diff --git a/docs/releases/v2.3.0.md b/docs/releases/v2.3.0.md
index ee4951618e6a94b723043d410c410b2eb65dafa9..396db42327544c2bc94914ac71ad524ec242fbdd 100644
--- a/docs/releases/v2.3.0.md
+++ b/docs/releases/v2.3.0.md
@@ -2,4 +2,8 @@
## New features
-- Updated `README.md`
\ No newline at end of file
+- update dataset preview functionality, allow the previewing of png
+- improved the previewing of maps
+ - parse min and max, if these metadata are provided
+ - allowing for color maps other than jet
+- Updated `README.md`
diff --git a/src/glue.ts b/src/glue.ts
index bf94ffeb1133885acbdbff350ad7f9691d1df6a8..7be1c6b576e6cd9fa9df0354567110892428b251 100644
--- a/src/glue.ts
+++ b/src/glue.ts
@@ -11,6 +11,8 @@ import { HttpClient } from "@angular/common/http"
import { DS_PREVIEW_URL, getShader, PMAP_DEFAULT_CONFIG } from 'src/util/constants'
import { ngViewerActionAddNgLayer, ngViewerActionRemoveNgLayer, INgLayerInterface } from "./services/state/ngViewerState.store.helper"
import { ARIA_LABELS } from 'common/constants'
+import { NgLayersService } from "src/ui/layerbrowser/ngLayerService.service"
+import { EnumColorMapName } from "./util/colorMaps"
const PREVIEW_FILE_TYPES_NO_UI = [
EnumPreviewFileTypes.NIFTI,
@@ -165,6 +167,7 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
constructor(
private store$: Store<any>,
private http: HttpClient,
+ private layersService: NgLayersService,
@Optional() @Inject(ACTION_TO_WIDGET_TOKEN) private actionOnWidget: TypeActionToWidget<any>
){
if (!this.actionOnWidget) console.warn(`actionOnWidget not provided in DatasetPreviewGlue. Did you forget to provide it?`)
@@ -227,26 +230,47 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
).subscribe(([ { prvToShow, prvToDismiss }, templateSelected ]) => {
// TODO consider where to check validity of previewed nifti file
for (const prv of prvToShow) {
- const { url, filename } = prv
+
+ const { url, filename, name, volumeMetadata = {} } = prv
+ const { min, max, colormap = EnumColorMapName.VIRIDIS } = volumeMetadata || {}
+
const previewFileId = DatasetPreviewGlue.GetDatasetPreviewId(prv)
+
+ const shaderObj = {
+ ...PMAP_DEFAULT_CONFIG,
+ ...{ colormap },
+ ...( typeof min !== 'undefined' ? { lowThreshold: min } : {} ),
+ ...( max ? { highThreshold: max } : { highThreshold: 1 } )
+ }
+
const layer = {
- name: filename,
+ // name: filename,
+ name: name || filename,
id: previewFileId,
source : `nifti://${url}`,
mixability : 'nonmixable',
- shader : getShader(PMAP_DEFAULT_CONFIG),
+ shader : getShader(shaderObj),
annotation: `${DATASET_PREVIEW_ANNOTATION} ${filename}`
}
+
+ const { name: layerName } = layer
+ const { colormap: cmap, lowThreshold, highThreshold, removeBg } = shaderObj
+
+ this.layersService.highThresholdMap.set(layerName, highThreshold)
+ this.layersService.lowThresholdMap.set(layerName, lowThreshold)
+ this.layersService.colorMapMap.set(layerName, cmap)
+ this.layersService.removeBgMap.set(layerName, removeBg)
+
this.store$.dispatch(
ngViewerActionAddNgLayer({ layer })
)
}
for (const prv of prvToDismiss) {
- const { url, filename } = prv
+ const { url, filename, name } = prv
const previewFileId = DatasetPreviewGlue.GetDatasetPreviewId(prv)
const layer = {
- name: filename,
+ name: name || filename,
id: previewFileId,
source : `nifti://${url}`,
mixability : 'nonmixable',
diff --git a/src/index.html b/src/index.html
index 65ddf0e75d50a6ec7823dfc908b7e2ebc21b0d7b..e716dff44957037f1629b62b5d96a8c1a5ad0f0b 100644
--- a/src/index.html
+++ b/src/index.html
@@ -11,7 +11,7 @@
<link rel="stylesheet" href="theme.css">
<link rel="stylesheet" href="version.css">
- <script src="https://unpkg.com/kg-dataset-previewer@0.0.18/dist/kg-dataset-previewer/kg-dataset-previewer.js" defer>
+ <script src="https://unpkg.com/kg-dataset-previewer@0.0.19/dist/kg-dataset-previewer/kg-dataset-previewer.js" defer>
</script>
<title>Interactive Atlas Viewer</title>
diff --git a/src/main-common.ts b/src/main-common.ts
index 0ee0604988782cb519e4c9995e8d9ed80b831af7..6062eff8c344234b09fb1d20b1ea4af5f4b03882 100644
--- a/src/main-common.ts
+++ b/src/main-common.ts
@@ -2,6 +2,7 @@
import '!!file-loader?context=third_party&name=vanilla.html!third_party/vanilla.html'
import '!!file-loader?context=third_party&name=vanilla_styles.css!third_party/styles.css'
import '!!file-loader?context=third_party&name=vanilla_nehuba.js!third_party/vanilla_nehuba.js'
+import '!!file-loader?context=third_party&name=preinit_vanilla.html!third_party/preinit_vanilla.html'
/**
* Catching Safari 10 bug:
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index 1d7876bee0c9e0d46989e1cd52f37df23e64e3a0..e72d8a90d757ef16b9314d168fd11ab39ace6f5f 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -9516,6 +9516,35793 @@
]
}
]
+ },
+ {
+ "name": "DiFuMo Atlas (64 dimensions)",
+ "ngId": "DiFuMo Atlas (64 dimensions)",
+ "auxillaryMeshIndices": [
+ 65535
+ ],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2"
+ }
+ ],
+ "regions": [
+ {
+ "name": "Superior frontal sulcus",
+ "labelIndex": "1",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "1.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DefaultB",
+ "Yeo_networks17": "DefaultA",
+ "GM": "0.6899956156495173",
+ "WM": "0.18570919448320866",
+ "CSF": "0.11688445498918655"
+ }
+ },
+ {
+ "name": "Fusiform gyrus",
+ "labelIndex": "2",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "2.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "No network found",
