simind-python-connector 1.0.0__tar.gz

simind_python_connector-1.0.0/LICENSE

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simind_python_connector-1.0.0/MANIFEST.in

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+include README.md
+include LICENSE
+include requirements.txt
+include requirements-dev.txt
+recursive-include simind_python_connector/data *.atn
+recursive-include simind_python_connector/data *.json
+recursive-include simind_python_connector/configs *.smc *.yaml
+recursive-include docs *.rst *.py
+recursive-include tests *.py
+recursive-include examples *.py
+global-exclude __pycache__
+global-exclude *.py[co]
+global-exclude .DS_Store

simind_python_connector-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: simind-python-connector
+Version: 1.0.0
+Summary: Python SIMIND Monte Carlo connector with STIR/SIRF/PyTomography adaptors
+Author-email: Sam Porter <sam.porter.18@ucl.ac.uk>, Rebecca Gillen <rebecca.gillen.18@ucl.ac.uk>, "Efstathios (Stahis) Varzakis" <efstathios.varzakis.22@ucl.ac.uk>
+Maintainer-email: Sam Porter <sam.porter.18@ucl.ac.uk>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/samdporter/simind-python-connector
+Project-URL: Documentation, https://simind-python-connector.readthedocs.io/
+Project-URL: Repository, https://github.com/samdporter/simind-python-connector
+Project-URL: Issues, https://github.com/samdporter/simind-python-connector/issues
+Project-URL: Changelog, https://github.com/samdporter/simind-python-connector/blob/main/CHANGELOG.md
+Keywords: SPECT,Monte Carlo,medical imaging,SIMIND,SIRF,STIR
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: pydicom>=2.0.0
+Requires-Dist: pyyaml>=5.4.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
+Requires-Dist: myst-parser; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: twine; extra == "dev"
+Provides-Extra: examples
+Requires-Dist: matplotlib>=3.0.0; extra == "examples"
+Dynamic: license-file
+
+# simind-python-connector
+
+Python SIMIND Monte Carlo Connector.
+
+[![Tests](https://github.com/samdporter/simind-python-connector/workflows/Tests/badge.svg)](https://github.com/samdporter/simind-python-connector/actions)
+[![Documentation Status](https://readthedocs.org/projects/simind-python-connector/badge/?version=latest)](https://simind-python-connector.readthedocs.io/en/latest/?badge=latest)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Python Version](https://img.shields.io/badge/python-3.9%2B-blue.svg)](https://www.python.org/downloads/)
+
+A Python toolkit that lets you run SIMIND from Python and use the outputs in
+common reconstruction ecosystems (STIR, SIRF, PyTomography).
+
+## Disclaimer
+
+This project is an independent Python connector toolkit and is **not
+affiliated with, endorsed by, or maintained by** the SIMIND project or Lund
+University.
+
+SIMIND is **not distributed** with this package. You must separately obtain and
+install a licensed SIMIND installation.
+
+## Quick Links
+- [Full Documentation](https://simind-python-connector.readthedocs.io/)
+- [Installation](https://simind-python-connector.readthedocs.io/en/latest/installation.html)
+- [Backend Support](https://simind-python-connector.readthedocs.io/en/latest/backends.html) - adaptor dependency matrix
+
+## What This Package Does
+1. Runs SIMIND from Python with a minimal, explicit API.
+2. Adapts SIMIND data for widely used Python reconstruction packages.
+
+## Key Features
+- **Connector-first API** - `SimindPythonConnector` for direct SIMIND execution from Python
+- **Package Adaptors** - STIR/SIRF/PyTomography adaptors for reconstruction workflows
+- **Native reconstruction workflows** - Use STIR/SIRF/PyTomography reconstruction tools with generated SIMIND data
+- **Dual scoring support** - SCATTWIN and PENETRATE
+- **DICOM builders** - DICOM-driven setup utilities for scanner/input preparation
+- **Advanced Schneider2000 density conversion** - 44-segment HU-to-density mapping
+
+## Installation
+
+### Basic Installation
+
+```bash
+pip install simind-python-connector
+```
+
+Import path remains:
+
+```python
+import simind_python_connector
+```
+
+### Adaptor Dependencies
+
+`SimindPythonConnector` works without SIRF/STIR/PyTomography.
+
+Install optional packages only for the adaptor paths you need:
+
+- **STIR Python** for `StirSimindAdaptor` workflows (example 07A)
+- **SIRF** for `SirfSimindAdaptor` workflows (example 07B)
+- **PyTomography** for `PyTomographySimindAdaptor` workflows (example 07C)
+
+#### Option 1: STIR Python (Recommended for basic usage)
+
+Install from conda:
+```bash
