diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 358df42f562fa469aecf40ad8344f9aeac07f340..ea17df9c9056ce0f4add92d35bc52ed3611a32b7 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,6 +2,21 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+
+2.8.4 (Monday 2nd March 2020)
+-----------------------------
+
+
+Added
+^^^^^
+
+
+* Added a new ``partial_fill`` option to :meth:`.FileTree.read`, which
+ effectively eliminates any variables which only have one value. This was
+ added to accommodate some behavioural changes that were introduced in 2.8.2.
+
+
+
2.8.3 (Friday 28th February 2020)
---------------------------------
diff --git a/fsl/utils/filetree/filetree.py b/fsl/utils/filetree/filetree.py
index 0b077d6c300611c783aee1cbbe7dbc0788342a6f..3159fefa842f986115921ae4166df7411ac93893 100644
--- a/fsl/utils/filetree/filetree.py
+++ b/fsl/utils/filetree/filetree.py
@@ -28,11 +28,11 @@ class FileTree(object):
- ``name``: descriptive name of the tree
"""
def __init__(self,
- templates: Dict[str, str],
- variables: Dict[str, Any],
- sub_trees: Dict[str, "FileTree"] = None,
- parent: Optional["FileTree"] = None,
- name: str = None):
+ templates: Dict[str, str],
+ variables: Dict[str, Any],
+ sub_trees: Dict[str, "FileTree"] = None,
+ parent: Optional["FileTree"] = None,
+ name: str = None):
"""
Creates a new filename tree.
"""
@@ -51,7 +51,6 @@ class FileTree(object):
"""
return self._parent
-
@property
def name(self, ):
"""
@@ -59,7 +58,6 @@ class FileTree(object):
"""
return self._name
-
@property
def all_variables(self, ):
"""
@@ -328,8 +326,35 @@ class FileTree(object):
return False
return True
+ def partial_fill(self, ) -> "FileTree":
+ """
+ Fills in known variables into the templates
+
+ :return: The resulting tree will have empty `variables` dictionaries and updated templates
+ """
+ new_tree = deepcopy(self)
+ to_update = new_tree
+ while to_update.parent is not None:
+ to_update = to_update.parent
+ to_update._update_partial_fill()
+ return new_tree
+
+ def _update_partial_fill(self, ):
+ """
+ Helper function for `partial_fill` that updates the templates in place
+ """
+ new_templates = {}
+ for short_name in self.templates:
+ template, variables = self.get_template(short_name)
+ new_templates[short_name] = str(utils.Template.parse(template).fill_known(variables))
+ self.templates = new_templates
+
+ for tree in self.sub_trees.values():
+ tree._update_partial_fill()
+ self.variables = {}
+
@classmethod
- def read(cls, tree_name: str, directory='.', **variables) -> "FileTree":
+ def read(cls, tree_name: str, directory='.', partial_fill=True, **variables) -> "FileTree":
"""
Reads a FileTree from a specific file
@@ -339,6 +364,7 @@ class FileTree(object):
:param tree_name: file containing the filename tree.
Can provide the filename of a tree file or the name for a tree in the ``filetree.tree_directories``.
:param directory: parent directory of the full tree (defaults to current directory)
+ :param partial_fill: By default any known `variables` are filled into the `template` immediately
:param variables: variable settings
:return: dictionary from specifier to filename
"""
@@ -422,6 +448,8 @@ class FileTree(object):
res = get_registered(tree_name, cls)(templates, variables=file_variables, sub_trees=sub_trees, name=tree_name)
for tree in sub_trees.values():
tree._parent = res
+ if partial_fill:
+ res = res.partial_fill()
return res
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index 56ba6cc4991b30bb47aad00ed513cc3868465951..a2e215c848558f304e62c61ba529614bd05038f0 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -373,7 +373,7 @@ def scan(tree : FileTree) -> List[Match]:
filename = tree.update(**variables).get(template)
- if not op.isfile(tree.update(**variables).get(template)):
+ if not op.isfile(filename):
continue
matches.append(Match(filename, template, tree, variables))
diff --git a/fsl/utils/filetree/utils.py b/fsl/utils/filetree/utils.py
index 621d97eeaa9b4e2c40a5e6879a47fa82b09a136c..0dae44a66aefe85d00761b7f2876f3611bc85266 100644
--- a/fsl/utils/filetree/utils.py
+++ b/fsl/utils/filetree/utils.py
@@ -132,6 +132,9 @@ class Template:
Splits a template into its constituent parts
"""
def __init__(self, parts: Sequence[Part]):
+ if isinstance(parts, str):
+ raise ValueError("Input to Template should be a sequence of parts; " +
+ "did you mean to call `Template.parse` instead?")
