diff --git a/common/util.js b/common/util.js
new file mode 100644
index 0000000000000000000000000000000000000000..74a3ff1f21886fc60554fb60ee49bd66ee8773d2
--- /dev/null
+++ b/common/util.js
@@ -0,0 +1,15 @@
+(function(exports) {
+ exports.getIdFromFullId = fullId => {
+ if (!fullId) return null
+ if (typeof fullId === 'string') {
+ const re = /\/([a-z]{1,}\/[a-z]{1,}\/[a-z]{1,}\/v[0-9.]{1,}\/[0-9a-z-]{1,}$)/.exec(fullId)
+ if (re) return re[1]
+ return null
+ } else {
+ const { kg = {} } = fullId
+ const { kgSchema , kgId } = kg
+ if (!kgSchema || !kgId) return null
+ return `${kgSchema}/${kgId}`
+ }
+ }
+})(typeof exports === 'undefined' ? module.exports : exports)
diff --git a/common/util.spec.js b/common/util.spec.js
new file mode 100644
index 0000000000000000000000000000000000000000..4597a54db648521dd029fb002f22ef56436d3b51
--- /dev/null
+++ b/common/util.spec.js
@@ -0,0 +1,20 @@
+import { getIdFromFullId } from './util'
+
+describe('common/util.js', () => {
+ describe('getIdFromFullId', () => {
+ it('should return correct kgId for regions fetched from kg', () => {
+ const id = 'https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/675a6ce9-ef26-4e68-9852-54afeb24923c'
+ expect(getIdFromFullId(id)).toBe('minds/core/parcellationregion/v1.0.0/675a6ce9-ef26-4e68-9852-54afeb24923c')
+ })
+
+ it('should return correct id for regions in hierarchy', () => {
+ const fullId = {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a844d80f-1d94-41a0-901a-14ae257519db"
+ }
+ }
+ expect(getIdFromFullId(fullId)).toBe(`minds/core/parcellationregion/v1.0.0/a844d80f-1d94-41a0-901a-14ae257519db`)
+ })
+ })
+})
diff --git a/deploy/datasets/testData/mni152.js b/deploy/datasets/testData/mni152.js
deleted file mode 100644
index b7f11f1608db7a22c0b84558eb02ab547dfad6c1..0000000000000000000000000000000000000000
--- a/deploy/datasets/testData/mni152.js
+++ /dev/null
@@ -1,113 +0,0 @@
-module.exports = [
- {
- "formats": [
- "NIFTI"
- ],
- "datasetDOI": [
- {
- "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
- "doi": "10.1006/nimg.1999.0516"
- }
- ],
- "activity": [
- {
- "protocols": [
- "histology"
- ],
- "preparation": [
- "Ex vivo"
- ]
- },
- {
- "protocols": [
- "imaging"
- ],
- "preparation": [
- "Ex vivo"
- ]
- },
- {
- "protocols": [
- "brain mapping"
- ],
- "preparation": [
- "Ex vivo"
- ]
- }
- ],
- "referenceSpaces": [
- {
- "name": null,
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
- },
- {
- "name": "MNI Colin 27",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
- }
- ],
- "methods": [
- "silver staining",
- "magnetic resonance imaging (MRI)",
- "probability mapping",
- "cytoarchitectonic mapping"
- ],
- "custodians": [
- "Amunts, Katrin"
- ],
- "project": [
- "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
- ],
- "description": "This dataset contains the distinct architectonic Area hOc1 (V1, 17, CalcS) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the JuBrain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area hOc1 (V1, 17, CalcS). The probability map of Area hOc1 (V1, 17, CalcS) are provided in the NifTi format for each brain reference space and hemisphere. The JuBrain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
- "parcellationAtlas": [
- {
- "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
- "id": [
- "deec923ec31a82f89a9c7c76a6fefd6b",
- "e2d45e028b6da0f6d9fdb9491a4de80a"
- ]
- }
- ],
- "licenseInfo": [
- {
- "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
- "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
- }
- ],
- "embargoStatus": [
- "Free"
- ],
- "license": [],
- "parcellationRegion": [
- {
- "species": [],
- "name": "Area hOc1 (V1, 17, CalcS)",
- "alias": null
- }
- ],
- "species": [
- "Homo sapiens"
- ],
- "name": "Probabilistic cytoarchitectonic map of Area hOc1 (V1, 17, CalcS) (v2.4)",
- "files": [],
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/5c669b77-c981-424a-858d-fe9f527dbc07",
- "contributors": [
- "Zilles, Karl",
- "Schormann, Thorsten",
- "Mohlberg, Hartmut",
- "Malikovic, Aleksandar",
- "Amunts, Katrin"
- ],
- "id": "5c669b77-c981-424a-858d-fe9f527dbc07",
- "kgReference": [
- "10.25493/MXJ6-6DH"
- ],
- "publications": [
- {
- "name": "Brodmann's Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable?",
- "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
- "doi": "10.1006/nimg.1999.0516"
- }
- ]
- }
-]
\ No newline at end of file
diff --git a/deploy/datasets/testData/mni152JuBrain.js b/deploy/datasets/testData/mni152JuBrain.js
new file mode 100644
index 0000000000000000000000000000000000000000..788d622c47c85e9318868752bd2c14686df37f7e
--- /dev/null
+++ b/deploy/datasets/testData/mni152JuBrain.js
@@ -0,0 +1,337 @@
+module.exports = [
+ {
+ "formats": [
+ "NIFTI"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "imaging"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [
+ {
+ "name": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+ },
+ {
+ "name": "MNI Colin 27",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+ }
+ ],
+ "methods": [
+ "silver staining",
+ "magnetic resonance imaging (MRI)",
+ "probability mapping",
+ "cytoarchitectonic mapping"
+ ],
+ "custodians": [
+ "Amunts, Katrin"
+ ],
+ "project": [
+ "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
+ ],
+ "description": "This dataset contains the distinct architectonic Area hOc1 (V1, 17, CalcS) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the JuBrain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area hOc1 (V1, 17, CalcS). The probability map of Area hOc1 (V1, 17, CalcS) are provided in the NifTi format for each brain reference space and hemisphere. The JuBrain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "parcellationAtlas": [
+ {
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "id": [
+ "deec923ec31a82f89a9c7c76a6fefd6b",
+ "e2d45e028b6da0f6d9fdb9491a4de80a"
+ ]
+ }
+ ],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1 (V1, 17, CalcS)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Probabilistic cytoarchitectonic map of Area hOc1 (V1, 17, CalcS) (v2.4)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/5c669b77-c981-424a-858d-fe9f527dbc07",
+ "contributors": [
+ "Zilles, Karl",
+ "Schormann, Thorsten",
+ "Mohlberg, Hartmut",
+ "Malikovic, Aleksandar",
+ "Amunts, Katrin"
+ ],
+ "id": "5c669b77-c981-424a-858d-fe9f527dbc07",
+ "kgReference": [
+ "10.25493/MXJ6-6DH"
+ ],
+ "publications": [
+ {
+ "name": "Brodmann's Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable?",
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ]
+ },{
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area hOc1 using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area hOc1",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/e715e1f7-2079-45c4-a67f-f76b102acfce",
+ "contributors": [
+ "Scheperjans, Filip",
+ "Schleicher, Axel",
+ "Eickhoff, Simon B.",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "0616d1e97b8be75de526bc265d9af540",
+ "kgReference": [
+ "10.25493/P8SD-JMH"
+ ],
+ "publications": [
+ {
+ "name": "Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex",
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+ },{
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area 44d using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area 44d",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area 44d",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/cb875c0d-97f4-4dbc-a9ce-472d8ba58c99",
+ "contributors": [
+ "Morosan, Patricia",
+ "Schleicher, Axel",
+ "Lenzen, Marianne",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "31397abd7aebcf13bf3b1d5eb2e2d400",
+ "kgReference": [
+ "10.25493/YQCR-1DQ"
+ ],
+ "publications": [
+ {
+ "name": "Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping",
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+ }
+]
\ No newline at end of file
diff --git a/deploy/datasets/testData/waxholmv2.js b/deploy/datasets/testData/waxholmv2.js
index 7c3afd5e2d0b4021446d7402ff6c44805fb4f3ec..91c198d28a131a55de5a44e5b4c2b1ca7ec888b7 100644
--- a/deploy/datasets/testData/waxholmv2.js
+++ b/deploy/datasets/testData/waxholmv2.js
@@ -65,7 +65,8 @@ module.exports = [
{
"species": [],
"name": "Mouse Whole brain (v3 2015)",
- "alias": "Whole brain"
+ "alias": "Whole brain",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/2bdfac7a-b38c-4c55-9843-0b56cb90bb67"
},
{
"species": [
@@ -78,8 +79,9 @@ module.exports = [
"@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/f3490d7f-8f7f-4b40-b238-963dcac84412"
}
],
- "name": "Whole Brain ",
- "alias": "Whole brain"
+ "name": "Rat Whole brain (v2)",
+ "alias": "Whole brain",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b2b56201-472c-4f70-842f-cf2133eacaba"
}
],
"species": [
@@ -87,118 +89,6 @@ module.exports = [
"Mus musculus"
],
"name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)",
- "files": [],
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/f7a7d460-8724-4cd1-a06e-457eb8954fbd",
- "contributors": [
- "Danbolt, Nils C.",
- "Bjaalie, Jan G.",
- "Leergaard, Trygve B.",
- "Lehre, K.P.",
- "Real, Katia",
- "Scott, Heather A.",
- "Holmseth, Silvia"
- ],
- "id": "63bbb845ac6d2f1839f919c2ef0455bc",
- "kgReference": [
- "10.25493/Y147-2CE"
- ],
- "publications": [
- {
- "name": "The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation",
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ]
- },
- {
- "formats": [],
- "datasetDOI": [
- {
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ],
- "activity": [
- {
- "protocols": [
- "Immunohistochemistry",
- "Atlas",
- "Brain-wide",
- "Synaptic transmission",
- "Neurtransmitter transport",
- "Glutamate uptake",
- "GLT1"
- ],
- "preparation": [
- "Ex vivo"
- ]
- }
- ],
- "referenceSpaces": [],
- "methods": [
- "Immunohistochemistry"
- ],
- "custodians": [
- "Danbolt, Niels C."
