Helper script that downloads the 2D CHO dataset from the Murphy Lab at Carnegie Mellon University

script.sh

#!/bin/bash

echo "*********************"
echo "* LICENSE AGREEMENT *"
echo "*********************"
echo "All data downloaded from the Murphy Lab web site (http://murphylab.web.cmu.edu) remain the property of the 
Murphy" 
echo "Lab. You are granted a non-exclusive license to use these images for non-commercial, research purposes, with the" 
echo "following conditions: (a) you agree to include a reference to"
echo ""
echo "M. V. Boland, M. K. Markey and R. F. Murphy (1998) Automated Recognition of Patterns Characteristic of Subcellular Structures in Fluorescence Microscopy Images. Cytometry 33: 366-375."
echo "M. K. Markey, M. V. Boland and R. F. Murphy (1999). Towards Objective Selection of Representative Microscope Images. Biophys. J. 76:2230-2237."
echo ""
echo "when presenting or publishing your results, (b) you agree to send a copy of any paper or abstract (upon its"
echo "acceptance for publication or presentation) by FAX, email or regular mail to Dr. Murphy, and (c) you agree not to "
echo "distribute these images without inclusion of this notice."

echo "Dr. Robert F. Murphy"
echo "Professor of Biological Sciences, Biomedical Engineering and Machine Learning"
echo "Carnegie Mellon University"
echo "4400 Fifth Ave., Pittsburgh, PA 15213"
echo "FAX: 412-268-6571"
echo "email: murphy@cmu.edu"
 
WEBSITE='http://murphylab.web.cmu.edu/data/cho'
 
URLS=( 'giant.zip'
'hoech.zip'
'lamp2.zip'
'nop4.zip'
'tubul.zip'
'giantin.tgz'
'hoechst.tgz'
'lamp2.tgz'
'nop4.tgz'
'tubulin.tgz'
'image.txt' )
 
for URL in "${URLS[@]}"
do
	echo Downloading "$WEBSITE"/"$URL" to `pwd`
	wget --quiet -nc "$WEBSITE"/"$URL"
done
 
echo ""

if [ ! -d "dat" ]; then
	mkdir "dat"
fi

if [ ! -d "tiff" ]; then
	mkdir "tiff"
fi

mv -v *.zip "dat"
mv -v *.tgz "tiff"

cd "dat"
for FILE in *.zip
do
	if [ -f "$FILE" ]; then
		echo "Decompressing" "$FILE"
		unzip -v $FILE
		echo "Removing file" "$FILE"
		rm -fv $FILE
	fi
done
cd ..
 
cd "tiff"
for FILE in *.tgz
do
	if [ -f "$FILE" ]; then
		echo "Decompressing" "$FILE"
		tar -xf $FILE
		echo "Removing file" "$FILE"
		rm -fv $FILE
	fi
done
cd ..