diff --git a/.github/workflows/e2e.yml b/.github/workflows/e2e.yml
index 5bfbf74482e1f33272073afa9917fdd75f12614b..e8f8aed0c0c4717bc1eaf2f9c09d52c7548c33ec 100644
--- a/.github/workflows/e2e.yml
+++ b/.github/workflows/e2e.yml
@@ -8,9 +8,10 @@ on:
env:
DOCKER_IMAGE_NAME: interactive-viewer
DOCKER_IMAGE_TAG: ${{ github.sha }}
- DOCKER_SAVE_FILENAME: iav.tar.gz
- ARTEFACT_NAME: iav_docker_image
- DOCKER_CONTAINER_NAME: github-actions-iav-dkr-container
+ DOCKER_CONTAINER_NAME: gha-iav-built-${{ github.sha }}
+ DOCKER_E2E_PPTR: gha-iav-e2e-pptr-${{ github.sha }}
+ DOCKER_E2E_NETWORK: gha-dkr-network-${{ github.sha }}
+ ATLAS_URL: http://gha-iav-built-${{ github.sha }}:3000/
jobs:
buildimage:
@@ -26,23 +27,47 @@ jobs:
run: |
docker build --build-arg BACKEND_URL=${BACKEND_URL} -t ${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG} .
env:
- BACKEND_URL: http://localhost:3001
+ BACKEND_URL: ${{ env.ATLAS_URL }}
test:
runs-on: self-hosted
needs: buildimage
steps:
- - uses: actions/checkout@v2
- with:
- fetch-depth: 2
- repository: 'FZJ-INM1-BDA/iv-automated-tests'
- - name: Install dependencies
+ - name: run docker image ${{ env.DOCKER_IMAGE_NAME }}:${{ env.DOCKER_IMAGE_TAG }} as container ${{ env.DOCKER_CONTAINER_NAME }}
+ run: |
+ docker run \
+ --rm \
+ --name ${DOCKER_CONTAINER_NAME} \
+ --env HBP_CLIENTID=${{ secrets.HBP_CLIENTID }} \
+ --env HBP_CLIENTSECRET=${{ secrets.HBP_CLIENTSECRET }} \
+ --env REFRESH_TOKEN=${{ secrets.REFRESH_TOKEN }} \
+ -dit \
+ ${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG}
+
+ - uses: actions/checkout@v1
+ - name: Start pptr docker container with name ${{ env.DOCKER_E2E_PPTR }}
+ run: |
+ docker run --rm \
+ --name ${DOCKER_E2E_PPTR} \
+ -dt \
+ puppeteer
+ docker cp . ${DOCKER_E2E_PPTR}:/iav
+ docker exec -u root ${DOCKER_E2E_PPTR} chown -R pptruser:pptruser /iav
+ docker exec -t -w /iav ${DOCKER_E2E_PPTR} npm i
+ docker exec -t -w /iav ${DOCKER_E2E_PPTR} npm run wd -- update --versions.chrome latest
+ docker exec -t ${DOCKER_E2E_PPTR} npm i puppeteer
+ - name: Setup docker network
+ run: |
+ docker network create ${{ env.DOCKER_E2E_NETWORK }}
+ docker network connect ${{ env.DOCKER_E2E_NETWORK }} ${{ env.DOCKER_E2E_PPTR }}
+ docker network connect ${{ env.DOCKER_E2E_NETWORK }} ${{ env.DOCKER_CONTAINER_NAME }}
+ - name: run pptr tests - ${{ env.ATLAS_URL }}
+ run: |
+ docker exec --env ATLAS_URL=${ATLAS_URL} -t -w /iav ${DOCKER_E2E_PPTR} npm run e2e
+ - name: cleanup, stop container ${{ env.DOCKER_CONTAINER_NAME }}
+ if: success()
run: |
- npm i
- - name: run docker image ${{ env.DOCKER_IMAGE_NAME }}:${{ env.DOCKER_IMAGE_TAG }}
- run: docker run -p 3001:3000 --rm --name ${DOCKER_CONTAINER_NAME} -dit ${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG}
- - name: run pptr tests
- run: node ./node_modules/.bin/mocha ./test/databrowser.spec.js --timeout 1800000
- - name: cleanup
- if: always()
- run: docker stop ${DOCKER_CONTAINER_NAME} && docker rmi ${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG}
+ docker stop ${DOCKER_CONTAINER_NAME}
+ docker stop ${DOCKER_E2E_PPTR}
+ docker network rm ${DOCKER_E2E_NETWORK}
+ docker rmi ${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG}
diff --git a/Dockerfile b/Dockerfile
index 87199619f483ddfe45793a012c87171032ece2b7..588e1efca446da79f6d454c1b7c3153522e9117b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -34,6 +34,9 @@ RUN apk --no-cache add ca-certificates
RUN mkdir /iv-app
WORKDIR /iv-app
+# Copy common folder
+COPY --from=builder /iv/common /common
+
# Copy the express server
COPY --from=builder /iv/deploy .
diff --git a/common/util.js b/common/util.js
new file mode 100644
index 0000000000000000000000000000000000000000..871481b91fc3d3b021aa4302a9d5aa71dd0a1e38
--- /dev/null
+++ b/common/util.js
@@ -0,0 +1,36 @@
+(function(exports) {
+ exports.getIdFromFullId = fullId => {
+ if (!fullId) return null
+ if (typeof fullId === 'string') {
+ const re = /\/([a-z]{1,}\/[a-z]{1,}\/[a-z]{1,}\/v[0-9.]{1,}\/[0-9a-z-]{1,}$)/.exec(fullId)
+ if (re) return re[1]
+ return null
+ } else {
+ const { kg = {} } = fullId
+ const { kgSchema , kgId } = kg
+ if (!kgSchema || !kgId) return null
+ return `${kgSchema}/${kgId}`
+ }
+ }
+
+ const defaultConfig = {
+ timeout: 5000,
+ retries: 3
+ }
+
+ exports.retry = async (fn, { timeout = defaultConfig.timeout, retries = defaultConfig.retries } = defaultConfig) => {
+ let retryNo = 0
+ while (retryNo < retries) {
+ retryNo ++
+ try {
+ const result = await fn()
+ return result
+ } catch (e) {
+ console.warn(`fn failed, retry after ${timeout} milliseconds`)
+ await (() => new Promise(rs => setTimeout(rs, timeout)))()
+ }
+ }
+
+ throw new Error(`fn failed ${retries} times. Aborting.`)
+ }
+})(typeof exports === 'undefined' ? module.exports : exports)
diff --git a/common/util.spec.js b/common/util.spec.js
new file mode 100644
index 0000000000000000000000000000000000000000..4597a54db648521dd029fb002f22ef56436d3b51
--- /dev/null
+++ b/common/util.spec.js
@@ -0,0 +1,20 @@
+import { getIdFromFullId } from './util'
+
+describe('common/util.js', () => {
+ describe('getIdFromFullId', () => {
+ it('should return correct kgId for regions fetched from kg', () => {
+ const id = 'https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/675a6ce9-ef26-4e68-9852-54afeb24923c'
+ expect(getIdFromFullId(id)).toBe('minds/core/parcellationregion/v1.0.0/675a6ce9-ef26-4e68-9852-54afeb24923c')
+ })
+
+ it('should return correct id for regions in hierarchy', () => {
+ const fullId = {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a844d80f-1d94-41a0-901a-14ae257519db"
+ }
+ }
+ expect(getIdFromFullId(fullId)).toBe(`minds/core/parcellationregion/v1.0.0/a844d80f-1d94-41a0-901a-14ae257519db`)
+ })
+ })
+})
diff --git a/deploy/datasets/testData/allen2015.js b/deploy/datasets/testData/allen2015.js
index 7c3afd5e2d0b4021446d7402ff6c44805fb4f3ec..d8d00647d1ac2eb5dcf42993590e359d2a0c36e9 100644
--- a/deploy/datasets/testData/allen2015.js
+++ b/deploy/datasets/testData/allen2015.js
@@ -1,23 +1,10 @@
module.exports = [
{
"formats": [],
- "datasetDOI": [
- {
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ],
+ "datasetDOI": [],
"activity": [
{
- "protocols": [
- "Immunohistochemistry",
- "Atlas",
- "Brain-wide",
- "Synaptic transmission",
- "Neurtransmitter transport",
- "Glutamate uptake",
- "GLT1"
- ],
+ "protocols": [],
"preparation": [
"Ex vivo"
]
@@ -25,200 +12,72 @@ module.exports = [
],
"referenceSpaces": [],
"methods": [
- "Immunohistochemistry"
+ "Patch clamp techniques",
+ "Voltage clamp recording",
+ "Single electrode recording",
+ "Knockin"
],
"custodians": [
- "Danbolt, Niels C."
+ "Cherubini, Enrico"
],
"project": [
- "Rodent brain neurotransporter atlas: GLT1"
+ "STDP"
],
- "description": "Glutamate is the major excitatory transmitter in the central nervous system (Danbolt, Prog. Neurobiol. 65:1-105, 2001). It is inactivated by cellular uptake, mostly catalyzed by the glutamate transporters GLT1 (slc1a2, excitatory amino acid transporter [EAAT2]) subtype expressed at high levels in brain astrocytes and at lower levels in neurons. Three C-terminal variants of EAAT2 exist: GLT1a (Pines et al., Nature 360:464-467, 1992), GLT1b (Utsunomiya-Tate et al., FEBS Lett 416:312-326,1997), and GLT1c (Rauen et al., Neurochem. Int. 45:1095-1106, 2004). This dataset is brain-wide collection of microscopic images showing the brain-wide distribution of GLT1 in the mouse and rat brain, visualized by immunohistochemistry using antibodies against GLT1a and GLT1b. To facilitate identification of anatomical location adjacent section were stained to reveal cyto- and myeloarchitecture.",
+ "description": "Spike-time dependent plasticity (STDP is a particular form of Hebbian type of learning which consists in bidirectional modifications of synaptic strength according to the temporal order of pre- and postsynaptic spiking (*Dan Y1, Poo MM (2006) Spike timing-dependent plasticity: from synapse to perception. Physiol Rev 86:1033-1048*). Thus, positively correlated pre- and postsynaptic spiking (pre before post) within a critical window leads to long term potentiation (LTP), whereas a negative correlation (post before pre) leads to long term depression (LTD). \nAt the neonatal stage, the hippocampal mossy fiber (MF)-CA3 is GABAergic and exhibits STDP. Our data demonstrate that, at the same age, positive pairing fails to induce STD-LTP at MF-CA3 synapses in hippocampal slices obtained from neuroligin-3 (NL3) knock-in (NL3<sup>R451C</sup> KI) and NL3 knock-out (KO) mice. Similarly, in NLR<sup>451C</sup> KI mice, negative pairing failed to cause STD-LTD. In contrast, STD-LTP and STD-LTD can be readily produced in control age-matched WT littermates. In NLR<sup>451C</sup> KI mice, the impairment in STD-LTP is maintained in adulthood when MF are glutamatergic. This set of data refers to the neonate, NLR<sup>451C</sup> KI, positive pairing condition.",
"parcellationAtlas": [
{
"name": "Allen Mouse Common Coordinate Framework v3 2015",
"fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f",
"id": "39a1384b-8413-4d27-af8d-22432225401f"
- },
- {
- "name": "Waxholm Space rat brain atlas v2",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d",
- "id": "2449a7f0-6dd0-4b5a-8f1e-aec0db03679d"
}
],
"licenseInfo": [
{
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "url": "https://creativecommons.org/licenses/by-sa/4.0"
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
}
],
"embargoStatus": [
- "Free"
+ "Embargoed"
],
"license": [
{
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "relativeUrl": "minds/core/licensetype/v1.0.0/78a3bfb2-f4b9-40f0-869c-34b5e48a45bd"
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "relativeUrl": "minds/core/licensetype/v1.0.0/88e71f2d-4fcc-4cb1-bc9f-cbab9ab2058b"
}
],
"parcellationRegion": [
- {
- "species": [],
- "name": "Mouse Whole brain (v3 2015)",
- "alias": "Whole brain"
- },
{
"species": [
{
"identifier": [
- "e9a384ea8a4edf817710b6edef5f2940",
- "5401fdb1d638c2bc5b68241560cddac0"
+ "899694120d41aab8054900b51d369ef8",
+ "e07b81dd7bbdf2727f6df2f4013ed025"
],
- "name": "Rattus norvegicus",
- "@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/f3490d7f-8f7f-4b40-b238-963dcac84412"
+ "name": "Mus musculus",
+ "@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/cfc1656c-67d1-4d2c-a17e-efd7ce0df88c"
}
],
- "name": "Whole Brain ",
- "alias": "Whole brain"
+ "name": "Mouse Hippocampal region (v3 2015)",
+ "alias": "Hippocampal region",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/fc429031-1632-49a4-b9c6-00ab72100c85"
}
],
"species": [
- "Rattus norvegicus",
"Mus musculus"
],
- "name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)",
+ "name": "Spike time dependent plasticity (STDP) data from neonate neuroligin-3 knock-in mice, positive pairing",
"files": [],
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/f7a7d460-8724-4cd1-a06e-457eb8954fbd",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/88e4e64e-b053-48b3-828b-306e386621e0",
"contributors": [
- "Danbolt, Nils C.",
- "Bjaalie, Jan G.",
- "Leergaard, Trygve B.",
- "Lehre, K.P.",
- "Real, Katia",
- "Scott, Heather A.",
- "Holmseth, Silvia"
+ "Cherubini, Enrico",
+ "Sgritta, Martina",
+ "Marchetti, Cristina"
],
- "id": "63bbb845ac6d2f1839f919c2ef0455bc",
+ "id": "1a6cbd0b55a13e7b8775d3417281a83f",
"kgReference": [
- "10.25493/Y147-2CE"
- ],
- "publications": [
- {
- "name": "The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation",
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ]
- },
- {
- "formats": [],
- "datasetDOI": [
- {
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ],
- "activity": [
- {
- "protocols": [
- "Immunohistochemistry",
- "Atlas",
- "Brain-wide",
- "Synaptic transmission",
- "Neurtransmitter transport",
- "Glutamate uptake",
- "GLT1"
- ],
- "preparation": [
- "Ex vivo"
- ]
- }
- ],
- "referenceSpaces": [],
- "methods": [
- "Immunohistochemistry"
- ],
- "custodians": [
- "Danbolt, Niels C."
+ "10.25493/PF1P-YSE"
],
- "project": [
- "Rodent brain neurotransporter atlas: GLT1"
- ],
- "description": "Glutamate is the major excitatory transmitter in the central nervous system (Danbolt, Prog. Neurobiol. 65:1-105, 2001). It is inactivated by cellular uptake, mostly catalyzed by the glutamate transporters GLT1 (slc1a2, excitatory amino acid transporter [EAAT2]) subtype expressed at high levels in brain astrocytes and at lower levels in neurons. Three C-terminal variants of EAAT2 exist: GLT1a (Pines et al., Nature 360:464-467, 1992), GLT1b (Utsunomiya-Tate et al., FEBS Lett 416:312-326,1997), and GLT1c (Rauen et al., Neurochem. Int. 45:1095-1106, 2004). This dataset is brain-wide collection of microscopic images showing the brain-wide distribution of GLT1 in the mouse and rat brain, visualized by immunohistochemistry using antibodies against GLT1a and GLT1b. To facilitate identification of anatomical location adjacent section were stained to reveal cyto- and myeloarchitecture.",
- "parcellationAtlas": [
- {
- "name": "Allen Mouse Common Coordinate Framework v3 2015",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f",
- "id": "39a1384b-8413-4d27-af8d-22432225401f"
- },
- {
- "name": "Waxholm Space rat brain atlas v2",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d",
- "id": "2449a7f0-6dd0-4b5a-8f1e-aec0db03679d"
- }
- ],
- "licenseInfo": [
- {
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "url": "https://creativecommons.org/licenses/by-sa/4.0"
- }
- ],
- "embargoStatus": [
- "Free"
- ],
- "license": [
- {
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "relativeUrl": "minds/core/licensetype/v1.0.0/78a3bfb2-f4b9-40f0-869c-34b5e48a45bd"
- }
- ],
- "parcellationRegion": [
- {
- "species": [],
- "name": "Mouse Whole brain (v3 2015)",
- "alias": "Whole brain"
- },
- {
- "species": [
- {
- "identifier": [
- "e9a384ea8a4edf817710b6edef5f2940",
- "5401fdb1d638c2bc5b68241560cddac0"
- ],
- "name": "Rattus norvegicus",
- "@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/f3490d7f-8f7f-4b40-b238-963dcac84412"
- }
- ],
- "name": "Whole Brain ",
- "alias": "Whole brain"
- }
- ],
- "species": [
- "Rattus norvegicus",
- "Mus musculus"
- ],
- "name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)",
- "files": [],
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/f7a7d460-8724-4cd1-a06e-457eb8954fbd",
- "contributors": [
- "Danbolt, Nils C.",
- "Bjaalie, Jan G.",
- "Leergaard, Trygve B.",
- "Lehre, K.P.",
- "Real, Katia",
- "Scott, Heather A.",
- "Holmseth, Silvia"
- ],
- "id": "63bbb845ac6d2f1839f919c2ef0455bc",
- "kgReference": [
- "10.25493/Y147-2CE"
- ],
- "publications": [
- {
- "name": "The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation",
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ]
+ "publications": []
}
]
\ No newline at end of file
diff --git a/deploy/datasets/testData/mni152.js b/deploy/datasets/testData/hoc1pmap.js
similarity index 65%
rename from deploy/datasets/testData/mni152.js
rename to deploy/datasets/testData/hoc1pmap.js
index b7f11f1608db7a22c0b84558eb02ab547dfad6c1..3cd032968a85c4696ed35c9554dd0dc6c93f333c 100644
--- a/deploy/datasets/testData/mni152.js
+++ b/deploy/datasets/testData/hoc1pmap.js
@@ -82,14 +82,46 @@ module.exports = [
{
"species": [],
"name": "Area hOc1 (V1, 17, CalcS)",
- "alias": null
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/5151ab8f-d8cb-4e67-a449-afe2a41fb007"
}
],
"species": [
"Homo sapiens"
],
"name": "Probabilistic cytoarchitectonic map of Area hOc1 (V1, 17, CalcS) (v2.4)",
- "files": [],
+ "files": [
+ {
+ "byteSize": 199561,
+ "name": "Area-hOc1_r_N10_nlin2Stdcolin27_2.4_publicP_b3b742528b1d1a933c89b2604d23028d.nii.gz",
+ "absolutePath": "https://object.cscs.ch/v1/AUTH_227176556f3c4bb38df9feea4b91200c/hbp-d000001_jubrain-cytoatlas-Area-hOc1_pub/2.4/Area-hOc1_r_N10_nlin2Stdcolin27_2.4_publicP_b3b742528b1d1a933c89b2604d23028d.nii.gz",
+ "contentType": "application/octet-stream"
+ },
+ {
+ "byteSize": 217968,
+ "name": "Area-hOc1_l_N10_nlin2Stdcolin27_2.4_publicP_788fe1ea663b1fa4e7e9a8b5cf26c5d6.nii.gz",
+ "absolutePath": "https://object.cscs.ch/v1/AUTH_227176556f3c4bb38df9feea4b91200c/hbp-d000001_jubrain-cytoatlas-Area-hOc1_pub/2.4/Area-hOc1_l_N10_nlin2Stdcolin27_2.4_publicP_788fe1ea663b1fa4e7e9a8b5cf26c5d6.nii.gz",
+ "contentType": "application/octet-stream"
+ },
+ {
+ "byteSize": 188966,
+ "name": "Area-hOc1_l_N10_nlin2MNI152ASYM2009C_2.4_publicP_d3045ee3c0c4de9820eb1516d2cc72bb.nii.gz",
+ "absolutePath": "https://object.cscs.ch/v1/AUTH_227176556f3c4bb38df9feea4b91200c/hbp-d000001_jubrain-cytoatlas-Area-hOc1_pub/2.4/Area-hOc1_l_N10_nlin2MNI152ASYM2009C_2.4_publicP_d3045ee3c0c4de9820eb1516d2cc72bb.nii.gz",
+ "contentType": "application/octet-stream"
+ },
+ {
+ "byteSize": 181550,
+ "name": "Area-hOc1_r_N10_nlin2MNI152ASYM2009C_2.4_publicP_a48ca5d938781ebaf1eaa25f59df74d0.nii.gz",
+ "absolutePath": "https://object.cscs.ch/v1/AUTH_227176556f3c4bb38df9feea4b91200c/hbp-d000001_jubrain-cytoatlas-Area-hOc1_pub/2.4/Area-hOc1_r_N10_nlin2MNI152ASYM2009C_2.4_publicP_a48ca5d938781ebaf1eaa25f59df74d0.nii.gz",
+ "contentType": "application/octet-stream"
+ },
+ {
+ "byteSize": 20,
+ "name": "subjects_Area-hOc1.csv",
+ "absolutePath": "https://object.cscs.ch/v1/AUTH_227176556f3c4bb38df9feea4b91200c/hbp-d000001_jubrain-cytoatlas-Area-hOc1_pub/subjects_Area-hOc1.csv",
+ "contentType": "text/csv"
+ }
+ ],
"fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/5c669b77-c981-424a-858d-fe9f527dbc07",
"contributors": [
"Zilles, Karl",
@@ -108,6 +140,7 @@ module.exports = [
"cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
"doi": "10.1006/nimg.1999.0516"
}
- ]
+ ],
+ "preview": true
}
]
\ No newline at end of file
diff --git a/deploy/datasets/testData/mni152JuBrain.js b/deploy/datasets/testData/mni152JuBrain.js
new file mode 100644
index 0000000000000000000000000000000000000000..788d622c47c85e9318868752bd2c14686df37f7e
--- /dev/null
+++ b/deploy/datasets/testData/mni152JuBrain.js
@@ -0,0 +1,337 @@
+module.exports = [
+ {
+ "formats": [
+ "NIFTI"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "imaging"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [
+ {
+ "name": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+ },
+ {
+ "name": "MNI Colin 27",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+ }
+ ],
+ "methods": [
+ "silver staining",
+ "magnetic resonance imaging (MRI)",
+ "probability mapping",
+ "cytoarchitectonic mapping"
+ ],
+ "custodians": [
+ "Amunts, Katrin"
+ ],
+ "project": [
+ "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
+ ],
+ "description": "This dataset contains the distinct architectonic Area hOc1 (V1, 17, CalcS) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the JuBrain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area hOc1 (V1, 17, CalcS). The probability map of Area hOc1 (V1, 17, CalcS) are provided in the NifTi format for each brain reference space and hemisphere. The JuBrain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "parcellationAtlas": [
+ {
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "id": [
+ "deec923ec31a82f89a9c7c76a6fefd6b",
+ "e2d45e028b6da0f6d9fdb9491a4de80a"
+ ]
+ }
+ ],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1 (V1, 17, CalcS)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Probabilistic cytoarchitectonic map of Area hOc1 (V1, 17, CalcS) (v2.4)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/5c669b77-c981-424a-858d-fe9f527dbc07",
+ "contributors": [
+ "Zilles, Karl",
+ "Schormann, Thorsten",
+ "Mohlberg, Hartmut",
+ "Malikovic, Aleksandar",
+ "Amunts, Katrin"
+ ],
+ "id": "5c669b77-c981-424a-858d-fe9f527dbc07",
+ "kgReference": [
+ "10.25493/MXJ6-6DH"
+ ],
+ "publications": [
+ {
+ "name": "Brodmann's Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable?",
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ]
+ },{
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area hOc1 using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area hOc1",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/e715e1f7-2079-45c4-a67f-f76b102acfce",
+ "contributors": [
+ "Scheperjans, Filip",
+ "Schleicher, Axel",
+ "Eickhoff, Simon B.",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "0616d1e97b8be75de526bc265d9af540",
+ "kgReference": [
+ "10.25493/P8SD-JMH"
+ ],
+ "publications": [
+ {
+ "name": "Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex",
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+ },{
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area 44d using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area 44d",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area 44d",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/cb875c0d-97f4-4dbc-a9ce-472d8ba58c99",
+ "contributors": [
+ "Morosan, Patricia",
+ "Schleicher, Axel",
+ "Lenzen, Marianne",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "31397abd7aebcf13bf3b1d5eb2e2d400",
+ "kgReference": [
+ "10.25493/YQCR-1DQ"
+ ],
+ "publications": [
+ {
+ "name": "Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping",
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+ }
+]
\ No newline at end of file
diff --git a/deploy/datasets/testData/waxholmv2.js b/deploy/datasets/testData/waxholmv2.js
index 7c3afd5e2d0b4021446d7402ff6c44805fb4f3ec..91c198d28a131a55de5a44e5b4c2b1ca7ec888b7 100644
--- a/deploy/datasets/testData/waxholmv2.js
+++ b/deploy/datasets/testData/waxholmv2.js
@@ -65,7 +65,8 @@ module.exports = [
{
"species": [],
"name": "Mouse Whole brain (v3 2015)",
- "alias": "Whole brain"
+ "alias": "Whole brain",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/2bdfac7a-b38c-4c55-9843-0b56cb90bb67"
},
{
"species": [
@@ -78,8 +79,9 @@ module.exports = [
"@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/f3490d7f-8f7f-4b40-b238-963dcac84412"
}
],
- "name": "Whole Brain ",
- "alias": "Whole brain"
+ "name": "Rat Whole brain (v2)",
+ "alias": "Whole brain",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b2b56201-472c-4f70-842f-cf2133eacaba"
}
],
"species": [
@@ -87,118 +89,6 @@ module.exports = [
"Mus musculus"
],
"name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)",
- "files": [],
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/f7a7d460-8724-4cd1-a06e-457eb8954fbd",
- "contributors": [
- "Danbolt, Nils C.",
- "Bjaalie, Jan G.",
- "Leergaard, Trygve B.",
- "Lehre, K.P.",
- "Real, Katia",
- "Scott, Heather A.",
- "Holmseth, Silvia"
- ],
- "id": "63bbb845ac6d2f1839f919c2ef0455bc",
- "kgReference": [
- "10.25493/Y147-2CE"
- ],
- "publications": [
- {
- "name": "The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation",
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ]
- },
- {
- "formats": [],
- "datasetDOI": [
- {
- "cite": "Holmseth, S., Scott, H. A., Real, K., Lehre, K. P., Leergaard, T. B., Bjaalie, J. G., & Danbolt, N. C. (2009). The concentrations and distributions of three C-terminal variants of the GLT1 (EAAT2; slc1a2) glutamate transporter protein in rat brain tissue suggest differential regulation. Neuroscience, 162(4), 1055–1071. ",
- "doi": "10.1016/j.neuroscience.2009.03.048"
- }
- ],
- "activity": [
- {
- "protocols": [
- "Immunohistochemistry",
- "Atlas",
- "Brain-wide",
- "Synaptic transmission",
- "Neurtransmitter transport",
- "Glutamate uptake",
- "GLT1"
- ],
- "preparation": [
- "Ex vivo"
- ]
- }
- ],
- "referenceSpaces": [],
- "methods": [
- "Immunohistochemistry"
- ],
- "custodians": [
- "Danbolt, Niels C."
