diff --git a/.github/workflows/docker_img.yml b/.github/workflows/docker_img.yml
index 057a93d7864f37820b14b5cf8f6ce141a6a08f85..cebe9aa4dcbb2e175ea620288786aaab7d67a022 100644
--- a/.github/workflows/docker_img.yml
+++ b/.github/workflows/docker_img.yml
@@ -20,7 +20,7 @@ jobs:
SIIBRA_API_STABLE: 'https://siibra-api-stable.apps.hbp.eu/v2_0,https://siibra-api-stable-ns.apps.hbp.eu/v2_0,https://siibra-api-stable.apps.jsc.hbp.eu/v2_0'
SIIBRA_API_RC: 'https://siibra-api-rc.apps.hbp.eu/v2_0'
- SIIBRA_API_LATEST: 'https://siibra-api-latest.apps-dev.hbp.eu/v2_0'
+ SIIBRA_API_LATEST: 'https://siibra-api-latest.apps-dev.hbp.eu/v3_0'
steps:
diff --git a/package.json b/package.json
index a38aed3a21dee98a92205763be72d4d0b0202e92..2475726f3dc9a83f540f6b9a170d6294af33f5e4 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
{
- "name": "interactive-viewer",
- "version": "2.9.0",
+ "name": "siibra-explorer",
+ "version": "2.10.0",
"description": "siibra-explorer - explore brain atlases. Based on humanbrainproject/nehuba & google/neuroglancer. Built with angular",
"scripts": {
"lint": "eslint src --ext .ts",
@@ -11,7 +11,7 @@
"watch": "ng build --watch --configuration development",
"test": "ng test",
"test-ci": "ng test --progress false --watch false --browsers=ChromeHeadless",
- "sapi-schema": "npx openapi-typescript@5.1.1 https://siibra-api-stable.apps.hbp.eu/v2_0/openapi.json --output ./src/atlasComponents/sapi/schema.ts && eslint ./src/atlasComponents/sapi/schema.ts --no-ignore --fix",
+ "sapi-schema": "npx openapi-typescript@6.1.0 https://siibra-api-latest.apps-dev.hbp.eu/v3_0/openapi.json --output ./src/atlasComponents/sapi/schema_v3.ts && eslint ./src/atlasComponents/sapi/schema_v3.ts --no-ignore --fix",
"api-schema": "node src/plugin/generateTypes.js",
"docs:json": "compodoc -p ./tsconfig.json -e json -d .",
"storybook": "npm run docs:json && start-storybook -p 6006",
diff --git a/spec/util.ts b/spec/util.ts
index 9925589fefa2a49339b67a696b69eae2ef8476f8..4b7affa862bd32d295e40c0518482e16f0ddf20b 100644
--- a/spec/util.ts
+++ b/spec/util.ts
@@ -57,14028 +57,3 @@ export const JUBRAIN_COLIN_CH123_RIGHT = {
-8347692
]
}
-
-export const COLIN = {
- "name": "MNI Colin 27",
- "fullId": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
- "type": "template",
- "species": "Human",
- "useTheme": "dark",
- "ngId": "colin",
- "nehubaConfigURL": "nehubaConfig/colinNehubaConfig",
- "parcellations": [
- {
- "name": "JuBrain Cytoarchitectonic Atlas",
- "ngId": "jubrain colin v18 left",
- "auxillaryMeshIndices": [
- 65535
- ],
- "hasAdditionalViewMode": [
- "connectivity"
- ],
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
- }
- ],
- "properties": {
- "version": "1.0",
- "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
- "publications": [
- {
- "doi": "https://doi.org/10.1038/nrn2776",
- "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 "
- },
- {
- "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037",
- "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065"
- },
- {
- "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X",
- "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602."
- }
- ]
- },
- "regions": [
- {
- "name": "telencephalon",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "cerebral nuclei",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "basal forebrain",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "magnocellular group within septum",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": [
- 124,
- 233,
- 167
- ],
- "children": [
- {
- "name": "Ch 123 (Basal Forebrain) - left hemisphere",
- "rgb": [
- 124,
- 233,
- 167
- ],
- "labelIndex": 286,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -2339339,
- 4405405,
- -8804805
- ]
- },
- {
- "name": "Ch 123 (Basal Forebrain) - right hemisphere",
- "rgb": [
- 124,
- 233,
- 167
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 286,
- "children": [],
- "status": "publicP",
- "position": [
- 3240000,
- 5153846,
- -8347692
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "sublenticular part of basal forebrain",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Ch 4 (Basal Forebrain)",
- "arealabel": "Ch-4",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/VZJ5-8WJ",
- "synonyms": [],
- "rgb": [
- 116,
- 243,
- 12
- ],
- "children": [
- {
- "name": "Ch 4 (Basal Forebrain) - left hemisphere",
- "rgb": [
- 116,
- 243,
- 12
- ],
- "labelIndex": 264,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -16053628,
- -454259,
- -12470032
- ]
- },
- {
- "name": "Ch 4 (Basal Forebrain) - right hemisphere",
- "rgb": [
- 116,
- 243,
- 12
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 264,
- "children": [],
- "status": "publicP",
- "position": [
- 17655072,
- 263768,
- -11539130
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "magnocellular group within horizontal limb of diagnoal band",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Ch 123 (Basal Forebrain)",
- "arealabel": "Ch-123",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": [
- 124,
- 233,
- 167
- ],
- "children": [
- {
- "name": "Ch 123 (Basal Forebrain) - left hemisphere",
- "rgb": [
- 124,
- 233,
- 167
- ],
- "labelIndex": 286,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -2339339,
- 4405405,
- -8804805
- ]
- },
- {
- "name": "Ch 123 (Basal Forebrain) - right hemisphere",
- "rgb": [
- 124,
- 233,
- 167
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 286,
- "children": [],
- "status": "publicP",
- "position": [
- 3240000,
- 5153846,
- -8347692
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
- }
- },
- "relatedAreas": []
- }
- ]
- }
- ]
- },
- {
- "name": "amygdala",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "laterobasal group",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "LB (Amygdala)",
- "arealabel": "LB",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/C3X0-NV3",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "LB (Amygdala) - left hemisphere",
- "rgb": null,
- "labelIndex": 15,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP"
- },
- {
- "name": "LB (Amygdala) - right hemisphere",
- "rgb": null,
- "ngId": "jubrain colin v18 right",
- "labelIndex": 15,
- "children": [],
- "status": "publicP"
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "LB (Amygdala)",
- "arealabel": "LB",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/C3X0-NV3",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "LB (Amygdala) - left hemisphere",
- "rgb": null,
- "labelIndex": 11,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP"
- },
- {
- "name": "LB (Amygdala) - right hemisphere",
- "rgb": null,
- "ngId": "jubrain colin v18 right",
- "labelIndex": 11,
- "children": [],
- "status": "publicP"
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "LB (Amygdala)",
- "arealabel": "LB",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/C3X0-NV3",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "LB (Amygdala) - left hemisphere",
- "rgb": null,
- "labelIndex": 19,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP"
- },
- {
- "name": "LB (Amygdala) - right hemisphere",
- "rgb": null,
- "ngId": "jubrain colin v18 right",
- "labelIndex": 19,
- "children": [],
- "status": "publicP"
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "LB (Amygdala)",
- "arealabel": "LB",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/C3X0-NV3",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "LB (Amygdala) - left hemisphere",
- "rgb": null,
- "labelIndex": 13,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -25304803,
- -1696429,
- -23766626
- ]
- },
- {
- "name": "LB (Amygdala) - right hemisphere",
- "rgb": null,
- "ngId": "jubrain colin v18 right",
- "labelIndex": 13,
- "children": [],
- "status": "publicP",
- "position": [
- 28015494,
- -81343,
- -24045836
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "superficial group",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "SF (Amygdala)",
- "arealabel": "SF",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/WD31-SEA",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "SF (Amygdala) - left hemisphere",
- "rgb": null,
- "labelIndex": 236,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -16044471,
- 530048,
- -20831731
- ]
- },
- {
- "name": "SF (Amygdala) - right hemisphere",
- "rgb": null,
- "ngId": "jubrain colin v18 right",
- "labelIndex": 236,
- "children": [],
- "status": "publicP",
- "position": [
- 19382770,
- 1539804,
- -19413304
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "48929163-bf7b-4471-9f14-991c5225eced"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "SF (Amygdala)",
- "arealabel": "SF",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/WD31-SEA",
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "SF (Amygdala) - left hemisphere",
- "rgb": null,
- "labelIndex": 17,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP"
- },
- {
- "name": "SF (Amygdala) - right hemisphere",
- "rgb": null,
- "ngId": "jubrain colin v18 right",
- "labelIndex": 17,
- "children": [],
- "status": "publicP"
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "48929163-bf7b-4471-9f14-991c5225eced"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "SF (Amygdala)",
- "arealabel": "SF",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/WD31-SEA",
- "synonyms": [],
- "rgb": [
- 18,
- 168,
- 22
- ],
- "children": [
- {
- "name": "SF (Amygdala) - left hemisphere",
- "rgb": [
- 18,
- 168,
- 22
- ],
- "labelIndex": 186,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP"
- },
- {
- "name": "SF (Amygdala) - right hemisphere",
- "rgb": [
- 18,
- 168,
- 22
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 186,
- "children": [],
- "status": "publicP"
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "48929163-bf7b-4471-9f14-991c5225eced"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "CM (Amygdala)",
- "arealabel": "CM",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/36FR-C95",
- "synonyms": [],
- "rgb": [
- 102,
- 180,
- 202
- ],
- "children": [
- {
- "name": "CM (Amygdala) - left hemisphere",
- "rgb": [
- 102,
- 180,
- 202
- ],
- "labelIndex": 22,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP"
- },
- {
- "name": "CM (Amygdala) - right hemisphere",
- "rgb": [
- 102,
- 180,
- 202
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 22,
- "children": [],
- "status": "publicP"
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "7aba8aef-6430-4fa7-ab54-8ecac558faed"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "fiber masses",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "VTM (Amygdala)",
- "arealabel": "VTM",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/99HN-XRE",
- "synonyms": [],
- "rgb": [
- 89,
- 178,
- 185
- ],
- "children": [
- {
- "name": "VTM (Amygdala) - left hemisphere",
- "rgb": [
- 89,
- 178,
- 185
- ],
- "labelIndex": 228,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -23377907,
- -9837209,
- -14848837
- ]
- },
- {
- "name": "VTM (Amygdala) - right hemisphere",
- "rgb": [
- 89,
- 178,
- 185
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 228,
- "children": [],
- "status": "publicP",
- "position": [
- 25513514,
- -8881081,
- -15551351
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "a964e6e6-8014-41a2-b975-754d75cbb6f2"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "IF (Amygdala)",
- "arealabel": "IF",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/GWPR-G6K",
- "synonyms": [],
- "rgb": [
- 120,
- 190,
- 129
- ],
- "children": [
- {
- "name": "IF (Amygdala) - left hemisphere",
- "rgb": [
- 120,
- 190,
- 129
- ],
- "labelIndex": 237,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -27588235,
- -1431373,
- -17460784
- ]
- },
- {
- "name": "IF (Amygdala) - right hemisphere",
- "rgb": [
- 120,
- 190,
- 129
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 237,
- "children": [],
- "status": "publicP",
- "position": [
- 29372549,
- -813725,
- -16578431
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "5a1391c8-6056-40e4-a19b-3774df42bd07"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "MF (Amygdala)",
- "arealabel": "MF",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/9375-55V",
- "synonyms": [],
- "rgb": [
- 190,
- 200,
- 9
- ],
- "children": [
- {
- "name": "MF (Amygdala) - left hemisphere",
- "rgb": [
- 190,
- 200,
- 9
- ],
- "labelIndex": 235,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -18714286,
- -6523810,
- -15428571
- ]
- },
- {
- "name": "MF (Amygdala) - right hemisphere",
- "rgb": [
- 190,
- 200,
- 9
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 235,
- "children": [],
- "status": "publicP",
- "position": [
- 20976744,
- -4930233,
- -14441860
- ]
- }
- ],
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- "ngId": "jubrain colin v18 right",
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- {
- "name": "emboliform nucleus",
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- "children": [
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- "synonyms": [],
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- "labelIndex": 251,
- "ngId": "jubrain colin v18 left",
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- "name": "Interposed Nucleus (Cerebellum) - right hemisphere",
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- "ngId": "jubrain colin v18 right",
- "labelIndex": 251,
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- "properties": {
- "name": "MNI Colin 27",
- "description": "A stereotaxic average of 27 T1-weighted MRI scans of the same individual. (Holmes et al., 1998), mapped to fit the MNI305 space. Although not capturing brain variability, it is well established in neuroscience due to its high definition. HBP provides the JuBrain probabilistic cytoarchitectonic atlas (Amunts et al.) in this space."
- }
-}
-
-export const JUBRAIN_COLIN = {
- "name": "JuBrain Cytoarchitectonic Atlas",
- "ngId": "jubrain colin v18 left",
- "auxillaryMeshIndices": [
- 65535
- ],
- "hasAdditionalViewMode": [
- "connectivity"
- ],
- "originDatasets": [
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
- }
- ],
- "properties": {
- "version": "1.0",
- "description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
- "publications": [
- {
- "doi": "https://doi.org/10.1038/nrn2776",
- "citation": "Zilles K, Amunts K (2010) Centenary of Brodmann’s map – conception and fate. Nature Reviews Neuroscience 11(2): 139-145 "
- },
- {
- "doi": "https://doi.org/10.1016/j.neuroimage.2007.02.037",
- "citation": "Amunts K, Schleicher A, Zilles K (2007) Cytoarchitecture of the cerebral cortex – more than localization. Neuroimage 37: 1061-1065"
- },
- {
- "doi": "http://dx.doi.org/10.1016/B978-012693019-1/50023-X",
- "citation": "Zilles K, Schleicher A, Palomero-Gallagher N, Amunts K (2002) Quantitative analysis of cyto- and receptor architecture of the human brain. In: /Brain Mapping: The Methods/, J. C. Mazziotta and A. Toga (eds.), USA: Elsevier, 2002, p. 573-602."
- }
- ]
- },
- "regions": [
- {
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- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
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- "status": null,
- "labelIndex": null,
- "synonyms": [],
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- "children": [
- {
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- "status": null,
- "labelIndex": null,
- "synonyms": [],
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- "children": [
- {
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- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
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- "arealabel": "Ch-123",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/7SEP-P2V",
- "synonyms": [],
- "rgb": [
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- 233,
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- ],
- "children": [
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- ],
- "labelIndex": 286,
- "ngId": "jubrain colin v18 left",
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- },
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- "ngId": "jubrain colin v18 right",
- "labelIndex": 286,
- "children": [],
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- {
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- "status": null,
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- "rgb": null,
- "children": [
- {
- "name": "Ch 4 (Basal Forebrain)",
- "arealabel": "Ch-4",
- "status": "publicP",
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- "doi": "https://doi.org/10.25493/VZJ5-8WJ",
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- "rgb": [
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- "children": [
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- ],
- "labelIndex": 264,
- "ngId": "jubrain colin v18 left",
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- },
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- "ngId": "jubrain colin v18 right",
- "labelIndex": 264,
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- {
- "name": "amygdala",
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- "children": [
- {
- "name": "laterobasal group",
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- "children": [
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- },
- {
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- {
- "name": "superficial group",
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- "children": [
- {
- "name": "SF (Amygdala)",
- "arealabel": "SF",
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- "doi": "https://doi.org/10.25493/WD31-SEA",
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- "name": "Area p32 (pACC)",
- "arealabel": "Area-p32",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/3JX0-7E5",
- "synonyms": [],
- "rgb": [
- 87,
- 135,
- 14
- ],
- "children": [
- {
- "name": "Area p32 (pACC) - left hemisphere",
- "rgb": [
- 87,
- 135,
- 14
- ],
- "labelIndex": 47,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -6122937,
- 49256108,
- 11929896
- ]
- },
- {
- "name": "Area p32 (pACC) - right hemisphere",
- "rgb": [
- 87,
- 135,
- 14
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 47,
- "children": [],
- "status": "publicP",
- "position": [
- 7759613,
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- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "b09aaa77-f41b-4008-b8b9-f984b0417cf3"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "Area s24 (sACC)",
- "arealabel": "Area-s24",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/HXWM-NRX",
- "synonyms": [],
- "rgb": [
- 133,
- 34,
- 201
- ],
- "children": [
- {
- "name": "Area s24 (sACC) - left hemisphere",
- "rgb": [
- 133,
- 34,
- 201
- ],
- "labelIndex": 183,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -3247887,
- 24596479,
- -9615493
- ]
- },
- {
- "name": "Area s24 (sACC) - right hemisphere",
- "rgb": [
- 133,
- 34,
- 201
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 183,
- "children": [],
- "status": "publicP",
- "position": [
- 3259899,
- 23813535,
- -9257019
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "d4ea6cc5-1e1d-4212-966f-81fed01eb648"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "hippocampal formation",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "HATA (Hippocampus)",
- "arealabel": "HATA",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/M1XP-VSQ",
- "synonyms": [],
- "rgb": [
- 137,
- 12,
- 73
- ],
- "children": [
- {
- "name": "HATA (Hippocampus) - left hemisphere",
- "rgb": [
- 137,
- 12,
- 73
- ],
- "labelIndex": 68,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -13947917,
- -9576389,
- -18975694
- ]
- },
- {
- "name": "HATA (Hippocampus) - right hemisphere",
- "rgb": [
- 137,
- 12,
- 73
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 68,
- "children": [],
- "status": "publicP",
- "position": [
- 15080586,
- -8358974,
- -17871795
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "9ec4a423-70fa-43cd-90b3-fbc26a3cbc6c"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "Entorhinal Cortex",
- "arealabel": "Entorhinal-Cortex",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/KNXY-B1Z",
- "synonyms": [],
- "rgb": [
- 35,
- 159,
- 214
- ],
- "children": [
- {
- "name": "Entorhinal Cortex - left hemisphere",
- "rgb": [
- 35,
- 159,
- 214
- ],
- "labelIndex": 60,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -20926052,
- -6082765,
- -33357509
- ]
- },
- {
- "name": "Entorhinal Cortex - right hemisphere",
- "rgb": [
- 35,
- 159,
- 214
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 60,
- "children": [],
- "status": "publicP",
- "position": [
- 22877203,
- -3501469,
- -32577556
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "030827d4-e0d1-4406-b71f-3f58dc2f9cca"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "CA (Hippocampus)",
- "arealabel": "CA",
- "status": "publicP",
- "labelIndex": null,
- "relatedAreas": [
- {
- "name": "CA1 (Hippocampus)",
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "bfc0beb7-310c-4c57-b810-2adc464bd02c"
- }
- }
- }
- ],
- "doi": "https://doi.org/10.25493/B85T-D88",
- "synonyms": [],
- "rgb": [
- 250,
- 191,
- 217
- ],
- "children": [
- {
- "name": "CA (Hippocampus) - left hemisphere",
- "rgb": [
- 250,
- 191,
- 217
- ],
- "labelIndex": 191,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -27476326,
- -26068931,
- -11082817
- ]
- },
- {
- "name": "CA (Hippocampus) - right hemisphere",
- "rgb": [
- 250,
- 191,
- 217
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 191,
- "children": [],
- "status": "publicP",
- "position": [
- 29426785,
- -24801145,
- -11142814
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "a0d14d3e-bc30-41cf-8b28-540067897f80"
- }
- }
- },
- {
- "name": "DG (Hippocampus)",
- "arealabel": "DG",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/M8JP-XQT",
- "synonyms": [],
- "rgb": [
- 149,
- 55,
- 120
- ],
- "children": [
- {
- "name": "DG (Hippocampus) - left hemisphere",
- "rgb": [
- 149,
- 55,
- 120
- ],
- "labelIndex": 61,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -26946498,
- -26708171,
- -9589494
- ]
- },
- {
- "name": "DG (Hippocampus) - right hemisphere",
- "rgb": [
- 149,
- 55,
- 120
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 61,
- "children": [],
- "status": "publicP",
- "position": [
- 28316456,
- -24674684,
- -10596203
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "0bea7e03-bfb2-4907-9d45-db9071ce627d"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "Subiculum (Hippocampus)",
- "arealabel": "Subiculum",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/QKJH-F45",
- "synonyms": [],
- "rgb": [
- 111,
- 125,
- 219
- ],
- "children": [
- {
- "name": "Subiculum (Hippocampus) - left hemisphere",
- "rgb": [
- 111,
- 125,
- 219
- ],
- "labelIndex": 192,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -20352171,
- -24057796,
- -16326997
- ]
- },
- {
- "name": "Subiculum (Hippocampus) - right hemisphere",
- "rgb": [
- 111,
- 125,
- 219
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 192,
- "children": [],
- "status": "publicP",
- "position": [
- 22543982,
- -23195614,
- -15923499
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "7e2dab4c-a140-440d-a322-c1679adef2d4"
- }
- },
- "relatedAreas": []
- }
- ]
- }
- ]
- }
- ]
- }
- ]
- },
- {
- "name": "metencephalon",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "cerebellum",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "cerebellar nuclei",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "globose nucleus",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Interposed Nucleus (Cerebellum)",
- "arealabel": "Interposed-Nucleus",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/8PTB-JDH",
- "synonyms": [],
- "rgb": [
- 170,
- 29,
- 10
- ],
- "children": [
- {
- "name": "Interposed Nucleus (Cerebellum) - left hemisphere",
- "rgb": [
- 170,
- 29,
- 10
- ],
- "labelIndex": 251,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -8457921,
- -55262376,
- -30235149
- ]
- },
- {
- "name": "Interposed Nucleus (Cerebellum) - right hemisphere",
- "rgb": [
- 170,
- 29,
- 10
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 251,
- "children": [],
- "status": "publicP",
- "position": [
- 7917989,
- -54201058,
- -31489418
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "dentate nucleus",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Dorsal Dentate Nucleus (Cerebellum)",
- "arealabel": "Dorsal-Dentate-Nucleus",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/M5QG-SHH",
- "synonyms": [],
- "rgb": [
- 89,
- 201,
- 99
- ],
- "children": [
- {
- "name": "Dorsal Dentate Nucleus (Cerebellum) - left hemisphere",
- "rgb": [
- 89,
- 201,
- 99
- ],
- "labelIndex": 240,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -16612782,
- -56036341,
- -36064536
- ]
- },
- {
- "name": "Dorsal Dentate Nucleus (Cerebellum) - right hemisphere",
- "rgb": [
- 89,
- 201,
- 99
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 240,
- "children": [],
- "status": "publicP",
- "position": [
- 15388967,
- -58303395,
- -36586280
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "58095aef-da69-43d4-887c-009c095cecce"
- }
- },
- "relatedAreas": []
- },
- {
- "name": "Ventral Dentate Nucleus (Cerebellum)",
- "arealabel": "Ventral-Dentate-Nucleus",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/FQE5-5QR",
- "synonyms": [],
- "rgb": [
- 39,
- 129,
- 9
- ],
- "children": [
- {
- "name": "Ventral Dentate Nucleus (Cerebellum) - left hemisphere",
- "rgb": [
- 39,
- 129,
- 9
- ],
- "labelIndex": 241,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -13112867,
- -56176072,
- -29957111
- ]
- },
- {
- "name": "Ventral Dentate Nucleus (Cerebellum) - right hemisphere",
- "rgb": [
- 39,
- 129,
- 9
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 241,
- "children": [],
- "status": "publicP",
- "position": [
- 12107011,
- -55974170,
- -31385609
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "57282342-5a75-4e07-bcdc-2d368c517b71"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "fastigial nucleus",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Fastigial Nucleus (Cerebellum)",
- "arealabel": "Fastigial-Nucleus",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/3YJ9-S6G",
- "synonyms": [],
- "rgb": [
- 200,
- 100,
- 10
- ],
- "children": [
- {
- "name": "Fastigial Nucleus (Cerebellum) - left hemisphere",
- "rgb": [
- 200,
- 100,
- 10
- ],
- "labelIndex": 219,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -3828877,
- -53149733,
- -29013369
- ]
- },
- {
- "name": "Fastigial Nucleus (Cerebellum) - right hemisphere",
- "rgb": [
- 200,
- 100,
- 10
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 219,
- "children": [],
- "status": "publicP",
- "position": [
- 3011287,
- -53069977,
- -29040632
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "e8abfe3d-8b64-45c2-8853-314d82873273"
- }
- },
- "relatedAreas": []
- }
- ]
- },
- {
- "name": "emboliform nucleus",
- "status": null,
- "labelIndex": null,
- "synonyms": [],
- "rgb": null,
- "children": [
- {
- "name": "Interposed Nucleus (Cerebellum)",
- "arealabel": "Interposed-Nucleus",
- "status": "publicP",
- "labelIndex": null,
- "doi": "https://doi.org/10.25493/8PTB-JDH",
- "synonyms": [],
- "rgb": [
- 170,
- 29,
- 10
- ],
- "children": [
- {
- "name": "Interposed Nucleus (Cerebellum) - left hemisphere",
- "rgb": [
- 170,
- 29,
- 10
- ],
- "labelIndex": 251,
- "ngId": "jubrain colin v18 left",
- "children": [],
- "status": "publicP",
- "position": [
- -8457921,
- -55262376,
- -30235149
- ]
- },
- {
- "name": "Interposed Nucleus (Cerebellum) - right hemisphere",
- "rgb": [
- 170,
- 29,
- 10
- ],
- "ngId": "jubrain colin v18 right",
- "labelIndex": 251,
- "children": [],
- "status": "publicP",
- "position": [
- 7917989,
- -54201058,
- -31489418
- ]
- }
- ],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
- }
- },
- "relatedAreas": []
- }
- ]
- }
- ]
- }
- ]
- }
- ]
- }
- ]
-}
diff --git a/src/api/service.ts b/src/api/service.ts
index 89a5f262aef9a15a03b795cc380e4286c3f0acc3..e2604e4320bfe6fee4d10850a52c1dc4facde280 100644
--- a/src/api/service.ts
+++ b/src/api/service.ts
@@ -1,9 +1,10 @@
import { Inject, Injectable, Optional } from "@angular/core";
import { select, Store } from "@ngrx/store";
import { Subject } from "rxjs";
-import { distinctUntilChanged, filter, map, take } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel, OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi";
-import { SxplrCoordinatePointExtension } from "src/atlasComponents/sapi/type";
+import { distinctUntilChanged, filter, map, switchMap, take } from "rxjs/operators";
+import { SAPI } from "src/atlasComponents/sapi";
+import { SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate, Point } from "src/atlasComponents/sapi/type_sxplr";
+import { SxplrCoordinatePointExtension } from "src/atlasComponents/sapi/type_v3";
import { MainState, atlasSelection, userInteraction, annotation, atlasAppearance } from "src/state"
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
import { CANCELLABLE_DIALOG, CANCELLABLE_DIALOG_OPTS } from "src/util/interfaces";
@@ -20,8 +21,8 @@ type AtId = {
}
type RequestUserTypes = {
- region: SapiRegionModel
- point: OpenMINDSCoordinatePoint
+ region: SxplrRegion
+ point: Point
confirm: void
input: string
}
@@ -38,15 +39,15 @@ type RequestUser<T extends keyof RequestUserTypes> = {
export type ApiBoothEvents = {
getAllAtlases: {
request: null
- response: SapiAtlasModel[]
+ response: SxplrAtlas[]
}
getSupportedTemplates: {
request: null
- response: SapiSpaceModel[]
+ response: SxplrTemplate[]
}
getSupportedParcellations: {
request: null
- response: SapiParcellationModel[]
+ response: SxplrParcellation[]
}
selectAtlas: {
@@ -72,7 +73,7 @@ export type ApiBoothEvents = {
type: 'region' | 'point'
message: string
}
- response: SapiRegionModel | OpenMINDSCoordinatePoint
+ response: SxplrRegion | Point
}
addAnnotations: {
@@ -135,11 +136,11 @@ export type HeartbeatEvents = {
}
export type BroadCastingApiEvents = {
- atlasSelected: SapiAtlasModel
- templateSelected: SapiSpaceModel
- parcellationSelected: SapiParcellationModel
- allRegions: SapiRegionModel[]
- regionsSelected: SapiRegionModel[]
+ atlasSelected: SxplrAtlas
+ templateSelected: SxplrTemplate
+ parcellationSelected: SxplrParcellation
+ allRegions: SxplrRegion[]
+ regionsSelected: SxplrRegion[]
navigation: MainState['[state.atlasSelection]']['navigation']
}
@@ -187,7 +188,7 @@ export class ApiService implements BoothResponder<ApiBoothEvents>{
const { type } = this.requestUserQueue[0]
if (type === "region") {
- let moRegion: SapiRegionModel
+ let moRegion: SxplrRegion
this.store.pipe(
select(userInteraction.selectors.mousingOverRegions),
filter(val => val.length > 0),
@@ -201,7 +202,7 @@ export class ApiService implements BoothResponder<ApiBoothEvents>{
}
if (type === "point") {
- let point: OpenMINDSCoordinatePoint
+ let point: Point
this.store.pipe(
select(userInteraction.selectors.mousingOverPosition),
take(1)
@@ -302,8 +303,9 @@ export class ApiService implements BoothResponder<ApiBoothEvents>{
case 'getSupportedParcellations': {
if (!event.id) return
const parcs = await this.store.pipe(
- atlasSelection.fromRootStore.allAvailParcs(this.sapi),
- take(1)
+ select(atlasSelection.selectors.selectedAtlas),
+ switchMap(atlas => this.sapi.getAllParcellations(atlas)),
+ take(1),
).toPromise()
return {
id: event.id,
@@ -314,7 +316,8 @@ export class ApiService implements BoothResponder<ApiBoothEvents>{
case 'getSupportedTemplates': {
if (!event.id) return
const spaces = await this.store.pipe(
- atlasSelection.fromRootStore.allAvailSpaces(this.sapi),
+ select(atlasSelection.selectors.selectedAtlas),
+ switchMap(atlas => this.sapi.getAllSpaces(atlas)),
take(1)
).toPromise()
return {
diff --git a/src/atlasComponents/sapi/core/base.ts b/src/atlasComponents/sapi/core/base.ts
new file mode 100644
index 0000000000000000000000000000000000000000..2fa7e18970aad13de91033422a7b2625c8a15870
--- /dev/null
+++ b/src/atlasComponents/sapi/core/base.ts
@@ -0,0 +1,34 @@
+import { Observable } from "rxjs"
+import { SAPI } from "../sapi.service"
+import { RouteParam, SapiQueryPriorityArg } from "../type_v3"
+
+const AllFeatures = {
+ // Feature: "Feature",
+ CorticalProfile: "CorticalProfile",
+ // EbrainsDataFeature: "EbrainsDataFeature",
+ RegionalConnectivity: "RegionalConnectivity",
+ Tabular: "Tabular",
+ GeneExpressions: "GeneExpressions",
+ VolumeOfInterest: "VolumeOfInterest",
+} as const
+
+type AF = keyof typeof AllFeatures
+
+export abstract class SAPIBase<T extends AF> {
+
+ public abstract features$: Observable<string[]>
+
+ constructor(
+ private _sapi: SAPI,
+ ){}
+
+ getFeatures(featureType: T, param: RouteParam<`/feature/${T}`> & Partial<SapiQueryPriorityArg>) {
+ const route = `/feature/${featureType}` as `/feature/${T}`
+ return this._sapi.v3Get(route, param)
+ }
+
+ getFeatureInstance(featureType: T, param: RouteParam<`/feature/${T}/{feature_id}`> & Partial<SapiQueryPriorityArg>) {
+ let route = `/feature/${featureType}/{feature_id}` as `/feature/${T}/{feature_id}`
+ return this._sapi.v3Get(route, param)
+ }
+}
diff --git a/src/atlasComponents/sapi/core/sapiParcellation.ts b/src/atlasComponents/sapi/core/sapiParcellation.ts
index 085c5a82b8136901136593aa0b2933d992efb22e..7d36e1202ca3e39140d037ca04a997372904714d 100644
--- a/src/atlasComponents/sapi/core/sapiParcellation.ts
+++ b/src/atlasComponents/sapi/core/sapiParcellation.ts
@@ -1,73 +1,36 @@
-import { Observable } from "rxjs"
+import { Observable, of } from "rxjs"
import { switchMap } from "rxjs/operators"
-import { SapiVolumeModel } from ".."
import { SAPI } from "../sapi.service"
-import {SapiParcellationFeatureModel, SapiParcellationModel, SapiQueryPriorityArg, SapiRegionModel} from "../type"
+import { SapiParcellationModel, SapiQueryPriorityArg, SapiRegionModel, RouteParam } from "../type_v3"
+import { SAPIBase } from "./base"
-type PaginationQuery = {
- size: number
- page: number
-}
+/**
+ * All valid parcellation features
+ */
+const ParcellationFeatures = {
+ RegionalConnectivity: "RegionalConnectivity",
+} as const
-type ParcellationPaginationQuery = {
- type?: string
- size?: number
- page: number
-}
+export type PF = keyof typeof ParcellationFeatures
-export class SAPIParcellation{
+export class SAPIParcellation extends SAPIBase<PF>{
constructor(private sapi: SAPI, public atlasId: string, public id: string){
-
+ super(sapi)
}
getDetail(queryParam?: SapiQueryPriorityArg): Observable<SapiParcellationModel>{
- return SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.sapi.httpGet<SapiParcellationModel>(
- `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.id)}`,
- null,
- queryParam
- ))
- )
+ return this.sapi.v3Get(`/parcellations/{parcellation_id}`, {
+ path: {
+ parcellation_id: this.id
+ },
+ priority: queryParam?.priority
+ })
}
- getRegions(spaceId: string, queryParam?: SapiQueryPriorityArg): Observable<SapiRegionModel[]> {
- return SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.sapi.httpGet<SapiRegionModel[]>(
- `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.id)}/regions`,
- {
- space_id: spaceId
- },
- queryParam
- ))
- )
- }
- getVolumes(): Observable<SapiVolumeModel[]>{
- return SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.sapi.httpGet<SapiVolumeModel[]>(
- `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.id)}/volumes`
- ))
- )
+ getLabelledMap(spaceId: string, queryParam?: SapiQueryPriorityArg) {
+ return this.sapi.getMap(this.id, spaceId, "LABELLED", queryParam)
}
- getFeatures(parcPagination?: ParcellationPaginationQuery, queryParam?: SapiQueryPriorityArg): Observable<SapiParcellationFeatureModel[]> {
- return SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.sapi.httpGet<SapiParcellationFeatureModel[]>(
- `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.id)}/features`,
- {
- type: parcPagination?.type,
- size: parcPagination?.size?.toString() || '5',
- page: parcPagination?.page.toString() || '0',
- },
- queryParam
- ))
- )
- }
-
- getFeatureInstance(instanceId: string): Observable<SapiParcellationFeatureModel> {
- return SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.sapi.http.get<SapiParcellationFeatureModel>(
- `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.id)}/features/${encodeURIComponent(instanceId)}`,
- ))
- )
- }
+ static Features$ = of(Object.keys(ParcellationFeatures) as PF[])
+ public features$ = SAPIParcellation.Features$
}
diff --git a/src/atlasComponents/sapi/core/sapiRegion.ts b/src/atlasComponents/sapi/core/sapiRegion.ts
index d9263cea03f0d7045e3a1f5043f8a4edc2209929..a8fd531d9d5f2e4746c7c4654512ca0c640e4121 100644
--- a/src/atlasComponents/sapi/core/sapiRegion.ts
+++ b/src/atlasComponents/sapi/core/sapiRegion.ts
@@ -1,22 +1,44 @@
import { SAPI } from "..";
-import { SapiRegionalFeatureModel, SapiRegionMapInfoModel, SapiRegionModel, cleanIeegSessionDatasets, SapiIeegSessionModel, CleanedIeegDataset, SapiVolumeModel, PaginatedResponse } from "../type";
+import { SapiRegionModel, RouteParam } from "../type_v3";
import { strToRgb, hexToRgb } from 'common/util'
-import { merge, Observable, of } from "rxjs";
-import { catchError, map, scan, switchMap } from "rxjs/operators";
+import { NEVER, Observable, of } from "rxjs";
+import { map } from "rxjs/operators";
+import { SAPIBase } from "./base";
+import { SxplrRegion } from "../type_sxplr";
-export class SAPIRegion{
+/**
+ * All valid region features
+ */
+const RegionFeatures = {
+ // ReceptorDensityFingerprint: "ReceptorDensityFingerprint",
+ // GeneExpressions: "GeneExpressions",
+ // EbrainsDataFeature: "EbrainsDataFeature",
+
+ // ReceptorDensityProfile: "ReceptorDensityProfile",
+ // BigBrainIntensityProfile: "BigBrainIntensityProfile",
+ // CellDensityProfile: "CellDensityProfile",
+ // LayerwiseBigBrainIntensities: "LayerwiseBigBrainIntensities",
+ // LayerwiseCellDensity: "LayerwiseCellDensity",
+
+ Tabular: "Tabular",
+ CorticalProfile: "CorticalProfile",
+} as const
- static GetDisplayColor(region: SapiRegionModel): [number, number, number]{
+type RF = keyof typeof RegionFeatures
+
+export class SAPIRegion extends SAPIBase<RF>{
+
+ static GetDisplayColor(region: SxplrRegion): [number, number, number]{
if (!region) {
throw new Error(`region must be provided!`)
}
- if (region.hasAnnotation?.displayColor) {
- return hexToRgb(region.hasAnnotation.displayColor)
- }
- return strToRgb(JSON.stringify(region))
+ return region.color
+ // if (region.hasAnnotation?.displayColor) {
+ // return hexToRgb(region.hasAnnotation.displayColor)
+ // }
+ // return strToRgb(JSON.stringify(region))
}
- private prefix$: Observable<string>
constructor(
private sapi: SAPI,
@@ -24,97 +46,81 @@ export class SAPIRegion{
public parcId: string,
public id: string,
){
- this.prefix$ = SAPI.BsEndpoint$.pipe(
- map(endpt => `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/parcellations/${encodeURIComponent(this.parcId)}/regions/${encodeURIComponent(this.id)}`)
- )
+ super(sapi)
}
- getFeatures(spaceId: string): Observable<(SapiRegionalFeatureModel | CleanedIeegDataset)[]> {
- return merge(
- this.prefix$.pipe(
- switchMap(prefix =>
- this.sapi.httpGet<SapiRegionalFeatureModel[]>(
- `${prefix}/features`,
- {
- space_id: spaceId
- }
- ).pipe(
- catchError((err, obs) => {
- return of([])
- })
- )
- )
- ),
- spaceId
- ? this.sapi.getSpace(this.atlasId, spaceId).getFeatures({ parcellationId: this.parcId, region: this.id }).pipe(
- catchError((err, obs) => {
- return of([])
- }),
- map(feats => {
- const ieegSessions: SapiIeegSessionModel[] = feats.filter(feat => feat["@type"] === "siibra/features/ieegSession")
- return cleanIeegSessionDatasets(ieegSessions)
- }),
- )
- : of([] as CleanedIeegDataset[])
- ).pipe(
- scan((acc, curr) => [...acc, ...curr], [])
- )
- }
+ static Features: RF[] = Object.keys(RegionFeatures) as RF[]
+ static Features$ = of(SAPIRegion.Features)
+ public features$ = SAPIRegion.Features$
- getFeatureInstance(instanceId: string, spaceId: string = null): Observable<SapiRegionalFeatureModel> {
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiRegionalFeatureModel>(
- `${prefix}/features/${encodeURIComponent(instanceId)}`,
- {
- space_id: spaceId
- }
- ))
- )
+ /**
+ * @param spaceId
+ * @returns
+ */
+ getMapInfo(spaceId: string): Observable<{min: number, max: number}> {
+ return this.sapi.v3Get("/map/statistical_map.info.json", {
+ query: {
+ parcellation_id: this.parcId,
+ region_id: this.id,
+ space_id: spaceId
+ }
+ })
}
- getMapInfo(spaceId: string): Observable<SapiRegionMapInfoModel> {
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.http.get<SapiRegionMapInfoModel>(
- `${prefix}/regional_map/info`,
- {
- params: {
+ /**
+ * @param spaceId
+ * @returns
+ */
+ getMapUrl(spaceId: string): Observable<string> {
+ return SAPI.BsEndpoint$.pipe(
+ map(endpoint => {
+ const { path, params } = this.sapi.v3GetRoute("/map/statistical_map.nii.gz", {
+ query: {
+ parcellation_id: this.parcId,
+ region_id: this.id,
space_id: spaceId
}
+ })
+
+ const search = new URLSearchParams()
+ for (const key in params) {
+ search.set(key, params[key].toString())
}
- ))
- )
- }
- getMapUrl(spaceId: string): Observable<string> {
- return this.prefix$.pipe(
- map(prefix => `${prefix}/regional_map/map?space_id=${encodeURI(spaceId)}`)
+ return `${endpoint}${path}?${search.toString()}`
+ })
)
}
- getVolumes(): Observable<PaginatedResponse<SapiVolumeModel>>{
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<PaginatedResponse<SapiVolumeModel>>(
- `${prefix}/volumes`
- ))
- )
+ /**
+ *
+ * @deprecated
+ * @param volumeId
+ * @returns
+ */
+ getVolumeInstance(volumeId: string): Observable<never> {
+ return NEVER
}
- getVolumeInstance(volumeId: string): Observable<SapiVolumeModel> {
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiVolumeModel>(
- `${prefix}/volumes/${encodeURIComponent(volumeId)}`
- ))
- )
+ getDetail(spaceId: string): Observable<SapiRegionModel> {
+ return this.sapi.v3Get("/regions/{region_id}", {
+ path: {
+ region_id: this.id
+ },
+ query: {
+ parcellation_id: this.parcId,
+ space_id: spaceId
+ }
+ })
}
- getDetail(spaceId: string): Observable<SapiRegionModel> {
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiRegionModel>(
- prefix,
- {
- space_id: spaceId
- }
- ))
- )
+ getMap(spaceId: string, mapType: RouteParam<"/map">['query']['map_type']) {
+ return this.sapi.v3Get("/map", {
+ query: {
+ space_id: spaceId,
+ parcellation_id: this.parcId,
+ map_type: mapType,
+ }
+ })
}
}
diff --git a/src/atlasComponents/sapi/core/sapiSpace.ts b/src/atlasComponents/sapi/core/sapiSpace.ts
index af2171077788d7a8a879590e6c89305883f90e7c..a11e997862de15d8c855d6e3bc8d522684e89c67 100644
--- a/src/atlasComponents/sapi/core/sapiSpace.ts
+++ b/src/atlasComponents/sapi/core/sapiSpace.ts
@@ -1,8 +1,18 @@
-import { Observable, throwError } from "rxjs"
+import { Observable, of, throwError } from "rxjs"
import { SAPI } from '../sapi.service'
-import { camelToSnake } from 'common/util'
-import {SapiQueryPriorityArg, SapiSpaceModel, SapiSpatialFeatureModel, SapiVolumeModel} from "../type"
+import { SxplrTemplate } from "../type_sxplr"
import { map, switchMap } from "rxjs/operators"
+import { SAPIBase } from "./base"
+import { SapiQueryPriorityArg } from "../type_v3"
+
+/**
+ * All valid parcellation features
+ */
+const SpaceFeatures = {
+ VolumeOfInterest: "VolumeOfInterest",
+} as const
+
+export type SF = keyof typeof SpaceFeatures
type FeatureResponse = {
features: {
@@ -21,9 +31,13 @@ type BBoxSpatialFEatureOpts = {
type SpatialFeatureOpts = RegionalSpatialFeatureOpts | BBoxSpatialFEatureOpts
-export class SAPISpace{
+export class SAPISpace extends SAPIBase<SF>{
+
+ static Features$ = of(Object.keys(SpaceFeatures) as SF[])
+ public features$ = SAPISpace.Features$
constructor(private sapi: SAPI, public atlasId: string, public id: string){
+ super(sapi)
this.prefix$ = SAPI.BsEndpoint$.pipe(
map(endpt => `${endpt}/atlases/${encodeURIComponent(this.atlasId)}/spaces/${encodeURIComponent(this.id)}`)
)
@@ -41,35 +55,9 @@ export class SAPISpace{
)
}
- getFeatures(opts: SpatialFeatureOpts): Observable<SapiSpatialFeatureModel[]> {
- const query: Record<string, string> = {}
- for (const [key, value] of Object.entries(opts)) {
- query[camelToSnake(key)] = value
- }
+ getDetail(param?: SapiQueryPriorityArg): Observable<SxplrTemplate>{
return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiSpatialFeatureModel[]>(
- `${prefix}/features`,
- query
- ))
- )
- }
-
- getFeatureInstance(instanceId: string, opts: SpatialFeatureOpts): Observable<SapiSpatialFeatureModel> {
- const query: Record<string, string> = {}
- for (const [key, value] of Object.entries(opts)) {
- query[camelToSnake(key)] = value
- }
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiSpatialFeatureModel>(
- `${prefix}/features/${encodeURIComponent(instanceId)}`,
- query
- ))
- )
- }
-
- getDetail(param?: SapiQueryPriorityArg): Observable<SapiSpaceModel>{
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiSpaceModel>(
+ switchMap(prefix => this.sapi.httpGet<SxplrTemplate>(
`${prefix}`,
null,
param
@@ -77,30 +65,4 @@ export class SAPISpace{
)
}
- getVolumes(): Observable<SapiVolumeModel[]>{
- return this.prefix$.pipe(
- switchMap(prefix => this.sapi.httpGet<SapiVolumeModel[]>(
- `${prefix}/volumes`,
- ))
- )
- }
-
- getTemplateSize() {
- return this.getVolumes().pipe(
- switchMap(volumes => {
- const ngVolumes = volumes.filter(vol => vol["@type"] === "spy/volume/neuroglancer/precomputed")
- if (ngVolumes.length === 0) return throwError(`template ${this.id} has no ng volume.`)
- return this.sapi.httpGet<any>(`${ngVolumes[0].data.url}/info`).pipe(
- map(infoJson => {
- const { resolution, size } = infoJson.scales[0]
- return {
- voxel: size as [number, number, number],
- real: [0, 1, 2].map(idx => resolution[idx] * size[idx]) as [number, number, number],
- transform: ngVolumes[0].data?.detail?.['neuroglancer/precomputed']?.['transform'] as number[][]
- }
- })
- )
- })
- )
- }
}
diff --git a/src/atlasComponents/sapi/features/sapiFeature.ts b/src/atlasComponents/sapi/features/sapiFeature.ts
index f2f341acce3aca72ba481f3eda6c68083320cfe1..73d6a8ea3a8a0efde7644e14904ad99e5eb0bc9b 100644
--- a/src/atlasComponents/sapi/features/sapiFeature.ts
+++ b/src/atlasComponents/sapi/features/sapiFeature.ts
@@ -1,6 +1,6 @@
+import { throwError } from "rxjs";
import { switchMap } from "rxjs/operators";
import { SAPI } from "../sapi.service";
-import { SapiFeatureModel } from "../type";
export class SAPIFeature {
constructor(private sapi: SAPI, public id: string, public opts: Record<string, string> = {}){
@@ -8,9 +8,6 @@ export class SAPIFeature {
}
public detail$ = SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.sapi.httpGet<SapiFeatureModel>(
- `${endpt}/features/${this.id}`,
- this.opts
- ))
+ switchMap(endpt => throwError(`IMPLEMENT ME`))
)
}
diff --git a/src/atlasComponents/sapi/index.ts b/src/atlasComponents/sapi/index.ts
index e5d8afd20e4e298a52db0b0edfc3fa61c55a5e74..356276003c98cafb620eaf5aa67df35acffcff4b 100644
--- a/src/atlasComponents/sapi/index.ts
+++ b/src/atlasComponents/sapi/index.ts
@@ -1,22 +1,5 @@
export { SAPIModule } from './module'
-export {
- SapiAtlasModel,
- SapiParcellationModel,
- SapiSpaceModel,
- SapiRegionModel,
- SapiVolumeModel,
- SapiDatasetModel,
- SapiRegionalFeatureModel,
- SapiSpatialFeatureModel,
- SapiFeatureModel,
- SapiParcellationFeatureModel,
- CleanedIeegDataset,
- SxplrCleanedFeatureModel,
- OpenMINDSCoordinatePoint,
- CLEANED_IEEG_DATASET_TYPE,
-} from "./type"
-
export { SAPI } from "./sapi.service"
export {
SAPIAtlas,
diff --git a/src/atlasComponents/sapi/sapi.service.ts b/src/atlasComponents/sapi/sapi.service.ts
index 8a44d6236a11bf41bb8d9df215a52e4b5b6c654f..34977f4b8c35a7e0b7d950dc088bb6c24f807a6e 100644
--- a/src/atlasComponents/sapi/sapi.service.ts
+++ b/src/atlasComponents/sapi/sapi.service.ts
@@ -1,18 +1,13 @@
import { Injectable } from "@angular/core";
import { HttpClient } from '@angular/common/http';
-import { map, shareReplay, switchMap, take } from "rxjs/operators";
+import { catchError, map, shareReplay, switchMap, take, tap } from "rxjs/operators";
import { SAPIAtlas, SAPISpace } from './core'
import {
- SapiAtlasModel,
- SapiModalityModel,
- SapiParcellationModel,
SapiQueryPriorityArg,
- SapiRegionalFeatureModel,
- SapiRegionModel,
- SapiSpaceModel,
- SpyNpArrayDataModel,
- SxplrCleanedFeatureModel
-} from "./type";
+} from "./type_v3";
+import {
+ translateV3Entities
+} from "./translate_v3"
import { getExportNehuba } from "src/util/fn";
import { SAPIParcellation } from "./core/sapiParcellation";
import { SAPIRegion } from "./core/sapiRegion"
@@ -20,22 +15,35 @@ import { MatSnackBar } from "@angular/material/snack-bar";
import { AtlasWorkerService } from "src/atlasViewer/atlasViewer.workerService.service";
import { EnumColorMapName } from "src/util/colorMaps";
import { PRIORITY_HEADER } from "src/util/priority";
-import { NEVER, Observable } from "rxjs";
+import { forkJoin, from, NEVER, Observable, of, throwError } from "rxjs";
import { SAPIFeature } from "./features";
import { environment } from "src/environments/environment"
+import { PathReturn, RouteParam, SapiRoute } from "./type_v3";
+import { BoundingBox, SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate, VoiFeature } from "./type_sxplr";
+
export const SIIBRA_API_VERSION_HEADER_KEY='x-siibra-api-version'
-export const SIIBRA_API_VERSION = '0.2.3'
+export const EXPECTED_SIIBRA_API_VERSION = '0.3.0'
type RegistryType = SAPIAtlas | SAPISpace | SAPIParcellation
let BS_ENDPOINT_CACHED_VALUE: Observable<string> = null
+type PaginatedResponse<T> = {
+ items: T[]
+ total: number
+ page: number
+ size: number
+ pages?: number
+}
+
@Injectable({
providedIn: 'root'
})
export class SAPI{
+ static API_VERSION = null
+
/**
* Used to clear BsEndPoint, so the next static get BsEndpoints$ will
* fetch again. Only used for unit test of BsEndpoint$
@@ -44,10 +52,43 @@ export class SAPI{
BS_ENDPOINT_CACHED_VALUE = null
}
+ iteratePages<T>(resp: PaginatedResponse<T>, cb: (page: number) => Observable<PaginatedResponse<T>>) {
+ /**
+ * technically, it's easier to use a concat + merge + reduce map rather than forkJoin + flatmap
+ * but merge does not guarantee same order, forkjoin does
+ * I don't know if page order matters, but it's good to be safe
+ */
+ const pages = Math.ceil(resp.total / resp.size)
+ return forkJoin([
+ of(resp.items),
+
+ /**
+ * similar to python's range function, this function generates a uniformly increasing array, to pages
+ * discarding first, since we already got it
+ */
+ ...Array(pages).fill(null).map((_, idx) => idx + 1).slice(1)
+ .map(page =>
+ cb(page).pipe(
+ map(v => v.items)
+ )
+ )
+ ]).pipe(
+ map(arrOfArr => arrOfArr.flatMap(v => v))
+ )
+ }
+
static async VerifyEndpoint(url: string): Promise<string> {
const resp = await fetch(`${url}/atlases`)
- const atlases = await resp.json()
- if (atlases.length > 0) return url
+ await resp.json()
+ if (resp.status >= 400) {
+ return Promise.reject(resp.statusText)
+ }
+
+ if (!SAPI.API_VERSION) {
+ SAPI.API_VERSION = resp.headers.get(SIIBRA_API_VERSION_HEADER_KEY)
+ console.log(`siibra-api::version::${SAPI.API_VERSION}, expecting::${EXPECTED_SIIBRA_API_VERSION}`)
+ }
+ return url
}
/**
@@ -123,11 +164,6 @@ export class SAPI{
this._map[id] = { func, args }
}
}
-
- getAtlas(atlasId: string): SAPIAtlas {
- return new SAPIAtlas(this, atlasId)
- }
-
getSpace(atlasId: string, spaceId: string): SAPISpace {
return new SAPISpace(this, atlasId, spaceId)
}
@@ -140,35 +176,116 @@ export class SAPI{
return new SAPIRegion(this, atlasId, parcId, regionId)
}
- getSpaceDetail(atlasId: string, spaceId: string, param?: SapiQueryPriorityArg): Observable<SapiSpaceModel> {
- return this.getSpace(atlasId, spaceId).getDetail(param)
+ getSpaceDetail(_atlasId: string, spaceId: string, param?: SapiQueryPriorityArg): Observable<SxplrTemplate> {
+ return this.v3Get("/spaces/{space_id}", {
+ path: {
+ space_id: spaceId
+ },
+ priority: param?.priority
+ }).pipe(
+ switchMap(v => translateV3Entities.translateTemplate(v))
+ )
}
- getParcDetail(atlasId: string, parcId: string, param?: SapiQueryPriorityArg): Observable<SapiParcellationModel> {
- return this.getParcellation(atlasId, parcId).getDetail(param)
+ getParcDetail(atlasId: string, parcId: string, param?: SapiQueryPriorityArg): Observable<SxplrParcellation> {
+ return this.v3Get("/parcellations/{parcellation_id}", {
+ path: {
+ parcellation_id: parcId
+ },
+ priority: param?.priority
+ }).pipe(
+ switchMap(v => translateV3Entities.translateParcellation(v))
+ )
}
- getParcRegions(atlasId: string, parcId: string, spaceId: string, queryParam?: SapiQueryPriorityArg): Observable<SapiRegionModel[]> {
- const parc = this.getParcellation(atlasId, parcId)
- return parc.getRegions(spaceId, queryParam)
+ getParcRegions(atlasId: string, parcId: string, spaceId: string, queryParam?: SapiQueryPriorityArg) {
+ const param = {
+ query: {
+ parcellation_id: parcId,
+ },
+ priority: queryParam?.priority
+ }
+ return this.v3Get("/regions", param).pipe(
+ switchMap(resp =>
+ this.iteratePages(
+ resp,
+ (page) => this.v3Get("/regions", {
+ ...param,
+ query: {
+ ...param.query,
+ page
+ },
+ })
+ ).pipe(
+ switchMap(regions => forkJoin(regions.map(r => translateV3Entities.translateRegion(r)))),
+ )
+ ),
+ )
+ }
+
+ getMap(parcId: string, spaceId: string, mapType: "LABELLED" | "STATISTICAL", queryParam?: SapiQueryPriorityArg) {
+ return this.v3Get("/map", {
+ query: {
+ map_type: mapType,
+ parcellation_id: parcId,
+ space_id: spaceId
+ }
+ })
}
getFeature(featureId: string, opts: Record<string, string> = {}) {
return new SAPIFeature(this, featureId, opts)
}
- getRegionFeatures(atlasId: string, parcId: string, spaceId: string, regionId: string, priority = 0): Observable<(SapiRegionalFeatureModel | SxplrCleanedFeatureModel)[]>{
+ getModalities() {
+ return this.v3Get("/feature/_types", { query: {} }).pipe(
+ map(v => v.items)
+ )
+ }
- const reg = this.getRegion(atlasId, parcId, regionId)
- return reg.getFeatures(spaceId)
+ v3GetRoute<T extends SapiRoute>(route: T, sapiParam: RouteParam<T>) {
+ const params: Record<string, string|number> = "query" in sapiParam ? sapiParam["query"] : {}
+ const _path: Record<string, string|number> = "path" in sapiParam ? sapiParam["path"] : {}
+ let path: string = route
+ for (const key in _path) {
+ path = path.replace(`{${key}}`, _path[key].toString())
+ }
+ return { path, params }
}
- getModalities(): Observable<SapiModalityModel[]> {
+ /**
+ * Should be privated. All components use this method forms a tight coupling to API
+ * Use this method sparingly!
