def test_generate_xml():
# Generate an xml mapping of the BDIS folder structure.
with tempfile.TemporaryDirectory() as tmp:
# copy the dst to a temp folder.
shutil.copytree(TESTPATH1, op.join(tmp, 'BIDSTEST1'))
folder = BIDSTree(op.join(tmp, 'BIDSTEST1'))
folder.generate_map(op.join(tmp, 'map.xml'))
tree = ET.ElementTree()
tree.parse(op.join(tmp, 'map.xml'))
assert len(tree.findall('Project')) == 2
# find the `test1` project
for _proj in tree.findall('Project'):
if _proj.attrib['ID'] == 'test1':
proj = _proj
assert len(proj.findall('Subject')) == 2
# find subject 1
for _subj in proj.findall('Subject'):
if _subj.attrib['ID'] == '1':
subj = _subj
assert subj.attrib['sex'] == 'F'
assert len(subj.findall('Session')) == 2
for _sess in subj.findall('Session'):
if _sess.attrib['ID'] == '1':
sess = _sess
assert len(sess.findall('Scan')) == 2
scan = None
for _scan in sess.findall('Scan'):
if (_scan.attrib['path'] ==
op.join(
'meg',
'sub-1_ses-1_task-resting_run-1_meg',
'sub-1_ses-1_task-resting_run-1_meg.con')):
scan = _scan
assert scan is not None
def _transfer(self):
"""Transfer all the files in each of the sources to the destination."""
copy_func = BIDSCopy(overwrite=self.force_override.get(),
verify=self.verify.get(),
file_name_tracker=self.curr_file,
file_num_tracker=self.transferred_count,
file_prog_tracker=self.curr_file_progress)
self.curr_file.set('Mapping destination BIDS structure...')
dst_folder = BIDSTree(self.dst)
for src in self.srcs:
dst_folder.add(src, copier=copy_func.copy_files)
if self.set_copied:
self._rename_complete(src)
self.transferred_count.set(self.file_count)
self.curr_file.set('Complete!')
def assign_bids_folder(fpath, treeview, data):
"""
Assign the filepath as a BIDS folder and associate all children as the
required type.
"""
try:
bids_folder = BIDSTree(fpath)
except MappingError:
return
if bids_folder.projects == []:
# Ie. no valid data
messagebox.showerror(
"Not valid",
"The folder you selected is does not contain valid BIDS "
"data.\nPlease select a folder containing BIDS-formatted "
"data.")
# Remove the bids folder just to be sure
del bids_folder
return None
# now we need to assign all the data to the filetree...
sid = treeview.sid_from_filepath(fpath)
data[sid] = bids_folder
for project in bids_folder:
sid = treeview.sid_from_filepath(project.path)
data[sid] = project
for subject in project:
sid = treeview.sid_from_filepath(subject.path)
data[sid] = subject
for session in subject:
sid = treeview.sid_from_filepath(session.path)
data[sid] = session
return bids_folder
def test_rename():
with tempfile.TemporaryDirectory() as tmp:
shutil.copytree(TESTPATH1, op.join(tmp, 'BIDSTEST1'))
src_bt = BIDSTree(op.join(tmp, 'BIDSTEST1'))
# renaming a subject
subj = src_bt.project('test1').subject(2)
subj.rename('4')
assert subj.ID == 'sub-4'
for _, _, files in os.walk(subj.path):
for fname in files:
assert 'sub-2' not in fname
sess = subj.session(2)
assert 'sub-4' in sess.scans[0].raw_file
# renaming a session
sess.rename('3')
assert sess.ID == 'ses-3'
for _, _, files in os.walk(subj.path):
for fname in files:
assert 'ses-2' not in fname
df = pd.read_csv(sess.scans_tsv, sep='\t')
for row in df['filename']:
assert 'ses-3' in row
assert 'sub-4' in row
# test renaming a folder-less session to have a session label
shutil.copytree(TESTPATH2, op.join(tmp, 'BIDSTEST2'))
src_bt = BIDSTree(op.join(tmp, 'BIDSTEST2'))
sess = src_bt.project('test1').subject(2).session('none')
orig_path = sess.path
sess.rename('1')
assert sess.path == op.join(orig_path, 'ses-1')
def test_bidstree_to_bidstree():
# Test writing one BIDSTree object to a new empty BIDSTree location.
with tempfile.TemporaryDirectory() as tmp:
dest_bf = BIDSTree(tmp, False)
src_bt = BIDSTree(TESTPATH2)
dest_bf.add(src_bt)
assert len(dest_bf.projects) == 1
assert dest_bf.project('test1').subject('1').subject_data['age'] == 2.0
def _import_bids_data(self):
"""Allow BIDS data to be imported into Biscuit."""
