large-image-source-tifffile 1.28.3.dev2__py3-none-any.whl → 1.30.7.dev12__py3-none-any.whl

large_image_source_tifffile/__init__.py

@@ -5,9 +5,9 @@ import os
 import threading
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
+from pathlib import Path
 
 import numpy as np
-import zarr
 
 import large_image
 from large_image.cache_util import LruCacheMetaclass, methodcache
@@ -16,6 +16,7 @@ from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource
 
 tifffile = None
+zarr = None
 
 try:
     __version__ = _importlib_version(__name__)
@@ -37,6 +38,7 @@ def _lazyImport():
     module initialization because it is slow.
     """
     global tifffile
+    global zarr
 
     if tifffile is None:
         try:
@@ -55,6 +57,8 @@ def _lazyImport():
         logging.getLogger('tifffile.tifffile').addHandler(checkForMissingDataHandler())
         logging.getLogger('tifffile').setLevel(logging.WARNING)
         logging.getLogger('tifffile').addHandler(checkForMissingDataHandler())
+    if zarr is None:
+        import zarr
 
 
 def et_findall(tag, text):
@@ -80,6 +84,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         'scn': SourcePriority.PREFERRED,
         'tif': SourcePriority.LOW,
         'tiff': SourcePriority.LOW,
+        'ome': SourcePriority.HIGHER,
     }
     mimeTypes = {
         None: SourcePriority.FALLBACK,
@@ -117,6 +122,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 raise TileSourceFileNotFoundError(self._largeImagePath) from None
             msg = 'File cannot be opened via tifffile.'
             raise TileSourceError(msg)
+        self._checkForOmeBinaryonly()
         maxseries, maxsamples = self._biggestSeries()
         self.tileWidth = self.tileHeight = self._tileSize
         s = self._tf.series[maxseries]
@@ -124,6 +130,9 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         if len(s.levels) == 1:
             self.tileWidth = self.tileHeight = self._singleTileSize
         page = s.pages[0]
+        if not hasattr(page, 'tags'):
+            msg = 'File will not be opened via tifffile.'
+            raise TileSourceError(msg)
         if ('TileWidth' in page.tags and
                 self._minTileSize <= page.tags['TileWidth'].value <= self._maxTileSize):
             self.tileWidth = page.tags['TileWidth'].value
@@ -134,6 +143,10 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             self._iccprofiles = [page.tags['InterColorProfile'].value]
         self.sizeX = s.shape[s.axes.index('X')]
         self.sizeY = s.shape[s.axes.index('Y')]
+        while (self.tileWidth // 2 >= self.sizeX and self.tileHeight // 2 >= self.sizeY and
+                min(self.tileWidth, self.tileHeight) // 2 >= self._minTileSize):
+            self.tileWidth //= 2
+            self.tileHeight //= 2
         self._mm_x = self._mm_y = None
         try:
             unit = {2: 25.4, 3: 10}[page.tags['ResolutionUnit'].value.real]
@@ -167,6 +180,35 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             msg = 'File cannot be opened via tifffile: axes and shape do not match access pattern.'
             raise TileSourceError(msg)
 
