From ba6f4406cc752992f13cb54fa9d01b185c4f5119 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Mon, 25 Sep 2023 08:58:45 +0200
Subject: [PATCH 01/24] Specify mc2 output file format for mcx

- resolves #245
---
 .../optical_forward_model_mcx_adapter.py                       | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
index 11aabb75..0e922c95 100644
--- a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
+++ b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
@@ -182,6 +182,9 @@ def get_command(self) -> List:
         # use 'C' order array format for binary input file
         cmd.append("-a")
         cmd.append("1")
+        # use mc2 binary output file format
+        cmd.append("-F")
+        cmd.append("mc2")
         return cmd
 
     @staticmethod

From 09569e968b04468950319d5878620969a45716e8 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Thu, 28 Sep 2023 14:13:43 +0200
Subject: [PATCH 02/24] Use gpu for noise generation if available

- `assert_array_well_defined` now accepts array or tensor
  - if the tensor is already on the gpu the assertions will also be done on the gpu
- increase number of noise samples in tests to make the statistical tests more robust
- convert final arrays back to float64 to maintain existing data format
  - these conversions can be removed when the simpy array datatype is changed to float32
---
 .pre-commit-config.yaml                       |  6 ++---
 simpa/core/processing_components/__init__.py  |  2 ++
 .../monospectral/noise/gamma_noise.py         | 15 +++++++----
 .../monospectral/noise/gaussian_noise.py      | 15 +++++++----
 .../monospectral/noise/poisson_noise.py       | 14 +++++++----
 .../noise/salt_and_pepper_noise.py            | 25 ++++++++++---------
 .../monospectral/noise/uniform_noise.py       | 13 +++++++---
 .../quality_assurance/data_sanity_testing.py  | 15 ++++++-----
 .../automatic_tests/test_noise_models.py      |  8 +++---
 9 files changed, 70 insertions(+), 43 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 81292682..529ef16a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
     -   id: check-added-large-files # prevents adding large files, above 500kB
 
 -   repo: https://github.com/pre-commit/mirrors-autopep8 # Uses MIT-License (MIT compatible) 
-    rev: v2.0.2  # Use the sha / tag you want to point at
+    rev: v2.0.4  # Use the sha / tag you want to point at
     hooks:
     -   id: autopep8 # formats code according to PEP8 standard. Lets commit fail if it needs to reformat code. Config for autopep8 is done in myproject.toml
 
@@ -17,7 +17,7 @@ repos:
       - id: validate-cff # validates cff citation files
 
 - repo: https://github.com/Lucas-C/pre-commit-hooks # Uses MIT License (MIT compatible)
-  rev: v1.5.1
+  rev: v1.5.4
   hooks:
     - id: insert-license    # Checks if the license header specified at license_header.txt is added in the first lines of each python file. If not, it suggests to insert them.
       types: [python]
@@ -31,7 +31,7 @@ repos:
     -   id: gitlint
 
 -   repo: https://github.com/tcort/markdown-link-check # Uses ISC-License (MIT compatible) 
-    rev: v3.10.3
+    rev: v3.11.2
     hooks:
       - id: markdown-link-check # checks if links in markdown files work
         exclude: docs/
diff --git a/simpa/core/processing_components/__init__.py b/simpa/core/processing_components/__init__.py
index ff831e5e..8c27b88c 100644
--- a/simpa/core/processing_components/__init__.py
+++ b/simpa/core/processing_components/__init__.py
@@ -4,6 +4,7 @@
 
 from abc import ABC
 from simpa.core import SimulationModule
+from simpa.utils.processing_device import get_processing_device
 
 
 class ProcessingComponent(SimulationModule, ABC):
@@ -19,3 +20,4 @@ def __init__(self, global_settings, component_settings_key: str):
         """
         super(ProcessingComponent, self).__init__(global_settings=global_settings)
         self.component_settings = global_settings[component_settings_key]
+        self.torch_device = get_processing_device(global_settings)
diff --git a/simpa/core/processing_components/monospectral/noise/gamma_noise.py b/simpa/core/processing_components/monospectral/noise/gamma_noise.py
index f8608cd8..011ddffa 100644
--- a/simpa/core/processing_components/monospectral/noise/gamma_noise.py
+++ b/simpa/core/processing_components/monospectral/noise/gamma_noise.py
@@ -3,6 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 import numpy as np
+import torch
 
 from simpa.core.processing_components import ProcessingComponent
 from simpa.io_handling import load_data_field, save_data_field
@@ -12,7 +13,7 @@
 
 class GammaNoise(ProcessingComponent):
     """
-    Applies Gaussian noise to the defined data field.
+    Applies Gamma noise to the defined data field.
     The noise will be applied to all wavelengths.
 
     Component Settings::
@@ -51,15 +52,19 @@ def run(self, device):
 
         wavelength = self.global_settings[Tags.WAVELENGTH]
         data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        data_tensor = torch.as_tensor(data_array, dtype=torch.float32, device=self.torch_device)
+        dist = torch.distributions.gamma.Gamma(torch.tensor(shape, dtype=torch.float32, device=self.torch_device),
+                                               torch.tensor(1.0/scale, dtype=torch.float32, device=self.torch_device))
 
         if mode == Tags.NOISE_MODE_ADDITIVE:
-            data_array = data_array + np.random.gamma(shape, scale, size=np.shape(data_array))
+            data_tensor += dist.sample(data_tensor.shape)
         elif mode == Tags.NOISE_MODE_MULTIPLICATIVE:
-            data_array = data_array * np.random.gamma(shape, scale, size=np.shape(data_array))
+            data_tensor *= dist.sample(data_tensor.shape)
 
         if not (Tags.IGNORE_QA_ASSERTIONS in self.global_settings and Tags.IGNORE_QA_ASSERTIONS):
-            assert_array_well_defined(data_array)
+            assert_array_well_defined(data_tensor)
 
-        save_data_field(data_array, self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        save_data_field(data_tensor.cpu().numpy().astype(np.float64, copy=False),
+                        self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
 
         self.logger.info("Applying Gamma Noise Model...[Done]")
diff --git a/simpa/core/processing_components/monospectral/noise/gaussian_noise.py b/simpa/core/processing_components/monospectral/noise/gaussian_noise.py
index 92d13d0e..5c31a50d 100644
--- a/simpa/core/processing_components/monospectral/noise/gaussian_noise.py
+++ b/simpa/core/processing_components/monospectral/noise/gaussian_noise.py
@@ -8,6 +8,7 @@
 from simpa.core.processing_components import ProcessingComponent
 from simpa.utils.quality_assurance.data_sanity_testing import assert_array_well_defined
 import numpy as np
+import torch
 
 
 class GaussianNoise(ProcessingComponent):
@@ -56,17 +57,21 @@ def run(self, device):
 
         wavelength = self.global_settings[Tags.WAVELENGTH]
         data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        data_tensor = torch.as_tensor(data_array, dtype=torch.float32, device=self.torch_device)
+        dist = torch.distributions.normal.Normal(torch.tensor(mean, dtype=torch.float32, device=self.torch_device),
+                                                 torch.tensor(std, dtype=torch.float32, device=self.torch_device))
 
         if mode == Tags.NOISE_MODE_ADDITIVE:
-            data_array = data_array + np.random.normal(mean, std, size=np.shape(data_array))
+            data_tensor += dist.sample(data_tensor.shape)
         elif mode == Tags.NOISE_MODE_MULTIPLICATIVE:
-            data_array = data_array * np.random.normal(mean, std, size=np.shape(data_array))
+            data_tensor *= dist.sample(data_tensor.shape)
 
         if not (Tags.IGNORE_QA_ASSERTIONS in self.global_settings and Tags.IGNORE_QA_ASSERTIONS):
-            assert_array_well_defined(data_array)
+            assert_array_well_defined(data_tensor)
 
         if non_negative:
-            data_array[data_array < EPS] = EPS
-        save_data_field(data_array, self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+            data_tensor[data_tensor < EPS] = EPS
+        save_data_field(data_tensor.cpu().numpy().astype(np.float64, copy=False),
+                        self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
 
         self.logger.info("Applying Gaussian Noise Model...[Done]")
diff --git a/simpa/core/processing_components/monospectral/noise/poisson_noise.py b/simpa/core/processing_components/monospectral/noise/poisson_noise.py
index df440c32..0fd544e6 100644
--- a/simpa/core/processing_components/monospectral/noise/poisson_noise.py
+++ b/simpa/core/processing_components/monospectral/noise/poisson_noise.py
@@ -7,11 +7,12 @@
 from simpa.core.processing_components import ProcessingComponent
 from simpa.utils.quality_assurance.data_sanity_testing import assert_array_well_defined
 import numpy as np
+import torch
 
 
 class PoissonNoise(ProcessingComponent):
     """
-    Applies Gaussian noise to the defined data field.
+    Applies Poisson noise to the defined data field.
     The noise will be applied to all wavelengths.
 
     Component Settings::
@@ -44,15 +45,18 @@ def run(self, device):
 
         wavelength = self.global_settings[Tags.WAVELENGTH]
         data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        data_tensor = torch.as_tensor(data_array, dtype=torch.float32, device=self.torch_device)
+        dist = torch.distributions.poisson.Poisson(torch.tensor(mean, dtype=torch.float32, device=self.torch_device))
 
         if mode == Tags.NOISE_MODE_ADDITIVE:
-            data_array = data_array + np.random.poisson(mean, size=np.shape(data_array))
+            data_tensor += dist.sample(data_tensor.shape)
         elif mode == Tags.NOISE_MODE_MULTIPLICATIVE:
-            data_array = data_array * np.random.poisson(mean, size=np.shape(data_array))
+            data_tensor *= dist.sample(data_tensor.shape)
 
         if not (Tags.IGNORE_QA_ASSERTIONS in self.global_settings and Tags.IGNORE_QA_ASSERTIONS):
-            assert_array_well_defined(data_array)
+            assert_array_well_defined(data_tensor)
 
-        save_data_field(data_array, self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        save_data_field(data_tensor.cpu().numpy().astype(np.float64, copy=False),
+                        self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
 
         self.logger.info("Applying Poisson Noise Model...[Done]")
diff --git a/simpa/core/processing_components/monospectral/noise/salt_and_pepper_noise.py b/simpa/core/processing_components/monospectral/noise/salt_and_pepper_noise.py
index 40dc5ce6..4204b32e 100644
--- a/simpa/core/processing_components/monospectral/noise/salt_and_pepper_noise.py
+++ b/simpa/core/processing_components/monospectral/noise/salt_and_pepper_noise.py
@@ -7,6 +7,7 @@
 from simpa.core.processing_components import ProcessingComponent
 from simpa.utils.quality_assurance.data_sanity_testing import assert_array_well_defined
 import numpy as np
+import torch
 
 
 class SaltAndPepperNoise(ProcessingComponent):
@@ -38,9 +39,10 @@ def run(self, device):
 
         wavelength = self.global_settings[Tags.WAVELENGTH]
         data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        data_tensor = torch.as_tensor(data_array, dtype=torch.float32, device=self.torch_device)
 
-        min_noise = np.min(data_array)
-        max_noise = np.max(data_array)
+        min_noise = torch.min(data_tensor).item()
+        max_noise = torch.max(data_tensor).item()
         noise_frequency = 0.01
 
         if Tags.NOISE_FREQUENCY in self.component_settings.keys():
@@ -56,18 +58,17 @@ def run(self, device):
         self.logger.debug(f"Noise model max: {max_noise}")
         self.logger.debug(f"Noise model frequency: {noise_frequency}")
 
