Update absorption and scattering test and ran pre-commit hooks

simpa/__init__.py

@@ -10,7 +10,7 @@
     __version__ = version("simpa")
 except PackageNotFoundError:
     __version__ = "unknown version"
-    
+
 from .core.simulation_modules.volume_creation_module.volume_creation_module_model_based_adapter import \
     ModelBasedVolumeCreationAdapter
 from .core.simulation_modules.volume_creation_module.volume_creation_module_segmentation_based_adapter import \

simpa/core/simulation.py

@@ -56,7 +56,7 @@ def simulate(simulation_pipeline: list, settings: Settings, digital_device_twin:
         simpa_output_path = path + settings[Tags.VOLUME_NAME]
 
     settings[Tags.SIMPA_OUTPUT_PATH] = simpa_output_path + ".hdf5"
-    
+
     simpa_output[Tags.SIMPA_VERSION] = __version__
     simpa_output[Tags.SETTINGS] = settings
     simpa_output[Tags.DIGITAL_DEVICE] = digital_device_twin

simpa/core/simulation_modules/reconstruction_module/reconstruction_module_time_reversal_adapter.py

@@ -170,7 +170,7 @@ def reconstruction_algorithm(self, time_series_sensor_data, detection_geometry):
 
         matlab_binary_path = self.component_settings[Tags.ACOUSTIC_MODEL_BINARY_PATH]
         cmd = generate_matlab_cmd(matlab_binary_path, time_reversal_script, acoustic_path, self.get_additional_flags())
-        
+
         cur_dir = os.getcwd()
         os.chdir(self.global_settings[Tags.SIMULATION_PATH])
         self.logger.info(cmd)

simpa/utils/matlab.py

@@ -21,7 +21,7 @@ def generate_matlab_cmd(matlab_binary_path: str, simulation_script_path: str, da
     :return: list of command parts
     :rtype: List[str]
     """
- 
+
     # get path of calling script to add to matlab path
     base_script_path = os.path.dirname(os.path.abspath(inspect.stack()[1].filename))
     # ensure data path is an absolute path

simpa_examples/minimal_optical_simulation.py

@@ -152,7 +152,7 @@ def __init__(self):
 
     device = ExampleDeviceSlitIlluminationLinearDetector()
 
-    sp.simulate(pipeline, settings, device)
+    sp.simulate(pipeline, settings, device, logging_level=Tags.LOGGER_ERROR)
 
     if Tags.WAVELENGTH in settings:
         WAVELENGTH = settings[Tags.WAVELENGTH]

simpa_examples/optical_and_acoustic_simulation.py

@@ -93,7 +93,7 @@ def create_example_tissue():
         Tags.DIM_VOLUME_Y_MM: VOLUME_PLANAR_DIM_IN_MM,
         Tags.VOLUME_CREATOR: Tags.VOLUME_CREATOR_VERSATILE,
         Tags.GPU: True,
-        Tags.WAVELENGTHS: [700, 800],
+        Tags.WAVELENGTHS: [700],
         Tags.DO_FILE_COMPRESSION: True,
         Tags.DO_IPASC_EXPORT: True
     }
@@ -115,7 +115,7 @@ def create_example_tissue():
     })
 
     settings.set_acoustic_settings({
-        Tags.ACOUSTIC_SIMULATION_3D: False,
+        # Tags.ACOUSTIC_SIMULATION_3D: False,
         Tags.ACOUSTIC_MODEL_BINARY_PATH: path_manager.get_matlab_binary_path(),
         Tags.KWAVE_PROPERTY_ALPHA_POWER: 0.00,
         Tags.KWAVE_PROPERTY_SENSOR_RECORD: "p",

simpa_tests/automatic_tests/test_additional_flags.py

@@ -1,24 +1,30 @@
+# SPDX-FileCopyrightText: 2021 Division of Intelligent Medical Systems, DKFZ
+# SPDX-FileCopyrightText: 2021 Janek Groehl
+# SPDX-License-Identifier: MIT
+
 import unittest
 import numpy as np
 
 from simpa import MCXAdapterReflectance, MCXAdapter, KWaveAdapter, TimeReversalAdapter, Tags, Settings
 from simpa.utils.matlab import generate_matlab_cmd
 
