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Ngff follow ups #544

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merged 4 commits into from
Oct 5, 2022
Merged

Ngff follow ups #544

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0c83dd2
BUG: Additional fixes following python 3.7 backport
thewtex Oct 4, 2022
a2061e7
DOC: Update 3DImage example screenshot
thewtex Oct 4, 2022
c060892
ENH: Add itk examples to notebook CI tests
thewtex Oct 4, 2022
ebfcd8e
BUG: Bump ngff-zarr required version to 0.1.2
thewtex Oct 5, 2022
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3 changes: 2 additions & 1 deletion .github/workflows/notebook-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
10 changes: 7 additions & 3 deletions examples/integrations/dask/DaskArray.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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>"
]
Expand Down Expand Up @@ -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>"
]
Expand Down Expand Up @@ -340,7 +344,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.6"
"version": "3.9.13"
}
},
"nbformat": 4,
Expand Down
41 changes: 14 additions & 27 deletions examples/integrations/itk/3DImage.ipynb
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22 changes: 12 additions & 10 deletions itkwidgets/integrations/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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):
Expand All @@ -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
2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
]
Expand Down