diff --git a/common/constants.js b/common/constants.js
index c5f7c056767d940539781b8a96efeee7d321fb6f..580136b22ef41d52cd3abebd38c0de8853ac7a6f 100644
--- a/common/constants.js
+++ b/common/constants.js
@@ -14,6 +14,9 @@
SHOW_ORIGIN_DATASET: `Show probabilistic map`,
SHOW_CONNECTIVITY_DATA: `Show connectivity data`,
SHOW_IN_OTHER_REF_SPACE: `Show in other reference space`,
- AVAILABILITY_IN_OTHER_REF_SPACE: 'Availability in other reference spaces'
+ AVAILABILITY_IN_OTHER_REF_SPACE: 'Availability in other reference spaces',
+
+ // additional volumes
+ TOGGLE_SHOW_LAYER_CONTROL: `Show layer control`,
}
})(typeof exports === 'undefined' ? module.exports : exports)
diff --git a/docs/releases/v2.2.1.md b/docs/releases/v2.2.1.md
new file mode 100644
index 0000000000000000000000000000000000000000..1934dc90e4a65c5cc990c948d392076602d4e490
--- /dev/null
+++ b/docs/releases/v2.2.1.md
@@ -0,0 +1,7 @@
+# v2.2.1
+
+26 May 2020
+
+## Bugfixes
+
+- fixed connectivity menu showing non existent connectivity data
diff --git a/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js b/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js
index b5cb270a7850655d8b580fa9f3f5ab7ff31935fb..42969809b7a962b46ac912fdcfeec99af8bec2ae 100644
--- a/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js
+++ b/e2e/src/advanced/browsingForDatasets.prod.e2e-spec.js
@@ -67,7 +67,7 @@ const area = 'Area hOc1 (V1, 17, CalcS)'
const receptorName = `Density measurements of different receptors for Area hOc1 (V1, 17, CalcS) [human, v1.0]`
-describe('> dataset previews', () => {
+describe('> receptor dataset previews', () => {
let iavPage
beforeEach(async () => {
iavPage = new AtlasPage()
@@ -121,4 +121,41 @@ describe('> dataset previews', () => {
const modalHasImage = await iavPage.modalHasChild('div[data-img-src]')
expect(modalHasImage).toEqual(true)
})
-})
\ No newline at end of file
+})
+
+describe('> pmap dataset preview', () => {
+ let iavPage
+
+ beforeAll(async () => {
+ // loads pmap and centers on hot spot
+ const url = `/?templateSelected=MNI+152+ICBM+2009c+Nonlinear+Asymmetric&parcellationSelected=JuBrain+Cytoarchitectonic+Atlas&cNavigation=0.0.0.-W000..2_ZG29.-ASCS.2-8jM2._aAY3..BSR0..dABI~.525x0~.7iMV..1EPC&niftiLayers=https%3A%2F%2Fneuroglancer.humanbrainproject.eu%2Fprecomputed%2FJuBrain%2F17%2Ficbm152casym%2Fpmaps%2FVisual_hOc1_l_N10_nlin2MNI152ASYM2009C_2.4_publicP_d3045ee3c0c4de9820eb1516d2cc72bb.nii.gz&previewingDatasetFiles=%5B%7B"datasetId"%3A"minds%2Fcore%2Fdataset%2Fv1.0.0%2F5c669b77-c981-424a-858d-fe9f527dbc07"%2C"filename"%3A"Area+hOc1+%28V1%2C+17%2C+CalcS%29+%5Bv2.4%2C+ICBM+2009c+Asymmetric%2C+left+hemisphere%5D"%7D%5D`
+ iavPage = new AtlasPage()
+ await iavPage.init()
+ await iavPage.goto(url)
+ await iavPage.waitUntilAllChunksLoaded()
+ })
+
+ it('> can display pmap', async () => {
+ const { red, green, blue } = await iavPage.getRgbAt({position: [200, 597]})
+ expect(red).toBeGreaterThan(green)
+ expect(red).toBeGreaterThan(blue)
+ })
+
+ it('> on update of layer control, pmap retains', async () => {
+ // by default, additional layer control is collapsed
+ await iavPage.toggleLayerControl()
+ await iavPage.wait(500)
+ await iavPage.toggleNthLayerControl(0)
+ await iavPage.wait(5500)
+
+ // interact with control
+ await iavPage.click(`[aria-label="Remove background"]`)
+ await iavPage.wait(500)
+
+ // color map should be unchanged
+ const { red, green, blue } = await iavPage.getRgbAt({position: [200, 597]})
+ expect(red).toBeGreaterThan(green)
+ expect(red).toBeGreaterThan(blue)
+
+ })
+})
diff --git a/e2e/src/advanced/urlParsing.prod.e2e-spec.js b/e2e/src/advanced/urlParsing.prod.e2e-spec.js
index 944dce4faf6e16b829a2496118803bac1150180a..21c9c6b33183574cd811e128e22fbd80b6ba2175 100644
--- a/e2e/src/advanced/urlParsing.prod.e2e-spec.js
+++ b/e2e/src/advanced/urlParsing.prod.e2e-spec.js
@@ -67,35 +67,7 @@ describe('> url parsing', () => {
