diff --git a/shapeworks_cloud/core/migrations/0037_landmarks_constraints.py b/shapeworks_cloud/core/migrations/0037_landmarks_constraints.py new file mode 100644 index 00000000..9f03f565 --- /dev/null +++ b/shapeworks_cloud/core/migrations/0037_landmarks_constraints.py @@ -0,0 +1,27 @@ +# Generated by Django 3.2.21 on 2023-11-13 17:30 + +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + dependencies = [ + ('core', '0036_analysis_multi_domain'), + ] + + operations = [ + migrations.RemoveField( + model_name='constraints', + name='optimized_particles', + ), + migrations.AddField( + model_name='constraints', + name='project', + field=models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name='constraints', + to='core.project', + ), + ), + ] diff --git a/shapeworks_cloud/core/models.py b/shapeworks_cloud/core/models.py index 83210457..e4ae00d0 100644 --- a/shapeworks_cloud/core/models.py +++ b/shapeworks_cloud/core/models.py @@ -271,11 +271,8 @@ class Constraints(TimeStampedModel, models.Model): file = S3FileField() subject = models.ForeignKey(Subject, on_delete=models.CASCADE, related_name='constraints') anatomy_type = models.CharField(max_length=255) - optimized_particles = models.ForeignKey( - OptimizedParticles, - on_delete=models.SET_NULL, - related_name='constraints', - null=True, + project = models.ForeignKey( + Project, on_delete=models.CASCADE, related_name='constraints', null=True ) diff --git a/shapeworks_cloud/core/rest.py b/shapeworks_cloud/core/rest.py index a85ac058..175699bc 100644 --- a/shapeworks_cloud/core/rest.py +++ b/shapeworks_cloud/core/rest.py @@ -1,10 +1,12 @@ import base64 +import json import os from pathlib import Path from tempfile import TemporaryDirectory, gettempdir from typing import Dict, Type from django.contrib.auth import logout +from django.core.files.base import ContentFile from django.db.models import Q from django.utils import timezone from django_filters.rest_framework import DjangoFilterBackend @@ -313,6 +315,105 @@ def download(self, request, **kwargs): project = self.get_object() return Response(serializers.ProjectDownloadSerializer(project).data) + @action( + detail=True, + url_path='landmarks', + url_name='landmarks', + methods=['POST'], + ) + def set_landmarks(self, request, **kwargs): + project = self.get_object() + form_data = request.data + landmarks_info = form_data.get('info') + landmarks_locations = form_data.get('locations') + + project.landmarks_info = landmarks_info + project_file_contents = json.loads(project.file.read()) + project_file_contents['landmarks'] = landmarks_info + project.file.save( + project.file.name.split('/')[-1], + ContentFile(json.dumps(project_file_contents).encode()), + ) + project.save() + + ids_existing_with_coords = [] + for subject_id, data in landmarks_locations.items(): + target_subject = models.Subject.objects.get(id=subject_id) + for anatomy_type, locations in data.items(): + landmarks_object, created = models.Landmarks.objects.get_or_create( + project=project, subject=target_subject, anatomy_type=anatomy_type + ) + file_content = '' + if ( + locations is not None + and len(locations) > 0 + and locations[0] is not None + and len(locations[0]) == 3 + ): + file_content = '\n'.join( + ' '.join(str(n) for n in (loc.values() if isinstance(loc, dict) else loc)) + for loc in locations + ) + file_name = 'landmarks.csv' + if landmarks_object.file: + file_name = landmarks_object.file.name.split('/')[-1] + landmarks_object.file.save( + file_name, + ContentFile(file_content.encode()), + ) + ids_existing_with_coords.append(landmarks_object.id) + + models.Landmarks.objects.filter(project=project).exclude( + id__in=ids_existing_with_coords + ).delete() + + log_write_access( + timezone.now(), + self.request.user.username, + 'Set Project Landmarks', + project.id, + ) + return Response(serializers.ProjectReadSerializer(project).data) + + @action( + detail=True, + url_path='constraints', + url_name='constraints', + methods=['POST'], + ) + def set_constraints(self, request, **kwargs): + project = self.get_object() + form_data = request.data + constraints_locations = form_data.get('locations') + + ids_existing_with_coords = [] + for subject_id, data in constraints_locations.items(): + target_subject = models.Subject.objects.get(id=subject_id) + for anatomy_type, locations in data.items(): + constraints_object, created = models.Constraints.objects.get_or_create( + project=project, subject=target_subject, anatomy_type=anatomy_type + ) + file_name = 'constraints.json' + if constraints_object.file: + file_name = constraints_object.file.name.split('/')[-1] + constraints_object.file.save( + file_name, + ContentFile(json.dumps(locations).encode()), + ) + ids_existing_with_coords.append(constraints_object.id) + + models.Constraints.objects.filter(project=project).exclude( + id__in=ids_existing_with_coords + ).delete() + + log_write_access( + timezone.now(), + self.request.user.username, + 'Set Project Constraints', + project.id, + ) + return Response(serializers.ProjectReadSerializer(project).data) + @action( detail=True, url_path='groom', diff --git a/shapeworks_cloud/core/serializers.py b/shapeworks_cloud/core/serializers.py index 267ee33c..34cc9b7b 100644 --- a/shapeworks_cloud/core/serializers.py +++ b/shapeworks_cloud/core/serializers.py @@ -12,6 +12,14 @@ class Meta: fields = '__all__' +class ConstraintsSerializer(serializers.ModelSerializer): + file = S3FileSerializerField() + + class Meta: + model = models.Constraints + fields = '__all__' + + class CachedAnalysisGroupSerializer(serializers.ModelSerializer): class Meta: model = models.CachedAnalysisGroup @@ -72,6 +80,7 @@ class ProjectReadSerializer(serializers.ModelSerializer): file = S3FileSerializerField() last_cached_analysis = CachedAnalysisReadSerializer(allow_null=True) landmarks = LandmarksSerializer(many=True) + constraints = ConstraintsSerializer(many=True) class Meta: model = models.Project @@ -168,18 +177,17 @@ class Meta: fields = '__all__' -class ConstraintsSerializer(serializers.ModelSerializer): - file = S3FileSerializerField() - - class Meta: - model = models.Constraints - fields = '__all__' - - class GroomedSegmentationSerializer(serializers.ModelSerializer): file = S3FileSerializerField() pre_cropping = S3FileSerializerField(required=False, allow_null=True) pre_alignment = S3FileSerializerField(required=False, allow_null=True) + anatomy_type = serializers.SerializerMethodField('get_anatomy_type') + + def get_anatomy_type(self, obj): + if obj.segmentation: + return obj.segmentation.anatomy_type + else: + return None class Meta: model = models.GroomedSegmentation @@ -190,6 +198,13 @@ class GroomedMeshSerializer(serializers.ModelSerializer): file = S3FileSerializerField() pre_cropping = S3FileSerializerField(required=False, allow_null=True) pre_alignment = S3FileSerializerField(required=False, allow_null=True) + anatomy_type = serializers.SerializerMethodField('get_anatomy_type') + + def get_anatomy_type(self, obj): + if obj.mesh: + return obj.mesh.anatomy_type + else: + return None class Meta: model = models.GroomedMesh @@ -215,6 +230,13 @@ class OptimizedParticlesReadSerializer(OptimizedParticlesSerializer): class ReconstructedSampleSerializer(serializers.ModelSerializer): file = S3FileSerializerField() particles = OptimizedParticlesReadSerializer(required=False) + anatomy_type = serializers.SerializerMethodField('get_anatomy_type') + + def get_anatomy_type(self, obj): + if obj.particles: + return obj.particles.anatomy_type + else: + return None class Meta: model = models.ReconstructedSample diff --git a/swcc/swcc/models/constants.py b/swcc/swcc/models/constants.py index 5a98f1e5..f9eed183 100644 --- a/swcc/swcc/models/constants.py +++ b/swcc/swcc/models/constants.py @@ -15,5 +15,6 @@ 'groomed', 'local', 'world', + 'landmarks_file', 'constraints', ] diff --git a/swcc/swcc/models/file.py b/swcc/swcc/models/file.py index 430ba263..9df99277 100644 --- a/swcc/swcc/models/file.py +++ b/swcc/swcc/models/file.py @@ -59,7 +59,7 @@ def upload(self): return self.field_value - def download(self, path: Union[str, Path]) -> Path: + def download(self, path: Union[str, Path], file_name=None) -> Path: from .utils import raise_for_status if self.url is None: @@ -75,7 +75,10 @@ def download(self, path: Union[str, Path]) -> Path: if not path.is_dir(): path.mkdir(parents=True, exist_ok=True) - path = path / self.url.path.split('/')[-1] + if file_name: + path = path / Path(file_name) + else: + path = path / self.url.path.split('/')[-1] r = requests.get(self.url, stream=True) raise_for_status(r) diff --git a/swcc/swcc/models/other_models.py b/swcc/swcc/models/other_models.py index 2ae46ee6..565629f6 100644 --- a/swcc/swcc/models/other_models.py +++ b/swcc/swcc/models/other_models.py @@ -109,7 +109,7 @@ class Constraints(ApiModel): file_source: Union[str, Path] subject: Subject anatomy_type: str = Field(min_length=1) - optimized_particles: Optional[OptimizedParticles] + project: Project class CachedAnalysisGroup(ApiModel): diff --git a/swcc/swcc/models/project.py b/swcc/swcc/models/project.py index 6a64a15a..bf3d0bae 100644 --- a/swcc/swcc/models/project.py +++ b/swcc/swcc/models/project.py @@ -131,7 +131,6 @@ def relative_path(filepath): groomed_shape: Union[GroomedMesh, GroomedSegmentation, None] = None world_particles_path = None local_particles_path = None - particles = None constraints_path = None transform = None @@ -183,7 +182,7 @@ def relative_path(filepath): transform = Path(temp_dir) / 'transform' with transform.open('w') as f: f.write(value) - elif key == 'landmarks': + elif key == 'landmarks_file': Landmarks( file_source=relative_path(value), subject=subject, @@ -201,7 +200,7 @@ def relative_path(filepath): groomed_mesh = groomed_shape elif type(groomed_shape) == GroomedSegmentation: groomed_segmentation = groomed_shape - particles = OptimizedParticles( + OptimizedParticles( world_source=world_particles_path, local_source=local_particles_path, transform_source=transform, @@ -212,12 +211,15 @@ def relative_path(filepath): anatomy_type=anatomy_id, ).create() if constraints_path: - Constraints( - file_source=constraints_path, - subject=subject, - optimized_particles=particles, - anatomy_type=anatomy_id, - ).create() + with open(constraints_path) as f: + constraints_contents = json.load(f) + if constraints_contents: + Constraints( + file_source=constraints_path, + subject=subject, + project=self.project, + anatomy_type=anatomy_id, + ).create() def load_analysis_from_json(self, file_path): project_root = Path(str(self.project.file.path)).parent @@ -234,12 +236,12 @@ def load_analysis_from_json(self, file_path): for mean_particle_path in contents['mean']['particle_files']: mean_particles.append(analysis_file_location.parent / Path(mean_particle_path)) - for i in range(len(mean_shapes)): - cams = CachedAnalysisMeanShape( - file_source=mean_shapes[i], - particles_source=mean_particles[i] if mean_particles else None, - ).create() - mean_shapes_cache.append(cams) + for i in range(len(mean_shapes)): + cams = CachedAnalysisMeanShape( + file_source=mean_shapes[i], + particles_source=mean_particles[i] if mean_particles else None, + ).create() + mean_shapes_cache.append(cams) modes = [] for mode in contents['modes']: @@ -402,7 +404,11 @@ def download(self, folder: Union[str, Path]): print_progress_bar(0, len(files)) for index, (path, url) in enumerate(files.items()): file_item: File = File(url) - file_item.download(Path(folder, *path.split('/')[:-1])) + path_split = path.split('/') + file_item.download( + Path(folder, *path_split[:-1]), + file_name=path_split[-1], + ) print_progress_bar(index + 1, len(files)) session.close() print() diff --git a/web/shapeworks/package.json b/web/shapeworks/package.json index 72e7d32c..570a4dc9 100644 --- a/web/shapeworks/package.json +++ b/web/shapeworks/package.json @@ -16,9 +16,10 @@ "echarts": "^5.4.1", "itk": "^14.1.1", "json-schema-defaults": "^0.4.0", + "kd-tree-javascript": "1.0.0", "lodash": "^4.17.21", "shader-loader": "^1.3.1", - "vtk.js": "*", + "vtk.js": ">=29.4.6", "vue": "^2.7.14", "vue-echarts": "^6.2.4", "vue-router": "^3.2.0", diff --git a/web/shapeworks/src/api/rest.ts b/web/shapeworks/src/api/rest.ts index 9fc1c98c..a2c748f7 100644 --- a/web/shapeworks/src/api/rest.ts +++ b/web/shapeworks/src/api/rest.ts @@ -1,4 +1,4 @@ -import { AnalysisParams, DataObject, Dataset, Project, Subject } from "@/types"; +import { AnalysisParams, DataObject, Dataset, LandmarkInfo, Constraints, Project, Subject } from "@/types"; import { apiClient } from "./auth"; import { loadGroomedShapeForObject, loadParticlesForObject } from "@/store"; @@ -154,3 +154,23 @@ export async function deleteTaskProgress(taskId: number){ export async function abortTask(taskId: number) { return (await apiClient.post(`/task-progress/${taskId}/abort/`)).data } + +export async function saveLandmarkData( + projectId: number, + landmarkInfo: LandmarkInfo[], + landmarkLocations: Record> +) { + return (await apiClient.post(`/projects/${projectId}/landmarks/`, { + info: landmarkInfo, + locations: landmarkLocations, + })).data +} + +export async function saveConstraintData( + projectId: number, + constraintLocations: Record> +) { + return (await apiClient.post(`/projects/${projectId}/constraints/`, { + locations: constraintLocations, + })).data +} diff --git a/web/shapeworks/src/components/Constraints.vue b/web/shapeworks/src/components/Constraints.vue new file mode 100644 index 00000000..802d8a91 --- /dev/null +++ b/web/shapeworks/src/components/Constraints.vue @@ -0,0 +1,401 @@ + + + + + diff --git a/web/shapeworks/src/components/DataList.vue b/web/shapeworks/src/components/DataList.vue index 92e569dd..b2e088bf 100644 --- a/web/shapeworks/src/components/DataList.vue +++ b/web/shapeworks/src/components/DataList.vue @@ -8,6 +8,7 @@ import { selectedDataset, allSubjectsForDataset, allDataObjectsInDataset, + anatomies, selectedDataObjects, loadingState, loadReconstructedSamplesForProject, @@ -30,7 +31,7 @@ export default { } }, setup(props) { - const anatomies = ref([]); + const selectedAnatomies = ref([]); const selectedSubjects = ref([]) const headers = [ @@ -85,6 +86,17 @@ export default { ) } + function selectedObjectsUpdated() { + const uniqueAnatomies = [...new Set(selectedDataObjects.value.map(item => item.anatomy_type))] + const uniqueSubjects = [...new Set(selectedDataObjects.value.map(item => item.subject))] + if (JSON.stringify(uniqueAnatomies) !== JSON.stringify(selectedAnatomies.value)) { + selectedAnatomies.value = uniqueAnatomies + } + if (JSON.stringify(uniqueSubjects) !== JSON.stringify(selectedSubjects.value)) { + selectedSubjects.value = uniqueSubjects + } + } + onMounted(async () => { if(!selectedDataset.value) { await fetchData(props.dataset) @@ -95,6 +107,7 @@ export default { watch(selectedAnatomies, updateSelectedObjects) watch(selectedSubjects, updateSelectedObjects) + watch(selectedDataObjects, selectedObjectsUpdated) return { anatomies, diff --git a/web/shapeworks/src/components/InfoTab.vue b/web/shapeworks/src/components/InfoTab.vue index 0fc370c6..60f6dcd1 100644 --- a/web/shapeworks/src/components/InfoTab.vue +++ b/web/shapeworks/src/components/InfoTab.vue @@ -1,80 +1,42 @@ - - - diff --git a/web/shapeworks/src/components/Landmarks.vue b/web/shapeworks/src/components/Landmarks.vue new file mode 100644 index 00000000..6c98289b --- /dev/null +++ b/web/shapeworks/src/components/Landmarks.vue @@ -0,0 +1,361 @@ + + + + + diff --git a/web/shapeworks/src/components/ShapeViewer/methods.js b/web/shapeworks/src/components/ShapeViewer/methods.js index 9f35d1dd..babe0c26 100644 --- a/web/shapeworks/src/components/ShapeViewer/methods.js +++ b/web/shapeworks/src/components/ShapeViewer/methods.js @@ -1,7 +1,7 @@ import vtkMapper from 'vtk.js/Sources/Rendering/Core/Mapper'; +import vtkPolyData from 'vtk.js/Sources/Common/DataModel/PolyData'; import vtkRenderer from 'vtk.js/Sources/Rendering/Core/Renderer'; import vtkSphereSource from 'vtk.js/Sources/Filters/Sources/SphereSource'; -import vtkCubeSource from 'vtk.js/Sources/Filters/Sources/CubeSource'; import vtkImageMarchingCubes from 'vtk.js/Sources/Filters/General/ImageMarchingCubes'; import vtkOrientationMarkerWidget from 'vtk.js/Sources/Interaction/Widgets/OrientationMarkerWidget'; import vtkArrowSource from 'vtk.js/Sources/Filters/Sources/ArrowSource' @@ -14,22 +14,38 @@ import { AttributeTypes } from 'vtk.js/Sources/Common/DataModel/DataSetAttribute import { ColorMode, ScalarMode } from 'vtk.js/Sources/Rendering/Core/Mapper/Constants'; import { FieldDataTypes } from 'vtk.js/Sources/Common/DataModel/DataSet/Constants'; -import vtkPolyData from 'vtk.js/Sources/Common/DataModel/PolyData'; import { - layers, layersShown, orientationIndicator, + renderLoading, layers, layersShown, orientationIndicator, cachedMarchingCubes, cachedParticleComparisonColors, vtkShapesByType, analysisFilesShown, currentAnalysisParticlesFiles, meanAnalysisParticlesFiles, - showDifferenceFromMeanMode, cachedParticleComparisonVectors, landmarkColorList, cacheComparison, calculateComparisons, + showDifferenceFromMeanMode, cachedParticleComparisonVectors, + cacheComparison, calculateComparisons, showGoodBadParticlesMode, goodBadMaxAngle, goodBadAngles, } from '@/store'; -import { COLORS, SPHERE_RESOLUTION } from '@/store/constants'; +import { SPHERE_RESOLUTION } from '@/store/constants'; +import widgetSync from './widgetSync'; export const GOOD_BAD_COLORS = [ [0, 255, 0], [255, 0, 0], ]; +const COLORS = [ + [166, 206, 227], + [31, 120, 180], + [178, 223, 138], + [51, 160, 44], + [251, 154, 153], + [227, 26, 28], + [253, 191, 111], + [255, 127, 0], + [202, 178, 214], + [106, 61, 154], + [255, 255, 153], + [177, 89, 40], +]; export default { + ...widgetSync, async resize() { await this.