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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Reads DICOM-Files exported with
% p:\doc\MeVisLab-Networks\2011\ExtractAcinusAndExport.mlab and save them
% as JPG image sequences to further peruse with the STEPanizer.com
% First version: 20.06.2011, reading and displaying the DICOM-file
% 28.07.2011: Now reads ALL the DICOM-Files in the directory selected on
% Line 16 and converts them in one batch.

clc
clear all

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## Makefile based on http://git.io/GIs6og
## Now at https://github.com/kjhealy/pandoc-templates/blob/master/examples/starting_from_markdown/Makefile

## Define standard Markdown extension
MEXT = md

## All markdown files in the working directory
SRC = $(wildcard *.$(MEXT))

## Bibliography

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# https://gist.github.com/habi/843646709a22004fb5654ab6d9a134d6#file-collage-sh
cd ~/tmp
# Get all images from our team website
wget https://www.anatomie.unibe.ch/pages/forsch_myct_team.php --page-requisites --accept .jpg --no-clobber --quiet
# Scale images to approximately the same size as my head (264x350)
mogrify -resize 264x350 www.anatomie.unibe.ch/users/hlushchuk/kopf.jpg
mogrify -resize 264x350 www.anatomie.unibe.ch/users/khoma/kopf.jpg
# See how big the files are (if needed)
#identify www.anatomie.unibe.ch/users/*/kopf.jpg
# Generate montage

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from scipy import ndimage
import numpy

def shiftimagetocentroid(image):
    imagecenter = [l/2 for l in numpy.shape(image)]
    centroid = ndimage.measurements.center_of_mass(image)
    print(centroid)
    shift = numpy.subtract(imagecenter, centroid)
    print(shift)
    image = scipy.ndimage.interpolation.shift(image, shift, mode='wrap')