diff --git a/.github/workflows/release-ci.yml b/.github/workflows/release-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..bdbaaec8eab1b2765bc7b8427518841597eaf93e
--- /dev/null
+++ b/.github/workflows/release-ci.yml
@@ -0,0 +1,42 @@
+name: Release CI
+on:
+ pull_request:
+ branches:
+ - master
+
+jobs:
+ check_version:
+ if: always()
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v1
+ - run: |
+ MASTER_VERSION=$(git show origin/master:package.json | jq '.version')
+ THIS_VERSION=$(jq '.version' < package.json)
+ test "$MASTER_VERSION" == "$THIS_VERSION" && exit 1 || exit 0
+
+ check_release:
+ if: always()
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v1
+ - run: |
+ VERSION_NUM=$(jq '.version' < package.json)
+ VERSION_NUM=${VERSION_NUM#\"}
+ VERSION_NUM=${VERSION_NUM%\"}
+ test -f docs/releases/v$VERSION_NUM.md && exit 0 || exit 1
+
+ release_linked_mkdocs:
+ if: always()
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v1
+ - run: |
+ VERSION_NUM=$(jq '.version' < package.json)
+ VERSION_NUM=${VERSION_NUM#\"}
+ VERSION_NUM=${VERSION_NUM%\"}
+ echo "VERSION_NUM: $VERSION_NUM"
+ cat mkdocs.yml
+ GREP_VERSION_NUM=$(cat mkdocs.yml | grep $VERSION_NUM)
+ echo GREP_VERSION_NUM: $GREP_VERSION_NUM
+ test -z "$GREP_VERSION_NUM" && exit 1 || exit 0
\ No newline at end of file
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index dc136836c17253be4056c83d497da3e3339fbc8c..e3766792780d1d42c25b17d98208b6193c286826 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -1,23 +1,26 @@
-name: '[release]'
-
-# on push to master, create release
+name: Release
on:
- push:
+ push:
branches:
- - 'master'
+ - master
jobs:
check-version:
+ outputs:
+ package-version: ${{ steps.set-version.outputs.package-version-from-json }}
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v1
- - run: |
+ - name: Set version
+ id: set-version
+ run: |
PACKAGEJSON_VER=v$(cat package.json | jq -r '.version')
- echo 'PACKAGEJSON_VER='$PACKAGEJSON_VER >> $GITHUB_ENV
-
+ echo "::set-output name=package-version-from-json::$PACKAGEJSON_VER"
+
create-release:
+ needs: check-version
if: success()
runs-on: ubuntu-latest
steps:
@@ -27,7 +30,7 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
- tag_name: ${{ env.PACKAGEJSON_VER }}
- release_name: Release ${{ env.PACKAGEJSON_VER }}
+ tag_name: ${{ needs.check-version.outputs.package-version }}
+ release_name: Release ${{ needs.check-version.outputs.package-version }}
draft: false
prerelease: false
diff --git a/common/helpOnePager.md b/common/helpOnePager.md
index 35b4ff7191af002402aa57c576dae3e2f2c14cb6..f23b9a498e529d2cfc65b5856c0b313142f29448 100644
--- a/common/helpOnePager.md
+++ b/common/helpOnePager.md
@@ -10,7 +10,7 @@
| Zoom | `[hover]` on any slice views, `[click]` magnifier |
| Next slice | `<ctrl>` + `[mousewheel]` |
| Next 10 slice | `<ctrl>` + `<shift>` + `[mousewheel]` |
-| Toggle delineation | |
+| Toggle delineation | `[q]` |
---
diff --git a/deploy/atlas/index.js b/deploy/atlas/index.js
index eb96d883cff1593df8dfd59cdeeae8b235567342..9bf745f2e071849efba3128ebb53f329bf44f27f 100644
--- a/deploy/atlas/index.js
+++ b/deploy/atlas/index.js
@@ -5,11 +5,12 @@ const path = require('path')
const { detEncoding } = require('nomiseco')
const { getAllAtlases, getAtlasById, isReady } = require('./query')
const HOSTNAME = process.env.HOSTNAME || 'http://localhost:3000'
-
+const HOST_PATHNAME = process.env.HOST_PATHNAME || ''
const { getTemplate } = require('../templates/query')
const { getHandleErrorFn } = require('../util/streamHandleError')
-const getPreviewFn = ({ res, lastpart }) => HOSTNAME.replace(/\/$/, '') + '/' +
+const getPreviewFn = ({ res, lastpart }) => HOSTNAME.replace(/\/$/, '') +
+ HOST_PATHNAME.replace(/\/$/, '') + '/' +
(res.locals.routePathname
? url.resolve(`${res.locals.routePathname}/`, lastpart)
: lastpart)
diff --git a/deploy/datasets/query.js b/deploy/datasets/query.js
index 47eef557694dbf01971ecd09d2bcf9a6eff81e60..1b4ce0d4c5d13479e6f59a05df634fa741b403d8 100644
--- a/deploy/datasets/query.js
+++ b/deploy/datasets/query.js
@@ -113,8 +113,11 @@ const getPublicDs = async () => {
throw `cached Data not yet resolved, neither is get public ds defined`
}
-
-const getDs = ({ user }) => (user
+/**
+ * force get only public ds
+ * getting individual ds is too slow
+ */
+const getDs = ({ user }) => (false && user
? fetchDatasetFromKg({ user }).then(({ results }) => results)
: getPublicDs()
).then(async datasets => {
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index c5487ed6dfd5458a46d28dd32845b87b6d68becf..229b03891d1c0b498d734d017655d6a7127ad892 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -21,8 +21,9 @@ const getUserKGRequestParam = async ({ user }) => {
let publicAccessToken
/**
* n.b. ACCESS_TOKEN env var is usually only set during dev
+ * user.type any other than 'hbp-oidc' (v1 of oidc) will result in timeout/error
*/
- const accessToken = (user && user.tokenset && user.tokenset.access_token) || process.env.ACCESS_TOKEN
+ const accessToken = (user && user.type === 'hbp-oidc' && user.tokenset && user.tokenset.access_token) || process.env.ACCESS_TOKEN
const releasedOnly = !accessToken
if (!accessToken && getPublicAccessToken) {
publicAccessToken = await getPublicAccessToken()
diff --git a/docs/releases/v2.3.0.md b/docs/releases/v2.3.0.md
index bd3c04a72e17891577f1027cb2da88d59d969b3d..2ffdd59932e3d4b2a5c66942f089ca30fa56717e 100644
--- a/docs/releases/v2.3.0.md
+++ b/docs/releases/v2.3.0.md
@@ -1,5 +1,7 @@
# v2.3.0
+11 Dec 2020
+
## New features
- update dataset preview functionality, allow the previewing of png
@@ -16,7 +18,7 @@
- reworked regional dataset previews (iEEG & receptor density)
- **experimental** : previewing of curated regional features: iEEG coordinates
-## Bugfixes:
+## Bugfixes
- dataset list view explicitly show loading status
- fixed a few typos
diff --git a/docs/releases/v2.3.1.md b/docs/releases/v2.3.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..5517468d33961969d036e9c12430c69785a72975
--- /dev/null
+++ b/docs/releases/v2.3.1.md
@@ -0,0 +1,7 @@
+# v2.3.1
+
+## Bugfixes
+
+- fixes iEEG panel sometimes not loading spatial data (#816 #744)
+- fixes fetching of non-existent data when in big brain reference space (#817)
+- restore CI for staging/release
\ No newline at end of file
diff --git a/docs/releases/v2.3.2.md b/docs/releases/v2.3.2.md
new file mode 100644
index 0000000000000000000000000000000000000000..0280a2ddffcd34b46c6c14198f724f365477a734
--- /dev/null
+++ b/docs/releases/v2.3.2.md
@@ -0,0 +1,5 @@
+# v2.3.2
+
+## Bugfixes
+
+- change URL source for connectivity browser.
diff --git a/docs/releases/v2.3.3.md b/docs/releases/v2.3.3.md
new file mode 100644
index 0000000000000000000000000000000000000000..daf21d1b8a1090df33fa4ff89351285bf271ea1e
--- /dev/null
+++ b/docs/releases/v2.3.3.md
@@ -0,0 +1,6 @@
+# v2.3.3
+
+## Bugfixes
+
+- fix backwards compatibility with some URLs
+- fix bug where fetching of regional features does not complete for logged in users (#826). (the viewer will only fetch released datasets)
diff --git a/docs/releases/v2.3.4.md b/docs/releases/v2.3.4.md
new file mode 100644
index 0000000000000000000000000000000000000000..7874ad49313a9e874ae5b80787a9e25c10ef0a35
--- /dev/null
+++ b/docs/releases/v2.3.4.md
@@ -0,0 +1,5 @@
+# v2.3.4
+
+## Bugfixes
+
+- fix connectivity dataset external link
diff --git a/docs/releases/v2.3.5.md b/docs/releases/v2.3.5.md
new file mode 100644
index 0000000000000000000000000000000000000000..b066cc07a9f4cde4b1df3d98c236967287ab9d16
--- /dev/null
+++ b/docs/releases/v2.3.5.md
@@ -0,0 +1,6 @@
+# v2.3.5
+
+## Under the hood stuff
+
+- Temporarily disable Colin 27 template.
