Scripts for Manipulation and Analysis of High Energy Diffraction Images (GE2 files)

misc_ge_scripts.sh

# 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
}