self.parts = tuple(parts)
@classmethod
diff --git a/tests/test_filetree/test_query.py b/tests/test_filetree/test_query.py
index 3d4bef6db3f229b88f0a7dfef21b38d41a1cb166..a85ac5d8d441111f0ac4cde7bade392facc4735d 100644
--- a/tests/test_filetree/test_query.py
+++ b/tests/test_filetree/test_query.py
@@ -396,6 +396,193 @@ def test_query_subtree():
op.join('subj-03', 'surf', 'R.white.gii')]
+def test_query_variable_partial_set():
+ tree1 = tw.dedent("""
+ subj-{participant}
+ T1w.nii.gz (T1w)
+ native
+ ->surface space=native (surf_native)
+ standard
+ ->surface (surf_standard)
+ """)
+ tree2 = tw.dedent("""
+ {hemi}.{space}.gii (surface)
+ """)
+
+ files = [
+ op.join('subj-01', 'T1w.nii.gz'),
+ op.join('subj-01', 'native', 'L.native.gii'),
+ op.join('subj-01', 'native', 'R.native.gii'),
+ op.join('subj-01', 'standard', 'L.mni.gii'),
+ op.join('subj-01', 'standard', 'R.mni.gii'),
+ op.join('subj-01', 'standard', 'L.freesurfer.gii'),
+ op.join('subj-01', 'standard', 'R.freesurfer.gii'),
+ op.join('subj-02', 'T1w.nii.gz'),
+ op.join('subj-02', 'native', 'L.native.gii'),
+ op.join('subj-02', 'native', 'R.native.gii'),
+ op.join('subj-02', 'standard', 'L.mni.gii'),
+ op.join('subj-02', 'standard', 'R.mni.gii'),
+ op.join('subj-02', 'standard', 'L.freesurfer.gii'),
+ op.join('subj-02', 'standard', 'R.freesurfer.gii'),
+ op.join('subj-03', 'T1w.nii.gz'),
+ op.join('subj-03', 'native', 'L.native.gii'),
+ op.join('subj-03', 'native', 'R.native.gii'),
+ op.join('subj-03', 'standard', 'L.mni.gii'),
+ op.join('subj-03', 'standard', 'R.mni.gii')]
+
+ with testdir(files):
+ with open('tree1.tree', 'wt') as f: f.write(tree1)
+ with open('surface.tree', 'wt') as f: f.write(tree2)
+
+ tree = filetree.FileTree.read('tree1.tree', '.')
+ query = filetree.FileTreeQuery(tree)
+
+ assert sorted(query.templates) == ['T1w',
+ 'surf_native/surface',
+ 'surf_standard/surface']
+
+ qvars = query.variables()
+ assert sorted(qvars.keys()) == ['hemi', 'participant', 'space']
+ assert qvars['hemi'] == ['L', 'R']
+ assert qvars['participant'] == ['01', '02', '03']
+ assert qvars['space'] == ['freesurfer', 'mni']
+
+ qvars = query.variables('T1w')
+ assert sorted(qvars.keys()) == ['participant']
+ assert qvars['participant'] == ['01', '02', '03']
+
+ qvars = query.variables('surf_native/surface')
+ assert sorted(qvars.keys()) == ['hemi', 'participant']
+ assert qvars['hemi'] == ['L', 'R']
+ assert qvars['participant'] == ['01', '02', '03']
+
+ qvars = query.variables('surf_standard/surface')
+ assert sorted(qvars.keys()) == ['hemi', 'participant', 'space']
+ assert qvars['hemi'] == ['L', 'R']
+ assert qvars['participant'] == ['01', '02', '03']
+ assert qvars['space'] == ['freesurfer', 'mni']
+
+ got = query.query('T1w')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'T1w.nii.gz'),
+ op.join('subj-02', 'T1w.nii.gz'),
+ op.join('subj-03', 'T1w.nii.gz')]
+
+ got = query.query('T1w', participant='01')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'T1w.nii.gz')]
+
+ got = query.query('surf_native/surface')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'native', 'L.native.gii'),
+ op.join('subj-01', 'native', 'R.native.gii'),
+ op.join('subj-02', 'native', 'L.native.gii'),
+ op.join('subj-02', 'native', 'R.native.gii'),
+ op.join('subj-03', 'native', 'L.native.gii'),
+ op.join('subj-03', 'native', 'R.native.gii')]
+
+ got = query.query('surf_native/surface', hemi='L')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'native', 'L.native.gii'),
+ op.join('subj-02', 'native', 'L.native.gii'),
+ op.join('subj-03', 'native', 'L.native.gii')]
+
+ got = query.query('surf_standard/surface', hemi='L')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'standard', 'L.freesurfer.gii'),
+ op.join('subj-01', 'standard', 'L.mni.gii'),
+ op.join('subj-02', 'standard', 'L.freesurfer.gii'),
+ op.join('subj-02', 'standard', 'L.mni.gii'),
+ # subj03/standard/L.freesurfer.gii was skipped when creating files
+ op.join('subj-03', 'standard', 'L.mni.gii')]
+
+
+def test_query_multi_subtree():
+ tree1 = tw.dedent("""
+ subj-{participant}
+ T1w.nii.gz (T1w)
+ native
+ ->surface space=native (surf_native)
+ mni
+ ->surface space=mni (surf_mni)
+ """)
+ tree2 = tw.dedent("""
+ {hemi}.{space}.gii (surface)
+ """)
+
+ files = [
+ op.join('subj-01', 'T1w.nii.gz'),
+ op.join('subj-01', 'native', 'L.native.gii'),
+ op.join('subj-01', 'native', 'R.native.gii'),
+ op.join('subj-01', 'mni', 'L.mni.gii'),
+ op.join('subj-01', 'mni', 'R.mni.gii'),
+ op.join('subj-02', 'T1w.nii.gz'),
+ op.join('subj-02', 'native', 'L.native.gii'),
+ op.join('subj-02', 'native', 'R.native.gii'),
+ op.join('subj-02', 'mni', 'L.mni.gii'),
+ op.join('subj-02', 'mni', 'R.mni.gii'),
+ op.join('subj-03', 'T1w.nii.gz'),
+ op.join('subj-03', 'native', 'L.native.gii'),
+ op.join('subj-03', 'native', 'R.native.gii'),
+ op.join('subj-03', 'mni', 'L.mni.gii'),
+ op.join('subj-03', 'mni', 'R.mni.gii')]
+
+ with testdir(files):
+ with open('tree1.tree', 'wt') as f: f.write(tree1)
+ with open('surface.tree', 'wt') as f: f.write(tree2)
+
+ tree = filetree.FileTree.read('tree1.tree', '.')
