Default adapter settings

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
       types: [python]
       args:
         - --license-filepath
-        - license_header.txt        # defaults to: LICENSE.txt
+        - pre_commit_configs/license_header.txt        # defaults to: LICENSE.txt
 
 -   repo: https://github.com/jorisroovers/gitlint # Uses MIT License (MIT compatible)
     rev:  v0.19.1
@@ -36,6 +36,10 @@ repos:
       - id: markdown-link-check # checks if links in markdown files work
         exclude: docs/
         types: [markdown]
+        args: 
+           - -c
+           - pre_commit_configs/link-config.json
+        always_run: true
 
 # toggle comment to perform git config user email check. Note that you have to place the check-email.sh script in your .git/hooks/ folder
 # -   repo: local

pre_commit_configs/link-config.json

@@ -0,0 +1,7 @@
+{
+    "ignorePatterns": [
+        {
+            "pattern": "https://doi.org/10.1117/1.JBO.27.8.083010"
+        }
+    ]
+}

simpa/core/__init__.py

@@ -5,7 +5,7 @@
 
 from simpa.core.device_digital_twins import DigitalDeviceTwinBase
 from simpa.log import Logger
-from simpa.utils import Settings
+from simpa.utils import Settings, Tags, PathManager
 from simpa.utils.processing_device import get_processing_device
 
 class PipelineModule:
@@ -18,9 +18,31 @@ def __init__(self, global_settings: Settings):
          :type global_settings: Settings
         """
         self.logger = Logger()
-        self.global_settings = global_settings
+        self.global_settings = self.get_default_global_settings()
+        self.global_settings.update(global_settings) # add and if necessary overrides default global settings by user given settings
         self.torch_device = get_processing_device(self.global_settings)
 
+    def get_default_global_settings(self) -> Settings:
+        """Return the default global settings
+
+        :return: default global settings
+        :rtype: Settings
+        """
+        path_manager = PathManager()
+
+        default_global_settings = {
+            Tags.RANDOM_SEED: 4711,
+            Tags.VOLUME_NAME: "CompletePipelineExample_4711",
+            Tags.SIMULATION_PATH: path_manager.get_hdf5_file_save_path(),
+            Tags.GPU: True,
+            Tags.DO_FILE_COMPRESSION: True,
+            Tags.DO_IPASC_EXPORT: True,
+            Tags.CONTINUE_SIMULATION: False 
+        }
+
+        return Settings(default_global_settings)
+
+
     @abstractmethod
     def run(self, digital_device_twin: DigitalDeviceTwinBase):
         """

simpa/core/simulation.py

@@ -91,6 +91,7 @@ def simulate(simulation_pipeline: list, settings: Settings, digital_device_twin:
 
         for pipeline_element in simulation_pipeline:
             logger.debug(f"Running {type(pipeline_element)}")
+            pipeline_element.global_settings = settings
             pipeline_element.run(digital_device_twin)
 
         logger.debug(f"Running pipeline for wavelength {wavelength}nm... [Done]")

simpa/core/simulation_modules/__init__.py

@@ -19,13 +19,28 @@ def __init__(self, global_settings: Settings):
          :type global_settings: Settings
         """
         super(SimulationModule, self).__init__(global_settings=global_settings)
-        self.component_settings = self.load_component_settings()
+
+        self.component_settings = self.get_default_component_settings()
+        self.component_settings.update(self.get_user_set_component_settings()) # adds and if necessary overrides default component settings by user given settings
         if self.component_settings is None:
             raise ValueError("The component settings should not be None at this point")
 
     @abstractmethod
-    def load_component_settings(self) -> Settings:
+    def get_user_set_component_settings(self) -> Settings:
+        """
+        :return: Loads component settings corresponding to this simulation component set by the user
         """
-        :return: Loads component settings corresponding to this simulation component
+        pass
+
+    @abstractmethod
+    def get_default_component_settings(self) -> Settings:
+        """Return the default component settings corresponding to this simulation component
+
+        :return: default component settings of this component
+        :rtype: Settings
         """
         pass
+
+
+
+

simpa/core/simulation_modules/acoustic_forward_module/__init__.py

@@ -34,13 +34,13 @@ class AcousticForwardModelBaseAdapter(SimulationModule):
     def __init__(self, global_settings: Settings):
         super(AcousticForwardModelBaseAdapter, self).__init__(global_settings=global_settings)
 
-    def load_component_settings(self) -> Settings:
-        """Implements abstract method to serve acoustic settings as component settings
+    def get_user_set_component_settings(self) -> Settings:
+        """Implements abstract method to serve user set acoustic settings as component settings
 
         :return: Settings: acoustic component settings
         """
         return self.global_settings.get_acoustic_settings()
-
+        
     @abstractmethod
     def forward_model(self, detection_geometry) -> np.ndarray:
         """

simpa/core/simulation_modules/acoustic_forward_module/acoustic_forward_model_test_adapter.py

