Add an open method to each source module.

CHANGELOG.md

@@ -9,17 +9,23 @@
 - Added a `canRead` method to the core module (#512)
 - Image conversion supports JPEG 2000 (jp2k) compression (#522)
 - Image conversion can now convert images readable by large_image sources but not by vips (#529)
+- Added an `open` method to the core module as an alias to `getTileSource` (#550)
+- Added an `open` method to each file source module (#550)
+- Numerous improvement to image converversion (#533, #535, #537, #541, #544, #545, #546, #549)
 
 ### Improvements
 - Better release bioformats resources (#502)
 - Better handling of tiff files with JPEG compression and RGB colorspace (#503)
 - The openjpeg tile source can decode with parallelism (#511)
 - Geospatial tile sources are preferred for geospatial files (#512)
 - Support decoding JP2k compressed tiles in the tiff tile source (#514)
+- Hardened tests against transient timing issues (#532, #536)
 
 ### Bug Fixes
 - Harden updates of the item view after making a large image (#508, #515)
 - Tiles in an unexpected color mode weren't consistently adjusted (#510)
+- Harden trying to add an annotation before the viewer is ready (#547)
+- Correctly report the tile size after resampling in the tileIterator (#538)
 
 ## Version 1.3.2
 

large_image/__init__.py

@@ -17,7 +17,7 @@
 from pkg_resources import DistributionNotFound, get_distribution
 
 from . import tilesource  # noqa
-from .tilesource import canRead, getTileSource  # noqa
+from .tilesource import canRead, getTileSource, open  # noqa
 
 
 try:

large_image/tilesource/__init__.py

@@ -123,6 +123,18 @@ def getTileSource(*args, **kwargs):
     return getTileSourceFromDict(AvailableTileSources, *args, **kwargs)
 
 
+def open(*args, **kwargs):
+    """
+    Alternate name of getTileSource.
+
+    Get a tilesource using the known sources.  If tile sources have not yet
+    been loaded, load them.
+
+    :returns: A tilesource for the passed arguments.
+    """
+    return getTileSource(*args, **kwargs)
+
+
 def canRead(*args, **kwargs):
     """
     Check if large_image can read a path or uri.

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -538,3 +538,17 @@ def _getAssociatedImage(self, imageKey):
                 if javabridge.get_env():
                     javabridge.detach()
         return large_image.tilesource.base._imageToPIL(image)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return BioformatsFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return BioformatsFileTileSource.canRead(*args, **kwargs)

sources/dummy/large_image_source_dummy/__init__.py

@@ -47,3 +47,17 @@ def canRead(cls, *args, **kwargs):
 
     def getTile(self, x, y, z, **kwargs):
         return b''
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return DummyTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return DummyTileSource.canRead(*args, **kwargs)

sources/gdal/large_image_source_gdal/__init__.py

@@ -940,3 +940,17 @@ def getPixel(self, **kwargs):
                         except RuntimeError:
                             pass
         return pixel
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return GDALFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return GDALFileTileSource.canRead(*args, **kwargs)

sources/mapnik/large_image_source_mapnik/__init__.py

@@ -414,3 +414,17 @@ def getTile(self, x, y, z, **kwargs):
         if overscan:
             pilimg = pilimg.crop((1, 1, pilimg.width - overscan, pilimg.height - overscan))
         return self._outputTile(pilimg, TILE_FORMAT_PIL, x, y, z, applyStyle=False, **kwargs)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return MapnikFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return MapnikFileTileSource.canRead(*args, **kwargs)

sources/nd2/large_image_source_nd2/__init__.py

@@ -318,3 +318,17 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
             tile = tileframe[y0:y1:step, x0:x1:step].copy()
         return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return ND2FileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return ND2FileTileSource.canRead(*args, **kwargs)

sources/ometiff/large_image_source_ometiff/__init__.py

@@ -353,3 +353,17 @@ def getPreferredLevel(self, level):
         while level - baselevel > self._maxSkippedLevels:
             level -= self._maxSkippedLevels
         return level
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return OMETiffFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return OMETiffFileTileSource.canRead(*args, **kwargs)

sources/openjpeg/large_image_source_openjpeg/__init__.py

@@ -14,6 +14,7 @@
 #  limitations under the License.
 ##############################################################################
 
+import builtins
 import glymur
 import io
 import math
@@ -203,7 +204,7 @@ def _readbox(self, box):
         if box.length > 16 * 1024 * 1024:
             return
         try:
-            fp = open(self._largeImagePath, 'rb')
+            fp = builtins.open(self._largeImagePath, 'rb')
             headerLength = 16
             fp.seek(box.offset + headerLength)
             data = fp.read(box.length - headerLength)
@@ -255,3 +256,17 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
             tile = tile[::scale, ::scale]
         return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return OpenjpegFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return OpenjpegFileTileSource.canRead(*args, **kwargs)

sources/openslide/large_image_source_openslide/__init__.py

@@ -370,3 +370,17 @@ def _getAssociatedImage(self, imageKey):
         _tiffFile.SetDirectory(images[imageKey])
         img = _tiffFile.read_image()
         return PIL.Image.fromarray(img)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return OpenslideFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return OpenslideFileTileSource.canRead(*args, **kwargs)

