Merge pull request #734 from thewtex/monai-updates

Monai updates

Author: thewtex

environment.yml

@@ -12,7 +12,7 @@ dependencies:
     - imjoy-elfinder
     - imjoy-jupyter-extension
     - imjoy-jupyterlab-extension
-    - monai-weekly[nibabel, matplotlib, tqdm]
+    - monai[nibabel, matplotlib, tqdm]
     - imageio
     - pyvista
     - dask[diagnostics]

examples/EnvironmentCheck.ipynb

@@ -111,7 +111,7 @@
     "    \"imjoy-jupyter-extension\",\n",
     "    \"imjoy-jupyterlab-extension\",\n",
     "    \"itk\",\n",
-    "    \"monai-weekly[nibabel, matplotlib, tqdm]\",\n",
+    "    \"monai[nibabel, matplotlib, tqdm]\",\n",
     "    \"imageio\",\n",
     "    \"pyvista\",\n",
     "    \"dask[diagnostics]\",\n",

examples/integrations/MONAI/transform_visualization.ipynb

@@ -6,6 +6,7 @@
 import dask
 from .itk import HAVE_ITK
 from .pytorch import HAVE_TORCH
+from .monai import HAVE_MONAI
 from .vtk import HAVE_VTK, vtk_image_to_ngff_image, vtk_polydata_to_vtkjs
 from .xarray import HAVE_XARRAY, HAVE_MULTISCALE_SPATIAL_IMAGE, xarray_data_array_to_numpy, xarray_data_set_to_numpy
 from ..render_types import RenderType
@@ -102,6 +103,15 @@ def _get_viewer_image(image, label=False):
         to_ngff_zarr(store, multiscales, chunk_store=chunk_store)
         return store
 
+    if HAVE_MONAI:
+        from monai.data import MetaTensor, metatensor_to_itk_image
+        if isinstance(image, MetaTensor):
+            itk_image = metatensor_to_itk_image(image)
+            ngff_image = itk_image_to_ngff_image(itk_image)
+            multiscales = to_multiscales(ngff_image, method=method)
+            to_ngff_zarr(store, multiscales, chunk_store=chunk_store)
+            return store
+
     if HAVE_TORCH:
         import torch
         if isinstance(image, torch.Tensor):

itkwidgets/integrations/__init__.py

@@ -1,18 +1,20 @@
 import itkwasm
 
 from packaging import version
+import importlib_metadata
 HAVE_ITK = False
 try:
-    import itk
-    if not hasattr(itk, '__version__') or version.parse(itk.__version__) < version.parse('5.3.0'):
-      raise RuntimeError('itk 5.3 or newer is required. `pip install itk>=5.3.0`')
+    itk_version = importlib_metadata.version('itk')
+    if version.parse(itk_version) < version.parse('5.3.0'):
+        raise RuntimeError('itk 5.3 or newer is required. `pip install itk>=5.3.0`')
     HAVE_ITK = True
-except ImportError:
+except importlib_metadata.PackageNotFoundError:
     pass
-    
+
 
 if HAVE_ITK:
     def itk_group_spatial_object_to_wasm_point_set(point_set):
+        import itk
         point_set_dict = itk.dict_from_pointset(point_set)
         wasm_point_set = itkwasm.PointSet(**point_set_dict)
         return wasm_point_set

itkwidgets/integrations/itk.py

@@ -0,0 +1,8 @@
+import importlib_metadata
+
+HAVE_MONAI = False
+try:
+    importlib_metadata.metadata("monai")
+    HAVE_MONAI = True
+except importlib_metadata.PackageNotFoundError:
+    pass

itkwidgets/integrations/monai.py

@@ -1,6 +1,8 @@
+import importlib_metadata
+
 HAVE_TORCH = False
 try:
-    import torch
+    importlib_metadata.metadata("torch")
     HAVE_TORCH = True
-except ImportError:
+except importlib_metadata.PackageNotFoundError:
     pass

itkwidgets/integrations/pytorch.py

@@ -1,15 +1,17 @@
+import importlib_metadata
+
 HAVE_VTK = False
 try:
-    import vtk
+    importlib_metadata.metadata("vtk")
     HAVE_VTK = True
-    from vtk.util.numpy_support import vtk_to_numpy
-except ImportError:
+except importlib_metadata.PackageNotFoundError:
     pass
 
-from ngff_zarr import ngff_image, to_ngff_image
+from ngff_zarr import to_ngff_image
 
 
 def vtk_image_to_ngff_image(image):
+    from vtk.util.numpy_support import vtk_to_numpy
     array = vtk_to_numpy(image.GetPointData().GetScalars())
     dimensions = list(image.GetDimensions())
     array.shape = dimensions[::-1]
@@ -25,5 +27,6 @@ def vtk_image_to_ngff_image(image):
     return ngff_image
 
 def vtk_polydata_to_vtkjs(point_set):
+    from vtk.util.numpy_support import vtk_to_numpy
     array = vtk_to_numpy(point_set.GetPoints().GetData())
     return array

itkwidgets/integrations/vtk.py

@@ -1,15 +1,17 @@
+import importlib_metadata
+
 HAVE_XARRAY = False
 try:
-    import xarray
+    importlib_metadata.metadata("xarray")
     HAVE_XARRAY = True
-except ImportError:
+except importlib_metadata.PackageNotFoundError:
     pass
 
 HAVE_MULTISCALE_SPATIAL_IMAGE = False
 try:
-    import multiscale_spatial_image
+    importlib_metadata.metadata("multiscale-spatial-image")
     HAVE_MULTISCALE_SPATIAL_IMAGE = True
-except ImportError:
+except importlib_metadata.PackageNotFoundError:
     pass
 
 def xarray_data_array_to_numpy(data_array):

itkwidgets/integrations/xarray.py

@@ -39,6 +39,7 @@ dependencies = [
     "itkwasm >= 1.0b.78",
     "imjoy-rpc >= 0.5.42",
     "imjoy-utils >= 0.1.2",
+    "importlib_metadata",
     "ngff-zarr[dask-image] >= 0.4.3",
     "numcodecs",
     "zarr",