+conda install -c conda-forge stir "numpy<2.0"
+```
+
+**Important**: As of November 2025, the STIR conda package (v6.3.0) requires NumPy < 2.0 due to binary compatibility issues with NumPy 2.x. The package was compiled against NumPy 1.x and will crash with memory errors if NumPy 2.x is installed. This should be resolved in future STIR releases.
+
+Or build from source:
+```bash
+git clone https://github.com/UCL/STIR.git
+cd STIR
+# Follow build instructions in the repository
+```
+
+#### Option 2: SIRF
+
+Install from source:
+```bash
+git clone https://github.com/SyneRBI/SIRF.git
+cd SIRF
+# Follow build instructions in the repository
+```
+
+**Note**: SIRF includes STIR, so a separate STIR install is usually unnecessary.
+
+#### Option 3: PyTomography
+
+Install PyTomography for the PyTomography adaptor workflow:
+
+```bash
+pip install pytomography
+```
+
+### SIMIND Requirement
+
+SIMIND is **not included** with this package and must be installed separately.
+
+Use the official SIMIND resources:
+
+- SIMIND site (Medical Radiation Physics, Lund University): https://www.msf.lu.se/en/research/simind-monte-carlo-program
+- SIMIND manual/docs: https://www.msf.lu.se/en/research/simind-monte-carlo-program/manual
+
+For local use with this package's scripts, place your SIMIND installation under:
+
+```text
+./simind
+```
+
+and make sure the executable is available at:
+
+```text
+./simind/simind
+```
+
+and ensure SIMIND data files are available under:
+
+```text
+./simind/smc_dir/
+```
+
+The Docker helper scripts use this layout and automatically wire SIMIND paths
+when the binary exists at `./simind/simind`.
+
+## Quick Start
+```python
+import numpy as np
+from simind_python_connector import SimindPythonConnector
+from simind_python_connector.configs import get
+
+source = np.zeros((32, 32, 32), dtype=np.float32)  # z, y, x
+source[12:20, 12:20, 12:20] = 1.0
+mu_map = np.zeros_like(source)
+mu_map[source > 0] = 0.15
+
+connector = SimindPythonConnector(
+    config_source=get("Example.yaml"),
+    output_dir="output/basic",
+    output_prefix="case01",
+    quantization_scale=0.05,
+)
+
+connector.configure_voxel_phantom(
+    source=source,
+    mu_map=mu_map,
+    voxel_size_mm=4.0,
+)
+connector.set_energy_windows([126], [154], [0])  # Tc-99m ± 10%
+connector.add_runtime_switch("FI", "tc99m")
+connector.add_runtime_switch("CC", "ma-lehr")
+connector.add_runtime_switch("NN", 1)
+connector.add_runtime_switch("RR", 12345)
+
+outputs = connector.run()
+total = outputs["tot_w1"].projection
+print(total.shape)
+```
+
+### Advanced Density Conversion
+
+```python
+from simind_python_connector.converters.attenuation import hu_to_density_schneider
+import numpy as np
+
+# Convert HU image to densities using Schneider2000 model
+hu_image = np.array([[-1000, 0, 500], [800, 1200, 2000]])
+density_map = hu_to_density_schneider(hu_image)  # 44-segment clinical model
+```
+
+### Pure Python Connector (NumPy Outputs)
+
+```python
+from simind_python_connector import RuntimeOperator, SimindPythonConnector
+from simind_python_connector.configs import get
+
+connector = SimindPythonConnector(
+    config_source=get("AnyScan.yaml"),
+    output_dir="output/python_connector",
+    output_prefix="case01",
+    quantization_scale=1.0,
+)
+
+outputs = connector.run(RuntimeOperator(switches={"NN": 1, "RR": 12345}))
+total = outputs["tot_w1"]
+print(total.projection.shape)
+print(total.header_path)
+```
+
+For minimal toy runs with smaller projection/image settings, use
+`get("Example.yaml")`.
+
+`quantization_scale` controls source integer quantization before writing SIMIND
+`.smi` files:
+
+- `1.0`: uses full internal source integer range (best numeric precision)
+- `< 1.0`: reduces integer scale for faster toy runs but increases rounding error
+
+SIMIND treats source maps as integer weights; absolute activity/time scaling is
+controlled separately by simulation settings.
+
+## Docker Environments
+
+Dedicated container definitions are provided in [`docker/`](docker/):
+
+- `docker/stir/Dockerfile`
+- `docker/sirf/Dockerfile`
+- `docker/pytomography/Dockerfile`
+
+Use Docker Compose:
+
+```bash
+docker compose -f docker/compose.yaml build stir
+docker compose -f docker/compose.yaml run --rm stir
+```
+
+Run per-backend validation and separated examples:
+
+```bash
+bash scripts/run_container_validation.sh
+bash scripts/run_container_validation.sh --with-simind
+bash scripts/run_container_examples.sh
+```
+
+## Contributing
+Please see our [Contributing Guide](CONTRIBUTING.md).
+
+## License
+Apache License 2.0