Merge remote branch 'stephan/gilabel' into main-master

* stephan/gilabel:
  ENH - Add missing test
  ENH - Adding test for gifti labeltable
  ENH - Supporting key attribute for Gifti labeltables

Author: matthew-brett

nibabel/gifti/gifti.py

@@ -77,7 +77,7 @@ def __init__(self):
     def get_labels_as_dict(self):
         self.labels_as_dict = {}
         for ele in self.labels:
-            self.labels_as_dict[ele.index] = ele.label
+            self.labels_as_dict[ele.key] = ele.label
         return self.labels_as_dict
 
     def to_xml(self):
@@ -94,8 +94,8 @@ def to_xml(self):
                 col += ' Blue="%s"' % str(ele.blue)
             if not ele.alpha is None:
                 col += ' Alpha="%s"' % str(ele.alpha)
-            lab = """\t<Label Index="%s"%s><![CDATA[%s]]></Label>\n""" % \
-                (str(ele.index), col, ele.label)
+            lab = """\t<Label Key="%s"%s><![CDATA[%s]]></Label>\n""" % \
+                (str(ele.key), col, ele.label)
             res = res + lab
         res = res + "</LabelTable>\n" 
         return res
@@ -105,7 +105,7 @@ def print_summary(self):
 
 
 class GiftiLabel(object):
-    index = int
+    key = int
     label = str
     # rgba
     # freesurfer examples seem not to conform
@@ -116,9 +116,9 @@ class GiftiLabel(object):
     blue = float
     alpha = float
 
-    def __init__(self, index = 0, label = '', red = None,\
+    def __init__(self, key = 0, label = '', red = None,\
                   green = None, blue = None, alpha = None):
-        self.index = index
+        self.key = key
         self.label = label
         self.red = red
         self.green = green

nibabel/gifti/parse_gifti_fast.py

@@ -134,7 +134,9 @@ def StartElementHandler(self, name, attrs):
         elif name == 'Label':
             self.label = gi.GiftiLabel()
             if "Index" in attrs:
-                self.label.index = int(attrs["Index"])
+                self.label.key = int(attrs["Index"])
+            if "Key" in attrs:
+                self.label.key = int(attrs["Key"])
             if "Red" in attrs:
                 self.label.red = float(attrs["Red"])
             if "Green" in attrs:

nibabel/gifti/tests/data/rh.aparc.annot.gii

@@ -33,9 +33,10 @@
 DATA_FILE3 = pjoin(IO_DATA_PATH, 'label.gii')
 DATA_FILE4 = pjoin(IO_DATA_PATH, 'rh.shape.curv.gii')
 DATA_FILE5 = pjoin(IO_DATA_PATH, 'base64bin.gii')
+DATA_FILE6 = pjoin(IO_DATA_PATH, 'rh.aparc.annot.gii')
 
-datafiles = [DATA_FILE1, DATA_FILE2, DATA_FILE3, DATA_FILE4, DATA_FILE5]
-numda = [2, 1, 1, 1, 2]
+datafiles = [DATA_FILE1, DATA_FILE2, DATA_FILE3, DATA_FILE4, DATA_FILE5, DATA_FILE6]
+numda = [2, 1, 1, 1, 2, 1]
 
 DATA_FILE1_darr1 = np.array(
        [[-16.07201 , -66.187515,  21.266994],
@@ -66,6 +67,8 @@
        [-0.48011276],
        [-0.45624232],
        [-0.31101292]], dtype=np.float32)
+       
+DATA_FILE6_darr1 = np.array([9182740, 9182740, 9182740], dtype=np.float32)
 
 DATA_FILE5_darr1 = np.array([[ 155.17539978,  135.58103943,   98.30715179],
        [ 140.33973694,  190.0491333 ,   73.24776459],
@@ -181,3 +184,16 @@ def test_getbyintent():
     assert_equal(len(da), 0)
     assert_equal(da, [])
 
+def test_labeltable():
+    img = gi.read(DATA_FILE6)
+    assert_array_almost_equal(img.darrays[0].data[:3], DATA_FILE6_darr1)
+    assert_equal(len(img.labeltable.labels), 36)
+    labeldict = img.labeltable.get_labels_as_dict()
+    assert_true(labeldict.has_key(660700))
+    assert_equal(labeldict[660700], u'entorhinal')
+    assert_equal(img.labeltable.labels[1].key, 2647065)
+    assert_equal(img.labeltable.labels[1].red, 0.0980392)
+    assert_equal(img.labeltable.labels[1].green, 0.392157)
+    assert_equal(img.labeltable.labels[1].blue, 0.156863)
+    assert_equal(img.labeltable.labels[1].alpha, 1)
+