- ],
- "project": [
- "Rodent brain neurotransporter atlas: GLT1"
- ],
- "description": "Glutamate is the major excitatory transmitter in the central nervous system (Danbolt, Prog. Neurobiol. 65:1-105, 2001). It is inactivated by cellular uptake, mostly catalyzed by the glutamate transporters GLT1 (slc1a2, excitatory amino acid transporter [EAAT2]) subtype expressed at high levels in brain astrocytes and at lower levels in neurons. Three C-terminal variants of EAAT2 exist: GLT1a (Pines et al., Nature 360:464-467, 1992), GLT1b (Utsunomiya-Tate et al., FEBS Lett 416:312-326,1997), and GLT1c (Rauen et al., Neurochem. Int. 45:1095-1106, 2004). This dataset is brain-wide collection of microscopic images showing the brain-wide distribution of GLT1 in the mouse and rat brain, visualized by immunohistochemistry using antibodies against GLT1a and GLT1b. To facilitate identification of anatomical location adjacent section were stained to reveal cyto- and myeloarchitecture.",
- "parcellationAtlas": [
- {
- "name": "Allen Mouse Common Coordinate Framework v3 2015",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/39a1384b-8413-4d27-af8d-22432225401f",
- "id": "39a1384b-8413-4d27-af8d-22432225401f"
- },
- {
- "name": "Waxholm Space rat brain atlas v2",
- "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/2449a7f0-6dd0-4b5a-8f1e-aec0db03679d",
- "id": "2449a7f0-6dd0-4b5a-8f1e-aec0db03679d"
- }
- ],
- "licenseInfo": [
- {
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "url": "https://creativecommons.org/licenses/by-sa/4.0"
- }
- ],
- "embargoStatus": [
- "Free"
- ],
- "license": [
- {
- "name": "Creative Commons Attribution-ShareAlike 4.0 International",
- "relativeUrl": "minds/core/licensetype/v1.0.0/78a3bfb2-f4b9-40f0-869c-34b5e48a45bd"
- }
- ],
- "parcellationRegion": [
- {
- "species": [],
- "name": "Mouse Whole brain (v3 2015)",
- "alias": "Whole brain"
- },
- {
- "species": [
- {
- "identifier": [
- "e9a384ea8a4edf817710b6edef5f2940",
- "5401fdb1d638c2bc5b68241560cddac0"
- ],
- "name": "Rattus norvegicus",
- "@id": "https://nexus.humanbrainproject.org/v0/data/minds/core/species/v1.0.0/f3490d7f-8f7f-4b40-b238-963dcac84412"
- }
- ],
- "name": "Whole Brain ",
- "alias": "Whole brain"
- }
- ],
- "species": [
- "Rattus norvegicus",
- "Mus musculus"
- ],
- "name": "Brain-wide distribution of glutamate type 1 transporter protein (GLT1)",
- "files": [],
"fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/f7a7d460-8724-4cd1-a06e-457eb8954fbd",
"contributors": [
"Danbolt, Nils C.",
diff --git a/deploy/datasets/util.js b/deploy/datasets/util.js
index bda610f0bdb7f4e6ec89146dc2c9e1333f7d4f10..d37ff932fd1b4a3025ec7267039f2736f4c79449 100644
--- a/deploy/datasets/util.js
+++ b/deploy/datasets/util.js
@@ -3,6 +3,7 @@ const { getCommonSenseDsFilter } = require('./supplements/commonSense')
const { hasPreview } = require('./supplements/previewFile')
const path = require('path')
const fs = require('fs')
+const { getIdFromFullId, retry } = require('../../common/util')
let getPublicAccessToken
@@ -58,12 +59,18 @@ const populateSet = (flattenedRegions, set = new Set()) => {
if (!(set instanceof Set)) throw `set needs to be an instance of Set`
if (!(flattenedRegions instanceof Array)) throw `flattenedRegions needs to be an instance of Array`
for (const region of flattenedRegions) {
- const { name, relatedAreas } = region
- if (name) set.add(name)
- if (relatedAreas && relatedAreas instanceof Array && relatedAreas.length > 0) {
+ const { name, relatedAreas, fullId } = region
+ if (fullId) {
+ set.add(
+ getIdFromFullId(fullId)
+ )
+ }
+ if (relatedAreas && Array.isArray(relatedAreas)) {
for (const relatedArea of relatedAreas) {
- if(typeof relatedArea === 'string') set.add(relatedArea)
- else console.warn(`related area not an instance of String. skipping`, relatedArea)
+ const { fullId } = relatedArea
+ set.add(
+ getIdFromFullId(fullId)
+ )
}
}
}
@@ -137,7 +144,9 @@ initPrArray.push(
const datasetRegionExistsInParcellationRegion = async (prs, atlasPrSet = new Set()) => {
if (!(atlasPrSet instanceof Set)) throw `atlasPrSet needs to be a set!`
await Promise.all(initPrArray)
- return prs.some(({ name, alias }) => atlasPrSet.has(alias) || atlasPrSet.has(name))
+ return prs.some(({ fullId }) => atlasPrSet.has(
+ getIdFromFullId(fullId)
+ ))
}
const templateNameToIdMap = new Map([
@@ -287,28 +296,9 @@ const init = async () => {
getPublicAccessToken = getPublic
}
-const defaultConfig = {
- timeout: 5000,
- retries: 3
-}
-
-const retry = async (fn, { timeout = defaultConfig.timeout, retries = defaultConfig.retries } = defaultConfig) => {
- let retryNo = 0
- while (retryNo < retries) {
- retryNo ++
- try {
- const result = await fn()
- return result
- } catch (e) {
- console.warn(`fn failed, retry after ${timeout} milliseconds`)
- await (() => new Promise(rs => setTimeout(rs, timeout)))()
- }
- }
-
- throw new Error(`fn failed ${retries} times. Aborting.`)
-}
-
module.exports = {
+ getIdFromFullId,
+ populateSet,
init,
getUserKGRequestParam,
retry,
diff --git a/deploy/datasets/util.spec.js b/deploy/datasets/util.spec.js
index a84b78208f395922cf9389954420bfd62f0409e0..48de1ddfa584b597cc3d38bd737633f207c6b436 100644
--- a/deploy/datasets/util.spec.js
+++ b/deploy/datasets/util.spec.js
@@ -1,56 +1,57 @@
-const { retry, datasetBelongsInTemplate, filterDatasets, datasetRegionExistsInParcellationRegion, _getParcellations } = require('./util')
+const { populateSet, datasetBelongToParcellation, retry, datasetBelongsInTemplate, filterDatasets, datasetRegionExistsInParcellationRegion, _getParcellations } = require('./util')
const { fake } = require('sinon')
const { assert, expect } = require('chai')
const waxholmv2 = require('./testData/waxholmv2')
const allen2015 = require('./testData/allen2015')
const bigbrain = require('./testData/bigbrain')
const humanReceptor = require('./testData/humanReceptor')
-const mni152 = require('./testData/mni152')
+const mni152JuBrain = require('./testData/mni152JuBrain')
const colin27 = require('./testData/colin27')
+const hoc1Pmap = require('./testData/hoc1pmap')
describe('datasets/util.js', () => {
- describe('retry', () => {
+ // describe('retry', () => {
- let val = 0
+ // let val = 0
- const failCall = fake()
- const succeedCall = fake()
+ // const failCall = fake()
+ // const succeedCall = fake()
- const prFn = () => {
- val++
- return val >=3
- ? (succeedCall(), Promise.resolve())
- : (failCall(), Promise.reject())
- }
+ // const prFn = () => {
+ // val++
+ // return val >=3
+ // ? (succeedCall(), Promise.resolve())
+ // : (failCall(), Promise.reject())
+ // }
- beforeEach(() => {
- val = 0
- succeedCall.resetHistory()
- failCall.resetHistory()
- })
+ // beforeEach(() => {
+ // val = 0
+ // succeedCall.resetHistory()
+ // failCall.resetHistory()
+ // })
- it('retry until succeed', async () => {
- await retry(prFn)
- assert(succeedCall.called)
- assert(failCall.calledTwice)
- })
+ // it('retry until succeed', async () => {
+ // await retry(prFn)
+ // assert(succeedCall.called)
+ // assert(failCall.calledTwice)
+ // })
- it('retry with shorter timeouts', async () => {
- await retry(prFn, { timeout: 100 })
- assert(succeedCall.called)
- assert(failCall.calledTwice)
- })
+ // it('retry with shorter timeouts', async () => {
+ // await retry(prFn, { timeout: 100 })
+ // assert(succeedCall.called)
+ // assert(failCall.calledTwice)
+ // })
- it('when retries excceeded, retry fn throws', async () => {
- try {
- await retry(prFn, { timeout: 100, retries: 2 })
- assert(false, 'retry fn should throw if retries exceed')
- } catch (e) {
- assert(true)
- }
- })
- })
+ // it('when retries excceeded, retry fn throws', async () => {
+ // try {
+ // await retry(prFn, { timeout: 100, retries: 2 })
+ // assert(false, 'retry fn should throw if retries exceed')
+ // } catch (e) {
+ // assert(true)
+ // }
+ // })
+ // })
describe('datasetBelongsInTemplate', () => {
it('should filter datasets with template defined', () => {
@@ -60,11 +61,6 @@ describe('datasets/util.js', () => {
expect(belong).to.be.true
}
- for (const ds of mni152) {
-
- const belong = datasetBelongsInTemplate({ templateName: 'MNI 152 ICBM 2009c Nonlinear Asymmetric' })(ds)
- expect(belong).to.be.true
- }
for (const ds of colin27) {
const belong = datasetBelongsInTemplate({ templateName: 'MNI Colin 27' })(ds)
@@ -86,7 +82,7 @@ describe('datasets/util.js', () => {
const belong = datasetBelongsInTemplate({ templateName: 'MNI 152 ICBM 2009c Nonlinear Asymmetric' })(ds)
expect(belong).to.be.false
}
- for (const ds of mni152) {
+ for (const ds of mni152JuBrain) {
const belong = datasetBelongsInTemplate({ templateName: 'Big Brain (Histology)' })(ds)
expect(belong).to.be.false
@@ -108,6 +104,41 @@ describe('datasets/util.js', () => {
expect(flag).to.be.true
}
})
+
+ it('should filter mni152JuBrain jubrain properly', async () => {
+ const { juBrainSet } = await _getParcellations()
+ for (const ds of mni152JuBrain){
+
+ const { parcellationRegion: prs } = ds
+ const flag = await datasetRegionExistsInParcellationRegion(prs, juBrainSet)
+ expect(flag).to.be.true
+ }
+ })
+
+ it('should filter allen2015 properly', async () => {
+ const { allen2015Set } = await _getParcellations()
+ for (const ds of allen2015){
+
+ const flag2015 = await datasetRegionExistsInParcellationRegion(ds.parcellationRegion, allen2015Set)
+ expect(
+ flag2015
+ ).to.be.true
+
+ }
+ })
+
+ it('should filterout allen2015 datasets in allen2017', async () => {
+
+ const { allen2017Set } = await _getParcellations()
+ for (const ds of allen2015){
+
+ const flag2017 = await datasetRegionExistsInParcellationRegion(ds.parcellationRegion, allen2017Set)
+ expect(
+ flag2017
+ ).to.be.false
+ }
+ })
+
})
describe('filterDatasets', () => {
@@ -118,14 +149,140 @@ describe('datasets/util.js', () => {
it('should filter waxholm v2 properly', async () => {
const filteredResult = await filterDatasets(waxholmv2, { parcellationName: 'Waxholm Space rat brain atlas v2' })
- expect(filteredResult).to.have.length(2)
+ expect(filteredResult).to.have.length(1)
})
it('should filter allen 2015 properly', async () => {
const filteredResult = await filterDatasets(allen2015, { parcellationName: 'Allen Mouse Common Coordinate Framework v3 2015' })
- expect(filteredResult).to.have.length(2)
+ expect(filteredResult).to.have.length(1)
+ })
+ })
+
+ describe('datasetBelongToParcellation', () => {
+ const dataset = {
+ parcellationAtlas:[{
+ name: 'jubrain v17'
+ }]
+ }
+ const parcellationName = 'jubrain v17'
+ const dataset2 = {
+ parcellationAtlas:[{
+ name: 'jubrain v18'
+ }]
+ }
+ const parcellationName2 = 'jubrain v18'
+ it('if parcellation name is undefined, will always return true', () => {
+ expect(
+ datasetBelongToParcellation({
+ parcellationName: null,
+ dataset
+ })
+ ).to.be.true
+ })
+ it('if parcellationAtlas of dataset is empty array, will always return true', () => {
+ expect(
+ datasetBelongToParcellation({
+ dataset: { parcellationAtlas: [] },
+ parcellationName
+ })).to.be.true
+ })
+ it('if parcellationAtlas of dataset is non empty array, and parcellationName is defined, should return false if they do not match', () => {
+ expect(
+ datasetBelongToParcellation({
+ dataset,
+ parcellationName: parcellationName2
+ })
+ ).to.be.false
+ })
+
+ it('if parcellationAtlas of dataset is non empty array, and parcellationName is defined, should return true if they do match', () => {
+ expect(
+ datasetBelongToParcellation({
+ dataset,
+ parcellationName
+ })
+ ).to.be.true
+ })
+
+ it('allen2015 belong to parcellation', () => {
+ for (const ds of allen2015){
+
+ expect(
+ datasetBelongToParcellation({
+ dataset: ds,
+ parcellationName: 'Allen Mouse Common Coordinate Framework v3 2015'
+ })
+ ).to.be.true
+ }
+ })
+
+ it('hoc1pmap should not belong to bundle parcellation', () => {
+ for (const ds of hoc1Pmap){
+ expect(
+ datasetBelongToParcellation({
+ dataset: ds,
+ parcellationName: 'Fibre Bundle Atlas - Long Bundle'
+ })
+ ).to.be.false
+ expect(
+ datasetBelongToParcellation({
+ dataset: ds,
+ parcellationName: 'Fibre Bundle Atlas - Short Bundle'
+ })
+ ).to.be.false
+ }
+ })
+ })
+
+ describe('populateSet', () => {
+ it('should populate relatedAreas', () => {
+ const area44 = {
+ "name": "Area 44 (IFG)",
+ "arealabel": "Area-44",
+ "status": "publicP",
+ "labelIndex": null,
+ "synonyms": [],
+ "relatedAreas": [
+ {
+ "name": "Area 44v",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
+ }
+ }
+ },
+ {
+ "name": "Area 44d",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ }
+ }
+ ],
+ "rgb": [
+ 54,
+ 74,
+ 75
+ ],
+ "children": [
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
+ }
+ }
+ }
+ const set = populateSet([area44])
+ expect(Array.from(set)).to.contain.members([
+ 'minds/core/parcellationregion/v1.0.0/7e5e7aa8-28b8-445b-8980-2a6f3fa645b3',
+ 'minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052',
+ 'minds/core/parcellationregion/v1.0.0/8a6be82c-5947-4fff-8348-cf9bf73e4f40',
+ ])
})
})
-
})
diff --git a/e2e/chromeOpts.js b/e2e/chromeOpts.js
new file mode 100644
index 0000000000000000000000000000000000000000..1098647da939f5ee6664e3767ffd77dade1b5041
--- /dev/null
+++ b/e2e/chromeOpts.js
@@ -0,0 +1,8 @@
+module.exports = [
+ '--headless',
+ '--no-sandbox',
+ '--disable-gpu',
+ '--disable-setuid-sandbox',
+ "--disable-extensions",
+ '--window-size=1600,800'
+]
\ No newline at end of file
diff --git a/e2e/protractor.conf.js b/e2e/protractor.conf.js
index dc04206e5c9d5762246b1c6ef5a302f065845f17..531d037f1401c1114262d955a63b59bc263cd37f 100644
--- a/e2e/protractor.conf.js
+++ b/e2e/protractor.conf.js
@@ -1,8 +1,29 @@
+
+// n.b. to start selenium, run npm run wd -- update && npm run wd -- start
+// n.b. you will need to run `npm i --no-save puppeteer`, so that normal download script does not download chrome binary
+const pptr = require('puppeteer')
+const chromeOpts = require('./chromeOpts')
+const SELENIUM_ADDRESS = process.env.SELENIUM_ADDRESS
+
exports.config = {
- seleniumAddress: 'http://localhost:4444/wd/hub',
+ ...(SELENIUM_ADDRESS
+ ? { seleniumAddress: SELENIUM_ADDRESS }
+ : { directConnect: true }
+ ),
specs: ['./src/**/*.e2e-spec.js'],
- // params: {
- // interactiveViewer : 'interactiveViewer',
- // viewer: 'viewer'
- // }
+ capabilities: {
+
+ // Use headless chrome
+ browserName: 'chrome',
+ chromeOptions: {
+ args: [
+ ...chromeOpts
+ ],
+ ...(
+ SELENIUM_ADDRESS
+ ? {}
+ : { binary: pptr.executablePath() }
+ )
+ }
+ }
}
\ No newline at end of file
diff --git a/e2e/src/iv.e2e-spec.js b/e2e/src/iv.e2e-spec.js
index 34fdb7c386b2c97e8f1858bd2c7356810bf0d820..79f2d1ae64e038339e26acf2617f0f3664ac2833 100644
--- a/e2e/src/iv.e2e-spec.js
+++ b/e2e/src/iv.e2e-spec.js
@@ -1,8 +1,10 @@
-const url = 'http://localhost:8081/'
-
+const chromeOpts = require('../chromeOpts')
const noErrorLog = require('./noErrorLog')
-const { getSelectedTemplate, getSelectedParcellation } = require('./ivApi')
+const { getSelectedTemplate, getSelectedParcellation, getSelectedRegions, getCurrentNavigationState, awaitNehubaViewer } = require('./ivApi')
const { getSearchParam, wait } = require('./util')
+const { URLSearchParams } = require('url')
+
+const { waitMultiple } = require('./util')
describe('protractor works', () => {
it('protractor works', () => {
@@ -10,89 +12,95 @@ describe('protractor works', () => {
})
})
-describe('Home screen', () => {
- beforeEach(() => {
- browser.waitForAngularEnabled(false)
- browser.get(url)
+const pptr = require('puppeteer')
+const ATLAS_URL = (process.env.ATLAS_URL || 'http://localhost:3000').replace(/\/$/, '')
+if (ATLAS_URL.length === 0) throw new Error(`ATLAS_URL must either be left unset or defined.`)
+if (ATLAS_URL[ATLAS_URL.length - 1] === '/') throw new Error(`ATLAS_URL should not trail with a slash: ${ATLAS_URL}`)
+
+let browser
+describe('IAV', () => {
+ beforeAll(async () => {
+ browser = await pptr.launch({
+ ...(
+ chromeOpts.indexOf('--headless') >= 0
+ ? { headless: true }
+ : {}
+ ),
+ args: [
+ ...chromeOpts
+ ]
+ })
})
- it('get title works', () => {
- browser.getTitle()
- .then(title => {
- expect(title).toEqual('Interactive Atlas Viewer')
+ // TODO figure out how to get jasmine to compare array members
+ describe('api', () => {
+ const urlMni152JuBrain = `${ATLAS_URL}/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&cRegionsSelected=%7B%22jubrain+mni152+v18+left%22%3A%222%22%2C%22jubrain+mni152+v18+right%22%3A%222%22%7D&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..70hl~.1w4W0~.70hk..1Pl9`
+ describe('selectRegion obs', () => {
+ it('should populate selected region with inherited properties', async () => {
+ const page = await browser.newPage()
+ await page.goto(urlMni152JuBrain, {waitUntil: 'networkidle2'})
+ const regions = await getSelectedRegions(page)
+ for (const region of regions){
+ expect(region.relatedAreas).toBeDefined()
+ expect(
+ region.relatedAreas.map(({ name }) => name).sort()
+ ).toEqual(
+ [
+ 'Area 44v',
+ 'Area 44d'
+ ].sort()
+ )
+ }
})
- .catch(error => {
- console.error('error', error)
- })
-
- browser.executeScript('window.interactiveViewer')
- .then(result => expect(result).toBeDefined())
- browser.executeScript('window.viewer')
- .then(result => expect(result).toBeNull())
-
- noErrorLog(browser)
+ })
})
-})
-
-describe('Query param: ', () => {
-
- it('correctly defined templateSelected and selectedParcellation works', async () => {
-
- const searchParam = '?templateSelected=MNI+Colin+27&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas'
- browser.get(url + searchParam)
- browser.executeScript('window.interactiveViewer').then(result => expect(result).toBeDefined())
- browser.executeScript('window.viewer').then(result => expect(result).toBeDefined())
+
+ describe('Url parsing', () => {
- await wait(browser)
-
- getSelectedTemplate(browser)
- .then(template => {
- expect(template.name).toBe('MNI Colin 27')
- })
-
- getSelectedParcellation(browser)
- .then(parcellation => {
- expect(parcellation.name).toBe('JuBrain Cytoarchitectonic Atlas')
- })
-
- noErrorLog(browser)
+ // tracking issue: https://github.com/HumanBrainProject/interactive-viewer/issues/455
+ // reenable when fixed
+ // it('incorrectly defined templateSelected should clear searchparam', async () => {
+ // const search = '/?templateSelected=NoName2&parcellationSelected=NoName'
+ // const page = await browser.newPage()
+ // await page.goto(`${ATLAS_URL}${search}`, {waitUntil: 'networkidle2'})
+ // await page.waitFor(500)
+ // const searchParam = await getSearchParam(page)
+ // const searchParamObj = new URLSearchParams(searchParam)
+ // expect(searchParamObj.get('templateSelected')).toBeNull()
+ // })
+
+
+ it('navigation state should be perserved', async () => {
+ const searchParam = `/?templateSelected=Big+Brain+%28Histology%29&parcellationSelected=Cytoarchitectonic+Maps&cNavigation=zvyba.z0UJ7._WMxv.-TTch..2_cJ0e.2-OUQG._a9qP._QPHw..7LIx..2CQ3O.1FYC.259Wu..2r6`
+ const expectedNav = {
+ "position": [
+ 36806872,
+ 325772,
+ 34904120
+ ],
+ "orientation": [
+ 0.1131771132349968,
+ 0.031712327152490616,
+ 0.2527998387813568,
+ 0.9603527784347534
+ ],
+ "zoom": 11590,
+ "perspectiveZoom": 1922235,
+ "perspectiveOrientation": [
+ -0.2991955280303955,
+ -0.8824243545532227,
+ 0.28244855999946594,
+ 0.22810545563697815
+ ]
+ }
+
+ const page = await browser.newPage()
+ await page.goto(`${ATLAS_URL}${searchParam}`, { waitUntil: 'networkidle2' })
+ await awaitNehubaViewer(page)
+ await page.waitFor(1000 * waitMultiple)
+
+ const actualNav = await getCurrentNavigationState(page)
+ expect(expectedNav).toEqual(actualNav)
+ })
})
-
- it('correctly defined templateSelected but incorrectly defined selectedParcellation work', async () => {
- const searchParam = '?templateSelected=MNI+Colin+27&parcellationSelected=NoName'
- browser.get(url + searchParam)
-
- await wait(browser)
-
- getSelectedTemplate(browser)
- .then(template => {
- expect(template.name).toBe('MNI Colin 27')
- })
- .catch(fail)
-
- Promise.all([
- getSelectedTemplate(browser),
- getSelectedParcellation(browser)
- ])
- .then(([template, parcellation]) => {
- expect(parcellation.name).toBe(template.parcellations[0].name)
- })
- .catch(fail)
-
- noErrorLog(browser)
- })
-
- it('incorrectly defined templateSelected should clear searchparam', async () => {
- const searchParam = '?templateSelected=NoName2&parcellationSelected=NoName'
- browser.get(url + searchParam)
-
- await wait(browser)
-
- getSearchParam(browser)
- .then(searchParam => {
- const templateSelected = searchParam.get('templateSelected')
- expect(templateSelected).toBeNull()
- })
- .catch(fail)
- })
-})
\ No newline at end of file
+})
diff --git a/e2e/src/ivApi.js b/e2e/src/ivApi.js
index 825bee506911fff68b5dfd80924b73ed3f83df2f..83d5a48a81f9195f7c9d98c61f6be37bc487b694 100644
--- a/e2e/src/ivApi.js
+++ b/e2e/src/ivApi.js
@@ -1,3 +1,6 @@
+const { retry } = require('../../common/util')
+const { waitMultiple } = require('./util')
+
exports.getSelectedTemplate = (browser) => new Promise((resolve, reject) => {
browser.executeAsyncScript('let sub = window.interactiveViewer.metadata.selectedTemplateBSubject.subscribe(obj => arguments[arguments.length - 1](obj));sub.unsubscribe()')
.then(resolve)
@@ -8,4 +11,56 @@ exports.getSelectedParcellation = (browser) => new Promise((resolve, reject) =>
browser.executeAsyncScript('let sub = window.interactiveViewer.metadata.selectedParcellationBSubject.subscribe(obj => arguments[arguments.length - 1](obj));sub.unsubscribe()')
.then(resolve)
.catch(reject)
-})
\ No newline at end of file
+})
+
+exports.getSelectedRegions = async (page) => {
+ return await page.evaluate(async () => {
+ let region, sub
+ const getRegion = () => new Promise(rs => {
+ sub = interactiveViewer.metadata.selectedRegionsBSubject.subscribe(rs)
+ })
+
+ region = await getRegion()
+ sub.unsubscribe()
+ return region
+ })
+}
+
+exports.getCurrentNavigationState = page => new Promise(async rs => {
+ const rObj = await page.evaluate(async () => {
+
+ let returnObj, sub
+ const getPr = () => new Promise(rs => {
+
+ sub = nehubaViewer.navigationState.all
+ .subscribe(({ orientation, perspectiveOrientation, perspectiveZoom, position, zoom }) => {
+ returnObj = {
+ orientation: Array.from(orientation),
+ perspectiveOrientation: Array.from(perspectiveOrientation),
+ perspectiveZoom,
+ zoom,
+ position: Array.from(position)
+ }
+ rs()
+ })
+ })
+
+ await getPr()
+ sub.unsubscribe()
+
+ return returnObj
+ })
+ rs(rObj)
+})
+
+exports.awaitNehubaViewer = async (page) => {
+ const getNVAvailable = () => new Promise(async (rs, rj) => {
+ const result = await page.evaluate(() => {
+ return !!window.nehubaViewer
+ })
+ if (result) return rs()
+ else return rj()
+ })
+
+ await retry(getNVAvailable, { timeout: 2000 * waitMultiple, retries: 10 })
+}
diff --git a/e2e/src/util.js b/e2e/src/util.js
index 030f2ccad62151ce4392c95704b211d57fb7af43..149e3edc26c0e890095e2930462b20fb9cf7c362 100644
--- a/e2e/src/util.js
+++ b/e2e/src/util.js
@@ -1,12 +1,5 @@
-const {URLSearchParams} = require('url')
-
-exports.getSearchParam = (browser) => {
- const script = `
- const search = window.location.search;
- return search
- `
- return browser.executeScript(script)
- .then(search => new URLSearchParams(search))
+exports.getSearchParam = page => {
+ return page.evaluate(`window.location.search`)
}
exports.wait = (browser) => new Promise(resolve => {
@@ -17,4 +10,6 @@ exports.wait = (browser) => new Promise(resolve => {
browser.sleep(1000)
.then(resolve)
-})
\ No newline at end of file
+})
+
+exports.waitMultiple = process.env.WAIT_ULTIPLE || 1
\ No newline at end of file
diff --git a/package.json b/package.json
index 05771f5d2fe1fddf8da20c1369e70e4be49e407f..b40068d878e38c6d24dcf9ea43d245c280487043 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,8 @@
"test": "karma start spec/karma.conf.js",