await iavPage.goto(url)
await iavPage.clearAlerts()
- // TODO use screenshot API when merg v2.3.0
- const screenshotData = await iavPage._driver.takeScreenshot()
- const [ red, green, blue ] = await iavPage._driver.executeAsyncScript(() => {
-
- const dataUri = arguments[0]
- const pos = arguments[1]
- const dim = arguments[2]
- const cb = arguments[arguments.length - 1]
-
- const img = new Image()
- img.onload = () => {
- const canvas = document.createElement('canvas')
- canvas.width = dim[0]
- canvas.height = dim[1]
-
- const ctx = canvas.getContext('2d')
- ctx.drawImage(img, 0, 0)
- const imgData = ctx.getImageData(0, 0, dim[0], dim[1])
-
- const idx = (dim[0] * pos[1] + pos[0]) * 4
- const red = imgData.data[idx]
- const green = imgData.data[idx + 1]
- const blue = imgData.data[idx + 2]
- cb([red, green, blue])
- }
- img.src = dataUri
-
- }, `data:image/png;base64,${screenshotData}`, [600, 490], [800, 796])
-
+ const { red, green, blue } = await iavPage.getRgbAt({ position: [600, 490] })
expect(red).toBeGreaterThan(0)
expect(red).toEqual(green)
expect(red).toEqual(blue)
@@ -106,34 +78,7 @@ describe('> url parsing', () => {
await iavPage.goto(url)
await iavPage.clearAlerts()
- // TODO use screenshot API when merg v2.3.0
- const screenshotData = await iavPage._driver.takeScreenshot()
- const [ red, green, blue ] = await iavPage._driver.executeAsyncScript(() => {
-
- const dataUri = arguments[0]
- const pos = arguments[1]
- const dim = arguments[2]
- const cb = arguments[arguments.length - 1]
-
- const img = new Image()
- img.onload = () => {
- const canvas = document.createElement('canvas')
- canvas.width = dim[0]
- canvas.height = dim[1]
-
- const ctx = canvas.getContext('2d')
- ctx.drawImage(img, 0, 0)
- const imgData = ctx.getImageData(0, 0, dim[0], dim[1])
-
- const idx = (dim[0] * pos[1] + pos[0]) * 4
- const red = imgData.data[idx]
- const green = imgData.data[idx + 1]
- const blue = imgData.data[idx + 2]
- cb([red, green, blue])
- }
- img.src = dataUri
-
- }, `data:image/png;base64,${screenshotData}`, [600, 490], [800, 796])
+ const { red, green, blue } = await iavPage.getRgbAt({ position: [600, 490] })
expect(red).toBeGreaterThan(0)
expect(red).toEqual(green)
diff --git a/e2e/src/layout/scrollDatasetContainer.prod.e2e-spec.js b/e2e/src/layout/scrollDatasetContainer.prod.e2e-spec.js
index 7d80e04fcb7edce754ba20e99afcd28c562c2b19..198be8f230c3c3acddcad6e70dd7123cd57221cf 100644
--- a/e2e/src/layout/scrollDatasetContainer.prod.e2e-spec.js
+++ b/e2e/src/layout/scrollDatasetContainer.prod.e2e-spec.js
@@ -37,6 +37,8 @@ describe('> scroll dataset container', () => {
countdown --
}while(countdown > 0)
+ await iavPage.wait(500)
+
const val = await iavPage.getScrollStatus(scrollContainerCssSelector)
expect(val).toBeGreaterThanOrEqual(10000)
})
diff --git a/e2e/src/material-util.js b/e2e/src/material-util.js
new file mode 100644
index 0000000000000000000000000000000000000000..04f9c994fac5310b6d1c50ab915ec3f1ddcc215f
--- /dev/null
+++ b/e2e/src/material-util.js
@@ -0,0 +1,19 @@
+const { By } = require('selenium-webdriver')
+
+async function polyFillClick(cssSelector){
+ if (!cssSelector) throw new Error(`click method needs to define a css selector`)
+ const webEl = this._browser.findElement( By.css(cssSelector) )
+ try {
+ await webEl.click()
+ } catch (e) {
+ const id = await webEl.getAttribute('id')
+ const newId = id.replace(/-input$/, '')
+ await this._browser.findElement(
+ By.id(newId)
+ ).click()
+ }
+}
+
+module.exports = {
+ polyFillClick
+}
diff --git a/e2e/src/util.js b/e2e/src/util.js
index 134ca978f603c656f3b11210ea8984e2615d1219..2830aad1c7c81f861237514157ed24cb3db95917 100644
--- a/e2e/src/util.js
+++ b/e2e/src/util.js
@@ -6,6 +6,9 @@ if (ATLAS_URL.length === 0) throw new Error(`ATLAS_URL must either be left unset
if (ATLAS_URL[ATLAS_URL.length - 1] === '/') throw new Error(`ATLAS_URL should not trail with a slash: ${ATLAS_URL}`)