+
 class TestAdditionalFlags(unittest.TestCase):
     def setUp(self) -> None:
         self.additional_flags = ('-l', '-a')
         self.settings = Settings()
-       
+
     def test_get_cmd_mcx_reflectance_adapter(self):
         self.settings.set_optical_settings({
             Tags.OPTICAL_MODEL_BINARY_PATH: '.',
             Tags.ADDITIONAL_FLAGS: self.additional_flags
         })
-        mcx_reflectance_adapter =  MCXAdapterReflectance(global_settings=self.settings)
+        mcx_reflectance_adapter = MCXAdapterReflectance(global_settings=self.settings)
         cmd = mcx_reflectance_adapter.get_command()
         for flag in self.additional_flags:
-            self.assertIn(flag, cmd, f"{flag} was not in command returned by mcx reflectance adapter but was defined as additional flag")
-
+            self.assertIn(
+                flag, cmd, f"{flag} was not in command returned by mcx reflectance adapter but was defined as additional flag")
+
     def test_get_cmd_mcx_adapter(self):
         self.settings.set_optical_settings({
             Tags.OPTICAL_MODEL_BINARY_PATH: '.',
@@ -27,27 +33,30 @@ def test_get_cmd_mcx_adapter(self):
         mcx_adapter = MCXAdapter(global_settings=self.settings)
         cmd = mcx_adapter.get_command()
         for flag in self.additional_flags:
-            self.assertIn(flag, cmd, f"{flag} was not in command returned by mcx adapter but was defined as additional flag")
-
+            self.assertIn(
+                flag, cmd, f"{flag} was not in command returned by mcx adapter but was defined as additional flag")
+
     def test_get_cmd_kwave_adapter(self):
         self.settings.set_acoustic_settings({
             Tags.ADDITIONAL_FLAGS: self.additional_flags
         })
         kwave_adapter = KWaveAdapter(global_settings=self.settings)
         cmd = generate_matlab_cmd("./matlab.exe", "simulate_2D.m", "my_hdf5.mat", kwave_adapter.get_additional_flags())
         for flag in self.additional_flags:
-            self.assertIn(flag, cmd, f"{flag} was not in command returned by kwave adapter but was defined as additional flag")
+            self.assertIn(
+                flag, cmd, f"{flag} was not in command returned by kwave adapter but was defined as additional flag")
 
     def test_get_cmd_time_reversal_adapter(self):
         self.settings.set_reconstruction_settings({
             Tags.ADDITIONAL_FLAGS: self.additional_flags
         })
         time_reversal_adapter = TimeReversalAdapter(global_settings=self.settings)
-        cmd = generate_matlab_cmd("./matlab.exe", "time_reversal_2D.m", "my_hdf5.mat", time_reversal_adapter.get_additional_flags())
+        cmd = generate_matlab_cmd("./matlab.exe", "time_reversal_2D.m", "my_hdf5.mat",
+                                  time_reversal_adapter.get_additional_flags())
         for flag in self.additional_flags:
-            self.assertIn(flag, cmd, f"{flag} was not in command returned by time reversal adapter but was defined as additional flag")            
-
-    
+            self.assertIn(
+                flag, cmd, f"{flag} was not in command returned by time reversal adapter but was defined as additional flag")
+
 
 if __name__ == '__main__':
-    unittest.main()
+    unittest.main()

simpa_tests/manual_tests/digital_device_twins/VisualiseDevices.py

@@ -35,6 +35,7 @@ def visualise_result(self, show_figure_on_screen=True, save_path=None):
         sp.visualise_device(sp.RSOMExplorerP50(device_position_mm=np.asarray([50, 10, 0])),
                             figure_save_path[2])
 
+
 if __name__ == "__main__":
     test = DeviceVisualisationTest()
     test.run_test(show_figure_on_screen=False)

simpa_tests/manual_tests/executables/MATLABAdditionalFlags.py

@@ -34,7 +34,7 @@ def setup(self):
         """
 
         path_manager = PathManager()
-        
+
         self.settings = Settings({
             Tags.WAVELENGTHS: [800],
             Tags.WAVELENGTH: 800,
@@ -79,12 +79,12 @@ def setup(self):
                                                                          0]))
         self.device.add_illumination_geometry(PencilBeamIlluminationGeometry())
         self.device.set_detection_geometry(LinearArrayDetectionGeometry(device_position_mm=self.device.device_position_mm,
-                                                              pitch_mm=0.25,
-                                                              number_detector_elements=100,
-                                                              field_of_view_extent_mm=np.asarray([-15, 15, 0, 0, 0, 20])))
+                                                                        pitch_mm=0.25,
+                                                                        number_detector_elements=100,
+                                                                        field_of_view_extent_mm=np.asarray([-15, 15, 0, 0, 0, 20])))
 
         output_name = f'{os.path.join(self.settings[Tags.SIMULATION_PATH], self.settings[Tags.VOLUME_NAME])}'
-        self.output_file_name = f'{output_name}.log' 
+        self.output_file_name = f'{output_name}.log'
 
     def run_simulation(self):
         # run pipeline including volume creation and optical mcx simulation and acoustic matlab kwave simulation
@@ -100,36 +100,38 @@ def test_execution_of_additional_flag(self):
 
         :raises FileNotFoundError: if log file does not exist at expected location
         """
-        
-        # perform cleaning before test 
+
+        # perform cleaning before test
         if os.path.exists(self.output_file_name):
             os.remove(self.output_file_name)
-        
+
         # run simulation
         self.settings.get_acoustic_settings()[Tags.ADDITIONAL_FLAGS] = ['-logfile', self.output_file_name]
         self.run_simulation()
 