-        shape = np.shape(data_array)
-        num_data_points = int(np.round(np.prod(shape) * noise_frequency / 2))
-
-        coords_min = tuple([np.random.randint(0, i - 1, int(num_data_points)) for i in shape])
-        coords_max = tuple([np.random.randint(0, i - 1, int(num_data_points)) for i in shape])
-
-        data_array[coords_min] = min_noise
-        data_array[coords_max] = max_noise
+        dist = torch.distributions.uniform.Uniform(torch.tensor(-1.0, dtype=torch.float32, device=self.torch_device),
+                                                   torch.tensor(1.0, dtype=torch.float32, device=self.torch_device))
+        sample = dist.sample(data_tensor.shape)
+        sample_cutoff = 1.0 - noise_frequency
+        data_tensor[sample > sample_cutoff] = min_noise
+        data_tensor[-sample > sample_cutoff] = max_noise
 
         if not (Tags.IGNORE_QA_ASSERTIONS in self.global_settings and Tags.IGNORE_QA_ASSERTIONS):
-            assert_array_well_defined(data_array)
+            assert_array_well_defined(data_tensor)
 
-        save_data_field(data_array, self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        save_data_field(data_tensor.cpu().numpy().astype(np.float64, copy=False),
+                        self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
 
         self.logger.info("Applying Salt And Pepper Noise Model...[Done]")
diff --git a/simpa/core/processing_components/monospectral/noise/uniform_noise.py b/simpa/core/processing_components/monospectral/noise/uniform_noise.py
index 7cc5f799..5610dc43 100644
--- a/simpa/core/processing_components/monospectral/noise/uniform_noise.py
+++ b/simpa/core/processing_components/monospectral/noise/uniform_noise.py
@@ -7,6 +7,7 @@
 from simpa.core.processing_components import ProcessingComponent
 from simpa.utils.quality_assurance.data_sanity_testing import assert_array_well_defined
 import numpy as np
+import torch
 
 
 class UniformNoise(ProcessingComponent):
@@ -52,15 +53,19 @@ def run(self, device):
 
         wavelength = self.global_settings[Tags.WAVELENGTH]
         data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        data_tensor = torch.as_tensor(data_array, dtype=torch.float32, device=self.torch_device)
+        dist = torch.distributions.uniform.Uniform(torch.tensor(min_noise, dtype=torch.float32, device=self.torch_device),
+                                                   torch.tensor(max_noise, dtype=torch.float32, device=self.torch_device))
 
         if mode == Tags.NOISE_MODE_ADDITIVE:
-            data_array = data_array + (np.random.random(size=np.shape(data_array)) * (max_noise-min_noise) + min_noise)
+            data_tensor += dist.sample(data_tensor.shape)
         elif mode == Tags.NOISE_MODE_MULTIPLICATIVE:
-            data_array = data_array * (np.random.random(size=np.shape(data_array)) * (max_noise-min_noise) + min_noise)
+            data_tensor *= dist.sample(data_tensor.shape)
 
         if not (Tags.IGNORE_QA_ASSERTIONS in self.global_settings and Tags.IGNORE_QA_ASSERTIONS):
-            assert_array_well_defined(data_array)
+            assert_array_well_defined(data_tensor)
 
-        save_data_field(data_array, self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+        save_data_field(data_tensor.cpu().numpy().astype(np.float64, copy=False),
+                        self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
 
         self.logger.info("Applying Uniform Noise Model...[Done]")
diff --git a/simpa/utils/quality_assurance/data_sanity_testing.py b/simpa/utils/quality_assurance/data_sanity_testing.py
index 0433ff8a..32cee0be 100644
--- a/simpa/utils/quality_assurance/data_sanity_testing.py
+++ b/simpa/utils/quality_assurance/data_sanity_testing.py
@@ -3,7 +3,9 @@
 # SPDX-License-Identifier: MIT
 
 import numpy as np
+import torch
 import inspect
+from typing import Union
 
 
 def assert_equal_shapes(numpy_arrays: list):
@@ -29,13 +31,13 @@ def assert_equal_shapes(numpy_arrays: list):
                              f" parameters. Called from {inspect.stack()[1].function}")
 
 
-def assert_array_well_defined(array: np.ndarray, assume_non_negativity: bool = False,
+def assert_array_well_defined(array: Union[np.ndarray, torch.Tensor], assume_non_negativity: bool = False,
                               assume_positivity=False, array_name: str = None):
     """
-    This method tests if all entries of the given array are well-defined (i.e. not np.inf, np.nan, or None).
+    This method tests if all entries of the given array or tensor are well-defined (i.e. not np.inf, np.nan, or None).
     The method can be parametrised to be more strict.
 
-    :param array: The input np.ndarray
+    :param array: The input np.ndarray or torch.Tensor
     :param assume_non_negativity: bool (default: False). If true, all values must be greater than or equal to 0.
     :param assume_positivity: bool (default: False). If true, all values must be greater than 0.
     :param array_name: a string that gives more information in case of an error.
@@ -43,11 +45,12 @@ def assert_array_well_defined(array: np.ndarray, assume_non_negativity: bool = F
     """
 
     error_message = None
-    if not np.isfinite(array).all():
+    array_as_tensor = torch.as_tensor(array)
+    if not torch.all(torch.isfinite(array_as_tensor)):
         error_message = "nan, inf or -inf"
-    if assume_positivity and (array <= 0).any():
+    if assume_positivity and torch.any(array_as_tensor <= 0):
         error_message = "not positive"
-    if assume_non_negativity and (array < 0).any():
+    if assume_non_negativity and torch.any(array_as_tensor < 0):
         error_message = "negative"
     if error_message:
         if array_name is None:
diff --git a/simpa_tests/automatic_tests/test_noise_models.py b/simpa_tests/automatic_tests/test_noise_models.py
index 61750380..87b12a18 100644
--- a/simpa_tests/automatic_tests/test_noise_models.py
+++ b/simpa_tests/automatic_tests/test_noise_models.py
@@ -5,6 +5,7 @@
 import unittest
 import os
 import numpy as np
+import torch
 
 from simpa.core.processing_components.monospectral.noise import *
 from simpa.utils import Tags, Settings
@@ -32,6 +33,7 @@ def validate_noise_model_results(self, noise_model, noise_model_settings,
                                      expected_mean, expected_std,
                                      error_margin=0.05):
         np.random.seed(self.RANDOM_SEED)
+        torch.manual_seed(self.RANDOM_SEED)
 
         settings = {
             # These parameters set the general propeties of the simulated volume
@@ -78,7 +80,7 @@ def validate_noise_model_results(self, noise_model, noise_model_settings,
                             f"The mean was not as expected. Expected {expected_mean} but was {actual_mean}")
             self.assertTrue(np.abs(actual_std - expected_std) < 1e-10 or
                             np.abs(actual_std - expected_std) / expected_std < error_margin,
-                            f"The mean was not as expected. Expected {expected_std} but was {actual_std}")
+                            f"The std was not as expected. Expected {expected_std} but was {actual_std}")
         finally:
             if (os.path.exists(settings[Tags.SIMPA_OUTPUT_PATH]) and
                     os.path.isfile(settings[Tags.SIMPA_OUTPUT_PATH])):
@@ -87,8 +89,8 @@ def validate_noise_model_results(self, noise_model, noise_model_settings,
 
     def setUp(self):
 
-        self.VOLUME_WIDTH_IN_MM = 10
-        self.VOLUME_HEIGHT_IN_MM = 10
+        self.VOLUME_WIDTH_IN_MM = 20
+        self.VOLUME_HEIGHT_IN_MM = 20
         self.SPACING = 1
         self.RANDOM_SEED = 4711
 

From 7feace012e7a5d17e07d4e8984af18e0b1efd5a9 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Mon, 2 Oct 2023 14:59:22 +0200
Subject: [PATCH 03/24] further increase number of noise samples in test code

---
 simpa_tests/automatic_tests/test_noise_models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/simpa_tests/automatic_tests/test_noise_models.py b/simpa_tests/automatic_tests/test_noise_models.py
index 87b12a18..b23ac50d 100644
--- a/simpa_tests/automatic_tests/test_noise_models.py
+++ b/simpa_tests/automatic_tests/test_noise_models.py
@@ -89,8 +89,8 @@ def validate_noise_model_results(self, noise_model, noise_model_settings,
 
     def setUp(self):
 
-        self.VOLUME_WIDTH_IN_MM = 20
-        self.VOLUME_HEIGHT_IN_MM = 20
+        self.VOLUME_WIDTH_IN_MM = 40
+        self.VOLUME_HEIGHT_IN_MM = 40
         self.SPACING = 1
         self.RANDOM_SEED = 4711
 

From 98f6a7f5612bda3e2c2395fe1df010d781ef6293 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Wed, 6 Mar 2024 08:31:08 +0100
Subject: [PATCH 04/24] Use mcx SLIT source for MSOTAcuity and MSOTInvision

- MSOTAcuityIlluminationGeometry
  - Change in source due to fixing of sign error
- MSOTInVisionIlluminationGeometry
  - Change in source due to use of gaussian broadening instead of step function
  - Now only requires a single mcx run using the new multiple sources feature
- Note: requires mcx version >= v2024.2
---
 .../ithera_msot_acuity_illumination.py        | 20 ++--
 .../ithera_msot_invision_illumination.py      | 94 +++++++------------
 .../pa_devices/ithera_msot_invision.py        |  4 +-
 3 files changed, 47 insertions(+), 71 deletions(-)

diff --git a/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_acuity_illumination.py b/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_acuity_illumination.py
index 57729c9a..f1b665d1 100644
--- a/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_acuity_illumination.py
+++ b/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_acuity_illumination.py
@@ -29,21 +29,25 @@ def __init__(self):
         self.normalized_source_direction_vector = self.source_direction_vector / np.linalg.norm(
             self.source_direction_vector)
 
-    def get_mcx_illuminator_definition(self, global_settings: Settings):
+        divergence_angle = 8.66  # full beam divergence angle measured at Full Width at Half Maximum (FWHM)
+        full_width_at_half_maximum = 2.0 * np.tan(0.5 * np.deg2rad(divergence_angle))  # FWHM of beam divergence
+        # standard deviation of gaussian with FWHM
+        self.sigma = full_width_at_half_maximum / (2.0 * np.sqrt(2.0 * np.log(2.0)))
 
-        source_type = Tags.ILLUMINATION_TYPE_MSOT_ACUITY_ECHO
+    def get_mcx_illuminator_definition(self, global_settings: Settings):
+        source_type = Tags.ILLUMINATION_TYPE_SLIT
         spacing = global_settings[Tags.SPACING_MM]
         device_position = list(self.device_position_mm / spacing + 0.5)
-
+        device_length = 30 / spacing
+        source_pos = device_position
+        source_pos[0] -= 0.5 * device_length
         source_direction = list(self.normalized_source_direction_vector)
-
-        source_param1 = [30 / spacing, 0, 0, 0]
-
-        source_param2 = [0, 0, 0, 0]
+        source_param1 = [device_length, 0.0, 0.0, 0.0]
+        source_param2 = [self.sigma, self.sigma, 0.0, 0.0]
 
         return {
             "Type": source_type,
-            "Pos": device_position,
+            "Pos": source_pos,
             "Dir": source_direction,
             "Param1": source_param1,
             "Param2": source_param2
diff --git a/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_invision_illumination.py b/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_invision_illumination.py
index 4dbdfbd0..5713fb54 100644
--- a/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_invision_illumination.py
+++ b/simpa/core/device_digital_twins/illumination_geometries/ithera_msot_invision_illumination.py
@@ -13,11 +13,7 @@ class MSOTInVisionIlluminationGeometry(IlluminationGeometryBase):
     This class represents the illumination geometry of the MSOT InVision photoacoustic device.
     """
 
-    def __init__(self, invision_position=None, geometry_id=0):
-        """
-        :param geometry_id: ID of the specific InVision illuminator.
-        :type geometry_id: int
-        """
+    def __init__(self, invision_position=None):
         super().__init__()
 
         if invision_position is None:
@@ -25,75 +21,53 @@ def __init__(self, invision_position=None, geometry_id=0):
         else:
             self.invision_position = invision_position
 