const { By, WebDriver, Key } = require('selenium-webdriver')
const CITRUS_LIGHT_URL = `https://unpkg.com/citruslight@0.1.0/citruslight.js`
+const { polyFillClick } = require('./material-util')
+
+const { ARIA_LABELS } = require('../../common/constants')
function getActualUrl(url) {
return /^http\:\/\//.test(url) ? url : `${ATLAS_URL}/${url.replace(/^\//, '')}`
@@ -92,6 +95,40 @@ class WdBase{
return result
}
+ async getRgbAt({ position } = {}, cssSelector = null){
+ if (!position) throw new Error(`position is required for getRgbAt`)
+ const { x, y } = verifyPosition(position)
+ const screenshotData = await this.takeScreenshot(cssSelector)
+ const [ red, green, blue ] = await this._driver.executeAsyncScript(() => {
+
+ const dataUri = arguments[0]
+ const pos = arguments[1]
+ const dim = arguments[2]
+ const cb = arguments[arguments.length - 1]
+
+ const img = new Image()
+ img.onload = () => {
+ const canvas = document.createElement('canvas')
+ canvas.width = dim[0]
+ canvas.height = dim[1]
+
+ const ctx = canvas.getContext('2d')
+ ctx.drawImage(img, 0, 0)
+ const imgData = ctx.getImageData(0, 0, dim[0], dim[1])
+
+ const idx = (dim[0] * pos[1] + pos[0]) * 4
+ const red = imgData.data[idx]
+ const green = imgData.data[idx + 1]
+ const blue = imgData.data[idx + 2]
+ cb([red, green, blue])
+ }
+ img.src = dataUri
+
+ }, `data:image/png;base64,${screenshotData}`, [x, y], [800, 796])
+
+ return { red, green, blue }
+ }
+
async switchIsChecked(cssSelector){
if (!cssSelector) throw new Error(`switchChecked method requies css selector`)
const checked = await this._browser
@@ -101,8 +138,7 @@ class WdBase{
}
async click(cssSelector){
- if (!cssSelector) throw new Error(`click method needs to define a css selector`)
- await this._browser.findElement( By.css(cssSelector) ).click()
+ return await polyFillClick.bind(this)(cssSelector)
}
async getText(cssSelector){
@@ -561,6 +597,13 @@ class WdLayoutPage extends WdBase{
.click()
}
+ async toggleNthLayerControl(idx) {
+ const els = await this._getAdditionalLayerControl()
+ .findElements( By.css(`[aria-label="${ARIA_LABELS.TOGGLE_SHOW_LAYER_CONTROL}"]`))
+ if (!els[idx]) throw new Error(`toggleNthLayerControl index out of bound: accessor ${idx} with length ${els.length}`)
+ await els[idx].click()
+ }
+
// Signin banner
_getToolsIcon(){
return this._driver
diff --git a/mkdocs.yml b/mkdocs.yml
index e2436413086040713a7cc5eef21856c5a5d2ae8b..25324af62f39c497367e7fa3f87218518c948af8 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -40,6 +40,7 @@ pages:
- Fetching datasets: 'advanced/datasets.md'
- Display non-atlas volumes: 'advanced/otherVolumes.md'
- Release notes:
+ - v2.2.1: 'releases/v2.2.1.md'
- v2.2.0: 'releases/v2.2.0.md'
- v2.1.3: 'releases/v2.1.3.md'
- v2.1.2: 'releases/v2.1.2.md'
diff --git a/src/atlasViewer/atlasViewer.constantService.service.ts b/src/atlasViewer/atlasViewer.constantService.service.ts
index 30cde5aded6877e7df1624f37333c1e17135d61b..ce7645f1ee5fa466f61470866c3a92b2fd1b1463 100644
--- a/src/atlasViewer/atlasViewer.constantService.service.ts
+++ b/src/atlasViewer/atlasViewer.constantService.service.ts
@@ -9,8 +9,6 @@ import { IavRootStoreInterface } from "../services/stateStore.service";
import { AtlasWorkerService } from "./atlasViewer.workerService.service";
export const CM_THRESHOLD = `0.05`
-export const CM_MATLAB_JET = `float r;if( x < 0.7 ){r = 4.0 * x - 1.5;} else {r = -4.0 * x + 4.5;}float g;if (x < 0.5) {g = 4.0 * x - 0.5;} else {g = -4.0 * x + 3.5;}float b;if (x < 0.3) {b = 4.0 * x + 0.5;} else {b = -4.0 * x + 2.5;}float a = 1.0;`
-export const GLSL_COLORMAP_JET = `void main(){float x = toNormalized(getDataValue());${CM_MATLAB_JET}if(x>${CM_THRESHOLD}){emitRGB(vec3(r,g,b));}else{emitTransparent();}}`
const getUniqueId = () => Math.round(Math.random() * 1e16).toString(16)
diff --git a/src/atlasViewer/atlasViewer.urlUtil.ts b/src/atlasViewer/atlasViewer.urlUtil.ts
