Add a Zarr tile source.

This mostly reads omezarr (ome-ngff).
girder · Oct 30, 2023 · 05e0f1d · 05e0f1d
1 parent df16ea8
commit 05e0f1d
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Showing 16 changed files with 565 additions and 5 deletions.
diff --git a/.circleci/make_wheels.sh b/.circleci/make_wheels.sh
@@ -55,3 +55,5 @@ cd "$ROOTPATH/sources/tifffile"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
 cd "$ROOTPATH/sources/vips"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
+cd "$ROOTPATH/sources/zarr"
+pip wheel . --no-deps -w ~/wheels && rm -rf build
diff --git a/.circleci/release_pypi.sh b/.circleci/release_pypi.sh
@@ -136,3 +136,9 @@ cp "$ROOTPATH/LICENSE" .
 python setup.py sdist
 pip wheel . --no-deps -w dist
 twine upload --verbose dist/*
+cd "$ROOTPATH/sources/zarr"
+cp "$ROOTPATH/README.rst" .
+cp "$ROOTPATH/LICENSE" .
+python setup.py sdist
+pip wheel . --no-deps -w dist
+twine upload --verbose dist/*
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,9 @@
 # Change Log
 
-## 1.25.1
+## 1.26.0
+
+### Features
+- Add a Zarr tile source (including ome.zarr) ([#1350](../../pull/1350))
 
 ### Improvements
 - Style can specify a dtype of 'source' to maintain the original dtype even when compositing frames ([#1326](../../pull/1326))

diff --git a/README.rst b/README.rst
@@ -142,6 +142,8 @@ Large Image consists of several Python modules designed to work together.  These
 
   - ``large-image-source-vips``: A tile source for reading any files handled by libvips.  This also can be used for writing tiled images from numpy arrays.
 
+  - ``large-image-source-zarr``: A tile source using the zarr library that can handle OME-Zarr (OME-NGFF) files as well as some other zarr files.
+
   - ``large-image-source-test``: A tile source that generates test tiles, including a simple fractal pattern.  Useful for testing extreme zoom levels.
 
   - ``large-image-source-dummy``: A tile source that does nothing.

diff --git a/docs/index.rst b/docs/index.rst
@@ -34,6 +34,7 @@
    _build/large_image_source_tiff/modules
    _build/large_image_source_tifffile/modules
    _build/large_image_source_vips/modules
+   _build/large_image_source_zarr/modules
    _build/large_image_converter/modules
    _build/large_image_tasks/modules
    _build/girder_large_image/modules

diff --git a/docs/make_docs.sh b/docs/make_docs.sh
@@ -35,6 +35,7 @@ sphinx-apidoc -f -o _build/large_image_source_test ../sources/test/large_image_s
 sphinx-apidoc -f -o _build/large_image_source_tiff ../sources/tiff/large_image_source_tiff
 sphinx-apidoc -f -o _build/large_image_source_tifffile ../sources/tifffile/large_image_source_tifffile
 sphinx-apidoc -f -o _build/large_image_source_vips ../sources/vips/large_image_source_vips
+sphinx-apidoc -f -o _build/large_image_source_zarr ../sources/zarr/large_image_source_zarr
 sphinx-apidoc -f -o _build/large_image_converter ../utilities/converter/large_image_converter
 sphinx-apidoc -f -o _build/large_image_tasks ../utilities/tasks/large_image_tasks
 sphinx-apidoc -f -o _build/girder_large_image ../girder/girder_large_image

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -16,6 +16,7 @@ girder-jobs>=3.0.3
 -e sources/tiff
 -e sources/tifffile
 -e sources/vips
+-e sources/zarr
 # must be after sources/tiff
 -e sources/ometiff
 # must be after source/gdal

diff --git a/requirements-test-core.txt b/requirements-test-core.txt
@@ -14,6 +14,7 @@ sources/test
 sources/tiff
 sources/tifffile ; python_version >= '3.7'
 sources/vips
+sources/zarr
 # must be after sources/tiff
 sources/ometiff
 # must be after source/gdal

diff --git a/requirements-test.txt b/requirements-test.txt
@@ -16,6 +16,7 @@ sources/test
 sources/tiff
 sources/tifffile ; python_version >= '3.7'
 sources/vips
+sources/zarr
 # must be after sources/tiff
 sources/ometiff
 # must be after source/gdal

diff --git a/setup.py b/setup.py
@@ -63,6 +63,7 @@ def prerelease_local_scheme(version):
     'tiff': [f'large-image-source-tiff{limit_version}'],
     'tifffile': [f'large-image-source-tifffile{limit_version} ; python_version >= "3.7"'],
     'vips': [f'large-image-source-vips{limit_version}'],
+    'zarr': [f'large-image-source-zarr{limit_version}'],
 }
 extraReqs.update(sources)
 extraReqs['sources'] = list(set(itertools.chain.from_iterable(sources.values())))
@@ -74,7 +75,7 @@ def prerelease_local_scheme(version):
 # from pypi with all needed dependencies.
 extraReqs['common'] = list(set(itertools.chain.from_iterable(extraReqs[key] for key in {
     'memcached', 'colormaps', 'performance',
-    'deepzoom', 'dicom', 'multi', 'nd2', 'test', 'tifffile',
+    'deepzoom', 'dicom', 'multi', 'nd2', 'test', 'tifffile', 'zarr',
 })) | {
     f'large-image-source-pil[all]{limit_version}',
     f'large-image-source-rasterio[all]{limit_version} ; python_version >= "3.8"',

diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -62,7 +62,7 @@
 
 # Default to ignoring files with no extension and some specific extensions.
 config.ConfigValues['source_bioformats_ignored_names'] = \
-    r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|isyntax|mrxs))$'
+    r'(^[^.]*|\.(jpg|jpeg|jpe|png|tif|tiff|ndpi|nd2|ome|nc|json|isyntax|mrxs|zarr(\.db|\.zip)))$'
 
 
 def _monitor_thread():