large-image 1.27.5.dev6__tar.gz → 1.27.5.dev71__tar.gz

{large-image-1.27.5.dev6/large_image.egg-info → large-image-1.27.5.dev71}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image
-Version: 1.27.5.dev6
+Version: 1.27.5.dev71
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

large-image-1.27.5.dev71/docs/formats.rst

@@ -0,0 +1,21 @@
+Image Formats
+=============
+
+Preferred Extensions and Mime Types
+-----------------------------------
+
+Images can generally be read regardless of their name.  By default, when opening an image with ``large_image.open()``, each tile source reader is tried in turn until one source can open the file.  Each source lists preferred file extensions and mime types with a priority level.  If the file ends with one of these extensions or had one of these mimetypes, the order that the source readers are tried is adjusted based on the listed priority.
+
+The file extensions and mime types that are listed by the core sources that can affect source processing order are listed below.  See ``large_image.listSources()`` for details about priority of the different source and the ``large_image.constants.SourcePriority`` for the priority meaning.
+
+Extensions
+~~~~~~~~~~
+
+.. include:: ../build/docs-work/known_extensions.txt
+   :literal:
+
+Mime Types
+~~~~~~~~~~
+
+.. include:: ../build/docs-work/known_mimetypes.txt
+   :literal:

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/docs/index.rst

@@ -14,6 +14,7 @@
    example_usage
    config_options
    image_conversion
+   formats
    upgrade
    _build/large_image/modules
    _build/large_image_source_bioformats/modules

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/docs/make_docs.sh

@@ -16,6 +16,8 @@ ln -s ../build/docs-work _build
 large_image_converter --help > _build/large_image_converter.txt
 python -c 'from girder_large_image_annotation.models import annotation;import json;print(json.dumps(annotation.AnnotationSchema.annotationSchema, indent=2))' > _build/annotation_schema.json
 python -c 'import large_image_source_multi, json;print(json.dumps(large_image_source_multi.MultiSourceSchema, indent=2))' > _build/multi_source_schema.json
+python -c 'import large_image, yaml;print("\n".join(large_image.listExtensions()))' > _build/known_extensions.txt
+python -c 'import large_image, yaml;print("\n".join(large_image.listMimeTypes()))' > _build/known_mimetypes.txt
 
 sphinx-apidoc -f -o _build/large_image ../large_image
 sphinx-apidoc -f -o _build/large_image_source_bioformats ../sources/bioformats/large_image_source_bioformats

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/large_image/__init__.py

@@ -18,7 +18,8 @@ from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
 from . import tilesource  # noqa
-from .tilesource import canRead, canReadList, getTileSource, new, open  # noqa
+from .tilesource import (canRead, canReadList, getTileSource,  # noqa
+                         listExtensions, listMimeTypes, listSources, new, open)
 
 try:
     __version__ = _importlib_version(__name__)

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/large_image/constants.py

@@ -25,9 +25,11 @@ class SourcePriority(enum.IntEnum):
     MEDIUM = 4
     LOW = 5
     LOWER = 6
-    FALLBACK_HIGH = 7
-    FALLBACK = 8
-    MANUAL = 9   # Will never be selected automatically
+    IMPLICIT_HIGH = 7
+    IMPLICIT = 8
+    FALLBACK_HIGH = 9
+    FALLBACK = 10
+    MANUAL = 11  # This and higher values will never be selected automatically
 
 
 TILE_FORMAT_IMAGE = 'image'

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/large_image/tilesource/__init__.py

@@ -1,9 +1,10 @@
 import os
 import re
+import sys
 import uuid
 from importlib.metadata import entry_points
 from pathlib import PosixPath
-from typing import Dict, List, Optional, Tuple, Type, Union
+from typing import Any, Dict, List, Optional, Tuple, Type, Union, cast
 