@@ -3,12 +3,20 @@
 # SPDX-License-Identifier: MIT
 
 import numpy as np
-from simpa.utils import Tags
+from simpa.utils import Tags, Settings
 from simpa.core.simulation_modules.acoustic_forward_module import AcousticForwardModelBaseAdapter
 
 
 class AcousticForwardModelTestAdapter(AcousticForwardModelBaseAdapter):
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default acoustic component settings 
+        """
+
+        default_settings = {}
+        return Settings(default_settings)      
+
     def forward_model(self, device) -> np.ndarray:
 
         if Tags.ACOUSTIC_SIMULATION_3D in self.component_settings \

simpa/core/simulation_modules/acoustic_forward_module/acoustic_forward_module_k_wave_adapter.py

@@ -66,6 +66,30 @@ class KWaveAdapter(AcousticForwardModelBaseAdapter):
 
     """
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default acoustic component settings 
+        """
+
+        path_manager = PathManager()
+
+        default_settings = {
+            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",
+            Tags.KWAVE_PROPERTY_PMLInside: False,
+            Tags.KWAVE_PROPERTY_PMLSize: [31, 32],
+            Tags.KWAVE_PROPERTY_PMLAlpha: 1.5,
+            Tags.KWAVE_PROPERTY_PlotPML: False,
+            Tags.RECORDMOVIE: False,
+            Tags.MOVIENAME: "visualization_log",
+            Tags.ACOUSTIC_LOG_SCALE: True
+        }
+
+        return Settings(default_settings)      
+
+
     def forward_model(self, detection_geometry: DetectionGeometryBase) -> np.ndarray:
         """
         Runs the acoustic forward model and performs reading parameters and values from an hdf5 file

simpa/core/simulation_modules/optical_simulation_module/__init__.py

@@ -30,12 +30,13 @@ def __init__(self, global_settings: Settings):
         self.nz = None
         self.temporary_output_files = []
 
-    def load_component_settings(self) -> Settings:
-        """Implements abstract method to serve optical settings as component settings
+    def get_user_set_component_settings(self) -> Settings:
+        """Implements abstract method to serve user set optical settings as component settings
 
         :return: Settings: optical component settings
         """
         return self.global_settings.get_optical_settings()
+
 
     @abstractmethod
     def forward_model(self,

simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py

@@ -4,7 +4,7 @@
 
 import numpy as np
 import subprocess
-from simpa.utils import Tags, Settings
+from simpa.utils import Tags, Settings, PathManager
 from simpa.core.simulation_modules.optical_simulation_module import OpticalForwardModuleBase
 from simpa.core.device_digital_twins.illumination_geometries import IlluminationGeometryBase
 import json
@@ -13,6 +13,7 @@
 from typing import List, Dict, Tuple
 
 
+
 class MCXAdapter(OpticalForwardModuleBase):
     """
     This class implements a bridge to the mcx framework to integrate mcx into SIMPA. This adapter only allows for
@@ -38,6 +39,22 @@ def __init__(self, global_settings: Settings):
         self.frames = None
         self.mcx_output_suffixes = {'mcx_volumetric_data_file': '.jnii'}
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default optical component settings 
+        """
+
+        path_manager = PathManager()
+
+        default_settings = {
+            Tags.MCX_ASSUMED_ANISOTROPY: 0.9,
+            Tags.OPTICAL_MODEL_BINARY_PATH: path_manager.get_mcx_binary_path(),
+            Tags.COMPUTE_DIFFUSE_REFLECTANCE: False,
+            Tags.COMPUTE_PHOTON_DIRECTION_AT_EXIT: False
+        }
+
+        return Settings(default_settings)      
+
     def forward_model(self,
                       absorption_cm: np.ndarray,
                       scattering_cm: np.ndarray,

simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py

@@ -7,7 +7,7 @@
 import os
 from typing import List, Tuple, Dict, Union
 
-from simpa.utils import Tags, Settings
+from simpa.utils import Tags, Settings, PathManager
 from simpa.core.simulation_modules.optical_simulation_module.optical_forward_model_mcx_adapter import MCXAdapter
 from simpa.core.device_digital_twins import IlluminationGeometryBase, PhotoacousticDevice
 
