gadgetron-starter

A starter project for new Gadgetron developers that includes a dockerfile for building out of tree gadgets into new docker images, a few simple template gadgets with common reference structures for Acquisition and Image datatypes, and a reference cmakelist file for building out of tree gadgets.

This example also includes scaffolding for generating ReadTheDocs/Doxygen documentation for the included sample gadget, as well as performing integration tests on new data and configuration files using Gadgetron's test infrastructure.

Included Samples/Templates

AcquisitionPassthroughChannelGadget

ChannelGadget that accepts and returns Core::Acquisition, without modifying the acquisition at all

ImagePassthroughPureGadget

PureGadget that accepts and returns Core::Image<complex>, without modifying the image at all

ImageFixedScalePureGadget

PureGadget that accepts and returns Core::Image and has one parameter (scaleFactor). Uses an iterator to scale all pixels in the input image via multiplying by scaleFactor

ImageFixedScalePythonChannelGadget

ChannelGadget that accepts and returns Core::Image and has one parameter (scaleFactor). Uses a python script to perform scaling of all pixels in the input image via multiplying by scaleFactor.

SaveImageToStorageServer

ChannelGadget that saves incoming image data to the ISMRMRD Storage Server instance

LoadImageFromStorageServer

ChannelGadget that loads previously-stored image data from the ISMRMRD Storage Server instance

Getting Started

Using vscode's devcontainer tools is the easiest way to get started. In vscode, a popup should appear when opening this repository offering to rebuild and reopen in a devcontainer - click yes, and The included docker file will be built and the repository will be mapped in so you can immediately start modifying code.

Dependencies for Devcontainer Environment

1. Docker
2. VSCode
3. Devcontainer extension for VSCode

Opening Devcontainer

1. Open vscode
2. Press F1-> Rebuild and Reopen in Devcontainer

Building in dev environment

1. mkdir build
2. cd build
3. cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} ../
4. ninja install

Running Tests

1. cd test
2. Run: ./getData.sh
3. Run: ./runTests.sh cases/*

Building Deployment Image

Once your code is in a stable state, a final docker container can be built using docker build . that strips out code and all dev dependencies to create a runtime environment including the new OOT gadgets.