large-image-source-tiff 1.28.2.dev10__py3-none-any.whl → 1.28.2.dev14__py3-none-any.whl

large_image_source_tiff/__init__.py

@@ -73,6 +73,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     }
 
     _maxAssociatedImageSize = 8192
+    _maxUntiledImage = 4096
 
     def __init__(self, path, **kwargs):  # noqa
         """
@@ -85,18 +86,18 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
 
         self._largeImagePath = str(self._getLargeImagePath())
 
+        lastException = None
         try:
             self._initWithTiffTools()
             return
         except Exception as exc:
             self.logger.debug('Cannot read with tifftools route; %r', exc)
+            lastException = exc
 
         alldir = []
         try:
             if hasattr(self, '_info'):
                 alldir = self._scanDirectories()
-            else:
-                lastException = 'Could not parse file with tifftools'
         except IOOpenTiffError:
             msg = 'File cannot be opened via tiff source.'
             raise TileSourceError(msg)
@@ -157,7 +158,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             tifftools.constants.SampleFormat[sampleformat or 1].name,
             bitspersample,
         ))
-        self._bandCount = highest._tiffInfo.get('samplesperpixel')
+        self._bandCount = highest._tiffInfo.get('samplesperpixel', 1)
         # Sort the directories so that the highest resolution is the last one;
         # if a level is missing, put a None value in its place.
         self._tiffDirectories = [directories.get(key) for key in
@@ -252,8 +253,13 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         sizeX = ifd['tags'][tifftools.Tag.ImageWidth.value]['data'][0]
         sizeY = ifd['tags'][tifftools.Tag.ImageLength.value]['data'][0]
-        tileWidth = baseifd['tags'][tifftools.Tag.TileWidth.value]['data'][0]
-        tileHeight = baseifd['tags'][tifftools.Tag.TileLength.value]['data'][0]
+        if tifftools.Tag.TileWidth.value in baseifd['tags']:
+            tileWidth = baseifd['tags'][tifftools.Tag.TileWidth.value]['data'][0]
+            tileHeight = baseifd['tags'][tifftools.Tag.TileLength.value]['data'][0]
+        else:
+            tileWidth = sizeX
+            tileHeight = baseifd['tags'][tifftools.Tag.RowsPerStrip.value]['data'][0]
+
         for tag in {
                 tifftools.Tag.SamplesPerPixel.value,
                 tifftools.Tag.BitsPerSample.value,
@@ -298,7 +304,7 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         directories are the same size and format; all non-tiled directories are
         treated as associated images.
         """
-        dir0 = self.getTiffDir(0)
+        dir0 = self.getTiffDir(0, mustBeTiled=None)
         self.tileWidth = dir0.tileWidth
         self.tileHeight = dir0.tileHeight
         self.sizeX = dir0.imageWidth
@@ -312,12 +318,11 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             tifftools.constants.SampleFormat[sampleformat or 1].name,
             bitspersample,
         ))
-        self._bandCount = dir0._tiffInfo.get('samplesperpixel')
+        self._bandCount = dir0._tiffInfo.get('samplesperpixel', 1)
         info = _cached_read_tiff(self._largeImagePath)
         self._info = info
         frames = []
         associated = []  # for now, a list of directories
-        curframe = -1
         for idx, ifd in enumerate(info['ifds']):
             # if not tiles, add to associated images
             if tifftools.Tag.tileWidth.value not in ifd['tags']:
@@ -326,7 +331,6 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             level = self._levelFromIfd(ifd, info['ifds'][0])
             # if the same resolution as the main image, add a frame
             if level == self.levels - 1:
-                curframe += 1
                 frames.append({'dirs': [None] * self.levels})
                 frames[-1]['dirs'][-1] = (idx, 0)
                 try:
@@ -365,6 +369,35 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     else:
                         msg = 'Tile layers are in a surprising order'
                         raise TileSourceError(msg)
+        # If we have a single untiled ifd that is "small", use it
+        if tifftools.Tag.tileWidth.value not in info['ifds'][0]['tags']:
+            if (
+                self.sizeX > self._maxUntiledImage or self.sizeY > self._maxUntiledImage or
+                (len(info['ifds']) != 1 or tifftools.Tag.SubIfd.value in ifd['tags']) or
+                (tifftools.Tag.ImageDescription.value in ifd['tags'] and
+                 'ImageJ' in ifd['tags'][tifftools.Tag.ImageDescription.value]['data'])
+            ):
+                msg = 'A tiled TIFF is required.'
+                raise ValidationTiffError(msg)
+            associated = []
+            level = self._levelFromIfd(ifd, info['ifds'][0])
+            frames.append({'dirs': [None] * self.levels})
+            frames[-1]['dirs'][-1] = (idx, 0)
+            try:
+                frameMetadata = json.loads(
+                    ifd['tags'][tifftools.Tag.ImageDescription.value]['data'])
+                for key in {'channels', 'frame'}:
+                    if key in frameMetadata:
+                        frames[-1][key] = frameMetadata[key]
+            except Exception:
+                pass
+            if tifftools.Tag.ICCProfile.value in ifd['tags']:
+                if not hasattr(self, '_iccprofiles'):
+                    self._iccprofiles = []
+                while len(self._iccprofiles) < len(frames) - 1:
+                    self._iccprofiles.append(None)
+                self._iccprofiles.append(ifd['tags'][
+                    tifftools.Tag.ICCProfile.value]['data'])
         self._associatedImages = {}
         for dirNum in associated:
             self._addAssociatedImage(dirNum)

large_image_source_tiff/tiff_reader.py

@@ -207,8 +207,8 @@ class TiledTiffDirectory:
         # the create_image.py script, such as flatten or colourspace.  These
         # should only be done if necessary, which would require the conversion
         # job to check output and perform subsequent processing as needed.
-        if (not self._tiffInfo.get('samplesperpixel') or
-                self._tiffInfo.get('samplesperpixel') < 1):
+        if (not self._tiffInfo.get('samplesperpixel', 1) or
+                self._tiffInfo.get('samplesperpixel', 1) < 1):
             msg = 'Only RGB and greyscale TIFF files are supported'
             raise ValidationTiffError(msg)
 