+ * @param route
+ * @param sapiParam
+ * @returns
+ */
+ v3Get<T extends SapiRoute>(route: T, sapiParam: RouteParam<T> & Partial<{ priority: number }>){
return SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.http.get<SapiModalityModel[]>(`${endpt}/modalities`))
+ switchMap(endpoint => {
+ const headers: Record<string, string> = {}
+ if (sapiParam?.priority) {
+ headers[PRIORITY_HEADER] = sapiParam.priority.toString()
+ }
+ const { path, params } = this.v3GetRoute(route, sapiParam)
+ return this.http.get<PathReturn<T>>(
+ `${endpoint}${path}`,
+ {
+ headers,
+ params
+ }
+ )
+ })
)
}
+ /**
+ * @deprecated
+ * @param url
+ * @param params
+ * @param sapiParam
+ * @returns
+ */
httpGet<T>(url: string, params?: Record<string, string>, sapiParam?: SapiQueryPriorityArg){
const headers: Record<string, string> = {}
if (sapiParam?.priority) {
@@ -183,25 +300,183 @@ export class SAPI{
)
}
- public atlases$ = SAPI.BsEndpoint$.pipe(
- switchMap(endpt => this.http.get<SapiAtlasModel[]>(
- `${endpt}/atlases`,
- {
- observe: "response"
- }
+ public atlases$ = this.v3Get("/atlases", {
+ query: {}
+ }).pipe(
+ switchMap(atlases => forkJoin(
+ atlases.items.map(atlas => translateV3Entities.translateAtlas(atlas))
)),
- map(resp => {
- const respVersion = resp.headers.get(SIIBRA_API_VERSION_HEADER_KEY)
- if (respVersion !== SIIBRA_API_VERSION) {
- this.snackbar.open(`Expecting ${SIIBRA_API_VERSION}, got ${respVersion}. Some functionalities may not work as expected.`, 'Dismiss', {
+ tap(() => {
+ const respVersion = SAPI.API_VERSION
+ if (respVersion !== EXPECTED_SIIBRA_API_VERSION) {
+ this.snackbar.open(`Expecting ${EXPECTED_SIIBRA_API_VERSION}, got ${respVersion}. Some functionalities may not work as expected.`, 'Dismiss', {
duration: 5000
})
}
- console.log(`siibra-api::version::${respVersion}, expecting::${SIIBRA_API_VERSION}`)
- return resp.body
}),
- shareReplay(1)
+ shareReplay(1),
)
+
+
+ public getAllSpaces(atlas: SxplrAtlas): Observable<SxplrTemplate[]> {
+ return forkJoin(
+ translateV3Entities.retrieveAtlas(atlas).spaces.map(
+ spc => this.v3Get("/spaces/{space_id}", { path: { space_id: spc["@id"] } }).pipe(
+ switchMap(v => translateV3Entities.translateTemplate(v))
+ )
+ )
+ )
+ }
+
+ public getAllParcellations(atlas: SxplrAtlas): Observable<SxplrParcellation[]> {
+ return forkJoin(
+ translateV3Entities.retrieveAtlas(atlas).parcellations.map(
+ parc => this.v3Get("/parcellations/{parcellation_id}", { path: { parcellation_id: parc["@id"] } }).pipe(
+ switchMap(v => translateV3Entities.translateParcellation(v))
+ )
+ )
+ )
+ }
+
+ #tmplToParcMap = new Map<string, SxplrParcellation[]>()
+ public getSupportedParcellations(atlas: SxplrAtlas, template: SxplrTemplate): Observable<any|SxplrParcellation[]> {
+ if (!template) {
+ return throwError(`template cannot be empty!`)
+ }
+ if (this.#tmplToParcMap.has(template.id)) {
+ return of(this.#tmplToParcMap.get(template.id))
+ }
+ return this.getAllParcellations(atlas).pipe(
+ switchMap(parcs => forkJoin(
+ parcs.map(
+ parc => this.getMap(
+ parc.id,
+ template.id,
+ "LABELLED"
+ ).pipe(
+ catchError((err, obs) => of(null as SxplrParcellation)),
+ map(_map => _map && parc)
+ )
+ )
+ ).pipe(
+ map(arr => {
+ const val = arr.filter(v => !!v)
+ this.#tmplToParcMap.set(template.id, val)
+ return val
+ })
+ ))
+ )
+ }
+
+ #parcIdToTmplMap = new Map<string, SxplrTemplate[]>()
+ public getSupportedTemplates(atlas: SxplrAtlas, parc: SxplrParcellation): Observable<SxplrTemplate[]> {
+ if (!parc) {
+ return throwError(`parc cannot be empty!`)
+ }
+ if (this.#parcIdToTmplMap.has(parc.id)) {
+ return of(this.#parcIdToTmplMap.get(parc.id))
+ }
+ return this.getAllSpaces(atlas).pipe(
+ switchMap(spaces => forkJoin(
+ spaces.map(
+ space => this.getMap(
+ parc.id,
+ space.id,
+ "LABELLED"
+ ).pipe(
+ catchError((err, obs) => of(null)),
+ map(_map => _map && space)
+ )
+ )
+ ).pipe(
+ map(arr => {
+ const val = arr.filter(v => !!v)
+ this.#parcIdToTmplMap.set(parc.id, val)
+ return val
+ })
+ ))
+ )
+ }
+
+ public getVoiFeatures(bbox: BoundingBox): Observable<VoiFeature[]> {
+ /**
+ * FIXME iterate over all pages
+ */
+ return this.v3Get("/feature/VolumeOfInterest", {
+ query: {
+ space_id: bbox.space.id,
+ bbox: JSON.stringify([bbox.minpoint, bbox.maxpoint]),
+ }
+ }).pipe(
+ switchMap(v => Promise.all(v.items.map(item => translateV3Entities.translateVoi(item))))
+ )
+ }
+
+ private async getLabelledMap(parcellation: SxplrParcellation, template: SxplrTemplate) {
+ // No need to retrieve sapi object, since we know @id maps to id
+ return await this.v3Get("/map", {
+ query: {
+ map_type: "LABELLED",
+ parcellation_id: parcellation.id,
+ space_id: template.id
+ }
+ }).toPromise()
+ }
+
+ public getVoxelTemplateImage(template: SxplrTemplate) {
+ return from(translateV3Entities.translateSpaceToVolumeImage(template))
+ }
+
+ public getVoxelAuxMesh(template: SxplrTemplate) {
+ return from(translateV3Entities.translateSpaceToAuxMesh(template))
+ }
+
+ public getSurfaceTemplateImage(template: SxplrTemplate) {
+ return from(translateV3Entities.translateSpaceToSurfaceImage(template))
+ }
+ /**
+ * Even though this creates a rather tight coupling between sapi.server and nehuba viewer module
+ * This is better than the alternative, which is creating a tight coupling between nehuba viewer module and siibra-api
+ */
+
+ public async getTranslatedLabelledNgMap(parcellation: SxplrParcellation, template: SxplrTemplate) {
+ if (!parcellation || !template) return {}
+ const map = await this.getLabelledMap(parcellation, template)
+ return await translateV3Entities.translateLabelledMapToNgSegLayers(map)
+ }
+
+ public async getTranslatedLabelledThreeMap(parcellation: SxplrParcellation, template: SxplrTemplate){
+ if (!parcellation || !template) return {}
+ const map = await this.getLabelledMap(parcellation, template)
+ return await translateV3Entities.translateLabelledMapToThreeLabel(map)
+ }
+
+ #tmplParcMap = new Map<string, PathReturn<"/map">>()
+ public async getRegionLabelIndices(tmpl: SxplrTemplate, parc: SxplrParcellation, region: SxplrRegion) {
+ const key = `${tmpl.id}::${parc.id}`
+
+ if (!this.#tmplParcMap.has(key)) {
+ const _map = await this.v3Get("/map", {
+ query: {
+ map_type: "LABELLED",
+ parcellation_id: parc.id,
+ space_id: tmpl.id
+ }
+ }).toPromise()
+ this.#tmplParcMap.set(key, _map)
+ }
+
+ const { indices } = this.#tmplParcMap.get(key)
+ const index = indices[region.name] || []
+ if (index.length === 0) {
+ throw new Error(`No map index found for ${region.name}`)
+ }
+ if (index.length !== 1) {
+ console.warn(`Multiple map indicies found... Using the first one`)
+ }
+ const _index = index[0]
+ return _index.label
+ }
constructor(
public http: HttpClient,
@@ -213,11 +488,12 @@ export class SAPI{
}
this.atlases$.subscribe(atlases => {
for (const atlas of atlases) {
- for (const space of atlas.spaces) {
+ const sapiAtlas = translateV3Entities.retrieveAtlas(atlas)
+ for (const space of sapiAtlas.spaces) {
this.registry.set(space["@id"], this.getSpace.bind(this), [atlas["@id"], space["@id"]])
this.getSpaceDetail(atlas["@id"], space["@id"])
}
- for (const parc of atlas.parcellations) {
+ for (const parc of sapiAtlas.parcellations) {
this.registry.set(parc["@id"], this.getParcellation.bind(this), [atlas["@id"], parc["@id"]])
this.getParcDetail(atlas["@id"], parc["@id"])
}
@@ -225,8 +501,16 @@ export class SAPI{
})
}
- async processNpArrayData<T extends keyof ProcessTypedArrayResult>(input: SpyNpArrayDataModel, method: PARSE_TYPEDARRAY = PARSE_TYPEDARRAY.RAW_ARRAY, params: ProcessTypedArrayResult[T]['input'] = null): Promise<ProcessTypedArrayResult[T]['output']> {
-
+ /**
+ *
+ * @deprecated
+ * @param input
+ * @param method
+ * @param params
+ * @returns
+ */
+ async processNpArrayData<T extends keyof ProcessTypedArrayResult>(input: any /*SpyNpArrayDataModel*/, method: PARSE_TYPEDARRAY = PARSE_TYPEDARRAY.RAW_ARRAY, params: ProcessTypedArrayResult[T]['input'] = null): Promise<ProcessTypedArrayResult[T]['output']> {
+ return null
const supportedDtype = [
"uint8",
"int32",
@@ -300,6 +584,9 @@ export class SAPI{
}
}
+/**
+ * @deprecated
+ */
export enum PARSE_TYPEDARRAY {
CANVAS_FORTRAN_RGBA="CANVAS_FORTRAN_RGBA",
CANVAS_COLORMAP_RGBA="CANVAS_COLORMAP_RGBA",
diff --git a/src/atlasComponents/sapi/schema.ts b/src/atlasComponents/sapi/schema.ts
index 49f3d1b3f257f321dd8704cf10ae93c55ee9e1e5..abec3c87032beadb1865bef6b3a97f9834138871 100644
--- a/src/atlasComponents/sapi/schema.ts
+++ b/src/atlasComponents/sapi/schema.ts
@@ -1,2035 +1,2035 @@
-/**
- * This file was auto-generated by openapi-typescript.
- * Do not make direct changes to the file.
- */
+// /**
+// * This file was auto-generated by openapi-typescript.
+// * Do not make direct changes to the file.
+// */
-export interface paths {
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions": {
- /** Returns all regions for a given parcellation id. */
- get: operations["get_all_regions_from_atlas_parc_space_atlases__atlas_id__parcellations__parcellation_id__regions_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features": {
- /** Returns all regional features for a region. */
- get: operations["get_all_regional_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features/{feature_id}": {
- /** Returns a feature for a region, as defined by the modality and feature ID */
- get: operations["get_single_detailed_regional_feature_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/regional_map/info": {
- /** Returns information about a regional map for given region name. */
- get: operations["get_regional_map_info_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_info_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/regional_map/map": {
- /** Returns a regional map for given region name. */
- get: operations["get_regional_map_file_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_map_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/volumes": {
- get: operations["get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/volumes/{volume_id}": {
- get: operations["get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes__volume_id__get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}": {
- get: operations["get_single_region_detail_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__get"]
- }
- "/atlases/{atlas_id}/parcellations": {
- /** Returns all parcellations that are defined in the siibra client for given atlas. */
- get: operations["get_all_parcellations_atlases__atlas_id__parcellations_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/features/{feature_id}": {
- /** Returns a global feature for a specific modality id. */
- get: operations["get_single_detailed_global_feature_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/features": {
- /** Returns all global features for a parcellation. */
- get: operations["get_all_global_features_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__features_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}/volumes": {
- /** Returns one parcellation for given id. */
- get: operations["get_volumes_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__volumes_get"]
- }
- "/atlases/{atlas_id}/parcellations/{parcellation_id}": {
- /** Returns one parcellation for given id. */
- get: operations["get_single_parcellation_detail_atlases__atlas_id__parcellations__parcellation_id__get"]
- }
- "/atlases/{atlas_id}/spaces": {
- /** Returns all spaces that are defined in the siibra client. */
- get: operations["get_all_spaces_atlases__atlas_id__spaces_get"]
- }
- "/atlases/{atlas_id}/spaces/{space_id}/templates": {
- /** Returns a template for a given space id. */
- get: operations["get_template_by_space_id_atlases__atlas_id__spaces__space_id__templates_get"]
- }
- "/atlases/{atlas_id}/spaces/{space_id}/parcellation_maps": {
- /** Returns all parcellation maps for a given space id. */
- get: operations["get_parcellation_map_for_space_atlases__atlas_id__spaces__space_id__parcellation_maps_get"]
- }
- "/atlases/{atlas_id}/spaces/{space_id}/features/{feature_id}": {
- /**
- * Get a detailed view on a single spatial feature.
- * A parcellation id and region id can be provided optional to get more details.
- */
- get: operations["get_single_detailed_spatial_feature_atlases__atlas_id__spaces__space_id__features__feature_id__get"]
- }
- "/atlases/{atlas_id}/spaces/{space_id}/features": {
- /** Return all possible feature names and links to get more details */
- get: operations["get_all_spatial_features_for_space_atlases__atlas_id__spaces__space_id__features_get"]
- }
- "/atlases/{atlas_id}/spaces/{space_id}/volumes": {
- get: operations["get_volumes_for_space_atlases__atlas_id__spaces__space_id__volumes_get"]
- }
- "/atlases/{atlas_id}/spaces/{space_id}": {
- /** Returns one space for given id, with links to further resources */
- get: operations["get_single_space_detail_atlases__atlas_id__spaces__space_id__get"]
- }
- "/atlases": {
- /** Get all atlases known by siibra. */
- get: operations["get_all_atlases_atlases_get"]
- }
- "/atlases/{atlas_id}": {
- /** Get more information for a specific atlas with links to further objects. */
- get: operations["get_atlas_by_id_atlases__atlas_id__get"]
- }
- "/genes": {
- /** Return all genes (name, acronym) in siibra */
- get: operations["get_gene_names_genes_get"]
- }
- "/modalities": {
- /** Return all possible modalities */
- get: operations["get_all_available_modalities_modalities_get"]
- }
- "/features/{feature_id}": {
- /**
- * Get all details for one feature by id.
- * Since the feature id is unique, no atlas concept is required.
- *
- * Further optional params can extend the result.
- * :param feature_id:
- * :param atlas_id:
- * :param space_id:
- * :param parcellation_id:
- * :param region_id:
- * :return: FeatureModels
- */
- get: operations["get_feature_details_features__feature_id__get"]
- }
-}
+// export interface paths {
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions": {
+// /** Returns all regions for a given parcellation id. */
+// get: operations["get_all_regions_from_atlas_parc_space_atlases__atlas_id__parcellations__parcellation_id__regions_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features": {
+// /** Returns all regional features for a region. */
+// get: operations["get_all_regional_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features/{feature_id}": {
+// /** Returns a feature for a region, as defined by the modality and feature ID */
+// get: operations["get_single_detailed_regional_feature_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/regional_map/info": {
+// /** Returns information about a regional map for given region name. */
+// get: operations["get_regional_map_info_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_info_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/regional_map/map": {
+// /** Returns a regional map for given region name. */
+// get: operations["get_regional_map_file_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_map_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/volumes": {
+// get: operations["get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/volumes/{volume_id}": {
+// get: operations["get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes__volume_id__get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}": {
+// get: operations["get_single_region_detail_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__get"]
+// }
+// "/atlases/{atlas_id}/parcellations": {
+// /** Returns all parcellations that are defined in the siibra client for given atlas. */
+// get: operations["get_all_parcellations_atlases__atlas_id__parcellations_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/features/{feature_id}": {
+// /** Returns a global feature for a specific modality id. */
+// get: operations["get_single_detailed_global_feature_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/features": {
+// /** Returns all global features for a parcellation. */
+// get: operations["get_all_global_features_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__features_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}/volumes": {
+// /** Returns one parcellation for given id. */
+// get: operations["get_volumes_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__volumes_get"]
+// }
+// "/atlases/{atlas_id}/parcellations/{parcellation_id}": {
+// /** Returns one parcellation for given id. */
+// get: operations["get_single_parcellation_detail_atlases__atlas_id__parcellations__parcellation_id__get"]
+// }
+// "/atlases/{atlas_id}/spaces": {
+// /** Returns all spaces that are defined in the siibra client. */
+// get: operations["get_all_spaces_atlases__atlas_id__spaces_get"]
+// }
+// "/atlases/{atlas_id}/spaces/{space_id}/templates": {
+// /** Returns a template for a given space id. */
+// get: operations["get_template_by_space_id_atlases__atlas_id__spaces__space_id__templates_get"]
+// }
+// "/atlases/{atlas_id}/spaces/{space_id}/parcellation_maps": {
+// /** Returns all parcellation maps for a given space id. */
+// get: operations["get_parcellation_map_for_space_atlases__atlas_id__spaces__space_id__parcellation_maps_get"]
+// }
+// "/atlases/{atlas_id}/spaces/{space_id}/features/{feature_id}": {
+// /**
+// * Get a detailed view on a single spatial feature.
+// * A parcellation id and region id can be provided optional to get more details.
+// */
+// get: operations["get_single_detailed_spatial_feature_atlases__atlas_id__spaces__space_id__features__feature_id__get"]
+// }
+// "/atlases/{atlas_id}/spaces/{space_id}/features": {
+// /** Return all possible feature names and links to get more details */
+// get: operations["get_all_spatial_features_for_space_atlases__atlas_id__spaces__space_id__features_get"]
+// }
+// "/atlases/{atlas_id}/spaces/{space_id}/volumes": {
+// get: operations["get_volumes_for_space_atlases__atlas_id__spaces__space_id__volumes_get"]
+// }
+// "/atlases/{atlas_id}/spaces/{space_id}": {
+// /** Returns one space for given id, with links to further resources */
+// get: operations["get_single_space_detail_atlases__atlas_id__spaces__space_id__get"]
+// }
+// "/atlases": {
+// /** Get all atlases known by siibra. */
+// get: operations["get_all_atlases_atlases_get"]
+// }
+// "/atlases/{atlas_id}": {
+// /** Get more information for a specific atlas with links to further objects. */
+// get: operations["get_atlas_by_id_atlases__atlas_id__get"]
+// }
+// "/genes": {
+// /** Return all genes (name, acronym) in siibra */
+// get: operations["get_gene_names_genes_get"]
+// }
+// "/modalities": {
+// /** Return all possible modalities */
+// get: operations["get_all_available_modalities_modalities_get"]
+// }
+// "/features/{feature_id}": {
+// /**
+// * Get all details for one feature by id.
+// * Since the feature id is unique, no atlas concept is required.
+// *
+// * Further optional params can extend the result.
+// * :param feature_id:
+// * :param atlas_id:
+// * :param space_id:
+// * :param parcellation_id:
+// * :param region_id:
+// * :return: FeatureModels
+// */
+// get: operations["get_feature_details_features__feature_id__get"]
+// }
+// }
-export interface components {
- schemas: {
- /** AutoradiographyDataModel */
- AutoradiographyDataModel: {
- /**
- * Content Type
- * @default application/octet-stream
- */
- content_type?: string
- /**
- * Content Encoding
- * @default gzip; base64
- */
- content_encoding?: string
- /** X-Width */
- "x-width": number
- /** X-Height */
- "x-height": number
- /** X-Channel */
- "x-channel": number
- /** Dtype */
- dtype: string
- /** Content */
- content: string
- }
- /** AxesOrigin */
- AxesOrigin: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * typeOfUncertainty
- * @description Distinct technique used to quantify the uncertainty of a measurement.
- */
- typeOfUncertainty?: unknown
- /**
- * uncertainty
- * @description Quantitative value range defining the uncertainty of a measurement.
- */
- uncertainty?: number[]
- /**
- * unit
- * @description Determinate quantity adopted as a standard of measurement.
- */
- unit?: unknown
- /**
- * value
- * @description Entry for a property.
- */
- value: number
- }
- /** BaseDatasetJsonModel */
- BaseDatasetJsonModel: {
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "https://openminds.ebrains.eu/core/DatasetVersion"
- metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
- /** Urls */
- urls: components["schemas"]["Url"][]
- }
- /** BestViewPoint */
- BestViewPoint: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * coordinateSpace
- * @description Two or three dimensional geometric setting.
- */
- coordinateSpace: unknown
- /**
- * Coordinates
- * @description Structured information on a quantitative value.
- */
- coordinates: components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Coordinates"][]
- }
- /** BoundingBoxModel */
- BoundingBoxModel: {
- /** @Type */
- "@type": string
- /** Space */
- space: { [key: string]: string }
- center: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
- minpoint: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
- maxpoint: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
- /** Shape */
- shape: number[]
- /** Isplanar */
- isPlanar: boolean
- }
- /** ConnectivityMatrixDataModel */
- ConnectivityMatrixDataModel: {
- /** @Id */
- "@id": string
- /** @Type */
- "@type": string
- /** Name */
- name?: string
- /** Description */
- description?: string
- /** Citation */
- citation?: string
- /** Authors */
- authors?: string[]
- /** Cohort */
- cohort?: string
- /** Subject */
- subject?: string
- /** Filename */
- filename?: string
- /** Dataset Id */
- dataset_id?: string
- /** Parcellations */
- parcellations: { [key: string]: string }[]
- matrix?: components["schemas"]["NpArrayDataModel"]
- /** Columns */
- columns?: string[]
- }
- /** CorticalCellDistributionModel */
- CorticalCellDistributionModel: {
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "siibra/features/cells"
- metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
- /** Urls */
- urls: components["schemas"]["Url"][]
- /** Cells */
- cells?: components["schemas"]["CorticalCellModel"][]
- /** Section */
- section?: string
- /** Patch */
- patch?: string
- }
- /** CorticalCellModel */
- CorticalCellModel: {
- /** X */
- x: number
- /** Y */
- y: number
- /** Area */
- area: number
- /** Layer */
- layer: number
- /** Instance Label */
- "instance label": number
- }
- /** DatasetJsonModel */
- DatasetJsonModel: {
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "https://openminds.ebrains.eu/core/DatasetVersion"
- metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
- /** Urls */
- urls: components["schemas"]["Url"][]
- }
- /** FingerPrintDataModel */
- FingerPrintDataModel: {
- /** Mean */
- mean: number
- /** Std */
- std: number
- /** Unit */
- unit: string
- }
- /** HTTPValidationError */
- HTTPValidationError: {
- /** Detail */
- detail?: components["schemas"]["ValidationError"][]
- }
- /** HasAnnotation */
- HasAnnotation: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * Bestviewpoint
- * @description Structured information on a coordinate point.
- */
- bestViewPoint?: components["schemas"]["BestViewPoint"]
- /**
- * criteria
- * @description Aspects or standards on which a judgement or decision is based.
- */
- criteria?: unknown
- /**
- * criteriaQualityType
- * @description Distinct class that defines how the judgement or decision was made for a particular criteria.
- */
- criteriaQualityType: unknown
- /**
- * displayColor
- * @description Preferred coloring.
- */
- displayColor?: string
- /**
- * inspiredBy
- * @description Reference to an inspiring element.
- */
- inspiredBy?: unknown[]
- /**
- * internalIdentifier
- * @description Term or code that identifies someone or something within a particular product.
- */
- internalIdentifier: string
- /**
- * laterality
- * @description Differentiation between a pair of lateral homologous parts of the body.
- */
- laterality?: unknown[]
- /**
- * visualizedIn
- * @description Reference to an image in which something is visible.
- */
- visualizedIn?: unknown
- }
- /** HasTerminologyVersion */
- HasTerminologyVersion: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * definedIn
- * @description Reference to a file instance in which something is stored.
- */
- definedIn?: unknown[]
- /** hasEntityVersion */
- hasEntityVersion: unknown[]
- /**
- * ontologyIdentifier
- * @description Term or code used to identify something or someone registered within a particular ontology.
- */
- ontologyIdentifier?: string[]
- }
- /** HrefModel */
- HrefModel: {
- /** Href */
- href: string
- }
- /** IEEGContactPointModel */
- IEEGContactPointModel: {
- /** Inroi */
- inRoi?: boolean
- /** Id */
- id: string
- point: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
- }
- /** IEEGElectrodeModel */
- IEEGElectrodeModel: {
- /** Inroi */
- inRoi?: boolean
- /** Electrode Id */
- electrode_id: string
- /** Contact Points */
- contact_points: {
- [key: string]: components["schemas"]["IEEGContactPointModel"]
- }
- }
- /** IEEGSessionModel */
- IEEGSessionModel: {
- /** Inroi */
- inRoi?: boolean
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "siibra/features/ieegSession"
- dataset: components["schemas"]["DatasetJsonModel"]
- /** Sub Id */
- sub_id: string
- /** Electrodes */
- electrodes: {
- [key: string]: components["schemas"]["IEEGElectrodeModel"]
- }
- }
- /** NeurotransmitterMarkupModel */
- NeurotransmitterMarkupModel: {
- /** Latex */
- latex: string
- /** Markdown */
- markdown: string
- /** Name */
- name: string
- /** Label */
- label: string
- }
- /** NiiMetadataModel */
- NiiMetadataModel: {
- /** Min */
- min: number
- /** Max */
- max: number
- }
- /** NpArrayDataModel */
- NpArrayDataModel: {
- /**
- * Content Type
- * @default application/octet-stream
- */
- content_type?: string
- /**
- * Content Encoding
- * @default gzip; base64
- */
- content_encoding?: string
- /** X-Width */
- "x-width": number
- /** X-Height */
- "x-height": number
- /** X-Channel */
- "x-channel": number
- /** Dtype */
- dtype: string
- /** Content */
- content: string
- }
- /** Page[Union[siibra.features.connectivity.ConnectivityMatrixDataModel, app.models.SerializationErrorModel]] */
- "Page_Union_siibra.features.connectivity.ConnectivityMatrixDataModel__app.models.SerializationErrorModel__": {
- /** Items */
- items: (Partial<components["schemas"]["ConnectivityMatrixDataModel"]> &
- Partial<components["schemas"]["SerializationErrorModel"]>)[]
- /** Total */
- total: number
- /** Page */
- page: number
- /** Size */
- size: number
- }
- /** Page[VolumeModel] */
- Page_VolumeModel_: {
- /** Items */
- items: components["schemas"]["VolumeModel"][]
- /** Total */
- total: number
- /** Page */
- page: number
- /** Size */
- size: number
- }
- /** ProfileDataModel */
- ProfileDataModel: {
- density: components["schemas"]["NpArrayDataModel"]
- /** Unit */
- unit: string
- }
- /** QuantitativeOverlapItem */
- QuantitativeOverlapItem: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * typeOfUncertainty
- * @description Distinct technique used to quantify the uncertainty of a measurement.
- */
- typeOfUncertainty?: unknown
- /**
- * uncertainty
- * @description Quantitative value range defining the uncertainty of a measurement.
- */
- uncertainty?: number[]
- /**
- * unit
- * @description Determinate quantity adopted as a standard of measurement.
- */
- unit?: unknown
- /**
- * value
- * @description Entry for a property.
- */
- value: number
- }
- /** QuantitativeOverlapItem1 */
- QuantitativeOverlapItem1: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * maxValue
- * @description Greatest quantity attained or allowed.
- */
- maxValue: number
- /** maxValueUnit */
- maxValueUnit?: unknown
- /**
- * minValue
- * @description Smallest quantity attained or allowed.
- */
- minValue: number
- /** minValueUnit */
- minValueUnit?: unknown
- }
- /** ReceptorDataModel */
- ReceptorDataModel: {
- /** Autoradiographs */
- autoradiographs: {
- [key: string]: components["schemas"]["AutoradiographyDataModel"]
- }
- /** Profiles */
- profiles: { [key: string]: components["schemas"]["ProfileDataModel"] }
- /** Fingerprints */
- fingerprints: {
- [key: string]: components["schemas"]["FingerPrintDataModel"]
- }
- /** Receptor Symbols */
- receptor_symbols: {
- [key: string]: components["schemas"]["SymbolMarkupClass"]
- }
- }
- /** ReceptorDatasetModel */
- ReceptorDatasetModel: {
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "siibra/features/receptor"
- metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
- /** Urls */
- urls: components["schemas"]["Url"][]
- data?: components["schemas"]["ReceptorDataModel"]
- }
- /** ReceptorMarkupModel */
- ReceptorMarkupModel: {
- /** Latex */
- latex: string
- /** Markdown */
- markdown: string
- /** Name */
- name: string
- }
- /** RelationAssessmentItem */
- RelationAssessmentItem: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * criteria
- * @description Aspects or standards on which a judgement or decision is based.
- */
- criteria?: unknown
- /**
- * inRelationTo
- * @description Reference to a related element.
- */
- inRelationTo: unknown
- /**
- * qualitativeOverlap
- * @description Semantic characterization of how much two things occupy the same space.
- */
- qualitativeOverlap: unknown
- }
- /** RelationAssessmentItem1 */
- RelationAssessmentItem1: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * criteria
- * @description Aspects or standards on which a judgement or decision is based.
- */
- criteria?: unknown
- /**
- * inRelationTo
- * @description Reference to a related element.
- */
- inRelationTo: unknown
- /** Quantitativeoverlap */
- quantitativeOverlap: Partial<
- components["schemas"]["QuantitativeOverlapItem"]
- > &
- Partial<components["schemas"]["QuantitativeOverlapItem1"]>
- }
- /** SapiAtlasModel */
- SapiAtlasModel: {
- /** Links */
- links: { [key: string]: components["schemas"]["HrefModel"] }
- /** @Id */
- "@id": string
- /** Name */
- name: string
- /**
- * @Type
- * @constant
- */
- "@type"?: "juelich/iav/atlas/v1.0.0"
- /** Spaces */
- spaces: components["schemas"]["SiibraAtIdModel"][]
- /** Parcellations */
- parcellations: components["schemas"]["SiibraAtIdModel"][]
- species: components["schemas"]["SpeciesModel"]
- }
- /** SapiParcellationModel */
- SapiParcellationModel: {
- /** Links */
- links: { [key: string]: components["schemas"]["HrefModel"] }
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "minds/core/parcellationatlas/v1.0.0"
- /** Name */
- name: string
- /** Modality */
- modality?: string
- /** Datasets */
- datasets: components["schemas"]["DatasetJsonModel"][]
- /** Brainatlasversions */
- brainAtlasVersions: components["schemas"]["siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Model"][]
- version?: components["schemas"]["SiibraParcellationVersionModel"]
- }
- /** SapiSpaceModel */
- SapiSpaceModel: {
- /** Links */
- links: { [key: string]: components["schemas"]["HrefModel"] }
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * @Id
- * @description Metadata node identifier.
- */
- "@id": string
- /** @Type */
- "@type": string
- /**
- * anatomicalAxesOrientation
- * @description Relation between reference planes used in anatomy and mathematics.
- */
- anatomicalAxesOrientation: { [key: string]: unknown }
- /**
- * Axesorigin
- * @description Structured information on a quantitative value.
- */
- axesOrigin: components["schemas"]["AxesOrigin"][]
- /**
- * defaultImage
- * @description Two or three dimensional image that particluarly represents a specific coordinate space.
- */
- defaultImage?: unknown[]
- /**
- * digitalIdentifier
- * @description Digital handle to identify objects or legal persons.
- */
- digitalIdentifier?: { [key: string]: unknown }
- /**
- * fullName
- * @description Whole, non-abbreviated name of something or somebody.
- */
- fullName: string
- /**
- * homepage
- * @description Main website of something or someone.
- */
- homepage?: { [key: string]: unknown }
- /**
- * howToCite
- * @description Preferred format for citing a particular object or legal person.
- */
- howToCite?: string
- /**
- * nativeUnit
- * @description Determinate quantity used in the original measurement.
- */
- nativeUnit: { [key: string]: unknown }
- /**
- * ontologyIdentifier
- * @description Term or code used to identify something or someone registered within a particular ontology.
- */
- ontologyIdentifier?: string[]
- /**
- * releaseDate
- * Format: date
- * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
- */
- releaseDate: string
- /**
- * shortName
- * @description Shortened or fully abbreviated name of something or somebody.
- */
- shortName: string
- /**
- * versionIdentifier
- * @description Term or code used to identify the version of something.
- */
- versionIdentifier: string
- }
- /** SerializationErrorModel */
- SerializationErrorModel: {
- /**
- * Type
- * @constant
- */
- type?: "spy/serialization-error"
- /** Message */
- message: string
- }
- /** SiibraAtIdModel */
- SiibraAtIdModel: {
- /** @Id */
- "@id": string
- }
- /** SiibraParcellationVersionModel */
- SiibraParcellationVersionModel: {
- /** Name */
- name: string
- /** Deprecated */
- deprecated?: boolean
- prev?: components["schemas"]["SiibraAtIdModel"]
- next?: components["schemas"]["SiibraAtIdModel"]
- }
- /** SpeciesModel */
- SpeciesModel: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * @Id
- * @description Metadata node identifier.
- */
- "@id": string
- /** @Type */
- "@type": string
- /**
- * definition
- * @description Short, but precise statement of the meaning of a word, word group, sign or a symbol.
- */
- definition?: string
- /**
- * description
- * @description Longer statement or account giving the characteristics of someone or something.
- */
- description?: string
- /**
- * interlexIdentifier
- * @description Persistent identifier for a term registered in the InterLex project.
- */
- interlexIdentifier?: string
- /**
- * knowledgeSpaceLink
- * @description Persistent link to an encyclopedia entry in the Knowledge Space project.
- */
- knowledgeSpaceLink?: string
- /**
- * name
- * @description Word or phrase that constitutes the distinctive designation of a being or thing.
- */
- name: string
- /**
- * preferredOntologyIdentifier
- * @description Persistent identifier of a preferred ontological term.
- */
- preferredOntologyIdentifier?: string
- /**
- * synonym
- * @description Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.
- */
- synonym?: string[]
- /** Kgv1Id */
- kgV1Id: string
- }
- /** SymbolMarkupClass */
- SymbolMarkupClass: {
- receptor: components["schemas"]["ReceptorMarkupModel"]
- neurotransmitter: components["schemas"]["NeurotransmitterMarkupModel"]
- }
- /** Url */
- Url: {
- /** Doi */
- doi: string
- /** Cite */
- cite?: string
- }
- /** VOIDataModel */
- VOIDataModel: {
- /** @Id */
- "@id": string
- /**
- * @Type
- * @constant
- */
- "@type"?: "siibra/features/voi"
- metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
- /** Urls */
- urls: components["schemas"]["Url"][]
- /** Volumes */
- volumes: components["schemas"]["VolumeModel"][]
- location: components["schemas"]["BoundingBoxModel"]
- }
- /** ValidationError */
- ValidationError: {
- /** Location */
- loc: (Partial<string> & Partial<number>)[]
- /** Message */
- msg: string
- /** Error Type */
- type: string
- }
- /** VocabModel */
- VocabModel: {
- /** @Vocab */
- "@vocab": string
- }
- /** VolumeDataModel */
- VolumeDataModel: {
- /** Type */
- type: string
- /** Is Volume */
- is_volume: boolean
- /** Is Surface */
- is_surface: boolean
- /** Detail */
- detail: { [key: string]: unknown }
- space: components["schemas"]["SiibraAtIdModel"]
- /** Url */
- url?: string
- /** Url Map */
- url_map?: { [key: string]: string }
- /** Map Type */
- map_type?: string
- /** Volume Type */
- volume_type?: string
- }
- /** VolumeModel */
- VolumeModel: {
- /** @Id */
- "@id": string
- /** @Type */
- "@type": string
- metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
- /** Urls */
- urls: components["schemas"]["Url"][]
- data: components["schemas"]["VolumeDataModel"]
- }
- /** Copyright */
- siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Copyright: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * holder
- * @description Legal person in possession of something.
- */
- holder: unknown[]
- /**
- * year
- * @description Cycle in the Gregorian calendar specified by a number and comprised of 365 or 366 days divided into 12 months beginning with January and ending with December.
- */
- year: string
- }
- /** Model */
- siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Model: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * @Id
- * @description Metadata node identifier.
- */
- "@id": string
- /** @Type */
- "@type": string
- /** abbreviation */
- abbreviation?: string
- /**
- * accessibility
- * @description Level to which something is accessible to someone or something.
- */
- accessibility: { [key: string]: unknown }
- /** atlasType */
- atlasType?: { [key: string]: unknown }
- /**
- * author
- * @description Creator of a literary or creative work, as well as a dataset publication.
- */
- author?: unknown[]
- /**
- * coordinateSpace
- * @description Two or three dimensional geometric setting.
- */
- coordinateSpace: { [key: string]: unknown }
- /**
- * Copyright
- * @description Structured information on the copyright.
- */
- copyright?: components["schemas"]["siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Copyright"]
- /**
- * custodian
- * @description The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
- */
- custodian?: unknown[]
- /**
- * description
- * @description Longer statement or account giving the characteristics of someone or something.
- */
- description?: string
- /**
- * digitalIdentifier
- * @description Digital handle to identify objects or legal persons.
- */
- digitalIdentifier?: { [key: string]: unknown }
- /**
- * fullDocumentation
- * @description Non-abridged instructions, comments, and information for using a particular product.
- */
- fullDocumentation: { [key: string]: unknown }
- /**
- * fullName
- * @description Whole, non-abbreviated name of something or somebody.
- */
- fullName?: string
- /**
- * funding
- * @description Money provided by a legal person for a particular purpose.
- */
- funding?: unknown[]
- hasTerminologyVersion: components["schemas"]["HasTerminologyVersion"]
- /**
- * homepage
- * @description Main website of something or someone.
- */
- homepage?: { [key: string]: unknown }
- /**
- * howToCite
- * @description Preferred format for citing a particular object or legal person.
- */
- howToCite?: string
- /**
- * isAlternativeVersionOf
- * @description Reference to an original form where the essence was preserved, but presented in an alternative form.
- */
- isAlternativeVersionOf?: unknown[]
- /**
- * isNewVersionOf
- * @description Reference to a previous (potentially outdated) particular form of something.
- */
- isNewVersionOf?: { [key: string]: unknown }
- /**
- * keyword
- * @description Significant word or concept that are representative of something or someone.
- */
- keyword?: unknown[]
- /**
- * license
- * @description Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
- */
- license: { [key: string]: unknown }
- /**
- * ontologyIdentifier
- * @description Term or code used to identify something or someone registered within a particular ontology.
- */
- ontologyIdentifier?: string[]
- /**
- * Othercontribution
- * @description Structured information on the contribution made to a research product.
- */
- otherContribution?: components["schemas"]["siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__OtherContribution"]
- /**
- * relatedPublication
- * @description Reference to something that was made available for the general public to see or buy.
- */
- relatedPublication?: unknown[]
- /**
- * releaseDate
- * Format: date
- * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
- */
- releaseDate: string
- /**
- * repository
- * @description Place, room, or container where something is deposited or stored.
- */
- repository?: { [key: string]: unknown }
- /**
- * shortName
- * @description Shortened or fully abbreviated name of something or somebody.
- */
- shortName: string
- /**
- * supportChannel
- * @description Way of communication used to interact with users or customers.
- */
- supportChannel?: string[]
- /**
- * versionIdentifier
- * @description Term or code used to identify the version of something.
- */
- versionIdentifier: string
- /**
- * versionInnovation
- * @description Documentation on what changed in comparison to a previously published form of something.
- */
- versionInnovation: string
- }
- /** OtherContribution */
- siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__OtherContribution: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * contributionType
- * @description Distinct class of what was given or supplied as a part or share.
- */
- contributionType: unknown[]
- /**
- * contributor
- * @description Legal person that gave or supplied something as a part or share.
- */
- contributor: unknown
- }
- /** Coordinates */
- siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Coordinates: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * typeOfUncertainty
- * @description Distinct technique used to quantify the uncertainty of a measurement.
- */
- typeOfUncertainty?: unknown
- /**
- * uncertainty
- * @description Quantitative value range defining the uncertainty of a measurement.
- */
- uncertainty?: number[]
- /**
- * unit
- * @description Determinate quantity adopted as a standard of measurement.
- */
- unit?: unknown
- /**
- * value
- * @description Entry for a property.
- */
- value: number
- }
- /** Model */
- siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * @Id
- * @description Metadata node identifier.
- */
- "@id": string
- /** @Type */
- "@type": string
- hasAnnotation?: components["schemas"]["HasAnnotation"]
- /**
- * hasParent
- * @description Reference to a parent object or legal person.
- */
- hasParent?: unknown[]
- /** lookupLabel */
- lookupLabel?: string
- /**
- * name
- * @description Word or phrase that constitutes the distinctive designation of a being or thing.
- */
- name?: string
- /**
- * ontologyIdentifier
- * @description Term or code used to identify something or someone registered within a particular ontology.
- */
- ontologyIdentifier?: string[]
- /** Relationassessment */
- relationAssessment?: Partial<
- components["schemas"]["RelationAssessmentItem"]
- > &
- Partial<components["schemas"]["RelationAssessmentItem1"]>
- /**
- * versionIdentifier
- * @description Term or code used to identify the version of something.
- */
- versionIdentifier: string
- /**
- * versionInnovation
- * @description Documentation on what changed in comparison to a previously published form of something.
- */
- versionInnovation?: string
- }
- /** Coordinates */
- siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Coordinates: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * typeOfUncertainty
- * @description Distinct technique used to quantify the uncertainty of a measurement.
- */
- typeOfUncertainty?: unknown
- /**
- * uncertainty
- * @description Quantitative value range defining the uncertainty of a measurement.
- */
- uncertainty?: number[]
- /**
- * unit
- * @description Determinate quantity adopted as a standard of measurement.
- */
- unit?: unknown
- /**
- * value
- * @description Entry for a property.
- */
- value: number
- }
- /** Model */
- siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * @Id
- * @description Metadata node identifier.
- */
- "@id": string
- /** @Type */
- "@type": string
- /**
- * coordinateSpace
- * @description Two or three dimensional geometric setting.
- */
- coordinateSpace: { [key: string]: unknown }
- /**
- * Coordinates
- * @description Structured information on a quantitative value.
- */
- coordinates: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Coordinates"][]
- }
- /** Copyright */
- siibra__openminds__core__v4__products__datasetVersion__Copyright: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * holder
- * @description Legal person in possession of something.
- */
- holder: unknown[]
- /**
- * year
- * @description Cycle in the Gregorian calendar specified by a number and comprised of 365 or 366 days divided into 12 months beginning with January and ending with December.
- */
- year: string
- }
- /** Model */
- siibra__openminds__core__v4__products__datasetVersion__Model: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * @Id
- * @description Metadata node identifier.
- */
- "@id": string
- /** @Type */
- "@type": string
- /**
- * accessibility
- * @description Level to which something is accessible to someone or something.
- */
- accessibility: { [key: string]: unknown }
- /**
- * author
- * @description Creator of a literary or creative work, as well as a dataset publication.
- */
- author?: unknown[]
- /** behavioralProtocol */
- behavioralProtocol?: unknown[]
- /**
- * Copyright
- * @description Structured information on the copyright.
- */
- copyright?: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Copyright"]
- /**
- * custodian
- * @description The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
- */
- custodian?: unknown[]
- /** dataType */
- dataType: unknown[]
- /**
- * description
- * @description Longer statement or account giving the characteristics of someone or something.
- */
- description?: string
- /**
- * digitalIdentifier
- * @description Digital handle to identify objects or legal persons.
- */
- digitalIdentifier: { [key: string]: unknown }
- /**
- * ethicsAssessment
- * @description Judgment about the applied principles of conduct governing an individual or a group.
- */
- ethicsAssessment: { [key: string]: unknown }
- /** experimentalApproach */
- experimentalApproach: unknown[]
- /**
- * fullDocumentation
- * @description Non-abridged instructions, comments, and information for using a particular product.
- */
- fullDocumentation: { [key: string]: unknown }
- /**
- * fullName
- * @description Whole, non-abbreviated name of something or somebody.
- */
- fullName?: string
- /**
- * funding
- * @description Money provided by a legal person for a particular purpose.
- */
- funding?: unknown[]
- /**
- * homepage
- * @description Main website of something or someone.
- */
- homepage?: { [key: string]: unknown }
- /**
- * howToCite
- * @description Preferred format for citing a particular object or legal person.
- */
- howToCite?: string
- /**
- * inputData
- * @description Data that is put into a process or machine.
- */
- inputData?: unknown[]
- /**
- * isAlternativeVersionOf
- * @description Reference to an original form where the essence was preserved, but presented in an alternative form.
- */
- isAlternativeVersionOf?: unknown[]
- /**
- * isNewVersionOf
- * @description Reference to a previous (potentially outdated) particular form of something.
- */
- isNewVersionOf?: { [key: string]: unknown }
- /**
- * keyword
- * @description Significant word or concept that are representative of something or someone.
- */
- keyword?: unknown[]
- /**
- * license
- * @description Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
- */
- license: { [key: string]: unknown }
- /**
- * Othercontribution
- * @description Structured information on the contribution made to a research product.
- */
- otherContribution?: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__OtherContribution"]
- /** preparationDesign */
- preparationDesign?: unknown[]
- /**
- * relatedPublication
- * @description Reference to something that was made available for the general public to see or buy.
- */
- relatedPublication?: unknown[]
- /**
- * releaseDate
- * Format: date
- * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
- */
- releaseDate: string
- /**
- * repository
- * @description Place, room, or container where something is deposited or stored.
- */
- repository?: { [key: string]: unknown }
- /**
- * shortName
- * @description Shortened or fully abbreviated name of something or somebody.
- */
- shortName: string
- /** studiedSpecimen */
- studiedSpecimen?: unknown[]
- /**
- * studyTarget
- * @description Structure or function that was targeted within a study.
- */
- studyTarget?: unknown[]
- /**
- * supportChannel
- * @description Way of communication used to interact with users or customers.
- */
- supportChannel?: string[]
- /**
- * technique
- * @description Method of accomplishing a desired aim.
- */
- technique: unknown[]
- /**
- * versionIdentifier
- * @description Term or code used to identify the version of something.
- */
- versionIdentifier: string
- /**
- * versionInnovation
- * @description Documentation on what changed in comparison to a previously published form of something.
- */
- versionInnovation: string
- }
- /** OtherContribution */
- siibra__openminds__core__v4__products__datasetVersion__OtherContribution: {
- /**
- * @Context
- * @default [object Object]
- */
- "@context"?: components["schemas"]["VocabModel"]
- /**
- * contributionType
- * @description Distinct class of what was given or supplied as a part or share.