index 025980709189be5ae41b6189e782011ecd9976ea..6447f1f7fb7b7d8860121eb3ef573cbe1a64f524 100644
--- a/src/atlasViewer/atlasViewer.urlUtil.ts
+++ b/src/atlasViewer/atlasViewer.urlUtil.ts
@@ -2,8 +2,9 @@ import { getGetRegionFromLabelIndexId } from "src/services/effect/effect";
import { mixNgLayers } from "src/services/state/ngViewerState.store";
import { PLUGINSTORE_CONSTANTS } from 'src/services/state/pluginState.store'
import { generateLabelIndexId, getNgIdLabelIndexFromRegion, IavRootStoreInterface } from "../services/stateStore.service";
-import { decodeToNumber, encodeNumber, GLSL_COLORMAP_JET, separator } from "./atlasViewer.constantService.service";
+import { decodeToNumber, encodeNumber, separator } from "./atlasViewer.constantService.service";
import { GetKgSchemaIdFromFullIdPipe } from "src/ui/databrowserModule/util/getKgSchemaIdFromFullId.pipe";
+import { getShader, PMAP_DEFAULT_CONFIG } from "src/util/constants";
const getKgSchemaIdFromFullIdPipe = new GetKgSchemaIdFromFullIdPipe()
@@ -304,7 +305,7 @@ export const cvtSearchParamToState = (searchparams: URLSearchParams, state: IavR
name : layer,
source : `nifti://${layer}`,
mixability : 'nonmixable',
- shader : GLSL_COLORMAP_JET,
+ shader : getShader(PMAP_DEFAULT_CONFIG),
} as any
})
const { ngViewerState } = returnState
diff --git a/src/ui/cookieAgreement/data/readmore.md b/src/ui/cookieAgreement/data/readmore.md
index 243cfe802f6e3ea3bef24c0238b5e6c12308e54a..6692141e5199aa2c7270c70e1ba7dce9f302ea2b 100644
--- a/src/ui/cookieAgreement/data/readmore.md
+++ b/src/ui/cookieAgreement/data/readmore.md
@@ -1,6 +1,6 @@
**Data controller(s)**: HBP Atlas Viewer is the data controller for your login information.
**List of partners responsible**: HBP Atlas Viewer is the data controller for your login information.
-**HBP Data Protection Officer (HBP DPO)**: FZJ-INM1 <inm1-bda@fz-juelich.de>
+**HBP Data Protection Officer (HBP DPO)**: <data.protection@humanbrainproject.eu>
**Legal basis for data processing**: You can find out about HBP Data Protection policies here: <https://www.humanbrainproject.eu/en/social-ethical-reflective/ethics-support/data-protection/> and you can contact HBP Data Protection Officer at <data.protection@humanbrainproject.eu>
**General categories of personal data collected**: consent
**Data shared within the HBP Consortium**: Name, ORC ID, JWT ID Token
diff --git a/src/ui/databrowserModule/databrowser.useEffect.ts b/src/ui/databrowserModule/databrowser.useEffect.ts
index 7a55fe649643910505bf5c09e541e1740f6137ab..74eb19f0218e1df91ddd40d81f50b28a4b868d12 100644
--- a/src/ui/databrowserModule/databrowser.useEffect.ts
+++ b/src/ui/databrowserModule/databrowser.useEffect.ts
@@ -6,10 +6,9 @@ import { filter, map, scan, switchMap, withLatestFrom, mapTo, shareReplay, start
import { LoggingService } from "src/logging";
import { DATASETS_ACTIONS_TYPES, IDataEntry, ViewerPreviewFile, DatasetPreview } from "src/services/state/dataStore.store";
import { IavRootStoreInterface, ADD_NG_LAYER, CHANGE_NAVIGATION } from "src/services/stateStore.service";
-import { LOCAL_STORAGE_CONST, DS_PREVIEW_URL } from "src/util/constants";
+import { LOCAL_STORAGE_CONST, DS_PREVIEW_URL, getShader, PMAP_DEFAULT_CONFIG } from "src/util/constants";
import { KgSingleDatasetService } from "./kgSingleDatasetService.service";
import { determinePreviewFileType, PREVIEW_FILE_TYPES, PREVIEW_FILE_TYPES_NO_UI } from "./preview/previewFileIcon.pipe";
-import { GLSL_COLORMAP_JET } from "src/atlasViewer/atlasViewer.constantService.service";
import { SHOW_BOTTOM_SHEET } from "src/services/state/uiState.store";
import { MatSnackBar } from "@angular/material/snack-bar";
import { MatDialog } from "@angular/material/dialog";
@@ -293,7 +292,7 @@ export class DataBrowserUseEffect implements OnDestroy {
name: filename,
source : `nifti://${url}`,
mixability : 'nonmixable',
- shader : GLSL_COLORMAP_JET,
+ shader : getShader(PMAP_DEFAULT_CONFIG),
