Merge pull request #463 from girder/bioformats

Add a bioformats tilesource.

.circleci/make_wheels.sh

@@ -18,6 +18,8 @@ cd "$ROOTPATH/girder_annotation"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
 cd "$ROOTPATH/tasks"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
+cd "$ROOTPATH/sources/bioformats"
+pip wheel . --no-deps -w ~/wheels && rm -rf build
 cd "$ROOTPATH/sources/dummy"
 pip wheel . --no-deps -w ~/wheels && rm -rf build
 cd "$ROOTPATH/sources/gdal"

.circleci/release_pypi.sh

@@ -15,6 +15,9 @@ twine upload --verbose dist/*
 cd "$ROOTPATH/tasks"
 python setup.py sdist
 twine upload --verbose dist/*
+cd "$ROOTPATH/sources/bioformats"
+python setup.py sdist
+twine upload --verbose dist/*
 cd "$ROOTPATH/sources/dummy"
 python setup.py sdist
 twine upload --verbose dist/*

CHANGELOG.md

@@ -2,6 +2,9 @@
 
 ## Unreleased
 
+### Features
+- Added bioformats tile source (#463)
+
 ## Version 1.2.0
 
 ### Features

README.rst

@@ -45,6 +45,8 @@ Large Image consists of several Python modules designed to work together.  These
 
   - ``large-image-source-nd2``: A tile source for reading nd2 (NIS Element) images.
 
+  - ``large-image-source-bioformats``: A tile source for reading any file handled by the Java Bioformats library.
+
   - ``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.

large_image/tilesource/base.py

@@ -102,6 +102,14 @@ def _imageToPIL(image, setMode=None):
             image = numpy.resize(image, image.shape[:2])
         if image.dtype == numpy.uint16:
             image = numpy.floor_divide(image, 256).astype(numpy.uint8)
+        # TODO: The scaling of float data needs to be identical across all
+        # tiles of an image.  This means that we need a reference to the parent
+        # tile source or some other way of regulating it.
+        # elif image.dtype.kind == 'f':
+        #     if numpy.max(image) > 1:
+        #         maxl2 = math.ceil(math.log(numpy.max(image) + 1) / math.log(2))
+        #         image = image / ((2 ** maxl2) - 1)
+        #     image = (image * 255).astype(numpy.uint8)
         elif image.dtype != numpy.uint8:
             image = image.astype(numpy.uint8)
         image = PIL.Image.fromarray(image, mode)
@@ -1322,7 +1330,7 @@ def _getMinMax(self, minmax, value, dtype, bandidx=None, frame=None):
                 value = self._bandRanges[frame]['max'][bandidx]
             elif dtype == numpy.uint16:
                 value = 65535
-            elif dtype == numpy.float:
+            elif dtype.kind == 'f':
                 value = 1
             else:
                 value = 255

requirements-dev.txt

@@ -3,6 +3,7 @@ girder>=3.0.4 ; python_version < '3.8'
 girder>=3.0.13.dev6 ; python_version >= '3.8'
 girder-jobs>=3.0.3,<3.1 ; python_version < '3.6'
 girder-jobs>=3.0.3 ; python_version >= '3.6'
+-e sources/bioformats ; python_version >= '3.5'
 -e sources/dummy
 -e sources/gdal
 -e sources/nd2

setup.py

@@ -5,6 +5,7 @@
 import os
 import platform
 from setuptools import setup, find_packages
+import sys
 
 with open('README.rst') as readme_file:
     readme = readme_file.read()
@@ -24,6 +25,10 @@
     'tiff': ['large-image-source-tiff'],
     'test': ['large-image-source-test'],
 }
+if sys.version_info >= (3, ):
+    sources.update({
+        'bioformats': ['large-image-source-bioformats'],
+    })
 extraReqs.update(sources)
 extraReqs['sources'] = list(set(itertools.chain.from_iterable(sources.values())))
 extraReqs['all'] = list(set(itertools.chain.from_iterable(extraReqs.values())))