+- Update to JulichBrain v2.5
diff --git a/docs/releases/v2.3.6.md b/docs/releases/v2.3.6.md
new file mode 100644
index 0000000000000000000000000000000000000000..4249e5ba896565f7ab2c6f3bac6e965ea3629201
--- /dev/null
+++ b/docs/releases/v2.3.6.md
@@ -0,0 +1,5 @@
+# v2.3.6
+
+## Bugfixes
+
+- fix backwards compatibility with some URLs
\ No newline at end of file
diff --git a/docs/releases/v2.3.7.md b/docs/releases/v2.3.7.md
new file mode 100644
index 0000000000000000000000000000000000000000..ad4b523b115c3ff80f37fe14df676e899cc13933
--- /dev/null
+++ b/docs/releases/v2.3.7.md
@@ -0,0 +1,5 @@
+# v2.3.7
+
+## Under the hood stuff
+
+- Enable CI for release workflow.
diff --git a/docs/releases/v2.3.8.md b/docs/releases/v2.3.8.md
new file mode 100644
index 0000000000000000000000000000000000000000..9a10601b60180d727fc0e1b0fa9e91314df882c4
--- /dev/null
+++ b/docs/releases/v2.3.8.md
@@ -0,0 +1,5 @@
+# v2.3.8
+
+## New Features
+
+- Adding control allowing delineation control
\ No newline at end of file
diff --git a/docs/releases/v2.3.9.md b/docs/releases/v2.3.9.md
new file mode 100644
index 0000000000000000000000000000000000000000..510ef7cf02181199f427e52b6c65a1d425dbab4d
--- /dev/null
+++ b/docs/releases/v2.3.9.md
@@ -0,0 +1,5 @@
+# v2.3.9
+
+## Bugfixes
+
+- Explore in other templates sometimes bugs out.
\ No newline at end of file
diff --git a/e2e/src/advanced/urlParsing.prod.e2e-spec.js b/e2e/src/advanced/urlParsing.prod.e2e-spec.js
index 832da7bc2f04294e37b033bef18d74b609efec10..7e239a89d51b86fd02e0fd8e31466e1af18482e5 100644
--- a/e2e/src/advanced/urlParsing.prod.e2e-spec.js
+++ b/e2e/src/advanced/urlParsing.prod.e2e-spec.js
@@ -70,8 +70,23 @@ describe('> url parsing', () => {
expect(red).toEqual(blue)
})
+ it('> [bkwards compat] if ill defined labelIndex for regionsSelected are defined, should handle gracefully', async () => {
+ const url = '/?parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&templateSelected=MNI+Colin+27&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__-17800000_-6700000_-7500000__200000®ionsSelected=142&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FJuBrain%2Fv2.2c%2FPMaps%2FBforebrain_4.nii'
+ await iavPage.goto(url)
+ await iavPage.clearAlerts()
+ await iavPage.wait(5000)
+ await iavPage.waitForAsync()
+ const log = await iavPage.getLog()
+ const filteredLog = log.filter(({ message }) => !/Access-Control-Allow-Origin/.test(message))
+
+ // expecting some errors in the console. In catastrophic event, there will most likely be looped errors (on each render cycle)
+ expect(
+ filteredLog.length
+ ).toBeLessThan(50)
+ })
+
it('> if niftiLayers are defined, parcellation layer should be hidden', async () => {
- const url = `/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.eu%2Fprecomputed%2FJuBrain%2F17%2Ficbm152casym%2Fpmaps%2FVisual_hOc1_r_N10_nlin2MNI152ASYM2009C_2.4_publicP_a48ca5d938781ebaf1eaa25f59df74d0.nii.gz`
+ const url = `/?parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&templateSelected=MNI+Colin+27&navigation=0_0_0_1__-0.2753947079181671_0.6631333827972412_-0.6360703706741333_0.2825356423854828__3000000__-17800000_-6700000_-7500000__200000®ionsSelected=142&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.org%2Fprecomputed%2FJuBrain%2Fv2.2c%2FPMaps%2FBforebrain_4.nii`
await iavPage.goto(url)
await iavPage.clearAlerts()
@@ -121,38 +136,4 @@ describe('> url parsing', () => {
))
})
- /**
- * encoding of dataset previews in url is current not enabled
- */
- it('> if datasetPreview is set, should load with previews',
- // async () => {
- // const url = `http://localhost:3000/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&previewingDatasetFiles=%5B%7B%22datasetId%22%3A%22e715e1f7-2079-45c4-a67f-f76b102acfce%22%2C%22filename%22%3A%22fingerprint%22%7D%2C%7B%22datasetId%22%3A%22e715e1f7-2079-45c4-a67f-f76b102acfce%22%2C%22filename%22%3A%22GABA%E1%B4%80%28BZ%29%2Fautoradiography%22%7D%2C%7B%22datasetId%22%3A%22e715e1f7-2079-45c4-a67f-f76b102acfce%22%2C%22filename%22%3A%22GABA%E1%B4%80%28BZ%29%2Fprofile%22%7D%5D`
- // const datasetPreview = [
- // {
- // "datasetId": "e715e1f7-2079-45c4-a67f-f76b102acfce",
- // "filename": "fingerprint"
- // },
- // {
- // "datasetId": "e715e1f7-2079-45c4-a67f-f76b102acfce",
- // "filename": "GABAá´€(BZ)/autoradiography"
- // },
- // {
- // "datasetId": "e715e1f7-2079-45c4-a67f-f76b102acfce",
- // "filename": "GABAá´€(BZ)/profile"
- // }
- // ]
-
- // const searchParam = new URLSearchParams()
-
- // searchParam.set('templateSelected', 'MNI 152 ICBM 2009c Nonlinear Asymmetric')
- // searchParam.set('parcellationSelected', 'JuBrain Cytoarchitectonic Atlas')
- // searchParam.set('previewingDatasetFiles', JSON.stringify(datasetPreview))
- // await iavPage.goto(`/?${searchParam.toString()}`)
-
- // const visibleArr = await iavPage.areVisible(`[aria-label="${ARIA_LABELS.DATASET_FILE_PREVIEW}"]`)
- // expect(visibleArr.length).toEqual(3)
- // expect(visibleArr).toEqual([true, true, true])
- // }
-
- )
})
diff --git a/e2e/util/selenium/base.js b/e2e/util/selenium/base.js
index e16f7465664396a0cad688e34e81e7a197f8ccdd..88312daf3cd2eadb52f2b47a390e9d1e6d33c89b 100644
--- a/e2e/util/selenium/base.js
+++ b/e2e/util/selenium/base.js
@@ -99,6 +99,11 @@ class WdBase{
return result
}
+ async getLog() {
+ const browserLog = await this._browser.manage().logs().get('browser')
+ return browserLog
+ }
+
async getRgbAt({ position } = {}, cssSelector = null){
if (!position) throw new Error(`position is required for getRgbAt`)
const { x, y } = verifyPosition(position)
diff --git a/mkdocs.yml b/mkdocs.yml
index 02d1d42676e5cae500b176d9800c6c1eacef7574..cf071e557a17313d0771db193adeebe6258c0aa7 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -41,6 +41,15 @@ pages:
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
- v2.4.0: 'releases/v2.4.0.md'
+ - v2.3.9: 'releases/v2.3.9.md'
+ - v2.3.8: 'releases/v2.3.8.md'
+ - v2.3.7: 'releases/v2.3.7.md'
+ - v2.3.6: 'releases/v2.3.6.md'
+ - v2.3.5: 'releases/v2.3.5.md'
+ - v2.3.4: 'releases/v2.3.4.md'
+ - v2.3.3: 'releases/v2.3.3.md'
+ - v2.3.2: 'releases/v2.3.2.md'
+ - v2.3.1: 'releases/v2.3.1.md'
- v2.3.0: 'releases/v2.3.0.md'
- v2.2.7: 'releases/v2.2.7.md'
- v2.2.6: 'releases/v2.2.6.md'
@@ -61,4 +70,4 @@ pages:
- v0.2.9: 'releases/v0.2.9.md'
- v0.2.0: 'releases/v0.2.0.md'
- v0.1.0: 'releases/v0.1.0.md'
- - legacy: 'releases/legacy.md'
\ No newline at end of file
+ - legacy: 'releases/legacy.md'
diff --git a/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.component.ts b/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.component.ts
index d9764a702610d555906f45360e715f017849543b..bc8a23b8e1fec20fef9fd6b7bebaf64c88a453b1 100644
--- a/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.component.ts
+++ b/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.component.ts
@@ -44,7 +44,7 @@ export class ConnectivityBrowserComponent implements OnInit, AfterViewInit, OnDe
*/
private _isFirstUpdate = true
- public connectivityUrl = 'https://connectivity-query-v1-1-connectivity.apps-dev.hbp.eu/v1.1/studies'
+ public connectivityUrl = 'https://connectivity-query-v1-1-connectivity.apps.hbp.eu/v1.1/studies'
private accordionIsExpanded = false
@@ -115,6 +115,8 @@ export class ConnectivityBrowserComponent implements OnInit, AfterViewInit, OnDe
public datasetList: any[] = []
public selectedDataset: any
public selectedDatasetDescription: string = ''
+ public selectedDatasetKgId: string = ''
+ public selectedDatasetKgSchema: string = ''
public connectedAreas = []
private selectedParcellationFlatRegions$ = this.store$.pipe(
@@ -304,7 +306,10 @@ export class ConnectivityBrowserComponent implements OnInit, AfterViewInit, OnDe
changeDataset(event = null) {
if (event) {
this.selectedDataset = event.value
- this.selectedDatasetDescription = this.datasetList.find(d => d.name === this.selectedDataset).description
+ const foundDataset = this.datasetList.find(d => d.name === this.selectedDataset)
+ this.selectedDatasetDescription = foundDataset?.description
+ this.selectedDatasetKgId = foundDataset?.kgId || null
+ this.selectedDatasetKgSchema = foundDataset?.kgschema || null
}
if (this.datasetList.length && this.selectedDataset) {
const selectedDatasetId = this.datasetList.find(d => d.name === this.selectedDataset).id
@@ -407,7 +412,7 @@ export class ConnectivityBrowserComponent implements OnInit, AfterViewInit, OnDe
