T417 Adding possibility of wavelength-dependant laser energy

.gitignore

@@ -157,3 +157,6 @@ dmypy.json
 # numpy files
 *npy
 /.mailmap
+
+# Data
+data/

docs/source/simpa.core.simulation_modules.acoustic_module.rst

@@ -0,0 +1,24 @@
+acoustic\_module
+=======================================================
+
+.. automodule:: simpa.core.simulation_modules.acoustic_module
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: simpa.core.simulation_modules.acoustic_module.acoustic_adapter_base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: simpa.core.simulation_modules.acoustic_module.acoustic_test_adapter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: simpa.core.simulation_modules.acoustic_module.k_wave_adapter
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/simpa.core.simulation_modules.optical_module.rst

@@ -0,0 +1,30 @@
+optical\_module
+======================================================
+
+.. automodule:: simpa.core.simulation_modules.optical_module
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+.. automodule:: simpa.core.simulation_modules.optical_module.mcx_adapter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: simpa.core.simulation_modules.optical_module.mcx_reflectance_adapter
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: simpa.core.simulation_modules.optical_module.optical_adapter_base
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: simpa.core.simulation_modules.optical_module.optical_test_adapter
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/simpa_examples.rst

@@ -4,15 +4,16 @@ simpa\_examples
 .. toctree::
    :maxdepth: 2
 
-   create_a_custom_digital_device_twin
-   create_custom_tissues
-   linear_unmixing
-   minimal_optical_simulation
-   minimal_optical_simulation_heterogeneous_tissue
-   minimal_optical_simulation_uniform_cube
-   msot_invision_simulation
-   optical_and_acoustic_simulation
-   perform_image_reconstruction
-   perform_iterative_qPAI_reconstruction
-   segmentation_loader
-   three_vs_two_dimensional_simulation_example
+   simpa_examples\__init__
+   simpa_examples\create_a_custom_digital_device_twin
+   simpa_examples\create_custom_tissues
+   simpa_examples\linear_unmixing
+   simpa_examples\minimal_optical_simulation
+   simpa_examples\minimal_optical_simulation_heterogeneous_tissue
+   simpa_examples\minimal_optical_simulation_uniform_cube
+   simpa_examples\msot_invision_simulation
+   simpa_examples\optical_and_acoustic_simulation
+   simpa_examples\perform_image_reconstruction
+   simpa_examples\perform_iterative_qPAI_reconstruction
+   simpa_examples\segmentation_loader
+   simpa_examples\three_vs_two_dimensional_simulation_example

docs/source/simpa_examples/__init__.rst

@@ -0,0 +1,7 @@
+simpa_examples\__init__
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\__init__.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/create_a_custom_digital_device_twin.rst

@@ -0,0 +1,7 @@
+simpa_examples\create_a_custom_digital_device_twin
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\create_a_custom_digital_device_twin.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/create_custom_tissues.rst

@@ -0,0 +1,7 @@
+simpa_examples\create_custom_tissues
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\create_custom_tissues.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/linear_unmixing.rst

@@ -0,0 +1,7 @@
+simpa_examples\linear_unmixing
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\linear_unmixing.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/minimal_optical_simulation.rst

@@ -0,0 +1,7 @@
+simpa_examples\minimal_optical_simulation
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\minimal_optical_simulation.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/minimal_optical_simulation_heterogeneous_tissue.rst

@@ -0,0 +1,7 @@
+simpa_examples\minimal_optical_simulation_heterogeneous_tissue
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\minimal_optical_simulation_heterogeneous_tissue.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/minimal_optical_simulation_uniform_cube.rst

@@ -0,0 +1,7 @@
+simpa_examples\minimal_optical_simulation_uniform_cube
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\minimal_optical_simulation_uniform_cube.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/msot_invision_simulation.rst

@@ -0,0 +1,7 @@
+simpa_examples\msot_invision_simulation
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\msot_invision_simulation.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/optical_and_acoustic_simulation.rst

@@ -0,0 +1,7 @@
+simpa_examples\optical_and_acoustic_simulation
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\optical_and_acoustic_simulation.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/perform_image_reconstruction.rst

@@ -0,0 +1,7 @@
+simpa_examples\perform_image_reconstruction
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\perform_image_reconstruction.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/perform_iterative_qPAI_reconstruction.rst

@@ -0,0 +1,7 @@
+simpa_examples\perform_iterative_qPAI_reconstruction
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\perform_iterative_qPAI_reconstruction.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/segmentation_loader.rst

@@ -0,0 +1,7 @@
+simpa_examples\segmentation_loader
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\segmentation_loader.py
+   :language: python
+   :lines: 1-
+

docs/source/simpa_examples/three_vs_two_dimensional_simulation_example.rst

@@ -0,0 +1,7 @@
+simpa_examples\three_vs_two_dimensional_simulation_example
+=========================================
+
+.. literalinclude:: ../../simpa_examples/simpa_examples\three_vs_two_dimensional_simulation_example.py
+   :language: python
+   :lines: 1-
+

simpa/core/simulation_modules/optical_module/optical_adapter_base.py

@@ -67,8 +67,8 @@ def run(self, device: Union[IlluminationGeometryBase, PhotoacousticDevice]) -> N
 
         file_path = self.global_settings[Tags.SIMPA_OUTPUT_FILE_PATH]
         wl = self.global_settings[Tags.WAVELENGTH]
-        wl_str = str(wl)
 
