diff --git a/deploy/package-lock.json b/deploy/package-lock.json
index 99b93fe79026380a2f1ca7f051b65e97774a31f5..5d707a769ac807f9c1473f3940fe0464dba4657b 100644
--- a/deploy/package-lock.json
+++ b/deploy/package-lock.json
@@ -257,9 +257,9 @@
},
"dependencies": {
"lodash": {
- "version": "4.17.20",
- "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.20.tgz",
- "integrity": "sha512-PlhdFcillOINfeV7Ni6oF1TAEayyZBoZ8bcshTHqOYJYlrqzRK5hagpagky5o4HfCzzd1TRkXPMFq6cKk9rGmA=="
+ "version": "4.17.21",
+ "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz",
+ "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg=="
}
}
},
@@ -735,9 +735,9 @@
"integrity": "sha1-3zrhmayt+31ECqrgsp4icrJOxhk="
},
"denque": {
- "version": "1.5.0",
- "resolved": "https://registry.npmjs.org/denque/-/denque-1.5.0.tgz",
- "integrity": "sha512-CYiCSgIF1p6EUByQPlGkKnP1M9g0ZV3qMIrqMqZqdwazygIA/YP2vrbcyl1h/WppKJTdl1F85cXIle+394iDAQ=="
+ "version": "1.5.1",
+ "resolved": "https://registry.npmjs.org/denque/-/denque-1.5.1.tgz",
+ "integrity": "sha512-XwE+iZ4D6ZUB7mfYRMb5wByE8L74HCn30FBN7sWnXksWc1LO1bPDl67pBR9o/kC4z/xSNAwkMYcGgqDV3BE3Hw=="
},
"depd": {
"version": "1.1.2",
@@ -1352,9 +1352,9 @@
"integrity": "sha1-R+Y/evVa+m+S4VAOaQ64uFKcCZo="
},
"jose": {
- "version": "2.0.4",
- "resolved": "https://registry.npmjs.org/jose/-/jose-2.0.4.tgz",
- "integrity": "sha512-EArN9f6aq1LT/fIGGsfghOnNXn4noD+3dG5lL/ljY3LcRjw1u9w+4ahu/4ahsN6N0kRLyyW6zqdoYk7LNx3+YQ==",
+ "version": "2.0.5",
+ "resolved": "https://registry.npmjs.org/jose/-/jose-2.0.5.tgz",
+ "integrity": "sha512-BAiDNeDKTMgk4tvD0BbxJ8xHEHBZgpeRZ1zGPPsitSyMgjoMWiLGYAE7H7NpP5h0lPppQajQs871E8NHUrzVPA==",
"requires": {
"@panva/asn1.js": "^1.0.0"
}
@@ -1446,9 +1446,9 @@
}
},
"lodash": {
- "version": "4.17.20",
- "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.20.tgz",
- "integrity": "sha512-PlhdFcillOINfeV7Ni6oF1TAEayyZBoZ8bcshTHqOYJYlrqzRK5hagpagky5o4HfCzzd1TRkXPMFq6cKk9rGmA==",
+ "version": "4.17.21",
+ "resolved": "https://registry.npmjs.org/lodash/-/lodash-4.17.21.tgz",
+ "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==",
"dev": true
},
"lodash.defaults": {
@@ -1801,9 +1801,9 @@
"integrity": "sha512-6eZs5Ls3WtCisHWp9S2GUy8dqkpGi4BVSz3GaqiE6ezub0512ESztXUwUB6C6IKbQkY2Pnb/mD4WYojCRwcwLA=="
},
"normalize-url": {
- "version": "4.5.0",
- "resolved": "https://registry.npmjs.org/normalize-url/-/normalize-url-4.5.0.tgz",
- "integrity": "sha512-2s47yzUxdexf1OhyRi4Em83iQk0aPvwTddtFz4hnSSw9dCEsLEGf6SwIO8ss/19S9iBb5sJaOuTvTGDeZI00BQ=="
+ "version": "4.5.1",
+ "resolved": "https://registry.npmjs.org/normalize-url/-/normalize-url-4.5.1.tgz",
+ "integrity": "sha512-9UZCFRHQdNrfTpGg8+1INIg93B6zE0aXMVFkw1WFwvO4SlZywU6aLg5Of0Ap/PgcbSw4LNxvMWXMeugwMCX0AA=="
},
"npm-run-path": {
"version": "2.0.2",
@@ -2194,20 +2194,20 @@
}
},
"redis": {
- "version": "3.0.2",
- "resolved": "https://registry.npmjs.org/redis/-/redis-3.0.2.tgz",