- ],
- "project": [
- "Rodent brain neurotransporter atlas: GLT1"
- ],
- "description": "Glutamate is the major excitatory transmitter in the central nervous system (Danbolt, Prog. Neurobiol. 65:1-105, 2001). It is inactivated by cellular uptake, mostly catalyzed by the glutamate transporters GLT1 (slc1a2, excitatory amino acid transporter [EAAT2]) subtype expressed at high levels in brain astrocytes and at lower levels in neurons. Three C-terminal variants of EAAT2 exist: GLT1a (Pines et al., Nature 360:464-467, 1992), GLT1b (Utsunomiya-Tate et al., FEBS Lett 416:312-326,1997), and GLT1c (Rauen et al., Neurochem. Int. 45:1095-1106, 2004). This dataset is brain-wide collection of microscopic images showing the brain-wide distribution of GLT1 in the mouse and rat brain, visualized by immunohistochemistry using antibodies against GLT1a and GLT1b. To facilitate identification of anatomical location adjacent section were stained to reveal cyto- and myeloarchitecture.",
- "parcellationAtlas": [
- {
- "name": "Allen Mouse Common Coordinate Framework v3 2015",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f",
- "id": "39a1384b-8413-4d27-af8d-22432225401f"
- },
- {
- "name": "Waxholm Space rat brain atlas v2",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d",
- "id": "2449a7f0-6dd0-4b5a-8f1e-aec0db03679d"
- }
- ],
- "licenseInfo": [
- {
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "url": "https://creativecommons.org/licenses/by-sa/4.0"
- }
- ],
- "embargoStatus": [
- "Free"
- ],
- "license": [
- {
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "relativeUrl": "minds/core/licensetype/v1.0.0/78a3bfb2-f4b9-40f0-869c-34b5e48a45bd"
- }
- ],
- "parcellationRegion": [
- {
- "species": [],
- "name": "Mouse Whole brain (v3 2015)",
- "alias": "Whole brain"
- },
- {
- "species": [
- {
- "identifier": [
- "e9a384ea8a4edf817710b6edef5f2940",
- "5401fdb1d638c2bc5b68241560cddac0"
- ],
- "name": "Rattus norvegicus",
- "@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/f3490d7f-8f7f-4b40-b238-963dcac84412"
- }
- ],
- "name": "Whole Brain ",
- "alias": "Whole brain"
- }
- ],
- "species": [
- "Rattus norvegicus",
- "Mus musculus"
- ],
- "name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)",
- "files": [],
"fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/f7a7d460-8724-4cd1-a06e-457eb8954fbd",
"contributors": [
"Danbolt, Nils C.",
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index bda610f0bdb7f4e6ec89146dc2c9e1333f7d4f10..e693ad311d68ca9a450a5e40c3a4d488e942da71 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -3,6 +3,7 @@ const { getCommonSenseDsFilter } = require('./supplements/commonSense')
const { hasPreview } = require('./supplements/previewFile')
const path = require('path')
const fs = require('fs')
+const { getIdFromFullId } = require('../../common/util')
let getPublicAccessToken
@@ -58,12 +59,18 @@ const populateSet = (flattenedRegions, set = new Set()) => {
if (!(set instanceof Set)) throw `set needs to be an instance of Set`
if (!(flattenedRegions instanceof Array)) throw `flattenedRegions needs to be an instance of Array`
for (const region of flattenedRegions) {
- const { name, relatedAreas } = region
- if (name) set.add(name)
- if (relatedAreas && relatedAreas instanceof Array && relatedAreas.length > 0) {
+ const { name, relatedAreas, fullId } = region
+ if (fullId) {
+ set.add(
+ getIdFromFullId(fullId)
+ )
+ }
+ if (relatedAreas && Array.isArray(relatedAreas)) {
for (const relatedArea of relatedAreas) {
- if(typeof relatedArea === 'string') set.add(relatedArea)
- else console.warn(`related area not an instance of String. skipping`, relatedArea)
+ const { fullId } = relatedArea
+ set.add(
+ getIdFromFullId(fullId)
+ )
}
}
}
@@ -137,7 +144,9 @@ initPrArray.push(
const datasetRegionExistsInParcellationRegion = async (prs, atlasPrSet = new Set()) => {
if (!(atlasPrSet instanceof Set)) throw `atlasPrSet needs to be a set!`
await Promise.all(initPrArray)
- return prs.some(({ name, alias }) => atlasPrSet.has(alias) || atlasPrSet.has(name))
+ return prs.some(({ fullId }) => atlasPrSet.has(
+ getIdFromFullId(fullId)
+ ))
}
const templateNameToIdMap = new Map([
@@ -309,6 +318,8 @@ const retry = async (fn, { timeout = defaultConfig.timeout, retries = defaultCon
}
module.exports = {
+ getIdFromFullId,
+ populateSet,
init,
getUserKGRequestParam,
retry,
diff --git a/deploy/datasets/util.spec.js b/deploy/datasets/util.spec.js
index a84b78208f395922cf9389954420bfd62f0409e0..4a84aa85f8f043d8e40680ff58af0acda789b3a5 100644
--- a/deploy/datasets/util.spec.js
+++ b/deploy/datasets/util.spec.js
@@ -1,11 +1,11 @@
-const { retry, datasetBelongsInTemplate, filterDatasets, datasetRegionExistsInParcellationRegion, _getParcellations } = require('./util')
+const { populateSet, datasetBelongToParcellation, retry, datasetBelongsInTemplate, filterDatasets, datasetRegionExistsInParcellationRegion, _getParcellations } = require('./util')
const { fake } = require('sinon')
const { assert, expect } = require('chai')
const waxholmv2 = require('./testData/waxholmv2')
const allen2015 = require('./testData/allen2015')
const bigbrain = require('./testData/bigbrain')
const humanReceptor = require('./testData/humanReceptor')
-const mni152 = require('./testData/mni152')
+const mni152JuBrain = require('./testData/mni152JuBrain')
const colin27 = require('./testData/colin27')
describe('datasets/util.js', () => {
@@ -60,11 +60,6 @@ describe('datasets/util.js', () => {
expect(belong).to.be.true
}
- for (const ds of mni152) {
-
- const belong = datasetBelongsInTemplate({ templateName: 'MNI 152 ICBM 2009c Nonlinear Asymmetric' })(ds)
- expect(belong).to.be.true
- }
for (const ds of colin27) {
const belong = datasetBelongsInTemplate({ templateName: 'MNI Colin 27' })(ds)
@@ -86,7 +81,7 @@ describe('datasets/util.js', () => {
const belong = datasetBelongsInTemplate({ templateName: 'MNI 152 ICBM 2009c Nonlinear Asymmetric' })(ds)
expect(belong).to.be.false
}
- for (const ds of mni152) {
+ for (const ds of mni152JuBrain) {
const belong = datasetBelongsInTemplate({ templateName: 'Big Brain (Histology)' })(ds)
expect(belong).to.be.false
@@ -108,6 +103,16 @@ describe('datasets/util.js', () => {
expect(flag).to.be.true
}
})
+
+ it('should filter mni152JuBrain jubrain properly', async () => {
+ const { juBrainSet } = await _getParcellations()
+ for (const ds of mni152JuBrain){
+
+ const { parcellationRegion: prs } = ds
+ const flag = await datasetRegionExistsInParcellationRegion(prs, juBrainSet)
+ expect(flag).to.be.true
+ }
+ })
})
describe('filterDatasets', () => {
@@ -118,7 +123,7 @@ describe('datasets/util.js', () => {
it('should filter waxholm v2 properly', async () => {
const filteredResult = await filterDatasets(waxholmv2, { parcellationName: 'Waxholm Space rat brain atlas v2' })
- expect(filteredResult).to.have.length(2)
+ expect(filteredResult).to.have.length(1)
})
it('should filter allen 2015 properly', async () => {
@@ -127,5 +132,104 @@ describe('datasets/util.js', () => {
expect(filteredResult).to.have.length(2)
})
})
+
+ describe('datasetBelongToParcellation', () => {
+ const dataset = {
+ parcellationAtlas:[{
+ name: 'jubrain v17'
+ }]
+ }
+ const parcellationName = 'jubrain v17'
+ const dataset2 = {
+ parcellationAtlas:[{
+ name: 'jubrain v18'
+ }]
+ }
+ const parcellationName2 = 'jubrain v18'
+ it('if parcellation name is undefined, will always return true', () => {
+ expect(
+ datasetBelongToParcellation({
+ parcellationName: null,
+ dataset
+ })
+ ).to.be.true
+ })
+ it('if parcellationAtlas of dataset is empty array, will always return true', () => {
+ expect(
+ datasetBelongToParcellation({
+ dataset: { parcellationAtlas: [] },
+ parcellationName
+ })).to.be.true
+ })
+ it('if parcellationAtlas of dataset is non empty array, and parcellationName is defined, should return false if they do not match', () => {
+ expect(
+ datasetBelongToParcellation({
+ dataset,
+ parcellationName: parcellationName2
+ })
+ ).to.be.false
+ })
+
+ it('if parcellationAtlas of dataset is non empty array, and parcellationName is defined, should return true if they do match', () => {
+ expect(
+ datasetBelongToParcellation({
+ dataset,
+ parcellationName
+ })
+ ).to.be.true
+ })
+ })
+
+ describe('populateSet', () => {
+ it('should populate relatedAreas', () => {
+ const area44 = {
+ "name": "Area 44 (IFG)",
+ "arealabel": "Area-44",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "relatedAreas": [
+ {
+ "name": "Area 44v",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
+ }
+ }
+ },
+ {
+ "name": "Area 44d",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ }
+ }
+ ],
+ "rgb": [
+ 54,
+ 74,
+ 75
+ ],
+ "children": [
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
+ }
+ }
+ }
+ const set = populateSet([area44])
+ expect(Array.from(set)).to.contain.members([
+ 'minds/core/parcellationregion/v1.0.0/7e5e7aa8-28b8-445b-8980-2a6f3fa645b3',
+ 'minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052',
+ 'minds/core/parcellationregion/v1.0.0/8a6be82c-5947-4fff-8348-cf9bf73e4f40',
+ ])
+ })
+
+ })
})
diff --git a/e2e/protractor.conf.js b/e2e/protractor.conf.js
index dc04206e5c9d5762246b1c6ef5a302f065845f17..344f4ca0ab7d79c29267d8419c30076cdeddca90 100644
--- a/e2e/protractor.conf.js
+++ b/e2e/protractor.conf.js
@@ -1,8 +1,23 @@
+
+// n.b. to start selenium, run npm run wd -- update && npm run wd -- start
+// n.b. you will need to run `npm i --no-save puppeteer`, so that normal download script does not download chrome binary
+const pptr = require('puppeteer')
+
+const SELENIUM_ADDRESS = process.env.SELENIUM_ADDRESS
+
exports.config = {
- seleniumAddress: 'http://localhost:4444/wd/hub',
+ ...(SELENIUM_ADDRESS
+ ? { seleniumAddress: SELENIUM_ADDRESS }
+ : { directConnect: true }
+ ),
specs: ['./src/**/*.e2e-spec.js'],
- // params: {
- // interactiveViewer : 'interactiveViewer',
- // viewer: 'viewer'
- // }
+ capabilities: {
+
+ // Use headless chrome
+ browserName: 'chrome',
+ chromeOptions: {
+ args: [ "--headless", "--disable-gpu", "--window-size=800,600"],
+ binary: pptr.executablePath()
+ }
+ }
}
\ No newline at end of file
diff --git a/e2e/src/iv.e2e-spec.js b/e2e/src/iv.e2e-spec.js
index 34fdb7c386b2c97e8f1858bd2c7356810bf0d820..fe1827499b897350eb09ac6c72b86d56c7ce08b2 100644
--- a/e2e/src/iv.e2e-spec.js
+++ b/e2e/src/iv.e2e-spec.js
@@ -1,8 +1,9 @@
-const url = 'http://localhost:8081/'
+const url = 'http://localhost:3000/'
const noErrorLog = require('./noErrorLog')
-const { getSelectedTemplate, getSelectedParcellation } = require('./ivApi')
+const { getSelectedTemplate, getSelectedParcellation, getSelectedRegions } = require('./ivApi')
const { getSearchParam, wait } = require('./util')
+const { URLSearchParams } = require('url')
describe('protractor works', () => {
it('protractor works', () => {
@@ -10,89 +11,52 @@ describe('protractor works', () => {
})
})
-describe('Home screen', () => {
- beforeEach(() => {
- browser.waitForAngularEnabled(false)
- browser.get(url)
- })
-
- it('get title works', () => {
- browser.getTitle()
- .then(title => {
- expect(title).toEqual('Interactive Atlas Viewer')
- })
- .catch(error => {
- console.error('error', error)
- })
+const pptr = require('puppeteer')
+const ATLAS_URL = process.env.ATLAS_URL || 'http://localhost:3000'
+if (ATLAS_URL.length === 0) throw new Error(`ATLAS_URL must either be left unset or defined.`)
+if (ATLAS_URL[ATLAS_URL.length - 1] === '/') throw new Error(`ATLAS_URL should not trail with a slash: ${ATLAS_URL}`)
- browser.executeScript('window.interactiveViewer')
- .then(result => expect(result).toBeDefined())
- browser.executeScript('window.viewer')
- .then(result => expect(result).toBeNull())
-
- noErrorLog(browser)
+let browser
+describe('IAV', () => {
+ beforeAll(async () => {
+ browser = await pptr.launch()
})
-})
-
-describe('Query param: ', () => {
- it('correctly defined templateSelected and selectedParcellation works', async () => {
-
- const searchParam = '?templateSelected=MNI+Colin+27&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas'
- browser.get(url + searchParam)
- browser.executeScript('window.interactiveViewer').then(result => expect(result).toBeDefined())
- browser.executeScript('window.viewer').then(result => expect(result).toBeDefined())
-
- await wait(browser)
-
- getSelectedTemplate(browser)
- .then(template => {
- expect(template.name).toBe('MNI Colin 27')
+ // TODO figure out how to get jasmine to compare array members
+ describe('api', () => {
+ const urlMni152JuBrain = `${ATLAS_URL}/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&cRegionsSelected=%7B%22jubrain+mni152+v18+left%22%3A%222%22%2C%22jubrain+mni152+v18+right%22%3A%222%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..70hl~.1w4W0~.70hk..1Pl9`
+ describe('selectRegion obs', () => {
+ it('should populate selected region with inherited properties', async () => {
+ const page = await browser.newPage()
+ await page.goto(urlMni152JuBrain, {waitUntil: 'networkidle2'})
+ const regions = await getSelectedRegions(page)
+ for (const region of regions){
+ expect(region.relatedAreas).toBeDefined()
+ expect(
+ region.relatedAreas.map(({ name }) => name).sort()
+ ).toEqual(
+ [
+ 'Area 44v',
+ 'Area 44d'
+ ].sort()
+ )
+ }
})
-
- getSelectedParcellation(browser)
- .then(parcellation => {
- expect(parcellation.name).toBe('JuBrain Cytoarchitectonic Atlas')
- })
-
- noErrorLog(browser)
+ })
})
-
- it('correctly defined templateSelected but incorrectly defined selectedParcellation work', async () => {
- const searchParam = '?templateSelected=MNI+Colin+27&parcellationSelected=NoName'
- browser.get(url + searchParam)
-
- await wait(browser)
-
- getSelectedTemplate(browser)
- .then(template => {
- expect(template.name).toBe('MNI Colin 27')
- })
- .catch(fail)
-
- Promise.all([
- getSelectedTemplate(browser),
- getSelectedParcellation(browser)
- ])
- .then(([template, parcellation]) => {
- expect(parcellation.name).toBe(template.parcellations[0].name)
- })
- .catch(fail)
-
- noErrorLog(browser)
- })
-
- it('incorrectly defined templateSelected should clear searchparam', async () => {
- const searchParam = '?templateSelected=NoName2&parcellationSelected=NoName'
- browser.get(url + searchParam)
-
- await wait(browser)
-
- getSearchParam(browser)
- .then(searchParam => {
