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Scripts for Manipulation and Analysis of High Energy Diffraction Images (GE2 files)
# Miscellaneous Diffraction Image Processing Commands
# This file defines aliases for several common image processing
# functions for GE2 diffraction images. This uses ImageMagick
# program, which is typically available on all Linux and Mac
# systems - http://www.imagemagick.org/script/index.php
# USAGE:
# Copy the contents of this file to the bottom of ~/.bashrc
# Run from terminal: source ~/.bashrc
# After this, following commands should be available
# 1. Convert TIFF to GE. Saves input.ge2
# tiff2ge input.tiff
# 2. Convert GE to TIFF. Saves input.tiff (Note: The produced TIFF may seem to have very low
# intensity. That is because, GE2 has 16-bit depth. So the intensity
# can go from 0 to 65000. Detectors at APS and CHESS generally max out
# at 16000 counts. So even high intensity points have only 25% intensity.
# You can stretch the intensity range of the TIFF using ImageMagick -
# convert -normalize original.tiff bright_output.tiff). If the GE2 file has
# multiple frames, TIFF is multipage. You can split TIFF into individual frames
# using - convert multipage.tiff frame_%05d.tiff
# ge2tiff input.ge2
# 3. Maximum over frames (saves a single frame with maximum intensity. Name: input-max.[ge2 | tiff])
# max_over_frames input.[ge2 | tiff]
# 4. Mean over frames (saves a single frame with mean intensity.
# Good for creating a dark frame from a sequence. Name: input-mean.[ge2 | tiff])
# mean_over_frames input.[ge2 | tiff]
# 5. Extract a single frame from a multi-frame image. Saves multiframe_frame_num.[ge2 | tiff]
# extract_frame multiframe.[ge2 | tiff] frame_num
# 6. Subtract dark frame from a (single or multi-frame) image. Saves input-dark-subtracted.[ge2 | tiff]
# subtract_dark input.[ge2 | tiff] dark_image.[ge2 | tiff]
# 7. Show FF data in a parent directory. This lists all ge2 files inside
# subdirectories. The output format is such that the GE2 list can be
# used e.g. in a heXRD config file.
# show_ff_data path/to/parent/directory
#
# Convert TIFF/PNG etc to GE2 (single or multi frame, works on multiple files)
function tiff2ge() {
for var in "$@"
do
echo "Processing : tiff2ge : $var"
filename=$(basename "$var")
extension="${filename##*.}"
filename="${filename%.*}"
convert "$var" -endian LSB -depth 16 -size 2048x2048 gray:"$filename".ge2.tmp
dd if="$filename".ge2.tmp of="$filename".ge2 obs=8192 seek=1
rm -f "$filename.ge2.tmp"
done
}
# Convert GE2 image to tiff
function ge2tiff() {
for var in "$@"
do
echo "Processing : ge2tiff : $var"
filename=$(basename "$var")
extension="${filename##*.}"
filename="${filename%.*}"
convert -endian LSB -depth 16 -size 2048x2048+8192 gray:"$var" "$filename".tiff
done
}
# Max over all frames
function max_over_frames() {
for var in "$@"
do
filename=$(basename "$var")
extension="${filename##*.}"
filename="${filename%.*}"
if [ ${extension^^} == "TIF" ] || [ ${extension^^} == "TIFF" ]
then
echo "Processing : max over : $extension : $var"
convert "$var" -evaluate-sequence max "$filename"-max."$extension"
elif [ ${extension^^} == "GE2" ]
then
echo "Processing : max over : $extension : $var"
convert -endian LSB -depth 16 -size 2048x2048+8192 gray:"$var" \
-endian LSB -depth 16 -size 2048x2048 -evaluate-sequence max gray:"$filename"."$extension".max
dd if="$filename"."$extension".max of="$filename"-max."$extension" obs=8192 seek=1
rm -f "$filename"."$extension".max
fi
done
}
# Mean over all frames
function mean_over_frames() {
for var in "$@"
do
filename=$(basename "$var")
extension="${filename##*.}"
filename="${filename%.*}"
if [ ${extension^^} == "TIF" ] || [ ${extension^^} == "TIFF" ]