- "integrity": "sha512-PNhLCrjU6vKVuMOyFu7oSP296mwBkcE6lrAjruBYG5LgdSqtRBoVQIylrMyVZD/lkF24RSNNatzvYag6HRBHjQ==",
+ "version": "3.1.2",
+ "resolved": "https://registry.npmjs.org/redis/-/redis-3.1.2.tgz",
+ "integrity": "sha512-grn5KoZLr/qrRQVwoSkmzdbw6pwF+/rwODtrOr6vuBRiR/f3rjSTGupbF90Zpqm2oenix8Do6RV7pYEkGwlKkw==",
"requires": {
- "denque": "^1.4.1",
- "redis-commands": "^1.5.0",
+ "denque": "^1.5.0",
+ "redis-commands": "^1.7.0",
"redis-errors": "^1.2.0",
"redis-parser": "^3.0.0"
}
},
"redis-commands": {
- "version": "1.6.0",
- "resolved": "https://registry.npmjs.org/redis-commands/-/redis-commands-1.6.0.tgz",
- "integrity": "sha512-2jnZ0IkjZxvguITjFTrGiLyzQZcTvaw8DAaCXxZq/dsHXz7KfMQ3OUJy7Tz9vnRtZRVz6VRCPDvruvU8Ts44wQ=="
+ "version": "1.7.0",
+ "resolved": "https://registry.npmjs.org/redis-commands/-/redis-commands-1.7.0.tgz",
+ "integrity": "sha512-nJWqw3bTFy21hX/CPKHth6sfhZbdiHP6bTawSgQBlKOVRG7EZkfHbbHwQJnrE4vsQf0CMNE+3gJ4Fmm16vdVlQ=="
},
"redis-errors": {
"version": "1.2.0",
@@ -2819,9 +2819,9 @@
"integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
},
"y18n": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.0.tgz",
- "integrity": "sha512-r9S/ZyXu/Xu9q1tYlpsLIsa3EeLXXk0VwlxqTcFRfg9EhMW+17kbt9G0NrgCmhGb5vT2hyhJZLfDGx+7+5Uj/w=="
+ "version": "4.0.3",
+ "resolved": "https://registry.npmjs.org/y18n/-/y18n-4.0.3.tgz",
+ "integrity": "sha512-JKhqTOwSrqNA1NY5lSztJ1GrBiUodLMmIZuLiDaMRJ+itFd+ABVE8XBjOvIWL+rSqNDC74LCSFmlb/U4UZ4hJQ=="
},
"yallist": {
"version": "3.1.1",
diff --git a/deploy/package.json b/deploy/package.json
index 95da8df0bd39afe6c3076fe360260e3b4f81995b..8a165a87192525bf0b6bcd9ba86df86fe5ddb30c 100644
--- a/deploy/package.json
+++ b/deploy/package.json
@@ -26,7 +26,7 @@
"nomiseco": "0.0.2",
"openid-client": "^4.4.0",
"passport": "^0.4.0",
- "redis": "^3.0.2",
+ "redis": "^3.1.2",
"request": "^2.88.0",
"showdown": "^1.9.1",
"soswrap": "^0.0.2",
diff --git a/docs/releases/v2.5.2.md b/docs/releases/v2.5.2.md
new file mode 100644
index 0000000000000000000000000000000000000000..200aab57206daa94f58fa4a931e1081adf72380b
--- /dev/null
+++ b/docs/releases/v2.5.2.md
@@ -0,0 +1,5 @@
+# v2.5.2
+
+## Bugfixes
+
+- fix big brain high resolution maps
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 80ad8c9d6d9c41957994b8138aeb124132e78e2e..b7e247316f838021293df1ef5f887cc486abef56 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -40,6 +40,7 @@ pages:
- Fetching datasets: 'advanced/datasets.md'
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
+ - v2.5.2: 'releases/v2.5.2.md'
- v2.5.1: 'releases/v2.5.1.md'
- v2.5.0: 'releases/v2.5.0.md'
- v2.4.8: 'releases/v2.4.8.md'
diff --git a/src/routerModule/util.spec.ts b/src/routerModule/util.spec.ts
index ac15ff5981b022ed662be9c7796e07fff9e941a0..b2ed55ea82db7f09f581114c2157a40ad2731bb6 100644
--- a/src/routerModule/util.spec.ts
+++ b/src/routerModule/util.spec.ts
@@ -6,6 +6,8 @@ import { cvtFullRouteToState, cvtStateToHashedRoutes, DummyCmp, routes } from '.
