diff --git a/README b/README
deleted file mode 100644
index e69de29b..00000000
diff --git a/bin/convert_vlsift_to_lowesift.pl b/bin/convert_vlsift_to_lowesift.pl
deleted file mode 100755
index 153e780e..00000000
--- a/bin/convert_vlsift_to_lowesift.pl
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/local/bin/perl
-
-$filename = $ARGV[0];
-
-open (DEST, ">$filename.key");
-open (SRC, "$filename.key.tmp");
-
-$resolution_line = `jhead $filename.jpg | grep "Resolution"`;
-($res_x, $res_y) = $resolution_line =~ /: ([0-9]*) x ([0-9]*)/;
-
-$linecount = 0;
-$linecount += tr/\n/\n/ while sysread(SRC, $_, 2 ** 16);
-
-seek(SRC, 0, 0);
-
-print DEST $linecount;
-print DEST " 128\n";
-
-printf ("found %d features in %s.jpg\n\n", $linecount, $filename);
-
-while ($record = <SRC>) {
-	@parts = split(/ /, $record);
-	
-	$counter = 0;
-	
-	$parts[0] = $res_x-$parts[0];
-	
-	foreach (@parts) {
-		
-		if((($counter-4) % 20) == 0) {
-			print DEST "\n ";
-		} else {
-			if($counter != 0){
-				print DEST " ";
-			}
-		}
-		
-		print DEST $_;
-		
-		$counter++;
-	}
-}
-
-close(DEST);
-close(SRC);
\ No newline at end of file
diff --git a/defs.sh b/defs.sh
deleted file mode 100755
index 439066d8..00000000
--- a/defs.sh
+++ /dev/null
@@ -1,47 +0,0 @@
-set -o nounset
-set -o errexit
-
-#if [ ! -n "$0" ]; then
-	TOOLS_PATH=$PWD/$(dirname $0)
-#else
-#	TOOLS_PATH=$PWD
-#fi
-
-IMAGE_DIR="."
-
-## paths for the tools
-TOOLS_BIN_PATH=$TOOLS_PATH/bin
-TOOLS_INC_PATH=$TOOLS_PATH/include
-TOOLS_LIB_PATH=$TOOLS_PATH/lib
-TOOLS_SRC_PATH=$TOOLS_PATH/src
-TOOLS_LOG_PATH=$TOOLS_PATH/logs
-
-## loacal dest paths
-LIB_PATH="/usr/local/lib"
-INC_PATH="/usr/local/include"
-
-## source paths
-BUNDLER_PATH="$TOOLS_SRC_PATH/bundler"
-CMVS_PATH="$TOOLS_SRC_PATH/cmvs"
-PMVS_PATH="$TOOLS_SRC_PATH/pmvs"
-GRACLUS_PATH="$TOOLS_SRC_PATH/graclus"
-CLAPACK_PATH="$TOOLS_SRC_PATH/clapack"
-OPENCV_PATH="$TOOLS_SRC_PATH/openCv"
-VLFEAT_PATH="$TOOLS_SRC_PATH/vlfeat"
-SIFT_PATH="$TOOLS_SRC_PATH/sift"
-PARALLEL_PATH="$TOOLS_SRC_PATH/parallel"
-PSR_PATH="$TOOLS_SRC_PATH/PoissonRecon"
-
-## executables
-EXTRACT_FOCAL=$TOOLS_BIN_PATH/extract_focal.pl
-MATCHKEYS=$TOOLS_BIN_PATH/KeyMatchFull
-BUNDLER=$TOOLS_BIN_PATH/bundler
-BUNDLE2PVMS=$TOOLS_BIN_PATH/Bundle2PMVS
-CMVS=$TOOLS_BIN_PATH/cmvs
-PMVS=$TOOLS_BIN_PATH/pmvs2
-GENOPTION=$TOOLS_BIN_PATH/genOption
-SIFT=$TOOLS_BIN_PATH/sift
-VLSIFT=$TOOLS_BIN_PATH/vlsift
-PARALLEL=$TOOLS_BIN_PATH/parallel
-PSR=$TOOLS_BIN_PATH/PoissonRecon
-VLSIFT_TO_LOWESIFT=$TOOLS_BIN_PATH/convert_vlsift_to_lowesift.pl
\ No newline at end of file
diff --git a/run-0-mogrify.sh b/run-0-mogrify.sh
deleted file mode 100755
index 30fd7be2..00000000
--- a/run-0-mogrify.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - scaling images"
-echo
-
-# Rename ".JPG" to ".jpg"
-for d in `ls -1 $IMAGE_DIR | egrep ".JPG$"`
-do 
-    mv $d `echo $d | sed 's/\.JPG/\.jpg/'`
-done
-
-mogrify -resize 1600x1200 -quality 100 *
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-1-get-keypoints.sh b/run-1-get-keypoints.sh
deleted file mode 100755
index 081dfc0f..00000000
--- a/run-1-get-keypoints.sh
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $VLSIFT (will take some time ...)"
