def concatenate_runs(subj_num):
"""
Concatenates data from all runs for a particular subject and saves that
data into a designated file. If file already exists, uses that cached file
instead.
Parameters
----------
subj_num : int
Returns
-------
None
"""
npy_file_name = dp.get_concatenated_path(subj_num)
if not exists(npy_file_name) or not USE_CACHED_DATA:
run_data = []
for j in range(NUM_RUNS):
img = nib.load(dp.get_raw_path(subj_num, j + 1))
data = img.get_data()
if j == 0:
run_data.append(data[..., :-4])
elif j >= 1 and j <= NUM_RUNS - 2:
run_data.append(data[..., 4:-4])
else:
run_data.append(data[..., 4:])
concatenated_run_data = np.concatenate(run_data, axis=3)
np.save(npy_file_name, concatenated_run_data)
print("Saved {0}".format(npy_file_name))
else:
print("Using cached version of {0}".format(npy_file_name))
def concatenate_runs(subj_num):
"""
Concatenates data from all runs for a particular subject and saves that
data into a designated file. If file already exists, uses that cached file
instead.
Parameters
----------
subj_num : int
Returns
-------
None
"""
npy_file_name = dp.get_concatenated_path(subj_num)
if not exists(npy_file_name) or not USE_CACHED_DATA:
run_data = []
for j in range(NUM_RUNS):
img = nib.load(dp.get_raw_path(subj_num, j + 1))
data = img.get_data()
if j == 0:
run_data.append(data[..., :-4])
elif j >= 1 and j <= NUM_RUNS - 2:
run_data.append(data[..., 4:-4])
else:
run_data.append(data[..., 4:])
concatenated_run_data = np.concatenate(run_data, axis=3)
np.save(npy_file_name, concatenated_run_data)
print('Saved {0}'.format(npy_file_name))
else:
print('Using cached version of {0}'.format(npy_file_name))
def get_affine():
affine_path = '{0}/data/affine.npy'.format(REPO_HOME_PATH)
if not exists(affine_path):
subj_num, run_num = 1, 1
img = nib.load(dp.get_raw_path(subj_num, run_num))
affine = img.get_affine()
np.save(affine_path, affine)
return affine
return np.load(affine_path)
def test_get_raw_path():
paths = [dp.get_raw_path(subject, RUN_NUM) for subject in SUBJECTS]
assert paths[0] == '{0}/data/raw/sub001/task001_run001/bold_dico_dico_rcds_nl.nii'.format(
REPO_HOME_PATH)
assert paths[1] == '{0}/data/raw/sub002/task001_run001/bold_dico_dico_rcds_nl.nii'.format(
REPO_HOME_PATH)
assert paths[2] == '{0}/data/raw/sub003/task001_run001/bold_dico_dico_rcds_nl.nii'.format(
REPO_HOME_PATH)
assert paths[3] == '{0}/data/raw/sub004/task001_run001/bold_dico_dico_rcds_nl.nii'.format(
REPO_HOME_PATH)
assert paths[4] == '{0}/data/raw/sub005/task001_run001/bold_dico_dico_rcds_nl.nii'.format(
REPO_HOME_PATH)
def concatenate_runs(subj_num):
npy_file_name = dp.get_concatenated_path(subj_num)
if not exists(npy_file_name) or not USE_CACHED_DATA:
run_data = []
for j in range(NUM_RUNS):
img = nib.load(dp.get_raw_path(subj_num, j + 1))
data = img.get_data()
if j == 0:
run_data.append(data[..., :-4])
elif j >= 1 and j <= NUM_RUNS - 2:
run_data.append(data[..., 4:-4])
else:
run_data.append(data[..., 4:])
concatenated_run_data = np.concatenate(run_data, axis=3)
np.save(npy_file_name, concatenated_run_data)
print('Saved {0}'.format(npy_file_name))
else:
print('Using cached version of {0}'.format(npy_file_name))
def get_affine():
"""
Retrieves the absolute path to the affine.npy file and loads the data from
that file
Parameters
----------
None
Returns
-------
affine_data : array
"""
affine_path = "{0}/data/affine.npy".format(REPO_HOME_PATH)
if not exists(affine_path):
subj_num, run_num = 1, 1
img = nib.load(dp.get_raw_path(subj_num, run_num))
affine = img.get_affine()
np.save(affine_path, affine)
return affine
return np.load(affine_path)
def get_affine():
"""
Retrieves the absolute path to the affine.npy file and loads the data from
that file
Parameters
----------
None
Returns
-------
affine_data : array
"""
affine_path = '{0}/data/affine.npy'.format(REPO_HOME_PATH)
if not exists(affine_path):
subj_num, run_num = 1, 1
img = nib.load(dp.get_raw_path(subj_num, run_num))
affine = img.get_affine()
np.save(affine_path, affine)
return affine
return np.load(affine_path)
def test_get_raw_path():
paths = [dp.get_raw_path(subject, RUN_NUM) for subject in SUBJECTS]
assert paths[0] == '{0}/data/raw/sub1_run1_raw.nii'.format(REPO_HOME_PATH)
assert paths[1] == '{0}/data/raw/sub2_run1_raw.nii'.format(REPO_HOME_PATH)
def test_get_raw_path():
paths = [dp.get_raw_path(subject, RUN_NUM) for subject in SUBJECTS]
assert paths[0] == '{0}/data/raw/sub1_run1_raw.nii'.format(
REPO_HOME_PATH)
assert paths[1] == '{0}/data/raw/sub2_run1_raw.nii'.format(
REPO_HOME_PATH)
