Merge pull request #576 from PaulHax/auto-seg

Automatically convert SEG DICOMs to Segment Groups

src/components/DataBrowser.vue

@@ -8,6 +8,7 @@ import PatientList from './dicom-web/PatientList.vue';
 import { useDICOMStore } from '../store/datasets-dicom';
 import { useImageStore } from '../store/datasets-images';
 import { useDataBrowserStore } from '../store/data-browser';
+import { useDatasetStore } from '../store/datasets';
 import { removeFromArray } from '../utils';
 
 const SAMPLE_DATA_KEY = 'sampleData';
@@ -27,6 +28,7 @@ export default defineComponent({
     const imageStore = useImageStore();
     const dicomWeb = useDicomWebStore();
     const dataBrowserStore = useDataBrowserStore();
+    const datasetStore = useDatasetStore();
 
     // TODO show patient ID in parens if there is a name conflict
     const patients = computed(() =>
@@ -65,10 +67,16 @@ export default defineComponent({
 
     const hideSampleData = computed(() => dataBrowserStore.hideSampleData);
 
+    const deletePatient = (key: string) => {
+      dicomStore.patientStudies[key]
+        .flatMap((study) => dicomStore.studyVolumes[study])
+        .forEach(datasetStore.remove);
+    };
+
     return {
       panels,
       patients,
-      deletePatient: dicomStore.deletePatient,
+      deletePatient,
       hasAnonymousImages,
       dicomWeb,
       SAMPLE_DATA_KEY,

src/components/ImageDataBrowser.vue

@@ -5,14 +5,15 @@ import GroupableItem from '@/src/components/GroupableItem.vue';
 import ImageListCard from '@/src/components/ImageListCard.vue';
 import { createVTKImageThumbnailer } from '@/src/core/thumbnailers/vtk-image';
 import { useSegmentGroupStore } from '@/src/store/segmentGroups';
-import { useImageStore } from '../store/datasets-images';
-import { useDICOMStore } from '../store/datasets-dicom';
 import {
   DataSelection,
   ImageSelection,
   selectionEquals,
-  useDatasetStore,
-} from '../store/datasets';
+} from '@/src/utils/dataSelection';
+import { useImageStore } from '../store/datasets-images';
+import { useDICOMStore } from '../store/datasets-dicom';
+import { useDatasetStore } from '../store/datasets';
+
 import { useMultiSelection } from '../composables/useMultiSelection';
 import { useLayersStore } from '../store/datasets-layers';
 
@@ -129,9 +130,7 @@ export default defineComponent({
       useMultiSelection(nonDICOMImages);
 
     function removeSelection() {
-      selected.value.forEach((id) => {
-        imageStore.deleteData(id);
-      });
+      selected.value.forEach(dataStore.remove);
       selected.value = [];
     }
 
@@ -145,7 +144,7 @@ export default defineComponent({
     }
 
     function removeData(id: string) {
-      imageStore.deleteData(id);
+      dataStore.remove(id);
     }
 
     return {

src/components/LayerProperties.vue

@@ -1,11 +1,11 @@
 <script lang="ts">
 import { computed, defineComponent, PropType, toRefs } from 'vue';
+import { getImageID } from '@/src/utils/dataSelection';
 import { InitViewSpecs } from '../config';
 import { useImageStore } from '../store/datasets-images';
 import { BlendConfig } from '../types/views';
 import { Layer } from '../store/datasets-layers';
 import useLayerColoringStore from '../store/view-configs/layers';
-import { getImageID } from '../store/datasets';
 
 const VIEWS_2D = Object.entries(InitViewSpecs)
   .filter(([, { viewType }]) => viewType === '2D')

src/components/PatientBrowser.vue

@@ -1,12 +1,9 @@
 <script lang="ts">
 import { computed, defineComponent, ref, toRefs, watch } from 'vue';
 import ItemGroup from '@/src/components/ItemGroup.vue';
+import { DataSelection, selectionEquals } from '@/src/utils/dataSelection';
 import { useDICOMStore } from '../store/datasets-dicom';
-import {
-  DataSelection,
-  selectionEquals,
-  useDatasetStore,
-} from '../store/datasets';
+import { useDatasetStore } from '../store/datasets';
 import { useMultiSelection } from '../composables/useMultiSelection';
 import PatientStudyVolumeBrowser from './PatientStudyVolumeBrowser.vue';
 
