def test_do_calculation_calculation_process(self, tmpdir, data_test_dir):
plan = self.create_calculation_plan3()
file_path = os.path.join(data_test_dir, "stack1_components",
"stack1_component1.tif")
calc = Calculation(
[file_path],
base_prefix=data_test_dir,
result_prefix=data_test_dir,
measurement_file_path=os.path.join(tmpdir, "test3.xlsx"),
sheet_name="Sheet1",
calculation_plan=plan,
voxel_size=(1, 1, 1),
)
calc_process = CalculationProcess()
res = calc_process.do_calculation(FileCalculation(file_path, calc))
assert isinstance(res, list)
assert isinstance(res[0], ResponseData)
def do_calculation(file_info: Tuple[int, str],
calculation: BaseCalculation) -> WrappedResult:
"""
Main function which will be used for run calculation.
It create :py:class:`.CalculationProcess` and call it method
:py:meth:`.CalculationProcess.do_calculation`
:param file_info: index and path to file which should be processed
:param calculation: calculation description
"""
calc = CalculationProcess()
index, file_path = file_info
try:
return index, calc.do_calculation(
FileCalculation(file_path, calculation))
except Exception as e:
# traceback.print_exc()
return index, [prepare_error_data(e)]
def do_calculation(file_info: Tuple[int, str],
calculation: BaseCalculation) -> WrappedResult:
"""
Main function which will be used for run calculation.
It create :py:class:`.CalculationProcess` and call it method
:py:meth:`.CalculationProcess.do_calculation`
:param file_info: index and path to file which should be processed
:param calculation: calculation description
"""
SimpleITK.ProcessObject_SetGlobalDefaultNumberOfThreads(1)
calc = CalculationProcess()
index, file_path = file_info
try:
return index, calc.do_calculation(
FileCalculation(file_path, calculation))
except Exception as e:
return index, [prepare_error_data(e)]
def test_do_calculation_save(self, tmpdir, data_test_dir, file_name,
root_type, save_method: SaveBase):
save_desc = Save("_test", "", save_method.get_name(),
save_method.get_short_name(),
save_method.get_default_values())
plan = self.create_simple_plan(root_type, save_desc)
file_path = os.path.join(data_test_dir, file_name)
calc = Calculation(
[file_path],
base_prefix=os.path.dirname(file_path),
result_prefix=tmpdir,
measurement_file_path=os.path.join(tmpdir, "test3.xlsx"),
sheet_name="Sheet1",
calculation_plan=plan,
voxel_size=(1, 1, 1),
)
calc_process = CalculationProcess()
res = calc_process.do_calculation(FileCalculation(file_path, calc))
assert isinstance(res, list)
assert isinstance(res[0], ResponseData)
def test_full_pipeline_base(self, tmpdir, data_test_dir, monkeypatch):
monkeypatch.setattr(batch_backend, "CalculationProcess",
MockCalculationProcess)
plan = self.create_calculation_plan()
file_pattern = os.path.join(data_test_dir, "stack1_components",
"stack1_component*[0-9].tif")
file_paths = sorted(glob(file_pattern))
assert os.path.basename(file_paths[0]) == "stack1_component1.tif"
calc = Calculation(
file_paths,
base_prefix=data_test_dir,
result_prefix=data_test_dir,
measurement_file_path=os.path.join(tmpdir, "test.xlsx"),
sheet_name="Sheet1",
calculation_plan=plan,
voxel_size=(1, 1, 1),
)
calc_process = CalculationProcess()
for file_path in file_paths:
res = calc_process.do_calculation(FileCalculation(file_path, calc))
assert isinstance(res, list)
assert isinstance(res[0], ResponseData)