$nextTick(); if (this.vtk.renderWindow) { @@ -59,7 +75,7 @@ export default { position: {}, viewUp: {}, } - this.vtk.renderers.forEach((renderer, index) => { + Object.values(this.vtk.renderers).forEach((renderer, index) => { const camera = renderer.getActiveCamera(); this.initialCameraStates.position[`renderer_${index}`] = [...camera.getReferenceByName('position')] this.initialCameraStates.viewUp[`renderer_${index}`] = [...camera.getReferenceByName('viewUp')] @@ -71,9 +87,10 @@ export default { viewUpDelta: undefined, } const targetCamera = renderer.getActiveCamera(); + const rendererIndex = Object.values(this.vtk.renderers).indexOf(renderer) - if (this.vtk.renderers.indexOf(renderer) >= 0) { - const targetRendererID = `renderer_${this.vtk.renderers.indexOf(renderer)}` + if (rendererIndex >= 0) { + const targetRendererID = `renderer_${rendererIndex}` this.initialCameraPosition = this.initialCameraStates.position[targetRendererID] this.initialCameraViewUp = this.initialCameraStates.viewUp[targetRendererID] this.newCameraPosition = targetCamera.getReferenceByName('position') @@ -92,7 +109,8 @@ export default { }, applyCameraDelta(renderer, positionDelta, viewUpDelta) { const camera = renderer.getActiveCamera(); - const rendererID = `renderer_${this.vtk.renderers.indexOf(renderer)}` + const rendererIndex = Object.values(this.vtk.renderers).indexOf(renderer) + const rendererID = `renderer_${rendererIndex}` if (this.initialCameraStates.position[rendererID]) { camera.setPosition( ...this.initialCameraStates.position[rendererID].map( @@ -111,13 +129,13 @@ export default { const targetRenderer = animation.pokedRenderer; const { positionDelta, viewUpDelta } = this.getCameraDelta(targetRenderer) - this.vtk.renderers.filter( + Object.values(this.vtk.renderers).filter( (renderer) => renderer !== targetRenderer ).forEach((renderer) => { this.applyCameraDelta(renderer, positionDelta, viewUpDelta) }) }, - createColorFilter(domainIndex = 0, landmarks = false, goodBad = false) { + createColorFilter(domainIndex = 0, goodBad = false) { const filter = vtkCalculator.newInstance() filter.setFormula({ getArrays() { @@ -139,13 +157,6 @@ export default { const n = coords.length / 3; for (let i = 0; i < n; i += 1) { let c = COLORS[i % COLORS.length]; - if (landmarks) { - if (landmarkColorList.value[i]) { - c = landmarkColorList.value[i] - } else { - c = [0, 0, 0] - } - } if (goodBad && analysisFilesShown.value?.length) { if (goodBadAngles.value[domainIndex][i] < goodBadMaxAngle.value) { @@ -154,33 +165,29 @@ export default { c = GOOD_BAD_COLORS[1] // red } } - color[3 * i] = c[0]; - color[3 * i + 1] = c[1]; - color[3 * i + 2] = c[2]; + if (c) { + color[3 * i] = c[0]; + color[3 * i + 1] = c[1]; + color[3 * i + 2] = c[2]; + } } input.forEach((x) => x.modified()); }, }); return filter; }, - addPoints(renderer, points, i, landmarks = false) { + addPoints(renderer, points, i) { let size = this.glyphSize let source = vtkSphereSource.newInstance({ thetaResolution: SPHERE_RESOLUTION, phiResolution: SPHERE_RESOLUTION, }); - if (landmarks) { - size *= 2 - source = vtkCubeSource.newInstance( - { xLength: 1, yLength: 1, zLength: 1 } - ) - } const mapper = vtkGlyph3DMapper.newInstance({ scaleMode: vtkGlyph3DMapper.SCALE_BY_CONSTANT, scaleFactor: size, }); const actor = vtkActor.newInstance(); - const filter = this.createColorFilter(i, landmarks, showGoodBadParticlesMode.value); + const filter = this.createColorFilter(i, showGoodBadParticlesMode.value); filter.setInputData(points, 0); mapper.setInputConnection(filter.getOutputPort(), 0); @@ -190,7 +197,11 @@ export default { renderer.addActor(actor); this.vtk.pointMappers.push(mapper); }, - addShapes(renderer, label, shapes) { + addShapes(renderer, shapes) { + let label; + Object.entries(this.vtk.renderers).forEach(([l, r]) => { + if (renderer == r) label = l + }) shapes.forEach( (shapeDatas, domainIndex) => { shapeDatas.forEach( @@ -378,66 +389,81 @@ export default { this.labelCanvasContext.font = "16px Arial"; this.labelCanvasContext.fillStyle = "white"; }, - populateRenderer(renderer, label, bounds, shapes) { - this.labelCanvasContext.fillText( - label, - this.labelCanvas.width * bounds[0], - this.labelCanvas.height * (1 - bounds[1]) - 20 - ); - - this.addShapes(renderer, label, shapes.map(({ shape }) => shape)); + populateRenderer(renderer, shapes) { + this.addShapes(renderer, shapes.map(({ shape }) => shape)); shapes.map(({ points }) => points).forEach((pointSet, i) => { if (pointSet.getNumberOfPoints() > 0) { this.addPoints(renderer, pointSet, i); } }) - shapes.map(({ landmarks }) => landmarks).forEach((landmarkSet, i) => { - if (landmarkSet && landmarkSet.getNumberOfPoints() > 0) { - this.addPoints(renderer, landmarkSet, i, true); - } - }) const camera = vtkCamera.newInstance(); renderer.setActiveCamera(camera); renderer.resetCamera(); }, renderGrid() { - this.prepareLabelCanvas(); + this.vtk.interactor.disable() + Object.values(this.vtk.widgetManagers).forEach((wm) => { + wm.disablePicking() + }) - let { positionDelta, viewUpDelta } = this.getCameraDelta(this.vtk.renderers[0]) + this.prepareLabelCanvas(); + let positionDelta, viewUpDelta - for (let i = 0; i < this.vtk.renderers.length; i += 1) { - this.vtk.renderWindow.removeRenderer(this.vtk.renderers[i]); + const renderers = Object.values(this.vtk.renderers) + for (let i = 0; i < renderers.length; i += 1) { + if (!positionDelta || !viewUpDelta) { + ({ positionDelta, viewUpDelta } = this.getCameraDelta(Object.values(this.vtk.renderers)[0])) + } + this.vtk.renderWindow.removeRenderer(renderers[i]); } if (this.vtk.orientationCube) this.vtk.orientationCube.setEnabled(false) - this.vtk.renderers = []; + this.vtk.renderers = {}; this.vtk.pointMappers = []; const data = Object.entries(this.data) - for (let i = 0; i < this.grid.length; i += 1) { - let newRenderer = vtkRenderer.newInstance({ background: [0.115, 0.115, 0.115] }); + for (let i = 0; i < data.length; i += 1) { + const [label, shapes] = data[i]; + const newRenderer = vtkRenderer.newInstance({ background: [0.115, 0.115, 0.115] }); + const bounds = this.grid[i]; + + this.labelCanvasContext.fillText( + label, + this.labelCanvas.width * bounds[0], + this.labelCanvas.height * (1 - bounds[1]) - 20 + ); + newRenderer.setViewport.apply(newRenderer, bounds); + this.vtk.renderers[label] = newRenderer; + this.vtk.renderWindow.addRenderer(newRenderer); if (i < data.length) { - this.populateRenderer(newRenderer, data[i][0], this.grid[i], data[i][1]) + this.populateRenderer(newRenderer, shapes) } - newRenderer.setViewport.apply(newRenderer, this.grid[i]); - this.vtk.renderers.push(newRenderer); - this.vtk.renderWindow.addRenderer(newRenderer); } this.initializeCameras() + this.initializeWidgets() - this.vtk.renderers.forEach((renderer) => { - if (positionDelta && viewUpDelta) { + if (positionDelta && viewUpDelta) { + Object.values(this.vtk.renderers).forEach((renderer) => { this.applyCameraDelta(renderer, positionDelta, viewUpDelta) - } - }) - const targetRenderer = this.vtk.renderers[this.columns - 1] + }) + } + + const targetRenderer = Object.values(this.vtk.renderers)[this.columns - 1] this.vtk.orientationCube = this.newOrientationCube(this.vtk.interactor) if (targetRenderer) { this.vtk.orientationCube.setParentRenderer(targetRenderer) this.vtk.orientationCube.setEnabled(true); - - this.render(); + this.vtk.interactor.enable() } + this.render(); + renderLoading.value = false; + setTimeout( + () => { + Object.values(this.vtk.widgetManagers).forEach((wm) => { + wm.enablePicking() + }) + }, 100 + ) }, render() { this.vtk.renderWindow.render(); diff --git a/web/shapeworks/src/components/ShapeViewer/scripting.js b/web/shapeworks/src/components/ShapeViewer/scripting.js index 51b1e5f1..414e8f5c 100644 --- a/web/shapeworks/src/components/ShapeViewer/scripting.js +++ b/web/shapeworks/src/components/ShapeViewer/scripting.js @@ -99,6 +99,7 @@ export default { interactor.initialize(); interactor.setInteractorStyle(vtkInteractorStyleTrackballCamera.newInstance()); interactor.onAnimation(this.syncCameras) + interactor.disable() const orientationCube = this.newOrientationCube(interactor) @@ -114,8 +115,9 @@ export default { interactor, openglRenderWindow, orientationCube, - renderers: [], + renderers: {}, pointMappers: [], + widgetManagers: {}, }; vtkInstance.value = this.vtk @@ -127,6 +129,7 @@ export default { this.updateSize(); this.renderGrid(); + this.watchWidgetStates(); }, updated() { this.prepareColorScale() diff --git a/web/shapeworks/src/components/ShapeViewer/widgetSync.js b/web/shapeworks/src/components/ShapeViewer/widgetSync.js new file mode 100644 index 00000000..737a01ff --- /dev/null +++ b/web/shapeworks/src/components/ShapeViewer/widgetSync.js @@ -0,0 +1,603 @@ +import _ from 'lodash'; + +import vtkPickerManipulator from 'vtk.js/Sources/Widgets/Manipulators/PickerManipulator'; +import