@@ -62,15 +59,10 @@ export default defineComponent({
       useMultiSelection(studyKeys);
 
     const removeSelectedStudies = () => {
-      selected.value.forEach(async (study) => {
-        dicomStore.deleteStudy(study);
-      });
+      selected.value
+        .flatMap((study) => dicomStore.studyVolumes[study])
+        .forEach(dataStore.remove);
       selected.value = [];
-
-      // Handle the case where we are deleting the selected study
-      // if (selected.value.indexOf(selectedStudy.value) !== -1) {
-      //   dataStore.setPrimarySelection(null);
-      // }
     };
 
     return {

src/components/PatientStudyVolumeBrowser.vue

@@ -3,12 +3,9 @@ import { computed, defineComponent, reactive, toRefs, watch } from 'vue';
 import { Image } from 'itk-wasm';
 import type { PropType } from 'vue';
 import GroupableItem from '@/src/components/GroupableItem.vue';
+import { DataSelection, DICOMSelection } from '@/src/utils/dataSelection';
 import { getDisplayName, useDICOMStore } from '../store/datasets-dicom';
-import {
-  DataSelection,
-  DICOMSelection,
-  useDatasetStore,
-} from '../store/datasets';
+import { useDatasetStore } from '../store/datasets';
 import { useMultiSelection } from '../composables/useMultiSelection';
 import { useMessageStore } from '../store/messages';
 import { useLayersStore } from '../store/datasets-layers';
@@ -75,9 +72,10 @@ export default defineComponent({
     const datasetStore = useDatasetStore();
     const layersStore = useLayersStore();
 
+    const primarySelectionRef = computed(() => datasetStore.primarySelection);
     const volumes = computed(() => {
-      const { volumeInfo } = dicomStore;
-      const { primarySelection } = datasetStore;
+      const volumeInfo = dicomStore.volumeInfo;
+      const primarySelection = primarySelectionRef.value;
       const layerVolumes = layersStore
         .getLayers(primarySelection)
         .filter(({ selection }) => selection.type === 'dicom');
@@ -167,13 +165,12 @@ export default defineComponent({
       useMultiSelection(volumeKeys);
 
     const removeData = (key: string) => {
-      dicomStore.deleteVolume(key);
+      datasetStore.remove(key);
     };
 
     const removeSelectedDICOMVolumes = () => {
-      selected.value.forEach((volumeKey) => {
-        removeData(volumeKey);
-      });
+      // make copy of selected as removing selected will change the array
+      [...selected.value].forEach(removeData);
 
       selected.value = [];
     };

src/components/SegmentGroupControls.vue

@@ -3,9 +3,12 @@ import SegmentList from '@/src/components/SegmentList.vue';
 import CloseableDialog from '@/src/components/CloseableDialog.vue';
 import SaveSegmentGroupDialog from '@/src/components/SaveSegmentGroupDialog.vue';
 import { useCurrentImage } from '@/src/composables/useCurrentImage';
-import { selectionEquals, useDatasetStore } from '@/src/store/datasets';
-import { useDICOMStore } from '@/src/store/datasets-dicom';
-import { useImageStore } from '@/src/store/datasets-images';
+import { useDatasetStore } from '@/src/store/datasets';
+import {
+  getSelectionName,
+  selectionEquals,
+  DataSelection,
+} from '@/src/utils/dataSelection';
 import { useSegmentGroupStore } from '@/src/store/segmentGroups';
 import { usePaintToolStore } from '@/src/store/tools/paint';
 import { Maybe } from '@/src/types';
@@ -15,8 +18,6 @@ const UNNAMED_GROUP_NAME = 'Unnamed Segment Group';
 
 const segmentGroupStore = useSegmentGroupStore();
 const { currentImageID } = useCurrentImage();
-const imageStore = useImageStore();
-const dicomStore = useDICOMStore();
 const dataStore = useDatasetStore();
 
 const currentSegmentGroups = computed(() => {
@@ -119,31 +120,25 @@ function createSegmentGroup() {
   startEditing(id);
 }
 
-// Filter and collect all acceptable images, excluding
-// the current background image, that can be converted into
-// a SegmentGroup (labelmap) for the current background image.
-const nonDICOMImages = computed(() => {
+// Collect images that can be converted into
+// a SegmentGroup for the current background image.
+const segmentGroupConvertibles = computed(() => {
   const primarySelection = dataStore.primarySelection;
-  const ids = imageStore.idList.filter(
-    (id) =>
-      !(id in dicomStore.imageIDToVolumeKey) &&
-      primarySelection &&
-      !selectionEquals({ type: 'image', dataID: id }, primarySelection)
-  );
-  return ids.map((id) => ({ id, name: imageStore.metadata[id].name }));
+  if (!primarySelection) return [];
+  return dataStore.idsAsSelections
+    .filter((selection) => !selectionEquals(selection, primarySelection))
+    .map((selection) => ({
+      selection,
+      name: getSelectionName(selection),
+    }));
 });
 