-        self.geometry_id = geometry_id
-
-        angle = 0.0
         det_sep_half = 24.74 / 2
         detector_iso_distance = 74.05 / 2
-        illumination_angle = -0.41608649
-
-        if geometry_id == 0:
-            angle = 0.0
-        elif geometry_id == 1:
-            angle = 0.0
-            det_sep_half = -det_sep_half
-            illumination_angle = -illumination_angle
-        elif geometry_id == 2:
-            angle = 1.25664
-        elif geometry_id == 3:
-            angle = 1.25664
-            det_sep_half = -det_sep_half
-            illumination_angle = -illumination_angle
-        elif geometry_id == 4:
-            angle = -1.25664
-        elif geometry_id == 5:
-            angle = -1.25664
-            det_sep_half = -det_sep_half
-            illumination_angle = -illumination_angle
-        elif geometry_id == 6:
-            angle = 2.51327
-        elif geometry_id == 7:
-            angle = 2.51327
-            det_sep_half = -det_sep_half
-            illumination_angle = -illumination_angle
-        elif geometry_id == 8:
-            angle = -2.51327
-        elif geometry_id == 9:
-            angle = -2.51327
-            det_sep_half = -det_sep_half
-            illumination_angle = -illumination_angle
-
-        self.device_position_mm = [self.invision_position[0] + np.sin(angle) * detector_iso_distance,
-                                   self.invision_position[1] + det_sep_half,
-                                   self.invision_position[2] + np.cos(angle) * detector_iso_distance]
-
-        self.source_direction_vector = np.array([-np.sin(angle),
-                                                 np.sin(illumination_angle),
-                                                 np.cos(angle)])
-
-        self.normalized_source_direction_vector = self.source_direction_vector / np.linalg.norm(
-            self.source_direction_vector)
+        detector_width = 2 * 6.12
+
+        self.device_positions_mm = list()
+        self.source_direction_vectors = list()
+        self.slit_vectors_mm = list()
+
+        for index in [0, 1, 2, 3, 4]:
+            for y_offset_factor in [+1, -1]:
+                angle = index * 2.0 * np.pi / 5.0
+                illumination_angle = -0.41608649 * y_offset_factor
+                v = np.array([-np.sin(angle), np.sin(illumination_angle), -np.cos(angle)])
+                v /= np.linalg.norm(v)
+                slit_vector = np.array([np.cos(angle), 0, -np.sin(angle)]) * detector_width
+                slit_middle_on_circle = np.array([np.sin(angle), 0.0, np.cos(angle)]) * detector_iso_distance
+                y_offset = np.array([0.0, det_sep_half * y_offset_factor, 0.0])
+                pos = np.array(self.invision_position) + slit_middle_on_circle + y_offset - 0.5*slit_vector
+                self.device_positions_mm.append(pos)
+                self.source_direction_vectors.append(v)
+                self.slit_vectors_mm.append(slit_vector)
+
+        divergence_angle = 0.165806  # full beam divergence angle measured at Full Width at Half Maximum (FWHM)
+        full_width_at_half_maximum = 2.0 * np.tan(0.5 * divergence_angle)  # FWHM of beam divergence
+        # standard deviation of gaussian with FWHM
+        self.sigma = full_width_at_half_maximum / (2.0 * np.sqrt(2.0 * np.log(2.0)))
 
     def get_mcx_illuminator_definition(self, global_settings):
         self.logger.debug(self.invision_position)
-        source_type = Tags.ILLUMINATION_TYPE_MSOT_INVISION
+        source_type = Tags.ILLUMINATION_TYPE_SLIT
 
         spacing = global_settings[Tags.SPACING_MM]
 
-        source_position = list(np.array(self.device_position_mm) / spacing + 1)
+        source_positions = list(list(pos / spacing + 1) for pos in self.device_positions_mm)
 
-        source_direction = list(self.normalized_source_direction_vector)
+        source_directions = list(list(v) for v in self.source_direction_vectors)
 
-        source_param1 = [spacing, self.geometry_id, 0, 0]
+        source_param1s = list(list(slit_vector / spacing) + [0.0] for slit_vector in self.slit_vectors_mm)
 
-        source_param2 = [0, 0, 0, 0]
+        source_param2s = [[self.sigma, 0, 0, 0]]*len(self.device_positions_mm)
 
         return {
             "Type": source_type,
-            "Pos": source_position,
-            "Dir": source_direction,
-            "Param1": source_param1,
-            "Param2": source_param2
+            "Pos": source_positions,
+            "Dir": source_directions,
+            "Param1": source_param1s,
+            "Param2": source_param2s
         }
 
     def serialize(self) -> dict:
diff --git a/simpa/core/device_digital_twins/pa_devices/ithera_msot_invision.py b/simpa/core/device_digital_twins/pa_devices/ithera_msot_invision.py
index 59abcdd3..f2e42945 100644
--- a/simpa/core/device_digital_twins/pa_devices/ithera_msot_invision.py
+++ b/simpa/core/device_digital_twins/pa_devices/ithera_msot_invision.py
@@ -54,9 +54,7 @@ def __init__(self, device_position_mm: np.ndarray = None,
 
         self.field_of_view_extent_mm = detection_geometry.field_of_view_extent_mm
         self.set_detection_geometry(detection_geometry)
-        for i in range(10):
-            self.add_illumination_geometry(MSOTInVisionIlluminationGeometry(invision_position=self.device_position_mm,
-                                                                            geometry_id=i))
+        self.add_illumination_geometry(MSOTInVisionIlluminationGeometry(invision_position=self.device_position_mm))
 
     def serialize(self) -> dict:
         serialized_device = self.__dict__

From 347c9f80ded7f0ffabea58e0c4fa72661044f92c Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Fri, 8 Mar 2024 13:04:46 +0100
Subject: [PATCH 05/24] Update DigitalDeviceTwinBase __eq__ to work with lists
 of numpy arrays

---
 .../digital_device_twin_base.py                 | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/simpa/core/device_digital_twins/digital_device_twin_base.py b/simpa/core/device_digital_twins/digital_device_twin_base.py
index c9280ca2..56c90128 100644
--- a/simpa/core/device_digital_twins/digital_device_twin_base.py
+++ b/simpa/core/device_digital_twins/digital_device_twin_base.py
@@ -12,6 +12,15 @@
 from simpa.utils.serializer import SerializableSIMPAClass
 
 
+def is_equal(a, b) -> bool:
+    if isinstance(a, list):
+        return all(is_equal(ai, bi) for ai, bi in zip(a, b))
+    elif isinstance(a, np.ndarray):
+        return (a == b).all
+    else:
+        return a == b
+
+
 class DigitalDeviceTwinBase(SerializableSIMPAClass):
     """
     This class represents a device that can be used for illumination, detection or a combined photoacoustic device
@@ -49,14 +58,8 @@ def __eq__(self, other):
                 return False
             for self_key, self_value in self.__dict__.items():
                 other_value = other.__dict__[self_key]
-                if isinstance(self_value, np.ndarray):
-                    boolean = (other_value != self_value).all()
-                else:
-                    boolean = other_value != self_value
-                if boolean:
+                if not is_equal(self_value, other_value):
                     return False
-                else:
-                    continue
             return True
         return False
 

From 50d87771e9eb42bcd479a95d1f1df3bb1c1718cc Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Fri, 8 Mar 2024 15:51:55 +0100
Subject: [PATCH 06/24] Fixed minor bug regarding path management inside the
 simpa output

---
 simpa/utils/dict_path_manager.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/simpa/utils/dict_path_manager.py b/simpa/utils/dict_path_manager.py
index 86d17a62..2dfa7f68 100644
--- a/simpa/utils/dict_path_manager.py
+++ b/simpa/utils/dict_path_manager.py
@@ -54,7 +54,7 @@ def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
         if wavelength is not None:
             dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + wl
         else:
-            dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field
+            dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + "/"
     elif data_field in simulation_output:
         if data_field in [Tags.DATA_FIELD_FLUENCE, Tags.DATA_FIELD_INITIAL_PRESSURE, Tags.OPTICAL_MODEL_UNITS,
                           Tags.DATA_FIELD_DIFFUSE_REFLECTANCE, Tags.DATA_FIELD_DIFFUSE_REFLECTANCE_POS,
@@ -62,12 +62,12 @@ def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
             if wavelength is not None:
                 dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.OPTICAL_MODEL_OUTPUT_NAME + "/" + data_field + wl
             else:
-                dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.OPTICAL_MODEL_OUTPUT_NAME + "/" + data_field
+                dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.OPTICAL_MODEL_OUTPUT_NAME + "/" + data_field + "/"
         else:
             if wavelength is not None:
                 dict_path = "/" + Tags.SIMULATIONS + "/" + data_field + wl
             else:
-                dict_path = "/" + Tags.SIMULATIONS + "/" + data_field
+                dict_path = "/" + Tags.SIMULATIONS + "/" + data_field + "/"
 
     elif data_field in wavelength_independent_properties:
         dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + "/"
@@ -77,7 +77,7 @@ def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
         if wavelength is not None:
             dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + wl
         else:
-            dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field
+            dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + "/"
 
     elif data_field in wavelength_independent_image_processing_output:
         dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + "/"

From ec01e0556ab31e387d93a139f6963a603130b14b Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Fri, 8 Mar 2024 16:31:13 +0100
Subject: [PATCH 07/24] Added possibility to continue a simulation based on a
 previously existing simulation

---
 simpa/core/simulation.py | 18 ++++++++++++++++--
 simpa/utils/tags.py      |  8 ++++++++
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/simpa/core/simulation.py b/simpa/core/simulation.py
index 990c018e..267661ab 100644
--- a/simpa/core/simulation.py
+++ b/simpa/core/simulation.py
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 from simpa.utils import Tags
-from simpa.io_handling.io_hdf5 import save_hdf5, load_hdf5
+from simpa.io_handling.io_hdf5 import save_hdf5, load_hdf5, save_data_field, load_data_field
 from simpa.io_handling.ipasc import export_to_ipasc
 from simpa.utils.settings import Settings
 from simpa.log import Logger
@@ -61,7 +61,21 @@ def simulate(simulation_pipeline: list, settings: Settings, digital_device_twin:
     simpa_output[Tags.SIMULATION_PIPELINE] = [type(x).__name__ for x in simulation_pipeline]
 
     logger.debug("Saving settings dictionary...")
-    save_hdf5(simpa_output, settings[Tags.SIMPA_OUTPUT_PATH])
+
+    # In case of continuation, the simulation script doesn't overwrite the existing file.
+
+    if Tags.CONTINUE_SIMULATION in settings and settings[Tags.CONTINUE_SIMULATION]:
+        simpa_output[Tags.SIMULATION_PIPELINE] = (load_data_field(settings[Tags.SIMPA_OUTPUT_PATH],
+                                                                  Tags.SIMULATION_PIPELINE)
+                                                  + simpa_output[Tags.SIMULATION_PIPELINE])
+        previous_settings = load_hdf5(settings[Tags.SIMPA_OUTPUT_PATH], Tags.SETTINGS)
+        previous_settings.update(settings)
+        simpa_output[Tags.SETTINGS] = previous_settings
+
+        for i in [Tags.SETTINGS, Tags.DIGITAL_DEVICE, Tags.SIMULATION_PIPELINE]:
+            save_data_field(simpa_output[i], settings[Tags.SIMPA_OUTPUT_PATH], i)
+    else:
+        save_hdf5(simpa_output, settings[Tags.SIMPA_OUTPUT_PATH])
     logger.debug("Saving settings dictionary...[Done]")
 
     for wavelength in settings[Tags.WAVELENGTHS]:
diff --git a/simpa/utils/tags.py b/simpa/utils/tags.py
index 49c89288..4e3d6634 100644
--- a/simpa/utils/tags.py
+++ b/simpa/utils/tags.py
@@ -34,6 +34,14 @@ class Tags:
     Usage: SIMPA package
     """
 
+    CONTINUE_SIMULATION = ("continue_simulation", bool)
+    """
+    Boolean whether the user just wants to continue a previously existing simulation or 
+    if they want to start a new simulation from scratch. In case of continuation, 
+    the simulation script doesn't overwrite the existing file.
+    Usage: SIMPA package
+    """
+
     VOLUME_NAME = ("volume_name", str)
     """
     Name of the SIMPA output file.\n

From d030fd75f01a26d0b91029506c7a997a58b4ec1e Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Mon, 11 Mar 2024 10:26:10 +0100
Subject: [PATCH 08/24] update required MCX version

---
 .../optical_forward_model_mcx_reflectance_adapter.py          | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
index 4c802771..a5f41b9d 100644
--- a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
+++ b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
@@ -18,8 +18,8 @@ class MCXAdapterReflectance(MCXAdapter):
     diffuse reflectance simulations. Specifically, it implements the capability to run diffuse reflectance simulations.
 
