diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 6ec39a89701554f55c4a943cdd3315e02cf2b004..b28eb952c98ccbda29f2097ca8eda9ae660cba4c 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -366,6 +366,15 @@ class AtlasLabel(object):
"""
return self.index < other.index
+ def __repr__(self):
+ """
+ Represents AtlasLabel as string
+ """
+ return '{}({}, index={}, value={})'.format(
+ self.__class__.__name__, self.name,
+ self.index, self.value,
+ )
+
class AtlasDescription(object):
"""An ``AtlasDescription`` instance parses and stores the information
@@ -574,11 +583,11 @@ class AtlasDescription(object):
self.labels = list(sorted(self.labels))
- def find(self, index=None, value=None):
+ def find(self, index=None, value=None, name=None):
"""Find an :class:`.AtlasLabel` either by ``index``, or by ``value``.
- Exactly one of ``index`` or ``value`` may be specified - a
- ``ValueError`` is raised otherwise. If an invalid ``index`` or
+ Exactly one of ``index``, ``value``, or ``name`` may be specified - a
+ ``ValueError`` is raised otherwise. If an invalid ``index``, ``name``, or
``value`` is specified, an ``IndexError`` or ``KeyError`` will be
raised.
@@ -586,12 +595,25 @@ class AtlasDescription(object):
labels, and a 3D ``LabelAtlas`` may have more values
than labels.
"""
- if (index is None and value is None) or \
- (index is not None and value is not None):
- raise ValueError('Only one of index or value may be specified')
+ if ((index is not None) + (value is not None) + (name is not None)) != 1:
+ raise ValueError('Only one of index, value, or name may be specified')
+ if index is not None: return self.labels[ index]
+ elif value is not None: return self.__labelsByValue[int(value)]
+ else:
+ matches = [l for l in self.labels if l.name == name]
+ if len(matches) == 0:
+ # look for partial matches only if there are no full matches
+ matches = [l for l in self.labels if l.name[:len(name)] == name]
+ if len(matches) == 0:
+ raise IndexError('No match for {} found in labels {}'.format(
+ name, tuple(l.name for l in self.labels)
+ ))
+ elif len(matches) > 1:
+ raise IndexError('Multiple matches for {} found in labels {}'.format(
+ name, tuple(l.name for l in self.labels)
+ ))
+ return matches[0]
- if index is not None: return self.labels[ index]
- else: return self.__labelsByValue[int(value)]
def __eq__(self, other):
@@ -612,6 +634,12 @@ class AtlasDescription(object):
"""
return self.name.lower() < other.name.lower()
+ def __repr__(self, ):
+ """
+ String representation of AtlasDescription
+ """
+ return '{}({})'.format(self.__class__.__name__, self.atlasID)
+
class Atlas(fslimage.Image):
"""This is the base class for the :class:`LabelAtlas` and
@@ -849,6 +877,28 @@ class LabelAtlas(Atlas):
return values, props
+ def get(self, label=None, index=None, value=None, name=None):
+ """
+ Returns the binary image for given label
+
+ Only one of the arguments should be used to define the label
+
+ :arg label: AtlasLabel contained within this atlas
+ :arg index: index of the label
+ :arg value: value of the label
+ :arg name: string of the label
+ :return: image.Image with the mask
+ """
+ if ((label is not None) + (index is not None) +
+ (value is not None) + (name is not None)) != 1:
+ raise ValueError('Only one of label, index, value, or name may be specified')
+ if label is None:
+ label = self.find(index=index, name=name, value=value)
+ elif label not in self.desc.labels:
+ raise ValueError("Unknown label provided")
+ arr = (self.data == label.value).astype(int)
+ return fslimage.Image(arr, name=label.name, header=self.header)
+
class ProbabilisticAtlas(Atlas):
"""A 4D atlas which contains one volume for each region.