- const templateSelected = searchParam.get('templateSelected')
- expect(templateSelected).toBeNull()
- })
- .catch(fail)
- })
-})
\ No newline at end of file
+
+ // tracking issue: https://github.com/HumanBrainProject/interactive-viewer/issues/455
+ // reenable when fixed
+ // describe('Url parsing', () => {
+
+ // it('incorrectly defined templateSelected should clear searchparam', async () => {
+ // const search = '/?templateSelected=NoName2&parcellationSelected=NoName'
+ // const page = await browser.newPage()
+ // await page.goto(`${ATLAS_URL}${search}`, {waitUntil: 'networkidle2'})
+ // await page.waitFor(500)
+ // const searchParam = await getSearchParam(page)
+ // const searchParamObj = new URLSearchParams(searchParam)
+ // expect(searchParamObj.get('templateSelected')).toBeNull()
+ // })
+ // })
+})
diff --git a/e2e/src/ivApi.js b/e2e/src/ivApi.js
index 825bee506911fff68b5dfd80924b73ed3f83df2f..ed5cc821e384c2d8b41e24eafa92da99dec835dc 100644
--- a/e2e/src/ivApi.js
+++ b/e2e/src/ivApi.js
@@ -8,4 +8,17 @@ exports.getSelectedParcellation = (browser) => new Promise((resolve, reject) =>
browser.executeAsyncScript('let sub = window.interactiveViewer.metadata.selectedParcellationBSubject.subscribe(obj => arguments[arguments.length - 1](obj));sub.unsubscribe()')
.then(resolve)
.catch(reject)
-})
\ No newline at end of file
+})
+
+exports.getSelectedRegions = async (page) => {
+ return await page.evaluate(async () => {
+ let region, sub
+ const getRegion = () => new Promise(rs => {
+ sub = interactiveViewer.metadata.selectedRegionsBSubject.subscribe(rs)
+ })
+
+ region = await getRegion()
+ sub.unsubscribe()
+ return region
+ })
+}
\ No newline at end of file
diff --git a/e2e/src/util.js b/e2e/src/util.js
index 030f2ccad62151ce4392c95704b211d57fb7af43..49892e2939ed39841494905fae28ab3f840d8790 100644
--- a/e2e/src/util.js
+++ b/e2e/src/util.js
@@ -1,12 +1,5 @@
-const {URLSearchParams} = require('url')
-
-exports.getSearchParam = (browser) => {
- const script = `
- const search = window.location.search;
- return search
- `
- return browser.executeScript(script)
- .then(search => new URLSearchParams(search))
+exports.getSearchParam = page => {
+ return page.evaluate(`window.location.search`)
}
exports.wait = (browser) => new Promise(resolve => {
diff --git a/package.json b/package.json
index 05771f5d2fe1fddf8da20c1369e70e4be49e407f..379e7f6290ab1c71387e8f93154f0c96908fd028 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,8 @@
"test": "karma start spec/karma.conf.js",
"e2e": "protractor e2e/protractor.conf",
"lint": "eslint src --ext .ts",
- "eslint": "eslint"
+ "eslint": "eslint",
+ "wd": "webdriver-manager"
},
"keywords": [],
"author": "",
diff --git a/spec/test.ts b/spec/test.ts
index 3d805584bd3e83f877957c738a748c010843c631..d2b2c152b7022cc9b536001f4602ec8e88017fef 100644
--- a/spec/test.ts
+++ b/spec/test.ts
@@ -19,4 +19,6 @@ getTestBed().initTestEnvironment(
);
const testContext = require.context('../src', true, /\.spec\.ts$/)
-testContext.keys().map(testContext)
\ No newline at end of file
+testContext.keys().map(testContext)
+
+require('../common/util.spec.js')
\ No newline at end of file
diff --git a/src/atlasViewer/atlasViewer.pluginService.service.spec.ts b/src/atlasViewer/atlasViewer.pluginService.service.spec.ts
index e9dd0b1fbce6e6c0c173ed429a34923675dfe694..acb0d9425edc4d4e54b72ab59ce658f9448f65b1 100644
--- a/src/atlasViewer/atlasViewer.pluginService.service.spec.ts
+++ b/src/atlasViewer/atlasViewer.pluginService.service.spec.ts
@@ -56,7 +56,6 @@
// expect(mockScript).toBeTruthy()
// })
// )
-
// it(
// 'template overrides templateURL',
// inject([HttpTestingController], (httpMock: HttpTestingController) => {
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index 3ce8bc85cc9c1bd30b2f6465c5cf2cb870390f18..315b9cf10744b9ce868fcd00e0630f9062272ccc 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -108,7 +108,14 @@
-8461290
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -163,7 +170,14 @@
-12582822
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -218,7 +232,14 @@
-8461290
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -272,7 +293,14 @@
"labelIndex": 187,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -317,7 +345,14 @@
"labelIndex": 22,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7aba8aef-6430-4fa7-ab54-8ecac558faed"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "SF (Amygdala)",
@@ -353,7 +388,14 @@
"labelIndex": 186,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "48929163-bf7b-4471-9f14-991c5225eced"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -408,7 +450,14 @@
-15985714
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3741c788-9412-4b8e-9ab4-9ca2d3a715ca"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "VTM (Amygdala)",
@@ -454,7 +503,14 @@
-17326733
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a964e6e6-8014-41a2-b975-754d75cbb6f2"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "IF (Amygdala)",
@@ -500,7 +556,14 @@
-17973684
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5a1391c8-6056-40e4-a19b-3774df42bd07"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -545,7 +608,14 @@
"labelIndex": 16,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7aba8aef-6430-4fa7-ab54-8ecac558faed"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "CM (Amygdala)",
@@ -591,7 +661,14 @@
-13743499
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7aba8aef-6430-4fa7-ab54-8ecac558faed"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -664,7 +741,14 @@
55690476
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "af9c4f39-63a4-409f-b306-e5965d639f37"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 5M (SPL)",
@@ -710,7 +794,14 @@
59763933
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "abe105cf-2c29-46af-af75-6b46fdb75137"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 7PC (SPL)",
@@ -756,7 +847,14 @@
62336656
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "763140d3-7ba0-4f28-b0ac-c6cbda2d14e1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 5L (SPL)",
@@ -802,7 +900,14 @@
69561773
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "64555f7f-1b33-4ffe-9853-be41e7a21096"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 7M (SPL)",
@@ -848,7 +953,14 @@
38515152
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "0aacea5c-bc9e-483f-8376-25f176ada158"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 7A (SPL)",
@@ -856,8 +968,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area 7A"
+ "relatedAreas": [
+ {
+ "name": "Area 7A",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "811f4adb-4a7c-45c1-8034-4afa9edf586a"
+ }
+ }
+ }
],
"rgb": [
38,
@@ -897,7 +1017,13 @@
62051683
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e26e999f-77ad-4934-9569-8290ed05ebda"
+ }
+ }
},
{
"name": "Area 5Ci (SPL)",
@@ -943,7 +1069,14 @@
45477854
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "07d08f74-af3d-4cbe-bc3c-f32b7f5c989f"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -998,7 +1131,14 @@
18500000
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "ab26cefd-f7d6-4442-8020-a6e418e673ff"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area OP4 (POperc)",
@@ -1044,7 +1184,14 @@
12300125
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b1e7f0d2-6d37-4047-9c2e-a08c3f1e2a16"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area OP3 (POperc)",
@@ -1090,7 +1237,14 @@
18514977
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f6f10b01-6c10-42cf-8129-f5aaf307a36b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area OP1 (POperc)",
@@ -1136,7 +1290,14 @@
18151001
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "402ec28d-0809-4226-91a4-900d9303291b"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -1191,7 +1352,14 @@
56291435
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "c9753e82-80ca-4074-a704-9dd2c4c0d58b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 3b (PostCG)",
@@ -1200,7 +1368,15 @@
"labelIndex": null,
"synonyms": [],
"relatedAreas": [
- "Area 3b"
+ {
+ "name": "Area 3b",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "74304fe9-452e-4ca3-97a3-8cf3459bb1a0"
+ }
+ }
+ }
],
"rgb": [
239,
@@ -1240,7 +1416,13 @@
47310887
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b84f67bb-5d9f-4daf-a8d6-15f63f901bd4"
+ }
+ }
},
{
"name": "Area 3a (PostCG)",
@@ -1286,7 +1468,14 @@
36367169
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2657ecc1-da69-4a37-9b37-66ae95f9623c"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 2 (PostCS)",
@@ -1332,7 +1521,14 @@
52910085
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9147ae9-5cf0-41b2-89a3-e6e6df07bef1"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -1349,8 +1545,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PFm"
+ "relatedAreas": [
+ {
+ "name": "Area PFm",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3455ada4-48c3-4748-ae38-2fe3f376f0fc"
+ }
+ }
+ }
],
"rgb": [
53,
@@ -1390,7 +1594,13 @@
39537196
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "411edde9-685f-464b-970c-a929f9a4067c"
+ }
+ }
},
{
"name": "Area PFop (IPL)",
@@ -1398,8 +1608,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PFop"
+ "relatedAreas": [
+ {
+ "name": "Area PFop",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b4397c40-82e1-4d62-b97a-44e8d04b428b"
+ }
+ }
+ }
],
"rgb": [
146,
@@ -1439,7 +1657,13 @@
26279323
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e8262e56-88fe-4006-b078-def4d78416b8"
+ }
+ }
},
{
"name": "Area PF (IPL)",
@@ -1447,8 +1671,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PF"
+ "relatedAreas": [
+ {
+ "name": "Area PF",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f4e177a6-1b2c-48d5-a62c-91949ba636e4"
+ }
+ }
+ }
],
"rgb": [
226,
@@ -1488,7 +1720,13 @@
31797118
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "18e5e1b0-6c25-4f55-a967-0834d2bd3ee4"
+ }
+ }
},
{
"name": "Area PGp (IPL)",
@@ -1496,8 +1734,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PGp"
+ "relatedAreas": [
+ {
+ "name": "Area PGp",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "1b00a0e4-9493-43ff-bfbd-b02119064813"
+ }
+ }
+ }
],
"rgb": [
92,
@@ -1537,7 +1783,13 @@
31755974
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b3ef6947-76c9-4935-bbc6-8b2329c0967b"
+ }
+ }
},
{
"name": "Area PGa (IPL)",
@@ -1545,8 +1797,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PGa"
+ "relatedAreas": [
+ {
+ "name": "Area PGa",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d5b168a3-a92e-4ab3-8b4d-61e58e5b7a1c"
+ }
+ }
+ }
],
"rgb": [
42,
@@ -1586,7 +1846,13 @@
31733304
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d7f6c5be-93c6-4a16-8939-4420329d4147"
+ }
+ }
},
{
"name": "Area PFt (IPL)",
@@ -1594,8 +1860,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PFt"
+ "relatedAreas": [
+ {
+ "name": "Area PFt",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9ff7fcc4-a88b-4bf8-be07-1386a3760a96"
+ }
+ }
+ }
],
"rgb": [
120,
@@ -1635,7 +1909,13 @@
39924515
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "847cef50-7340-470d-8580-327b4ce9db19"
+ }
+ }
},
{
"name": "Area PFcm (IPL)",
@@ -1643,8 +1923,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area PFcm"
+ "relatedAreas": [
+ {
+ "name": "Area PFcm",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f07d441f-452f-471b-ac7c-0d3c2ae16fb2"
+ }
+ }
+ }
],
"rgb": [
98,
@@ -1684,7 +1972,13 @@
24592525
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "10502c3a-f20e-44fa-b985-786d6888d4bb"
+ }
+ }
}
]
},
@@ -1739,7 +2033,14 @@
37156498
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a78998c2-99d4-4738-bbda-82a317f713f1"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -1794,7 +2095,14 @@
34275566
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9717dec-0310-4078-a4ae-294170b4fb37"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP3 (IPS)",
@@ -1840,7 +2148,14 @@
50509215
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "700ac6db-870d-44f1-8786-0c01207f992b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP8 (IPS)",
@@ -1886,7 +2201,14 @@
41158435
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a2c1acc7-7fdc-4fbd-90ee-729eda7fdff3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP4 (IPS)",
@@ -1932,7 +2254,14 @@
22440217
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5875bfe2-99ca-4e50-bce2-61c201c3dd54"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP7 (IPS)",
@@ -1978,7 +2307,14 @@
27718516
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
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{
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@@ -2024,7 +2360,14 @@
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{
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@@ -2070,7 +2413,14 @@
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]
}
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{
"name": "Area hIP2 (IPS)",
@@ -2116,7 +2466,14 @@
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]
}
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]
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{
"name": "Area hOc3d (Cuneus)",
@@ -2226,7 +2590,14 @@
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]
}
- ]
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{
"name": "Area hOc6 (POS)",
@@ -2272,7 +2643,14 @@
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]
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@@ -2327,7 +2705,14 @@
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]
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{
"name": "Area hOc3v (LingG)",
@@ -2373,7 +2758,14 @@
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]
}
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@@ -2428,7 +2820,14 @@
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+ "relatedAreas": []
},
{
"name": "Area hOc1 (V1, 17, CalcS)",
@@ -2436,8 +2835,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
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- "Area hOc1"
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@@ -2532,7 +2945,14 @@
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]
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{
"name": "Area hOc4la (LOC)",
@@ -2578,7 +2998,14 @@
