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Upgrade ome-zarr package (#315)
* Upgrade ome-zarr package * Sphinx fixes * Pin pulp version for snakemake * Fix test * Lint
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‎.github/workflows/test_demos.yml‎

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Original file line numberDiff line numberDiff line change
@@ -11,6 +11,7 @@ jobs:
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with:
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python-version: '3.9'
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- run: |
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pip install "pulp==2.7.0"
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pip install snakemake
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pip install pyyaml
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- name: Install vitessce

‎pyproject.toml‎

Lines changed: 11 additions & 1 deletion
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@@ -34,7 +34,7 @@ dependencies = [
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'numpy>=1.21.2',
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'anndata>=0.7.8,<0.9',
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'scanpy>=1.9.3',
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'ome-zarr==0.2.1',
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'ome-zarr==0.8.3',
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'tifffile>=2020.10.1',
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'jsonschema>=3.2'
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]
@@ -50,6 +50,16 @@ dev = [
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docs = [
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'sphinx==4.2.0',
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'sphinx-rtd-theme==1.0.0',
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# Pin sub-dependencies of sphinx
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# Reference: https://github.com/sphinx-doc/sphinx/issues/11130
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'sphinxcontrib-applehelp==1.0.4',
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'sphinxcontrib-devhelp==1.0.2',
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'sphinxcontrib-htmlhelp==2.0.1',
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'sphinxcontrib-jsmath==1.0.1',
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'sphinxcontrib-qthelp==1.0.3',
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'sphinxcontrib-serializinghtml==1.1.5',
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'nbsphinx==0.8.8',
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'nbclean==0.3.2',
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# Pin sqlalchemy to before 1.4 to fix issue importing nbclean.NotebookCleaner

‎tests/test_ome_utils.py‎

Lines changed: 26 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -50,41 +50,44 @@ def setUp(self):
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def test_rgb_img_to_ome_zarr(self):
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img_arr = self.img_arr
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out_path = data_path / "rgb_out.ome.zarr"
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rgb_img_to_ome_zarr(img_arr, out_path, img_name="Test", axes="cyx", chunks=(1, 3, 3))
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rgb_img_to_ome_zarr(img_arr, out_path, img_name="Test", axes="cyx", chunks=(1, 3, 3), scaler=None)
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z_root = zarr.open(out_path, mode="r")
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assert dict(z_root.attrs) == {
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'multiscales': [
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{
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'axes': ['c', 'y', 'x'],
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'axes': [
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{'name': 'c', 'type': 'channel'},
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{'name': 'y', 'type': 'space'},
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{'name': 'x', 'type': 'space'}
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],
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'datasets': [
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{'path': '0'},
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{'path': '1'},
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{'path': '2'},
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{'path': '3'},
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{'path': '4'}
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{
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'coordinateTransformations': [
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{'scale': [1.0, 1.0, 1.0], 'type': 'scale'}
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],
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'path': '0'
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}
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],
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'version': '0.3'
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'name': '/',
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'version': '0.4'
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}
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],
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'omero': {
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'channels': [
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{
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'color': 'FF0000',
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'label': 'R',
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'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
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},
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{
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'color': '00FF00',
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'label': 'G',
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'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
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},
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{
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'color': '0000FF',
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'label': 'B',
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'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
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}
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{'color': 'FF0000',
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'label': 'R',
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'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
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},
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{'color': '00FF00',
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'label': 'G',
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'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
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},
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{'color': '0000FF',
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'label': 'B',
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'window': {'end': 255, 'max': 255, 'min': 0, 'start': 0}
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}
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],
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'name': 'Test',
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'rdefs': {},

‎vitessce/data_utils/ome.py‎

Lines changed: 40 additions & 39 deletions
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@ def multiplex_img_to_ome_tiff(img_arr, channel_names, output_path, axes="CYX"):
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tiff_writer.close()
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def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx"):
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def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx", **kwargs):
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"""
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Convert an RGB image to OME-Zarr v0.3.
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@@ -75,30 +75,31 @@ def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256,
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image=img_arr,
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group=z_root,
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axes=axes,
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omero={
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"name": img_name,
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"version": "0.3",
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"rdefs": {},
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"channels": [
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{
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"label": "R",
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"color": "FF0000",
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"window": default_window
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},
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{
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"label": "G",
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"color": "00FF00",
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"window": default_window
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},
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{
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"label": "B",
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"color": "0000FF",
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"window": default_window
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}
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]
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},
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chunks=chunks
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storage_options=dict(chunks=chunks),
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**kwargs,
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)
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z_root.attrs["omero"] = {
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"name": img_name,
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"version": "0.3",
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"rdefs": {},
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"channels": [
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{
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"label": "R",
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"color": "FF0000",
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"window": default_window
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},
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{
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"label": "G",
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"color": "00FF00",
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"window": default_window
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},
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{
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"label": "B",
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"color": "0000FF",
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"window": default_window
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}
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]
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}
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def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx", channel_colors=None):
@@ -132,19 +133,19 @@ def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Ima
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image=img_arr,
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group=z_root,
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axes=axes,
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omero={
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"name": img_name,
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"version": "0.3",
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"rdefs": {},
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"channels": [
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{
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"label": channel_name,
142-
"color": channel_colors[channel_name] if channel_colors is not None else "FFFFFF",
143-
"window": default_window
144-
}
145-
for channel_name
146-
in channel_names
147-
]
148-
},
149-
chunks=chunks
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storage_options=dict(chunks=chunks)
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)
138+
z_root.attrs["omero"] = {
139+
"name": img_name,
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"version": "0.3",
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"rdefs": {},
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"channels": [
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{
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"label": channel_name,
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"color": channel_colors[channel_name] if channel_colors is not None else "FFFFFF",
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"window": default_window
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}
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for channel_name
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in channel_names
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]
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}

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