src_dir = filedialog.askdirectory(
title="Select the BIDS folder to import")
if src_dir != '':
try:
bt = BIDSTree(src_dir)
except MappingError:
messagebox.showerror(
'Invalid folder', 'Can only import entire BIDS folders '
'currently.')
return
dst_dir = filedialog.askdirectory(
title="Select the BIDS folder to import into")
if dst_dir != '':
SendFilesWindow(self, bt, dst_dir, opt_verify=True)
def test_copy_errors():
# Test trying to copy the wrong things into the wrong places.
with tempfile.TemporaryDirectory() as tmp:
# copy the dst to a temp folder
shutil.copytree(TESTPATH2, op.join(tmp, 'BIDSTEST2'))
src_bt = BIDSTree(TESTPATH1)
dst_bt = BIDSTree(op.join(tmp, 'BIDSTEST2'))
# try add one project to another with different ID's
# try and add an object you shouldn't do:
proj = src_bt.project('test1')
with pytest.raises(TypeError):
dst_bt.project('test1').subject('1').session('1').add(proj)
with pytest.raises(TypeError):
dst_bt.project('test1').subject('1').add(proj)
with pytest.raises(TypeError):
dst_bt.project('test1').add(src_bt)
proj = src_bt.project('test2')
sub = proj.subject('3')
ses = sub.session('1')
scan = ses.scan(task='resting', run='1')
# try and add objects in the wrong project:
with pytest.raises(ValueError):
dst_bt.project('test1').add(proj)
with pytest.raises(AssociationError):
dst_bt.project('test1').add(sub)
with pytest.raises(AssociationError):
dst_bt.project('test1').add(ses)
with pytest.raises(AssociationError):
dst_bt.project('test1').add(scan)
# try and add objects to the wrong subject:
with pytest.raises(ValueError):
dst_bt.project('test1').subject('1').add(sub)
with pytest.raises(AssociationError):
dst_bt.project('test1').subject('1').add(ses)
with pytest.raises(AssociationError):
dst_bt.project('test1').subject('1').add(scan)
# try and add objects to the wrong session:
with pytest.raises(ValueError):
session = src_bt.project('test1').subject('1').session('2')
dst_bt.project('test1').subject('1').session('1').add(session)
with pytest.raises(AssociationError):
dst_bt.project('test1').subject('1').session('1').add(scan)
def test_merge_bidstrees():
# Test completely merging one BIDS folder into another.
with tempfile.TemporaryDirectory() as tmp:
# copy the dst to a temp folder
shutil.copytree(TESTPATH2, op.join(tmp, 'BIDSTEST2'))
src_bt = BIDSTree(TESTPATH1)
dst_bt = BIDSTree(op.join(tmp, 'BIDSTEST2'))
with pytest.warns(UserWarning):
dst_bt.add(src_bt)
assert len(dst_bt.projects) == 2
# proj:test1, subj:2, sess: 1 will not have been merged
assert (src_bt.project('test1').subject(2).session(2)
not in dst_bt.project('test1').subject(2))
# To rectify this, rename the folder-less session then re-add
dst_bt.project('test1').subject(2).session('none').rename('1')
dst_bt.project('test1').subject(2).add(
src_bt.project('test1').subject(2).session(2))
assert len(dst_bt.project('test1').subject(2).sessions) == 2
# check that extra files are brought along
sess = dst_bt.project('test2').subject(3).session(1)
assert 'code' in sess.extra_data
assert 'extradata' in sess.extra_data
assert op.exists(op.join(sess.path, 'code', 'analysis.py'))
assert op.exists(op.join(sess.path, 'extradata', 'extra.txt'))
def test_add_new_project_recursively():
