Merge branch 'test/new_atlas' into 'master'

Updates to atlases

See merge request fsl/fslpy!51

.ci/build_conda_dist.sh

@@ -6,7 +6,7 @@ name=$1
 version=$2
 
 # add any extra channels that are needed
-for channel in $CONDA_CHANNELS; do
+for channel in $FSL_CONDA_CHANNELS; do
     conda config  --append channels $channel
 done
 

fsl/scripts/atlasq.py

@@ -275,17 +275,27 @@ def ohi(namespace):
         dumpatlases()
         return
 
+    # atlasquery always uses 2mm atlas
+    # versions when a 2mm is available
+    reses = [p[0] for p in atlasDesc.pixdims]
+
+    if 2 in reses: res = 2
+    else:          res = max(reses)
+
     # Mask query.
     if namespace.ohiMask is not None:
 
-        # atlasquery always uses 2mm atlas versions
         mask          = fslimage.Image(namespace.ohiMask)
-        labels, props = maskQuery(atlasDesc, [mask], resolution=2)
+        labels, props = maskQuery(atlasDesc, [mask], resolution=res)
         labels        = labels[0]
         props         = props[ 0]
 
         for lbl, prop in zip(labels, props):
-            lbl = atlasDesc.labels[int(lbl)].name
+
+            if atlasDesc.atlasType == 'probabilistic':
+                lbl = atlasDesc.labels[int(lbl)].name
+            elif atlasDesc.atlasType == 'label':
+                lbl = atlasDesc.find(value=int(lbl)).name
             print('{}:{:0.4f}'.format(lbl, prop))
 
     # Coordinate query
@@ -295,7 +305,7 @@ def ohi(namespace):
         labels, props = coordQuery(atlasDesc,
                                    [coord],
                                    False,
-                                   resolution=2)
+                                   resolution=res)
 
         labels = labels[0]
         props  = props[ 0]

tests/test_atlases_query.py

@@ -41,7 +41,7 @@ def _get_atlas(atlasID, res, summary=False):
     atlas = _atlases.get((atlasID, res, summary), default=None)
     if atlas is None:
         if summary or atlasID in ('talairach', 'striatum-structural',
-                                  'jhu-labels'):
+                                  'jhu-labels', 'smatt'):
             kwargs = {}
         else:
             kwargs = {'loadData'  : False,

tests/test_atlasq_ohi.py

@@ -155,8 +155,8 @@ def test_mask(seed):
         exp           = []
 
         for lbl, prop in zip(labels, props):
-            exp.append('{}:{:0.4f}'.format(desc.labels[int(lbl)].name,
-                                           prop))
+            name = desc.find(value=int(lbl)).name
+            exp.append('{}:{:0.4f}'.format(name, prop))
 
         return '\n'.join(exp)