-echo
-
-# Create the list of images
-find $IMAGE_DIR -maxdepth 1 | egrep ".jpg$" | sort > list_tmp.txt
-$EXTRACT_FOCAL list_tmp.txt
-cp prepare/list.txt .
-
-rm -f match_jobs.txt
-
-for d in `ls -1 $IMAGE_DIR | egrep "jpg$"`
-do 
-    key_file=`echo $d | sed 's/jpg$/key/'`
-    pgm_file=`echo $d | sed 's/jpg$/pgm/'`
-    base_file=`echo $d | sed 's/\.jpg$//'`
-    jpg_file=`echo $d`
-
-	VLSIFT_CMD="mogrify -format pgm $IMAGE_DIR/$jpg_file; $VLSIFT -o $IMAGE_DIR/$key_file.tmp $IMAGE_DIR/$pgm_file; rm $IMAGE_DIR/$pgm_file; perl $VLSIFT_TO_LOWESIFT $base_file; rm $IMAGE_DIR/$key_file.tmp; gzip -f $IMAGE_DIR/$key_file"	
-	SIFT_CMD="mogrify -format pgm $IMAGE_DIR/$jpg_file; $SIFT < $IMAGE_DIR/$pgm_file > $IMAGE_DIR/$key_file; rm $IMAGE_DIR/$pgm_file; gzip -f $IMAGE_DIR/$key_file"
-
-	echo $SIFT_CMD >> match_jobs.txt
-
-##	eval $SIFT_CMD
-done
-
-$PARALLEL -j+0 < match_jobs.txt
-
-wait
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-1.sh b/run-1.sh
deleted file mode 100755
index 5a072767..00000000
--- a/run-1.sh
+++ /dev/null
@@ -1,50 +0,0 @@
-#!/bin/bash
-
-BASE_PATH=$(dirname $(which $0));
-IMAGE_DIR="."
-
-EXTRACT_FOCAL=$BASE_PATH/bin/extract_focal.pl
-MATCHKEYS=$BASE_PATH/bin/KeyMatchFull
-BUNDLER=$BASE_PATH/bin/bundler
-BUNDLE2PVMS=$BASE_PATH/bin/Bundle2PMVS
-CMVS=$BASE_PATH/bin/cmvs
-PMVS=$BASE_PATH/bin/pmvs2
-GENOPTION=$BASE_PATH/bin/genOption
-SIFT=$BASE_PATH/bin/sift
-SIFTFEAT=$BASE_PATH/siftfeat
-VLSIFT=$BASE_PATH/bin/vlsift
-
-if [ $# -eq 1 ]
-then
-    echo "Using directory '$1'"
-    IMAGE_DIR=$1
-fi
-
-# Rename ".JPG" to ".jpg"
-for d in `ls -1 $IMAGE_DIR | egrep ".JPG$"`
-do 
-    mv $d `echo $d | sed 's/\.JPG/\.jpg/'`
-done
-
-# Create the list of images
-find $IMAGE_DIR -maxdepth 1 | egrep ".jpg$" | sort > list_tmp.txt
-$EXTRACT_FOCAL list_tmp.txt
-cp prepare/list.txt .
-
-echo
-echo '[- Extracting keypoints -]'
-echo
-
-for d in `ls -1 $IMAGE_DIR | egrep "jpg$"`
-do 
-    key_file=`echo $d | sed 's/jpg$/key/'`
-    pgm_file=`echo $d | sed 's/jpg$/pgm/'`
-    jpg_file=`echo $d`
-
-#	SIFT_CMD="$VLSIFT -o $IMAGE_DIR/$key_file -x $IMAGE_DIR/$jpg_file; gzip -f $IMAGE_DIR/$key_file"
-#	SIFT_CMD="mogrify -format pgm $IMAGE_DIR/$jpg_file; $VLSIFT < $IMAGE_DIR/$pgm_file > $IMAGE_DIR/$key_file; rm $IMAGE_DIR/$pgm_file; gzip -f $IMAGE_DIR/$key_file"
-	SIFT_CMD="mogrify -format pgm $IMAGE_DIR/$jpg_file; $SIFT < $IMAGE_DIR/$pgm_file > $IMAGE_DIR/$key_file; rm $IMAGE_DIR/$pgm_file; gzip -f $IMAGE_DIR/$key_file"
-	eval $SIFT_CMD
-done
-
-exit
diff --git a/run-2-match-keypoints.sh b/run-2-match-keypoints.sh
deleted file mode 100755
index f59b7713..00000000
--- a/run-2-match-keypoints.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $MATCHKEYS (will take some time ...)"
