Ani branch

.github/workflows/build_package.yml

@@ -0,0 +1,58 @@
+name: Build Package
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build_docs:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -e ".[docs]"
+
+      - name: Build API
+        run: |
+          python tools/build/create_api.py
+
+      - name: Build Docs
+        run: |
+          cd tools/docs
+          make clean
+          python create_templates.py
+          python create_documents.py
+          make dirhtml
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: tools/docs/_build/dirhtml
+
+  deploy_docs:
+    needs: build_docs
+    runs-on: ubuntu-latest
+
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -8,4 +8,10 @@ venv/
 
 # OS files
 .DS_Store
-Thumbs.db
+Thumbs.db
+
+# pytest
+.pytest_cache/
+
+# dev tests
+*.ipynb

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.12.0  # use the latest Ruff version you prefer
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

README.rst

@@ -0,0 +1,41 @@
+im2sim
+======
+
+``im2sim`` is a library designed to simplify the development of ML-accelerated
+digital twins based on medical images.
+
+This includes two main components:
+
+1. Deep Learning (DL) frameworks based on
+   `PyTorch <https://pytorch.org>`_ and
+   `PyTorch Geometric <https://pytorch-geometric.readthedocs.io/en/latest/>`_
+
+2. Mesh processing frameworks based on
+   `VTK <https://vtk.org>`_ and
+   `PyVista <https://docs.pyvista.org/index.html>`_
+
+Features
+--------
+
+* Image and Mesh Data Processing
+* DL models for medical imaging applications
+* DL models for digital twin applications
+* Hybrid DL models for simulation outputs directly from images
+* Building blocks for custom DL models
+* Visualisation utilities
+
+Installation
+------------
+
+1. Install the CUDA dependencies:
+
+.. code-block:: bash
+
+   pip install torch-scatter torch-cluster \
+      -f https://data.pydata.org/whl/torch-2.3.1+cu121.html
+
+2. Install the repository:
+
+.. code-block:: bash
+
+   pip install git+https://github.com/mrphys/im2sim.git

im2sim/__about__.py

@@ -0,0 +1,38 @@
+# Copyright 2026 University College London. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+"""About IM2SIM"""
+
+__all__ = [
+    "__title__",
+    "__summary__",
+    "__uri__",
+    "__version__",
+    "__author__",
+    "__email__",
+    "__license__",
+    "__copyright__",
+]
+
+__title__ = "im2sim"
+__summary__ = "A library to accelerate the development of deep learning models for medical image analysis and simulation."
+__uri__ = "https://github.com/mrphys/im2sim"
+
+__version__ = "0.1.0"
+
+__author__ = "Anirudh Raman, Vivek Muthurangu, Javier Montalt-Tordera"
+__email__ = "v.muthurangu@ucl.ac.uk"
+
+__license__ = "Apache 2.0"
+__copyright__ = "2026 University College London"

im2sim/__init__.py

@@ -1 +1,28 @@
-from . import callbacks, data, layers, losses, metrics, models, utils
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""IM2SIM."""
+import os as _os
+import sys as _sys
+
+from im2sim.__about__ import *
+
+# Import submodules.
+from im2sim._api import data
+from im2sim._api import layers
+from im2sim._api import configs
+from im2sim._api import ops
+from im2sim._api import losses
+from im2sim._api import models
+from im2sim._api import plot
+
+# Make sure directory containing top level submodules is in
+# the __path__ so that "from tensorflow_mri.foo import bar" works.
+# We're using callbacks, but there's nothing special about that.
+_API_MODULE = _sys.modules[__name__].layers
+_im2sim_api_dir = _os.path.dirname(_os.path.dirname(_API_MODULE.__file__))
+_current_module = _sys.modules[__name__]
+
+if not hasattr(_current_module, '__path__'):
+  __path__ = [_im2sim_api_dir]
+elif _im2sim_api_dir not in __path__:
+  __path__.append(_im2sim_api_dir)

im2sim/_api/configs/__init__.py

@@ -0,0 +1,6 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Configuration classes for model and training settings."""
+
+from im2sim.src.layers.image_conv_blocks import ImageConvBlockConfig as ImageConvBlockConfig
+from im2sim.src.layers.halfunet import HalfUNetConfig as HalfUNetConfig

im2sim/_api/data/__init__.py

@@ -0,0 +1,5 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Data loading and preprocessing utilities."""
+
+

im2sim/_api/layers/__init__.py

@@ -0,0 +1,15 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Custom layers for building deep learning models."""
+
+from im2sim.src.layers.graph_blocks import DefaultGraphNorm as DefaultGraphNorm
+from im2sim.src.layers.graph_blocks import GraphConvBlock as GraphConvBlock
+from im2sim.src.layers.graph_blocks import GraphConvResBlock as GraphConvResBlock
+from im2sim.src.layers.graph_blocks import GraphResDecoderBlock as GraphResDecoderBlock
+from im2sim.src.layers.custom_image_layers import DepthwiseConv as DepthwiseConv
+from im2sim.src.layers.custom_image_layers import DepthwiseSeparableConv as DepthwiseSeparableConv
+from im2sim.src.layers.custom_image_layers import GhostConv as GhostConv
+from im2sim.src.layers.custom_image_layers import EfficientChannelAttn as EfficientChannelAttn
+from im2sim.src.layers.custom_image_layers import SqueezeExcite as SqueezeExcite
+from im2sim.src.layers.custom_image_layers import ConditionedSqueezeExcite as ConditionedSqueezeExcite
+from im2sim.src.layers.image_conv_blocks import ImageConvBlock as ImageConvBlock

im2sim/_api/losses/__init__.py

@@ -0,0 +1,5 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Custom loss functions for training deep learning models."""
+
+

im2sim/_api/models/__init__.py

@@ -0,0 +1,5 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Predefined deep learning models for various tasks."""
+
+from im2sim.src.layers.halfunet import HalfUNet as HalfUNet

im2sim/_api/ops/__init__.py

@@ -0,0 +1,5 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Custom operations for deep learning models."""
+
+from im2sim.src.data.ops import normtorange as normtorange

im2sim/_api/plot/__init__.py

@@ -0,0 +1,5 @@
+# This file was automatically generated by tools/build/create_api.py.
+# Do not edit.
+"""Utilities for visualizing data and model outputs."""
+
+