large-image-source-tifffile 1.27.5.dev4__tar.gz → 1.30.7.dev10__tar.gz

{large-image-source-tifffile-1.27.5.dev4 → large_image_source_tifffile-1.30.7.dev10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.27.5.dev4
+Version: 1.30.7.dev10
 Summary: A tifffile tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -15,9 +15,16 @@ 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
-Provides-Extra: girder
+Description-Content-Type: text/x-rst
 License-File: LICENSE
+Requires-Dist: large-image>=1.30.7.dev10
+Requires-Dist: dask[array]
+Requires-Dist: tifffile[all]
+Requires-Dist: zarr
+Provides-Extra: girder
+Requires-Dist: girder-large-image>=1.30.7.dev10; extra == "girder"
 
 A tifffile tilesource for large_image.
 

{large-image-source-tifffile-1.27.5.dev4 → large_image_source_tifffile-1.30.7.dev10}/README.rst

@@ -15,7 +15,7 @@ Large Image
    :target: https://codecov.io/github/girder/large_image?branch=master
    :alt: codecov.io
 
-.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4723355-blue
+.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4723355-blue.svg
    :target: https://zenodo.org/badge/latestdoi/45569214
 
 .. |pypi-badge| image:: https://img.shields.io/pypi/v/large-image.svg?logo=python&logoColor=white
@@ -39,7 +39,7 @@ Highlights
 Installation
 ------------
 
-In addition to installing the ``large-image`` package, you'll need at least one tile source (a ``large-image-source-xxx`` package).   You can install everything from the main project with one of these commands:
+In addition to installing the base ``large-image`` package, you'll need at least one tile source which corresponds to your target file format(s) (a ``large-image-source-xxx`` package).   You can install everything from the main project with one of these commands:
 
 Pip
 ~~~
@@ -52,7 +52,7 @@ Install all tile sources on linux::
 
     pip install large-image[all] --find-links https://girder.github.io/large_image_wheels
 
-Install all tile sources and all Girder plugins on linux::
+When using large-image with an instance of `Girder`_, install all tile sources and all Girder plugins on linux::
 
     pip install large-image[all] girder-large-image-annotation[tasks] --find-links https://girder.github.io/large_image_wheels
 
@@ -60,8 +60,9 @@ Install all tile sources and all Girder plugins on linux::
 Conda
 ~~~~~
 
-Conda makes dependency management a bit easier if not on Linux. Some of the source modules are available on conda-forge. You can install the following::
+Conda makes dependency management a bit easier if not on Linux. The base module, converter module, and two of the source modules are available on conda-forge. You can install the following::
 
+    conda install -c conda-forge large-image
     conda install -c conda-forge large-image-source-gdal
     conda install -c conda-forge large-image-source-tiff
     conda install -c conda-forge large-image-converter
@@ -118,7 +119,7 @@ Large Image consists of several Python modules designed to work together.  These
 
   - ``large-image-source-deepzoom``: A tile source for reading Deepzoom tiles.
 
-  - ``large-image-source-dicom``: A tile source for reading DICOM WSI images.
+  - ``large-image-source-dicom``: A tile source for reading DICOM Whole Slide Images (WSI).
 
   - ``large-image-source-gdal``: A tile source for reading geotiff files via GDAL.  This handles source data with more complex transforms than the mapnik tile source.
 
@@ -128,62 +129,41 @@ 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-ometiff``: A tile source using the tiff library that can handle some multi-frame OMETiff files.
+  - ``large-image-source-ometiff``: A tile source using the tiff library that can handle most multi-frame OMETiff files that are compliant with the specification.
 
   - ``large-image-source-openjpeg``: A tile source using the Glymur library to read jp2 (JPEG 2000) files.
 
   - ``large-image-source-openslide``: A tile source using the OpenSlide library.  This works with svs, ndpi, Mirax, tiff, vms, and other file formats.
 
-  - ``large-image-source-pil``: A tile source for small images via the Python Imaging Library (Pillow).
+  - ``large-image-source-pil``: A tile source for small images via the Python Imaging Library (Pillow). By default, the maximum size is 4096, but the maximum size can be configured.
 
   - ``large-image-source-tiff``: A tile source for reading pyramidal tiff files in common compression formats.
 
   - ``large-image-source-tifffile``: A tile source using the tifffile library that can handle a wide variety of tiff-like files.
 
-  - ``large-image-source-vips``: A tile source for reading any files handled by libvips.  This also can be used for writing tiled images from numpy arrays.
+  - ``large-image-source-vips``: A tile source for reading any files handled by libvips.  This also can be used for writing tiled images from numpy arrays (up to 4 dimensions).
 