- */
- contributionType: unknown[]
- /**
- * contributor
- * @description Legal person that gave or supplied something as a part or share.
- */
- contributor: unknown
- }
- }
-}
+// export interface components {
+// schemas: {
+// /** AutoradiographyDataModel */
+// AutoradiographyDataModel: {
+// /**
+// * Content Type
+// * @default application/octet-stream
+// */
+// content_type?: string
+// /**
+// * Content Encoding
+// * @default gzip; base64
+// */
+// content_encoding?: string
+// /** X-Width */
+// "x-width": number
+// /** X-Height */
+// "x-height": number
+// /** X-Channel */
+// "x-channel": number
+// /** Dtype */
+// dtype: string
+// /** Content */
+// content: string
+// }
+// /** AxesOrigin */
+// AxesOrigin: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * typeOfUncertainty
+// * @description Distinct technique used to quantify the uncertainty of a measurement.
+// */
+// typeOfUncertainty?: unknown
+// /**
+// * uncertainty
+// * @description Quantitative value range defining the uncertainty of a measurement.
+// */
+// uncertainty?: number[]
+// /**
+// * unit
+// * @description Determinate quantity adopted as a standard of measurement.
+// */
+// unit?: unknown
+// /**
+// * value
+// * @description Entry for a property.
+// */
+// value: number
+// }
+// /** BaseDatasetJsonModel */
+// BaseDatasetJsonModel: {
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "https://openminds.ebrains.eu/core/DatasetVersion"
+// metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
+// /** Urls */
+// urls: components["schemas"]["Url"][]
+// }
+// /** BestViewPoint */
+// BestViewPoint: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * coordinateSpace
+// * @description Two or three dimensional geometric setting.
+// */
+// coordinateSpace: unknown
+// /**
+// * Coordinates
+// * @description Structured information on a quantitative value.
+// */
+// coordinates: components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Coordinates"][]
+// }
+// /** BoundingBoxModel */
+// BoundingBoxModel: {
+// /** @Type */
+// "@type": string
+// /** Space */
+// space: { [key: string]: string }
+// center: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
+// minpoint: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
+// maxpoint: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
+// /** Shape */
+// shape: number[]
+// /** Isplanar */
+// isPlanar: boolean
+// }
+// /** ConnectivityMatrixDataModel */
+// ConnectivityMatrixDataModel: {
+// /** @Id */
+// "@id": string
+// /** @Type */
+// "@type": string
+// /** Name */
+// name?: string
+// /** Description */
+// description?: string
+// /** Citation */
+// citation?: string
+// /** Authors */
+// authors?: string[]
+// /** Cohort */
+// cohort?: string
+// /** Subject */
+// subject?: string
+// /** Filename */
+// filename?: string
+// /** Dataset Id */
+// dataset_id?: string
+// /** Parcellations */
+// parcellations: { [key: string]: string }[]
+// matrix?: components["schemas"]["NpArrayDataModel"]
+// /** Columns */
+// columns?: string[]
+// }
+// /** CorticalCellDistributionModel */
+// CorticalCellDistributionModel: {
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "siibra/features/cells"
+// metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
+// /** Urls */
+// urls: components["schemas"]["Url"][]
+// /** Cells */
+// cells?: components["schemas"]["CorticalCellModel"][]
+// /** Section */
+// section?: string
+// /** Patch */
+// patch?: string
+// }
+// /** CorticalCellModel */
+// CorticalCellModel: {
+// /** X */
+// x: number
+// /** Y */
+// y: number
+// /** Area */
+// area: number
+// /** Layer */
+// layer: number
+// /** Instance Label */
+// "instance label": number
+// }
+// /** DatasetJsonModel */
+// DatasetJsonModel: {
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "https://openminds.ebrains.eu/core/DatasetVersion"
+// metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
+// /** Urls */
+// urls: components["schemas"]["Url"][]
+// }
+// /** FingerPrintDataModel */
+// FingerPrintDataModel: {
+// /** Mean */
+// mean: number
+// /** Std */
+// std: number
+// /** Unit */
+// unit: string
+// }
+// /** HTTPValidationError */
+// HTTPValidationError: {
+// /** Detail */
+// detail?: components["schemas"]["ValidationError"][]
+// }
+// /** HasAnnotation */
+// HasAnnotation: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * Bestviewpoint
+// * @description Structured information on a coordinate point.
+// */
+// bestViewPoint?: components["schemas"]["BestViewPoint"]
+// /**
+// * criteria
+// * @description Aspects or standards on which a judgement or decision is based.
+// */
+// criteria?: unknown
+// /**
+// * criteriaQualityType
+// * @description Distinct class that defines how the judgement or decision was made for a particular criteria.
+// */
+// criteriaQualityType: unknown
+// /**
+// * displayColor
+// * @description Preferred coloring.
+// */
+// displayColor?: string
+// /**
+// * inspiredBy
+// * @description Reference to an inspiring element.
+// */
+// inspiredBy?: unknown[]
+// /**
+// * internalIdentifier
+// * @description Term or code that identifies someone or something within a particular product.
+// */
+// internalIdentifier: string
+// /**
+// * laterality
+// * @description Differentiation between a pair of lateral homologous parts of the body.
+// */
+// laterality?: unknown[]
+// /**
+// * visualizedIn
+// * @description Reference to an image in which something is visible.
+// */
+// visualizedIn?: unknown
+// }
+// /** HasTerminologyVersion */
+// HasTerminologyVersion: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * definedIn
+// * @description Reference to a file instance in which something is stored.
+// */
+// definedIn?: unknown[]
+// /** hasEntityVersion */
+// hasEntityVersion: unknown[]
+// /**
+// * ontologyIdentifier
+// * @description Term or code used to identify something or someone registered within a particular ontology.
+// */
+// ontologyIdentifier?: string[]
+// }
+// /** HrefModel */
+// HrefModel: {
+// /** Href */
+// href: string
+// }
+// /** IEEGContactPointModel */
+// IEEGContactPointModel: {
+// /** Inroi */
+// inRoi?: boolean
+// /** Id */
+// id: string
+// point: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model"]
+// }
+// /** IEEGElectrodeModel */
+// IEEGElectrodeModel: {
+// /** Inroi */
+// inRoi?: boolean
+// /** Electrode Id */
+// electrode_id: string
+// /** Contact Points */
+// contact_points: {
+// [key: string]: components["schemas"]["IEEGContactPointModel"]
+// }
+// }
+// /** IEEGSessionModel */
+// IEEGSessionModel: {
+// /** Inroi */
+// inRoi?: boolean
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "siibra/features/ieegSession"
+// dataset: components["schemas"]["DatasetJsonModel"]
+// /** Sub Id */
+// sub_id: string
+// /** Electrodes */
+// electrodes: {
+// [key: string]: components["schemas"]["IEEGElectrodeModel"]
+// }
+// }
+// /** NeurotransmitterMarkupModel */
+// NeurotransmitterMarkupModel: {
+// /** Latex */
+// latex: string
+// /** Markdown */
+// markdown: string
+// /** Name */
+// name: string
+// /** Label */
+// label: string
+// }
+// /** NiiMetadataModel */
+// NiiMetadataModel: {
+// /** Min */
+// min: number
+// /** Max */
+// max: number
+// }
+// /** NpArrayDataModel */
+// NpArrayDataModel: {
+// /**
+// * Content Type
+// * @default application/octet-stream
+// */
+// content_type?: string
+// /**
+// * Content Encoding
+// * @default gzip; base64
+// */
+// content_encoding?: string
+// /** X-Width */
+// "x-width": number
+// /** X-Height */
+// "x-height": number
+// /** X-Channel */
+// "x-channel": number
+// /** Dtype */
+// dtype: string
+// /** Content */
+// content: string
+// }
+// /** Page[Union[siibra.features.connectivity.ConnectivityMatrixDataModel, app.models.SerializationErrorModel]] */
+// "Page_Union_siibra.features.connectivity.ConnectivityMatrixDataModel__app.models.SerializationErrorModel__": {
+// /** Items */
+// items: (Partial<components["schemas"]["ConnectivityMatrixDataModel"]> &
+// Partial<components["schemas"]["SerializationErrorModel"]>)[]
+// /** Total */
+// total: number
+// /** Page */
+// page: number
+// /** Size */
+// size: number
+// }
+// /** Page[VolumeModel] */
+// Page_VolumeModel_: {
+// /** Items */
+// items: components["schemas"]["VolumeModel"][]
+// /** Total */
+// total: number
+// /** Page */
+// page: number
+// /** Size */
+// size: number
+// }
+// /** ProfileDataModel */
+// ProfileDataModel: {
+// density: components["schemas"]["NpArrayDataModel"]
+// /** Unit */
+// unit: string
+// }
+// /** QuantitativeOverlapItem */
+// QuantitativeOverlapItem: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * typeOfUncertainty
+// * @description Distinct technique used to quantify the uncertainty of a measurement.
+// */
+// typeOfUncertainty?: unknown
+// /**
+// * uncertainty
+// * @description Quantitative value range defining the uncertainty of a measurement.
+// */
+// uncertainty?: number[]
+// /**
+// * unit
+// * @description Determinate quantity adopted as a standard of measurement.
+// */
+// unit?: unknown
+// /**
+// * value
+// * @description Entry for a property.
+// */
+// value: number
+// }
+// /** QuantitativeOverlapItem1 */
+// QuantitativeOverlapItem1: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * maxValue
+// * @description Greatest quantity attained or allowed.
+// */
+// maxValue: number
+// /** maxValueUnit */
+// maxValueUnit?: unknown
+// /**
+// * minValue
+// * @description Smallest quantity attained or allowed.
+// */
+// minValue: number
+// /** minValueUnit */
+// minValueUnit?: unknown
+// }
+// /** ReceptorDataModel */
+// ReceptorDataModel: {
+// /** Autoradiographs */
+// autoradiographs: {
+// [key: string]: components["schemas"]["AutoradiographyDataModel"]
+// }
+// /** Profiles */
+// profiles: { [key: string]: components["schemas"]["ProfileDataModel"] }
+// /** Fingerprints */
+// fingerprints: {
+// [key: string]: components["schemas"]["FingerPrintDataModel"]
+// }
+// /** Receptor Symbols */
+// receptor_symbols: {
+// [key: string]: components["schemas"]["SymbolMarkupClass"]
+// }
+// }
+// /** ReceptorDatasetModel */
+// ReceptorDatasetModel: {
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "siibra/features/receptor"
+// metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
+// /** Urls */
+// urls: components["schemas"]["Url"][]
+// data?: components["schemas"]["ReceptorDataModel"]
+// }
+// /** ReceptorMarkupModel */
+// ReceptorMarkupModel: {
+// /** Latex */
+// latex: string
+// /** Markdown */
+// markdown: string
+// /** Name */
+// name: string
+// }
+// /** RelationAssessmentItem */
+// RelationAssessmentItem: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * criteria
+// * @description Aspects or standards on which a judgement or decision is based.
+// */
+// criteria?: unknown
+// /**
+// * inRelationTo
+// * @description Reference to a related element.
+// */
+// inRelationTo: unknown
+// /**
+// * qualitativeOverlap
+// * @description Semantic characterization of how much two things occupy the same space.
+// */
+// qualitativeOverlap: unknown
+// }
+// /** RelationAssessmentItem1 */
+// RelationAssessmentItem1: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * criteria
+// * @description Aspects or standards on which a judgement or decision is based.
+// */
+// criteria?: unknown
+// /**
+// * inRelationTo
+// * @description Reference to a related element.
+// */
+// inRelationTo: unknown
+// /** Quantitativeoverlap */
+// quantitativeOverlap: Partial<
+// components["schemas"]["QuantitativeOverlapItem"]
+// > &
+// Partial<components["schemas"]["QuantitativeOverlapItem1"]>
+// }
+// /** SapiAtlasModel */
+// SapiAtlasModel: {
+// /** Links */
+// links: { [key: string]: components["schemas"]["HrefModel"] }
+// /** @Id */
+// "@id": string
+// /** Name */
+// name: string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "juelich/iav/atlas/v1.0.0"
+// /** Spaces */
+// spaces: components["schemas"]["SiibraAtIdModel"][]
+// /** Parcellations */
+// parcellations: components["schemas"]["SiibraAtIdModel"][]
+// species: components["schemas"]["SpeciesModel"]
+// }
+// /** SapiParcellationModel */
+// SapiParcellationModel: {
+// /** Links */
+// links: { [key: string]: components["schemas"]["HrefModel"] }
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "minds/core/parcellationatlas/v1.0.0"
+// /** Name */
+// name: string
+// /** Modality */
+// modality?: string
+// /** Datasets */
+// datasets: components["schemas"]["DatasetJsonModel"][]
+// /** Brainatlasversions */
+// brainAtlasVersions: components["schemas"]["siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Model"][]
+// version?: components["schemas"]["SiibraParcellationVersionModel"]
+// }
+// /** SapiSpaceModel */
+// SapiSpaceModel: {
+// /** Links */
+// links: { [key: string]: components["schemas"]["HrefModel"] }
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * @Id
+// * @description Metadata node identifier.
+// */
+// "@id": string
+// /** @Type */
+// "@type": string
+// /**
+// * anatomicalAxesOrientation
+// * @description Relation between reference planes used in anatomy and mathematics.
+// */
+// anatomicalAxesOrientation: { [key: string]: unknown }
+// /**
+// * Axesorigin
+// * @description Structured information on a quantitative value.
+// */
+// axesOrigin: components["schemas"]["AxesOrigin"][]
+// /**
+// * defaultImage
+// * @description Two or three dimensional image that particluarly represents a specific coordinate space.
+// */
+// defaultImage?: unknown[]
+// /**
+// * digitalIdentifier
+// * @description Digital handle to identify objects or legal persons.
+// */
+// digitalIdentifier?: { [key: string]: unknown }
+// /**
+// * fullName
+// * @description Whole, non-abbreviated name of something or somebody.
+// */
+// fullName: string
+// /**
+// * homepage
+// * @description Main website of something or someone.
+// */
+// homepage?: { [key: string]: unknown }
+// /**
+// * howToCite
+// * @description Preferred format for citing a particular object or legal person.
+// */
+// howToCite?: string
+// /**
+// * nativeUnit
+// * @description Determinate quantity used in the original measurement.
+// */
+// nativeUnit: { [key: string]: unknown }
+// /**
+// * ontologyIdentifier
+// * @description Term or code used to identify something or someone registered within a particular ontology.
+// */
+// ontologyIdentifier?: string[]
+// /**
+// * releaseDate
+// * Format: date
+// * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
+// */
+// releaseDate: string
+// /**
+// * shortName
+// * @description Shortened or fully abbreviated name of something or somebody.
+// */
+// shortName: string
+// /**
+// * versionIdentifier
+// * @description Term or code used to identify the version of something.
+// */
+// versionIdentifier: string
+// }
+// /** SerializationErrorModel */
+// SerializationErrorModel: {
+// /**
+// * Type
+// * @constant
+// */
+// type?: "spy/serialization-error"
+// /** Message */
+// message: string
+// }
+// /** SiibraAtIdModel */
+// SiibraAtIdModel: {
+// /** @Id */
+// "@id": string
+// }
+// /** SiibraParcellationVersionModel */
+// SiibraParcellationVersionModel: {
+// /** Name */
+// name: string
+// /** Deprecated */
+// deprecated?: boolean
+// prev?: components["schemas"]["SiibraAtIdModel"]
+// next?: components["schemas"]["SiibraAtIdModel"]
+// }
+// /** SpeciesModel */
+// SpeciesModel: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * @Id
+// * @description Metadata node identifier.
+// */
+// "@id": string
+// /** @Type */
+// "@type": string
+// /**
+// * definition
+// * @description Short, but precise statement of the meaning of a word, word group, sign or a symbol.
+// */
+// definition?: string
+// /**
+// * description
+// * @description Longer statement or account giving the characteristics of someone or something.
+// */
+// description?: string
+// /**
+// * interlexIdentifier
+// * @description Persistent identifier for a term registered in the InterLex project.
+// */
+// interlexIdentifier?: string
+// /**
+// * knowledgeSpaceLink
+// * @description Persistent link to an encyclopedia entry in the Knowledge Space project.
+// */
+// knowledgeSpaceLink?: string
+// /**
+// * name
+// * @description Word or phrase that constitutes the distinctive designation of a being or thing.
+// */
+// name: string
+// /**
+// * preferredOntologyIdentifier
+// * @description Persistent identifier of a preferred ontological term.
+// */
+// preferredOntologyIdentifier?: string
+// /**
+// * synonym
+// * @description Words or expressions used in the same language that have the same or nearly the same meaning in some or all senses.
+// */
+// synonym?: string[]
+// /** Kgv1Id */
+// kgV1Id: string
+// }
+// /** SymbolMarkupClass */
+// SymbolMarkupClass: {
+// receptor: components["schemas"]["ReceptorMarkupModel"]
+// neurotransmitter: components["schemas"]["NeurotransmitterMarkupModel"]
+// }
+// /** Url */
+// Url: {
+// /** Doi */
+// doi: string
+// /** Cite */
+// cite?: string
+// }
+// /** VOIDataModel */
+// VOIDataModel: {
+// /** @Id */
+// "@id": string
+// /**
+// * @Type
+// * @constant
+// */
+// "@type"?: "siibra/features/voi"
+// metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
+// /** Urls */
+// urls: components["schemas"]["Url"][]
+// /** Volumes */
+// volumes: components["schemas"]["VolumeModel"][]
+// location: components["schemas"]["BoundingBoxModel"]
+// }
+// /** ValidationError */
+// ValidationError: {
+// /** Location */
+// loc: (Partial<string> & Partial<number>)[]
+// /** Message */
+// msg: string
+// /** Error Type */
+// type: string
+// }
+// /** VocabModel */
+// VocabModel: {
+// /** @Vocab */
+// "@vocab": string
+// }
+// /** VolumeDataModel */
+// VolumeDataModel: {
+// /** Type */
+// type: string
+// /** Is Volume */
+// is_volume: boolean
+// /** Is Surface */
+// is_surface: boolean
+// /** Detail */
+// detail: { [key: string]: unknown }
+// space: components["schemas"]["SiibraAtIdModel"]
+// /** Url */
+// url?: string
+// /** Url Map */
+// url_map?: { [key: string]: string }
+// /** Map Type */
+// map_type?: string
+// /** Volume Type */
+// volume_type?: string
+// }
+// /** VolumeModel */
+// VolumeModel: {
+// /** @Id */
+// "@id": string
+// /** @Type */
+// "@type": string
+// metadata: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Model"]
+// /** Urls */
+// urls: components["schemas"]["Url"][]
+// data: components["schemas"]["VolumeDataModel"]
+// }
+// /** Copyright */
+// siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Copyright: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * holder
+// * @description Legal person in possession of something.
+// */
+// holder: unknown[]
+// /**
+// * year
+// * @description Cycle in the Gregorian calendar specified by a number and comprised of 365 or 366 days divided into 12 months beginning with January and ending with December.
+// */
+// year: string
+// }
+// /** Model */
+// siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Model: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * @Id
+// * @description Metadata node identifier.
+// */
+// "@id": string
+// /** @Type */
+// "@type": string
+// /** abbreviation */
+// abbreviation?: string
+// /**
+// * accessibility
+// * @description Level to which something is accessible to someone or something.
+// */
+// accessibility: { [key: string]: unknown }
+// /** atlasType */
+// atlasType?: { [key: string]: unknown }
+// /**
+// * author
+// * @description Creator of a literary or creative work, as well as a dataset publication.
+// */
+// author?: unknown[]
+// /**
+// * coordinateSpace
+// * @description Two or three dimensional geometric setting.
+// */
+// coordinateSpace: { [key: string]: unknown }
+// /**
+// * Copyright
+// * @description Structured information on the copyright.
+// */
+// copyright?: components["schemas"]["siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__Copyright"]
+// /**
+// * custodian
+// * @description The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
+// */
+// custodian?: unknown[]
+// /**
+// * description
+// * @description Longer statement or account giving the characteristics of someone or something.
+// */
+// description?: string
+// /**
+// * digitalIdentifier
+// * @description Digital handle to identify objects or legal persons.
+// */
+// digitalIdentifier?: { [key: string]: unknown }
+// /**
+// * fullDocumentation
+// * @description Non-abridged instructions, comments, and information for using a particular product.
+// */
+// fullDocumentation: { [key: string]: unknown }
+// /**
+// * fullName
+// * @description Whole, non-abbreviated name of something or somebody.
+// */
+// fullName?: string
+// /**
+// * funding
+// * @description Money provided by a legal person for a particular purpose.
+// */
+// funding?: unknown[]
+// hasTerminologyVersion: components["schemas"]["HasTerminologyVersion"]
+// /**
+// * homepage
+// * @description Main website of something or someone.
+// */
+// homepage?: { [key: string]: unknown }
+// /**
+// * howToCite
+// * @description Preferred format for citing a particular object or legal person.
+// */
+// howToCite?: string
+// /**
+// * isAlternativeVersionOf
+// * @description Reference to an original form where the essence was preserved, but presented in an alternative form.
+// */
+// isAlternativeVersionOf?: unknown[]
+// /**
+// * isNewVersionOf
+// * @description Reference to a previous (potentially outdated) particular form of something.
+// */
+// isNewVersionOf?: { [key: string]: unknown }
+// /**
+// * keyword
+// * @description Significant word or concept that are representative of something or someone.
+// */
+// keyword?: unknown[]
+// /**
+// * license
+// * @description Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
+// */
+// license: { [key: string]: unknown }
+// /**
+// * ontologyIdentifier
+// * @description Term or code used to identify something or someone registered within a particular ontology.
+// */
+// ontologyIdentifier?: string[]
+// /**
+// * Othercontribution
+// * @description Structured information on the contribution made to a research product.
+// */
+// otherContribution?: components["schemas"]["siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__OtherContribution"]
+// /**
+// * relatedPublication
+// * @description Reference to something that was made available for the general public to see or buy.
+// */
+// relatedPublication?: unknown[]
+// /**
+// * releaseDate
+// * Format: date
+// * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
+// */
+// releaseDate: string
+// /**
+// * repository
+// * @description Place, room, or container where something is deposited or stored.
+// */
+// repository?: { [key: string]: unknown }
+// /**
+// * shortName
+// * @description Shortened or fully abbreviated name of something or somebody.
+// */
+// shortName: string
+// /**
+// * supportChannel
+// * @description Way of communication used to interact with users or customers.
+// */
+// supportChannel?: string[]
+// /**
+// * versionIdentifier
+// * @description Term or code used to identify the version of something.
+// */
+// versionIdentifier: string
+// /**
+// * versionInnovation
+// * @description Documentation on what changed in comparison to a previously published form of something.
+// */
+// versionInnovation: string
+// }
+// /** OtherContribution */
+// siibra__openminds__SANDS__v3__atlas__brainAtlasVersion__OtherContribution: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * contributionType
+// * @description Distinct class of what was given or supplied as a part or share.
+// */
+// contributionType: unknown[]
+// /**
+// * contributor
+// * @description Legal person that gave or supplied something as a part or share.
+// */
+// contributor: unknown
+// }
+// /** Coordinates */
+// siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Coordinates: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * typeOfUncertainty
+// * @description Distinct technique used to quantify the uncertainty of a measurement.
+// */
+// typeOfUncertainty?: unknown
+// /**
+// * uncertainty
+// * @description Quantitative value range defining the uncertainty of a measurement.
+// */
+// uncertainty?: number[]
+// /**
+// * unit
+// * @description Determinate quantity adopted as a standard of measurement.
+// */
+// unit?: unknown
+// /**
+// * value
+// * @description Entry for a property.
+// */
+// value: number
+// }
+// /** Model */
+// siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * @Id
+// * @description Metadata node identifier.
+// */
+// "@id": string
+// /** @Type */
+// "@type": string
+// hasAnnotation?: components["schemas"]["HasAnnotation"]
+// /**
+// * hasParent
+// * @description Reference to a parent object or legal person.
+// */
+// hasParent?: unknown[]
+// /** lookupLabel */
+// lookupLabel?: string
+// /**
+// * name
+// * @description Word or phrase that constitutes the distinctive designation of a being or thing.
+// */
+// name?: string
+// /**
+// * ontologyIdentifier
+// * @description Term or code used to identify something or someone registered within a particular ontology.
+// */
+// ontologyIdentifier?: string[]
+// /** Relationassessment */
+// relationAssessment?: Partial<
+// components["schemas"]["RelationAssessmentItem"]
+// > &
+// Partial<components["schemas"]["RelationAssessmentItem1"]>
+// /**
+// * versionIdentifier
+// * @description Term or code used to identify the version of something.
+// */
+// versionIdentifier: string
+// /**
+// * versionInnovation
+// * @description Documentation on what changed in comparison to a previously published form of something.
+// */
+// versionInnovation?: string
+// }
+// /** Coordinates */
+// siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Coordinates: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * typeOfUncertainty
+// * @description Distinct technique used to quantify the uncertainty of a measurement.
+// */
+// typeOfUncertainty?: unknown
+// /**
+// * uncertainty
+// * @description Quantitative value range defining the uncertainty of a measurement.
+// */
+// uncertainty?: number[]
+// /**
+// * unit
+// * @description Determinate quantity adopted as a standard of measurement.
+// */
+// unit?: unknown
+// /**
+// * value
+// * @description Entry for a property.
+// */
+// value: number
+// }
+// /** Model */
+// siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * @Id
+// * @description Metadata node identifier.
+// */
+// "@id": string
+// /** @Type */
+// "@type": string
+// /**
+// * coordinateSpace
+// * @description Two or three dimensional geometric setting.
+// */
+// coordinateSpace: { [key: string]: unknown }
+// /**
+// * Coordinates
+// * @description Structured information on a quantitative value.
+// */
+// coordinates: components["schemas"]["siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Coordinates"][]
+// }
+// /** Copyright */
+// siibra__openminds__core__v4__products__datasetVersion__Copyright: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * holder
+// * @description Legal person in possession of something.
+// */
+// holder: unknown[]
+// /**
+// * year
+// * @description Cycle in the Gregorian calendar specified by a number and comprised of 365 or 366 days divided into 12 months beginning with January and ending with December.
+// */
+// year: string
+// }
+// /** Model */
+// siibra__openminds__core__v4__products__datasetVersion__Model: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * @Id
+// * @description Metadata node identifier.
+// */
+// "@id": string
+// /** @Type */
+// "@type": string
+// /**
+// * accessibility
+// * @description Level to which something is accessible to someone or something.
+// */
+// accessibility: { [key: string]: unknown }
+// /**
+// * author
+// * @description Creator of a literary or creative work, as well as a dataset publication.
+// */
+// author?: unknown[]
+// /** behavioralProtocol */
+// behavioralProtocol?: unknown[]
+// /**
+// * Copyright
+// * @description Structured information on the copyright.
+// */
+// copyright?: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__Copyright"]
+// /**
+// * custodian
+// * @description The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
+// */
+// custodian?: unknown[]
+// /** dataType */
+// dataType: unknown[]
+// /**
+// * description
+// * @description Longer statement or account giving the characteristics of someone or something.
+// */
+// description?: string
+// /**
+// * digitalIdentifier
+// * @description Digital handle to identify objects or legal persons.
+// */
+// digitalIdentifier: { [key: string]: unknown }
+// /**
+// * ethicsAssessment
+// * @description Judgment about the applied principles of conduct governing an individual or a group.
+// */
+// ethicsAssessment: { [key: string]: unknown }
+// /** experimentalApproach */
+// experimentalApproach: unknown[]
+// /**
+// * fullDocumentation
+// * @description Non-abridged instructions, comments, and information for using a particular product.
+// */
+// fullDocumentation: { [key: string]: unknown }
+// /**
+// * fullName
+// * @description Whole, non-abbreviated name of something or somebody.
+// */
+// fullName?: string
+// /**
+// * funding
+// * @description Money provided by a legal person for a particular purpose.
+// */
+// funding?: unknown[]
+// /**
+// * homepage
+// * @description Main website of something or someone.
+// */
+// homepage?: { [key: string]: unknown }
+// /**
+// * howToCite
+// * @description Preferred format for citing a particular object or legal person.
+// */
+// howToCite?: string
+// /**
+// * inputData
+// * @description Data that is put into a process or machine.
+// */
+// inputData?: unknown[]
+// /**
+// * isAlternativeVersionOf
+// * @description Reference to an original form where the essence was preserved, but presented in an alternative form.
+// */
+// isAlternativeVersionOf?: unknown[]
+// /**
+// * isNewVersionOf
+// * @description Reference to a previous (potentially outdated) particular form of something.
+// */
+// isNewVersionOf?: { [key: string]: unknown }
+// /**
+// * keyword
+// * @description Significant word or concept that are representative of something or someone.
+// */
+// keyword?: unknown[]
+// /**
+// * license
+// * @description Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
+// */
+// license: { [key: string]: unknown }
+// /**
+// * Othercontribution
+// * @description Structured information on the contribution made to a research product.
+// */
+// otherContribution?: components["schemas"]["siibra__openminds__core__v4__products__datasetVersion__OtherContribution"]
+// /** preparationDesign */
+// preparationDesign?: unknown[]
+// /**
+// * relatedPublication
+// * @description Reference to something that was made available for the general public to see or buy.
+// */
+// relatedPublication?: unknown[]
+// /**
+// * releaseDate
+// * Format: date
+// * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
+// */
+// releaseDate: string
+// /**
+// * repository
+// * @description Place, room, or container where something is deposited or stored.
+// */
+// repository?: { [key: string]: unknown }
+// /**
+// * shortName
+// * @description Shortened or fully abbreviated name of something or somebody.
+// */
+// shortName: string
+// /** studiedSpecimen */
+// studiedSpecimen?: unknown[]
+// /**
+// * studyTarget
+// * @description Structure or function that was targeted within a study.
+// */
+// studyTarget?: unknown[]
+// /**
+// * supportChannel
+// * @description Way of communication used to interact with users or customers.
+// */
+// supportChannel?: string[]
+// /**
+// * technique
+// * @description Method of accomplishing a desired aim.
+// */
+// technique: unknown[]
+// /**
+// * versionIdentifier
+// * @description Term or code used to identify the version of something.
+// */
+// versionIdentifier: string
+// /**
+// * versionInnovation
+// * @description Documentation on what changed in comparison to a previously published form of something.
+// */
+// versionInnovation: string
+// }
+// /** OtherContribution */
+// siibra__openminds__core__v4__products__datasetVersion__OtherContribution: {
+// /**
+// * @Context
+// * @default [object Object]
+// */
+// "@context"?: components["schemas"]["VocabModel"]
+// /**
+// * contributionType
+// * @description Distinct class of what was given or supplied as a part or share.
+// */
+// contributionType: unknown[]
+// /**
+// * contributor
+// * @description Legal person that gave or supplied something as a part or share.
+// */
+// contributor: unknown
+// }
+// }
+// }
-export interface operations {
- /** Returns all regions for a given parcellation id. */
- get_all_regions_from_atlas_parc_space_atlases__atlas_id__parcellations__parcellation_id__regions_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- }
- query: {
- space_id?: string
- find?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"][]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns all regional features for a region. */
- get_all_regional_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- }
- query: {
- space_id?: string
- type?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": (Partial<
- components["schemas"]["ReceptorDatasetModel"]
- > &
- Partial<components["schemas"]["BaseDatasetJsonModel"]> &
- Partial<components["schemas"]["CorticalCellDistributionModel"]>)[]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns a feature for a region, as defined by the modality and feature ID */
- get_single_detailed_regional_feature_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- feature_id: string
- }
- query: {
- space_id?: string
- gene?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": Partial<
- components["schemas"]["ReceptorDatasetModel"]
- > &
- Partial<components["schemas"]["BaseDatasetJsonModel"]> &
- Partial<components["schemas"]["CorticalCellDistributionModel"]>
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns information about a regional map for given region name. */
- get_regional_map_info_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_info_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- }
- query: {
- space_id?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["NiiMetadataModel"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns a regional map for given region name. */
- get_regional_map_file_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_map_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- }
- query: {
- space_id?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": unknown
- "application/octet-stream": string
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- }
- query: {
- space_id?: string
- type?: string
- page?: number
- size?: number
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["Page_VolumeModel_"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes__volume_id__get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- volume_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["VolumeModel"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- get_single_region_detail_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- region_id: string
- }
- query: {
- space_id?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns all parcellations that are defined in the siibra client for given atlas. */
- get_all_parcellations_atlases__atlas_id__parcellations_get: {
- parameters: {
- path: {
- atlas_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["SapiParcellationModel"][]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns a global feature for a specific modality id. */
- get_single_detailed_global_feature_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- feature_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": Partial<
- components["schemas"]["ConnectivityMatrixDataModel"]
- > &
- Partial<components["schemas"]["SerializationErrorModel"]>
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns all global features for a parcellation. */
- get_all_global_features_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__features_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- }
- query: {
- type?: string
- page?: number
- size?: number
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["Page_Union_siibra.features.connectivity.ConnectivityMatrixDataModel__app.models.SerializationErrorModel__"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns one parcellation for given id. */
- get_volumes_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__volumes_get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["VolumeModel"][]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns one parcellation for given id. */
- get_single_parcellation_detail_atlases__atlas_id__parcellations__parcellation_id__get: {
- parameters: {
- path: {
- atlas_id: string
- parcellation_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["SapiParcellationModel"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns all spaces that are defined in the siibra client. */
- get_all_spaces_atlases__atlas_id__spaces_get: {
- parameters: {
- path: {
- atlas_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["SapiSpaceModel"][]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns a template for a given space id. */
- get_template_by_space_id_atlases__atlas_id__spaces__space_id__templates_get: {
- parameters: {
- path: {
- atlas_id: string
- space_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": unknown
- "application/octet-stream": string
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns all parcellation maps for a given space id. */
- get_parcellation_map_for_space_atlases__atlas_id__spaces__space_id__parcellation_maps_get: {
- parameters: {
- path: {
- atlas_id: string
- space_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": unknown
- "application/octet-stream": string
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /**
- * Get a detailed view on a single spatial feature.
- * A parcellation id and region id can be provided optional to get more details.
- */
- get_single_detailed_spatial_feature_atlases__atlas_id__spaces__space_id__features__feature_id__get: {
- parameters: {
- path: {
- feature_id: string
- atlas_id: string
- space_id: string
- }
- query: {
- parcellation_id?: string
- region?: string
- bbox?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": Partial<
- components["schemas"]["IEEGSessionModel"]
- > &
- Partial<components["schemas"]["VOIDataModel"]>
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Return all possible feature names and links to get more details */
- get_all_spatial_features_for_space_atlases__atlas_id__spaces__space_id__features_get: {
- parameters: {
- path: {
- atlas_id: string
- space_id: string
- }
- query: {
- parcellation_id?: string
- type?: string
- region?: string
- bbox?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": (Partial<
- components["schemas"]["IEEGSessionModel"]
- > &
- Partial<components["schemas"]["VOIDataModel"]>)[]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- get_volumes_for_space_atlases__atlas_id__spaces__space_id__volumes_get: {
- parameters: {
- path: {
- atlas_id: string
- space_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["VolumeModel"][]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Returns one space for given id, with links to further resources */
- get_single_space_detail_atlases__atlas_id__spaces__space_id__get: {
- parameters: {
- path: {
- atlas_id: string
- space_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["SapiSpaceModel"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Get all atlases known by siibra. */
- get_all_atlases_atlases_get: {
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["SapiAtlasModel"][]
- }
- }
- }
- }
- /** Get more information for a specific atlas with links to further objects. */
- get_atlas_by_id_atlases__atlas_id__get: {
- parameters: {
- path: {
- atlas_id: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": components["schemas"]["SapiAtlasModel"]
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
- /** Return all genes (name, acronym) in siibra */
- get_gene_names_genes_get: {
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": unknown
- }
- }
- }
- }
- /** Return all possible modalities */
- get_all_available_modalities_modalities_get: {
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": unknown
- }
- }
- }
- }
- /**
- * Get all details for one feature by id.
- * Since the feature id is unique, no atlas concept is required.
- *
- * Further optional params can extend the result.
- * :param feature_id:
- * :param atlas_id:
- * :param space_id:
- * :param parcellation_id:
- * :param region_id:
- * :return: FeatureModels
- */
- get_feature_details_features__feature_id__get: {
- parameters: {
- path: {
- feature_id: string
- }
- query: {
- atlas_id?: string
- space_id?: string
- parcellation_id?: string
- region_id?: string
- }
- }
- responses: {
- /** Successful Response */
- 200: {
- content: {
- "application/json": Partial<
- components["schemas"]["ReceptorDatasetModel"]
- > &
- Partial<components["schemas"]["BaseDatasetJsonModel"]> &
- Partial<components["schemas"]["CorticalCellDistributionModel"]> &
- Partial<components["schemas"]["IEEGSessionModel"]> &
- Partial<components["schemas"]["VOIDataModel"]> &
- Partial<components["schemas"]["ConnectivityMatrixDataModel"]> &
- Partial<components["schemas"]["SerializationErrorModel"]>
- }
- }
- /** Validation Error */
- 422: {
- content: {
- "application/json": components["schemas"]["HTTPValidationError"]
- }
- }
- }
- }
-}
+// export interface operations {
+// /** Returns all regions for a given parcellation id. */
+// get_all_regions_from_atlas_parc_space_atlases__atlas_id__parcellations__parcellation_id__regions_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// }
+// query: {
+// space_id?: string
+// find?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"][]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns all regional features for a region. */
+// get_all_regional_features_for_region_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// }
+// query: {
+// space_id?: string
+// type?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": (Partial<
+// components["schemas"]["ReceptorDatasetModel"]
+// > &
+// Partial<components["schemas"]["BaseDatasetJsonModel"]> &
+// Partial<components["schemas"]["CorticalCellDistributionModel"]>)[]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns a feature for a region, as defined by the modality and feature ID */
+// get_single_detailed_regional_feature_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__features__feature_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// feature_id: string
+// }
+// query: {
+// space_id?: string
+// gene?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": Partial<
+// components["schemas"]["ReceptorDatasetModel"]
+// > &
+// Partial<components["schemas"]["BaseDatasetJsonModel"]> &
+// Partial<components["schemas"]["CorticalCellDistributionModel"]>
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns information about a regional map for given region name. */
+// get_regional_map_info_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_info_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// }
+// query: {
+// space_id?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["NiiMetadataModel"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns a regional map for given region name. */
+// get_regional_map_file_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__regional_map_map_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// }
+// query: {
+// space_id?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": unknown
+// "application/octet-stream": string
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// }
+// query: {
+// space_id?: string
+// type?: string
+// page?: number
+// size?: number
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["Page_VolumeModel_"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// get_regional_volumes_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__volumes__volume_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// volume_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["VolumeModel"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// get_single_region_detail_atlases__atlas_id__parcellations__parcellation_id__regions__region_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// region_id: string
+// }
+// query: {
+// space_id?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns all parcellations that are defined in the siibra client for given atlas. */
+// get_all_parcellations_atlases__atlas_id__parcellations_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["SapiParcellationModel"][]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns a global feature for a specific modality id. */
+// get_single_detailed_global_feature_atlases__atlas_id__parcellations__parcellation_id__features__feature_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// feature_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": Partial<
+// components["schemas"]["ConnectivityMatrixDataModel"]
+// > &
+// Partial<components["schemas"]["SerializationErrorModel"]>
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns all global features for a parcellation. */
+// get_all_global_features_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__features_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// }
+// query: {
+// type?: string
+// page?: number
+// size?: number
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["Page_Union_siibra.features.connectivity.ConnectivityMatrixDataModel__app.models.SerializationErrorModel__"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns one parcellation for given id. */
+// get_volumes_for_parcellation_atlases__atlas_id__parcellations__parcellation_id__volumes_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["VolumeModel"][]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns one parcellation for given id. */
+// get_single_parcellation_detail_atlases__atlas_id__parcellations__parcellation_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// parcellation_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["SapiParcellationModel"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns all spaces that are defined in the siibra client. */
+// get_all_spaces_atlases__atlas_id__spaces_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["SapiSpaceModel"][]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns a template for a given space id. */
+// get_template_by_space_id_atlases__atlas_id__spaces__space_id__templates_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// space_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": unknown
+// "application/octet-stream": string
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns all parcellation maps for a given space id. */
+// get_parcellation_map_for_space_atlases__atlas_id__spaces__space_id__parcellation_maps_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// space_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": unknown
+// "application/octet-stream": string
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /**
+// * Get a detailed view on a single spatial feature.
+// * A parcellation id and region id can be provided optional to get more details.
+// */
+// get_single_detailed_spatial_feature_atlases__atlas_id__spaces__space_id__features__feature_id__get: {
+// parameters: {
+// path: {
+// feature_id: string
+// atlas_id: string
+// space_id: string
+// }
+// query: {
+// parcellation_id?: string
+// region?: string
+// bbox?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": Partial<
+// components["schemas"]["IEEGSessionModel"]
+// > &
+// Partial<components["schemas"]["VOIDataModel"]>
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Return all possible feature names and links to get more details */
+// get_all_spatial_features_for_space_atlases__atlas_id__spaces__space_id__features_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// space_id: string
+// }
+// query: {
+// parcellation_id?: string
+// type?: string
+// region?: string
+// bbox?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": (Partial<
+// components["schemas"]["IEEGSessionModel"]
+// > &
+// Partial<components["schemas"]["VOIDataModel"]>)[]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// get_volumes_for_space_atlases__atlas_id__spaces__space_id__volumes_get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// space_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["VolumeModel"][]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Returns one space for given id, with links to further resources */
+// get_single_space_detail_atlases__atlas_id__spaces__space_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// space_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["SapiSpaceModel"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Get all atlases known by siibra. */
+// get_all_atlases_atlases_get: {
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["SapiAtlasModel"][]
+// }
+// }
+// }
+// }
+// /** Get more information for a specific atlas with links to further objects. */
+// get_atlas_by_id_atlases__atlas_id__get: {
+// parameters: {
+// path: {
+// atlas_id: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": components["schemas"]["SapiAtlasModel"]
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// /** Return all genes (name, acronym) in siibra */
+// get_gene_names_genes_get: {
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": unknown
+// }
+// }
+// }
+// }
+// /** Return all possible modalities */
+// get_all_available_modalities_modalities_get: {
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": unknown
+// }
+// }
+// }
+// }
+// /**
+// * Get all details for one feature by id.
+// * Since the feature id is unique, no atlas concept is required.
+// *
+// * Further optional params can extend the result.
+// * :param feature_id:
+// * :param atlas_id:
+// * :param space_id:
+// * :param parcellation_id:
+// * :param region_id:
+// * :return: FeatureModels
+// */
+// get_feature_details_features__feature_id__get: {
+// parameters: {
+// path: {
+// feature_id: string
+// }
+// query: {
+// atlas_id?: string
+// space_id?: string
+// parcellation_id?: string
+// region_id?: string
+// }
+// }
+// responses: {
+// /** Successful Response */
+// 200: {
+// content: {
+// "application/json": Partial<
+// components["schemas"]["ReceptorDatasetModel"]
+// > &
+// Partial<components["schemas"]["BaseDatasetJsonModel"]> &
+// Partial<components["schemas"]["CorticalCellDistributionModel"]> &
+// Partial<components["schemas"]["IEEGSessionModel"]> &
+// Partial<components["schemas"]["VOIDataModel"]> &
+// Partial<components["schemas"]["ConnectivityMatrixDataModel"]> &
+// Partial<components["schemas"]["SerializationErrorModel"]>
+// }
+// }
+// /** Validation Error */
+// 422: {
+// content: {
+// "application/json": components["schemas"]["HTTPValidationError"]
+// }
+// }
+// }
+// }
+// }
-export interface external {}
+// export interface external {}
diff --git a/src/atlasComponents/sapi/schema_v3.ts b/src/atlasComponents/sapi/schema_v3.ts
new file mode 100644
index 0000000000000000000000000000000000000000..7147fd8c7a5b5c5511895b02e296518108ac20d1
--- /dev/null
+++ b/src/atlasComponents/sapi/schema_v3.ts
@@ -0,0 +1,1803 @@
+/**
+ * This file was auto-generated by openapi-typescript.
+ * Do not make direct changes to the file.
+ */
+
+
+export interface paths {
+ "/atlases": {
+ /** Get All Atlases */
+ get: operations["get_all_atlases_atlases_get"]
+ }
+ "/atlases/{atlas_id}": {
+ /** Get Single Atlas */
+ get: operations["get_single_atlas_atlases__atlas_id__get"]
+ }
+ "/spaces": {
+ /** Get All Spaces */
+ get: operations["get_all_spaces_spaces_get"]
+ }
+ "/spaces/{space_id}": {
+ /** Get Single Space */
+ get: operations["get_single_space_spaces__space_id__get"]
+ }
+ "/parcellations": {
+ /** Get All Parcellations */
+ get: operations["get_all_parcellations_parcellations_get"]
+ }
+ "/parcellations/{parcellation_id}": {
+ /** Get Single Parcellation */
+ get: operations["get_single_parcellation_parcellations__parcellation_id__get"]
+ }
+ "/regions": {
+ /** Get All Regions */
+ get: operations["get_all_regions_regions_get"]
+ }
+ "/regions/{region_id}": {
+ /** Get All Regions */
+ get: operations["get_all_regions_regions__region_id__get"]
+ }
+ "/map": {
+ /** Route Get Map */
+ get: operations["route_get_map_map_get"]
+ }
+ "/map/labelled_map.nii.gz": {
+ /** Route Get Parcellation Labelled Map */
+ get: operations["route_get_parcellation_labelled_map_map_labelled_map_nii_gz_get"]
+ }
+ "/map/statistical_map.nii.gz": {
+ /** Route Get Region Statistical Map */
+ get: operations["route_get_region_statistical_map_map_statistical_map_nii_gz_get"]
+ }
+ "/map/statistical_map.info.json": {
+ /** Route Get Region Statistical Map */
+ get: operations["route_get_region_statistical_map_map_statistical_map_info_json_get"]
+ }
+ "/feature/_types": {
+ /** Get All Feature Types */
+ get: operations["get_all_feature_types_feature__types_get"]
+ }
+ "/feature/RegionalConnectivity": {
+ /** Get All Connectivity Features */
+ get: operations["get_all_connectivity_features_feature_RegionalConnectivity_get"]
+ }
+ "/feature/RegionalConnectivity/{feature_id}": {
+ /** Get Single Connectivity Feature */
+ get: operations["get_single_connectivity_feature_feature_RegionalConnectivity__feature_id__get"]
+ }
+ "/feature/CorticalProfile": {
+ /** Get All Connectivity Features */
+ get: operations["get_all_connectivity_features_feature_CorticalProfile_get"]
+ }
+ "/feature/CorticalProfile/{feature_id}": {
+ /** Get Single Connectivity Feature */
+ get: operations["get_single_connectivity_feature_feature_CorticalProfile__feature_id__get"]
+ }
+ "/feature/Tabular": {
+ /** Get All Tabular */
+ get: operations["get_all_tabular_feature_Tabular_get"]
+ }
+ "/feature/Tabular/{feature_id}": {
+ /** Get Single Tabular */
+ get: operations["get_single_tabular_feature_Tabular__feature_id__get"]
+ }
+ "/feature/VolumeOfInterest": {
+ /** Get All Voi */
+ get: operations["get_all_voi_feature_VolumeOfInterest_get"]
+ }
+ "/feature/VolumeOfInterest/{feature_id}": {
+ /** Get Single Voi */
+ get: operations["get_single_voi_feature_VolumeOfInterest__feature_id__get"]
+ }
+ "/feature/GeneExpressions": {
+ /** Get All Gene */
+ get: operations["get_all_gene_feature_GeneExpressions_get"]
+ }
+ "/feature/GeneExpressions/{feature_id}": {
+ /** Get All Gene */
+ get: operations["get_all_gene_feature_GeneExpressions__feature_id__get"]
+ }
+}
+
+export type webhooks = Record<string, never>;
+
+export interface components {
+ schemas: {
+ /** AxesOrigin */
+ AxesOrigin: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * typeOfUncertainty
+ * @description Distinct technique used to quantify the uncertainty of a measurement.
+ */
+ typeOfUncertainty?: Record<string, never>
+ /**
+ * uncertainty
+ * @description Quantitative value range defining the uncertainty of a measurement.
+ */
+ uncertainty?: (number)[]
+ /**
+ * unit
+ * @description Determinate quantity adopted as a standard of measurement.
+ */
+ unit?: Record<string, never>
+ /**
+ * value
+ * @description Entry for a property.
+ */
+ value: number
+ }
+ /** BestViewPoint */
+ BestViewPoint: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * coordinateSpace
+ * @description Two or three dimensional geometric setting.
+ */
+ coordinateSpace: Record<string, never>
+ /**
+ * Coordinates
+ * @description Structured information on a quantitative value.
+ */
+ coordinates: (components["schemas"]["api__models__openminds__SANDS__v3__atlas__parcellationEntityVersion__Coordinates"])[]
+ }
+ /** BoundingBoxModel */
+ BoundingBoxModel: {
+ /** @Type */
+ "@type": string
+ space: components["schemas"]["SiibraAtIdModel"]
+ center: components["schemas"]["CoordinatePointModel"]
+ minpoint: components["schemas"]["CoordinatePointModel"]
+ maxpoint: components["schemas"]["CoordinatePointModel"]
+ /** Shape */
+ shape: (number)[]
+ /** Isplanar */
+ isPlanar: boolean
+ }
+ /** BrainAtlasVersionModel */
+ BrainAtlasVersionModel: {
+ /** @Type */
+ "@type": string
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * @Id
+ * @description Metadata node identifier.
+ */
+ "@id": string
+ /** abbreviation */
+ abbreviation?: string
+ /**
+ * accessibility
+ * @description Level to which something is accessible to someone or something.
+ */
+ accessibility: Record<string, never>
+ /** atlasType */
+ atlasType?: Record<string, never>
+ /**
+ * author
+ * @description Creator of a literary or creative work, as well as a dataset publication.
+ */
+ author?: (Record<string, never>)[]
+ /**
+ * coordinateSpace
+ * @description Two or three dimensional geometric setting.
+ */
+ coordinateSpace: Record<string, never>
+ /**
+ * Copyright
+ * @description Structured information on the copyright.
+ */
+ copyright?: components["schemas"]["Copyright"]
+ /**
+ * custodian
+ * @description The 'custodian' is a legal person who is responsible for the content and quality of the data, metadata, and/or code of a research product.
+ */
+ custodian?: (Record<string, never>)[]
+ /**
+ * description
+ * @description Longer statement or account giving the characteristics of someone or something.
+ */
+ description?: string
+ /**
+ * digitalIdentifier
+ * @description Digital handle to identify objects or legal persons.
+ */
+ digitalIdentifier?: Record<string, never>
+ /**
+ * fullDocumentation
+ * @description Non-abridged instructions, comments, and information for using a particular product.
+ */
+ fullDocumentation: Record<string, never>
+ /**
+ * fullName
+ * @description Whole, non-abbreviated name of something or somebody.
+ */
+ fullName?: string
+ /**
+ * funding
+ * @description Money provided by a legal person for a particular purpose.
+ */
+ funding?: (Record<string, never>)[]
+ hasTerminologyVersion: components["schemas"]["HasTerminologyVersion"]
+ /**
+ * homepage
+ * @description Main website of something or someone.
+ */
+ homepage?: Record<string, never>
+ /**
+ * howToCite
+ * @description Preferred format for citing a particular object or legal person.
+ */
+ howToCite?: string
+ /**
+ * isAlternativeVersionOf
+ * @description Reference to an original form where the essence was preserved, but presented in an alternative form.
+ */
+ isAlternativeVersionOf?: (Record<string, never>)[]
+ /**
+ * isNewVersionOf
+ * @description Reference to a previous (potentially outdated) particular form of something.