}
public exportFullConnectivity() {
- this.fullConnectivityGridElement.nativeElement['downloadCSV']()
+ this.fullConnectivityGridElement?.nativeElement['downloadCSV']()
}
}
diff --git a/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.template.html b/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.template.html
index fa47192a66062082a8d29c557871a35bb6726a49..178cab32f593d5eb1690fcd46c89ab1cb44b4ea5 100644
--- a/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.template.html
+++ b/src/atlasComponents/connectivity/connectivityBrowser/connectivityBrowser.template.html
@@ -39,7 +39,10 @@
<button class="flex-grow-0 flex-shrink-0" mat-icon-button
iav-dataset-show-dataset-dialog
[iav-dataset-show-dataset-dialog-name]="selectedDataset"
- [iav-dataset-show-dataset-dialog-description]="selectedDatasetDescription">
+ [iav-dataset-show-dataset-dialog-description]="selectedDatasetDescription"
+ [iav-dataset-show-dataset-dialog-kgid]="selectedDatasetKgId? selectedDatasetKgId : null"
+ [iav-dataset-show-dataset-dialog-kgschema]="selectedDatasetKgSchema? selectedDatasetKgSchema : null"
+ >
<i class="fas fa-info"></i>
</button>
<button class="flex-grow-0 flex-shrink-0"
diff --git a/src/atlasComponents/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html b/src/atlasComponents/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html
index 78daaefedf86e26108902a5d0004084cfc6e3245..455219a1825c31e207e94e6ea46a36774c6871ad 100644
--- a/src/atlasComponents/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html
+++ b/src/atlasComponents/databrowserModule/singleDataset/sideNavView/sDsSideNavView.template.html
@@ -135,7 +135,8 @@
<ng-template [ngIf]="matExpansionPanel.expanded">
<feature-container
[feature]="feature"
- [region]="region$ | async">
+ [region]="region$ | async"
+ (viewChanged)="detectChange()">
</feature-container>
</ng-template>
</mat-expansion-panel>
diff --git a/src/atlasComponents/parcellationRegion/region.base.spec.ts b/src/atlasComponents/parcellationRegion/region.base.spec.ts
index 93899584dd99b1fbc99d994e0432e280263087bd..712e323298045aa049c7e8e2961fbb58480f9be2 100644
--- a/src/atlasComponents/parcellationRegion/region.base.spec.ts
+++ b/src/atlasComponents/parcellationRegion/region.base.spec.ts
@@ -1,5 +1,6 @@
import { TestBed } from '@angular/core/testing'
import { MockStore, provideMockStore } from '@ngrx/store/testing'
+import { viewerStateNewViewer } from 'src/services/state/viewerState/actions'
import { RegionBase, regionInOtherTemplateSelector, getRegionParentParcRefSpace } from './region.base'
const util = require('common/util')
@@ -329,16 +330,22 @@ const getRegionInOtherTemplateSelectorBundle = (version: EnumParcRegVersion) =>
describe('> region.base.ts', () => {
describe('> regionInOtherTemplateSelector', () => {
+ // TODO
+ it('> only selects region in the template specified by selected atlas')
+
for (const enumKey of Object.keys(EnumParcRegVersion)) {
describe(`> selector version for ${enumKey}`, () => {
const { mockFetchedTemplates, mr0, mt2, mt0, mp0, mt1, mp1h, mr0lh, mt3, mr0rh } = getRegionInOtherTemplateSelectorBundle(enumKey as EnumParcRegVersion)
+ let selectedAtlas = {
+ templateSpaces: mockFetchedTemplates
+ }
describe('> no hemisphere selected, simulates big brain cyto map', () => {
let result: any[]
beforeAll(() => {
- result = regionInOtherTemplateSelector.projector(mockFetchedTemplates, mt0, { region: mr0 })
+ result = regionInOtherTemplateSelector.projector(selectedAtlas, mockFetchedTemplates, mt0, { region: mr0 })
})
it('> length checks out', () => {
@@ -410,7 +417,7 @@ describe('> region.base.ts', () => {
describe('> hemisphere data selected (left hemisphere), simulates julich-brain in mni152', () => {
let result
beforeAll(() => {
- result = regionInOtherTemplateSelector.projector(mockFetchedTemplates, mt2, { region: mr0lh })
+ result = regionInOtherTemplateSelector.projector(selectedAtlas, mockFetchedTemplates, mt2, { region: mr0lh })
})
it('> length checks out', () => {
@@ -444,19 +451,20 @@ describe('> region.base.ts', () => {
})
describe('> RegionBase', () => {
+ let regionBase: RegionBase
+ let mockStore: MockStore
beforeEach(() => {
TestBed.configureTestingModule({
providers: [
provideMockStore()
]
})
+ mockStore = TestBed.inject(MockStore)
+ mockStore.overrideSelector(regionInOtherTemplateSelector, [])
+ mockStore.overrideSelector(getRegionParentParcRefSpace, { template: null, parcellation: null })
})
describe('> position', () => {
- let regionBase: RegionBase
beforeEach(() => {
- const mockStore = TestBed.inject(MockStore)
- mockStore.overrideSelector(regionInOtherTemplateSelector, [])
- mockStore.overrideSelector(getRegionParentParcRefSpace, { template: null, parcellation: null })
regionBase = new RegionBase(mockStore)
})
it('> does not populate if position property is absent', () => {
@@ -609,7 +617,85 @@ describe('> region.base.ts', () => {
regionBase.rgbString
).toEqual(`rgb(255,200,200)`)
})
+ })
+ })
+ describe('> changeView', () => {
+ const fakeTmpl = {
+ name: 'fakeTmpl'
+ }
+ const fakeParc = {
+ name: 'fakeParc'
+ }
+ beforeEach(() => {
+ regionBase = new RegionBase(mockStore)
+ })
+
+ describe('> if sameRegion has position attribute', () => {
+ let dispatchSpy: jasmine.Spy
+
+ beforeEach(() => {
+ dispatchSpy = spyOn(mockStore, 'dispatch')
+ })
+ afterEach(() => {
+ dispatchSpy.calls.reset()
+ })
+ it('> malformed position is not an array > do not pass position', () => {
+ regionBase.changeView({
+ template: fakeTmpl,
+ parcellation: fakeParc,
+ region: {
+ position: 'hello wolrd'
+ }
+ })
+
+ expect(dispatchSpy).toHaveBeenCalledWith(
+ viewerStateNewViewer({
+ selectTemplate: fakeTmpl,
+ selectParcellation: fakeParc,
+ navigation: {}
+ })
+ )
+ })
+
+ it('> malformed position is an array of incorrect size > do not pass position', () => {
+
+ regionBase.changeView({
+ template: fakeTmpl,
+ parcellation: fakeParc,
+ region: {
+ position: []
+ }
+ })
+
+ expect(dispatchSpy).toHaveBeenCalledWith(
+ viewerStateNewViewer({
+ selectTemplate: fakeTmpl,
+ selectParcellation: fakeParc,
+ navigation: {}
+ })
+ )
+ })
+
+ it('> correct position > pass position', () => {
+ regionBase.changeView({
+ template: fakeTmpl,
+ parcellation: fakeParc,
+ region: {
+ position: [1,2,3]
+ }
+ })
+
+ expect(dispatchSpy).toHaveBeenCalledWith(
+ viewerStateNewViewer({
+ selectTemplate: fakeTmpl,
+ selectParcellation: fakeParc,
+ navigation: {
+ position: [1,2,3]
+ }
+ })
+ )
+ })
})
})
})
diff --git a/src/atlasComponents/parcellationRegion/region.base.ts b/src/atlasComponents/parcellationRegion/region.base.ts
index 68b83999af0e147d48eaf7fc7a2bab91e13c67db..33f84531de4c0bcc599b53542d8c5209ccd9f8e7 100644
--- a/src/atlasComponents/parcellationRegion/region.base.ts
+++ b/src/atlasComponents/parcellationRegion/region.base.ts
@@ -173,6 +173,9 @@ export class RegionBase {
region
} = sameRegion
const { position } = region
+ const navigation = Array.isArray(position) && position.length === 3
+ ? { position }
+ : { }
this.closeRegionMenu.emit()
/**
@@ -182,9 +185,7 @@ export class RegionBase {
this.store$.dispatch(viewerStateNewViewer ({
selectTemplate: template,
selectParcellation: parcellation,
- navigation: {
- position
- },
+ navigation,
}))
}
@@ -261,9 +262,11 @@ export class RenderViewOriginDatasetLabelPipe implements PipeTransform{
}
export const regionInOtherTemplateSelector = createSelector(
+ viewerStateGetSelectedAtlas,
viewerStateFetchedTemplatesSelector,
viewerStateSelectedTemplateSelector,
- (fetchedTemplates, templateSelected, prop) => {
+ (atlas, fetchedTemplates, templateSelected, prop) => {
+ const atlasTemplateSpacesIds = atlas.templateSpaces.map(({ ['@id']: id, fullId }) => id || fullId)
const { region: regionOfInterest } = prop
const returnArr = []
@@ -272,7 +275,13 @@ export const regionInOtherTemplateSelector = createSelector(
const regionOfInterestId = getIdFromFullId(regionOfInterest.fullId)
if (!templateSelected) return []
const selectedTemplateId = getIdFromFullId(templateSelected.fullId)
- const otherTemplates = fetchedTemplates.filter(({ fullId }) => getIdFromFullId(fullId) !== selectedTemplateId)
+
+ // need to ensure that the templates are defined in atlas definition
+ // atlas is the single source of truth
+
+ const otherTemplates = fetchedTemplates
+ .filter(({ fullId }) => getIdFromFullId(fullId) !== selectedTemplateId)