-function createSegmentGroupFromImage(selectedImageID: string) {
-  if (!selectedImageID) {
-    throw new Error('Cannot create a labelmap without a base image');
-  }
+function createSegmentGroupFromImage(selection: DataSelection) {
   const primarySelection = dataStore.primarySelection;
-  if (primarySelection) {
-    segmentGroupStore.convertImageToLabelmap(
-      { type: 'image', dataID: selectedImageID },
-      primarySelection
-    );
+  if (!primarySelection) {
+    throw new Error('No primary selection');
   }
+  segmentGroupStore.convertImageToLabelmap(selection, primarySelection);
 }
 
 const saveId = ref('');
@@ -178,11 +173,11 @@ function openSaveDialog(id: string) {
             <v-icon class="mr-1">mdi-chevron-down</v-icon>From Image
           </v-btn>
         </template>
-        <v-list v-if="nonDICOMImages.length !== 0">
+        <v-list v-if="segmentGroupConvertibles.length !== 0">
           <v-list-item
-            v-for="(item, index) in nonDICOMImages"
+            v-for="(item, index) in segmentGroupConvertibles"
             :key="index"
-            @click="createSegmentGroupFromImage(item.id)"
+            @click="createSegmentGroupFromImage(item.selection)"
           >
             {{ item.name }}
             <v-tooltip activator="parent" location="end" max-width="200px">

src/components/vtk/VtkSegmentationSliceRepresentation.vue

@@ -6,7 +6,10 @@ import { LPSAxis } from '@/src/types/lps';
 import { onVTKEvent } from '@/src/composables/onVTKEvent';
 import { SlicingMode } from '@kitware/vtk.js/Rendering/Core/ImageMapper/Constants';
 import { VtkViewContext } from '@/src/components/vtk/context';
-import { useSegmentGroupStore } from '@/src/store/segmentGroups';
+import {
+  useSegmentGroupStore,
+  SegmentGroupMetadata,
+} from '@/src/store/segmentGroups';
 import { InterpolationType } from '@kitware/vtk.js/Rendering/Core/ImageProperty/Constants';
 import vtkColorTransferFunction from '@kitware/vtk.js/Rendering/Core/ColorTransferFunction';
 import vtkPiecewiseFunction from '@kitware/vtk.js/Common/DataModel/PiecewiseFunction';
@@ -29,7 +32,7 @@ const view = inject(VtkViewContext);
 if (!view) throw new Error('No VtkView');
 
 const segmentationStore = useSegmentGroupStore();
-const metadata = computed(
+const metadata = computed<SegmentGroupMetadata | undefined>(
   () => segmentationStore.metadataByID[segmentationId.value]
 );
 const imageData = computed(
@@ -64,7 +67,7 @@ watchEffect(() => {
 });
 
 // set slicing mode
-const parentImageId = computed(() => metadata.value.parentImage);
+const parentImageId = computed(() => metadata.value?.parentImage);
 const { metadata: parentMetadata } = useImage(parentImageId);
 
 watchEffect(() => {
@@ -89,6 +92,8 @@ const applySegmentColoring = () => {
 
   let maxValue = 0;
 
+  if (!metadata.value) return; // segment group just deleted
+
   const { segments } = metadata.value;
   segments.order.forEach((segId) => {
     const segment = segments.byValue[segId];

src/composables/useCurrentImage.ts

@@ -14,11 +14,8 @@ import {
 } from '@/src/store/datasets-images';
 import { useLayersStore } from '@/src/store/datasets-layers';
 import { createLPSBounds, getAxisBounds } from '@/src/utils/lps';
-import {
-  getDataSelection,
-  getImageID,
-  useDatasetStore,
-} from '@/src/store/datasets';
+import { useDatasetStore } from '@/src/store/datasets';
+import { getDataSelection, getImageID } from '@/src/utils/dataSelection';
 import { storeToRefs } from 'pinia';
 
 export interface CurrentImageContext {

src/io/dicom.ts

@@ -219,36 +219,6 @@ export class DICOMIO {
     return result.outputs[0].data as Image;
   }
 
-  async resample(fixed: SpatialParameters, moving: Image) {
-    await this.initialize();
-
-    const { size, spacing, origin, direction } = fixed;
-    const args = [
-      '--action',
-      'resample',
-      '0', // space for input image
-
-      '--size',
-      size.join(','),
-      '--spacing',
-      spacing.join(','),
-      '--origin',
-      origin.join(','),
-      '--direction',
-      direction.join(','),
-
-      '--memory-io',
-      '0',
-    ];
-
-    const inputs = [{ type: InterfaceTypes.Image, data: moving }];
-    const outputs = [{ type: InterfaceTypes.Image }];
-
-    const result = await this.runTask('dicom', args, inputs, outputs);
-    const image = result.outputs[0].data as Image;
-    return image;
-  }
-
   /**
    * Builds a volume for a set of files.
    * @async

src/io/import/common.ts

@@ -14,6 +14,10 @@ export interface LoadableResult extends DataResult {
   dataType: 'image' | 'dicom' | 'model';
 }
 
+export interface VolumeResult extends LoadableResult {
+  dataType: 'image' | 'dicom';
+}
+
 export interface ConfigResult extends DataResult {
   config: Config;
 }
@@ -46,6 +50,15 @@ export function isLoadableResult(
   return 'dataID' in importResult && 'dataType' in importResult;
 }
 
+export function isVolumeResult(
+  importResult: ImportResult
+): importResult is VolumeResult {
+  return (
+    isLoadableResult(importResult) &&
+    (importResult.dataType === 'image' || importResult.dataType === 'dicom')
+  );
+}
+
 export function isConfigResult(
   importResult: ImportResult
 ): importResult is ConfigResult {