sources/pil/large_image_source_pil/__init__.py

@@ -170,3 +170,17 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
             raise TileSourceException('y is outside layer')
         return self._outputTile(self._pilImage, TILE_FORMAT_PIL, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return PILFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return PILFileTileSource.canRead(*args, **kwargs)

sources/test/large_image_source_test/__init__.py

@@ -178,3 +178,17 @@ def getState(self):
         return 'test %r %r %r %r %r %r' % (
             super().getState(), self.minLevel,
             self.maxLevel, self.tileWidth, self.tileHeight, self.fractal)
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return TestTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return TestTileSource.canRead(*args, **kwargs)

sources/tiff/large_image_source_tiff/__init__.py

@@ -647,3 +647,17 @@ def _getAssociatedImage(self, imageKey):
         if imageKey in self._associatedImages:
             return PIL.Image.fromarray(self._associatedImages[imageKey])
         return None
+
+
+def open(*args, **kwargs):
+    """
+    Create an instance of the module class.
+    """
+    return TiffFileTileSource(*args, **kwargs)
+
+
+def canRead(*args, **kwargs):
+    """
+    Check if an input can be read by the module class.
+    """
+    return TiffFileTileSource.canRead(*args, **kwargs)

test/test_converter.py

@@ -141,7 +141,7 @@ def testConvertJp2kCompression(tmpdir):
     info = tifftools.read_tiff(outputPath)
     assert (info['ifds'][0]['tags'][tifftools.Tag.Compression.value]['data'][0] ==
             tifftools.constants.Compression.JP2000.value)
-    source = large_image_source_tiff.TiffFileTileSource(outputPath)
+    source = large_image_source_tiff.open(outputPath)
     image, _ = source.getRegion(
         output={'maxWidth': 200, 'maxHeight': 200}, format=constants.TILE_FORMAT_NUMPY)
     assert (image[12][167] == [215, 135, 172]).all()
@@ -160,7 +160,7 @@ def testConvertFromLargeImage(tmpdir):
     imagePath = utilities.externaldata('data/sample_image.jp2.sha512')
     outputPath = os.path.join(tmpdir, 'out.tiff')
     large_image_converter.convert(imagePath, outputPath)
-    source = large_image_source_tiff.TiffFileTileSource(outputPath)
+    source = large_image_source_tiff.open(outputPath)
     metadata = source.getMetadata()
     assert metadata['levels'] == 6
 
@@ -169,7 +169,7 @@ def testConvertFromMultiframeImage(tmpdir):
     imagePath = utilities.externaldata('data/sample.ome.tif.sha512')
     outputPath = os.path.join(tmpdir, 'out.tiff')
     large_image_converter.convert(imagePath, outputPath)
-    source = large_image_source_tiff.TiffFileTileSource(outputPath)
+    source = large_image_source_tiff.open(outputPath)
     metadata = source.getMetadata()
     assert metadata['levels'] == 5
     assert len(metadata['frames']) == 3
@@ -181,7 +181,7 @@ def testConvertFromMultiframeImageNoSubIFDS(tmpdir):
     imagePath = utilities.externaldata('data/sample.ome.tif.sha512')
     outputPath = os.path.join(tmpdir, 'out.tiff')
     large_image_converter.convert(imagePath, outputPath, subifds=False)
-    source = large_image_source_tiff.TiffFileTileSource(outputPath)
+    source = large_image_source_tiff.open(outputPath)
     metadata = source.getMetadata()
     assert metadata['levels'] == 5
     assert len(metadata['frames']) == 3

test/test_source_bioformats.py

@@ -9,7 +9,7 @@ def testTilesFromBioformats():
     import large_image_source_bioformats
 
     imagePath = utilities.externaldata('data/HENormalN801.czi.sha512')
-    source = large_image_source_bioformats.BioformatsFileTileSource(imagePath)
+    source = large_image_source_bioformats.open(imagePath)
     tileMetadata = source.getMetadata()
 
     assert tileMetadata['tileWidth'] == 1024
@@ -28,7 +28,7 @@ def testInternalMetadata():
     import large_image_source_bioformats
 
     imagePath = utilities.externaldata('data/HENormalN801.czi.sha512')
-    source = large_image_source_bioformats.BioformatsFileTileSource(imagePath)
+    source = large_image_source_bioformats.open(imagePath)
     metadata = source.getInternalMetadata()
     assert 'sizeColorPlanes' in metadata
 

test/test_source_dummy.py

@@ -1,9 +1,9 @@
-from large_image import getTileSource
+import large_image
 import large_image_source_dummy
 
 
 def testDummyTileSource():
-    source = large_image_source_dummy.DummyTileSource()
+    source = large_image_source_dummy.open()
     tileMetadata = source.getMetadata()
     assert tileMetadata['tileWidth'] == 0
     assert tileMetadata['tileHeight'] == 0
@@ -17,5 +17,5 @@ def testDummyTileSource():
 
 
 def testGetDummyTileSource():
-    source = getTileSource('large_image://dummy')
+    source = large_image.open('large_image://dummy')
     assert isinstance(source, large_image_source_dummy.DummyTileSource)