+        wl_str = str(wl)
         absorption = load_data_field(file_path, Tags.DATA_FIELD_ABSORPTION_PER_CM, wl_str)
         scattering = load_data_field(file_path, Tags.DATA_FIELD_SCATTERING_PER_CM, wl_str)
         anisotropy = load_data_field(file_path, Tags.DATA_FIELD_ANISOTROPY, wl_str)
@@ -92,23 +92,29 @@ def run(self, device: Union[IlluminationGeometryBase, PhotoacousticDevice]) -> N
             assert_array_well_defined(fluence, assume_non_negativity=True, array_name="fluence")
 
         if Tags.LASER_PULSE_ENERGY_IN_MILLIJOULE in self.component_settings:
+            laser_energies = self.component_settings[Tags.LASER_PULSE_ENERGY_IN_MILLIJOULE]
+
+            if type(laser_energies) in (list, range, tuple, np.ndarray):
+
+                list_laser_energies = list(laser_energies)
+                wls = self.global_settings[Tags.WAVELENGTHS]
+
+                if len(list_laser_energies) != len(wls):
+                    raise ValueError(
+                        "The wavelength dependant laser energies need to have compatible dimension \
+                        with the wavelengths.")
+                else:
+                    laser_energy = laser_energies[wls.index(wl)]
+
+            elif type(laser_energies) in (float, int, np.integer):
+                laser_energy = laser_energies
+
             units = Tags.UNITS_PRESSURE
             # Initial pressure should be given in units of Pascale
             conversion_factor = 1e6  # 1 J/cm^3 = 10^6 N/m^2 = 10^6 Pa
+            initial_pressure = (absorption * fluence * gruneisen_parameter * (laser_energy / 1000)
+                                * conversion_factor)
 
-            energy_setting = self.component_settings[Tags.LASER_PULSE_ENERGY_IN_MILLIJOULE]
-            if np.isscalar(energy_setting):
-                energy_mJ = float(energy_setting)
-            else:
-                energies = list(energy_setting)
-                wavelengths = self.global_settings[Tags.WAVELENGTHS]
-                if len(energies) != len(wavelengths):
-                    raise ValueError("Length of LASER_PULSE_ENERGY_IN_MILLIJOULE must be equal to number of wavelengths.")
-                idx = list(wavelengths).index(wl)
-                energy_mJ = float(energies[idx])
-
-            initial_pressure = (absorption * fluence * gruneisen_parameter *
-                                (energy_mJ / 1000.0) * conversion_factor)
         else:
             units = Tags.UNITS_ARBITRARY
             initial_pressure = absorption * fluence

simpa/utils/tags.py

@@ -374,7 +374,9 @@ class Tags:
     LASER_PULSE_ENERGY_IN_MILLIJOULE = ("laser_pulse_energy_in_millijoule", (int, np.integer, float, list,
                                                                              range, tuple, np.ndarray))
     """
-    Laser pulse energy used in the optical simulation. Can be an iterable if energy varies with wavelength.\n
+    Laser pulse energy used in the optical simulation. If it is considered wavelength dependant, should be
+    an iterable compatible with the size of the wavelength list. \n
+
     Usage: module optical_simulation_module
     """
 

simpa_examples/benchmarking/benchmarking_mean.md

@@ -0,0 +1,22 @@
+| Example                                                                                                         |   Spacing |   MEMORY_mean |   MEMORY_std |   TIME_mean |   TIME_std |
+|:----------------------------------------------------------------------------------------------------------------|----------:|--------------:|-------------:|------------:|-----------:|
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation                      |      0.2  |         nan   |          nan |     19107.2 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation                      |      0.25 |         nan   |          nan |      9383.2 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation_uniform_cube         |      0.2  |         nan   |          nan |     12850.5 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation_uniform_cube         |      0.25 |         nan   |          nan |      6496.2 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\optical_and_acoustic_simulation                 |      0.2  |         nan   |          nan |     60223.9 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\optical_and_acoustic_simulation                 |      0.25 |         nan   |          nan |     39334.8 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\segmentation_loader                             |      0.2  |         nan   |          nan |     11956.5 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\segmentation_loader                             |      0.25 |         nan   |          nan |      7739.1 |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\three_vs_two_dimensional_simulation_example     |      0.2  |         nan   |          nan |    172377   |        nan |
+| File: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\three_vs_two_dimensional_simulation_example     |      0.25 |         nan   |          nan |     85203.1 |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation                  |      0.2  |         419.1 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation                  |      0.25 |         224.5 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation_uniform_cube     |      0.2  |         -43.7 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\minimal_optical_simulation_uniform_cube     |      0.25 |          24.1 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\optical_and_acoustic_simulation             |      0.2  |           4.9 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\optical_and_acoustic_simulation             |      0.25 |         -15.5 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\segmentation_loader                         |      0.2  |         153.8 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\segmentation_loader                         |      0.25 |          85   |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\three_vs_two_dimensional_simulation_example |      0.2  |        -132.1 |          nan |       nan   |        nan |
+| Filename: C:\Users\jeremie.gillet\Desktop\T417\simpa\simpa_examples\three_vs_two_dimensional_simulation_example |      0.25 |         -29.8 |          nan |       nan   |        nan |