         # checking if file exists afterwards
         if not os.path.exists(self.output_file_name):
             raise FileNotFoundError(f"Log file wasn't created at expected path {self.output_file_name}")
-        
+
     def test_if_last_flag_is_used(self):
         """Tests if log file is created with correct last given name by setting multiple additional parameters
 
         :raises FileNotFoundError: if correct log file does not exist at expected location
         """
-        
+
         # perform cleaning before test
         if os.path.exists(self.output_file_name):
             os.remove(self.output_file_name)
-        
+
         # run simulation
-        self.settings.get_acoustic_settings()[Tags.ADDITIONAL_FLAGS] = ['-logfile', 'temp_name', '-logfile', self.output_file_name]
+        self.settings.get_acoustic_settings()[Tags.ADDITIONAL_FLAGS] = [
+            '-logfile', 'temp_name', '-logfile', self.output_file_name]
         self.run_simulation()
 
         # checking if file exists afterwards
         if not os.path.exists(self.output_file_name):
-            raise FileNotFoundError(f"Log file wasn't created with correct last given name at expected path {self.output_file_name}")
+            raise FileNotFoundError(
+                f"Log file wasn't created with correct last given name at expected path {self.output_file_name}")
 
     def perform_test(self):
         """
@@ -139,8 +141,9 @@ def perform_test(self):
         self.test_if_last_flag_is_used()
 
     def visualise_result(self, show_figure_on_screen=True, save_path=None):
-        pass # no figures are created that could be visualized
-
+        pass  # no figures are created that could be visualized
+
+
 if __name__ == '__main__':
     test = MATLABAdditionalFlags()
     test.run_test(show_figure_on_screen=False)

simpa_tests/manual_tests/executables/MCXAdditionalFlags.py

@@ -31,7 +31,7 @@ def setup(self):
         """
 
         path_manager = PathManager()
-        
+
         self.settings = Settings({
             Tags.WAVELENGTHS: [800],
             Tags.WAVELENGTH: 800,
@@ -63,7 +63,7 @@ def setup(self):
         self.device.add_illumination_geometry(PencilBeamIlluminationGeometry())
 
         self.output_name = f'{os.path.join(self.settings[Tags.SIMULATION_PATH], self.settings[Tags.VOLUME_NAME])}_output'
-        self.output_file_name = f'{self.output_name}.log' 
+        self.output_file_name = f'{self.output_name}.log'
 
     def run_simulation(self):
         # run pipeline including volume creation and optical mcx simulation
@@ -78,38 +78,39 @@ def test_execution_of_additional_flag(self):
 
         :raises FileNotFoundError: if log file does not exist at expected location
         """
-        
-        # perform cleaning before test 
+
+        # perform cleaning before test
         if os.path.exists(self. output_file_name):
             os.remove(self.output_file_name)
-        
+
         # run simulation
         self.settings.get_optical_settings()[Tags.ADDITIONAL_FLAGS] = ['-l', 1, '-s', self.output_name]
         self.run_simulation()
 
         # checking if file exists afterwards
         if not os.path.exists(self.output_file_name):
             raise FileNotFoundError(f"Log file wasn't created at expected path {self.output_file_name}")
-        
+
     def test_if_last_flag_is_used(self):
         """Tests if log file is created with correct last given name by setting multiple additional parameters
 
         :raises FileNotFoundError: if correct log file does not exist at expected location
         """
         output_name = f'{os.path.join(self.settings[Tags.SIMULATION_PATH], self.settings[Tags.VOLUME_NAME])}_output'
-        output_file_name = f'{output_name}.log' 
+        output_file_name = f'{output_name}.log'
 
-        # perform cleaning before test 
+        # perform cleaning before test
         if os.path.exists(output_file_name):
             os.remove(output_file_name)
-        
+
         # run simulation
         self.settings.get_optical_settings()[Tags.ADDITIONAL_FLAGS] = ['-l', 1, '-s', 'temp_name',  '-s', output_name]
         self.run_simulation()
 
         # checking if file exists afterwards
         if not os.path.exists(output_file_name):
-            raise FileNotFoundError(f"Log file wasn't created with correct last given name at expected path {output_file_name}")
+            raise FileNotFoundError(
+                f"Log file wasn't created with correct last given name at expected path {output_file_name}")
 
     def perform_test(self):
         """
@@ -119,8 +120,9 @@ def perform_test(self):
         self.test_if_last_flag_is_used()
 
     def visualise_result(self, show_figure_on_screen=True, save_path=None):
-        pass # no figures are created that could be visualized
-
+        pass  # no figures are created that could be visualized
+
+
 if __name__ == '__main__':
     test = MCXAdditionalFlags()
     test.run_test(show_figure_on_screen=False)