pydicom/dicom
Docker container to easily get started with common dicom tools
6.9K
pydicom/dicom repository overview
Getting Started With Dicom
These are Singularity and Docker images that will provide you with installations of pydicom and The Dicom Toolkit. You can use this environment if you don't want to install the dependencies for both on your system.
Singularity
First you should install Singularity (note this is for the development branch):
git clone -b development https://www.github.com/singularityware/singularity.git
cd singularity
./autogen.sh
./configure --prefix=/usr/local
make
sudo make install
Create the image
The image is created with a bootstrap, meaning we create the image, then use a build specification file called Singularity to build it easily with one command.
git clone https://www.github.com/pydicom/singularity-dicom
cd singularity-dicom
singularity create --size 3000 dcm.img
sudo singularity bootstrap dcm.img Singularity
Shell into the container
If you want to interactively shell into the container, you can do it in read or writable mode (writable requires sudo):
singularity shell dcm.img
sudo singularity shell --writable dcm.img
Dicom Toolkit
If you run the container without any input arguments, it will spit out the various dcm2k tools it provides:
$ singularity run dcm2k.img
dcm2json dcmdrle dcmnet_tests dcmqrscp dconvlum mkreport
dcm2pdf dcmdspfn dcmodify dcmqrti drtdump movescu
dcm2pnm dcmdump dcmp2pgm dcmquant drttest ofstd_tests
dcm2xml dcmftest dcmprscp dcmrecv dsr2html pdf2dcm
dcmcjpeg dcmgpdir dcmprscu dcmrt_tests dsr2xml storescp
dcmcjpls dcmiod_tests dcmpschk dcmscale dsrdump storescu
dcmconv dcmj2pnm dcmpsmk dcmseg_tests dump2dcm termscu
dcmcrle dcml2pnm dcmpsprt dcmsend echoscu wlmscpfs
dcmdata_tests dcmmkcrv dcmpsrcv dcmsign findscu xml2dcm
dcmdjpeg dcmmkdir dcmpssnd dcmsr_tests getscu xml2dsr
dcmdjpls dcmmklut dcmqridx dcod2lum img2dcm
You can issue any of the above commands to the container.
singularity shell [image] and run python for pydicom.
You can then run a specific command (in the example below, dcm2json), and we just ask for help.
singularity run dcm.img dcm2json --help
$dcmtk: dcm2json v3.6.1 2017-02-28 $
dcm2json: Convert DICOM file and data set to JSON
usage: dcm2json [options] dcmfile-in [jsonfile-out]
parameters:
dcmfile-in DICOM input filename to be converted
jsonfile-out JSON output filename (default: stdout)
general options:
-h --help print this help text and exit
--version print version information and exit
--arguments print expanded command line arguments
-q --quiet quiet mode, print no warnings and errors
-v --verbose verbose mode, print processing details
-d --debug debug mode, print debug information
-ll --log-level [l]evel: string constant
(fatal, error, warn, info, debug, trace)
use level l for the logger
-lc --log-config [f]ilename: string
use config file f for the logger
input options:
input file format:
+f --read-file read file format or data set (default)
+fo --read-file-only read file format only
-f --read-dataset read data set without file meta information
input transfer syntax:
-t= --read-xfer-auto use TS recognition (default)
-td --read-xfer-detect ignore TS specified in the file meta header
-te --read-xfer-little read with explicit VR little endian TS
-tb --read-xfer-big read with explicit VR big endian TS
-ti --read-xfer-implicit read with implicit VR little endian TS
output options:
output format:
+fc --formatted-code output file with human readable formatting (def.)
-fc --compact-code output without formatting (single line of code)
+m --write-meta write data set with meta information
By default, your $HOME and temporary file locations are mounted. If you need to mount additional data folders, you can do that with -B or --bind. A /data folder has been created in the container for you to do this easily. Eg:
singularity run --bind /path/on/host:/data dcm.img [COMMANDS] --output=/data
Notice that I am outputting to /data in the container, which is mounted at /path/to/host on my local machine.
Pydicom Tools
Python is installed at /opt/conda and added to the path, so if you shell into the image and run python, you should be able to easily import both and get started with pydicom. The minimal installation has been done for both pydicom and pynetdicom3 and if there is a library or other dependency missing, please post an issue.
Singularity Hub
We also provide this image for you to use on Singularity Hub (I'm hiding this down here so you might have tried building it yourself first! We provide the image on , so you can just pull it from there:
singularity pull --name dcm.img shub://pydicom/singularity-dicom
If you don't specify a --name it will pull as pydicom-singularity-dicom-master.img.
Docker
I've added an equivalent Docker image too - hey why not! You can either build locally first,
docker build -t pydicom/dicom .
or just skip and run as follows from Docker Hub
docker run pydicom/dicom
and then the equivalent command would be:
docker run --volume /path/on/host:/data pydicom/dicom storescu --help
Need help? 
Tag summary
Content type
Image
Digest
Size
753.7 MB
Last updated
over 6 years ago
docker pull pydicom/dicom