+ */
+ isNewVersionOf?: Record<string, never>
+ /**
+ * keyword
+ * @description Significant word or concept that are representative of something or someone.
+ */
+ keyword?: (Record<string, never>)[]
+ /**
+ * license
+ * @description Grant by a party to another party as an element of an agreement between those parties that permits to do, use, or own something.
+ */
+ license: Record<string, never>
+ /**
+ * ontologyIdentifier
+ * @description Term or code used to identify something or someone registered within a particular ontology.
+ */
+ ontologyIdentifier?: (string)[]
+ /**
+ * Othercontribution
+ * @description Structured information on the contribution made to a research product.
+ */
+ otherContribution?: components["schemas"]["OtherContribution"]
+ /**
+ * relatedPublication
+ * @description Reference to something that was made available for the general public to see or buy.
+ */
+ relatedPublication?: (Record<string, never>)[]
+ /**
+ * releaseDate
+ * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
+ */
+ releaseDate: string
+ /**
+ * repository
+ * @description Place, room, or container where something is deposited or stored.
+ */
+ repository?: Record<string, never>
+ /**
+ * shortName
+ * @description Shortened or fully abbreviated name of something or somebody.
+ */
+ shortName: string
+ /**
+ * supportChannel
+ * @description Way of communication used to interact with users or customers.
+ */
+ supportChannel?: (string)[]
+ /**
+ * versionIdentifier
+ * @description Term or code used to identify the version of something.
+ */
+ versionIdentifier: string
+ /**
+ * versionInnovation
+ * @description Documentation on what changed in comparison to a previously published form of something.
+ */
+ versionInnovation: string
+ }
+ /** CommonCoordinateSpaceModel */
+ CommonCoordinateSpaceModel: {
+ /** @Type */
+ "@type": string
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * @Id
+ * @description Metadata node identifier.
+ */
+ "@id": string
+ /**
+ * anatomicalAxesOrientation
+ * @description Relation between reference planes used in anatomy and mathematics.
+ */
+ anatomicalAxesOrientation: Record<string, never>
+ /**
+ * Axesorigin
+ * @description Structured information on a quantitative value.
+ */
+ axesOrigin: (components["schemas"]["AxesOrigin"])[]
+ /**
+ * defaultImage
+ * @description Two or three dimensional image that particluarly represents a specific coordinate space.
+ */
+ defaultImage?: components["schemas"]["VolumeModel"][]
+ /**
+ * digitalIdentifier
+ * @description Digital handle to identify objects or legal persons.
+ */
+ digitalIdentifier?: Record<string, never>
+ /**
+ * fullName
+ * @description Whole, non-abbreviated name of something or somebody.
+ */
+ fullName: string
+ /**
+ * homepage
+ * @description Main website of something or someone.
+ */
+ homepage?: Record<string, never>
+ /**
+ * howToCite
+ * @description Preferred format for citing a particular object or legal person.
+ */
+ howToCite?: string
+ /**
+ * nativeUnit
+ * @description Determinate quantity used in the original measurement.
+ */
+ nativeUnit: Record<string, never>
+ /**
+ * ontologyIdentifier
+ * @description Term or code used to identify something or someone registered within a particular ontology.
+ */
+ ontologyIdentifier?: (string)[]
+ /**
+ * releaseDate
+ * @description Fixed date on which a product is due to become or was made available for the general public to see or buy
+ */
+ releaseDate: string
+ /**
+ * shortName
+ * @description Shortened or fully abbreviated name of something or somebody.
+ */
+ shortName: string
+ /**
+ * versionIdentifier
+ * @description Term or code used to identify the version of something.
+ */
+ versionIdentifier: string
+ }
+ /**
+ * ConnectivityTypes
+ * @description An enumeration.
+ * @enum {unknown}
+ */
+ ConnectivityTypes: "FunctionalConnectivity" | "StreamlineCounts" | "StreamlineLengths"
+ /** CoordinatePointModel */
+ CoordinatePointModel: {
+ /** @Type */
+ "@type": string
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * @Id
+ * @description Metadata node identifier.
+ */
+ "@id": string
+ /**
+ * coordinateSpace
+ * @description Two or three dimensional geometric setting.
+ */
+ coordinateSpace: Record<string, never>
+ /**
+ * Coordinates
+ * @description Structured information on a quantitative value.
+ */
+ coordinates: (components["schemas"]["api__models__openminds__SANDS__v3__miscellaneous__coordinatePoint__Coordinates"])[]
+ }
+ /** Copyright */
+ Copyright: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * holder
+ * @description Legal person in possession of something.
+ */
+ holder: (Record<string, never>)[]
+ /**
+ * year
+ * @description Cycle in the Gregorian calendar specified by a number and comprised of 365 or 366 days divided into 12 months beginning with January and ending with December.
+ */
+ year: string
+ }
+ /**
+ * CorticalProfileTypes
+ * @description An enumeration.
+ * @enum {unknown}
+ */
+ CorticalProfileTypes: "ReceptorDensityProfile" | "CellDensityProfile" | "BigBrainIntensityProfile"
+ /** DataFrameModel */
+ DataFrameModel: {
+ /** @Type */
+ "@type": string
+ /** Index */
+ index: (Record<string, never>)[]
+ /** Dtype */
+ dtype: string
+ /** Columns */
+ columns: (Record<string, never>)[]
+ /** Ndim */
+ ndim: number
+ /** Data */
+ data: ((number | string | (number)[])[])[]
+ }
+ /** EbrainsDatasetModel */
+ EbrainsDatasetModel: {
+ /** @Type */
+ "@type": string
+ /** @Id */
+ "@id": string
+ /** Name */
+ name: string
+ /** Urls */
+ urls: (components["schemas"]["EbrainsDsUrl"])[]
+ /** Description */
+ description: string
+ /** Contributors */
+ contributors: (components["schemas"]["EbrainsDsPerson"])[]
+ /** Ebrains Page */
+ ebrains_page: string
+ /** Custodians */
+ custodians: (components["schemas"]["EbrainsDsPerson"])[]
+ }
+ /** EbrainsDsPerson */
+ EbrainsDsPerson: {
+ /** @Type */
+ "@type": string
+ /** @Id */
+ "@id": string
+ /** Schema.Org/Shortname */
+ "schema.org/shortName": string
+ /** Identifier */
+ identifier: string
+ /** Shortname */
+ shortName: string
+ /** Name */
+ name: string
+ }
+ /** EbrainsDsUrl */
+ EbrainsDsUrl: {
+ /** @Type */
+ "@type": string
+ /** Url */
+ url: string
+ }
+ /** HTTPValidationError */
+ HTTPValidationError: {
+ /** Detail */
+ detail?: (components["schemas"]["ValidationError"])[]
+ }
+ /** HasAnnotation */
+ HasAnnotation: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * Bestviewpoint
+ * @description Structured information on a coordinate point.
+ */
+ bestViewPoint?: components["schemas"]["BestViewPoint"]
+ /**
+ * criteria
+ * @description Aspects or standards on which a judgement or decision is based.
+ */
+ criteria?: Record<string, never>
+ /**
+ * criteriaQualityType
+ * @description Distinct class that defines how the judgement or decision was made for a particular criteria.
+ */
+ criteriaQualityType: Record<string, never>
+ /**
+ * displayColor
+ * @description Preferred coloring.
+ */
+ displayColor?: string
+ /**
+ * inspiredBy
+ * @description Reference to an inspiring element.
+ */
+ inspiredBy?: (Record<string, never>)[]
+ /**
+ * internalIdentifier
+ * @description Term or code that identifies someone or something within a particular product.
+ */
+ internalIdentifier: string
+ /**
+ * laterality
+ * @description Differentiation between a pair of lateral homologous parts of the body.
+ */
+ laterality?: (Record<string, never>)[]
+ /**
+ * visualizedIn
+ * @description Reference to an image in which something is visible.
+ */
+ visualizedIn?: Record<string, never>
+ }
+ /** HasTerminologyVersion */
+ HasTerminologyVersion: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * definedIn
+ * @description Reference to a file instance in which something is stored.
+ */
+ definedIn?: (Record<string, never>)[]
+ /** hasEntityVersion */
+ hasEntityVersion: (Record<string, never>)[]
+ /**
+ * ontologyIdentifier
+ * @description Term or code used to identify something or someone registered within a particular ontology.
+ */
+ ontologyIdentifier?: (string)[]
+ }
+ /** LocationModel */
+ LocationModel: {
+ /** @Type */
+ "@type": string
+ space: components["schemas"]["SiibraAtIdModel"]
+ }
+ /** MapIndexModel */
+ MapIndexModel: {
+ /** @Type */
+ "@type": string
+ /** Volume */
+ volume: number
+ /** Label */
+ label?: number
+ /** Fragment */
+ fragment?: string
+ }
+ /** MapModel */
+ MapModel: {
+ /** @Type */
+ "@type": string
+ /** @Id */
+ "@id": string
+ /** Name */
+ name: string
+ /** Shortname */
+ shortname?: string
+ /** Modality */
+ modality?: string
+ /** Description */
+ description?: string
+ /** Publications */
+ publications: (components["schemas"]["SiibraPublication"])[]
+ /** Datasets */
+ datasets: (components["schemas"]["EbrainsDatasetModel"])[]
+ /** Species */
+ species: string
+ /** Indices */
+ indices: {
+ [key: string]: (components["schemas"]["MapIndexModel"])[] | undefined
+ }
+ /** Volumes */
+ volumes: (components["schemas"]["VolumeModel"])[]
+ }
+ /**
+ * MapType
+ * @description An enumeration.
+ * @enum {string}
+ */
+ MapType: "LABELLED" | "STATISTICAL"
+ /** OtherContribution */
+ OtherContribution: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * contributionType
+ * @description Distinct class of what was given or supplied as a part or share.
+ */
+ contributionType: (Record<string, never>)[]
+ /**
+ * contributor
+ * @description Legal person that gave or supplied something as a part or share.
+ */
+ contributor: Record<string, never>
+ }
+ /** Page[CommonCoordinateSpaceModel] */
+ Page_CommonCoordinateSpaceModel_: {
+ /** Items */
+ items: (components["schemas"]["CommonCoordinateSpaceModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[ParcellationEntityVersionModel] */
+ Page_ParcellationEntityVersionModel_: {
+ /** Items */
+ items: (components["schemas"]["ParcellationEntityVersionModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[SiibraAtlasModel] */
+ Page_SiibraAtlasModel_: {
+ /** Items */
+ items: (components["schemas"]["SiibraAtlasModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[SiibraCorticalProfileModel] */
+ Page_SiibraCorticalProfileModel_: {
+ /** Items */
+ items: (components["schemas"]["SiibraCorticalProfileModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[SiibraParcellationModel] */
+ Page_SiibraParcellationModel_: {
+ /** Items */
+ items: (components["schemas"]["SiibraParcellationModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[SiibraRegionalConnectivityModel] */
+ Page_SiibraRegionalConnectivityModel_: {
+ /** Items */
+ items: (components["schemas"]["SiibraRegionalConnectivityModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[SiibraTabularModel] */
+ Page_SiibraTabularModel_: {
+ /** Items */
+ items: (components["schemas"]["SiibraTabularModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[SiibraVoiModel] */
+ Page_SiibraVoiModel_: {
+ /** Items */
+ items: (components["schemas"]["SiibraVoiModel"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[Union[SiibraCorticalProfileModel, SiibraTabularModel, SiibraReceptorDensityFp]] */
+ Page_Union_SiibraCorticalProfileModel__SiibraTabularModel__SiibraReceptorDensityFp__: {
+ /** Items */
+ items: (components["schemas"]["SiibraCorticalProfileModel"] | components["schemas"]["SiibraTabularModel"] | components["schemas"]["SiibraReceptorDensityFp"])[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** Page[str] */
+ Page_str_: {
+ /** Items */
+ items: (string)[]
+ /** Total */
+ total: number
+ /** Page */
+ page: number
+ /** Size */
+ size: number
+ /** Pages */
+ pages?: number
+ }
+ /** ParcellationEntityVersionModel */
+ ParcellationEntityVersionModel: {
+ /** @Type */
+ "@type": string
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * @Id
+ * @description Metadata node identifier.
+ */
+ "@id": string
+ hasAnnotation?: components["schemas"]["HasAnnotation"]
+ /**
+ * hasParent
+ * @description Reference to a parent object or legal person.
+ */
+ hasParent?: (Record<string, never>)[]
+ /** lookupLabel */
+ lookupLabel?: string
+ /**
+ * name
+ * @description Word or phrase that constitutes the distinctive designation of a being or thing.
+ */
+ name?: string
+ /**
+ * ontologyIdentifier
+ * @description Term or code used to identify something or someone registered within a particular ontology.
+ */
+ ontologyIdentifier?: (string)[]
+ /** Relationassessment */
+ relationAssessment?: components["schemas"]["RelationAssessmentItem"] | components["schemas"]["RelationAssessmentItem1"]
+ /**
+ * versionIdentifier
+ * @description Term or code used to identify the version of something.
+ */
+ versionIdentifier: string
+ /**
+ * versionInnovation
+ * @description Documentation on what changed in comparison to a previously published form of something.
+ */
+ versionInnovation?: string
+ }
+ /** QuantitativeOverlapItem */
+ QuantitativeOverlapItem: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * typeOfUncertainty
+ * @description Distinct technique used to quantify the uncertainty of a measurement.
+ */
+ typeOfUncertainty?: Record<string, never>
+ /**
+ * uncertainty
+ * @description Quantitative value range defining the uncertainty of a measurement.
+ */
+ uncertainty?: (number)[]
+ /**
+ * unit
+ * @description Determinate quantity adopted as a standard of measurement.
+ */
+ unit?: Record<string, never>
+ /**
+ * value
+ * @description Entry for a property.
+ */
+ value: number
+ }
+ /** QuantitativeOverlapItem1 */
+ QuantitativeOverlapItem1: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * maxValue
+ * @description Greatest quantity attained or allowed.
+ */
+ maxValue: number
+ /** maxValueUnit */
+ maxValueUnit?: Record<string, never>
+ /**
+ * minValue
+ * @description Smallest quantity attained or allowed.
+ */
+ minValue: number
+ /** minValueUnit */
+ minValueUnit?: Record<string, never>
+ }
+ /** RelationAssessmentItem */
+ RelationAssessmentItem: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * criteria
+ * @description Aspects or standards on which a judgement or decision is based.
+ */
+ criteria?: Record<string, never>
+ /**
+ * inRelationTo
+ * @description Reference to a related element.
+ */
+ inRelationTo: Record<string, never>
+ /**
+ * qualitativeOverlap
+ * @description Semantic characterization of how much two things occupy the same space.
+ */
+ qualitativeOverlap: Record<string, never>
+ }
+ /** RelationAssessmentItem1 */
+ RelationAssessmentItem1: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * criteria
+ * @description Aspects or standards on which a judgement or decision is based.
+ */
+ criteria?: Record<string, never>
+ /**
+ * inRelationTo
+ * @description Reference to a related element.
+ */
+ inRelationTo: Record<string, never>
+ /** Quantitativeoverlap */
+ quantitativeOverlap: components["schemas"]["QuantitativeOverlapItem"] | components["schemas"]["QuantitativeOverlapItem1"]
+ }
+ /** SeriesModel */
+ SeriesModel: {
+ /** @Type */
+ "@type": string
+ /** Name */
+ name?: string
+ /** Dtype */
+ dtype: string
+ /** Index */
+ index: (string | number | number)[]
+ /** Data */
+ data: (number)[]
+ }
+ /** SiibraAnchorModel */
+ SiibraAnchorModel: {
+ /** @Type */
+ "@type": string
+ location?: components["schemas"]["LocationModel"]
+ /** Regions */
+ regions: (components["schemas"]["SiibraRegionAssignmentQual"])[]
+ }
+ /** SiibraAtIdModel */
+ SiibraAtIdModel: {
+ /** @Id */
+ "@id": string
+ }
+ /** SiibraAtlasModel */
+ SiibraAtlasModel: {
+ /** @Type */
+ "@type": string
+ /** @Id */
+ "@id": string
+ /** Name */
+ name: string
+ /** Spaces */
+ spaces: (components["schemas"]["SiibraAtIdModel"])[]
+ /** Parcellations */
+ parcellations: (components["schemas"]["SiibraAtIdModel"])[]
+ /** Species */
+ species: string
+ }
+ /** SiibraCorticalProfileModel */
+ SiibraCorticalProfileModel: {
+ /** @Type */
+ "@type": string
+ /** Id */
+ id: string
+ /** Modality */
+ modality: string
+ /** Description */
+ description: string
+ /** Name */
+ name: string
+ /** Datasets */
+ datasets: (components["schemas"]["EbrainsDatasetModel"])[]
+ anchor?: components["schemas"]["SiibraAnchorModel"]
+ /** Unit */
+ unit?: string
+ /** Boundary Positions */
+ boundary_positions: {
+ [key: string]: number | undefined
+ }
+ /** Boundaries Mapped */
+ boundaries_mapped: boolean
+ data?: components["schemas"]["SeriesModel"]
+ }
+ /** SiibraParcellationModel */
+ SiibraParcellationModel: {
+ /** @Type */
+ "@type": string
+ /** @Id */
+ "@id": string
+ /** Name */
+ name: string
+ /** Modality */
+ modality?: string
+ /** Brainatlasversions */
+ brainAtlasVersions: (components["schemas"]["BrainAtlasVersionModel"])[]
+ version?: components["schemas"]["SiibraParcellationVersionModel"]
+ }
+ /** SiibraParcellationVersionModel */
+ SiibraParcellationVersionModel: {
+ /** @Type */
+ "@type": string
+ /** Name */
+ name: string
+ /** Deprecated */
+ deprecated?: boolean
+ prev?: components["schemas"]["SiibraAtIdModel"]
+ next?: components["schemas"]["SiibraAtIdModel"]
+ }
+ /** SiibraPublication */
+ SiibraPublication: {
+ /** @Type */
+ "@type": string
+ /** Citation */
+ citation: string
+ /** Url */
+ url: string
+ }
+ /** SiibraReceptorDensityFp */
+ SiibraReceptorDensityFp: {
+ /** @Type */
+ "@type": string
+ /** Id */
+ id: string
+ /** Modality */
+ modality: string
+ /** Description */
+ description: string
+ /** Name */
+ name: string
+ /** Datasets */
+ datasets: (components["schemas"]["EbrainsDatasetModel"])[]
+ anchor?: components["schemas"]["SiibraAnchorModel"]
+ data?: components["schemas"]["DataFrameModel"]
+ /** Neurotransmitters */
+ neurotransmitters?: (string)[]
+ /** Receptors */
+ receptors?: (string)[]
+ }
+ /** SiibraRegionAssignmentQual */
+ SiibraRegionAssignmentQual: {
+ /** @Type */
+ "@type": string
+ region: components["schemas"]["ParcellationEntityVersionModel"]
+ /** Qualification */
+ qualification: string
+ }
+ /** SiibraRegionalConnectivityModel */
+ SiibraRegionalConnectivityModel: {
+ /** @Type */
+ "@type": string
+ /** Id */
+ id: string
+ /** Modality */
+ modality: string
+ /** Description */
+ description: string
+ /** Name */
+ name: string
+ /** Datasets */
+ datasets: (components["schemas"]["EbrainsDatasetModel"])[]
+ anchor?: components["schemas"]["SiibraAnchorModel"]
+ /** Cohort */
+ cohort: string
+ /** Subjects */
+ subjects: (string)[]
+ /** Matrices */
+ matrices?: {
+ [key: string]: components["schemas"]["DataFrameModel"] | undefined
+ }
+ }
+ /** SiibraTabularModel */
+ SiibraTabularModel: {
+ /** @Type */
+ "@type": string
+ /** Id */
+ id: string
+ /** Modality */
+ modality: string
+ /** Description */
+ description: string
+ /** Name */
+ name: string
+ /** Datasets */
+ datasets: (components["schemas"]["EbrainsDatasetModel"])[]
+ anchor?: components["schemas"]["SiibraAnchorModel"]
+ data?: components["schemas"]["DataFrameModel"]
+ }
+ /** SiibraVoiModel */
+ SiibraVoiModel: {
+ /** @Type */
+ "@type": string
+ /** Id */
+ id: string
+ /** Modality */
+ modality: string
+ /** Description */
+ description: string
+ /** Name */
+ name: string
+ /** Datasets */
+ datasets: (components["schemas"]["EbrainsDatasetModel"])[]
+ anchor?: components["schemas"]["SiibraAnchorModel"]
+ volume: components["schemas"]["VolumeModel"]
+ boundingbox: components["schemas"]["BoundingBoxModel"]
+ }
+ /** StatisticModelInfo */
+ StatisticModelInfo: {
+ /** Min */
+ min: number
+ /** Max */
+ max: number
+ }
+ /**
+ * TabularTypes
+ * @description An enumeration.
+ * @enum {unknown}
+ */
+ TabularTypes: "ReceptorDensityFingerprint" | "LayerwiseBigBrainIntensities" | "LayerwiseCellDensity"
+ /** ValidationError */
+ ValidationError: {
+ /** Location */
+ loc: (string | number)[]
+ /** Message */
+ msg: string
+ /** Error Type */
+ type: string
+ }
+ /** VocabModel */
+ VocabModel: {
+ /** @Vocab */
+ "@vocab": string
+ }
+ /** VolumeModel */
+ VolumeModel: {
+ /** @Type */
+ "@type": string
+ /** Name */
+ name: string
+ /** Formats */
+ formats: (string)[]
+ /** Providesmesh */
+ providesMesh: boolean
+ /** Providesimage */
+ providesImage: boolean
+ /** Fragments */
+ fragments: {
+ [key: string]: (string)[] | undefined
+ }
+ /** Variant */
+ variant?: string
+ /** Providedvolumes */
+ providedVolumes: {
+ [key: string]: (string | ({
+ [key: string]: string | undefined
+ })) | undefined
+ }
+ space: components["schemas"]["SiibraAtIdModel"]
+ }
+ /** Coordinates */
+ api__models__openminds__SANDS__v3__atlas__parcellationEntityVersion__Coordinates: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * typeOfUncertainty
+ * @description Distinct technique used to quantify the uncertainty of a measurement.
+ */
+ typeOfUncertainty?: Record<string, never>
+ /**
+ * uncertainty
+ * @description Quantitative value range defining the uncertainty of a measurement.
+ */
+ uncertainty?: (number)[]
+ /**
+ * unit
+ * @description Determinate quantity adopted as a standard of measurement.
+ */
+ unit?: Record<string, never>
+ /**
+ * value
+ * @description Entry for a property.
+ */
+ value: number
+ }
+ /** Coordinates */
+ api__models__openminds__SANDS__v3__miscellaneous__coordinatePoint__Coordinates: {
+ /**
+ * @Context
+ * @default {
+ * "@vocab": "https://openminds.ebrains.eu/vocab/"
+ * }
+ */
+ "@context"?: components["schemas"]["VocabModel"]
+ /**
+ * typeOfUncertainty
+ * @description Distinct technique used to quantify the uncertainty of a measurement.
+ */
+ typeOfUncertainty?: Record<string, never>
+ /**
+ * uncertainty
+ * @description Quantitative value range defining the uncertainty of a measurement.
+ */
+ uncertainty?: (number)[]
+ /**
+ * unit
+ * @description Determinate quantity adopted as a standard of measurement.
+ */
+ unit?: Record<string, never>
+ /**
+ * value
+ * @description Entry for a property.
+ */
+ value: number
+ }
+ }
+ responses: never
+ parameters: never
+ requestBodies: never
+ headers: never
+ pathItems: never
+}
+
+export type external = Record<string, never>;
+
+export interface operations {
+
+ get_all_atlases_atlases_get: {
+ /** Get All Atlases */
+ parameters?: {
+ query?: {
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_SiibraAtlasModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_atlas_atlases__atlas_id__get: {
+ /** Get Single Atlas */
+ parameters: {
+ path: {
+ atlas_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraAtlasModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_spaces_spaces_get: {
+ /** Get All Spaces */
+ parameters?: {
+ query?: {
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_CommonCoordinateSpaceModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_space_spaces__space_id__get: {
+ /** Get Single Space */
+ parameters: {
+ path: {
+ space_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["CommonCoordinateSpaceModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_parcellations_parcellations_get: {
+ /** Get All Parcellations */
+ parameters?: {
+ query?: {
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_SiibraParcellationModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_parcellation_parcellations__parcellation_id__get: {
+ /** Get Single Parcellation */
+ parameters: {
+ path: {
+ parcellation_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraParcellationModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_regions_regions_get: {
+ /** Get All Regions */
+ parameters: {
+ query: {
+ parcellation_id: string
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_ParcellationEntityVersionModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_regions_regions__region_id__get: {
+ /** Get All Regions */
+ parameters: {
+ query: {
+ parcellation_id: string
+ space_id: string
+ }
+ path: {
+ region_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["ParcellationEntityVersionModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ route_get_map_map_get: {
+ /** Route Get Map */
+ parameters: {
+ query: {
+ parcellation_id: string
+ space_id: string
+ map_type: components["schemas"]["MapType"]
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["MapModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ route_get_parcellation_labelled_map_map_labelled_map_nii_gz_get: {
+ /** Route Get Parcellation Labelled Map */
+ parameters: {
+ query: {
+ parcellation_id: string
+ space_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: never
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ route_get_region_statistical_map_map_statistical_map_nii_gz_get: {
+ /** Route Get Region Statistical Map */
+ parameters: {
+ query: {
+ parcellation_id: string
+ space_id: string
+ region_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: never
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ route_get_region_statistical_map_map_statistical_map_info_json_get: {
+ /** Route Get Region Statistical Map */
+ parameters: {
+ query: {
+ parcellation_id: string
+ space_id: string
+ region_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["StatisticModelInfo"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_feature_types_feature__types_get: {
+ /** Get All Feature Types */
+ parameters?: {
+ query?: {
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_str_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_connectivity_features_feature_RegionalConnectivity_get: {
+ /** Get All Connectivity Features */
+ parameters: {
+ query: {
+ parcellation_id: string
+ type?: components["schemas"]["ConnectivityTypes"]
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_SiibraRegionalConnectivityModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_connectivity_feature_feature_RegionalConnectivity__feature_id__get: {
+ /** Get Single Connectivity Feature */
+ parameters: {
+ query: {
+ parcellation_id: string
+ subject: string
+ type?: components["schemas"]["ConnectivityTypes"]
+ }
+ path: {
+ feature_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraRegionalConnectivityModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_connectivity_features_feature_CorticalProfile_get: {
+ /** Get All Connectivity Features */
+ parameters: {
+ query: {
+ parcellation_id: string
+ region_id: string
+ type?: components["schemas"]["CorticalProfileTypes"]
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_SiibraCorticalProfileModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_connectivity_feature_feature_CorticalProfile__feature_id__get: {
+ /** Get Single Connectivity Feature */
+ parameters: {
+ query: {
+ parcellation_id: string
+ region_id: string
+ type?: components["schemas"]["CorticalProfileTypes"]
+ }
+ path: {
+ feature_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraCorticalProfileModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_tabular_feature_Tabular_get: {
+ /** Get All Tabular */
+ parameters: {
+ query: {
+ parcellation_id: string
+ region_id: string
+ type?: components["schemas"]["TabularTypes"]
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_Union_SiibraCorticalProfileModel__SiibraTabularModel__SiibraReceptorDensityFp__"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_tabular_feature_Tabular__feature_id__get: {
+ /** Get Single Tabular */
+ parameters: {
+ query: {
+ parcellation_id: string
+ region_id: string
+ type?: components["schemas"]["TabularTypes"]
+ }
+ path: {
+ feature_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraCorticalProfileModel"] | components["schemas"]["SiibraTabularModel"] | components["schemas"]["SiibraReceptorDensityFp"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_voi_feature_VolumeOfInterest_get: {
+ /** Get All Voi */
+ parameters: {
+ query: {
+ space_id: string
+ bbox?: string
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_SiibraVoiModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_single_voi_feature_VolumeOfInterest__feature_id__get: {
+ /** Get Single Voi */
+ parameters: {
+ query: {
+ space_id: string
+ bbox?: string
+ }
+ path: {
+ feature_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraVoiModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_gene_feature_GeneExpressions_get: {
+ /** Get All Gene */
+ parameters: {
+ query: {
+ parcellation_id: string
+ region_id: string
+ gene: string
+ page?: number
+ size?: number
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["Page_SiibraTabularModel_"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+ get_all_gene_feature_GeneExpressions__feature_id__get: {
+ /** Get All Gene */
+ parameters: {
+ query: {
+ parcellation_id: string
+ region_id: string
+ gene: string
+ }
+ path: {
+ feature_id: string
+ }
+ }
+ responses: {
+ /** @description Successful Response */
+ 200: {
+ content: {
+ "application/json": components["schemas"]["SiibraTabularModel"]
+ }
+ }
+ /** @description Validation Error */
+ 422: {
+ content: {
+ "application/json": components["schemas"]["HTTPValidationError"]
+ }
+ }
+ }
+ }
+}
diff --git a/src/atlasComponents/sapi/translate_v3.ts b/src/atlasComponents/sapi/translate_v3.ts
new file mode 100644
index 0000000000000000000000000000000000000000..b8eeff87e951b583e2c7b5cb54470f1bdaf7ddd3
--- /dev/null
+++ b/src/atlasComponents/sapi/translate_v3.ts
@@ -0,0 +1,338 @@
+import {
+ SxplrAtlas, SxplrParcellation, SxplrTemplate, SxplrRegion, NgLayerSpec, NgPrecompMeshSpec, NgSegLayerSpec, VoiFeature, Point, TemplateDefaultImage, TThreeSurferMesh, TThreeMesh, LabelledMap
+} from "./type_sxplr"
+import { PathReturn } from "./type_v3"
+import { hexToRgb } from 'common/util'
+import { components } from "./schema_v3"
+
+
+class TranslateV3 {
+
+ #atlasMap: Map<string, PathReturn<"/atlases/{atlas_id}">> = new Map()
+ retrieveAtlas(atlas: SxplrAtlas): PathReturn<"/atlases/{atlas_id}"> {
+ return this.#atlasMap.get(atlas.id)
+ }
+ async translateAtlas(atlas:PathReturn<"/atlases/{atlas_id}">): Promise<SxplrAtlas> {
+ this.#atlasMap.set(atlas["@id"], atlas)
+ return {
+ id: atlas["@id"],
+ name: atlas.name
+ }
+ }
+
+ #parcellationMap: Map<string, PathReturn<"/parcellations/{parcellation_id}">> = new Map()
+ retrieveParcellation(parcellation: SxplrParcellation): PathReturn<"/parcellations/{parcellation_id}"> {
+ return this.#parcellationMap.get(parcellation.id)
+ }
+ async translateParcellation(parcellation:PathReturn<"/parcellations/{parcellation_id}">): Promise<SxplrParcellation> {
+ return {
+ id: parcellation["@id"],
+ name: parcellation.name,
+ modality: parcellation.modality,
+ }
+ }
+
+ #templateMap: Map<string, PathReturn<"/spaces/{space_id}">> = new Map()
+ retrieveTemplate(template:SxplrTemplate): PathReturn<"/spaces/{space_id}"> {
+ if (!template) debugger
+ return this.#templateMap.get(template.id)
+ }
+ async translateTemplate(template:PathReturn<"/spaces/{space_id}">): Promise<SxplrTemplate> {
+ this.#templateMap.set(template["@id"], template)
+ return {
+ id: template["@id"],
+ name: template.fullName
+ }
+ }
+
+ /**
+ * map of both name and id to region
+ */
+ #regionMap: Map<string, PathReturn<"/regions/{region_id}">> = new Map()
+ retrieveRegion(region: SxplrRegion): PathReturn<"/regions/{region_id}"> {
+ return this.#regionMap.get(region.name)
+ }
+ async translateRegion(region: PathReturn<"/regions/{region_id}">): Promise<SxplrRegion> {
+ const { ['@id']: regionId } = region
+ this.#regionMap.set(regionId, region)
+ this.#regionMap.set(region.name, region)
+ return {
+ id: region["@id"],
+ name: region.name,
+ color: hexToRgb(region.hasAnnotation?.displayColor) as [number, number, number],
+ parentIds: region.hasParent.map( v => v["@id"] )
+ }
+ }
+
+ async translateSpaceToVolumeImage(template: SxplrTemplate): Promise<NgLayerSpec[]> {
+ if (!template) return []
+ const space = this.retrieveTemplate(template)
+ if (!space) return []
+ const returnObj: NgLayerSpec[] = []
+ const validImages = space.defaultImage.filter(di => di.formats.includes("neuroglancer/precomputed"))
+
+ for (const defaultImage of validImages) {
+
+ const { providedVolumes } = defaultImage
+
+ const { ['neuroglancer/precomputed']: precomputedVol } = providedVolumes
+ if (!precomputedVol) {
+ console.error(`neuroglancer/precomputed data source has not been found!`)
+ continue
+ }
+ if (typeof precomputedVol === "object") {
+ console.error(`template default image cannot have fragment`)
+ continue
+ }
+ const [transform, info] = await Promise.all([
+ (async () => {
+
+ const resp = await fetch(`${precomputedVol}/transform.json`)
+ if (resp.status >= 400) {
+ console.error(`cannot retrieve transform: ${resp.status}`)
+ return null
+ }
+ const transform: number[][] = await resp.json()
+ return transform
+ })(),
+ (async () => {
+ const resp = await fetch(`${precomputedVol}/info`)
+ if (resp.status >= 400) {
+ console.error(`cannot retrieve transform: ${resp.status}`)
+ return null
+ }
+ const info = await resp.json()
+ const { resolution, size } = info.scales[0]
+ return {
+ voxel: info.scales[0].size as [number, number, number],
+ real: [0, 1, 2].map(idx => resolution[idx] * size[idx]) as [number, number, number],
+ }
+ })()
+ ])
+ returnObj.push({
+ source: `precomputed://${precomputedVol}`,
+ transform,
+ info,
+ })
+ }
+ return returnObj
+ }
+
+ async translateSpaceToSurfaceImage(template: SxplrTemplate): Promise<TThreeMesh[]> {
+ if (!template) return []
+ const space = this.retrieveTemplate(template)
+ if (!space) return []
+ const returnObj: TThreeMesh[] = []
+ const validImages = space.defaultImage.filter(di => di.formats.includes("gii-mesh"))
+ for (const defaultImage of validImages) {
+ const { providedVolumes, variant } = defaultImage
+ if (!variant) {
+ console.warn(`variant is not defined!`)
+ continue
+ }
+
+ const { ['gii-mesh']: giiMesh } = providedVolumes
+ if (!giiMesh) {
+ console.warn(`default image does not have gii-mesh in provided volumes`)
+ continue
+ }
+
+ if (typeof giiMesh === "string") {
+ console.warn(`three giiMesh is of type string, must be a dict!`)
+ continue
+ }
+
+ for (const lateriality in giiMesh) {
+ const url = giiMesh[lateriality]
+
+ returnObj.push({
+ id: `${template.name}-${variant}-${lateriality}`,
+ space: template.name,
+ variant,
+ laterality: /left/.test(lateriality)
+ ? 'left'
+ : /right/.test(lateriality)
+ ? 'right'
+ : null,
+ url,
+ })
+ }
+ }
+ return returnObj
+ }
+
+ async translateLabelledMapToThreeLabel(map:PathReturn<"/map">) {
+ const threeLabelMap: Record<string, { laterality: 'left' | 'right', url: string, regions: Record<string, number> }> = {}
+ const registerLayer = (url: string, laterality: 'left' | 'right', region: string, label: number) => {
+ if (!threeLabelMap[url]) {
+ threeLabelMap[url] = {
+ laterality,
+ regions: {},
+ url,
+ }
+ }
+
+ threeLabelMap[url].regions[region] = label
+ }
+ for (const regionname in map.indices) {
+ for (const { volume: volIdx, fragment, label } of map.indices[regionname]) {
+ const volume = map.volumes[volIdx || 0]
+ if (!volume.formats.includes("gii-label")) {
+ console.warn(`getting three label error! volume does not provide gii-label! skipping!`)
+ continue
+ }
+ const { ["gii-label"]: giiLabel } = volume.providedVolumes
+
+
+ if (!fragment || !["left hemisphere", "right hemisphere"].includes(fragment)) {
+ console.warn(`either fragment not defined, or fragment is not '{left|right} hemisphere'. Skipping!`)
+ continue
+ }
+ if (!giiLabel[fragment]) {
+ console.warn(`fragment '${fragment}' not provided by volume.gii-label! skipping!`)
+ continue
+ }
+ let laterality: 'left' | 'right'
+ if (fragment.includes("left")) laterality = "left"
+ if (fragment.includes("right")) laterality = "right"
+ if (!laterality) {
+ console.warn(`cannot determine the laterality! skipping`)
+ continue
+ }
+ registerLayer(giiLabel[fragment], laterality, regionname, label)
+ }
+ }
+ return threeLabelMap
+ }
+
+ async translateLabelledMapToNgSegLayers(map:PathReturn<"/map">): Promise<Record<string,{layer:NgSegLayerSpec, region: LabelledMap[]}>> {
+ const nglayerSpecMap: Record<string,{layer:NgSegLayerSpec, region: LabelledMap[]}> = {}
+
+ const registerLayer = async (url: string, label: number, region: LabelledMap) => {
+ let segLayerSpec: {layer:NgSegLayerSpec, region: LabelledMap[]}
+ if (url in nglayerSpecMap){
+ segLayerSpec = nglayerSpecMap[url]
+ } else {
+ const resp = await fetch(`${url}/transform.json`)
+ const transform = await resp.json()
+ segLayerSpec = {
+ layer: {
+ labelIndicies: [],
+ source: `precomputed://${url}`,
+ transform,
+ },
+ region: []
+ }
+ nglayerSpecMap[url] = segLayerSpec
+ }
+ segLayerSpec.layer.labelIndicies.push(label)
+ segLayerSpec.region.push(region)
+ }
+ for (const regionname in map.indices) {
+ for (const index of map.indices[regionname]) {
+ const { volume:volumeIdx=0, fragment, label } = index
+ if (!label) {
+ console.error(`Attempmting to add labelledmap with label '${label}'`)
+ }
+ let error = `Attempting to access map volume with idx '${volumeIdx}'`
+ if (!map.volumes[volumeIdx]) {
+ console.error(`${error}, IndexError, Skipping`)
+ continue
+ }
+ const volume = map.volumes[volumeIdx]
+
+ if (!volume.providedVolumes["neuroglancer/precomputed"]) {
+ console.error(`${error}, volume does not provide neuroglancer/precomputed. Skipping.`)
+ continue
+ }
+
+ const precomputedVol = volume.providedVolumes["neuroglancer/precomputed"]
+ if (typeof precomputedVol === "string") {
+ await registerLayer(precomputedVol, label, { name: regionname, label })
+ continue
+ }
+
+ if (!precomputedVol[fragment]) {
+ console.error(`${error}, fragment provided is '${fragment}', but was not available in volume: ${Object.keys(precomputedVol)}`)
+ continue
+ }
+ await registerLayer(precomputedVol[fragment], label, { name: regionname, label })
+ }
+ }
+
+ return nglayerSpecMap
+ }
+
+ async translateSpaceToAuxMesh(template: SxplrTemplate): Promise<NgPrecompMeshSpec[]>{
+ if (!template) return []
+ const space = this.retrieveTemplate(template)
+ if (!space) return []
+ const returnObj: NgPrecompMeshSpec[] = []
+ const validImages = space.defaultImage.filter(di => di.formats.includes("neuroglancer/precompmesh/surface"))
+
+ for (const defaultImage of validImages) {
+
+ const { providedVolumes } = defaultImage
+
+ const { ['neuroglancer/precompmesh/surface']: precompMeshVol } = providedVolumes
+ if (!precompMeshVol) {
+ console.error(`neuroglancer/precompmesh/surface data source has not been found!`)
+ continue
+ }
+ if (typeof precompMeshVol === "object") {
+ console.error(`template default image cannot have fragment`)
+ continue
+ }
+
+ const splitPrecompMeshVol = precompMeshVol.split(" ")
+ if (splitPrecompMeshVol.length !== 2) {
+ console.error(`Expecting exactly two fragments by splitting precompmeshvol, but got ${splitPrecompMeshVol.length}`)
+ continue
+ }
+ const resp = await fetch(`${splitPrecompMeshVol[0]}/transform.json`)
+ if (resp.status >= 400) {
+ console.error(`cannot retrieve transform: ${resp.status}`)
+ continue
+ }
+ const transform: number[][] = await resp.json()
+ returnObj.push({
+ source: `precompmesh://${splitPrecompMeshVol[0]}`,
+ transform,
+ auxMeshes: [{
+ labelIndicies: [Number(splitPrecompMeshVol[1])],
+ name: "auxmesh"
+ }]
+ })
+ }
+ return returnObj
+ }
+
+ async translatePoint(point: components["schemas"]["CoordinatePointModel"]): Promise<Point> {
+ const sapiSpace = this.#templateMap.get(point.coordinateSpace['@id'])
+ const space = await this.translateTemplate(sapiSpace)
+ return {
+ space,
+ loc: point.coordinates.map(v => v.value) as [number, number, number]
+ }
+ }
+
+ async translateVoi(voi: PathReturn<"/feature/VolumeOfInterest/{feature_id}">): Promise<VoiFeature> {
+ const { boundingbox } = voi
+ const { loc: center, space } = await this.translatePoint(boundingbox.center)
+ const { loc: maxpoint } = await this.translatePoint(boundingbox.maxpoint)
+ const { loc: minpoint } = await this.translatePoint(boundingbox.minpoint)
+ return {
+ bbox: {
+ center,
+ maxpoint,
+ minpoint,
+ space
+ },
+ name: voi.name,
+ desc: voi.description,
+ id: voi.id
+ }
+ }
+}
+
+export const translateV3Entities = new TranslateV3()
diff --git a/src/atlasComponents/sapi/type.ts b/src/atlasComponents/sapi/type.ts
index 905c0dee7f004cba521b96860e44c4da6e801d10..524d3d9a27748792217400a373ee83c97abf7c15 100644
--- a/src/atlasComponents/sapi/type.ts
+++ b/src/atlasComponents/sapi/type.ts
@@ -1,121 +1,121 @@
-import { OperatorFunction } from "rxjs"
-import { map } from "rxjs/operators"
-import { components, operations, paths } from "./schema"
-
-export type IdName = {
- id: string
- name: string
-}
-
-export type SapiModalityModel = {
- name: string
- types: string[]
-}
-
-type Point = [number, number, number]
-
-export type BoundingBoxConcept = [Point, Point]
-
-export type SapiAtlasModel = components["schemas"]["SapiAtlasModel"]
-export type SapiSpaceModel = components["schemas"]["SapiSpaceModel"]
-export type SapiParcellationModel = components["schemas"]["SapiParcellationModel"]
-export type SapiRegionModel = components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"]
-export type OpenMINDSCoordinatePoint = components['schemas']['siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model']
-export type SxplrCoordinatePointExtension = {
- openminds: OpenMINDSCoordinatePoint
- name: string
- description: string
- color: string
- '@id': string // should match the id of opendminds specs
-}
-
-export type SapiRegionMapInfoModel = components["schemas"]["NiiMetadataModel"]
-export type SapiVOIDataResponse = components["schemas"]["VOIDataModel"]
-export type SapiVolumeModel = components["schemas"]["VolumeModel"]
-export type SapiDatasetModel = components["schemas"]["DatasetJsonModel"]
-export type SpyNpArrayDataModel = components["schemas"]["NpArrayDataModel"]
-export type SapiIeegSessionModel = components["schemas"]["IEEGSessionModel"]
-
-/**
- * utility types
- */
-type PathReturn<T extends keyof paths> = Required<paths[T]["get"]["responses"][200]["content"]["application/json"]>
-export type PaginatedResponse<T> = {
- items: T[]
- total: number
- page: number
- size: number
-}
-
-/**
- * serialization error type
- */
-export type SapiSerializationErrorModel = components["schemas"]["SerializationErrorModel"]
-
-/**
- * datafeatures from operations
- */
-
-export type SapiRegionalFeatureModel = PathReturn<"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features/{feature_id}">
-export type SapiParcellationFeatureModel = PathReturn<"/atlases/{atlas_id}/parcellations/{parcellation_id}/features/{feature_id}">
-export type SapiSpatialFeatureModel = PathReturn<"/atlases/{atlas_id}/spaces/{space_id}/features/{feature_id}">
-
-export type SapiFeatureModel = SapiRegionalFeatureModel | SapiSpatialFeatureModel | SapiParcellationFeatureModel
-
-/**
- * specific data features
- */
-
-export type SapiRegionalFeatureReceptorModel = components["schemas"]["ReceptorDatasetModel"]
-export type SapiParcellationFeatureMatrixModel = components["schemas"]["ConnectivityMatrixDataModel"]
-
-
-export const CLEANED_IEEG_DATASET_TYPE = 'sxplr/cleanedIeegDataset'
-export type CleanedIeegDataset = Required<
- Omit<SapiDatasetModel, "@type"> & {
- '@type': 'sxplr/cleanedIeegDataset'
- sessions: Record<string, Omit<SapiIeegSessionModel, "dataset">>
- }
->
-
-export function cleanIeegSessionDatasets(ieegSessions: SapiIeegSessionModel[]): CleanedIeegDataset[]{
- const returnArr: CleanedIeegDataset[] = []
- for (const sess of ieegSessions) {
- const { dataset, ...itemToAppend } = sess
- const existing = returnArr.find(it => it["@id"] === dataset["@id"])
- if (!existing) {
- returnArr.push({
- ...dataset,
- '@type': CLEANED_IEEG_DATASET_TYPE,
- sessions: {
- [sess.sub_id]: itemToAppend
- }
- })
- continue
- }
- existing.sessions[sess.sub_id] = itemToAppend
- }
- return returnArr
-}
-
-export type SxplrCleanedFeatureModel = CleanedIeegDataset
-
-export function guardPipe<
- InputType,
- GuardType extends InputType
->(
- guardFn: (input: InputType) => input is GuardType
-): OperatorFunction<InputType, GuardType> {
- return src => src.pipe(
- map(val => {
- if (guardFn(val)) {
- return val
- }
- throw new Error(`TypeGuard Error`)
- })
- )
-}
-
-export type SapiQueryPriorityArg = {
- priority: number
-}
+// import { OperatorFunction } from "rxjs"
+// import { map } from "rxjs/operators"
+// import { components, operations, paths } from "./schema"
+
+// export type IdName = {
+// id: string
+// name: string
+// }
+
+// export type SapiModalityModel = {
+// name: string
+// types: string[]
+// }
+
+// type Point = [number, number, number]
+
+// export type BoundingBoxConcept = [Point, Point]
+
+// export type SapiAtlasModel = components["schemas"]["SapiAtlasModel"]
+// export type SapiSpaceModel = components["schemas"]["SapiSpaceModel"]
+// export type SapiParcellationModel = components["schemas"]["SapiParcellationModel"]
+// export type SapiRegionModel = components["schemas"]["siibra__openminds__SANDS__v3__atlas__parcellationEntityVersion__Model"]
+// export type OpenMINDSCoordinatePoint = components['schemas']['siibra__openminds__SANDS__v3__miscellaneous__coordinatePoint__Model']
+// export type SxplrCoordinatePointExtension = {
+// openminds: OpenMINDSCoordinatePoint
+// name: string
+// description: string
+// color: string
+// '@id': string // should match the id of opendminds specs
+// }
+
+// export type SapiRegionMapInfoModel = components["schemas"]["NiiMetadataModel"]
+// export type SapiVOIDataResponse = components["schemas"]["VOIDataModel"]
+// export type SapiVolumeModel = components["schemas"]["VolumeModel"]
+// export type SapiDatasetModel = components["schemas"]["DatasetJsonModel"]
+// export type SpyNpArrayDataModel = components["schemas"]["NpArrayDataModel"]
+// export type SapiIeegSessionModel = components["schemas"]["IEEGSessionModel"]
+
+// /**
+// * utility types
+// */
+// type PathReturn<T extends keyof paths> = Required<paths[T]["get"]["responses"][200]["content"]["application/json"]>
+// export type PaginatedResponse<T> = {
+// items: T[]
+// total: number
+// page: number
+// size: number
+// }
+
+// /**
+// * serialization error type
+// */
+// export type SapiSerializationErrorModel = components["schemas"]["SerializationErrorModel"]
+
+// /**
+// * datafeatures from operations
+// */
+
+// export type SapiRegionalFeatureModel = PathReturn<"/atlases/{atlas_id}/parcellations/{parcellation_id}/regions/{region_id}/features/{feature_id}">
+// export type SapiParcellationFeatureModel = PathReturn<"/atlases/{atlas_id}/parcellations/{parcellation_id}/features/{feature_id}">
+// export type SapiSpatialFeatureModel = PathReturn<"/atlases/{atlas_id}/spaces/{space_id}/features/{feature_id}">
+
+// export type SapiFeatureModel = SapiRegionalFeatureModel | SapiSpatialFeatureModel | SapiParcellationFeatureModel
+
+// /**
+// * specific data features
+// */
+
+// export type SapiRegionalFeatureReceptorModel = components["schemas"]["ReceptorDatasetModel"]