"e2e": "protractor e2e/protractor.conf",
"lint": "eslint src --ext .ts",
- "eslint": "eslint"
+ "eslint": "eslint",
+ "wd": "webdriver-manager"
},
"keywords": [],
"author": "",
@@ -91,6 +92,6 @@
"zone.js": "^0.9.1"
},
"dependencies": {
- "hbp-connectivity-component": "0.0.17"
+ "hbp-connectivity-component": "^0.1.0"
}
}
diff --git a/spec/test.ts b/spec/test.ts
index 3d805584bd3e83f877957c738a748c010843c631..d2b2c152b7022cc9b536001f4602ec8e88017fef 100644
--- a/spec/test.ts
+++ b/spec/test.ts
@@ -19,4 +19,6 @@ getTestBed().initTestEnvironment(
);
const testContext = require.context('../src', true, /\.spec\.ts$/)
-testContext.keys().map(testContext)
\ No newline at end of file
+testContext.keys().map(testContext)
+
+require('../common/util.spec.js')
\ No newline at end of file
diff --git a/src/atlasViewer/atlasViewer.apiService.service.spec.ts b/src/atlasViewer/atlasViewer.apiService.service.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..4f4d4c0de6d513a0ebad97e81bb8a9f107a201a7
--- /dev/null
+++ b/src/atlasViewer/atlasViewer.apiService.service.spec.ts
@@ -0,0 +1,55 @@
+import {} from 'jasmine'
+import {AtlasViewerAPIServices} from "src/atlasViewer/atlasViewer.apiService.service";
+import {async, TestBed} from "@angular/core/testing";
+import {provideMockActions} from "@ngrx/effects/testing";
+import {provideMockStore} from "@ngrx/store/testing";
+import {defaultRootState} from "src/services/stateStore.service";
+import {Observable, of} from "rxjs";
+import {Action} from "@ngrx/store";
+import {AngularMaterialModule} from "src/ui/sharedModules/angularMaterial.module";
+const actions$: Observable<Action> = of({type: 'TEST'})
+
+
+
+describe('atlasViewer.apiService.service.ts', () => {
+ describe('getUserToSelectARegion', () => {
+
+ beforeEach(async(() => {
+ TestBed.configureTestingModule({
+ imports: [
+ AngularMaterialModule,
+ ],
+ providers: [
+ AtlasViewerAPIServices,
+ provideMockActions(() => actions$),
+ provideMockStore({initialState: defaultRootState})
+ ]
+ })
+ }))
+
+ it('should return value on resolve', async () => {
+ const regionToSend = 'test-region'
+ let sentData: any
+ const apiService = TestBed.get(AtlasViewerAPIServices)
+ const callApi = apiService.interactiveViewer.uiHandle.getUserToSelectARegion('selecting Region mode message')
+ apiService.getUserToSelectARegionResolve(regionToSend)
+ await callApi.then(r => {
+ sentData = r
+ })
+ expect(sentData).toEqual(regionToSend)
+ })
+
+ it('pluginRegionSelectionEnabled should false after resolve', async () => {
+ const { uiState } = defaultRootState
+ const regionToSend = 'test-region'
+ let sentData: any
+ const apiService = TestBed.get(AtlasViewerAPIServices)
+ const callApi = apiService.interactiveViewer.uiHandle.getUserToSelectARegion('selecting Region mode message')
+ apiService.getUserToSelectARegionResolve(regionToSend)
+ await callApi.then(r => {
+ sentData = r
+ })
+ expect(uiState.pluginRegionSelectionEnabled).toBe(false)
+ })
+ })
+})
\ No newline at end of file
diff --git a/src/atlasViewer/atlasViewer.apiService.service.ts b/src/atlasViewer/atlasViewer.apiService.service.ts
index c68c60bf953f2cd2951278dab547dbd3a17d5460..c85e7f6a102a6a42051a0fa697c5a83a12269bf0 100644
--- a/src/atlasViewer/atlasViewer.apiService.service.ts
+++ b/src/atlasViewer/atlasViewer.apiService.service.ts
@@ -1,13 +1,20 @@
import { Injectable } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { Observable } from "rxjs";
-import { distinctUntilChanged, map, filter } from "rxjs/operators";
+import { Observable, Subscribable } from "rxjs";
+import { distinctUntilChanged, map, filter, startWith } from "rxjs/operators";
import { DialogService } from "src/services/dialogService.service";
import { LoggingService } from "src/services/logging.service";
-import { getLabelIndexMap, getMultiNgIdsRegionsLabelIndexMap, IavRootStoreInterface, safeFilter } from "src/services/stateStore.service";
+import {
+ DISABLE_PLUGIN_REGION_SELECTION,
+ getLabelIndexMap,
+ getMultiNgIdsRegionsLabelIndexMap,
+ IavRootStoreInterface,
+ safeFilter
+} from "src/services/stateStore.service";
import { ModalHandler } from "../util/pluginHandlerClasses/modalHandler";
import { ToastHandler } from "../util/pluginHandlerClasses/toastHandler";
import { IPluginManifest } from "./atlasViewer.pluginService.service";
+import {ENABLE_PLUGIN_REGION_SELECTION} from "src/services/state/uiState.store";
declare let window
@@ -23,6 +30,9 @@ export class AtlasViewerAPIServices {
public loadedLibraries: Map<string, {counter: number, src: HTMLElement|null}> = new Map()
+ public getUserToSelectARegionResolve
+ public getUserToSelectARegionReject
+
constructor(
private store: Store<IavRootStoreInterface>,
private dialogService: DialogService,
@@ -71,8 +81,8 @@ export class AtlasViewerAPIServices {
datasetsBSubject : this.store.pipe(
select('dataStore'),
- safeFilter('fetchedDataEntries'),
- map(state => state.fetchedDataEntries),
+ select('fetchedDataEntries'),
+ startWith([])
),
},
uiHandle : {
@@ -118,8 +128,27 @@ export class AtlasViewerAPIServices {
return Promise.reject('Needs to be overwritted')
},
- getUserInput: config => this.dialogService.getUserInput(config),
+ getUserInput: config => this.dialogService.getUserInput(config) ,
getUserConfirmation: config => this.dialogService.getUserConfirm(config),
+
+ getUserToSelectARegion: (selectingMessage) => new Promise((resolve, reject) => {
+ this.store.dispatch({
+ type: ENABLE_PLUGIN_REGION_SELECTION,
+ payload: selectingMessage
+ })
+
+ this.getUserToSelectARegionResolve = resolve
+ this.getUserToSelectARegionReject = reject
+ }),
+
+ // ToDo Method should be able to cancel any pending promise.
+ cancelPromise: (pr) => {
+ if (pr === this.interactiveViewer.uiHandle.getUserToSelectARegion) {
+ if (this.getUserToSelectARegionReject) this.getUserToSelectARegionReject('Rej')
+ this.store.dispatch({type: DISABLE_PLUGIN_REGION_SELECTION})
+ }
+ }
+
},
pluginControl : {
loadExternalLibraries : () => Promise.reject('load External Library method not over written')
@@ -131,11 +160,6 @@ export class AtlasViewerAPIServices {
}
window.interactiveViewer = this.interactiveViewer
this.init()
-
- /**
- * TODO debugger debug
- */
- window.uiHandle = this.interactiveViewer.uiHandle
}
private init() {
@@ -205,6 +229,8 @@ export interface IInteractiveViewerInterface {
launchNewWidget: (manifest: IPluginManifest) => Promise<any>
getUserInput: (config: IGetUserInputConfig) => Promise<string>
getUserConfirmation: (config: IGetUserConfirmation) => Promise<any>
+ getUserToSelectARegion: (selectingMessage: any) => Promise<any>
+ cancelPromise: (pr) => void
}
pluginControl: {
diff --git a/src/atlasViewer/atlasViewer.component.ts b/src/atlasViewer/atlasViewer.component.ts
index eb71bfd07cc1754ed2be6b759e6a63fa87b44be4..7b2659e3cfb08e3ecb498db89a99cb0e8502e6a0 100644
--- a/src/atlasViewer/atlasViewer.component.ts
+++ b/src/atlasViewer/atlasViewer.component.ts
@@ -1,5 +1,5 @@
import {
- AfterViewInit,
+ AfterViewInit, ChangeDetectorRef,
Component,
HostBinding,
OnDestroy,
@@ -117,6 +117,11 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
public onhoverSegmentsForFixed$: Observable<string[]>
+ private pluginRegionSelectionEnabled$: Observable<boolean>
+ private pluginRegionSelectionEnabled: boolean = false
+ private persistentStateNotifierTemplate$: Observable<string>
+ // private pluginRegionSelectionEnabled: boolean = false
+
constructor(
private store: Store<IavRootStoreInterface>,
private widgetServices: WidgetServices,
@@ -129,6 +134,7 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
private snackbar: MatSnackBar,
private bottomSheet: MatBottomSheet,
private log: LoggingService,
+ private changeDetectorRef: ChangeDetectorRef,
) {
this.snackbarMessage$ = this.store.pipe(
@@ -136,6 +142,17 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
select("snackbarMessage"),
)
+ this.pluginRegionSelectionEnabled$ = this.store.pipe(
+ select('uiState'),
+ select("pluginRegionSelectionEnabled"),
+ distinctUntilChanged(),
+ )
+ this.persistentStateNotifierTemplate$ = this.store.pipe(
+ select('uiState'),
+ select("persistentStateNotifierTemplate"),
+ distinctUntilChanged(),
+ )
+
this.bottomSheet$ = this.store.pipe(
select('uiState'),
select('bottomSheetTemplate'),
@@ -279,6 +296,10 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
}
}),
)
+
+ this.onhoverSegments$.subscribe(hr => {
+ this.hoveringRegions = hr
+ })
}
private selectedParcellation$: Observable<any>
@@ -361,6 +382,13 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
this.rd.setAttribute(document.body, 'darktheme', flag.toString())
}),
)
+
+ this.subscriptions.push(
+ this.pluginRegionSelectionEnabled$.subscribe(PRSE => {
+ this.pluginRegionSelectionEnabled = PRSE
+ this.changeDetectorRef.detectChanges()
+ })
+ )
}
public ngAfterViewInit() {
@@ -409,21 +437,26 @@ export class AtlasViewer implements OnDestroy, OnInit, AfterViewInit {
withLatestFrom(this.onhoverSegments$),
map(([_flag, onhoverSegments]) => onhoverSegments || []),
)
-
}
+ private hoveringRegions = []
+
public mouseDownNehuba(_event) {
this.rClContextualMenu.hide()
}
- public mouseUpNehuba(event) {
+ public mouseClickNehuba(event) {
// if (this.mouseUpLeftPosition === event.pageX && this.mouseUpTopPosition === event.pageY) {}
if (!this.rClContextualMenu) { return }
this.rClContextualMenu.mousePos = [
event.clientX,
event.clientY,
]
- this.rClContextualMenu.show()
+ if (!this.pluginRegionSelectionEnabled) {
+ this.rClContextualMenu.show()
+ } else {
+ if (this.hoveringRegions) this.apiService.getUserToSelectARegionResolve(this.hoveringRegions)
+ }
}
public toggleSideNavMenu(opened) {
diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts
index 919f2b9134aa99d59da652e142baf4ad6882a876..28f5b7c1c298da5db2ddc9e59e58ff8fd74295bf 100644
--- a/src/atlasViewer/atlasViewer.constantService.service.ts
+++ b/src/atlasViewer/atlasViewer.constantService.service.ts
@@ -1,16 +1,19 @@
import { HttpClient } from "@angular/common/http";
import { Injectable, OnDestroy } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { merge, Observable, of, Subscription, throwError } from "rxjs";
-import { catchError, map, shareReplay, switchMap, tap } from "rxjs/operators";
+import { merge, Observable, of, Subscription, throwError, fromEvent, forkJoin } from "rxjs";
+import { catchError, map, shareReplay, switchMap, tap, filter, take } from "rxjs/operators";
import { LoggingService } from "src/services/logging.service";
import { SNACKBAR_MESSAGE } from "src/services/state/uiState.store";
import { IavRootStoreInterface } from "../services/stateStore.service";
+import { AtlasWorkerService } from "./atlasViewer.workerService.service";
export const CM_THRESHOLD = `0.05`
export 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;`
export const GLSL_COLORMAP_JET = `void main(){float x = toNormalized(getDataValue());${CM_MATLAB_JET}if(x>${CM_THRESHOLD}){emitRGB(vec3(r,g,b));}else{emitTransparent();}}`
+const getUniqueId = () => Math.round(Math.random() * 1e16).toString(16)
+
@Injectable({
providedIn : 'root',
})
@@ -49,7 +52,7 @@ export class AtlasViewerConstantsServices implements OnDestroy {
}
// instead of using window.location.href, which includes query param etc
- public backendUrl = BACKEND_URL || `${window.location.origin}${window.location.pathname}`
+ public backendUrl = `${BACKEND_URL}/`.replace(/\/\/$/, '/') || `${window.location.origin}${window.location.pathname}`
private fetchTemplate = (templateUrl) => this.http.get(`${this.backendUrl}${templateUrl}`, { responseType: 'json' }).pipe(
switchMap((template: any) => {
@@ -69,10 +72,48 @@ export class AtlasViewerConstantsServices implements OnDestroy {
public totalTemplates = null
+ private workerUpdateParcellation$ = fromEvent(this.workerService.worker, 'message').pipe(
+ filter((message: MessageEvent) => message && message.data && message.data.type === 'UPDATE_PARCELLATION_REGIONS'),
+ map(({ data }) => data)
+ )
+
+ private processTemplate = template => forkJoin(
+ ...template.parcellations.map(parcellation => {
+
+ const id = getUniqueId()
+
+ this.workerService.worker.postMessage({
+ type: 'PROPAGATE_PARC_REGION_ATTR',
+ parcellation,
+ inheritAttrsOpts: {
+ ngId: (parcellation as any ).ngId,
+ relatedAreas: [],
+ fullId: null
+ },
+ id
+ })
+
+ return this.workerUpdateParcellation$.pipe(
+ filter(({ id: returnedId }) => id === returnedId),
+ take(1),
+ map(({ parcellation }) => parcellation)
+ )
+ })
+ )
+
public initFetchTemplate$ = this.http.get(`${this.backendUrl}templates`, { responseType: 'json' }).pipe(
tap((arr: any[]) => this.totalTemplates = arr.length),
switchMap((templates: string[]) => merge(
- ...templates.map(this.fetchTemplate),
+ ...templates.map(templateName => this.fetchTemplate(templateName).pipe(
+ switchMap(template => this.processTemplate(template).pipe(
+ map(parcellations => {
+ return {
+ ...template,
+ parcellations
+ }
+ })
+ ))
+ )),
)),
catchError((err) => {
this.log.warn(`fetching templates error`, err)
@@ -255,6 +296,7 @@ Send us an email: <a target = "_blank" href = "mailto:${this.supportEmailAddress
private store$: Store<IavRootStoreInterface>,
private http: HttpClient,
private log: LoggingService,
+ private workerService: AtlasWorkerService
) {
this.darktheme$ = this.store$.pipe(
diff --git a/src/atlasViewer/atlasViewer.pluginService.service.spec.ts b/src/atlasViewer/atlasViewer.pluginService.service.spec.ts
index e9dd0b1fbce6e6c0c173ed429a34923675dfe694..acb0d9425edc4d4e54b72ab59ce658f9448f65b1 100644
--- a/src/atlasViewer/atlasViewer.pluginService.service.spec.ts
+++ b/src/atlasViewer/atlasViewer.pluginService.service.spec.ts
@@ -56,7 +56,6 @@
// expect(mockScript).toBeTruthy()
// })
// )
-
// it(
// 'template overrides templateURL',
// inject([HttpTestingController], (httpMock: HttpTestingController) => {
diff --git a/src/atlasViewer/atlasViewer.template.html b/src/atlasViewer/atlasViewer.template.html
index e10c82d4cb40aba6e2d08355fe4b161421587f37..edf1cb961d858435682c621d47b0add5c213db91 100644
--- a/src/atlasViewer/atlasViewer.template.html
+++ b/src/atlasViewer/atlasViewer.template.html
@@ -47,7 +47,7 @@
[currentOnHover]="iavMouseHoverEl.currentOnHoverObs$ | async"
iav-captureClickListenerDirective
(iav-captureClickListenerDirective-onMousedown)="mouseDownNehuba($event)"
- (iav-captureClickListenerDirective-onClick)="mouseUpNehuba($event)">
+ (iav-captureClickListenerDirective-onClick)="mouseClickNehuba($event)">
</ui-nehuba-container>
<div class="z-index-10 position-absolute pe-none w-100 h-100">
@@ -108,6 +108,11 @@
</ng-container>
</div>
+ <div class="fixed-top pe-none d-flex justify-content-center m-4" *ngIf="pluginRegionSelectionEnabled">
+ <ng-container *ngTemplateOutlet="persistentStateNotifierTemplate">
+ </ng-container>
+ </div>
+
<div floatingMouseContextualContainerDirective>
<div *ngIf="!ismobile"
@@ -204,4 +209,9 @@
<!-- logo tmpl -->
<ng-template #logoTmpl>
<logo-container></logo-container>
-</ng-template>
\ No newline at end of file
+</ng-template>
+
+<ng-template #persistentStateNotifierTemplate>
+ <mat-card>{{persistentStateNotifierTemplate$ | async}}</mat-card>
+</ng-template>
+
diff --git a/src/main-aot.ts b/src/main-aot.ts
index 6555323d09903fc1bd7e145c57749d76755e8e6c..292c911a660728e31f71cfd75a42f899c9fe6bec 100644
--- a/src/main-aot.ts
+++ b/src/main-aot.ts
@@ -1,9 +1 @@
-import { enableProdMode } from '@angular/core';
-
-enableProdMode()
-
import './main-common'
-
-/* aot === production mode */
-
-if (PRODUCTION) { console.log(`Interactive Atlas Viewer: ${VERSION}`) }
diff --git a/src/main-common.ts b/src/main-common.ts
index ab8bf78a4710915655b355607300ccb35ee63026..14a3447d5a1c147f247771021dd3f613c3252af3 100644
--- a/src/main-common.ts
+++ b/src/main-common.ts
@@ -1,11 +1,14 @@
import 'zone.js'
-
import 'third_party/testSafari.js'
+import { enableProdMode } from '@angular/core';
import { defineCustomElements } from 'hbp-connectivity-component/dist/loader'
import { platformBrowserDynamic } from '@angular/platform-browser-dynamic'
import { MainModule } from './main.module';
+if (PRODUCTION) enableProdMode()
+if (PRODUCTION) { console.log(`Interactive Atlas Viewer: ${VERSION}`) }
+
const requireAll = (r: any) => {r.keys().forEach(r)}
requireAll(require.context('./res/ext', false, /\.json$/))
requireAll(require.context('./res/images', true, /\.jpg$|\.png$|\.svg$/))
diff --git a/src/res/ext/MNI152.json b/src/res/ext/MNI152.json
index 3ce8bc85cc9c1bd30b2f6465c5cf2cb870390f18..cc88e19c20b47c922116ffdb97b56756cd6b8f91 100644
--- a/src/res/ext/MNI152.json
+++ b/src/res/ext/MNI152.json
@@ -9,14 +9,18 @@
{
"name": "JuBrain Cytoarchitectonic Atlas",
"ngId": "jubrain mni152 v18 left",
- "auxillaryMeshIndices": [ 65535 ],
+ "auxillaryMeshIndices": [
+ 65535
+ ],
"hasAdditionalViewMode": [
"connectivity"
],
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
- }],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "4ac9f0bc-560d-47e0-8916-7b24da9bb0ce"
+ }
+ ],
"properties": {
"version": "1.0",
"description": "This dataset contains the whole-brain parcellation of the JuBrain Cytoarchitectonic Atlas (Amunts and Zilles, 2015) in the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. The parcellation is derived from the individual probability maps (PMs) of the cytoarchitectonic regions released in the JuBrain Atlas, that are further combined into a Maximum Probability Map (MPM). The MPM is calculated by considering for each voxel the probability of all cytoarchitectonic areas released in the atlas, and determining the most probable assignment (Eickhoff 2005). Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
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"status": "publicP",
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"synonyms": [],
- "relatedAreas":[
- "Area PGa"
+ "relatedAreas": [
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{
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"status": "publicP",
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"synonyms": [],
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+ "relatedAreas": [
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{
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@@ -1643,8 +1927,16 @@
"status": "publicP",
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"synonyms": [],
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{
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{
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{
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{
"name": "Area hOc3d (Cuneus)",
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{
"name": "Area hOc6 (POS)",
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{
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+ "kgId": "0d6392fd-b905-4bc3-bac9-fc44d8990a30"
+ }
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+ "relatedAreas": []
}
]
},
@@ -2428,7 +2824,14 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "04674a3c-bb3a-495e-a466-206355e630bd"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hOc1 (V1, 17, CalcS)",
@@ -2436,8 +2839,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area hOc1"
+ "relatedAreas": [
+ {
+ "name": "Area hOc1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ }
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],
"rgb": [
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@@ -2477,7 +2888,13 @@
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]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
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}
]
},
@@ -2532,7 +2949,14 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b40afb5a-e6a1-47b6-8a3e-1f8a20fbf99a"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hOc4la (LOC)",
@@ -2578,7 +3002,14 @@
251812
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "94365b82-6204-4937-8b86-fe0433287938"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hOc4lp (LOC)",
@@ -2624,7 +3055,14 @@
4946882
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9006ee6a-6dc1-4604-9f20-7e08b42d574d"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -2714,7 +3152,14 @@
"labelIndex": 247,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "472dacc9-c27d-49c2-9e6f-a1cc3309c4ab"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs1 (IFS)",
@@ -2750,7 +3195,14 @@
"labelIndex": 244,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d687d385-98d9-4b31-85db-4bc682cd0a31"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifj2 (IFS/PreS)",
@@ -2822,7 +3274,14 @@
"labelIndex": 245,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "658a67d8-60c2-4bb4-8eaf-e54725eda261"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs3 (IFS)",
@@ -2858,7 +3317,14 @@
"labelIndex": 246,
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e555881e-7082-4ac0-b6cc-cd096f30d3dc"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -2875,9 +3341,25 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area 44v",
- "Area 44d"
+ "relatedAreas": [
+ {
+ "name": "Area 44v",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
+ }
+ }
+ },
+ {
+ "name": "Area 44d",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ }
+ }
],
"rgb": [
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@@ -2917,7 +3399,13 @@
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]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
+ }
+ }
},
{
"name": "Area 45 (IFG)",
@@ -2926,7 +3414,15 @@
"labelIndex": null,
"synonyms": [],
"relatedAreas": [
- "Area 45"
+ {
+ "name": "Area 45",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "131e6de8-b073-4f01-8f60-1bdb5a6c9a9a"
+ }
+ }
+ }
],
"rgb": [
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@@ -2966,7 +3462,13 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "cb32e688-43f0-4ae3-9554-085973137663"
+ }
+ }
}
]
},
@@ -2978,7 +3480,7 @@
"rgb": null,
"children": [
{
- "name": "Area 6d1 (PreG)",
+ "name": "Area 6d1 (PreCG)",
"arealabel": "Area-6d1",
"status": "publicDOI",
"labelIndex": null,
@@ -2988,9 +3490,15 @@
33,
27
],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId":"a802f3dc-b7e5-48b7-9845-832a6e6f9b1c"
+ }
+ },
"children": [
{
- "name": "Area 6d1 (PreG) - left hemisphere",
+ "name": "Area 6d1 (PreCG) - left hemisphere",
"rgb": [
45,
33,
@@ -3006,7 +3514,7 @@
]
},
{
- "name": "Area 6d1 (PreG) - right hemisphere",
+ "name": "Area 6d1 (PreCG) - right hemisphere",
"rgb": [
45,
33,
@@ -3024,7 +3532,7 @@
]
},
{
- "name": "Area 6d2 (PreG)",
+ "name": "Area 6d2 (PreCG)",
"arealabel": "Area-6d2",
"status": "publicDOI",
"labelIndex": null,
@@ -3034,9 +3542,15 @@
151,
180
],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId":"963c5281-67df-4d41-9b91-60b31cf150c0"
+ }
+ },
"children": [
{
- "name": "Area 6d2 (PreG) - left hemisphere",
+ "name": "Area 6d2 (PreCG) - left hemisphere",
"rgb": [
170,
151,
@@ -3052,7 +3566,7 @@
]
},
{
- "name": "Area 6d2 (PreG) - right hemisphere",
+ "name": "Area 6d2 (PreCG) - right hemisphere",
"rgb": [
170,
151,
@@ -3122,7 +3636,14 @@
57073758
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "07b4c6a1-8a24-4f88-8f73-b2ea06e1c2f3"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -3177,7 +3698,14 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "266c1ada-1840-462f-8223-7ff2df457552"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -3232,7 +3760,14 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "10dc5343-941b-4e3e-80ed-df031c33bbc6"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fp2 (FPole)",
@@ -3278,7 +3813,14 @@
-3022228
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3bf7bde1-cc06-4657-b296-380275f9d4b8"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -3295,8 +3837,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area 4p"
+ "relatedAreas": [
+ {
+ "name": "Area 4p",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "861ab96a-c4b5-4ba6-bd40-1e80d4680f89"