+    def _checkForOmeBinaryonly(self):
+        from xml.etree import ElementTree as etree
+
+        omexml = getattr(self._tf, 'ome_metadata', None)
+        if not omexml:
+            return
+        try:
+            root = etree.fromstring(omexml)
+        except Exception:
+            return
+        metadatafile = None
+        for element in root:
+            if element.tag.endswith('BinaryOnly'):
+                metadatafile = element.attrib.get('MetadataFile', '')
+        if not metadatafile:
+            return
+        path = Path(self._largeImagePath).parent / metadatafile
+        if not path.is_file():
+            return
+        try:
+            newxml = path.open('r').read()
+        except Exception:
+            return
+        try:
+            root = etree.fromstring(newxml)
+        except Exception:
+            return
+        self._tf._omexml = newxml
+
     def _biggestSeries(self):
         """
         Find the series with the most pixels.  Use all series that have the
@@ -180,7 +222,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         ex = 'no maximum series'
         try:
             for idx, s in enumerate(self._tf.series):
-                samples = np.prod(s.shape)
+                samples = math.prod(s.shape)
                 if samples > maxsamples and 'X' in s.axes and 'Y' in s.axes:
                     maxseries = idx
                     maxsamples = samples
@@ -229,7 +271,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 'sizeX': s.shape[s.axes.index('X')], 'sizeY': s.shape[s.axes.index('Y')]})
             self.sizeX = max(self.sizeX, s.shape[s.axes.index('X')])
             self.sizeY = max(self.sizeY, s.shape[s.axes.index('Y')])
-        self._framecount = len(self._series) * np.prod(tuple(
+        self._framecount = len(self._series) * math.prod(tuple(
             1 if base.axes[sidx] in 'YXS' else v for sidx, v in enumerate(base.shape)))
         self._basis = {}
         basis = 1
@@ -256,14 +298,17 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         for p in self._tf.pages:
             if (p not in pagesInSeries and getattr(p, 'keyframe', None) is not None and
                     p.hash not in hashes and not len(set(p.axes) - set('YXS'))):
-                id = 'image_%s' % p.index
-                entry = {'page': p.index}
-                entry['width'] = p.shape[p.axes.index('X')]
-                entry['height'] = p.shape[p.axes.index('Y')]
-                if (id not in self._associatedImages and
-                        max(entry['width'], entry['height']) <= self._maxAssociatedImageSize and
-                        max(entry['width'], entry['height']) >= self._minAssociatedImageSize):
-                    self._associatedImages[id] = entry
+                try:
+                    id = 'image_%s' % p.index
+                    entry = {'page': p.index}
+                    entry['width'] = p.shape[p.axes.index('X')]
+                    entry['height'] = p.shape[p.axes.index('Y')]
+                    if (id not in self._associatedImages and
+                            max(entry['width'], entry['height']) <= self._maxAssociatedImageSize and
+                            max(entry['width'], entry['height']) >= self._minAssociatedImageSize):
+                        self._associatedImages[id] = entry
+                except Exception:
+                    pass
         for sidx, s in enumerate(self._tf.series):
             if sidx not in self._series and not len(set(s.axes) - set('YXS')):
                 id = 'series_%d' % sidx
@@ -286,6 +331,79 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
+    def _handle_indica(self):
+        import xml.etree.ElementTree
+
+        import large_image.tilesource.utilities
+
+        try:
+            root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
+            self._xml = large_image.tilesource.utilities.etreeToDict(root)
+            self._channels = [c['name'] for c in
+                              self._xml['indica']['image']['channels']['channel']]
+            if len(self._basis) == 1 and 'I' in self._basis:
+                self._basis['C'] = self._basis.pop('I')
+            self._associatedImages.clear()
+        except Exception:
+            pass
+
+    def _handle_ome(self):
+        """
+        For OME Tiff, if we didn't parse the mangification elsewhere, try to
+        parse it here.
+        """
+        import xml.etree.ElementTree
+
+        import large_image.tilesource.utilities
+
+        _omeUnitsToMeters = {
+            'Ym': 1e24,
+            'Zm': 1e21,
+            'Em': 1e18,
+            'Pm': 1e15,
+            'Tm': 1e12,
+            'Gm': 1e9,
+            'Mm': 1e6,
+            'km': 1e3,
+            'hm': 1e2,
+            'dam': 1e1,
+            'm': 1,
+            'dm': 1e-1,
+            'cm': 1e-2,
+            'mm': 1e-3,
+            '\u00b5m': 1e-6,
+            'nm': 1e-9,
+            'pm': 1e-12,
+            'fm': 1e-15,
+            'am': 1e-18,
+            'zm': 1e-21,
+            'ym': 1e-24,
+            '\u00c5': 1e-10,
+        }
+
+        try:
+            root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
+            self._xml = large_image.tilesource.utilities.etreeToDict(root)
+        except Exception:
+            return
+        try:
+            try:
+                base = self._xml['OME']['Image'][0]['Pixels']
+            except Exception:
+                base = self._xml['OME']['Image']['Pixels']
+            if self._mm_x is None and 'PhysicalSizeX' in base:
+                self._mm_x = (
+                    float(base['PhysicalSizeX']) * 1e3 *
+                    _omeUnitsToMeters[base.get('PhysicalSizeXUnit', '\u00b5m')])
+            if self._mm_y is None and 'PhysicalSizeY' in base:
+                self._mm_y = (
+                    float(base['PhysicalSizeY']) * 1e3 *
+                    _omeUnitsToMeters[base.get('PhysicalSizeYUnit', '\u00b5m')])
+            self._mm_x = self._mm_x or self._mm_y
+            self._mm_y = self._mm_y or self._mm_x
+        except Exception:
+            pass
+
     def _handle_scn(self):  # noqa
         """
         For SCN files, parse the xml and possibly adjust how associated images
@@ -351,6 +469,20 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
+    def _handle_internal_ndpi(self, intmeta):
+        try:
+            ndpi = intmeta.pop('65449')
+            intmeta['ndpi'] = {}
+            for line in ndpi.replace('\r', '\n').split('\n'):
+                if '=' in line:
+                    key, value = line.split('=', 1)
+                    key = key.strip()
+                    value = value.strip()
+                    if key and key not in intmeta['ndpi'] and value:
+                        intmeta['ndpi'][key] = value
+        except Exception:
+            pass
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -420,6 +552,10 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                                 json.dumps(result[key][subkey])
                             except Exception:
                                 del result[key][subkey]
+        for key in dir(self._tf):
+            if (key.startswith('is_') and hasattr(self, '_handle_internal_' + key[3:]) and
+                    getattr(self._tf, key)):
+                getattr(self, '_handle_internal_' + key[3:])(result)
         if hasattr(self, '_xml') and 'xml' not in result:
             result.pop('ImageDescription', None)
             result['xml'] = self._xml
@@ -490,6 +626,17 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._nonempty_levels_list[frame] = nonempty
         return nonempty
 
