def test_load_nifti_multiple_echoes(self, monkeypatch):
"""
Assert passes with correct data for multiple echoes
:return:
"""
if self.tmp_path.exists():
shutil.rmtree(self.data_path_volume)
monkeypatch.setattr('sys.stdin', StringIO('0\n'))
niftis, info, json_info = load_nifti(self.tmp_path)
assert (len(info) == 2), "Wrong number od info data 1"
assert (len(json_info) == 2), "Wrong number of JSON data 1"
self._json_phase['EchoNumber'] = 1
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)), \
"JSON file is not correctly loaded for first JSON1"
self._json_phase['EchoNumber'] = 2
assert (json.dumps(json_info[1], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)), \
"JSON file is not correctly loaded for second JSON 1"
assert (niftis.shape == (3, 3, 3, 2,
1)), "Wrong shape for the Nifti output data 1"
monkeypatch.setattr('sys.stdin', StringIO('1\n'))
niftis, info, json_info = load_nifti(self.tmp_path)
assert (len(info) == 2), "Wrong number of info data 2"
assert (len(json_info) == 2), "Wrong number of JSON data 2"
self._json_phase['EchoNumber'] = 1
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)), \
"JSON file is not correctly loaded for first JSON 2"
self._json_phase['EchoNumber'] = 2
assert (json.dumps(json_info[1], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)), \
"JSON file is not correctly loaded for second JSON 2"
assert (niftis.shape == (3, 3, 3, 2,
1)), "Wrong shape for the Nifti output data 2"
def test_load_nifti_modality_check(self, monkeypatch):
"""
Assert passes with correct data for multiple echoes
:return:
"""
if self.data_path_2.exists():
shutil.rmtree(self.data_path_2)
if self.data_path_volume.exists():
shutil.rmtree(self.data_path_volume)
os.remove(os.path.join(self.data_path, "dummy2.nii"))
os.remove(os.path.join(self.data_path, "dummy2.json"))
dummy_data = nib.nifti1.Nifti1Image(dataobj=self._data,
affine=self._aff)
nib.save(dummy_data, os.path.join(self.data_path, 'dummy2.nii'))
with open(os.path.join(self.data_path, 'dummy2.json'),
'w') as json_file:
json.dump(self._json_mag, json_file)
niftis, info, json_info = load_nifti(self.data_path)
assert (len(info) == 1), "Wrong number od info data 1"
assert (len(json_info) == 1), "Wrong number of JSON data 1"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)), \
"JSON file is not correctly loaded for first JSON1"
assert (niftis.shape == (3, 3, 3, 1,
1)), "Wrong shape for the Nifti output data 1"
niftis, info, json_info = load_nifti(self.data_path, "magnitude")
assert (len(info) == 1), "Wrong number of info data 2"
assert (len(json_info) == 1), "Wrong number of JSON data 2"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_mag, sort_keys=True)), \
"JSON file is not correctly loaded for first JSON 2"
assert (niftis.shape == (3, 3, 3, 1,
1)), "Wrong shape for the Nifti output data 2"
def test_load_nifti_no_folder_fail(self):
"""
Assert fails without existing path
:return:
"""
with pytest.raises(RuntimeError, match="Not an existing NIFTI path"):
load_nifti("dummy")
def test_load_nifti_json_missing_fail(self):
"""
Assert fails if json missing
:return:
"""
os.remove(os.path.join(self.data_path, "dummy.json"))
with pytest.raises(OSError, match="Missing json file"):
load_nifti(self.data_path)
def test_load_nifti_mix_file_types_fail(self):
"""
Assert fails if folder and files in path
:return:
"""
with pytest.raises(RuntimeError,
match="Directories and files in input path"):
load_nifti(self.toolbox_path)
def test_load_nifti_mix_file_types_fail(self):
"""
Assert fails if folder and files in path
:return:
"""
try:
load_nifti(self.toolbox_path)
except:
return 0
assert False, "Did not fail with folder and files in the same path"
def test_load_nifti_no_folder_fail(self):
"""
Assert fails without existing path
:return:
"""
try:
load_nifti("dummy")
except RuntimeError:
return 0
assert False, "Did not fail if no valid path given"
def test_load_nifti_json_missing_fail(self):
"""
Assert fails if json missing
:return:
"""