 from .. import config
 from ..constants import NEW_IMAGE_PATH_FLAG, SourcePriority
@@ -86,23 +87,26 @@ def getSortedSourceList(
     properties = {
         '_geospatial_source': isGeospatial(pathOrUri),
     }
+    isNew = str(pathOrUri).startswith(NEW_IMAGE_PATH_FLAG)
     sourceList = []
     for sourceName in availableSources:
         sourceExtensions = availableSources[sourceName].extensions
         priority = sourceExtensions.get(None, SourcePriority.MANUAL)
         fallback = True
+        if isNew and getattr(availableSources[sourceName], 'newPriority', None) is not None:
+            priority = min(priority, cast(SourcePriority, availableSources[sourceName].newPriority))
         if (mimeType and getattr(availableSources[sourceName], 'mimeTypes', None) and
                 mimeType in availableSources[sourceName].mimeTypes):
-            fallback = False
             priority = min(priority, availableSources[sourceName].mimeTypes[mimeType])
+            fallback = False
         for regex in getattr(availableSources[sourceName], 'nameMatches', {}):
             if re.match(regex, baseName):
-                fallback = False
                 priority = min(priority, availableSources[sourceName].nameMatches[regex])
+                fallback = False
         for ext in extensions:
             if ext in sourceExtensions:
-                fallback = False
                 priority = min(priority, sourceExtensions[ext])
+                fallback = False
         if isLargeImageUri and sourceName == uriWithoutProtocol:
             priority = SourcePriority.NAMED
         if priority >= SourcePriority.MANUAL:
@@ -130,7 +134,8 @@ def getSourceNameFromDict(
         there is no such source.
     """
     sourceList = getSortedSourceList(availableSources, pathOrUri, mimeType, *args, **kwargs)
-    for _clash, _fallback, _priority, sourceName in sorted(sourceList):
+    for entry in sorted(sourceList):
+        sourceName = entry[-1]
         if availableSources[sourceName].canRead(pathOrUri, *args, **kwargs):
             return sourceName
     return None
@@ -217,7 +222,8 @@ def canReadList(
     sourceList = getSortedSourceList(
         AvailableTileSources, pathOrUri, mimeType, *args, **kwargs)
     result = []
-    for _clash, _fallback, _priority, sourceName in sorted(sourceList):
+    for entry in sorted(sourceList):
+        sourceName = entry[-1]
         result.append((sourceName, AvailableTileSources[sourceName].canRead(
             pathOrUri, *args, **kwargs)))
     return result
@@ -232,6 +238,75 @@ def new(*args, **kwargs) -> TileSource:
     return getTileSource(NEW_IMAGE_PATH_FLAG + str(uuid.uuid4()), *args, **kwargs)
 
 
+def listSources(
+    availableSources: Optional[Dict[str, Type[FileTileSource]]] = None,
+) -> Dict[str, Dict[str, Any]]:
+    """
+    Get a dictionary with all sources, all known extensions, and all known
+    mimetypes.
+
+    :param availableSources: an ordered dictionary of sources to try.
+    :returns: a dictionary with sources, extensions, and mimeTypes.  The
+        extensions and mimeTypes list their matching sources in priority order.
+        The sources list their supported extensions and mimeTypes with their
+        priority.
+    """
+    if availableSources is None:
+        if not len(AvailableTileSources):
+            loadTileSources()
+        availableSources = AvailableTileSources
+    results: Dict[str, Dict[str, Any]] = {'sources': {}, 'extensions': {}, 'mimeTypes': {}}
+    for key, source in availableSources.items():
+        if hasattr(source, 'addKnownExtensions'):
+            source.addKnownExtensions()
+        results['sources'][key] = {
+            'extensions': {
+                k or 'default': v for k, v in source.extensions.items()},
+            'mimeTypes': {
+                k or 'default': v for k, v in source.mimeTypes.items()},
+        }
+        for k, v in source.extensions.items():
+            if k is not None:
+                results['extensions'].setdefault(k, [])
+                results['extensions'][k].append((v, key))
+                results['extensions'][k].sort()
+        for k, v in source.mimeTypes.items():
+            if k is not None:
+                results['mimeTypes'].setdefault(k, [])
+                results['mimeTypes'][k].append((v, key))
+                results['mimeTypes'][k].sort()
+        for cls in source.__mro__:
+            try:
+                if sys.modules[cls.__module__].__version__:
+                    results['sources'][key]['version'] = sys.modules[cls.__module__].__version__
+                    break
+            except Exception:
+                pass
+    return results
+
+
+def listExtensions(
+        availableSources: Optional[Dict[str, Type[FileTileSource]]] = None) -> List[str]:
+    """
+    Get a list of all known extensions.
+
+    :param availableSources: an ordered dictionary of sources to try.
+    :returns: a list of extensions (without leading dots).
+    """
+    return sorted(listSources(availableSources)['extensions'].keys())
+
+
+def listMimeTypes(
+        availableSources: Optional[Dict[str, Type[FileTileSource]]] = None) -> List[str]:
+    """
+    Get a list of all known mime types.
+
+    :param availableSources: an ordered dictionary of sources to try.
+    :returns: a list of mime types.
+    """
+    return sorted(listSources(availableSources)['mimeTypes'].keys())
+
+
 __all__ = [
     'TileSource', 'FileTileSource',
     'exceptions', 'TileGeneralError', 'TileSourceError',
@@ -240,5 +315,6 @@ __all__ = [
     'TileOutputMimeTypes', 'TILE_FORMAT_IMAGE', 'TILE_FORMAT_PIL', 'TILE_FORMAT_NUMPY',
     'AvailableTileSources', 'getTileSource', 'getSourceNameFromDict', 'nearPowerOfTwo',
     'canRead', 'open', 'new',
+    'listSources', 'listExtensions', 'listMimeTypes',
     'etreeToDict', 'dictToEtree',
 ]

