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Advanced documentation #160

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merged 11 commits into from
Dec 8, 2023
Merged

Advanced documentation #160

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9bf47a8
use function to read sitk image
pchlap Dec 5, 2023
5728d97
Guide for working with structure sets
pchlap Dec 5, 2023
ee49bb7
Add configuration guide
pchlap Dec 5, 2023
1d22ec7
Update to working with structures guide
pchlap Dec 5, 2023
8bf8486
Add object generation documentation
pchlap Dec 5, 2023
77cc0b8
Add nnUNet example
pchlap Dec 5, 2023
b887a97
Merge branch 'main' into advanced-documentation
pchlap Dec 6, 2023
c592d08
Add auto-segmentation example
pchlap Dec 6, 2023
7a0f3cd
Run poetry lock
pchlap Dec 6, 2023
c08b227
Use a different directory for the auto-seg example
pchlap Dec 6, 2023
9b33815
Clear outputs in example notebook
pchlap Dec 7, 2023
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9 changes: 6 additions & 3 deletions docs/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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")
6 changes: 6 additions & 0 deletions docs/dataset.rst
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Expand Up @@ -13,3 +13,9 @@ Preparation Functions

.. automodule:: pydicer.dataset.functions
:members:

Structure Sets
==============

.. automodule:: pydicer.dataset.structureset
:members:
23 changes: 23 additions & 0 deletions docs/generate.rst
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@@ -0,0 +1,23 @@
#####################
Generation
#####################

Objects
=======

.. automodule:: pydicer.generate.object
:members:

Auto-segmentation
=================

.. automodule:: pydicer.generate.segmentation
:members:


Models
======

.. automodule:: pydicer.generate.models
:members:

7 changes: 7 additions & 0 deletions docs/index.rst
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Expand Up @@ -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
Expand All @@ -35,9 +40,11 @@
tool
input
config
utils
preprocess
convert
visualise
dataset
analyse
generate
nnunet
6 changes: 6 additions & 0 deletions docs/utils.rst
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@@ -0,0 +1,6 @@
#####################
Utils
#####################

.. automodule:: pydicer.utils
:members:
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