Merge branch 'master' into jupyter-frame-selector

girder · Jan 28, 2025 · b831097 · b831097
2 parents 2f029fa + 4b2b390
commit b831097
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,10 +16,13 @@
 - Automatically set the JUPYTER_PROXY value ([#1781](../../pull/1781))
 - Add a general channelNames property to tile sources ([#1783](../../pull/1783))
 - Speed up compositing styles ([#1784](../../pull/1784))
+- Better repr of large_image classes ([#1787](../../pull/1787))
+- Better detect multiframe images in PIL ([#1791](../../pull/1791))
 
 ### Changes
 
 - Allow umap-learn for graphing in girder annotations in python 3.13 ([#1780](../../pull/1780))
+- List a few more known extensions for different sources ([#1790](../../pull/1790))
 
 ### Bug Fixes
 

diff --git a/large_image/constants.py b/large_image/constants.py
@@ -27,9 +27,10 @@ class SourcePriority(enum.IntEnum):
     LOWER = 6
     IMPLICIT_HIGH = 7
     IMPLICIT = 8
-    FALLBACK_HIGH = 9
-    FALLBACK = 10
-    MANUAL = 11  # This and higher values will never be selected automatically
+    IMPLICIT_LOW = 9
+    FALLBACK_HIGH = 10
+    FALLBACK = 11
+    MANUAL = 12  # This and higher values will never be selected automatically
 
 
 TILE_FORMAT_IMAGE = 'image'

diff --git a/large_image/tilesource/base.py b/large_image/tilesource/base.py
@@ -200,11 +200,30 @@ def __reduce__(self) -> Tuple[functools.partial, Tuple[str]]:
         return functools.partial(type(self), **self._initValues[1]), self._initValues[0]
 
     def __repr__(self) -> str:
-        return self.getState()
+        if hasattr(self, '_initValues') and not hasattr(self, '_unpickleable'):
+            param = [
+                f'{k}={v!r}' if k != 'style' or not isinstance(v, dict) or
+                not getattr(self, '_jsonstyle', None) else
+                f'style={json.loads(self._jsonstyle)}'
+                for k, v in self._initValues[1].items()]
+            return (
+                f'{self.__class__.__name__}('
+                f'{", ".join(repr(val) for val in self._initValues[0])}'
+                f'{", " if len(self._initValues[1]) else ""}'
+                f'{", ".join(param)}'
+                ')')
+        return '<' + self.getState() + '>'
 
     def _repr_png_(self) -> bytes:
         return self.getThumbnail(encoding='PNG')[0]
 
+    def __rich_repr__(self) -> Iterator[Any]:
+        if not hasattr(self, '_initValues') or hasattr(self, '_unpickleable'):
+            yield self.getState()
+        else:
+            yield from self._initValues[0]
+            yield from self._initValues[1].items()
+
     @property
     def geospatial(self) -> bool:
         return False

diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -767,6 +767,10 @@ def addKnownExtensions(cls):
                         'fake', 'no'}:
                     if ext not in cls.extensions:
                         cls.extensions[ext] = SourcePriority.IMPLICIT
+            # These were found by reading some OMERO test files
+            for ext in {'columbusidx', 'dv_vol', 'lifext'}:
+                if ext.lower() not in cls.extensions:
+                    cls.extensions[ext.lower()] = SourcePriority.IMPLICIT_LOW
 
 
 def open(*args, **kwargs):

diff --git a/sources/gdal/large_image_source_gdal/__init__.py b/sources/gdal/large_image_source_gdal/__init__.py
@@ -1075,6 +1075,16 @@ def addKnownExtensions(cls):
                     if drvmimes is not None:
                         if drvmimes not in cls.mimeTypes:
                             cls.mimeTypes[drvmimes] = SourcePriority.IMPLICIT
+            # This list was compiled by trying to read the test files in GDAL's
+            # repo.
+            for ext in {
+                    'adf', 'aux', 'demtif', 'dim', 'doq', 'flt', 'fst',
+                    'gdbtable', 'gsc', 'h3', 'idf', 'lan', 'los', 'lrc',
+                    'mapml', 'mint.bin', 'mtw', 'nsf', 'nws', 'on2', 'on9',
+                    'osm.pbf', 'pjg', 'prj', 'ptf', 'rasterlite', 'rdb', 'rl2',
+                    'shx', 'sos', 'tif.grd', 'til', 'vic', 'xlb'}:
+                if ext.lower() not in cls.extensions:
+                    cls.extensions[ext.lower()] = SourcePriority.IMPLICIT_LOW
 
