crkit-docker

Build:

name=sergeicu/crkit:2021
sudo docker build --no-cache -t $name .

OR Pull:

name=sergeicu/crkit:2021
sudo docker pull $name

Note that $name should follow convention <dockerhub_username>/<docker_name>:<build_release>.

Run:

Interactively:
sudo docker run -it --rm $name

Interactively, with access to local filesystem, mounted on /data in the container:

localfolder=/home/ch215616/code/docker/crkit/
chmod ugo+rwx $localfolder #full chmod is required  
sudo docker run -it --rm -v $localfolder:/data $name

Run CRL command on an individual file, without entering container:

cmd=crlConvertBetweenFileFormats
localfolder=/home/ch215616/code/docker/crkit/
input=example_image.nii.gz # make sure this file is inside $localfolder
chmod ugo+rwx $localfolder #full chmod is required 
sudo docker run -it --rm -v $localfolder:/data $name $cmd --in /data/$input --out /data/output.nrrd

Run a script and process multiple files:

Create script.sh
Place it within Dockerfile directory
Add the following lines to Dockerfile build instructions (above CMD)

COPY script.sh /
RUN chmod ugo+rwx /script.sh

Build docker image as shown above
Run docker sudo docker run -it --rm -v $localfolder:/data $name /script.sh /data/$localsubfolder /data/$localsubfolder
, where $localsubfolder is a subfolder inside $localfolder (or a symbolic link), which must have rwx chmod for all users.

Notes:

crkit binaries are located in /crkit folder inside the container

Current errors (TODO):

3 missing .so libraries cause 65 out of 213 binary executables to falter.

libITKNLOPTOptimizers
libvtkCommonDataModel
libcrlDWICommon
Solution: need to add install instructions OR copy these shared libraries directly during Dockerfile build.

To replicate:

localfolder=/home/ch215616/code/docker/crkit/ 
sudo docker run -it --rm -v $localfolder:/data $name
find /crkit/bin/crl* -executable -type f -exec {} \; > /data/stdout.log 2> /data/sterr.log