+ }
+ }
+ }
],
"rgb": [
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@@ -3336,7 +3886,13 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "82e6e826-a439-41db-84ff-4674ca3d643a"
+ }
+ }
},
{
"name": "Area 4a (PreCG)",
@@ -3382,7 +3938,14 @@
67748853
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "175848ff-4c55-47e3-a0ae-f905a14e03cd"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -3437,7 +4000,14 @@
56050065
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "def99e8e-ce8f-4a62-bd5d-739948c4b010"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -3492,7 +4062,14 @@
-20253609
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "741f6a9e-cfd7-4173-ac7d-ee616c29555e"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo1 (OFC)",
@@ -3538,7 +4115,14 @@
-25066859
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3864cb8c-f277-4de6-9f8d-c76d71d7e9a9"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo2 (OFC)",
@@ -3584,7 +4168,14 @@
-21936370
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "30a04d2b-58e1-43d7-8b8f-1f0b598382d0"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -3740,7 +4331,14 @@
-6858425
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3fd2e113-ec08-407b-bc88-172c9285694a"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo7 (OFC)",
@@ -3786,7 +4384,14 @@
-13535015
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "1b882148-fcdd-4dbe-b33d-659957840e9e"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo4 (OFC)",
@@ -3832,7 +4437,14 @@
-15390093
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2cdee956-207a-4d4d-b051-bef80045210b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo6 (OFC)",
@@ -3878,7 +4490,14 @@
-14205821
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "330ae178-557c-4bd0-a932-f138c0a05345"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -3942,7 +4561,14 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "46cf08af-8086-4e8a-9e9f-182ca583bdf0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Ig2 (Insula)",
@@ -3988,7 +4614,14 @@
5868966
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "49092952-1eef-4b89-b8bf-1bf1f25f149a"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -4043,7 +4676,14 @@
-8955882
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "110d0d7b-cb88-48ea-9caf-863f548dbe38"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -4098,7 +4738,14 @@
1550497
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3d5729f5-55c6-412a-8fc1-41a95c71b13a"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -4153,7 +4800,14 @@
-5112416
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "c22055c1-514f-4096-906b-abf57286053b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id5 (Insula)",
@@ -4199,7 +4853,14 @@
165741
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e03cd3c6-d0be-481c-b906-9b39c1d0b641"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id4 (Insula)",
@@ -4245,7 +4906,14 @@
10987327
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f480ed72-5ca5-4d1f-8905-cbe9bedcfaee"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id6 (Insula)",
@@ -4291,7 +4959,14 @@
2772938
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "31bbe92d-e5e8-4cf4-be5d-e6b12c71a107"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -4355,7 +5030,14 @@
-5666868
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "68784b66-ff15-4b09-b28a-a2146c0f8907"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area STS2 (STS)",
@@ -4401,7 +5083,14 @@
-16698805
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "278fc30f-2e24-4046-856b-95dfaf561635"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -4456,7 +5145,14 @@
-1006136
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e1a3291-efdc-4ca6-a3d0-6c496c34639f"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -4511,7 +5207,14 @@
-1426009
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "677cd48c-70fa-4bbd-9f0a-ffdc7744bc0f"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.1 (HESCHL)",
@@ -4557,7 +5260,14 @@
10842857
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e2969911-77eb-4b21-af70-216cab5285b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.0 (HESCHL)",
@@ -4565,8 +5275,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area Te1"
+ "relatedAreas": [
+ {
+ "name": "Area Te1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f424643e-9baf-4c50-9417-db1ac33dcd3e"
+ }
+ }
+ }
],
"rgb": [
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@@ -4606,7 +5324,13 @@
5319209
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "13e21153-2ba8-4212-b172-8894f1012225"
+ }
+ }
}
]
},
@@ -4623,8 +5347,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area FG1"
+ "relatedAreas": [
+ {
+ "name": "Area FG1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6318e160-4ad2-4eec-8a2e-2df6fe07d8f4"
+ }
+ }
+ }
],
"rgb": [
131,
@@ -4664,7 +5396,13 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "39fb34a8-fd6d-4fba-898c-2f6167e40459"
+ }
+ }
},
{
"name": "Area FG4 (FusG)",
@@ -4710,7 +5448,14 @@
-21712296
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "fa602743-5f6e-49d1-9734-29dffaa95ff5"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area FG3 (FusG)",
@@ -4756,7 +5501,14 @@
-15743424
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "023f8ef7-c266-4c45-8bf2-4a17dc52985b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area FG2 (FusG)",
@@ -4764,8 +5516,16 @@
"status": "publicP",
"labelIndex": null,
"synonyms": [],
- "relatedAreas":[
- "Area FG2"
+ "relatedAreas": [
+ {
+ "name": "Area FG2",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8f436328-4251-4706-ae38-767e1ab21c6f"
+ }
+ }
+ }
],
"rgb": [
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@@ -4805,7 +5565,13 @@
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]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6e7a0441-4baa-4355-921b-50d23d07d50f"
+ }
+ }
}
]
}
@@ -4869,7 +5635,14 @@
11145614
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e6507a3d-f2f8-4c17-84ff-0e7297e836a0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p24ab (pACC)",
@@ -4915,7 +5688,14 @@
6891142
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5dbb1035-487c-4f43-b551-ccadcf058340"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s32 (sACC)",
@@ -4961,7 +5741,14 @@
-15008494
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "61b44255-ae3a-4a23-b1bc-7d303a48dbd3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 25 (sACC)",
@@ -5007,7 +5794,14 @@
-13530501
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9010ef76-accd-4308-9951-f37b6a10f42b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s24 (sACC)",
@@ -5053,7 +5847,14 @@
-10923181
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d4ea6cc5-1e1d-4212-966f-81fed01eb648"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p32 (pACC)",
@@ -5099,7 +5900,14 @@
10022042
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b09aaa77-f41b-4008-b8b9-f984b0417cf3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 33 (ACC)",
@@ -5145,7 +5953,14 @@
15680187
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b83a3330-b80e-42a0-b8d2-82f38784aa1d"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5200,15 +6015,30 @@
-34844921
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "030827d4-e0d1-4406-b71f-3f58dc2f9cca"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "CA (Hippocampus)",
"arealabel": "CA",
"status": "publicP",
"labelIndex": null,
- "relatedAreas":[
- "CA1 (Hippocampus)"
+ "relatedAreas": [
+ {
+ "name": "CA1 (Hippocampus)",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bfc0beb7-310c-4c57-b810-2adc464bd02c"
+ }
+ }
+ }
],
"synonyms": [],
"rgb": [
@@ -5249,7 +6079,13 @@
-11735266
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a0d14d3e-bc30-41cf-8b28-540067897f80"
+ }
+ }
},
{
"name": "DG (Hippocampus)",
@@ -5295,7 +6131,14 @@
-11462629
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "0bea7e03-bfb2-4907-9d45-db9071ce627d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Subiculum (Hippocampus)",
@@ -5341,7 +6184,14 @@
-18015846
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e2dab4c-a140-440d-a322-c1679adef2d4"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "HATA (Hippocampus)",
@@ -5387,7 +6237,14 @@
-18866667
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9ec4a423-70fa-43cd-90b3-fbc26a3cbc6c"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -5469,7 +6326,14 @@
-32600000
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5524,7 +6388,14 @@
-37750665
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "58095aef-da69-43d4-887c-009c095cecce"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Ventral Dentate Nucleus (Cerebellum)",
@@ -5570,7 +6441,14 @@
-32527125
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "57282342-5a75-4e07-bcdc-2d368c517b71"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5625,7 +6503,14 @@
-30598446
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e8abfe3d-8b64-45c2-8853-314d82873273"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5680,7 +6565,14 @@
-32600000
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -5694,113 +6586,164 @@
},
{
"ngId": "fibre bundle long",
- "auxillaryMeshIndices": [ 65535 ],
+ "auxillaryMeshIndices": [
+ 65535
+ ],
"type": "parcellation",
"surfaceParcellation": true,
"ngData": null,
"name": "Fibre Bundle Atlas - Long Bundle",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "fcbb049b-edd5-4fb5-acbc-7bf8ee933e24"
- }],
- "properties": {
- },
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "fcbb049b-edd5-4fb5-acbc-7bf8ee933e24"
+ }
+ ],
+ "properties": {},
"regions": [
{
"name": "Arcuate - Left",
"children": [],
"labelIndex": "1",
- "relatedAreas": [
- "Direct segment of the left arcuate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7de080e0-fa5e-492f-9cbc-a4d7e498b1d5"
+ }
+ }
},
{
"name": "Arcuate - Right",
"children": [],
"labelIndex": "31",
- "relatedAreas": [
- "Direct segment of the right arcuate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "17cbf31c-f68b-4753-9014-44aa38e1cdcf"
+ }
+ }
},
{
"name": "Arcuate_Anterior - Left",
"children": [],
"labelIndex": "2",
- "relatedAreas": [
- "Anterior segment of the left arcuate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "1ed86a08-d720-427c-9796-ade24e34a36b"
+ }
+ }
},
{
"name": "Arcuate_Anterior - Right",
"children": [],
"labelIndex": "32",
- "relatedAreas": [
- "Anterior segment of the right arcuate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9f625fad-9329-4824-8751-8b27dc197d3e"
+ }
+ }
},
{
"name": "Arcuate_Posterior - Left",
"children": [],
"labelIndex": "3",
- "relatedAreas": [
- "Posterior segment of the left arcuate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f13ba46b-09ad-48bd-9301-282b0ee74d8d"
+ }
+ }
},
{
"name": "Arcuate_Posterior - Right",
"children": [],
"labelIndex": "33",
- "relatedAreas": [
- "Posterior segment of the right arcuate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2a6ea612-46c1-4a0f-a6f4-5ffc7ff09548"
+ }
+ }
},
{
"name": "Cingulum_Long - Left",
"children": [],
"labelIndex": "4",
- "relatedAreas": [
- "Left long cingulate fibres"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6fa27cc1-2efe-4fd3-83d7-973667a0b925"
+ }
+ }
},
{
"name": "Cingulum_Long - Right",
"children": [],
"labelIndex": "34",
- "relatedAreas": [
- "Right long cingulate fibres"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f5ae1188-8a10-4e17-9fa9-47b1dc4e50cd"
+ }
+ }
},
{
"name": "Cingulum_Short - Left",
"children": [],
"labelIndex": "5",
- "relatedAreas": [
- "Left short cingulate fibres"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "882d13c0-ffe4-4fd8-95a1-ba714cd25fbb"
+ }
+ }
},
{
"name": "Cingulum_Short - Right",
"children": [],
"labelIndex": "35",
- "relatedAreas": [
- "Right short cingulate fibres"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "4c5ecae5-17b4-4a65-8b66-c4d0882a2bca"
+ }
+ }
},
{
"name": "Cingulum_Temporal - Left",
"children": [],
"labelIndex": "6",
- "relatedAreas": [
- "Left temporal cingulate fibres"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2c71b329-5a32-4ba0-aacb-0fac99c46aca"
+ }
+ }
},
{
"name": "Cingulum_Temporal - Right",
"children": [],
"labelIndex": "36",
- "relatedAreas": [
- "Right temporal cingulate fibres"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e965e21-1d9b-4b8d-b77d-4a7ca17603e6"
+ }
+ }
},
{
"name": "CorpusCallosum_Body",
@@ -5826,17 +6769,25 @@
"name": "CorticoSpinalTract - Left",
"children": [],
"labelIndex": "11",
- "relatedAreas": [
- "Left corticospinal tract"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "afbb2642-5e90-412f-9847-3d7a831f8f07"
+ }
+ }
},
{
"name": "CorticoSpinalTract - Right",
"children": [],
"labelIndex": "41",
- "relatedAreas": [
- "Right corticospinal tract"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2f398c6e-6264-4615-8a28-18b3573d0732"
+ }
+ }
},
{
"name": "ExternalCapsule - Left",
@@ -5852,49 +6803,73 @@
"name": "Fornix - Left",
"children": [],
"labelIndex": "13",
- "relatedAreas": [
- "Left fornix"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "c8d1e4a0-d0c2-4101-a971-3ffb1ba65ef8"
+ }
+ }
},
{
"name": "Fornix - Right",
"children": [],
"labelIndex": "43",
- "relatedAreas": [
- "Right fornix"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e7e8fd6d-aa43-452e-9fc3-635aa0333910"
+ }
+ }
},
{
"name": "InferiorFrontoOccipital - Left",
"children": [],
"labelIndex": "14",
- "relatedAreas": [
- "Left inferior fronto-occipital fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "524cd5a0-7066-4149-83b8-c0c4aaa12820"
+ }
+ }
},
{
"name": "InferiorFrontoOccipital - Right",
"children": [],
"labelIndex": "44",
- "relatedAreas": [
- "Right inferior fronto-occipital fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "34e8f68d-0b00-4e9e-bd43-ccaf10deef6d"
+ }
+ }
},
{
"name": "InferiorLongitudinal - Left",
"children": [],
"labelIndex": "15",
- "relatedAreas": [
- "Left inferior longitudinal fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d3a458e1-6dbf-418d-bb52-c0b0c6acb920"
+ }
+ }
},
{
"name": "InferiorLongitudinal - Right",
"children": [],
"labelIndex": "45",
- "relatedAreas": [
- "Right inferior longitudinal fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "25326bc6-2b87-4483-9738-89ca249faccd"
+ }
+ }
},
{
"name": "InferiorLongitudinal_Lateral - Left",
@@ -5950,31 +6925,43 @@
"name": "Uncinate - Left",
"children": [],
"labelIndex": "21",
- "relatedAreas": [
- "Left uncinate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f36707b5-d4f3-480b-a1c9-651bf8cc49d5"
+ }
+ }
},
{
"name": "Uncinate - Right",
"children": [],
"labelIndex": "51",
- "relatedAreas": [
- "Right uncinate fasciculus"
- ]
+ "relatedAreas": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "84ea1a64-03a6-4a7e-9f64-a3d2127ebf3f"
+ }
+ }
}
]
},
{
"ngId": "fibre bundle short",
- "auxillaryMeshIndices": [ 65535 ],
+ "auxillaryMeshIndices": [
+ 65535
+ ],
"type": "parcellation",
"surfaceParcellation": true,
"ngData": null,
"name": "Fibre Bundle Atlas - Short Bundle",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "f58e4425-6614-4ad9-ac26-5e946b1296cb"
- }],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "f58e4425-6614-4ad9-ac26-5e946b1296cb"
+ }
+ ],
"regions": [
{
"name": "Left Hemisphere",
@@ -7008,4 +7995,4 @@
"name": "ICBM 2009c Nonlinear Asymmetric",
"description": "An unbiased non-linear average of multiple subjects from the MNI152 database, which provides high-spatial resolution and signal-to-noise while not being biased towards a single brain (Fonov et al., 2011). This template space is widely used as a reference space in neuroimaging. HBP provides the JuBrain probabilistic cytoarchitectonic atlas (Amunts/Zilles, 2015) as well as a probabilistic atlas of large fibre bundles (Guevara, Mangin et al., 2017) in this space."
}
-}
+}
\ No newline at end of file
diff --git a/src/res/ext/allenMouse.json b/src/res/ext/allenMouse.json
index 13ebc3c9f38106b9cd7d037544070be2abf7bb0f..b0fbfcceb3f57dbd8bd17adcdd8409ee49c9a6bb 100644
--- a/src/res/ext/allenMouse.json
+++ b/src/res/ext/allenMouse.json
@@ -3,7 +3,9 @@
"type": "template",
"species": "Mouse",
"ngId": "stpt",
- "otherNgIds": ["nissl"],
+ "otherNgIds": [
+ "nissl"
+ ],
"useTheme": "dark",
"nehubaConfigURL": "nehubaConfig/allenMouseNehubaConfig",
"parcellations": [
@@ -19106,9 +19108,11 @@
"properties": {
"name": "Allen Mouse Common Coordinate Framework v3 2017",
"description": "Allen Mouse Common Coordinate Framework v3, downloaded on 19/09/2019, 2017 (662 newly drawn structures, 1522 structures total)",
- "publications": [{
- "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
- }]
+ "publications": [
+ {
+ "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
+ }
+ ]
}
},
{
@@ -19851,7 +19855,14 @@
2337500,
1677500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "368c29b4-affd-46cf-ac89-ce6d520759b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Secondary motor area",
@@ -20128,7 +20139,14 @@
3027500,
1927500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "af019af1-3b69-42ac-be17-f1c2a1058329"
+ }
+ },
+ "relatedAreas": []
}
],
"ontologyMetadata": {
@@ -20771,7 +20789,14 @@
967500,
1577500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6321aaf1-e663-48ac-a2e4-a0b53b2a4941"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Primary somatosensory area, barrel field",
@@ -21249,7 +21274,14 @@
-102500,
2287500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a2c0a613-0507-4878-a305-0b8455121e3a"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Primary somatosensory area, lower limb",
@@ -21572,7 +21604,14 @@
667500,
2807500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2442b0a6-5a4b-433f-b24c-24973831f4f4"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Primary somatosensory area, mouth",
@@ -22218,7 +22257,14 @@
1187500,
2297500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "0b260c14-c381-4260-a958-505bfd6672d1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Primary somatosensory area, trunk",
@@ -22541,7 +22587,14 @@
-42500,
3097500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "4b9e5151-bf65-4d3c-9926-9f8e92061889"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Primary somatosensory area, unassigned",
@@ -22864,7 +22917,14 @@
777500,
2317500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "ac8f6062-6014-437d-b24a-715b211f2096"
+ }
+ },
+ "relatedAreas": []
}
],
"ontologyMetadata": {
@@ -22902,7 +22962,14 @@
897500,
1977500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6ffdfed4-d9bf-4c92-b6f7-e7de76dee881"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Supplemental somatosensory area",
@@ -25867,7 +25934,14 @@
-1622500,
2357500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6f17fd2c-94d7-4807-be28-12eb2b870e6d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Anteromedial visual area",
@@ -26190,7 +26264,14 @@
-1022500,
3317500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9925036-2394-48df-813e-150dce63aee4"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Lateral visual area",
@@ -26836,7 +26917,14 @@
-2432500,
2837500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9d426ec-d6b2-4370-8fa2-8e85d30168c6"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Posterolateral visual area",
@@ -28562,7 +28650,14 @@
2197500,
2097500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6f9e275f-e4b1-4b73-ab3c-61f3d386ed00"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Anterior cingulate area, ventral part",
@@ -29176,7 +29271,14 @@
3527500,
1257500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "157f0525-03ae-434b-8856-bac7abb0a2a3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Infralimbic area",
@@ -32136,7 +32238,14 @@
-1492500,
3217500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a43fe448-5035-4fb2-b141-3af62baf7c02"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Retrosplenial area, dorsal part",
@@ -32459,7 +32568,14 @@
-1382500,
3237500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "30517d4d-668e-40eb-a7a8-7112058ca906"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Retrosplenial area, ventral part",
@@ -32758,7 +32874,14 @@
-1152500,
2777500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "fc465f87-b153-4418-a526-52874591f64a"
+ }
+ },
+ "relatedAreas": []
}
],
"ontologyMetadata": {
@@ -33260,7 +33383,14 @@
-612500,
3177500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "cf5c7194-fe25-4828-8225-8a8125c30133"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Rostrolateral visual area",
@@ -33583,7 +33713,14 @@
-1162500,
2797500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d5ffb9fa-04e2-44dc-bcee-ab4a1467fa99"
+ }
+ },
+ "relatedAreas": []
}
],
"ontologyMetadata": {
@@ -37851,7 +37988,14 @@
-1332500,
797500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "fc429031-1632-49a4-b9c6-00ab72100c85"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Retrohippocampal region",
@@ -40539,7 +40683,14 @@
997500,
1107500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b4747984-ae71-4de2-bf18-e5965a27b490"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Cerebral nuclei",
@@ -43051,7 +43202,14 @@
867500,
297500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2f520589-1a89-427d-ac6b-3a561e0fa0f3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Brain stem",
@@ -57486,7 +57644,14 @@
-2602500,
-722500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a470f51b-bf1f-4c63-a18f-df2ea2c65f3f"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Cerebellum",
@@ -58840,7 +59005,14 @@
-5122500,
1147500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8b7490d6-bde7-438a-aee9-34820860fe12"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Hemispheric regions",
@@ -60098,7 +60270,14 @@
-4942500,
777500
]
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "caa2c52c-0d6c-4eba-b2b6-5414cc241553"
+ }
+ },
+ "relatedAreas": []
}
],
"ontologyMetadata": {
@@ -67952,28 +68131,35 @@
}
],
"properties": {
- "name":"Allen Mouse Common Coordinate Framework v3 2015",
- "description":"Allen Mouse Common Coordinate Framework v3, downloaded on 01/07/2017 2015 (178 newly drawn structures, 1045 structures total)",
- "publications": [{
- "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
- },{
- "doi": "10.1038/nature13186",
- "citation": "Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214. "
- }]
+ "name": "Allen Mouse Common Coordinate Framework v3 2015",
+ "description": "Allen Mouse Common Coordinate Framework v3, downloaded on 01/07/2017 2015 (178 newly drawn structures, 1045 structures total)",
+ "publications": [
+ {
+ "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
+ },
+ {
+ "doi": "10.1038/nature13186",
+ "citation": "Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214. "
+ }
+ ]
}
}
],
"properties": {
"name": "Allen Mouse Common Coordinate Framework v3 2015",
"description": "The Allen Mouse Common Coordinate Framework v3 2015 includes a full-color, high-resolution anatomical reference atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures. Anatomical annotations in classical histological atlas plates were extracted to create a comprehensive volumetric reference atlas of the mouse brain.",
- "publications":[{
- "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
- },{
- "cite":"Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214.",
- "doi": "10.1038/nature13186"
- }, {
- "cite": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/",
- "doi": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/"
- }]
+ "publications": [
+ {
+ "cite": "Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011. Available from: http://connectivity.brain-map.org/."
