Provide an option to output large regions as tiled tiffs.

This also will geotag geospatial outputs.

Specifically, when calling the getRegion function or endpoint, if an
encoding of `TILED` is used (previously this could have been one of
`JPEG`, `PNG`, or `TIFF`), a tiled tiff is output.  For non-geospatial
sources, this is tiled using vips.  For geospatial sources, this is
tiled using gdal.

When using the `TILED` option, a variety of parameters that can be used
in conversions can be used: `compression`, `quality`.  For
compatibility, these can also be `tiffCompression` and `jpegQuality`.

CHANGELOG.md

@@ -7,6 +7,7 @@
 - Add a convert endpoint to the Girder plugin (#578)
 - Added support for creating Aperio svs files (#580)
 - Added support for geospatial files with GCP (#588)
+- Regions can be output as tiled tiffs with scale or geospatial metadata (#594)
 
 ### Improvements
 - More untiled tiff files are handles by the bioformats reader (#569)

girder/girder_large_image/rest/tiles.py

@@ -18,6 +18,7 @@
 import hashlib
 import math
 import os
+import pathlib
 import re
 import urllib
 
@@ -29,6 +30,7 @@
 from girder.exceptions import RestException
 from girder.models.file import File
 from girder.models.item import Item
+from girder.utility.progress import setResponseTimeLimit
 
 from large_image.constants import TileInputUnits
 from large_image.exceptions import TileGeneralException
@@ -627,7 +629,6 @@ def getDZITile(self, item, level, xandy, params):
     @loadmodel(model='item', map={'itemId': 'item'}, level=AccessType.WRITE)
     def deleteTiles(self, item, params):
         deleted = self.imageItemModel.delete(item)
-        # TODO: a better response
         return {
             'deleted': deleted
         }
@@ -654,8 +655,11 @@ def deleteTiles(self, item, params):
         .param('frame', 'For multiframe images, the 0-based frame number.  '
                'This is ignored on non-multiframe images.', required=False,
                dataType='int')
-        .param('encoding', 'Thumbnail output encoding', required=False,
-               enum=['JPEG', 'PNG', 'TIFF'], default='JPEG')
+        .param('encoding', 'Output image encoding.  TILED generates a tiled '
+               'tiff without the upper limit on image size the other options '
+               'have.  For geospatial sources, TILED will also have '
+               'appropriate tagging.', required=False,
+               enum=['JPEG', 'PNG', 'TIFF', 'TILED'], default='JPEG')
         .param('contentDisposition', 'Specify the Content-Disposition response '
                'header disposition-type value.', required=False,
                enum=['inline', 'attachment'])
@@ -752,8 +756,11 @@ def getTilesThumbnail(self, item, params):
         .param('frame', 'For multiframe images, the 0-based frame number.  '
                'This is ignored on non-multiframe images.', required=False,
                dataType='int')
-        .param('encoding', 'Output image encoding', required=False,
-               enum=['JPEG', 'PNG', 'TIFF'], default='JPEG')
+        .param('encoding', 'Output image encoding.  TILED generates a tiled '
+               'tiff without the upper limit on image size the other options '
+               'have.  For geospatial sources, TILED will also have '
+               'appropriate tagging.', required=False,
+               enum=['JPEG', 'PNG', 'TIFF', 'TILED'], default='JPEG')
         .param('jpegQuality', 'Quality used for generating JPEG images',
                required=False, dataType='int', default=95)
         .param('jpegSubsampling', 'Chroma subsampling used for generating '
@@ -809,6 +816,7 @@ def getTilesRegion(self, item, params):
             ('contentDisposition', str),
         ])
         _handleETag('getTilesRegion', item, params)
+        setResponseTimeLimit(86400)
         try:
             regionData, regionMime = self.imageItemModel.getRegion(
                 item, **params)
@@ -819,6 +827,20 @@ def getTilesRegion(self, item, params):
         self._setContentDisposition(
             item, params.get('contentDisposition'), regionMime, 'region')
         setResponseHeader('Content-Type', regionMime)
+        if isinstance(regionData, pathlib.Path):
+            BUF_SIZE = 65536
+
+            def stream():
+                try:
+                    with regionData.open('rb') as f:
+                        while True:
+                            data = f.read(BUF_SIZE)
+                            if not data:
+                                break
+                            yield data
+                finally:
+                    regionData.unlink()
+            return stream
         setRawResponse()
         return regionData
 

girder/test_girder/girder_utilities.py

@@ -4,7 +4,7 @@
 from girder.models.upload import Upload
 
 from test.datastore import datastore
-from test.utilities import JFIFHeader, JPEGHeader, PNGHeader  # noqa
+from test.utilities import JFIFHeader, JPEGHeader, PNGHeader, TIFFHeader, BigTIFFHeader  # noqa
 
 
 def namedFolder(user, folderName='Public'):

girder/test_girder/test_tiles_rest.py

@@ -783,6 +783,15 @@ def testRegions(server, admin, fsAssetstore):
     assert width == 500
     assert height == 375
 
+    # Get a tiled image
+    params = {'regionWidth': 1000, 'regionHeight': 1000,
+              'left': 48000, 'top': 3000, 'encoding': 'TILED'}
+    resp = server.request(path='/item/%s/tiles/region' % itemId,
+                          user=admin, isJson=False, params=params)
+    assert utilities.respStatus(resp) == 200
+    image = origImage = utilities.getBody(resp, text=False)
+    assert image[:len(utilities.BigTIFFHeader)] == utilities.BigTIFFHeader
+
 
 @pytest.mark.usefixtures('unbindLargeImage')
 @pytest.mark.plugin('large_image')

large_image/constants.py

@@ -42,12 +42,13 @@ class SourcePriority:
     'JPEG': 'image/jpeg',
     'PNG': 'image/png',
     'TIFF': 'image/tiff',
+    # TILED indicates the region output should be generated as a tiled TIFF
+    'TILED': 'image/tiff',
 }
 TileOutputPILFormat = {
     'JFIF': 'JPEG'
 }
 
-
 TileInputUnits = {
     None: 'base_pixels',
     'base': 'base_pixels',
@@ -64,3 +65,17 @@ class SourcePriority:
     'millimeters': 'mm',
     'fraction': 'fraction',
 }
+
+# numpy dtype to pyvips GValue
+dtypeToGValue = {
+    'b': 'char',
+    'B': 'uchar',
+    'd': 'double',
+    'D': 'dpcomplex',
+    'f': 'float',
+    'F': 'complex',
+    'h': 'short',
+    'H': 'ushort',
+    'i': 'int',
+    'I': 'uint',
+}