# Add a scan existing in a project that doesn't exist in the dst folder
# This will recursively add the project, subject and session.
with tempfile.TemporaryDirectory() as tmp:
# copy the dst to a temp folder
shutil.copytree(TESTPATH2, op.join(tmp, 'BIDSTEST2'))
src_bt = BIDSTree(TESTPATH1)
dst_bt = BIDSTree(op.join(tmp, 'BIDSTEST2'))
scan = src_bt.project('test2').subject('3').session('1').scan(
task='resting', run='1')
assert scan.emptyroom is not None
dst_bt.add(scan)
# make sure the project was added
assert len(dst_bt.projects) == 2
assert op.exists(dst_bt.project('test2').readme)
assert op.exists(dst_bt.project('test2').description)
# make sure the subject was added and the empty room data was too
assert len(dst_bt.project('test2').subjects) == 2
# make sure the scan was added
scans_tsv = dst_bt.project('test2').subject('3').session('1').scans_tsv
assert op.exists(scans_tsv)
dst_bt.project('test2').subject('emptyroom')
def test_query():
folder = BIDSTree(TESTPATH1)
# query a BIDSTree object
# query some subject information
assert len(folder.query('subject', 'age', '=', 4)) == 1
assert len(folder.query('subject', 'age', '>', 2)) == 2
assert len(folder.query('subject', 'age', '>=', 2)) == 3
assert len(folder.query('subject', 'sex', '=', 'M')) == 1
assert len(folder.query('subject', 'sex', '!=', 'M')) == 3
assert len(folder.query('subject', 'group', '=', 'autistic')) == 2
# query some tasks
assert len(folder.query('scan', 'task', '=', 'resting')) == 2
# ask if any of the subjects has *any* tasks that aren't 'resting'
assert (folder.project('test1').subject('1')
in folder.query('subject', 'task', '!=', 'resting'))
# ask if any of the subjects have not got a task called 'resting'
assert (folder.project('test1').subject('2')
in folder.query('subject', 'task', '!!=', 'resting'))
with pytest.raises(ValueError, match='Condition'):
folder.query('subject', 'task', '>', 'resting')
# query the recording date
ref_datetime = '2018-10-26T11:32:33'
ref_date = '2018-10-26'
assert len(folder.query('scan', 'rec_date', '=', ref_datetime)) == 1
assert len(folder.query('scan', 'rec_date', '<=', ref_datetime)) == 5
assert len(folder.query('scan', 'rec_date', '>', ref_datetime)) == 1
assert len(folder.query('scan', 'rec_date', '=', ref_date)) == 6
assert len(folder.query('session', 'rec_date', '=', ref_date)) == 5
# query some data in the sidecar.json:
assert len(folder.query('project', 'PowerLineFrequency', '=', 50)) == 2
assert len(folder.query('subject', 'MiscChannelCount', '=', 93)) == 4
assert len(folder.query('session', 'TaskName', '=', 'resting')) == 2
assert len(folder.query('scan', 'RecordingDuration', '>=', 5)) == 6
# query for number of subjects, sessions, or scans
assert len(folder.query('project', 'subjects', '=', 2)) == 2
assert len(folder.query('project', 'sessions', '!=', 3)) == 1
assert len(folder.query('subject', 'sessions', '<', 2)) == 3
assert len(folder.query('project', 'scans', '>', 4)) == 0
assert len(folder.query('subject', 'scans', '<=', 2)) == 3
assert len(folder.query('session', 'scans', '<', 2)) == 4
with pytest.raises(ValueError):
folder.query('subject', 'subjects', '=', 2)
with pytest.raises(ValueError):
folder.query('session', 'sessions', '=', 1)
with pytest.raises(ValueError):
folder.query('scan', 'scans', '=', 1)
# query a Project object (test1):
proj = folder.query('project', 'sessions', '=', 3)
assert len(proj.query('subject', 'sessions', '=', 2)) == 1
assert len(proj.query('subject', 'group', '=', 'neurotypical')) == 1
assert len(proj.query('session', 'scans', '<=', 3)) == 3
# query a Subject object (sub-1):
subj = proj.query('subject', 'sessions', '=', 2)[0]
assert len(subj.query('session', 'scans', '>=', 1)) == 2
with pytest.raises(ValueError, match='Invalid query'):
subj.query('project', 'subjects', '=', 1)
# query a Session object (ses-1):
sess = subj.query('session', 'scans', '>', 1)[0]
assert len(sess.query('scan', 'task', '=', 'resting')) == 1
# query a scan object:
scan = sess.query('scan', 'task', '=', 'resting')[0]
assert len(scan.query('scan', 'MEGChannelCount', '=', 160)) == 1
# perform a compound query:
subjs = folder.query('subject', 'age', '>', 2)
assert len(subjs.query('scan', 'task', '=', 'resting')) == 1
projs = folder.query('project', 'subjects', '>', 1)
assert (folder.project('test1') in projs.query('project', 'sessions', '=',
3))
subjs = folder.query('subject', 'sex', '=', 'F')
assert (folder.project('test2').subject('3')
in subjs.query('subject', 'sessions', '=', 1))
sesss = folder.query('session', 'scans', '=', 1)
assert len(sesss) == 4
assert (folder.project('test2').subject('3').session('1')
in sesss.query('session', 'TaskName', '=', 'resting'))