+// export type SapiParcellationFeatureMatrixModel = components["schemas"]["ConnectivityMatrixDataModel"]
+
+
+// export const CLEANED_IEEG_DATASET_TYPE = 'sxplr/cleanedIeegDataset'
+// export type CleanedIeegDataset = Required<
+// Omit<SapiDatasetModel, "@type"> & {
+// '@type': 'sxplr/cleanedIeegDataset'
+// sessions: Record<string, Omit<SapiIeegSessionModel, "dataset">>
+// }
+// >
+
+// export function cleanIeegSessionDatasets(ieegSessions: SapiIeegSessionModel[]): CleanedIeegDataset[]{
+// const returnArr: CleanedIeegDataset[] = []
+// for (const sess of ieegSessions) {
+// const { dataset, ...itemToAppend } = sess
+// const existing = returnArr.find(it => it["@id"] === dataset["@id"])
+// if (!existing) {
+// returnArr.push({
+// ...dataset,
+// '@type': CLEANED_IEEG_DATASET_TYPE,
+// sessions: {
+// [sess.sub_id]: itemToAppend
+// }
+// })
+// continue
+// }
+// existing.sessions[sess.sub_id] = itemToAppend
+// }
+// return returnArr
+// }
+
+// export type SxplrCleanedFeatureModel = CleanedIeegDataset
+
+// export function guardPipe<
+// InputType,
+// GuardType extends InputType
+// >(
+// guardFn: (input: InputType) => input is GuardType
+// ): OperatorFunction<InputType, GuardType> {
+// return src => src.pipe(
+// map(val => {
+// if (guardFn(val)) {
+// return val
+// }
+// throw new Error(`TypeGuard Error`)
+// })
+// )
+// }
+
+// export type SapiQueryPriorityArg = {
+// priority: number
+// }
diff --git a/src/atlasComponents/sapi/type_sxplr.ts b/src/atlasComponents/sapi/type_sxplr.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0e5d6f8a7f21d1799eb592db59563b2c25c3a9fc
--- /dev/null
+++ b/src/atlasComponents/sapi/type_sxplr.ts
@@ -0,0 +1,104 @@
+/**
+ * Here, you will find the type interface used by siibra-explorer
+ * SAPI types can change in the future, but hopefully, the setup can allow
+ * a much smoother transition to new API
+ */
+
+
+/**
+ * TODO do a global search on type_v3
+ * anything outside src/atlasComponent should directly import from type_sxplr, and not from type_v3, or worse type, schema_v3
+ */
+
+export type SxplrRegion = {
+ id: string
+ name: string
+ centroid?: Point
+ color?: [number, number, number]
+ parentIds:string[]
+} & Partial<AdditionalInfo>
+
+export type SxplrParcellation = {
+ id: string
+ name: string
+ modality?: string
+} & Partial<AdditionalInfo>
+
+export type SxplrTemplate = {
+ id: string
+ name: string
+} & Partial<AdditionalInfo>
+
+export type SxplrAtlas = {
+ id: string
+ name: string
+} & Partial<AdditionalInfo>
+
+export type AdditionalInfo = {
+ desc: string
+ link: {
+ text: string
+ href: string
+ }[]
+}
+
+type Location = {
+ space: SxplrTemplate
+}
+type LocTuple = [number, number, number]
+
+export type Point = {
+ loc: LocTuple
+} & Location
+
+export type BoundingBox = {
+ maxpoint: LocTuple
+ minpoint: LocTuple
+ center: LocTuple
+} & Location
+
+import { NgLayerSpec } from "src/viewerModule/nehuba/config.service/type"
+
+export { NgLayerSpec }
+export {
+ NgPrecompMeshSpec,
+ NgSegLayerSpec,
+} from "src/viewerModule/nehuba/config.service/type"
+
+import { TThreeSurferMesh, TThreeMesh, TThreeMeshLabel } from "src/viewerModule/threeSurfer/types"
+export { TThreeSurferMesh, TThreeMesh, TThreeMeshLabel }
+
+/**
+ * Union of processed image
+ */
+export type TemplateDefaultImage = NgLayerSpec | TThreeMesh
+
+/**
+ * Features
+ */
+
+export type Feature = {
+ id: string
+ name: string
+} & Partial<AdditionalInfo>
+
+type DataFrame = {
+ index: Record<string, string>
+}
+
+export type VoiFeature = {
+ bbox: BoundingBox
+} & Feature
+
+type TabularDataType = number | string | number[]
+
+export type TabularFeature<T extends TabularDataType> = {
+ index: string[]
+ columns: string[]
+ data: T[][]
+} & Feature
+
+export type LabelledMap = {
+ name: string
+ label: number
+}
diff --git a/src/atlasComponents/sapi/type_v3.ts b/src/atlasComponents/sapi/type_v3.ts
new file mode 100644
index 0000000000000000000000000000000000000000..89c4e9d8887579a211b938b31cf49d64b10118c7
--- /dev/null
+++ b/src/atlasComponents/sapi/type_v3.ts
@@ -0,0 +1,47 @@
+import { components, paths, operations } from "./schema_v3"
+
+export type SapiAtlasModel = PathReturn<"/atlases/{atlas_id}">
+export type SapiSpaceModel = PathReturn<"/spaces/{space_id}">
+export type SapiParcellationModel = PathReturn<"/parcellations/{parcellation_id}">
+export type SapiRegionModel = PathReturn<"/regions/{region_id}">
+export type OpenMINDSCoordinatePoint = components['schemas']["CoordinatePointModel"]
+export type SxplrCoordinatePointExtension = {
+ openminds: OpenMINDSCoordinatePoint
+ name: string
+ description: string
+ color: string
+ '@id': string // should match the id of opendminds specs
+}
+export type SapiSpatialFeatureModel = PathReturn<"/feature/VolumeOfInterest/{feature_id}">
+export type SapiFeatureModel = SapiSpatialFeatureModel | PathReturn<"/feature/Tabular/{feature_id}"> | PathReturn<"/feature/RegionalConnectivity/{feature_id}"> | PathReturn<"/feature/CorticalProfile/{feature_id}">
+
+export type SapiRoute = keyof paths
+
+/**
+ * Support types
+ */
+export type RouteParam<T extends keyof paths> = paths[T]['get']['parameters']
+type Json200 = {
+ 200: {
+ content: {
+ "application/json": unknown
+ }
+ }
+}
+export type PathReturn<T extends keyof paths> = paths[T]["get"]["responses"] extends Json200
+ ? paths[T]["get"]["responses"][200]["content"]["application/json"]
+ : unknown
+export type PaginatedModel<T> = {
+ items: T[]
+ total: number
+ page: number
+ size: number
+}
+
+/**
+ * siibra-explorer types
+ * TODO: to be exported
+ */
+export type SapiQueryPriorityArg = {
+ priority: number
+}
diff --git a/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts b/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts
index 056e3660c4243ee41bff9e5090354bd6e6fb2deb..50a9a3f9bb4e1123aa8800e437ca07019872529a 100644
--- a/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts
+++ b/src/atlasComponents/sapiViews/core/atlas/splashScreen/splashScreen.component.ts
@@ -2,7 +2,7 @@ import { ChangeDetectionStrategy, Component } from "@angular/core";
import { Store } from "@ngrx/store";
import { tap } from 'rxjs/operators'
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
-import { SapiAtlasModel } from "src/atlasComponents/sapi/type";
+import { SxplrAtlas } from "src/atlasComponents/sapi/type_sxplr";
import { atlasSelection } from "src/state"
@Component({
@@ -28,7 +28,7 @@ export class SapiViewsCoreAtlasSplashScreen {
) {
}
- public selectAtlas(atlas: SapiAtlasModel){
+ public selectAtlas(atlas: SxplrAtlas){
this.store.dispatch(
atlasSelection.actions.selectAtlas({
atlas
diff --git a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts
index 22813095a37d1c1b8b6a12b44003995d8b7e8db5..4651fcefd57dc1627a8b1bc8fc1b6f10f7118394 100644
--- a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts
+++ b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.component.ts
@@ -1,6 +1,7 @@
import { ChangeDetectionStrategy, Component, Input, OnChanges, SimpleChanges } from "@angular/core";
-import { SapiDatasetModel } from "src/atlasComponents/sapi";
+import { Feature } from "src/atlasComponents/sapi/type_sxplr";
import { CONST } from "common/constants"
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
const RESTRICTED_ACCESS_ID = "https://nexus.humanbrainproject.org/v0/data/minds/core/embargostatus/v1.0.0/3054f80d-96a8-4dce-9b92-55c68a8b5efd"
@@ -15,7 +16,7 @@ const RESTRICTED_ACCESS_ID = "https://nexus.humanbrainproject.org/v0/data/minds/
export class DatasetView implements OnChanges{
@Input('sxplr-sapiviews-core-datasets-dataset-input')
- dataset: SapiDatasetModel
+ dataset: Feature
public isRestricted = false
public CONST = CONST
@@ -23,7 +24,8 @@ export class DatasetView implements OnChanges{
ngOnChanges(changes: SimpleChanges): void {
const { dataset } = changes
if (dataset) {
- this.isRestricted = (dataset.currentValue as SapiDatasetModel)?.metadata?.accessibility?.["@id"] === RESTRICTED_ACCESS_ID
+ throw new Error(`Fix this`)
+ // this.isRestricted = (dataset.currentValue as Feature)?.metadata?.accessibility?.["@id"] === RESTRICTED_ACCESS_ID
}
}
}
diff --git a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html
index a04996afbb8d961cba682ed0cd1cc9d5b2940d31..654af558fe9fa334634775926688851a0f6f03cf 100644
--- a/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html
+++ b/src/atlasComponents/sapiViews/core/datasets/dataset/dataset.template.html
@@ -15,7 +15,7 @@
<mat-card-title>
<ng-template [ngTemplateOutlet]="headerTmpl"></ng-template>
<span>
- {{ dataset.metadata.fullName }}
+ {{ dataset.name }}
</span>
</mat-card-title>
@@ -33,15 +33,15 @@
<mat-divider class="sxplr-pl-1" [vertical]="true"></mat-divider>
- <a mat-icon-button sxplr-hide-when-local *ngFor="let url of dataset.urls" [href]="url.doi | parseDoi" target="_blank">
+ <!-- <a mat-icon-button sxplr-hide-when-local *ngFor="let url of dataset.link" [href]="url.doi | parseDoi" target="_blank">
<i class="fas fa-external-link-alt"></i>
- </a>
+ </a> -->
</mat-card-subtitle>
</mat-card>
<mat-card *ngIf="dataset" class="sxplr-z-0">
<mat-card-content>
- <markdown-dom class="sxplr-muted" [markdown]="dataset?.metadata?.description">
+ <markdown-dom class="sxplr-muted" [markdown]="dataset?.desc">
</markdown-dom>
</mat-card-content>
</mat-card>
diff --git a/src/atlasComponents/sapiViews/core/parcellation/filterGroupedParcellations.pipe.ts b/src/atlasComponents/sapiViews/core/parcellation/filterGroupedParcellations.pipe.ts
index 62910eab45e5529ee22f137afa92e4978d42cfe4..b1c5176accb4207091672576307bfc07d74578b7 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/filterGroupedParcellations.pipe.ts
+++ b/src/atlasComponents/sapiViews/core/parcellation/filterGroupedParcellations.pipe.ts
@@ -1,5 +1,5 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { SapiParcellationModel } from "src/atlasComponents/sapi";
+import { SxplrParcellation } from "src/atlasComponents/sapi/type_sxplr";
import { GroupedParcellation } from "./groupedParcellation";
@Pipe({
@@ -8,11 +8,11 @@ import { GroupedParcellation } from "./groupedParcellation";
})
export class FilterGroupedParcellationPipe implements PipeTransform{
- public transform(parcs: SapiParcellationModel[], getGroupsFlag: boolean=false): (SapiParcellationModel|GroupedParcellation)[] {
+ public transform(parcs: SxplrParcellation[], getGroupsFlag: boolean=false): (SxplrParcellation|GroupedParcellation)[] {
if (!getGroupsFlag) {
return parcs.filter(p => !p.modality)
}
- const map: Record<string, SapiParcellationModel[]> = {}
+ const map: Record<string, SxplrParcellation[]> = {}
for (const parc of parcs.filter(p => !!p.modality)) {
if (!map[parc.modality]) {
map[parc.modality] = []
diff --git a/src/atlasComponents/sapiViews/core/parcellation/filterUnsupportedParc.pipe.ts b/src/atlasComponents/sapiViews/core/parcellation/filterUnsupportedParc.pipe.ts
index 222020d7296acd3555b08c2b69c05fd49ceba80c..5c80f96bf33e911d5689f4ed263c61fa79bde389 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/filterUnsupportedParc.pipe.ts
+++ b/src/atlasComponents/sapiViews/core/parcellation/filterUnsupportedParc.pipe.ts
@@ -1,8 +1,9 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { SapiParcellationModel } from "src/atlasComponents/sapi/type";
+import { SxplrParcellation } from "src/atlasComponents/sapi/type_sxplr";
import { GroupedParcellation } from "./groupedParcellation";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
-type Filterables = SapiParcellationModel | GroupedParcellation
+type Filterables = SxplrParcellation | GroupedParcellation
const unsupportedIds = [
"https://doi.org/10.1016/j.jneumeth.2020.108983/mni152",
@@ -23,11 +24,12 @@ export class FilterUnsupportedParcPipe implements PipeTransform{
if (p instanceof GroupedParcellation) {
return hideGroup.indexOf(p.name) < 0
}
- if (unsupportedIds.includes(p["@id"])) {
+ if (unsupportedIds.includes(p.id)) {
return false
}
- if (p.version) {
- return !p.version.deprecated
+ const apiP = translateV3Entities.retrieveParcellation(p)
+ if (apiP.version) {
+ return !apiP.version.deprecated
}
return true
})
diff --git a/src/atlasComponents/sapiViews/core/parcellation/groupedParcellation.ts b/src/atlasComponents/sapiViews/core/parcellation/groupedParcellation.ts
index c66d6e9818a3884cb0c48fc58de56bee4373e113..1f0eb3789fa6ca8ca102a905e9bf24d3be056535 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/groupedParcellation.ts
+++ b/src/atlasComponents/sapiViews/core/parcellation/groupedParcellation.ts
@@ -1,9 +1,9 @@
-import { SapiParcellationModel } from "src/atlasComponents/sapi"
+import { SxplrParcellation } from "src/atlasComponents/sapi/type_sxplr"
export class GroupedParcellation{
name: string
- parcellations: SapiParcellationModel[]
- constructor(name: string, parcellations: SapiParcellationModel[]){
+ parcellations: SxplrParcellation[]
+ constructor(name: string, parcellations: SxplrParcellation[]){
this.name = name
this.parcellations = parcellations
}
diff --git a/src/atlasComponents/sapiViews/core/parcellation/parcellationDoi.pipe.ts b/src/atlasComponents/sapiViews/core/parcellation/parcellationDoi.pipe.ts
index 8652365e1bb40d6565ccfd9d88e30eb94492c6d4..8eba5f152abc68ae63ecd60f6aae9d8517ea2ae8 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/parcellationDoi.pipe.ts
+++ b/src/atlasComponents/sapiViews/core/parcellation/parcellationDoi.pipe.ts
@@ -1,5 +1,6 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { SapiParcellationModel } from "src/atlasComponents/sapi/type";
+import { SxplrParcellation } from "src/atlasComponents/sapi/type_sxplr";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
@Pipe({
name: 'parcellationDoiPipe',
@@ -7,7 +8,8 @@ import { SapiParcellationModel } from "src/atlasComponents/sapi/type";
})
export class ParcellationDoiPipe implements PipeTransform {
- public transform(parc: SapiParcellationModel): string[] {
+ public transform(_parc: SxplrParcellation): string[] {
+ const parc = translateV3Entities.retrieveParcellation(_parc)
const urls = (parc?.brainAtlasVersions || []).filter(
v => v.digitalIdentifier && v.digitalIdentifier['@type'] === 'https://openminds.ebrains.eu/core/DOI'
).map(
diff --git a/src/atlasComponents/sapiViews/core/parcellation/parcellationGroupSelected.pipe.ts b/src/atlasComponents/sapiViews/core/parcellation/parcellationGroupSelected.pipe.ts
index cd31e439157a8e34182c03427fb70c35031241b9..e73322143f96e2746e040414f599605c5b6db7df 100644
--- a/src/atlasComponents/sapiViews/core/parcellation/parcellationGroupSelected.pipe.ts
+++ b/src/atlasComponents/sapiViews/core/parcellation/parcellationGroupSelected.pipe.ts
@@ -1,10 +1,9 @@
import { Pipe, PipeTransform } from "@angular/core";
-import { SapiParcellationModel } from "src/atlasComponents/sapi/type";
+import { SxplrParcellation } from "src/atlasComponents/sapi/type_sxplr";
import { GroupedParcellation } from "./groupedParcellation";
function isGroupedParc(parc: GroupedParcellation|unknown): parc is GroupedParcellation {
- if (!parc['parcellations']) return false
- return (parc['parcellations'] as SapiParcellationModel[]).every(p => p["@type"] === "minds/core/parcellationatlas/v1.0.0")
+ return !!parc['parcellations']
}
@Pipe({
@@ -13,7 +12,7 @@ function isGroupedParc(parc: GroupedParcellation|unknown): parc is GroupedParcel
})
export class ParcellationGroupSelectedPipe implements PipeTransform {
- public transform(parc: GroupedParcellation|unknown, selectedParcellation: SapiParcellationModel): boolean {
+ public transform(parc: GroupedParcellation|unknown, selectedParcellation: SxplrParcellation): boolean {
if (!isGroupedParc(parc)) return false
return parc.parcellations.some(p => p["@id"] === selectedParcellation["@id"])
}
diff --git a/src/atlasComponents/sapiViews/core/region/module.ts b/src/atlasComponents/sapiViews/core/region/module.ts
index 60fd2425cc9b9f67008b8caa8c386dcf32614bd8..50759b93a63e6993946a337212559589c38e31a6 100644
--- a/src/atlasComponents/sapiViews/core/region/module.ts
+++ b/src/atlasComponents/sapiViews/core/region/module.ts
@@ -4,7 +4,7 @@ import { MarkdownModule } from "src/components/markdown";
import { SpinnerModule } from "src/components/spinner";
import { AngularMaterialModule } from "src/sharedModules";
import { StrictLocalModule } from "src/strictLocal";
-import { SapiViewsFeaturesModule } from "../../features";
+// import { SapiViewsFeaturesModule } from "../../features";
import { SapiViewsUtilModule } from "../../util/module";
import { SapiViewsCoreRegionRegionChip } from "./region/chip/region.chip.component";
import { SapiViewsCoreRegionRegionListItem } from "./region/listItem/region.listItem.component";
@@ -17,7 +17,7 @@ import { SapiViewsCoreRegionRegionRich } from "./region/rich/region.rich.compone
CommonModule,
AngularMaterialModule,
SapiViewsUtilModule,
- SapiViewsFeaturesModule,
+ // SapiViewsFeaturesModule,
SpinnerModule,
MarkdownModule,
StrictLocalModule,
diff --git a/src/atlasComponents/sapiViews/core/region/region/region.base.directive.ts b/src/atlasComponents/sapiViews/core/region/region/region.base.directive.ts
index 96f374b267ced1fb700333654b7e62a39a9e311a..ef053700699acbd5655db0739eaba8f4153c43c3 100644
--- a/src/atlasComponents/sapiViews/core/region/region/region.base.directive.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/region.base.directive.ts
@@ -1,9 +1,11 @@
import { Directive, EventEmitter, Input, OnDestroy, Output } from "@angular/core";
-import { SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
import { rgbToHsl } from 'common/util'
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
import { BehaviorSubject, Subject } from "rxjs";
import { SAPIRegion } from "src/atlasComponents/sapi/core";
+import { switchMap } from "rxjs/operators";
@Directive({
selector: `[sxplr-sapiviews-core-region]`,
@@ -17,19 +19,19 @@ export class SapiViewsCoreRegionRegionBase {
public fetchInProgress$ = new BehaviorSubject<boolean>(false)
@Input('sxplr-sapiviews-core-region-atlas')
- atlas: SapiAtlasModel
+ atlas: SxplrAtlas
@Input('sxplr-sapiviews-core-region-template')
- template: SapiSpaceModel
+ template: SxplrTemplate
@Input('sxplr-sapiviews-core-region-parcellation')
- parcellation: SapiParcellationModel
+ parcellation: SxplrParcellation
@Output('sxplr-sapiviews-core-region-navigate-to')
onNavigateTo = new EventEmitter<number[]>()
- protected region$ = new Subject<SapiRegionModel>()
- private _region: SapiRegionModel
+ protected region$ = new Subject<SxplrRegion>()
+ private _region: SxplrRegion
@Input('sxplr-sapiviews-core-region-region')
- set region(val: SapiRegionModel) {
+ set region(val: SxplrRegion) {
this.region$.next(val)
@@ -76,7 +78,7 @@ export class SapiViewsCoreRegionRegionBase {
/**
* color
*/
- const rgb = SAPIRegion.GetDisplayColor(this.region)
+ const rgb = SAPIRegion.GetDisplayColor(this.region) || [200, 200, 200]
this.regionRgbString = `rgb(${rgb.join(',')})`
const [_h, _s, l] = rgbToHsl(...rgb)
this.regionDarkmode = l < 0.4
@@ -84,14 +86,12 @@ export class SapiViewsCoreRegionRegionBase {
/**
* position
*/
- this.regionPosition = this.region.hasAnnotation?.bestViewPoint?.coordinates.map(v => v.value)
+ this.regionPosition = this.region.centroid?.loc
/**
* dois
*/
- this.dois = (this.region.hasAnnotation?.inspiredBy || [])
- .map(insp => insp["@id"] as string)
- .filter(id => /^https?:\/\/doi\.org/.test(id))
+ this.dois = (this.region.link || []).map(link => link.href)
}
}
@@ -99,8 +99,18 @@ export class SapiViewsCoreRegionRegionBase {
this.onNavigateTo.emit(position.map(v => v*1e6))
}
- protected async fetchDetail(region: SapiRegionModel) {
- return this.sapi.getRegion(this.atlas["@id"],this.parcellation["@id"], region.name).getDetail(this.template["@id"]).toPromise()
+ protected async fetchDetail(region: SxplrRegion): Promise<SxplrRegion> {
+ return this.sapi.v3Get("/regions/{region_id}", {
+ path: {
+ region_id: region.name
+ },
+ query: {
+ parcellation_id: this.parcellation.id,
+ space_id: this.template.id
+ }
+ }).pipe(
+ switchMap(r => translateV3Entities.translateRegion(r))
+ ).toPromise()
}
constructor(protected sapi: SAPI){
diff --git a/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts b/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts
index 47a4b6912c7a701b116fae6e13c0591c4005ab19..de2084a760923d103c7972febd69f75e2aaa5a52 100644
--- a/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/region.features.directive.ts
@@ -1,8 +1,8 @@
import { Directive, OnChanges, SimpleChanges } from "@angular/core";
-import { BehaviorSubject, Observable } from "rxjs";
-import { switchMap, filter, startWith, shareReplay, finalize } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionalFeatureModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
-import { SxplrCleanedFeatureModel } from "src/atlasComponents/sapi/type";
+import { BehaviorSubject, merge } from "rxjs";
+import { switchMap, filter, startWith, shareReplay, scan } from "rxjs/operators";
+import { SAPI, SAPIRegion } from "src/atlasComponents/sapi";
+import { SxplrAtlas, SxplrParcellation, SxplrTemplate, SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
import { SapiViewsCoreRegionRegionBase } from "./region.base.directive";
@Directive({
@@ -13,10 +13,10 @@ import { SapiViewsCoreRegionRegionBase } from "./region.base.directive";
export class SapiViewsCoreRegionRegionalFeatureDirective extends SapiViewsCoreRegionRegionBase implements OnChanges{
private ATPR$ = new BehaviorSubject<{
- atlas: SapiAtlasModel
- template: SapiSpaceModel
- parcellation: SapiParcellationModel
- region: SapiRegionModel
+ atlas: SxplrAtlas
+ template: SxplrTemplate
+ parcellation: SxplrParcellation
+ region: SxplrRegion
}>(null)
ngOnChanges(sc: SimpleChanges): void {
@@ -28,7 +28,7 @@ export class SapiViewsCoreRegionRegionalFeatureDirective extends SapiViewsCoreRe
super(sapi)
}
- private features$: Observable<(SapiRegionalFeatureModel|SxplrCleanedFeatureModel)[]> = this.ATPR$.pipe(
+ private features$ = this.ATPR$.pipe(
filter(arg => {
if (!arg) return false
const { atlas, parcellation, region, template } = arg
@@ -36,13 +36,31 @@ export class SapiViewsCoreRegionRegionalFeatureDirective extends SapiViewsCoreRe
}),
switchMap(({ atlas, parcellation, region, template }) => {
this.busy$.next(true)
- return this.sapi.getRegionFeatures(atlas["@id"], parcellation["@id"], template["@id"], region.name).pipe(
- finalize(() => this.busy$.next(false))
+ const parcId = parcellation["@id"]
+ const regionId = region.name
+ const atlasId = atlas["@id"]
+ const reg = this.sapi.getRegion(atlasId, parcId, regionId)
+ return SAPIRegion.Features$.pipe(
+ switchMap(features => merge(
+ ...features.map(
+ feature => reg.getFeatures(
+ feature,
+ {
+ query: {
+ parcellation_id: parcId,
+ region_id: regionId,
+ },
+ priority: 1
+ }
+ )
+ )
+ )),
+ scan((acc, curr) => [...acc, ...curr.items], [])
)
}),
)
- public listOfFeatures$: Observable<(SapiRegionalFeatureModel|SxplrCleanedFeatureModel)[]> = this.features$.pipe(
+ public listOfFeatures$ = this.features$.pipe(
startWith([]),
shareReplay(1),
)
diff --git a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.component.ts b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.component.ts
index 0d506febda44ca7366f7366a622403b06a488228..02ed169e0ff45ea97188872f01ba56a61018b004 100644
--- a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.component.ts
+++ b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.component.ts
@@ -3,7 +3,7 @@ import { Component, EventEmitter, Inject, Output } from "@angular/core";
import { DARKTHEME } from "src/util/injectionTokens";
import { SapiViewsCoreRegionRegionBase } from "../region.base.directive";
import { ARIA_LABELS, CONST } from 'common/constants'
-import { SapiRegionalFeatureModel } from "src/atlasComponents/sapi";
+import { Feature } from "src/atlasComponents/sapi/type_sxplr";
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
import { environment } from "src/environments/environment";
@@ -24,7 +24,7 @@ export class SapiViewsCoreRegionRegionRich extends SapiViewsCoreRegionRegionBase
public CONST = CONST
@Output('sxplr-sapiviews-core-region-region-rich-feature-clicked')
- featureClicked = new EventEmitter<SapiRegionalFeatureModel>()
+ featureClicked = new EventEmitter<Feature>()
public expandedPanel: string
@@ -35,7 +35,7 @@ export class SapiViewsCoreRegionRegionRich extends SapiViewsCoreRegionRegionBase
super(sapi)
}
- handleRegionalFeatureClicked(feat: SapiRegionalFeatureModel) {
+ handleRegionalFeatureClicked(feat: Feature) {
this.featureClicked.emit(feat)
}
diff --git a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
index 18f77fc1b93f298b44f0a0abca283971145655fe..461fcf176f48d78582a92a6f7e2149ee0b500450 100644
--- a/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
+++ b/src/atlasComponents/sapiViews/core/region/region/rich/region.rich.template.html
@@ -68,17 +68,17 @@
<spinner-cmp *ngIf="rfDir.busy$ | async"></spinner-cmp>
- <sxplr-sapiviews-features-entry-list-item
+ <!-- <sxplr-sapiviews-features-entry-list-item
*ngFor="let feat of rfDir.listOfFeatures$ | async | orderFilterFeatures"
[sxplr-sapiviews-features-entry-list-item-feature]="feat"
(click)="handleRegionalFeatureClicked(feat)">
- </sxplr-sapiviews-features-entry-list-item>
+ </sxplr-sapiviews-features-entry-list-item> -->
</div>
</ng-template>
<ng-template #regionDesc>
- <markdown-dom class="sxplr-muted" [markdown]="region?.versionInnovation || 'No description provided.'">
+ <markdown-dom class="sxplr-muted" [markdown]="region?.desc || 'No description provided.'">
</markdown-dom>
</ng-template>
@@ -91,7 +91,7 @@
content: regionDesc,
desc: '',
iconTooltip: 'Description',
- iavNgIf: !!region?.versionInnovation
+ iavNgIf: !!region?.desc
}">
</ng-container>
@@ -112,7 +112,7 @@
<!-- connectivity -->
<ng-template #sxplrSapiviewsFeaturesConnectivityBrowser>
- <sxplr-sapiviews-features-connectivity-browser
+ <!-- <sxplr-sapiviews-features-connectivity-browser
class="pe-all flex-shrink-1"
[region]="region"
[sxplr-sapiviews-features-connectivity-browser-atlas]="atlas"
@@ -120,23 +120,23 @@
[accordionExpanded]="expandedPanel === CONST.CONNECTIVITY"
[types]="hasConnectivityDirective.availableModalities"
>
- </sxplr-sapiviews-features-connectivity-browser>
+ </sxplr-sapiviews-features-connectivity-browser> -->
</ng-template>
- <ng-container *ngTemplateOutlet="ngMatAccordionTmpl; context: {
+ <!-- <ng-container *ngTemplateOutlet="ngMatAccordionTmpl; context: {
title: CONST.CONNECTIVITY,
iconClass: 'fab fa-connectdevelop',
content: sxplrSapiviewsFeaturesConnectivityBrowser,
iavNgIf: hasConnectivityDirective.hasConnectivity
}">
- </ng-container>
+ </ng-container> -->
- <div sxplr-sapiviews-features-connectivity-check
+ <!-- <div sxplr-sapiviews-features-connectivity-check
[sxplr-sapiviews-features-connectivity-check-atlas]="atlas"
[sxplr-sapiviews-features-connectivity-check-parcellation]="parcellation"
[region]="region"
#hasConnectivityDirective="hasConnectivityDirective">
- </div>
+ </div> -->
</ng-template>
</mat-accordion>
diff --git a/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.components.ts b/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.components.ts
index 13c9abbb1da7cf2bce5db618c999f9c46d543777..4cddf5bde6ac04d647088d4b9370f4e9f489ebba 100644
--- a/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.components.ts
+++ b/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.components.ts
@@ -1,5 +1,5 @@
import { ChangeDetectionStrategy, Component, EventEmitter, Input, OnChanges, Output, SimpleChanges } from "@angular/core";
-import { SapiAtlasModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi/type";
+import { SxplrAtlas, SxplrParcellation, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
import { FilterGroupedParcellationPipe, GroupedParcellation } from "src/atlasComponents/sapiViews/core/parcellation";
export const darkThemePalette = [
@@ -15,9 +15,9 @@ export const lightThemePalette = [
]
export type ATP = {
- atlas: SapiAtlasModel
- template: SapiSpaceModel
- parcellation: SapiParcellationModel
+ atlas: SxplrAtlas
+ template: SxplrTemplate
+ parcellation: SxplrParcellation
}
function isATPGuard(atp: Record<string, unknown>): atp is Partial<ATP> {
@@ -51,15 +51,15 @@ export class PureATPSelector implements OnChanges{
public selectedIds: string[] = []
@Input(`sxplr-pure-atp-selector-atlases`)
- public allAtlases: SapiAtlasModel[] = []
+ public allAtlases: SxplrAtlas[] = []
@Input(`sxplr-pure-atp-selector-templates`)
- public availableTemplates: SapiSpaceModel[] = []
+ public availableTemplates: SxplrTemplate[] = []
@Input(`sxplr-pure-atp-selector-parcellations`)
- public parcellations: SapiParcellationModel[] = []
+ public parcellations: SxplrParcellation[] = []
- public parcAndGroup: (GroupedParcellation|SapiParcellationModel)[] = []
+ public parcAndGroup: (GroupedParcellation|SxplrParcellation)[] = []
@Input('sxplr-pure-atp-selector-is-busy')
public isBusy: boolean = false
@@ -67,7 +67,7 @@ export class PureATPSelector implements OnChanges{
@Output('sxplr-pure-atp-selector-on-select')
selectLeafEmitter = new EventEmitter<Partial<ATP>>()
- getChildren(parc: GroupedParcellation|SapiParcellationModel){
+ getChildren(parc: GroupedParcellation|SxplrParcellation){
return (parc as GroupedParcellation).parcellations || []
}
@@ -83,7 +83,7 @@ export class PureATPSelector implements OnChanges{
this.selectedIds = []
} else {
const { atlas, parcellation, template } = changes.selectedATP.currentValue as ATP
- this.selectedIds = [atlas?.["@id"], parcellation?.["@id"], template?.["@id"]].filter(v => !!v)
+ this.selectedIds = [atlas?.id, parcellation?.id, template?.id].filter(v => !!v)
}
}
diff --git a/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.template.html b/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.template.html
index 5814b72ab091e6a09e6cbc7e2759abff11e336f2..044965ed56ec6ad515764fb75a503bcea7269220 100644
--- a/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.template.html
+++ b/src/atlasComponents/sapiViews/core/rich/ATPSelector/pureDumb/pureATPSelector.template.html
@@ -24,8 +24,8 @@
sxplr-dialog
[sxplr-dialog-size]="null"
[sxplr-dialog-data]="{
- title: ATP.parcellation.name || ATP.parcellation.fullName,
- descMd: (ATP.parcellation.brainAtlasVersions || [])[0]?.versionInnovation,
+ title: ATP.parcellation.name,
+ descMd: ATP.parcellation.desc,
actions: ATP.parcellation | parcellationDoiPipe
}">
<i class="fas fa-info"></i>
@@ -52,7 +52,7 @@
[disabled]="isBusy">
<ng-template sxplrSmartChipContent>
<span class="chip-text">
- {{ ATP.template.fullName }}
+ {{ ATP.template.name }}
</span>
</ng-template>
<ng-template sxplrSmartChipMenu let-space>
diff --git a/src/atlasComponents/sapiViews/core/rich/ATPSelector/wrapper/wrapper.component.ts b/src/atlasComponents/sapiViews/core/rich/ATPSelector/wrapper/wrapper.component.ts
index e5a3ef9eeebef4e6a2cdaba8d5a50aa000cdb06a..ea738098fdbd9732d66fc01e39843f322884a091 100644
--- a/src/atlasComponents/sapiViews/core/rich/ATPSelector/wrapper/wrapper.component.ts
+++ b/src/atlasComponents/sapiViews/core/rich/ATPSelector/wrapper/wrapper.component.ts
@@ -1,10 +1,9 @@
import { Component, Inject, OnDestroy } from "@angular/core";
import { MatDialog } from "@angular/material/dialog";
-import { Store } from "@ngrx/store";
+import { select, Store } from "@ngrx/store";
import { Observable, of, Subject, Subscription } from "rxjs";
import { filter, map, switchMap, tap, withLatestFrom } from "rxjs/operators";
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
-import { ParcellationSupportedInSpacePipe } from "src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe";
import { atlasSelection } from "src/state";
import { fromRootStore } from "src/state/atlasSelection";
import { DialogFallbackCmp } from "src/ui/dialogInfo";
@@ -30,7 +29,6 @@ export class WrapperATPSelector implements OnDestroy{
lightThemePalette = lightThemePalette
#subscription: Subscription[] = []
- #parcSupportedInSpacePipe = new ParcellationSupportedInSpacePipe(this.sapi)
#askUser(title: string, descMd: string): Observable<boolean> {
const agree = "OK"
@@ -51,10 +49,12 @@ export class WrapperATPSelector implements OnDestroy{
allAtlases$ = this.sapi.atlases$
availableTemplates$ = this.store$.pipe(
- fromRootStore.allAvailSpaces(this.sapi),
+ select(atlasSelection.selectors.selectedAtlas),
+ switchMap(atlas => this.sapi.getAllSpaces(atlas))
)
parcs$ = this.store$.pipe(
- fromRootStore.allAvailParcs(this.sapi),
+ select(atlasSelection.selectors.selectedAtlas),
+ switchMap(atlas => this.sapi.getAllParcellations(atlas))
)
isBusy$ = new Subject<boolean>()
@@ -79,21 +79,28 @@ export class WrapperATPSelector implements OnDestroy{
return of({ atlas })
}
if (template) {
- return this.#parcSupportedInSpacePipe.transform(selectedATP.parcellation, template).pipe(
- switchMap(supported => supported
- ? of({ template })
- : this.#askUser(`Incompatible parcellation`, `Attempting to load template **${template.fullName}**, which does not support parcellation **${selectedATP.parcellation.name}**. Proceed anyway and load the default parcellation?`).pipe(
+ return this.sapi.getSupportedTemplates(selectedATP.atlas, selectedATP.parcellation).pipe(
+ switchMap(tmpls => {
+ const supported = tmpls.some(tmpl => tmpl.id === template.id)
+ if (supported) return of({ template })
+ return this.#askUser(
+ `Incompatible parcellation`, `Attempting to load template **${template.name}**, which does not support parcellation **${selectedATP.parcellation.name}**. Proceed anyway and load the default parcellation?`
+ ).pipe(
switchMap(flag => of(flag ? { template } : null))
- ))
+ )
+ })
)
}
if (parcellation) {
- return this.#parcSupportedInSpacePipe.transform(parcellation, selectedATP.template).pipe(
- switchMap(supported=> supported
- ? of({ parcellation })
- : this.#askUser(`Incompatible template`, `Attempting to load parcellation **${parcellation.name}**, which is not supported in template **${selectedATP.template.fullName}**. Proceed anyway and load the default template?`).pipe(
- switchMap(flag => of(flag ? { parcellation } : null))
- ))
+ return this.sapi.getSupportedParcellations(selectedATP.atlas, selectedATP.template).pipe(
+ switchMap(parcs => {
+ const supported = parcs.some(parc => parc.id === parcellation.id)
+ return supported
+ ? of ({ parcellation })
+ : this.#askUser(`Incompatible template`, `Attempting to load parcellation **${parcellation.name}**, which is not supported in template **${selectedATP.template.name}**. Proceed anyway and load the default template?`).pipe(
+ switchMap(flag => of(flag ? { parcellation } : null))
+ )
+ })
)
}
return of(null)
@@ -125,8 +132,8 @@ export class WrapperATPSelector implements OnDestroy{
)
}
- private selectLeaf$ = new Subject<ATP>()
- selectLeaf(atp: ATP) {
+ private selectLeaf$ = new Subject<Partial<ATP>>()
+ selectLeaf(atp: Partial<ATP>) {
this.selectLeaf$.next(atp)
}
diff --git a/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.component.ts b/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.component.ts
index b82c2ba05f70cbca2247b464e1d2de29b6a9a838..22b0f837c245c0939431a3751bcccf03b4f742d0 100644
--- a/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.component.ts
+++ b/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.component.ts
@@ -2,7 +2,8 @@ import { ChangeDetectionStrategy, ChangeDetectorRef, Component, EventEmitter, In
import { UntypedFormControl } from "@angular/forms";
import { Subscription } from "rxjs";
import { debounceTime, distinctUntilChanged, filter, startWith } from "rxjs/operators";
-import { SapiRegionModel } from "src/atlasComponents/sapi/type";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
import { SxplrFlatHierarchyTreeView } from "src/components/flatHierarchy/treeView/treeView.component";
import { FilterByRegexPipe } from "./filterByRegex.pipe";
import { RegionTreeFilterPipe } from "./regionTreeFilter.pipe";
@@ -21,11 +22,17 @@ const filterByRegexPipe = new FilterByRegexPipe()
export class SapiViewsCoreRichRegionsHierarchy {
- static IsParent(region: SapiRegionModel, parentRegion: SapiRegionModel) {
- return region.hasParent?.some(parent => parent['@id'] === parentRegion["@id"])
+ static IsParent(region: SxplrRegion, parentRegion: SxplrRegion): boolean {
+ const _region = translateV3Entities.retrieveRegion(region)
+ const _parentRegion = translateV3Entities.retrieveRegion(parentRegion)
+ const { ["@id"]: parentRegionId } = _parentRegion
+ return _region.hasParent?.some(parent => {
+ const { ["@id"]: pId } = parent
+ return pId === parentRegionId
+ })
}
- static FilterRegions(regions: SapiRegionModel[], searchTerm: string): SapiRegionModel[]{
+ static FilterRegions(regions: SxplrRegion[], searchTerm: string): SxplrRegion[]{
if (searchTerm === '' || !searchTerm) {
return regions
}
@@ -37,19 +44,19 @@ export class SapiViewsCoreRichRegionsHierarchy {
}
@Input('sxplr-sapiviews-core-rich-regionshierarchy-accent-regions')
- accentedRegions: SapiRegionModel[] = []
+ accentedRegions: SxplrRegion[] = []
@Input('sxplr-sapiviews-core-rich-regionshierarchy-placeholder')
placeholderText: string = 'Search all regions'
- passedRegions: SapiRegionModel[] = []
+ passedRegions: SxplrRegion[] = []
- private _regions: SapiRegionModel[] = []
+ private _regions: SxplrRegion[] = []
get regions(){
return this._regions
}
@Input('sxplr-sapiviews-core-rich-regionshierarchy-regions')
- set regions(val: SapiRegionModel[]){
+ set regions(val: SxplrRegion[]){
this._regions = val
this.passedRegions = SapiViewsCoreRichRegionsHierarchy.FilterRegions(
this._regions,
@@ -58,10 +65,10 @@ export class SapiViewsCoreRichRegionsHierarchy {
}
@Output('sxplr-sapiviews-core-rich-regionshierarchy-region-select')
- nodeClicked = new EventEmitter<SapiRegionModel>()
+ nodeClicked = new EventEmitter<SxplrRegion>()
@ViewChild(SxplrFlatHierarchyTreeView)
- treeView: SxplrFlatHierarchyTreeView<SapiRegionModel>
+ treeView: SxplrFlatHierarchyTreeView<SxplrRegion>
isParent = SapiViewsCoreRichRegionsHierarchy.IsParent
diff --git a/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.template.html b/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.template.html
index f3a4e82d473fcb11a80abf856c560f79e722ac89..7dc6a9cc5f9f963727081fa5dbe7a5b7da5ddb52 100644
--- a/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.template.html
+++ b/src/atlasComponents/sapiViews/core/rich/regionsHierarchy/regionsHierarchy.template.html
@@ -28,6 +28,6 @@
[sxplr-flat-hierarchy-is-parent]="isParent"
[sxplr-flat-hierarchy-render-node-tmpl]="tmplRef"
[sxplr-flat-hierarchy-tree-view-expand-on-init]="true"
- sxplr-flat-hierarchy-tree-view-lineheight="24"
+ [sxplr-flat-hierarchy-tree-view-lineheight]="24"
(sxplr-flat-hierarchy-tree-view-node-clicked)="nodeClicked.emit($event)">
</sxplr-flat-hierarchy-tree-view>
\ No newline at end of file
diff --git a/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearch.component.ts b/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearch.component.ts
index d169eb904f4ce01fe5d9753a95acce50180d326b..e455ccc4aa06111b00092198e1ddae87dfbeda5c 100644
--- a/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearch.component.ts
+++ b/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearch.component.ts
@@ -1,5 +1,5 @@
import { ChangeDetectionStrategy, Component, ContentChild, EventEmitter, Input, Output, TemplateRef } from "@angular/core";
-import { SapiRegionModel } from "src/atlasComponents/sapi/type";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
import { ARIA_LABELS } from "common/constants"
import { UntypedFormControl } from "@angular/forms";
import { debounceTime, distinctUntilChanged, map, startWith } from "rxjs/operators";
@@ -13,12 +13,11 @@ import { SapiViewsCoreRichRegionListTemplateDirective } from "./regionListSearch
* @param region input region
* @returns {boolean} whether or not to include the region in the list search
*/
-const filterRegionForListSearch = (region: SapiRegionModel): boolean => {
- const visualizedIn = region.hasAnnotation?.visualizedIn
- return !!visualizedIn
+const filterRegionForListSearch = (region: SxplrRegion): boolean => {
+ return !!region.color
}
-const filterRegionViaSearch = (searchTerm: string) => (region:SapiRegionModel) => {
+const filterRegionViaSearch = (searchTerm: string) => (region:SxplrRegion) => {
return region.name.toLocaleLowerCase().includes(searchTerm.toLocaleLowerCase())
}
@@ -37,12 +36,12 @@ export class SapiViewsCoreRichRegionListSearch {
showNOptions = 4
- private _regions: SapiRegionModel[] = []
+ private _regions: SxplrRegion[] = []
get regions(){
return this._regions
}
@Input('sxplr-sapiviews-core-rich-regionlistsearch-regions')
- set regions(val: SapiRegionModel[]) {
+ set regions(val: SxplrRegion[]) {
this._regions = val.filter(filterRegionForListSearch)
}
@@ -56,7 +55,7 @@ export class SapiViewsCoreRichRegionListSearch {
currentSearch: string = ''
@Output('sxplr-sapiviews-core-rich-regionlistsearch-region-select')
- onOptionSelected = new EventEmitter<SapiRegionModel>()
+ onOptionSelected = new EventEmitter<SxplrRegion>()
public searchFormControl = new UntypedFormControl()
@@ -64,7 +63,7 @@ export class SapiViewsCoreRichRegionListSearch {
startWith(''),
distinctUntilChanged(),
debounceTime(160),
- map((searchTerm: string | SapiRegionModel) => {
+ map((searchTerm: string | SxplrRegion) => {
if (typeof searchTerm === "string") {
return this.regions.filter(filterRegionViaSearch(searchTerm))
}
@@ -76,12 +75,12 @@ export class SapiViewsCoreRichRegionListSearch {
map(list => list.slice(0, this.showNOptions))
)
- displayFn(region: SapiRegionModel){
+ displayFn(region: SxplrRegion){
return region?.name || ''
}
optionSelected(opt: MatAutocompleteSelectedEvent) {
- const selectedRegion = opt.option.value as SapiRegionModel
+ const selectedRegion = opt.option.value as SxplrRegion
this.onOptionSelected.emit(selectedRegion)
}
}
diff --git a/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearchTmpl.directive.ts b/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearchTmpl.directive.ts
index ecc282ee47ba3a328c13444d7890afcd8c62047b..b3efbe51bb910b607ee0940e02e2348990495aef 100644
--- a/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearchTmpl.directive.ts
+++ b/src/atlasComponents/sapiViews/core/rich/regionsListSearch/regionListSearchTmpl.directive.ts
@@ -1,10 +1,10 @@
import { Directive, TemplateRef } from "@angular/core";
-import { SapiRegionModel } from "src/atlasComponents/sapi/type";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
@Directive({
selector: 'ng-template[region-template],ng-template[regionTemplate]'
})
export class SapiViewsCoreRichRegionListTemplateDirective{
- constructor(public tmplRef: TemplateRef<SapiRegionModel>){}
+ constructor(public tmplRef: TemplateRef<SxplrRegion>){}
}
diff --git a/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts b/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts
index 3d592f3974c5db9b91fb6172fdf05df516b8ad63..0fa95bbbade15e2ea809a6cbfbf2c3ba439e291d 100644
--- a/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts
+++ b/src/atlasComponents/sapiViews/core/space/boundingBox.directive.ts
@@ -1,7 +1,7 @@
import { Directive, Input, OnChanges, SimpleChanges } from "@angular/core";
import { BehaviorSubject, Observable } from "rxjs";
import { distinctUntilChanged } from "rxjs/operators";
-import { BoundingBoxConcept, SapiAtlasModel, SapiSpaceModel } from "src/atlasComponents/sapi/type";
+import { BoundingBox, SxplrTemplate, SxplrAtlas } from "src/atlasComponents/sapi/type_sxplr"
function validateBbox(input: any): boolean {
if (!Array.isArray(input)) return false
@@ -16,19 +16,27 @@ function validateBbox(input: any): boolean {
export class SapiViewsCoreSpaceBoundingBox implements OnChanges{
@Input('sxplr-sapiviews-core-space-boundingbox-atlas')
- atlas: SapiAtlasModel
+ atlas: SxplrAtlas
@Input('sxplr-sapiviews-core-space-boundingbox-space')
- space: SapiSpaceModel
+ space: SxplrTemplate
- private _bbox: BoundingBoxConcept
+ private _bbox: BoundingBox
@Input('sxplr-sapiviews-core-space-boundingbox-spec')
- set bbox(val: string | BoundingBoxConcept ) {
+ set bbox(val: string | BoundingBox ) {
if (typeof val === "string") {
try {
- const [min, max] = JSON.parse(val)
- this._bbox = [min, max]
+ const [min, max]: [
+ [number, number, number],
+ [number, number, number],
+ ] = JSON.parse(val)
+ this._bbox = {
+ minpoint: min,
+ maxpoint: max,
+ center: min.map((v, idx) => (v + max[idx]) / 2) as [number, number, number],
+ space: this.space
+ }
} catch (e) {
console.warn(`Parse bbox input error`)
}
@@ -40,14 +48,14 @@ export class SapiViewsCoreSpaceBoundingBox implements OnChanges{
}
this._bbox = val
}
- get bbox(): BoundingBoxConcept {
+ get bbox(): BoundingBox {
return this._bbox
}
private _bbox$: BehaviorSubject<{
- atlas: SapiAtlasModel
- space: SapiSpaceModel
- bbox: BoundingBoxConcept
+ atlas: SxplrAtlas
+ space: SxplrTemplate
+ bbox: BoundingBox
}> = new BehaviorSubject({
atlas: null,
space: null,
@@ -55,9 +63,9 @@ export class SapiViewsCoreSpaceBoundingBox implements OnChanges{
})
public bbox$: Observable<{
- atlas: SapiAtlasModel
- space: SapiSpaceModel
- bbox: BoundingBoxConcept
+ atlas: SxplrAtlas
+ space: SxplrTemplate
+ bbox: BoundingBox
}> = this._bbox$.asObservable().pipe(
distinctUntilChanged(
(prev, curr) => prev.atlas?.["@id"] === curr.atlas?.['@id']
diff --git a/src/atlasComponents/sapiViews/module.ts b/src/atlasComponents/sapiViews/module.ts
index ff029f0362be7205bec3a45957debcc25f87197c..dd53fa9756db3e026c90a5c95c6b2ec228cec616 100644
--- a/src/atlasComponents/sapiViews/module.ts
+++ b/src/atlasComponents/sapiViews/module.ts
@@ -1,14 +1,13 @@
import { NgModule } from "@angular/core";
import { SapiViewsCoreModule } from "./core";
-import { SapiViewsFeaturesModule } from "./features";
@NgModule({
imports: [
- SapiViewsFeaturesModule,
+ // SapiViewsFeaturesModule,
SapiViewsCoreModule,
],
exports: [
- SapiViewsFeaturesModule,
+ // SapiViewsFeaturesModule,
SapiViewsCoreModule,
]
})
diff --git a/src/atlasComponents/sapiViews/util/module.ts b/src/atlasComponents/sapiViews/util/module.ts
index 2ab8ff874d96216b9ad2528ac1ed83a3e95c204d..8d092a8c809ad7b3a42888a92b9becbf54ef6578 100644
--- a/src/atlasComponents/sapiViews/util/module.ts
+++ b/src/atlasComponents/sapiViews/util/module.ts
@@ -3,7 +3,6 @@ import { AddUnitAndJoin } from "./addUnitAndJoin.pipe";
import { EqualityPipe } from "./equality.pipe";
import { IncludesPipe } from "./includes.pipe";
import { NumbersPipe } from "./numbers.pipe";
-import { ParcellationSupportedInSpacePipe } from "./parcellationSupportedInSpace.pipe";
import { ParseDoiPipe } from "./parseDoi.pipe";
@NgModule({
@@ -13,7 +12,6 @@ import { ParseDoiPipe } from "./parseDoi.pipe";
NumbersPipe,
AddUnitAndJoin,
IncludesPipe,