os.remove(os.path.join(self.data_path, "dummy.json"))
try:
load_nifti(self.data_path)
except ValueError:
return 0
assert (False), "Did not fail with missing JSON file"
def test_load_nifti_quit(self, monkeypatch):
"""
Assert q quits loading with return 0
:return:
"""
monkeypatch.setattr('sys.stdin', StringIO('q\n'))
ret = load_nifti(self.tmp_path)
assert (ret == 0), "Should have returned 0 for quit input"
def test_load_nifti_multiple_run(self, monkeypatch):
"""
Assert data is correctly separated between runs
:return:
"""
if self.data_path_2.exists():
shutil.rmtree(self.data_path_2)
if self.data_path_volume.exists():
shutil.rmtree(self.data_path_volume)
os.remove(os.path.join(self.data_path, "dummy2.nii"))
os.remove(os.path.join(self.data_path, "dummy2.json"))
dummy_data = nib.nifti1.Nifti1Image(dataobj=self._data,
affine=self._aff)
nib.save(dummy_data, os.path.join(self.data_path, 'dummy2.nii'))
with open(os.path.join(self.data_path, 'dummy2.json'),
'w') as json_file:
self._json_phase['AcquisitionNumber'] = 2
json.dump(self._json_phase, json_file)
monkeypatch.setattr('sys.stdin', StringIO('1\n'))
niftis, info, json_info = load_nifti(self.data_path)
self._json_phase['AcquisitionNumber'] = 1
assert (len(info) == 1), "Wrong number od info data"
assert (len(json_info) == 1), "Wrong number of JSON data"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(
self._json_phase,
sort_keys=True)), "JSON file is not correctly loaded"
assert (niftis.shape == (3, 3, 3, 1,
1)), "Wrong shape for the Nifti output data"
monkeypatch.setattr('sys.stdin', StringIO('2\n'))
niftis, info, json_info = load_nifti(self.data_path)
self._json_phase['AcquisitionNumber'] = 2
assert (len(info) == 1), "Wrong number od info data"
assert (len(json_info) == 1), "Wrong number of JSON data"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(
self._json_phase,
sort_keys=True)), "JSON file is not correctly loaded"
assert (niftis.shape == (3, 3, 3, 1,
1)), "Wrong shape for the Nifti output data"
self._json_phase['AcquisitionNumber'] = 1
def test_load_nifti_volume(self):
"""
Assert data containing volume is correctly parsed
:return:
"""
if self.data_path_2.exists():
shutil.rmtree(self.data_path_2)
if self.data_path.exists():
shutil.rmtree(self.data_path)
niftis, info, json_info = load_nifti(self.data_path_volume)
assert (len(info) == 1), "Wrong number of info data"
assert (len(json_info) == 1), "Wrong number of JSON data"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)),\
"JSON file is not correctly loaded"
assert (niftis.shape == (3, 3, 3, 1,
2)), "Wrong shape for the Nifti output data"
def test_load_nifti_folders(self, monkeypatch):
"""
Assert that pass if path contains only folders
:return:
"""
if self.data_path_2.exists():
shutil.rmtree(self.data_path_2)
os.remove(os.path.join(self.data_path, "dummy2.nii"))
os.remove(os.path.join(self.data_path, "dummy2.json"))
monkeypatch.setattr('sys.stdin', StringIO('0\n'))
niftis, info, json_info = load_nifti(self.tmp_path)
assert (len(info) == 1), "Wrong number od info data"
assert (len(json_info) == 1), "Wrong number of JSON data"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)),\
"JSON file is not correctly loaded"
assert (niftis.shape == (3, 3, 3, 1,
1)), "Wrong shape for the Nifti output data"
def test_load_nifti_files(self):
"""
Assert that pass if path contains only files
:return:
"""
if self.data_path_2.exists():
shutil.rmtree(self.data_path_2)
if self.data_path_volume.exists():
shutil.rmtree(self.data_path_volume)
os.remove(os.path.join(self.data_path, "dummy2.nii"))
os.remove(os.path.join(self.data_path, "dummy2.json"))
niftis, info, json_info = load_nifti(self.data_path)
assert (len(info) == 1), "Wrong number of info data"
assert (len(json_info) == 1), "Wrong number of JSON data"
assert (json.dumps(json_info[0], sort_keys=True) == json.dumps(self._json_phase, sort_keys=True)),\
"JSON file is not correctly loaded"
assert (niftis.shape == (3, 3, 3, 1,
1)), "Wrong shape for the Nifti output data"