-echo
-
-sed 's/\.jpg$/\.key/' $IMAGE_DIR/list_tmp.txt > $IMAGE_DIR/list_keys.txt
-
-echo $MATCHKEYS $IMAGE_DIR/list_keys.txt $IMAGE_DIR/matches.init.txt
-$MATCHKEYS $IMAGE_DIR/list_keys.txt $IMAGE_DIR/matches.init.txt
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-3-bundler.sh b/run-3-bundler.sh
deleted file mode 100755
index 973732b2..00000000
--- a/run-3-bundler.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $BUNDLER"
-echo
-
-mkdir bundle
-rm -f $IMAGE_DIR/options.txt
-
-echo "--match_table matches.init.txt" >> options.txt
-echo "--output bundle.out" >> options.txt
-echo "--output_all bundle_" >> options.txt
-echo "--output_dir bundle" >> options.txt
-echo "--variable_focal_length" >> options.txt
-echo "--use_focal_estimate" >> options.txt
-echo "--constrain_focal" >> options.txt
-echo "--constrain_focal_weight 0.0001" >> options.txt
-echo "--estimate_distortion" >> options.txt
-echo "--run_bundle" >> options.txt
-
-rm -f $IMAGE_DIR/constraints.txt
-rm -f $IMAGE_DIR/pairwise_scores.txt
-$BUNDLER $IMAGE_DIR/list.txt --options_file $IMAGE_DIR/options.txt > $IMAGE_DIR/bundle/out
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-4-bundle2pmvs.sh b/run-4-bundle2pmvs.sh
deleted file mode 100755
index 7f264dd6..00000000
--- a/run-4-bundle2pmvs.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $BUNDLE2PVMS"
-echo
-
-$BUNDLE2PVMS list.txt bundle/bundle.out
-
-sed -i $IMAGE_DIR/pmvs/prep_pmvs.sh -e "4c\BUNDLER_BIN_PATH=\"$TOOLS_BIN_PATH\""
-sh $IMAGE_DIR/pmvs/prep_pmvs.sh
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-5-cmvs.sh b/run-5-cmvs.sh
deleted file mode 100755
index 176d8417..00000000
--- a/run-5-cmvs.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $CMVS"
-echo
-
-$CMVS pmvs/ 100 4
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-6-genOption.sh b/run-6-genOption.sh
deleted file mode 100755
index 34bd7f8e..00000000
--- a/run-6-genOption.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $GENOPTION"
-echo
-
-$GENOPTION pmvs/
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-7-pmvs.sh b/run-7-pmvs.sh
deleted file mode 100755
index 7ff7df8b..00000000
--- a/run-7-pmvs.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/bash
-
-script_dir=$(dirname $0)
-. $script_dir/defs.sh
-
-echo
-echo "  - running $PMVS"
-echo
-
-
-$PMVS pmvs/ option-0000
-
-echo
-echo "  < done - `date`"
-
-exit
diff --git a/run-all.sh b/run-all.sh
deleted file mode 100755
index bc3f8499..00000000
--- a/run-all.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/bash
-
-BASE_PATH=$(dirname $(which $0));
-
-sh $BASE_PATH/run-0-mogrify.sh
-sh $BASE_PATH/run-1-get-keypoints.sh
-sh $BASE_PATH/run-2-match-keypoints.sh
-sh $BASE_PATH/run-3-bundler.sh
-sh $BASE_PATH/run-4-bundle2pmvs.sh
-sh $BASE_PATH/run-5-cmvs.sh
-sh $BASE_PATH/run-6-genOption.sh
-sh $BASE_PATH/run-7-pmvs.sh
-
-exit
diff --git a/run.sh b/run.sh
deleted file mode 100755
index cc290cb5..00000000
--- a/run.sh
+++ /dev/null
@@ -1,124 +0,0 @@
-BASE_PATH=$(dirname $(which $0));
-IMAGE_DIR="."
