Resync to cardiotensor

.github/workflows/draft-pdf.yml

@@ -14,6 +14,8 @@ jobs:
       # Step 1: Checkout repository
       - name: Checkout
         uses: actions/checkout@v4
+        with:
+          lfs: true
 
       # Step 2: Build draft PDF using Open Journals action
       - name: Build draft PDF
@@ -34,4 +36,4 @@ jobs:
         uses: EndBug/add-and-commit@v9
         with:
           message: '(auto) Paper PDF Draft'
-          add: 'paper/*.pdf'       # or 'paper/*.pdf' for multiple PDFs
+          add: 'paper/*.pdf'       # or 'paper/*.pdf' for multiple PDFs

README.md

@@ -1,4 +1,4 @@
-<h1 align="center">Cardiotensor</h1>
+<h1 align="center">CardioTensor</h1>
 
 <p align="center">
   <picture>
@@ -14,7 +14,7 @@
 [![CI](https://github.com/JosephBrunet/cardiotensor/actions/workflows/ci.yml/badge.svg)](https://github.com/JosephBrunet/cardiotensor/actions/workflows/ci.yml)
 [![Doc](https://img.shields.io/badge/docs-dev-blue.svg)](https://JosephBrunet.github.io/cardiotensor/)
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/b0e80972e3104ffa890532738882f42e)](https://app.codacy.com?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
-[![License](https://img.shields.io/github/license/JosephBrunet/cardiotensor)](https://github.com/JosephBrunet/cardiotensor/blob/main/LICENSE)
+[![License](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/JosephBrunet/cardiotensor/blob/main/LICENSE)
 [![Python Version](https://img.shields.io/pypi/pyversions/cardiotensor.svg)](https://pypi.python.org/pypi/cardiotensor)
 [![PyPI version](https://img.shields.io/pypi/v/cardiotensor.svg)](https://pypi.org/project/cardiotensor/)
 

docs/advanced/index.md

@@ -6,6 +6,7 @@ Pages:
 
 - [Transmural Analysis](./cardio-analysis.md): Extract transmural profiles from angle and FA maps with `cardio-analysis`.
 - [Streamlines](./streamlines.md): Generate and visualize 3D streamlines with `cardio-generate-streamlines` and `cardio-visualize-streamlines`.
+- [SLURM Launcher](./slurm-launcher.md): Submit chunked `cardio-tensor` jobs on HPC clusters.
 
 See also:
 

docs/advanced/slurm-launcher.md

@@ -0,0 +1,63 @@
+# SLURM Launcher
+
+Use `cardio-tensor-slurm` to submit chunked orientation jobs as SLURM array tasks.
+
+## What It Does
+
+- Splits a dataset into chunks.
+- Generates a `.slurm` script.
+- Submits one or more SLURM arrays with `sbatch`.
+- Monitors output progress.
+
+The launcher calls `cardio-tensor` on each task with:
+
+```bash
+cardio-tensor <conf_file> --start_index <start> --end_index <end>
+```
+
+## Basic Usage
+
+```bash
+cardio-tensor-slurm path/to/parameters.conf
+```
+
+## Useful Options
+
+```bash
+cardio-tensor-slurm path/to/parameters.conf \
+  --start_index 0 \                     # First slice index (inclusive)
+  --end_index 5000 \                    # Last slice index (exclusive)
+  --chunk_size 100 \                    # Slices processed per SLURM task
+  --time_limit 4:00:00 \                # Wall-time limit for each task
+  --cpus_per_task 8 \                   # CPU cores requested per task
+  --mem_gb 64 \                         # Memory requested per task (GB)
+  --array_parallel 50 \                 # Max concurrent tasks in the SLURM array
+  --partition nice \                    # Optional partition/queue name
+  --log_dir /path/to/logs \             # Where SLURM stdout/stderr logs are written
+  --submit_dir /path/to/slurm_scripts   # Where generated .slurm scripts are saved
+```
+
+Other useful flags:
+
+- `--no_monitor`: submit jobs and return immediately (do not watch output progress).
+- `--dry_run`: generate the `.slurm` script and print `sbatch` command without submitting.
+
+Run help for the full list:
+
+```bash
+cardio-tensor-slurm -h
+```
+
+## Troubleshooting
+
+- **`sbatch` fails**  
+  Verify partition/account/time/memory policy on your cluster.
+
+- **Job fails before running `cardio-tensor`**  
+  Check logs in `OUTPUT_PATH/slurm/log/`.
+
+- **No progress in monitor**  
+  Confirm output folder permissions and that tasks can write outputs.
+
+- **Want to debug without submitting jobs**  
+  Use `--dry_run`.

docs/getting-started/examples.md

@@ -13,7 +13,7 @@ The `./examples/` directory contains:
 
 1. **Heart Volume**:
     - Path: `./data/635.2um_LADAF-2021-17_heart_overview_/`
-    - Description: A downsampled 3D heart image volume designed for testing. The full-resolution dataset is available at the [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/1659197537).
+    - Description: A 3D heart image volume, downsampled 32 times from the original 19.85 µm/voxel dataset, resulting in an effective voxel size of 635.2 µm. The full-resolution dataset is available at the [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/1659197537).
 
 2. **Binary Mask**:
     - Path: `./data/mask/`

docs/reference/cli.md

@@ -9,6 +9,10 @@ Compute myocyte orientation from a 3D volume using a configuration file.
 - `cardio-tensor`
   Computes structure tensor, helix/transverse angle, FA, and eigenvectors.
 
+- `cardio-tensor-slurm`
+  Submits chunked `cardio-tensor` runs as SLURM array jobs.
+  See [SLURM Launcher](../advanced/slurm-launcher.md).
+
 See the [example](../getting-started/examples.md) to get started.
 
 ---