def test_check_for_custom_measure_stats_files_mgh_format():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list, hemi='rh')
bdi.check_for_custom_measure_stats_files(["aparc"], ["area"], morph_file_format="mgh")
def test_braindescriptors_init_with_invalid_hemi():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
with pytest.raises(ValueError) as exc_info:
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list, hemi='nosuchhemi')
assert "hemi must be one of {'lh', 'rh', 'both'} but is" in str(exc_info.value)
assert "nosuchhemi" in str(exc_info.value)
def test_check_for_NaNs_no_descriptors_yet():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list, hemi='lh')
subjects_over_threshold, descriptors_over_threshold, nan_share_per_subject, nan_share_per_descriptor = bdi.check_for_NaNs()
assert len(subjects_over_threshold) == 0
assert len(descriptors_over_threshold) == 0
def test_braindescriptors_add_standard_stats():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list)
bdi.add_standard_stats()
assert len(bdi.descriptor_names) == 3426
assert bdi.descriptor_values.shape == (2, 3426)
def test_check_for_custom_measure_stats_files_invalid_format():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list, hemi='rh')
with pytest.raises(ValueError) as exc_info:
bdi.check_for_custom_measure_stats_files(["aparc"], ["area"], morph_file_format="nosuchformat")
assert "nosuchformat" in str(exc_info.value)
assert "morph_file_format must be one of" in str(exc_info.value)
def test_braindescriptors_init_with_hemi():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list, hemi='lh')
bdi.report_descriptors()
bdi.check_for_hemi_dependent_file([])
assert len(bdi.subjects_list) == 2
assert len(bdi.descriptor_names) == 0
assert bdi.descriptor_values.shape == (2, 0)
assert len(bdi.hemis) == 1
def test_braindescriptors_parcellation_stats():
expected_subject2_testdata_dir = os.path.join(TEST_DATA_DIR, 'subject2')
if not os.path.isdir(expected_subject2_testdata_dir):
pytest.skip("Test data missing: e.g., directory '%s' does not exist. You can get all test data by running './develop/get_test_data_all.bash' in the repo root." % expected_subject2_testdata_dir)
subjects_list = ['subject1', 'subject2']
bdi = bd.BrainDescriptors(TEST_DATA_DIR, subjects_list)
bdi.add_parcellation_stats(['aparc', 'aparc.a2009s'])
bdi.add_segmentation_stats(['aseg'])
bdi.add_custom_measure_stats(['aparc'], ['area'])
bdi.add_curv_stats()
assert len(bdi.descriptor_names) == 3089
assert bdi.descriptor_values.shape == (2, 3089)
def run_desc():
#subjects_list = ['subject1', 'subject2']
#subjects_dir = os.path.join("tests", "test_data")
subjects_dir = os.path.join(os.getenv("HOME"), "data", "abide",
"structural")
#subjects_dir = os.path.join("/Volumes", "shared-1", "projects", "abide", "structural")
subjects_file = os.path.join(subjects_dir, 'subjects.txt')
subjects_list = brainload.nitools.read_subjects_file(subjects_file)
logging.basicConfig(level=logging.INFO)
bdi = bd.BrainDescriptors(subjects_dir, subjects_list)
bdi.add_parcellation_stats(['aparc', 'aparc.a2009s'])
bdi.add_segmentation_stats(['aseg'])
#bdi.add_custom_measure_stats(['aparc'], ['area'])
bdi.add_custom_measure_stats(['aparc', 'aparc.a2009s'], [
'area', 'area.pial', 'curv', 'curv.pial', 'jacobian_white', 'sulc',
'thickness', 'truncation', 'volume'
])
#bdi.report_descriptors()
bdi._check_for_duplicate_descriptor_names()
subjects_over_threshold, descriptors_over_threshold, nan_share_per_subject, nan_share_per_descriptor = bdi.check_for_NaNs(
)
do_plot_nans = False
if do_plot_nans:
plot_hist(nan_share_per_subject, "NaN share per subject")
plot_hist(nan_share_per_descriptor, "NaN share per descriptor")
data_output_file = "braindescriptors.csv"
subjects_output_file = "subjects.txt"
bdi.save(data_output_file, subjects_file=subjects_output_file)
logging.info(
"Saved values of %d descriptors for each of the %d subjects to file '%s'. Subject order for data written to file '%s'."
% (len(bdi.descriptor_names), len(
bdi.subjects_list), data_output_file, subjects_output_file))
