Merge pull request #486 from girder/openslide-associated-images

Show additional associated image for some openslides.

Dockerfile

@@ -11,7 +11,6 @@ ENV DEBIAN_FRONTEND=noninteractive \
     LANG=en_US.UTF-8 \
     PYENV_ROOT="/.pyenv" \
     PATH="/.pyenv/bin:/.pyenv/shims:$PATH" \
-    GOSU_VERSION=1.10 \
     PYTHON_VERSIONS="3.7.9 2.7.18 3.5.9 3.6.12 3.8.6" \
     LOCAL_PYTHON_VERSION="3.7.9"
     # PYTHON_VERSIONS="2.7.18 3.5.9 3.6.12 3.7.9 3.8.6 pypy2.7-7.3.1 pypy3.5-7.0.0 pypy3.6-7.3.1"
@@ -26,6 +25,7 @@ RUN apt-get update && \
       fonts-dejavu \
       fuse \
       git \
+      gosu \
       gpg-agent \
       libbz2-dev \
       libffi-dev \
@@ -61,22 +61,10 @@ RUN pyenv update && \
     find $PYENV_ROOT/versions -type f '(' -name '*.py[co]' -o -name '*.exe' ')' -exec rm -fv '{}' + && \
     echo $PYTHON_VERSIONS | tr " " "\n" > $PYENV_ROOT/version
 
+# Create a user that can be used with gosu or chroot when running tox
 RUN groupadd -r tox --gid=999 && \
     useradd -m -r -g tox --uid=999 tox
 
-# Install gosu to run tox as the "tox" user instead of as root.
-# https://github.com/tianon/gosu#from-debian
-RUN set -x && \
-    dpkgArch="$(dpkg --print-architecture | awk -F- '{ print $NF }')" && \
-    wget -O /usr/local/bin/gosu "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$dpkgArch" && \
-    wget -O /usr/local/bin/gosu.asc "https://github.com/tianon/gosu/releases/download/$GOSU_VERSION/gosu-$dpkgArch.asc" && \
-    export GNUPGHOME="$(mktemp -d)" && \
-    gpg --keyserver ha.pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4 && \
-    gpg --batch --verify /usr/local/bin/gosu.asc /usr/local/bin/gosu && \
-    rm -r "$GNUPGHOME" /usr/local/bin/gosu.asc && \
-    chmod +x /usr/local/bin/gosu && \
-    gosu nobody true
-
 RUN pyenv local ${PYTHON_VERSIONS%% *} && \
     python -m pip install -U pip && \
     python -m pip install tox && \

sources/openslide/large_image_source_openslide/__init__.py

@@ -25,12 +25,22 @@
 import PIL
 from pkg_resources import DistributionNotFound, get_distribution
 
+try:
+    import tifftools
+except ImportError:
+    tifftools = None
+
 from large_image import config
 from large_image.cache_util import LruCacheMetaclass, methodcache
 from large_image.constants import SourcePriority, TILE_FORMAT_PIL
 from large_image.exceptions import TileSourceException
 from large_image.tilesource import FileTileSource, nearPowerOfTwo
 
+try:
+    from libtiff import libtiff_ctypes
+except ImportError:
+    libtiff_ctypes = False
+
 
 try:
     __version__ = get_distribution(__name__).version
@@ -85,6 +95,11 @@ def __init__(self, path, **kwargs):
             raise TileSourceException('File cannot be opened via OpenSlide.')
         except openslide.lowlevel.OpenSlideError:
             raise TileSourceException('File will not be opened via OpenSlide.')
+        if tifftools and libtiff_ctypes:
+            try:
+                self._tiffinfo = tifftools.read_tiff(largeImagePath)
+            except Exception:
+                pass
 
         svsAvailableLevels = self._getAvailableLevels(largeImagePath)
         if not len(svsAvailableLevels):
@@ -309,16 +324,38 @@ def getPreferredLevel(self, level):
             scale /= 2
         return level
 
+    def _getAssociatedImagesDict(self):
+        images = {}
+        try:
+            for key in self._openslide.associated_images:
+                images[key] = 'openslide'
+        except openslide.lowlevel.OpenSlideError:
+            pass
+        if hasattr(self, '_tiffinfo'):
+            vendor = self._openslide.properties['openslide.vendor']
+            for ifdidx, ifd in enumerate(self._tiffinfo['ifds']):
+                key = None
+                if vendor == 'hamamatsu':
+                    if tifftools.Tag.NDPI_SOURCELENS.value in ifd['tags']:
+                        lens = ifd['tags'][tifftools.Tag.NDPI_SOURCELENS.value]['data'][0]
+                        key = {-1: 'macro', -2: 'nonempty'}.get(lens)
+                elif vendor == 'aperio':
+                    if (ifd['tags'].get(tifftools.Tag.NewSubfileType.value) and
+                            ifd['tags'][tifftools.Tag.NewSubfileType.value]['data'][0] &
+                            tifftools.Tag.NewSubfileType.bitfield.Page.value):
+                        key = 'label' if ifd['tags'][
+                            tifftools.Tag.NewSubfileType.value]['data'][0] == 1 else 'macro'
+                if key and key not in images:
+                    images[key] = ifdidx
+        return images
+
     def getAssociatedImagesList(self):
         """
         Get a list of all associated images.
 
         :return: the list of image keys.
         """
-        try:
-            return sorted(self._openslide.associated_images)
-        except openslide.lowlevel.OpenSlideError:
-            return []
+        return sorted(self._getAssociatedImagesDict().keys())
 
     def _getAssociatedImage(self, imageKey):
         """
@@ -327,9 +364,18 @@ def _getAssociatedImage(self, imageKey):
         :param imageKey: the key of the associated image.
         :return: the image in PIL format or None.
         """
-        try:
-            if imageKey in self._openslide.associated_images:
+        images = self._getAssociatedImagesDict()
+        if imageKey not in images:
+            return None
+        if images[imageKey] == 'openslide':
+            try:
                 return self._openslide.associated_images[imageKey]
-        except openslide.lowlevel.OpenSlideError:
-            pass
-        return None
+            except openslide.lowlevel.OpenSlideError:
+                return None
+        bytePath = self._getLargeImagePath()
+        if not isinstance(bytePath, six.binary_type):
+            bytePath = bytePath.encode('utf8')
+        _tiffFile = libtiff_ctypes.TIFF.open(bytePath)
+        _tiffFile.SetDirectory(images[imageKey])
+        img = _tiffFile.read_image()
+        return PIL.Image.fromarray(img)

sources/openslide/setup.py

@@ -44,6 +44,7 @@ def prerelease_local_scheme(version):
     install_requires=[
         'large-image>=1.0.0',
         'openslide-python>=1.1.0',
+        'tifftools;python_version>="3.6"',
     ],
     extras_require={
         'girder': 'girder-large-image>=1.0.0',