Convert to svs

.gitignore

@@ -60,4 +60,6 @@ node_modules/
 .eslintcache
 test/externaldata
 
-docs/source
+docs/source/*
+!docs/source/*.py
+!docs/source/*.rst

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Features
 - Allow converting a single frame of a multiframe image (#579)
 - Add a convert endpoint to the Girder plugin (#578)
+- Added support for creating Aperio svs files (#580)
 
 ### Improvements
 - More untiled tiff files are handles by the bioformats reader (#569)

docs/make_docs.sh

@@ -10,6 +10,8 @@ pip install -e . -r requirements-dev.txt --find-links https://girder.github.io/l
 popd
 # git clean -fxd .
 
+large_image_converter --help > source/large_image_converter.txt
+
 sphinx-apidoc -f -o source/large_image ../large_image
 sphinx-apidoc -f -o source/large_image_source_dummy ../sources/dummy/large_image_source_dummy
 sphinx-apidoc -f -o source/large_image_source_gdal ../sources/gdal/large_image_source_gdal

docs/source/image_conversion.rst

@@ -0,0 +1,10 @@
+Image Conversion
+================
+
+The large_image library can read a variety of images with the various tile source modules.  Some image files that cannot be read directly can be converted into a format that can be read by the large_image library.  Additionally, some images that can be read are very slow to handle because they are stored inefficiently, and converting them will make a equivalent file that is more efficient.
+
+Installing the ``large-image-converter`` module adds a ``large_image_converter`` command to the local environment.  Running ``large_image_converter --help`` displays the various options.
+
+.. include:: large_image_converter.txt
+   :literal:
+

docs/source/index.rst

@@ -15,6 +15,7 @@ large_image also works as a Girder plugin with optional annotation support.
    :caption: Contents:
 
    tilesource_options
+   image_conversion
    large_image/modules
    large_image_source_dummy/modules
    large_image_source_gdal/modules

docs/source/tilesource_options.rst

@@ -39,7 +39,7 @@ A band definition is an object which can contain the following keys:
 
 - ``frame``: if specified, override the frame parameter used in the tile query for this band.  Note that it is more efficient to have at least one band not specify a frame parameter or use the same value as the basic query.  Defaults to the frame value of the core query.
 
-- ``frameidelta``: if specified, and ``frame`` is not specified, override the frame parameter used in the tile query for this band by adding the value to the current frame number.  If many different frames are being requested, all with the same ``framedelta``, this is more efficient than varying the ``frame`` within the style.
+- ``framedelta``: if specified, and ``frame`` is not specified, override the frame parameter used in the tile query for this band by adding the value to the current frame number.  If many different frames are being requested, all with the same ``framedelta``, this is more efficient than varying the ``frame`` within the style.
 
 - ``min``: the value to map to the first palette value.  Defaults to 0.  'auto' to use 0 if the reported minimum and maximum of the band are between [0, 255] or use the reported minimum otherwise.  'min' or 'max' to always uses the reported minimum or maximum.
 

girder/girder_large_image/rest/tiles.py

@@ -207,6 +207,8 @@ def createTiles(self, item, params):
         .param('onlyFrame', 'Only convert a specific 0-based frame of a '
                'multiframe file.  If not specified, all frames are converted.',
                dataType='int', required=False)
+        .param('format', 'File format', required=False,
+               enum=['tiff', 'aperio'])
         .param('compression', 'Internal compression format', required=False,
                enum=['none', 'jpeg', 'deflate', 'lzw', 'zstd', 'packbits', 'webp', 'jp2k'])
         .param('quality', 'JPEG compression quality where 0 is small and 100 '

large_image/tilesource/__init__.py

@@ -16,7 +16,7 @@ def isGeospatial(path):
     """
     Check if a path is likely to be a geospatial file.
 
-    :params path: The path to the file
+    :param path: The path to the file
     :returns: True if geospatial.
     """
     try:

sources/openslide/large_image_source_openslide/__init__.py

@@ -360,6 +360,7 @@ def _getAssociatedImage(self, imageKey):
             return None
         if images[imageKey] == 'openslide':
             try:
+                print('YYYYYYY')
                 return self._openslide.associated_images[imageKey]
             except openslide.lowlevel.OpenSlideError:
                 return None

sources/tiff/large_image_source_tiff/__init__.py

@@ -319,6 +319,36 @@ def _initWithTiffTools(self):  # noqa
                 'It will be inefficient to read lower resolution tiles.', maxMissing)
         return True
 