+ },
+ {
+ "cite": "Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214.",
+ "doi": "10.1038/nature13186"
+ },
+ {
+ "cite": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/",
+ "doi": "http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/"
+ }
+ ]
}
}
\ No newline at end of file
diff --git a/src/res/ext/bigbrain.json b/src/res/ext/bigbrain.json
index 2440a1ee9b1c54631a4fa82215c7b58123c1b5f5..abff253c1bcfe71b4fc29561fb23804a84882302 100644
--- a/src/res/ext/bigbrain.json
+++ b/src/res/ext/bigbrain.json
@@ -4,10 +4,12 @@
"species": "Human",
"useTheme": "light",
"ngId": " grey value: ",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "e32f9053-38c9-4911-b868-845c56828f4d"
- }],
+ "originDatasets": [
+ {
+ "kgSchema": "minds/core/dataset/v1.0.0",
+ "kgId": "e32f9053-38c9-4911-b868-845c56828f4d"
+ }
+ ],
"nehubaConfigURL": "nehubaConfig/bigbrainNehubaConfig",
"parcellations": [
{
@@ -43,6 +45,23 @@
4363384,
836825,
4887117
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "13e21153-2ba8-4212-b172-8894f1012225"
+ }
+ },
+ "relatedAreas": [
+ {
+ "name": "Area Te1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f424643e-9baf-4c50-9417-db1ac33dcd3e"
+ }
+ }
+ }
]
},
{
@@ -60,7 +79,14 @@
-11860944,
-3841071,
6062770
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e2969911-77eb-4b21-af70-216cab5285b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.2 (HESCHL)",
@@ -77,7 +103,14 @@
19474750,
7932494,
3511322
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "677cd48c-70fa-4bbd-9f0a-ffdc7744bc0f"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -99,7 +132,14 @@
3479937,
2702958,
3819372
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e1a3291-efdc-4ca6-a3d0-6c496c34639f"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -116,7 +156,14 @@
-3185950,
3919067,
-8346900
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "68784b66-ff15-4b09-b28a-a2146c0f8907"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area STS2 (STS)",
@@ -128,7 +175,14 @@
8584703,
6170348,
-11790982
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "278fc30f-2e24-4046-856b-95dfaf561635"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -150,7 +204,13 @@
-10496194,
13643679,
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- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a802f3dc-b7e5-48b7-9845-832a6e6f9b1c"
+ }
+ }
},
{
"name": "Area 6d2 (PreCG)",
@@ -162,7 +222,13 @@
-9255504,
27432072,
43445689
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "963c5281-67df-4d41-9b91-60b31cf150c0"
+ }
+ }
},
{
"name": "Area 6ma (preSMA, mesial SFG)",
@@ -174,7 +240,14 @@
-9349145,
27783957,
38734627
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "07b4c6a1-8a24-4f88-8f73-b2ea06e1c2f3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 6mp (SMA, mesial SFG)",
@@ -186,7 +259,14 @@
-11566856,
15797100,
42172031
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "def99e8e-ce8f-4a62-bd5d-739948c4b010"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -203,7 +283,14 @@
-8973604,
28973429,
35691250
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "266c1ada-1840-462f-8223-7ff2df457552"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -220,7 +307,14 @@
-7394436,
33562602,
19086364
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a6a83284-829b-4385-9f83-7f1bc832c5a5"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifj2 (IFS/PreCS)",
@@ -244,7 +338,14 @@
-4044465,
40212624,
17596493
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d687d385-98d9-4b31-85db-4bc682cd0a31"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs2 (IFS)",
@@ -256,7 +357,14 @@
6807265,
40114241,
18114896
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "658a67d8-60c2-4bb4-8eaf-e54725eda261"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs3 (IFS)",
@@ -268,7 +376,14 @@
-2260366,
37593844,
19960703
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e555881e-7082-4ac0-b6cc-cd096f30d3dc"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area ifs4 (IFS)",
@@ -280,7 +395,14 @@
-3440565,
37895181,
17378851
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "472dacc9-c27d-49c2-9e6f-a1cc3309c4ab"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -307,7 +429,14 @@
4800238,
8859989,
-24872710
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "030827d4-e0d1-4406-b71f-3f58dc2f9cca"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -329,7 +458,14 @@
-5671181,
-44793673,
21692004
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5875bfe2-99ca-4e50-bce2-61c201c3dd54"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP5 (IPS)",
@@ -341,7 +477,14 @@
-13546343,
-38230309,
26252296
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9717dec-0310-4078-a4ae-294170b4fb37"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP6 (IPS)",
@@ -353,7 +496,14 @@
-3723403,
-33064127,
32569712
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b9975f8e-f484-4e82-883a-5fd765855ae0"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area hIP7 (IPS)",
@@ -365,7 +515,14 @@
-5344588,
-43655931,
24702722
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9c6c3c96-8129-4e0e-aa22-a0fb435aab45"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -382,7 +539,14 @@
-4455614,
-44097379,
28855803
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a78998c2-99d4-4738-bbda-82a317f713f1"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -409,7 +573,24 @@
30,
250
],
- "children": []
+ "children": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
+ },
+ "relatedAreas": [
+ {
+ "name": "Area hOc1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ }
+ }
+ }
+ ]
},
{
"name": "Area hOc2 (V2, 18)",
@@ -426,7 +607,14 @@
100,
250
],
- "children": []
+ "children": [],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "04674a3c-bb3a-495e-a466-206355e630bd"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "dorsal occipital cortex",
@@ -441,7 +629,14 @@
-4399437,
-36706104,
15113374
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d72e0210-a910-4b15-bcaf-80c3433cd3e0"
+ }
+ },
+ "relatedAreas": []
}
]
}
diff --git a/src/res/ext/colin.json b/src/res/ext/colin.json
index 9094492116566be46ff2869c02b27d01e40198d9..c9a3d19638ccd97efbd20da73e12547e6ce87a5a 100644
--- a/src/res/ext/colin.json
+++ b/src/res/ext/colin.json
@@ -115,7 +115,14 @@
-8347692
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -173,7 +180,14 @@
-11539130
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a5c9d95f-8e7c-4454-91b6-a790387370fc"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -231,7 +245,14 @@
-8347692
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bb111a95-e04c-4987-8254-4af4ed8b0022"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -276,7 +297,14 @@
"children": [],
"status": "publicP"
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "LB (Amygdala)",
@@ -303,7 +331,14 @@
"children": [],
"status": "publicP"
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "708df0fa-e9a4-4c23-bd85-8957f6d30faf"
+ }
+ },
+ "relatedAreas": []
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{
"name": "LB (Amygdala)",
@@ -330,7 +365,14 @@
"children": [],
"status": "publicP"
}
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@@ -367,7 +409,14 @@
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]
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@@ -413,7 +462,14 @@
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{
"name": "SF (Amygdala)",
@@ -440,7 +496,14 @@
"children": [],
"status": "publicP"
}
- ]
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "48929163-bf7b-4471-9f14-991c5225eced"
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{
"name": "SF (Amygdala)",
@@ -479,7 +542,14 @@
"children": [],
"status": "publicP"
}
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "48929163-bf7b-4471-9f14-991c5225eced"
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+ "relatedAreas": []
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{
"name": "CM (Amygdala)",
@@ -518,7 +588,14 @@
"children": [],
"status": "publicP"
}
- ]
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@@ -576,7 +653,14 @@
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{
"name": "IF (Amygdala)",
@@ -625,7 +709,14 @@
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]
}
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{
"name": "MF (Amygdala)",
@@ -674,7 +765,14 @@
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]
}
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@@ -722,7 +820,14 @@
"children": [],
"status": "publicP"
}
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+ "kgId": "7aba8aef-6430-4fa7-ab54-8ecac558faed"
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{
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@@ -771,7 +876,14 @@
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]
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@@ -847,7 +959,14 @@
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{
"name": "Area 7M (SPL)",
@@ -896,7 +1015,14 @@
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]
}
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+ "kgId": "0aacea5c-bc9e-483f-8376-25f176ada158"
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},
{
"name": "Area 7PC (SPL)",
@@ -945,7 +1071,14 @@
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]
}
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+ "kgId": "763140d3-7ba0-4f28-b0ac-c6cbda2d14e1"
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+ "relatedAreas": []
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{
"name": "Area 5M (SPL)",
@@ -994,7 +1127,14 @@
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]
}
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+ "kgId": "abe105cf-2c29-46af-af75-6b46fdb75137"
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{
"name": "Area 7P (SPL)",
@@ -1043,7 +1183,14 @@
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]
}
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{
"name": "Area 5Ci (SPL)",
@@ -1092,7 +1239,14 @@
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]
}
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},
{
"name": "Area 7A (SPL)",
@@ -1143,8 +1297,22 @@
}
],
"relatedAreas": [
- "Area 7A"
- ]
+ {
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+ "fullId": {
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@@ -1202,7 +1370,14 @@
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]
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{
"name": "Area OP4 (POperc)",
@@ -1251,7 +1426,14 @@
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]
}
- ]
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+ "relatedAreas": []
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{
"name": "Area OP2 (POperc)",
@@ -1300,7 +1482,14 @@
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]
}
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+ "kgId": "ab26cefd-f7d6-4442-8020-a6e418e673ff"
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+ "relatedAreas": []
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{
"name": "Area OP1 (POperc)",
@@ -1349,7 +1538,14 @@
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]
}
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}
]
},
@@ -1368,7 +1564,15 @@
"doi": "https://doi.org/10.25493/2JK3-QXR",
"synonyms": [],
"relatedAreas": [
- "Area 3b"
+ {
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+ "kgId": "74304fe9-452e-4ca3-97a3-8cf3459bb1a0"
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@@ -1410,7 +1614,13 @@
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+ "kgId": "b84f67bb-5d9f-4daf-a8d6-15f63f901bd4"
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},
{
"name": "Area 1 (PostCG)",
@@ -1459,7 +1669,14 @@
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]
}
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{
"name": "Area 2 (PostCS)",
@@ -1508,7 +1725,14 @@
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]
}
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{
"name": "Area 3a (PostCG)",
@@ -1557,7 +1781,14 @@
36284571
]
}
- ]
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}
]
},
@@ -1576,7 +1807,15 @@
"doi": "https://doi.org/10.25493/F1TJ-54W",
"synonyms": [],
"relatedAreas": [
- "Area PF"
+ {
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+ "kgId": "f4e177a6-1b2c-48d5-a62c-91949ba636e4"
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@@ -1618,7 +1857,13 @@
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+ "kgId": "18e5e1b0-6c25-4f55-a967-0834d2bd3ee4"
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},
{
"name": "Area PFcm (IPL)",
@@ -1628,7 +1873,15 @@
"doi": "https://doi.org/10.25493/8DP8-8HE",
"synonyms": [],
"relatedAreas": [
- "Area PFcm"
+ {
+ "name": "Area PFcm",
+ "fullId": {
+ "kg": {
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+ "kgId": "f07d441f-452f-471b-ac7c-0d3c2ae16fb2"
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],
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@@ -1670,7 +1923,13 @@
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]
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+ "kgId": "10502c3a-f20e-44fa-b985-786d6888d4bb"
+ }
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},
{
"name": "Area PGa (IPL)",
@@ -1680,7 +1939,15 @@
"doi": "https://doi.org/10.25493/V5HY-XTS",
"synonyms": [],
"relatedAreas": [
- "Area PGa"
+ {
+ "name": "Area PGa",
+ "fullId": {
+ "kg": {
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+ "kgId": "d5b168a3-a92e-4ab3-8b4d-61e58e5b7a1c"
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@@ -1722,7 +1989,13 @@
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]
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+ "kgId": "d7f6c5be-93c6-4a16-8939-4420329d4147"
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},
{
"name": "Area PFt (IPL)",
@@ -1732,7 +2005,15 @@
"doi": "https://doi.org/10.25493/JGM9-ZET",
"synonyms": [],
"relatedAreas": [
- "Area PFt"
+ {
+ "name": "Area PFt",
+ "fullId": {
+ "kg": {
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+ "kgId": "9ff7fcc4-a88b-4bf8-be07-1386a3760a96"
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],
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@@ -1774,7 +2055,13 @@
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]
}
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+ "kgId": "847cef50-7340-470d-8580-327b4ce9db19"
+ }
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},
{
"name": "Area PFm (IPL)",
@@ -1784,7 +2071,15 @@
"doi": "https://doi.org/10.25493/TB94-HRK",
"synonyms": [],
"relatedAreas": [
- "Area PFm"
+ {
+ "name": "Area PFm",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3455ada4-48c3-4748-ae38-2fe3f376f0fc"
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],
"rgb": [
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@@ -1826,7 +2121,13 @@
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]
}
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+ "kgId": "411edde9-685f-464b-970c-a929f9a4067c"
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},
{
"name": "Area PGp (IPL)",
@@ -1877,8 +2178,22 @@
}
],
"relatedAreas": [
- "Area PGp"
- ]
+ {
+ "name": "Area PGp",
+ "fullId": {
+ "kg": {
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+ "kgId": "1b00a0e4-9493-43ff-bfbd-b02119064813"
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+ "kgId": "b3ef6947-76c9-4935-bbc6-8b2329c0967b"
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},
{
"name": "Area PFop (IPL)",
@@ -1929,8 +2244,22 @@
}
],
"relatedAreas": [
- "Area PFop"
- ]
+ {
+ "name": "Area PFop",
+ "fullId": {
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+ "kgId": "b4397c40-82e1-4d62-b97a-44e8d04b428b"
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]
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@@ -1988,7 +2317,14 @@
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]
}
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+ "fullId": {
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+ "kgId": "a78998c2-99d4-4738-bbda-82a317f713f1"
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]
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@@ -2046,7 +2382,14 @@
39158853
]
}
- ]
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+ "fullId": {
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+ "kgId": "7722c71f-fe84-4deb-8f6b-98e2aecf2e31"
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+ "relatedAreas": []
},
{
"name": "Area hIP7 (IPS)",
@@ -2095,7 +2438,14 @@
27046207
]
}
- ]
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+ "fullId": {
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+ "kgId": "9c6c3c96-8129-4e0e-aa22-a0fb435aab45"
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+ "relatedAreas": []
},
{
"name": "Area hIP3 (IPS)",
@@ -2144,7 +2494,14 @@
50461950
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "700ac6db-870d-44f1-8786-0c01207f992b"
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+ "relatedAreas": []
},
{
"name": "Area hIP2 (IPS)",
@@ -2193,7 +2550,14 @@
45130872
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "4490ef3e-ce60-4453-9e9f-85388d0603cb"
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+ "relatedAreas": []
},
{
"name": "Area hIP4 (IPS)",
@@ -2242,7 +2606,14 @@
22338021
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5875bfe2-99ca-4e50-bce2-61c201c3dd54"
+ }
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+ "relatedAreas": []
},
{
"name": "Area hIP5 (IPS)",
@@ -2291,7 +2662,14 @@
33299252
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f9717dec-0310-4078-a4ae-294170b4fb37"
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+ "relatedAreas": []
},
{
"name": "Area hIP6 (IPS)",
@@ -2340,7 +2718,14 @@
45628006
]
}
- ]
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+ "fullId": {
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+ "kgId": "b9975f8e-f484-4e82-883a-5fd765855ae0"
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+ "relatedAreas": []
},
{
"name": "Area hIP8 (IPS)",
@@ -2389,7 +2774,14 @@
41680048
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a2c1acc7-7fdc-4fbd-90ee-729eda7fdff3"
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]
}
@@ -2456,7 +2848,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "d72e0210-a910-4b15-bcaf-80c3433cd3e0"
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+ "relatedAreas": []
},
{
"name": "Area hOc4d (Cuneus)",
@@ -2505,7 +2904,14 @@
27253227
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8120426c-f65b-4426-8a58-3060e2334921"
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+ "relatedAreas": []
},
{
"name": "Area hOc3d (Cuneus)",
@@ -2554,7 +2960,14 @@
23080617
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d7ec4342-ae58-41e3-a68c-28e90a719d41"
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]
},
@@ -2612,7 +3025,14 @@
-10031193
]
}
- ]
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+ "fullId": {
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+ "kgId": "0d6392fd-b905-4bc3-bac9-fc44d8990a30"
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+ "relatedAreas": []
},
{
"name": "Area hOc4v (LingG)",
@@ -2661,7 +3081,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "27d91cbb-5611-4d38-bd17-c0f1ac22b4cc"
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]
},
@@ -2719,7 +3146,14 @@
2905309
]
}
- ]
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+ "fullId": {
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+ "kgId": "04674a3c-bb3a-495e-a466-206355e630bd"
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+ },
+ "relatedAreas": []
},
{
"name": "Area hOc1 (V1, 17, CalcS)",
@@ -2770,8 +3204,22 @@
}
],
"relatedAreas": [
- "Area hOc1"
- ]
+ {
+ "name": "Area hOc1",
+ "fullId": {
+ "kg": {
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@@ -2829,7 +3277,14 @@
4086228
]
}
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{
"name": "Area hOc5 (LOC)",
@@ -2878,7 +3333,14 @@
3121699
]
}
- ]
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+ "relatedAreas": []
},
{
"name": "Area hOc4la (LOC)",
@@ -2927,7 +3389,14 @@
-779202
]
}
- ]
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+ "fullId": {
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+ "relatedAreas": []
}
]
}
@@ -2955,8 +3424,24 @@
"doi": "https://doi.org/10.25493/F9P8-ZVW",
"synonyms": [],
"relatedAreas": [
- "Area 44v",
- "Area 44d"
+ {
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+ "fullId": {
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+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
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+ {
+ "name": "Area 44d",
+ "fullId": {
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+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
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],
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+ "kgId": "8a6be82c-5947-4fff-8348-cf9bf73e4f40"
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},
{
"name": "Area 45 (IFG)",
@@ -3008,7 +3499,15 @@
"doi": "https://doi.org/10.25493/MR1V-BJ3",
"synonyms": [],
"relatedAreas": [
- "Area 45"
+ {
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+ "fullId": {
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],
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@@ -3050,7 +3549,13 @@
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+ "kgId": "cb32e688-43f0-4ae3-9554-085973137663"
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]
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@@ -3108,7 +3613,14 @@
68442439
]
}
- ]
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+ "relatedAreas": []
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{
"name": "Area 6d1 (PreCG)",
@@ -3157,7 +3669,14 @@
68870890
]
}
- ]
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]
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@@ -3215,7 +3734,14 @@
58355079
]
}
- ]
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@@ -3273,7 +3799,14 @@
53334281
]
}
- ]
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+ "fullId": {
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+ "kgId": "266c1ada-1840-462f-8223-7ff2df457552"
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]
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@@ -3331,7 +3864,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "10dc5343-941b-4e3e-80ed-df031c33bbc6"
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+ "relatedAreas": []
},
{
"name": "Area Fp2 (FPole)",
@@ -3380,7 +3920,14 @@
-509606
]
}
- ]
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+ "fullId": {
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+ "relatedAreas": []
}
]
},
@@ -3399,7 +3946,15 @@
"doi": "https://doi.org/10.25493/5HSF-81J",
"synonyms": [],
"relatedAreas": [
- "Area 4p"
+ {
+ "name": "Area 4p",
+ "fullId": {
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+ "kgId": "861ab96a-c4b5-4ba6-bd40-1e80d4680f89"
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],
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@@ -3441,7 +3996,13 @@
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]
}
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+ "kgId": "82e6e826-a439-41db-84ff-4674ca3d643a"
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},
{
"name": "Area 4a (PreCG)",
@@ -3490,7 +4051,14 @@
68068112
]
}
- ]
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+ "fullId": {
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]
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@@ -3548,7 +4116,14 @@
57534028
]
}
- ]
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]
},
@@ -3606,7 +4181,14 @@
-22481988
]
}
- ]
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+ "kgId": "3864cb8c-f277-4de6-9f8d-c76d71d7e9a9"
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+ "relatedAreas": []
},
{
"name": "Area Fo3 (OFC)",
@@ -3655,7 +4237,14 @@
-20231493
]
}
- ]
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+ "fullId": {
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+ "kgId": "741f6a9e-cfd7-4173-ac7d-ee616c29555e"
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+ "relatedAreas": []
},
{
"name": "Area Fo2 (OFC)",
@@ -3704,7 +4293,14 @@
-20593342
]
}
- ]
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+ "fullId": {
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]
},
@@ -3869,7 +4465,14 @@
-4983615
]
}
- ]
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+ "fullId": {
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+ "kgId": "3fd2e113-ec08-407b-bc88-172c9285694a"
+ }
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+ "relatedAreas": []
},
{
"name": "Area Fo4 (OFC)",
@@ -3918,7 +4521,14 @@
-15509742
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "2cdee956-207a-4d4d-b051-bef80045210b"
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+ "relatedAreas": []
},
{
"name": "Area Fo6 (OFC)",
@@ -3967,7 +4577,14 @@
-12457353
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "330ae178-557c-4bd0-a932-f138c0a05345"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Fo7 (OFC)",
@@ -4016,7 +4633,14 @@
-13777644
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "1b882148-fcdd-4dbe-b33d-659957840e9e"
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+ "relatedAreas": []
}
]
}
@@ -4083,7 +4707,14 @@
9071429
]
}
- ]
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+ "fullId": {
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+ "kgId": "46cf08af-8086-4e8a-9e9f-182ca583bdf0"
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+ "relatedAreas": []
},
{
"name": "Area Ig3 (Insula)",
@@ -4132,7 +4763,14 @@
13916877
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "10dba769-4f6c-40f9-8ffd-e0cce71c5adb"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Ig2 (Insula)",
@@ -4181,7 +4819,14 @@
5703657
]
}
- ]
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+ "fullId": {
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+ "kgId": "49092952-1eef-4b89-b8bf-1bf1f25f149a"
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]