import { encodeNumber } from './cipher'
import { Router } from '@angular/router'
import { RouterTestingModule } from '@angular/router/testing'
+import * as parsedRoute from './parseRouteToTmplParcReg'
+import { spaceMiscInfoMap } from 'src/util/pureConstant.service'
describe('> util.ts', () => {
describe('> cvtFullRouteToState', () => {
@@ -61,6 +63,53 @@ describe('> util.ts', () => {
})
})
+ describe('> navigation', () => {
+ let parseSpy: jasmine.Spy
+ let mapGetSpy: jasmine.Spy
+ beforeEach(() => {
+ parseSpy = spyOnProperty(parsedRoute, 'parseSearchParamForTemplateParcellationRegion')
+ mapGetSpy = spyOn(spaceMiscInfoMap, 'get')
+ })
+ it('> if not present, should show something palatable', () => {
+ parseSpy.and.returnValue(() => ({
+ parcellationSelected: {
+ id: 'dummpy-id-parc'
+ },
+ regionsSelected: [],
+ templateSelected: {
+ id: 'dummpy-id-tmpl-sel'
+ },
+ }))
+
+ const scale = 0.25
+
+ mapGetSpy.and.returnValue({ scale })
+
+ const router = TestBed.inject(Router)
+ const route = `/a:juelich:iav:atlas:v1.0.0:1/t:minds:core:referencespace:v1.0.0:dafcffc5-4826-4bf1-8ff6-46b8a31ff8e2/p:minds:core:parcellationatlas:v1.0.0:94c1125b-b87e-45e4-901c-00daee7f2579-290`
+ const parsedUrl = router.parseUrl(route)
+ const { viewerState = {} } = cvtFullRouteToState(parsedUrl, {}) || {}
+ const { navigation } = viewerState
+ const {
+ orientation,
+ perspectiveOrientation,
+ position,
+ zoom,
+ perspectiveZoom,
+ } = navigation
+
+ expect(orientation).toEqual([0,0,0,1])
+ expect(perspectiveOrientation).toEqual([
+ 0.3140767216682434,
+ -0.7418519854545593,
+ 0.4988985061645508,
+ -0.3195493221282959
+ ])
+ expect(position).toEqual([0,0,0])
+ expect(zoom).toEqual(350000 * scale)
+ expect(perspectiveZoom).toEqual(1922235.5293810747 * scale)
+ })
+ })
})
describe('> cvtStateToHashedRoutes', () => {
diff --git a/src/routerModule/util.ts b/src/routerModule/util.ts
index 21ccdc6e7bbbb9bab69a399a96ac388d5fbc7439..e0115ee6268f033cf55a17e1ddac3c39e1b8839f 100644
--- a/src/routerModule/util.ts
+++ b/src/routerModule/util.ts
@@ -18,6 +18,7 @@ import {
parseSearchParamForTemplateParcellationRegion,
encodeId,
} from './parseRouteToTmplParcReg'
+import { spaceMiscInfoMap } from "src/util/pureConstant.service"
const endcodePath = (key: string, val: string|string[]) =>
key[0] === '?'
@@ -34,6 +35,17 @@ const decodePath = (path: string) => {
}
}
+export const DEFAULT_NAV = {
+ orientation: [0, 0, 0, 1],
+ perspectiveOrientation: [
+ 0.3140767216682434,
+ -0.7418519854545593,
+ 0.4988985061645508,
+ -0.3195493221282959
+ ],
+ position: [0, 0, 0],
+}
+
export const cvtFullRouteToState = (fullPath: UrlTree, state: any, _warnCb?: (arg: string) => void) => {
const warnCb = _warnCb || ((...e: any[]) => console.warn(...e))
@@ -78,7 +90,7 @@ export const cvtFullRouteToState = (fullPath: UrlTree, state: any, _warnCb?: (ar
// nav obj is almost always defined, regardless if standaloneVolume or not
const cViewerState = returnObj['@'] && returnObj['@'][0]
- let parsedNavObj = {}
+ let parsedNavObj: any
if (cViewerState) {
try {
const [ cO, cPO, cPZ, cP, cZ ] = cViewerState.split(`${separator}${separator}`)
@@ -171,7 +183,12 @@ export const cvtFullRouteToState = (fullPath: UrlTree, state: any, _warnCb?: (ar
returnState['viewerState']['regionsSelected'] = regionsSelected
returnState['viewerState']['templateSelected'] = templateSelected
- returnState['viewerState']['navigation'] = parsedNavObj
+ const { scale } = spaceMiscInfoMap.get(templateSelected.id) || { scale: 1 }
+ returnState['viewerState']['navigation'] = parsedNavObj || ({
+ ...DEFAULT_NAV,
+ zoom: 350000 * scale,
+ perspectiveZoom: 1922235.5293810747 * scale
+ })
} catch (e) {
// if error, show error on UI?