     .. warning::
-        This MCX adapter requires a version of MCX containing the revision: `Rev::077060`, which was published in the
-        Nightly build  on `2022-01-26`.
+        This MCX adapter requires a version of MCX containing the commit 56eca8ae7e9abde309053759d6d6273ac4795fc5,
+        which was published in the Nightly build on `2024-03-10`.
 
     .. note::
         MCX is a GPU-enabled Monte-Carlo model simulation of photon transport in tissue:

From 5df4a70a46569db4f495111fe6e9a9dedfbce43f Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Mon, 11 Mar 2024 15:36:59 +0100
Subject: [PATCH 09/24] Update MCXAdapterReflectance to account for change in
 NIFTIData format in mcx 2024.1

---
 .../optical_forward_model_mcx_reflectance_adapter.py        | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
index a5f41b9d..54c4a876 100644
--- a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
+++ b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
@@ -101,6 +101,9 @@ def get_command(self) -> List:
         cmd.append(self.mcx_json_config_file)
         cmd.append("-O")
         cmd.append("F")
+        # use 'C' order array format for binary input file
+        cmd.append("-a")
+        cmd.append("1")
         cmd.append("-F")
         cmd.append("jnii")
         if Tags.COMPUTE_PHOTON_DIRECTION_AT_EXIT in self.component_settings and \
@@ -128,6 +131,9 @@ def read_mcx_output(self, **kwargs) -> Dict:
                 self.mcx_output_suffixes['mcx_volumetric_data_file']):
             content = jdata.load(self.mcx_volumetric_data_file)
             fluence = content['NIFTIData']
+            if fluence.ndim > 3:
+                # mcx >= v2024.1 includes additional dimensions in this data structure for the source and detector ids
+                fluence = np.squeeze(fluence)
             ref, ref_pos, fluence = self.extract_reflectance_from_fluence(fluence=fluence)
             fluence = self.post_process_volumes(**{'arrays': (fluence,)})[0]
             fluence *= 100  # Convert from J/mm^2 to J/cm^2

From 15d2d02ec3d6a7538c8ec709a3daa66a256fc2a1 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Mon, 11 Mar 2024 15:53:41 +0100
Subject: [PATCH 10/24] update docs on mcx installation

---
 README.md                   | 22 +++++-----------------
 docs/source/introduction.md | 22 +++++-----------------
 2 files changed, 10 insertions(+), 34 deletions(-)

diff --git a/README.md b/README.md
index 99de8b48..f61481dc 100755
--- a/README.md
+++ b/README.md
@@ -75,25 +75,13 @@ acoustic simulations possible.
 
 ### mcx (Optical Forward Model)
 
-Either download suitable executables or build yourself from the following sources:
+Download the latest nightly build of [mcx](http://mcx.space/) for your operating system:
 
-[http://mcx.space/](http://mcx.space/)
+- [Linux](http://mcx.space/nightly/github/mcx-linux-x64-github-latest.zip)
+- [MacOS](http://mcx.space/nightly/github/mcx-macos-x64-github-latest.zip)
+- [Windows](http://mcx.space/nightly/github/mcx-windows-x64-github-latest.zip)
 
-In order to obtain access to all custom sources that we implemented, please build mcx yourself from the
-following mcx Github fork:
-[https://github.com/IMSY-DKFZ/mcx](https://github.com/IMSY-DKFZ/mcx)
-
-For the installation, please follow steps 1-4:
-1. `git clone https://github.com/IMSY-DKFZ/mcx.git`
-2. `cd mcx/src`
-3. In `MAKEFILE` adapt line 111 the sm version [according to your GPU](https://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/).
-4. `make`
-
-The built binary can be found in `src/bin`.
-Note, in case you can’t build mcx with the GPU-specific sm version you need to install a more recent NVIDIA driver and nvcc toolkit. 
-One option would be to install cuda in a conda environment via `conda install cuda -c nvidia`.
-Please note that there might be compatibility issues using mcx-cl with the MCX Adapter as this use case is not 
-being tested and supported by the SIMPA developers.
+Then extract the files and set `MCX_BINARY_PATH=/.../mcx/bin/mcx` in your path_config.env.
 
 ### k-Wave (Acoustic Forward Model)
 
diff --git a/docs/source/introduction.md b/docs/source/introduction.md
index f211279d..593b74d1 100644
--- a/docs/source/introduction.md
+++ b/docs/source/introduction.md
@@ -39,25 +39,13 @@ acoustic simulations possible.
 
 ### mcx (Optical Forward Model)
 
-Either download suitable executables or build yourself from the following sources:
+Download the latest nightly build of [mcx](http://mcx.space/) for your operating system:
 
-[http://mcx.space/](http://mcx.space/)
+- [Linux](http://mcx.space/nightly/github/mcx-linux-x64-github-latest.zip)
+- [MacOS](http://mcx.space/nightly/github/mcx-macos-x64-github-latest.zip)
+- [Windows](http://mcx.space/nightly/github/mcx-windows-x64-github-latest.zip)
 
-In order to obtain access to all custom sources that we implemented, please build mcx yourself from the
-following mcx Github fork:
-[https://github.com/IMSY-DKFZ/mcx](https://github.com/IMSY-DKFZ/mcx)
-
-For the installation, please follow steps 1-4:
-1. `git clone https://github.com/IMSY-DKFZ/mcx.git`
-2. `cd mcx/src`
-3. In `MAKEFILE` adapt line 111 the sm version [according to your GPU](https://arnon.dk/matching-sm-architectures-arch-and-gencode-for-various-nvidia-cards/).
-4. `make`
-
-The built binary can be found in `src/bin`.
-Note, in case you can’t build mcx with the GPU-specific sm version you need to install a more recent NVIDIA driver and nvcc toolkit. 
-One option would be to install cuda in a conda environment via `conda install cuda -c nvidia`.
-Please note that there might be compatibility issues using mcx-cl with the MCX Adapter as this use case is not 
-being tested and supported by the SIMPA developers.
+Then extract the files and set `MCX_BINARY_PATH=/.../mcx/bin/mcx` in your path_config.env.
 
 ### k-Wave (Acoustic Forward Model)
 

From b717904e6e8a4ed2edf6e0ea8a689c86dbf617fb Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Mon, 11 Mar 2024 16:43:46 +0100
Subject: [PATCH 11/24] Update MCXAdapter to use jnii data file format and
 ensure we end up with a 3d fluence array

- shape of mc2 file depends on mcx version and this format is now deprecated in mcx
---
 .../optical_forward_model_mcx_adapter.py      | 19 ++++++++++---------
 ...l_forward_model_mcx_reflectance_adapter.py |  4 ++--
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
index 0e922c95..ed4617a4 100644
--- a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
+++ b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_adapter.py
@@ -8,8 +8,8 @@
 from simpa.core.simulation_modules.optical_simulation_module import OpticalForwardModuleBase
 from simpa.core.device_digital_twins.illumination_geometries.illumination_geometry_base import IlluminationGeometryBase
 import json
+import jdata
 import os
-import gc
 from typing import List, Dict, Tuple
 
 
@@ -36,7 +36,7 @@ def __init__(self, global_settings: Settings):
         self.mcx_json_config_file = None
         self.mcx_volumetric_data_file = None
         self.frames = None
-        self.mcx_output_suffixes = {'mcx_volumetric_data_file': '.mc2'}
+        self.mcx_output_suffixes = {'mcx_volumetric_data_file': '.jnii'}
 
     def forward_model(self,
                       absorption_cm: np.ndarray,
@@ -182,9 +182,8 @@ def get_command(self) -> List:
         # use 'C' order array format for binary input file
         cmd.append("-a")
         cmd.append("1")
-        # use mc2 binary output file format
         cmd.append("-F")
-        cmd.append("mc2")
+        cmd.append("jnii")
         return cmd
 
     @staticmethod
@@ -237,11 +236,13 @@ def read_mcx_output(self, **kwargs) -> Dict:
         :param kwargs: dummy, used for class inheritance compatibility
         :return: `Dict` instance containing the MCX output
         """
-        shape = [self.nx, self.ny, self.nz, self.frames]
-        fluence = np.fromfile(self.mcx_volumetric_data_file, dtype=np.float32).reshape(shape, order='F')
-        fluence *= 100  # Convert from J/mm^2 to J/cm^2
-        if np.shape(fluence)[3] == 1:
-            fluence = np.squeeze(fluence, 3)
+        content = jdata.load(self.mcx_volumetric_data_file)
+        fluence = content['NIFTIData']
+        print(f"fluence.shape {fluence.shape}")
+        if fluence.ndim > 3:
+            # remove the 1 or 2 (for mcx >= v2024.1) additional dimensions of size 1 if present to obtain a 3d array
+            fluence = fluence.reshape(fluence.shape[0], fluence.shape[1], -1)
+        print(f"fluence.shape {fluence.shape}")
         results = dict()
         results[Tags.DATA_FIELD_FLUENCE] = fluence
         return results
diff --git a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
index 54c4a876..fa9a64a7 100644
--- a/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
+++ b/simpa/core/simulation_modules/optical_simulation_module/optical_forward_model_mcx_reflectance_adapter.py
@@ -132,8 +132,8 @@ def read_mcx_output(self, **kwargs) -> Dict:
             content = jdata.load(self.mcx_volumetric_data_file)
             fluence = content['NIFTIData']
             if fluence.ndim > 3:
-                # mcx >= v2024.1 includes additional dimensions in this data structure for the source and detector ids
-                fluence = np.squeeze(fluence)
+                # remove the 1 or 2 (for mcx >= v2024.1) additional dimensions of size 1 if present to obtain a 3d array
+                fluence = fluence.reshape(fluence.shape[0], fluence.shape[1], -1)
             ref, ref_pos, fluence = self.extract_reflectance_from_fluence(fluence=fluence)
             fluence = self.post_process_volumes(**{'arrays': (fluence,)})[0]
             fluence *= 100  # Convert from J/mm^2 to J/cm^2

From aebeec2f4e250f4a39987ea0aed40efc1d1f86ac Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam@keegan.ch>
Date: Tue, 12 Mar 2024 08:51:22 +0100
Subject: [PATCH 12/24] Fix assert_array_well_defined to also work on arrays
 with negative strides

---
 simpa/utils/quality_assurance/data_sanity_testing.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/simpa/utils/quality_assurance/data_sanity_testing.py b/simpa/utils/quality_assurance/data_sanity_testing.py
index 32cee0be..dd20c2f2 100644
--- a/simpa/utils/quality_assurance/data_sanity_testing.py
+++ b/simpa/utils/quality_assurance/data_sanity_testing.py
@@ -45,7 +45,11 @@ def assert_array_well_defined(array: Union[np.ndarray, torch.Tensor], assume_non
     """
 
     error_message = None
-    array_as_tensor = torch.as_tensor(array)
+    if isinstance(array, np.ndarray) and any(stride < 0 for stride in array.strides):
+        # torch does not support tensors with negative strides so we need to make a copy of the array
+        array_as_tensor = torch.as_tensor(array.copy())
+    else:
+        array_as_tensor = torch.as_tensor(array)
     if not torch.all(torch.isfinite(array_as_tensor)):
         error_message = "nan, inf or -inf"
     if assume_positivity and torch.any(array_as_tensor <= 0):

From e165ead14820ec308190b2546e6b812bf4e2a249 Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 12 Mar 2024 11:33:34 +0100
Subject: [PATCH 13/24] Fixed bug in simulation continuation

---
 simpa/core/simulation.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/simpa/core/simulation.py b/simpa/core/simulation.py
index 267661ab..ce53cc45 100644
--- a/simpa/core/simulation.py
+++ b/simpa/core/simulation.py
@@ -65,10 +65,12 @@ def simulate(simulation_pipeline: list, settings: Settings, digital_device_twin:
     # In case of continuation, the simulation script doesn't overwrite the existing file.
 