+ .filter(({ ['@id']: id, fullId }) => atlasTemplateSpacesIds.includes(id || fullId))
for (const template of otherTemplates) {
for (const parcellation of template.parcellations) {
const flattenedRegions = flattenRegions(parcellation.regions)
diff --git a/src/atlasComponents/regionalFeatures/featureContainer/featureContainer.component.ts b/src/atlasComponents/regionalFeatures/featureContainer/featureContainer.component.ts
index d6752dae47b53d81f94c067ff653366f59c1a375..6a66668fe1ac2c287ff382026bdbd8f9bc2062df 100644
--- a/src/atlasComponents/regionalFeatures/featureContainer/featureContainer.component.ts
+++ b/src/atlasComponents/regionalFeatures/featureContainer/featureContainer.component.ts
@@ -1,4 +1,4 @@
-import { ChangeDetectionStrategy, ChangeDetectorRef, Component, ComponentFactoryResolver, ComponentRef, Input, OnChanges, SimpleChanges, ViewContainerRef } from "@angular/core";
+import { ChangeDetectionStrategy, ChangeDetectorRef, Component, ComponentFactoryResolver, ComponentRef, Input, OnChanges, Output, SimpleChanges, ViewContainerRef, EventEmitter } from "@angular/core";
import { Subscription } from "rxjs";
import { IFeature, RegionalFeaturesService } from "../regionalFeature.service";
import { ISingleFeature } from "../singleFeatures/interfaces";
@@ -16,13 +16,15 @@ export class FeatureContainer implements OnChanges{
@Input()
region: any
+ @Output()
+ viewChanged: EventEmitter<boolean> = new EventEmitter()
+
private cr: ComponentRef<ISingleFeature>
constructor(
private vCRef: ViewContainerRef,
private rService: RegionalFeaturesService,
private cfr: ComponentFactoryResolver,
- private cdr: ChangeDetectorRef
){
}
@@ -33,15 +35,22 @@ export class FeatureContainer implements OnChanges{
const { currentValue, previousValue } = simpleChanges.feature
if (currentValue === previousValue) return
this.clear()
+
+ /**
+ * catching instances where currentValue for feature is falsy
+ */
+ if (!currentValue) return
+
/**
* TODO catch if map is undefined
*/
const comp = this.rService.mapFeatToCmp.get(currentValue.type)
+ if (!comp) throw new Error(`mapFeatToCmp for ${currentValue.type} not defined`)
const cf = this.cfr.resolveComponentFactory<ISingleFeature>(comp)
this.cr = this.vCRef.createComponent(cf)
this.cr.instance.feature = this.feature
this.cr.instance.region = this.region
- this.viewChangedSub = this.cr.instance.viewChanged.subscribe(() => this.cdr.detectChanges())
+ this.viewChangedSub = this.cr.instance.viewChanged.subscribe(() => this.viewChanged.emit(true))
}
clear(){
diff --git a/src/atlasComponents/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts b/src/atlasComponents/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts
index af0dcab8913fa06d2f7ad55f6ffadc309aae69dc..072cbabf90ec1d731fe4a767dcd78ee76ba7d4b9 100644
--- a/src/atlasComponents/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts
+++ b/src/atlasComponents/regionalFeatures/singleFeatures/iEEGRecordings/iEEGRecordings/iEEGRecordings.component.ts
@@ -31,7 +31,7 @@ export class IEEGRecordingsCmp extends RegionFeatureBase implements ISingleFeatu
super(regionFeatureService)
}
- public viewChanged = new EventEmitter<null>()
+ public viewChanged = new EventEmitter<boolean>()
ngOnInit(){
if (this.regClickIntp) {
@@ -71,7 +71,7 @@ export class IEEGRecordingsCmp extends RegionFeatureBase implements ISingleFeatu
)
this.sub.push(
- this.dataIsLoading$.subscribe(() => this.viewChanged.emit(null))
+ this.dataIsLoading$.subscribe(() => this.viewChanged.emit(true))
)
this.onDestroyCb.push(() => {
diff --git a/src/atlasComponents/regionalFeatures/singleFeatures/interfaces.ts b/src/atlasComponents/regionalFeatures/singleFeatures/interfaces.ts
index 37abcd4479aa87e9dabed72e589d2a3b82a091bd..bd3861d391b4bcc90d262ee16e124b51e4affee2 100644
--- a/src/atlasComponents/regionalFeatures/singleFeatures/interfaces.ts
+++ b/src/atlasComponents/regionalFeatures/singleFeatures/interfaces.ts
@@ -4,5 +4,5 @@ import { IFeature } from "../regionalFeature.service";
export interface ISingleFeature{
feature: IFeature
region: any
- viewChanged: EventEmitter<null>
+ viewChanged: EventEmitter<boolean>
}
diff --git a/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.component.ts b/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.component.ts
index 088c98dbefb4b85f4eb19b0f88ff9efcf59cf263..046aa3448b8566a3c9fcd0179560e5d6aa1908ef 100644
--- a/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.component.ts
+++ b/src/atlasComponents/uiSelectors/atlasLayerSelector/atlasLayerSelector.component.ts
@@ -1,6 +1,6 @@
import { Component, OnInit, ViewChildren, QueryList, HostBinding } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { distinctUntilChanged, map, withLatestFrom, shareReplay, groupBy, mergeMap, toArray, switchMap, scan, filter } from "rxjs/operators";
+import { distinctUntilChanged, map, withLatestFrom, shareReplay, groupBy, mergeMap, toArray, switchMap, scan, filter, startWith } from "rxjs/operators";
import { Observable, Subscription, from, zip, of, combineLatest } from "rxjs";
import { viewerStateSelectTemplateWithId, viewerStateToggleLayer } from "src/services/state/viewerState.store.helper";
import { MatMenuTrigger } from "@angular/material/menu";
diff --git a/src/glue.ts b/src/glue.ts
index d2c6756cd0d534834fddb900464e406317641cb7..451e16b0968e76c0b5c0d0d677fc2c5cf012374e 100644
--- a/src/glue.ts
+++ b/src/glue.ts
@@ -631,6 +631,7 @@ export class DatasetPreviewGlue implements IDatasetPreviewGlue, OnDestroy{
}
public datasetPreviewDisplayed(file: DatasetPreview, dataset?: IKgDataEntry){
+ if (!file) return of(false)
return this.previewingDatasetFiles$.pipe(
map(datasetPreviews => {
const { filename, datasetId } = file
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index f7b08d8e701937661663eb5d3ebbaca05a710952..c20593fc588bbefd0b80de33340c624f217362c0 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -23,7 +23,7 @@
"originDatasets": [
{
"kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6"
+ "kgId": "2eaa3dc6-a21b-41c1-b703-bf06f82adf25"
}
],
"properties": {
@@ -62,12 +62,20 @@
{
"name": "Ch 123 (Basal Forebrain)",
"status": "left hemisphere",
- "labelIndex": 62,
+ "labelIndex": 79,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ch 123 (Basal Forebrain)",
"gray": "79"
+ },
+ "xml253": {
+ "_": "Ch 123 (Basal Forebrain)",
+ "$": {
+ "num": "78",
+ "id": "286",
+ "grayvalue": "79"
+ }
}
},
"originDatasets": [
@@ -97,12 +105,20 @@
{
"name": "Ch 123 (Basal Forebrain)",
"status": "right hemisphere",
- "labelIndex": 62,
+ "labelIndex": 79,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ch 123 (Basal Forebrain)",
"gray": "79"
+ },
+ "xml253": {
+ "_": "Ch 123 (Basal Forebrain)",
+ "$": {
+ "num": "78",
+ "id": "286",
+ "grayvalue": "79"
+ }
}
},
"originDatasets": [
@@ -153,12 +169,20 @@
{
"name": "Ch 4 (Basal Forebrain)",
"status": "left hemisphere",
- "labelIndex": 97,
+ "labelIndex": 13,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ch 4 (Basal Forebrain)",
"gray": "13"
+ },
+ "xml253": {
+ "_": "Ch 4 (Basal Forebrain)",
+ "$": {
+ "num": "12",
+ "id": "264",
+ "grayvalue": "13"
+ }
}
},
"originDatasets": [
@@ -188,12 +212,20 @@
{
"name": "Ch 4 (Basal Forebrain)",
"status": "right hemisphere",
- "labelIndex": 97,
+ "labelIndex": 13,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ch 4 (Basal Forebrain)",
"gray": "13"
+ },
+ "xml253": {
+ "_": "Ch 4 (Basal Forebrain)",
+ "$": {
+ "num": "12",
+ "id": "264",
+ "grayvalue": "13"
+ }
}
},
"originDatasets": [
@@ -244,12 +276,20 @@
{
"name": "Ch 123 (Basal Forebrain)",
"status": "left hemisphere",
- "labelIndex": 62,
+ "labelIndex": 79,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ch 123 (Basal Forebrain)",
"gray": "79"
+ },
+ "xml253": {
+ "_": "Ch 123 (Basal Forebrain)",
+ "$": {
+ "num": "78",
+ "id": "286",
+ "grayvalue": "79"
+ }
}
},
"originDatasets": [
@@ -279,12 +319,20 @@
{
"name": "Ch 123 (Basal Forebrain)",
"status": "right hemisphere",
- "labelIndex": 62,
+ "labelIndex": 79,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ch 123 (Basal Forebrain)",
"gray": "79"
+ },
+ "xml253": {
+ "_": "Ch 123 (Basal Forebrain)",
+ "$": {
+ "num": "78",
+ "id": "286",
+ "grayvalue": "79"
+ }
}
},
"originDatasets": [
@@ -340,12 +388,20 @@
{
"name": "LB (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 41,
+ "labelIndex": 94,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "LB (Amygdala)",