warnCb(`parse template, parc, region error`, e)
diff --git a/src/util/patchPureConstants.ts b/src/util/patchPureConstants.ts
index 55ff455615c145c59ac2906fba55625fabdf6d1a..681860add48b6393c202f3377f7afc217acd1682 100644
--- a/src/util/patchPureConstants.ts
+++ b/src/util/patchPureConstants.ts
@@ -46,25 +46,21 @@ async function getInterpolatedPatchObj(targetName: string, labelIndex: number){
'@id': 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
}],
"payload": {
- "volumeSrc": {
- 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588': {
- "collect": [{
- "@type": "fzj/tmp/volume_type/v0.0.1" as const,
- "@id": "fzj/tmp/volume_type/v0.0.1/interpolated",
- "name": "Julich Brain v2.5 interpolated map",
- "volume_type": "neuroglancer/precomputed" as const,
- "url": "https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/2019_05_22_interpolated_areas",
- "detail": {
- "neuroglancer/precomputed": {
- "labelIndex": labelIndex,
- "transform": [[1,0,0,-70677184],[0,1,0,-51990000],[0,0,1,-58788284],[0,0,0,1]]
- }
- },
- "space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
- map_type: 'labelled'
- }]
- }
- }
+ _dataset_specs: [{
+ "@type": "fzj/tmp/volume_type/v0.0.1" as const,
+ "@id": "fzj/tmp/volume_type/v0.0.1/interpolated",
+ "name": "Julich Brain v2.5 interpolated map",
+ "volume_type": "neuroglancer/precomputed" as const,
+ "url": "https://neuroglancer.humanbrainproject.org/precomputed/BigBrainRelease.2015/2019_05_22_interpolated_areas",
+ "detail": {
+ "neuroglancer/precomputed": {
+ "labelIndex": labelIndex,
+ "transform": [[1,0,0,-70677184],[0,1,0,-51990000],[0,0,1,-58788284],[0,0,0,1]]
+ }
+ },
+ "space_id": "minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588",
+ map_type: 'labelled'
+ }],
}
}
const hex = await getShaDigest(JSON.stringify(returnObj))
@@ -78,9 +74,9 @@ async function getIndividualMap(parentName: string, regionName: string, url: str
const volumeId = await getShaDigest(url)
const returnObj: TPatchRegion = {
'@id': '',
- "@type": 'julich/siibra/append-region/v0.0.1',
- "parent": {
- "name": parentName
+ "@type": 'julich/siibra/patch-region/v0.0.1',
+ "target": {
+ "name": regionName
},
"targetParcellation": [{
"@id": 'minds/core/parcellationatlas/v1.0.0/94c1125b-b87e-45e4-901c-00daee7f2579-290'
@@ -89,26 +85,21 @@ async function getIndividualMap(parentName: string, regionName: string, url: str
'@id': 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588'
}],
"payload": {
- "name": regionName,
- "volumeSrc": {
- 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588': {
- "collect": [{
- "@type": "fzj/tmp/volume_type/v0.0.1" as const,
- "@id": `fzj/tmp/volume_type/v0.0.1/${volumeId}`,
- "name": "Julich Brain v2.5 detailed map",
- "volume_type": "neuroglancer/precomputed" as const,
- "url": url,
- "detail": {
- "neuroglancer/precomputed": {
- "labelIndex": labelIndex,
- "transform": transform
- }
- },
- space_id: 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
- map_type: 'labelled'
- }]
- }
- }
+ '_dataset_specs': [{
+ "@type": "fzj/tmp/volume_type/v0.0.1" as const,
+ "@id": `fzj/tmp/volume_type/v0.0.1/${volumeId}`,
+ "name": "Julich Brain v2.5 detailed map",
+ "volume_type": "neuroglancer/precomputed" as const,
+ "url": url,
+ "detail": {
