Commit 76bf1a8a authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Merge branch 'rel/2.8.4' into 'v2.8'

Rel/2.8.4

See merge request fsl/fslpy!204
parents d4d0d342 fb171f95
Pipeline #5081 passed with stages
in 3 minutes and 37 seconds
...@@ -2,6 +2,21 @@ This document contains the ``fslpy`` release history in reverse chronological ...@@ -2,6 +2,21 @@ This document contains the ``fslpy`` release history in reverse chronological
order. 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) 2.8.3 (Friday 28th February 2020)
--------------------------------- ---------------------------------
......
...@@ -28,11 +28,11 @@ class FileTree(object): ...@@ -28,11 +28,11 @@ class FileTree(object):
- ``name``: descriptive name of the tree - ``name``: descriptive name of the tree
""" """
def __init__(self, def __init__(self,
templates: Dict[str, str], templates: Dict[str, str],
variables: Dict[str, Any], variables: Dict[str, Any],
sub_trees: Dict[str, "FileTree"] = None, sub_trees: Dict[str, "FileTree"] = None,
parent: Optional["FileTree"] = None, parent: Optional["FileTree"] = None,
name: str = None): name: str = None):
""" """
Creates a new filename tree. Creates a new filename tree.
""" """
...@@ -51,7 +51,6 @@ class FileTree(object): ...@@ -51,7 +51,6 @@ class FileTree(object):
""" """
return self._parent return self._parent
@property @property
def name(self, ): def name(self, ):
""" """
...@@ -59,7 +58,6 @@ class FileTree(object): ...@@ -59,7 +58,6 @@ class FileTree(object):
""" """
return self._name return self._name
@property @property
def all_variables(self, ): def all_variables(self, ):
""" """
...@@ -328,8 +326,35 @@ class FileTree(object): ...@@ -328,8 +326,35 @@ class FileTree(object):
return False return False
return True 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 @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 Reads a FileTree from a specific file
...@@ -339,6 +364,7 @@ class FileTree(object): ...@@ -339,6 +364,7 @@ class FileTree(object):
:param tree_name: file containing the filename tree. :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``. 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 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 :param variables: variable settings
:return: dictionary from specifier to filename :return: dictionary from specifier to filename
""" """
...@@ -422,6 +448,8 @@ class FileTree(object): ...@@ -422,6 +448,8 @@ class FileTree(object):
res = get_registered(tree_name, cls)(templates, variables=file_variables, sub_trees=sub_trees, name=tree_name) res = get_registered(tree_name, cls)(templates, variables=file_variables, sub_trees=sub_trees, name=tree_name)
for tree in sub_trees.values(): for tree in sub_trees.values():
tree._parent = res tree._parent = res
if partial_fill:
res = res.partial_fill()
return res return res
......
...@@ -373,7 +373,7 @@ def scan(tree : FileTree) -> List[Match]: ...@@ -373,7 +373,7 @@ def scan(tree : FileTree) -> List[Match]:
filename = tree.update(**variables).get(template) filename = tree.update(**variables).get(template)
if not op.isfile(tree.update(**variables).get(template)): if not op.isfile(filename):
continue continue
matches.append(Match(filename, template, tree, variables)) matches.append(Match(filename, template, tree, variables))
......
...@@ -132,6 +132,9 @@ class Template: ...@@ -132,6 +132,9 @@ class Template:
Splits a template into its constituent parts Splits a template into its constituent parts
""" """
def __init__(self, parts: Sequence[Part]): 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) self.parts = tuple(parts)
@classmethod @classmethod
......
...@@ -47,7 +47,7 @@ import re ...@@ -47,7 +47,7 @@ import re
import string import string
__version__ = '2.8.3' __version__ = '2.8.4'
"""Current version number, as a string. """ """Current version number, as a string. """
......
...@@ -396,6 +396,193 @@ def test_query_subtree(): ...@@ -396,6 +396,193 @@ def test_query_subtree():
op.join('subj-03', 'surf', 'R.white.gii')] 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(): def test_scan():
with _test_data(): with _test_data():
......
...@@ -13,18 +13,25 @@ def same_path(p1, p2): ...@@ -13,18 +13,25 @@ def same_path(p1, p2):
def test_simple_tree(): def test_simple_tree():
tree = filetree.FileTree.read('eddy') 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('basename'), './eddy_output')
same_path(tree.get('image'), './eddy_output.nii.gz') same_path(tree.get('image'), './eddy_output.nii.gz')
tree = filetree.FileTree.read('eddy.tree', basename='out') tree = filetree.FileTree.read('eddy.tree', basename='out')
same_path(tree.get('basename'), './out') assert 'basename' not in tree.variables
same_path(tree.update(basename='test').get('basename'), './test')
same_path(tree.get('basename'), './out') same_path(tree.get('basename'), './out')
with pytest.raises(ValueError): with pytest.raises(ValueError):
filetree.FileTree.read('non_existing') 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(): def test_complicated_tree():
tree = filetree.FileTree.read('HCP_directory').update(subject='100307') tree = filetree.FileTree.read('HCP_directory').update(subject='100307')
......
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