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@@ -4239,7 +4884,14 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "110d0d7b-cb88-48ea-9caf-863f548dbe38"
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]
},
@@ -4297,7 +4949,14 @@
2446009
]
}
- ]
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+ "fullId": {
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]
},
@@ -4355,7 +5014,14 @@
3759834
]
}
- ]
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+ "fullId": {
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+ "kgId": "cf9dea67-649d-4034-ae57-ec389f339277"
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+ "relatedAreas": []
},
{
"name": "Area Id1 (Insula)",
@@ -4404,7 +5070,14 @@
-4688027
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "c22055c1-514f-4096-906b-abf57286053b"
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+ "relatedAreas": []
},
{
"name": "Area Id3 (Insula)",
@@ -4453,7 +5126,14 @@
-9042586
]
}
- ]
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+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "3dcfcfc2-035c-4785-a820-a671f2104ac3"
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+ },
+ "relatedAreas": []
},
{
"name": "Area Id5 (Insula)",
@@ -4502,7 +5182,14 @@
607357
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e03cd3c6-d0be-481c-b906-9b39c1d0b641"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id6 (Insula)",
@@ -4551,7 +5238,14 @@
3041624
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "31bbe92d-e5e8-4cf4-be5d-e6b12c71a107"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area Id4 (Insula)",
@@ -4600,7 +5294,14 @@
10858017
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f480ed72-5ca5-4d1f-8905-cbe9bedcfaee"
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+ "relatedAreas": []
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]
}
@@ -4667,7 +5368,14 @@
-16067930
]
}
- ]
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+ "fullId": {
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+ "kgId": "278fc30f-2e24-4046-856b-95dfaf561635"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area STS1 (STS)",
@@ -4716,7 +5424,14 @@
-5712544
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "68784b66-ff15-4b09-b28a-a2146c0f8907"
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}
]
},
@@ -4774,7 +5489,14 @@
-1027621
]
}
- ]
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+ "fullId": {
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]
},
@@ -4832,7 +5554,14 @@
52747
]
}
- ]
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+ "fullId": {
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+ "kgId": "677cd48c-70fa-4bbd-9f0a-ffdc7744bc0f"
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+ "relatedAreas": []
},
{
"name": "Area TE 1.1 (HESCHL)",
@@ -4881,7 +5610,14 @@
10308962
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e2969911-77eb-4b21-af70-216cab5285b1"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area TE 1.0 (HESCHL)",
@@ -4891,7 +5627,15 @@
"doi": "https://doi.org/10.25493/MV3G-RET",
"synonyms": [],
"relatedAreas": [
- "Area Te1"
+ {
+ "name": "Area Te1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "f424643e-9baf-4c50-9417-db1ac33dcd3e"
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],
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@@ -4933,7 +5677,13 @@
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]
}
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+ "kgId": "13e21153-2ba8-4212-b172-8894f1012225"
+ }
+ }
}
]
},
@@ -4952,7 +5702,15 @@
"doi": "https://doi.org/10.25493/F2JH-KVV",
"synonyms": [],
"relatedAreas": [
- "Area FG2"
+ {
+ "name": "Area FG2",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8f436328-4251-4706-ae38-767e1ab21c6f"
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],
"rgb": [
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@@ -4994,7 +5752,13 @@
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]
}
- ]
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+ "fullId": {
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+ "kgId": "6e7a0441-4baa-4355-921b-50d23d07d50f"
+ }
+ }
},
{
"name": "Area FG3 (FusG)",
@@ -5043,7 +5807,14 @@
-15533822
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "023f8ef7-c266-4c45-8bf2-4a17dc52985b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area FG1 (FusG)",
@@ -5094,8 +5865,22 @@
}
],
"relatedAreas": [
- "Area FG1"
- ]
+ {
+ "name": "Area FG1",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "6318e160-4ad2-4eec-8a2e-2df6fe07d8f4"
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+ "fullId": {
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+ }
+ }
},
{
"name": "Area FG4 (FusG)",
@@ -5105,7 +5890,15 @@
"doi": "https://doi.org/10.25493/13RG-FYV",
"synonyms": [],
"relatedAreas": [
- "Area FG2"
+ {
+ "name": "Area FG2",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8f436328-4251-4706-ae38-767e1ab21c6f"
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],
"rgb": [
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@@ -5147,7 +5940,13 @@
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]
}
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}
]
}
@@ -5214,7 +6013,14 @@
12002406
]
}
- ]
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+ "fullId": {
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+ "kgId": "e6507a3d-f2f8-4c17-84ff-0e7297e836a0"
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+ },
+ "relatedAreas": []
},
{
"name": "Area 25 (sACC)",
@@ -5263,7 +6069,14 @@
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]
}
- ]
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+ "fullId": {
+ "kg": {
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+ "kgId": "9010ef76-accd-4308-9951-f37b6a10f42b"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p24ab (pACC)",
@@ -5312,7 +6125,14 @@
7809963
]
}
- ]
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+ "fullId": {
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+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "5dbb1035-487c-4f43-b551-ccadcf058340"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area s32 (sACC)",
@@ -5361,7 +6181,14 @@
-12141905
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "61b44255-ae3a-4a23-b1bc-7d303a48dbd3"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area 33 (ACC)",
@@ -5410,7 +6237,14 @@
16125051
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b83a3330-b80e-42a0-b8d2-82f38784aa1d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Area p32 (pACC)",
@@ -5459,7 +6293,14 @@
12436058
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b09aaa77-f41b-4008-b8b9-f984b0417cf3"
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+ },
+ "relatedAreas": []
},
{
"name": "Area s24 (sACC)",
@@ -5508,7 +6349,14 @@
-9257019
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "d4ea6cc5-1e1d-4212-966f-81fed01eb648"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5566,7 +6414,14 @@
-17871795
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "9ec4a423-70fa-43cd-90b3-fbc26a3cbc6c"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Entorhinal Cortex",
@@ -5615,15 +6470,30 @@
-32577556
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "030827d4-e0d1-4406-b71f-3f58dc2f9cca"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "CA (Hippocampus)",
"arealabel": "CA",
"status": "publicP",
"labelIndex": null,
- "relatedAreas":[
- "CA1 (Hippocampus)"
+ "relatedAreas": [
+ {
+ "name": "CA1 (Hippocampus)",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "bfc0beb7-310c-4c57-b810-2adc464bd02c"
+ }
+ }
+ }
],
"doi": "https://doi.org/10.25493/B85T-D88",
"synonyms": [],
@@ -5667,7 +6537,13 @@
-11142814
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a0d14d3e-bc30-41cf-8b28-540067897f80"
+ }
+ }
},
{
"name": "DG (Hippocampus)",
@@ -5716,7 +6592,14 @@
-10596203
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "0bea7e03-bfb2-4907-9d45-db9071ce627d"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Subiculum (Hippocampus)",
@@ -5765,7 +6648,14 @@
-15923499
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e2dab4c-a140-440d-a322-c1679adef2d4"
+ }
+ },
+ "relatedAreas": []
}
]
}
@@ -5850,7 +6740,14 @@
-31489418
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -5908,7 +6805,14 @@
-36586280
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "58095aef-da69-43d4-887c-009c095cecce"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "Ventral Dentate Nucleus (Cerebellum)",
@@ -5957,7 +6861,14 @@
-31385609
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "57282342-5a75-4e07-bcdc-2d368c517b71"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -6015,7 +6926,14 @@
-29040632
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "e8abfe3d-8b64-45c2-8853-314d82873273"
+ }
+ },
+ "relatedAreas": []
}
]
},
@@ -6073,7 +6991,14 @@
-31489418
]
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "85e7bb13-4b73-4f6f-8222-3adb7b800788"
+ }
+ },
+ "relatedAreas": []
}
]
}
diff --git a/src/res/ext/waxholmRatV2_0.json b/src/res/ext/waxholmRatV2_0.json
index 58c045cb923f560434ec224ee815a2bd800e22d9..6b0c9fd80c19f7692d1473dfc4819d08b159a7f1 100644
--- a/src/res/ext/waxholmRatV2_0.json
+++ b/src/res/ext/waxholmRatV2_0.json
@@ -4,7 +4,7 @@
"species": "Rat",
"useTheme": "dark",
"ngId": "template",
- "otherNgIds":[
+ "otherNgIds": [
"templateUnMasked"
],
"nehubaConfigURL": "nehubaConfig/waxholmRatV2_0NehubaConfig",
@@ -13,1545 +13,1576 @@
"ngId": "v3",
"type": "parcellation",
"name": "Waxholm Space rat brain atlas v3",
- "originDatasets":[{
- "kgSchema": "minds/core/dataset/v1.0.0",
- "kgId": "e80f9946-1aa9-494b-b81a-9048ca9afdbe"
- }],
- "regions": [{
- "ngId": "v3",
- "name": "Whole brain",
- "labelIndex": null,
- "rgb": null,
- "children":[
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "White matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 67,
- "name": "corpus callosum and associated subcortical white matter",
- "rgb": [
- 255,
- 110,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Anterior commissure",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 36,
- "name": "anterior commissure, anterior part",
- "rgb": [
- 124,
- 252,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 37,
- "name": "anterior commissure, posterior part",
- "rgb": [
- 255,
- 186,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 73,
- "name": "anterior commissure",
- "rgb": [
- 255,
- 79,
- 206
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Hippocampal white matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 6,
- "name": "alveus of the hippocampus",
- "rgb": [
- 255,
- 0,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 38,
- "name": "ventral hippocampal commissure",
- "rgb": [
- 174,
- 0,
- 232
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 52,
- "name": "fornix",
- "rgb": [
- 21,
- 192,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 59,
- "name": "fimbria of the hippocampus",
- "rgb": [
- 0,
- 255,
- 29
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Corticofugal pathways",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 1,
- "name": "descending corticofugal pathways",
- "rgb": [
- 255,
- 52,
- 39
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 85,
- "name": "pyramidal decussation",
- "rgb": [
- 114,
- 9,
- 212
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Medial lemniscus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 34,
- "name": "medial lemniscus",
- "rgb": [
- 212,
- 255,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 84,
- "name": "medial lemniscus decussation",
- "rgb": [
- 65,
- 150,
- 255
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Thalamic tracts",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 53,
- "name": "mammillothalamic tract",
- "rgb": [
- 238,
- 186,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 54,
- "name": "commissural stria terminalis",
- "rgb": [
- 173,
- 255,
- 47
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 60,
- "name": "fasciculus retroflexus",
- "rgb": [
- 244,
- 67,
- 69
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 61,
- "name": "stria medullaris of the thalamus",
- "rgb": [
- 0,
- 255,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 62,
- "name": "stria terminalis",
- "rgb": [
- 238,
- 117,
- 51
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 80,
- "name": "habenular commissure",
- "rgb": [
- 69,
- 235,
- 202
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 63,
- "name": "posterior commissure",
- "rgb": [
- 255,
- 0,
- 218
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Facial nerve",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 35,
- "name": "facial nerve",
- "rgb": [
- 255,
- 25,
- 240
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 72,
- "name": "ascending fibers of the facial nerve",
- "rgb": [
- 179,
- 28,
- 53
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 57,
- "name": "genu of the facial nerve",
- "rgb": [
- 250,
- 244,
- 247
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Optic fiber system and supraoptic decussation",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 41,
- "name": "optic nerve",
- "rgb": [
- 48,
- 218,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 42,
- "name": "optic tract and optic chiasm",
- "rgb": [
- 38,
- 126,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 83,
- "name": "supraoptic decussation",
- "rgb": [
- 250,
- 170,
- 64
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 76,
- "name": "spinal trigeminal tract",
- "rgb": [
- 250,
- 128,
- 114
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "White matter of the tectum",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 46,
- "name": "commissure of the superior colliculus",
- "rgb": [
- 33,
- 230,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 68,
- "name": "brachium of the superior colliculus",
- "rgb": [
- 188,
- 32,
- 173
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 69,
- "name": "inferior colliculus, commissure",
- "rgb": [
- 255,
- 42,
- 39
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 146,
- "name": "inferior colliculus, brachium",
- "rgb": [
- 176,
- 58,
- 72
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Cerebellar and precerebellar white matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 7,
- "name": "inferior cerebellar peduncle",
- "rgb": [
- 52,
- 255,
- 13
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 78,
- "name": "middle cerebellar peduncle",
- "rgb": [
- 134,
- 204,
- 76
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 79,
- "name": "transverse fibers of the pons",
- "rgb": [
- 128,
- 170,
- 255
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "White matter of the brainstem",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Lateral lemniscus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 140,
- "name": "lateral lemniscus, commissure",
- "rgb": [
- 255,
- 29,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 141,
- "name": "lateral lemniscus",
- "rgb": [
- 255,
- 166,
- 0
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 129,
- "name": "acoustic striae",
- "rgb": [
- 255,
- 217,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 130,
- "name": "trapezoid body",
- "rgb": [
- 213,
- 255,
- 0
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 157,
- "name": "auditory radiation",
- "rgb": [
- 244,
- 156,
- 255
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Gray matter",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Olfactory system",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 64,
- "name": "glomerular layer of the accessory olfactory bulb",
- "rgb": [
- 15,
- 109,
- 230
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 65,
- "name": "glomerular layer of the olfactory bulb",
- "rgb": [
- 255,
- 227,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 66,
- "name": "olfactory bulb",
- "rgb": [
- 255,
- 135,
- 0
- ],
- "children": []
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Cerebral cortex including the neocortex and the hippocampus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Neocortex",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 77,
- "name": "frontal association cortex",
- "rgb": [
- 206,
- 211,
- 7
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 92,
- "name": "neocortex",
- "rgb": [
- 3,
- 193,
- 45
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 10,
- "name": "cingulate cortex, area 2",
- "rgb": [
- 29,
- 104,
- 235
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 108,
- "name": "postrhinal cortex",
- "rgb": [
- 40,
- 112,
- 130
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 109,
- "name": "presubiculum",
- "rgb": [
- 80,
- 123,
- 175
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 110,
- "name": "parasubiculum",
- "rgb": [
- 23,
- 54,
- 96
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 112,
- "name": "perirhinal area 35",
- "rgb": [
- 205,
- 51,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 113,
- "name": "perirhinal area 36",
- "rgb": [
- 112,
- 48,
- 160
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 114,
- "name": "entorhinal cortex",
- "rgb": [
- 122,
- 187,
- 51
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 115,
- "name": "lateral entorhinal cortex",
- "rgb": [
- 90,
- 111,
- 47
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Auditory cortex",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 151,
- "name": "primary auditory cortex",
- "rgb": [
- 255,
- 215,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 152,
- "name": "secondary auditory cortex, dorsal area",
- "rgb": [
- 240,
- 255,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 153,
- "name": "secondary auditory cortex, ventral area",
- "rgb": [
- 216,
- 191,
- 216
- ],
- "children": []
- }
- ]
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Allocortex",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 95,
- "name": "cornu ammonis 3",
- "rgb": [
- 165,
- 131,
- 107
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 96,
- "name": "dentate gyrus",
- "rgb": [
- 91,
- 45,
- 10
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 97,
- "name": "cornu ammonis 2",
- "rgb": [
- 255,
- 255,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 98,
- "name": "cornu ammonis 1",
- "rgb": [
- 217,
- 104,
- 13
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 99,
- "name": "fasciola cinereum",
- "rgb": [
- 255,
- 0,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 100,
- "name": "subiculum",
- "rgb": [
- 255,
- 192,
- 0
- ],
- "children": []
- }
- ]
- }
- ]
- },
- {
- "ngId": "v3",
- "labelIndex": 30,
- "name": "striatum",
- "rgb": [
- 129,
- 79,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 31,
- "name": "globus pallidus",
- "rgb": [
- 255,
- 145,
- 186
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 32,
- "name": "entopeduncular nucleus",
- "rgb": [
- 26,
- 231,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 3,
- "name": "subthalamic nucleus",
- "rgb": [
- 0,
- 0,
- 255
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 82,
- "name": "basal forebrain region",
- "rgb": [
- 225,
- 240,
- 13
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 40,
- "name": "septal region",
- "rgb": [
- 255,
- 8,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": null,
- "name": "Thalamus",
- "children": [
- {
- "ngId": "v3",
- "labelIndex": 39,
- "name": "thalamus",
- "rgb": [
- 0,
- 100,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 147,
- "name": "medial geniculate body, medial division",
- "rgb": [
- 10,
- 244,
- 217
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 148,
- "name": "medial geniculate body, dorsal division",
- "rgb": [
- 239,
- 163,
- 0
- ],
- "children": []
- },
- {
- "ngId": "v3",
- "labelIndex": 149,
- "name": "medial geniculate body, ventral division",
- "rgb": [
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"name": "Whole brain",
"labelIndex": null,
"rgb": null,
- "children":[
-
+ "children": [
{
"name": "White matter",
"labelIndex": null,
@@ -4718,7 +4767,14 @@
},
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "a844d80f-1d94-41a0-901a-14ae257519db"
+ }
+ },
+ "relatedAreas": []
},
{
"name": "inferior olive",
@@ -4885,33 +4941,47 @@
},
"children": []
}
- ]
+ ],
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "b2b56201-472c-4f70-842f-cf2133eacaba"
+ }
+ },
+ "relatedAreas": []
}
],
"properties": {
"name": "Waxholm Space rat brain atlas v1",
"description": "Waxholm Space atlas of the Sprague Dawley rat brain, first iteration with major brain regions delineated (76 structures).",
- "publications": [{
- "cite": "https://www.nitrc.org/frs/?group_id=1081",
- "doi": "https://www.nitrc.org/frs/?group_id=1081"
- },{
- "doi": "10.1016/j.neuroimage.2014.04.001",
- "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
- }]
+ "publications": [
+ {
+ "cite": "https://www.nitrc.org/frs/?group_id=1081",
+ "doi": "https://www.nitrc.org/frs/?group_id=1081"
+ },
+ {
+ "doi": "10.1016/j.neuroimage.2014.04.001",
+ "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
+ }
+ ]
}
}
],
"properties": {
"name": "Waxholm Space rat brain MRI/DTI",
"description": "MRI/DTI template of adult male Sprague Dawley rat brain.",
- "publications": [{
- "doi": "10.1016/j.neuroimage.2014.04.001",
- "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
- },{
- "cite": "RRID: SCR_017124"
- },{
- "doi": "https://www.nitrc.org/projects/whs-sd-atlas",
- "cite": "https://www.nitrc.org/projects/whs-sd-atlas"
- }]
+ "publications": [
+ {
+ "doi": "10.1016/j.neuroimage.2014.04.001",
+ "cite": "Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386"
+ },
+ {
+ "cite": "RRID: SCR_017124"
+ },
+ {
+ "doi": "https://www.nitrc.org/projects/whs-sd-atlas",
+ "cite": "https://www.nitrc.org/projects/whs-sd-atlas"
+ }
+ ]
}
}
\ No newline at end of file
diff --git a/src/services/effect/effect.ts b/src/services/effect/effect.ts
index 043ff4c116bd86a34155c4048e35d61c8c9b4400..a1ade573150dc87aa589e1d5a7d867cc0060be69 100644
--- a/src/services/effect/effect.ts
+++ b/src/services/effect/effect.ts
@@ -1,12 +1,11 @@
import { Injectable, OnDestroy } from "@angular/core";
import { Actions, Effect, ofType } from "@ngrx/effects";
import { select, Store } from "@ngrx/store";
-import { fromEvent, merge, Observable, Subscription } from "rxjs";
+import { merge, Observable, Subscription } from "rxjs";
import { filter, map, shareReplay, switchMap, take, withLatestFrom } from "rxjs/operators";
-import { worker } from 'src/atlasViewer/atlasViewer.workerService.service'
import { LoggingService } from "../logging.service";
-import { ADD_TO_REGIONS_SELECTION_WITH_IDS, DESELECT_REGIONS, NEWVIEWER, SELECT_PARCELLATION, SELECT_REGIONS, SELECT_REGIONS_WITH_ID, UPDATE_PARCELLATION } from "../state/viewerState.store";
-import { generateLabelIndexId, getNgIdLabelIndexFromId, IavRootStoreInterface, recursiveFindRegionWithLabelIndexId } from '../stateStore.service';
+import { ADD_TO_REGIONS_SELECTION_WITH_IDS, DESELECT_REGIONS, NEWVIEWER, SELECT_PARCELLATION, SELECT_REGIONS, SELECT_REGIONS_WITH_ID } from "../state/viewerState.store";
+import { generateLabelIndexId, getNgIdLabelIndexFromId, IavRootStoreInterface, recursiveFindRegionWithLabelIndexId, getMultiNgIdsRegionsLabelIndexMap, GENERAL_ACTION_TYPES } from '../stateStore.service';
@Injectable({
providedIn: 'root',
@@ -18,15 +17,6 @@ export class UseEffects implements OnDestroy {
private store$: Store<IavRootStoreInterface>,
private log: LoggingService,
) {
- this.subscriptions.push(
- this.newParcellationSelected$.subscribe(parcellation => {
- worker.postMessage({
- type: `PROPAGATE_NG_ID`,
- parcellation,
- })
- }),
- )
-
this.regionsSelected$ = this.store$.pipe(
select('viewerState'),
select('regionsSelected'),
@@ -105,11 +95,24 @@ export class UseEffects implements OnDestroy {
ofType(NEWVIEWER),
)
+ // trigger for rebuilding the parcellation
private newParcellationSelected$ = merge(
- this.newViewer$,
- this.parcellationSelected$,
+ this.actions$.pipe(
+ ofType(NEWVIEWER)
+ ),
+ this.actions$.pipe(
+ ofType(SELECT_PARCELLATION)
+ ),
+ this.actions$.pipe(
+ ofType(GENERAL_ACTION_TYPES.APPLY_STATE)
+ )
).pipe(
- map(({selectParcellation}) => selectParcellation),
+ withLatestFrom(this.store$.pipe(
+ select('viewerState'),
+ select('parcellationSelected')
+ )),
+ map(([_, parcellation]) => parcellation),
+ filter(v => !!v)
)
private updatedParcellation$ = this.store$.pipe(
@@ -198,35 +201,12 @@ export class UseEffects implements OnDestroy {
* side effect of selecting a parcellation means deselecting all regions
*/
@Effect()
- public onParcellationSelected$ = this.newParcellationSelected$.pipe(
+ public onParcellationSelected$ = this.parcellationSelected$.pipe(
map(() => ({
type: SELECT_REGIONS,
selectRegions: [],
})),
)
-
- /**
- * calculating propagating ngId from worker thread
- */
- @Effect()
- public updateParcellation$ = fromEvent(worker, 'message').pipe(
- filter((message: MessageEvent) => message && message.data && message.data.type === 'UPDATE_PARCELLATION_REGIONS'),
- map(({data}) => data.parcellation),
- withLatestFrom(this.newParcellationSelected$),
- filter(([ propagatedP, selectedP ]: [any, any]) => {
- /**
- * TODO
- * use id
- * but jubrain may have same id for different template spaces
- */
- return propagatedP.name === selectedP.name
- }),
- map(([ propagatedP, _ ]) => propagatedP),
- map(parcellation => ({
- type: UPDATE_PARCELLATION,
- updatedParcellation: parcellation,
- })),
- )
}
export const getGetRegionFromLabelIndexId = ({ parcellation }) => {
diff --git a/src/services/state/uiState.store.ts b/src/services/state/uiState.store.ts
index 595df963cc01870bd831a4f9abed7137184e9f99..18c29e926e90b85da53013c154f6c0ff4373f38a 100644
--- a/src/services/state/uiState.store.ts
+++ b/src/services/state/uiState.store.ts
@@ -23,6 +23,9 @@ export const defaultState: StateInterface = {
bottomSheetTemplate: null,
+ pluginRegionSelectionEnabled: false,
+ persistentStateNotifierTemplate: null,
+
/**
* replace with server side logic (?)
