feat(segmentGroups): resample when converting to image

src/io/resample/CMakeLists.txt

@@ -8,6 +8,7 @@ find_package(ITK REQUIRED
     WebAssemblyInterface
     ITKImageGrid
     ITKImageFunction
+    GenericLabelInterpolator
   )
 include(${ITK_USE_FILE})
 

src/io/resample/itkWasmUtils.js

@@ -8,6 +8,7 @@ import {
 
 import itkConfig from '@/src/io/itk/itkConfig';
 
+// Splits the input image into multiple slices and processes them in parallel
 export async function runWasm(
   pipeline,
   args,

src/io/resample/resample.cxx

@@ -19,6 +19,7 @@
 #include "itkVectorImage.h"
 #include "itkResampleImageFilter.h"
 #include "itkLinearInterpolateImageFunction.h"
+#include "itkLabelImageGenericInterpolateImageFunction.h"
 #include "itkImageRegionSplitterSlowDimension.h"
 #include "itkExtractImageFilter.h"
 #include "itkRGBPixel.h"
@@ -53,6 +54,9 @@ int Resample(itk::wasm::Pipeline &pipeline, itk::wasm::InputImage<TImage> &input
   OutputImageType outputImage;
   pipeline.add_option("OutputImage", outputImage, "Output image")->required();
 
+  bool label = false;
+  pipeline.add_flag("-l,--label", label, "Interpolate for label image")->default_val(false);
+
   std::vector<unsigned int> outSize;
   pipeline.add_option("-z,--size", outSize, "New image size for each direction")->expected(2, 3)->delimiter(',');
 
@@ -81,6 +85,12 @@ int Resample(itk::wasm::Pipeline &pipeline, itk::wasm::InputImage<TImage> &input
 
   using ResampleFilterType = itk::ResampleImageFilter<ImageType, ImageType>;
   auto resampleFilter = ResampleFilterType::New();
+  if (label)
+  {
+    using InterpolatorType = itk::LabelImageGenericInterpolateImageFunction<ImageType, itk::LinearInterpolateImageFunction>;
+    resampleFilter->SetInterpolator(InterpolatorType::New());
+  }
+
   resampleFilter->SetInput(inImage);
 
   typename ImageType::SizeType outputSize;

src/io/resample/resample.ts

@@ -1,10 +1,15 @@
 import { Image } from 'itk-wasm';
+import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
+import vtkITKHelper from '@kitware/vtk.js/Common/DataModel/ITKHelper';
+import { compareImageSpaces } from '@/src/utils/imageSpace';
 import { runWasm } from './itkWasmUtils';
 
 
-export async function resample(fixed: Image, moving: Image) {
+export async function resample(fixed: Image, moving: Image, label = false) {
+  const labelFlag = label ? ['--label'] : [];
   const { size, spacing, origin, direction } = fixed;
   const args = [
+    ...labelFlag,
     '--size',
     size.join(','),
     '--spacing',
@@ -17,3 +22,15 @@ export async function resample(fixed: Image, moving: Image) {
 
   return runWasm('resample', args, [moving]);
 }
+
+export async function ensureSameSpace(target: vtkImageData, resampleCandidate: vtkImageData, label = false) {
+  if (compareImageSpaces(target, resampleCandidate)) {
+    return resampleCandidate; // could still be different pixel dimensions
+  } 
+  const itkImage = await resample(
+    vtkITKHelper.convertVtkToItkImage(target),
+    vtkITKHelper.convertVtkToItkImage(resampleCandidate),
+    label
+  );
+  return vtkITKHelper.convertItkToVtkImage(itkImage);
+}

src/store/segmentGroups.ts

@@ -1,13 +1,13 @@
 import { computed, reactive, ref, toRaw, watch } from 'vue';
 import vtkDataArray from '@kitware/vtk.js/Common/Core/DataArray';
 import vtkImageData from '@kitware/vtk.js/Common/DataModel/ImageData';
+import vtkBoundingBox from '@kitware/vtk.js/Common/DataModel/BoundingBox';
 import { defineStore } from 'pinia';
 import { useImageStore } from '@/src/store/datasets-images';
 import { join, normalize } from '@/src/utils/path';
 import { useIdStore } from '@/src/store/id';
 import { onImageDeleted } from '@/src/composables/onImageDeleted';
 import { normalizeForStore, removeFromArray } from '@/src/utils';
-import { compareImageSpaces } from '@/src/utils/imageSpace';
 import { SegmentMask } from '@/src/types/segment';
 import { DEFAULT_SEGMENT_MASKS } from '@/src/config';
 import { readImage, writeImage } from '@/src/io/readWriteImage';
@@ -27,6 +27,7 @@ import {
   getImageID,
   selectionEquals,
 } from './datasets';
+import { ensureSameSpace } from '../io/resample/resample';
 
 const LabelmapArrayType = Uint8Array;
 export type LabelmapArrayType = Uint8Array;
@@ -215,8 +216,9 @@ export const useSegmentGroupStore = defineStore('segmentGroup', () => {
       throw new Error('Cannot convert an image to be a labelmap of itself');
 
     // Build vtkImageData for DICOMs
-    await getImage(image);
-    await getImage(parent);
+    const [childImage, parentImage] = await Promise.all(
+      [image, parent].map(getImage)
+    );
 
     const imageID = getImageID(image);
     const parentID = getImageID(parent);
@@ -225,18 +227,25 @@ export const useSegmentGroupStore = defineStore('segmentGroup', () => {
       throw new Error('Image and/or parent datasets do not exist');
 
     const imageStore = useImageStore();
-    const parentImage = imageStore.dataIndex[parentID];
-    const childImage = imageStore.dataIndex[imageID];
 
-    if (!compareImageSpaces(childImage, parentImage))
-      throw new Error('Image does not match parent image space');
+    const intersects = vtkBoundingBox.intersects(
+      parentImage.getBounds(),
+      childImage.getBounds()
+    );
+    if (!intersects) {
+      throw new Error(
+        'Segment group and parent image bounds do not intersect. So no overlap in physical space.'
+      );
+    }
+
+    const resampled = await ensureSameSpace(parentImage, childImage, true);
+    const labelmapImage = toLabelMap(resampled);
 
-    const segmentGroupStore = useSegmentGroupStore();
-    const labelmapImage = toLabelMap(childImage);
     const { order, byKey } = normalizeForStore(
       structuredClone(DEFAULT_SEGMENT_MASKS),
       'value'
     );
+    const segmentGroupStore = useSegmentGroupStore();
     segmentGroupStore.addLabelmap(labelmapImage, {
       name: imageStore.metadata[imageID].name,
       parentImage: parentID,