     if Tags.CONTINUE_SIMULATION in settings and settings[Tags.CONTINUE_SIMULATION]:
-        simpa_output[Tags.SIMULATION_PIPELINE] = (load_data_field(settings[Tags.SIMPA_OUTPUT_PATH],
-                                                                  Tags.SIMULATION_PIPELINE)
-                                                  + simpa_output[Tags.SIMULATION_PIPELINE])
-        previous_settings = load_hdf5(settings[Tags.SIMPA_OUTPUT_PATH], Tags.SETTINGS)
+        try:
+            old_pipe = load_data_field(settings[Tags.SIMPA_OUTPUT_PATH], Tags.SIMULATION_PIPELINE)
+        except KeyError as e:
+            old_pipe = list()
+        simpa_output[Tags.SIMULATION_PIPELINE] = old_pipe + simpa_output[Tags.SIMULATION_PIPELINE]
+        previous_settings = load_data_field(settings[Tags.SIMPA_OUTPUT_PATH], Tags.SETTINGS)
         previous_settings.update(settings)
         simpa_output[Tags.SETTINGS] = previous_settings
 

From bb502f514311b1c8ab5d2123f432cefeec4e4718 Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Wed, 13 Mar 2024 13:36:55 +0100
Subject: [PATCH 14/24] Exclude first layer voxels from last layer for single
 voxel layers

---
 .../libraries/structure_library/HorizontalLayerStructure.py     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/simpa/utils/libraries/structure_library/HorizontalLayerStructure.py b/simpa/utils/libraries/structure_library/HorizontalLayerStructure.py
index 5053b33d..152b1cf0 100644
--- a/simpa/utils/libraries/structure_library/HorizontalLayerStructure.py
+++ b/simpa/utils/libraries/structure_library/HorizontalLayerStructure.py
@@ -83,7 +83,7 @@ def get_enclosed_indices(self):
 
             bools_fully_filled_layers = ((target_vector_voxels >= 0) & (target_vector_voxels < floored_depth_voxels))
 
-            bools_last_layer = ((target_vector_voxels >= floored_depth_voxels) &
+            bools_last_layer = ((target_vector_voxels >= 0) & (target_vector_voxels >= floored_depth_voxels) &
                                 (target_vector_voxels <= floored_depth_voxels + 1))
 
             volume_fractions[bools_last_layer] = depth_voxels - target_vector_voxels[bools_last_layer]

From a718b797abbcd3d08b04f850b3b0b32a6b5486a2 Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Wed, 13 Mar 2024 15:33:06 +0100
Subject: [PATCH 15/24] Plit up wavelength_independent_tags and toolkit tags in
 a unified place in constants.py instead of multiple definitions

---
 .../volume_creation_module/__init__.py        |  8 +--
 ...ation_module_segmentation_based_adapter.py |  5 +-
 simpa/utils/constants.py                      | 35 ++++++++++++
 simpa/utils/dict_path_manager.py              | 56 ++++---------------
 simpa/utils/tissue_properties.py              | 25 ++-------
 .../test_utils/tissue_composition_tests.py    |  7 ++-
 6 files changed, 60 insertions(+), 76 deletions(-)

diff --git a/simpa/core/simulation_modules/volume_creation_module/__init__.py b/simpa/core/simulation_modules/volume_creation_module/__init__.py
index 991c7669..bb9a5ba9 100644
--- a/simpa/core/simulation_modules/volume_creation_module/__init__.py
+++ b/simpa/core/simulation_modules/volume_creation_module/__init__.py
@@ -5,11 +5,9 @@
 from abc import abstractmethod
 from simpa.utils.settings import Settings
 from simpa.utils import Tags
-from simpa.utils.tissue_properties import TissueProperties
-import numpy as np
+from simpa.utils.constants import wavelength_independent_properties, property_tags
 import torch
 from simpa.core import SimulationModule
-from simpa.utils.dict_path_manager import generate_dict_path
 from simpa.io_handling import save_data_field
 from simpa.utils.quality_assurance.data_sanity_testing import assert_equal_shapes, assert_array_well_defined
 from simpa.utils.processing_device import get_processing_device
@@ -37,9 +35,9 @@ def create_empty_volumes(self):
         wavelength = self.global_settings[Tags.WAVELENGTH]
         first_wavelength = self.global_settings[Tags.WAVELENGTHS][0]
 
-        for key in TissueProperties.property_tags:
+        for key in property_tags:
             # Create wavelength-independent properties only in the first wavelength run
-            if key in TissueProperties.wavelength_independent_properties and wavelength != first_wavelength:
+            if key in wavelength_independent_properties and wavelength != first_wavelength:
                 continue
             volumes[key] = torch.zeros(sizes, dtype=torch.float, device=self.torch_device)
 
diff --git a/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py b/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
index 4e2d9732..f766b109 100644
--- a/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
+++ b/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
@@ -4,9 +4,8 @@
 
 from simpa.core.simulation_modules.volume_creation_module import VolumeCreatorModuleBase
 from simpa.utils import Tags
-from simpa.utils.tissue_properties import TissueProperties
+from simpa.utils.constants import property_tags
 from simpa.io_handling import save_hdf5
-import h5py
 import numpy as np
 
 
@@ -42,7 +41,7 @@ def create_simulation_volume(self) -> dict:
 
         for seg_class in segmentation_classes:
             class_properties = class_mapping[seg_class].get_properties_for_wavelength(wavelength)
-            for prop_tag in TissueProperties.property_tags:
+            for prop_tag in property_tags:
                 volumes[prop_tag][segmentation_volume == seg_class] = class_properties[prop_tag]
 
         save_hdf5(self.global_settings, self.global_settings[Tags.SIMPA_OUTPUT_PATH], "/settings/")
diff --git a/simpa/utils/constants.py b/simpa/utils/constants.py
index 8e8520e8..b4b7c17c 100644
--- a/simpa/utils/constants.py
+++ b/simpa/utils/constants.py
@@ -2,6 +2,8 @@
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
 
+from simpa.utils.tags import Tags
+
 EPS = 1e-20
 """
 Defines the smallest increment that should be considered by SIMPA.
@@ -27,3 +29,36 @@ class SegmentationClasses:
     MEDIPRENE = 11
     SOFT_TISSUE = 12
     LYMPH_NODE = 13
+
+
+wavelength_dependent_properties = [
+    Tags.DATA_FIELD_ABSORPTION_PER_CM,
+    Tags.DATA_FIELD_SCATTERING_PER_CM,
+    Tags.DATA_FIELD_ANISOTROPY
+]
+
+wavelength_independent_properties = [
+    Tags.DATA_FIELD_GRUNEISEN_PARAMETER,
+    Tags.DATA_FIELD_SEGMENTATION,
+    Tags.DATA_FIELD_OXYGENATION,
+    Tags.DATA_FIELD_DENSITY,
+    Tags.DATA_FIELD_SPEED_OF_SOUND,
+    Tags.DATA_FIELD_ALPHA_COEFF
+]
+
+property_tags = wavelength_dependent_properties + wavelength_independent_properties
+
+toolkit_tags = [Tags.KWAVE_PROPERTY_SENSOR_MASK, Tags.KWAVE_PROPERTY_DIRECTIVITY_ANGLE]
+
+simulation_output = [Tags.DATA_FIELD_FLUENCE,
+                     Tags.DATA_FIELD_INITIAL_PRESSURE,
+                     Tags.OPTICAL_MODEL_UNITS,
+                     Tags.DATA_FIELD_TIME_SERIES_DATA,
+                     Tags.DATA_FIELD_RECONSTRUCTED_DATA,
+                     Tags.DATA_FIELD_DIFFUSE_REFLECTANCE,
+                     Tags.DATA_FIELD_DIFFUSE_REFLECTANCE_POS,
+                     Tags.DATA_FIELD_PHOTON_EXIT_POS,
+                     Tags.DATA_FIELD_PHOTON_EXIT_DIR]
+
+simulation_output_fields = [Tags.OPTICAL_MODEL_OUTPUT_NAME,
+                            Tags.SIMULATION_PROPERTIES]
diff --git a/simpa/utils/dict_path_manager.py b/simpa/utils/dict_path_manager.py
index 2dfa7f68..c4e5e105 100644
--- a/simpa/utils/dict_path_manager.py
+++ b/simpa/utils/dict_path_manager.py
@@ -3,6 +3,8 @@
 # SPDX-License-Identifier: MIT
 
 from simpa.utils import Tags
+from simpa.utils.constants import (wavelength_dependent_properties, wavelength_independent_properties,
+                                   toolkit_tags, simulation_output, simulation_output_fields)
 
 
 def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
@@ -17,31 +19,7 @@ def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
     if data_field in [Tags.SIMULATIONS, Tags.SETTINGS, Tags.DIGITAL_DEVICE, Tags.SIMULATION_PIPELINE]:
         return "/" + data_field + "/"
 
-    wavelength_dependent_properties = [Tags.DATA_FIELD_ABSORPTION_PER_CM,
-                                       Tags.DATA_FIELD_SCATTERING_PER_CM,
-                                       Tags.DATA_FIELD_ANISOTROPY]
-
-    wavelength_independent_properties = [Tags.DATA_FIELD_OXYGENATION,
-                                         Tags.DATA_FIELD_SEGMENTATION,
-                                         Tags.DATA_FIELD_GRUNEISEN_PARAMETER,
-                                         Tags.DATA_FIELD_SPEED_OF_SOUND,
-                                         Tags.DATA_FIELD_DENSITY,
-                                         Tags.DATA_FIELD_ALPHA_COEFF,
-                                         Tags.KWAVE_PROPERTY_SENSOR_MASK,
-                                         Tags.KWAVE_PROPERTY_DIRECTIVITY_ANGLE]
-
-    simulation_output = [Tags.DATA_FIELD_FLUENCE,
-                         Tags.DATA_FIELD_INITIAL_PRESSURE,
-                         Tags.OPTICAL_MODEL_UNITS,
-                         Tags.DATA_FIELD_TIME_SERIES_DATA,
-                         Tags.DATA_FIELD_RECONSTRUCTED_DATA,
-                         Tags.DATA_FIELD_DIFFUSE_REFLECTANCE,
-                         Tags.DATA_FIELD_DIFFUSE_REFLECTANCE_POS,
-                         Tags.DATA_FIELD_PHOTON_EXIT_POS,
-                         Tags.DATA_FIELD_PHOTON_EXIT_DIR]
-
-    simulation_output_fields = [Tags.OPTICAL_MODEL_OUTPUT_NAME,
-                                Tags.SIMULATION_PROPERTIES]
+    all_wl_independent_properties = wavelength_independent_properties + toolkit_tags
 
     wavelength_dependent_image_processing_output = [Tags.ITERATIVE_qPAI_RESULT]
 
@@ -49,41 +27,31 @@ def generate_dict_path(data_field, wavelength: (int, float) = None) -> str:
 
     if wavelength is not None:
         wl = "/{}/".format(wavelength)
+    else:
+        wl = "/"
 
     if data_field in wavelength_dependent_properties:
-        if wavelength is not None:
-            dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + wl
-        else:
-            dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + "/"
+        dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + wl
     elif data_field in simulation_output:
         if data_field in [Tags.DATA_FIELD_FLUENCE, Tags.DATA_FIELD_INITIAL_PRESSURE, Tags.OPTICAL_MODEL_UNITS,
                           Tags.DATA_FIELD_DIFFUSE_REFLECTANCE, Tags.DATA_FIELD_DIFFUSE_REFLECTANCE_POS,
                           Tags.DATA_FIELD_PHOTON_EXIT_POS, Tags.DATA_FIELD_PHOTON_EXIT_DIR]:
-            if wavelength is not None:
-                dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.OPTICAL_MODEL_OUTPUT_NAME + "/" + data_field + wl
-            else:
-                dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.OPTICAL_MODEL_OUTPUT_NAME + "/" + data_field + "/"
+            dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.OPTICAL_MODEL_OUTPUT_NAME + "/" + data_field + wl
         else:
-            if wavelength is not None:
-                dict_path = "/" + Tags.SIMULATIONS + "/" + data_field + wl
-            else:
-                dict_path = "/" + Tags.SIMULATIONS + "/" + data_field + "/"
+            dict_path = "/" + Tags.SIMULATIONS + "/" + data_field + wl
 
