Merge pull request #1088 from girder/pil-frames

Support multi-frame PIL sources.

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Speed up validating annotation colors ([#1080](../../pull/1080))
 - Support more complex bands from the test source ([#1082](../../pull/1082))
 - Improve error thrown for invalid schema with multi source ([#1083](../../pull/1083))
+- Support multi-frame PIL sources ([#1088](../../pull/1088))
 
 ### Bug Fixes
 - The cache could reuse a class inappropriately ([#1070](../../pull/1070))

requirements-dev.txt

@@ -11,7 +11,7 @@ girder-jobs>=3.0.3
 -e sources/nd2
 -e sources/openjpeg
 -e sources/openslide
--e sources/pil
+-e sources/pil[all]
 -e sources/test
 -e sources/tiff
 -e sources/tifffile

requirements-test-core.txt

@@ -8,7 +8,7 @@ sources/multi
 sources/nd2 ; python_version >= '3.7'
 sources/openjpeg
 sources/openslide
-sources/pil
+sources/pil[all]
 sources/test
 sources/tiff
 sources/tifffile ; python_version >= '3.7'

requirements-test.txt

@@ -11,7 +11,7 @@ sources/multi
 sources/nd2 ; python_version >= '3.7'
 sources/openjpeg
 sources/openslide
-sources/pil
+sources/pil[all]
 sources/test
 sources/tiff
 sources/tifffile ; python_version >= '3.7'

sources/pil/large_image_source_pil/__init__.py

@@ -17,16 +17,27 @@
 import json
 import math
 import os
+import threading
 
 import numpy
 import PIL.Image
 
+import large_image
 from large_image import config
 from large_image.cache_util import LruCacheMetaclass, methodcache, strhash
 from large_image.constants import TILE_FORMAT_PIL, SourcePriority
 from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource
 
+# Optionally extend PIL with some additional formats
+try:
+    from pillow_heif import register_heif_opener
+    register_heif_opener()
+    from pillow_heif import register_avif_opener
+    register_avif_opener()
+except Exception:
+    pass
+
 try:
     from importlib.metadata import PackageNotFoundError
     from importlib.metadata import version as _importlib_version
@@ -111,12 +122,15 @@ def __init__(self, path, maxSize=None, **kwargs):
         # such misses most of the data.
         self._ignoreSourceNames('pil', largeImagePath)
 
-        try:
-            self._pilImage = PIL.Image.open(largeImagePath)
-        except OSError:
-            if not os.path.isfile(largeImagePath):
-                raise TileSourceFileNotFoundError(largeImagePath) from None
-            raise TileSourceError('File cannot be opened via PIL.')
+        self._pilImage = None
+        self._fromRawpy(largeImagePath)
+        if self._pilImage is None:
+            try:
+                self._pilImage = PIL.Image.open(largeImagePath)
+            except OSError:
+                if not os.path.isfile(largeImagePath):
+                    raise TileSourceFileNotFoundError(largeImagePath) from None
+                raise TileSourceError('File cannot be opened via PIL.')
         minwh = min(self._pilImage.width, self._pilImage.height)
         maxwh = max(self._pilImage.width, self._pilImage.height)
         # Throw an exception if too small or big before processing further
@@ -125,6 +139,7 @@ def __init__(self, path, maxSize=None, **kwargs):
         maxWidth, maxHeight = getMaxSize(maxSize, self.defaultMaxSize())
         if maxwh > max(maxWidth, maxHeight):
             raise TileSourceError('PIL tile size is too large.')
+        self._checkForFrames()
         if self._pilImage.info.get('icc_profile', None):
             self._iccprofiles = [self._pilImage.info.get('icc_profile')]
         # If the rotation flag exists, loading the image may change the width
@@ -136,11 +151,13 @@ def __init__(self, path, maxSize=None, **kwargs):
         # maximum of 1, 2^8-1, 2^16-1, 2^24-1, or 2^32-1, and scales it to
         # [0, 255]
         pilImageMode = self._pilImage.mode.split(';')[0]
+        self._factor = None
         if pilImageMode in ('I', 'F'):
             imgdata = numpy.asarray(self._pilImage)
             maxval = 256 ** math.ceil(math.log(numpy.max(imgdata) + 1, 256)) - 1
+            self._factor = 255.0 / maxval
             self._pilImage = PIL.Image.fromarray(numpy.uint8(numpy.multiply(
-                imgdata, 255.0 / maxval)))
+                imgdata, self._factor)))
         self.sizeX = self._pilImage.width
         self.sizeY = self._pilImage.height
         # We have just one tile which is the entire image.
@@ -151,6 +168,40 @@ def __init__(self, path, maxSize=None, **kwargs):
         if self.tileWidth > maxWidth or self.tileHeight > maxHeight:
             raise TileSourceError('PIL tile size is too large.')
 
