This is currently under development, and builds a Docker image to run text (letter detection) on a demo image. You can either detect (just find and report) or clean the data (and save cleaned png images). If this is a route we want to go, the data can be saved as dicom proper.
First, to build the image (or just skip to download and use version built on Docker Hub):
docker build -t vanessa/dicom-scraper .
Then to run it, you can first see if it works:
docker run vanessa/dicom-scraper --help
and you should see usage
docker run vanessa/dicom-scraper --help usage: main.py [-h] [--input FOLDER] [--outfolder OUTFOLDER] [--detect] [--verbose] Deid (de-identification) pixel scaping tool. optional arguments: -h, --help show this help message and exit --input FOLDER, -i FOLDER input folder to search for images. --outfolder OUTFOLDER, -o OUTFOLDER full path to save output, will use /data folder if not specified --detect, -d Only detect, but don't try to scrub --verbose, -v if set, print more image debugging to screen.
We see that you should provide a folder with dicom files to the
--input argument. If you want to see the image files preprocessed (with contenders in red boxes), you should also map a
--volume. If you only want to detect (and not clean) you can use
Let's cd to some folder with dicom images, and then map it (the
$PWD to /data) in the container. We will specify
--input to be
/data, meaning the mapped folder with our images. Let's try just detection first
cd dicom_folder docker run --volume $PWD:/data vanessa/dicom-scraper --input /data --detect
You'll see overly verbose output (this would be nice to replace with a progress bar) followed by the final summary of detection:
1.2.840.1136126.96.36.1997437170.19835.1075923296.44 DETECTED: 84 SKIPPED: 27 CLEAN: 1 TOTAL: 112
Clean after Detection
Now we will specify the same command, but without
--detect so we also perform cleaning (note this is under development).
cd dicom_folder docker run --volume $PWD:/data vanessa/dicom-scraper --input /data
You'll see the pixels that are being cleaned, and the output (png files for preview) in the same folder (the deprecation warnings need to be disabled):
$ docker run --volume $PWD:/data vanessa/dicom-scraper --input /data DEBUG Found 5 contender files in data DEBUG Checking 5 dicom files for validation. /opt/anaconda2/lib/python2.7/site-packages/skimage/transform/_warps.py:84: UserWarning: The default mode, 'constant', will be changed to 'reflect' in skimage 0.15. warn("The default mode, 'constant', will be changed to 'reflect' in " /opt/anaconda2/lib/python2.7/site-packages/skimage/feature/_hog.py:119: skimage_deprecation: Default value of `block_norm`==`L1` is deprecated and will be changed to `L2-Hys` in v0.15 'be changed to `L2-Hys` in v0.15', skimage_deprecation) Found 5 valid dicom files Scrubbing (108,0,408,512) Scrubbing (418,200,431,230) Scrubbing (418,241,431,245) Scrubbing (418,255,431,263) Scrubbing (422,268,431,287) Scrubbing (422,288,435,296) Scrubbing (437,202,452,214) Scrubbing (437,214,450,222) Scrubbing (437,223,452,236) Scrubbing (437,239,450,245) ============================================================ Scrubbing (48,255,63,271) Scrubbing (50,249,63,253) Scrubbing (54,276,63,295) Scrubbing (54,296,67,304) ============================================================ Scrubbing (64,0,447,512) Scrubbing (438,268,447,287) Scrubbing (438,288,451,296) Scrubbing (453,202,468,214) Scrubbing (453,214,466,222) Scrubbing (453,223,468,236) Scrubbing (453,239,466,245) ============================================================ Scrubbing (90,184,103,214) Scrubbing (90,225,103,229) Scrubbing (90,239,103,247) Scrubbing (94,252,103,271) Scrubbing (94,272,107,280) Scrubbing (109,0,474,512) Scrubbing (109,198,122,206) Scrubbing (109,223,122,229) ============================================================ Scrubbing (62,283,69,288) Scrubbing (73,302,80,307) Scrubbing (90,330,97,335) ============================================================
Complete credit for the base work goes to @FraPochetti, I just wrapped the functions in a container, added xvfb and other dependencies to (hopefully) reproduce most of the versions that he used, and then added functions to save to file.