"gray": "94"
+ },
+ "xml253": {
+ "_": "LB (Amygdala)",
+ "$": {
+ "num": "93",
+ "id": "187",
+ "grayvalue": "94"
+ }
}
},
"originDatasets": [
@@ -375,12 +431,20 @@
{
"name": "LB (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 41,
+ "labelIndex": 94,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "LB (Amygdala)",
"gray": "94"
+ },
+ "xml253": {
+ "_": "LB (Amygdala)",
+ "$": {
+ "num": "93",
+ "id": "187",
+ "grayvalue": "94"
+ }
}
},
"originDatasets": [
@@ -431,12 +495,20 @@
{
"name": "CM (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 85,
+ "labelIndex": 44,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CM (Amygdala)",
"gray": "44"
+ },
+ "xml253": {
+ "_": "CM (Amygdala)",
+ "$": {
+ "num": "43",
+ "id": "290",
+ "grayvalue": "44"
+ }
}
},
"originDatasets": [
@@ -466,12 +538,20 @@
{
"name": "CM (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 85,
+ "labelIndex": 44,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CM (Amygdala)",
"gray": "44"
+ },
+ "xml253": {
+ "_": "CM (Amygdala)",
+ "$": {
+ "num": "43",
+ "id": "290",
+ "grayvalue": "44"
+ }
}
},
"originDatasets": [
@@ -517,12 +597,20 @@
{
"name": "SF (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 5,
+ "labelIndex": 111,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "SF (Amygdala)",
"gray": "110"
+ },
+ "xml253": {
+ "_": "SF (Amygdala)",
+ "$": {
+ "num": "110",
+ "id": "185",
+ "grayvalue": "111"
+ }
}
},
"originDatasets": [
@@ -552,12 +640,20 @@
{
"name": "SF (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 5,
+ "labelIndex": 110,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "SF (Amygdala)",
"gray": "110"
+ },
+ "xml253": {
+ "_": "SF (Amygdala)",
+ "$": {
+ "num": "109",
+ "id": "185",
+ "grayvalue": "110"
+ }
}
},
"originDatasets": [
@@ -608,12 +704,20 @@
{
"name": "VTM (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 109,
+ "labelIndex": 83,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "VTM (Amygdala)",
"gray": "83"
+ },
+ "xml253": {
+ "_": "VTM (Amygdala)",
+ "$": {
+ "num": "82",
+ "id": "228",
+ "grayvalue": "83"
+ }
}
},
"originDatasets": [
@@ -643,12 +747,20 @@
{
"name": "VTM (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 109,
+ "labelIndex": 83,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "VTM (Amygdala)",
"gray": "83"
+ },
+ "xml253": {
+ "_": "VTM (Amygdala)",
+ "$": {
+ "num": "82",
+ "id": "228",
+ "grayvalue": "83"
+ }
}
},
"originDatasets": [
@@ -694,12 +806,20 @@
{
"name": "IF (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 46,
+ "labelIndex": 61,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "IF (Amygdala)",
"gray": "61"
+ },
+ "xml253": {
+ "_": "IF (Amygdala)",
+ "$": {
+ "num": "60",
+ "id": "237",
+ "grayvalue": "61"
+ }
}
},
"originDatasets": [
@@ -729,12 +849,20 @@
{
"name": "IF (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 46,
+ "labelIndex": 61,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "IF (Amygdala)",
"gray": "61"
+ },
+ "xml253": {
+ "_": "IF (Amygdala)",
+ "$": {
+ "num": "60",
+ "id": "237",
+ "grayvalue": "61"
+ }
}
},
"originDatasets": [
@@ -780,12 +908,20 @@
{
"name": "MF (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 123,
+ "labelIndex": 104,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "MF (Amygdala)",
"gray": "104"
+ },
+ "xml253": {
+ "_": "MF (Amygdala)",
+ "$": {
+ "num": "103",
+ "id": "235",
+ "grayvalue": "104"
+ }
}
},
"originDatasets": [
@@ -815,12 +951,20 @@
{
"name": "MF (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 123,
+ "labelIndex": 104,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "MF (Amygdala)",
"gray": "104"
+ },
+ "xml253": {
+ "_": "MF (Amygdala)",
+ "$": {
+ "num": "103",
+ "id": "235",
+ "grayvalue": "104"
+ }
}
},
"originDatasets": [
@@ -871,12 +1015,20 @@
{
"name": "CM (Amygdala)",
"status": "left hemisphere",
- "labelIndex": 85,
+ "labelIndex": 44,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CM (Amygdala)",
"gray": "44"
+ },
+ "xml253": {
+ "_": "CM (Amygdala)",
+ "$": {
+ "num": "43",
+ "id": "290",
+ "grayvalue": "44"
+ }
}
},
"originDatasets": [
@@ -906,12 +1058,20 @@
{
"name": "CM (Amygdala)",
"status": "right hemisphere",
- "labelIndex": 85,
+ "labelIndex": 44,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CM (Amygdala)",
"gray": "44"
+ },
+ "xml253": {
+ "_": "CM (Amygdala)",
+ "$": {
+ "num": "43",
+ "id": "290",
+ "grayvalue": "44"
+ }
}
},
"originDatasets": [
@@ -972,12 +1132,20 @@
{
"name": "Area 5L (SPL)",
"status": "left hemisphere",
- "labelIndex": 83,
+ "labelIndex": 97,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Area 5L (SPL)",
"gray": "98"
+ },
+ "xml253": {
+ "_": "Area 5L (SPL)",
+ "$": {
+ "num": "96",
+ "id": "130",
+ "grayvalue": "97"
+ }
}
},
"originDatasets": [
@@ -1007,12 +1175,20 @@
{
"name": "Area 5L (SPL)",
"status": "right hemisphere",
- "labelIndex": 83,
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@@ -9997,12 +11821,20 @@
{
"name": "CA3 (Hippocampus)",
"status": "left hemisphere",
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+ "labelIndex": 91,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CA3 (Hippocampus)",
"gray": "91"
+ },
+ "xml253": {
+ "_": "CA3 (Hippocampus)",
+ "$": {
+ "num": "90",
+ "id": "59",
+ "grayvalue": "91"
+ }
}
},
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@@ -10032,12 +11864,20 @@
{
"name": "CA3 (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 119,
+ "labelIndex": 92,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CA3 (Hippocampus)",
"gray": "90"
+ },
+ "xml253": {
+ "_": "CA3 (Hippocampus)",
+ "$": {
+ "num": "91",
+ "id": "59",
+ "grayvalue": "92"
+ }
}
},
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@@ -10083,12 +11923,20 @@
{
"name": "HC-Transsubiculum (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 66,
+ "labelIndex": 87,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Transsubiculum (Hippocampus)",
"gray": "87"
+ },
+ "xml253": {
+ "_": "HC-Transsubiculum (Hippocampus)",
+ "$": {
+ "num": "86",
+ "id": "305",
+ "grayvalue": "87"
+ }
}
},
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@@ -10112,12 +11960,20 @@
{
"name": "HC-Transsubiculum (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 66,
+ "labelIndex": 87,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Transsubiculum (Hippocampus)",
"gray": "87"
+ },
+ "xml253": {
+ "_": "HC-Transsubiculum (Hippocampus)",
+ "$": {
+ "num": "86",
+ "id": "305",
+ "grayvalue": "87"
+ }
}
},
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@@ -10157,12 +12013,20 @@
{
"name": "HC-Subiculum (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 10,
+ "labelIndex": 63,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Subiculum (Hippocampus)",
"gray": "63"
+ },
+ "xml253": {
+ "_": "HC-Subiculum (Hippocampus)",
+ "$": {
+ "num": "62",
+ "id": "67",
+ "grayvalue": "63"
+ }
}
},
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@@ -10186,12 +12050,20 @@
{
"name": "HC-Subiculum (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 10,
+ "labelIndex": 63,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Subiculum (Hippocampus)",
"gray": "63"
+ },
+ "xml253": {
+ "_": "HC-Subiculum (Hippocampus)",
+ "$": {
+ "num": "62",
+ "id": "67",
+ "grayvalue": "63"
+ }
}
},
"originDatasets": [
@@ -10231,12 +12103,20 @@
{
"name": "HC-Prosubiculum (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 6,
+ "labelIndex": 49,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Prosubiculum (Hippocampus)",
"gray": "48"
+ },
+ "xml253": {
+ "_": "HC-Prosubiculum (Hippocampus)",
+ "$": {
+ "num": "48",
+ "id": "64",
+ "grayvalue": "49"
+ }
}
},
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@@ -10260,12 +12140,20 @@
{
"name": "HC-Prosubiculum (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 6,
+ "labelIndex": 48,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Prosubiculum (Hippocampus)",
"gray": "48"
+ },
+ "xml253": {
+ "_": "HC-Prosubiculum (Hippocampus)",
+ "$": {
+ "num": "47",
+ "id": "64",
+ "grayvalue": "48"
+ }
}
},
"originDatasets": [
@@ -10305,12 +12193,20 @@
{
"name": "HC-Parasubiculum (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 8,
+ "labelIndex": 60,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Parasubiculum (Hippocampus)",
"gray": "59"
+ },
+ "xml253": {
+ "_": "HC-Parasubiculum (Hippocampus)",
+ "$": {
+ "num": "59",