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]
}
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{
"name": "Area hOc4lp (LOC)",
@@ -2624,7 +3051,14 @@
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]
}
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@@ -2714,7 +3148,14 @@
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"children": []
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{
"name": "Area ifs1 (IFS)",
@@ -2750,7 +3191,14 @@
"labelIndex": 244,
"children": []
}
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{
"name": "Area ifj2 (IFS/PreS)",
@@ -2822,7 +3270,14 @@
"labelIndex": 245,
"children": []
}
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{
"name": "Area ifs3 (IFS)",
@@ -2858,7 +3313,14 @@
"labelIndex": 246,
"children": []
}
- ]
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]
},
@@ -2875,9 +3337,25 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
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- "Area 44d"
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+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
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+ {
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]
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+ "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
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},
{
"name": "Area 45 (IFG)",
@@ -2926,7 +3410,15 @@
"labelIndex": null,
"synonyms": [],
"relatedAreas": [
- "Area 45"
+ {
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+ "fullId": {
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@@ -3122,7 +3620,14 @@
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@@ -3177,7 +3682,14 @@
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]
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@@ -3232,7 +3744,14 @@
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]
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+ "kgId": "10dc5343-941b-4e3e-80ed-df031c33bbc6"
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},
{
"name": "Area Fp2 (FPole)",
@@ -3278,7 +3797,14 @@
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]
}
- ]
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}
]
},
@@ -3295,8 +3821,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area 4p"
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@@ -3336,7 +3870,13 @@
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]
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+ "kgId": "82e6e826-a439-41db-84ff-4674ca3d643a"
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},
{
"name": "Area 4a (PreCG)",
@@ -3382,7 +3922,14 @@
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]
}
- ]
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+ "kgId": "175848ff-4c55-47e3-a0ae-f905a14e03cd"
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@@ -3437,7 +3984,14 @@
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]
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]
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@@ -3492,7 +4046,14 @@
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]
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+ "relatedAreas": []
},
{
"name": "Area Fo1 (OFC)",
@@ -3538,7 +4099,14 @@
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]
}
- ]
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{
"name": "Area Fo2 (OFC)",
@@ -3584,7 +4152,14 @@
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]
}
- ]
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@@ -3740,7 +4315,14 @@
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]
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+ "kgId": "3fd2e113-ec08-407b-bc88-172c9285694a"
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+ "relatedAreas": []
},
{
"name": "Area Fo7 (OFC)",
@@ -3786,7 +4368,14 @@
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]
}
- ]
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+ "relatedAreas": []
},
{
"name": "Area Fo4 (OFC)",
@@ -3832,7 +4421,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "2cdee956-207a-4d4d-b051-bef80045210b"
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+ "relatedAreas": []
},
{
"name": "Area Fo6 (OFC)",
@@ -3878,7 +4474,14 @@
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]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "330ae178-557c-4bd0-a932-f138c0a05345"
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}
]
}
@@ -3942,7 +4545,14 @@
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]
}
- ]
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+ "kgId": "46cf08af-8086-4e8a-9e9f-182ca583bdf0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Ig2 (Insula)",
@@ -3988,7 +4598,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "49092952-1eef-4b89-b8bf-1bf1f25f149a"
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]
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@@ -4043,7 +4660,14 @@
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]
}
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+ "kgId": "110d0d7b-cb88-48ea-9caf-863f548dbe38"
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]
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@@ -4098,7 +4722,14 @@
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]
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- ]
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+ "kgId": "3d5729f5-55c6-412a-8fc1-41a95c71b13a"
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]
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@@ -4153,7 +4784,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "c22055c1-514f-4096-906b-abf57286053b"
+ }
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+ "relatedAreas": []
},
{
"name": "Area Id5 (Insula)",
@@ -4199,7 +4837,14 @@
165741
]
}
- ]
+ ],
+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e03cd3c6-d0be-481c-b906-9b39c1d0b641"
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+ "relatedAreas": []
},
{
"name": "Area Id4 (Insula)",
@@ -4245,7 +4890,14 @@
10987327
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f480ed72-5ca5-4d1f-8905-cbe9bedcfaee"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id6 (Insula)",
@@ -4291,7 +4943,14 @@
2772938
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
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}
]
}
@@ -4355,7 +5014,14 @@
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]
}
- ]
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+ "kgId": "68784b66-ff15-4b09-b28a-a2146c0f8907"
+ }
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+ "relatedAreas": []
},
{
"name": "Area STS2 (STS)",
@@ -4401,7 +5067,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "278fc30f-2e24-4046-856b-95dfaf561635"
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]
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@@ -4456,7 +5129,14 @@
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]
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- ]
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+ "fullId": {
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]
},
@@ -4511,7 +5191,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "677cd48c-70fa-4bbd-9f0a-ffdc7744bc0f"
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+ "relatedAreas": []
},
{
"name": "Area TE 1.1 (HESCHL)",
@@ -4557,7 +5244,14 @@
10842857
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e2969911-77eb-4b21-af70-216cab5285b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.0 (HESCHL)",
@@ -4565,8 +5259,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area Te1"
+ "relatedAreas": [
+ {
+ "name": "Area Te1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f424643e-9baf-4c50-9417-db1ac33dcd3e"
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],
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@@ -4606,7 +5308,13 @@
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]
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+ "kgId": "13e21153-2ba8-4212-b172-8894f1012225"
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}
]
},
@@ -4623,8 +5331,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area FG1"
+ "relatedAreas": [
+ {
+ "name": "Area FG1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6318e160-4ad2-4eec-8a2e-2df6fe07d8f4"
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],
"rgb": [
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@@ -4664,7 +5380,13 @@
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]
}
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+ "kgId": "39fb34a8-fd6d-4fba-898c-2f6167e40459"
+ }
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},
{
"name": "Area FG4 (FusG)",
@@ -4710,7 +5432,14 @@
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]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "fa602743-5f6e-49d1-9734-29dffaa95ff5"
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+ "relatedAreas": []
},
{
"name": "Area FG3 (FusG)",
@@ -4756,7 +5485,14 @@
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]
}
- ]
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+ "fullId": {
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+ }
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+ "relatedAreas": []
},
{
"name": "Area FG2 (FusG)",
@@ -4764,8 +5500,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area FG2"
+ "relatedAreas": [
+ {
+ "name": "Area FG2",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8f436328-4251-4706-ae38-767e1ab21c6f"
+ }
+ }
+ }
],
"rgb": [
67,
@@ -4805,7 +5549,13 @@
-16661544
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6e7a0441-4baa-4355-921b-50d23d07d50f"
+ }
+ }
}
]
}
@@ -4869,7 +5619,14 @@
11145614
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e6507a3d-f2f8-4c17-84ff-0e7297e836a0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p24ab (pACC)",
@@ -4915,7 +5672,14 @@
6891142
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5dbb1035-487c-4f43-b551-ccadcf058340"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s32 (sACC)",
@@ -4961,7 +5725,14 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "61b44255-ae3a-4a23-b1bc-7d303a48dbd3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 25 (sACC)",
@@ -5007,7 +5778,14 @@
-13530501
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9010ef76-accd-4308-9951-f37b6a10f42b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s24 (sACC)",
@@ -5053,7 +5831,14 @@
-10923181
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d4ea6cc5-1e1d-4212-966f-81fed01eb648"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p32 (pACC)",
@@ -5099,7 +5884,14 @@
10022042
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b09aaa77-f41b-4008-b8b9-f984b0417cf3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 33 (ACC)",
@@ -5145,7 +5937,14 @@
15680187
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b83a3330-b80e-42a0-b8d2-82f38784aa1d"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5200,15 +5999,30 @@
-34844921
]
}
- ]
+ ],
+ "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":[
- "CA1 (Hippocampus)"
+ "relatedAreas": [
+ {
+ "name": "CA1 (Hippocampus)",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bfc0beb7-310c-4c57-b810-2adc464bd02c"
+ }
+ }
+ }
],
"synonyms": [],
"rgb": [
@@ -5249,7 +6063,13 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a0d14d3e-bc30-41cf-8b28-540067897f80"
+ }
+ }
},
{
"name": "DG (Hippocampus)",
@@ -5295,7 +6115,14 @@
-11462629
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "0bea7e03-bfb2-4907-9d45-db9071ce627d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Subiculum (Hippocampus)",
@@ -5341,7 +6168,14 @@
-18015846
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e2dab4c-a140-440d-a322-c1679adef2d4"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "HATA (Hippocampus)",
@@ -5387,7 +6221,14 @@
-18866667
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9ec4a423-70fa-43cd-90b3-fbc26a3cbc6c"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -5469,7 +6310,14 @@
-32600000
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5524,7 +6372,14 @@
-37750665
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "58095aef-da69-43d4-887c-009c095cecce"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Ventral Dentate Nucleus (Cerebellum)",
@@ -5570,7 +6425,14 @@
-32527125
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "57282342-5a75-4e07-bcdc-2d368c517b71"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5625,7 +6487,14 @@
-30598446
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e8abfe3d-8b64-45c2-8853-314d82873273"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5680,7 +6549,14 @@
-32600000
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -5694,17 +6570,20 @@
},
{
"ngId": "fibre bundle long",
- "auxillaryMeshIndices": [ 65535 ],
+ "auxillaryMeshIndices": [
+ 65535
+ ],
"type": "parcellation",
"surfaceParcellation": true,
"ngData": null,
"name": "Fibre Bundle Atlas - Long Bundle",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "fcbb049b-edd5-4fb5-acbc-7bf8ee933e24"
- }],
- "properties": {
- },
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "fcbb049b-edd5-4fb5-acbc-7bf8ee933e24"
+ }
+ ],
+ "properties": {},
"regions": [
{
"name": "Arcuate - Left",
@@ -5966,15 +6845,19 @@
},
{
"ngId": "fibre bundle short",
- "auxillaryMeshIndices": [ 65535 ],
+ "auxillaryMeshIndices": [
+ 65535
+ ],
"type": "parcellation",
"surfaceParcellation": true,
"ngData": null,
"name": "Fibre Bundle Atlas - Short Bundle",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "f58e4425-6614-4ad9-ac26-5e946b1296cb"
- }],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "f58e4425-6614-4ad9-ac26-5e946b1296cb"
+ }
+ ],
"regions": [
{
"name": "Left Hemisphere",
@@ -7008,4 +7891,4 @@
"name": "ICBM 2009c Nonlinear Asymmetric",
"description": "An unbiased non-linear average of multiple subjects from the MNI152 database, which provides high-spatial resolution and signal-to-noise while not being biased towards a single brain (Fonov et al., 2011). This template space is widely used as a reference space in neuroimaging. HBP provides the JuBrain probabilistic cytoarchitectonic atlas (Amunts/Zilles, 2015) as well as a probabilistic atlas of large fibre bundles (Guevara, Mangin et al., 2017) in this space."