+ "GM": "0.8447325231765037",
+ "WM": "0.02102643141862085",
+ "CSF": "0.13378859201455914"
+ }
+ },
+ {
+ "name": "Calcarine cortex posterior",
+ "labelIndex": "3",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "3.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "VisCent",
+ "Yeo_networks17": "VisPeri",
+ "GM": "0.601767818274053",
+ "WM": "0.3020671197728652",
+ "CSF": "0.0912973216275698"
+ }
+ },
+ {
+ "name": "Cingulate cortex posterior",
+ "labelIndex": "4",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "4.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DefaultB",
+ "Yeo_networks17": "DefaultA",
+ "GM": "0.7400859593248862",
+ "WM": "0.14036828520239494",
+ "CSF": "0.1195668910655905"
+ }
+ },
+ {
+ "name": "Parieto-occipital sulcus superior",
+ "labelIndex": "5",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "5.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "ContA",
+ "Yeo_networks17": "ContC",
+ "GM": "0.6401569112237818",
+ "WM": "0.2414921597679687",
+ "CSF": "0.11782554915712587"
+ }
+ },
+ {
+ "name": "Insula antero-superior",
+ "labelIndex": "6",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "6.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SalVentAttnA",
+ "Yeo_networks17": "SalVentAttnB",
+ "GM": "0.786372865071193",
+ "WM": "0.06417080012874092",
+ "CSF": "0.14549075149397567"
+ }
+ },
+ {
+ "name": "Superior temporal sulcus with angular gyrus",
+ "labelIndex": "7",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "7.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DefaultB",
+ "Yeo_networks17": "TempPar",
+ "GM": "0.7289689261090406",
+ "WM": "0.19352618334003086",
+ "CSF": "0.0760887281183381"
+ }
+ },
+ {
+ "name": "Planum temporale",
+ "labelIndex": "8",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "8.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SomMotA",
+ "Yeo_networks17": "SomMotB",
+ "GM": "0.6698659209540166",
+ "WM": "0.1910266837459853",
+ "CSF": "0.13332598308951646"
+ }
+ },
+ {
+ "name": "Cerebellum Crus II",
+ "labelIndex": "9",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "9.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "No network found",
+ "GM": "0.8185904861148258",
+ "WM": "0.1338739033486082",
+ "CSF": "0.04542831413786549"
+ }
+ },
+ {
+ "name": "Superior parts of Postcentral and Precentral gyri",
+ "labelIndex": "10",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "10.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SomMotA",
+ "Yeo_networks17": "DorsAttnB",
+ "GM": "0.3708748845575369",
+ "WM": "0.06203569095447033",
+ "CSF": "0.1800623844186744"
+ }
+ },
+ {
+ "name": "Transverse sinus",
+ "labelIndex": "11",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "11.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "No network found",
+ "GM": "0.7683739104554709",
+ "WM": "0.023967151704877586",
+ "CSF": "0.18954300759709386"
+ }
+ },
+ {
+ "name": "Paracentral gyrus RH",
+ "labelIndex": "12",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "12.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SomMotA",
+ "Yeo_networks17": "SomMotA",
+ "GM": "0.5306374774591351",
+ "WM": "0.3479044488382695",
+ "CSF": "0.1176783513756604"
+ }
+ },
+ {
+ "name": "Superior occipital gyrus",
+ "labelIndex": "13",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "13.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "VisCent",
+ "Yeo_networks17": "VisPeri",
+ "GM": "0.5586152516127496",
+ "WM": "0.28697033183706605",
+ "CSF": "0.11869489252408445"
+ }
+ },
+ {
+ "name": "Cingulate gyrus mid-posterior",
+ "labelIndex": "14",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "14.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DefaultB",
+ "Yeo_networks17": "ContC",
+ "GM": "0.7452027221344231",
+ "WM": "0.11458104451974745",
+ "CSF": "0.1401896263361808"
+ }
+ },
+ {
+ "name": "ventricles",
+ "labelIndex": "15",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "15.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "No network found",
+ "GM": "0.5967024501902108",
+ "WM": "0.2403387753233659",
+ "CSF": "0.16296436839860015"
+ }
+ },
+ {
+ "name": "Fusiform gyrus posterior",
+ "labelIndex": "16",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "16.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "VisCent",
+ "Yeo_networks17": "VisCent",
+ "GM": "0.7626315127910275",
+ "WM": "0.1665671393414221",
+ "CSF": "0.06815565457970252"
+ }
+ },
+ {
+ "name": "Superior frontal gyrus medial",
+ "labelIndex": "17",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "17.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SalVentAttnA",
+ "Yeo_networks17": "SalVentAttnA",
+ "GM": "0.6587145979633471",
+ "WM": "0.07825500493180974",
+ "CSF": "0.25475311800672945"
+ }
+ },
+ {
+ "name": "Precuneus superior",
+ "labelIndex": "18",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "18.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DorsAttnB",
+ "Yeo_networks17": "ContC",
+ "GM": "0.5608419562056097",
+ "WM": "0.05959337009837265",
+ "CSF": "0.2562661761850908"
+ }
+ },
+ {
+ "name": "Planum polare",
+ "labelIndex": "19",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "19.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SalVentAttnA",
+ "Yeo_networks17": "SomMotB",
+ "GM": "0.7553942181635669",
+ "WM": "0.0331071169214432",
+ "CSF": "0.2060875317942941"
+ }
+ },
+ {