+ "id": "62",
+ "grayvalue": "60"
+ }
}
},
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@@ -10334,12 +12230,20 @@
{
"name": "HC-Parasubiculum (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 8,
+ "labelIndex": 59,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "HC-Parasubiculum (Hippocampus)",
"gray": "59"
+ },
+ "xml253": {
+ "_": "HC-Parasubiculum (Hippocampus)",
+ "$": {
+ "num": "58",
+ "id": "62",
+ "grayvalue": "59"
+ }
}
},
"originDatasets": [
@@ -10379,12 +12283,20 @@
{
"name": "DG (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 91,
+ "labelIndex": 22,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "DG (Hippocampus)",
"gray": "22"
+ },
+ "xml253": {
+ "_": "DG (Hippocampus)",
+ "$": {
+ "num": "21",
+ "id": "61",
+ "grayvalue": "22"
+ }
}
},
"originDatasets": [
@@ -10414,12 +12326,20 @@
{
"name": "DG (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 91,
+ "labelIndex": 22,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "DG (Hippocampus)",
"gray": "22"
+ },
+ "xml253": {
+ "_": "DG (Hippocampus)",
+ "$": {
+ "num": "21",
+ "id": "61",
+ "grayvalue": "22"
+ }
}
},
"originDatasets": [
@@ -10465,12 +12385,20 @@
{
"name": "CA2 (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 23,
+ "labelIndex": 51,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CA2 (Hippocampus)",
"gray": "51"
+ },
+ "xml253": {
+ "_": "CA2 (Hippocampus)",
+ "$": {
+ "num": "50",
+ "id": "58",
+ "grayvalue": "51"
+ }
}
},
"originDatasets": [
@@ -10500,12 +12428,20 @@
{
"name": "CA2 (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 23,
+ "labelIndex": 51,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CA2 (Hippocampus)",
"gray": "51"
+ },
+ "xml253": {
+ "_": "CA2 (Hippocampus)",
+ "$": {
+ "num": "50",
+ "id": "58",
+ "grayvalue": "51"
+ }
}
},
"originDatasets": [
@@ -10551,12 +12487,20 @@
{
"name": "CA1 (Hippocampus)",
"status": "left hemisphere",
- "labelIndex": 61,
+ "labelIndex": 56,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CA1 (Hippocampus)",
"gray": "57"
+ },
+ "xml253": {
+ "_": "CA1 (Hippocampus)",
+ "$": {
+ "num": "55",
+ "id": "66",
+ "grayvalue": "56"
+ }
}
},
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@@ -10586,12 +12530,20 @@
{
"name": "CA1 (Hippocampus)",
"status": "right hemisphere",
- "labelIndex": 61,
+ "labelIndex": 57,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "CA1 (Hippocampus)",
"gray": "56"
+ },
+ "xml253": {
+ "_": "CA1 (Hippocampus)",
+ "$": {
+ "num": "56",
+ "id": "66",
+ "grayvalue": "57"
+ }
}
},
"originDatasets": [
@@ -10657,12 +12609,20 @@
{
"name": "Interposed Nucleus (Cerebellum)",
"status": "left hemisphere",
- "labelIndex": 30,
+ "labelIndex": 109,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Interposed Nucleus (Cerebellum)",
"gray": "109"
+ },
+ "xml253": {
+ "_": "Interposed Nucleus (Cerebellum)",
+ "$": {
+ "num": "108",
+ "id": "251",
+ "grayvalue": "109"
+ }
}
},
"originDatasets": [
@@ -10692,12 +12652,20 @@
{
"name": "Interposed Nucleus (Cerebellum)",
"status": "right hemisphere",
- "labelIndex": 30,
+ "labelIndex": 109,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Interposed Nucleus (Cerebellum)",
"gray": "109"
+ },
+ "xml253": {
+ "_": "Interposed Nucleus (Cerebellum)",
+ "$": {
+ "num": "108",
+ "id": "251",
+ "grayvalue": "109"
+ }
}
},
"originDatasets": [
@@ -10748,12 +12716,20 @@
{
"name": "Dorsal Dentate Nucleus (Cerebellum)",
"status": "left hemisphere",
- "labelIndex": 111,
+ "labelIndex": 16,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Dorsal Dentate Nucleus (Cerebellum)",
"gray": "16"
+ },
+ "xml253": {
+ "_": "Dorsal Dentate Nucleus (Cerebellum)",
+ "$": {
+ "num": "15",
+ "id": "240",
+ "grayvalue": "16"
+ }
}
},
"originDatasets": [
@@ -10783,12 +12759,20 @@
{
"name": "Dorsal Dentate Nucleus (Cerebellum)",
"status": "right hemisphere",
- "labelIndex": 111,
+ "labelIndex": 18,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Dorsal Dentate Nucleus (Cerebellum)",
"gray": "16"
+ },
+ "xml253": {
+ "_": "Dorsal Dentate Nucleus (Cerebellum)",
+ "$": {
+ "num": "17",
+ "id": "240",
+ "grayvalue": "18"
+ }
}
},
"originDatasets": [
@@ -10834,12 +12818,20 @@
{
"name": "Ventral Dentate Nucleus (Cerebellum)",
"status": "left hemisphere",
- "labelIndex": 38,
+ "labelIndex": 66,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ventral Dentate Nucleus (Cerebellum)",
"gray": "65"
+ },
+ "xml253": {
+ "_": "Ventral Dentate Nucleus (Cerebellum)",
+ "$": {
+ "num": "65",
+ "id": "241",
+ "grayvalue": "66"
+ }
}
},
"originDatasets": [
@@ -10869,12 +12861,20 @@
{
"name": "Ventral Dentate Nucleus (Cerebellum)",
"status": "right hemisphere",
- "labelIndex": 38,
+ "labelIndex": 65,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Ventral Dentate Nucleus (Cerebellum)",
"gray": "65"
+ },
+ "xml253": {
+ "_": "Ventral Dentate Nucleus (Cerebellum)",
+ "$": {
+ "num": "64",
+ "id": "241",
+ "grayvalue": "65"
+ }
}
},
"originDatasets": [
@@ -10925,12 +12925,20 @@
{
"name": "Fastigial Nucleus (Cerebellum)",
"status": "left hemisphere",
- "labelIndex": 89,
+ "labelIndex": 102,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Fastigial Nucleus (Cerebellum)",
"gray": "103"
+ },
+ "xml253": {
+ "_": "Fastigial Nucleus (Cerebellum)",
+ "$": {
+ "num": "101",
+ "id": "219",
+ "grayvalue": "102"
+ }
}
},
"originDatasets": [
@@ -10960,12 +12968,20 @@
{
"name": "Fastigial Nucleus (Cerebellum)",
"status": "right hemisphere",
- "labelIndex": 89,
+ "labelIndex": 102,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Fastigial Nucleus (Cerebellum)",
"gray": "102"
+ },
+ "xml253": {
+ "_": "Fastigial Nucleus (Cerebellum)",
+ "$": {
+ "num": "101",
+ "id": "219",
+ "grayvalue": "102"
+ }
}
},
"originDatasets": [
@@ -11016,12 +13032,20 @@
{
"name": "Interposed Nucleus (Cerebellum)",
"status": "left hemisphere",
- "labelIndex": 30,
+ "labelIndex": 109,
"ngId": "MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Interposed Nucleus (Cerebellum)",
"gray": "109"
+ },
+ "xml253": {
+ "_": "Interposed Nucleus (Cerebellum)",
+ "$": {
+ "num": "108",
+ "id": "251",
+ "grayvalue": "109"
+ }
}
},
"originDatasets": [
@@ -11051,12 +13075,20 @@
{
"name": "Interposed Nucleus (Cerebellum)",
"status": "right hemisphere",
- "labelIndex": 30,
+ "labelIndex": 109,
"ngId": "MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE",
"_": {
"xml": {
"name": "Interposed Nucleus (Cerebellum)",
"gray": "109"
+ },
+ "xml253": {
+ "_": "Interposed Nucleus (Cerebellum)",
+ "$": {
+ "num": "108",
+ "id": "251",
+ "grayvalue": "109"
+ }
}
},
"originDatasets": [
@@ -11107,7 +13139,7 @@
]
,
"_": {
- "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20201204_JulichBrainV3_0_hemisphereSplit_metadata/src/58efbff4f6599cd66246945eb1ffbbb239840295/output/nehubaUI/julich-brain-v3.0-icbm152-pos.json"
+ "@src": "https://gin.g-node.org/FZJ-INM1-BDA/20210209_JulichBrain_v2_5_3_hierarchy/src/5ea4494af794d24406672b189a04eea70d03c8b9/output/newHierarchy.json"
}
},{
"@id": "juelich/iav/atlas/v1.0.0/79cbeaa4ee96d5d3dfe2876e9f74b3dc3d3ffb84304fb9b965b1776563a1069c",
diff --git a/src/res/ext/MNI152NehubaConfig.json b/src/res/ext/MNI152NehubaConfig.json
index a19a6ba72d7a8e02e32f1326b7bd080ef89401cf..32f89fb2eceeec97268024776561287a36761fc5 100644
--- a/src/res/ext/MNI152NehubaConfig.json
+++ b/src/res/ext/MNI152NehubaConfig.json
@@ -220,7 +220,7 @@
"MNI152_V25_RIGHT_NG_SPLIT_HEMISPHERE": {
"type": "segmentation",
"visible": true,
- "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_icbm_v30_r",
+ "source": "precomputed://https://neuroglancer-dev.humanbrainproject.eu/precomputed/data-repo-ng-bot/JulichBrainV2_5_3/precomputed/JulichBrain_MPMAtlas_r_N10_nlin2Stdicbm152asym2009c_publicDOI_453c4c95827e38dcce5372b200065cba",
"transform": [
[
1,
@@ -251,7 +251,7 @@
"MNI152_V25_LEFT_NG_SPLIT_HEMISPHERE": {
"type": "segmentation",
"visible": true,
- "source": "precomputed://https://neuroglancer.humanbrainproject.eu/precomputed/data-repo/20201204_JulichBrainV3_0_hemisphereSplit/precomputed/JuBrain_Map_icbm_v30_l",
+ "source": "precomputed://https://neuroglancer-dev.humanbrainproject.eu//precomputed/data-repo-ng-bot/JulichBrainV2_5_3/precomputed/JulichBrain_MPMAtlas_l_N10_nlin2Stdicbm152asym2009c_publicDOI_3f5ec6016bc2242769c41befdbc1b2e0",
"transform": [
[
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diff --git a/src/res/ext/atlas/atlas_multiLevelHuman.json b/src/res/ext/atlas/atlas_multiLevelHuman.json