}
-}
+}
\ No newline at end of file
diff --git a/src/res/ext/bigbrain.json b/src/res/ext/bigbrain.json
index 2440a1ee9b1c54631a4fa82215c7b58123c1b5f5..601642cbacac7f21583452163add21ed3a97f4b4 100644
--- a/src/res/ext/bigbrain.json
+++ b/src/res/ext/bigbrain.json
@@ -4,10 +4,12 @@
"species": "Human",
"useTheme": "light",
"ngId": " grey value: ",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "e32f9053-38c9-4911-b868-845c56828f4d"
- }],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "e32f9053-38c9-4911-b868-845c56828f4d"
+ }
+ ],
"nehubaConfigURL": "nehubaConfig/bigbrainNehubaConfig",
"parcellations": [
{
@@ -43,7 +45,14 @@
4363384,
836825,
4887117
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "13e21153-2ba8-4212-b172-8894f1012225"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.1 (HESCHL)",
@@ -60,7 +69,14 @@
-11860944,
-3841071,
6062770
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e2969911-77eb-4b21-af70-216cab5285b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.2 (HESCHL)",
@@ -77,7 +93,14 @@
19474750,
7932494,
3511322
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "677cd48c-70fa-4bbd-9f0a-ffdc7744bc0f"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -99,7 +122,14 @@
3479937,
2702958,
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- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e1a3291-efdc-4ca6-a3d0-6c496c34639f"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -116,7 +146,14 @@
-3185950,
3919067,
-8346900
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "68784b66-ff15-4b09-b28a-a2146c0f8907"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area STS2 (STS)",
@@ -128,7 +165,14 @@
8584703,
6170348,
-11790982
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "278fc30f-2e24-4046-856b-95dfaf561635"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -150,7 +194,14 @@
-10496194,
13643679,
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- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a802f3dc-b7e5-48b7-9845-832a6e6f9b1c"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 6d2 (PreCG)",
@@ -162,7 +213,14 @@
-9255504,
27432072,
43445689
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "963c5281-67df-4d41-9b91-60b31cf150c0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 6ma (preSMA, mesial SFG)",
@@ -174,7 +232,14 @@
-9349145,
27783957,
38734627
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "07b4c6a1-8a24-4f88-8f73-b2ea06e1c2f3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 6mp (SMA, mesial SFG)",
@@ -186,7 +251,14 @@
-11566856,
15797100,
42172031
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "def99e8e-ce8f-4a62-bd5d-739948c4b010"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -203,7 +275,14 @@
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28973429,
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- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "266c1ada-1840-462f-8223-7ff2df457552"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -220,7 +299,14 @@
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33562602,
19086364
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a6a83284-829b-4385-9f83-7f1bc832c5a5"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifj2 (IFS/PreCS)",
@@ -244,7 +330,14 @@
-4044465,
40212624,
17596493
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d687d385-98d9-4b31-85db-4bc682cd0a31"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs2 (IFS)",
@@ -256,7 +349,14 @@
6807265,
40114241,
18114896
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "658a67d8-60c2-4bb4-8eaf-e54725eda261"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs3 (IFS)",
@@ -268,7 +368,14 @@
-2260366,
37593844,
19960703
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e555881e-7082-4ac0-b6cc-cd096f30d3dc"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs4 (IFS)",
@@ -280,7 +387,14 @@
-3440565,
37895181,
17378851
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "472dacc9-c27d-49c2-9e6f-a1cc3309c4ab"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -307,7 +421,14 @@
4800238,
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-24872710
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "030827d4-e0d1-4406-b71f-3f58dc2f9cca"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -329,7 +450,14 @@
-5671181,
-44793673,
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- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5875bfe2-99ca-4e50-bce2-61c201c3dd54"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP5 (IPS)",
@@ -341,7 +469,14 @@
-13546343,
-38230309,
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- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9717dec-0310-4078-a4ae-294170b4fb37"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP6 (IPS)",
@@ -353,7 +488,14 @@
-3723403,
-33064127,
32569712
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b9975f8e-f484-4e82-883a-5fd765855ae0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP7 (IPS)",
@@ -365,7 +507,14 @@
-5344588,
-43655931,
24702722
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9c6c3c96-8129-4e0e-aa22-a0fb435aab45"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -382,7 +531,14 @@
-4455614,
-44097379,
28855803
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a78998c2-99d4-4738-bbda-82a317f713f1"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -409,7 +565,14 @@
30,
250
],
- "children": []
+ "children": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hOc2 (V2, 18)",
@@ -426,7 +589,14 @@
100,
250
],
- "children": []
+ "children": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "04674a3c-bb3a-495e-a466-206355e630bd"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "dorsal occipital cortex",
@@ -441,7 +611,14 @@
-4399437,
-36706104,
15113374
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d72e0210-a910-4b15-bcaf-80c3433cd3e0"
+ }
+ },
+ "relatedAreas": []
}
]
}
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 9094492116566be46ff2869c02b27d01e40198d9..c9a3d19638ccd97efbd20da73e12547e6ce87a5a 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -115,7 +115,14 @@
-8347692
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -173,7 +180,14 @@
-11539130
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -231,7 +245,14 @@
-8347692
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -276,7 +297,14 @@
"children": [],
"status": "publicP"
}
- ]
+ ],
+ "fullId": {
+ "kg": {
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"name": "LB (Amygdala)",
@@ -303,7 +331,14 @@
"children": [],
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@@ -330,7 +365,14 @@
"children": [],
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{
"name": "SF (Amygdala)",
@@ -440,7 +496,14 @@
"children": [],
"status": "publicP"
}
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{
"name": "SF (Amygdala)",
@@ -479,7 +542,14 @@
"children": [],
"status": "publicP"
}
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{
"name": "CM (Amygdala)",
@@ -518,7 +588,14 @@
"children": [],
"status": "publicP"
}
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{
"name": "IF (Amygdala)",
@@ -625,7 +709,14 @@
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{
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@@ -674,7 +765,14 @@
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@@ -722,7 +820,14 @@
"children": [],
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{
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@@ -847,7 +959,14 @@
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{
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@@ -896,7 +1015,14 @@
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{
"name": "Area 7PC (SPL)",
@@ -945,7 +1071,14 @@
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{
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@@ -994,7 +1127,14 @@
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]
}
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{
"name": "Area 7P (SPL)",
@@ -1043,7 +1183,14 @@
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{
"name": "Area 5Ci (SPL)",
@@ -1092,7 +1239,14 @@
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{
"name": "Area 7A (SPL)",
@@ -1143,8 +1297,22 @@
}
],
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- "Area 7A"
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{
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@@ -1251,7 +1426,14 @@
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}
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{
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@@ -1300,7 +1482,14 @@
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]
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{
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]
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@@ -1368,7 +1564,15 @@
"doi": "https://doi.org/10.25493/2JK3-QXR",
"synonyms": [],
"relatedAreas": [
- "Area 3b"
+ {
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{
"name": "Area 1 (PostCG)",
@@ -1459,7 +1669,14 @@
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]
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{
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]
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{
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@@ -1557,7 +1781,14 @@
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@@ -1576,7 +1807,15 @@
"doi": "https://doi.org/10.25493/F1TJ-54W",
"synonyms": [],
"relatedAreas": [
- "Area PF"
+ {
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},
{
"name": "Area PFcm (IPL)",
@@ -1628,7 +1873,15 @@
"doi": "https://doi.org/10.25493/8DP8-8HE",
"synonyms": [],
"relatedAreas": [
- "Area PFcm"
+ {
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},
{
"name": "Area PGa (IPL)",
@@ -1680,7 +1939,15 @@
"doi": "https://doi.org/10.25493/V5HY-XTS",
"synonyms": [],
"relatedAreas": [
- "Area PGa"
+ {
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@@ -1722,7 +1989,13 @@
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},
{
"name": "Area PFt (IPL)",
@@ -1732,7 +2005,15 @@
"doi": "https://doi.org/10.25493/JGM9-ZET",
"synonyms": [],
"relatedAreas": [
- "Area PFt"
+ {
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+ "fullId": {
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},
{
"name": "Area PFm (IPL)",
@@ -1784,7 +2071,15 @@
"doi": "https://doi.org/10.25493/TB94-HRK",
"synonyms": [],
"relatedAreas": [
- "Area PFm"
+ {
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+ "fullId": {
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+ "kgId": "3455ada4-48c3-4748-ae38-2fe3f376f0fc"
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@@ -1826,7 +2121,13 @@
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},
{
"name": "Area PGp (IPL)",
@@ -1877,8 +2178,22 @@
}
],
"relatedAreas": [
- "Area PGp"
- ]
+ {
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},
{
"name": "Area PFop (IPL)",
@@ -1929,8 +2244,22 @@
}
],
"relatedAreas": [
- "Area PFop"
- ]
+ {
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@@ -1988,7 +2317,14 @@
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@@ -2046,7 +2382,14 @@
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{
"name": "Area hIP7 (IPS)",
@@ -2095,7 +2438,14 @@
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]
}
- ]
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+ "fullId": {
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{
"name": "Area hIP3 (IPS)",
@@ -2144,7 +2494,14 @@
50461950
]
}
- ]
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+ "fullId": {
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},
{
"name": "Area hIP2 (IPS)",
@@ -2193,7 +2550,14 @@
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]
}
- ]
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{
"name": "Area hIP4 (IPS)",
@@ -2242,7 +2606,14 @@
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]
}
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{
"name": "Area hIP5 (IPS)",
@@ -2291,7 +2662,14 @@
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]
}
- ]
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{
"name": "Area hIP6 (IPS)",
@@ -2340,7 +2718,14 @@
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]
}
- ]
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{
"name": "Area hIP8 (IPS)",
@@ -2389,7 +2774,14 @@
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]
}
- ]
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@@ -2456,7 +2848,14 @@
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{
"name": "Area hOc4d (Cuneus)",
@@ -2505,7 +2904,14 @@
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]
}
- ]
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+ "fullId": {
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{
"name": "Area hOc3d (Cuneus)",
@@ -2554,7 +2960,14 @@
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]
}
- ]
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@@ -2612,7 +3025,14 @@
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]
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{
"name": "Area hOc4v (LingG)",
@@ -2661,7 +3081,14 @@
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]
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@@ -2719,7 +3146,14 @@
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]
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{
"name": "Area hOc1 (V1, 17, CalcS)",
@@ -2770,8 +3204,22 @@
}
],
"relatedAreas": [
- "Area hOc1"
- ]
+ {
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+ "fullId": {
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+ "kgId": "b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
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]
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@@ -2829,7 +3277,14 @@
4086228
]
}
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+ "kgId": "9006ee6a-6dc1-4604-9f20-7e08b42d574d"
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+ "relatedAreas": []
},
{
"name": "Area hOc5 (LOC)",
@@ -2878,7 +3333,14 @@
3121699
]
}
- ]
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+ "fullId": {
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+ "relatedAreas": []
},
{
"name": "Area hOc4la (LOC)",
@@ -2927,7 +3389,14 @@
-779202
]
}
- ]
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+ "fullId": {
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+ "kgId": "94365b82-6204-4937-8b86-fe0433287938"
+ }
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+ "relatedAreas": []