+ "name": "Parieto-occipital sulcus middle",
+ "labelIndex": "20",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "20.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "VisCent",
+ "Yeo_networks17": "VisPeri",
+ "GM": "0.590863624165701",
+ "WM": "0.2897505050215277",
+ "CSF": "0.11865591921166073"
+ }
+ },
+ {
+ "name": "Cerebellum I-V",
+ "labelIndex": "21",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "21.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "No network found",
+ "GM": "0.7930338315508172",
+ "WM": "0.18133515241841824",
+ "CSF": "0.02562201265613615"
+ }
+ },
+ {
+ "name": "Superior fornix and isthmus",
+ "labelIndex": "22",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "22.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "DefaultC",
+ "GM": "0.395778158074814",
+ "WM": "0.05192834296459222",
+ "CSF": "0.552281473643165"
+ }
+ },
+ {
+ "name": "Anterior Cingulate Cortex",
+ "labelIndex": "23",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "23.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DefaultB",
+ "Yeo_networks17": "SalVentAttnB",
+ "GM": "0.7826330767531011",
+ "WM": "0.07566979891167905",
+ "CSF": "0.14171656568181354"
+ }
+ },
+ {
+ "name": "Descending occipital gyrus",
+ "labelIndex": "24",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "24.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "VisCent",
+ "Yeo_networks17": "VisCent",
+ "GM": "0.5837077720023389",
+ "WM": "0.3483014386740513",
+ "CSF": "0.06531219840042406"
+ }
+ },
+ {
+ "name": "Putamen",
+ "labelIndex": "25",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "25.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "No network found",
+ "Yeo_networks17": "No network found",
+ "GM": "0.5931855707283495",
+ "WM": "0.40345738952725374",
+ "CSF": "0.0033452801249732565"
+ }
+ },
+ {
+ "name": "Cingulate gyrus mid-anterior",
+ "labelIndex": "26",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "26.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "SalVentAttnA",
+ "Yeo_networks17": "SalVentAttnA",
+ "GM": "0.772303700700098",
+ "WM": "0.05080428803067855",
+ "CSF": "0.1659924892724604"
+ }
+ },
+ {
+ "name": "Superior parietal lobule posterior",
+ "labelIndex": "27",
+ "originDatasets": [
+ {
+ "kgId": "e472a8c7-d9f9-4e75-9d0b-b137cecbc6a2",
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "filename": "27.nii.gz"
+ }
+ ],
+ "ontologyMetadata": {
+ "Yeo_networks7": "DorsAttnB",
+ "Yeo_networks17": "DorsAttnA",
+ "GM": "0.5043998362415332",
+ "WM": "0.3680702636995562",
+ "CSF": "0.12285828269239095"
+ }
+ },
+ {
+ "name": "Paracentral lobule",
+ "labelIndex": "28",
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diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
index 69dd2a1de6769d5637c4641baf9097e68c49d69e..e8e145cf7f80374435b170d71915dc4cccc5faae 100644
--- a/src/res/ext/MNI152NehubaConfig.json
+++ b/src/res/ext/MNI152NehubaConfig.json
@@ -215,6 +215,161 @@
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diff --git a/src/res/ext/waxholmRatV2_0.json b/src/res/ext/waxholmRatV2_0.json
index a3800e9509ac9fa57d8782f3d85328d48b76a25e..c1c5851ebeabc305ef3dedc99e8a0bf602bf6bb3 100644
--- a/src/res/ext/waxholmRatV2_0.json
+++ b/src/res/ext/waxholmRatV2_0.json
@@ -9,6 +9,3196 @@
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+ "labelIndex": 262,
+ "name": "Paraventricular hypothalamic nucleus, anterior parvicellular part",
+ "rgb": [
+ 0,
+ 255,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 256,
+ "name": "Paraventricular hypothalamic nucleus, medial parvicellular part",
+ "rgb": [
+ 138,
+ 43,
+ 226
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 48,
+ "name": "hypothalamic region",
+ "rgb": [
+ 226,
+ 120,
+ 161
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 43,
+ "name": "pineal gland",
+ "rgb": [
+ 218,
+ 170,
+ 62
+ ],
+ "children": []
+ },
+ {
+ "name": "Midbrain",
+ "children": [
+ {
+ "name": "Substantia nigra",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 187,
+ "name": "Substantia nigra, reticular part",
+ "rgb": [
+ 99,
+ 197,
+ 18
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 188,
+ "name": "Substantia nigra, compact part",
+ "rgb": [
+ 255,
+ 255,
+ 127
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 189,
+ "name": "Substantia nigra, lateral part",
+ "rgb": [
+ 0,
+ 159,
+ 159
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 3,
+ "name": "subthalamic nucleus",
+ "rgb": [
+ 0,
+ 0,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 196,
+ "name": "Ventral tegmental area",
+ "rgb": [
+ 127,
+ 255,
+ 212
+ ],
+ "children": []
+ },
+ {
+ "name": "Tectum",
+ "children": [
+ {
+ "name": "Inferior colliculus",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 142,
+ "name": "inferior colliculus, dorsal cortex",
+ "rgb": [
+ 206,
+ 255,
+ 142
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 143,
+ "name": "inferior colliculus, central nucleus",
+ "rgb": [
+ 0,
+ 238,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 145,
+ "name": "inferior colliculus, external cortex",
+ "rgb": [
+ 48,
+ 136,
+ 203
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 94,
+ "name": "pretectal region",
+ "rgb": [
+ 255,
+ 87,
+ 30
+ ],
+ "children": []
+ },
+ {
+ "name": "Superior colliculus",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 50,
+ "name": "superficial gray layer of the superior colliculus",
+ "rgb": [
+ 86,
+ 0,
+ 221
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 55,
+ "name": "deeper layers of the superior colliculus",
+ "rgb": [
+ 225,
+ 151,
+ 15
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 317,
+ "name": "Intermediate gray layer of the superior colliculus",
+ "rgb": [
+ 250,
+ 240,
+ 230
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 318,
+ "name": "Intermediate white layer of the superior colliculus",
+ "rgb": [
+ 128,
+ 0,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 319,
+ "name": "Optic nerve layer of the superior colliculus",
+ "rgb": [
+ 50,
+ 205,
+ 50
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 320,
+ "name": "Zonal layer of the superior colliculus",
+ "rgb": [
+ 215,
+ 244,
+ 96
+ ],
+ "children": []
+ }
+ ]
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "Cerebellum",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 4,
+ "name": "molecular layer of the cerebellum",
+ "rgb": [
+ 255,
+ 255,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 5,
+ "name": "granule cell level of the cerebellum",
+ "rgb": [
+ 0,
+ 255,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "name": "Cerebellar nuclei",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 321,
+ "name": "Lateral (dentate) cerebellar nucleus",
+ "rgb": [
+ 80,
+ 244,
+ 62
+ ],
+ "children": [
+ {
+ "name": "Lateral (dentate) cerebellar nucleus",
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 326,
+ "name": "Lateral cerebellar nucleus, parvicellular part",
+ "rgb": [
+ 127,
+ 255,
+ 212
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 325,
+ "name": "Medial (fastigial) cerebellar nucleus",
+ "rgb": [
+ 255,
+ 192,
+ 203
+ ],
+ "children": [
+ {
+ "name": "Medial (fastigial) cerebellar nucleus",
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 327,
+ "name": "Medial cerebellar nucleus, lateral part",
+ "rgb": [
+ 255,
+ 140,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 328,
+ "name": "Medial cerebellar nucleus, dorsolateral protuberance",
+ "rgb": [
+ 143,
+ 188,
+ 143
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Interposed cerebellar nucleus",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 322,
+ "name": "Interposed cerebellar nucleus, anterior part",
+ "rgb": [
+ 123,
+ 104,
+ 238
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 323,
+ "name": "Interposed cerebellar nucleus, dorsolateral part",
+ "rgb": [
+ 255,
+ 165,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 324,
+ "name": "Interposed cerebellar nucleus, dorsomedial part",
+ "rgb": [
+ 173,
+ 216,
+ 230
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 329,
+ "name": "Interposed cerebellar nucleus, posterior parvicellular part",
+ "rgb": [
+ 220,
+ 20,
+ 60
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 330,
+ "name": "Interposed cerebellar nucleus, posterior part",
+ "rgb": [
+ 244,
+ 71,
+ 201
+ ],
+ "children": []
+ }
+ ]
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "Brainstem",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 47,
+ "name": "brainstem",
+ "rgb": [
+ 153,
+ 83,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "name": "Cochlear nucleus, ventral part",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 158,
+ "name": "ventral cochlear nucleus, anterior part",
+ "rgb": [
+ 34,
+ 152,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 159,
+ "name": "ventral cochlear nucleus, posterior part",
+ "rgb": [
+ 0,
+ 230,
+ 207
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 160,
+ "name": "ventral cochlear nucleus, cap area",
+ "rgb": [
+ 0,
+ 255,
+ 106
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 123,
+ "name": "ventral cochlear nucleus, granule cell layer",
+ "rgb": [
+ 0,
+ 12,
+ 255
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Cochlear nucleus, dorsal part",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 126,
+ "name": "dorsal cochlear nucleus, molecular layer",
+ "rgb": [
+ 92,
+ 156,
+ 211
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 127,
+ "name": "dorsal cochlear nucleus, fusiform and granule layer",
+ "rgb": [
+ 0,
+ 80,
+ 156
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 128,
+ "name": "dorsal cochlear nucleus, deep core",
+ "rgb": [
+ 197,
+ 238,
+ 255
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Superior olivary complex",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 131,
+ "name": "nucleus of the trapezoid body",
+ "rgb": [
+ 0,
+ 255,
+ 81
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 132,
+ "name": "superior paraolivary nucleus",
+ "rgb": [
+ 0,
+ 238,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 133,
+ "name": "medial superior olive",
+ "rgb": [
+ 219,
+ 239,
+ 61
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 134,
+ "name": "lateral superior olive",
+ "rgb": [
+ 35,
+ 76,
+ 190
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 135,
+ "name": "superior periolivary region",
+ "rgb": [
+ 1,
+ 153,
+ 21
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 136,
+ "name": "ventral periolivary nuclei",
+ "rgb": [
+ 0,
+ 174,
+ 255
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Nuclei of the lateral lemniscus",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 137,
+ "name": "lateral lemniscus, ventral nucleus",
+ "rgb": [
+ 255,
+ 0,
+ 115
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 138,
+ "name": "lateral lemniscus, intermediate nucleus",
+ "rgb": [
+ 171,
+ 16,