-    elif data_field in wavelength_independent_properties:
+    elif data_field in all_wl_independent_properties:
         dict_path = "/" + Tags.SIMULATIONS + "/" + Tags.SIMULATION_PROPERTIES + "/" + data_field + "/"
     elif data_field in simulation_output_fields:
         dict_path = "/" + Tags.SIMULATIONS + "/" + data_field + "/"
     elif data_field in wavelength_dependent_image_processing_output:
-        if wavelength is not None:
-            dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + wl
-        else:
-            dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + "/"
+        dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + wl
 
     elif data_field in wavelength_independent_image_processing_output:
         dict_path = "/" + Tags.IMAGE_PROCESSING + "/" + data_field + "/"
     else:
-        raise ValueError("The requested data_field is not a valid argument. Please specify a valid data_field using "
-                         "the Tags from simpa/utils/tags.py!")
+        raise ValueError(f"The requested data_field: '{data_field}: is not a valid argument. "
+                         f"Please specify a valid data_field using the Tags from simpa/utils/tags.py!")
 
     return dict_path
 
diff --git a/simpa/utils/tissue_properties.py b/simpa/utils/tissue_properties.py
index 2496a117..02f35013 100644
--- a/simpa/utils/tissue_properties.py
+++ b/simpa/utils/tissue_properties.py
@@ -2,38 +2,21 @@
 # SPDX-FileCopyrightText: 2021 Janek Groehl
 # SPDX-License-Identifier: MIT
 
-from simpa.utils import Tags
+from simpa.utils.constants import property_tags
 
 
 class TissueProperties(dict):
 
-    wavelength_dependent_properties = [
-        Tags.DATA_FIELD_ABSORPTION_PER_CM,
-        Tags.DATA_FIELD_SCATTERING_PER_CM,
-        Tags.DATA_FIELD_ANISOTROPY
-    ]
-
-    wavelength_independent_properties = [
-        Tags.DATA_FIELD_GRUNEISEN_PARAMETER,
-        Tags.DATA_FIELD_SEGMENTATION,
-        Tags.DATA_FIELD_OXYGENATION,
-        Tags.DATA_FIELD_DENSITY,
-        Tags.DATA_FIELD_SPEED_OF_SOUND,
-        Tags.DATA_FIELD_ALPHA_COEFF
-    ]
-
-    property_tags = wavelength_dependent_properties + wavelength_independent_properties
-
     def __init__(self):
         super().__init__()
         self.volume_fraction = 0
-        for key in TissueProperties.property_tags:
+        for key in property_tags:
             self[key] = 0
 
     @staticmethod
     def normalized_merge(property_list: list):
         return_property = TissueProperties.weighted_merge(property_list)
-        for key in return_property.property_tags:
+        for key in property_tags:
             return_property[key] = return_property[key] / return_property.volume_fraction
         return return_property
 
@@ -41,7 +24,7 @@ def normalized_merge(property_list: list):
     def weighted_merge(property_list: list):
         return_property = TissueProperties()
         for target_property in property_list:
-            for key in return_property.property_tags:
+            for key in property_tags:
                 if target_property[key] is not None:
                     return_property[key] += target_property.volume_fraction * target_property[key]
             return_property.volume_fraction += target_property.volume_fraction
diff --git a/simpa_tests/test_utils/tissue_composition_tests.py b/simpa_tests/test_utils/tissue_composition_tests.py
index 8e73f8ec..daa9f067 100644
--- a/simpa_tests/test_utils/tissue_composition_tests.py
+++ b/simpa_tests/test_utils/tissue_composition_tests.py
@@ -5,6 +5,7 @@
 from simpa.utils import Tags, SegmentationClasses, calculate_gruneisen_parameter_from_temperature
 from simpa.utils.libraries.molecule_library import MolecularComposition
 from simpa.utils.tissue_properties import TissueProperties
+from simpa.utils.constants import property_tags
 from simpa.utils.libraries.tissue_library import TISSUE_LIBRARY
 import numpy as np
 import matplotlib.patches as patches
@@ -37,7 +38,7 @@ def compare_molecular_composition_against_expected_values(molecular_composition:
     if visualise_values:
         plt.figure(figsize=(12, 8))
         plt.suptitle(title + f" [green=expected, blue=actual, red={tolerated_margin_in_percent*100}% margin]")
-        num_subplots = len(TissueProperties.property_tags)
+        num_subplots = len(property_tags)
 
     for wavelength in expected_values.keys():
         molecular_composition.update_internal_properties()
@@ -45,7 +46,7 @@ def compare_molecular_composition_against_expected_values(molecular_composition:
         expected_properties = expected_values[wavelength]
 
         if visualise_values:
-            for tag_idx, tag in enumerate(TissueProperties.property_tags):
+            for tag_idx, tag in enumerate(property_tags):
                 ax = plt.subplot(3, int(np.ceil(num_subplots/3)), (tag_idx+1))
                 ax.set_title(tag)
                 ax.set_xlabel("wavelength [nm]")
@@ -57,7 +58,7 @@ def compare_molecular_composition_against_expected_values(molecular_composition:
                 ax.scatter(x=wavelength, y=composition_properties[tag], c="blue")
                 ax.scatter(x=wavelength, y=expected_properties[tag], c="green")
         else:
-            for tag in TissueProperties.property_tags:
+            for tag in property_tags:
                 if expected_properties[tag] is not None:
                     if (not (composition_properties[tag] is None and expected_properties[tag] is None)) and \
                         ((np.abs(composition_properties[tag] - expected_properties[tag]) /

From 4c0f8dd092419f22ab0055fad6a087b2099cf07b Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Wed, 13 Mar 2024 15:33:32 +0100
Subject: [PATCH 16/24] Fixed minor fov bug

---
 .../monospectral/field_of_view_cropping.py    | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/simpa/core/processing_components/monospectral/field_of_view_cropping.py b/simpa/core/processing_components/monospectral/field_of_view_cropping.py
index 0653096b..b950dc8f 100644
--- a/simpa/core/processing_components/monospectral/field_of_view_cropping.py
+++ b/simpa/core/processing_components/monospectral/field_of_view_cropping.py
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: MIT
 
 from simpa.utils import Tags, Settings
-from simpa.utils.tissue_properties import TissueProperties
+from simpa.utils.constants import property_tags, wavelength_independent_properties, toolkit_tags
 from simpa.io_handling import load_data_field, save_data_field
 from simpa.core.processing_components import ProcessingComponent
 from simpa.core.device_digital_twins import DigitalDeviceTwinBase, PhotoacousticDevice
@@ -14,11 +14,9 @@ class FieldOfViewCropping(ProcessingComponent):
 
     def __init__(self, global_settings, settings_key=None):
         if settings_key is None:
-            # TODO Extract from global settings all the fields that should be cropped
             global_settings["FieldOfViewCropping"] = Settings({
-                Tags.DATA_FIELD: TissueProperties.property_tags +
-                [Tags.DATA_FIELD_FLUENCE,
-                 Tags.DATA_FIELD_INITIAL_PRESSURE]})
+                Tags.DATA_FIELD: property_tags + toolkit_tags
+                + [Tags.DATA_FIELD_FLUENCE, Tags.DATA_FIELD_INITIAL_PRESSURE]})
         super(FieldOfViewCropping, self).__init__(global_settings, "FieldOfViewCropping")
     """
     Applies Gaussian noise to the defined data field.
@@ -61,13 +59,17 @@ def run(self, device: DigitalDeviceTwinBase):
 
         for data_field in data_fields:
             # Crop wavelength-independent properties only in the last wavelength run
-            if (data_field in TissueProperties.wavelength_independent_properties
+            if (data_field in wavelength_independent_properties
                     and wavelength != self.global_settings[Tags.WAVELENGTHS][-1]):
                 continue
-            self.logger.debug(f"Cropping data field {data_field}...")
-            data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
-            self.logger.debug(f"data array shape before cropping: {np.shape(data_array)}")
-            self.logger.debug(f"data array shape len: {len(np.shape(data_array))}")
+            try:
+                self.logger.debug(f"Cropping data field {data_field}...")
+                data_array = load_data_field(self.global_settings[Tags.SIMPA_OUTPUT_PATH], data_field, wavelength)
+
+                self.logger.debug(f"data array shape before cropping: {np.shape(data_array)}")
+                self.logger.debug(f"data array shape len: {len(np.shape(data_array))}")
+            except KeyError:
+                continue
 
             # input validation
             if not isinstance(data_array, np.ndarray):

From 0bfa7f9333d89ce43778b42f074002acb8e4795c Mon Sep 17 00:00:00 2001
From: kdreher <40358298+kdreher@users.noreply.github.com>
Date: Thu, 14 Mar 2024 10:17:29 +0100
Subject: [PATCH 17/24] Update README.md

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index f61481dc..ce75f572 100755
--- a/README.md
+++ b/README.md
@@ -75,11 +75,11 @@ acoustic simulations possible.
 
 ### mcx (Optical Forward Model)
 
-Download the latest nightly build of [mcx](http://mcx.space/) for your operating system:
+Download the latest nightly build of [mcx](http://mcx.space/) on [this page](http://mcx.space/nightly/github/) for your operating system:
 
-- [Linux](http://mcx.space/nightly/github/mcx-linux-x64-github-latest.zip)
-- [MacOS](http://mcx.space/nightly/github/mcx-macos-x64-github-latest.zip)
-- [Windows](http://mcx.space/nightly/github/mcx-windows-x64-github-latest.zip)
+- Linux: `mcx-linux-x64-github-latest.zip`
+- MacOS: `mcx-macos-x64-github-latest.zip`
+- Windows: `mcx-windows-x64-github-latest.zip`
 
 Then extract the files and set `MCX_BINARY_PATH=/.../mcx/bin/mcx` in your path_config.env.
 
@@ -221,4 +221,4 @@ Gröhl, Janek, Kris K. Dreher, Melanie Schellenberg, Tom Rix, Niklas Holzwarth,
 
 This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. [101002198]).
 