index 9eb2e035cb96cf9643689065f67c873be0bf5c0a..8bff76f3ec6d19cd1c975824bad57841f8bae5d4 100644
--- a/src/res/ext/atlas/atlas_multiLevelHuman.json
+++ b/src/res/ext/atlas/atlas_multiLevelHuman.json
@@ -51,20 +51,6 @@
}
]
},
- {
- "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
- "name": "MNI Colin 27",
- "availableIn": [
- {
- "@id": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
- "name": "Cytoarchitectonic maps - v2.5"
- },
- {
- "@id": "juelich/iav/atlas/v1.0.0/8",
- "name": "Cytoarchitectonic Maps - v1.18"
- }
- ]
- },
{
"@id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
"name": "Big Brain (Histology)",
@@ -111,13 +97,6 @@
"originalDatasetFormats": [{
"name": "probability map"
}]
- },
- {
- "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
- "name": "MNI Colin 27",
- "originalDatasetFormats": [{
- "name": "probability map"
- }]
}
]
},
@@ -145,7 +124,7 @@
"@version": {
"@next": null,
"@this": "minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-25",
- "name": "v2.5",
+ "name": "v2.6",
"@previous": "juelich/iav/atlas/v1.0.0/8"
},
"availableIn": [
@@ -155,13 +134,6 @@
"originalDatasetFormats": [{
"name": "probability map"
}]
- },
- {
- "@id": "minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992",
- "name": "MNI Colin 27",
- "originalDatasetFormats": [{
- "name": "probability map"
- }]
}
]
},
diff --git a/src/res/ext/bigbrain.json b/src/res/ext/bigbrain.json
index 85d502866ec6af1f5f8efc425b82ff33940781d9..22556883653d752f26da1a8cd644d808279810dd 100644
--- a/src/res/ext/bigbrain.json
+++ b/src/res/ext/bigbrain.json
@@ -852,36 +852,6 @@
"ngId": "v3v",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
- "rgb": [
- 83,
- 179,
- 155
- ],
- "children": [],
- "fullId": {
- "kg": {
- "kgSchema": "minds/core/parcellationregion/v1.0.0",
- "kgId": "04674a3c-bb3a-495e-a466-206355e630bd"
- }
- },
- "relatedAreas": [],
- "originDatasets":[
- {
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "f746514d-b79a-48e2-9c07-39f7c62459cf",
- "format": {
- "name": "Full 3D map"
- }
- }
- ]
- },
- {
- "name": "Area hOc3v (LingG)",
- "ngId": "v3v",
- "status": "fully mapped",
- "labelIndex": 1,
- "position": [],
"rgb": [
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179,
@@ -937,7 +907,6 @@
"ngId": "v5",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
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@@ -991,7 +960,6 @@
"ngId": "LGB-lam1",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
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@@ -1020,7 +988,6 @@
"ngId": "LGB-lam2",
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- "position": [],
"rgb": [
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@@ -1049,7 +1016,6 @@
"ngId": "LGB-lam3",
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- "position": [],
"rgb": [
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@@ -1078,7 +1044,6 @@
"ngId": "LGB-lam4",
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"rgb": [
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@@ -1107,7 +1072,6 @@
"ngId": "LGB-lam5",
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"rgb": [
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@@ -1136,7 +1100,6 @@
"ngId": "LGB-lam6",
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- "position": [],
"rgb": [
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@@ -1170,7 +1133,6 @@
"ngId": "v5",
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- "position": [],
"rgb": [
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@@ -1215,7 +1177,6 @@
"ngId": "LGB-lam1",
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- "position": [],
"rgb": [
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@@ -1235,7 +1196,6 @@
"ngId": "LGB-lam2",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
222,
74,
@@ -1255,7 +1215,6 @@
"ngId": "LGB-lam3",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
132,
90,
@@ -1275,7 +1234,6 @@
"ngId": "LGB-lam4",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
41,
123,
@@ -1295,7 +1253,6 @@
"ngId": "LGB-lam5",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
82,
214,
@@ -1315,7 +1272,6 @@
"ngId": "LGB-lam6",
"status": "fully mapped",
"labelIndex": 1,
- "position": [],
"rgb": [
99,
231,
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 932ccb8a54b4caa2e0306a81f27941dfa5547911..2c1d0cd2639a41c661fb6e45c8f695e84299ee33 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -22,7 +22,7 @@
"originDatasets": [
{
"kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "ef48c5e9-6b3c-4d5a-a9a9-e678fe10bdf6"
+ "kgId": "2eaa3dc6-a21b-41c1-b703-bf06f82adf25"
}
],
"properties": {
diff --git a/src/ui/connectivityBrowser/connectivityBrowser.component.spec.ts b/src/ui/connectivityBrowser/connectivityBrowser.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..72aa760cb486d4a0457df4669ea12559ec446ee3
--- /dev/null
+++ b/src/ui/connectivityBrowser/connectivityBrowser.component.spec.ts
@@ -0,0 +1,78 @@
+import {ConnectivityBrowserComponent} from "src/ui/connectivityBrowser/connectivityBrowser.component";
+import {async, ComponentFixture, TestBed} from "@angular/core/testing";
+import {Action} from "@ngrx/store";
+import {
+ defaultRootState,
+} from "src/services/stateStore.service";
+import {HttpClientModule} from "@angular/common/http";
+import {CUSTOM_ELEMENTS_SCHEMA} from "@angular/core";
+import {DatabrowserModule} from "src/ui/databrowserModule";
+import {provideMockActions} from "@ngrx/effects/testing";
+import {provideMockStore} from "@ngrx/store/testing";
+import {Observable, of} from "rxjs";
+
+describe('ConnectivityComponent', () => {
+
+ let component: ConnectivityBrowserComponent;
+ let fixture: ComponentFixture<ConnectivityBrowserComponent>;
+ const actions$: Observable<Action> = of({type: 'TEST'})
+
+ let datasetList = [
+ {
+ id: 'id1',
+ name: 'n1',
+ description: 'd1',
+ kgId: 'kgId1',
+ kgschema: 'kgschema1'
+ }, {
+ id: 'id2',
+ name: 'n2',
+ description: 'd2',
+ kgId: 'kgId2',
+ kgschema: 'kgschema2'
+ }
+ ]
+
+ beforeEach(async (() => {
+ TestBed.configureTestingModule({
+ imports: [
+ HttpClientModule,
+ DatabrowserModule
+ ],
+ providers: [
+ provideMockActions(() => actions$),
+ provideMockStore({ initialState: defaultRootState })
+ ],
+ declarations: [ConnectivityBrowserComponent],
+ schemas: [
+ CUSTOM_ELEMENTS_SCHEMA,
+ ],
+ }).compileComponents()
+ }));
+
+ it('> component can be created', async () => {
+ fixture = TestBed.createComponent(ConnectivityBrowserComponent)
+ component = fixture.componentInstance
+ expect(component).toBeTruthy()
+ })
+
+ it('> change dataset changes description, kgId and kgschema', () => {
+ fixture = TestBed.createComponent(ConnectivityBrowserComponent)
+ component = fixture.componentInstance
+
+ component.datasetList = datasetList
+
+ component.changeDataset({value: 'n1'})
+
+ expect(component.selectedDatasetDescription).toEqual('d1')
+ expect(component.selectedDatasetKgId).toEqual('kgId1')
+ expect(component.selectedDatasetKgSchema).toEqual('kgschema1')
+
+ component.changeDataset({value: 'n2'})
+
+ expect(component.selectedDatasetDescription).toEqual('d2')
+ expect(component.selectedDatasetKgId).toEqual('kgId2')
+ expect(component.selectedDatasetKgSchema).toEqual('kgschema2')
+ })
+
+});
\ No newline at end of file
diff --git a/src/ui/regionalFeatures/featureContainer/featureContainer.component.spec.ts b/src/ui/regionalFeatures/featureContainer/featureContainer.component.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..627b097c977eb8fbef6171fb205a0b6f690abd6e
--- /dev/null
+++ b/src/ui/regionalFeatures/featureContainer/featureContainer.component.spec.ts
@@ -0,0 +1,169 @@
+import { CommonModule } from "@angular/common"
+import { ChangeDetectorRef, Component, ComponentRef, EventEmitter, NgModule } from "@angular/core"
+import { async, TestBed } from "@angular/core/testing"
+import { By } from "@angular/platform-browser"
+import { RegionalFeaturesService } from "../regionalFeature.service"
+import { ISingleFeature } from "../singleFeatures/interfaces"
+import { FeatureContainer } from "./featureContainer.component"
+
+const dummyCmpType = 'dummyType'
+
+@Component({
+ template: `{{ text }}`
+})
+
+class DummyComponent implements ISingleFeature{
+ text = 'hello world'
+ feature: any
+ region: any
+ viewChanged = new EventEmitter<boolean>()
+}
