Merge pull request #160 from AustralianCancerDataNetwork/advanced-doc…

…umentation Advanced documentation
AustralianCancerDataNetwork · Dec 8, 2023 · d53ec2c · d53ec2c
2 parents 3096e2c + 9b33815
commit d53ec2c
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Showing 16 changed files with 3,473 additions and 1,273 deletions.
diff --git a/docs/conf.py b/docs/conf.py
@@ -85,7 +85,10 @@ def setup(app):
 shutil.copy("../examples/VisualiseData.ipynb", "_examples/VisualiseData.ipynb")
 shutil.copy("../examples/DoseMetrics.ipynb", "_examples/DoseMetrics.ipynb")
 shutil.copy("../examples/Radiomics.ipynb", "_examples/Radiomics.ipynb")
-shutil.copy(
-    "../examples/DatasetPreparation.ipynb", "_examples/DatasetPreparation.ipynb"
-)
+shutil.copy("../examples/DatasetPreparation.ipynb", "_examples/DatasetPreparation.ipynb")
 shutil.copy("../examples/WorkingWithData.ipynb", "_examples/WorkingWithData.ipynb")
+shutil.copy("../examples/WorkingWithStructures.ipynb", "_examples/WorkingWithStructures.ipynb")
+shutil.copy("../examples/Configuration.ipynb", "_examples/Configuration.ipynb")
+shutil.copy("../examples/ObjectGeneration.ipynb", "_examples/ObjectGeneration.ipynb")
+shutil.copy("../examples/AutoSegmentation.ipynb", "_examples/AutoSegmentation.ipynb")
+shutil.copy("../examples/nnUNet.ipynb", "_examples/nnUNet.ipynb")
diff --git a/docs/dataset.rst b/docs/dataset.rst
@@ -13,3 +13,9 @@ Preparation Functions
 
 .. automodule:: pydicer.dataset.functions
     :members:
+
+Structure Sets
+==============
+
+.. automodule:: pydicer.dataset.structureset
+    :members:
diff --git a/docs/generate.rst b/docs/generate.rst
@@ -0,0 +1,23 @@
+#####################
+Generation
+#####################
+
+Objects
+=======
+
+.. automodule:: pydicer.generate.object
+    :members:
+
+Auto-segmentation
+=================
+
+.. automodule:: pydicer.generate.segmentation
+    :members:
+
+
+Models
+======
+
+.. automodule:: pydicer.generate.models
+    :members:
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -11,13 +11,18 @@
     _examples/Radiomics
     _examples/DoseMetrics
     _examples/DatasetPreparation
+    _examples/AutoSegmentation
+    _examples/nnUNet
 
 .. toctree::
     :caption: Guides
     :maxdepth: 2
     :hidden:
 
     _examples/WorkingWithData
+    _examples/WorkingWithStructures
+    _examples/ObjectGeneration
+    _examples/Configuration
 
 .. toctree::
     :caption: Developers
@@ -35,9 +40,11 @@
    tool
    input
    config
+   utils
    preprocess
    convert
    visualise
    dataset
    analyse
+   generate
    nnunet
diff --git a/docs/utils.rst b/docs/utils.rst
@@ -0,0 +1,6 @@
+#####################
+Utils
+#####################
+
+.. automodule:: pydicer.utils
+    :members: