Merge pull request #659 from girder/band-number-basis

Always have band number start at 1.

CHANGELOG.md

@@ -8,6 +8,7 @@
 
 ### Bug Fixes
 - getBandInformation could fail on high bands in some cases (#651)
+- Band information should always be 1-indexed (#659)
 
 ## Version 1.8.0
 

girder/test_girder/test_tiles_rest.py

@@ -1202,8 +1202,8 @@ def testTilesBandInformation(server, admin, fsAssetstore):
     server.request(path='/item/%s/tiles' % itemId, method='POST', user=admin)
     resp = server.request(path='/item/%s/tiles/bands' % itemId)
     assert len(resp.json) == 4
-    assert resp.json[0]['interpretation'] == 'red'
-    assert 'mean' in resp.json[0]
+    assert resp.json['1']['interpretation'] == 'red'
+    assert 'mean' in resp.json['1']
 
 
 @pytest.mark.usefixtures('unbindLargeImage')

large_image/tilesource/base.py

@@ -1320,7 +1320,7 @@ def getOneBandInformation(self, band):
         """
         Get band information for a single band.
 
-        :param band: a 0-based band.
+        :param band: a 1-based band.
         :returns: a dictionary of band information.  See getBandInformation.
         """
         return self.getBandInformation()[band]
@@ -1331,8 +1331,9 @@ def getBandInformation(self, statistics=False, **kwargs):
 
         :param statistics: if True, compute statistics if they don't already
             exist.
-        :returns: a list of one dictionary per band.  Each dictionary contains
-            known values such as interpretation, min, max, mean, stdev.
+        :returns: a dictionary of one dictionary per band.  Each dictionary
+            contains known values such as interpretation, min, max, mean,
+            stdev.
         """
         if not getattr(self, '_bandInfo', None):
             bandInterp = {
@@ -1345,8 +1346,9 @@ def getBandInformation(self, statistics=False, **kwargs):
                     tile = self.getSingleTile()['tile']
                     bands = tile.shape[2] if len(tile.shape) > 2 else 1
                     interp = bandInterp.get(bands, bandInterp[3])
-                    bandInfo = [{'interpretation': interp[idx] if idx < len(interp) else 'unknown'}
-                                for idx in range(bands)]
+                    bandInfo = {
+                        idx + 1: {'interpretation': interp[idx] if idx < len(interp)
+                                  else 'unknown'} for idx in range(bands)}
                     self._bandInfoNoStats = bandInfo
                 return self._bandInfoNoStats
             analysisSize = 2048
@@ -1358,12 +1360,13 @@ def getBandInformation(self, statistics=False, **kwargs):
                 **kwargs)
             bands = histogram['min'].shape[0]
             interp = bandInterp.get(bands, 3)
-            bandInfo = [{'interpretation': interp[idx] if idx < len(interp) else 'unknown'}
-                        for idx in range(bands)]
+            bandInfo = {
+                idx + 1: {'interpretation': interp[idx] if idx < len(interp)
+                          else 'unknown'} for idx in range(bands)}
             for key in {'min', 'max', 'mean', 'stdev'}:
                 if key in histogram:
                     for idx in range(bands):
-                        bandInfo[idx][key] = histogram[key][idx]
+                        bandInfo[idx + 1][key] = histogram[key][idx]
             self._bandInfo = bandInfo
         return self._bandInfo
 

test/test_source_base.py

@@ -90,21 +90,29 @@ def testSourcesCanRead(source, filename):
 
 @pytest.mark.parametrize('filename', registry)
 @pytest.mark.parametrize('source', SourceAndFiles)
-def testSourcesTiles(source, filename):
+def testSourcesTilesAndMethods(source, filename):
     sourceInfo = SourceAndFiles[source]
     canRead = sourceInfo.get('any') or (
         re.search(sourceInfo.get('read', r'^$'), filename) and
         not re.search(sourceInfo.get('noread', r'^$'), filename))
     if not canRead:
-        return
+        pytest.skip('source does not work with this file')
     if re.search(sourceInfo.get('skipTiles', r'^$'), filename):
-        return
+        pytest.skip('source fails tile tests from this file')
     imagePath = datastore.fetch(filename)
     large_image.tilesource.loadTileSources()
     sourceClass = large_image.tilesource.AvailableTileSources[source]
     ts = sourceClass(imagePath)
     tileMetadata = ts.getMetadata()
     utilities.checkTilesZXY(ts, tileMetadata)
+    # All of these should succeed
+    assert ts.getInternalMetadata() is not None
+    assert ts.getOneBandInformation(1) is not None
+    assert len(ts.getBandInformation()) >= 1
+    # Histograms are too slow to test in this way
+    #  assert len(ts.histogram()['histogram']) >= 1
+    #  assert ts.histogram(onlyMinMax=True)['min'][0] is not None
+    # Test multiple frames if they exist
     if len(tileMetadata.get('frames', [])) > 1:
         tsf = sourceClass(imagePath, frame=len(tileMetadata['frames']) - 1)
         tileMetadata = tsf.getMetadata()

test/test_source_pil.py

@@ -78,8 +78,8 @@ def testGetBandInformation():
     source = large_image_source_pil.open(imagePath)
     bandInfo = source.getBandInformation(False)
     assert len(bandInfo) == 4
-    assert bandInfo[0] == {'interpretation': 'red'}
+    assert bandInfo[1] == {'interpretation': 'red'}
 
     bandInfo = source.getBandInformation(True)
     assert len(bandInfo) == 4
-    assert 'mean' in bandInfo[0]
+    assert 'mean' in bandInfo[1]