+ query = filetree.FileTreeQuery(tree)
+
+ assert sorted(query.templates) == ['T1w',
+ 'surf_mni/surface',
+ 'surf_native/surface']
+
+ qvars = query.variables()
+ assert sorted(qvars.keys()) == ['hemi', 'participant']
+ assert qvars['hemi'] == ['L', 'R']
+ assert qvars['participant'] == ['01', '02', '03']
+
+ qvars = query.variables('T1w')
+ assert sorted(qvars.keys()) == ['participant']
+ assert qvars['participant'] == ['01', '02', '03']
+
+ qvars = query.variables('surf_mni/surface')
+ assert sorted(qvars.keys()) == ['hemi', 'participant']
+ assert qvars['hemi'] == ['L', 'R']
+ assert qvars['participant'] == ['01', '02', '03']
+
+ qvars = query.variables('surf_native/surface')
+ assert sorted(qvars.keys()) == ['hemi', 'participant']
+ assert qvars['hemi'] == ['L', 'R']
+ assert qvars['participant'] == ['01', '02', '03']
+
+ got = query.query('T1w')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'T1w.nii.gz'),
+ op.join('subj-02', 'T1w.nii.gz'),
+ op.join('subj-03', 'T1w.nii.gz')]
+
+ got = query.query('T1w', participant='01')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'T1w.nii.gz')]
+
+ got = query.query('surf_mni/surface')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'mni', 'L.mni.gii'),
+ op.join('subj-01', 'mni', 'R.mni.gii'),
+ op.join('subj-02', 'mni', 'L.mni.gii'),
+ op.join('subj-02', 'mni', 'R.mni.gii'),
+ op.join('subj-03', 'mni', 'L.mni.gii'),
+ op.join('subj-03', 'mni', 'R.mni.gii')]
+
+ got = query.query('surf_native/surface', hemi='L')
+ assert [m.filename for m in sorted(got)] == [
+ op.join('subj-01', 'native', 'L.native.gii'),
+ op.join('subj-02', 'native', 'L.native.gii'),
+ op.join('subj-03', 'native', 'L.native.gii')]
+
+
def test_scan():
with _test_data():
diff --git a/tests/test_filetree/test_read.py b/tests/test_filetree/test_read.py
index 4895ce1d9e303a3e7c19b40ef30cf4b9adfcc2ed..6627969e343094ca8a8cc8797c09872195ab9774 100644
--- a/tests/test_filetree/test_read.py
+++ b/tests/test_filetree/test_read.py
@@ -13,18 +13,25 @@ def same_path(p1, p2):
def test_simple_tree():
tree = filetree.FileTree.read('eddy')
- assert tree.variables['basename'] == 'eddy_output'
+ assert 'basename' not in tree.variables
+
same_path(tree.get('basename'), './eddy_output')
same_path(tree.get('image'), './eddy_output.nii.gz')
tree = filetree.FileTree.read('eddy.tree', basename='out')
- same_path(tree.get('basename'), './out')
- same_path(tree.update(basename='test').get('basename'), './test')
+ assert 'basename' not in tree.variables
same_path(tree.get('basename'), './out')
with pytest.raises(ValueError):
filetree.FileTree.read('non_existing')
+ # without partial_fill
+ tree_no_fill = filetree.FileTree.read('eddy', partial_fill=False)
+ tree_no_fill.variables['basename'] == 'eddy_output'
+ same_path(tree_no_fill.get('basename'), './eddy_output')
+ same_path(tree_no_fill.update(basename='test').get('basename'), './test')
+ same_path(tree_no_fill.get('basename'), './eddy_output')
+
def test_complicated_tree():
tree = filetree.FileTree.read('HCP_directory').update(subject='100307')