vtkWidgetManager from 'vtk.js/Sources/Widgets/Core/WidgetManager'; +import vtkSeedWidget from 'vtk.js/Sources/Widgets/Widgets3D/SeedWidget'; +import vtkPaintWidget from 'vtk.js/Sources/Widgets/Widgets3D/PaintWidget'; +import vtkImplicitPlaneWidget from 'vtk.js/Sources/Widgets/Widgets3D/ImplicitPlaneWidget' +import vtkColorTransferFunction from 'vtk.js/Sources/Rendering/Core/ColorTransferFunction'; +import vtkDataArray from 'vtk.js/Sources/Common/Core/DataArray'; + +import { kdTree } from 'kd-tree-javascript'; +import { distance } from '@/helper' +import { ref, watch } from 'vue' + +import { + layersShown, + landmarkInfo, landmarkSize, currentLandmarkPlacement, + getLandmarkLocation, setLandmarkLocation, + allSetLandmarks, reassignLandmarkNumSetValues, + constraintInfo, constraintsShown, allSetConstraints, currentConstraintPlacement, + getConstraintLocation, setConstraintLocation, + constraintPaintRadius, constraintPaintExclusion, +} from '@/store'; + +const manipulators = ref({}); // organized by label, domain +const dataKDTrees = ref({}); // organized by label, domain +const shapeKDTrees = ref({}); // organized by label, domain +const seedWidgets = ref({}); // organized by label, domain, id +const planeWidgets = ref({}); // organized by label, domain, id +const paintWidgets = ref({}); // organized by label, domain, id + +export default { + // --------------------- + // Initialization + // --------------------- + initializeWidgets() { + // called when shapes or layers shown have changed + this.vtk.widgetManagers = {} + Object.entries(this.vtk.renderers).forEach(([label, renderer]) => { + manipulators.value[label] = {} + const wm = vtkWidgetManager.newInstance() + wm.setRenderer(renderer) + wm.disablePicking(); + this.vtk.widgetManagers[label] = wm + renderer.getActors().forEach((actor) => { + const domain = actor.getMapper()?.getInputData()?.getFieldData()?.getArrayByName('domain')?.getData()[0] + if (!manipulators.value[label][domain]) { + const m = vtkPickerManipulator.newInstance() + m.getPicker().addPickList(actor) + manipulators.value[label][domain] = m + } + if (layersShown.value.includes('Landmarks')) { + const existingWidgets = seedWidgets.value[label] + if (existingWidgets) { + Object.values(existingWidgets).forEach((ws) => { + Object.values(ws).forEach((w) => { + const widgetHandle = wm.addWidget(w) + widgetHandle.setScaleInPixels(false) + widgetHandle.onEndInteractionEvent(() => { + this.seedWidgetEndInteraction(w) + }) + }) + }) + } + } + if (layersShown.value.includes('Constraints')) { + this.initializeConstraintColormap(actor) + const existingWidgets = planeWidgets.value[label] + if (existingWidgets) { + Object.values(existingWidgets).forEach((ws) => { + Object.values(ws).forEach((w) => { + const widgetHandle = wm.addWidget(w) + this.stylePlaneWidget(widgetHandle) + widgetHandle.onEndInteractionEvent(() => { + this.planeWidgetEndInteraction(w) + }) + }) + }) + } + } + }) + }) + if (layersShown.value.includes('Landmarks')) { + this.landmarkInfoUpdated(landmarkInfo.value) + } + if (layersShown.value.includes('Constraints')) { + this.constraintInfoUpdated(constraintInfo.value) + } + }, + initializeConstraintColormap(actor) { + const ctfun = vtkColorTransferFunction.newInstance(); + ctfun.addRGBPoint(1, ...actor.getProperty().getColor()); // 0: default color has not been excluded + ctfun.addRGBPoint(0, 0.5, 0.5, 0.5); // 1: gray has been excluded + ctfun.setMappingRange(0, 1) + ctfun.updateRange() + + const mapper = actor.getMapper() + mapper.setLookupTable(ctfun) + mapper.setColorByArrayName('color') + + const inputData = mapper.getInputData() + const allPoints = inputData.getPoints() + const colorArray = vtkDataArray.newInstance({ + name: 'color', + values: Array.from( + { length: allPoints.getNumberOfPoints() }, () => 1 + ) + }) + inputData.getPointData().addArray(colorArray) + }, + + // --------------------- + // Getters + // --------------------- + getWidgetManager(label) { + return this.vtk.widgetManagers[label] + }, + getManipulator(label, domain) { + if (!manipulators.value[label]) manipulators.value[label] = {} + return manipulators.value[label][domain] + }, + getDataKDTree(label, domain, cData) { + if (!dataKDTrees.value[label]) dataKDTrees.value[label] = {} + if (!dataKDTrees.value[label][domain]) { + const { points } = cData.data.field + const scalarPoints = points.map((p, i) => ({ x: p[0], y: p[1], z: p[2], i })) + dataKDTrees.value[label][domain] = new kdTree(scalarPoints, distance, ['x', 'y', 'z', 'i']); + } + return dataKDTrees.value[label][domain] + }, + getShapeKDTree(label, domain, shapeData) { + if (!shapeKDTrees.value[label]) shapeKDTrees.value[label] = {} + if (!shapeKDTrees.value[label][domain]) { + const pointData = Array.prototype.slice.call(shapeData.getPoints().getData()) + const allPoints = Array.from({ length: pointData.length / 3 }, () => pointData.splice(0, 3)); + const treePoints = allPoints.map((p) => ({ x: p[0], y: p[1], z: p[2] })) + shapeKDTrees.value[label][domain] = new kdTree( + treePoints, + distance, + ['x', 'y', 'z'] + ) + } + return shapeKDTrees.value[label][domain] + }, + getSeedWidget(label, domain, lInfo) { + if (!seedWidgets.value[label]) seedWidgets.value[label] = {} + if (!seedWidgets.value[label][domain]) seedWidgets.value[label][domain] = {} + if (!seedWidgets.value[label][domain][lInfo.id]) { + this.createSeedWidget(label, domain, lInfo) + } + return seedWidgets.value[label][domain][lInfo.id] + }, + getPlaneWidget(label, domain, cInfo) { + if (!planeWidgets.value[label]) planeWidgets.value[label] = {} + if (!planeWidgets.value[label][domain]) planeWidgets.value[label][domain] = {} + if (!planeWidgets.value[label][domain][cInfo.id]) { + this.createPlaneWidget(label, domain, cInfo) + } + return planeWidgets.value[label][domain][cInfo.id] + }, + getPaintWidget(label, domain, cInfo, inputData) { + if (!paintWidgets.value[label]) paintWidgets.value[label] = {} + if (!paintWidgets.value[label][domain]) paintWidgets.value[label][domain] = {} + // always create new paint widget + this.createPaintWidget(label, domain, cInfo, inputData) + return paintWidgets.value[label][domain][cInfo.id] + }, + + // --------------------- + // Widget creation + // --------------------- + createSeedWidget(label, domain, lInfo) { + const renderer = this.vtk.renderers[label] + const manipulator = this.getManipulator(label, domain) + const widgetManager = this.getWidgetManager(label) + if (renderer && manipulator) { + const widget = vtkSeedWidget.newInstance() + const widgetHandle = widgetManager.addWidget(widget) + widget.setManipulator(manipulator) + widgetHandle.setScaleInPixels(false) + widgetHandle.onEndInteractionEvent(() => { + this.seedWidgetEndInteraction(widget) + }) + seedWidgets.value[label][domain][lInfo.id] = widget + } + }, + createPlaneWidget(label, domain, cInfo) { + const renderer = this.vtk.renderers[label] + const manipulator = this.getManipulator(label, domain) + const widgetManager = this.getWidgetManager(label) + if (renderer && manipulator) { + const pickList = manipulator.getPicker().getPickList() + if (pickList.length > 0) { + const actor = pickList[0] + const bounds = actor.getBounds() + const widget = vtkImplicitPlaneWidget.newInstance() + widget.placeWidget(bounds) + widget.setPlaceFactor(2) + const widgetHandle = widgetManager.addWidget(widget) + widgetHandle.getRepresentations()[0].setLabels({ + 'subject': label, + 'domain': domain + }) + this.stylePlaneWidget(widgetHandle) + widgetHandle.onEndInteractionEvent(() => { + this.planeWidgetEndInteraction(widget) + }) + planeWidgets.value[label][domain][cInfo.id] = widget + } + } + }, + createPaintWidget(label, domain, cInfo, inputData) { + const widgetManager = this.getWidgetManager(label) + const manipulator = this.getManipulator(label, domain) + if (manipulator) { + const widget = vtkPaintWidget.newInstance({ manipulator }); + const widgetHandle = widgetManager.addWidget(widget) + paintWidgets.value[label][domain][cInfo.id] = widget + widgetHandle.onEndInteractionEvent(() => { + this.paintWidgetEndInteraction(widget, inputData) + }) + } + }, + stylePlaneWidget(widgetHandle) { + widgetHandle.setHandleSizeRatio(0.08) + widgetHandle.setAxisScale(0.25) + widgetHandle.setRepresentationStyle({ + static: { + outline: { + opacity: 0 + } + } + }) + }, + + // --------------------- + // Widget interaction events + // --------------------- + + seedWidgetEndInteraction(widget) { + Object.entries(seedWidgets.value).forEach(([label, subjectWidgets]) => { + Object.entries(subjectWidgets).forEach(([domain, shapeWidgets]) => { + Object.entries(shapeWidgets).forEach(([id, w]) => { + if (widget === w) { + const lInfo = { domain, id } + const wm = this.getWidgetManager(label) + // When widget moved, update value in allSetLandmarks + const landmarkCoord = widget.getWidgetState().getMoveHandle().getOrigin() + if (landmarkCoord) { + wm.releaseFocus(widget); + const previousLocation = getLandmarkLocation({ name: label }, lInfo, landmarkCoord) + if (!previousLocation || previousLocation.some((v, i) => landmarkCoord[i] != v)) { + setLandmarkLocation({ name: label }, lInfo, landmarkCoord) + // reassign store var for listeners + allSetLandmarks.value = Object.assign({}, allSetLandmarks.value) + reassignLandmarkNumSetValues() + currentLandmarkPlacement.value = undefined; + } + } + + } + }) + }) + }) + }, + planeWidgetEndInteraction(widget) { + Object.entries(planeWidgets.value).forEach(([label, subjectWidgets]) => { + Object.entries(subjectWidgets).forEach(([domain, shapeWidgets]) => { + Object.entries(shapeWidgets).forEach(([id, w]) => { + if (widget === w) { + const cInfo = { domain, id } + // When widget moved, update value in allSetConstraints + const widgetState = widget.getWidgetState() + setConstraintLocation({ name: label }, cInfo, { + type: 'plane', + data: { + origin: widgetState.getOrigin(), + normal: widgetState.getNormal(), + } + }) + this.updateConstraintColors() + } + }) + }) + }) + }, + paintWidgetEndInteraction(widget, inputData) { + Object.entries(paintWidgets.value).forEach(([label, subjectWidgets]) => { + Object.entries(subjectWidgets).forEach(([domain, shapeWidgets]) => { + Object.entries(shapeWidgets).forEach(([id, w]) => { + if (widget === w) { + const cInfo = { domain, id } + const allPoints = inputData.getPoints() + const tree = this.getShapeKDTree(label, domain, inputData) + let cData = getConstraintLocation({ name: label }, cInfo) + if (!cData) { + const numPoints = allPoints.getNumberOfPoints() + const points = Array.from({ length: numPoints }).map((v, i) => allPoints.getPoint(i)) + cData = { + type: 'paint', + data: { + field: { + points, + scalars: Array.from({ length: numPoints }).fill(1), + } + } + } + } + let paintedPoints = [] + widget.getWidgetState().getTrailList().forEach((state) => { + const currentPoint = state.getOrigin() + if (currentPoint) { + paintedPoints = [ + ...paintedPoints, + ...tree.nearest( + { x: currentPoint[0], y: currentPoint[1], z: currentPoint[2] }, + allPoints.getNumberOfPoints(), + constraintPaintRadius.value * 2 + ) + ] + } + }) + paintedPoints.forEach(([{ x, y, z },]) => { + const pointIndex = cData.data.field.points.findIndex( + (p) => p[0] === x && p[1] === y && p[2] === z + ) + if (pointIndex >= 0 && pointIndex < cData.data.field.scalars.length) { + cData.data.field.scalars[pointIndex] = constraintPaintExclusion.value ? 0 : 1 + } + }) + setConstraintLocation({ name: label }, cInfo, cData) + this.updateConstraintColors() + } + }) + }) + }) + }, + + // --------------------- + // Update widget states + // --------------------- + landmarkInfoUpdated(newInfo) { + const validWidgets = [] + Object.entries(manipulators.value).forEach(([label, records]) => { + Object.entries(records).forEach(([domain,]) => { + newInfo.filter((lInfo) => lInfo.domain === domain).forEach((lInfo) => { + const widget = this.getSeedWidget(label, domain, lInfo) + const handle = widget.getWidgetState().getMoveHandle(); + validWidgets.push(widget) + + const location = getLandmarkLocation({ name: label }, lInfo) + if (location && ( + !handle.getOrigin() || + handle.getOrigin().some((v, i) => v !== location[i]) + )) { + handle.setOrigin(location) + } + if (handle.getColor3().some((v, i) => v !== lInfo.color[i])) { + handle.setColor3(...lInfo.color); + } + if (handle.getScale1() != landmarkSize.value) { + handle.setScale1(landmarkSize.value); + } + }) + }) + }) + seedWidgets.value = Object.fromEntries( + Object.entries(seedWidgets.value).map(([label, labelRecords]) => { + return [label, Object.fromEntries( + Object.entries(labelRecords).map(([domain, shapeRecords]) => { + return [domain, Object.fromEntries( + Object.entries(shapeRecords).map(([id, seedWidget]) => { + if (!validWidgets.includes(seedWidget)) { + this.getWidgetManager(label).removeWidget(seedWidget) + return [id, undefined] + } + return [id, seedWidget] + }) + )] + }) + )] + }) + ) + this.render() + }, + landmarkSizeUpdated() { + Object.values(seedWidgets.value).forEach((subjectWidgets) => { + Object.values(subjectWidgets).forEach((shapeWidgets) => { + Object.values(shapeWidgets).forEach((widget) => { + const handle = widget.getWidgetState().getMoveHandle(); + if (handle.getScale1() != landmarkSize.value) { + handle.setScale1(landmarkSize.value); + } + }) + }) + }) + this.render() + }, + currentLandmarkPlacementUpdated(newPlacement) { + if (newPlacement) { + const label = newPlacement.subjectName + const domain = newPlacement.domain + const id = newPlacement.widgetID + const widgetManager = this.getWidgetManager(label) + const manipulator = this.getManipulator(label, domain) + if (manipulator) { + const widget = this.getSeedWidget(label, domain, { id, domain }) + const pickList = manipulator.getPicker().getPickList() + if (pickList.length > 0) { + const actor = pickList[0] + widget.placeWidget(actor.getBounds()); + widgetManager.grabFocus(widget) + } + } + } + }, + constraintInfoUpdated(newInfo) { + const validWidgets = [] + Object.entries(manipulators.value).forEach(([label, records]) => { + Object.entries(records).forEach(([domain,]) => { + newInfo.filter((cInfo) => cInfo.domain === domain).forEach((cInfo) => { + if (cInfo.type === 'plane') { + const widget = this.getPlaneWidget(label, domain, cInfo) + const widgetState = widget.getWidgetState() + const cData = getConstraintLocation({ name: label }, cInfo) + validWidgets.push(widget) + + let origin = cData?.data?.origin + if (origin && widgetState.getOrigin().some((v, i) => v != origin[i])) { + widgetState.setOrigin(origin) + } + let normal = cData?.data?.normal + if (normal && widgetState.getNormal().some((v, i) => v != normal[i])) { + widgetState.setNormal(normal) + } + + widget.setVisibility(origin && normal && constraintsShown.value.includes(cInfo.id)) + } + }) + }) + }) + planeWidgets.value = Object.fromEntries( + Object.entries(planeWidgets.value).map(([label, labelRecords]) => { + return [label, Object.fromEntries( + Object.entries(labelRecords).map(([domain, shapeRecords]) => { + return [domain, Object.fromEntries( + Object.entries(shapeRecords).map(([id, planeWidget]) => { + if (!validWidgets.includes(planeWidget)) { + this.getWidgetManager(label).removeWidget(planeWidget) + return [id, undefined] + } + return [id, planeWidget] + }) + )] + }) + )] + }) + ) + this.updateConstraintColors() + this.render() + }, + constraintsShownUpdated() { + this.constraintInfoUpdated(constraintInfo.value) + }, + currentConstraintPlacementUpdated(newPlacement) { + if (newPlacement) { + const label = newPlacement.subjectName + const domain = newPlacement.domain + const id = newPlacement.widgetID + const widgetManager = this.getWidgetManager(label) + const manipulator = this.getManipulator(label, domain) + const cInfo = constraintInfo.value.find((c) => + c.id == id && c.domain == domain + ) + if (manipulator) { + const pickList = manipulator.getPicker().getPickList() + if (pickList.length > 0) { + const actor = pickList[0] + if (cInfo?.type === 'plane') { + const bounds = actor.getBounds() + const origin = [ + (bounds[0] + bounds[1]) / 2, + (bounds[2] + bounds[3]) / 2, + (bounds[4] + bounds[5]) / 2, + ] + const normal = [0, 0, 1] + setConstraintLocation( + { name: label }, + { id, domain }, + { type: 'plane', data: { origin, normal } }, + ) + currentConstraintPlacement.value = undefined + this.constraintInfoUpdated(constraintInfo.value) + } else if (manipulator && cInfo?.type === 'paint') { + const mapper = actor.getMapper() + const inputData = mapper.getInputData() + const widget = this.getPaintWidget(label, domain, cInfo, inputData) + widget.setRadius(constraintPaintRadius.value) + widget.getWidgetState().getHandle().setVisible(true) + widgetManager.grabFocus(widget); + widget.getWidgetState().setActive(true) + } + } + } + } else { + Object.entries(paintWidgets.value).forEach(([label, subjectRecords]) => { + const widgetManager = this.getWidgetManager(label) + if (widgetManager) { + Object.values(subjectRecords).forEach((shapeRecords) => { + Object.values(shapeRecords).forEach((widget) => { + widget.getWidgetState().getHandle().setVisible(false) + widget.getWidgetState().setActive(false) + widgetManager.releaseFocus(widget) + }) + }) + } + }) + } + }, + updateConstraintColors() { + Object.entries(manipulators.value).forEach(([label, shapeManipulators]) => { + if (!allSetConstraints.value[label]) return + Object.entries(shapeManipulators).forEach(([domain, manipulator]) => { + const pickList = manipulator.getPicker().getPickList() + if (!pickList.length || !allSetConstraints.value[label][domain]) return + const actor = pickList[0] + const mapper = actor.getMapper() + const inputData = mapper.getInputData() + const allPoints = inputData.getPoints() + const allPointColors = inputData.getPointData().getArrayByName('color') + allPointColors.setData( + new Uint8Array(allPoints.getNumberOfPoints()).fill(1) + ) + Object.entries(allSetConstraints.value[label][domain]).forEach( + ([id, cData]) => { + if (constraintsShown.value.includes(parseInt(id))) { + if (cData?.type === 'plane') { + const { normal, origin } = cData.data + let dot = (a, b) => a.map((x, i) => a[i] * b[i]).reduce((m, n) => m + n); + for (let i = 0; i < allPoints.getNumberOfPoints(); i++) { + const point = allPoints.getPoint(i) + const pointColor = allPointColors.getValue(i) + if (pointColor == 1) { + // has not been excluded yet, check for exclusion + const dotProduct = dot(normal, [ + origin[0] - point[0], + origin[1] - point[1], + origin[2] - point[2], + ]) + if (dotProduct <= 0) { + // negative dotProduct means point is below plane + allPointColors.setValue(i, 0) + } + } + } + } else if (cData?.type === 'paint') { + const { scalars } = cData.data.field + const tree = this.getDataKDTree(label, domain, cData) + if (scalars.length === allPoints.getNumberOfPoints()) { + for (let i = 0; i < scalars.length; i++) { + const pointColor = allPointColors.getValue(i) + if (pointColor == 1) { + // has not been excluded yet, check for exclusion + const currentPoint = allPoints.getPoint(i) + const currentPointObj = { + x: currentPoint[0], + y: currentPoint[1], + z: currentPoint[2], + } + const nearests = tree.nearest(currentPointObj, 1) + if (nearests.length) { + const [nearest,] = nearests[0] + if (nearest.i && nearest.i >= 0 && nearest.i < cData.data.field.scalars.length) { + allPointColors.setValue(i, cData.data.field.scalars[nearest.i]) + } + } + } + } + } + } + } + } + ) + allPointColors.modified() + inputData.modified() + }) + }) + this.render() + }, + + // --------------------- + // Listeners + // --------------------- + watchWidgetStates() { + watch(landmarkInfo, _.debounce(this.landmarkInfoUpdated, 1000)) + watch(landmarkSize, _.debounce(this.landmarkSizeUpdated, 1000)) + watch(currentLandmarkPlacement, _.debounce(this.currentLandmarkPlacementUpdated, 1000)) + watch(constraintInfo, _.debounce(this.constraintInfoUpdated, 1000)) + watch(constraintsShown, _.debounce(this.constraintsShownUpdated, 1000)) + watch(currentConstraintPlacement, _.debounce(this.currentConstraintPlacementUpdated, 1000)) + watch(allSetConstraints, _.debounce(this.updateConstraintColors, 1000)) + }, +} diff --git a/web/shapeworks/src/helper.ts b/web/shapeworks/src/helper.ts index 48bf1721..1aef38fd 100644 --- a/web/shapeworks/src/helper.ts +++ b/web/shapeworks/src/helper.ts @@ -39,5 +39,17 @@ export function hexToRgb(hex: string) { parseInt(result[1], 16), parseInt(result[2], 16), parseInt(result[3], 16) - ] : [0, 0, 0]; + ] : [0, 0, 0]; +} + +export function rgbToHex(rgb) { + const components = rgb.map((c) => { + const hex = c.toString(16); + return hex.length == 1 ? "0" + hex : hex; + }) + return "#" + components.join(""); } + +export function distance(a, b){ + return Math.pow(a.x - b.x, 2) + Math.pow(a.y - b.y, 2) + Math.pow(a.z - b.z, 2); +} diff --git a/web/shapeworks/src/reader/constraints.ts b/web/shapeworks/src/reader/constraints.ts new file mode 100644 index 00000000..c982edae --- /dev/null +++ b/web/shapeworks/src/reader/constraints.ts @@ -0,0 +1,109 @@ +function crossProduct(v1, v2) { + return [ + (v1[1] * v2[2] - v1[2] * v2[1]), + (v1[2] * v2[0] - v1[0] * v2[2]), + (v1[0] * v2[1] - v1[1] * v2[0]), + ] +} + +function addVectors(v1, v2) { + return [ + v1[0] + v2[0], + v1[1] + v2[1], + v1[2] + v2[2], + ] +} + +function subtractVectors(v1, v2) { + return [ + v1[0] - v2[0], + v1[1] - v2[1], + v1[2] - v2[2], + ] +} + +function normalizeVector(v) { + const magnitude = Math.sqrt( + Math.pow(v[0], 2) + + Math.pow(v[1], 2) + + Math.pow(v[2], 2) + ) + return [ + v[0] / magnitude, + v[1] / magnitude, + v[2] / magnitude, + ] +} + +export default async function (url: string | undefined) { + const constraintList: {type: string, data: any, name: string}[] = [] + if (url) { + const resp = await fetch(url); + const json = await resp.json() + json.planes?.forEach(({points, name}) => { + // must contain 3 points + if (points && points.length === 3) { + const [p1, p2, p3] = points + const v1 = subtractVectors(p1, p3) + const v2 = subtractVectors(p1, p2) + // v1 and v2 are parallel to plane, normal is vector product of v1 and v2 + const normal = normalizeVector(crossProduct(v1, v2)) + const origin = p1 + constraintList.push({ + type: 'plane', + data : { origin, normal }, + name + }) + } + }) + if (json.free_form_constraints) { + constraintList.push({ + type: 'paint', + data: json.free_form_constraints, + name: json.free_form_constraints.name, + }) + } + } + return constraintList +} + + + +export function convertConstraintDataForDB(shapeLocations, shapeInfos) { + const constraintJSON: Record = {} + shapeInfos.forEach((cInfo) => { + const indexForShape = shapeInfos + .filter((info) => info.type === cInfo.type && info.domain === cInfo.domain) + .findIndex((info) => info.id === cInfo.id) + const locations = shapeLocations.filter((cData) => cData.type === cInfo.type) + + // location not set, skip this iteration + if (locations.length <= indexForShape) return + const cData = locations[indexForShape] + if (cInfo.type === 'plane') { + if (!constraintJSON.planes) constraintJSON.planes = [] + const { origin, normal } = cData.data + + const v1 = crossProduct(normal, [1, 0, 0]) + const v2 = crossProduct(normal, [0, 1, 0]) + + const p1 = origin; + const p2 = addVectors(origin, normal[2] > 0 ? v2 : v1) + const p3 = addVectors(origin, normal[2] > 0 ? v1 : v2) + + const planeData: Record = {points: [p1, p2, p3]} + if (cInfo.name) { + planeData.name = cInfo.name + } + constraintJSON.planes.push(planeData) + } else if (cInfo.type === 'paint') { + const paintData: Record = cData.data + if (cInfo.name) { + paintData.name = cInfo.name + } + constraintJSON.free_form_constraints = paintData + } + }) + + return constraintJSON +} diff --git a/web/shapeworks/src/reader/image.ts b/web/shapeworks/src/reader/image.ts index a725973e..16522fe9 100644 --- a/web/shapeworks/src/reader/image.ts +++ b/web/shapeworks/src/reader/image.ts @@ -3,6 +3,7 @@ import vtkPolyData from 'vtk.js/Sources/Common/DataModel/PolyData'; import vtkPLYReader from 'vtk.js/Sources/IO/Geometry/PLYReader'; import vtkSTLReader from 'vtk.js/Sources/IO/Geometry/STLReader'; import vtkPolyDataReader from 'vtk.js/Sources/IO/Legacy/PolyDataReader'; +import vtkStringArray from 'vtk.js/Sources/Common/Core/StringArray' import readImageArrayBuffer from 'itk/readImageArrayBuffer'; import ITKHelper from 'vtk.js/Sources/Common/DataModel/ITKHelper'; import axios from 'axios'; @@ -14,7 +15,7 @@ const { convertItkToVtkImage } = ITKHelper; export default async function ( - url: string | undefined, filename='', type="Original", + url: string | undefined, filename='', type="Original", metadata={}, ): Promise { let shape: vtkImageData | vtkPolyData = vtkPolyData.newInstance() if(!url) return shape @@ -49,6 +50,20 @@ export default async function ( shape = vtkPolyData.newInstance() } + // Add metadata to field data + const fieldData = shape.getFieldData() + Object.entries(metadata).forEach(([key, value]) => { + // @ts-ignore + const str: string = value.toString() + const arr = vtkStringArray.newInstance({ + name: key, + size: 1, + }) + arr.setData([str], 1) + // @ts-ignore + fieldData.addArray(arr) + }) + vtkShapesByType.value[type].push(shape) return shape } diff --git a/web/shapeworks/src/store/constants.ts b/web/shapeworks/src/store/constants.ts index 229d5c75..8942ccd5 100644 --- a/web/shapeworks/src/store/constants.ts +++ b/web/shapeworks/src/store/constants.ts @@ -44,7 +44,15 @@ export const layers = ref[]>([ color: undefined, rgb: undefined, available: () => { - return selectedProject.value?.landmarks && selectedProject.value.landmarks.length > 0 + return selectedProject.value?.landmarks_info && selectedProject.value.landmarks_info.length > 0 + } + }, + { + name: 'Constraints', + color: undefined, + rgb: undefined, + available: () => { + return selectedProject.value?.constraints && selectedProject.value.constraints.length > 0 } } ]) diff --git a/web/shapeworks/src/store/index.ts b/web/shapeworks/src/store/index.ts index a170da47..08843c50 100644 --- a/web/shapeworks/src/store/index.ts +++ b/web/shapeworks/src/store/index.ts @@ -3,7 +3,7 @@ import { DataObject, Dataset, Subject, Particles, GroomedShape, Project, ReconstructedSample, VTKInstance, - Analysis, Task + Analysis, Task, LandmarkInfo, Constraints } from '@/types' import { ref } from 'vue' @@ -13,6 +13,8 @@ export * from './constants' export const loadingState = ref(false) +export const renderLoading = ref(false) + export const currentError = ref() export const vtkInstance = ref() @@ -31,6 +33,8 @@ export const allSubjectsForDataset = ref([]) export const allDataObjectsInDataset = ref([]) +export const anatomies = ref([]); + export const selectedDataObjects = ref([]) export const orientationIndicator = ref(vtkAnnotatedCubeActor.newInstance()) @@ -67,9 +71,29 @@ export const cachedParticleComparisonVectors = ref<{[key: string]: number[][]}>( export const cachedParticleComparisonColors = ref<{[key: string]: number[]}>({}) -export const landmarkInfo = ref(); +export const landmarkInfo = ref([]); + +export const landmarksLoading = ref(true); + +export const landmarkSize = ref(2); + +export const allSetLandmarks = ref>(); + +export const currentLandmarkPlacement = ref(); + +export const constraintInfo = ref([]); + +export const constraintsLoading = ref(true); + +export const constraintsShown = ref([]); + +export const allSetConstraints = ref>(); + +export const currentConstraintPlacement = ref(); + +export const constraintPaintRadius = ref(3); -export const landmarkColorList = ref([]) +export const constraintPaintExclusion = ref(true); export const currentTasks = ref>>({}) diff --git a/web/shapeworks/src/store/methods.ts b/web/shapeworks/src/store/methods.ts index 24dc842d..ab50d99c 100644 --- a/web/shapeworks/src/store/methods.ts +++ b/web/shapeworks/src/store/methods.ts @@ -1,4 +1,4 @@ -import { AnalysisParams, CacheComparison, LandmarkInfo, Project, Task } from "@/types"; +import { AnalysisParams, CacheComparison, Project, Task, Constraints } from "@/types"; import { loadingState, selectedDataset, @@ -17,7 +17,6 @@ import { cachedParticleComparisonVectors, allDatasets, goodBadAngles, - landmarkColorList, landmarkInfo, analysisExpandedTab, selectedDataObjects, @@ -29,10 +28,16 @@ import { showDifferenceFromMeanMode, showGoodBadParticlesMode, analysisAnimate, + allSetLandmarks, + allSubjectsForDataset, + anatomies, + constraintInfo, + allSetConstraints, } from "."; import imageReader from "@/reader/image"; import pointsReader from "@/reader/points"; import generateMapper from "@/reader/mapper"; +import constraintsReader from "@/reader/constraints"; import { abortTask, analyzeProject, @@ -52,8 +57,7 @@ import router from "@/router"; export const resetState = () => { selectedDataObjects.value = []; layersShown.value = ['Original']; - landmarkInfo.value = undefined; - landmarkColorList.value = []; + landmarkInfo.value = []; currentTasks.value = {}; jobProgressPoll.value = undefined; particleSize.value = 2; @@ -69,8 +73,6 @@ export const resetState = () => { cachedMarchingCubes.value = {}; cachedParticleComparisonVectors.value = {}; cachedParticleComparisonColors.value = {}; - landmarkInfo.value = undefined; - landmarkColorList.value = []; analysisExpandedTab.value = 0; analysisAnimate.value = false; } @@ -98,7 +100,6 @@ export async function getAllDatasets() { export const loadProjectForDataset = async (projectId: number) => { refreshProject(projectId).then((proj) => { selectedProject.value = proj - getLandmarks() }); } @@ -119,7 +120,6 @@ export const selectProject = (projectId: number | undefined) => { selectedProject.value = allProjectsForDataset.value.find( (project: Project) => project.id == projectId, ) - getLandmarks(); } } @@ -392,47 +392,232 @@ export async function cacheAllComparisons(comparisons: CacheComparison[][]) { } } -export function updateLandmarkColorList() { - landmarkColorList.value = landmarkInfo.value.map( - (info: LandmarkInfo) => info.color - ) + +export function isShapeShown(subjectID, domain) { + return selectedDataObjects.value.some((d) => ( + d.subject === subjectID && d.anatomy_type.replace('anatomy_', '') === domain + )) } -export async function getLandmarks() { - if (selectedProject.value?.landmarks){ - const subjectParticles = await Promise.all( - selectedProject.value.landmarks.map( - async (subjectLandmarks) => { - const locations = await pointsReader(subjectLandmarks.file) - return locations.getPoints().getNumberOfPoints() - } +export function toggleSubjectShown(subjectID, domain) { + const shape = allDataObjectsInDataset.value.find((d) => ( + d.subject === subjectID && d.anatomy_type.replace('anatomy_', '') === domain + )) + if (shape) { + if (selectedDataObjects.value.includes(shape)) { + selectedDataObjects.value = selectedDataObjects.value.filter( + (s) => s !== shape ) + } else { + selectedDataObjects.value = [ + ...selectedDataObjects.value, + shape + ] + } + } +} + +export function getWidgetInfo(subject, item) { + return { + subjectName: subject.name, + domain: item.domain, + widgetID: item.id, + } +} + +export function getLandmarkLocation(subject, item) { + if ( + allSetLandmarks.value && + allSetLandmarks.value[subject.name] + && allSetLandmarks.value[subject.name][item.domain] + ) + return allSetLandmarks.value[subject.name][item.domain][item.id] +} + +export function setLandmarkLocation(subject, item, location) { + if (!allSetLandmarks.value) allSetLandmarks.value = {} + if (!allSetLandmarks.value[subject.name]) allSetLandmarks.value[subject.name] = {} + if (!allSetLandmarks.value[subject.name][item.domain]) allSetLandmarks.value[subject.name][item.domain] = {} + allSetLandmarks.value[subject.name][item.domain][item.id] = location +} + + +export function reassignLandmarkIDsByIndex() { + const reassignedIds = {} + landmarkInfo.value = landmarkInfo.value.map((info, index) => { + if (info.id !== undefined) reassignedIds[info.id] = index + return Object.assign(info, {id: index}) + }) + if (allSetLandmarks.value) { + allSetLandmarks.value = Object.fromEntries( + Object.entries(allSetLandmarks.value) + .map(([subjectName, subjectRecords]) => { + return [subjectName, Object.fromEntries( + Object.entries(subjectRecords).map(([domain, domainRecords]) => { + domainRecords = Object.fromEntries( + Object.entries(domainRecords) + .filter(([lId,]) => Object.keys(reassignedIds).includes(lId)) + .map(([lId, lData]) => { + return [reassignedIds[lId], lData] + }) + ) + return [domain, domainRecords] + }) + )] + }) ) - if (subjectParticles.length > 0){ - const numRows = Math.max(...subjectParticles) - landmarkInfo.value = [...Array(numRows).keys()].map((index) => { - let currentInfo = { - id: index, - color: COLORS[index % COLORS.length], - name: `L${index}`, - num_set: subjectParticles.filter( - (numLocations) => numLocations > index - ).length, - comment: undefined, + } +} - } - if (selectedProject.value?.landmarks_info && selectedProject.value.landmarks_info.length > index) { - currentInfo = Object.assign( - currentInfo, - selectedProject.value?.landmarks_info[index] - ) - } - if (currentInfo.color.toString().includes("#")) { - currentInfo.color = hexToRgb(currentInfo.color.toString()) - } - return currentInfo +export function reassignLandmarkNumSetValues() { + // only reassign if a value has changed + const reassign = false + const newInfo = landmarkInfo.value.map((lInfo) => { + const newNumSet = allSubjectsForDataset.value.filter((s) => !!getLandmarkLocation(s, lInfo)).length + if (newNumSet != lInfo.num_set) { + lInfo.num_set = newNumSet + } + return lInfo + }) + if (reassign) landmarkInfo.value = newInfo +} + + +export async function getLandmarks() { + allSetLandmarks.value = {} + if(selectedProject.value?.landmarks) { + landmarkInfo.value = selectedProject.value.landmarks_info.map((lInfo, index) => { + if (!lInfo.id) { + lInfo.id = index + } + if (!lInfo.name) { + lInfo.name = `L${index}` + } + if (!lInfo.color) { + lInfo.color = COLORS[index % COLORS.length] + } + if (lInfo.color.toString().includes('#')) { + lInfo.color = hexToRgb(lInfo.color.toString()) + } + lInfo.num_set = 0 + return lInfo + }) + + for (let i = 0; i < selectedProject.value.landmarks.length; i++) { + const landmarksObject = selectedProject.value.landmarks[i] + const subject = allSubjectsForDataset.value.find((s) => s.id === landmarksObject.subject) + const pointData = await pointsReader(landmarksObject.file) + const locationData = pointData.getPoints().getData() + const locations: number[][] = [] + for (let p = 0; p < locationData.length; p+=3) { + const location = locationData.slice(p, p+3) as number[] + locations.push(location) + } + const lInfos = landmarkInfo.value.filter((lInfo) => lInfo.domain === landmarksObject.anatomy_type.replace('anatomy_', '')) + locations.forEach((location, index) => { + const lInfo = lInfos[index] + setLandmarkLocation(subject, lInfo, location) }) - updateLandmarkColorList() } + // reassign store var for listeners + allSetLandmarks.value = Object.assign({}, allSetLandmarks.value) + reassignLandmarkNumSetValues(); + } +} + +export function getConstraintLocation(subject, item) { + if ( + allSetConstraints.value && + allSetConstraints.value[subject.name] + && allSetConstraints.value[subject.name][item.domain] + ) + return allSetConstraints.value[subject.name][item.domain][item.id] +} + +export function setConstraintLocation(subject, item, location) { + if (!allSetConstraints.value) allSetConstraints.value = {} + if (!allSetConstraints.value[subject.name]) allSetConstraints.value[subject.name] = {} + if (!allSetConstraints.value[subject.name][item.domain]) allSetConstraints.value[subject.name][item.domain] = {} + allSetConstraints.value[subject.name][item.domain][item.id] = location + allSetConstraints.value = Object.assign({}, allSetConstraints.value) + reassignConstraintNumSetValues() +} + + +export function reassignConstraintIDsByIndex() { + const reassignedIds = {} + constraintInfo.value = constraintInfo.value.map((info, index) => { + if (info.id !