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/large_image/tilesource/base.py

@@ -57,6 +57,10 @@ class TileSource(IPyLeafletMixin):
     nameMatches: Dict[str, SourcePriority] = {
     }
 
+    # If a source supports creating new tiled images, specify its basic
+    # priority based on expected feature set
+    newPriority: Optional[SourcePriority] = None
+
     # When getting tiles for otherwise empty levels (missing powers of two), we
     # composite the tile from higher resolution levels.  This can use excessive
     # memory if there are too many missing levels.  For instance, if there are
@@ -1956,7 +1960,7 @@ class TileSource(IPyLeafletMixin):
         image = None
         tiledimage = None
         if max_workers is not None and max_workers < 0:
-            max_workers = max(-max_workers, utilities.cpu_count(False))
+            max_workers = min(-max_workers, utilities.cpu_count(False))
         with concurrent.futures.ThreadPoolExecutor(max_workers=max_workers) as pool:
             futures = []
             for idx, frame in enumerate(frameList):

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/large_image/tilesource/utilities.py

@@ -815,7 +815,12 @@ def _addSubimageToImage(
             dtype=subimage.dtype)
     elif len(image.shape) != len(subimage.shape) or image.shape[-1] != subimage.shape[-1]:
         image, subimage = _makeSameChannelDepth(image, subimage)
-    image[y:y + subimage.shape[0], x:x + subimage.shape[1]] = subimage
+    if subimage.shape[-1] in {2, 4}:
+        mask = (subimage[:, :, -1] > 0)[:, :, np.newaxis]
+        image[y:y + subimage.shape[0], x:x + subimage.shape[1]] = np.where(
+            mask, subimage, image[y:y + subimage.shape[0], x:x + subimage.shape[1]])
+    else:
+        image[y:y + subimage.shape[0], x:x + subimage.shape[1]] = subimage
     return image
 
 

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71/large_image.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image
-Version: 1.27.5.dev6
+Version: 1.27.5.dev71
 Summary: Python modules to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{large-image-1.27.5.dev6 → large-image-1.27.5.dev71}/large_image.egg-info/SOURCES.txt

@@ -8,6 +8,7 @@ docs/conf.py
 docs/config_options.rst
 docs/development.rst
 docs/example_usage.rst
+docs/formats.rst
 docs/girder_annotation_config_options.rst
 docs/girder_config_options.rst
 docs/image_conversion.rst

