Merge pull request #885 from girder/tifffile-source

Add a tifffile tile source.

.circleci/make_wheels.sh

@@ -47,5 +47,7 @@ cd "$ROOTPATH/sources/test"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
 cd "$ROOTPATH/sources/tiff"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
+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

.circleci/release_pypi.sh

@@ -112,6 +112,12 @@ cp "$ROOTPATH/LICENSE" .
 python setup.py sdist
 pip wheel . --no-deps -w dist
 twine upload --verbose dist/*
+cd "$ROOTPATH/sources/tifffile"
+cp "$ROOTPATH/README.rst" .
+cp "$ROOTPATH/LICENSE" .
+python setup.py sdist
+pip wheel . --no-deps -w dist
+twine upload --verbose dist/*
 cd "$ROOTPATH/sources/vips"
 cp "$ROOTPATH/README.rst" .
 cp "$ROOTPATH/LICENSE" .

README.rst

@@ -132,6 +132,8 @@ 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-tifffile``: A tile source using the tifffile library that can handle a wide variety of tiff-like 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.

docs/index.rst

@@ -30,6 +30,7 @@
    _build/large_image_source_pil/modules
    _build/large_image_source_test/modules
    _build/large_image_source_tiff/modules
+   _build/large_image_source_tifffile/modules
    _build/large_image_source_vips/modules
    _build/large_image_converter/modules
    _build/large_image_tasks/modules

docs/make_docs.sh

@@ -31,6 +31,7 @@ sphinx-apidoc -f -o _build/large_image_source_openslide ../sources/openslide/lar
 sphinx-apidoc -f -o _build/large_image_source_pil ../sources/pil/large_image_source_pil
 sphinx-apidoc -f -o _build/large_image_source_test ../sources/test/large_image_source_test
 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_converter ../utilities/converter/large_image_converter
 sphinx-apidoc -f -o _build/large_image_tasks ../utilities/tasks/large_image_tasks

requirements-dev-core.txt

@@ -10,6 +10,7 @@
 -e sources/pil
 -e sources/test
 -e sources/tiff
+-e sources/tifffile
 -e sources/vips
 # must be after sources/tiff
 -e sources/ometiff

requirements-dev.txt

@@ -13,6 +13,7 @@ girder-jobs>=3.0.3
 -e sources/pil
 -e sources/test
 -e sources/tiff
+-e sources/tifffile ; python_version >= '3.7'
 -e sources/vips
 # must be after sources/tiff
 -e sources/ometiff

requirements-worker.txt

@@ -9,6 +9,7 @@
 -e sources/pil
 -e sources/test
 -e sources/tiff
+-e sources/tifffile
 -e sources/vips
 # must be after sources/tiff
 -e sources/ometiff

setup.py

@@ -56,6 +56,7 @@ def prerelease_local_scheme(version):
     'pil': [f'large-image-source-pil{limit_version}'],
     'test': [f'large-image-source-test{limit_version}'],
     'tiff': [f'large-image-source-tiff{limit_version}'],
+    'tifffile': [f'large-image-source-tifffile{limit_version}'],
     'vips': [f'large-image-source-vips{limit_version}'],
 }
 if sys.version_info >= (3, 7):

sources/tiff/large_image_source_tiff/__init__.py

@@ -712,7 +712,6 @@ def _getAssociatedImage(self, imageKey):
                 return PIL.Image.open(io.BytesIO(base64.b64decode(td._embeddedImages[imageKey])))
         if imageKey in self._associatedImages:
             return PIL.Image.fromarray(self._associatedImages[imageKey])
-        return None
 
 
 def open(*args, **kwargs):