+ 91
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 139,
+ "name": "lateral lemniscus, dorsal nucleus",
+ "rgb": [
+ 108,
+ 18,
+ 91
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 163,
+ "name": "nucleus sagulum",
+ "rgb": [
+ 99,
+ 205,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "name": "Vestibular nuclei",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 301,
+ "name": "Superior vestibular nucleus",
+ "rgb": [
+ 238,
+ 232,
+ 170
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 304,
+ "name": "Lateral vestibular nucleus",
+ "rgb": [
+ 184,
+ 134,
+ 11
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 305,
+ "name": "Nucleus Y of the vestibular complex",
+ "rgb": [
+ 45,
+ 36,
+ 178
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 306,
+ "name": "Spinal vestibular nucleus",
+ "rgb": [
+ 255,
+ 20,
+ 147
+ ],
+ "children": []
+ },
+ {
+ "name": "Medial vestibular nucleus",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 308,
+ "name": "Medial vestibular nucleus, magnocellular part",
+ "rgb": [
+ 112,
+ 128,
+ 144
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 309,
+ "name": "Medial vestibular nucleus, parvicellular part",
+ "rgb": [
+ 34,
+ 139,
+ 34
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 337,
+ "name": "Medial vestibular nucleus, caudal part",
+ "rgb": [
+ 4,
+ 25,
+ 159
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 343,
+ "name": "Nucleus X of the vestibular nucleus",
+ "rgb": [
+ 40,
+ 117,
+ 10
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 312,
+ "name": "Abducens nucleus",
+ "rgb": [
+ 255,
+ 160,
+ 122
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 336,
+ "name": "Nucleus of efferents of vestibular nerve",
+ "rgb": [
+ 250,
+ 128,
+ 114
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 339,
+ "name": "Locus coeruleus",
+ "rgb": [
+ 255,
+ 127,
+ 80
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 310,
+ "name": "Vestibulocerebellar nucleus",
+ "rgb": [
+ 223,
+ 216,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 74,
+ "name": "inferior olive",
+ "rgb": [
+ 0,
+ 246,
+ 14
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 75,
+ "name": "spinal trigeminal nucleus",
+ "rgb": [
+ 91,
+ 241,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 56,
+ "name": "periventricular gray",
+ "rgb": [
+ 235,
+ 87,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 71,
+ "name": "interpeduncular nucleus",
+ "rgb": [
+ 63,
+ 192,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 51,
+ "name": "periaqueductal gray",
+ "rgb": [
+ 7,
+ 255,
+ 89
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 58,
+ "name": "pontine nuclei",
+ "rgb": [
+ 0,
+ 215,
+ 11
+ ],
+ "children": []
+ }
+ ]
+ }
+ ]
+ },
+ {
+ "name": "Ventricular system",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 33,
+ "name": "ventricular system",
+ "rgb": [
+ 2,
+ 44,
+ 255
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 125,
+ "name": "4th ventricle",
+ "rgb": [
+ 52,
+ 29,
+ 144
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Spinal cord",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 45,
+ "name": "spinal cord",
+ "rgb": [
+ 134,
+ 255,
+ 90
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 70,
+ "name": "central canal",
+ "rgb": [
+ 39,
+ 244,
+ 253
+ ],
+ "children": []
+ }
+ ]
+ },
+ {
+ "name": "Inner ear",
+ "children": [
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 119,
+ "name": "vestibular apparatus",
+ "rgb": [
+ 0,
+ 144,
+ 55
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 120,
+ "name": "cochlea",
+ "rgb": [
+ 0,
+ 255,
+ 29
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 121,
+ "name": "cochlear nerve",
+ "rgb": [
+ 253,
+ 148,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 122,
+ "name": "vestibular nerve",
+ "rgb": [
+ 253,
+ 50,
+ 0
+ ],
+ "children": []
+ },
+ {
+ "ngId": "WHS_SD_rat_atlas_v4_beta",
+ "labelIndex": 162,
+ "name": "spiral ganglion",
+ "rgb": [
+ 185,
+ 255,
+ 233
+ ],
+ "children": []
+ }
+ ]
+ }
+ ]
+ },
{
"ngId": "v3",
"type": "parcellation",
diff --git a/src/res/ext/waxholmRatV2_0NehubaConfig.json b/src/res/ext/waxholmRatV2_0NehubaConfig.json
index 0b76891b3b1ce20fdc08788c35c7ba506edc8984..e98b6ee833f6a6cb86c857e9114b0ec3d9294f09 100644
--- a/src/res/ext/waxholmRatV2_0NehubaConfig.json
+++ b/src/res/ext/waxholmRatV2_0NehubaConfig.json
@@ -204,6 +204,37 @@
1
]
]
+ },
+ "WHS_SD_rat_atlas_v4_beta": {
+ "type": "segmentation",
+ "source": "precomputed://https://neuroglancer-dev.humanbrainproject.org/precomputed/WHS_SD_rat/parcellations/WHS_SD_rat_atlas_v4_beta",
+ "selectedAlpha": 0.35,
+ "transform": [
+ [
+ 1,
+ 0,
+ 0,
+ -9550781
+ ],
+ [
+ 0,
+ 1,
+ 0,
+ -24355468
+ ],
+ [
+ 0,
+ 0,
+ 1,
+ -9707031
+ ],
+ [
+ 0,
+ 0,
+ 0,
+ 1
+ ]
+ ]
}
},
"navigation": {
diff --git a/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts b/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts
index 5161a4ed7c52d03b989f800e42d25cc57ffbd041..984f89702fc1f4df4e255c4bff4233a607cf300d 100644
--- a/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts
+++ b/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.component.ts
@@ -5,6 +5,7 @@ import { Observable, fromEvent, Subscription, of, throwError } from "rxjs";
import { switchMapTo, catchError, take, concatMap, map, retryWhen, delay } from "rxjs/operators";
import { DomSanitizer, SafeResourceUrl } from "@angular/platform-browser";
