Merge pull request #544 from thewtex/ngff-follow-ups

Ngff follow ups

Author: thewtex

.github/workflows/notebook-test.yml

@@ -28,7 +28,8 @@ jobs:
           python3 -m pip install -e ".[test]"
           python3 -m pip install pyimagej
           python3 -c "import imagej; ij = imagej.init('2.5.0'); print(ij.getVersion())"
+          python3 -m pip install --upgrade --pre itk
 
       - name: Test notebooks
         run: |
-          pytest --nbmake --nbmake-timeout=3000  examples/*.ipynb examples/integrations/dask/*.ipynb
+          pytest --nbmake --nbmake-timeout=3000  examples/*.ipynb examples/integrations/dask/*.ipynb examples/integrations/itk/*.ipynb

examples/integrations/dask/DaskArray.ipynb

@@ -82,7 +82,9 @@
     },
     {
      "data": {
-      "application/javascript": "window.connectPlugin && window.connectPlugin(\"f73b9611-a293-4994-8215-809777c33496\")",
+      "application/javascript": [
+       "window.connectPlugin && window.connectPlugin(\"f73b9611-a293-4994-8215-809777c33496\")"
+      ],
       "text/plain": [
        "<IPython.core.display.Javascript object>"
       ]
@@ -288,7 +290,9 @@
     },
     {
      "data": {
-      "application/javascript": "window.connectPlugin && window.connectPlugin(\"f73b9611-a293-4994-8215-809777c33496\")",
+      "application/javascript": [
+       "window.connectPlugin && window.connectPlugin(\"f73b9611-a293-4994-8215-809777c33496\")"
+      ],
       "text/plain": [
        "<IPython.core.display.Javascript object>"
       ]
@@ -340,7 +344,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.9.13"
   }
  },
  "nbformat": 4,

examples/integrations/itk/3DImage.ipynb

@@ -47,10 +47,11 @@ def _get_viewer_image(image, label=False):
         method = Methods.DASK_IMAGE_NEAREST
     else:
         method = Methods.DASK_IMAGE_GAUSSIAN
-    
+
     store, chunk_store = _make_multiscale_store()
 
     if HAVE_MULTISCALE_SPATIAL_IMAGE:
+        from multiscale_spatial_image import MultiscaleSpatialImage
         if isinstance(image, MultiscaleSpatialImage):
             image.to_zarr(store, compute=True)
             return store
@@ -59,6 +60,7 @@ def _get_viewer_image(image, label=False):
         ngff_image = itk_image_to_ngff_image(image)
         multiscales = to_multiscales(ngff_image, method=method)
         to_ngff_zarr(store, multiscales, chunk_store=chunk_store)
+        return store
 
     if HAVE_ITK:
         import itk
@@ -152,10 +154,6 @@ def _detect_render_type(data, input_type) -> RenderType:
         return RenderType.IMAGE
     elif isinstance(data, itkwasm.PointSet):
         return RenderType.POINT_SET
-    elif HAVE_MULTISCALE_SPATIAL_IMAGE:
-        from multiscale_spatial_image import MultiscaleSpatialImage
-        if isinstance(data, MultiscaleSpatialImage):
-            return RenderType.IMAGE
     elif isinstance(data, (zarr.Array, zarr.Group)):
         # For now assume zarr.Group is an image
         # In the future, once NGFF supports point sets fully
@@ -175,6 +173,10 @@ def _detect_render_type(data, input_type) -> RenderType:
         import itk
         if isinstance(data, itk.Image):
             return RenderType.IMAGE
+    if HAVE_MULTISCALE_SPATIAL_IMAGE:
+        from multiscale_spatial_image import MultiscaleSpatialImage
+        if isinstance(data, MultiscaleSpatialImage):
+            return RenderType.IMAGE
     if HAVE_VTK:
         import vtk
         if isinstance(data, vtk.vtkImageData):
@@ -200,8 +202,8 @@ def _detect_render_type(data, input_type) -> RenderType:
                 return RenderType.POINT_SET
             else:
                 return RenderType.IMAGE
-    if isinstance(data, xr.Dataset):
-        if input_type == 'point_sets':
-            return RenderType.POINT_SET
-        else:
-            return RenderType.IMAGE
+        if isinstance(data, xr.Dataset):
+            if input_type == 'point_sets':
+                return RenderType.POINT_SET
+            else:
+                return RenderType.IMAGE

itkwidgets/integrations/__init__.py

@@ -38,7 +38,7 @@ dependencies = [
     "itkwasm >= 1.0b1",
     "imjoy-rpc >= 0.5.16",
     "imjoy-utils >= 0.1.2",
-    "ngff-zarr[dask-image] >= 0.1.0",
+    "ngff-zarr[dask-image] >= 0.1.2",
     "numcodecs",
     "zarr",
 ]