+    def getPreferredLevel(self, level):
+        """
+        Given a desired level (0 is minimum resolution, self.levels - 1 is max
+        resolution), return the level that contains actual data that is no
+        lower resolution.
+
+        :param level: desired level
+        :returns level: a level with actual data that is no lower resolution.
+        """
+        return max(0, min(level, self.levels - 1))
+
     def _getZarrArray(self, series, sidx):
         with self._zarrlock:
             if sidx not in self._zarrcache:
@@ -533,7 +680,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         else:
             bza = za
         if step > 2 ** self._maxSkippedLevels:
-            tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
+            tile, _format = self._getTileFromEmptyLevel(x, y, z, **kwargs)
             tile = large_image.tilesource.base._imageToNumpy(tile)[0]
         else:
             sel = []
@@ -549,6 +696,8 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     sel.append(slice(series.shape[aidx]))
                     baxis += 'S'
                 else:
+                    if axis not in self._basis and axis == 'I':
+                        axis = 'C'
                     sel.append((frame // self._basis[axis][0]) % self._basis[axis][2])
             tile = bza[tuple(sel)]
             # rotate

{large_image_source_tifffile-1.28.3.dev2.dist-info → large_image_source_tifffile-1.30.7.dev12.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: large-image-source-tifffile
-Version: 1.28.3.dev2
+Version: 1.30.7.dev12
 Summary: A tifffile tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -15,14 +15,28 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image >=1.28.3.dev2
+Requires-Dist: large-image>=1.30.7.dev12
 Requires-Dist: dask[array]
 Requires-Dist: tifffile[all]
 Requires-Dist: zarr
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.28.3.dev2 ; extra == 'girder'
+Requires-Dist: girder-large-image>=1.30.7.dev12; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 A tifffile tilesource for large_image.
 

large_image_source_tifffile-1.30.7.dev12.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_tifffile/__init__.py,sha256=WsyPJKR2Iij1V7maAfv4-m1xEhEUHLlRsO3qOK9IIWc,30244
+large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
+large_image_source_tifffile-1.30.7.dev12.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_tifffile-1.30.7.dev12.dist-info/METADATA,sha256=DwwJpYFWMtn8Tp7_mYPoplHzoqmMpoZ43B9xK7nZuZc,1405
+large_image_source_tifffile-1.30.7.dev12.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+large_image_source_tifffile-1.30.7.dev12.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
+large_image_source_tifffile-1.30.7.dev12.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
+large_image_source_tifffile-1.30.7.dev12.dist-info/RECORD,,

{large_image_source_tifffile-1.28.3.dev2.dist-info → large_image_source_tifffile-1.30.7.dev12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_tifffile-1.28.3.dev2.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_tifffile/__init__.py,sha256=7hREWGbhyYOcz94l_vxMAOTUSJKtJY37TEIZdkvamNw,25001
-large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
-large_image_source_tifffile-1.28.3.dev2.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_tifffile-1.28.3.dev2.dist-info/METADATA,sha256=2XRfComEY1H1fO7m6luWIfzukgRCnPmPJw6RVkiDpZw,1061
-large_image_source_tifffile-1.28.3.dev2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_tifffile-1.28.3.dev2.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
-large_image_source_tifffile-1.28.3.dev2.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
-large_image_source_tifffile-1.28.3.dev2.dist-info/RECORD,,