def test_bids_naming():
from samri.pipelines.extra_functions import get_data_selection
from samri.pipelines.utils import bids_naming
import pandas as pd
import os
bruker_data_dir = path.join(DATA_DIR, 'bruker')
f_data_selection = get_data_selection(
bruker_data_dir,
match={
'task': ['JogB', 'CogB', 'CogB2m'],
},
)
s_data_selection = get_data_selection(
bruker_data_dir,
match={
'acquisition': ['TurboRARE', 'TurboRARElowcov'],
},
)
name = bids_naming(
subject_session=('5706', 'ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,
'sub-5706_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz',
debug=f_data_selection)
name = bids_naming(
subject_session=('4011', 'ofMaF'),
metadata=s_data_selection,
)
assert_and_feedback(name,
'sub-4011_ses-ofMaF_acq-TurboRARElowcov_T2w.nii.gz',
debug=s_data_selection)
name = bids_naming(
subject_session=('5704', 'ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,
'sub-5704_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz',
debug=f_data_selection)
name = bids_naming(
subject_session=('5704', 'ofMpF'),
metadata=s_data_selection,
)
assert_and_feedback(name,
'sub-5704_ses-ofMpF_acq-TurboRARE_T2w.nii.gz',
debug=s_data_selection)
def test_bids_naming():
from samri.pipelines.extra_functions import get_data_selection
from samri.pipelines.utils import bids_naming
import pandas as pd
import os
bruker_data_dir = path.join(DATA_DIR,'bruker')
f_data_selection = get_data_selection(bruker_data_dir,
match={
'task':['JogB','CogB','CogB2m'],
},
)
s_data_selection = get_data_selection(bruker_data_dir,
match={
'acquisition':['TurboRARE', 'TurboRARElowcov'],
},
)
name = bids_naming(
subject_session=('5706','ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,'sub-5706_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz', debug=f_data_selection)
name = bids_naming(
subject_session=('4011','ofMaF'),
metadata=s_data_selection,
)
assert_and_feedback(name,'sub-4011_ses-ofMaF_acq-TurboRARElowcov_T2w.nii.gz', debug=s_data_selection)
name = bids_naming(
subject_session=('5704','ofMpF'),
metadata=f_data_selection,
)
assert_and_feedback(name,'sub-5704_ses-ofMpF_task-CogB_acq-EPI_cbv.nii.gz', debug=f_data_selection)
name = bids_naming(
subject_session=('5704','ofMpF'),
metadata=s_data_selection,
)
assert_and_feedback(name,'sub-5704_ses-ofMpF_acq-TurboRARE_T2w.nii.gz', debug=s_data_selection)
def get_bids_scan(data_selection,
bids_base="",
ind_type="",
selector=None,
subject=None,
session=None,
extra=['acq','run'],
):
"""Description...
Parameters
----------
bids_base : str
Path to the bids base path.
data_selection : pandas.DataFrame
A `pandas.DataFrame` object as produced by `samri.preprocessing.extra_functions.get_data_selection()`.
selector : iterable, optional
The first method of selecting the subject and scan, this value should be a length-2 list or tuple containing the subject and sthe session to be selected.
subject : string, optional
This has to be defined if `selector` is not defined. The subject for which to return a scan directory.
session : string, optional
This has to be defined if `selector` is not defined. The session for which to return a scan directory.
"""
import os #for some reason the import outside the function fails
import pandas as pd
from samri.pipelines.utils import bids_naming
filtered_data = []
if selector:
subject = selector[0]
session = selector[1]
filtered_data = data_selection[(data_selection["session"] == session)&(data_selection["subject"] == subject)]
else:
filtered_data = data_selection[data_selection.index==ind_type]
if filtered_data.empty:
raise Exception("SAMRIError: Does not exist: " + str(selector[0]) + str(selector[1]) + str(ind_type))
else:
subject = filtered_data['subject'].item()
session = filtered_data['session'].item()
try:
typ = filtered_data['type'].item()
except:
typ = ""
try:
task = filtered_data['task'].item()
except:
task = ""
subject_session = [subject, session]
#scan_path = os.path.join(bids_base, 'sub-' + subject + '/', 'ses-' + session + '/', typ )
try:
nii_path = filtered_data['path'].item()
except KeyError:
nii_path = filtered_data['measurement'].item()
nii_path += '/'+filtered_data['scan'].item()
nii_name = bids_naming(subject_session, filtered_data,
extra=extra,
extension='',
)
scan_path = nii_path
else:
scan_path = os.path.dirname(nii_path)
nii_name = os.path.basename(nii_path)
eventfile_name = bids_naming(subject_session, filtered_data,
extra=extra,
extension='.tsv',
suffix='events'
)
metadata_filename = bids_naming(subject_session, filtered_data,
extra=extra,
extension='.json',
)
dict_slice = filtered_data.to_dict('records')[0]
return scan_path, typ, task, nii_path, nii_name, eventfile_name, subject_session, metadata_filename, dict_slice
def get_bids_scan(
data_selection,
bids_base="",
ind_type="",
selector=None,
subject=None,
session=None,
extra=['acq', 'run'],
):
"""Description...
Parameters
----------
bids_base : str
Path to the bids base path.
data_selection : pandas.DataFrame
A `pandas.DataFrame` object as produced by `samri.preprocessing.extra_functions.get_data_selection()`.
selector : iterable, optional
The first method of selecting the subject and scan, this value should be a length-2 list or tuple containing the subject and sthe session to be selected.
subject : string, optional
This has to be defined if `selector` is not defined. The subject for which to return a scan directory.
session : string, optional
This has to be defined if `selector` is not defined. The session for which to return a scan directory.
"""
import os #for some reason the import outside the function fails
import pandas as pd
from samri.pipelines.utils import bids_naming
filtered_data = []
if selector:
subject = selector[0]
session = selector[1]
filtered_data = data_selection[(data_selection["session"] == session) &
(data_selection["subject"] == subject)]
else:
filtered_data = data_selection[data_selection.index == ind_type]
if filtered_data.empty:
raise Exception("SAMRIError: Does not exist: " + str(selector[0]) +
str(selector[1]) + str(ind_type))
else:
subject = filtered_data['subject'].item()
session = filtered_data['session'].item()
try:
typ = filtered_data['type'].item()
except:
typ = ""
try:
task = filtered_data['task'].item()
except:
task = ""
subject_session = [subject, session]
#scan_path = os.path.join(bids_base, 'sub-' + subject + '/', 'ses-' + session + '/', typ )
try:
nii_path = filtered_data['path'].item()
except KeyError:
nii_path = filtered_data['measurement'].item()
nii_path += '/' + filtered_data['scan'].item()
nii_name = bids_naming(
subject_session,
filtered_data,
extra=extra,
extension='',
)
scan_path = nii_path
else:
scan_path = os.path.dirname(nii_path)
nii_name = os.path.basename(nii_path)
eventfile_name = bids_naming(subject_session,
filtered_data,
extra=extra,
extension='.tsv',
suffix='events')
metadata_filename = bids_naming(
subject_session,
filtered_data,
extra=extra,
extension='.json',
)
dict_slice = filtered_data.to_dict('records')[0]
return scan_path, typ, task, nii_path, nii_name, eventfile_name, subject_session, metadata_filename, dict_slice