Add tile source bandCount attribute

CHANGELOG.md

@@ -1,6 +1,9 @@
 # Change Log
 
-## 1.22.5
+## 1.23.0
+
+### Features
+- Add tile source bandCount attribute ([#1214](../../pull/1214))
 
 ### Improvements
 - Harden the nd2 source to allow it to read more files ([#1207](../../pull/1207))

large_image/tilesource/base.py

@@ -141,6 +141,7 @@ def __init__(self, encoding='JPEG', jpegQuality=95, jpegSubsampling=0,
         self.sizeY = None
         self._styleLock = threading.RLock()
         self._dtype = None
+        self._bandCount = None
 
         if encoding not in TileOutputMimeTypes:
             raise ValueError('Invalid encoding "%s"' % encoding)
@@ -214,7 +215,7 @@ def getBounds(self, *args, **kwargs):
         }
 
     def getCenter(self, *args, **kwargs):
-        """Retruns (Y, X) center location."""
+        """Returns (Y, X) center location."""
         if self.geospatial:
             bounds = self.getBounds(*args, **kwargs)
             return (
@@ -239,13 +240,21 @@ def dtype(self):
                             region=dict(left=0, top=0, width=1, height=1),
                             format=TILE_FORMAT_NUMPY)
                         self._dtype = sample.dtype
+                        self._bandCount = sample.shape[-1] if len(sample.shape) == 3 else 1
                     finally:
                         self._setSkipStyle(False)
                 else:
                     return None
 
         return self._dtype
 
+    @property
+    def bandCount(self):
+        if not self._bandCount:
+            if not self.dtype:
+                return None
+        return self._bandCount
+
     @staticmethod
     def getLRUHash(*args, **kwargs):
         """
@@ -1604,10 +1613,14 @@ def _outputTile(self, tile, tileEncoding, x, y, z, pilImageAllowed=False,
         if self._dtype is None:
             if tileEncoding == TILE_FORMAT_NUMPY:
                 self._dtype = tile.dtype
+                self._bandCount = tile.shape[-1] if len(tile.shape) == 3 else 1
             elif tileEncoding == TILE_FORMAT_PIL:
                 self._dtype = numpy.uint8 if ';16' not in tile.mode else numpy.uint16
+                self._bandCount = len(tile.mode)
             else:
-                self._dtype = _imageToNumpy(tile)[0].dtype
+                _img = _imageToNumpy(tile)[0]
+                self._dtype = _img.dtype
+                self._bandCount = _img.shape[-1] if len(_img.shape) == 3 else 1
 
         mode = None
         if (numpyAllowed == 'always' or tileEncoding == TILE_FORMAT_NUMPY or
@@ -1717,6 +1730,7 @@ def getMetadata(self):
             'mm_x': mag['mm_x'],
             'mm_y': mag['mm_y'],
             'dtype': str(self.dtype),
+            'bandCount': self.bandCount,
         })
 
     @property

sources/gdal/large_image_source_gdal/__init__.py

@@ -580,22 +580,17 @@ def geospatial(self):
             hasattr(self, '_netcdf'))
 
     def getMetadata(self):
+        metadata = super().getMetadata()
         with self._getDatasetLock:
-            metadata = JSONDict({
+            metadata.update({
                 'geospatial': self.geospatial,
-                'levels': self.levels,
-                'sizeX': self.sizeX,
-                'sizeY': self.sizeY,
                 'sourceLevels': self.sourceLevels,
                 'sourceSizeX': self.sourceSizeX,
                 'sourceSizeY': self.sourceSizeY,
-                'tileWidth': self.tileWidth,
-                'tileHeight': self.tileHeight,
                 'bounds': self.getBounds(self.projection),
                 'sourceBounds': self.getBounds(),
                 'bands': self.getBandInformation(),
             })
-        metadata.update(self.getNativeMagnification())
         if hasattr(self, '_netcdf'):
             # To ensure all band information from all subdatasets in netcdf,
             # we could do the following:

sources/rasterio/large_image_source_rasterio/__init__.py

@@ -493,30 +493,22 @@ def getBandInformation(self, statistics=True, dataset=None, **kwargs):
         return infoSet
 
     def getMetadata(self):
+        metadata = super().getMetadata()
         with self._getDatasetLock:
             # check if the file is geospatial
             has_projection = self.dataset.crs
             has_gcps = len(self.dataset.gcps[0]) != 0 and self.dataset.gcps[1]
             has_affine = self.dataset.transform
 
-            metadata = JSONDict({
+            metadata.update({
                 'geospatial': bool(has_projection or has_gcps or has_affine),
-                'levels': self.levels,
-                'sizeX': self.sizeX,
-                'sizeY': self.sizeY,
                 'sourceLevels': self.sourceLevels,
                 'sourceSizeX': self.sourceSizeX,
                 'sourceSizeY': self.sourceSizeY,
-                'tileWidth': self.tileWidth,
-                'tileHeight': self.tileHeight,
                 'bounds': self.getBounds(self.projection),
                 'sourceBounds': self.getBounds(),
                 'bands': self.getBandInformation(),
             })
-
-        # magnification is computed elswhere
-        metadata.update(self.getNativeMagnification())
-
         return metadata
 
     def getInternalMetadata(self, **kwargs):

sources/tiff/large_image_source_tiff/__init__.py

@@ -165,6 +165,7 @@ def __init__(self, path, **kwargs):  # noqa
             tifftools.constants.SampleFormat[sampleformat or 1].name,
             bitspersample
         ))
+        self._bandCount = highest._tiffInfo.get('samplesperpixel')
         # 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
@@ -298,6 +299,7 @@ def _initWithTiffTools(self):  # noqa
             tifftools.constants.SampleFormat[sampleformat or 1].name,
             bitspersample
         ))
+        self._bandCount = dir0._tiffInfo.get('samplesperpixel')
         info = _cached_read_tiff(self._largeImagePath)
         frames = []
         associated = []  # for now, a list of directories

sources/tiff/large_image_source_tiff/tiff_reader.py

@@ -787,7 +787,10 @@ def getTile(self, x, y):
         # a form we expect.  If this isn't done, then PIL can load the image
         # multiple times, which sometimes throws an exception in PIL's JPEG
         # 2000 module.
-        image = image.convert('RGB')
+        if image.mode != 'L':
+            image = image.convert('RGB')
+        else:
+            image.load()
         return image
 
     def parse_image_description(self, meta=None):  # noqa

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -309,7 +309,8 @@ def _handle_scn(self):  # noqa
                         self._channelInfo = channels
                         try:
                             self._channels = [
-                                channels.get(idx)['name'] for idx in range(len(channels))]
+                                channels.get(idx)['name'].split('|')[0]
+                                for idx in range(len(channels))]
                         except Exception:
                             pass
 

test/test_source_base.py

@@ -196,6 +196,7 @@ def testSourcesTilesAndMethods(source, filename):
     assert ts.getInternalMetadata() is not None
     assert ts.getOneBandInformation(1) is not None
     assert len(ts.getBandInformation()) >= 1
+    assert len(ts.getBandInformation()) == tileMetadata['bandCount']
     assert ts.getPixel(region=dict(left=0, top=0)) is not None
     # Histograms are too slow to test in this way
     #  assert len(ts.histogram()['histogram']) >= 1