import { ARIA_LABELS } from 'common/constants'
+import { DS_PREVIEW_URL } from 'src/util/constants'
const {
DOWNLOAD_PREVIEW,
@@ -39,6 +40,7 @@ const fromPromiseRetry = ({ retries = 10, timeout = 100 } = {}) => {
export class PreviewComponentWrapper{
+ public DS_PREVIEW_URL = DS_PREVIEW_URL
public touched: boolean = false
public untouchedIndex: number = 0
diff --git a/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.template.html b/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.template.html
index 71c478682921cef2df732e485c0dc69594d33099..5419402d30a93f76016e49a793647bcbc1ca42d3 100644
--- a/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.template.html
+++ b/src/ui/databrowserModule/preview/previewComponentWrapper/previewCW.template.html
@@ -39,7 +39,7 @@
[darkmode]="darktheme$ | async"
[filename]="filename"
[kgId]="kgId"
- [backendUrl]="backendUrl"
+ [backendUrl]="backendUrl || DS_PREVIEW_URL"
#dataPreviewerStencilCmp>
</kg-dataset-previewer>
diff --git a/src/ui/layerbrowser/layerDetail/layerDetail.component.ts b/src/ui/layerbrowser/layerDetail/layerDetail.component.ts
index ce525450d66af85854ae715723c14ff6ad6ffd35..414bab57e2f2ef11e8232a7405e8b206d5707cda 100644
--- a/src/ui/layerbrowser/layerDetail/layerDetail.component.ts
+++ b/src/ui/layerbrowser/layerDetail/layerDetail.component.ts
@@ -2,7 +2,7 @@ import { Component, Input, OnChanges, ChangeDetectionStrategy, Optional, Inject
import { NgLayersService } from "../ngLayerService.service";
import { MatSliderChange } from "@angular/material/slider";
import { MatSlideToggleChange } from "@angular/material/slide-toggle";
-import { COLORMAP_IS_JET, getShader, PMAP_DEFAULT_CONFIG } from "src/util/constants";
+import { getShader } from "src/util/constants";
export const VIEWER_INJECTION_TOKEN = `VIEWER_INJECTION_TOKEN`
@@ -28,19 +28,12 @@ export class LayerDetailComponent implements OnChanges{
ngOnChanges(){
if (!this.layerName) return
- const isPmap = (this.fragmentMain.value as string).includes(COLORMAP_IS_JET)
- const { colormap, lowThreshold, removeBg } = PMAP_DEFAULT_CONFIG
- if (isPmap) {
- this.colormap = colormap
- this.lowThreshold = lowThreshold
- this.removeBg = removeBg
- }
-
this.lowThreshold = this.layersService.lowThresholdMap.get(this.layerName) || this.lowThreshold
this.highThreshold = this.layersService.highThresholdMap.get(this.layerName) || this.highThreshold
this.brightness = this.layersService.brightnessMap.get(this.layerName) || this.brightness
this.contrast = this.layersService.contrastMap.get(this.layerName) || this.contrast
this.removeBg = this.layersService.removeBgMap.get(this.layerName) || this.removeBg
+ this.colormap = this.layersService.colorMapMap.get(this.layerName) || this.colormap
}
public lowThreshold: number = 0
diff --git a/src/ui/layerbrowser/ngLayerService.service.ts b/src/ui/layerbrowser/ngLayerService.service.ts
index baf59a9a4191c27ea5ddffb72629148cdb1a1ab9..35bd949ba6885423862692dacdac94e35dc96a7b 100644
--- a/src/ui/layerbrowser/ngLayerService.service.ts
+++ b/src/ui/layerbrowser/ngLayerService.service.ts
@@ -1,4 +1,5 @@
import { Injectable } from "@angular/core";
+import { EnumColorMapName } from "src/util/colorMaps";
@Injectable({
providedIn: 'root'
@@ -10,4 +11,5 @@ export class NgLayersService{
public brightnessMap: Map<string, number> = new Map()
public contrastMap: Map<string, number> = new Map()
public removeBgMap: Map<string, boolean> = new Map()
+ public colorMapMap: Map<string, EnumColorMapName> = new Map()
}
diff --git a/src/ui/searchSideNav/searchSideNav.template.html b/src/ui/searchSideNav/searchSideNav.template.html
index d9f0f5b8aa3d25548cde01e6a735243afbc2e747..eb1ae006e424599bda673f2aa471b4e5a8ab93ec 100644
--- a/src/ui/searchSideNav/searchSideNav.template.html
+++ b/src/ui/searchSideNav/searchSideNav.template.html
@@ -69,7 +69,7 @@
</div>
-<div [hidden]>
+<div class="d-none">
<layer-browser
(nonBaseLayersChanged)="handleNonbaseLayerEvent($event)"
#layerBrowser>
diff --git a/src/util/colorMaps.ts b/src/util/colorMaps.ts
new file mode 100644
index 0000000000000000000000000000000000000000..ad3ab450b293f301dc90182328e1bd2b06002a7a
--- /dev/null
+++ b/src/util/colorMaps.ts
@@ -0,0 +1,204 @@
+export const COLORMAP_IS_DEFAULT = `// iav-colormap-default`
+
+export const COLORMAP_IS_JET = `// iav-colormap-is-jet`
+
+export const COLORMAP_IS_VIRIDIS = `// iav-colormap-is-viridis`
+export const COLORMAP_IS_MAGMA = `// iav-colormap-is-magma`
+export const COLORMAP_IS_PLASMA = `// iav-colormap-is-plasma`
+export const COLORMAP_IS_INFERNO = `// iav-colormap-is-inferno`
+
+export const COLORMAP_IS_GREYSCALE = `// iav-colormap-is-greyscale`
+
+export enum EnumColorMapName{
+ JET='jet',
+
+ VIRIDIS='viridis',
+ PLASMA='plasma',
+ MAGMA='magma',
+ INFERNO='inferno',
+
+ GREYSCALE='greyscale',
+}
+
+interface IColorMap{
+ /**
+ * header
+ */
+ header: string
+ /**
+ * appended before void main() {} block
+ */
+ premain: string
+ /**
+ * appended in void main(){} block
+ *
+ * input:
+ *
+ * float x;
+ *
+ * populate:
+ *
+ * vec3 rgb;
+ */
+ main: string
+}
+
+export const mapKeyColorMap = new Map<EnumColorMapName, IColorMap>([
+ [ EnumColorMapName.JET, {
+ header: COLORMAP_IS_JET,
+ /**
+ * The MIT License (MIT)
+
+ Copyright (c) 2015 kbinani
+
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+
+ The above copyright notice and this permission notice shall be included in all
+ copies or substantial portions of the Software.
