From 6732185d155222bcba64ef67e1930a452a0492e3 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Tue, 20 Jul 2021 16:51:01 +0200
Subject: [PATCH] bugfix: change tmpl spatial backend
---
.../parcellationRegion/region.base.spec.ts | 138 ++++++++++++------
.../parcellationRegion/region.base.ts | 26 ++--
...eCoordinatesTransformation.service.spec.ts | 47 ++++--
...mplateCoordinatesTransformation.service.ts | 24 ++-
4 files changed, 164 insertions(+), 71 deletions(-)
diff --git a/src/atlasComponents/parcellationRegion/region.base.spec.ts b/src/atlasComponents/parcellationRegion/region.base.spec.ts
index 0fb3792e9..c9ee29648 100644
--- a/src/atlasComponents/parcellationRegion/region.base.spec.ts
+++ b/src/atlasComponents/parcellationRegion/region.base.spec.ts
@@ -1,6 +1,6 @@
import { TestBed } from '@angular/core/testing'
import { MockStore, provideMockStore } from '@ngrx/store/testing'
-import { viewerStateNewViewer } from 'src/services/state/viewerState/actions'
+import { viewerStateSelectTemplateWithId } from 'src/services/state/viewerState/actions'
import { RegionBase, regionInOtherTemplateSelector, getRegionParentParcRefSpace } from './region.base'
const util = require('common/util')
@@ -620,16 +620,18 @@ describe('> region.base.ts', () => {
})
describe('> changeView', () => {
const fakeTmpl = {
+ '@id': 'faketmplid',
name: 'fakeTmpl'
}
const fakeParc = {
+ '@id': 'fakeparcid',
name: 'fakeParc'
}
beforeEach(() => {
regionBase = new RegionBase(mockStore)
})
- describe('> if sameRegion has position attribute', () => {
+ describe('> [tmp] sameRegion to use transform backend', () => {
let dispatchSpy: jasmine.Spy
beforeEach(() => {
@@ -638,64 +640,106 @@ describe('> region.base.ts', () => {
afterEach(() => {
dispatchSpy.calls.reset()
})
- it('> malformed position is not an array > do not pass position', () => {
- regionBase.changeView({
- template: fakeTmpl,
- parcellation: fakeParc,
- region: {
- position: 'hello wolrd'
- }
- })
-
- expect(dispatchSpy).toHaveBeenCalledWith(
- viewerStateNewViewer({
- selectTemplate: fakeTmpl,
- selectParcellation: fakeParc,
- navigation: {}
- })
- )
- })
-
- it('> malformed position is an array of incorrect size > do not pass position', () => {
+ it('> calls viewerStateSelectTemplateWithId', () => {
regionBase.changeView({
template: fakeTmpl,
parcellation: fakeParc,
- region: {
- position: []
- }
})
expect(dispatchSpy).toHaveBeenCalledWith(
- viewerStateNewViewer({
- selectTemplate: fakeTmpl,
- selectParcellation: fakeParc,
- navigation: {}
- })
- )
- })
-
- it('> correct position > pass position', () => {
- regionBase.changeView({
- template: fakeTmpl,
- parcellation: fakeParc,
- region: {
- position: [1,2,3]
- }
- })
-
- expect(dispatchSpy).toHaveBeenCalledWith(
- viewerStateNewViewer({
- selectTemplate: fakeTmpl,
- selectParcellation: fakeParc,
- navigation: {
- position: [1,2,3]
+ viewerStateSelectTemplateWithId({
+ payload: {
+ '@id': fakeTmpl['@id']
+ },
+ config: {
+ selectParcellation: {
+ "@id": fakeParc['@id']
+ }
}
})
)
})
})
+
+ /**
+ * currently, without position metadata, the navigation is broken
+ * fix changeView to fetch position metadata. If cannot, fallback to spatial backend
+ */
+
+ // describe('> if sameRegion has position attribute', () => {
+ // let dispatchSpy: jasmine.Spy
+
+ // beforeEach(() => {
+ // dispatchSpy = spyOn(mockStore, 'dispatch')
+ // })
+ // afterEach(() => {
+ // dispatchSpy.calls.reset()
+ // })
+ // it('> malformed position is not an array > do not pass position', () => {
+
+ // regionBase.changeView({
+ // template: fakeTmpl,
+ // parcellation: fakeParc,
+ // region: {
+ // position: 'hello wolrd'
+ // }
+ // })
+
+ // expect(dispatchSpy).toHaveBeenCalledWith(
+ // viewerStateNewViewer({
+ // selectTemplate: fakeTmpl,
+ // selectParcellation: fakeParc,
+ // navigation: {}
+ // })
+ // )
+ // })
+
+ // it('> malformed position is an array of incorrect size > do not pass position', () => {
+
+ // regionBase.changeView({
+ // template: fakeTmpl,
+ // parcellation: fakeParc,
+ // region: {
