Added fig_grid first version

scripts/fig_grid

@@ -0,0 +1,203 @@
+#!/bin/bash
+
+# This script uses imagemagick to create grids of images and automatically adds captions to them.
+# There are various grid styles which can be made outlined below
+
+# Style 1 - n by m grid with caption for every row
+# for a 3 by 2 grid it will look like:
+#       ------       ------
+#      |      |     |      |
+#      |      |     |      |
+#       ------       ------
+#       ------       ------
+#      |      |     |      |
+#      |      |     |      |
+#       ------       ------
+#       ------       ------
+#      |      |     |      |
+#      |      |     |      |
+#       ------       ------
+#       
+
+####
+#Help
+####
+Help(){
+    echo "fig_grid combines images into a grid, useful for creating complex figures that can be moved between pandoc/latex and other sources such as word or powerpoint."
+    echo
+    echo "Syntax: fig_grid [-h|-o filename|-c captionfile | -s size | -b | -p padding] style inputs"
+    echo "options:"
+    echo "-h: Prints this help"
+    echo "-o: Specify output file as filename"
+    echo "-c: Path to caption file. Caption file must have specific syntax, please check documentation"
+    echo "-s: Font size for captions in pixels"
+    echo "-b: Add thin black border around images"
+    echo "-p: Add padding around images before combining them "
+    echo "style: Represents the style of the output figure. Currently only accepts:"
+    echo "          - nxm (example: 3x2): Arranges a grid into n rows and m columns populating the rows first"
+    echo "inputs: Input files to be processed"
+}
+
+####
+#Error
+####
+function fail {
+    printf 'Error: %s\n' "$1" >&2
+    exit "${2-1}"
+}
+
+
+####
+#Add caption to image
+# First argument should be image file path
+# Second argument should be the message
+# Third argument is the padding to add to the image 
+# Fourth argument is the size of the font
+####
+function add_caption {
+    file=$1
+    msg=$2
+    pad=$3
+    size=$4
+    width=$(identify -format '%w' $file)
+    height=$(identify -format '%h' $file)
+    (( height = height+pad ))
+    convert -extent x"$height" $file $file
+    captmp="$RANDOM$RANDOM$RANDOM$RANDOM.png"
+    convert -background " #FFF " -fill black -font Helvetica -size x$size label:"$msg" $captmp
+    convert -append -gravity center $file $captmp $file
+    rm $captmp
+}
+
+args=()
+argnum=0
+csize=0
+cpad=0
+border=0
+pad=0
+output="output.png"
+while [ $# -gt 0 ]; do
+    unset OPTIND
+    unset OPTARG
+    #Parse Flags
+    while getopts ':ho:c:s:bp:' options; do 
+        case $options in
+            h)
+                Help
+                break;;
+            o)
+                output=$OPTARG;;
+            c)
+                captionfile=$OPTARG;;
+            s)
+                csize=$OPTARG;;
+            b)
+                border=2;;
+            p)
+                pad=$OPTARG;;
+        esac
+    done
+    shift $((OPTIND-1))
+    args+=("$1")
+     (( argnum++ ))
+     shift
+ done
+
+if [ $argnum -eq 0 ]; then
+    Help
+    exit
+fi
+
+#Specify tmp file prefix
+tmp=$(echo $RANDOM$RANDOM$RANDOM)
+#First calculate the number of inputs to be expected, then check to make sure enough images are provided
+style=${args[0]}
+calc_style="${style/x/\*}"
+expfiles=$(echo $calc_style | bc)
+
+if [ $expfiles -ne $(( argnum -1 )) ]; then
+    fail "expected $expfiles files but only got $(( argnum - 1 )) files"
+fi
+
+#Now read the caption file into an array if it exists
+if [ "$captionfile" != "" ]; then
+    mapfile -t captions < $captionfile
+fi
+
+#Finally generate the correct images. By default this will size all images to the size of the largest image to create regular spacings. It does this by scaling and the extent command
+
+#First find max image size
+max_x=0
+max_y=0
+
+for i in $(seq 1 $((argnum-1)) ); do
+    if [ ! -f ${args[$i]} ]; then
+        fail "File ${args[$i]} doesn't exist"
+    fi
+    x=$(identify -format '%w' ${args[$i]})
+    y=$(identify -format '%h' ${args[$i]})
+    if [ "$x" -gt "$max_x" ]; then
+        max_x=$x
+    fi
+    if [ "$y" -gt "$max_y" ]; then
+        max_y=$y
+    fi
+done
+
+echo "Resizing all images to $max_x $max_y"
+
+#Get caption size 
+
+if [ $csize -eq 0 ]; then
+    csize=$(echo "scale=0; $max_y*10/100" | bc)
+fi
+
+#Get padding if necessary
+if [ $pad -eq 0 ]; then 
+    pad=$(echo "scale=0; $max_y*5/100" | bc)
+    cpad=$(echo "scale=0; $csize/2" | bc)
+fi
+#Now resize all of the images
+for i in $(seq 1 $((argnum-1)) ); do
+    info=$(identify ${args[$i]} ) || fail "Failed to identify image ${args[$i]}"
+    x=$(identify -format '%w' ${args[$i]})
+    y=$(identify -format '%h' ${args[$i]})
+
+    if [ $x -gt $y ]; then
+        convert -scale "$max_x"x ${args[$i]} $tmp$i.png || fail "Failed to scale image"
+    fi
+    if [ $y -gt $x ]; then
+        convert -scale x"$max_y" ${args[$i]} $tmp$i.png || fail "Failed to scale image"
+    fi
+    convert -extent "$max_x"x"$max_y" -gravity center -border "$border"x$border -bordercolor black $tmp$i.png $tmp$i.png || fail "Failed to add padding to image"
+done
+
+k=$(( i+1 ))
+cap_num=1
+#Now build the actually images based on style
+if [[ "$style" == *"x"* ]]; then
+    vertappend=""
+    rows=${style%x*}
+    columns=${style#*x}
+    echo "Combining images into an $rows by $columns grid"
+    l=1
+    for i in $(seq 1 $rows); do 
+        horizappend=""
+        for j in $(seq 1 $columns); do 
+            horizappend="$horizappend ( -border $pad -bordercolor white $tmp$l.png )"
+            (( l++ ))
+        done
+        convert $horizappend +append $tmp$k.png
+        if [ "${captions[0]}" = "rows" ]; then 
+            add_caption $tmp$k.png ${captions[$cap_num]} $cpad $csize || fail "Couldn't add caption"
+            (( cap_num++ ))
+        fi 
+        vertappend="$vertappend $tmp$k.png"
+        (( k++ ))
+    done
+    convert $vertappend -append $output
+fi
+
+rm $tmp*.png
+
+