Merge pull request #496 from girder/expose-more-region-options

Expose more resample options for region and histogram.

CHANGELOG.md

@@ -6,6 +6,8 @@
 - Reduce caching associated images when the parent item changes (#491)
 - Test with Python 3.9 (#493)
 - Add a hideAnnotation function in the client (#490)
+- Expose more resample options for region and histogram endpoints (#496)
+- Improve OME tiff preferred level calculation for OME tiffs with subifds (#496)
 
 ### Changes
 - Include the annotationType to the annotation conversion method in the client (#490)

girder/girder_large_image/rest/tiles.py

@@ -206,6 +206,9 @@ def _parseParams(cls, params, keepUnknownParams, typeList):
         for entry in typeList:
             key, dataType, outkey1, outkey2 = (list(entry) + [None] * 2)[:4]
             if key in params:
+                if dataType == 'boolOrInt':
+                    dataType = bool if str(params[key]).lower() in (
+                        'true', 'false', 'on', 'off', 'yes', 'no') else int
                 try:
                     if dataType is bool:
                         results[key] = str(params[key]).lower() in (
@@ -670,6 +673,12 @@ def getTilesThumbnail(self, item, params):
                'image', required=False,
                enum=['raw', 'tiff_lzw', 'jpeg', 'tiff_adobe_deflate'])
         .param('style', 'JSON-encoded style string', required=False)
+        .param('resample', 'If false, an existing level of the image is used '
+               'for the histogram.  If true, the internal values are '
+               'interpolated to match the specified size as needed.  0-3 for '
+               'a specific interpolation method (0-nearest, 1-lanczos, '
+               '2-bilinear, 3-bicubic)', required=False,
+               enum=['false', 'true', '0', '1', '2', '3'], default='false')
         .param('contentDisposition', 'Specify the Content-Disposition response '
                'header disposition-type value.', required=False,
                enum=['inline', 'attachment'])
@@ -704,6 +713,7 @@ def getTilesRegion(self, item, params):
             ('jpegSubsampling', int),
             ('tiffCompression', str),
             ('style', str),
+            ('resample', 'boolOrInt'),
             ('contentDisposition', str),
         ])
         _handleETag('getTilesRegion', item, params)
@@ -773,8 +783,10 @@ def getTilesPixel(self, item, params):
                default=2048, required=False, dataType='int')
         .param('resample', 'If false, an existing level of the image is used '
                'for the histogram.  If true, the internal values are '
-               'interpolated to match the specified size as needed.',
-               required=False, dataType='boolean', default=False)
+               'interpolated to match the specified size as needed.  0-3 for '
+               'a specific interpolation method (0-nearest, 1-lanczos, '
+               '2-bilinear, 3-bicubic)', required=False,
+               enum=['false', 'true', '0', '1', '2', '3'], default='false')
         .param('frame', 'For multiframe images, the 0-based frame number.  '
                'This is ignored on non-multiframe images.', required=False,
                dataType='int')
@@ -817,7 +829,7 @@ def getHistogram(self, item, params):
             ('jpegSubsampling', int),
             ('tiffCompression', str),
             ('style', str),
-            ('resample', bool),
+            ('resample', 'boolOrInt'),
             ('bins', int),
             ('rangeMin', int),
             ('rangeMax', int),

sources/ometiff/large_image_source_ometiff/__init__.py

@@ -332,3 +332,27 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                 x, y, z, pilImageAllowed=pilImageAllowed,
                 numpyAllowed=numpyAllowed, sparseFallback=sparseFallback,
                 exception=e, **kwargs)
+
+    def getPreferredLevel(self, level):
+        """
+        Given a desired level (0 is minimum resolution, self.levels - 1 is max
+        resolution), return the level that contains actual data that is no
+        lower resolution.
+
+        :param level: desired level
+        :returns level: a level with actual data that is no lower resolution.
+        """
+        level = max(0, min(level, self.levels - 1))
+        baselevel = level
+        while self._tiffDirectories[level] is None and level < self.levels - 1:
+            try:
+                dirnum = int(self._omeLevels[-1]['TiffData'][0].get('IFD', 0))
+                subdir = self.levels - 1 - level
+                if self._getDirFromCache(dirnum, subdir):
+                    break
+            except Exception:
+                pass
+            level += 1
+        while level - baselevel > self._maxSkippedLevels:
+            level -= self._maxSkippedLevels
+        return level

tox.ini

@@ -15,6 +15,7 @@ python =
   3.6: py36
   3.7: py37, docs, flake8, lintclient, lintannotationclient
   3.8: py38
+  3.9: py39
 
 [testenv]
 passenv = PYTEST_*
@@ -29,6 +30,7 @@ deps =
   pytest-girder>=3.0.4,<3.1; python_version < '3.6'
   pytest-xdist
   celery!=4.4.4,<5
+  urllib3<1.26
 # celery 4.4.4 is broken; avoid it until a new version is released
 whitelist_externals =
   rm