+
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.
+
+ * <https://github.com/kbinani/colormap-shaders/blob/master/shaders/glsl/MATLAB_jet.frag>
+ */
+ premain: `
+ float colormap_red(float x) {
+ if (x < 0.7) {
+ return 4.0 * x - 1.5;
+ } else {
+ return -4.0 * x + 4.5;
+ }
+ }
+
+ float colormap_green(float x) {
+ if (x < 0.5) {
+ return 4.0 * x - 0.5;
+ } else {
+ return -4.0 * x + 3.5;
+ }
+ }
+
+ float colormap_blue(float x) {
+ if (x < 0.3) {
+ return 4.0 * x + 0.5;
+ } else {
+ return -4.0 * x + 2.5;
+ }
+ }
+ `,
+ main: `
+ float r = clamp(colormap_red(x), 0.0, 1.0);
+ float g = clamp(colormap_green(x), 0.0, 1.0);
+ float b = clamp(colormap_blue(x), 0.0, 1.0);
+ rgb=vec3(r,g,b);
+ `
+ } ],
+
+ [ EnumColorMapName.VIRIDIS, {
+ header: COLORMAP_IS_VIRIDIS,
+ /**
+ * created by mattz CC/0
+ * https://www.shadertoy.com/view/WlfXRN
+ */
+ premain: `
+ vec3 viridis(float t) {
+
+ const vec3 c0 = vec3(0.2777273272234177, 0.005407344544966578, 0.3340998053353061);
+ const vec3 c1 = vec3(0.1050930431085774, 1.404613529898575, 1.384590162594685);
+ const vec3 c2 = vec3(-0.3308618287255563, 0.214847559468213, 0.09509516302823659);
+ const vec3 c3 = vec3(-4.634230498983486, -5.799100973351585, -19.33244095627987);
+ const vec3 c4 = vec3(6.228269936347081, 14.17993336680509, 56.69055260068105);
+ const vec3 c5 = vec3(4.776384997670288, -13.74514537774601, -65.35303263337234);
+ const vec3 c6 = vec3(-5.435455855934631, 4.645852612178535, 26.3124352495832);
+
+ return c0+t*(c1+t*(c2+t*(c3+t*(c4+t*(c5+t*c6)))));
+ }
+ `,
+ main: 'rgb=viridis(x);'
+ } ],
+ [ EnumColorMapName.PLASMA, {
+ header: COLORMAP_IS_PLASMA,
+ /**
+ * created by mattz CC/0
+ * https://www.shadertoy.com/view/WlfXRN
+ */
+ premain: `
+ vec3 plasma(float t) {
+
+ const vec3 c0 = vec3(0.05873234392399702, 0.02333670892565664, 0.5433401826748754);
+ const vec3 c1 = vec3(2.176514634195958, 0.2383834171260182, 0.7539604599784036);
+ const vec3 c2 = vec3(-2.689460476458034, -7.455851135738909, 3.110799939717086);
+ const vec3 c3 = vec3(6.130348345893603, 42.3461881477227, -28.51885465332158);
+ const vec3 c4 = vec3(-11.10743619062271, -82.66631109428045, 60.13984767418263);
+ const vec3 c5 = vec3(10.02306557647065, 71.41361770095349, -54.07218655560067);
+ const vec3 c6 = vec3(-3.658713842777788, -22.93153465461149, 18.19190778539828);
+
+ return c0+t*(c1+t*(c2+t*(c3+t*(c4+t*(c5+t*c6)))));
+
+ }
+ `,
+ main: 'rgb=plasma(x);'
+ } ],
+ [ EnumColorMapName.MAGMA, {
+ header: COLORMAP_IS_MAGMA,
+ /**
+ * created by mattz CC/0
+ * https://www.shadertoy.com/view/WlfXRN
+ */
+ premain: `
+ vec3 magma(float t) {
+
+ const vec3 c0 = vec3(-0.002136485053939582, -0.000749655052795221, -0.005386127855323933);
+ const vec3 c1 = vec3(0.2516605407371642, 0.6775232436837668, 2.494026599312351);
+ const vec3 c2 = vec3(8.353717279216625, -3.577719514958484, 0.3144679030132573);
+ const vec3 c3 = vec3(-27.66873308576866, 14.26473078096533, -13.64921318813922);
+ const vec3 c4 = vec3(52.17613981234068, -27.94360607168351, 12.94416944238394);
+ const vec3 c5 = vec3(-50.76852536473588, 29.04658282127291, 4.23415299384598);
+ const vec3 c6 = vec3(18.65570506591883, -11.48977351997711, -5.601961508734096);
+
+ return c0+t*(c1+t*(c2+t*(c3+t*(c4+t*(c5+t*c6)))));
+
+ }
+ `,
+ main: 'rgb=magma(x);'
+ } ],
+ [ EnumColorMapName.INFERNO, {
+ header: '',
+ /**
+ * created by mattz CC/0
+ * https://www.shadertoy.com/view/WlfXRN
+ */
+ premain: `
+ vec3 inferno(float t) {
+
+ const vec3 c0 = vec3(0.0002189403691192265, 0.001651004631001012, -0.01948089843709184);
+ const vec3 c1 = vec3(0.1065134194856116, 0.5639564367884091, 3.932712388889277);
