Merge pull request #1155 from girder/getpixel-improvement

getPixel method and endpoint now returns rawer values
girder · May 12, 2023 · 851d921 · 851d921
2 parents 2bcc4f0 + f7dbee3
commit 851d921
Show file tree

Hide file tree

Showing 5 changed files with 42 additions and 14 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Change Log
 
+## 1.20.7
+
+### Improvements
+- getPixel method and endpoint now returns rawer values ([#1155](../../pull/1155))
+
 ## 1.20.6
 
 ### Improvements

diff --git a/large_image/tilesource/base.py b/large_image/tilesource/base.py
@@ -2716,12 +2716,13 @@ def getPixel(self, includeTileRecord=False, **kwargs):
         #  img, format = self.getRegion(format=TILE_FORMAT_PIL, **regionArgs)
         # where img is the PIL image (rather than tile['tile'], but using
         # _tileIteratorInfo and the _tileIterator is slightly more efficient.
-        iterInfo = self._tileIteratorInfo(format=TILE_FORMAT_PIL, **regionArgs)
+        iterInfo = self._tileIteratorInfo(format=TILE_FORMAT_NUMPY, **regionArgs)
         if iterInfo is not None:
             tile = next(self._tileIterator(iterInfo), None)
             if includeTileRecord:
                 pixel['tile'] = tile
-            img = tile['tile']
+            pixel['value'] = [v.item() for v in tile['tile'][0][0]]
+            img = _imageToPIL(tile['tile'])
             if img.size[0] >= 1 and img.size[1] >= 1:
                 if len(img.mode) > 1:
                     pixel.update(dict(zip(img.mode.lower(), img.load()[0, 0])))

diff --git a/test/test_source_gdal.py b/test/test_source_gdal.py
@@ -170,6 +170,8 @@ def testPixel():
     # Test in pixel coordinates
     source = large_image_source_gdal.open(imagePath)
     pixel = source.getPixel(region={'left': 212, 'top': 198})
+    assert 'value' in pixel
+    pixel.pop('value')
     assert pixel == {
         'r': 76, 'g': 78, 'b': 77, 'a': 255, 'bands': {1: 62.0, 2: 65.0, 3: 66.0}}
     pixel = source.getPixel(region={'left': 2120, 'top': 198})
@@ -178,6 +180,7 @@ def testPixel():
     # Test with a projection
     source = large_image_source_gdal.open(imagePath, projection='EPSG:3857')
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'projection'})
+    pixel.pop('value')
     assert pixel == {
         'r': 94, 'g': 98, 'b': 99, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
 
@@ -187,6 +190,7 @@ def testPixel():
     source = large_image_source_gdal.open(
         imagePath, projection='EPSG:3857', style=style)
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'projection'})
+    pixel.pop('value')
     assert pixel == {
         'r': 247, 'g': 156, 'b': 60, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
 
@@ -196,21 +200,25 @@ def testPixel():
     source = large_image_source_gdal.open(
         imagePath, projection='EPSG:3857', style=style)
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'projection'})
+    pixel.pop('value')
     assert pixel == {
         'r': 137, 'g': 117, 'b': 0, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
 
     # Test with projection units
     source = large_image_source_gdal.open(imagePath, projection='EPSG:3857')
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'EPSG:3857'})
+    pixel.pop('value')
     assert pixel == {
         'r': 94, 'g': 98, 'b': 99, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
     pixel = source.getPixel(region={'left': -117.975, 'top': 33.865, 'units': 'WGS84'})
+    pixel.pop('value')
     assert pixel == {
         'r': 94, 'g': 98, 'b': 99, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
     # When the tile has a different projection, the pixel is the same as
     # the band values.
     source = large_image_source_gdal.open(imagePath)
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'EPSG:3857'})
+    pixel.pop('value')
     assert pixel == {
         'r': 94, 'g': 98, 'b': 99, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
 

diff --git a/test/test_source_mapnik.py b/test/test_source_mapnik.py
@@ -192,15 +192,19 @@ def testPixel():
     source = large_image_source_mapnik.open(imagePath)
     pixel = source.getPixel(region={'left': 212, 'top': 198})
     assert pixel == {
-        'r': 62, 'g': 65, 'b': 66, 'a': 255, 'bands': {1: 62.0, 2: 65.0, 3: 66.0}}
+        'r': 62, 'g': 65, 'b': 66, 'a': 255,
+        'bands': {1: 62.0, 2: 65.0, 3: 66.0},
+        'value': [62, 65, 66, 255]}
     pixel = source.getPixel(region={'left': 2120, 'top': 198})
     assert pixel == {}
 