@@ -867,6 +917,27 @@ class ProbabilisticAtlas(Atlas):
"""
Atlas.__init__(self, atlasDesc, resolution, False, **kwargs)
+ def get(self, label=None, index=None, value=None, name=None):
+ """
+ Returns the probabilistic image for given label
+
+ Only one of the arguments should be used to define the label
+
+ :arg label: AtlasLabel contained within this atlas
+ :arg index: index of the label
+ :arg value: value of the label
+ :arg name: string of the label
+ :return: image.Image with the probabilistic mask
+ """
+ if ((label is not None) + (index is not None) +
+ (value is not None) + (name is not None)) != 1:
+ raise ValueError('Only one of label, index, value, or name may be specified')
+ if label is None:
+ label = self.find(index=index, value=value, name=name)
+ elif label not in self.desc.labels:
+ raise ValueError("Unknown label provided")
+ arr = self[..., label.index]
+ return fslimage.Image(arr, name=label.name, header=self.header)
def proportions(self, location, *args, **kwargs):
"""Looks up and returns the proportions of of all regions at the given
diff --git a/fsl/utils/filetree/trees/ProbtrackX.tree b/fsl/utils/filetree/trees/ProbtrackX.tree
index 38db04c26930365b9046b8171ba28bfbd116ff39..06daa454663e653654814de6b36e8cb6f1214672 100644
--- a/fsl/utils/filetree/trees/ProbtrackX.tree
+++ b/fsl/utils/filetree/trees/ProbtrackX.tree
@@ -1,4 +1,4 @@
-basename=fdt
+basename=fdt_paths
probtrackx.log (log_cmd)
{basename}.log (log_settings)
diff --git a/tests/test_atlases.py b/tests/test_atlases.py
index c2d257f601da2eaf61b5de4eb6f4cd3e148d8d7d..b2dfec113a00349dea0601f781f565561fa18b2c 100644
--- a/tests/test_atlases.py
+++ b/tests/test_atlases.py
@@ -99,6 +99,8 @@ def test_AtlasDescription():
tal = registry.getAtlasDescription('talairach')
cort = registry.getAtlasDescription('harvardoxford-cortical')
+ assert str(tal) == 'AtlasDescription(talairach)'
+ assert str(cort) == 'AtlasDescription(harvardoxford-cortical)'
assert tal.atlasID == 'talairach'
assert tal.name == 'Talairach Daemon Labels'
@@ -140,8 +142,6 @@ def test_AtlasDescription():
registry.getAtlasDescription('non-existent-atlas')
-
-
def test_add_remove_atlas():
with tests.testdir() as testdir:
@@ -235,6 +235,23 @@ def test_load_atlas():
assert isinstance(lblatlas, atlases.LabelAtlas)
+def test_get():
+
+ reg = atlases.registry
+ reg.rescanAtlases()
+
+ probatlas = reg.loadAtlas('harvardoxford-cortical')
+ lblatlas = reg.loadAtlas('talairach')
+ for atlas in (probatlas, lblatlas):
+ for idx, label in enumerate(atlas.desc.labels[:10]):
+ target = probatlas[..., idx] if atlas is probatlas else lblatlas.data == label.value
+ assert (target == atlas.get(label).data).all()
+ assert label.name == atlas.get(label).name
+ assert (target == atlas.get(index=label.index).data).all()
+ assert (target == atlas.get(value=label.value).data).all()
+ assert (target == atlas.get(name=label.name).data).all()
+
+
def test_find():
reg = atlases.registry
@@ -252,16 +269,31 @@ def test_find():
assert atlas .find(value=label.value) == label
assert atlas .find(index=label.index) == label
+ assert atlas .find(name=label.name) == label
assert atlas.desc.find(value=label.value) == label
assert atlas.desc.find(index=label.index) == label
+ assert atlas.desc.find(name=label.name) == label
+
+ if atlas is not lblatlas:
+ # lblatlas has a lot of very similar label names
+ assert atlas .find(name=label.name[:-2]) == label
+ assert atlas.desc.find(name=label.name[:-2]) == label
with pytest.raises(ValueError):
atlas.find()
with pytest.raises(ValueError):
atlas.find(index=1, value=1)
+ with pytest.raises(ValueError):
+ atlas.find(index=1, name=1)
+ with pytest.raises(ValueError):
+ atlas.find(value=1, name=1)
with pytest.raises(IndexError):
atlas.find(index=len(labels))
+ with pytest.raises(IndexError):
+ atlas.find(name='InvalidROI')
+ with pytest.raises(IndexError):
+ atlas.find(name='')
maxval = max([l.value for l in labels])
with pytest.raises(KeyError):