- ParcellationSupportedInSpacePipe,
],
exports: [
EqualityPipe,
@@ -21,7 +19,6 @@ import { ParseDoiPipe } from "./parseDoi.pipe";
NumbersPipe,
AddUnitAndJoin,
IncludesPipe,
- ParcellationSupportedInSpacePipe,
]
})
diff --git a/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts b/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts
deleted file mode 100644
index 8d69ecf0ce16d1df1227b985471003a8280110d5..0000000000000000000000000000000000000000
--- a/src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe.ts
+++ /dev/null
@@ -1,48 +0,0 @@
-import { Pipe, PipeTransform } from "@angular/core";
-import { NEVER, Observable, of } from "rxjs";
-import { map } from "rxjs/operators";
-import { SAPIParcellation } from "src/atlasComponents/sapi/core";
-import { SAPI } from "src/atlasComponents/sapi/sapi.service";
-import { SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi/type";
-
-export const knownExceptions = {
- supported: {
- /**
- * jba29
- */
- 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290': [
- /**
- * big brain
- */
- 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
- ]
- }
-}
-
-@Pipe({
- name: 'parcellationSuppportedInSpace',
- pure: false,
-})
-
-export class ParcellationSupportedInSpacePipe implements PipeTransform{
-
- constructor(private sapi: SAPI){}
-
- public transform(parc: SapiParcellationModel|string, tmpl: SapiSpaceModel|string): Observable<boolean> {
- if (!parc) return NEVER
- const parcId = typeof parc === "string"
- ? parc
- : parc["@id"]
- const tmplId = typeof tmpl === "string"
- ? tmpl
- : tmpl["@id"]
- for (const key in knownExceptions.supported) {
- if (key === parcId && knownExceptions.supported[key].indexOf(tmplId) >= 0) {
- return of(true)
- }
- }
- return this.sapi.registry.get<SAPIParcellation>(parcId).getVolumes().pipe(
- map(volumes => volumes.some(v => v.data.space["@id"] === tmplId))
- )
- }
-}
\ No newline at end of file
diff --git a/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts b/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts
index 5eacf72e95c4baadee42cbb70d28a09ddb84dc62..accf24d9ec78d3d0d1503e62d9b2717bee468aa3 100644
--- a/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts
+++ b/src/atlasComponents/userAnnotations/annotationMode/annotationMode.component.ts
@@ -18,13 +18,7 @@ export class AnnotationMode implements OnDestroy{
public ARIA_LABELS = ARIA_LABELS
- public moduleAnnotationTypes: {
- instance: {
- name: string
- iconClass: string
- }
- onClick: () => void
- }[] = []
+ public moduleAnnotationTypes = this.modularToolSvc.moduleAnnotationTypes
private onDestroyCb: (() => void)[] = []
@@ -34,7 +28,6 @@ export class AnnotationMode implements OnDestroy{
@Optional() @Inject(CLICK_INTERCEPTOR_INJECTOR) clickInterceptor: ClickInterceptor,
@Optional() @Inject(CONTEXT_MENU_ITEM_INJECTOR) ctxMenuInterceptor: TContextMenu<TContextMenuReg<TContextArg<'nehuba' | 'threeSurfer'>>>
) {
- this.moduleAnnotationTypes = this.modularToolSvc.moduleAnnotationTypes
const stopClickProp = () => false
if (clickInterceptor) {
const { register, deregister } = clickInterceptor
diff --git a/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts b/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
index d339398c0a55865d2a4fce6e2feb9246e4a5606b..23f1de2aa3ebbc08ccd76833e270d3fa9c633cbd 100644
--- a/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
+++ b/src/atlasComponents/userAnnotations/filterAnnotationBySpace.pipe.ts
@@ -1,5 +1,6 @@
import { Pipe, PipeTransform } from "@angular/core";
import { IAnnotationGeometry } from "./tools/type";
+import { SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr"
type TOpts = {
reverse?: boolean
@@ -11,10 +12,10 @@ type TOpts = {
})
export class FilterAnnotationsBySpace implements PipeTransform{
- public transform(annotations: IAnnotationGeometry[], space: { '@id': string }, opts?: TOpts): IAnnotationGeometry[]{
+ public transform(annotations: IAnnotationGeometry[], space: SxplrTemplate, opts?: TOpts): IAnnotationGeometry[]{
const { reverse = false } = opts || {}
return reverse
- ? annotations.filter(ann => ann.space?.["@id"] !== space?.["@id"])
- : annotations.filter(ann => ann.space?.["@id"] === space?.["@id"])
+ ? annotations.filter(ann => ann.space?.id !== space?.id)
+ : annotations.filter(ann => ann.space?.id === space?.id)
}
}
diff --git a/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.template.html b/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.template.html
index 51f1c004700f834b92c3afd81d6cd93ee3d01026..0f35d07e6d352172a7790ad68662c8eb48aaccfe 100644
--- a/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.template.html
+++ b/src/atlasComponents/userAnnotations/singleAnnotationUnit/singleAnnotationUnit.template.html
@@ -5,7 +5,7 @@
</mat-label>
<mat-select formControlName="spaceId">
<mat-option *ngFor="let tmpl of tmpls$ | async" [value]="tmpl['@id']">
- {{ tmpl.fullName }}
+ {{ tmpl.name }}
</mat-option>
</mat-select>
</mat-form-field>
diff --git a/src/atlasComponents/userAnnotations/tools/line.ts b/src/atlasComponents/userAnnotations/tools/line.ts
index 3d01d57dc41678c9958d1c52b41e734fce28ae28..c156a9e09544fb3e82b50820f49d50668a4ea094 100644
--- a/src/atlasComponents/userAnnotations/tools/line.ts
+++ b/src/atlasComponents/userAnnotations/tools/line.ts
@@ -127,6 +127,7 @@ export class Line extends IAnnotationGeometry{
coordinatesFrom,
coordinatesTo
} = json
+ const { ['@id']: spaceId } = coordinateSpace
if (type !== 'tmp/line') throw new Error(`cannot parse line from sands`)
const fromPt = coordinatesFrom.map(c => {
if (c.unit["@id"] !== 'id.link/mm') throw new Error(`Cannot parse unit`)
@@ -145,17 +146,17 @@ export class Line extends IAnnotationGeometry{
x: fromPt[0],
y: fromPt[1],
z: fromPt[2],
- space: coordinateSpace
+ space: { id: spaceId }
}),
new Point({
'@type': "siibra-ex/annotation/point",
x: toPoint[0],
y: toPoint[1],
z: toPoint[2],
- space: coordinateSpace
+ space: { id: spaceId }
})
],
- space: coordinateSpace
+ space: { id: spaceId }
})
return line
}
diff --git a/src/atlasComponents/userAnnotations/tools/line/line.template.html b/src/atlasComponents/userAnnotations/tools/line/line.template.html
index 3f72bd1d7a590f34b3f20636a44a7ff46f9ce2e2..2cff6f5feb88b61d0bdaed4008b2435fd30d0da4 100644
--- a/src/atlasComponents/userAnnotations/tools/line/line.template.html
+++ b/src/atlasComponents/userAnnotations/tools/line/line.template.html
@@ -7,7 +7,7 @@
<mat-chip-list>
<mat-chip *ngFor="let point of (updateAnnotation?.points || []) ; let i = index"
(click)="gotoRoi(point)"
- [matTooltip]="point">
+ [matTooltip]="point.toString()">
{{ i }}
</mat-chip>
</mat-chip-list>
diff --git a/src/atlasComponents/userAnnotations/tools/point.ts b/src/atlasComponents/userAnnotations/tools/point.ts
index f69baf0e4045e8300de93c42a086b57ceee7292e..a2e10804108682e14e844481094063cfac3fad5c 100644
--- a/src/atlasComponents/userAnnotations/tools/point.ts
+++ b/src/atlasComponents/userAnnotations/tools/point.ts
@@ -56,6 +56,7 @@ export class Point extends IAnnotationGeometry {
coordinateSpace,
coordinates
} = sands
+ const { ['@id']: spaceId } = coordinateSpace
if (type === 'https://openminds.ebrains.eu/sands/CoordinatePoint') {
const parsedCoordinate = coordinates.map(coord => {
const { value, unit } = coord
@@ -64,7 +65,7 @@ export class Point extends IAnnotationGeometry {
})
const point = new Point({
id,
- space: coordinateSpace,
+ space: { id: spaceId },
"@type": 'siibra-ex/annotation/point',
x: parsedCoordinate[0],
y: parsedCoordinate[1],
diff --git a/src/atlasComponents/userAnnotations/tools/point/point.template.html b/src/atlasComponents/userAnnotations/tools/point/point.template.html
index 805ab08767a59c9f202ae053b814150678bef881..90f1b5807dad478c8c519736a144258de0e19d30 100644
--- a/src/atlasComponents/userAnnotations/tools/point/point.template.html
+++ b/src/atlasComponents/userAnnotations/tools/point/point.template.html
@@ -5,7 +5,7 @@
</span>
<mat-chip-list>
- <mat-chip [matTooltip]="updateAnnotation"
+ <mat-chip [matTooltip]="updateAnnotation.toString()"
(click)="gotoRoi()">
0
</mat-chip>
diff --git a/src/atlasComponents/userAnnotations/tools/poly.ts b/src/atlasComponents/userAnnotations/tools/poly.ts
index 47dd27c7dc56924a1be4911045523577e7e9d1ad..37a0fdbd397fe43fa136409af1503a2cb2443bbe 100644
--- a/src/atlasComponents/userAnnotations/tools/poly.ts
+++ b/src/atlasComponents/userAnnotations/tools/poly.ts
@@ -166,6 +166,7 @@ export class Polygon extends IAnnotationGeometry{
coordinateSpace,
coordinates
} = sands
+ const { ["@id"]: spaceId } = coordinateSpace
if (type === 'tmp/poly') {
const points: Point[] = []
const edges: [number, number][] = []
@@ -175,7 +176,9 @@ export class Polygon extends IAnnotationGeometry{
return c.value * 1e6
})
const p = new Point({
- space: coordinateSpace,
+ space: {
+ id: spaceId
+ },
x: parsedValue[0],
y: parsedValue[1],
z: parsedValue[2],
@@ -190,7 +193,7 @@ export class Polygon extends IAnnotationGeometry{
const poly = new Polygon({
id,
"@type": 'siibra-ex/annotation/polyline',
- space: coordinateSpace,
+ space: { id: spaceId },
points,
edges
})
diff --git a/src/atlasComponents/userAnnotations/tools/poly/poly.template.html b/src/atlasComponents/userAnnotations/tools/poly/poly.template.html
index 6827915b80ecfb04504184c6519b9670cfa62cf0..71158649f12a4f782a0f149da06ce81b3bd7a25c 100644
--- a/src/atlasComponents/userAnnotations/tools/poly/poly.template.html
+++ b/src/atlasComponents/userAnnotations/tools/poly/poly.template.html
@@ -7,7 +7,7 @@
<mat-chip-list>
<mat-chip *ngFor="let point of (updateAnnotation?.points || []); let i = index"
(click)="gotoRoi(point)"
- [matTooltip]="point">
+ [matTooltip]="point.toString()">
{{ i }}
</mat-chip>
</mat-chip-list>
diff --git a/src/atlasComponents/userAnnotations/tools/service.ts b/src/atlasComponents/userAnnotations/tools/service.ts
index e998c9c53a65be4965b8cad62e84d1b45df3c3f3..17d58ebe0dac79780b6ff699885209f9bea7cf7e 100644
--- a/src/atlasComponents/userAnnotations/tools/service.ts
+++ b/src/atlasComponents/userAnnotations/tools/service.ts
@@ -16,7 +16,7 @@ import { retry } from 'common/util'
import { MatSnackBar } from "@angular/material/snack-bar";
import { actions } from "src/state/atlasSelection";
import { atlasSelection } from "src/state";
-import { SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
import { AnnotationLayer } from "src/atlasComponents/annotations";
const LOCAL_STORAGE_KEY = 'userAnnotationKey'
@@ -91,7 +91,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
private activeToolName: string
private forcedAnnotationRefresh$ = new BehaviorSubject(null)
- private selectedTmpl: SapiSpaceModel
+ private selectedTmpl: SxplrTemplate
private selectedTmpl$ = this.store.pipe(
select(atlasSelection.selectors.selectedTemplate),
)
@@ -501,7 +501,7 @@ export class ModularUserAnnotationToolService implements OnDestroy{
this.annotnEvSubj.next({
type: 'metadataEv',
detail: {
- space: tmpl && { ['@id']: tmpl['@id'] }
+ space: tmpl
}
})
this.forcedAnnotationRefresh$.next(null)
diff --git a/src/atlasComponents/userAnnotations/tools/type.ts b/src/atlasComponents/userAnnotations/tools/type.ts
index 763a58fcb59efc5aeee758008f2d5a6c710ac7c7..eb6f15882be83d17ed7ff30870a879e39ca8101f 100644
--- a/src/atlasComponents/userAnnotations/tools/type.ts
+++ b/src/atlasComponents/userAnnotations/tools/type.ts
@@ -41,7 +41,9 @@ export abstract class AbsToolClass<T extends IAnnotationGeometry> {
init(){
this.subs.push(
this.metadataEv$.subscribe(ev => {
- this.space = ev.detail.space
+ this.space = ev.detail.space && ({
+ id: ev.detail.space.id
+ })
})
)
}
@@ -225,7 +227,7 @@ export type TCallbackFunction = <T extends keyof TCallback>(arg: TCallback[T]['c
export type TBaseAnnotationGeomtrySpec = {
id?: string
space?: {
- ['@id']: string
+ id: string
}
name?: string
desc?: string
@@ -377,7 +379,7 @@ export type TNgMouseEvent = {
}
export type TMetaEvent = {
- space: { ['@id']: string }
+ space: { id: string }
}
export interface IAnnotationEvents {
diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts
index 15dbb49421acaec542c842562853d946422e64d6..5f510e7fda57199da499e2922ead4451b772bb84 100644
--- a/src/atlasViewer/atlasViewer.component.ts
+++ b/src/atlasViewer/atlasViewer.component.ts
@@ -26,6 +26,7 @@ import { environment } from 'src/environments/environment'
import { DOCUMENT } from "@angular/common";
import { userPreference } from "src/state"
import { DARKTHEME } from "src/util/injectionTokens";
+import { EnumQuickTourSeverity } from "src/ui/quickTour/constrants";
/**
* TODO
@@ -207,7 +208,8 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
If you have any comments or need further support, please contact us at [${this.supportEmailAddress}](mailto:${this.supportEmailAddress})`,
description: `That's it! We hope you enjoy your stay. If you have any comments or need further support, please contact us at ${this.supportEmailAddress}`,
- position: 'center'
+ position: 'center' as const,
+ priority: EnumQuickTourSeverity.LOW
}
@HostBinding('attr.version')
diff --git a/src/atlasViewer/atlasViewer.template.html b/src/atlasViewer/atlasViewer.template.html
index ed2e2c6da37077aeea63cf59942a0b7dc7386986..864976bc6901450056408aecc096df0c0254e7ce 100644
--- a/src/atlasViewer/atlasViewer.template.html
+++ b/src/atlasViewer/atlasViewer.template.html
@@ -30,7 +30,7 @@
[quick-tour-description-md]="quickTourFinale.descriptionMd"
[quick-tour-order]="quickTourFinale.order"
[quick-tour-overwrite-arrow]="emptyArrowTmpl"
- quick-tour-severity="low">
+ [quick-tour-severity]="quickTourFinale.priority">
<!-- prevent default is required so that user do not zoom in on UI or scroll on mobile UI -->
<iav-cmp-viewer-container
class="w-100 h-100 d-block"
diff --git a/src/components/dynamicMaterialBtn/dynamicMaterialBtn.component.ts b/src/components/dynamicMaterialBtn/dynamicMaterialBtn.component.ts
index d0a19e9ba7a5343c35f025cc7d2c51b90ac96c3e..57c20da0e5163f5676d6f0c8da887b65dc03ceb5 100644
--- a/src/components/dynamicMaterialBtn/dynamicMaterialBtn.component.ts
+++ b/src/components/dynamicMaterialBtn/dynamicMaterialBtn.component.ts
@@ -1,7 +1,7 @@
import { Component, Input } from "@angular/core";
-type TypeMatBtnStyle = 'mat-button' | 'mat-raised-button' | 'mat-stroked-button' | 'mat-flat-button' | 'mat-icon-button' | 'mat-fab' | 'mat-mini-fab'
-type TypeMatBtnColor = 'basic' | 'primary' | 'accent' | 'warn'
+export type TypeMatBtnStyle = 'mat-button' | 'mat-raised-button' | 'mat-stroked-button' | 'mat-flat-button' | 'mat-icon-button' | 'mat-fab' | 'mat-mini-fab'
+export type TypeMatBtnColor = 'basic' | 'primary' | 'accent' | 'warn'
@Component({
selector: 'iav-dynamic-mat-button',
diff --git a/src/environments/environment.common.ts b/src/environments/environment.common.ts
index 129a0fe9e32d74a76fcc365fdc33a48e81604afc..a8511509d93b2e4b80abadfc5b814006f4a56611 100644
--- a/src/environments/environment.common.ts
+++ b/src/environments/environment.common.ts
@@ -4,7 +4,7 @@ export const environment = {
VERSION: 'unknown version',
PRODUCTION: true,
BACKEND_URL: null,
- SIIBRA_API_ENDPOINTS: 'https://siibra-api-stable.apps.hbp.eu/v2_0,https://siibra-api-stable.apps.jsc.hbp.eu/v2_0,https://siibra-api-stable-ns.apps.hbp.eu/v2_0',
+ SIIBRA_API_ENDPOINTS: 'https://siibra-api-latest.apps-dev.hbp.eu/v3_0', //'https://siibra-api-stable.apps.hbp.eu/v2_0,https://siibra-api-stable.apps.jsc.hbp.eu/v2_0,https://siibra-api-stable-ns.apps.hbp.eu/v2_0',
SPATIAL_TRANSFORM_BACKEND: 'https://hbp-spatial-backend.apps.hbp.eu',
MATOMO_URL: null,
MATOMO_ID: null,
diff --git a/src/getFileInput/fileInputModal/fileInputModal.component.ts b/src/getFileInput/fileInputModal/fileInputModal.component.ts
index b402c272261e01cf13047a0d9c3c65776ada7850..40bfa6d8f14c922df7b2b6ce4155418c7c58de33 100644
--- a/src/getFileInput/fileInputModal/fileInputModal.component.ts
+++ b/src/getFileInput/fileInputModal/fileInputModal.component.ts
@@ -68,7 +68,7 @@ export class FileInputModal implements IFileInputConfig{
get fileInput(){
return this._fileInput
}
- handleFileInputChange(ev: InputEvent){
+ handleFileInputChange(ev: Event){
const target = ev.target as HTMLInputElement
this.fileInput = target.files[0]
}
diff --git a/src/messagingGlue.ts b/src/messagingGlue.ts
index 724841a7d13e9255e76ba5c4b0ad94e7393e91ad..45a7fb37ef39ad91894b9badaeaf6c461d2e82f5 100644
--- a/src/messagingGlue.ts
+++ b/src/messagingGlue.ts
@@ -3,6 +3,7 @@ import { Store } from "@ngrx/store";
import { IMessagingActionTmpl, IWindowMessaging } from "./messaging/types";
import { atlasAppearance, atlasSelection, generalActions } from "src/state"
import { SAPI } from "./atlasComponents/sapi";
+import { translateV3Entities } from "./atlasComponents/sapi/translate_v3"
@Injectable()
export class MessagingGlue implements IWindowMessaging, OnDestroy {
@@ -22,7 +23,8 @@ export class MessagingGlue implements IWindowMessaging, OnDestroy {
const sub = sapi.atlases$.subscribe(atlases => {
for (const atlas of atlases) {
- const { ['@id']: atlasId, spaces } = atlas
+ const sapiAtlas = translateV3Entities.retrieveAtlas(atlas)
+ const { ['@id']: atlasId, spaces } = sapiAtlas
for (const tmpl of spaces) {
const { ['@id']: tmplId } = tmpl
this.tmplSpIdToAtlasId.set(tmplId, atlasId)
diff --git a/src/mouseoverModule/util.ts b/src/mouseoverModule/util.ts
index 0811db26a592492f396f27f1d61cae1b4c7e2cb6..771b7ae4a5b2717fc6ec34025d06fc969e46c02d 100644
--- a/src/mouseoverModule/util.ts
+++ b/src/mouseoverModule/util.ts
@@ -1,8 +1,8 @@
-import { SapiRegionModel } from "src/atlasComponents/sapi"
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
import { IAnnotationGeometry } from "src/atlasComponents/userAnnotations/tools/type"
export type TOnHoverObj = {
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
annotation: IAnnotationGeometry
landmark: {
landmarkName: number
diff --git a/src/plugin/generateTypes.js b/src/plugin/generateTypes.js
index 52f69d8f99921f02bbaf4f3949fdc212a2cd4203..5b92c7e0ce2c9cefe30e3061e79e24df7c564f2f 100644
--- a/src/plugin/generateTypes.js
+++ b/src/plugin/generateTypes.js
@@ -1,3 +1,8 @@
+/**
+ * This node script generates API doc for plugins.
+ * Check npm run api-schema for usage.
+ */
+
const ts = require('typescript')
const fs = require('fs')
const path = require('path')
diff --git a/src/routerModule/routeStateTransform.service.spec.ts b/src/routerModule/routeStateTransform.service.spec.ts
index 590619e9e2f428f4ebd07591e14d6e911862701c..5be8c163f477f7a4da1b46be1178d6bef92dbb3a 100644
--- a/src/routerModule/routeStateTransform.service.spec.ts
+++ b/src/routerModule/routeStateTransform.service.spec.ts
@@ -153,21 +153,21 @@ describe("> routeStateTransform.service.ts", () => {
}
})
- it('> calls correct functions', () => {
+ it('> calls correct functions', async () => {
getRegionLabelIndexSpy.and.returnValue(11)
getParcNgId.and.returnValue('foo-bar')
const state = {}
const svc = TestBed.inject(RouteStateTransformSvc)
- const s = svc.cvtStateToRoute(state as any)
+ const s = await svc.cvtStateToRoute(state as any)
for (const key in atlasSelectionSpy) {
expect(atlasSelectionSpy[key]).toHaveBeenCalledTimes(1)
}
})
- it('> regular ngId', () => {
+ it('> regular ngId', async () => {
const ngId = 'foobar'
const labelIndex = 124
@@ -176,12 +176,12 @@ describe("> routeStateTransform.service.ts", () => {
const state = {}
const svc = TestBed.inject(RouteStateTransformSvc)
- const s = svc.cvtStateToRoute(state as any)
+ const s = await svc.cvtStateToRoute(state as any)
expect(s).toContain(`r:${ngId}::${encodeNumber(labelIndex, { float: false })}`)
})
- it('> ngId containing ()', () => {
+ it('> ngId containing ()', async () => {
const ngId = 'foobar(1)'
const labelIndex = 124
@@ -190,7 +190,7 @@ describe("> routeStateTransform.service.ts", () => {
const state = {}
const svc = TestBed.inject(RouteStateTransformSvc)
- const s = svc.cvtStateToRoute(state as any)
+ const s = await svc.cvtStateToRoute(state as any)
expect(s).toContain(`r:foobar%25281%2529::${encodeNumber(labelIndex, { float: false })}`)
})
})
diff --git a/src/routerModule/routeStateTransform.service.ts b/src/routerModule/routeStateTransform.service.ts
index d464b6eeaf5b90f400be66b1f100ee292b94d8ac..93b6dd82fac39328caadf1096757b2ab8da54d0b 100644
--- a/src/routerModule/routeStateTransform.service.ts
+++ b/src/routerModule/routeStateTransform.service.ts
@@ -1,9 +1,10 @@
import { Injectable } from "@angular/core";
import { UrlSegment, UrlTree } from "@angular/router";
import { map } from "rxjs/operators";
-import { SAPI, SapiRegionModel } from "src/atlasComponents/sapi";
+import { SAPI } from "src/atlasComponents/sapi";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
import { atlasSelection, defaultState, MainState, plugins, userInteraction } from "src/state";
-import { getParcNgId, getRegionLabelIndex } from "src/viewerModule/nehuba/config.service";
+import { getParcNgId, } from "src/viewerModule/nehuba/config.service";
import { decodeToNumber, encodeNumber, encodeURIFull, separator } from "./cipher";
import { TUrlAtlas, TUrlPathObj, TUrlStandaloneVolume } from "./type";
import { decodePath, encodeId, decodeId, endcodePath } from "./util";
@@ -43,7 +44,7 @@ export class RouteStateTransformSvc {
this.sapi.getParcRegions(selectedAtlasId, selectedParcellationId, selectedTemplateId, { priority: 10 }).toPromise(),
])
- const ngIdToRegionMap: Map<string, Map<number, SapiRegionModel[]>> = new Map()
+ const ngIdToRegionMap: Map<string, Map<number, SxplrRegion[]>> = new Map()
for (const region of allParcellationRegions) {
const ngId = getParcNgId(selectedAtlas, selectedTemplate, selectedParcellation, region)
@@ -52,7 +53,7 @@ export class RouteStateTransformSvc {
}
const map = ngIdToRegionMap.get(ngId)
- const idx = getRegionLabelIndex(selectedAtlas, selectedTemplate, selectedParcellation, region)
+ const idx = await this.sapi.getRegionLabelIndices(selectedTemplate, selectedParcellation, region)
if (!map.has(idx)) {
map.set(idx, [])
}
@@ -201,7 +202,7 @@ export class RouteStateTransformSvc {
return returnState
}
- cvtStateToRoute(_state: MainState) {
+ async cvtStateToRoute(_state: MainState) {
/**
* need to create new references here
@@ -238,7 +239,7 @@ export class RouteStateTransformSvc {
let selectedRegionsString: string
if (selectedRegions.length === 1) {
const region = selectedRegions[0]
- const labelIndex = getRegionLabelIndex(selectedAtlas, selectedTemplate, selectedParcellation, region)
+ const labelIndex = await this.sapi.getRegionLabelIndices(selectedTemplate, selectedParcellation, region)
const ngId = getParcNgId(selectedAtlas, selectedTemplate, selectedParcellation, region)
selectedRegionsString = `${ngId}::${encodeNumber(labelIndex, { float: false })}`
diff --git a/src/routerModule/router.service.ts b/src/routerModule/router.service.ts
index 3a060971d4f2d51a4223f16c86cb218362e75095..7a2047489958038b0d4dcd36d2759ec7ffdc7e4f 100644
--- a/src/routerModule/router.service.ts
+++ b/src/routerModule/router.service.ts
@@ -3,9 +3,9 @@ import { APP_BASE_HREF } from "@angular/common";
import { Inject } from "@angular/core";
import { NavigationEnd, Router } from '@angular/router'
import { Store } from "@ngrx/store";
-import { debounceTime, distinctUntilChanged, filter, map, mapTo, shareReplay, startWith, switchMap, switchMapTo, take, withLatestFrom } from "rxjs/operators";
+import { catchError, debounceTime, distinctUntilChanged, filter, map, mapTo, shareReplay, startWith, switchMap, switchMapTo, take, withLatestFrom } from "rxjs/operators";
import { encodeCustomState, decodeCustomState, verifyCustomState } from "./util";
-import { BehaviorSubject, combineLatest, concat, merge, Observable, timer } from 'rxjs'
+import { BehaviorSubject, combineLatest, concat, from, merge, Observable, of, timer } from 'rxjs'
import { scan } from 'rxjs/operators'
import { RouteStateTransformSvc } from "./routeStateTransform.service";
import { SAPI } from "src/atlasComponents/sapi";
@@ -145,22 +145,21 @@ export class RouterService {
})
),
withLatestFrom(
- store$,
+ store$.pipe(
+ switchMap(state =>
+ from(routeToStateTransformSvc.cvtStateToRoute(state)).pipe(
+ catchError(() => of(``))
+ )
+ )
+ ),
this.customRoute$.pipe(
startWith({})
)
)
).subscribe(arg => {
- const [{ stateFromRoute, url }, currentState, customRoutes] = arg
+ const [{ stateFromRoute, url }, _routeFromState, customRoutes] = arg
const fullPath = url
-
- let routeFromState: string
- try {
- routeFromState = routeToStateTransformSvc.cvtStateToRoute(currentState)
- } catch (_e) {
- routeFromState = ``
- }
-
+ let routeFromState = _routeFromState
for (const key in customRoutes) {
const customStatePath = encodeCustomState(key, customRoutes[key])
if (!customStatePath) continue
@@ -203,14 +202,14 @@ export class RouterService {
combineLatest([
store$.pipe(
debounceTime(160),
- map(state => {
- try {
- return routeToStateTransformSvc.cvtStateToRoute(state)
- } catch (e) {
- this.logError(e)
- return ``
- }
- })
+ switchMap(state =>
+ from(routeToStateTransformSvc.cvtStateToRoute(state)).pipe(
+ catchError(err => {
+ this.logError(err)
+ return of(``)
+ })
+ )
+ ),
),
this.customRoute$,
]).pipe(
diff --git a/src/state/annotations/store.ts b/src/state/annotations/store.ts
index 21198ff816f5315721746a0cbeba8d8f55c90d47..26a52261bcc69ae39b6bdf549066cea3375b26ef 100644
--- a/src/state/annotations/store.ts
+++ b/src/state/annotations/store.ts
@@ -1,5 +1,5 @@
import { createReducer, on } from "@ngrx/store"
-import { OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi"
+import { OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi/type_v3"
import * as actions from "./actions"
type Line = {
diff --git a/src/state/atlasAppearance/const.ts b/src/state/atlasAppearance/const.ts
index c6c24f31b6ffc7e8bebf9647f9b0b4f538c0f710..32a78b0f0e590411e68adf95ba8cb8f7964bdad3 100644
--- a/src/state/atlasAppearance/const.ts
+++ b/src/state/atlasAppearance/const.ts
@@ -1,4 +1,4 @@
-import { SapiRegionModel } from "src/atlasComponents/sapi"
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
export const nameSpace = `[state.atlasAppearance]`
type CustomLayerBase = {
@@ -7,7 +7,7 @@ type CustomLayerBase = {
export type ColorMapCustomLayer = {
clType: 'customlayer/colormap' | 'baselayer/colormap'
- colormap: WeakMap<SapiRegionModel, number[]>
+ colormap: WeakMap<SxplrRegion, number[]>
} & CustomLayerBase
export type ThreeSurferCustomLayer = {
diff --git a/src/state/atlasSelection/actions.ts b/src/state/atlasSelection/actions.ts
index 7cf6d778a8549575c94b8244266ad5cc213cb0a8..36e61174c8255944054e02b1da96b9d595789f83 100644
--- a/src/state/atlasSelection/actions.ts
+++ b/src/state/atlasSelection/actions.ts
@@ -1,25 +1,25 @@
import { createAction, props } from "@ngrx/store";
-import { SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
import { BreadCrumb, nameSpace, ViewerMode, AtlasSelectionState } from "./const"
export const selectAtlas = createAction(
`${nameSpace} selectAtlas`,
props<{
- atlas: SapiAtlasModel
+ atlas: SxplrAtlas
}>()
)
export const selectTemplate = createAction(
`${nameSpace} selectTemplate`,
props<{
- template: SapiSpaceModel
+ template: SxplrTemplate
}>()
)
export const selectParcellation = createAction(
`${nameSpace} selectParcellation`,
props<{
- parcellation: SapiParcellationModel
+ parcellation: SxplrParcellation
}>()
)
@@ -44,21 +44,21 @@ export const setAtlasSelectionState = createAction(
export const setSelectedParcellationAllRegions = createAction(
`${nameSpace} setSelectedParcellationAllRegions`,
props<{
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
}>()
)
export const selectRegion = createAction(
`${nameSpace} selectRegion`,
props<{
- region: SapiRegionModel
+ region: SxplrRegion
}>()
)
export const setSelectedRegions = createAction(
`${nameSpace} setSelectedRegions`,
props<{
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
}>()
)
@@ -146,7 +146,7 @@ export const navigateTo = createAction(
export const navigateToRegion = createAction(
`${nameSpace} navigateToRegion`,
props<{
- region: SapiRegionModel
+ region: SxplrRegion
}>()
)
@@ -157,7 +157,7 @@ export const clearViewerMode = createAction(
export const toggleRegionSelect = createAction(
`${nameSpace} toggleRegionSelect`,
props<{
- region: SapiRegionModel
+ region: SxplrRegion
}>()
)
@@ -171,7 +171,7 @@ export const toggleRegionSelectById = createAction(
export const viewSelRegionInNewSpace = createAction(
`${nameSpace} viewSelRegionInNewSpace`,
props<{
- region: SapiRegionModel
- template: SapiSpaceModel
+ region: SxplrRegion
+ template: SxplrTemplate
}>()
)
diff --git a/src/state/atlasSelection/const.ts b/src/state/atlasSelection/const.ts
index 1499e2472a896352406389a50a6eacaa14752539..b5ad6084ab41a90cce85b4ea182beaa3b8a76a5e 100644
--- a/src/state/atlasSelection/const.ts
+++ b/src/state/atlasSelection/const.ts
@@ -1,4 +1,4 @@
-import { SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi"
+import { SxplrAtlas, SxplrTemplate, SxplrParcellation, SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
export const nameSpace = `[state.atlasSelection]`
export type ViewerMode = 'annotating' | 'key frame'
@@ -8,12 +8,12 @@ export type BreadCrumb = {
}
export type AtlasSelectionState = {
- selectedAtlas: SapiAtlasModel
- selectedTemplate: SapiSpaceModel
- selectedParcellation: SapiParcellationModel
- selectedParcellationAllRegions: SapiRegionModel[]
+ selectedAtlas: SxplrAtlas
+ selectedTemplate: SxplrTemplate
+ selectedParcellation: SxplrParcellation
+ selectedParcellationAllRegions: SxplrRegion[]
- selectedRegions: SapiRegionModel[]
+ selectedRegions: SxplrRegion[]
standAloneVolumes: string[]
/**
diff --git a/src/state/atlasSelection/effects.ts b/src/state/atlasSelection/effects.ts
index a84da1c3dfaa44031c79b46a04dfe5334522e434..b610696172c04ec863b3cdf71fc998596352bc23 100644
--- a/src/state/atlasSelection/effects.ts
+++ b/src/state/atlasSelection/effects.ts
@@ -1,26 +1,28 @@
import { Injectable } from "@angular/core";
import { Actions, createEffect, ofType } from "@ngrx/effects";
-import { concat, forkJoin, merge, Observable, of } from "rxjs";
+import { forkJoin, merge, Observable, of } from "rxjs";
import { catchError, filter, map, mapTo, switchMap, switchMapTo, take, withLatestFrom } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiParcellationModel, SAPIRegion, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SAPI, SAPIRegion } from "src/atlasComponents/sapi";
import * as mainActions from "../actions"
import { select, Store } from "@ngrx/store";
import { selectors, actions } from '.'
import { AtlasSelectionState } from "./const"
import { atlasAppearance, atlasSelection } from "..";
-import { ParcellationSupportedInSpacePipe } from "src/atlasComponents/sapiViews/util/parcellationSupportedInSpace.pipe";
+
import { InterSpaceCoordXformSvc } from "src/atlasComponents/sapi/core/space/interSpaceCoordXform.service";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
+import { SxplrAtlas, SxplrParcellation, SxplrRegion, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
type OnTmplParcHookArg = {
previous: {
- atlas: SapiAtlasModel
- template: SapiSpaceModel
- parcellation: SapiParcellationModel
+ atlas: SxplrAtlas
+ template: SxplrTemplate
+ parcellation: SxplrParcellation
}
current: {
- atlas: SapiAtlasModel
- template: SapiSpaceModel
- parcellation: SapiParcellationModel
+ atlas: SxplrAtlas
+ template: SxplrTemplate
+ parcellation: SxplrParcellation
}
}
@@ -36,7 +38,7 @@ export class Effect {
const { atlas, parcellation, template } = current
return (
!!atlas && !!parcellation && !!template
- ? this.sapiSvc.getParcRegions(atlas["@id"], parcellation["@id"], template["@id"])
+ ? this.sapiSvc.getParcRegions(atlas.id, parcellation.id, template.id)
: of([])
).pipe(
map(regions => {
@@ -47,13 +49,13 @@ export class Effect {
)
},
({ current, previous }) => {
- const prevSpcName = InterSpaceCoordXformSvc.TmplIdToValidSpaceName(previous?.template?.["@id"])
- const currSpcName = InterSpaceCoordXformSvc.TmplIdToValidSpaceName(current?.template?.["@id"])
+ const prevSpcName = InterSpaceCoordXformSvc.TmplIdToValidSpaceName(previous?.template?.id)
+ const currSpcName = InterSpaceCoordXformSvc.TmplIdToValidSpaceName(current?.template?.id)
/**
* if trans-species, return default state for navigation
*/
- if (previous?.atlas?.["@id"] !== current?.atlas?.["@id"]) {
+ if (previous?.atlas?.id !== current?.atlas?.id) {
return of({
navigation: null
})
@@ -89,14 +91,13 @@ export class Effect {
}
]
- parcSupportedInSpacePipe = new ParcellationSupportedInSpacePipe(this.sapiSvc)
- onTemplateParcSelection = createEffect(() => merge<{ template: SapiSpaceModel, parcellation: SapiParcellationModel }>(
+ onTemplateParcSelection = createEffect(() => merge(
this.action.pipe(
ofType(actions.selectTemplate),
map(({ template }) => {
return {
template,
- parcellation: null
+ parcellation: null as SxplrParcellation
}
})
),
@@ -104,7 +105,7 @@ export class Effect {
ofType(actions.selectParcellation),
map(({ parcellation }) => {
return {
- template: null,
+ template: null as SxplrTemplate,
parcellation
}
})
@@ -115,14 +116,9 @@ export class Effect {
const currTmpl = selectors.selectedTemplate(store)
const currParc = selectors.selectedParcellation(store)
const currAtlas = selectors.selectedAtlas(store)
- return this.parcSupportedInSpacePipe.transform(
- parcellation || currParc,
- template || currTmpl
- ).pipe(
- switchMap(flag => {
- /**
- * if desired parc is supported in tmpl, emit them
- */
+ return this.sapiSvc.getSupportedTemplates(currAtlas, parcellation || currParc).pipe(
+ switchMap(tmpls => {
+ const flag = tmpls.some(tmpl => tmpl.id === (template || currTmpl).id)
if (flag) {
return of({
atlas: currAtlas,
@@ -134,38 +130,28 @@ export class Effect {
* if template is defined, find the first parcellation that is supported
*/
if (!!template) {
- return concat(
- ...currAtlas.parcellations.map(
- p => this.parcSupportedInSpacePipe.transform(p["@id"], template).pipe(
- filter(flag => flag),
- switchMap(() => this.sapiSvc.getParcDetail(currAtlas["@id"], p['@id'])),
- )
- )
- ).pipe(
- take(1),
- map(parcellation => {
+ return this.sapiSvc.getSupportedParcellations(currAtlas, template).pipe(
+ map(parcs => {
+ if (parcs.length === 0) {
+ throw new Error(`Cannot find any supported parcellations for template ${template.name}`)
+ }
return {
atlas: currAtlas,
template,
- parcellation
+ parcellation: parcs[0]
}
})
)
}
if (!!parcellation) {
- return concat(
- ...currAtlas.spaces.map(
- sp => this.parcSupportedInSpacePipe.transform(parcellation["@id"], sp["@id"]).pipe(
- filter(flag => flag),
- switchMap(() => this.sapiSvc.getSpaceDetail(currAtlas["@id"], sp['@id'])),
- )
- )
- ).pipe(
- take(1),
- map(template => {
+ return this.sapiSvc.getSupportedTemplates(currAtlas, parcellation).pipe(
+ map(templates => {
+ if (templates.length === 0) {
+ throw new Error(`Cannot find any supported templates for parcellation ${parcellation.name}`)
+ }
return {
atlas: currAtlas,
- template,
+ template: templates[0],
parcellation
}
})
@@ -178,6 +164,7 @@ export class Effect {
this.onTemplateParcSelectionPostHook.map(fn => fn({ previous: { atlas: currAtlas, template: currTmpl, parcellation: currParc }, current: { atlas, template, parcellation } }))
).pipe(
map(partialStates => {
+ console.log('selected teplate', template, parcellation)
let returnState: Partial<AtlasSelectionState> = {
selectedAtlas: atlas,
selectedTemplate: template,
@@ -200,28 +187,21 @@ export class Effect {
onAtlasSelectionSelectTmplParc = createEffect(() => this.action.pipe(
ofType(actions.selectAtlas),
filter(action => !!action.atlas),
- switchMap(({ atlas }) => {
- const selectedParc = atlas.parcellations.find(p => /290/.test(p["@id"])) || atlas.parcellations[0]
- return this.sapiSvc.getParcDetail(atlas["@id"], selectedParc["@id"], { priority: 10 }).pipe(
- map(parcellation => {
+ switchMap(({ atlas }) =>
+ this.sapiSvc.getAllParcellations(atlas).pipe(
+ map(parcellations => {
+ const selectedParc = parcellations.find(p => p.id.includes("290")) || parcellations[0]
return {
- parcellation,
+ parcellation: selectedParc,
atlas
}
})
)
- }),
+ ),
switchMap(({ atlas, parcellation }) => {
- const spacdIds = parcellation.brainAtlasVersions.map(bas => bas.coordinateSpace) as { "@id": string }[]
- return forkJoin(
- spacdIds.filter(
- spaceId => atlas.spaces.map(spc => spc["@id"]).indexOf(spaceId["@id"]) >= 0
- ).map(spaceId =>
- this.sapiSvc.getSpaceDetail(atlas["@id"], spaceId["@id"])
- )
- ).pipe(
+ return this.sapiSvc.getSupportedTemplates(atlas, parcellation).pipe(
switchMap(spaces => {
- const selectedSpace = spaces.find(s => /152/.test(s.fullName)) || spaces[0]
+ const selectedSpace = spaces.find(s => s.name.includes("152")) || spaces[0]
return forkJoin(
this.onTemplateParcSelectionPostHook.map(fn => fn({ previous: null, current: { atlas, parcellation, template: selectedSpace } }))
).pipe(
@@ -255,7 +235,7 @@ export class Effect {
)
),
switchMap(([regions, layers]) => {
- const map = new Map<SapiRegionModel, number[]>()
+ const map = new Map<SxplrRegion, number[]>()
for (const region of regions) {
map.set(region, SAPIRegion.GetDisplayColor(region))
}
@@ -336,8 +316,8 @@ export class Effect {
select(selectors.selectedParcellation)
)
),
- switchMap(([{ region }, selectedTemplate, selectedAtlas, selectedParcellation]) => {
- if (!selectedAtlas || !selectedTemplate || !selectedParcellation || !region) {
+ switchMap(([{ region: _region }, selectedTemplate, selectedAtlas, selectedParcellation]) => {
+ if (!selectedAtlas || !selectedTemplate || !selectedParcellation || !_region) {
return of(
mainActions.generalActionError({
message: `atlas, template, parcellation or region not set`
@@ -345,6 +325,8 @@ export class Effect {
)
}
+ const region = translateV3Entities.retrieveRegion(_region)
+
if (region.hasAnnotation?.bestViewPoint && region.hasAnnotation.bestViewPoint.coordinateSpace['@id'] === selectedTemplate["@id"]) {
return of(
actions.navigateTo({
diff --git a/src/state/atlasSelection/store.ts b/src/state/atlasSelection/store.ts
index ebea8a78dd3015d9b0b050c3902e40fb8ab2a0c8..1138c493706646809b09753841a10ec9c6a9095b 100644
--- a/src/state/atlasSelection/store.ts
+++ b/src/state/atlasSelection/store.ts
@@ -1,14 +1,7 @@
import { createReducer, on } from "@ngrx/store";
-import { SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
import * as actions from "./actions"
import { AtlasSelectionState } from "./const"
-function getRegionLabelIndex(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: SapiParcellationModel, region: SapiRegionModel) {
- const lblIdx = Number(region?.hasAnnotation?.internalIdentifier)
- if (isNaN(lblIdx)) return null
- return lblIdx
-}
-
export const defaultState: AtlasSelectionState = {
selectedAtlas: null,
selectedParcellation: null,
@@ -50,13 +43,6 @@ const reducer = createReducer(
*
* ignore
*/
- const { selectedAtlas, selectedParcellation, selectedTemplate } = state
- if (
- !region.hasAnnotation?.visualizedIn
- && !getRegionLabelIndex(selectedAtlas, selectedTemplate, selectedParcellation, region)
- ) {
- return { ...state }
- }
const selected = state.selectedRegions.includes(region)
return {
...state,
@@ -117,14 +103,12 @@ const reducer = createReducer(
on(
actions.selectAtlas,
(state, { atlas }) => {
- if (atlas?.["@id"] === state?.selectedAtlas?.["@id"]) {
- return state
+ if (atlas?.id === state?.selectedAtlas?.id) {
+ return { ...state }
}
return {
...state,
selectedAtlas: atlas,
- selectedTemplate: null,
- selectedParcellation: null,
}
}
),
diff --git a/src/state/atlasSelection/util.ts b/src/state/atlasSelection/util.ts
index 2ee06893cafa819dc5a13784f74a9425f6645804..0f21d0095d1456bf7df858d9518a2e7817478035 100644
--- a/src/state/atlasSelection/util.ts
+++ b/src/state/atlasSelection/util.ts
@@ -1,45 +1,12 @@
import { createSelector, select } from "@ngrx/store";
import { forkJoin, of, pipe } from "rxjs";
import { distinctUntilChanged, map, switchMap } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SAPI } from "src/atlasComponents/sapi";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
+import { SxplrAtlas, SxplrParcellation, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
import { jsonEqual } from "src/util/json";
import * as selectors from "./selectors"
-const allAvailSpaces = (sapi: SAPI) => {
- return pipe(
- select(selectors.selectedAtlas),
- switchMap(atlas => atlas
- ? forkJoin(
- atlas.spaces.map(spcWId => sapi.getSpaceDetail(atlas["@id"], spcWId["@id"]))
- )
- : of([])
- )
- )
-}
-
-const allAvailParcs = (sapi: SAPI) => pipe(
- select(selectors.selectedAtlas),
- switchMap(atlas => atlas
- ? forkJoin(
- atlas.parcellations.map(parcWId => sapi.getParcDetail(atlas["@id"], parcWId["@id"]))
- )
- : of([])
- )
-)
-const allAvailSpacesParcs = (sapi: SAPI) => pipe(
- select(selectors.selectedAtlas),
- switchMap(atlas => atlas
- ? forkJoin({
- spaces: atlas.spaces.map(spcWId => sapi.getSpaceDetail(atlas["@id"], spcWId["@id"])),
- parcellation: atlas.parcellations.map(parcWId => sapi.getParcDetail(atlas["@id"], parcWId["@id"])),
- })
- : of({
- spaces: [],
- parcellation: []
- })
- )
-)
-
const nonDistinctATP = createSelector(
selectors.selectedAtlas,
selectors.selectedTemplate,
@@ -50,14 +17,11 @@ const nonDistinctATP = createSelector(
const distinctATP = () => pipe(
select(nonDistinctATP),
distinctUntilChanged(
- jsonEqual((o, n) => o?.["@id"] === n?.["@id"])
+ jsonEqual((o, n) => o?.id === n?.id)
),
- map(val => val as { atlas: SapiAtlasModel, parcellation: SapiParcellationModel, template: SapiSpaceModel })
+ map(val => val as { atlas: SxplrAtlas, parcellation: SxplrParcellation, template: SxplrTemplate })
)
export const fromRootStore = {
- allAvailSpaces,
- allAvailParcs,
- allAvailSpacesParcs,
distinctATP,
}
diff --git a/src/state/index.ts b/src/state/index.ts
index 4d63d64e5d893fae4008bc9bad0f906471385f65..40e84c234c4bca8d7eb7fece2c2c999ab249629f 100644
--- a/src/state/index.ts
+++ b/src/state/index.ts
@@ -26,7 +26,6 @@ function debug(reducer: ActionReducer<MainState>): ActionReducer<MainState> {
return function(state, action) {
console.log('state', state);
console.log('action', action);
-
return reducer(state, action);
};
}
diff --git a/src/state/userInteraction/actions.ts b/src/state/userInteraction/actions.ts
index 3df6c1b9780d6d0f9fde7e14e205a0d179445093..42de09fe8e3100733952564f6fcd18266f5b576a 100644
--- a/src/state/userInteraction/actions.ts
+++ b/src/state/userInteraction/actions.ts
@@ -1,6 +1,6 @@
import { createAction, props } from "@ngrx/store"
import { nameSpace } from "./const"
-import { SapiRegionModel, SapiFeatureModel, OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi"
+import { SxplrRegion, Feature, Point } from "src/atlasComponents/sapi/type_sxplr"
export const mouseOverAnnotations = createAction(
`${nameSpace} mouseOverAnnotations`,
@@ -14,21 +14,21 @@ export const mouseOverAnnotations = createAction(
export const mouseoverRegions = createAction(
`${nameSpace} mouseoverRegions`,
props<{
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
}>()
)
export const mouseoverPosition = createAction(
`${nameSpace} mouseoverPosition`,
props<{
- position: OpenMINDSCoordinatePoint
+ position: Point
}>()
)
export const showFeature = createAction(
`${nameSpace} showFeature`,
props<{
- feature: SapiFeatureModel
+ feature: Feature
}>()
)
diff --git a/src/state/userInteraction/store.ts b/src/state/userInteraction/store.ts
index ab75700289c279969ac2bba0eaafe3a6da3286e4..7426ba02eca4f1f5ede5f148ba5e788120bb0061 100644
--- a/src/state/userInteraction/store.ts
+++ b/src/state/userInteraction/store.ts
@@ -1,11 +1,11 @@
import { createReducer, on } from "@ngrx/store";
-import { SapiRegionModel, SapiFeatureModel, OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi";
+import { SxplrRegion, Feature, Point } from "src/atlasComponents/sapi/type_sxplr";
import * as actions from "./actions"
export type UserInteraction = {
- mouseoverRegions: SapiRegionModel[]
- selectedFeature: SapiFeatureModel
- mouseoverPosition: OpenMINDSCoordinatePoint
+ mouseoverRegions: SxplrRegion[]
+ selectedFeature: Feature
+ mouseoverPosition: Point
}
export const defaultState: UserInteraction = {
diff --git a/src/strictLocal/strictLocal.directive.ts b/src/strictLocal/strictLocal.directive.ts
index b5f0c83ad82310ec40b64906c3f6d5c266fb7a2f..a3141e7019a50b48a12962423c0f658624e073f1 100644
--- a/src/strictLocal/strictLocal.directive.ts
+++ b/src/strictLocal/strictLocal.directive.ts
@@ -1,4 +1,4 @@
-import { ComponentFactoryResolver, Directive, HostBinding, ViewContainerRef } from "@angular/core";
+import { Directive, HostBinding, ViewContainerRef } from "@angular/core";
import { environment } from "src/environments/environment"
import { StrictLocalInfo } from "./strictLocalCmp/strictLocalCmp.component";
@@ -12,11 +12,9 @@ export class HideWhenLocal {
hideWhenLocal = environment.STRICT_LOCAL ? 'none!important' : null
constructor(
private vc: ViewContainerRef,
- private cfr: ComponentFactoryResolver,
){
if (environment.STRICT_LOCAL) {
- const cf = this.cfr.resolveComponentFactory(StrictLocalInfo)
- this.vc.createComponent(cf)
+ this.vc.createComponent(StrictLocalInfo)
}
}
}
diff --git a/src/ui/dialogInfo/dialog.directive.ts b/src/ui/dialogInfo/dialog.directive.ts
index eccb689f25f5e35c65375e3d5ebe32124f16c2b9..3b24370b99282a6b8386e4c81b35c8b7286f552f 100644
--- a/src/ui/dialogInfo/dialog.directive.ts
+++ b/src/ui/dialogInfo/dialog.directive.ts
@@ -31,7 +31,7 @@ const sizeDict: Record<DialogSize, Partial<MatDialogConfig>> = {
export class DialogDirective{
@Input('sxplr-dialog')
- templateRef: TemplateRef<unknown>
+ templateRef: TemplateRef<unknown>|string
@Input('sxplr-dialog-size')
size: DialogSize = 'm'
@@ -43,7 +43,11 @@ export class DialogDirective{
@HostListener('click')
onClick(){
- this.matDialog.open(this.templateRef || DialogFallbackCmp, {
+ const tmpl = this.templateRef instanceof TemplateRef
+ ? this.templateRef
+ : DialogFallbackCmp
+
+ this.matDialog.open(tmpl, {
data: this.data,
...(sizeDict[this.size] || {})
})
diff --git a/src/ui/quickTour/constrants.ts b/src/ui/quickTour/constrants.ts
index 375ecc3f933a7e1d653e1c311148653a78d6dcf5..0cac96e3b651ff805f8e3c516a8bc9ed214f316d 100644
--- a/src/ui/quickTour/constrants.ts
+++ b/src/ui/quickTour/constrants.ts
@@ -3,8 +3,8 @@ import { InjectionToken, TemplateRef } from "@angular/core"
type TPosition = 'top' | 'top-right' | 'right' | 'bottom-right' | 'bottom' | 'bottom-left' | 'left' | 'top-left' | 'center'
type TCustomPosition = {
- left: number
- top: number
+ left: string
+ top: string
}
export interface IQuickTourData {
@@ -31,6 +31,12 @@ export enum EnumQuickTourSeverity {
HIGH = 'hight',
}
+export const QuickTourSeverity = {
+ "low": EnumQuickTourSeverity.LOW,
+ "medium": EnumQuickTourSeverity.MEDIUM,
+ "high": EnumQuickTourSeverity.HIGH,
+} as const
+
export const PERMISSION_DIALOG_ACTIONS = {