+ "neuroglancer/precomputed": {
+ "labelIndex": labelIndex,
+ "transform": transform
+ }
+ },
+ space_id: 'minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588',
+ map_type: 'labelled'
+ }],
}
}
const hex = await getShaDigest(JSON.stringify(returnObj))
diff --git a/src/util/pureConstant.service.ts b/src/util/pureConstant.service.ts
index 09b2e1898137bcedd28fd9a0f3181d17b6d32778..c6145b3d2a7617850815eb6bf9212c81481b5efd 100644
--- a/src/util/pureConstant.service.ts
+++ b/src/util/pureConstant.service.ts
@@ -52,7 +52,7 @@ type TIAVAtlas = {
} & THasId)[]
} & THasId
-const spaceMiscInfoMap = new Map([
+export const spaceMiscInfoMap = new Map([
['minds/core/referencespace/v1.0.0/a1655b99-82f1-420f-a3c2-fe80fd4c8588', {
name: 'bigbrain',
scale: 1,
@@ -532,20 +532,16 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
* this should work for both fully mapped and interpolated
* in the case of interpolated, it sucks that the ngLayerObj will be set multiple times
*/
- if (
- tmpl.id in (region.volumeSrc || {})
- && 'collect' in region.volumeSrc[tmpl.id]
- ) {
- const dedicatedMap = region.volumeSrc[tmpl.id]['collect'].filter(v => v.volume_type === 'neuroglancer/precomputed')
- if (dedicatedMap.length === 1) {
- const ngId = getNgId(atlas['@id'], tmpl.id, parc.id, dedicatedMap[0]['@id'])
- region['ngId'] = ngId
- region['labelIndex'] = dedicatedMap[0].detail['neuroglancer/precomputed'].labelIndex
- ngLayerObj[tmpl.id][ngId] = {
- source: `precomputed://${dedicatedMap[0].url}`,
- type: "segmentation",
- transform: dedicatedMap[0].detail['neuroglancer/precomputed'].transform
- }
+
+ const dedicatedMap = region._dataset_specs.filter(spec => spec.space_id === tmpl.id && spec['volume_type'] === 'neuroglancer/precomputed')
+ if (dedicatedMap.length === 1) {
+ const ngId = getNgId(atlas['@id'], tmpl.id, parc.id, dedicatedMap[0]['@id'])
+ region['ngId'] = ngId
+ region['labelIndex'] = dedicatedMap[0].detail['neuroglancer/precomputed'].labelIndex
+ ngLayerObj[tmpl.id][ngId] = {
+ source: `precomputed://${dedicatedMap[0].url}`,
+ type: "segmentation",
+ transform: dedicatedMap[0].detail['neuroglancer/precomputed'].transform
}
}
@@ -579,10 +575,11 @@ Raise/track issues at github repo: <a target = "_blank" href = "${this.repoUrl}"
&& hemisphereKey === 'whole brain'
) {
region.children = []
- return
}
- const hemispheredNgId = getNgId(atlas['@id'], tmpl.id, parc.id, hemisphereKey)
- region['ngId'] = hemispheredNgId
+ if (!region['ngId']) {
+ const hemispheredNgId = getNgId(atlas['@id'], tmpl.id, parc.id, hemisphereKey)
+ region['ngId'] = hemispheredNgId
+ }
}
}
)
diff --git a/src/util/siibraApiConstants/types.ts b/src/util/siibraApiConstants/types.ts
index 62fc6057d749a4123da76bcce3bf2d6b2fd738be..7f3170ad6f7f665ba13202a833b7342f86d36037 100644
--- a/src/util/siibraApiConstants/types.ts
+++ b/src/util/siibraApiConstants/types.ts
@@ -180,11 +180,6 @@ export type TRegionDetail = {
export type TRegion = {
name: string
children: TRegion[]
- volumeSrc: {
- [key: string]: {
- [key: string]: TVolumeSrc<keyof IVolumeTypeDetail>[]
- }
- }
labelIndex?: number
rgb?: number[]
@@ -192,6 +187,8 @@ export type TRegion = {
kg: TKgIdentifier
}
+ _dataset_specs: TVolumeSrc<keyof IVolumeTypeDetail>[]
+
/**
* missing
*/