}
]
}
@@ -2955,8 +3424,24 @@
"doi": "https://doi.org/10.25493/F9P8-ZVW",
"synonyms": [],
"relatedAreas": [
- "Area 44v",
- "Area 44d"
+ {
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+ "fullId": {
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+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
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+ {
+ "name": "Area 44d",
+ "fullId": {
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+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
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],
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@@ -2998,7 +3483,13 @@
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]
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+ "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
+ }
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},
{
"name": "Area 45 (IFG)",
@@ -3008,7 +3499,15 @@
"doi": "https://doi.org/10.25493/MR1V-BJ3",
"synonyms": [],
"relatedAreas": [
- "Area 45"
+ {
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+ "fullId": {
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+ "kgId": "131e6de8-b073-4f01-8f60-1bdb5a6c9a9a"
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],
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@@ -3050,7 +3549,13 @@
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]
}
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+ "kgId": "cb32e688-43f0-4ae3-9554-085973137663"
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}
]
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@@ -3108,7 +3613,14 @@
68442439
]
}
- ]
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+ "kgId": "963c5281-67df-4d41-9b91-60b31cf150c0"
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+ "relatedAreas": []
},
{
"name": "Area 6d1 (PreCG)",
@@ -3157,7 +3669,14 @@
68870890
]
}
- ]
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+ "fullId": {
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]
},
@@ -3215,7 +3734,14 @@
58355079
]
}
- ]
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]
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@@ -3273,7 +3799,14 @@
53334281
]
}
- ]
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+ "fullId": {
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+ "kgId": "266c1ada-1840-462f-8223-7ff2df457552"
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]
},
@@ -3331,7 +3864,14 @@
-317043
]
}
- ]
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+ "fullId": {
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+ "kgId": "10dc5343-941b-4e3e-80ed-df031c33bbc6"
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+ "relatedAreas": []
},
{
"name": "Area Fp2 (FPole)",
@@ -3380,7 +3920,14 @@
-509606
]
}
- ]
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+ "fullId": {
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+ "kgId": "3bf7bde1-cc06-4657-b296-380275f9d4b8"
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+ "relatedAreas": []
}
]
},
@@ -3399,7 +3946,15 @@
"doi": "https://doi.org/10.25493/5HSF-81J",
"synonyms": [],
"relatedAreas": [
- "Area 4p"
+ {
+ "name": "Area 4p",
+ "fullId": {
+ "kg": {
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+ "kgId": "861ab96a-c4b5-4ba6-bd40-1e80d4680f89"
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],
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@@ -3441,7 +3996,13 @@
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]
}
- ]
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+ "kgId": "82e6e826-a439-41db-84ff-4674ca3d643a"
+ }
+ }
},
{
"name": "Area 4a (PreCG)",
@@ -3490,7 +4051,14 @@
68068112
]
}
- ]
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+ "fullId": {
+ "kg": {
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+ "kgId": "175848ff-4c55-47e3-a0ae-f905a14e03cd"
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}
]
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@@ -3548,7 +4116,14 @@
57534028
]
}
- ]
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+ "fullId": {
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+ "kgId": "def99e8e-ce8f-4a62-bd5d-739948c4b010"
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}
]
},
@@ -3606,7 +4181,14 @@
-22481988
]
}
- ]
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+ "fullId": {
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+ "kgId": "3864cb8c-f277-4de6-9f8d-c76d71d7e9a9"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo3 (OFC)",
@@ -3655,7 +4237,14 @@
-20231493
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "741f6a9e-cfd7-4173-ac7d-ee616c29555e"
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+ "relatedAreas": []
},
{
"name": "Area Fo2 (OFC)",
@@ -3704,7 +4293,14 @@
-20593342
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "30a04d2b-58e1-43d7-8b8f-1f0b598382d0"
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]
},
@@ -3869,7 +4465,14 @@
-4983615
]
}
- ]
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+ "fullId": {
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+ "kgId": "3fd2e113-ec08-407b-bc88-172c9285694a"
+ }
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+ "relatedAreas": []
},
{
"name": "Area Fo4 (OFC)",
@@ -3918,7 +4521,14 @@
-15509742
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2cdee956-207a-4d4d-b051-bef80045210b"
+ }
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+ "relatedAreas": []
},
{
"name": "Area Fo6 (OFC)",
@@ -3967,7 +4577,14 @@
-12457353
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "330ae178-557c-4bd0-a932-f138c0a05345"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo7 (OFC)",
@@ -4016,7 +4633,14 @@
-13777644
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "1b882148-fcdd-4dbe-b33d-659957840e9e"
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+ "relatedAreas": []
}
]
}
@@ -4083,7 +4707,14 @@
9071429
]
}
- ]
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+ "fullId": {
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+ "kgId": "46cf08af-8086-4e8a-9e9f-182ca583bdf0"
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+ "relatedAreas": []
},
{
"name": "Area Ig3 (Insula)",
@@ -4132,7 +4763,14 @@
13916877
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "10dba769-4f6c-40f9-8ffd-e0cce71c5adb"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Ig2 (Insula)",
@@ -4181,7 +4819,14 @@
5703657
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "49092952-1eef-4b89-b8bf-1bf1f25f149a"
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}
]
},
@@ -4239,7 +4884,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "110d0d7b-cb88-48ea-9caf-863f548dbe38"
+ }
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+ "relatedAreas": []
}
]
},
@@ -4297,7 +4949,14 @@
2446009
]
}
- ]
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+ "fullId": {
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+ "kgId": "3d5729f5-55c6-412a-8fc1-41a95c71b13a"
+ }
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}
]
},
@@ -4355,7 +5014,14 @@
3759834
]
}
- ]
+ ],
+ "fullId": {
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+ "kgId": "cf9dea67-649d-4034-ae57-ec389f339277"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id1 (Insula)",
@@ -4404,7 +5070,14 @@
-4688027
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "c22055c1-514f-4096-906b-abf57286053b"
+ }
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+ "relatedAreas": []
},
{
"name": "Area Id3 (Insula)",
@@ -4453,7 +5126,14 @@
-9042586
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3dcfcfc2-035c-4785-a820-a671f2104ac3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id5 (Insula)",
@@ -4502,7 +5182,14 @@
607357
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e03cd3c6-d0be-481c-b906-9b39c1d0b641"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id6 (Insula)",
@@ -4551,7 +5238,14 @@
3041624
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "31bbe92d-e5e8-4cf4-be5d-e6b12c71a107"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id4 (Insula)",
@@ -4600,7 +5294,14 @@
10858017
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f480ed72-5ca5-4d1f-8905-cbe9bedcfaee"
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+ "relatedAreas": []
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]
}
@@ -4667,7 +5368,14 @@
-16067930
]
}
- ]
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+ "fullId": {
+ "kg": {
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+ "kgId": "278fc30f-2e24-4046-856b-95dfaf561635"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area STS1 (STS)",
@@ -4716,7 +5424,14 @@
-5712544
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "68784b66-ff15-4b09-b28a-a2146c0f8907"
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}
]
},
@@ -4774,7 +5489,14 @@
-1027621
]
}
- ]
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+ "fullId": {
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]
},
@@ -4832,7 +5554,14 @@
52747
]
}
- ]
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+ "fullId": {
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+ "kgId": "677cd48c-70fa-4bbd-9f0a-ffdc7744bc0f"
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+ "relatedAreas": []
},
{
"name": "Area TE 1.1 (HESCHL)",
@@ -4881,7 +5610,14 @@
10308962
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e2969911-77eb-4b21-af70-216cab5285b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.0 (HESCHL)",
@@ -4891,7 +5627,15 @@
"doi": "https://doi.org/10.25493/MV3G-RET",
"synonyms": [],
"relatedAreas": [
- "Area Te1"
+ {
+ "name": "Area Te1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f424643e-9baf-4c50-9417-db1ac33dcd3e"
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],
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@@ -4933,7 +5677,13 @@
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]
}
- ]
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+ "kgId": "13e21153-2ba8-4212-b172-8894f1012225"
+ }
+ }
}
]
},
@@ -4952,7 +5702,15 @@
"doi": "https://doi.org/10.25493/F2JH-KVV",
"synonyms": [],
"relatedAreas": [
- "Area FG2"
+ {
+ "name": "Area FG2",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8f436328-4251-4706-ae38-767e1ab21c6f"
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],
"rgb": [
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@@ -4994,7 +5752,13 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "6e7a0441-4baa-4355-921b-50d23d07d50f"
+ }
+ }
},
{
"name": "Area FG3 (FusG)",
@@ -5043,7 +5807,14 @@
-15533822
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "023f8ef7-c266-4c45-8bf2-4a17dc52985b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area FG1 (FusG)",
@@ -5094,8 +5865,22 @@
}
],
"relatedAreas": [
- "Area FG1"
- ]
+ {
+ "name": "Area FG1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6318e160-4ad2-4eec-8a2e-2df6fe07d8f4"
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+ }
+ }
},
{
"name": "Area FG4 (FusG)",
@@ -5105,7 +5890,15 @@
"doi": "https://doi.org/10.25493/13RG-FYV",
"synonyms": [],
"relatedAreas": [
- "Area FG2"
+ {
+ "name": "Area FG2",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8f436328-4251-4706-ae38-767e1ab21c6f"
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],
"rgb": [
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@@ -5147,7 +5940,13 @@
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]
}
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}
]
}
@@ -5214,7 +6013,14 @@
12002406
]
}
- ]
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+ "fullId": {
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+ "kgId": "e6507a3d-f2f8-4c17-84ff-0e7297e836a0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 25 (sACC)",
@@ -5263,7 +6069,14 @@
-12174863
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9010ef76-accd-4308-9951-f37b6a10f42b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p24ab (pACC)",
@@ -5312,7 +6125,14 @@
7809963
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5dbb1035-487c-4f43-b551-ccadcf058340"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s32 (sACC)",
@@ -5361,7 +6181,14 @@
-12141905
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "61b44255-ae3a-4a23-b1bc-7d303a48dbd3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 33 (ACC)",
@@ -5410,7 +6237,14 @@
16125051
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b83a3330-b80e-42a0-b8d2-82f38784aa1d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p32 (pACC)",
@@ -5459,7 +6293,14 @@
12436058
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b09aaa77-f41b-4008-b8b9-f984b0417cf3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s24 (sACC)",
@@ -5508,7 +6349,14 @@
-9257019
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d4ea6cc5-1e1d-4212-966f-81fed01eb648"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5566,7 +6414,14 @@
-17871795
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9ec4a423-70fa-43cd-90b3-fbc26a3cbc6c"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Entorhinal Cortex",
@@ -5615,15 +6470,30 @@
-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":[
- "CA1 (Hippocampus)"
+ "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": [],
@@ -5667,7 +6537,13 @@
-11142814
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a0d14d3e-bc30-41cf-8b28-540067897f80"
+ }
+ }
},
{
"name": "DG (Hippocampus)",
@@ -5716,7 +6592,14 @@
-10596203
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "0bea7e03-bfb2-4907-9d45-db9071ce627d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Subiculum (Hippocampus)",
@@ -5765,7 +6648,14 @@
-15923499
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e2dab4c-a140-440d-a322-c1679adef2d4"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -5850,7 +6740,14 @@
-31489418
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5908,7 +6805,14 @@
-36586280
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "58095aef-da69-43d4-887c-009c095cecce"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Ventral Dentate Nucleus (Cerebellum)",
@@ -5957,7 +6861,14 @@
-31385609
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "57282342-5a75-4e07-bcdc-2d368c517b71"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -6015,7 +6926,14 @@
-29040632
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e8abfe3d-8b64-45c2-8853-314d82873273"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -6073,7 +6991,14 @@
-31489418
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
}
diff --git a/src/res/ext/waxholmRatV2_0.json b/src/res/ext/waxholmRatV2_0.json