+    def _checkForFrames(self):
+        self._frames = None
+        self._frameCount = 1
+        if hasattr(self._pilImage, 'seek'):
+            baseSize, baseMode = self._pilImage.size, self._pilImage.mode
+            self._frames = [
+                idx for idx, frame in enumerate(PIL.ImageSequence.Iterator(self._pilImage))
+                if frame.size == baseSize and frame.mode == baseMode]
+            self._pilImage.seek(0)
+            self._frameImage = self._pilImage
+            self._frameCount = len(self._frames)
+            self._tileLock = threading.RLock()
+
+    def _fromRawpy(self, largeImagePath):
+        """
+        Try to use rawpy to read an image.
+        """
+        # if rawpy is present, try reading via that library first
+        try:
+            import rawpy
+
+            rgb = rawpy.imread(largeImagePath).postprocess()
+            rgb = large_image.tilesource.utilities._imageToNumpy(rgb)
+            if rgb.shape[2] == 2:
+                rgb = rgb[:, :, :1]
+            elif rgb.shape[2] > 3:
+                rgb = rgb[:, :, :3]
+            self._pilImage = PIL.Image.fromarray(
+                rgb.astype(numpy.uint8) if rgb.dtype != numpy.uint16 else rgb,
+                ('RGB' if rgb.dtype != numpy.uint16 else 'RGB;16') if rgb.shape[2] == 3 else
+                ('L' if rgb.dtype != numpy.uint16 else 'L;16'))
+        except Exception:
+            pass
+
     def defaultMaxSize(self):
         """
         Get the default max size from the config settings.
@@ -170,6 +221,19 @@ def getState(self):
         return super().getState() + ',' + str(
             self._maxSize)
 
+    def getMetadata(self):
+        """
+        Return a dictionary of metadata containing levels, sizeX, sizeY,
+        tileWidth, tileHeight, magnification, mm_x, mm_y, and frames.
+
+        :returns: metadata dictionary.
+        """
+        result = super().getMetadata()
+        if getattr(self, '_frames', None) is not None and len(self._frames) > 1:
+            result['frames'] = [{} for idx in range(len(self._frames))]
+            self._addMetadataFrameInformation(result)
+        return result
+
     def getInternalMetadata(self, **kwargs):
         """
         Return additional known metadata about the tile source.  Data returned
@@ -189,8 +253,23 @@ def getInternalMetadata(self, **kwargs):
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                 mayRedirect=False, **kwargs):
-        self._xyzInRange(x, y, z)
-        return self._outputTile(self._pilImage, TILE_FORMAT_PIL, x, y, z,
+        frame = self._getFrame(**kwargs)
+        self._xyzInRange(x, y, z, frame, self._frameCount)
+        if frame != 0:
+            with self._tileLock:
+                self._frameImage.seek(self._frames[frame])
+                try:
+                    img = self._frameImage.copy()
+                except Exception:
+                    pass
+                self._frameImage.seek(0)
+            img.load()
+            if self._factor:
+                img = PIL.Image.fromarray(numpy.uint8(numpy.multiply(
+                    numpy.asarray(img), self._factor)))
+        else:
+            img = self._pilImage
+        return self._outputTile(img, TILE_FORMAT_PIL, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
 
 

sources/pil/setup.py

@@ -57,6 +57,7 @@ def prerelease_local_scheme(version):
         'importlib-metadata<5 ; python_version < "3.8"',
     ],
     extras_require={
+        'all': ['rawpy', 'pillow-heif'],
         'girder': f'girder-large-image{limit_version}',
     },
     keywords='large_image, tile source',

test/test_source_base.py

@@ -193,11 +193,11 @@ def testSourcesTilesAndMethods(source, filename):
     #  assert ts.histogram(onlyMinMax=True)['min'][0] is not None
     # Test multiple frames if they exist
     assert ts.frames >= 1
-    if len(tileMetadata.get('frames', [])) > 1:
+    open('/tmp/junk.txt', 'a').write('%r\n' % ([source, filename, ts.frames], ))
+    if ts.frames > 1:
         assert ts.frames == len(tileMetadata['frames'])
-        tsf = sourceClass(imagePath, frame=len(tileMetadata['frames']) - 1)
-        tileMetadata = tsf.getMetadata()
-        utilities.checkTilesZXY(tsf, tileMetadata)
+        utilities.checkTilesZXY(
+            ts, tileMetadata, tileParams=dict(frame=ts.frames - 1))
     # Test if we can fetch an associated image if any exist
     assert ts.getAssociatedImagesList() is not None
     if len(ts.getAssociatedImagesList()):