START: `start`,
CANCEL: `cancel`,
diff --git a/src/ui/quickTour/quickTour.service.ts b/src/ui/quickTour/quickTour.service.ts
index 3aed96edf8d1cde0ff32642954be57f735a634a5..e593328e8ecf45e6e351c3460aab66934a4ba8e7 100644
--- a/src/ui/quickTour/quickTour.service.ts
+++ b/src/ui/quickTour/quickTour.service.ts
@@ -4,11 +4,18 @@ import { Overlay, OverlayRef } from "@angular/cdk/overlay";
import { ComponentPortal } from "@angular/cdk/portal";
import { QuickTourThis } from "./quickTourThis.directive";
import { DoublyLinkedList, IDoublyLinkedItem } from 'src/util'
-import { EnumQuickTourSeverity, PERMISSION_DIALOG_ACTIONS, QUICK_TOUR_CMP_INJTKN } from "./constrants";
+import { EnumQuickTourSeverity, PERMISSION_DIALOG_ACTIONS, QuickTourSeverity, QUICK_TOUR_CMP_INJTKN } from "./constrants";
import { LOCAL_STORAGE_CONST } from "src/util/constants";
import { MatDialog, MatDialogRef } from "@angular/material/dialog";
import { StartTourDialogDialog } from "src/ui/quickTour/startTourDialog/startTourDialog.component";
+const autoPlayPriority: Set<EnumQuickTourSeverity | keyof typeof QuickTourSeverity> = new Set([
+ EnumQuickTourSeverity.HIGH,
+ EnumQuickTourSeverity.MEDIUM,
+ "medium",
+ "high"
+])
+
@Injectable()
export class QuickTourService {
@@ -51,7 +58,7 @@ export class QuickTourService {
)
- if (dir.quickTourSeverity === EnumQuickTourSeverity.MEDIUM || dir.quickTourSeverity === EnumQuickTourSeverity.HIGH) {
+ if (autoPlayPriority.has(dir.quickTourSeverity)) {
this.autoStart()
}
}
diff --git a/src/ui/quickTour/quickTourThis.directive.ts b/src/ui/quickTour/quickTourThis.directive.ts
index 1908166452147779e29c35e08d9838f60e1479bc..9dc6a2bd34b8c085d3e2b5461e48a042849a2d49 100644
--- a/src/ui/quickTour/quickTourThis.directive.ts
+++ b/src/ui/quickTour/quickTourThis.directive.ts
@@ -1,7 +1,6 @@
import { Directive, ElementRef, Input, OnChanges, OnDestroy, OnInit, TemplateRef } from "@angular/core";
import { QuickTourService } from "src/ui/quickTour/quickTour.service";
-import { EnumQuickTourSeverity, IQuickTourOverwritePosition, TQuickTourPosition } from "src/ui/quickTour/constrants";
-import {LOCAL_STORAGE_CONST} from "src/util/constants";
+import { EnumQuickTourSeverity, IQuickTourOverwritePosition, TQuickTourPosition, QuickTourSeverity } from "src/ui/quickTour/constrants";
@Directive({
selector: '[quick-tour]',
@@ -15,7 +14,7 @@ export class QuickTourThis implements OnInit, OnChanges, OnDestroy {
@Input('quick-tour-position') position: TQuickTourPosition
@Input('quick-tour-overwrite-position') overwritePosition: IQuickTourOverwritePosition
@Input('quick-tour-overwrite-arrow') overWriteArrow: TemplateRef<any> | string
- @Input('quick-tour-severity') quickTourSeverity: EnumQuickTourSeverity = EnumQuickTourSeverity.MEDIUM
+ @Input('quick-tour-severity') quickTourSeverity: EnumQuickTourSeverity | keyof typeof QuickTourSeverity = EnumQuickTourSeverity.MEDIUM
private attachedTmpl: ElementRef
diff --git a/src/ui/topMenu/topMenuCmp/topMenu.components.ts b/src/ui/topMenu/topMenuCmp/topMenu.components.ts
index 0d464d59a1fe19491977f384eb0a3cb83f61788c..c2ed29672c1caffcaf41257b8c1fa5448f6149bc 100644
--- a/src/ui/topMenu/topMenuCmp/topMenu.components.ts
+++ b/src/ui/topMenu/topMenuCmp/topMenu.components.ts
@@ -13,6 +13,7 @@ import { MatBottomSheet } from "@angular/material/bottom-sheet";
import { CONST, QUICKTOUR_DESC, ARIA_LABELS } from 'common/constants'
import { IQuickTourData } from "src/ui/quickTour/constrants";
import { environment } from 'src/environments/environment'
+import { TypeMatBtnColor, TypeMatBtnStyle } from "src/components/dynamicMaterialBtn/dynamicMaterialBtn.component";
@Component({
selector: 'top-menu-cmp',
@@ -30,8 +31,8 @@ export class TopMenuCmp {
public ARIA_LABELS = ARIA_LABELS
public PINNED_DATASETS_BADGE_DESC = CONST.PINNED_DATASETS_BADGE_DESC
- public matBtnStyle = 'mat-icon-button'
- public matBtnColor = 'primary'
+ public matBtnStyle: TypeMatBtnStyle = 'mat-icon-button'
+ public matBtnColor: TypeMatBtnColor = 'primary'
private _ismobile = false
@Input()
@@ -103,9 +104,9 @@ export class TopMenuCmp {
}
private keyListenerConfigBase = {
- type: 'keydown',
+ type: 'keydown' as const,
stop: true,
- target: 'document',
+ target: 'document' as const,
}
public keyListenerConfig = [{
diff --git a/src/util/priority.ts b/src/util/priority.ts
index 79ef1b043e4d5bb13a99e157995315e05e94b8d5..b12abb243d9c984ea9f9d3ec7dd608d375357e9e 100644
--- a/src/util/priority.ts
+++ b/src/util/priority.ts
@@ -31,7 +31,7 @@ export const DISABLE_PRIORITY_HEADER = 'x-sxplr-disable-priority'
})
export class PriorityHttpInterceptor implements HttpInterceptor{
- private retry = 5
+ private retry = 0
private disablePriority = false
private priorityQueue: Queue[] = []
@@ -73,8 +73,7 @@ export class PriorityHttpInterceptor implements HttpInterceptor{
this.counter --
}),
catchError((err, obs) => {
- if (retry >= 0) {
- retry --
+ if (--retry >= 0) {
return obs
}
return of(new Error(err))
diff --git a/src/viewerModule/nehuba/base.service/base.service.ts b/src/viewerModule/nehuba/base.service/base.service.ts
new file mode 100644
index 0000000000000000000000000000000000000000..0e7020fb0cce143b6b52349550c8e7f20e50245f
--- /dev/null
+++ b/src/viewerModule/nehuba/base.service/base.service.ts
@@ -0,0 +1,99 @@
+import { Injectable } from "@angular/core";
+import { select, Store } from "@ngrx/store";
+import { from, Observable, pipe, UnaryFunction } from "rxjs";
+import { map, shareReplay, switchMap } from "rxjs/operators";
+import { SAPI } from "src/atlasComponents/sapi";
+import { NgSegLayerSpec, SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
+import { atlasSelection } from "src/state";
+import { getParcNgId } from "../config.service";
+
+type NgMapReturnType = {
+ region: SxplrRegion
+ layer: NgSegLayerSpec
+}
+
+@Injectable({
+ providedIn: 'root'
+})
+export class BaseService {
+
+ constructor(private sapi: SAPI, private store$: Store){}
+
+ public selectedATP$ = this.store$.pipe(
+ atlasSelection.fromRootStore.distinctATP(),
+ )
+
+ public selectedATPR$ = this.selectedATP$.pipe(
+ switchMap(({ atlas, template, parcellation }) =>
+ this.store$.pipe(
+ select(atlasSelection.selectors.selectedParcAllRegions),
+ map(regions => ({
+ atlas, template, parcellation, regions
+ })),
+ )
+ )
+ )
+
+ #translatedNgMap = this.selectedATPR$.pipe(
+ switchMap(({ atlas, parcellation, regions, template }) =>
+ from(this.sapi.getTranslatedLabelledNgMap(parcellation, template)).pipe(
+ map(record => {
+
+ const regionmap = new Map<string, SxplrRegion>()
+ for (const r of regions) {
+ regionmap.set(r.name, r)
+ }
+ const returnVal: Record<string, Record<number, NgMapReturnType>> = {}
+ for (const [url, { layer, region }] of Object.entries(record)) {
+
+
+ for (const { name, label } of region) {
+ const actualRegion = regionmap.get(name)
+ if (!actualRegion) {
+ console.warn(`region with name ${name} cannot be found, skipping`)
+ continue
+ }
+ const ngId = getParcNgId(atlas, template, parcellation, actualRegion)
+ if (!returnVal[ngId]) {
+ returnVal[ngId] = {}
+ }
+ returnVal[ngId][label] = {
+ region: actualRegion,
+ layer
+ }
+ }
+ }
+ return returnVal
+ })
+ )
+ )
+ )
+
+
+ public completeNgIdNgSegLayerSpec$: Observable<Record<string, NgSegLayerSpec>> = this.#translatedNgMap.pipe(
+ map(val => {
+ const returnObj: Record<string, NgSegLayerSpec> = {}
+ for (const [ ngId, obj ] of Object.entries(val)) {
+ for (const [_label, layer] of Object.entries(obj)) {
+ returnObj[ngId] = layer.layer
+ }
+ }
+ return returnObj
+ })
+ )
+
+ public completeNgIdLabelRegionMap$: Observable<Record<string, Record<number, SxplrRegion>>> = this.#translatedNgMap.pipe(
+ map(val => {
+ const returnObj: Record<string, Record<number, SxplrRegion>> = {}
+ for (const [ ngId, obj ] of Object.entries(val)) {
+ for (const [label, layer] of Object.entries(obj)) {
+ if (!returnObj[ngId]) {
+ returnObj[ngId] = {}
+ }
+ returnObj[ngId][label] = layer.region
+ }
+ }
+ return returnObj
+ })
+ )
+}
diff --git a/src/viewerModule/nehuba/config.service/index.ts b/src/viewerModule/nehuba/config.service/index.ts
index 1d0fd090589abf2a94209c68e8da7eff87c9b630..c4587bc97f641a10dc5d27261ca6e6a59738813d 100644
--- a/src/viewerModule/nehuba/config.service/index.ts
+++ b/src/viewerModule/nehuba/config.service/index.ts
@@ -7,10 +7,7 @@ export {
NgSegLayerSpec,
} from "./type"
export {
- getParcNgLayers,
- getTmplAuxNgLayer,
- getTmplNgLayer,
- getNgLayersFromVolumesATP,
+
getParcNgId,
getRegionLabelIndex,
getNehubaConfig,
diff --git a/src/viewerModule/nehuba/config.service/type.ts b/src/viewerModule/nehuba/config.service/type.ts
index c8154dd44432e6efe3d7920977f5dd287c557726..ea17a3b69d8668beab9aab95152396671cb0c5a8 100644
--- a/src/viewerModule/nehuba/config.service/type.ts
+++ b/src/viewerModule/nehuba/config.service/type.ts
@@ -96,13 +96,23 @@ interface _NehubaConfig {
export type NehubaConfig = RecursivePartial<_NehubaConfig>
+/**
+ * source MUST contain format, e.g. precomputed://
+ */
export type NgLayerSpec = {
source: string
transform: number[][]
+ info?: {
+ voxel: [number, number, number]
+ real: [number, number, number]
+ }
opacity?: number
visible?: boolean
}
+/**
+ * source MUST contain format, e.g. precomputed://
+ */
export type NgPrecompMeshSpec = {
auxMeshes: {
name: string
@@ -110,6 +120,9 @@ export type NgPrecompMeshSpec = {
}[]
} & NgLayerSpec
+/**
+ * source MUST contain format, e.g. precomputed://
+ */
export type NgSegLayerSpec = {
labelIndicies: number[]
} & NgLayerSpec
diff --git a/src/viewerModule/nehuba/config.service/util.ts b/src/viewerModule/nehuba/config.service/util.ts
index 8f2b0de2dc144f287815a503dd95e35c741e82fb..62cfa5b05d1069f9ee6490e696a193b9ccbb66fd 100644
--- a/src/viewerModule/nehuba/config.service/util.ts
+++ b/src/viewerModule/nehuba/config.service/util.ts
@@ -1,17 +1,12 @@
-import { SapiParcellationModel, SapiSpaceModel, SapiAtlasModel, SapiRegionModel } from 'src/atlasComponents/sapi'
-import { SapiVolumeModel, IDS } from 'src/atlasComponents/sapi'
+import { SxplrAtlas, SxplrTemplate, SxplrParcellation, SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
+import { IDS } from 'src/atlasComponents/sapi/constants'
import { atlasSelection } from 'src/state'
import { MultiDimMap } from 'src/util/fn'
-import { ParcVolumeSpec } from "../store/util"
import {
NehubaConfig,
NgConfig,
RecursivePartial,
- NgLayerSpec,
- NgPrecompMeshSpec,
- NgSegLayerSpec,
} from "./type"
-
// fsaverage uses threesurfer, which, whilst do not use ngId, uses 'left' and 'right' as keys
const fsAverageKeyVal = {
[IDS.PARCELLATION.JBA29]: {
@@ -160,33 +155,7 @@ const BACKCOMAP_KEY_DICT = {
}
-export function getTmplNgLayer(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, spaceVolumes: SapiVolumeModel[]): Record<string, NgLayerSpec>{
- if (!atlas || !tmpl) return {}
- const ngId = `_${MultiDimMap.GetKey(atlas["@id"], tmpl["@id"], "tmplImage")}`
- const tmplImage = spaceVolumes.find(v => "neuroglancer/precomputed" in v.data.detail)
- if (!tmplImage) return {}
- return {
- [ngId]: {
- source: `precomputed://${tmplImage.data.url.replace(/^precomputed:\/\//, '')}`,
- ...tmplImage.data.detail["neuroglancer/precomputed"] as NgLayerSpec
- }
- }
-}
-
-export function getTmplAuxNgLayer(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, spaceVolumes: SapiVolumeModel[]): Record<string, NgPrecompMeshSpec>{
- if (!atlas || !tmpl) return {}
- const ngId = `_${MultiDimMap.GetKey(atlas["@id"], tmpl["@id"], "auxLayer")}`
- const tmplImage = spaceVolumes.find(v => "neuroglancer/precompmesh" in v.data.detail)
- if (!tmplImage) return {}
- return {
- [ngId]: {
- source: `precompmesh://${tmplImage.data.url.replace(/^precompmesh:\/\//, '')}`,
- ...tmplImage.data.detail["neuroglancer/precompmesh"] as NgPrecompMeshSpec
- }
- }
-}
-
-export function getParcNgId(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: SapiParcellationModel, region: SapiRegionModel): string {
+export function getParcNgId(atlas: SxplrAtlas, tmpl: SxplrTemplate, parc: SxplrParcellation, region: SxplrRegion): string {
let laterality: string = "whole brain"
if (region.name.indexOf("left") >= 0) laterality = "left hemisphere"
@@ -195,77 +164,44 @@ export function getParcNgId(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: S
/**
* for JBA29 in big brain, there exist several volumes. (e.g. v1, v2, v5, interpolated, etc)
*/
- if (tmpl['@id'] === IDS.TEMPLATES.BIG_BRAIN && parc['@id'] === IDS.PARCELLATION.JBA29) {
- laterality = region.hasAnnotation.visualizedIn?.['@id']
+ if (tmpl.id === IDS.TEMPLATES.BIG_BRAIN && parc.id === IDS.PARCELLATION.JBA29) {
+ // laterality = region.hasAnnotation.visualizedIn?.['@id']
+ throw new Error(`FIXME figure out what region.hasAnnotation id is`)
}
if (!laterality) {
return null
}
- let ngId = BACKCOMAP_KEY_DICT[atlas["@id"]]?.[tmpl["@id"]]?.[parc["@id"]]?.[laterality]
+ let ngId = BACKCOMAP_KEY_DICT[atlas.id]?.[tmpl.id]?.[parc.id]?.[laterality]
if (!ngId) {
- ngId = `_${MultiDimMap.GetKey(atlas["@id"], tmpl["@id"], parc["@id"], laterality)}`
+ ngId = `_${MultiDimMap.GetKey(atlas.id, tmpl.id, parc.id, laterality)}`
}
return ngId
}
const labelIdxRegex = /siibra_python_ng_precomputed_labelindex:\/\/(.*?)#([0-9]+)$/
-export function getRegionLabelIndex(_atlas: SapiAtlasModel, _tmpl: SapiSpaceModel, _parc: SapiParcellationModel, region: SapiRegionModel): number {
- const overwriteLabelIndex = region.hasAnnotation.inspiredBy.map(({ "@id": id }) => labelIdxRegex.exec(id)).filter(v => !!v)
- if (overwriteLabelIndex.length > 0) {
- const match = overwriteLabelIndex[0]
- const volumeId = match[1]
- const labelIndex = match[2]
- const _labelIndex = Number(labelIndex)
- if (!isNaN(_labelIndex)) return _labelIndex
- }
- const lblIdx = Number(region?.hasAnnotation?.internalIdentifier)
- if (isNaN(lblIdx)) return null
- return lblIdx
-}
-
-export function getParcNgLayers(atlas: SapiAtlasModel, tmpl: SapiSpaceModel, parc: SapiParcellationModel, parcVolumes: { volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec }[]): Record<string, NgSegLayerSpec>{
- const returnVal: Record<string, NgSegLayerSpec> = {}
- for (const parcVol of parcVolumes) {
- if ("spy/volume/neuroglancer/precomputed" !== parcVol.volume['@type']) continue
- const { volume, volumeMetadata } = parcVol
- const { regions } = volumeMetadata
- if (regions.length === 0) {
- console.warn(`parc volume with no associated region`)
- continue
- }
- const ngId = getParcNgId(atlas, tmpl, parc, regions[0].region)
-
- returnVal[ngId] = {
- source: `precomputed://${volume.data.url.replace(/^precomputed:\/\//, '')}`,
- transform: (volume.data.detail["neuroglancer/precomputed"] as any).transform,
- labelIndicies: regions.map(v => v.labelIndex)
- }
- }
- return returnVal
-}
-
-type CongregatedVolume = {
- tmplVolumes: SapiVolumeModel[]
- tmplAuxMeshVolumes: SapiVolumeModel[]
- parcVolumes: { volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec}[]
-}
-
-export const getNgLayersFromVolumesATP = (volumes: CongregatedVolume, ATP: { atlas: SapiAtlasModel, template: SapiSpaceModel, parcellation: SapiParcellationModel }): {
- tmplNgLayers: Record<string, NgLayerSpec>
- tmplAuxNgLayers: Record<string, NgPrecompMeshSpec>
- parcNgLayers: Record<string, NgSegLayerSpec>
-} => {
-
- const { tmplVolumes, tmplAuxMeshVolumes, parcVolumes } = volumes
- const { atlas, template, parcellation } = ATP
- return {
- tmplNgLayers: getTmplNgLayer(atlas, template, tmplVolumes),
- tmplAuxNgLayers: getTmplAuxNgLayer(atlas, template, tmplAuxMeshVolumes),
- parcNgLayers: getParcNgLayers(atlas, template, parcellation, parcVolumes)
- }
+/**
+ * @deprecated
+ * @param _atlas
+ * @param tmpl
+ * @param parc
+ * @param region
+ */
+export function getRegionLabelIndex(_atlas: SxplrAtlas, tmpl: SxplrTemplate, parc: SxplrParcellation, region: SxplrRegion): number {
+ throw new Error(`TODO fix me`)
+ // const overwriteLabelIndex = region.hasAnnotation.inspiredBy.map(({ "@id": id }) => labelIdxRegex.exec(id)).filter(v => !!v)
+ // if (overwriteLabelIndex.length > 0) {
+ // const match = overwriteLabelIndex[0]
+ // const volumeId = match[1]
+ // const labelIndex = match[2]
+ // const _labelIndex = Number(labelIndex)
+ // if (!isNaN(_labelIndex)) return _labelIndex
+ // }
+ // const lblIdx = Number(region?.hasAnnotation?.internalIdentifier)
+ // if (isNaN(lblIdx)) return null
+ // return lblIdx
}
export const defaultNehubaConfig: NehubaConfig = {
@@ -362,7 +298,7 @@ export const spaceMiscInfoMap = new Map([
}],
])
-export function getNehubaConfig(space: SapiSpaceModel): NehubaConfig {
+export function getNehubaConfig(space: SxplrTemplate): NehubaConfig {
const darkTheme = space["@id"] !== "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588"
const { scale } = spaceMiscInfoMap.get(space["@id"]) || { scale: 1 }
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
index c052d1109674137db6e5fa941167c6af2283f21e..973b7d4d39fbe61ce028810783eb7afd1e436406 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.effects.ts
@@ -1,20 +1,38 @@
import { Injectable } from "@angular/core";
import { createEffect } from "@ngrx/effects";
import { select, Store } from "@ngrx/store";
-import { forkJoin, of } from "rxjs";
+import { forkJoin, from, of } from "rxjs";
import { mapTo, switchMap, withLatestFrom, filter, catchError, map, debounceTime, shareReplay, distinctUntilChanged, startWith, pairwise, tap } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiFeatureModel, SapiParcellationModel, SapiSpaceModel, SapiRegionModel } from "src/atlasComponents/sapi";
-import { SapiVOIDataResponse, SapiVolumeModel } from "src/atlasComponents/sapi/type";
+import { NgSegLayerSpec, SxplrAtlas, SxplrParcellation, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
+import { SAPI } from "src/atlasComponents/sapi"
+import {
+ SapiFeatureModel,
+ SapiSpatialFeatureModel,
+} from "src/atlasComponents/sapi/type_v3";
+import { translateV3Entities } from "src/atlasComponents/sapi/translate_v3"
import { atlasAppearance, atlasSelection, userInteraction } from "src/state";
import { arrayEqual } from "src/util/array";
import { EnumColorMapName } from "src/util/colorMaps";
import { getShader } from "src/util/constants";
-import { getNgLayersFromVolumesATP, getRegionLabelIndex } from "../config.service";
-import { ParcVolumeSpec } from "../store/util";
import { PMAP_LAYER_NAME } from "../constants";
+import { QuickHash } from "src/util/fn";
+import { BaseService } from "../base.service/base.service";
+import { getParcNgId } from "../config.service";
@Injectable()
export class LayerCtrlEffects {
+ static TransformVolumeModel(volumeModel: SapiSpatialFeatureModel['volume']): atlasAppearance.NgLayerCustomLayer[] {
+ /**
+ * TODO implement
+ */
+ throw new Error(`IMPLEMENT ME`)
+ for (const volumeFormat in volumeModel.providedVolumes) {
+
+ }
+
+ return []
+ }
+
onRegionSelectClearPmapLayer = createEffect(() => this.store.pipe(
select(atlasSelection.selectors.selectedRegions),
distinctUntilChanged(
@@ -67,44 +85,26 @@ export class LayerCtrlEffects {
onATP$ = this.store.pipe(
atlasSelection.fromRootStore.distinctATP(),
- map(val => val as { atlas: SapiAtlasModel, parcellation: SapiParcellationModel, template: SapiSpaceModel }),
+ map(val => val as { atlas: SxplrAtlas, parcellation: SxplrParcellation, template: SxplrTemplate }),
)
onShownFeature = createEffect(() => this.store.pipe(
select(userInteraction.selectors.selectedFeature),
startWith(null as SapiFeatureModel),
- pairwise(),
+ pairwise<SapiFeatureModel>(),
map(([ prev, curr ]) => {
const removeLayers: atlasAppearance.NgLayerCustomLayer[] = []
const addLayers: atlasAppearance.NgLayerCustomLayer[] = []
- if (prev?.["@type"] === "siibra/features/voi") {
+ if (prev?.["@type"].includes("feature/volume_of_interest")) {
+ const prevVoi = prev as SapiSpatialFeatureModel
removeLayers.push(
- ...(prev as SapiVOIDataResponse).volumes.map(v => {
- return {
- id: v.metadata.fullName,
- clType: "customlayer/nglayer",
- source: v.data.url,
- transform: v.data.detail['neuroglancer/precomputed']['transform'],
- opacity: 1.0,
- visible: true,
- shader: v.data.detail['neuroglancer/precomputed']['shader'] || getShader()
- } as atlasAppearance.NgLayerCustomLayer
- })
+ ...LayerCtrlEffects.TransformVolumeModel(prevVoi.volume)
)
}
- if (curr?.["@type"] === "siibra/features/voi") {
+ if (curr?.["@type"].includes("feature/volume_of_interest")) {
+ const currVoi = curr as SapiSpatialFeatureModel
addLayers.push(
- ...(curr as SapiVOIDataResponse).volumes.map(v => {
- return {
- id: v.metadata.fullName,
- clType: "customlayer/nglayer",
- source: `precomputed://${v.data.url}`,
- transform: v.data.detail['neuroglancer/precomputed']['transform'],
- opacity: v.data.detail['neuroglancer/precomputed']['opacity'] || 1.0,
- visible: true,
- shader: v.data.detail['neuroglancer/precomputed']['shader'] || getShader()
- } as atlasAppearance.NgLayerCustomLayer
- })
+ ...LayerCtrlEffects.TransformVolumeModel(currVoi.volume)
)
}
return { removeLayers, addLayers }
@@ -143,155 +143,47 @@ export class LayerCtrlEffects {
)
))
- private getNgLayers(atlas: SapiAtlasModel, parcellation: SapiParcellationModel, template: SapiSpaceModel){
-
- if (!!parcellation && !template) {
- throw new Error(`parcellation defined, but template not defined!`)
- }
-
- /**
- * some labelled maps (such as julich brain in big brain) do not have the volumes defined on the parcellation level.
- * While we have the URLs of these volumes (the method we use is also kind of hacky), and in theory, we could construct a volume object directly
- * It is probably better to fetch the correct volume object to begin with
- */
- const parcVolumes$ = !parcellation
- ? of([] as {volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec}[])
- : forkJoin([
- this.sapi.getParcellation(atlas["@id"], parcellation["@id"]).getRegions(template["@id"]).pipe(
- map(regions => {
-
- const volumeIdToRegionMap = new Map<string, {
- labelIndex: number
- region: SapiRegionModel
- }[]>()
-
- for (const r of regions) {
- const volumeId = r?.hasAnnotation?.visualizedIn?.["@id"]
- if (!volumeId) continue
-
- const labelIndex = getRegionLabelIndex(atlas, template, parcellation, r)
- if (!labelIndex) continue
-
- if (!volumeIdToRegionMap.has(volumeId)) {
- volumeIdToRegionMap.set(volumeId, [])
- }
- volumeIdToRegionMap.get(volumeId).push({
- labelIndex,
- region: r
- })
+ onATPDebounceNgLayers$ = this.onATP$.pipe(
+ debounceTime(16),
+ switchMap(({ atlas, template, parcellation }) =>
+ forkJoin({
+ tmplNgLayers: this.sapi.getVoxelTemplateImage(template).pipe(
+ map(templateImages => {
+ const returnObj = {}
+ for (const img of templateImages) {
+ returnObj[QuickHash.GetHash(img.source)] = img
}
- return volumeIdToRegionMap
+ return returnObj
})
),
- this.sapi.getParcellation(atlas["@id"], parcellation["@id"]).getVolumes()
- ]).pipe(
- switchMap(([ volumeIdToRegionMap, volumes ]) => {
- const missingVolumeIds = Array.from(volumeIdToRegionMap.keys()).filter(id => volumes.map(v => v["@id"]).indexOf(id) < 0)
-
- const volumesFromParc: {volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec}[] = volumes.map(
- volume => {
- const found = volumeIdToRegionMap.get(volume["@id"])
- if (!found) return null
-
- try {
-
- const volumeMetadata: ParcVolumeSpec = {
- regions: found,
- parcellation,
- volumeSrc: volume.data.url
- }
- return {
- volume,
- volumeMetadata,
- }
- } catch (e) {
- console.error(e)
- return null
- }
+ tmplAuxNgLayers: this.sapi.getVoxelAuxMesh(template).pipe(
+ map(auxMeshes => {
+ const returnObj = {}
+ for (const img of auxMeshes) {
+ returnObj[QuickHash.GetHash(`${img.source}_auxMesh`)] = img
}
- ).filter(v => v?.volumeMetadata?.regions)
-
- if (missingVolumeIds.length === 0) return of([...volumesFromParc])
- return forkJoin(
- missingVolumeIds.map(missingId => {
- if (!volumeIdToRegionMap.has(missingId)) {
- console.warn(`volumeIdToRegionMap does not have volume with id ${missingId}`)
- return of(null as SapiVolumeModel)
- }
- const { region } = volumeIdToRegionMap.get(missingId)[0]
- return this.sapi.getRegion(atlas["@id"], parcellation["@id"], region.name).getVolumeInstance(missingId).pipe(
- catchError((err, obs) => of(null as SapiVolumeModel))
- )
- })
- ).pipe(
- map((missingVolumes: SapiVolumeModel[]) => {
-
- const volumesFromRegion: { volume: SapiVolumeModel, volumeMetadata: ParcVolumeSpec }[] = missingVolumes.map(
- volume => {
- if (!volume || !volumeIdToRegionMap.has(volume['@id'])) {
- return null
- }
-
- try {
-
- const found = volumeIdToRegionMap.get(volume['@id'])
- const volumeMetadata: ParcVolumeSpec = {
- regions: found,
- parcellation,
- volumeSrc: volume.data.url
- }
- return {
- volume,
- volumeMetadata
- }
- } catch (e) {
- console.error(`volume from region error`, e)
- return null
- }
- }
- ).filter(
- v => !!v
- )
-
- return [
- ...volumesFromParc,
- ...volumesFromRegion
- ]
- })
- )
- })
- )
-
- const spaceVols$ = !!template
- ? this.sapi.getSpace(atlas["@id"], template["@id"]).getVolumes().pipe(
- shareReplay(1),
- )
- : of([] as SapiVolumeModel[])
-
- return forkJoin({
- tmplVolumes: spaceVols$.pipe(
- map(
- volumes => volumes.filter(vol => "neuroglancer/precomputed" in vol.data.detail)
- ),
- ),
- tmplAuxMeshVolumes: spaceVols$.pipe(
- map(
- volumes => volumes.filter(vol => "neuroglancer/precompmesh" in vol.data.detail)
+ return returnObj
+ })
),
- ),
- parcVolumes: parcVolumes$.pipe(
- )
- })
- }
-
- onATPDebounceNgLayers$ = this.onATP$.pipe(
- debounceTime(16),
- switchMap(({ atlas, parcellation, template }) => {
- return this.getNgLayers(atlas, parcellation, template).pipe(
- map(volumes => getNgLayersFromVolumesATP(volumes, { atlas, parcellation, template }))
- )
- }),
- shareReplay(1)
+ parcNgLayers: from(this.sapi.getTranslatedLabelledNgMap(parcellation, template)).pipe(
+ map(val => {
+ const returnVal: Record<string, NgSegLayerSpec> = {}
+ for (const [ url, { layer, region } ] of Object.entries(val)) {
+ const { name } = region[0]
+ const ngId = getParcNgId(atlas, template, parcellation, {
+ id: '',
+ name,
+ parentIds: []
+ })
+ returnVal[ngId] = layer
+ continue
+ }
+ return returnVal
+ })
+ )
+ })
+ ),
+ shareReplay(1),
)
onATPDebounceAddBaseLayers$ = createEffect(() => this.onATPDebounceNgLayers$.pipe(
@@ -322,5 +214,9 @@ export class LayerCtrlEffects {
})
))
- constructor(private store: Store<any>,private sapi: SAPI){}
+ constructor(
+ private store: Store<any>,
+ private sapi: SAPI,
+ private baseService: BaseService,
+ ){}
}
\ No newline at end of file
diff --git a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
index da9855ecb93b0344c2239776590f0625dd20117a..0281479fbbc03b5f58bacd71a7ce0415009e75f5 100644
--- a/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
+++ b/src/viewerModule/nehuba/layerCtrl.service/layerCtrl.service.ts
@@ -1,21 +1,20 @@
import { Injectable, OnDestroy } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { combineLatest, merge, Observable, Subject, Subscription } from "rxjs";
+import { combineLatest, from, merge, Observable, Subject, Subscription } from "rxjs";
import { debounceTime, distinctUntilChanged, filter, map, pairwise, shareReplay, startWith, switchMap, withLatestFrom } from "rxjs/operators";
import { IColorMap, INgLayerCtrl, TNgLayerCtrl } from "./layerCtrl.util";
-import { SAPIRegion } from "src/atlasComponents/sapi/core";
import { getParcNgId } from "../config.service"
-import { getRegionLabelIndex } from "../config.service/util";
import { annotation, atlasAppearance, atlasSelection } from "src/state";
import { serializeSegment } from "../util";
import { LayerCtrlEffects } from "./layerCtrl.effects";
import { arrayEqual } from "src/util/array";
import { ColorMapCustomLayer } from "src/state/atlasAppearance";
-import { SapiRegionModel } from "src/atlasComponents/sapi";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
import { AnnotationLayer } from "src/atlasComponents/annotations";
import { PMAP_LAYER_NAME } from "../constants"
-import { EnumColorMapName, mapKeyColorMap } from "src/util/colorMaps";
import { getShader } from "src/util/constants";
+import { SAPI } from "src/atlasComponents/sapi";
+import { BaseService } from "../base.service/base.service";
export const BACKUP_COLOR = {
red: 255,
@@ -36,34 +35,24 @@ export class NehubaLayerControlService implements OnDestroy{
private defaultNgLayers$ = this.layerEffects.onATPDebounceNgLayers$
- private selectedATP$ = this.store$.pipe(
- atlasSelection.fromRootStore.distinctATP(),
- shareReplay(1),
- )
+ private selectedATP$ = this.baseService.selectedATP$
- public selectedATPR$ = this.selectedATP$.pipe(
- switchMap(({ atlas, template, parcellation }) =>
- this.store$.pipe(
- select(atlasSelection.selectors.selectedParcAllRegions),
- map(regions => ({
- atlas, template, parcellation, regions
- })),
- shareReplay(1)
- )
- )
- )
+ public selectedATPR$ = this.baseService.selectedATPR$
private customLayers$ = this.store$.pipe(
select(atlasAppearance.selectors.customLayers),
distinctUntilChanged(arrayEqual((o, n) => o.id === n.id)),
shareReplay(1)
)
+
+ public completeNgIdLabelRegionMap$ = this.baseService.completeNgIdLabelRegionMap$
+
private activeColorMap$ = combineLatest([
combineLatest([
- this.selectedATPR$,
+ this.completeNgIdLabelRegionMap$,
this.customLayers$,
]).pipe(
- map(([{ atlas, parcellation, regions, template }, layers]) => {
+ map(([record, layers]) => {
const returnVal: IColorMap = {}
const cmCustomLayers = layers.filter(l => l.clType === "customlayer/colormap") as ColorMapCustomLayer[]
@@ -85,25 +74,19 @@ export class NehubaLayerControlService implements OnDestroy{
set: () => {
throw new Error(`cannot set`)
},
- get: (r: SapiRegionModel) => SAPIRegion.GetDisplayColor(r)
+ get: (r: SxplrRegion) => r.color
}
})()
- for (const r of regions) {
-
- if (!r.hasAnnotation) continue
- if (!r.hasAnnotation.visualizedIn) continue
-
- const ngId = getParcNgId(atlas, template, parcellation, r)
- const labelIndex = getRegionLabelIndex(atlas, template, parcellation, r)
- if (!labelIndex) continue
-
- const [ red, green, blue ] = useCm.get(r)
-
- if (!returnVal[ngId]) {
- returnVal[ngId] = {}
+ for (const [ngId, labelRecord] of Object.entries(record)) {
+ for (const [label, region] of Object.entries(labelRecord)) {
+ if (!region.color) continue
+ const [ red, green, blue ] = useCm.get(region)
+ if (!returnVal[ngId]) {
+ returnVal[ngId] = {}
+ }
+ returnVal[ngId][label] = { red, green, blue }
}
- returnVal[ngId][labelIndex] = { red, green, blue }
}
return returnVal
})
@@ -140,6 +123,7 @@ export class NehubaLayerControlService implements OnDestroy{
constructor(
private store$: Store<any>,
private layerEffects: LayerCtrlEffects,
+ private baseService: BaseService,
){
this.sub.push(
@@ -248,8 +232,8 @@ export class NehubaLayerControlService implements OnDestroy{
map(layers => layers.filter(l => l.clType === "customlayer/nglayer").length > 0),
),
]).pipe(
- withLatestFrom(this.selectedATPR$),
- map(([[ selectedRegions, customMapExists, nonmixableLayerExists ], { atlas, parcellation, template, regions }]) => {
+ withLatestFrom(this.completeNgIdLabelRegionMap$),
+ map(([[ selectedRegions, customMapExists, nonmixableLayerExists ], completeNgIdLabelRegion]) => {
/**
* if non mixable layer exist (e.g. pmap)
* and no custom color map exist
@@ -263,15 +247,17 @@ export class NehubaLayerControlService implements OnDestroy{
* if custom map exists, roi is all regions
* otherwise, roi is only selectedRegions
*/
- const roi = customMapExists ? regions : selectedRegions
-
- const roiIndexSet = new Set<string>(
- roi.map(r => {
- const ngId = getParcNgId(atlas, template, parcellation, r)
- const label = getRegionLabelIndex(atlas, template, parcellation, r)
- return ngId && label && serializeSegment(ngId, label)
- }).filter(v => !!v)
- )
+ const selectedRegionNameSet = new Set(selectedRegions.map(r => r.name))
+ const roiIndexSet = new Set<string>()
+ for (const ngId in completeNgIdLabelRegion) {
+ for (const label in completeNgIdLabelRegion[ngId]) {
+ const val = completeNgIdLabelRegion[ngId][label]
+ if (!customMapExists && !selectedRegionNameSet.has(val.name)) {
+ continue
+ }
+ roiIndexSet.add(serializeSegment(ngId, label))
+ }
+ }
if (roiIndexSet.size > 0) {
return [...roiIndexSet]
} else {
diff --git a/src/viewerModule/nehuba/mesh.service/mesh.service.ts b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
index d372ce460746d01c5cf560518e1532f38616b882..4ad0dbf18a1f6a88d84a080c89efafa0c443fa1f 100644
--- a/src/viewerModule/nehuba/mesh.service/mesh.service.ts
+++ b/src/viewerModule/nehuba/mesh.service/mesh.service.ts
@@ -1,13 +1,13 @@
import { Injectable, OnDestroy } from "@angular/core";
import { select, Store } from "@ngrx/store";
import { combineLatest, merge, Observable, of } from "rxjs";
-import { map, switchMap } from "rxjs/operators";
+import { map, switchMap, tap } from "rxjs/operators";
import { IMeshesToLoad } from '../constants'
import { selectorAuxMeshes } from "../store";
import { LayerCtrlEffects } from "../layerCtrl.service/layerCtrl.effects";
import { atlasSelection } from "src/state";
import { Tree } from "src/components/flatHierarchy/treeView/treeControl"
-import { getParcNgId, getRegionLabelIndex } from "../config.service";
+import { BaseService } from "../base.service/base.service";
/**
* control mesh loading etc
@@ -21,6 +21,7 @@ export class NehubaMeshService implements OnDestroy {
constructor(
private store$: Store<any>,
private effect: LayerCtrlEffects,
+ private baseService: BaseService,
){
}
@@ -30,66 +31,44 @@ export class NehubaMeshService implements OnDestroy {
public auxMeshes$ = this.effect.onATPDebounceNgLayers$.pipe(
- map(({ tmplAuxNgLayers }) => tmplAuxNgLayers)
+ map(({ tmplAuxNgLayers }) => tmplAuxNgLayers),
+ tap(v => console.log('mesh.service', v))
)
public loadMeshes$: Observable<IMeshesToLoad> = merge(
combineLatest([
- this.store$.pipe(
- atlasSelection.fromRootStore.distinctATP(),
- ),
+ this.baseService.completeNgIdLabelRegionMap$,
this.store$.pipe(
select(atlasSelection.selectors.selectedParcAllRegions),
),
this.store$.pipe(
select(atlasSelection.selectors.selectedRegions),
- )
+ ),
+
]).pipe(
- switchMap(([{ atlas, template, parcellation }, regions, selectedRegions]) => {
+ switchMap(([record, regions, selectedRegions]) => {
const ngIdRecord: Record<string, number[]> = {}
const tree = new Tree(
regions,
- (c, p) => (c.hasParent || []).some(_p => _p["@id"] === p["@id"])
+ (c, p) => (c.parentIds.some( id => p.id === id))
)
+
+ const selectedRegionFlag = selectedRegions.length > 0
+ const selectedRegionNameSet = new Set(selectedRegions.map(r => r.name))
- for (const r of regions) {
- const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
- if (!regionLabelIndex) {
- continue
- }
- if (
- tree.someAncestor(r, anc => !!getRegionLabelIndex(atlas, template, parcellation, anc))
- ) {
- continue
- }
- const ngId = getParcNgId(atlas, template, parcellation, r)
- if (!ngIdRecord[ngId]) {
- ngIdRecord[ngId] = []
- }
- ngIdRecord[ngId].push(regionLabelIndex)
- }
-
- if (selectedRegions.length > 0) {
- /**
- * If regions are selected, reset the meshes
- */
- for (const key in ngIdRecord) {
- ngIdRecord[key] = []
- }
-
- /**
- * only show selected region
- */
- for (const r of selectedRegions) {
- const ngId = getParcNgId(atlas, template, parcellation, r)
- const regionLabelIndex = getRegionLabelIndex( atlas, template, parcellation, r )
+ for (const [ngId, labelToRegion] of Object.entries(record)) {
+ for (const [label, region] of Object.entries(labelToRegion)) {
+ if (selectedRegionFlag && !selectedRegionNameSet.has(region.name)) {
+ continue
+ }
if (!ngIdRecord[ngId]) {
ngIdRecord[ngId] = []
}
- ngIdRecord[ngId].push(regionLabelIndex)
+ ngIdRecord[ngId].push(Number(label))
}
}
+
const arr: IMeshesToLoad[] = []
for (const ngId in ngIdRecord) {
diff --git a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
index 465d3144979c3e6997e4dbefcb12f6009ab9ea21..10d7ba68683f16c5a09b0df46a954380480fe645 100644
--- a/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewer/nehubaViewer.component.ts
@@ -147,7 +147,6 @@ export class NehubaViewerUnit implements OnDestroy {
if (this.nehubaViewer$) {
this.nehubaViewer$.next(this)
}
-
getImportNehubaPr()
.then(() => {
this.nehubaLoaded = true
diff --git a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
index e570bcd5f01ea7b0ef4d19556773aa11285c4e4d..10d71071e03fb0abada6f5ded62e1740171daf29 100644
--- a/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerGlue/nehubaViewerGlue.component.ts
@@ -6,7 +6,7 @@ import { IViewer, TViewerEvent } from "../../viewer.interface";
import { NehubaMeshService } from "../mesh.service";
import { NehubaLayerControlService, SET_COLORMAP_OBS, SET_LAYER_VISIBILITY } from "../layerCtrl.service";
import { NG_LAYER_CONTROL, SET_SEGMENT_VISIBILITY } from "../layerCtrl.service/layerCtrl.util";
-import { SapiRegionModel } from "src/atlasComponents/sapi";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
import { NehubaConfig } from "../config.service";
import { SET_MESHES_TO_LOAD } from "../constants";
import { atlasSelection, userInteraction } from "src/state";
@@ -54,7 +54,7 @@ import { atlasSelection, userInteraction } from "src/state";
export class NehubaGlueCmp implements IViewer<'nehuba'>, OnDestroy {
- private onhoverSegments: SapiRegionModel[] = []
+ private onhoverSegments: SxplrRegion[] = []
private onDestroyCb: (() => void)[] = []
public nehubaConfig: NehubaConfig
diff --git a/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerContainer.component.ts b/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerContainer.component.ts
index f4ad7e41191010356daec181ad362ce655cc661c..f3c063b51ffb646e2eb9a9be701b3670ee00585d 100644
--- a/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerContainer.component.ts
+++ b/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerContainer.component.ts
@@ -1,13 +1,12 @@
import { AfterViewInit, Component, EventEmitter, OnDestroy, Output, ViewChild } from "@angular/core";
-import { concat, Observable, of, Subscription } from "rxjs";
-import { map, withLatestFrom } from "rxjs/operators";
-import { SapiRegionModel } from "src/atlasComponents/sapi";
+import { concat, of, Subscription } from "rxjs";
+import { withLatestFrom } from "rxjs/operators";
import { EnumViewerEvt, TViewerEvent } from "../../viewer.interface";
import { NehubaLayerControlService } from "../layerCtrl.service";
import { NehubaViewerContainerDirective } from "./nehubaViewerInterface.directive";
-import { getParcNgId, getRegionLabelIndex } from "../config.service";
import { Store } from "@ngrx/store";
import { atlasSelection } from "src/state";
+import { SAPI } from "src/atlasComponents/sapi";
@Component({
selector: `sxplr-nehuba-viewer-container`,
@@ -47,26 +46,29 @@ export class NehubaViewerContainer implements AfterViewInit, OnDestroy {
}),
concat(
- of(null),
+ of('start' as const),
mouseOverSegments
).pipe(
withLatestFrom(
- this.multiNgIdsRegionsLabelMap$
+ this.layerCtrlService.completeNgIdLabelRegionMap$
)
).subscribe(([seg, multiNgIdsRegionsLabelIndexMap]) => {
+ const isStart = seg === "start"
this.viewerEvent.emit({
type: EnumViewerEvt.VIEWER_CTX,
data: {
viewerType: 'nehuba',
payload: {
- nehuba: seg && seg.map(v => {
+ nehuba: isStart
+ ? []
+ : seg.map(v => {
return {
layerName: v.layer.name,
labelIndices: [ Number(v.segmentId) ],
regions: (() => {
- const map = multiNgIdsRegionsLabelIndexMap.get(v.layer.name)
- if (!map) return []
- return [map.get(Number(v.segmentId))]
+ const record = multiNgIdsRegionsLabelIndexMap[v.layer.name] || {}
+ if (!record) return []
+ return [record[Number(v.segmentId)]]
})()
}
})
@@ -117,23 +119,6 @@ export class NehubaViewerContainer implements AfterViewInit, OnDestroy {
@ViewChild(NehubaViewerContainerDirective, { static: true })
private nehubaContainerDirective: NehubaViewerContainerDirective
- private multiNgIdsRegionsLabelMap$: Observable<Map<string, Map<number, SapiRegionModel>>> = this.layerCtrlService.selectedATPR$.pipe(
- map(( { atlas, parcellation, template, regions } ) => {
-
- const retMap = new Map<string, Map<number, SapiRegionModel>>()
- for (const r of regions) {
- const ngId = getParcNgId(atlas, template, parcellation, r)
- if (!ngId) continue
- if (!retMap.has(ngId)) {
- retMap.set(ngId, new Map())
- }
- const labelIndex = getRegionLabelIndex(atlas, template, parcellation, r)
- if (!labelIndex) continue
- retMap.get(ngId).set(labelIndex, r)
- }
- return retMap
- })
- )
private subscriptions: Subscription[] = []
}
diff --git a/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerInterface.directive.ts b/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerInterface.directive.ts
index 0b7f185aa8d4530a561d779f45274a9a3b13cff7..baa371a0ac122708ea997445cfe0ddf49644f2ab 100644
--- a/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerInterface.directive.ts
+++ b/src/viewerModule/nehuba/nehubaViewerInterface/nehubaViewerInterface.directive.ts
@@ -2,14 +2,14 @@ import { Directive, ViewContainerRef, ComponentRef, OnDestroy, Output, EventEmit
import { NehubaViewerUnit } from "../nehubaViewer/nehubaViewer.component";
import { Store, select } from "@ngrx/store";
import { Subscription, Observable, asyncScheduler, combineLatest } from "rxjs";
-import { distinctUntilChanged, filter, debounceTime, scan, map, throttleTime, switchMap, take } from "rxjs/operators";
+import { distinctUntilChanged, filter, debounceTime, scan, map, throttleTime, switchMap, take, tap } from "rxjs/operators";
import { serializeSegment } from "../util";
import { LoggingService } from "src/logging";
import { arrayOfPrimitiveEqual } from 'src/util/fn'
import { INavObj, NehubaNavigationService } from "../navigation.service";
import { NehubaConfig, defaultNehubaConfig, getNehubaConfig } from "../config.service";
import { atlasAppearance, atlasSelection, userPreference } from "src/state";
-import { SapiAtlasModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SxplrAtlas, SxplrParcellation, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
import { NgLayerCustomLayer } from "src/state/atlasAppearance";
import { arrayEqual } from "src/util/array";
import { cvtNavigationObjToNehubaConfig } from "../config.service/util";
@@ -175,7 +175,7 @@ export class NehubaViewerContainerDirective implements OnDestroy{
this.store$.pipe(
atlasSelection.fromRootStore.distinctATP(),
debounceTime(16),
- switchMap((ATP: { atlas: SapiAtlasModel, parcellation: SapiParcellationModel, template: SapiSpaceModel }) => this.store$.pipe(
+ switchMap((ATP: { atlas: SxplrAtlas, parcellation: SxplrParcellation, template: SxplrTemplate }) => this.store$.pipe(
select(atlasAppearance.selectors.customLayers),
debounceTime(16),
map(cl => cl.filter(l => l.clType === "baselayer/nglayer") as NgLayerCustomLayer[]),
diff --git a/src/viewerModule/nehuba/statusCard/statusCard.component.ts b/src/viewerModule/nehuba/statusCard/statusCard.component.ts
index c658f2c65368d9b8c7187f4742d5a4805880206e..50fa2c0faddda60c3c47e14cccaee9b760659995 100644
--- a/src/viewerModule/nehuba/statusCard/statusCard.component.ts
+++ b/src/viewerModule/nehuba/statusCard/statusCard.component.ts
@@ -21,7 +21,7 @@ import { NEHUBA_INSTANCE_INJTKN } from '../util'
import { IQuickTourData } from "src/ui/quickTour/constrants";
import { actions } from "src/state/atlasSelection";
import { atlasSelection } from "src/state";
-import { SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
import { getNehubaConfig } from "../config.service";
@Component({
@@ -45,7 +45,7 @@ export class StatusCardComponent implements OnInit, OnChanges{
public arialabel = ARIA_LABELS.STATUS_PANEL
public showFull = false
- private selectedTemplate: SapiSpaceModel
+ private selectedTemplate: SxplrTemplate
private currentNavigation: any
private subscriptions: Subscription[] = []
diff --git a/src/viewerModule/nehuba/types.ts b/src/viewerModule/nehuba/types.ts
index 6fd0dddab5fce72039cd81a92ac3b377c294f8fe..f61a467b37e8427867aab0d938cc6f69df7de3dc 100644
--- a/src/viewerModule/nehuba/types.ts
+++ b/src/viewerModule/nehuba/types.ts
@@ -1,4 +1,4 @@
-import { SapiRegionModel } from "src/atlasComponents/sapi";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr";
import { INavObj } from "./navigation.service";
export type TNehubaContextInfo = {
@@ -10,6 +10,6 @@ export type TNehubaContextInfo = {
nehuba: {
layerName: string
labelIndices: number[]
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
}[]
}
diff --git a/src/viewerModule/nehuba/viewerCtrl/perspectiveViewSlider/perspectiveViewSlider.component.ts b/src/viewerModule/nehuba/viewerCtrl/perspectiveViewSlider/perspectiveViewSlider.component.ts
index 56a3621904da2da3743b66e6b415cca5c2d70724..721a27550bc28c11c65c3219fe181a03d20790af 100644
--- a/src/viewerModule/nehuba/viewerCtrl/perspectiveViewSlider/perspectiveViewSlider.component.ts
+++ b/src/viewerModule/nehuba/viewerCtrl/perspectiveViewSlider/perspectiveViewSlider.component.ts
@@ -1,9 +1,10 @@
import { Component, OnDestroy, Inject, ViewChild, ChangeDetectionStrategy } from "@angular/core";
import { FormControl } from "@angular/forms";
import { select, Store } from "@ngrx/store";
-import { combineLatest, concat, NEVER, Observable, of, Subject, Subscription } from "rxjs";
+import { combineLatest, concat, forkJoin, NEVER, Observable, of, Subject, Subscription, throwError } from "rxjs";
import { switchMap, distinctUntilChanged, map, debounceTime, shareReplay, take, withLatestFrom } from "rxjs/operators";
-import { SAPI, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SAPI } from "src/atlasComponents/sapi";
+import { SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr"
import { fromRootStore } from "src/state/atlasSelection";
import { selectedTemplate } from "src/state/atlasSelection/selectors";
import { panelMode, panelOrder } from "src/state/userInterface/selectors";
@@ -147,9 +148,21 @@ export class PerspectiveViewSlider implements OnDestroy {
private currentTemplateSize$ = this.store$.pipe(
fromRootStore.distinctATP(),
- switchMap(({ atlas, template }) =>
- atlas && template
- ? this.sapi.getSpace(atlas['@id'], template['@id']).getTemplateSize()
+ switchMap(({ template }) =>
+ template
+ ? this.sapi.getVoxelTemplateImage(template).pipe(
+ map(defaultImage => {
+ if (defaultImage.length == 0) {
+ const errMsg = `template ${template.name} has no ng volume`
+ throw new Error(errMsg)
+ }
+ const img = defaultImage[0]
+ return {
+ ...img.info || {},
+ transform: img.transform
+ }
+ })
+ )
: NEVER),
)
@@ -394,8 +407,8 @@ const viewToSuffix = {
[EnumClassicalView.CORONAL]: 'coronal',
}
-function getScreenshotUrl(space: SapiSpaceModel, requestedView: EnumClassicalView): string {
- const prefix = spaceIdToPrefix[space?.['@id']]
+function getScreenshotUrl(space: SxplrTemplate, requestedView: EnumClassicalView): string {