*/
@@ -105,6 +108,22 @@ export const getStateStore = ({ state = defaultState } = {}) => (prevState: Stat
...prevState,
sidePanelCurrentViewContent: 'Dataset',
}
+
+ case ENABLE_PLUGIN_REGION_SELECTION: {
+ return {
+ ...prevState,
+ pluginRegionSelectionEnabled: true,
+ persistentStateNotifierTemplate: action.payload
+ }
+ }
+ case DISABLE_PLUGIN_REGION_SELECTION: {
+ return {
+ ...prevState,
+ pluginRegionSelectionEnabled: false,
+ persistentStateNotifierTemplate: null
+ }
+ }
+
case AGREE_COOKIE: {
/**
* TODO replace with server side logic
@@ -168,6 +187,9 @@ export interface StateInterface {
snackbarMessage: symbol
+ pluginRegionSelectionEnabled: boolean
+ persistentStateNotifierTemplate: TemplateRef<any>
+
agreedCookies: boolean
agreedKgTos: boolean
@@ -243,6 +265,9 @@ export const HIDE_SIDE_PANEL_CONNECTIVITY = `HIDE_SIDE_PANEL_CONNECTIVITY`
export const COLLAPSE_SIDE_PANEL_CURRENT_VIEW = `COLLAPSE_SIDE_PANEL_CURRENT_VIEW`
export const EXPAND_SIDE_PANEL_CURRENT_VIEW = `EXPAND_SIDE_PANEL_CURRENT_VIEW`
+export const ENABLE_PLUGIN_REGION_SELECTION = `ENABLE_PLUGIN_REGION_SELECTION`
+export const DISABLE_PLUGIN_REGION_SELECTION = `DISABLE_PLUGIN_REGION_SELECTION`
+
export const AGREE_COOKIE = `AGREE_COOKIE`
export const AGREE_KG_TOS = `AGREE_KG_TOS`
export const SHOW_KG_TOS = `SHOW_KG_TOS`
diff --git a/src/services/state/viewerState.store.ts b/src/services/state/viewerState.store.ts
index fabc68c7a468842409150579b527c2af9a7a0972..4310e2185d1af89421ee4711e0cc3ba847a79fbe 100644
--- a/src/services/state/viewerState.store.ts
+++ b/src/services/state/viewerState.store.ts
@@ -88,15 +88,10 @@ export const getStateStore = ({ state = defaultState } = {}) => (prevState: Part
case NEWVIEWER: {
const { selectParcellation: parcellation } = action
- // const parcellation = propagateNgId( selectParcellation ): parcellation
- const { regions, ...parcellationWORegions } = parcellation
return {
...prevState,
templateSelected : action.selectTemplate,
- parcellationSelected : {
- ...parcellationWORegions,
- regions: null,
- },
+ parcellationSelected : parcellation,
// taken care of by effect.ts
// regionsSelected : [],
landmarksSelected : [],
@@ -117,25 +112,14 @@ export const getStateStore = ({ state = defaultState } = {}) => (prevState: Part
}
}
case SELECT_PARCELLATION : {
- const { selectParcellation: sParcellation } = action
- const { regions, ...sParcellationWORegions } = sParcellation
+ const { selectParcellation } = action
return {
...prevState,
- parcellationSelected: sParcellationWORegions,
+ parcellationSelected: selectParcellation,
// taken care of by effect.ts
// regionsSelected: []
}
}
- case UPDATE_PARCELLATION: {
- const { updatedParcellation } = action
- return {
- ...prevState,
- parcellationSelected: {
- ...updatedParcellation,
- updated: true,
- },
- }
- }
case SELECT_REGIONS: {
const { selectRegions } = action
return {
@@ -225,7 +209,6 @@ export const FETCHED_TEMPLATE = 'FETCHED_TEMPLATE'
export const CHANGE_NAVIGATION = 'CHANGE_NAVIGATION'
export const SELECT_PARCELLATION = `SELECT_PARCELLATION`
-export const UPDATE_PARCELLATION = `UPDATE_PARCELLATION`
export const DESELECT_REGIONS = `DESELECT_REGIONS`
export const SELECT_REGIONS = `SELECT_REGIONS`
diff --git a/src/services/stateStore.service.ts b/src/services/stateStore.service.ts
index dadde7dc67e49a1d0d041f611a953aa825f432cc..45aee75b421a35e660d3060cdd5082ec3150afae 100644
--- a/src/services/stateStore.service.ts
+++ b/src/services/stateStore.service.ts
@@ -52,7 +52,7 @@ export { userConfigState, USER_CONFIG_ACTION_TYPES}
export { ADD_NG_LAYER, FORCE_SHOW_SEGMENT, HIDE_NG_LAYER, REMOVE_NG_LAYER, SHOW_NG_LAYER } from './state/ngViewerState.store'
export { CHANGE_NAVIGATION, DESELECT_LANDMARKS, FETCHED_TEMPLATE, NEWVIEWER, SELECT_LANDMARKS, SELECT_PARCELLATION, SELECT_REGIONS, USER_LANDMARKS } from './state/viewerState.store'
export { IDataEntry, IParcellationRegion, FETCHED_DATAENTRIES, FETCHED_SPATIAL_DATA, ILandmark, IOtherLandmarkGeometry, IPlaneLandmarkGeometry, IPointLandmarkGeometry, IProperty, IPublication, IReferenceSpace, IFile, IFileSupplementData } from './state/dataStore.store'
-export { CLOSE_SIDE_PANEL, MOUSE_OVER_LANDMARK, MOUSE_OVER_SEGMENT, OPEN_SIDE_PANEL, SHOW_SIDE_PANEL_CONNECTIVITY, HIDE_SIDE_PANEL_CONNECTIVITY, COLLAPSE_SIDE_PANEL_CURRENT_VIEW, EXPAND_SIDE_PANEL_CURRENT_VIEW } from './state/uiState.store'
+export { CLOSE_SIDE_PANEL, MOUSE_OVER_LANDMARK, MOUSE_OVER_SEGMENT, OPEN_SIDE_PANEL, SHOW_SIDE_PANEL_CONNECTIVITY, HIDE_SIDE_PANEL_CONNECTIVITY, COLLAPSE_SIDE_PANEL_CURRENT_VIEW, EXPAND_SIDE_PANEL_CURRENT_VIEW, ENABLE_PLUGIN_REGION_SELECTION, DISABLE_PLUGIN_REGION_SELECTION } from './state/uiState.store'
export { UserConfigStateUseEffect } from './state/userConfigState.store'
export const GENERAL_ACTION_TYPES = {
@@ -216,8 +216,3 @@ export const defaultRootState: IavRootStoreInterface = {
viewerConfigState: viewerConfigDefaultState,
viewerState: viewerDefaultState,
}
-
-// export const getInitialState = (): IavRootStoreInterface => {
-// const search = new URLSearchParams( window.location.search )
-// cvtSearchParamToState(search, defaultRootState)
-// }
diff --git a/src/ui/connectivityBrowser/connectivityBrowser.component.ts b/src/ui/connectivityBrowser/connectivityBrowser.component.ts
index 1e9f33a59b14938be3918b1b62db642ee5609d22..8d3ad0fd8df80eae0373600c9176766cd6f0a384 100644
--- a/src/ui/connectivityBrowser/connectivityBrowser.component.ts
+++ b/src/ui/connectivityBrowser/connectivityBrowser.component.ts
@@ -1,4 +1,6 @@
import {
+ AfterContentChecked,
+ AfterContentInit, AfterViewChecked,
AfterViewInit, ChangeDetectorRef,
Component,
ElementRef,
@@ -8,28 +10,30 @@ import {
import {select, Store} from "@ngrx/store";
import {fromEvent, Observable, Subscription} from "rxjs";
import {distinctUntilChanged, filter, map} from "rxjs/operators";
-import {AtlasViewerConstantsServices} from "src/atlasViewer/atlasViewer.constantService.service";
import {CLEAR_CONNECTIVITY_REGION, SET_CONNECTIVITY_REGION} from "src/services/state/viewerState.store";
import {HIDE_SIDE_PANEL_CONNECTIVITY, isDefined, safeFilter} from "src/services/stateStore.service";
+import {VIEWERSTATE_CONTROLLER_ACTION_TYPES} from "src/ui/viewerStateController/viewerState.base";
@Component({
selector: 'connectivity-browser',
templateUrl: './connectivityBrowser.template.html',
})
-export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
+export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy, AfterContentChecked {
public region: string
+ public datasetList: any[] = []
+ public selectedDataset: any
private connectedAreas = []
+ public componentHeight: any
private connectivityRegion$: Observable<any>
private selectedParcellation$: Observable<any>
+ public selectedRegions$: Observable<any[]>
+
private subscriptions: Subscription[] = []
public expandMenuIndex = -1
public allRegions = []
public defaultColorMap: Map<string, Map<number, {red: number, green: number, blue: number}>>
- public parcellationHasConnectivityData = true
- private areaHemisphere: string
-
public math = Math
@ViewChild('connectivityComponent', {read: ElementRef}) public connectivityComponentElement: ElementRef
@@ -51,13 +55,22 @@ export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
map(state => state.connectivityRegion),
)
+ this.selectedRegions$ = this.store$.pipe(
+ select('viewerState'),
+ filter(state => isDefined(state) && isDefined(state.regionsSelected)),
+ map(state => state.regionsSelected),
+ distinctUntilChanged(),
+ )
+ }
+
+ public ngAfterContentChecked(): void {
+ this.componentHeight = this.connectivityComponentElement.nativeElement.clientHeight
}
public ngAfterViewInit(): void {
this.subscriptions.push(
this.selectedParcellation$.subscribe(parcellation => {
if (parcellation && parcellation.hasAdditionalViewMode && parcellation.hasAdditionalViewMode.includes('connectivity')) {
- this.parcellationHasConnectivityData = true
if (parcellation.regions && parcellation.regions.length) {
this.allRegions = []
this.getAllRegionsFromParcellation(parcellation.regions)
@@ -66,12 +79,11 @@ export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
}
}
} else {
- this.parcellationHasConnectivityData = false
+ this.closeConnectivityView()
}
}),
this.connectivityRegion$.subscribe(cr => {
this.region = cr
- this.areaHemisphere = cr.includes('left hemisphere') ? ' - left hemisphere' : ' - right hemisphere'
this.changeDetectionRef.detectChanges()
}),
)
@@ -86,12 +98,21 @@ export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
.subscribe((e: CustomEvent) => {
this.expandMenuIndex = e.detail
}),
+ fromEvent(this.connectivityComponentElement.nativeElement, 'datasetDataReceived', { capture: true })
+ .subscribe((e: CustomEvent) => {
+ this.datasetList = e.detail
+ this.selectedDataset = this.datasetList[0]
+ }),
)
}
+ // ToDo Affect on component
+ changeDataset(event) {
+ this.selectedDataset = event.value
+ }
+
public ngOnDestroy(): void {
- this.setDefaultMap()
this.subscriptions.forEach(s => s.unsubscribe())
}
@@ -102,9 +123,18 @@ export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
})
}
- public closeConnectivityView() {
- this.setDefaultMap()
+ navigateToRegion(region) {
+ this.store$.dispatch({
+ type: VIEWERSTATE_CONTROLLER_ACTION_TYPES.NAVIGATETO_REGION,
+ payload: { region: this.getRegionWithName(region) },
+ })
+ }
+ getRegionWithName(region) {
+ return this.allRegions.find(ar => ar.name === region)
+ }
+
+ public closeConnectivityView() {
this.store$.dispatch({
type: HIDE_SIDE_PANEL_CONNECTIVITY,
})
@@ -127,11 +157,9 @@ export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
this.defaultColorMap = new Map(getWindow().interactiveViewer.viewerHandle.getLayersSegmentColourMap())
const existingMap: Map<string, Map<number, {red: number, green: number, blue: number}>> = (getWindow().interactiveViewer.viewerHandle.getLayersSegmentColourMap())
-
const colorMap = new Map(existingMap)
this.allRegions.forEach(r => {
-
if (r.ngId) {
colorMap.get(r.ngId).set(r.labelIndex, {red: 255, green: 255, blue: 255})
}
@@ -139,7 +167,7 @@ export class ConnectivityBrowserComponent implements AfterViewInit, OnDestroy {
this.connectedAreas.forEach(area => {
const areaAsRegion = this.allRegions
- .filter(r => r.name === area.name + this.areaHemisphere)
+ .filter(r => r.name === area.name)
.map(r => r)
if (areaAsRegion && areaAsRegion.length && areaAsRegion[0].ngId) {
diff --git a/src/ui/connectivityBrowser/connectivityBrowser.template.html b/src/ui/connectivityBrowser/connectivityBrowser.template.html
index cbde664d53a0824ca2dcc029559d12c9f7f5854e..61ef3010b3a960b6d8677d1ffceaffa40bd85ea3 100644
--- a/src/ui/connectivityBrowser/connectivityBrowser.template.html
+++ b/src/ui/connectivityBrowser/connectivityBrowser.template.html
@@ -1,77 +1,101 @@
-<div class="w-100 h-100 overflow-auto d-block d-flex flex-column pb-2" #connectivityComponent *ngIf="parcellationHasConnectivityData; else noConnectivity">
- <!--ToDo set show-description="true" when data will available-->
+<div class="w-100 h-100 d-block d-flex flex-column pb-2" #connectivityComponent>
<hbp-connectivity-matrix-row
[region]="region"
theme="dark"
loadurl="https://connectivityquery-connectivity.apps-dev.hbp.eu/connectivity"
+ dataset-url="https://connectivityquery-connectivity.apps-dev.hbp.eu/studies"
show-export="true"
show-source="true"
- show-title="true"
- show-toolbar="true">
- <div slot="header" class="w-100 d-flex justify-content-end mt-3"><span
- class="cursorPointer" (click)="closeConnectivityView()">X</span></div>
+ show-title="false"
+ show-toolbar="false"
+ show-description="false"
+ show-dataset-name="false"
+ custom-dataset-selector="true"
+ [customHeight]="componentHeight + 'px'">
+ <div slot="header" class="w-100 d-flex justify-content-between mt-3">
+ <span>Connectivity Browser</span>
+ <i (click)="closeConnectivityView(); setDefaultMap()" class="far fa-times-circle cursorPointer"></i>
+ </div>
- <div slot="connectedRegionMenu">
+ <div slot="dataset">
+ <div *ngIf="datasetList.length && selectedDataset" class=" flex-grow-0 flex-shrink-0 d-flex flex-row flex-nowrap">
+ <mat-form-field class="flex-grow-1 flex-shrink-1 w-0">
+ <mat-label>
+ Dataset
+ </mat-label>
- <div class="d-flex flex-column" *ngIf="expandMenuIndex >= 0">
- <mat-divider></mat-divider>
- <span class="mt-2 mr-2 ml-2">
- <small>Region: {{connectedAreas[expandMenuIndex].name}}</small>
- <br>
- <small>Number of Connection: {{connectedAreas[expandMenuIndex].numberOfConnections}}</small>
- <br>
- <small>Log(123) = {{math.log10(connectedAreas[expandMenuIndex].numberOfConnections)}}</small>
- </span>
- <div class="d-flex align-items-center justify-content-around">
- <small class="d-flex flex-column align-items-center w-100">
- <!--ToDo Implement function when Hemisphere information will be available -->
- <!-- *ngIf="(selectedRegions$ | async) as selectedRegions"-->
- <!-- (click)="toggleRegionWithId(region.ngId, region.labelIndex, regionIsSelected(selectedRegions, region.ngId, region.labelIndex))">-->
+ <mat-select
+ panelClass="no-max-width"
+ [value]="selectedDataset"
+ (selectionChange)="changeDataset($event)">
+ <mat-option
+ *ngFor="let dataset of datasetList"
+ [value]="dataset"
+ >
+ {{ dataset.title }}
+ </mat-option>
+ </mat-select>
+ </mat-form-field>
+ <ng-container *ngIf="selectedDataset && selectedDataset.description" >
+ <!-- show on hover component -->
+ <sleight-of-hand class="d-inline-block flex-grow-0 flex-shrink-0 pe-all">
- <button mat-icon-button class="border">
- <!-- <i class="fas fa-hand-pointer mt-n1"></i>-->
- <span class="fa-stack fa-1x ">
- <i class="fas fa-hand-pointer fa-stack-1x"></i>
- <!--ToDo Implement function when Hemisphere information will be available -->
- <!-- <i class="fas fa-slash fa-stack-1x fa-inverse"-->
- <!-- *ngIf="regionIsSelected(selectedRegions, region.ngId, region.labelIndex)"></i>-->
- </span>
- </button>
- <!-- <span [innerText]="regionIsSelected(selectedRegions, region.ngId, region.labelIndex)? 'Deselect' : 'Select'"></span>-->
- <span>Select</span>
- </small>
+ <!-- shown when off -->
+ <div sleight-of-hand-front>
+ <button
+ mat-icon-button>
+ <i class="fas fa-info"></i>
+ </button>
+ </div>
- <small class="d-flex flex-column align-items-center w-100">
- <button mat-icon-button class="border">
- <i class="fas fa-crosshairs mt-n1"></i>
- </button>
- Navigate
- </small>
+ <!-- shown on hover -->
+ <div class="d-flex flex-row align-items-start" sleight-of-hand-back>
+ <button class="flex-grow-0 flex-shrink-0" mat-icon-button>
+ <i class="fas fa-info"></i>
+ </button>
- <small class="d-flex flex-column align-items-center w-100">
- <button mat-icon-button class="border" (click)="updateConnevtivityRegion(connectedAreas[expandMenuIndex].name)">
- <i class="fab fa-connectdevelop mt-n1"></i>
- </button>
- Connectivity
- </small>
- </div>
- </div>
+ <div class="position-relative">
+ <button class="position-relative invisible pe-none" mat-icon-button>
+ <i class="fas fa-info"></i>
+ </button>
+ <mat-card class="position-absolute left-0 top-0 w-40em">
+ <single-dataset-view
+ [name]="selectedDataset.title"
+ [description]="selectedDataset.description">
+ </single-dataset-view>
+ </mat-card>
+ </div>
- </div>
- </hbp-connectivity-matrix-row>
-</div>
+ </div>
+ </sleight-of-hand>
+
+ </ng-container>
-<ng-template #noConnectivity>
- <mat-card class="p-2 w-100 h-100 overflow-auto d-block">
- <div class="w-100 d-flex justify-content-end mt-3"><span
- class="cursorPointer" (click)="closeConnectivityView()">X</span></div>
- <h5>
- Connectivity Matrix Browser
- </h5>
- <div>
- No Connectivity for selected Parcellation!
+ </div>
</div>
- </mat-card>
-</ng-template>
\ No newline at end of file
+ <div slot="connectedRegionMenu">
+ <div class="d-flex flex-column p-0 m-0" *ngIf="expandMenuIndex >= 0">
+ <mat-divider></mat-divider>
+ <mat-card-subtitle class="pt-2 pr-2 pl-2 pb-0">
+ {{connectedAreas[expandMenuIndex].name}}
+ </mat-card-subtitle>
+ <div class="d-flex align-items-center justify-content-around">
+ <button mat-button (click)="navigateToRegion(navigateToRegion(connectedAreas[expandMenuIndex].name))">
+ <i class="fas fa-map-marked-alt"></i>
+ <span>
+ Navigate
+ </span>
+ </button>
+ <button mat-button (click)="updateConnevtivityRegion(connectedAreas[expandMenuIndex].name)">
+ <i class="fab fa-connectdevelop"></i>
+ <span>
+ Connectivity
+ </span>
+ </button>
+ </div>
+ </div>
+ </div>
+ </hbp-connectivity-matrix-row>
+</div>
\ No newline at end of file
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.spec.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.spec.ts
new file mode 100644
index 0000000000000000000000000000000000000000..d0fe83f9512cfb7b595fe059b67646823e0f6012
--- /dev/null
+++ b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.spec.ts
@@ -0,0 +1,472 @@
+import { regionsEqual, FilterDataEntriesByRegion } from './filterDataEntriesByRegion.pipe'
+
+const cytoPmapHoc1 = {
+ "formats": [
+ "NIFTI"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "imaging"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [
+ {
+ "name": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2"
+ },
+ {
+ "name": "MNI Colin 27",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+ }
+ ],
+ "methods": [
+ "silver staining",
+ "magnetic resonance imaging (MRI)",
+ "probability mapping",
+ "cytoarchitectonic mapping"
+ ],
+ "custodians": [
+ "Amunts, Katrin"
+ ],
+ "project": [
+ "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
+ ],
+ "description": "This dataset contains the distinct architectonic Area hOc1 (V1, 17, CalcS) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the JuBrain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area hOc1 (V1, 17, CalcS). The probability map of Area hOc1 (V1, 17, CalcS) are provided in the NifTi format for each brain reference space and hemisphere. The JuBrain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets.",
+ "parcellationAtlas": [
+ {
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "id": [
+ "deec923ec31a82f89a9c7c76a6fefd6b",
+ "e2d45e028b6da0f6d9fdb9491a4de80a"
+ ]
+ }
+ ],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1 (V1, 17, CalcS)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/5151ab8f-d8cb-4e67-a449-afe2a41fb007"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Probabilistic cytoarchitectonic map of Area hOc1 (V1, 17, CalcS) (v2.4)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/5c669b77-c981-424a-858d-fe9f527dbc07",
+ "contributors": [
+ "Zilles, Karl",
+ "Schormann, Thorsten",
+ "Mohlberg, Hartmut",
+ "Malikovic, Aleksandar",
+ "Amunts, Katrin"
+ ],
+ "id": "5c669b77-c981-424a-858d-fe9f527dbc07",
+ "kgReference": [
+ "10.25493/MXJ6-6DH"
+ ],
+ "publications": [
+ {
+ "name": "Brodmann's Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable?",
+ "cite": "Amunts, K., Malikovic, A., Mohlberg, H., Schormann, T., & Zilles, K. (2000). Brodmann’s Areas 17 and 18 Brought into Stereotaxic Space—Where and How Variable? NeuroImage, 11(1), 66–84. ",
+ "doi": "10.1006/nimg.1999.0516"
+ }
+ ]
+} as any
+
+const receptorhoc1 = {
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area hOc1 using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area hOc1",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/b851eb9d-9502-45e9-8dd8-2861f0e6da3f"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area hOc1",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/e715e1f7-2079-45c4-a67f-f76b102acfce",
+ "contributors": [
+ "Scheperjans, Filip",
+ "Schleicher, Axel",
+ "Eickhoff, Simon B.",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "0616d1e97b8be75de526bc265d9af540",
+ "kgReference": [
+ "10.25493/P8SD-JMH"
+ ],
+ "publications": [
+ {
+ "name": "Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex",
+ "cite": "Eickhoff, S. B., Schleicher, A., Scheperjans, F., Palomero-Gallagher, N., & Zilles, K. (2007). Analysis of neurotransmitter receptor distribution patterns in the cerebral cortex. NeuroImage, 34(4), 1317–1330. ",
+ "doi": "10.1016/j.neuroimage.2006.11.016"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+} as any
+
+const receptor44d = {
+ "formats": [
+ "xlsx, tif, txt"
+ ],
+ "datasetDOI": [
+ {
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ],
+ "activity": [
+ {
+ "protocols": [
+ "brain mapping"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ },
+ {
+ "protocols": [
+ "histology"
+ ],
+ "preparation": [
+ "Ex vivo"
+ ]
+ }
+ ],
+ "referenceSpaces": [],
+ "methods": [
+ "receptor autoradiography plot",
+ "receptor density fingerprint analysis",
+ "receptor density profile analysis",
+ "autoradiography with [³H] SCH23390",
+ "autoradiography with [³H] ketanserin",
+ "autoradiography with [³H] 8-OH-DPAT",
+ "autoradiography with [³H] UK-14,304",
+ "autoradiography with [³H] epibatidine",
+ "autoradiography with [³H] 4-DAMP",
+ "autoradiography with [³H] oxotremorine-M",
+ "autoradiography with [³H] flumazenil",
+ "autoradiography with [³H] CGP 54626",
+ "autoradiography with [³H] prazosin",
+ "autoradiography with [³H] muscimol",
+ "autoradiography with [³H]LY 341 495",
+ "autoradiography with [³H] pirenzepine",
+ "autoradiography with [³H] MK-801",
+ "autoradiography with [³H] kainate",
+ "autoradiography with [³H] AMPA"
+ ],
+ "custodians": [
+ "Palomero-Gallagher, Nicola",
+ "Zilles, Karl"
+ ],
+ "project": [
+ "Quantitative Receptor data"
+ ],
+ "description": "This dataset contains the densities (in fmol/mg protein) of 16 receptors for classical neurotransmitters in Area 44d using quantitative in vitro autoradiography. The receptor density measurements can be provided in three ways: (fp) as density fingerprints (average across samples; mean density and standard deviation for each of the 16 receptors), (pr) as laminar density profiles (exemplary data from one sample; average course of the density from the pial surface to the border between layer VI and the white matter for each receptor), and (ar) as color-coded autoradiographs (exemplary data from one sample; laminar density distribution patterns for each receptor labeling). \nThis dataset contains the following receptor density measurements based on the labeling of these receptor binding sites: \n\nAMPA (glutamate; labelled with [³H]AMPA): fp, pr, ar\n\nkainate (glutamate; [³H]kainate): fp, pr, ar\n\nNMDA (glutamate; [³H]MK-801): fp, pr, ar\n\nmGluR2/3 (glutamate; [³H] LY 341 495): pr, ar\n\nGABA<sub>A</sub> (GABA; [³H]muscimol): fp, pr, ar\n\nGABA<sub>B</sub> (GABA; [³H] CGP54626): fp, pr, ar\n\nGABA<sub>A</sub> associated benzodiazepine binding sites (BZ; [³H]flumazenil): fp, pr, ar\n\nmuscarinic Mâ‚ (acetylcholine; [³H]pirenzepine): fp, pr, ar\n\nmuscarinic Mâ‚‚ (acetylcholine; [³H]oxotremorine-M): fp, pr, ar\n\nmuscarinic M₃ (acetylcholine; [³H]4-DAMP): fp, pr, ar\n\nnicotinic α₄β₂ (acetylcholine; [³H]epibatidine): fp, pr, ar\n\nα₠(noradrenalin; [³H]prazosin): fp, pr, ar\n\nα₂ (noradrenalin; [³H]UK-14,304): fp, pr, ar\n\n5-HTâ‚<sub>A</sub> (serotonin; [³H]8-OH-DPAT): fp, pr, ar\n\n5-HTâ‚‚ (serotonin; [³H]ketanserin): fp, pr, ar\n\nDâ‚ (dopamine; [³H]SCH23390): fp, pr, ar\n\nWhich sample was used for which receptor density measurement is stated in metadata files accompanying the main data repository. For methodological details, see Zilles et al. (2002), and in Palomero-Gallagher and Zilles (2018).\n\nZilles, K. et al. (2002). Quantitative analysis of cyto- and receptorarchitecture of the human brain, pp. 573-602. In: Brain Mapping: The Methods, 2nd edition (A.W. Toga and J.C. Mazziotta, eds.). San Diego, Academic Press.\n\nPalomero-Gallagher N, Zilles K. (2018) Cyto- and receptorarchitectonic mapping of the human brain. In: Handbook of Clinical Neurology 150: 355-387",