large-image-1.27.5.dev71/large_image.egg-info/requires.txt

@@ -0,0 +1,145 @@
+cachetools
+palettable
+Pillow
+numpy
+typing-extensions
+
+[all]
+large-image-source-mapnik>=1.27.5.dev71
+psutil>=4.2.0
+large-image-source-dicom>=1.27.5.dev71
+large-image-source-zarr>=1.27.5.dev71
+large-image-source-pil[all]>=1.27.5.dev71
+large-image-source-tiff>=1.27.5.dev71
+large-image-source-dummy>=1.27.5.dev71
+large-image-source-rasterio>=1.27.5.dev71
+large-image-converter>=1.27.5.dev71
+large-image-source-pil>=1.27.5.dev71
+matplotlib
+large-image-source-bioformats>=1.27.5.dev71
+large-image-source-openslide>=1.27.5.dev71
+large-image-source-test>=1.27.5.dev71
+large-image-source-nd2>=1.27.5.dev71
+large-image-source-gdal>=1.27.5.dev71
+large-image-source-multi[all]>=1.27.5.dev71
+simplejpeg
+large-image-source-openjpeg>=1.27.5.dev71
+large-image-source-tifffile>=1.27.5.dev71
+large-image-source-rasterio[all]>=1.27.5.dev71
+large-image-source-multi>=1.27.5.dev71
+pyvips
+large-image-source-deepzoom>=1.27.5.dev71
+large-image-source-ometiff>=1.27.5.dev71
+large-image-source-vips>=1.27.5.dev71
+
+[all:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[bioformats]
+large-image-source-bioformats>=1.27.5.dev71
+
+[colormaps]
+matplotlib
+
+[common]
+large-image-source-nd2>=1.27.5.dev71
+psutil>=4.2.0
+large-image-source-dicom>=1.27.5.dev71
+large-image-source-zarr>=1.27.5.dev71
+simplejpeg
+large-image-source-tifffile>=1.27.5.dev71
+large-image-source-pil[all]>=1.27.5.dev71
+large-image-source-rasterio[all]>=1.27.5.dev71
+large-image-source-multi>=1.27.5.dev71
+matplotlib
+large-image-source-deepzoom>=1.27.5.dev71
+large-image-source-test>=1.27.5.dev71
+
+[common:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[converter]
+large-image-converter>=1.27.5.dev71
+
+[deepzoom]
+large-image-source-deepzoom>=1.27.5.dev71
+
+[dicom]
+large-image-source-dicom>=1.27.5.dev71
+
+[dummy]
+large-image-source-dummy>=1.27.5.dev71
+
+[gdal]
+large-image-source-gdal>=1.27.5.dev71
+
+[mapnik]
+large-image-source-mapnik>=1.27.5.dev71
+
+[memcached]
+
+[memcached:platform_system != "Windows"]
+pylibmc>=1.5.1
+
+[multi]
+large-image-source-multi>=1.27.5.dev71
+
+[nd2]
+large-image-source-nd2>=1.27.5.dev71
+
+[ometiff]
+large-image-source-ometiff>=1.27.5.dev71
+
+[openjpeg]
+large-image-source-openjpeg>=1.27.5.dev71
+
+[openslide]
+large-image-source-openslide>=1.27.5.dev71
+
+[performance]
+psutil>=4.2.0
+simplejpeg
+
+[pil]
+large-image-source-pil>=1.27.5.dev71
+
+[rasterio]
+large-image-source-rasterio>=1.27.5.dev71
+
+[sources]
+large-image-source-nd2>=1.27.5.dev71
+large-image-source-mapnik>=1.27.5.dev71
+large-image-source-gdal>=1.27.5.dev71
+large-image-source-dicom>=1.27.5.dev71
+large-image-source-zarr>=1.27.5.dev71
+large-image-source-test>=1.27.5.dev71
+large-image-source-openjpeg>=1.27.5.dev71
+large-image-source-tiff>=1.27.5.dev71
+large-image-source-dummy>=1.27.5.dev71
+large-image-source-rasterio>=1.27.5.dev71
+large-image-source-multi>=1.27.5.dev71
+large-image-source-tifffile>=1.27.5.dev71
+large-image-source-pil>=1.27.5.dev71
+large-image-source-bioformats>=1.27.5.dev71
+large-image-source-openslide>=1.27.5.dev71
+large-image-source-deepzoom>=1.27.5.dev71
+large-image-source-ometiff>=1.27.5.dev71
+large-image-source-vips>=1.27.5.dev71
+
+[test]
+large-image-source-test>=1.27.5.dev71
+
+[tiff]
+large-image-source-tiff>=1.27.5.dev71
+
+[tifffile]
+large-image-source-tifffile>=1.27.5.dev71
+
+[tiledoutput]
+pyvips
+
+[vips]
+large-image-source-vips>=1.27.5.dev71
+
+[zarr]
+large-image-source-zarr>=1.27.5.dev71

