pyimagingdock

Image processing methods from Python and SimpleITK exposed through Docker. Based off of the pysciencedock design here: http://github.com/Kitware/pysciencedock

Local usage

List methods available with JSON descriptions of inputs and outputs:

python -m pyimagingdock

Print help information for a method:

python -m pyimagingdock <method> --help

Run one of the methods:

python -m pyimagingdock <method> <arg1> ...

Usage through Docker

List the methods available through Docker:

docker run pyimagingdock

Run a method through Docker:

docker run <docker_options> pyimagingdock <method> <arg1> ...

In order to send data files to Docker, mount a volume and use the mounted volume prefix for the input and output paths. For example, if myinput.csv is in your current directory, the following will produce myoutput.csv in the current directory:

docker run -v $PWD:/data pyimagingdock ImagePassThroughFilter --image=/data/myinput.png --output=/data/myoutput.png

Build the Docker image:

git clone https://github.com/curtislisle/pyimagingdock.git
cd pyimagingdock
docker build -t pyimagingdock .

Usage through Girder

Install Girder.
Enable the "Item tasks" plugin.
Start a girder_worker Celery worker and point it and the Worker plugin settings to use the same task queue.
From any folder you have write access to (you must be admin), select "Add tasks" from the actions menu.
Enter "kitware/pyimagingdock" as the image name and click Run.
When that task completes, navigate to a created task item and select "Run task" from the actions menu.
Fill in the task parameters and click Run.

Testing

To run the unit tests:

python -m unittest tests