annotation: `${DATASET_PREVIEW_ANNOTATION} ${filename}`
}
return {
diff --git a/src/ui/layerbrowser/layerDetail/layerDetail.component.spec.ts b/src/ui/layerbrowser/layerDetail/layerDetail.component.spec.ts
index 9d88ec67995546615a0a3e9d6c261b11495460cb..c628d46e0476638c993a44d86a6975d2b17041aa 100644
--- a/src/ui/layerbrowser/layerDetail/layerDetail.component.spec.ts
+++ b/src/ui/layerbrowser/layerDetail/layerDetail.component.spec.ts
@@ -1,8 +1,9 @@
-import { LayerDetailComponent } from './layerDetail.component'
+import { LayerDetailComponent, VIEWER_INJECTION_TOKEN } from './layerDetail.component'
import { async, TestBed } from '@angular/core/testing'
import { NgLayersService } from '../ngLayerService.service'
import { UIModule } from 'src/ui/ui.module'
import { By } from '@angular/platform-browser'
+import * as CONSTANT from 'src/util/constants'
const getSpies = (service: NgLayersService) => {
const lowThMapGetSpy = spyOn(service.lowThresholdMap, 'get').and.callThrough()
@@ -65,8 +66,19 @@ const getSliderChangeTest = ctrlName => describe(`testing: ${ctrlName}`, () => {
})
})
-describe('layerDetail.component.ts', () => {
- describe('LayerDetailComponent', () => {
+const fragmentMainSpy = {
+ value: `test value`,
+ restoreState: () => {}
+}
+
+const defaultViewer = {
+ layerManager: {
+ getLayerByName: jasmine.createSpy('getLayerByName').and.returnValue({layer: {fragmentMain: fragmentMainSpy}})
+ }
+}
+
+describe('> layerDetail.component.ts', () => {
+ describe('> LayerDetailComponent', () => {
beforeEach(async(() => {
TestBed.configureTestingModule({
@@ -74,21 +86,28 @@ describe('layerDetail.component.ts', () => {
UIModule
],
providers: [
- NgLayersService
+ NgLayersService,
+ {
+ provide: VIEWER_INJECTION_TOKEN,
+ useValue: defaultViewer
+ }
]
}).compileComponents()
}))
- describe('basic', () => {
+ describe('> basic funcitonalities', () => {
- it('should be created', () => {
+ it('> it should be created', () => {
const fixture = TestBed.createComponent(LayerDetailComponent)
const element = fixture.debugElement.componentInstance
expect(element).toBeTruthy()
})
- it('on bind input, if input is truthy, calls get on layerService maps', () => {
+ it('> on bind input, if input is truthy, calls get on layerService maps', () => {
const service = TestBed.inject(NgLayersService)
+ TestBed.overrideProvider(VIEWER_INJECTION_TOKEN, {
+ useValue: {}
+ })
const {
brightnessMapGetSpy,
contractMapGetSpy,
@@ -109,7 +128,7 @@ describe('layerDetail.component.ts', () => {
expect(removeBgMapGetSpy).toHaveBeenCalledWith(layerName)
})
- it('on bind input, if input is falsy, does not call layerService map get', () => {
+ it('> on bind input, if input is falsy, does not call layerService map get', () => {
const service = TestBed.inject(NgLayersService)
const {
brightnessMapGetSpy,
@@ -144,8 +163,6 @@ describe('layerDetail.component.ts', () => {
getSliderChangeTest(sliderCtrl)
}
- // TODO test remove bg toggle
-
describe('testing: removeBG toggle', () => {
it('on change, calls window', () => {
@@ -177,6 +194,9 @@ describe('layerDetail.component.ts', () => {
describe('triggerChange', () => {
it('should throw if viewer is not defined', () => {
+ TestBed.overrideProvider(VIEWER_INJECTION_TOKEN, {
+ useValue: null
+ })
const fixutre = TestBed.createComponent(LayerDetailComponent)
expect(function(){
fixutre.componentInstance.triggerChange()
@@ -184,16 +204,21 @@ describe('layerDetail.component.ts', () => {
})
it('should throw if layer is not found', () => {
- const fixutre = TestBed.createComponent(LayerDetailComponent)
- const layerName = `test-kitty`
const fakeGetLayerByName = jasmine.createSpy().and.returnValue(undefined)
const fakeNgInstance = {
layerManager: {
getLayerByName: fakeGetLayerByName
}
}
+
+ TestBed.overrideProvider(VIEWER_INJECTION_TOKEN, {
+ useValue: fakeNgInstance
+ })
+
+ const fixutre = TestBed.createComponent(LayerDetailComponent)