-![ERC](docs/source/images/LOGO_ERC-FLAG_EU_.jpg "ERC")
\ No newline at end of file
+![ERC](docs/source/images/LOGO_ERC-FLAG_EU_.jpg "ERC")

From c2f30f1e9143848ca3d1370e293772813c1f226c Mon Sep 17 00:00:00 2001
From: kdreher <40358298+kdreher@users.noreply.github.com>
Date: Thu, 14 Mar 2024 10:18:15 +0100
Subject: [PATCH 18/24] Bump version number

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 979b6fd8..41d08c9b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "simpa"
-version = "0.8.20"
+version = "0.9.0"
 description = "Simulation and Image Processing for Photonics and Acoustics"
 authors = [
     "Division of Intelligent Medical Systems (IMSY), DKFZ <k.dreher@dkfz-heidelberg.de>",

From dda1befc6a8f5b7065a9c8e4ec75625d93a77177 Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 2 Apr 2024 14:18:57 +0200
Subject: [PATCH 19/24] Fixes #273

---
 ...olume_creation_module_segmentation_based_adapter.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py b/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
index f766b109..490ce2eb 100644
--- a/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
+++ b/simpa/core/simulation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py
@@ -7,6 +7,7 @@
 from simpa.utils.constants import property_tags
 from simpa.io_handling import save_hdf5
 import numpy as np
+import torch
 
 
 class SegmentationBasedVolumeCreationAdapter(VolumeCreatorModuleBase):
@@ -42,8 +43,15 @@ def create_simulation_volume(self) -> dict:
         for seg_class in segmentation_classes:
             class_properties = class_mapping[seg_class].get_properties_for_wavelength(wavelength)
             for prop_tag in property_tags:
-                volumes[prop_tag][segmentation_volume == seg_class] = class_properties[prop_tag]
+                assigned_prop = class_properties[prop_tag]
+                if assigned_prop is None:
+                    assigned_prop = torch.nan
+                volumes[prop_tag][segmentation_volume == seg_class] = assigned_prop
 
         save_hdf5(self.global_settings, self.global_settings[Tags.SIMPA_OUTPUT_PATH], "/settings/")
 
+        # convert volumes back to CPU
+        for key in volumes.keys():
+            volumes[key] = volumes[key].cpu().numpy().astype(np.float64, copy=False)
+
         return volumes

From eee19e19d77c0df706d791cae56182b0c1e23526 Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 2 Apr 2024 14:20:13 +0200
Subject: [PATCH 20/24] Bump version number to 0.9.1

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 41d08c9b..e97d1632 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "simpa"
-version = "0.9.0"
+version = "0.9.1"
 description = "Simulation and Image Processing for Photonics and Acoustics"
 authors = [
     "Division of Intelligent Medical Systems (IMSY), DKFZ <k.dreher@dkfz-heidelberg.de>",

From a0ebf3000480e97405175446e079882149e4407e Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 2 Apr 2024 15:13:56 +0200
Subject: [PATCH 21/24] Updated docs

---
 .readthedocs.yaml              |    2 +-
 docs/source/introduction.md    |   16 +-
 docs/source/simpa.utils.rst    |    6 +
 docs/source/simpa_examples.rst |    8 +-
 poetry.lock                    | 1710 ++++++++++++++++++++------------
 pyproject.toml                 |    2 +-
 6 files changed, 1073 insertions(+), 671 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 86e7a6d4..a492a325 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -12,7 +12,7 @@ build:
       - asdf global poetry latest
       - poetry config virtualenvs.create true
     post_install:
-      - poetry install
+      - poetry install --all-extras
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
diff --git a/docs/source/introduction.md b/docs/source/introduction.md
index 593b74d1..c1dde86d 100644
--- a/docs/source/introduction.md
+++ b/docs/source/introduction.md
@@ -39,11 +39,11 @@ acoustic simulations possible.
 
 ### mcx (Optical Forward Model)
 
-Download the latest nightly build of [mcx](http://mcx.space/) for your operating system:
+Download the latest nightly build of [mcx](http://mcx.space/) on [this page](http://mcx.space/nightly/github/) for your operating system:
 
-- [Linux](http://mcx.space/nightly/github/mcx-linux-x64-github-latest.zip)
-- [MacOS](http://mcx.space/nightly/github/mcx-macos-x64-github-latest.zip)
-- [Windows](http://mcx.space/nightly/github/mcx-windows-x64-github-latest.zip)
+- Linux: `mcx-linux-x64-github-latest.zip`
+- MacOS: `mcx-macos-x64-github-latest.zip`
+- Windows: `mcx-windows-x64-github-latest.zip`
 
 Then extract the files and set `MCX_BINARY_PATH=/.../mcx/bin/mcx` in your path_config.env.
 
@@ -55,12 +55,10 @@ for further (and much better) guidance under:
 [http://www.k-wave.org/](http://www.k-wave.org/)
 
 1. Install MATLAB with the core, image processing and parallel computing toolboxes activated at the minimum.
-2. Download the kWave toolbox
+2. Download the kWave toolbox (version >= 1.4)
 3. Add the kWave toolbox base path to the toolbox paths in MATLAB
-4. Download the kWaveArray addition from the link given in this user forum post [http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources](http://www.k-wave.org/forum/topic/alpha-version-of-kwavearray-off-grid-sources)
-5. Add the kWaveArray folder to the toolbox paths in MATLAB as well
-6. If wanted: Download the CPP and CUDA binary files and place them in the k-Wave/binaries folder
-7. Note down the system path to the `matlab` executable file.
+4. If wanted: Download the CPP and CUDA binary files and place them in the k-Wave/binaries folder
+5. Note down the system path to the `matlab` executable file.
 
 ## Path management
 
diff --git a/docs/source/simpa.utils.rst b/docs/source/simpa.utils.rst
index c8b151b9..a7aa845d 100644
--- a/docs/source/simpa.utils.rst
+++ b/docs/source/simpa.utils.rst
@@ -36,6 +36,12 @@ utils
    :show-inheritance:
 
 
+.. automodule:: simpa.utils.matlab
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
 .. automodule:: simpa.utils.path_manager
    :members:
    :undoc-members:
diff --git a/docs/source/simpa_examples.rst b/docs/source/simpa_examples.rst
index 458cd47a..7f54dbbb 100644
--- a/docs/source/simpa_examples.rst
+++ b/docs/source/simpa_examples.rst
@@ -4,12 +4,12 @@ simpa\_examples
 .. toctree::
    :maxdepth: 2
 
-   linear_unmixing
    create_a_custom_digital_device_twin
+   create_custom_tissues
+   linear_unmixing
+   minimal_optical_simulation
    msot_invision_simulation
-   perform_image_reconstruction
    perform_iterative_qPAI_reconstruction
-   create_custom_tissues
    segmentation_loader
-   minimal_optical_simulation
+   perform_image_reconstruction
    optical_and_acoustic_simulation
diff --git a/poetry.lock b/poetry.lock
index 03a20b61..d59220a5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -13,122 +13,140 @@ files = [
 
 [[package]]
 name = "babel"
-version = "2.12.1"
+version = "2.14.0"
 description = "Internationalization utilities"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Babel-2.12.1-py3-none-any.whl", hash = "sha256:b4246fb7677d3b98f501a39d43396d3cafdc8eadb045f4a31be01863f655c610"},
-    {file = "Babel-2.12.1.tar.gz", hash = "sha256:cc2d99999cd01d44420ae725a21c9e3711b3aadc7976d6147f622d8581963455"},
+    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
+    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
 ]
 
 [package.dependencies]
 pytz = {version = ">=2015.7", markers = "python_version < \"3.9\""}
 
+[package.extras]
+dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+
 [[package]]
 name = "certifi"
-version = "2023.7.22"
+version = "2024.2.2"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.7.22-py3-none-any.whl", hash = "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9"},
-    {file = "certifi-2023.7.22.tar.gz", hash = "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082"},
+    {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+    {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
 ]
 
 [[package]]
 name = "cfgv"
-version = "3.3.1"
+version = "3.4.0"
 description = "Validate configuration and produce human readable error messages."
 optional = false
-python-versions = ">=3.6.1"
+python-versions = ">=3.8"
 files = [
-    {file = "cfgv-3.3.1-py2.py3-none-any.whl", hash = "sha256:c6a0883f3917a037485059700b9e75da2464e6c27051014ad85ba6aaa5884426"},
-    {file = "cfgv-3.3.1.tar.gz", hash = "sha256:f5a830efb9ce7a445376bb66ec94c638a9787422f96264c98edc6bdeed8ab736"},
+    {file = "cfgv-3.4.0-py2.py3-none-any.whl", hash = "sha256:b7265b1f29fd3316bfcd2b330d63d024f2bfd8bcb8b0272f8e19a504856c48f9"},
+    {file = "cfgv-3.4.0.tar.gz", hash = "sha256:e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.2.0"
+version = "3.3.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.2.0.tar.gz", hash = "sha256:3bb3d25a8e6c0aedd251753a79ae98a093c7e7b471faa3aa9a93a81431987ace"},
-    {file = "charset_normalizer-3.2.0-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:0b87549028f680ca955556e3bd57013ab47474c3124dc069faa0b6545b6c9710"},
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 test = ["Pillow", "contourpy[test-no-images]", "matplotlib"]
 test-no-images = ["pytest", "pytest-cov", "wurlitzer"]
 
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 ]
 
 [package.dependencies]
@@ -277,15 +362,19 @@ toml = ["tomli"]
 
 [[package]]
 name = "cycler"
-version = "0.11.0"
+version = "0.12.1"
 description = "Composable style cycles"
 optional = false
-python-versions = ">=3.6"
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 ]
 
+[package.extras]
+docs = ["ipython", "matplotlib", "numpydoc", "sphinx"]
+tests = ["pytest", "pytest-cov", "pytest-xdist"]
+
 [[package]]
 name = "deprecated"
 version = "1.2.14"
@@ -305,13 +394,13 @@ dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "distlib"
-version = "0.3.7"
+version = "0.3.8"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [[package]]
@@ -327,13 +416,13 @@ files = [
 
 [[package]]
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-version = "1.1.2"
+version = "1.2.0"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
@@ -341,104 +430,152 @@ test = ["pytest (>=6)"]
 
 [[package]]
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+version = "3.13.3"
 description = "A platform independent file lock."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
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+docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
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+typing = ["typing-extensions (>=4.8)"]
 
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 ]
 
 [package.dependencies]
@@ -446,13 +583,13 @@ numpy = ">=1.17.3"
 
 [[package]]
 name = "identify"
-version = "2.5.26"
+version = "2.5.35"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -460,24 +597,24 @@ license = ["ukkonen"]
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.6"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
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-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
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+    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
 ]
 
 [[package]]
 name = "imageio"
-version = "2.31.1"
+version = "2.34.0"
 description = "Library for reading and writing a wide range of image, video, scientific, and volumetric data formats."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "imageio-2.34.0.tar.gz", hash = "sha256:ae9732e10acf807a22c389aef193f42215718e16bd06eed0c5bb57e1034a4d53"},
 ]
 
 [package.dependencies]
@@ -485,17 +622,18 @@ numpy = "*"
 pillow = ">=8.3.2"
 
 [package.extras]
-all-plugins = ["astropy", "av", "imageio-ffmpeg", "psutil", "tifffile"]
-all-plugins-pypy = ["av", "imageio-ffmpeg", "psutil", "tifffile"]
+all-plugins = ["astropy", "av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
+all-plugins-pypy = ["av", "imageio-ffmpeg", "pillow-heif", "psutil", "tifffile"]
 build = ["wheel"]
 dev = ["black", "flake8", "fsspec[github]", "pytest", "pytest-cov"]
 docs = ["numpydoc", "pydata-sphinx-theme", "sphinx (<6)"]
 ffmpeg = ["imageio-ffmpeg", "psutil"]
 fits = ["astropy"]
-full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpydoc", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
+full = ["astropy", "av", "black", "flake8", "fsspec[github]", "gdal", "imageio-ffmpeg", "itk", "numpydoc", "pillow-heif", "psutil", "pydata-sphinx-theme", "pytest", "pytest-cov", "sphinx (<6)", "tifffile", "wheel"]
 gdal = ["gdal"]
 itk = ["itk"]
 linting = ["black", "flake8"]
+pillow-heif = ["pillow-heif"]
 pyav = ["av"]
 test = ["fsspec[github]", "pytest", "pytest-cov"]
 tifffile = ["tifffile"]
@@ -513,40 +651,40 @@ files = [
 
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "7.1.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
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 [[package]]
 name = "importlib-resources"
-version = "6.0.0"
+version = "6.4.0"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
 zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
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+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -561,13 +699,13 @@ files = [
 
 [[package]]
 name = "jdata"
-version = "0.5.3"
+version = "0.6.0"
 description = "Encoding and decoding Python data structrues using portable JData-annotated formats"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -575,13 +713,13 @@ numpy = ">=1.8.0"
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.3"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -592,79 +730,115 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "kiwisolver"
-version = "1.4.4"
+version = "1.4.5"
 description = "A fast implementation of the Cassowary constraint solver"
 optional = false
 python-versions = ">=3.7"
 files = [
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@@ -708,111 +882,127 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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 [package.dependencies]
@@ -821,10 +1011,10 @@ cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
 kiwisolver = ">=1.0.1"
-numpy = ">=1.20"
+numpy = ">=1.20,<2"
 packaging = ">=20.0"
 pillow = ">=6.2.0"
-pyparsing = ">=2.3.1,<3.1"
+pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
 
 [[package]]
@@ -991,6 +1181,148 @@ files = [
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 ]
 
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 docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinx-removed-in", "sphinxext-opengraph"]
+fpx = ["olefile"]
+mic = ["olefile"]
 tests = ["check-manifest", "coverage", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout"]
+typing = ["typing-extensions"]
+xmp = ["defusedxml"]
 