index 58c045cb923f560434ec224ee815a2bd800e22d9..6b0c9fd80c19f7692d1473dfc4819d08b159a7f1 100644
--- a/src/res/ext/waxholmRatV2_0.json
+++ b/src/res/ext/waxholmRatV2_0.json
@@ -4,7 +4,7 @@
"species": "Rat",
"useTheme": "dark",
"ngId": "template",
- "otherNgIds":[
+ "otherNgIds": [
"templateUnMasked"
],
"nehubaConfigURL": "nehubaConfig/waxholmRatV2_0NehubaConfig",
@@ -13,1545 +13,1576 @@
"ngId": "v3",
"type": "parcellation",
"name": "Waxholm Space rat brain atlas v3",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "e80f9946-1aa9-494b-b81a-9048ca9afdbe"
- }],
- "regions": [{
- "ngId": "v3",
- "name": "Whole brain",
- "labelIndex": null,
- "rgb": null,
- "children":[
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "White matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 67,
- "name": "corpus callosum and associated subcortical white matter",
- "rgb": [
- 255,
- 110,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Anterior commissure",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 36,
- "name": "anterior commissure, anterior part",
- "rgb": [
- 124,
- 252,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 37,
- "name": "anterior commissure, posterior part",
- "rgb": [
- 255,
- 186,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 73,
- "name": "anterior commissure",
- "rgb": [
- 255,
- 79,
- 206
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Hippocampal white matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 6,
- "name": "alveus of the hippocampus",
- "rgb": [
- 255,
- 0,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 38,
- "name": "ventral hippocampal commissure",
- "rgb": [
- 174,
- 0,
- 232
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 52,
- "name": "fornix",
- "rgb": [
- 21,
- 192,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 59,
- "name": "fimbria of the hippocampus",
- "rgb": [
- 0,
- 255,
- 29
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Corticofugal pathways",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 1,
- "name": "descending corticofugal pathways",
- "rgb": [
- 255,
- 52,
- 39
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 85,
- "name": "pyramidal decussation",
- "rgb": [
- 114,
- 9,
- 212
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Medial lemniscus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 34,
- "name": "medial lemniscus",
- "rgb": [
- 212,
- 255,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 84,
- "name": "medial lemniscus decussation",
- "rgb": [
- 65,
- 150,
- 255
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Thalamic tracts",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 53,
- "name": "mammillothalamic tract",
- "rgb": [
- 238,
- 186,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 54,
- "name": "commissural stria terminalis",
- "rgb": [
- 173,
- 255,
- 47
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 60,
- "name": "fasciculus retroflexus",
- "rgb": [
- 244,
- 67,
- 69
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 61,
- "name": "stria medullaris of the thalamus",
- "rgb": [
- 0,
- 255,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 62,
- "name": "stria terminalis",
- "rgb": [
- 238,
- 117,
- 51
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 80,
- "name": "habenular commissure",
- "rgb": [
- 69,
- 235,
- 202
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 63,
- "name": "posterior commissure",
- "rgb": [
- 255,
- 0,
- 218
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Facial nerve",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 35,
- "name": "facial nerve",
- "rgb": [
- 255,
- 25,
- 240
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 72,
- "name": "ascending fibers of the facial nerve",
- "rgb": [
- 179,
- 28,
- 53
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 57,
- "name": "genu of the facial nerve",
- "rgb": [
- 250,
- 244,
- 247
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Optic fiber system and supraoptic decussation",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 41,
- "name": "optic nerve",
- "rgb": [
- 48,
- 218,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 42,
- "name": "optic tract and optic chiasm",
- "rgb": [
- 38,
- 126,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 83,
- "name": "supraoptic decussation",
- "rgb": [
- 250,
- 170,
- 64
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 76,
- "name": "spinal trigeminal tract",
- "rgb": [
- 250,
- 128,
- 114
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "White matter of the tectum",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 46,
- "name": "commissure of the superior colliculus",
- "rgb": [
- 33,
- 230,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 68,
- "name": "brachium of the superior colliculus",
- "rgb": [
- 188,
- 32,
- 173
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 69,
- "name": "inferior colliculus, commissure",
- "rgb": [
- 255,
- 42,
- 39
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 146,
- "name": "inferior colliculus, brachium",
- "rgb": [
- 176,
- 58,
- 72
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Cerebellar and precerebellar white matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 7,
- "name": "inferior cerebellar peduncle",
- "rgb": [
- 52,
- 255,
- 13
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 78,
- "name": "middle cerebellar peduncle",
- "rgb": [
- 134,
- 204,
- 76
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 79,
- "name": "transverse fibers of the pons",
- "rgb": [
- 128,
- 170,
- 255
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "White matter of the brainstem",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Lateral lemniscus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 140,
- "name": "lateral lemniscus, commissure",
- "rgb": [
- 255,
- 29,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 141,
- "name": "lateral lemniscus",
- "rgb": [
- 255,
- 166,
- 0
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 129,
- "name": "acoustic striae",
- "rgb": [
- 255,
- 217,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 130,
- "name": "trapezoid body",
- "rgb": [
- 213,
- 255,
- 0
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 157,
- "name": "auditory radiation",
- "rgb": [
- 244,
- 156,
- 255
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Gray matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Olfactory system",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 64,
- "name": "glomerular layer of the accessory olfactory bulb",
- "rgb": [
- 15,
- 109,
- 230
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 65,
- "name": "glomerular layer of the olfactory bulb",
- "rgb": [
- 255,
- 227,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 66,
- "name": "olfactory bulb",
- "rgb": [
- 255,
- 135,
- 0
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Cerebral cortex including the neocortex and the hippocampus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Neocortex",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 77,
- "name": "frontal association cortex",
- "rgb": [
- 206,
- 211,
- 7
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 92,
- "name": "neocortex",
- "rgb": [
- 3,
- 193,
- 45
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 10,
- "name": "cingulate cortex, area 2",
- "rgb": [
- 29,
- 104,
- 235
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 108,
- "name": "postrhinal cortex",
- "rgb": [
- 40,
- 112,
- 130
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 109,
- "name": "presubiculum",
- "rgb": [
- 80,
- 123,
- 175
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 110,
- "name": "parasubiculum",
- "rgb": [
- 23,
- 54,
- 96
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 112,
- "name": "perirhinal area 35",
- "rgb": [
- 205,
- 51,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 113,
- "name": "perirhinal area 36",
- "rgb": [
- 112,
- 48,
- 160
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 114,
- "name": "entorhinal cortex",
- "rgb": [
- 122,
- 187,
- 51
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 115,
- "name": "lateral entorhinal cortex",
- "rgb": [
- 90,
- 111,
- 47
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Auditory cortex",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 151,
- "name": "primary auditory cortex",
- "rgb": [
- 255,
- 215,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 152,
- "name": "secondary auditory cortex, dorsal area",
- "rgb": [
- 240,
- 255,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 153,
- "name": "secondary auditory cortex, ventral area",
- "rgb": [
- 216,
- 191,
- 216
- ],
- "children": []
- }
- ]
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Allocortex",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 95,
- "name": "cornu ammonis 3",
- "rgb": [
- 165,
- 131,
- 107
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 96,
- "name": "dentate gyrus",
- "rgb": [
- 91,
- 45,
- 10
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 97,
- "name": "cornu ammonis 2",
- "rgb": [
- 255,
- 255,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 98,
- "name": "cornu ammonis 1",
- "rgb": [
- 217,
- 104,
- 13
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 99,
- "name": "fasciola cinereum",
- "rgb": [
- 255,
- 0,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 100,
- "name": "subiculum",
- "rgb": [
- 255,
- 192,
- 0
- ],
- "children": []
- }
- ]
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 30,
- "name": "striatum",
- "rgb": [
- 129,
- 79,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 31,
- "name": "globus pallidus",
- "rgb": [
- 255,
- 145,
- 186
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 32,
- "name": "entopeduncular nucleus",
- "rgb": [
- 26,
- 231,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 3,
- "name": "subthalamic nucleus",
- "rgb": [
- 0,
- 0,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 82,
- "name": "basal forebrain region",
- "rgb": [
- 225,
- 240,
- 13
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 40,
- "name": "septal region",
- "rgb": [
- 255,
- 8,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Thalamus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 39,
- "name": "thalamus",
- "rgb": [
- 0,
- 100,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 147,
- "name": "medial geniculate body, medial division",
- "rgb": [
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"name": "Waxholm Space rat brain atlas v1",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "f40e466b-8247-463a-a4cb-56dfe68e7059"
- }],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "f40e466b-8247-463a-a4cb-56dfe68e7059"
+ }
+ ],
"regions": [
{
"ngId": "v1_01",
"name": "Whole brain",
"labelIndex": null,
"rgb": null,
- "children":[
-
+ "children": [
{
"name": "White matter",
"labelIndex": null,
@@ -4718,7 +4767,14 @@
},
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a844d80f-1d94-41a0-901a-14ae257519db"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "inferior olive",
@@ -4885,33 +4941,47 @@
},
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b2b56201-472c-4f70-842f-cf2133eacaba"
+ }
+ },
+ "relatedAreas": []
}
],
"properties": {
"name": "Waxholm Space rat brain atlas v1",
"description": "Waxholm Space atlas of the Sprague Dawley rat brain, first iteration with major brain regions delineated (76 structures).",
- "publications": [{
- "cite": "https://www.nitrc.org/frs/?group_id=1081",
- "doi": "https://www.nitrc.org/frs/?group_id=1081"
- },{
- "doi": "10.1016/j.neuroimage.2014.04.001",
- "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
- }]
+ "publications": [
+ {
+ "cite": "https://www.nitrc.org/frs/?group_id=1081",
+ "doi": "https://www.nitrc.org/frs/?group_id=1081"
+ },
+ {
+ "doi": "10.1016/j.neuroimage.2014.04.001",
+ "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
+ }
+ ]
}
}
],
"properties": {
"name": "Waxholm Space rat brain MRI/DTI",
"description": "MRI/DTI template of adult male Sprague Dawley rat brain.",
- "publications": [{
- "doi": "10.1016/j.neuroimage.2014.04.001",
- "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
- },{
- "cite": "RRID: SCR_017124"
- },{
- "doi": "https://www.nitrc.org/projects/whs-sd-atlas",
- "cite": "https://www.nitrc.org/projects/whs-sd-atlas"
- }]
+ "publications": [
+ {
+ "doi": "10.1016/j.neuroimage.2014.04.001",
+ "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
+ },
+ {
+ "cite": "RRID: SCR_017124"
+ },
+ {
+ "doi": "https://www.nitrc.org/projects/whs-sd-atlas",
+ "cite": "https://www.nitrc.org/projects/whs-sd-atlas"
+ }
+ ]
}
}
\ No newline at end of file
diff --git a/src/services/effect/effect.ts b/src/services/effect/effect.ts
index 043ff4c116bd86a34155c4048e35d61c8c9b4400..f6565910f7d9da8e9949fc698065bd0971d4e4b6 100644
--- a/src/services/effect/effect.ts
+++ b/src/services/effect/effect.ts
@@ -2,11 +2,11 @@ import { Injectable, OnDestroy } from "@angular/core";
import { Actions, Effect, ofType } from "@ngrx/effects";
import { select, Store } from "@ngrx/store";
import { fromEvent, merge, Observable, Subscription } from "rxjs";
-import { filter, map, shareReplay, switchMap, take, withLatestFrom } from "rxjs/operators";
+import { filter, map, shareReplay, switchMap, take, withLatestFrom, startWith, tap, distinctUntilChanged, mapTo } from "rxjs/operators";
import { worker } from 'src/atlasViewer/atlasViewer.workerService.service'
import { LoggingService } from "../logging.service";
import { ADD_TO_REGIONS_SELECTION_WITH_IDS, DESELECT_REGIONS, NEWVIEWER, SELECT_PARCELLATION, SELECT_REGIONS, SELECT_REGIONS_WITH_ID, UPDATE_PARCELLATION } from "../state/viewerState.store";
-import { generateLabelIndexId, getNgIdLabelIndexFromId, IavRootStoreInterface, recursiveFindRegionWithLabelIndexId } from '../stateStore.service';
+import { generateLabelIndexId, getNgIdLabelIndexFromId, IavRootStoreInterface, recursiveFindRegionWithLabelIndexId, getMultiNgIdsRegionsLabelIndexMap, GENERAL_ACTION_TYPES } from '../stateStore.service';
@Injectable({
providedIn: 'root',
@@ -21,8 +21,12 @@ export class UseEffects implements OnDestroy {
this.subscriptions.push(
this.newParcellationSelected$.subscribe(parcellation => {
worker.postMessage({
- type: `PROPAGATE_NG_ID`,
+ type: `PROPAGATE_PARC_REGION_ATTR`,
parcellation,
+ inheritAttrsOpts: {
+ ngId: (parcellation as any ).ngId,
+ relatedAreas: []
+ }
})
}),
)
@@ -85,6 +89,19 @@ export class UseEffects implements OnDestroy {
}
}),
)
+
+ this.updateSelectedRegion$ = this.actions$.pipe(