@@ -41,6 +41,22 @@ def __init__(self, global_settings: Settings):
         self.mcx_output_suffixes = {'mcx_volumetric_data_file': '.jnii',
                                     'mcx_photon_data_file': '_detp.jdat'}
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default optical component settings 
+        """
+
+        path_manager = PathManager()
+
+        default_settings = {
+            Tags.MCX_ASSUMED_ANISOTROPY: 0.9,
+            Tags.OPTICAL_MODEL_BINARY_PATH: path_manager.get_mcx_binary_path(),
+            Tags.COMPUTE_DIFFUSE_REFLECTANCE: True,
+            Tags.COMPUTE_PHOTON_DIRECTION_AT_EXIT: False
+        }
+
+        return Settings(default_settings)      
+
     def forward_model(self,
                       absorption_cm: np.ndarray,
                       scattering_cm: np.ndarray,

simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_test_adapter.py

@@ -3,14 +3,22 @@
 # SPDX-License-Identifier: MIT
 
 from simpa.core.simulation_modules.optical_simulation_module import OpticalForwardModuleBase
-from simpa import Tags
+from simpa import Tags, Settings
 
 
 class OpticalForwardModelTestAdapter(OpticalForwardModuleBase):
     """
     This Adapter was created for testing purposes and only
     """
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default optical component settings 
+        """
+
+        default_settings = {}
+        return Settings(default_settings)      
+
     def forward_model(self, absorption_cm, scattering_cm, anisotropy, illumination_geometry):
         results = {Tags.DATA_FIELD_FLUENCE: absorption_cm / ((1 - anisotropy) * scattering_cm)}
         return results

simpa/core/simulation_modules/reconstruction_module/__init__.py

@@ -26,8 +26,8 @@ class ReconstructionAdapterBase(SimulationModule):
     def __init__(self, global_settings: Settings):
         super(ReconstructionAdapterBase, self).__init__(global_settings=global_settings)
 
-    def load_component_settings(self) -> Settings:
-        """Implements abstract method to serve reconstruction settings as component settings
+    def get_user_set_component_settings(self) -> Settings:
+        """Implements abstract method to serve user set reconstruction settings as component settings
 
         :return: Settings: reconstruction component settings
         """

simpa/core/simulation_modules/reconstruction_module/reconstruction_module_delay_and_sum_adapter.py

@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
 
-from simpa.utils import Tags
+from simpa.utils import Tags, Settings
 from simpa.core.simulation_modules.reconstruction_module import ReconstructionAdapterBase
 import numpy as np
 import torch
@@ -14,6 +14,23 @@
 
 class DelayAndSumAdapter(ReconstructionAdapterBase):
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default reconstruction component settings 
+        """
+
+        default_settings = {
+            Tags.RECONSTRUCTION_PERFORM_BANDPASS_FILTERING: True,
+            Tags.TUKEY_WINDOW_ALPHA: 0.5,
+            Tags.BANDPASS_CUTOFF_LOWPASS_IN_HZ: int(8e6),
+            Tags.BANDPASS_CUTOFF_HIGHPASS_IN_HZ: int(0.1e6),
+            Tags.RECONSTRUCTION_BMODE_METHOD: Tags.RECONSTRUCTION_BMODE_METHOD_HILBERT_TRANSFORM,
+            Tags.RECONSTRUCTION_APODIZATION_METHOD: Tags.RECONSTRUCTION_APODIZATION_BOX,
+            Tags.RECONSTRUCTION_MODE: Tags.RECONSTRUCTION_MODE_PRESSURE,
+        }
+
+        return Settings(default_settings) 
+
     def reconstruction_algorithm(self, time_series_sensor_data, detection_geometry: DetectionGeometryBase):
         """
         Applies the Delay and Sum beamforming algorithm [1] to the time series sensor data (2D numpy array where the

simpa/core/simulation_modules/reconstruction_module/reconstruction_module_delay_multiply_and_sum_adapter.py

@@ -2,7 +2,7 @@
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
 
-from simpa.utils import Tags
+from simpa.utils import Tags, Settings
 from simpa.core.simulation_modules.reconstruction_module import ReconstructionAdapterBase
 from simpa.core.device_digital_twins import DetectionGeometryBase
 import numpy as np
@@ -14,6 +14,23 @@
 
 class DelayMultiplyAndSumAdapter(ReconstructionAdapterBase):
 
+    def get_default_component_settings(self) -> Settings:
+        """
+        :return: Loads default reconstruction component settings 
+        """
+
+        default_settings = {
+            Tags.RECONSTRUCTION_PERFORM_BANDPASS_FILTERING: True,
+            Tags.TUKEY_WINDOW_ALPHA: 0.5,
+            Tags.BANDPASS_CUTOFF_LOWPASS_IN_HZ: int(8e6),
+            Tags.BANDPASS_CUTOFF_HIGHPASS_IN_HZ: int(0.1e6),
+            Tags.RECONSTRUCTION_BMODE_METHOD: Tags.RECONSTRUCTION_BMODE_METHOD_HILBERT_TRANSFORM,
+            Tags.RECONSTRUCTION_APODIZATION_METHOD: Tags.RECONSTRUCTION_APODIZATION_BOX,
+            Tags.RECONSTRUCTION_MODE: Tags.RECONSTRUCTION_MODE_PRESSURE,
+        }
+
+        return Settings(default_settings)      
+
     def reconstruction_algorithm(self, time_series_sensor_data, detection_geometry: DetectionGeometryBase):
         """
         Applies the Delay Multiply and Sum beamforming algorithm [1] to the time series sensor data (2D numpy array where the