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mkdocs.yml
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site_name: ShapeWorks
site_url: https://www.sci.utah.edu/software/shapeworks.html
repo_url: https://github.com/SCIInstitute/ShapeWorks
repo_name: SCIInstitute/ShapeWorks
edit_uri: edit/master/docs/ # should be changed to master branch
site_description: The official documentation of ShapeWorks
site_author: Shireen Elhabian et al.
use_directory_urls: false
docs_dir: 'docs/'
copyright: Copyright © 1998 - 2024 Scientific Computing and Imaging Institute. All rights reserved. This project is supported by the National Institutes of Health under grant numbers NIBIB-U24EB029011, NIAMS-R01AR076120, NHLBI-R01HL135568, and NIBIB-R01EB016701. Software maintenance and support are provided within the funding period.
google_analytics: ['UA-36723568-3', 'mkdocs.org']
nav:
- Home: 'index.md'
- Getting Started:
- 'Shapes, What & From Where?': 'getting-started/shapes.md'
- 'Shape Modeling Workflow': 'getting-started/workflow.md'
- 'ShapeWorks Success Stories': 'getting-started/sw-stories.md'
- 'ShapeWorks Interfaces': 'getting-started/interfaces.md'
- 'Examples': 'getting-started/examples.md'
- 'How-Tos': 'getting-started/how-tos.md'
- For Users:
- 'How to Install ShapeWorks?': 'users/install.md'
- 'How to Cite ShapeWorks?': 'users/citation.md'
- 'Revelant Papers': 'users/papers.md'
- Workflow:
- 'How to Groom Your Dataset?': 'workflow/groom.md'
- Shape Model Optimization:
- 'How to Optimize Your Shape Model?': 'workflow/optimize.md'
- 'Optimization Parameters': 'workflow/parameters.md'
- 'How to Analyze Your Shape Model?' : 'workflow/analyze.md'
- What is New?:
- 'New in ShapeWorks Studio': 'new/new-studio.md'
- 'ShapeWorks Takes ~85% Less Memory': 'new/openvdb.md'
- 'ShapeWorks Directly on Meshes': 'new/sw-meshes.md'
- 'ShapeWorks Command': 'new/shapeworks-command.md'
- 'Shape Model Evaluation': 'new/ssm-eval.md'
- 'ShapeWorks in Python': 'new/shapeworks-python.md'
- 'Ellipsoid Joint Generation': 'new/ellipsoid-joint-generation.md'
- ShapeWorks Studio:
- 'Getting Started': 'studio/getting-started-with-studio.md'
- 'Viewer Controls': 'studio/studio-viewer.md'
- 'Export Options': 'studio/studio-export.md'
- 'Data Module': 'studio/studio-data.md'
- 'Groom Module': 'studio/studio-groom.md'
- 'Optimize Module': 'studio/studio-optimize.md'
- 'Analyze Module': 'studio/studio-analyze.md'
- 'DeepSSM Module': 'studio/deepssm-in-studio.md'
- 'Multiple Domains SSM': 'studio/multiple-domains.md'
- 'Shared Boundaries': 'studio/studio-shared-boundary.md'
- ShapeWorks Cloud:
- 'Getting Started': 'cloud/getting-started-with-cloud.md'
- 'Datasets': 'cloud/cloud-dataset.md'
- 'Projects': 'cloud/cloud-project.md'
- 'Data Module': 'cloud/cloud-data-module.md'
- 'Groom Module': 'cloud/cloud-groom-module.md'
- 'Optimize Module': 'cloud/cloud-optimize-module.md'
- 'Analyze Module': 'cloud/cloud-analyze-module.md'
- 'Shape Viewer': 'cloud/cloud-shape-viewer.md'
- 'ShapeWorks Cloud Client': 'cloud/swcc.md'
- ShapeWorks Tools:
- 'ShapeWorks Commands': 'tools/ShapeWorksCommands.md'
- ShapeWorks in Python:
- 'Getting Started with Notebooks' : 'notebooks/getting-started-with-notebooks.ipynb'
- 'Getting Started with Segmentations' : 'notebooks/getting-started-with-segmentations.ipynb'
- 'Getting Started with Meshes' : 'notebooks/getting-started-with-meshes.ipynb'
- 'Getting Started with Exploring Segmentations' : 'notebooks/getting-started-with-exploring-segmentations.ipynb'
- 'Getting Started with Data Augmentation' : 'notebooks/getting-started-with-data-augmentation.ipynb'
- 'Getting Started with Shape Cohort Generation' : 'notebooks/getting-started-with-shape-cohort-generation.ipynb'
- 'Array passing without copying' : 'notebooks/array-passing-without-copying.ipynb'
- 'Create and apply Image transforms' : 'notebooks/create-and-apply-image-transforms.ipynb'
- 'Create and apply Mesh transforms' : 'notebooks/create-and-apply-mesh-transforms.ipynb'
- Deep Learning & SSMs:
- 'PyTorch GPU Support for ShapeWorks': 'deep-learning/pytorch-gpu.md'
- 'Data Augmentation for Deep Learning': 'deep-learning/data-augmentation.md'
- 'SSMs Directly from Images': 'deep-learning/deep-ssm.md'
- Use Cases:
- 'Getting Started with Use Cases': 'use-cases/use-cases.md'
- Segmentation Based Use Cases:
- 'Ellipsoid: Basic Example': 'use-cases/segmentation-based/ellipsoid.md'
- 'Left Atrium: Shape Model from Segmentations': 'use-cases/segmentation-based/left-atrium.md'
- 'Shape Model for Multiple Domains from Segmentations': 'use-cases/segmentation-based/ellipsoid-multiple-domain.md'
- Mesh Based Use Cases:
- 'Ellipsoid Mesh: Basic Example': 'use-cases/mesh-based/ellipsoid_mesh.md'