@@ -607,7 +607,7 @@ class TiledTiffDirectory:
             self._tiffInfo.get('bitspersample'),
             self._tiffInfo.get('sampleformat') if self._tiffInfo.get(
                 'sampleformat') is not None else libtiff_ctypes.SAMPLEFORMAT_UINT)
-        image = np.empty((th, tw, self._tiffInfo['samplesperpixel']),
+        image = np.empty((th, tw, self._tiffInfo.get('samplesperpixel', 1)),
                          dtype=_ctypesFormattbl[format])
         imageBuffer = image.ctypes.data_as(ctypes.POINTER(ctypes.c_char))
         if self._tiffInfo.get('istiled'):
@@ -635,7 +635,7 @@ class TiledTiffDirectory:
             raise IOTiffError(
                 'Read an unexpected number of bytes from an encoded tile' if readSize >= 0 else
                 'Failed to read from an encoded tile')
-        if (self._tiffInfo.get('samplesperpixel') == 3 and
+        if (self._tiffInfo.get('samplesperpixel', 1) == 3 and
                 self._tiffInfo.get('photometric') == libtiff_ctypes.PHOTOMETRIC_YCBCR):
             if self._tiffInfo.get('bitspersample') == 16:
                 image = np.floor_divide(image, 256).astype(np.uint8)

{large_image_source_tiff-1.28.2.dev10.dist-info → large_image_source_tiff-1.28.2.dev14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tiff
-Version: 1.28.2.dev10
+Version: 1.28.2.dev14
 Summary: A TIFF tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,11 +17,11 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.8
 License-File: LICENSE
-Requires-Dist: large-image >=1.28.2.dev10
+Requires-Dist: large-image >=1.28.2.dev14
 Requires-Dist: pylibtiff
 Requires-Dist: tifftools >=1.2.0
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.28.2.dev10 ; extra == 'girder'
+Requires-Dist: girder-large-image >=1.28.2.dev14 ; extra == 'girder'
 
 A TIFF tilesource for large_image.
 

large_image_source_tiff-1.28.2.dev14.dist-info/RECORD

@@ -0,0 +1,10 @@
+large_image_source_tiff/__init__.py,sha256=jviPOv6MViHA6Lfq8rm4TNFvnO_9dqho9Lt_xAQLLjQ,35736
+large_image_source_tiff/exceptions.py,sha256=NgdwloaDCtbtUMe2BU2lXEU8IwQSYtaokIwGIFypCps,617
+large_image_source_tiff/girder_source.py,sha256=Dp2e3O4VTANYXZI_eybgzs5BcyuMcw2-MAzCUJ8zzPg,1031
+large_image_source_tiff/tiff_reader.py,sha256=xrutsp0YGeVeURN0Yf53whbYmKghpEzWC6349WhsMR8,38650
+large_image_source_tiff-1.28.2.dev14.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_tiff-1.28.2.dev14.dist-info/METADATA,sha256=tPOBFIewSbYhr4K0DtfQSyqNkGEsDn0kskqcEOxXtXI,1034
+large_image_source_tiff-1.28.2.dev14.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+large_image_source_tiff-1.28.2.dev14.dist-info/entry_points.txt,sha256=iZ43sIcj98SND7nDUC-_4qroBL6apyXN4iSbPXZ8LE4,166
+large_image_source_tiff-1.28.2.dev14.dist-info/top_level.txt,sha256=QRx_D2oeiOOz_5FlBOAoDPF-E4Q-aFmerUWlaeP14B8,24
+large_image_source_tiff-1.28.2.dev14.dist-info/RECORD,,

large_image_source_tiff-1.28.2.dev10.dist-info/RECORD

@@ -1,10 +0,0 @@
-large_image_source_tiff/__init__.py,sha256=pJmuf2byaUWyTmCQpRa03V3wRfaoM7S46DUONY0aZds,34024
-large_image_source_tiff/exceptions.py,sha256=NgdwloaDCtbtUMe2BU2lXEU8IwQSYtaokIwGIFypCps,617
-large_image_source_tiff/girder_source.py,sha256=Dp2e3O4VTANYXZI_eybgzs5BcyuMcw2-MAzCUJ8zzPg,1031
-large_image_source_tiff/tiff_reader.py,sha256=xZGz9P97LHfL5kmxVCL1ek0ry259LNp39yGls6tnpnM,38634
-large_image_source_tiff-1.28.2.dev10.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_tiff-1.28.2.dev10.dist-info/METADATA,sha256=glBMrldnmGoMkRJnLhgUVVGvEYBkKQIlCfzaJSnuL74,1034
-large_image_source_tiff-1.28.2.dev10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_tiff-1.28.2.dev10.dist-info/entry_points.txt,sha256=iZ43sIcj98SND7nDUC-_4qroBL6apyXN4iSbPXZ8LE4,166
-large_image_source_tiff-1.28.2.dev10.dist-info/top_level.txt,sha256=QRx_D2oeiOOz_5FlBOAoDPF-E4Q-aFmerUWlaeP14B8,24
-large_image_source_tiff-1.28.2.dev10.dist-info/RECORD,,