+ const prefix = spaceIdToPrefix[space?.id]
if (!prefix) return null
const suffix = viewToSuffix[requestedView]
if (!suffix) return null
diff --git a/src/viewerModule/threeSurfer/store/actions.ts b/src/viewerModule/threeSurfer/store/actions.ts
index 613fcbbfc7b943dfc412717987314a2b34fb5fb6..90d736a27f282918ed629ea59be789301f91f6c2 100644
--- a/src/viewerModule/threeSurfer/store/actions.ts
+++ b/src/viewerModule/threeSurfer/store/actions.ts
@@ -1,9 +1,9 @@
import { createAction, props } from "@ngrx/store";
import { nameSpace } from "./const"
-export const selectVolumeById = createAction(
- `${nameSpace} selectVolumeById`,
+export const selectSurfaceVariant = createAction(
+ `${nameSpace} selectSurfaceVariant`,
props<{
- id: string
+ variant: string
}>()
)
diff --git a/src/viewerModule/threeSurfer/store/effects.ts b/src/viewerModule/threeSurfer/store/effects.ts
index 4fa4c9f190783d18fac844ec69019352bfb6c855..cfdf2bfec67eccfec3f5d3de1e5f65c184a0bd0f 100644
--- a/src/viewerModule/threeSurfer/store/effects.ts
+++ b/src/viewerModule/threeSurfer/store/effects.ts
@@ -3,7 +3,8 @@ import { createEffect } from "@ngrx/effects";
import { select, Store } from "@ngrx/store";
import { EMPTY, forkJoin, merge, Observable, of, pipe, throwError } from "rxjs";
import { debounceTime, map, switchMap, withLatestFrom, filter, shareReplay, distinctUntilChanged } from "rxjs/operators";
-import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi";
+import { SAPI } from "src/atlasComponents/sapi";
+import { SxplrAtlas, SxplrParcellation, SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr"
import { atlasAppearance, atlasSelection } from "src/state";
import { ThreeSurferCustomLabelLayer, ThreeSurferCustomLayer } from "src/state/atlasAppearance/const";
import * as selectors from "./selectors"
@@ -13,25 +14,14 @@ export const fromATP = {
getThreeSurfaces: (sapi: SAPI) => {
return pipe(
filter(
- ({ atlas, template, parcellation }: {atlas: SapiAtlasModel, template: SapiSpaceModel, parcellation: SapiParcellationModel}) => !!atlas && !!template && !!parcellation
+ ({ atlas, template, parcellation }: {atlas: SxplrAtlas, template: SxplrTemplate, parcellation: SxplrParcellation}) => !!atlas && !!template && !!parcellation
),
- switchMap(({ atlas, template, parcellation }: {atlas: SapiAtlasModel, template: SapiSpaceModel, parcellation: SapiParcellationModel}) =>
- forkJoin({
- surfaces: sapi.getSpace(atlas["@id"], template["@id"]).getVolumes().pipe(
- map(
- volumes => volumes.filter(vol => vol.data.type === "gii")
- )
- ),
- labels: sapi.getParcellation(atlas["@id"], parcellation["@id"]).getVolumes().pipe(
- map(
- volumes => volumes.filter(vol =>
- vol.data.type === "gii-label" &&
- vol.data.space["@id"] === template["@id"]
- )
- )
- )
+ switchMap(({ template, parcellation }: {atlas: SxplrAtlas, template: SxplrTemplate, parcellation: SxplrParcellation}) => {
+ return forkJoin({
+ surfaces: sapi.getSurfaceTemplateImage(template),
+ labels: sapi.getTranslatedLabelledThreeMap(parcellation, template),
})
- )
+ })
)
}
}
@@ -44,7 +34,7 @@ export class ThreeSurferEffects {
)
private selectedSurfaceId$ = this.store.pipe(
- select(selectors.getSelectedVolumeId),
+ select(selectors.getSelectedSurfaceVariant),
distinctUntilChanged()
)
@@ -81,18 +71,19 @@ export class ThreeSurferEffects {
onATPDebounceHasSurfaceVolumes = createEffect(() => this.onATPDebounceThreeSurferLayers$.pipe(
switchMap(({ surfaces }) => {
- const defaultSurface = surfaces.find(s => s.metadata.shortName === "pial") || surfaces[0]
+
+ const defaultSurface = surfaces.find(s => s.variant === "pial") || surfaces[0]
if (!defaultSurface) return EMPTY
return of(
- actions.selectVolumeById({
- id: defaultSurface["@id"]
+ actions.selectSurfaceVariant({
+ variant: defaultSurface.variant
})
)
})
))
onSurfaceSelected = createEffect(() => this.selectedSurfaceId$.pipe(
- switchMap(id => this.onATPDebounceThreeSurferLayers$.pipe(
+ switchMap(variant => this.onATPDebounceThreeSurferLayers$.pipe(
switchMap(({ surfaces }) => {
if (surfaces.length === 0) return EMPTY
@@ -100,19 +91,16 @@ export class ThreeSurferEffects {
/**
* select the pial or first one by default
*/
- const selectedSrc = surfaces.find(s => s["@id"] === id)
-
- if (!(selectedSrc.data?.url_map)) {
- return throwError(`Expecting surfaces[0].data.url_map to be defined, but is not.`)
- }
+ const selectedSrc = surfaces.filter(surface => surface.variant === variant)
- for (const key in selectedSrc.data.url_map) {
+ for (const src of selectedSrc) {
layers.push({
+
clType: 'baselayer/threesurfer',
- id: `${selectedSrc["@id"]}-${key}`,
- name: `${selectedSrc["@id"]}-${key}`,
- laterality: key as 'left' | 'right',
- source: selectedSrc.data.url_map[key]
+ id: src.id,
+ name: src.id,
+ laterality: src.laterality,
+ source: src.url
})
}
return of(...[
@@ -127,14 +115,15 @@ export class ThreeSurferEffects {
))
onATPDebounceAddBaseLayers$ = createEffect(() => this.onATPDebounceThreeSurferLayers$.pipe(
- switchMap(({ labels }) => {
+ switchMap(({ labels, surfaces }) => {
const labelMaps: ThreeSurferCustomLabelLayer[] = []
- for (const label of labels) {
+ for (const key in labels) {
+ const { laterality, regions, url } = labels[key]
labelMaps.push({
clType: 'baselayer/threesurfer-label',
- id: `${label["@id"]}-${label.metadata.shortName}`,
- laterality: label.metadata.shortName as 'left' | 'right',
- source: label.data.url
+ id: `${url}-${laterality}`,
+ laterality,
+ source: url
})
}
return of(
diff --git a/src/viewerModule/threeSurfer/store/selectors.ts b/src/viewerModule/threeSurfer/store/selectors.ts
index 82c32604a57a26efac7881f9345fdb6c38cf9c2c..017d9aa8916e2024c4f21696b5fdb8eb8d9b7709 100644
--- a/src/viewerModule/threeSurfer/store/selectors.ts
+++ b/src/viewerModule/threeSurfer/store/selectors.ts
@@ -4,7 +4,7 @@ import { Store } from "./store"
const selectStore = state => state[nameSpace] as Store
-export const getSelectedVolumeId = createSelector(
+export const getSelectedSurfaceVariant = createSelector(
selectStore,
- ({ selectedVolumeId }) => selectedVolumeId
+ ({ selectedSurfaceVariant }) => selectedSurfaceVariant
)
diff --git a/src/viewerModule/threeSurfer/store/store.ts b/src/viewerModule/threeSurfer/store/store.ts
index b830d4278e88bfea95ca9a5f0697fb68f7db2171..713003dce599a80508661f9c672d2d3763cbc5ad 100644
--- a/src/viewerModule/threeSurfer/store/store.ts
+++ b/src/viewerModule/threeSurfer/store/store.ts
@@ -2,22 +2,22 @@ import { createReducer, on } from "@ngrx/store";
import * as actions from "./actions"
export type Store = {
- selectedVolumeId: string
+ selectedSurfaceVariant: string
}
export const defaultStore: Store = {
- selectedVolumeId: null
+ selectedSurfaceVariant: null
}
export const reducer = createReducer(
defaultStore,
on(
- actions.selectVolumeById,
- (state, { id }) => {
+ actions.selectSurfaceVariant,
+ (state, { variant }) => {
return {
...state,
- selectedVolumeId: id
+ selectedSurfaceVariant: variant
}
}
)
diff --git a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
index f04ad6cc1b0a5b85875c6bc247150b737eb5605c..a5292817e5b160fa2108e5c5bd62b0eea939c43d 100644
--- a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
+++ b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
@@ -1,7 +1,7 @@
import { Component, Output, EventEmitter, ElementRef, OnDestroy, AfterViewInit, Inject, Optional, ChangeDetectionStrategy } from "@angular/core";
import { EnumViewerEvt, IViewer, TViewerEvent } from "src/viewerModule/viewer.interface";
-import { combineLatest, Observable, Subject } from "rxjs";
-import { debounceTime, distinctUntilChanged, filter, map, shareReplay } from "rxjs/operators";
+import { combineLatest, forkJoin, from, merge, Observable, Subject } from "rxjs";
+import { debounceTime, distinctUntilChanged, filter, map, scan, shareReplay, switchMap } from "rxjs/operators";
import { ComponentStore } from "src/viewerModule/componentStore";
import { select, Store } from "@ngrx/store";
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
@@ -11,11 +11,11 @@ import { getUuid } from "src/util/fn";
import { AUTO_ROTATE, TInteralStatePayload, ViewerInternalStateSvc } from "src/viewerModule/viewerInternalState.service";
import { atlasAppearance, atlasSelection } from "src/state";
import { ThreeSurferCustomLabelLayer, ThreeSurferCustomLayer, ColorMapCustomLayer } from "src/state/atlasAppearance/const";
-import { SapiRegionModel, SapiVolumeModel } from "src/atlasComponents/sapi";
-import { getRegionLabelIndex } from "src/viewerModule/nehuba/config.service";
+import { SxplrRegion } from "src/atlasComponents/sapi/type_sxplr"
import { arrayEqual } from "src/util/array";
import { ThreeSurferEffects } from "../store/effects";
import { selectors, actions } from "../store"
+import { SAPI } from "src/atlasComponents/sapi";
const viewerType = 'ThreeSurfer'
type TInternalState = {
@@ -30,7 +30,7 @@ type TInternalState = {
const pZoomFactor = 5e3
type THandlingCustomEv = {
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
error?: string
evMesh?: {
faceIndex: number
@@ -112,7 +112,7 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
}> = {}
private internalStateNext: (arg: TInteralStatePayload<TInternalState>) => void
- private mouseoverRegions: SapiRegionModel[] = []
+ private mouseoverRegions: SxplrRegion[] = []
private selectedRegions$ = this.store$.pipe(
select(atlasSelection.selectors.selectedRegions)
@@ -136,8 +136,8 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
/**
* maps laterality to label index to sapi region
*/
- private latLblIdxToRegionRecord: LateralityRecord<Record<number, SapiRegionModel>> = {}
- private latLblIdxToRegionRecord$: Observable<LateralityRecord<Record<number, SapiRegionModel>>> = combineLatest([
+ private latLblIdxToRegionRecord: LateralityRecord<Record<number, SxplrRegion>> = {}
+ private latLblIdxToRegionRecord$: Observable<LateralityRecord<Record<number, SxplrRegion>>> = combineLatest([
this.store$.pipe(
atlasSelection.fromRootStore.distinctATP()
),
@@ -145,15 +145,21 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
select(atlasSelection.selectors.selectedParcAllRegions),
)
]).pipe(
- map(([ { atlas, parcellation, template }, regions]) => {
+ switchMap(([ { atlas, parcellation, template }, regions]) => {
const returnObj = {
- 'left': {} as Record<number, SapiRegionModel>,
- 'right': {} as Record<number, SapiRegionModel>
+ 'left': {} as Record<number, SxplrRegion>,
+ 'right': {} as Record<number, SxplrRegion>
}
-
- for (const region of regions) {
- const idx = getRegionLabelIndex(atlas, template, parcellation, region)
- if (idx) {
+ return merge(
+ ...regions.map(region =>
+ from(this.sapi.getRegionLabelIndices(template, parcellation, region)).pipe(
+ map(label => ({ region, label }))
+ )
+ )
+ ).pipe(
+ scan((acc, curr) => {
+ const { label, region } = curr
+
let key : 'left' | 'right'
if ( /left/i.test(region.name) ) key = 'left'
if ( /right/i.test(region.name) ) key = 'right'
@@ -162,12 +168,17 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
* TODO
* there are ... more regions than expected, which has label index without laterality
*/
- continue
+ return { ...acc }
}
- returnObj[key][idx] = region
- }
- }
- return returnObj
+ return {
+ ...acc,
+ [key]: {
+ ...acc[key],
+ [label]: region
+ }
+ }
+ }, {'left': {}, 'right': {}})
+ )
})
)
@@ -185,11 +196,11 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
*/
private showDelineation: boolean = true
- public threeSurferSurfaceLayers$ = this.effect.onATPDebounceThreeSurferLayers$.pipe(
- map(({ surfaces }) => surfaces)
+ public threeSurferSurfaceVariants$ = this.effect.onATPDebounceThreeSurferLayers$.pipe(
+ map(({ surfaces }) => surfaces.reduce((acc, val) => acc.includes(val.variant) ? acc : [...acc, val.variant] ,[] as string[]))
)
public selectedSurfaceLayerId$ = this.store$.pipe(
- select(selectors.getSelectedVolumeId)
+ select(selectors.getSelectedSurfaceVariant)
)
constructor(
@@ -197,6 +208,7 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
private el: ElementRef,
private store$: Store,
private navStateStoreRelay: ComponentStore<{ perspectiveOrientation: [number, number, number, number], perspectiveZoom: number }>,
+ private sapi: SAPI,
private snackbar: MatSnackBar,
@Optional() intViewerStateSvc: ViewerInternalStateSvc,
@Optional() @Inject(CLICK_INTERCEPTOR_INJECTOR) clickInterceptor: ClickInterceptor,
@@ -369,7 +381,7 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
}
private tsRef: TThreeSurfer
- private selectedRegions: SapiRegionModel[] = []
+ private selectedRegions: SxplrRegion[] = []
private relayStoreLock: () => void = null
private tsRefInitCb: ((tsRef: any) => void)[] = []
@@ -673,10 +685,10 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
}
}
- switchSurfaceLayer(layer: SapiVolumeModel): void{
+ switchSurfaceLayer(variant: string): void{
this.store$.dispatch(
- actions.selectVolumeById({
- id: layer["@id"]
+ actions.selectSurfaceVariant({
+ variant
})
)
}
diff --git a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.template.html b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.template.html
index 2a9703618ce87100f39bbd6470f88d4cd5bd5a57..fcef001a1ff56073a379a11d82573f85b109f069 100644
--- a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.template.html
+++ b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.template.html
@@ -29,16 +29,16 @@
</div>
<mat-divider></mat-divider>
- <button *ngFor="let surfaceLayer of threeSurferSurfaceLayers$ | async"
+ <button *ngFor="let surfaceLayer of (threeSurferSurfaceVariants$ | async)"
mat-menu-item
(click)="switchSurfaceLayer(surfaceLayer)"
color="primary">
<mat-icon
fontSet="fas"
- [fontIcon]="surfaceLayer['@id'] === (selectedSurfaceLayerId$ | async) ? 'fa-circle' : 'fa-none'">
+ [fontIcon]="surfaceLayer === (selectedSurfaceLayerId$ | async) ? 'fa-circle' : 'fa-none'">
</mat-icon>
<span>
- {{ surfaceLayer.metadata.shortName }}
+ {{ surfaceLayer }}
</span>
</button>
</mat-menu>
diff --git a/src/viewerModule/threeSurfer/types.ts b/src/viewerModule/threeSurfer/types.ts
index 9a15c5642d7c04e5c5057a412532eaabe51be8fe..1a4cdf152e08d1b6459a9383e6387e477c85b181 100644
--- a/src/viewerModule/threeSurfer/types.ts
+++ b/src/viewerModule/threeSurfer/types.ts
@@ -1,4 +1,4 @@
-import { SapiRegionModel } from 'src/atlasComponents/sapi'
+import { SxplrRegion } from 'src/atlasComponents/sapi/type_sxplr'
export type TThreeSurferMesh = {
colormap: string
@@ -6,11 +6,25 @@ export type TThreeSurferMesh = {
hemisphere: 'left' | 'right'
}
+export type TThreeMesh = {
+ id: string
+ variant: string
+ space: string
+ url: string
+ laterality: 'left' | 'right'
+}
+
+export type TThreeMeshLabel = {
+ url: string
+ space: string
+ laterality: 'left' | 'right'
+}
+
export type TThreeSurferContextInfo = {
position: number[]
faceIndex: number
vertexIndices: number[]
fsversion: string
- regions: SapiRegionModel[]
+ regions: SxplrRegion[]
error?: string
}
diff --git a/src/viewerModule/viewerCmp/viewerCmp.component.ts b/src/viewerModule/viewerCmp/viewerCmp.component.ts
index cef42ef50ec244b4f503d545935bc9548d167d4d..08df7f8b49884a7b094b7152abf21ae7cc398320 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.component.ts
+++ b/src/viewerModule/viewerCmp/viewerCmp.component.ts
@@ -1,6 +1,6 @@
import { ChangeDetectionStrategy, ChangeDetectorRef, Component, OnDestroy, TemplateRef, ViewChild, ViewContainerRef } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { combineLatest, Observable, of, Subscription } from "rxjs";
+import { combineLatest, forkJoin, Observable, of, Subscription } from "rxjs";
import { debounceTime, distinctUntilChanged, map, shareReplay, startWith, switchMap } from "rxjs/operators";
import { CONST, ARIA_LABELS, QUICKTOUR_DESC } from 'common/constants'
import { animate, state, style, transition, trigger } from "@angular/animations";
@@ -8,13 +8,14 @@ import { IQuickTourData } from "src/ui/quickTour";
import { EnumViewerEvt, TContextArg, TSupportedViewers, TViewerEvent } from "../viewer.interface";
import { ContextMenuService, TContextMenuReg } from "src/contextMenuModule";
import { DialogService } from "src/services/dialogService.service";
-import {SAPI, SapiAtlasModel, SapiRegionModel} from "src/atlasComponents/sapi";
-import { atlasSelection, userInteraction, } from "src/state";
-import { SapiSpatialFeatureModel, SapiFeatureModel, SapiParcellationModel, SapiSpaceModel } from "src/atlasComponents/sapi/type";
-import { getUuid } from "src/util/fn";
+import { SAPI } from "src/atlasComponents/sapi";
+import { Feature, NgLayerSpec, SxplrAtlas, SxplrRegion, TThreeMesh } from "src/atlasComponents/sapi/type_sxplr"
+import { atlasSelection, userInteraction } from "src/state";
+
import { environment } from "src/environments/environment"
-import { SapiViewsFeaturesVoiQuery } from "src/atlasComponents/sapiViews/features";
+// import { SapiViewsFeaturesVoiQuery } from "src/atlasComponents/sapiViews/features";
import { SapiViewsCoreSpaceBoundingBox } from "src/atlasComponents/sapiViews/core";
+import { SxplrTemplate } from "src/atlasComponents/sapi/type_sxplr";
@Component({
selector: 'iav-cmp-viewer-container',
@@ -70,8 +71,8 @@ export class ViewerCmp implements OnDestroy {
@ViewChild('genericInfoVCR', { read: ViewContainerRef })
genericInfoVCR: ViewContainerRef
- @ViewChild('voiFeatures', { read: SapiViewsFeaturesVoiQuery })
- voiQueryDirective: SapiViewsFeaturesVoiQuery
+ // @ViewChild('voiFeatures', { read: SapiViewsFeaturesVoiQuery })
+ // voiQueryDirective: SapiViewsFeaturesVoiQuery
@ViewChild('bbox', { read: SapiViewsCoreSpaceBoundingBox })
boundingBoxDirective: SapiViewsCoreSpaceBoundingBox
@@ -94,7 +95,7 @@ export class ViewerCmp implements OnDestroy {
shareReplay(1)
)
- public fetchedAtlases$: Observable<SapiAtlasModel[]> = this.sapi.atlases$
+ public fetchedAtlases$: Observable<SxplrAtlas[]> = this.sapi.atlases$
public selectedAtlas$ = this.selectedATP.pipe(
map(({ atlas }) => atlas)
@@ -127,20 +128,24 @@ export class ViewerCmp implements OnDestroy {
public useViewer$: Observable<TSupportedViewers | 'notsupported'> = combineLatest([
this.store$.pipe(
atlasSelection.fromRootStore.distinctATP(),
- switchMap(({ atlas, template }) => atlas && template
- ? this.sapi.getSpace(atlas["@id"], template["@id"]).getVolumes()
- : of(null)),
+ switchMap(({ template }) => template
+ ? forkJoin({
+ voxel: this.sapi.getVoxelTemplateImage(template),
+ surface: this.sapi.getSurfaceTemplateImage(template),
+ })
+ : of(null as { voxel: NgLayerSpec[], surface: TThreeMesh[] })
+ ),
map(vols => {
if (!vols) return null
const flags = {
isNehuba: false,
isThreeSurfer: false
}
- if (vols.find(vol => vol.data.volume_type === "neuroglancer/precomputed")) {
+ if (vols.voxel.length > 0) {
flags.isNehuba = true
}
- if (vols.find(vol => vol.data.volume_type === "gii")) {
+ if (vols.surface.length > 0) {
flags.isThreeSurfer = true
}
return flags
@@ -166,7 +171,7 @@ export class ViewerCmp implements OnDestroy {
public viewerCtx$ = this.ctxMenuSvc.context$
- public selectedFeature$: Observable<SapiFeatureModel> = this.store$.pipe(
+ public selectedFeature$: Observable<Feature> = this.store$.pipe(
select(userInteraction.selectors.selectedFeature)
)
@@ -193,7 +198,7 @@ export class ViewerCmp implements OnDestroy {
private viewerStatusRegionCtxMenu: TemplateRef<any>
public context: TContextArg<TSupportedViewers>
- private templateSelected: SapiSpaceModel
+ private templateSelected: SxplrTemplate
constructor(
private store$: Store<any>,
@@ -227,7 +232,7 @@ export class ViewerCmp implements OnDestroy {
message.push(`- _${atlas.name}_`)
}
if (checkPrerelease(tmpl)) {
- message.push(`- _${tmpl.fullName}_`)
+ message.push(`- _${tmpl.name}_`)
}
if (checkPrerelease(parc)) {
message.push(`- _${parc.name}_`)
@@ -311,7 +316,7 @@ export class ViewerCmp implements OnDestroy {
)
}
- public selectRoi(roi: SapiRegionModel): void {
+ public selectRoi(roi: SxplrRegion): void {
this.store$.dispatch(
atlasSelection.actions.selectRegion({
region: roi
@@ -347,16 +352,8 @@ export class ViewerCmp implements OnDestroy {
this.store$.dispatch(
userInteraction.actions.mouseoverPosition({
position: {
- "@id": getUuid(),
- "@type": "https://openminds.ebrains.eu/sands/CoordinatePoint",
- coordinates: nav.position.map(p => {
- return {
- value: p,
- }
- }),
- coordinateSpace: {
- '@id': this.templateSelected["@id"]
- }
+ loc: nav.position as [number, number, number],
+ space: this.templateSelected
}
})
)
@@ -371,19 +368,22 @@ export class ViewerCmp implements OnDestroy {
this.ctxMenuSvc.dismissCtxMenu()
}
- showDataset(feat: SapiFeatureModel): void {
- if ((feat as SapiSpatialFeatureModel).location) {
- const feature = feat as SapiSpatialFeatureModel
- this.store$.dispatch(
- atlasSelection.actions.navigateTo({
- navigation: {
- orientation: [0, 0, 0, 1],
- position: feature.location.center.coordinates.map(v => v.value * 1e6)
- },
- animation: true
- })
- )
- }
+ showDataset(feat: Feature): void {
+ /**
+ * TODO if feat is spatial feature, navigate to region
+ */
+ // if ((feat as SapiSpatialFeatureModel).location) {
+ // const feature = feat as SapiSpatialFeatureModel
+ // this.store$.dispatch(
+ // atlasSelection.actions.navigateTo({
+ // navigation: {
+ // orientation: [0, 0, 0, 1],
+ // position: feature.location.center.coordinates.map(v => v.value * 1e6)
+ // },
+ // animation: true
+ // })
+ // )
+ // }
this.store$.dispatch(
userInteraction.actions.showFeature({
diff --git a/src/viewerModule/viewerCmp/viewerCmp.template.html b/src/viewerModule/viewerCmp/viewerCmp.template.html
index 6774d54ae5b2d38cf04d0eecf13412f0ca98092e..0731f9bf2aad326458d20373fc7395d174f7763b 100644
--- a/src/viewerModule/viewerCmp/viewerCmp.template.html
+++ b/src/viewerModule/viewerCmp/viewerCmp.template.html
@@ -29,7 +29,7 @@
</mat-list-item>
- <ng-template [ngIf]="voiQueryDirective && (voiQueryDirective.onhover | async)" let-feat>
+ <!-- <ng-template [ngIf]="voiQueryDirective && (voiQueryDirective.onhover | async)" let-feat>
<mat-list-item>
<mat-icon
fontSet="fas"
@@ -38,7 +38,8 @@
</mat-icon>
<div matLine>{{ feat?.metadata?.fullName || 'Feature' }}</div>
</mat-list-item>
- </ng-template>
+ </ng-template> -->
+
</mat-list>
<!-- TODO Potentially implementing plugin contextual info -->
</div>
@@ -230,11 +231,11 @@
<ng-container *ngTemplateOutlet="autocompleteTmpl; context: { showTour: true }">
</ng-container>
- <ng-template [ngIf]="VOI_QUERY_FLAG">
+ <!-- <ng-template [ngIf]="VOI_QUERY_FLAG">
<div *ngIf="!((selectedRegions$ | async)[0])" class="sxplr-p-2 w-100">
<ng-container *ngTemplateOutlet="spatialFeatureListViewTmpl"></ng-container>
</div>
- </ng-template>
+ </ng-template> -->
</div>
<!-- such a gross implementation -->
@@ -268,7 +269,7 @@
</div>
<!-- tab toggling hide/show of min search tray -->
- <div class="tab-toggle-container d-inline-block v-align-top">
+ <!-- <div class="tab-toggle-container d-inline-block v-align-top">
<ng-container *ngTemplateOutlet="tabTmpl; context: {
isOpen: minTrayVisSwitch.switchState$ | async,
regionSelected: selectedRegions$ | async,
@@ -276,7 +277,7 @@
badge: voiQueryDirective && (voiQueryDirective.features$ | async).length || null
}">
</ng-container>
- </div>
+ </div> -->
</ng-template>
@@ -796,7 +797,7 @@
<!-- context menu template -->
<ng-template #viewerCtxMenuTmpl let-tmplRefs="tmplRefs">
<mat-card class="sxplr-p-0 d-flex flex-column"
- [iav-key-listener]="[{type: 'keydown', target: 'document', capture: true}]"
+ [iav-key-listener]="[{type: 'keydown', target: 'document', capture: true, key: 'Esc'}]"
(iav-key-event)="disposeCtxMenu()"
(iav-outsideClick)="disposeCtxMenu()">
<mat-card-content *ngFor="let tmplRef of tmplRefs"
@@ -930,13 +931,14 @@
</sxplr-sapiviews-core-datasets-dataset>
- <sxplr-sapiviews-features-entry
+ <!-- TODO FIXME -->
+ <!-- <sxplr-sapiviews-features-entry
[sxplr-sapiviews-features-entry-atlas]="selectedAtlas$ | async"
[sxplr-sapiviews-features-entry-space]="templateSelected$ | async"
[sxplr-sapiviews-features-entry-parcellation]="parcellationSelected$ | async"
[sxplr-sapiviews-features-entry-region]="(selectedRegions$ | async)[0]"
[sxplr-sapiviews-features-entry-feature]="feature">
- </sxplr-sapiviews-features-entry>
+ </sxplr-sapiviews-features-entry> -->
</ng-template>
<!-- general feature tmpl -->
@@ -962,7 +964,7 @@
</ng-template>
-<ng-template #spatialFeatureListViewTmpl>
+<!-- <ng-template #spatialFeatureListViewTmpl>
<div *ngIf="voiQueryDirective && (voiQueryDirective.busy$ | async); else notBusyTmpl" class="fs-200">
<spinner-cmp></spinner-cmp>
</div>
@@ -973,7 +975,6 @@
Volumes of interest
</mat-card-title>
<mat-card-subtitle class="overflow-hidden">
- <!-- TODO in future, perhaps encapsulate this as a component? seems like a nature fit in sapiView/space/boundingbox -->
<ng-template let-bbox [ngIf]="boundingBoxDirective && (boundingBoxDirective.bbox$ | async | getProperty : 'bbox')" [ngIfElse]="bboxFallbackTmpl">
Bounding box: {{ bbox[0] | numbers | json }} - {{ bbox[1] | numbers | json }} mm
</ng-template>
@@ -996,9 +997,10 @@
</ng-template>
</mat-card>
</ng-template>
-</ng-template>
+</ng-template> -->
-<div class="d-none"
+<!-- TODO FIXME -->
+<!-- <div class="d-none"
*ngIf="VOI_QUERY_FLAG"
sxplr-sapiviews-core-space-boundingbox
[sxplr-sapiviews-core-space-boundingbox-atlas]="selectedAtlas$ | async"
@@ -1012,4 +1014,4 @@
(sxplr-sapiviews-features-voi-query-onclick)="showDataset($event)"
#voiFeatures="sxplrSapiViewsFeaturesVoiQuery">
-</div>
+</div> -->
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
rename to tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.spec.ts
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.component.ts
rename to tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.component.ts
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.stories.ts b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
rename to tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.style.scss b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.style.scss
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.style.scss
rename to tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.style.scss
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.template.html b/tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/connectivityBrowser/connectivityBrowser.template.html
rename to tmpFeatures/connectivity/connectivityBrowser/connectivityBrowser.template.html
diff --git a/src/atlasComponents/sapiViews/features/connectivity/connectivityDoi.pipe.ts b/tmpFeatures/connectivity/connectivityDoi.pipe.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/connectivityDoi.pipe.ts
rename to tmpFeatures/connectivity/connectivityDoi.pipe.ts
diff --git a/src/atlasComponents/sapiViews/features/connectivity/hasConnectivity.directive.ts b/tmpFeatures/connectivity/hasConnectivity.directive.ts
similarity index 99%
rename from src/atlasComponents/sapiViews/features/connectivity/hasConnectivity.directive.ts
rename to tmpFeatures/connectivity/hasConnectivity.directive.ts
index 122083f1d33a5ab54c2d2c78de59e0d39a7f552e..89168b6ada70caa0ac9de83c32edf9a2f0c0d856 100644
--- a/src/atlasComponents/sapiViews/features/connectivity/hasConnectivity.directive.ts
+++ b/tmpFeatures/connectivity/hasConnectivity.directive.ts
@@ -74,7 +74,6 @@ export class HasConnectivity implements OnDestroy {
if (this.region.name) {
this.connectivityModalities.forEach(m => {
const type = m.types[0]
-
this.sapi.getParcellation(this.atlas["@id"], this.parcellation["@id"])
.getFeatures({type, page: 1, size: 1}).pipe(take(1))
.subscribe((res: SapiParcellationFeatureModel[] | any) => {
diff --git a/src/atlasComponents/sapiViews/features/connectivity/index.ts b/tmpFeatures/connectivity/index.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/index.ts
rename to tmpFeatures/connectivity/index.ts
diff --git a/src/atlasComponents/sapiViews/features/connectivity/module.ts b/tmpFeatures/connectivity/module.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/connectivity/module.ts
rename to tmpFeatures/connectivity/module.ts
diff --git a/src/atlasComponents/sapiViews/features/entry/entry.component.ts b/tmpFeatures/entry/entry.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entry/entry.component.ts
rename to tmpFeatures/entry/entry.component.ts
diff --git a/src/atlasComponents/sapiViews/features/entry/entry.style.css b/tmpFeatures/entry/entry.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entry/entry.style.css
rename to tmpFeatures/entry/entry.style.css
diff --git a/src/atlasComponents/sapiViews/features/entry/entry.template.html b/tmpFeatures/entry/entry.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entry/entry.template.html
rename to tmpFeatures/entry/entry.template.html
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts b/tmpFeatures/entryListItem/entryListItem.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entryListItem/entryListItem.component.ts
rename to tmpFeatures/entryListItem/entryListItem.component.ts
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.style.css b/tmpFeatures/entryListItem/entryListItem.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entryListItem/entryListItem.style.css
rename to tmpFeatures/entryListItem/entryListItem.style.css
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListItem.template.html b/tmpFeatures/entryListItem/entryListItem.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entryListItem/entryListItem.template.html
rename to tmpFeatures/entryListItem/entryListItem.template.html
diff --git a/src/atlasComponents/sapiViews/features/entryListItem/entryListitem.stories.ts b/tmpFeatures/entryListItem/entryListitem.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/entryListItem/entryListitem.stories.ts
rename to tmpFeatures/entryListItem/entryListitem.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/featureBadgeColor.pipe.ts b/tmpFeatures/featureBadgeColor.pipe.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/featureBadgeColor.pipe.ts
rename to tmpFeatures/featureBadgeColor.pipe.ts
diff --git a/src/atlasComponents/sapiViews/features/featureBadgeFlag.pipe.ts b/tmpFeatures/featureBadgeFlag.pipe.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/featureBadgeFlag.pipe.ts
rename to tmpFeatures/featureBadgeFlag.pipe.ts
diff --git a/src/atlasComponents/sapiViews/features/featureBadgeName.pipe.ts b/tmpFeatures/featureBadgeName.pipe.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/featureBadgeName.pipe.ts
rename to tmpFeatures/featureBadgeName.pipe.ts
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.component.ts b/tmpFeatures/ieeg/ieegDataset/ieegDataset.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.component.ts
rename to tmpFeatures/ieeg/ieegDataset/ieegDataset.component.ts
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.stories.ts b/tmpFeatures/ieeg/ieegDataset/ieegDataset.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.stories.ts
rename to tmpFeatures/ieeg/ieegDataset/ieegDataset.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.style.css b/tmpFeatures/ieeg/ieegDataset/ieegDataset.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.style.css
rename to tmpFeatures/ieeg/ieegDataset/ieegDataset.style.css
diff --git a/src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.template.html b/tmpFeatures/ieeg/ieegDataset/ieegDataset.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/ieegDataset/ieegDataset.template.html
rename to tmpFeatures/ieeg/ieegDataset/ieegDataset.template.html
diff --git a/src/atlasComponents/sapiViews/features/ieeg/inRoi.pipe.ts b/tmpFeatures/ieeg/inRoi.pipe.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/inRoi.pipe.ts
rename to tmpFeatures/ieeg/inRoi.pipe.ts
diff --git a/src/atlasComponents/sapiViews/features/ieeg/index.ts b/tmpFeatures/ieeg/index.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/index.ts
rename to tmpFeatures/ieeg/index.ts
diff --git a/src/atlasComponents/sapiViews/features/ieeg/module.ts b/tmpFeatures/ieeg/module.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/ieeg/module.ts
rename to tmpFeatures/ieeg/module.ts
diff --git a/src/atlasComponents/sapiViews/features/index.ts b/tmpFeatures/index.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/index.ts
rename to tmpFeatures/index.ts
diff --git a/src/atlasComponents/sapiViews/features/module.ts b/tmpFeatures/module.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/module.ts
rename to tmpFeatures/module.ts
diff --git a/src/atlasComponents/sapiViews/features/orderFilterFeatureList.pipe.ts b/tmpFeatures/orderFilterFeatureList.pipe.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/orderFilterFeatureList.pipe.ts
rename to tmpFeatures/orderFilterFeatureList.pipe.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiograph.stories.ts b/tmpFeatures/receptors/autoradiography/autoradiograph.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiograph.stories.ts
rename to tmpFeatures/receptors/autoradiography/autoradiograph.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiography.component.ts b/tmpFeatures/receptors/autoradiography/autoradiography.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiography.component.ts
rename to tmpFeatures/receptors/autoradiography/autoradiography.component.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiography.style.css b/tmpFeatures/receptors/autoradiography/autoradiography.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiography.style.css
rename to tmpFeatures/receptors/autoradiography/autoradiography.style.css
diff --git a/src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiography.template.html b/tmpFeatures/receptors/autoradiography/autoradiography.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/autoradiography/autoradiography.template.html
rename to tmpFeatures/receptors/autoradiography/autoradiography.template.html
diff --git a/src/atlasComponents/sapiViews/features/receptors/base.ts b/tmpFeatures/receptors/base.ts
similarity index 95%
rename from src/atlasComponents/sapiViews/features/receptors/base.ts
rename to tmpFeatures/receptors/base.ts
index 2428c72f6e315c97f98a5914c867d7c6c7560af8..08dc8f46177f25d1f2071aa76844097eaf746ce6 100644
--- a/src/atlasComponents/sapiViews/features/receptors/base.ts
+++ b/tmpFeatures/receptors/base.ts
@@ -1,7 +1,7 @@
import { Directive, Input, SimpleChanges } from "@angular/core";
import { BehaviorSubject } from "rxjs";
import { SAPI, SapiAtlasModel, SapiParcellationModel, SapiRegionModel, SapiSpaceModel } from "src/atlasComponents/sapi";
-import { SapiRegionalFeatureReceptorModel } from "src/atlasComponents/sapi/type";
+import { TabularFeature } from "src/atlasComponents/sapi/type_sxplr"
@Directive()
export abstract class BaseReceptor{
@@ -22,7 +22,7 @@ export abstract class BaseReceptor{
featureId: string
@Input('sxplr-sapiviews-features-receptor-data')
- receptorData: SapiRegionalFeatureReceptorModel
+ receptorData: TabularFeature<number>
error: string
diff --git a/src/atlasComponents/sapiViews/features/receptors/entry/entry.component.ts b/tmpFeatures/receptors/entry/entry.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/entry/entry.component.ts
rename to tmpFeatures/receptors/entry/entry.component.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/entry/entry.stories.ts b/tmpFeatures/receptors/entry/entry.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/entry/entry.stories.ts
rename to tmpFeatures/receptors/entry/entry.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/entry/entry.style.css b/tmpFeatures/receptors/entry/entry.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/entry/entry.style.css
rename to tmpFeatures/receptors/entry/entry.style.css
diff --git a/src/atlasComponents/sapiViews/features/receptors/entry/entry.template.html b/tmpFeatures/receptors/entry/entry.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/entry/entry.template.html
rename to tmpFeatures/receptors/entry/entry.template.html
diff --git a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.component.ts b/tmpFeatures/receptors/fingerprint/fingerprint.component.ts
similarity index 82%
rename from src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.component.ts
rename to tmpFeatures/receptors/fingerprint/fingerprint.component.ts
index 98c5b0076da0350cd0a30fdc01633ee57b6e3bab..7780f53ad96c8a2fef661008ce83c8c57ffe7165 100644
--- a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.component.ts
+++ b/tmpFeatures/receptors/fingerprint/fingerprint.component.ts
@@ -2,7 +2,7 @@ import { AfterViewInit, Component, ElementRef, EventEmitter, HostListener, Injec
import { fromEvent, Observable, Subscription } from "rxjs";
import { distinctUntilChanged, map } from "rxjs/operators";
import { SAPI } from "src/atlasComponents/sapi";
-import { SapiRegionalFeatureReceptorModel } from "src/atlasComponents/sapi/type";
+import { TabularFeature } from "src/atlasComponents/sapi/type_sxplr";
import { DARKTHEME } from "src/util/injectionTokens";
import { BaseReceptor } from "../base";
@@ -21,22 +21,27 @@ type RequiredType = {
}
}
-function transformRadar(input: SapiRegionalFeatureReceptorModel['data']['fingerprints']): RequiredType[]{
+function transformRadar(input: TabularFeature<number>): RequiredType[]{
const listRequired: RequiredType[] = []
- for (const key in input) {
- const item = input[key]
+ if (input.index.length !== input.data.length) {
+ throw new Error(`Expecting index length: '${input.index.length}' to be the same as data length : '${input.data.length}'.`)
+ }
+ const rowLength = new Set([input.data.map(row => row.length)])
+ if (rowLength.size !== 1) {
+ throw new Error(`Expecting all row length to equal, but exists: ${JSON.stringify(Array.from(rowLength))}`)
+ }
+ input.index.forEach((label, idx) => {
listRequired.push({
receptor: {
- label: key
+ label
},
density: {
- mean: item.mean,
- sd: item.std,
- unit: item.unit
+ mean: input.data[idx][0],
+ sd: input.data[idx][1],
+ unit: ''
}
})
-
- }
+ })
return listRequired
}
diff --git a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.stories.ts b/tmpFeatures/receptors/fingerprint/fingerprint.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.stories.ts
rename to tmpFeatures/receptors/fingerprint/fingerprint.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.style.css b/tmpFeatures/receptors/fingerprint/fingerprint.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.style.css
rename to tmpFeatures/receptors/fingerprint/fingerprint.style.css
diff --git a/src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.template.html b/tmpFeatures/receptors/fingerprint/fingerprint.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/fingerprint/fingerprint.template.html
rename to tmpFeatures/receptors/fingerprint/fingerprint.template.html
diff --git a/src/atlasComponents/sapiViews/features/receptors/index.ts b/tmpFeatures/receptors/index.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/index.ts
rename to tmpFeatures/receptors/index.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/module.ts b/tmpFeatures/receptors/module.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/module.ts
rename to tmpFeatures/receptors/module.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/profile/profile.component.ts b/tmpFeatures/receptors/profile/profile.component.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/profile/profile.component.ts
rename to tmpFeatures/receptors/profile/profile.component.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/profile/profile.stories.ts b/tmpFeatures/receptors/profile/profile.stories.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/profile/profile.stories.ts
rename to tmpFeatures/receptors/profile/profile.stories.ts
diff --git a/src/atlasComponents/sapiViews/features/receptors/profile/profile.style.css b/tmpFeatures/receptors/profile/profile.style.css
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/profile/profile.style.css
rename to tmpFeatures/receptors/profile/profile.style.css
diff --git a/src/atlasComponents/sapiViews/features/receptors/profile/profile.template.html b/tmpFeatures/receptors/profile/profile.template.html
similarity index 100%
rename from src/atlasComponents/sapiViews/features/receptors/profile/profile.template.html
rename to tmpFeatures/receptors/profile/profile.template.html
diff --git a/src/atlasComponents/sapiViews/features/voi/index.ts b/tmpFeatures/voi/index.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/voi/index.ts
rename to tmpFeatures/voi/index.ts
diff --git a/src/atlasComponents/sapiViews/features/voi/module.ts b/tmpFeatures/voi/module.ts
similarity index 100%
rename from src/atlasComponents/sapiViews/features/voi/module.ts
rename to tmpFeatures/voi/module.ts
diff --git a/src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts b/tmpFeatures/voi/voiQuery.directive.ts
similarity index 75%
rename from src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts
rename to tmpFeatures/voi/voiQuery.directive.ts
index 623011d89b1d2385fec8ca30c3456082056128e7..fe76589bdf32503e3b14c6a32b5aabafe0a5d9cb 100644
--- a/src/atlasComponents/sapiViews/features/voi/voiQuery.directive.ts
+++ b/tmpFeatures/voi/voiQuery.directive.ts
@@ -3,7 +3,8 @@ import { interval, merge, Observable, of, Subject, Subscription } from "rxjs";
import { debounce, debounceTime, distinctUntilChanged, filter, pairwise, shareReplay, startWith, switchMap, take, tap } from "rxjs/operators";
import { AnnotationLayer, TNgAnnotationPoint, TNgAnnotationAABBox } from "src/atlasComponents/annotations";
import { SAPI } from "src/atlasComponents/sapi/sapi.service";
-import { BoundingBoxConcept, SapiAtlasModel, SapiSpaceModel, SapiVOIDataResponse, OpenMINDSCoordinatePoint } from "src/atlasComponents/sapi/type";
+import { BoundingBox, SxplrAtlas, SxplrTemplate, VoiFeature } from "src/atlasComponents/sapi/type_sxplr";
+
import { ClickInterceptor, CLICK_INTERCEPTOR_INJECTOR } from "src/util";
import { arrayEqual } from "src/util/array";
@@ -17,9 +18,9 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
static VOI_LAYER_NAME = 'voi-annotation-layer'
static VOI_ANNOTATION_COLOR = "#ffff00"
private voiQuerySpec = new Subject<{
- atlas: SapiAtlasModel
- space: SapiSpaceModel
- bbox: BoundingBoxConcept
+ atlas: SxplrAtlas
+ space: SxplrTemplate
+ bbox: BoundingBox
}>()
private canFetchVoi(){
@@ -27,22 +28,22 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
}
@Input('sxplr-sapiviews-features-voi-query-atlas')
- atlas: SapiAtlasModel
+ atlas: SxplrAtlas
@Input('sxplr-sapiviews-features-voi-query-space')
- space: SapiSpaceModel
+ space: SxplrTemplate
@Input('sxplr-sapiviews-features-voi-query-bbox')
- bbox: BoundingBoxConcept
+ bbox: BoundingBox
@Output('sxplr-sapiviews-features-voi-query-onhover')
- onhover = new EventEmitter<SapiVOIDataResponse>()
+ onhover = new EventEmitter<VoiFeature>()
@Output('sxplr-sapiviews-features-voi-query-onclick')
- onclick = new EventEmitter<SapiVOIDataResponse>()
+ onclick = new EventEmitter<VoiFeature>()
public busy$ = new EventEmitter<boolean>()
- public features$: Observable<SapiVOIDataResponse[]> = this.voiQuerySpec.pipe(
+ public features$: Observable<VoiFeature[]> = this.voiQuerySpec.pipe(
debounceTime(160),
tap(() => this.busy$.emit(true)),
switchMap(({ atlas, bbox, space }) => {
@@ -51,18 +52,14 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
}
return merge(
of([]),
- this.sapi.getSpace(atlas["@id"], space["@id"]).getFeatures({ bbox: JSON.stringify(bbox) }).pipe(
- tap(val => {
- this.busy$.emit(false)
- })
- )
+ this.sapi.getVoiFeatures(bbox)
)
}),
startWith([]),
shareReplay(1)
)
- private hoveredFeat: SapiVOIDataResponse
+ private hoveredFeat: VoiFeature
private onDestroyCb: (() => void)[] = []
private subscription: Subscription[] = []
ngOnChanges(simpleChanges: SimpleChanges): void {
@@ -131,7 +128,7 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
clickInterceptor.register(handle)
this.subscription.push(
this.features$.pipe(
- startWith([] as SapiVOIDataResponse[]),
+ startWith([] as VoiFeature[]),
distinctUntilChanged(arrayEqual((o, n) => o["@id"] === n["@id"])),
pairwise(),
debounce(() =>
@@ -142,8 +139,8 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
),
).subscribe(([ prev, curr ]) => {
for (const v of prev) {
- const box = this.pointsToAABB(v.location.maxpoint, v.location.minpoint)
- const point = this.pointToPoint(v.location.center)
+ const box = this.pointsToAABB(v.bbox.maxpoint, v.bbox.minpoint)
+ const point = this.pointToPoint(v.bbox.center)
this.annotationIdToFeature.delete(box.id)
this.annotationIdToFeature.delete(point.id)
if (!this.voiBBoxSvc) continue
@@ -154,8 +151,8 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
}
}
for (const v of curr) {
- const box = this.pointsToAABB(v.location.maxpoint, v.location.minpoint)
- const point = this.pointToPoint(v.location.center)
+ const box = this.pointsToAABB(v.bbox.maxpoint, v.bbox.minpoint)
+ const point = this.pointToPoint(v.bbox.center)
this.annotationIdToFeature.set(box.id, v)
this.annotationIdToFeature.set(point.id, v)
if (!this.voiBBoxSvc) {
@@ -170,20 +167,20 @@ export class SapiViewsFeaturesVoiQuery implements OnChanges, OnDestroy{
)
}
- private annotationIdToFeature = new Map<string, SapiVOIDataResponse>()
+ private annotationIdToFeature = new Map<string, VoiFeature>()
- private pointsToAABB(pointA: OpenMINDSCoordinatePoint, pointB: OpenMINDSCoordinatePoint): TNgAnnotationAABBox{
+ private pointsToAABB(pointA: [number, number, number], pointB: [number, number, number]): TNgAnnotationAABBox{
return {
id: `${SapiViewsFeaturesVoiQuery.VOI_LAYER_NAME}:${pointA["@id"]}:${pointB["@id"]}`,
- pointA: pointA.coordinates.map(v => v.value * 1e6) as [number, number, number],
- pointB: pointB.coordinates.map(v => v.value * 1e6) as [number, number, number],
+ pointA: pointA.map(v => v * 1e6) as [number, number, number],
+ pointB: pointB.map(v => v * 1e6) as [number, number, number],
type: "aabbox"
}
}
- private pointToPoint(point: OpenMINDSCoordinatePoint): TNgAnnotationPoint {
+ private pointToPoint(point: [number, number, number]): TNgAnnotationPoint {
return {
- id: `${SapiViewsFeaturesVoiQuery.VOI_LAYER_NAME}:${point["@id"]}`,
- point: point.coordinates.map(v => v.value * 1e6) as [number, number, number],
+ id: `${SapiViewsFeaturesVoiQuery.VOI_LAYER_NAME}:${JSON.stringify(point)}}`,
+ point: point.map(v => v * 1e6) as [number, number, number],
type: "point"
}
}
diff --git a/tsconfig.json b/tsconfig.json
index 7e2716b1f639eb80fe50f7ac5f3842c1a0ccbe18..bfd3effbebe1bbe4804212fd1188169c72d3937e 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -22,6 +22,7 @@
"angularCompilerOptions":{
"fullTemplateTypeCheck": true,
"strictInjectionParameters": true,
- "annotateForClosureCompiler" : true
+ "annotateForClosureCompiler" : true,
+ "strictTemplates": true
}
}
\ No newline at end of file