+ const layerName = `test-kitty`
+
fixutre.componentInstance.layerName = layerName
- fixutre.componentInstance.ngViewerInstance = fakeNgInstance
expect(function(){
fixutre.componentInstance.triggerChange()
@@ -201,8 +226,6 @@ describe('layerDetail.component.ts', () => {
})
it('should throw if layer.layer.fragmentMain is undefined', () => {
-
- const fixutre = TestBed.createComponent(LayerDetailComponent)
const layerName = `test-kitty`
const fakeLayer = {
@@ -214,8 +237,14 @@ describe('layerDetail.component.ts', () => {
getLayerByName: fakeGetLayerByName
}
}
+
+ TestBed.overrideProvider(VIEWER_INJECTION_TOKEN, {
+ useValue: fakeNgInstance
+ })
+
+ const fixutre = TestBed.createComponent(LayerDetailComponent)
+
fixutre.componentInstance.layerName = layerName
- fixutre.componentInstance.ngViewerInstance = fakeNgInstance
expect(function(){
fixutre.componentInstance.triggerChange()
@@ -225,13 +254,12 @@ describe('layerDetail.component.ts', () => {
it('should call getShader and restoreState if all goes right', () => {
const replacementShader = `blabla ahder`
-
- const service = TestBed.inject(NgLayersService)
- const getShaderSpy = spyOn(service, 'getShader').and.returnValue(replacementShader)
- const fixutre = TestBed.createComponent(LayerDetailComponent)
+ const getShaderSpy = jasmine.createSpy('getShader').and.returnValue(replacementShader)
+ spyOnProperty(CONSTANT, 'getShader').and.returnValue(getShaderSpy)
+
const layerName = `test-kitty`
- const fakeRestoreState = jasmine.createSpy()
+ const fakeRestoreState = jasmine.createSpy('fakeGetLayerByName')
const fakeLayer = {
layer: {
fragmentMain: {
@@ -239,14 +267,19 @@ describe('layerDetail.component.ts', () => {
}
}
}
- const fakeGetLayerByName = jasmine.createSpy().and.returnValue(fakeLayer)
+ const fakeGetLayerByName = jasmine.createSpy('fakeGetLayerByName').and.returnValue(fakeLayer)
const fakeNgInstance = {
layerManager: {
getLayerByName: fakeGetLayerByName
}
}
+ TestBed.overrideProvider(VIEWER_INJECTION_TOKEN, {
+ useValue: fakeNgInstance
+ })
+
+ const fixutre = TestBed.createComponent(LayerDetailComponent)
fixutre.componentInstance.layerName = layerName
- fixutre.componentInstance.ngViewerInstance = fakeNgInstance
+ fixutre.detectChanges()
fixutre.componentInstance.triggerChange()
diff --git a/src/ui/layerbrowser/layerDetail/layerDetail.component.ts b/src/ui/layerbrowser/layerDetail/layerDetail.component.ts
index ea6efeafc863f1d4a9db30254b31c9d3de5249d4..ce525450d66af85854ae715723c14ff6ad6ffd35 100644
--- a/src/ui/layerbrowser/layerDetail/layerDetail.component.ts
+++ b/src/ui/layerbrowser/layerDetail/layerDetail.component.ts
@@ -1,7 +1,10 @@
-import { Component, Input, OnChanges, ChangeDetectionStrategy } from "@angular/core";
+import { Component, Input, OnChanges, ChangeDetectionStrategy, Optional, Inject } from "@angular/core";
import { NgLayersService } from "../ngLayerService.service";
import { MatSliderChange } from "@angular/material/slider";
import { MatSlideToggleChange } from "@angular/material/slide-toggle";
+import { COLORMAP_IS_JET, getShader, PMAP_DEFAULT_CONFIG } from "src/util/constants";
+
+export const VIEWER_INJECTION_TOKEN = `VIEWER_INJECTION_TOKEN`
@Component({
selector: 'layer-detail-cmp',
@@ -13,15 +16,26 @@ export class LayerDetailComponent implements OnChanges{
@Input()
layerName: string
- @Input()
- ngViewerInstance: any
+ private colormap = null
- constructor(private layersService: NgLayersService){
+ constructor(
+ private layersService: NgLayersService,
+ @Optional() @Inject(VIEWER_INJECTION_TOKEN) private injectedViewer
+ ){
}
ngOnChanges(){
if (!this.layerName) return
+
+ const isPmap = (this.fragmentMain.value as string).includes(COLORMAP_IS_JET)
+ const { colormap, lowThreshold, removeBg } = PMAP_DEFAULT_CONFIG
+ if (isPmap) {
+ this.colormap = colormap
+ this.lowThreshold = lowThreshold
+ this.removeBg = removeBg
+ }
+