     # Test with a projection
     source = large_image_source_mapnik.open(imagePath, projection='EPSG:3857')
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'projection'})
     assert pixel == {
-        'r': 77, 'g': 82, 'b': 84, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
+        'r': 77, 'g': 82, 'b': 84, 'a': 255,
+        'bands': {1: 77.0, 2: 82.0, 3: 84.0},
+        'value': [77, 82, 84, 255]}
 
     # Check if the point is outside of the image
     pixel = source.getPixel(region={'left': 10000000, 'top': 4000000, 'units': 'projection'})
@@ -214,7 +218,9 @@ def testPixel():
         imagePath, projection='EPSG:3857', style=style)
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'projection'})
     assert pixel == {
-        'r': 225, 'g': 100, 'b': 98, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
+        'r': 225, 'g': 100, 'b': 98, 'a': 255,
+        'bands': {1: 77.0, 2: 82.0, 3: 84.0},
+        'value': [225, 100, 98, 255]}
 
     # Test with palette as an array of colors
     style = json.dumps({'band': 1, 'min': 0, 'max': 100,
@@ -224,22 +230,30 @@ def testPixel():
         imagePath, projection='EPSG:3857', style=style)
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'projection'})
     assert pixel == {
-        'r': 0, 'g': 255, 'b': 0, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
+        'r': 0, 'g': 255, 'b': 0, 'a': 255,
+        'bands': {1: 77.0, 2: 82.0, 3: 84.0},
+        'value': [0, 255, 0, 255]}
 
     # Test with projection units
     source = large_image_source_mapnik.open(imagePath, projection='EPSG:3857')
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'EPSG:3857'})
     assert pixel == {
-        'r': 77, 'g': 82, 'b': 84, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
+        'r': 77, 'g': 82, 'b': 84, 'a': 255,
+        'bands': {1: 77.0, 2: 82.0, 3: 84.0},
+        'value': [77, 82, 84, 255]}
     pixel = source.getPixel(region={'left': -117.975, 'top': 33.865, 'units': 'WGS84'})
     assert pixel == {
-        'r': 77, 'g': 82, 'b': 84, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
+        'r': 77, 'g': 82, 'b': 84, 'a': 255,
+        'bands': {1: 77.0, 2: 82.0, 3: 84.0},
+        'value': [77, 82, 84, 255]}
     # When the tile has a different projection, the pixel is the same as
     # the band values.
     source = large_image_source_mapnik.open(imagePath)
     pixel = source.getPixel(region={'left': -13132910, 'top': 4010586, 'units': 'EPSG:3857'})
     assert pixel == {
-        'r': 77, 'g': 82, 'b': 84, 'a': 255, 'bands': {1: 77.0, 2: 82.0, 3: 84.0}}
+        'r': 77, 'g': 82, 'b': 84, 'a': 255,
+        'bands': {1: 77.0, 2: 82.0, 3: 84.0},
+        'value': [77, 82, 84, 255]}
 
 
 def testSourceErrors():

diff --git a/test/test_source_openslide.py b/test/test_source_openslide.py
@@ -321,16 +321,16 @@ def testGetPixel():
     source = large_image_source_openslide.open(imagePath, style={'icc': False})
 
     pixel = source.getPixel(region={'left': 12125, 'top': 10640})
-    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
+    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255, 'value': [156, 98, 138, 255]}
 
     pixel = source.getPixel(region={'left': 3.0555, 'top': 2.68128, 'units': 'mm'})
-    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
+    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255, 'value': [156, 98, 138, 255]}
 
     pixel = source.getPixel(region={'top': 10640, 'right': 12126, 'bottom': 12000})
-    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
+    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255, 'value': [156, 98, 138, 255]}
 
     pixel = source.getPixel(region={'left': 12125, 'top': 10640, 'right': 13000})
-    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255}
+    assert pixel == {'r': 156, 'g': 98, 'b': 138, 'a': 255, 'value': [156, 98, 138, 255]}
 
     pixel = source.getPixel(region={'left': 12125, 'top': 10640}, includeTileRecord=True)
     assert 'tile' in pixel
@@ -342,7 +342,7 @@ def testGetPixelWithICCCorrection():
         '4a70-9ae3-50e3ab45e242.svs')
     source = large_image_source_openslide.open(imagePath)
     pixel = source.getPixel(region={'left': 12125, 'top': 10640})
-    assert pixel == {'r': 169, 'g': 99, 'b': 151, 'a': 255}
+    assert pixel == {'r': 169, 'g': 99, 'b': 151, 'a': 255, 'value': [169, 99, 151, 255]}
     source = large_image_source_openslide.open(imagePath, style={'icc': True})
     pixel2 = source.getPixel(region={'left': 12125, 'top': 10640})
     assert pixel == pixel2