+ // position: []
+ // }
+ // })
+
+ // expect(dispatchSpy).toHaveBeenCalledWith(
+ // viewerStateSelectTemplateWithId({
+ // payload: {
+ // '@id': fakeTmpl['@id']
+ // },
+ // config: {
+ // selectParcellation: {
+ // "@id": fakeParc['@id']
+ // }
+ // }
+ // })
+ // )
+ // })
+
+ // it('> correct position > pass position', () => {
+ // regionBase.changeView({
+ // template: fakeTmpl,
+ // parcellation: fakeParc,
+ // region: {
+ // position: [1,2,3]
+ // }
+ // })
+
+ // expect(dispatchSpy).toHaveBeenCalledWith(
+ // viewerStateNewViewer({
+ // selectTemplate: fakeTmpl,
+ // selectParcellation: fakeParc,
+ // navigation: {
+ // position: [1,2,3]
+ // }
+ // })
+ // )
+ // })
+ // })
})
})
})
diff --git a/src/atlasComponents/parcellationRegion/region.base.ts b/src/atlasComponents/parcellationRegion/region.base.ts
index d954d08b1..c91ef45d1 100644
--- a/src/atlasComponents/parcellationRegion/region.base.ts
+++ b/src/atlasComponents/parcellationRegion/region.base.ts
@@ -1,10 +1,10 @@
import { EventEmitter, Input, Output, Pipe, PipeTransform } from "@angular/core";
import { select, Store, createSelector } from "@ngrx/store";
import { uiStateOpenSidePanel, uiStateExpandSidePanel, uiActionShowSidePanelConnectivity } from 'src/services/state/uiState.store.helper'
-import { distinctUntilChanged, switchMap, filter, map, withLatestFrom } from "rxjs/operators";
+import { distinctUntilChanged, switchMap, filter, map, withLatestFrom, tap } from "rxjs/operators";
import { Observable, BehaviorSubject, combineLatest } from "rxjs";
import { flattenRegions, getIdFromKgIdObj, rgbToHsl } from 'common/util'
-import { viewerStateSetConnectivityRegion, viewerStateNavigateToRegion, viewerStateToggleRegionSelect, viewerStateNewViewer, isNewerThan } from "src/services/state/viewerState.store.helper";
+import { viewerStateSetConnectivityRegion, viewerStateNavigateToRegion, viewerStateToggleRegionSelect, viewerStateNewViewer, isNewerThan, viewerStateSelectTemplateWithId } from "src/services/state/viewerState.store.helper";
import { viewerStateFetchedTemplatesSelector, viewerStateGetSelectedAtlas, viewerStateSelectedTemplateFullInfoSelector, viewerStateSelectedTemplateSelector } from "src/services/state/viewerState/selectors";
import { strToRgb, verifyPositionArg, getRegionHemisphere } from 'common/util'
import { getPosFromRegion } from "src/util/siibraApiConstants/fn";
@@ -181,23 +181,25 @@ export class RegionBase {
const {
template,
parcellation,
- region
} = sameRegion
- const { position } = region
- const navigation = Array.isArray(position) && position.length === 3
- ? { position }
- : { }
this.closeRegionMenu.emit()
/**
* TODO use createAction in future
* for now, not importing const because it breaks tests
*/
- this.store$.dispatch(viewerStateNewViewer ({
- selectTemplate: template,
- selectParcellation: parcellation,
- navigation,
- }))
+ this.store$.dispatch(
+ viewerStateSelectTemplateWithId({
+ payload: {
+ '@id': template['@id'] || template['fullId']
+ },
+ config: {
+ selectParcellation: {
+ '@id': parcellation['@id'] || parcellation['fullId']
+ }
+ }
+ })
+ )
}
}
diff --git a/src/services/templateCoordinatesTransformation.service.spec.ts b/src/services/templateCoordinatesTransformation.service.spec.ts
index 08906f068..0aa477d10 100644
--- a/src/services/templateCoordinatesTransformation.service.spec.ts
+++ b/src/services/templateCoordinatesTransformation.service.spec.ts
@@ -33,8 +33,8 @@ describe('templateCoordinatesTransformation.service.spec.ts', () => {
// subscriptions are necessary for http fetch to occur
service.getPointCoordinatesForTemplate(
- 'from',
- 'target',
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.MNI152,
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
[1,2,3]
).subscribe((_ev) => {
@@ -44,8 +44,8 @@ describe('templateCoordinatesTransformation.service.spec.ts', () => {
expect(
JSON.parse(req.request.body)
).toEqual({
- 'source_space': 'from',
- 'target_space': 'target',
+ 'source_space': TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.MNI152,
