readme

Author: Jose Alonso Solis-Lemus

README.md

@@ -0,0 +1,68 @@
+# pycemrg-image-analysis
+
+A high-level framework for cardiac image segmentation post-processing and model creation, built on SimpleITK. Maintained by the [Cardiac Electromechanics Research Group (CEMRG)](https://www.cemrg.com/) at Imperial College London.
+
+---
+
+## Installation
+
+This library depends on [`pycemrg`](https://pypi.org/project/pycemrg/), which provides the core label management and configuration scaffolding utilities. Both packages should be installed together.
+
+### 1. Clone both repositories
+
+```bash
+git clone https://github.com/OpenHeartDevelopers/pycemrg.git
+git clone https://github.com/OpenHeartDevelopers/pycemrg-image-analysis.git
+```
+
+### 2. Create and activate a virtual environment
+
+**Preferred:** Conda 
+```bash
+conda create -n pycemrg-image-analysis python=3.10 -y 
+conda activate pycemrg-image-analysis
+```
+
+Or via python's venv 
+```bash
+python -m venv .venv
+source .venv/bin/activate   # on Windows: .venv\Scripts\activate
+```
+
+### 3. Install both packages in editable mode
+
+Install `pycemrg` first, then `pycemrg-image-analysis`:
+
+```bash
+pip install -e pycemrg/
+pip install -e pycemrg-image-analysis/
+```
+
+> **Why editable (`-e`)?** Editable installs link directly to the source tree so changes to either package take effect immediately without reinstalling.
+
+---
+
+## Running the tests
+
+```bash
+# Unit tests (no data required)
+pytest pycemrg-image-analysis/tests/unit/
+
+# Integration tests (requires segmentation data)
+PYCEMRG_TEST_DATA_ROOT=/path/to/your/data pytest pycemrg-image-analysis/tests/integration/
+
+# All tests
+pytest pycemrg-image-analysis/
+```
+
+Integration tests are skipped automatically when `PYCEMRG_TEST_DATA_ROOT` is not set.
+
+---
+
+## Requirements
+
+- Python ≥ 3.10
+- SimpleITK ≥ 2.4.0
+- `pycemrg` ≥ 0.1.0 (see above)
+
+All other dependencies are declared in `pyproject.toml` and installed automatically by `pip`.