+
+@Component({
+ template: ''
+})
+
+class HostCmp{
+ public feature: any
+ public region: any
+
+ constructor(public cdr: ChangeDetectorRef){
+
+ }
+
+ detectChange(){
+ this.cdr.detectChanges()
+ }
+}
+
+const serviceStub = {
+ mapFeatToCmp: new Map([
+ [dummyCmpType, DummyComponent]
+ ])
+}
+
+@NgModule({
+ declarations: [
+ FeatureContainer,
+ DummyComponent,
+ ],
+ entryComponents: [
+ DummyComponent
+ ],
+ providers: [
+ {
+ provide: RegionalFeaturesService,
+ useValue: serviceStub
+ }
+ ],
+ exports: [
+ FeatureContainer,
+ DummyComponent,
+ ]
+})
+
+class DummyModule{}
+
+describe('> featureContainer.component.ts', () => {
+ describe('> FeatureContainer', () => {
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ imports: [
+ CommonModule,
+ DummyModule,
+ ],
+ declarations: [
+ HostCmp,
+ ],
+ }).overrideComponent(HostCmp, {
+ set: {
+ template: `
+ <feature-container
+ [feature]="feature"
+ [region]="region"
+ (viewChanged)="detectChange()">
+ </feature-container>`
+ }
+ }).compileComponents()
+
+ }))
+
+ it('> can be created', () => {
+ const fixture = TestBed.createComponent(HostCmp)
+ expect(fixture).toBeTruthy()
+ const featContainer = fixture.debugElement.query(By.directive(FeatureContainer))
+ expect(featContainer).toBeTruthy()
+ })
+
+ describe('> if inputs change', () => {
+ it('> if input changed, but feature is not one of them, map.get will not be called', () => {
+ const fixture = TestBed.createComponent(HostCmp)
+ // const featContainer = fixture.debugElement.query(By.directive(FeatureContainer))
+ spyOn(serviceStub.mapFeatToCmp, 'get').and.callThrough()
+ fixture.componentInstance.region = {
+ name: 'tesla'
+ }
+ fixture.detectChanges()
+ expect(serviceStub.mapFeatToCmp.get).not.toHaveBeenCalled()
+ })
+
+ it('> if input changed, feature is one of them, will not call map.get', () => {
+ const fixture = TestBed.createComponent(HostCmp)
+ const dummyFeature = {
+ type: dummyCmpType
+ }
+ spyOn(serviceStub.mapFeatToCmp, 'get').and.callThrough()
+ fixture.componentInstance.feature = dummyFeature
+ fixture.detectChanges()
+ expect(serviceStub.mapFeatToCmp.get).toHaveBeenCalledWith(dummyCmpType)
+ })
+
+ it('> should render default txt', () => {
+ const fixture = TestBed.createComponent(HostCmp)
+ const dummyFeature = {
+ type: dummyCmpType
+ }
+ fixture.componentInstance.feature = dummyFeature
+ fixture.detectChanges()
+ const text = fixture.nativeElement.textContent
+ expect(text).toContain('hello world')
+ })
+
+ it('> if inner component changes, if view changed does not emit, will not change ui', () => {
+
+ const fixture = TestBed.createComponent(HostCmp)
+ const dummyFeature = {
+ type: dummyCmpType
+ }
+ fixture.componentInstance.feature = dummyFeature
+ fixture.detectChanges()
+ const featureContainer = fixture.debugElement.query(
+ By.directive(FeatureContainer)
+ )
+ const cr = (featureContainer.componentInstance as FeatureContainer)['cr'] as ComponentRef<DummyComponent>
+ cr.instance.text = 'foo bar'
+ const text = fixture.nativeElement.textContent
+ expect(text).toContain('hello world')
+ })
+
+ it('> if inner component changes, and viewChanged is emitted, ui should change accordingly', () => {
+
+ const fixture = TestBed.createComponent(HostCmp)
+ const dummyFeature = {
+ type: dummyCmpType
+ }
+ fixture.componentInstance.feature = dummyFeature
+ fixture.detectChanges()
+ const featureContainer = fixture.debugElement.query(
+ By.directive(FeatureContainer)
+ )
+ const cr = (featureContainer.componentInstance as FeatureContainer)['cr'] as ComponentRef<DummyComponent>
+ cr.instance.text = 'foo bar'
+ cr.instance.viewChanged.emit(true)
+ const text = fixture.nativeElement.textContent
+ expect(text).toContain('foo bar')
+ })
+ })
+ })
+})
diff --git a/src/ui/ui.module.ts b/src/ui/ui.module.ts
index 708649fd9aad63c7814d30eeea689076d68821a2..be64909fc1852861252a9729f5c173a8b8367017 100644
--- a/src/ui/ui.module.ts
+++ b/src/ui/ui.module.ts
@@ -51,6 +51,7 @@ import { HANDLE_SCREENSHOT_PROMISE, TypeHandleScrnShotPromise } from "./screensh
import { ParcellationRegionModule } from "src/atlasComponents/parcellationRegion";
import { AtlasCmpParcellationModule } from "src/atlasComponents/parcellation";
import { AtlasCmptConnModule } from "src/atlasComponents/connectivity";
+import { ViewerCtrlModule } from "src/viewerCtrl";
@NgModule({
imports : [
@@ -71,6 +72,7 @@ import { AtlasCmptConnModule } from "src/atlasComponents/connectivity";
ParcellationRegionModule,
AtlasCmpParcellationModule,
AtlasCmptConnModule,
+ ViewerCtrlModule,
],
declarations : [
// NehubaContainer,
diff --git a/src/viewerCtrl/index.ts b/src/viewerCtrl/index.ts
new file mode 100644
index 0000000000000000000000000000000000000000..32598a8ce9159499453bb4e35ae719bb7448e983
--- /dev/null
+++ b/src/viewerCtrl/index.ts
@@ -0,0 +1 @@
+export { ViewerCtrlModule } from './module'
\ No newline at end of file
diff --git a/src/viewerCtrl/module.ts b/src/viewerCtrl/module.ts
new file mode 100644
index 0000000000000000000000000000000000000000..dd1a100beeba314400417dc5ac19670bf090bde4
--- /dev/null
+++ b/src/viewerCtrl/module.ts
@@ -0,0 +1,21 @@
+import { CommonModule } from "@angular/common";
+import { NgModule } from "@angular/core";
+import { AngularMaterialModule } from "src/ui/sharedModules/angularMaterial.module";
+import { ViewerCtrlCmp } from "./viewerCtrlCmp/viewerCtrlCmp.component";
+
+// Migrate to viewer specific submodule when merged to dev
+
+@NgModule({
+ imports: [
+ CommonModule,
+ AngularMaterialModule,
+ ],
+ declarations: [
+ ViewerCtrlCmp,
+ ],
+ exports: [
+ ViewerCtrlCmp
+ ]
+})
+
+export class ViewerCtrlModule{}
\ No newline at end of file
diff --git a/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.component.ts b/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.component.ts
new file mode 100644
index 0000000000000000000000000000000000000000..93e6f3def9078f23195e9bea73dac0165214c17f
--- /dev/null
+++ b/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.component.ts
@@ -0,0 +1,65 @@
+import { Component, HostBinding } from "@angular/core";
+import { select, Store } from "@ngrx/store";
+import { Subscription } from "rxjs";
+import { viewerStateSelectedTemplatePureSelector } from "src/services/state/viewerState/selectors";
+
+
+@Component({
+ selector: 'viewer-ctrl-component',
+ templateUrl: './viewerCtrlCmp.template.html',
+ styleUrls: [
+ './viewerCtrlCmp.style.css'
+ ],
+ exportAs: 'viewerCtrlCmp'
+})
+
+export class ViewerCtrlCmp{
+
+ @HostBinding('attr.darktheme')
+ darktheme = false
+
+ private sub: Subscription[] = []
+ private hiddenLayerNames: string[] = []
+
+ constructor(
+ private store$: Store<any>
+ ){
+
+ this.sub.push(
+ this.store$.pipe(
+ select(viewerStateSelectedTemplatePureSelector)
+ ).subscribe(tmpl => {
+ const { useTheme } = tmpl || {}
+ this.darktheme = useTheme === 'dark'
+ })
+ )
+
+ }
+
+ public toggleParcVsbl(){
+ const visibleParcLayers = ((window as any).viewer.layerManager.managedLayers)
+ .slice(1)
+ .filter(({ visible }) => visible)
+
+ const allParcHidden = visibleParcLayers.length === 0
+
+ if (allParcHidden) {
+ for (const name of this.hiddenLayerNames) {
+ const l = (window as any).viewer.layerManager.getLayerByName(name)
+ l && l.setVisible(true)
+ }
+ this.hiddenLayerNames = []
+ } else {
+ this.hiddenLayerNames = []
+ for (const { name } of visibleParcLayers) {
+ const l = (window as any).viewer.layerManager.getLayerByName(name)
+ l && l.setVisible(false)
+ this.hiddenLayerNames.push( name )
+ }
+ }
+
+ setTimeout(() => {
+ (window as any).viewer.display.scheduleRedraw()
+ })
+ }
+}
\ No newline at end of file
diff --git a/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.style.css b/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.style.css
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.template.html b/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.template.html
new file mode 100644
index 0000000000000000000000000000000000000000..2ba8e30622edf364319af102febfd0fe26d6d30c
--- /dev/null
+++ b/src/viewerCtrl/viewerCtrlCmp/viewerCtrlCmp.template.html
@@ -0,0 +1,14 @@
+<h3 class="iv-custom-comp text mat-title">
+ Parcellations
+</h3>
+
+<mat-divider></mat-divider>
+
+<button mat-flat-button color="warn"
+ class="mt-2"
+ (click)="toggleParcVsbl()">
+ <i class="fas fa-eye-slash"></i>
+ <span>
+ Clear All
+ </span>
+</button>
\ No newline at end of file