+ 'target_space': TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
'source_points': [
[1e-6, 2e-6, 3e-6]
]
@@ -53,14 +53,41 @@ describe('templateCoordinatesTransformation.service.spec.ts', () => {
req.flush({})
})
+ it('transforms mapped space name(s)', () => {
+ const service = TestBed.inject(TemplateCoordinatesTransformation)
+ const httpTestingController = TestBed.inject(HttpTestingController)
+
+ const key = Array.from(TemplateCoordinatesTransformation.NameMap.keys())[0]
+ service.getPointCoordinatesForTemplate(
+ key,
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
+ [1,2,3]
+ ).subscribe((_ev) => {
+
+ })
+ const req = httpTestingController.expectOne(service.url)
+ expect(req.request.method).toEqual('POST')
+ expect(
+ JSON.parse(req.request.body)
+ ).toEqual({
+ 'source_space': TemplateCoordinatesTransformation.NameMap.get(key),
+ 'target_space': TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
+ 'source_points': [
+ [1e-6, 2e-6, 3e-6]
+ ]
+ })
+ req.flush({})
+ })
+
+
it('should transform response properly', () => {
const service = TestBed.inject(TemplateCoordinatesTransformation)
const httpTestingController = TestBed.inject(HttpTestingController)
service.getPointCoordinatesForTemplate(
- 'from',
- 'target',
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.MNI152,
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
[1,2,3]
).subscribe(({ status, result }) => {
expect(status).toEqual('completed')
@@ -79,8 +106,8 @@ describe('templateCoordinatesTransformation.service.spec.ts', () => {
const httpTestingController = TestBed.inject(HttpTestingController)
service.getPointCoordinatesForTemplate(
- 'from',
- 'target',
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.MNI152,
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
[1,2,3]
).subscribe(({ status }) => {
expect(status).toEqual('error')
@@ -96,8 +123,8 @@ describe('templateCoordinatesTransformation.service.spec.ts', () => {
const httpTestingController = TestBed.inject(HttpTestingController)
service.getPointCoordinatesForTemplate(
- 'from',
- 'target',
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.MNI152,
+ TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN,
[1,2,3]
).subscribe(({ status, statusText }) => {
expect(status).toEqual('error')
diff --git a/src/services/templateCoordinatesTransformation.service.ts b/src/services/templateCoordinatesTransformation.service.ts
index 6aaf98b99..2c6f4fce9 100644
--- a/src/services/templateCoordinatesTransformation.service.ts
+++ b/src/services/templateCoordinatesTransformation.service.ts
@@ -14,6 +14,18 @@ export interface ITemplateCoordXformResp{
})
export class TemplateCoordinatesTransformation {
+ static VALID_TEMPLATE_SPACE_NAMES = {
+ MNI152: 'MNI 152 ICBM 2009c Nonlinear Asymmetric',
+ COLIN27: 'MNI Colin 27',
+ BIG_BRAIN: 'Big Brain (Histology)',
+ INFANT: 'Infant Atlas',
+ }
+
+ static NameMap = new Map([
+ ['MNI152 2009c nonl asym', TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.MNI152],
+ ["Big Brain", TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES.BIG_BRAIN]
+ ])
+
constructor(private httpClient: HttpClient) {}
public url = `${SPATIAL_TRANSFORM_BACKEND.replace(/\/$/, '')}/v1/transform-points`
@@ -27,12 +39,20 @@ export class TemplateCoordinatesTransformation {
'Content-Type': 'application/json'
})
}
+ const srcTmplName = Object.values(TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES).includes(sourceTemplateName)
+ ? sourceTemplateName
+ : TemplateCoordinatesTransformation.NameMap.get(sourceTemplateName)
+
+ const targetTmplName = Object.values(TemplateCoordinatesTransformation.VALID_TEMPLATE_SPACE_NAMES).includes(targetTemplateName)
+ ? targetTemplateName
+ : TemplateCoordinatesTransformation.NameMap.get(targetTemplateName)
+
return this.httpClient.post(
this.url,
JSON.stringify({
'source_points': [[...coordinatesInNm.map(c => c/1e6)]],
- 'source_space': sourceTemplateName,
- 'target_space': targetTemplateName
+ 'source_space': srcTmplName,
+ 'target_space': targetTmplName
}),
httpOptions
).pipe(
--
GitLab