Merge pull request IMSY-DKFZ#274 from IMSY-DKFZ/develop

Merge fix for IMSY-DKFZ#273 from develop
invimg · Apr 2, 2024 · b2c2461 · b2c2461
2 parents c2f30f1 + 22b4c8e
commit b2c2461
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diff --git 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
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git 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
@@ -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
@@ -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
diff --git 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>",
@@ -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"
 

diff --git a/...ation_modules/volume_creation_module/volume_creation_module_segmentation_based_adapter.py b/...ation_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