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 name = "platformdirs"
-version = "3.9.1"
+version = "4.2.0"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.3.1)", "pytest-cov (>=4.1)", "pytest-mock (>=3.10)"]
+docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.4.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -1192,13 +1541,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
-version = "3.3.3"
+version = "3.5.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pre_commit-3.5.0.tar.gz", hash = "sha256:5804465c675b659b0862f07907f96295d490822a450c4c40e747d0b1c6ebcb32"},
 ]
 
 [package.dependencies]
@@ -1210,17 +1559,18 @@ virtualenv = ">=20.10.0"
 
 [[package]]
 name = "pygments"
-version = "2.15.1"
+version = "2.17.2"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.extras]
 plugins = ["importlib-metadata"]
+windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pynrrd"
@@ -1240,13 +1590,13 @@ typing-extensions = "*"
 
 [[package]]
 name = "pyparsing"
-version = "3.0.9"
+version = "3.1.2"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
 python-versions = ">=3.6.8"
 files = [
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-    {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
+    {file = "pyparsing-3.1.2-py3-none-any.whl", hash = "sha256:f9db75911801ed778fe61bb643079ff86601aca99fcae6345aa67292038fb742"},
+    {file = "pyparsing-3.1.2.tar.gz", hash = "sha256:a1bac0ce561155ecc3ed78ca94d3c9378656ad4c94c1270de543f621420f94ad"},
 ]
 
 [package.extras]
@@ -1254,13 +1604,13 @@ diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
-version = "7.4.0"
+version = "8.1.1"
 description = "pytest: simple powerful testing with Python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-7.4.0-py3-none-any.whl", hash = "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32"},
-    {file = "pytest-7.4.0.tar.gz", hash = "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a"},
+    {file = "pytest-8.1.1-py3-none-any.whl", hash = "sha256:2a8386cfc11fa9d2c50ee7b2a57e7d898ef90470a7a34c4b949ff59662bb78b7"},
+    {file = "pytest-8.1.1.tar.gz", hash = "sha256:ac978141a75948948817d360297b7aae0fcb9d6ff6bc9ec6d514b85d5a65c044"},
 ]
 
 [package.dependencies]
@@ -1268,21 +1618,21 @@ colorama = {version = "*", markers = "sys_platform == \"win32\""}
 exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
-tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
+pluggy = ">=1.4,<2.0"
+tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
+testing = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
-version = "4.1.0"
+version = "5.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
-    {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
+    {file = "pytest-cov-5.0.0.tar.gz", hash = "sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857"},
+    {file = "pytest_cov-5.0.0-py3-none-any.whl", hash = "sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652"},
 ]
 
 [package.dependencies]
@@ -1290,17 +1640,17 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "python-dateutil"
-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
-    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+    {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
+    {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
 
 [package.dependencies]
@@ -1308,13 +1658,13 @@ six = ">=1.5"
 
 [[package]]
 name = "python-dotenv"
-version = "1.0.0"
+version = "1.0.1"
 description = "Read key-value pairs from a .env file and set them as environment variables"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "python-dotenv-1.0.0.tar.gz", hash = "sha256:a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba"},
-    {file = "python_dotenv-1.0.0-py3-none-any.whl", hash = "sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a"},
+    {file = "python-dotenv-1.0.1.tar.gz", hash = "sha256:e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca"},
+    {file = "python_dotenv-1.0.1-py3-none-any.whl", hash = "sha256:f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a"},
 ]
 
 [package.extras]
@@ -1322,13 +1672,13 @@ cli = ["click (>=5.0)"]
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2024.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2023.3-py2.py3-none-any.whl", hash = "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"},
-    {file = "pytz-2023.3.tar.gz", hash = "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588"},
+    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
+    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
 ]
 
 [[package]]
@@ -1380,6 +1730,7 @@ files = [
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     {file = "PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:ba336e390cd8e4d1739f42dfe9bb83a3cc2e80f567d8805e11b46f4a943f5515"},
+    {file = "PyYAML-6.0.1-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:326c013efe8048858a6d312ddd31d56e468118ad4cdeda36c719bf5bb6192290"},
     {file = "PyYAML-6.0.1-cp310-cp310-win32.whl", hash = "sha256:bd4af7373a854424dabd882decdc5579653d7868b8fb26dc7d0e99f823aa5924"},
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@@ -1387,8 +1738,16 @@ files = [
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     {file = "PyYAML-6.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:bf07ee2fef7014951eeb99f56f39c9bb4af143d8aa3c21b1677805985307da34"},
+    {file = "PyYAML-6.0.1-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:855fb52b0dc35af121542a76b9a84f8d1cd886ea97c84703eaa6d88e37a2ad28"},
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+    {file = "PyYAML-6.0.1-cp312-cp312-win32.whl", hash = "sha256:d483d2cdf104e7c9fa60c544d92981f12ad66a457afae824d146093b8c294c54"},
+    {file = "PyYAML-6.0.1-cp312-cp312-win_amd64.whl", hash = "sha256:0d3304d8c0adc42be59c5f8a4d9e3d7379e6955ad754aa9d6ab7a398b59dd1df"},
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     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:1fe35611261b29bd1de0070f0b2f47cb6ff71fa6595c077e42bd0c419fa27b98"},
     {file = "PyYAML-6.0.1-cp36-cp36m-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:704219a11b772aea0d8ecd7058d0082713c3562b4e271b849ad7dc4a5c90c13c"},
@@ -1405,6 +1764,7 @@ files = [
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     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:28c119d996beec18c05208a8bd78cbe4007878c6dd15091efb73a30e90539696"},
     {file = "PyYAML-6.0.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:7e07cbde391ba96ab58e532ff4803f79c4129397514e1413a7dc761ccd755735"},
+    {file = "PyYAML-6.0.1-cp38-cp38-musllinux_1_1_x86_64.whl", hash = "sha256:49a183be227561de579b4a36efbb21b3eab9651dd81b1858589f796549873dd6"},
     {file = "PyYAML-6.0.1-cp38-cp38-win32.whl", hash = "sha256:184c5108a2aca3c5b3d3bf9395d50893a7ab82a38004c8f61c258d4428e80206"},
     {file = "PyYAML-6.0.1-cp38-cp38-win_amd64.whl", hash = "sha256:1e2722cc9fbb45d9b87631ac70924c11d3a401b2d7f410cc0e3bbf249f2dca62"},
     {file = "PyYAML-6.0.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8"},
@@ -1412,6 +1772,7 @@ files = [
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     {file = "PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:bc1bf2925a1ecd43da378f4db9e4f799775d6367bdb94671027b73b393a7c42c"},
+    {file = "PyYAML-6.0.1-cp39-cp39-musllinux_1_1_x86_64.whl", hash = "sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5"},
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     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
@@ -1528,19 +1889,19 @@ test = ["asv", "gmpy2", "mpmath", "pytest", "pytest-cov", "pytest-xdist", "sciki
 
 [[package]]
 name = "setuptools"
-version = "68.0.0"
+version = "69.2.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "setuptools-68.0.0-py3-none-any.whl", hash = "sha256:11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f"},
-    {file = "setuptools-68.0.0.tar.gz", hash = "sha256:baf1fdb41c6da4cd2eae722e135500da913332ab3f2f5c7d33af9b492acb5235"},
+    {file = "setuptools-69.2.0-py3-none-any.whl", hash = "sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c"},
+    {file = "setuptools-69.2.0.tar.gz", hash = "sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-hoverxref (<2)", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (==0.8.3)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pip-run (>=8.8)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv]", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -1601,18 +1962,18 @@ test = ["cython", "html5lib", "pytest (>=4.6)", "typed_ast"]
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.2.2"
+version = "2.0.0"
 description = "Read the Docs theme for Sphinx"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.6"
 files = [
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+    {file = "sphinx_rtd_theme-2.0.0-py2.py3-none-any.whl", hash = "sha256:ec93d0856dc280cf3aee9a4c9807c60e027c7f7b461b77aeffed682e68f0e586"},
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 ]
 
 [package.dependencies]
-docutils = "<0.19"
-sphinx = ">=1.6,<7"
+docutils = "<0.21"
+sphinx = ">=5,<8"
 sphinxcontrib-jquery = ">=4,<5"
 
 [package.extras]
@@ -1765,100 +2126,142 @@ files = [
 
 [[package]]
 name = "torch"
-version = "2.0.1"
+version = "2.2.2"
 description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration"
 optional = false
 python-versions = ">=3.8.0"
 files = [
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+    {file = "wrapt-1.16.0-py3-none-any.whl", hash = "sha256:6906c4100a8fcbf2fa735f6059214bb13b97f75b1a61777fcf6432121ef12ef1"},
+    {file = "wrapt-1.16.0.tar.gz", hash = "sha256:5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d"},
 ]
 
 [[package]]
@@ -1968,20 +2366,20 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.16.2"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.16.2-py3-none-any.whl", hash = "sha256:679e51dd4403591b2d6838a48de3d283f3d188412a9782faadf845f298736ba0"},
-    {file = "zipp-3.16.2.tar.gz", hash = "sha256:ebc15946aa78bd63458992fc81ec3b6f7b1e92d51c35e6de1c3804e73b799147"},
+    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8"
-content-hash = "df229890fcc3919670a7bd56fb82cd1dcacb9d3087b350ec62e9b2e4f7835ec2"
+content-hash = "f4aae213c4409d4c72aa6efe6efe6a3da367357a5a408e9a14faf4d5b1e45eeb"
diff --git a/pyproject.toml b/pyproject.toml
index e97d1632..2b836a84 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -41,7 +41,7 @@ jdata = ">=0.5.2"            # Uses Apache 2.0-License (MIT compatible)
 pre-commit = ">=3.2.2"       # Uses MIT-License (MIT compatible) 
 
 [tool.poetry.group.docs.dependencies]
-sphinx-rtd-theme = "^1.0.0"
+sphinx-rtd-theme = "^2.0.0"
 Sphinx = "^5.1.1"
 myst-parser = "0.18.0, <1.1"
 

From 39a836437ad67cc1632aae1509fff4ce63c0175a Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 2 Apr 2024 15:22:07 +0200
Subject: [PATCH 22/24] added sphinx rtd theme to sphinx extensions

---
 docs/source/conf.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 354a021a..49e0e7fd 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -45,7 +45,8 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
-    'myst_parser',
+    'myst_parser'
+    'sphinx_rtd_theme',
 ]
 
 # Napoleon settings

From 1218785d84171f52677b064404e0a4104193f70d Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 2 Apr 2024 15:32:13 +0200
Subject: [PATCH 23/24] Fixed sphinx extension bug

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 49e0e7fd..f8c9102b 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -45,7 +45,7 @@
     'sphinx.ext.intersphinx',
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
-    'myst_parser'
+    'myst_parser',
     'sphinx_rtd_theme',
 ]
 

From 22b4c8e223dd4d5ad32ecccc5e583ff59fdae67f Mon Sep 17 00:00:00 2001
From: Kris Dreher <k.dreher@dkfz-heidelberg.de>
Date: Tue, 2 Apr 2024 17:10:29 +0200
Subject: [PATCH 24/24] Changed to new way of installing poetry on rtd

---
 .readthedocs.yaml   | 13 +++++--------
 docs/source/conf.py |  1 -
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index a492a325..a1d14d08 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -3,16 +3,13 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
-  tools: {python: "3.9"}
+  os: ubuntu-22.04
+  tools: {python: "3.10"}
   jobs:
-    pre_create_environment:
-      - asdf plugin add poetry
-      - asdf install poetry latest
-      - asdf global poetry latest
-      - poetry config virtualenvs.create true
+    post_create_environment:
+      - pip install poetry
     post_install:
-      - poetry install --all-extras
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
diff --git a/docs/source/conf.py b/docs/source/conf.py
index f8c9102b..354a021a 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -46,7 +46,6 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.viewcode',
     'myst_parser',
-    'sphinx_rtd_theme',
 ]
 
 # Napoleon settings