- 'Lumps: Shape Model directly from Mesh': 'use-cases/mesh-based/lumps.md'
- 'Thin Cavity Bean: Shape Model with Geodesic Distances': 'use-cases/mesh-based/thin-cavity-bean.md'
- 'Shape Model for Multiple Domains directly from Mesh': 'use-cases/mesh-based/ellipsoid-multiple-domain-mesh.md'
- 'Hip: Multiple Domains Alignment': 'use-cases/mesh-based/hip.md'
- Contour Based Use Cases:
- 'Supershapes:Shape Model for Contour Domains': 'use-cases/contour-based/supershapes-contour.md'
- Constraints Based Use Cases:
- 'Ellipsoid: Shape Model with Cutting Planes': 'use-cases/constraint-based/ellipsoid-cutting-planes.md'
- 'Femur:Shape Model with Cutting Planes': 'use-cases//constraint-based/femur-cutting-planes.md'
- 'Studio Femur: Shape Model from Meshes with Cutting Planes Using Studio': 'use-cases//constraint-based/femur-cutting-planes-studio.md'
- Multi-Step Optimization Use Cases:
- 'Fixed Domains Ellipsoid: Shape Model on New Shapes': 'use-cases/multistep/fixed-domain-ellipsoid.md'
- 'Incremental Supershapes: Building a Shape Model Incrementally': 'use-cases/multistep/incremental_supershapes.md'
- Statistics Based Use Cases:
- 'Ellipsoid: Shape Statistics in Python': 'use-cases/stats-based/ellipsoid-pca.md'
- 'Femur: Group Difference Statistics in Python': 'use-cases/stats-based/femur-pvalues.md'
- 'Ellipsoid: Shape Evaluation in Python': 'use-cases/stats-based/ellipsoid-evaluate.md'
- Deep Learning Based Use Cases:
- 'Femur SSM Directly from Images': 'use-cases/deep-learning-based/deep-ssm-femur.md'
- Shared Boundary Use Cases:
- 'Peanut:Shape Model of Multiple Domains with Shared Boundaries': 'use-cases/shared-boundary-based/peanut.md'
- 'Right Ventricle: Highly Variable Shapes': 'use-cases/right-ventricle.md'
- For Developers:
- 'Onboarding': 'dev/onboarding.md'
- 'How to Build ShapeWorks from Source?': 'dev/build.md'
- 'How to Contribute to ShapeWorks?': 'dev/contribute.md'
- 'How to Add ShapeWorks Commands?': 'dev/commands.md'
- 'How to Add Python APIs?': 'dev/python-apis.md'
- 'How to Add and Run Unit Tests?': 'dev/tests.md'
- 'How to Add New Use Cases?': 'dev/new-use-case.md'
- 'How to Add New Datasets?': 'dev/datasets.md'
- 'How to Add New Notebooks?': 'dev/new-notebook.md'
- 'When Modifying Existing Datasets': 'dev/modify-datasets.md'
- 'Getting Started with Documentation': 'dev/docs.md'
- 'Getting Started with GitHub Actions': 'dev/gh-actions.md'
- 'Getting Started with Markdown': 'dev/markdown.md'
- 'Adding to PATH Environment Variable': 'dev/paths.md'
- 'Release Process': 'dev/release-process.md'
- Python API Reference: 'python/python-api.md'
- C++ API Reference:
- ShapeWorks as a Library: 'dev/shapeworks-library.md'
- Groups: 'api/Modules/index_groups.md'
- Namespaces: 'api/Namespaces/index_namespaces.md'
- Classes: 'api/Classes/index_classes.md'
- Files: 'api/Files/index_files.md'
- Java/Matlab Interface:
- Java Interface: 'java/java.md'
- Matlab Interface: 'java/matlab.md'
- About:
- 'Meet ShapeWorkers!': 'about/team.md'
- 'Release Notes': 'about/release-notes.md'
- 'License': 'about/license.md'
- 'Contact Us': 'about/contact.md'
theme:
name: material #readthedocs #rtd-dropdown #readthedocs #yeti #united #spacelab #sandstone #minty #lumen #flatly
logo: assets/shapeworks-logo-small.png
include_sidebar: true
highlightjs: true
hljs_languages:
- yaml
- python
- c++
# features: // pretty cool, and not necessarily problems, but leaving it off for now
# - navigation.instant
palette:
- scheme: default
toggle:
icon: material/eye-outline
name: Switch to dark mode
- scheme: slate
toggle:
icon: material/eye
name: Switch to light mode
markdown_extensions:
- attr_list
- pymdownx.tasklist
- mdx_math
- admonition
- pymdownx.superfences
- pymdownx.details
- pymdownx.arithmatex:
generic: true
extra_css:
- css/custom.css
extra_javascript:
- assets/mathjaxhelper.js
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
plugins:
- search
- mkdocstrings:
handlers:
python:
selection:
docstring_style: google
docstring_options:
ignore_init_summary: yes
setup_commands:
- "import sys"
- "print(sys.path)"
- "import shapeworks"
rendering:
merge_init_into_class: yes
- mkdocs-jupyter:
execute: False
include_source: True
- mike:
# these fields are all optional; the defaults are as below...
version_selector: true # set to false to leave out the version selector
css_dir: css # the directory to put the version selector's CSS
javascript_dir: js # the directory to put the version selector's JS
canonical_version: null # the version for <link rel="canonical">; `null`
# uses the version specified via `mike deploy`
# for material theme, mike versioning is supported as an extra
extra:
version:
provider: mike
analytics:
provider: google
property: UA-36723568-3