-
-EXTRACT_FOCAL=$BASE_PATH/extract_focal.pl
-MATCHKEYS=$BASE_PATH/KeyMatchFull
-BUNDLER=$BASE_PATH/bundler
-BUNDLE2PVMS=$BASE_PATH/Bundle2PMVS
-CMVS=$BASE_PATH/cmvs
-PMVS=$BASE_PATH/pmvs2
-GENOPTION=$BASE_PATH/genOption
-SIFT=$BASE_PATH/sift
-SIFTFEAT=$BASE_PATH/siftfeat
-
-if [ $# -eq 1 ]
-then
-    echo "Using directory '$1'"
-    IMAGE_DIR=$1
-fi
-
-# Rename ".JPG" to ".jpg"
-for d in `ls -1 $IMAGE_DIR | egrep ".JPG$"`
-do 
-    mv $d `echo $d | sed 's/\.JPG/\.jpg/'`
-done
-
-echo
-echo '[- Scaling images -]'
-echo
-
-mogrify -resize 1600x1200 -quality 100 *
-
-# Create the list of images
-find $IMAGE_DIR -maxdepth 1 | egrep ".jpg$" | sort > list_tmp.txt
-$EXTRACT_FOCAL list_tmp.txt
-cp prepare/list.txt .
-
-echo
-echo '[- Extracting keypoints -]'
-echo
-
-for d in `ls -1 $IMAGE_DIR | egrep "jpg$"`
-do 
-    key_file=`echo $d | sed 's/jpg$/key/'`
-    pgm_file=`echo $d | sed 's/jpg$/pgm/'`
-    jpg_file=`echo $d`
-
-	SIFT_CMD="$SIFTFEAT -o $IMAGE_DIR/$key_file -x $IMAGE_DIR/$jpg_file; gzip -f $IMAGE_DIR/$key_file"
-#	SIFT_CMD="mogrify -format pgm $IMAGE_DIR/$jpg_file; $SIFT < $IMAGE_DIR/$pgm_file > $IMAGE_DIR/$key_file; rm $IMAGE_DIR/$pgm_file; gzip -f $IMAGE_DIR/$key_file"
-	eval $SIFT_CMD
-done
-
-# Match images (can take a while)
-echo
-echo '[- Matching keypoints (this can take a while) -]'
-echo
-
-sed 's/\.jpg$/\.key/' $IMAGE_DIR/list_tmp.txt > $IMAGE_DIR/list_keys.txt
-
-echo $MATCHKEYS $IMAGE_DIR/list_keys.txt $IMAGE_DIR/matches.init.txt
-$MATCHKEYS $IMAGE_DIR/list_keys.txt $IMAGE_DIR/matches.init.txt
-
-mkdir bundle
-rm -f $IMAGE_DIR/options.txt
-
-echo "--match_table matches.init.txt" >> options.txt
-echo "--output bundle.out" >> options.txt
-echo "--output_all bundle_" >> options.txt
-echo "--output_dir bundle" >> options.txt
-echo "--variable_focal_length" >> options.txt
-echo "--use_focal_estimate" >> options.txt
-echo "--constrain_focal" >> options.txt
-echo "--constrain_focal_weight 0.0001" >> options.txt
-echo "--estimate_distortion" >> options.txt
-echo "--run_bundle" >> options.txt
-
-# Run Bundler!
-echo
-echo '[- Running Bundler -]'
-echo
-
-rm -f $IMAGE_DIR/constraints.txt
-rm -f $IMAGE_DIR/pairwise_scores.txt
-$BUNDLER $IMAGE_DIR/list.txt --options_file $IMAGE_DIR/options.txt > $IMAGE_DIR/bundle/out
-
-# Run Bundle2PMVS!
-echo
-echo '[- Running Bundle2PMVS -]'
-echo
-
-$BUNDLE2PVMS list.txt bundle/bundle.out
-
-# Run prep_pmvs!
-echo
-echo '[- Running prep_pmvs -]'
-echo
-
-sed -i $IMAGE_DIR/pmvs/prep_pmvs.sh -e "4c\BUNDLER_BIN_PATH=\"$BASE_PATH\""
-sh pmvs/prep_pmvs.sh
-
-# Run cmvs!
-echo
-echo '[- Running cmvs -]'
-echo
-
-$CMVS pmvs/ 20
-
-# Run pmvs!
-echo
-echo '[- Running genOption -]'
-echo
-
-$GENOPTION pmvs/
-
-# Run prep_pmvs!
-echo
-echo '[- Running pmvs -]'
-echo
-
-$PMVS pmvs/ option-0000
-#sh pmvs/pmvs.sh
-
-echo
-echo '[- Done -]'
-echo
\ No newline at end of file