+ ofType(UPDATE_PARCELLATION),
+ withLatestFrom(this.regionsSelected$),
+ map(([{ updatedParcellation }, regionsSelected]) => {
+ const map = getMultiNgIdsRegionsLabelIndexMap(updatedParcellation)
+ const newRS = regionsSelected.map(({ ngId, labelIndex }) => map.get(ngId).get(labelIndex))
+ return {
+ type: SELECT_REGIONS,
+ selectRegions: newRS
+ }
+ })
+ )
}
private regionsSelected$: Observable<any[]>
@@ -105,11 +122,24 @@ export class UseEffects implements OnDestroy {
ofType(NEWVIEWER),
)
+ // trigger for rebuilding the parcellation
private newParcellationSelected$ = merge(
- this.newViewer$,
- this.parcellationSelected$,
+ this.actions$.pipe(
+ ofType(NEWVIEWER)
+ ),
+ this.actions$.pipe(
+ ofType(SELECT_PARCELLATION)
+ ),
+ this.actions$.pipe(
+ ofType(GENERAL_ACTION_TYPES.APPLY_STATE)
+ )
).pipe(
- map(({selectParcellation}) => selectParcellation),
+ withLatestFrom(this.store$.pipe(
+ select('viewerState'),
+ select('parcellationSelected')
+ )),
+ map(([_, parcellation]) => parcellation),
+ filter(v => !!v)
)
private updatedParcellation$ = this.store$.pipe(
@@ -119,6 +149,9 @@ export class UseEffects implements OnDestroy {
shareReplay(1),
)
+ @Effect()
+ public updateSelectedRegion$: Observable<any>
+
@Effect()
public onDeselectRegions: Observable<any>
@@ -198,7 +231,7 @@ export class UseEffects implements OnDestroy {
* side effect of selecting a parcellation means deselecting all regions
*/
@Effect()
- public onParcellationSelected$ = this.newParcellationSelected$.pipe(
+ public onParcellationSelected$ = this.parcellationSelected$.pipe(
map(() => ({
type: SELECT_REGIONS,
selectRegions: [],
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.spec.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d0fe83f9512cfb7b595fe059b67646823e0f6012
--- /dev/null
+++ b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.spec.ts
@@ -0,0 +1,472 @@
+import { regionsEqual, FilterDataEntriesByRegion } from './filterDataEntriesByRegion.pipe'
+
+const cytoPmapHoc1 = {
+ "formats": [
+ "NIFTI"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "imaging"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [
+ {
+ "name": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+ },
+ {
+ "name": "MNI Colin 27",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+ }
+ ],
+ "methods": [
+ "silver staining",
+ "magnetic resonance imaging (MRI)",
+ "probability mapping",
+ "cytoarchitectonic mapping"
+ ],
+ "custodians": [
+ "Amunts, Katrin"
+ ],
+ "project": [
+ "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
+ ],
+ "description": "This dataset contains the distinct architectonic Area hOc1 (V1, 17, CalcS) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the JuBrain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area hOc1 (V1, 17, CalcS). The probability map of Area hOc1 (V1, 17, CalcS) are provided in the NifTi format for each brain reference space and hemisphere. The JuBrain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "parcellationAtlas": [
+ {
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "id": [
+ "deec923ec31a82f89a9c7c76a6fefd6b",
+ "e2d45e028b6da0f6d9fdb9491a4de80a"
+ ]
+ }
+ ],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1 (V1, 17, CalcS)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Probabilistic cytoarchitectonic map of Area hOc1 (V1, 17, CalcS) (v2.4)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/5c669b77-c981-424a-858d-fe9f527dbc07",
+ "contributors": [
+ "Zilles, Karl",
+ "Schormann, Thorsten",
+ "Mohlberg, Hartmut",
+ "Malikovic, Aleksandar",
+ "Amunts, Katrin"
+ ],
+ "id": "5c669b77-c981-424a-858d-fe9f527dbc07",
+ "kgReference": [
+ "10.25493/MXJ6-6DH"
+ ],
+ "publications": [
+ {
+ "name": "Brodmann's Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable?",
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ]
+} as any
+
+const receptorhoc1 = {
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area hOc1 using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area hOc1",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/e715e1f7-2079-45c4-a67f-f76b102acfce",
+ "contributors": [
+ "Scheperjans, Filip",
+ "Schleicher, Axel",
+ "Eickhoff, Simon B.",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "0616d1e97b8be75de526bc265d9af540",
+ "kgReference": [
+ "10.25493/P8SD-JMH"
+ ],
+ "publications": [
+ {
+ "name": "Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex",
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+} as any
+
+const receptor44d = {
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area 44d using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area 44d",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area 44d",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/cb875c0d-97f4-4dbc-a9ce-472d8ba58c99",
+ "contributors": [
+ "Morosan, Patricia",
+ "Schleicher, Axel",
+ "Lenzen, Marianne",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "31397abd7aebcf13bf3b1d5eb2e2d400",
+ "kgReference": [
+ "10.25493/YQCR-1DQ"
+ ],
+ "publications": [
+ {
+ "name": "Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping",
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+} as any
+
+const mni152JuBrain = [
+ cytoPmapHoc1,
+ receptorhoc1,
+ receptor44d
+]
+
+describe('filterDataEntriesByRegion.pipe', () => {
+
+ describe('regionsEqual', () => {
+ it('should return true when fullId is equal', () => {
+ const region1 = {
+ "referenceSpaces": [
+ {
+ "name": "MNI Colin 27",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+ }
+ ],
+ "project": [
+ "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
+ ],
+ "parcellationAtlas": [
+ {
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "id": [
+ "deec923ec31a82f89a9c7c76a6fefd6b",
+ "e2d45e028b6da0f6d9fdb9491a4de80a"
+ ]
+ }
+ ],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "CA1 (Hippocampus)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/bfc0beb7-310c-4c57-b810-2adc464bd02c"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/1bbe0651-f646-4366-84f1-d37dc3c39bb3",
+ "id": "ca2d24694a35504816e7aefa30754f80",
+ "kgReference": [
+ "10.25493/W4WK-QSK"
+ ],
+ "preview": false
+ }
+
+ const { parcellationRegion } = region1
+ regionsEqual(parcellationRegion[0], {})
+ })
+
+ it('should return true when there is a related area', () => {
+
+ const region1 = {
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area 4p",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/861ab96a-c4b5-4ba6-bd40-1e80d4680f89"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/b3cac84d-2146-4750-a5f1-174076f82292",
+ "id": "ef2de94a2b532b91031ecf65300283cb",
+ "kgReference": [
+ "10.25493/J5JR-YH0"
+ ],
+ "preview": true
+ }
+ })
+ })
+
+ describe('FilterDataEntriesByRegion', () => {
+ const pipe = new FilterDataEntriesByRegion()
+ it('if selectedRegions is an empty array, should return original dataentries', () => {
+ expect(
+ pipe.transform(mni152JuBrain, [], [])
+ ).toEqual(mni152JuBrain)
+ })
+
+ it('if selectedRegions include area 44, should return receptor data', () => {
+ const selectedRegions = [
+ {
+ "name": "Area 44 (IFG) - left hemisphere",
+ "rgb": [
+ 54,
+ 74,
+ 75
+ ],
+ "labelIndex": 2,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "position": [
+ -54134365,
+ 11216664,
+ 15641040
+ ],
+ "relatedAreas": [
+ {
+ "name": "Area 44v",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
+ }
+ }
+ },
+ {
+ "name": "Area 44d",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ }
+ }
+ ],
+ }
+ ]
+ expect(
+ pipe.transform(mni152JuBrain, selectedRegions, [])
+ ).toEqual([receptor44d])
+ })
+ })
+})
\ No newline at end of file
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
index b666190984e62679cf2ace4b082e6c1333f5c04e..d976cba7a58f733ac321420e21af3ec9f7ea3073 100644
--- a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
+++ b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
@@ -1,9 +1,19 @@
import { Pipe, PipeTransform } from "@angular/core";
import { IDataEntry } from "src/services/stateStore.service";
+import { getIdFromFullId } from "common/util"
-const isSubRegion = (high, low) => (high.id && low.id && high.id === low.id) || high.name === low.name
+export const regionsEqual = (r1, r2) => {
+ const { fullId: r1FId, relatedAreas: rA1 = [] } = r1
+ const { fullId: r2FId, relatedAreas: rA2 = [] } = r2
+ const region2Aliases = new Set([getIdFromFullId(r2FId), ...rA2.map(({ fullId }) => getIdFromFullId(fullId))])
+ const region1Aliases = new Set([getIdFromFullId(r1FId), ...rA1.map(({ fullId }) => getIdFromFullId(fullId))])
+ return region1Aliases.has(getIdFromFullId(r2FId))
+ || region2Aliases.has(getIdFromFullId(r1FId))
+}
+
+const isSubRegion = (high, low) => regionsEqual(high, low)
? true
- : high.children && high.children.some
+ : high.children && Array.isArray(high.children)
? high.children.some(r => isSubRegion(r, low))
: false
@@ -18,29 +28,6 @@ export class FilterDataEntriesByRegion implements PipeTransform {
public transform(dataentries: IDataEntry[], selectedRegions: any[], flattenedAllRegions: any[]) {
return dataentries && selectedRegions && selectedRegions.length > 0
? dataentries
- .map(de => {
- /**
- * translate parcellationRegion to region representation
- */
- const newParcellationRegion = de.parcellationRegion.map(({name, id, ...rest}) => {
-
- const found = flattenedAllRegions.find(r => {
- /**
- * TODO replace pseudo id with real uuid
- */
- return (r.id && id && r.id === id)
- || r.name === name
- || r.relatedAreas && r.relatedAreas.length && r.relatedAreas.some(syn => syn === name)
- })
- return found
- ? { name, id, ...rest, ...found }
- : { name, id, ...rest }
- })
- return {
- ...de,
- parcellationRegion: newParcellationRegion,
- }
- })
.filter(de => filterSubSelect(de, selectedRegions))
: dataentries
}
diff --git a/src/ui/viewerStateController/regionSearch/regionSearch.component.ts b/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
index 01fb37ceb42e8522275cf26f86377ad180c18bfa..a86f9f553a19e28fa83b014c8a5a72f3fe3444e7 100644
--- a/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
+++ b/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
@@ -12,7 +12,7 @@ import { VIEWERSTATE_CONTROLLER_ACTION_TYPES } from "../viewerState.base";
import { LoggingService } from "src/services/logging.service";
const filterRegionBasedOnText = searchTerm => region => region.name.toLowerCase().includes(searchTerm.toLowerCase())
- || (region.relatedAreas && region.relatedAreas.some(relatedArea => relatedArea.toLowerCase().includes(searchTerm.toLowerCase())))
+ || (region.relatedAreas && region.relatedAreas.some(relatedArea => relatedArea.name.toLowerCase().includes(searchTerm.toLowerCase())))
const compareFn = (it, item) => it.name === item.name
diff --git a/src/util/worker.js b/src/util/worker.js
index f5313880e961c533e72b8429bdf2e46d73e9fa27..7d60b6c469e785db1147241ab018b1a13bf6dac0 100644
--- a/src/util/worker.js
+++ b/src/util/worker.js
@@ -2,7 +2,7 @@ const validTypes = [
'GET_LANDMARKS_VTK',
'GET_USERLANDMARKS_VTK',
'BUILD_REGION_SELECTION_TREE',
- 'PROPAGATE_NG_ID'
+ 'PROPAGATE_PARC_REGION_ATTR'
]
const validOutType = [
@@ -246,21 +246,28 @@ const rebuildSelectedRegion = (payload) => {
rebuiltSomeSelectedRegions: someActiveTreeBranch
})
}
+const recursivePropagateAttri = (region, inheritAttrsOpts) => {
-const propagateNgId = (parcellation) => {
- const recursivePropagateNgId = (region, {ngId}) => {
- return {
- ngId,
- ...region,
- ...( region.children && region.children.map
- ? {
- children: region.children.map(c => recursivePropagateNgId(c, { ngId: region.ngId || ngId }))
- }
- : {} )
- }
+ const inheritAttrs = Object.keys(inheritAttrsOpts)
+
+ const returnRegion = {
+ ...region
+ }
+ const newInhAttrsOpts = {}
+ for (const attr of inheritAttrs){
+ returnRegion[attr] = returnRegion[attr] || inheritAttrsOpts[attr]
+ newInhAttrsOpts[attr] = returnRegion[attr] || inheritAttrsOpts[attr]
}
- const regions = parcellation.regions && parcellation.regions.map
- ? parcellation.regions.map(r => recursivePropagateNgId(r, { ngId: parcellation.ngId }))
+ returnRegion.children = returnRegion.children.map(c => recursivePropagateAttri(c, newInhAttrsOpts))
+ return returnRegion
+}
+
+const propagateAttri = (parcellation, inheritAttrsOpts) => {
+ const inheritAttrs = Object.keys(inheritAttrsOpts)
+ if (inheritAttrs.indexOf('children') >= 0) throw new Error(`children attr cannot be inherited`)
+
+ const regions = Array.isArray(parcellation.regions)
+ ? parcellation.regions.map(r => recursivePropagateAttri(r, inheritAttrsOpts))
: []
return {
@@ -269,11 +276,9 @@ const propagateNgId = (parcellation) => {
}
}
-const processPropagateNgId = (payload) => {
- const { parcellation } = payload
- const p = parcellation.ngId
- ? parcellation
- : propagateNgId(parcellation)
+const processParcRegionAttr = (payload) => {
+ const { parcellation, inheritAttrsOpts } = payload
+ const p = propagateAttri(parcellation, inheritAttrsOpts)
postMessage({
type: 'UPDATE_PARCELLATION_REGIONS',
parcellation: p
@@ -293,8 +298,8 @@ onmessage = (message) => {
case 'BUILD_REGION_SELECTION_TREE':
rebuildSelectedRegion(message.data)
return
- case 'PROPAGATE_NG_ID':
- processPropagateNgId(message.data)
+ case 'PROPAGATE_PARC_REGION_ATTR':
+ processParcRegionAttr(message.data)
return
default:
console.warn('unhandled worker action', message)
diff --git a/tsconfig-aot.json b/tsconfig-aot.json
index 3a4115d6cfbc48fe643b9e85be53edab3f03ff25..7e541551de2f10d6e188764fe44de55db26581f5 100644
--- a/tsconfig-aot.json
+++ b/tsconfig-aot.json
@@ -8,7 +8,8 @@
"baseUrl": ".",
"paths": {
"third_party/*" : ["third_party/*"],
- "src/*" : ["src/*"]
+ "src/*" : ["src/*"],
+ "common/*": ["common/*"]
}
},
"angularCompilerOptions":{
diff --git a/tsconfig.json b/tsconfig.json
index f8617eab74953284b4d1a3f9ed6e234b455c10ab..59ee73b188970995b9fc4b12331823aa5ffef17c 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -8,7 +8,8 @@
"baseUrl": ".",
"paths": {
"third_party/*" : ["third_party/*"],
- "src/*" : ["src/*"]
+ "src/*" : ["src/*"],
+ "common/*": ["common/*"]
}
}
}
\ No newline at end of file
diff --git a/webpack.common.js b/webpack.common.js
index 9f680d8ef445b10c2a672197ea510f1dba6033c8..b432b1d516e6e026f7ea57cb6207a13507866848 100644
--- a/webpack.common.js
+++ b/webpack.common.js
@@ -31,7 +31,8 @@ module.exports = {
],
alias : {
"third_party" : path.resolve(__dirname,'third_party'),
- "src" : path.resolve(__dirname,'src')
+ "src" : path.resolve(__dirname,'src'),
+ "common": path.resolve(__dirname, 'common')
}
},
}
\ No newline at end of file