+ const vec3 c2 = vec3(11.60249308247187, -3.972853965665698, -15.9423941062914);
+ const vec3 c3 = vec3(-41.70399613139459, 17.43639888205313, 44.35414519872813);
+ const vec3 c4 = vec3(77.162935699427, -33.40235894210092, -81.80730925738993);
+ const vec3 c5 = vec3(-71.31942824499214, 32.62606426397723, 73.20951985803202);
+ const vec3 c6 = vec3(25.13112622477341, -12.24266895238567, -23.07032500287172);
+
+ return c0+t*(c1+t*(c2+t*(c3+t*(c4+t*(c5+t*c6)))));
+
+ }
+ `,
+ main: 'rgb=inferno(x);'
+ } ],
+
+ [ EnumColorMapName.GREYSCALE, {
+ header: COLORMAP_IS_GREYSCALE,
+ premain: '',
+ main: 'rgb=vec3(x, x, x);'
+ } ]
+])
diff --git a/src/util/constants.ts b/src/util/constants.ts
index 8a56a7ceaa97c2c654be25e3d49df77dd191d1f4..0a0b993c6cfa54b69687f37479bf4ea704ace688 100644
--- a/src/util/constants.ts
+++ b/src/util/constants.ts
@@ -68,37 +68,41 @@ export const getHttpHeader: () => HttpHeaders = () => {
return header
}
-const CM_MATLAB_JET = `float r;if( x < 0.7 ){r = 4.0 * x - 1.5;} else {r = -4.0 * x + 4.5;}float g;if (x < 0.5) {g = 4.0 * x - 0.5;} else {g = -4.0 * x + 3.5;}float b;if (x < 0.3) {b = 4.0 * x + 0.5;} else {b = -4.0 * x + 2.5;}float a = 1.0;`
-const CM_DEFAULT = `float r = x; float g = x; float b = x;`
export const COLORMAP_IS_JET = `// iav-colormap-is-jet`
-export const COLORMAP_IS_DEFAULT = `// iav-colormap-default`
+import { EnumColorMapName, mapKeyColorMap } from './colorMaps'
export const getShader = ({
- colormap = null,
+ colormap = EnumColorMapName.GREYSCALE,
lowThreshold = 0,
highThreshold = 1,
brightness = 0,
contrast = 0,
removeBg = false
} = {}): string => {
- const header = colormap === 'jet' ? COLORMAP_IS_JET : COLORMAP_IS_DEFAULT
- const colormapGlsl = colormap === 'jet' ? CM_MATLAB_JET : CM_DEFAULT
+ const { header, main, premain } = mapKeyColorMap.get(colormap) || (() => {
+ console.warn(`colormap ${colormap} not found. Using default colormap instead`)
+ return mapKeyColorMap.get(EnumColorMapName.GREYSCALE)
+ })()
+
+ // so that if lowthreshold is defined to be 0, at least some background removal will be done
+ const _lowThreshold = lowThreshold + 1e-10
return `${header}
+${premain}
void main() {
float raw_x = toNormalized(getDataValue());
- float x = (raw_x - ${lowThreshold.toFixed(5)}) / (${highThreshold - lowThreshold}) ${ brightness > 0 ? '+' : '-' } ${Math.abs(brightness).toFixed(5)};
+ float x = (raw_x - ${_lowThreshold.toFixed(10)}) / (${highThreshold - _lowThreshold}) ${ brightness > 0 ? '+' : '-' } ${Math.abs(brightness).toFixed(10)};
${ removeBg ? 'if(x>1.0){emitTransparent();}else if(x<0.0){emitTransparent();}else{' : '' }
- ${colormapGlsl}
-
- emitRGB(vec3(r, g, b)*exp(${contrast.toFixed(5)}));
+ vec3 rgb;
+ ${main}
+ emitRGB(rgb*exp(${contrast.toFixed(10)}));
${ removeBg ? '}' : '' }
}
`
}
export const PMAP_DEFAULT_CONFIG = {
- colormap: 'jet',
+ colormap: EnumColorMapName.VIRIDIS,
lowThreshold: 0.05,
removeBg: true
}
diff --git a/third_party/preinit_vanilla.html b/third_party/preinit_vanilla.html
new file mode 100644
index 0000000000000000000000000000000000000000..5c7ce1097580ccc6ff9071895cd1995f36d7d02e
--- /dev/null
+++ b/third_party/preinit_vanilla.html
@@ -0,0 +1,14 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+ <meta charset="UTF-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
+ <meta http-equiv="X-UA-Compatible" content="ie=edge">
+ <title>nehuba</title>
+ <script src="main.bundle.js"></script>
+ <link rel="stylesheet" href="vanilla_styles.css">
+</head>
+<body>
+ <div id="neuroglancer-container"></div>
+</body>
+</html>
\ No newline at end of file