 
 def open(*args, **kwargs):

diff --git a/sources/pil/large_image_source_pil/__init__.py b/sources/pil/large_image_source_pil/__init__.py
@@ -101,6 +101,7 @@ class PILFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         'jpg': SourcePriority.LOW,
         'jpeg': SourcePriority.LOW,
         'jpe': SourcePriority.LOW,
+        'nef': SourcePriority.LOW,
     }
     mimeTypes = {
         None: SourcePriority.FALLBACK_HIGH,
@@ -222,11 +223,20 @@ def _fromRawpy(self, largeImagePath):
         """
         Try to use rawpy to read an image.
         """
-        # if rawpy is present, try reading via that library first
+        # if rawpy is present, try reading via that library first, but only
+        # if PIL reports a single frame
         try:
+            img = PIL.Image.open(largeImagePath)
+            if len(list(PIL.ImageSequence.Iterator(img))) > 1:
+                return
+        except Exception:
+            pass
+        try:
+            import builtins
+
             import rawpy
 
-            with contextlib.redirect_stderr(open(os.devnull, 'w')):
+            with contextlib.redirect_stderr(builtins.open(os.devnull, 'w')):
                 rgb = rawpy.imread(largeImagePath).postprocess()
                 rgb = large_image.tilesource.utilities._imageToNumpy(rgb)[0]
                 if rgb.shape[2] == 2:
@@ -323,6 +333,10 @@ def addKnownExtensions(cls):
             for mimeType in PIL.Image.MIME.values():
                 if mimeType not in cls.mimeTypes:
                     cls.mimeTypes[mimeType] = SourcePriority.IMPLICIT_HIGH
+            # These were found by reading various test files.
+            for ext in {'ppg'}:
+                if ext.lower() not in cls.extensions:
+                    cls.extensions[ext.lower()] = SourcePriority.IMPLICIT_LOW
 
 
 def open(*args, **kwargs):

diff --git a/sources/pil/setup.py b/sources/pil/setup.py
@@ -58,7 +58,8 @@ def prerelease_local_scheme(version):
         'all': [
             'rawpy',
             'pillow-heif',
-            'pillow-jxl-plugin',
+            'pillow-jxl-plugin < 1.3 ; python_version < "3.8"',
+            'pillow-jxl-plugin ; python_version >= "3.9"',
             'pillow-jpls',
         ],
         'girder': f'girder-large-image{limit_version}',

diff --git a/sources/rasterio/large_image_source_rasterio/__init__.py b/sources/rasterio/large_image_source_rasterio/__init__.py
@@ -1077,6 +1077,15 @@ def addKnownExtensions(cls):
             for ext in rasterio.drivers.raster_driver_extensions():
                 if ext not in cls.extensions:
                     cls.extensions[ext] = SourcePriority.IMPLICIT
+            # This list was compiled by trying to read the test files in GDAL's
+            # repo.
+            for ext in {
+                    'adf', 'aux', 'demtif', 'dim', 'doq', 'flt', 'fst', 'gsc',
+                    'h3', 'lan', 'los', 'lrc', 'mint.bin', 'mtw', 'nsf', 'nws',
+                    'on9', 'pjg', 'png.ovr', 'prj', 'ptf', 'rasterlite', 'rdb',
+                    'tif.grd', 'til', 'vic', 'xlb'}:
+                if ext.lower() not in cls.extensions:
+                    cls.extensions[ext.lower()] = SourcePriority.IMPLICIT_LOW
 
 
 def open(*args, **kwargs):

diff --git a/test/lisource_compare.py b/test/lisource_compare.py
@@ -568,6 +568,7 @@ def command():
     if not large_image.tilesource.AvailableTileSources:
         large_image.tilesource.loadTileSources()
     if opts.all:
+        large_image.config.setConfig('max_small_image_size', 16384)
         for key in list(large_image.config.ConfigValues):
             if '_ignored_names' in key:
                 del large_image.config.ConfigValues[key]