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
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)
---------------------------------
......
......@@ -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
......
......@@ -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))
......
......@@ -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
......
......@@ -47,7 +47,7 @@ import re
import string
__version__ = '2.8.3'
__version__ = '2.8.4'
"""Current version number, as a string. """
......
......@@ -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():
......
......@@ -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')
......
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