-  - ``large-image-source-zarr``: A tile source using the zarr library that can handle OME-Zarr (OME-NGFF) files as well as some other zarr files.
+  - ``large-image-source-zarr``: A tile source using the zarr library that can handle OME-Zarr (OME-NGFF) files as well as some other zarr files. This can also be used for writing N-dimensional tiled images from numpy arrays. Written images can be saved as any supported format.
 
   - ``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-source-dummy``: A tile source that does nothing. This is an absolutely minimal implementation of a tile source used for testing. If you want to create a custom tile source, start with this implementation.
 
-  Most tile sources can be used with girder-large-image.  You can specific an extras_require of ``girder`` to include ``girder-large-image`` with the source.
 
-- As a Girder plugin:
+As a `Girder`_ plugin, ``large-image`` adds end points to access all of the image formats it can read both to get metadata and to act as a tile server.
+In the Girder UI, ``large-image`` shows images on item pages, and can show thumbnails in item lists when browsing folders.
+There is also cache management to balance memory use and speed of response in Girder when ``large-image`` is used as a tile server.
 
-  - ``girder-large-image``: Large Image as a Girder_ 3.x plugin.
-    You can specify extras_require of ``tasks`` to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.
+Most tile sources can be used with Girder Large Image.  You can specify an extras_require of ``girder`` to install the following packages:
 
-  - ``girder-large-image-annotation``: Annotations for large images as a Girder_ 3.x plugin.
+  - ``girder-large-image``: Large Image as a Girder 3.x plugin.
+    You can install ``large-image[tasks]`` to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.
+
+  - ``girder-large-image-annotation``: Adds models to the Girder database for supporting annotating large images.  These annotations can be rendered on images. Annotations can include polygons, points, image overlays, and other types. Each annotation can have a label and metadata.
 
   - ``large-image-tasks``: A utility for running the converter via Girder Worker.
     You can specify an extras_require of ``girder`` to include modules needed to work with the Girder remote worker or ``worker`` to include modules needed on the remote side of the Girder remote worker.  If neither is specified, some conversion tasks can be run using Girder local jobs.
 
 
-Developer Installation
-----------------------
-
-To install all packages from source, clone the repository::
-
-    git clone https://github.com/girder/large_image.git
-    cd large_image
-
-Install all packages and dependencies::
-
-    pip install -e . -r requirements-dev.txt
-
-If you aren't developing with Girder 3, you can skip installing those components.  Use ``requirements-dev-core.txt`` instead of ``requirements-dev.txt``::
-
-    pip install -e . -r requirements-dev-core.txt
-
-
-Tile source prerequisites
-=========================
-
-Many tile sources have complex prerequisites.  These can be installed directly using your system's package manager or from some prebuilt Python wheels for Linux.  The prebuilt wheels are not official packages, but they can be used by instructing pip to use them by preference::
-
-    pip install -e . -r requirements-dev.txt --find-links https://girder.github.io/large_image_wheels
-
 
-.. _Girder: https://github.com/girder/girder
+.. _Girder: https://girder.readthedocs.io/en/latest/

{large-image-source-tifffile-1.27.5.dev4 → large_image_source_tifffile-1.30.7.dev10}/large_image_source_tifffile/__init__.py

@@ -7,7 +7,6 @@ from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
 import numpy as np
-import zarr
 
 import large_image
 from large_image.cache_util import LruCacheMetaclass, methodcache
@@ -16,6 +15,7 @@ from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource
 
 tifffile = None
+zarr = None
 
 try:
     __version__ = _importlib_version(__name__)
@@ -37,6 +37,7 @@ def _lazyImport():
     module initialization because it is slow.
     """
     global tifffile
+    global zarr
 
     if tifffile is None:
         try:
@@ -55,6 +56,8 @@ 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):
@@ -109,6 +112,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._largeImagePath = str(self._getLargeImagePath())
 