this.lowThreshold = this.layersService.lowThresholdMap.get(this.layerName) || this.lowThreshold
this.highThreshold = this.layersService.highThresholdMap.get(this.layerName) || this.highThreshold
this.brightness = this.layersService.brightnessMap.get(this.layerName) || this.brightness
@@ -65,21 +79,29 @@ export class LayerDetailComponent implements OnChanges{
}
triggerChange(){
+ const { lowThreshold, highThreshold, brightness, contrast, removeBg, colormap } = this
+ const shader = getShader({
+ lowThreshold,
+ highThreshold,
+ colormap,
+ brightness,
+ contrast,
+ removeBg
+ })
+ this.fragmentMain.restoreState(shader)
+ }
+
+ private get viewer(){
+ return this.injectedViewer || (window as any).viewer
+ }
+
+ private get fragmentMain(){
+
if (!this.viewer) throw new Error(`viewer is not defined`)
const layer = this.viewer.layerManager.getLayerByName(this.layerName)
if (!layer) throw new Error(`layer with name: ${this.layerName}, not found.`)
if (! (layer.layer?.fragmentMain?.restoreState) ) throw new Error(`layer.fragmentMain is not defined... is this an image layer?`)
- const shader = this.layersService.getShader(
- this.lowThreshold,
- this.highThreshold,
- this.brightness,
- this.contrast,
- this.removeBg
- )
- layer.layer.fragmentMain.restoreState(shader)
- }
- get viewer(){
- return this.ngViewerInstance || (window as any).viewer
+ return layer.layer.fragmentMain
}
}
diff --git a/src/ui/layerbrowser/layerDetail/layerDetail.template.html b/src/ui/layerbrowser/layerDetail/layerDetail.template.html
index ef47a9b904dcd3a1c72d9380b21073d4df62965b..376b875c3ffd924a5a69166d2555104cae0c0390 100644
--- a/src/ui/layerbrowser/layerDetail/layerDetail.template.html
+++ b/src/ui/layerbrowser/layerDetail/layerDetail.template.html
@@ -72,7 +72,7 @@
<mat-slide-toggle
aria-label="Remove background"
(change)="handleToggleBg($event)"
- [value]="removeBg">
+ [(ngModel)]="removeBg">
</mat-slide-toggle>
</div>
diff --git a/src/ui/layerbrowser/layerbrowser.component.ts b/src/ui/layerbrowser/layerbrowser.component.ts
index 91121d8f27731c516768eadbc6dc62de728a2c8b..aa6e069a4e53d763030bd53989ab89ff6cc762dc 100644
--- a/src/ui/layerbrowser/layerbrowser.component.ts
+++ b/src/ui/layerbrowser/layerbrowser.component.ts
@@ -9,6 +9,7 @@ import { getViewer } from "src/util/fn";
import { INgLayerInterface } from "../../atlasViewer/atlasViewer.component";
import { FORCE_SHOW_SEGMENT, getNgIds, isDefined, REMOVE_NG_LAYER, safeFilter, ViewerStateInterface, IavRootStoreInterface } from "../../services/stateStore.service";
import { MatSliderChange } from "@angular/material/slider";
+import { ARIA_LABELS } from 'common/constants'
@Component({
selector : 'layer-browser',
@@ -21,6 +22,8 @@ import { MatSliderChange } from "@angular/material/slider";
export class LayerBrowser implements OnInit, OnDestroy {
+ public TOGGLE_SHOW_LAYER_CONTROL_ARIA_LABEL = ARIA_LABELS.TOGGLE_SHOW_LAYER_CONTROL
+
@Output() public nonBaseLayersChanged: EventEmitter<INgLayerInterface[]> = new EventEmitter()
/**
diff --git a/src/ui/layerbrowser/layerbrowser.template.html b/src/ui/layerbrowser/layerbrowser.template.html
index 4c50cf9506371c4c236dc8d89dfd10e6cd1d6942..f34b2ea8b77315f7a2b54f39d237c21b469c4a5d 100644
--- a/src/ui/layerbrowser/layerbrowser.template.html
+++ b/src/ui/layerbrowser/layerbrowser.template.html
@@ -13,7 +13,7 @@
class="layer-expansion-unit"
#expansionPanel>
<mat-expansion-panel-header>
- <div class="align-items-center d-flex flex-nowrap pr-4">
+ <div class="align-items-center d-flex flex-nowrap pr-4 w-100">
<!-- toggle opacity -->
<div matTooltip="opacity">
@@ -70,11 +70,12 @@
<mat-label
[matTooltipPosition]="matTooltipPosition"
[matTooltip]="ngLayer.name | getFilenamePipe "
- [class]="((darktheme$ | async) ? 'text-light' : 'text-dark') + ' text-truncate'">
+ [class]="((darktheme$ | async) ? 'text-light' : 'text-dark') + ' text-truncate flex-grow-1 flex-shrink-1'">
{{ ngLayer.name | getFilenamePipe }}