then
echo "Processing : max over : $extension : $var"
convert "$var" -evaluate-sequence mean "$filename"-mean."$extension"
elif [ ${extension^^} == "GE2" ]
then
echo "Processing : max over : $extension : $var"
convert -endian LSB -depth 16 -size 2048x2048+8192 gray:"$var" \
-endian LSB -depth 16 -size 2048x2048 -evaluate-sequence mean gray:"$filename"."$extension".mean
dd if="$filename"."$extension".mean of="$filename"-mean."$extension" obs=8192 seek=1
rm -f "$filename"."$extension".mean
fi
done
}
# Extract a specific frame from multi-frame image
function extract_frame() {
filename=$(basename "$1")
extension="${filename##*.}"
filename="${filename%.*}"
if [ ${extension^^} == "TIF" ] || [ ${extension^^} == "TIFF" ]
then
echo "Processing : extract frame $2 : $extension : $1"
convert "$1"[$2] "$filename"_"$2"."$extension"
elif [ ${extension^^} == "GE2" ]
then
echo "Processing : extract frame $2 : $extension : $1"
convert -endian LSB -depth 16 -size 2048x2048+8192 gray:"$1"["$2"] \
-endian LSB -depth 16 -size 2048x2048 -evaluate-sequence max gray:"$filename"_"$2"."$extension".tmp
dd if="$filename"_"$2"."$extension".tmp of="$filename"_"$2"."$extension" obs=8192 seek=1
rm -f "$filename"_"$2"."$extension".tmp
fi
}
# Subtract a dark frame from an image (not tested for multiframe)
function subtract_dark() {
filename=$(basename "$1")
extension="${filename##*.}"
filename="${filename%.*}"
if [ ${extension^^} == "TIF" ] || [ ${extension^^} == "TIFF" ]
then
echo "Processing : subtract dark : $extension : $2 from $1"
convert $1 null: $2 -compose difference -layers composite "$filename"-dark-subtracted."$extension"
#composite -compose difference $1 $2 "$filename"-dark-subtracted."$extension"
elif [ ${extension^^} == "GE2" ]
then
echo "Processing : subtract dark : $extension : $2 from $1"
convert -endian LSB -depth 16 -size 2048x2048+8192 gray:$1 \
-endian LSB -depth 16 -size 2048x2048+8192 null: gray:$2 \
-compose difference -layers composite -endian LSB -depth 16 -size 2048x2048+8192 "$filename"-dark-subtracted."$extension".tmp
#composite -compose difference -endian LSB -depth 16 -size 2048x2048+8192 gray:"$1" \
# -endian LSB -depth 16 -size 2048x2048+8192 gray:"$2" \
# -endian LSB -depth 16 -size 2048x2048+8192 "$filename"-dark-subtracted."$extension".tmp
dd if="$filename"-dark-subtracted."$extension".tmp of="$filename"-dark-subtracted."$extension" obs=8192 seek=1
rm -f "$filename"-dark-subtracted."$extension".tmp
fi
}
# Display file numbers from an ff directory
function show_ff_data() {
# Find all directories with name ff and loop over them
find "$@" -not -empty -name "ff" -print | while read f; do
# Show directory name
echo "$f"
# Get size of all contents in the directory (in bytes)
tot_byte_size=$(du -b "$f")
# By default du prints the folder name too. Strip that.
tot_byte_size=($tot_byte_size)
tot_byte_size=${tot_byte_size[0]}
# Estimate number of FF frames assuming one frame = 2048*2048*2 bytes
num_frames_estimate=$( echo $tot_byte_size / 8388608 | bc )
# Get size of all contents in a human readable unit (M, G, T)
tot_file_size=$(du -h "$f")
tot_file_size=($tot_file_size)
# Print total size and frame number estimate
echo Total size = ${tot_file_size[0]}, Estimated frames = $num_frames_estimate
# List the contents of the folders
filenames1=$(eval ls \'"$f"\' | tr '\n' ' ')
filelist=''
# Clean up the filenames assuming ff_%5d.ge2 format
for filename in $filenames1
do
filenum1=${filename:3:5}
filenum=$(echo $filenum1 | sed 's/^0*//')
filelist+=", $filenum"
done
filelist1=${filelist:2}
# Print comma separated list of file numbers
echo $filelist1
done
}
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