== undefined) reassignedIds[info.id] = index + return Object.assign(info, {id: index}) + }) + if (allSetConstraints.value) { + allSetConstraints.value = Object.fromEntries( + Object.entries(allSetConstraints.value) + .map(([subjectName, subjectRecords]) => { + return [subjectName, Object.fromEntries( + Object.entries(subjectRecords).map(([domain, domainRecords]) => { + domainRecords = Object.fromEntries( + Object.entries(domainRecords) + .filter(([cId,]) => Object.keys(reassignedIds).includes(cId)) + .map(([cId, cData]) => { + return [reassignedIds[cId], cData] + }) + ) + return [domain, domainRecords] + }) + )] + }) + ) + } +} + +export function reassignConstraintNumSetValues() { + // only reassign if a value has changed + const reassign = false + const newInfo = constraintInfo.value.map((cInfo) => { + const newNumSet = allSubjectsForDataset.value.filter((s) => !!getConstraintLocation(s, cInfo)).length + if (newNumSet != cInfo.num_set) { + cInfo.num_set = newNumSet + } + return cInfo + }) + if (reassign) constraintInfo.value = newInfo +} + +export async function getConstraints() { + allSetConstraints.value = {} + constraintInfo.value = [] + if(selectedProject.value?.constraints) { + for (let i = 0; i < selectedProject.value.constraints.length; i++) { + const constraintsObject = selectedProject.value.constraints[i] + const subject = allSubjectsForDataset.value.find((s) => s.id === constraintsObject.subject) + const domain = constraintsObject.anatomy_type?.replace('anatomy_', '') || '0' + if (subject) { + const constraintsData = await constraintsReader(constraintsObject.file); + ['plane', 'paint'].forEach((constraintType) => { + const newConstraintsOfType = constraintsData.filter((cData) => cData.type === constraintType) + const existingConstraintsOfType = constraintInfo.value.filter((cData) => cData.type === constraintType && cData.domain === domain) + for(let i=0; i= existingConstraintsOfType.length) { + cInfo = { + id: constraintInfo.value.length, + type: constraintType, + name: cData.name, + domain + } + constraintInfo.value.push(cInfo) + } else { + cInfo = existingConstraintsOfType[i] + } + if(cInfo) setConstraintLocation(subject, cInfo, cData) + } + }) + } + } + // reassign store var for listeners + allSetConstraints.value = Object.assign({}, allSetConstraints.value) + reassignConstraintNumSetValues(); } } diff --git a/web/shapeworks/src/types/index.ts b/web/shapeworks/src/types/index.ts index 1f2a2d32..0ada57f4 100644 --- a/web/shapeworks/src/types/index.ts +++ b/web/shapeworks/src/types/index.ts @@ -94,6 +94,7 @@ export interface Project { dataset: number, landmarks: Landmarks[], landmarks_info: any, + constraints: Constraints[], last_cached_analysis: Analysis | undefined, } @@ -149,6 +150,7 @@ export interface Particles { export interface GroomedShape { id: number, file: string, + anatomy_type: string, pre_alignment: string, pre_cropping: string, project: number, @@ -163,6 +165,7 @@ export interface ReconstructedSample { file: string, project: number, particles: Particles, + anatomy_type: string } export interface Task { @@ -181,6 +184,7 @@ export interface Landmarks { subject: number, created: string, modified: string, + anatomy_type: string, } export interface LandmarkInfo { @@ -193,6 +197,19 @@ export interface LandmarkInfo { visible: "true" | "false", } +export interface Constraints { + id?: number, + file?: string, + type: string, + project?: number, + subject?: number, + created?: string, + modified?: string, + anatomy_type?: string, + domain?: string, + num_set?: number, +} + export interface CacheComparison { file: string, particles: string diff --git a/web/shapeworks/src/views/Main.vue b/web/shapeworks/src/views/Main.vue index d93fc0a7..7bf08937 100644 --- a/web/shapeworks/src/views/Main.vue +++ b/web/shapeworks/src/views/Main.vue @@ -15,6 +15,7 @@ import RenderControls from '../components/RenderControls.vue' import vtkImageData from 'vtk.js/Sources/Common/DataModel/ImageData'; import vtkPolyData from 'vtk.js/Sources/Common/DataModel/PolyData'; import { + renderLoading, selectedDataset, allSubjectsForDataset, selectedDataObjects, @@ -30,26 +31,32 @@ import { meanAnalysisParticlesFiles, currentAnalysisParticlesFiles, switchTab, - landmarkColorList, jobAlreadyDone, analysisExpandedTab, allProjectsForDataset, loadProjectsForDataset, + getLandmarks, + allSetLandmarks, + getConstraints, + allSetConstraints, + landmarksLoading, + constraintsLoading, } from '@/store'; import router from '@/router'; import TabForm from '@/components/TabForm.vue'; import AnalysisTab from '@/components/Analysis/AnalysisTab.vue'; import InfoTab from '@/components/InfoTab.vue'; +import { loadingState } from '../store/index'; export default { components: { ShapeViewer, DataList, + InfoTab, RenderControls, TabForm, AnalysisTab, - InfoTab, }, props: { dataset: { @@ -150,6 +157,35 @@ export default { } async function refreshRender() { + // Get landmarks and constraints the first time each layer is enabled, + // regardless of whether there are objects to render + let landmarksPromise; + if( + layersShown.value.includes("Landmarks") && + !allSetLandmarks.value + ) { + landmarksPromise = getLandmarks().then(() => { + landmarksLoading.value = false + }) + } + + let constraintsPromise; + if( + layersShown.value.includes("Constraints") && + !allSetConstraints.value + ) { + constraintsPromise = getConstraints().then(() => { + constraintsLoading.value = false + }) + } + + if (selectedDataObjects.value.length == 0) { + return Promise.all([ + landmarksPromise, + constraintsPromise, + ]) + } + renderLoading.value = true let newRenderData = {} let newRenderMetaData = {} const groupedSelections: Record = groupBy(selectedDataObjects.value, 'subject') @@ -215,6 +251,8 @@ export default { imageReader( dataObject.file, shortFileName(dataObject.file), + "Original", + { domain: dataObject.anatomy_type.replace('anatomy_', '') } ) ) } @@ -227,6 +265,7 @@ export default { shapeURL, shortFileName(shapeURL), "Groomed", + { domain: dataObject.anatomy_type.replace('anatomy_', '') } ) ) } @@ -249,7 +288,8 @@ export default { imageReader( shapeURL, shortFileName(shapeURL), - "Reconstructed" + "Reconstructed", + { domain: targetReconstruction.anatomy_type.replace('anatomy_', '') } ) ) } @@ -260,23 +300,20 @@ export default { particleURL = particlesForOriginalDataObjects.value[dataObject.type][dataObject.id]?.local } - let landmarksURL; - if(layersShown.value.includes("Landmarks")) { - landmarksURL = selectedProject.value?.landmarks?.find( - (l) => l.subject.toString() === subjectId - )?.file - } - return Promise.all([ Promise.all(shapePromises), pointsReader(particleURL), - pointsReader(landmarksURL) + landmarksPromise, + constraintsPromise, ]) } ))) - .map(([imageData, particleData, landmarkData]) => ( - {shape: imageData, points: particleData, landmarks: landmarkData} - )) + .map(([imageData, particleData, landmarkData, constraintData]) => ({ + shape: imageData, + points: particleData, + landmarks: landmarkData, + constraints: constraintData + })) return [ subjectName, shapeDatas ] @@ -308,11 +345,12 @@ export default { watch(selectedDataObjects, debouncedRefreshRender) watch(layersShown, debouncedRefreshRender) watch(analysisFilesShown, debouncedRefreshRender, {deep: true}) - watch(landmarkColorList, debouncedRefreshRender) watch(meanAnalysisParticlesFiles, debouncedRefreshRender, {deep: true}) watch(tab, switchTab) return { + loadingState, + renderLoading, drawer, drawerWidth, setDrawerWidth, @@ -426,6 +464,9 @@ export default { /> Select any number of data objects + + + diff --git a/web/shapeworks/yarn.lock b/web/shapeworks/yarn.lock index ba088b2e..acbac145 100644 --- a/web/shapeworks/yarn.lock +++ b/web/shapeworks/yarn.lock @@ -2,410 +2,329 @@ # yarn lockfile v1 -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.8.3": - version "7.12.13" - resolved "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.12.13.tgz" - integrity sha512-HV1Cm0Q3ZrpCR93tkWOYiuYIgLxZXZFVG2VgK+MBWjUqZTundupbfx2aXarXuw5Ko5aMcjtJgbSs4vUGBS5v6g== +"@achrinza/node-ipc@9.2.2": + version "9.2.2" + resolved "https://registry.npmjs.org/@achrinza/node-ipc/-/node-ipc-9.2.2.tgz" + integrity sha512-b90U39dx0cU6emsOvy5hxU4ApNXnE3+Tuo8XQZfiKTGelDwpMwBVgBP7QX6dGTcJgu/miyJuNJ/2naFBliNWEw== + dependencies: + "@node-ipc/js-queue" "2.0.3" + event-pubsub "4.3.0" + js-message 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