+ "parcellationAtlas": [],
+ "licenseInfo": [
+ {
+ "name": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International",
+ "url": "https://creativecommons.org/licenses/by-nc-sa/4.0/"
+ }
+ ],
+ "embargoStatus": [
+ "Free"
+ ],
+ "license": [],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area 44d",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "name": "Density measurements of different receptors for Area 44d",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/cb875c0d-97f4-4dbc-a9ce-472d8ba58c99",
+ "contributors": [
+ "Morosan, Patricia",
+ "Schleicher, Axel",
+ "Lenzen, Marianne",
+ "Friederici, Angela D.",
+ "Amunts, Katrin",
+ "Palomero-Gallagher, Nicola",
+ "Bacha-Trams, Maraike",
+ "Zilles, Karl"
+ ],
+ "id": "31397abd7aebcf13bf3b1d5eb2e2d400",
+ "kgReference": [
+ "10.25493/YQCR-1DQ"
+ ],
+ "publications": [
+ {
+ "name": "Broca's Region: Novel Organizational Principles and Multiple Receptor Mapping",
+ "cite": "Amunts, K., Lenzen, M., Friederici, A. D., Schleicher, A., Morosan, P., Palomero-Gallagher, N., & Zilles, K. (2010). Broca’s Region: Novel Organizational Principles and Multiple Receptor Mapping. PLoS Biology, 8(9), e1000489. ",
+ "doi": "10.1371/journal.pbio.1000489"
+ },
+ {
+ "name": "Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints",
+ "cite": "Zilles, K., Bacha-Trams, M., Palomero-Gallagher, N., Amunts, K., & Friederici, A. D. (2015). Common molecular basis of the sentence comprehension network revealed by neurotransmitter receptor fingerprints. Cortex, 63, 79–89. ",
+ "doi": "10.1016/j.cortex.2014.07.007"
+ }
+ ]
+} as any
+
+const mni152JuBrain = [
+ cytoPmapHoc1,
+ receptorhoc1,
+ receptor44d
+]
+
+describe('filterDataEntriesByRegion.pipe', () => {
+
+ describe('regionsEqual', () => {
+ it('should return true when fullId is equal', () => {
+ const region1 = {
+ "referenceSpaces": [
+ {
+ "name": "MNI Colin 27",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/referencespace/v1.0.0/7f39f7be-445b-47c0-9791-e971c0b6d992"
+ }
+ ],
+ "project": [
+ "JuBrain: cytoarchitectonic probabilistic maps of the human brain"
+ ],
+ "parcellationAtlas": [
+ {
+ "name": "Jülich Cytoarchitechtonic Brain Atlas (human)",
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579",
+ "id": [
+ "deec923ec31a82f89a9c7c76a6fefd6b",
+ "e2d45e028b6da0f6d9fdb9491a4de80a"
+ ]
+ }
+ ],
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "CA1 (Hippocampus)",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/bfc0beb7-310c-4c57-b810-2adc464bd02c"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/1bbe0651-f646-4366-84f1-d37dc3c39bb3",
+ "id": "ca2d24694a35504816e7aefa30754f80",
+ "kgReference": [
+ "10.25493/W4WK-QSK"
+ ],
+ "preview": false
+ }
+
+ const { parcellationRegion } = region1
+ regionsEqual(parcellationRegion[0], {})
+ })
+
+ it('should return true when there is a related area', () => {
+
+ const region1 = {
+ "parcellationRegion": [
+ {
+ "species": [],
+ "name": "Area 4p",
+ "alias": null,
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/parcellationregion/v1.0.0/861ab96a-c4b5-4ba6-bd40-1e80d4680f89"
+ }
+ ],
+ "species": [
+ "Homo sapiens"
+ ],
+ "fullId": "https://nexus.humanbrainproject.org/v0/data/minds/core/dataset/v1.0.0/b3cac84d-2146-4750-a5f1-174076f82292",
+ "id": "ef2de94a2b532b91031ecf65300283cb",
+ "kgReference": [
+ "10.25493/J5JR-YH0"
+ ],
+ "preview": true
+ }
+ })
+ })
+
+ describe('FilterDataEntriesByRegion', () => {
+ const pipe = new FilterDataEntriesByRegion()
+ it('if selectedRegions is an empty array, should return original dataentries', () => {
+ expect(
+ pipe.transform(mni152JuBrain, [], [])
+ ).toEqual(mni152JuBrain)
+ })
+
+ it('if selectedRegions include area 44, should return receptor data', () => {
+ const selectedRegions = [
+ {
+ "name": "Area 44 (IFG) - left hemisphere",
+ "rgb": [
+ 54,
+ 74,
+ 75
+ ],
+ "labelIndex": 2,
+ "ngId": "jubrain mni152 v18 left",
+ "children": [],
+ "position": [
+ -54134365,
+ 11216664,
+ 15641040
+ ],
+ "relatedAreas": [
+ {
+ "name": "Area 44v",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "7e5e7aa8-28b8-445b-8980-2a6f3fa645b3"
+ }
+ }
+ },
+ {
+ "name": "Area 44d",
+ "fullId": {
+ "kg": {
+ "kgSchema": "minds/core/parcellationregion/v1.0.0",
+ "kgId": "8aeae833-81c8-4e27-a8d6-deee339d6052"
+ }
+ }
+ }
+ ],
+ }
+ ]
+ expect(
+ pipe.transform(mni152JuBrain, selectedRegions, [])
+ ).toEqual([receptor44d])
+ })
+ })
+})
\ No newline at end of file
diff --git a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
index b666190984e62679cf2ace4b082e6c1333f5c04e..d976cba7a58f733ac321420e21af3ec9f7ea3073 100644
--- a/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
+++ b/src/ui/databrowserModule/util/filterDataEntriesByRegion.pipe.ts
@@ -1,9 +1,19 @@
import { Pipe, PipeTransform } from "@angular/core";
import { IDataEntry } from "src/services/stateStore.service";
+import { getIdFromFullId } from "common/util"
-const isSubRegion = (high, low) => (high.id && low.id && high.id === low.id) || high.name === low.name
+export const regionsEqual = (r1, r2) => {
+ const { fullId: r1FId, relatedAreas: rA1 = [] } = r1
+ const { fullId: r2FId, relatedAreas: rA2 = [] } = r2
+ const region2Aliases = new Set([getIdFromFullId(r2FId), ...rA2.map(({ fullId }) => getIdFromFullId(fullId))])
+ const region1Aliases = new Set([getIdFromFullId(r1FId), ...rA1.map(({ fullId }) => getIdFromFullId(fullId))])
+ return region1Aliases.has(getIdFromFullId(r2FId))
+ || region2Aliases.has(getIdFromFullId(r1FId))
+}
+
+const isSubRegion = (high, low) => regionsEqual(high, low)
? true
- : high.children && high.children.some
+ : high.children && Array.isArray(high.children)
? high.children.some(r => isSubRegion(r, low))
: false
@@ -18,29 +28,6 @@ export class FilterDataEntriesByRegion implements PipeTransform {
public transform(dataentries: IDataEntry[], selectedRegions: any[], flattenedAllRegions: any[]) {
return dataentries && selectedRegions && selectedRegions.length > 0
? dataentries
- .map(de => {
- /**
- * translate parcellationRegion to region representation
- */
- const newParcellationRegion = de.parcellationRegion.map(({name, id, ...rest}) => {
-
- const found = flattenedAllRegions.find(r => {
- /**
- * TODO replace pseudo id with real uuid
- */
- return (r.id && id && r.id === id)
- || r.name === name
- || r.relatedAreas && r.relatedAreas.length && r.relatedAreas.some(syn => syn === name)
- })
- return found
- ? { name, id, ...rest, ...found }
- : { name, id, ...rest }
- })
- return {
- ...de,
- parcellationRegion: newParcellationRegion,
- }
- })
.filter(de => filterSubSelect(de, selectedRegions))
: dataentries
}
diff --git a/src/ui/nehubaContainer/nehubaContainer.component.ts b/src/ui/nehubaContainer/nehubaContainer.component.ts
index 3eaf0b5e340c6346a906579b92172af259193a80..ac50c13fb5ad1a4c411caa6cae0f6d8b77b9aa95 100644
--- a/src/ui/nehubaContainer/nehubaContainer.component.ts
+++ b/src/ui/nehubaContainer/nehubaContainer.component.ts
@@ -1,6 +1,6 @@
import { Component, ComponentFactory, ComponentFactoryResolver, ComponentRef, ElementRef, Input, OnChanges, OnDestroy, OnInit, ViewChild, ViewContainerRef } from "@angular/core";
import { select, Store } from "@ngrx/store";
-import { combineLatest, fromEvent, merge, Observable, of, Subscription } from "rxjs";
+import { combineLatest, fromEvent, merge, Observable, of, Subscription, from } from "rxjs";
import { pipeFromArray } from "rxjs/internal/util/pipe";
import {
buffer,
@@ -242,8 +242,8 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
this.navigationChanges$ = this.store.pipe(
select('viewerState'),
- safeFilter('navigation'),
- map(state => state.navigation),
+ select('navigation'),
+ filter(v => !!v)
)
this.spatialResultsVisible$ = this.store.pipe(
@@ -587,10 +587,25 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
/* order of subscription will determine the order of execution */
this.subscriptions.push(
this.newViewer$.pipe(
- withLatestFrom(this.selectedParcellation$.pipe(
- startWith(null as object),
- )),
- ).subscribe(([templateSelected, parcellationSelected]) => {
+ map(templateSelected => {
+ const deepCopiedState = JSON.parse(JSON.stringify(templateSelected))
+ const navigation = deepCopiedState.nehubaConfig.dataset.initialNgState.navigation
+ if (!navigation) {
+ return deepCopiedState
+ }
+ navigation.zoomFactor = calculateSliceZoomFactor(navigation.zoomFactor)
+ deepCopiedState.nehubaConfig.dataset.initialNgState.navigation = navigation
+ return deepCopiedState
+ }),
+ withLatestFrom(
+ this.selectedParcellation$.pipe(
+ startWith(null),
+ ),
+ this.navigationChanges$.pipe(
+ startWith({})
+ )
+ ),
+ ).subscribe(([templateSelected, parcellationSelected, navigation]) => {
this.store.dispatch({
type: NEHUBA_READY,
nehubaReady: false,
@@ -598,7 +613,7 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
this.nehubaViewerSubscriptions.forEach(s => s.unsubscribe())
this.selectedTemplate = templateSelected
- this.createNewNehuba(templateSelected)
+ this.createNewNehuba(templateSelected, navigation)
const foundParcellation = parcellationSelected
&& templateSelected.parcellations.find(parcellation => parcellationSelected.name === parcellation.name)
this.handleParcellation(foundParcellation || templateSelected.parcellations[0])
@@ -967,7 +982,7 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
this.nehubaViewer = null
}
- private createNewNehuba(template: any) {
+ private createNewNehuba(template: any, overwriteInitNavigation: any) {
this.viewerLoaded = true
this.cr = this.container.createComponent(this.nehubaViewerFactory)
@@ -983,12 +998,20 @@ export class NehubaContainer implements OnInit, OnChanges, OnDestroy {
const { voxelSize = [1e6, 1e6, 1e6], voxelCoordinates = [0, 0, 0] } = (pose && pose.position) || {}
const { orientation = [0, 0, 0, 1] } = pose || {}
+ const {
+ orientation: owOrientation,
+ perspectiveOrientation: owPerspectiveOrientation,
+ perspectiveZoom: owPerspectiveZoom,
+ position: owPosition,
+ zoom: owZoom
+ } = overwriteInitNavigation
+
const initNavigation = {
- orientation: orientation,
- perspectiveOrientation,
- perspectiveZoom,
- position: [0, 1, 2].map(idx => voxelSize[idx] * voxelCoordinates[idx]),
- zoom: zoomFactor,
+ orientation: owOrientation || [0, 0, 0, 1],
+ perspectiveOrientation: owPerspectiveOrientation || perspectiveOrientation,
+ perspectiveZoom: owPerspectiveZoom || perspectiveZoom,
+ position: owPosition || [0, 1, 2].map(idx => voxelSize[idx] * voxelCoordinates[idx]),
+ zoom: owZoom || zoomFactor,
}
this.handleEmittedNavigationChange(initNavigation)
diff --git a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
index ad488c9ea3fa810464f6ed72d0c6f3c57f0a3f65..1cb264cde6a2c183fdf807ac0f26a5053dce9b81 100644
--- a/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
+++ b/src/ui/nehubaContainer/nehubaViewer/nehubaViewer.component.ts
@@ -1,5 +1,5 @@
import { Component, ElementRef, EventEmitter, NgZone, OnDestroy, OnInit, Output, Renderer2 } from "@angular/core";
-import { fromEvent, Subject, Subscription } from 'rxjs'
+import { fromEvent, Subscription, ReplaySubject } from 'rxjs'
import { pipeFromArray } from "rxjs/internal/util/pipe";
import { debounceTime, filter, map, scan } from "rxjs/operators";
import { AtlasViewerConstantsServices } from "src/atlasViewer/atlasViewer.constantService.service";
@@ -109,6 +109,11 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
public ondestroySubscriptions: Subscription[] = []
+ private createNehubaPromiseRs: Function
+ private createNehubaPromise = new Promise(rs => {
+ this.createNehubaPromiseRs = rs
+ })
+
constructor(
private rd: Renderer2,
public elementRef: ElementRef,
@@ -143,6 +148,10 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
this.layersChangedHandler = this.nehubaViewer.ngviewer.layerManager.layersChanged.add(() => this.layersChanged.emit(null))
this.nehubaViewer.ngviewer.registerDisposer(this.layersChangedHandler)
})
+ .then(() => {
+ // all mutation to this.nehubaViewer should await createNehubaPromise
+ this.createNehubaPromiseRs()
+ })
.catch(e => this.errorEmitter.emit(e))
this.ondestroySubscriptions.push(
@@ -258,20 +267,16 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
}
set ngIds(val: string[]) {
-
- if (this.nehubaViewer) {
- this._ngIds.forEach(id => {
- const oldlayer = this.nehubaViewer.ngviewer.layerManager.getLayerByName(id)
- if (oldlayer) {oldlayer.setVisible(false) } else { this.log.warn('could not find old layer', id) }
+ this.createNehubaPromise
+ .then(() => {
+ this._ngIds.forEach(id => {
+ const oldlayer = this.nehubaViewer.ngviewer.layerManager.getLayerByName(id)
+ if (oldlayer) {oldlayer.setVisible(false) } else { this.log.warn('could not find old layer', id) }
+ })
+ this._ngIds = val
+ this.loadNewParcellation()
+ this.showAllSeg()
})
- }
-
- this._ngIds = val
-
- if (this.nehubaViewer) {
- this.loadNewParcellation()
- this.showAllSeg()
- }
}
public spatialLandmarkSelectionChanged(labels: number[]) {
@@ -312,7 +317,7 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
this._multiNgIdColorMap = val
}
- private loadMeshes$: Subject<{labelIndicies: number[], layer: { name: string }}> = new Subject()
+ private loadMeshes$: ReplaySubject<{labelIndicies: number[], layer: { name: string }}> = new ReplaySubject()
private loadMeshes(labelIndicies: number[], { name }) {
this.loadMeshes$.next({
labelIndicies,
@@ -386,6 +391,7 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
this.subscriptions.push(
this.loadMeshes$.pipe(
scan(scanFn, []),
+ debounceTime(100)
).subscribe(layersLabelIndex => {
let totalMeshes = 0
for (const layerLayerIndex of layersLabelIndex) {
@@ -708,7 +714,7 @@ export class NehubaViewerUnit implements OnInit, OnDestroy {
this.setNavigationState(this.initNav)
}
- if (this.initRegions) {
+ if (this.initRegions && this.initRegions.length > 0) {
this.hideAllSeg()
this.showSegs(this.initRegions)
}
diff --git a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
index 1d7e78a1ad5484f51b35145ac258fcc73f278e04..68f7925fd672d87b5ce1b8e33d320f5dfd51902e 100644
--- a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
+++ b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
@@ -20,11 +20,25 @@
Navigate
</span>
</button>
- <button *ngIf="hasConnectivity" mat-button (click)="showConnectivity(region.name)">
+ <button *ngIf="hasConnectivity"
+ mat-button
+ [matMenuTriggerFor]="connectivitySourceDatasets"
+ #connectivityMenuButton="matMenuTrigger">
<i class="fab fa-connectdevelop"></i>
<span>
Connectivity
</span>
+ <i class="fas fa-angle-right"></i>
</button>
+
+ <!-- ToDo make dynamic with AVAILABLE CONNECTIVITY DATASETS data - get info from atlas viewer core -->
+ <mat-menu #connectivitySourceDatasets="matMenu" xPosition="before" (click)="$event.stopPropagation()" hasBackdrop="false">
+ <div>
+ <button mat-menu-item
+ (click)="showConnectivity(region.name)">
+ <span>1000 Brain Study - DTI connectivity</span>
+ </button>
+ </div>
+ </mat-menu>
</mat-card-actions>
</mat-card>
\ No newline at end of file
diff --git a/src/ui/searchSideNav/searchSideNav.style.css b/src/ui/searchSideNav/searchSideNav.style.css
index 4abec449498d3a8586f333d9003d001a100ec6f4..5bb036cfb94a7098f23e386101b641f6fbae208a 100644
--- a/src/ui/searchSideNav/searchSideNav.style.css
+++ b/src/ui/searchSideNav/searchSideNav.style.css
@@ -19,5 +19,5 @@
}
connectivity-browser {
- max-height: calc(100% - 220px);
+ max-height: calc(100% - 200px);
}
\ No newline at end of file
diff --git a/src/ui/viewerStateController/regionSearch/regionSearch.component.ts b/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
index 01fb37ceb42e8522275cf26f86377ad180c18bfa..a5c3b12a235d91ec21c7ec569b6ab5b1685e6c3d 100644
--- a/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
+++ b/src/ui/viewerStateController/regionSearch/regionSearch.component.ts
@@ -12,7 +12,7 @@ import { VIEWERSTATE_CONTROLLER_ACTION_TYPES } from "../viewerState.base";
import { LoggingService } from "src/services/logging.service";
const filterRegionBasedOnText = searchTerm => region => region.name.toLowerCase().includes(searchTerm.toLowerCase())
- || (region.relatedAreas && region.relatedAreas.some(relatedArea => relatedArea.toLowerCase().includes(searchTerm.toLowerCase())))
+ || (region.relatedAreas && region.relatedAreas.some(relatedArea => relatedArea.name && relatedArea.name.toLowerCase().includes(searchTerm.toLowerCase())))
const compareFn = (it, item) => it.name === item.name
@@ -60,7 +60,7 @@ export class RegionTextSearchAutocomplete {
map(parcellationSelected => {
try {
const returnArray = []
- const ngIdMap = getMultiNgIdsRegionsLabelIndexMap(parcellationSelected, { ngId: 'root', relatedAreas: [] })
+ const ngIdMap = getMultiNgIdsRegionsLabelIndexMap(parcellationSelected, { ngId: 'root', relatedAreas: [], fullId: null })
for (const [ngId, labelIndexMap] of ngIdMap) {
for (const [labelIndex, region] of labelIndexMap) {
returnArray.push({
diff --git a/src/ui/viewerStateController/viewerState.base.ts b/src/ui/viewerStateController/viewerState.base.ts
index be61afdff357ddf3c02af888ef5a881ad79b4fd3..6a3804835b723ac36106c27806be836211ceba6a 100644
--- a/src/ui/viewerStateController/viewerState.base.ts
+++ b/src/ui/viewerStateController/viewerState.base.ts
@@ -77,7 +77,7 @@ export class ViewerStateBase implements OnInit {
this.availableTemplates$ = viewerState$.pipe(
select('fetchedTemplates'),
- distinctUntilChanged(),
+ distinctUntilChanged()
)
this.availableParcellations$ = this.templateSelected$.pipe(
@@ -155,13 +155,7 @@ export class ViewerStateBase implements OnInit {
})
}
- public displayActiveParcellation(parcellation: any) {
- return `<div class="d-flex"><small>Parcellation</small> <small class = "flex-grow-1 mute-text">${parcellation ? '(' + parcellation.name + ')' : ''}</small> <span class = "fas fa-caret-down"></span></div>`
- }
-
- public displayActiveTemplate(template: any) {
- return `<div class="d-flex"><small>Template</small> <small class = "flex-grow-1 mute-text">${template ? '(' + template.name + ')' : ''}</small> <span class = "fas fa-caret-down"></span></div>`
- }
+ public trackByFn = ({ name }) => name
public loadSelection(_event: MouseEvent) {
this.focused = true
diff --git a/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html b/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html
index 5f72c5990590ccc7a949b14f8937a737b9b9fb3e..32675891bf3eb5ad67fefe2b83d80e78bf176157 100644
--- a/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html
+++ b/src/ui/viewerStateController/viewerStateCFull/viewerState.template.html
@@ -14,7 +14,7 @@
(selectionChange)="handleTemplateChange($event)"
(openedChange)="focused = $event">
<mat-option
- *ngFor="let template of (availableTemplates$ | async)"
+ *ngFor="let template of (availableTemplates$ | async); trackBy: trackByFn"
[value]="template.name">
{{ template.name }}
</mat-option>
diff --git a/src/util/worker.js b/src/util/worker.js
index f5313880e961c533e72b8429bdf2e46d73e9fa27..a46c50fccc19223a9f2fadd1c317eddea9b2d141 100644
--- a/src/util/worker.js
+++ b/src/util/worker.js
@@ -2,7 +2,7 @@ const validTypes = [
'GET_LANDMARKS_VTK',
'GET_USERLANDMARKS_VTK',
'BUILD_REGION_SELECTION_TREE',
- 'PROPAGATE_NG_ID'
+ 'PROPAGATE_PARC_REGION_ATTR'
]
const validOutType = [
@@ -246,21 +246,30 @@ const rebuildSelectedRegion = (payload) => {
rebuiltSomeSelectedRegions: someActiveTreeBranch
})
}
+const recursivePropagateAttri = (region, inheritAttrsOpts) => {
-const propagateNgId = (parcellation) => {
- const recursivePropagateNgId = (region, {ngId}) => {
- return {
- ngId,
- ...region,
- ...( region.children && region.children.map
- ? {
- children: region.children.map(c => recursivePropagateNgId(c, { ngId: region.ngId || ngId }))
- }
- : {} )
- }
+ const inheritAttrs = Object.keys(inheritAttrsOpts)
+
+ const returnRegion = {
+ ...region
+ }
+ const newInhAttrsOpts = {}
+ for (const attr of inheritAttrs){
+ returnRegion[attr] = returnRegion[attr] || inheritAttrsOpts[attr]
+ newInhAttrsOpts[attr] = returnRegion[attr] || inheritAttrsOpts[attr]
}
- const regions = parcellation.regions && parcellation.regions.map
- ? parcellation.regions.map(r => recursivePropagateNgId(r, { ngId: parcellation.ngId }))
+ returnRegion.children = returnRegion.children && Array.isArray(returnRegion.children)
+ ? returnRegion.children.map(c => recursivePropagateAttri(c, newInhAttrsOpts))
+ : null
+ return returnRegion
+}
+
+const propagateAttri = (parcellation, inheritAttrsOpts) => {
+ const inheritAttrs = Object.keys(inheritAttrsOpts)
+ if (inheritAttrs.indexOf('children') >= 0) throw new Error(`children attr cannot be inherited`)
+
+ const regions = Array.isArray(parcellation.regions)
+ ? parcellation.regions.map(r => recursivePropagateAttri(r, inheritAttrsOpts))
: []
return {
@@ -269,12 +278,11 @@ const propagateNgId = (parcellation) => {
}
}
-const processPropagateNgId = (payload) => {
- const { parcellation } = payload
- const p = parcellation.ngId
- ? parcellation
- : propagateNgId(parcellation)
+const processParcRegionAttr = (payload) => {
+ const { parcellation, inheritAttrsOpts } = payload
+ const p = propagateAttri(parcellation, inheritAttrsOpts)
postMessage({
+ ...payload,
type: 'UPDATE_PARCELLATION_REGIONS',
parcellation: p
})
@@ -293,8 +301,8 @@ onmessage = (message) => {
case 'BUILD_REGION_SELECTION_TREE':
rebuildSelectedRegion(message.data)
return
- case 'PROPAGATE_NG_ID':
- processPropagateNgId(message.data)
+ case 'PROPAGATE_PARC_REGION_ATTR':
+ processParcRegionAttr(message.data)
return
default:
console.warn('unhandled worker action', message)
diff --git a/tsconfig-aot.json b/tsconfig-aot.json
index 3a4115d6cfbc48fe643b9e85be53edab3f03ff25..7e541551de2f10d6e188764fe44de55db26581f5 100644
--- a/tsconfig-aot.json
+++ b/tsconfig-aot.json
@@ -8,7 +8,8 @@
"baseUrl": ".",
"paths": {
"third_party/*" : ["third_party/*"],
- "src/*" : ["src/*"]
+ "src/*" : ["src/*"],
+ "common/*": ["common/*"]
}
},
"angularCompilerOptions":{
diff --git a/tsconfig.json b/tsconfig.json
index f8617eab74953284b4d1a3f9ed6e234b455c10ab..59ee73b188970995b9fc4b12331823aa5ffef17c 100644
--- a/tsconfig.json
+++ b/tsconfig.json
@@ -8,7 +8,8 @@
"baseUrl": ".",
"paths": {
"third_party/*" : ["third_party/*"],
- "src/*" : ["src/*"]
+ "src/*" : ["src/*"],
+ "common/*": ["common/*"]
}
}
}
\ No newline at end of file
diff --git a/webpack.common.js b/webpack.common.js
index 9f680d8ef445b10c2a672197ea510f1dba6033c8..b432b1d516e6e026f7ea57cb6207a13507866848 100644
--- a/webpack.common.js
+++ b/webpack.common.js
@@ -31,7 +31,8 @@ module.exports = {
],
alias : {
"third_party" : path.resolve(__dirname,'third_party'),
- "src" : path.resolve(__dirname,'src')
+ "src" : path.resolve(__dirname,'src'),
+ "common": path.resolve(__dirname, 'common')
}
},
}
\ No newline at end of file