Merge pull request #380 from girder/openjpeg-source

Add an openjpeg source using the glymur library.

.circleci/release_pypi.sh

@@ -21,10 +21,13 @@ twine upload --verbose dist/*
 cd "$ROOTPATH/sources/mapnik"
 python setup.py sdist
 twine upload --verbose dist/*
-cd "$ROOTPATH/sources/openslide"
+cd "$ROOTPATH/sources/ometiff"
 python setup.py sdist
 twine upload --verbose dist/*
-cd "$ROOTPATH/sources/ometiff"
+cd "$ROOTPATH/sources/openjpeg"
+python setup.py sdist
+twine upload --verbose dist/*
+cd "$ROOTPATH/sources/openslide"
 python setup.py sdist
 twine upload --verbose dist/*
 cd "$ROOTPATH/sources/pil"

girder/girder_large_image/web_client/views/imageViewerWidget/leaflet.js

@@ -25,6 +25,7 @@ var LeafletImageViewerWidget = ImageViewerWidget.extend({
     },
 
     render: function () {
+        var errmsg;
         // If script or metadata isn't loaded, then abort
         if (!window.L || !this.tileWidth || !this.tileHeight || this.deleted) {
             return this;
@@ -36,7 +37,15 @@ var LeafletImageViewerWidget = ImageViewerWidget.extend({
         }
 
         if (this.tileWidth !== this.tileHeight) {
-            console.error('The Leaflet viewer only supports square tiles.');
+            errmsg = 'The Leaflet viewer only supports square tiles.';
+        }
+        if (this.tileWidth > 256) {
+            errmsg = 'The Leaflet viewer does not support tiles wider than 256 pixels.';
+        }
+        if (errmsg) {
+            this.viewer = $('<div/>').text(errmsg);
+            this.$el.append(this.viewer);
+            console.error(errmsg);
             return this;
         }
 

girder/girder_large_image/web_client/views/imageViewerWidget/slideatlas.js

@@ -25,6 +25,7 @@ var SlideAtlasImageViewerWidget = ImageViewerWidget.extend({
     },
 
     render: function () {
+        var errmsg;
         // If script or metadata isn't loaded, then abort
         if (!window.SA || !this.tileWidth || !this.tileHeight || this.deleted) {
             return this;
@@ -36,7 +37,15 @@ var SlideAtlasImageViewerWidget = ImageViewerWidget.extend({
         }
 
         if (this.tileWidth !== this.tileHeight) {
-            console.error('The SlideAtlas viewer only supports square tiles.');
+            errmsg = 'The SlideAtlas viewer only supports square tiles.';
+        }
+        if (this.tileWidth > 256) {
+            errmsg = 'The SlideAtlas viewer does not support tiles wider than 256 pixels.';
+        }
+        if (errmsg) {
+            this.viewer = $('<div/>').text(errmsg);
+            this.$el.append(this.viewer);
+            console.error(errmsg);
             return this;
         }
 

large_image/tilesource/__init__.py

@@ -4,7 +4,8 @@
 from pkg_resources import iter_entry_points
 
 from .base import TileSource, FileTileSource, TileOutputMimeTypes, \
-    TILE_FORMAT_IMAGE, TILE_FORMAT_PIL, TILE_FORMAT_NUMPY, nearPowerOfTwo
+    TILE_FORMAT_IMAGE, TILE_FORMAT_PIL, TILE_FORMAT_NUMPY, nearPowerOfTwo, \
+    etreeToDict
 from ..exceptions import TileGeneralException, TileSourceException, TileSourceAssetstoreException
 from .. import config
 from ..constants import SourcePriority
@@ -82,5 +83,5 @@ def getTileSource(*args, **kwargs):
     'TileSource', 'FileTileSource',
     'exceptions', 'TileGeneralException', 'TileSourceException', 'TileSourceAssetstoreException',
     'TileOutputMimeTypes', 'TILE_FORMAT_IMAGE', 'TILE_FORMAT_PIL', 'TILE_FORMAT_NUMPY',
-    'AvailableTileSources', 'getTileSource', 'nearPowerOfTwo',
+    'AvailableTileSources', 'getTileSource', 'nearPowerOfTwo', 'etreeToDict',
 ]

large_image/tilesource/base.py

@@ -7,6 +7,7 @@
 import PIL.ImageColor
 import PIL.ImageDraw
 import six
+from collections import defaultdict
 from six import BytesIO
 
 from ..cache_util import getTileCache, strhash, methodcache
@@ -95,6 +96,37 @@ def _letterboxImage(image, width, height, fill):
     return result
 
 
+def etreeToDict(t):
+    """
+    Convert an xml etree to a nested dictionary without schema names in the
+    keys.
+
+    @param t: an etree.
+    @returns: a python dictionary with the results.
+    """
+    # Remove schema
+    tag = t.tag.split('}', 1)[1] if t.tag.startswith('{') else t.tag
+    d = {tag: {}}
+    children = list(t)
+    if children:
+        entries = defaultdict(list)
+        for entry in map(etreeToDict, children):
+            for k, v in six.iteritems(entry):
+                entries[k].append(v)
+        d = {tag: {k: v[0] if len(v) == 1 else v
+                   for k, v in six.iteritems(entries)}}
+
+    if t.attrib:
+        d[tag].update({(k.split('}', 1)[1] if k.startswith('{') else k): v
+                       for k, v in six.iteritems(t.attrib)})
+    text = (t.text or '').strip()
+    if text and len(d[tag]):
+        d[tag]['text'] = text
+    elif text:
+        d[tag] = text
+    return d
+
+
 def nearPowerOfTwo(val1, val2, tolerance=0.02):
     """
     Check if two values are different by nearly a power of two.
@@ -979,8 +1011,7 @@ def _pilFormatMatches(self, image, match=True, **kwargs):
         # compatibility could be an issue.
         return False
 
-    def _outputTile(self, tile, tileEncoding, x, y, z, pilImageAllowed=False,
-                    **kwargs):
+    def _outputTile(self, tile, tileEncoding, x, y, z, pilImageAllowed=False, **kwargs):
         """
         Convert a tile from a PIL image or image in memory to the desired
         encoding.

requirements-dev.txt

@@ -3,6 +3,7 @@ girder>=3.0.3
 girder-jobs>=3.0.3
 -e sources/dummy
 -e sources/mapnik
+-e sources/openjpeg
 -e sources/openslide
 -e sources/pil
 -e sources/test

setup.py

@@ -16,6 +16,7 @@
     'dummy': ['large-image-source-dummy'],
     'mapnik': ['large-image-source-mapnik'],
     'ometiff': ['large-image-source-ometiff'],
+    'openjpeg': ['large-image-source-openjpeg'],
     'openslide': ['large-image-source-openslide'],
     'pil': ['large-image-source-pil'],
     'tiff': ['large-image-source-tiff'],