Landmark edits

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
@@ -302,6 +304,66 @@ 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():
+            for anatomy_type, locations in data.items():
+                target_subject = models.Subject.objects.get(id=subject_id)
+                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='groom',

swcc/swcc/models/constants.py

@@ -15,5 +15,6 @@
     'groomed',
     'local',
     'world',
+    'landmarks',
     'constraints',
 ]

web/shapeworks/package.json

@@ -18,7 +18,7 @@
     "json-schema-defaults": "^0.4.0",
     "lodash": "^4.17.21",
     "shader-loader": "^1.3.1",
-    "vtk.js": "*",
+    "vtk.js": ">=28.11.0",
     "vue": "^2.7.14",
     "vue-echarts": "^6.2.4",
     "vue-router": "^3.2.0",

web/shapeworks/src/api/rest.ts

@@ -1,4 +1,4 @@
-import { AnalysisParams, DataObject, Dataset, Project, Subject } from "@/types";
+import { AnalysisParams, DataObject, Dataset, LandmarkInfo, Project, Subject } from "@/types";
 import { apiClient } from "./auth";
 import { loadGroomedShapeForObject, loadParticlesForObject } from "@/store";
 
@@ -154,3 +154,14 @@ export async function deleteTaskProgress(taskId: number){
 export async function abortTask(taskId: number) {
     return (await apiClient.post(`/task-progress/${taskId}/abort/`)).data
 }
+
+export async function saveLandmarkData(
+    projectId: number,
+    landmarkInfo: LandmarkInfo[],
+    landmarkLocations: Record<number, Record<number, number[][]>>
+) {
+    return (await apiClient.post(`/projects/${projectId}/landmarks/`, {
+        info: landmarkInfo,
+        locations: landmarkLocations,
+    })).data
+}

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<string[]>([]);
+
         const selectedAnatomies = ref<string[]>([]);
         const selectedSubjects = ref<number[]>([])
         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,