large-image-1.27.5.dev6/large_image.egg-info/requires.txt

@@ -1,145 +0,0 @@
-cachetools
-palettable
-Pillow
-numpy
-typing-extensions
-
-[all]
-psutil>=4.2.0
-large-image-source-openslide>=1.27.5.dev6
-matplotlib
-large-image-source-deepzoom>=1.27.5.dev6
-large-image-source-vips>=1.27.5.dev6
-large-image-source-pil[all]>=1.27.5.dev6
-large-image-source-pil>=1.27.5.dev6
-large-image-source-bioformats>=1.27.5.dev6
-large-image-source-tifffile>=1.27.5.dev6
-large-image-source-multi>=1.27.5.dev6
-large-image-source-rasterio>=1.27.5.dev6
-large-image-source-ometiff>=1.27.5.dev6
-pyvips
-large-image-source-test>=1.27.5.dev6
-large-image-source-dummy>=1.27.5.dev6
-large-image-source-zarr>=1.27.5.dev6
-large-image-source-mapnik>=1.27.5.dev6
-large-image-source-multi[all]>=1.27.5.dev6
-large-image-source-openjpeg>=1.27.5.dev6
-large-image-source-gdal>=1.27.5.dev6
-large-image-source-nd2>=1.27.5.dev6
-large-image-source-dicom>=1.27.5.dev6
-large-image-converter>=1.27.5.dev6
-large-image-source-rasterio[all]>=1.27.5.dev6
-large-image-source-tiff>=1.27.5.dev6
-simplejpeg
-
-[all:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[bioformats]
-large-image-source-bioformats>=1.27.5.dev6
-
-[colormaps]
-matplotlib
-
-[common]
-psutil>=4.2.0
-matplotlib
-large-image-source-test>=1.27.5.dev6
-large-image-source-zarr>=1.27.5.dev6
-large-image-source-deepzoom>=1.27.5.dev6
-large-image-source-nd2>=1.27.5.dev6
-large-image-source-pil[all]>=1.27.5.dev6
-large-image-source-dicom>=1.27.5.dev6
-large-image-source-tifffile>=1.27.5.dev6
-large-image-source-multi>=1.27.5.dev6
-large-image-source-rasterio[all]>=1.27.5.dev6
-simplejpeg
-
-[common:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[converter]
-large-image-converter>=1.27.5.dev6
-
-[deepzoom]
-large-image-source-deepzoom>=1.27.5.dev6
-
-[dicom]
-large-image-source-dicom>=1.27.5.dev6
-
-[dummy]
-large-image-source-dummy>=1.27.5.dev6
-
-[gdal]
-large-image-source-gdal>=1.27.5.dev6
-
-[mapnik]
-large-image-source-mapnik>=1.27.5.dev6
-
-[memcached]
-
-[memcached:platform_system != "Windows"]
-pylibmc>=1.5.1
-
-[multi]
-large-image-source-multi>=1.27.5.dev6
-
-[nd2]
-large-image-source-nd2>=1.27.5.dev6
-
-[ometiff]
-large-image-source-ometiff>=1.27.5.dev6
-
-[openjpeg]
-large-image-source-openjpeg>=1.27.5.dev6
-
-[openslide]
-large-image-source-openslide>=1.27.5.dev6
-
-[performance]
-psutil>=4.2.0
-simplejpeg
-
-[pil]
-large-image-source-pil>=1.27.5.dev6
-
-[rasterio]
-large-image-source-rasterio>=1.27.5.dev6
-
-[sources]
-large-image-source-ometiff>=1.27.5.dev6
-large-image-source-openslide>=1.27.5.dev6
-large-image-source-test>=1.27.5.dev6
-large-image-source-deepzoom>=1.27.5.dev6
-large-image-source-dummy>=1.27.5.dev6
-large-image-source-mapnik>=1.27.5.dev6
-large-image-source-vips>=1.27.5.dev6
-large-image-source-zarr>=1.27.5.dev6
-large-image-source-openjpeg>=1.27.5.dev6
-large-image-source-gdal>=1.27.5.dev6
-large-image-source-nd2>=1.27.5.dev6
-large-image-source-pil>=1.27.5.dev6
-large-image-source-bioformats>=1.27.5.dev6
-large-image-source-dicom>=1.27.5.dev6
-large-image-source-tifffile>=1.27.5.dev6
-large-image-source-multi>=1.27.5.dev6
-large-image-source-tiff>=1.27.5.dev6
-large-image-source-rasterio>=1.27.5.dev6
-
-[test]
-large-image-source-test>=1.27.5.dev6
-
-[tiff]
-large-image-source-tiff>=1.27.5.dev6
-
-[tifffile]
-large-image-source-tifffile>=1.27.5.dev6
-
-[tiledoutput]
-pyvips
-
-[vips]
-large-image-source-vips>=1.27.5.dev6
-
-[zarr]
-large-image-source-zarr>=1.27.5.dev6