         _lazyImport()
+        self.addKnownExtensions()
         try:
             self._tf = tifffile.TiffFile(self._largeImagePath)
         except Exception:
@@ -179,7 +183,7 @@ 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
@@ -228,7 +232,7 @@ 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
@@ -255,14 +259,17 @@ 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
@@ -285,6 +292,79 @@ 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
@@ -350,6 +430,20 @@ 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.
@@ -419,6 +513,10 @@ 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
@@ -473,19 +571,12 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             sidx = frame // self._basis['P'][0]
         else:
             sidx = 0
-        series = self._tf.series[self._series[sidx]]
         nonempty = [None] * self.levels
         nonempty[self.levels - 1] = True
+        series = self._tf.series[self._series[sidx]]
+        za, hasgbs = self._getZarrArray(series, sidx)
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
-        with self._zarrlock:
-            if sidx not in self._zarrcache:
-                if len(self._zarrcache) > 10:
-                    self._zarrcache = {}
-                za = zarr.open(series.aszarr(), mode='r')
-                hasgbs = hasattr(za[0], 'get_basic_selection')
-                self._zarrcache[sidx] = (za, hasgbs)
-            za, hasgbs = self._zarrcache[sidx]
         for ll in range(1, len(series.levels)):
             scale = round(math.log(max(za[0].shape[xidx] / za[ll].shape[xidx],
                                        za[0].shape[yidx] / za[ll].shape[yidx])) / math.log(2))
@@ -496,6 +587,30 @@ 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:
+                if len(self._zarrcache) > 10:
+                    self._zarrcache = {}
+                za = zarr.open(series.aszarr(), mode='r')
+                hasgbs = hasattr(za[0], 'get_basic_selection')
+                if not hasgbs and math.prod(series.shape) < 256 * 1024 ** 2:
+                    za = series.asarray()
+                self._zarrcache[sidx] = (za, hasgbs)
+            za, hasgbs = self._zarrcache[sidx]
+        return za, hasgbs
+
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         frame = self._getFrame(**kwargs)
@@ -506,14 +621,7 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         else:
             sidx = 0
         series = self._tf.series[self._series[sidx]]
-        with self._zarrlock:
-            if sidx not in self._zarrcache:
-                if len(self._zarrcache) > 10:
-                    self._zarrcache = {}
-                za = zarr.open(series.aszarr(), mode='r')
-                hasgbs = hasattr(za[0], 'get_basic_selection')
-                self._zarrcache[sidx] = (za, hasgbs)
-            za, hasgbs = self._zarrcache[sidx]
+        za, hasgbs = self._getZarrArray(series, sidx)
         xidx = series.axes.index('X')
         yidx = series.axes.index('Y')
         if hasgbs:
@@ -533,7 +641,7 @@ 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 +657,8 @@ 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
@@ -558,6 +668,16 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
 
+    @classmethod
+    def addKnownExtensions(cls):
+        if not hasattr(cls, '_addedExtensions'):
+            _lazyImport()
+            cls._addedExtensions = True
+            cls.extensions = cls.extensions.copy()
+            for ext in tifffile.TIFF.FILE_EXTENSIONS:
+                if ext not in cls.extensions:
+                    cls.extensions[ext] = SourcePriority.IMPLICIT
+
 
 def open(*args, **kwargs):
     """

{large-image-source-tifffile-1.27.5.dev4 → large_image_source_tifffile-1.30.7.dev10}/large_image_source_tifffile.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.27.5.dev4
+Version: 1.30.7.dev10
 Summary: A tifffile tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -15,9 +15,16 @@ 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
-Provides-Extra: girder
+Description-Content-Type: text/x-rst
 License-File: LICENSE
+Requires-Dist: large-image>=1.30.7.dev10
+Requires-Dist: dask[array]
+Requires-Dist: tifffile[all]
+Requires-Dist: zarr
+Provides-Extra: girder
+Requires-Dist: girder-large-image>=1.30.7.dev10; extra == "girder"
 
 A tifffile tilesource for large_image.
 

large_image_source_tifffile-1.30.7.dev10/large_image_source_tifffile.egg-info/requires.txt

@@ -0,0 +1,7 @@
+large-image>=1.30.7.dev10
+dask[array]
+tifffile[all]
+zarr
+
+[girder]
+girder-large-image>=1.30.7.dev10

{large-image-source-tifffile-1.27.5.dev4 → large_image_source_tifffile-1.30.7.dev10}/setup.py

@@ -19,8 +19,7 @@ def prerelease_local_scheme(version):
 
     if os.getenv('CIRCLE_BRANCH') in ('master', ):
         return ''
-    else:
-        return get_local_node_and_date(version)
+    return get_local_node_and_date(version)
 
 
 try:
@@ -37,6 +36,7 @@ setup(
                      'fallback_version': '0.0.0'},
     description=description,
     long_description=long_description,
+    long_description_content_type='text/x-rst',
     license='Apache Software License 2.0',
     author='Kitware, Inc.',
     author_email='kitware@kitware.com',
@@ -49,6 +49,7 @@ setup(
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     install_requires=[
         f'large-image{limit_version}',

large-image-source-tifffile-1.27.5.dev4/large_image_source_tifffile.egg-info/requires.txt

@@ -1,7 +0,0 @@
-large-image>=1.27.5.dev4
-dask[array]
-tifffile[all]
-zarr
-
-[girder]
-girder-large-image>=1.27.5.dev4