</mat-label>
<button mat-icon-button
+ [attr.aria-label]="TOGGLE_SHOW_LAYER_CONTROL_ARIA_LABEL"
(click)="expansionPanel.toggle()">
<ng-container *ngIf="expansionPanel.expanded; else btnIconAlt">
<i class="fas fa-chevron-up"></i>
diff --git a/src/ui/layerbrowser/ngLayerService.service.ts b/src/ui/layerbrowser/ngLayerService.service.ts
index fefb5b7c4675cfac110a02c5008f462c0de5592f..baf59a9a4191c27ea5ddffb72629148cdb1a1ab9 100644
--- a/src/ui/layerbrowser/ngLayerService.service.ts
+++ b/src/ui/layerbrowser/ngLayerService.service.ts
@@ -1,22 +1,5 @@
import { Injectable } from "@angular/core";
-const setGetShaderFn = (normalizedIncomingColor) => (lowerThreshold, upperThreshold, brightness, contrast, removeBg: boolean) => `
-void main() {
- float raw_x = toNormalized(getDataValue());
- float x = (raw_x - ${lowerThreshold.toFixed(5)}) / (${(upperThreshold - lowerThreshold).toFixed(5)}) ${brightness > 0 ? '+' : '-'} ${Math.abs(brightness).toFixed(5)};
-
- ${ removeBg ? 'if(x>1.0){ emitTransparent(); }else if (x<0.0){ emitTransparent(); }else{' : '' }
-
- emitRGB(vec3(
- x * ${normalizedIncomingColor[0].toFixed(5)}, x * ${normalizedIncomingColor[1].toFixed(5)}, x * ${normalizedIncomingColor[2].toFixed(5)})
- * exp(${contrast.toFixed(5)})
- );
-
- ${ removeBg ? '}' : '' }
-
-}
-`
-
@Injectable({
providedIn: 'root'
})
@@ -27,5 +10,4 @@ export class NgLayersService{
public brightnessMap: Map<string, number> = new Map()
public contrastMap: Map<string, number> = new Map()
public removeBgMap: Map<string, boolean> = new Map()
- public getShader: (low: number, high: number, brightness: number, contrast: number, removeBg: boolean) => string = setGetShaderFn([1, 1, 1])
}
diff --git a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
index 4d538936d97e6f385673e486683d3f263b06ca5f..d4f008803fae1a52450fa862010319c168e7a609 100644
--- a/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
+++ b/src/ui/parcellationRegion/regionMenu/regionMenu.template.html
@@ -138,7 +138,7 @@
</mat-list-item>
<!-- connectivity -->
- <div iav-switch #connectivitySwitch="iavSwitch">
+ <div *ngIf="hasConnectivity" iav-switch #connectivitySwitch="iavSwitch">
<mat-list-item mat-ripple
(click)="connectivitySwitch.toggle()"
diff --git a/src/util/constants.ts b/src/util/constants.ts
index bfb83d130f37e87b74f201971016e38012127395..8a56a7ceaa97c2c654be25e3d49df77dd191d1f4 100644
--- a/src/util/constants.ts
+++ b/src/util/constants.ts
@@ -66,4 +66,39 @@ export const getHttpHeader: () => HttpHeaders = () => {
const header = new HttpHeaders()
header.set('referrer', getScopedReferer())
return header
-}
\ No newline at end of file
+}
+
+const CM_MATLAB_JET = `float r;if( x < 0.7 ){r = 4.0 * x - 1.5;} else {r = -4.0 * x + 4.5;}float g;if (x < 0.5) {g = 4.0 * x - 0.5;} else {g = -4.0 * x + 3.5;}float b;if (x < 0.3) {b = 4.0 * x + 0.5;} else {b = -4.0 * x + 2.5;}float a = 1.0;`
+const CM_DEFAULT = `float r = x; float g = x; float b = x;`
+export const COLORMAP_IS_JET = `// iav-colormap-is-jet`
+export const COLORMAP_IS_DEFAULT = `// iav-colormap-default`
+
+export const getShader = ({
+ colormap = null,
+ lowThreshold = 0,
+ highThreshold = 1,
+ brightness = 0,
+ contrast = 0,
+ removeBg = false
+} = {}): string => {
+ const header = colormap === 'jet' ? COLORMAP_IS_JET : COLORMAP_IS_DEFAULT
+ const colormapGlsl = colormap === 'jet' ? CM_MATLAB_JET : CM_DEFAULT
+ return `${header}
+void main() {
+ float raw_x = toNormalized(getDataValue());
+ float x = (raw_x - ${lowThreshold.toFixed(5)}) / (${highThreshold - lowThreshold}) ${ brightness > 0 ? '+' : '-' } ${Math.abs(brightness).toFixed(5)};
+
+ ${ removeBg ? 'if(x>1.0){emitTransparent();}else if(x<0.0){emitTransparent();}else{' : '' }
+ ${colormapGlsl}
+
+ emitRGB(vec3(r, g, b)*exp(${contrast.toFixed(5)}));
+ ${ removeBg ? '}' : '' }
+}
+`
+}
+
+export const PMAP_DEFAULT_CONFIG = {
+ colormap: 'jet',
+ lowThreshold: 0.05,
+ removeBg: true
+}