openrecon-template

This repo is a template made to help building OpenRecon apps.

The puropose is to build the i2i demo provided by Siemens for the SDK on https://www.magnetom.net, using a single build script, without any modification.

For later developments, the first step of a new OpenRecon project it to create a new repo based on this openrecon-template, then modify the app dir (or any other dir), to finnaly call the building process.

Requirement

A Python environment manager is strongly recomanded.

• Python
  • python 3.10 minimum : 100% sure
    OR
  • python 3.12 : don't know
• Additional (non-builtin) modules
  • jsonschema : a simple pip install jsonschema should work

Build

Simply run the build.py script :

python build.py

It will build the demo-i2i directory. All output files will be in the build directory

The script is quite verbose, helping troubleshooting at each step of the process in case of error.

To build a specific dir, such as the app dir :

python build.py --dirname app

Outputs

All output files will be placed in a build subdir. The finale file, ready for the upload on the magnet will be the .zip file.

Building the demo-i2i dir (default option) you should have this :

$ ls -1 build
i2i_json_ui.json
i2i.py
OpenReconSchema_1.1.0.json
OpenRecon_SiemensHealthineersAG_PythonMRDi2i_V1.0.0.Dockerfile
OpenRecon_SiemensHealthineersAG_PythonMRDi2i_V1.0.0.pdf
OpenRecon_SiemensHealthineersAG_PythonMRDi2i_V1.0.0.tar
OpenRecon_SiemensHealthineersAG_PythonMRDi2i_V1.0.0.zip

Building the app dir :

$ ls -1 build
i2i-save-original-images_json_ui.json
i2i-save-original-images.py
OpenRecon_openrecon-template_i2i-save-original-images_V1.0.0.Dockerfile
OpenRecon_openrecon-template_i2i-save-original-images_V1.0.0.pdf
OpenRecon_openrecon-template_i2i-save-original-images_V1.0.0.tar
OpenRecon_openrecon-template_i2i-save-original-images_V1.0.0.zip
OpenReconSchema_1.1.0.json

App

Objective : templatization & separation of environments

The app dir will contained the versioned code.
The python-ismrmrd-server dir is NOT versioned.
To add your app files files in the python-ismrmrd-server, create symbolic links.

How to test locally the reconstruction

Prepare the python environment

Open a Terminal in the repository directory, then :

# setup Conda environment
conda create --name openrecon-template
conda activate openrecon-template
conda install python=3.12
conda install ipython
pip install ismrmrd
pip install pydicom
pip install pynetdicom

# create .py file symbolic link in `python-ismrmrd-server`
# this is how the MRD client/server will behave : all files/modules in the same dir
cd python-ismrmrd-server
ln -s ../app/i2i-save-original-images.py .

Repeat the ln -s for the files you need.

Convert your test dicom into MRD

Put DICOMs in a dir then convert to MRD (.h5 file)

python python-ismrmrd-server/dicom2mrd.py -o <path_to_data>/in/test.h5 <path_to_data>/in/

Start the reco

In a terminal or an IDE like VSCode, start the main.py. This will help a lot debugging.

Send data using client.py

python python-ismrmrd-server/client.py -o <path_to_data>/out/reco_test.h5 -c <myrecon> <path_to_data>/in/test.h5 

Convert the output of your reco to DICOM for visualization

python python-ismrmrd-server/mrd2dicom.py -o <path_to_data>/out/ <path_to_data>/out/reco_test.h5

Use any DICOM viewer to check visually.

All-in-one

Start the main.py in VSCode. It can be in Debug mode, with breakpoints. Then :

#!/bin/bash

## path management
IN_DIR=data/in
OUT_DIR=data/out
DATASET_NAME=test

## clean out dir
rm $OUT_DIR/*dcm $OUT_DIR/*h5

## send h5 MRD dataset using th client -> the server will process them
TARGET_CONFIG=i2i-save-original-images
python python-ismrmrd-server/client.py -o $OUT_DIR/OR_$DATASET_NAME.h5 -c $TARGET_CONFIG $IN_DIR/$DATASET_NAME.h5

# convert fresh OR processed MRD dataset into DICOM for visu
python python-ismrmrd-server/mrd2dicom.py -o $OUT_DIR/ $OUT_DIR/OR_$DATASET_NAME.h5

# use your favorite DICOM viewer
mrview $OUT_DIR/ -mode 2

VSCode tips

I found that, when you modify the <reco>.py file when the main.py is running, the code is not updated => you need to restart the server (started by the main.py) so the <reco>.py is reloaded.