+    def _reorient_numpy_image(self, image, orientation):
+        """
+        Reorient a numpy image array based on a tiff orientation.
+
+        :param image: the numpy array to reorient.
+        :param orientation: one of the tiff orientation constants.
+        :returns: an image with top-left orientation.
+        """
+        if len(image.shape) == 2:
+            image = numpy.resize(image, (image.shape[0], image.shape[1], 1))
+        if orientation in {
+                tifftools.constants.Orientation.LeftTop.value,
+                tifftools.constants.Orientation.RightTop.value,
+                tifftools.constants.Orientation.LeftBottom.value,
+                tifftools.constants.Orientation.RightBottom.value}:
+            image = image.transpose(1, 0, 2)
+        if orientation in {
+                tifftools.constants.Orientation.BottomLeft.value,
+                tifftools.constants.Orientation.BottomRight.value,
+                tifftools.constants.Orientation.LeftBottom.value,
+                tifftools.constants.Orientation.RightBottom.value}:
+            image = image[::-1, ::, ::]
+        if orientation in {
+                tifftools.constants.Orientation.TopRight.value,
+                tifftools.constants.Orientation.BottomRight.value,
+                tifftools.constants.Orientation.RightTop.value,
+                tifftools.constants.Orientation.RightBottom.value}:
+            image = image[::, ::-1, ::]
+        return image
+
     def _addAssociatedImage(self, largeImagePath, directoryNum, mustBeTiled=False, topImage=None):
         """
         Check if the specified TIFF directory contains an image with a sensible
@@ -335,9 +365,11 @@ def _addAssociatedImage(self, largeImagePath, directoryNum, mustBeTiled=False, t
         try:
             associated = TiledTiffDirectory(largeImagePath, directoryNum, mustBeTiled)
             id = ''
-            if associated._tiffInfo.get('imagedescription'):
-                id = associated._tiffInfo.get(
-                    'imagedescription').strip().split(None, 1)[0].lower()
+            desc = associated._tiffInfo.get('imagedescription')
+            if desc:
+                id = desc.strip().split(None, 1)[0].lower()
+                if b'\n' in desc:
+                    id = desc.split(b'\n', 1)[1].strip().split(None, 1)[0].lower() or id
             elif mustBeTiled:
                 id = 'dir%d' % directoryNum
                 if not len(self._associatedImages):
@@ -357,6 +389,7 @@ def _addAssociatedImage(self, largeImagePath, directoryNum, mustBeTiled=False, t
                 if image.tobytes()[:6] == b'<?xml ':
                     self._parseImageXml(image.tobytes().rsplit(b'>', 1)[0] + b'>', topImage)
                     return
+                image = self._reorient_numpy_image(image, associated._tiffInfo.get('orientation'))
                 self._associatedImages[id] = image
         except (TiffException, AttributeError):
             # If we can't validate or read an associated image or it has no
@@ -374,8 +407,8 @@ def _parseImageXml(self, xml, topImage):
         Parse metadata stored in arbitrary xml and associate it with a specific
         image.
 
-        :params xml: the xml as a string or bytes object.
-        :params topImage: the image to add metadata to.
+        :param xml: the xml as a string or bytes object.
+        :param topImage: the image to add metadata to.
         """
         if not topImage or topImage.pixelInfo.get('magnificaiton'):
             return

test/test_converter.py

@@ -4,6 +4,7 @@
 import shutil
 import tifftools
 
+import large_image
 from large_image import constants
 import large_image_source_tiff
 
@@ -200,6 +201,23 @@ def testConvertFromMultiframeImageOnlyOneFrame(tmpdir):
     assert len(info['ifds']) == 5
 
 
+def testConvertToAperio(tmpdir):
+    imagePath = utilities.externaldata('data/huron.image2_jpeg2k.tif.sha512')
+    outputPath = os.path.join(tmpdir, 'out.svs')
+    large_image_converter.convert(imagePath, outputPath, format='aperio')
+    source = large_image.open(outputPath)
+    assert 'openslide' in source.name
+    assert 'label' in source.getAssociatedImagesList()
+
+
+def testConvertMultiframeToAperio(tmpdir):
+    imagePath = utilities.externaldata('data/sample.ome.tif.sha512')
+    outputPath = os.path.join(tmpdir, 'out.tiff')
+    large_image_converter.convert(imagePath, outputPath, format='aperio', compression='jp2k')
+    source = large_image.open(outputPath)
+    assert 'label' in source.getAssociatedImagesList()
+
+
 # Test main program
 
 def testConverterMain(tmpdir):