Imagemagick: Are there any operators that could convert all spots on b/w mages into pixel placed at geometric center?

Question

I have a huge set of black and white images with spots and want to replace every spot into pixel (or small circle) that is located in the geometric center of the spot.

Because the spots has different sizes, I could not consequently use dilate operator because it completely deletes small sports. Is there any way to do this automatical with Imagemagick?

Answer 1

Kudos (and upvotes) to Fred (@fmw42) for the original technique. As much for my own curiosity as anything (and to document the approach), I wanted to make a variant that is hopefully more CPU-friendly, I/O friendly and maybe more portable. This should also have advantages given that OP has large numbers of images to process.

I worked on the following aspects:

• rather than repeatedly load the image, draw a circle and re-save for every circle, I wanted to use a script that loads it once, draws all the circles and saves it

• reduce dependency on other tools, and their process creation times - so all the cut, grep, tr, convert, echo and so on are encapsulated inside a single, awk invocation leveraging its built-in ability to split fields, process text, and do math. Hopefully this makes it easier to port to Windows too as fewer binaries are needed.

So, it looks like this:

#!/bin/bash

magick black_spots.png \
   -threshold 50% -type bilevel \
   -define connected-components:mean-color=true \
   -define connected-components:area-threshold=0-300 \
   -define connected-components:verbose=true \
   -connected-components 8 null: | awk -F'[ x+]*' '
      BEGIN       { print "black_spots.png -fill white -colorize 100 -fill black" }
      /gray\(0\)/ {
                    w=$3; h=$4; x=$5; y=$6; cx=x+w/2; cy=y+h/2
                    printf("-draw \"translate %f,%f circle 0,0 0,5\"\n", cx, cy)
                  }
      END         { print "-write result.png"}
   ' | magick -script -

---

The awk part in the middle actually generates a script that looks like this:

black_spots.png -fill white -colorize 100 -fill black
-draw "translate 1429.000000,368.000000 circle 0,0 0,5"
-draw "translate 6.000000,1026.500000 circle 0,0 0,5"
-draw "translate 739.500000,378.000000 circle 0,0 0,5"
...
...
-write result.png

That is then piped into magick -script at the end. Hopefully it is clear that the input file is only read once, all the circles are drawn, then the output file is written - just once.

---

Some notes on the awk parts:

• -F'[ x+]*' means that multiple spaces, the letter x and + signs should all be treated as field separators

• BEGIN and END blocks are executed once at the start and end of the awk script

• the /gray\(0\)/ block is executed only on lines containing gray(0)

---

As regards processing large numbers of files, I would use GNU Parallel, but you have not indicated your operating system. Basically, modify the above script to accept a filename as a parameter, save it as ProcessOne, make it executable with chmod +x ProcessOne, then run:

parallel ./ProcessOne ::: *.png

and it will keep all your CPU cores busy processing all your files in parallel till they are all done. You can get progress bars and ETAs with various switches:

parallel --eta ...         # show ETA
parallel --progress ...    # report progress
parallel --bar ...         # add progress bar
parallel -j 4 ...          # just run 4 jobs in parallel

Answer 2

Here is how to use -connected-components in Imagemagick to put circles where the spots are located.

This is a Unix Bash script using Imagemagick.

1. Save the internal file separator
2. Set the internal file separator to a new line rather than a space
3. Create an array holding the dat and read the input
4. Make a copy of the input and write over it with white and save
5. Threshold the input and save a bilevel
6. Set the output of connected components to the mean-color of the regions
7. Threshold the regions to those that between 0 and 300 pixels in area (This will discard your long arc on the right for the most part. It may throw out large spots. So change as desired) 8) Set the connected components to verbose output to get the textual data
8. Set the connected components type to 8 connected rather than 4 connected
9. Save only black regions and filter to get only the second and third fields which are the bounding box and the centroid
10. Get the number of lines of data (one line per region)
11. Print to the terminal the number of lines of data
12. Start a For loop over each line of data
13. Get the bounding box width
14. Get the bounding box height
15. Compute the radius from the bounding box width and height
16. Get the centroid
17. Print to the terminal the line number, width, height, radius and centroid
18. Draw a black circle on the white image for each line of data, i.e. using the centroid and radius
19. end the loop
20. Set the internal file separator back to the save space separator

Input:

OLDIFS=$IFS
IFS=$'\n'
dataArr=(`convert black_spots.png \
\( +clone -fill white -colorize 100 -write black_spots_result.png +delete \) \
-threshold 50% -type bilevel \
-define connected-components:mean-color=true \
-define connected-components:area-threshold=0-300 \
-define connected-components:verbose=true \
-connected-components 8 null: |\
grep "gray(0)" | awk '{print $2, $3}' | tr "x" "+"`)
num=${#dataArr[*]}
echo $num
for ((i=0; i<num; i++)); do
ww=`echo ${dataArr[$i]} | cut -d\  -f1 | cut -d+ -f1`
hh=`echo ${dataArr[$i]} | cut -d\  -f1 | cut -d+ -f2`
rad=`convert xc: -format "%[fx:($ww+$hh)/4]" info:`
cent=`echo ${dataArr[$i]} | cut -d\  -f2`
echo "$i $ww $hh $rad $cent"
convert black_spots_result.png -fill black -draw "translate $cent circle 0,0 0,$rad" black_spots_result.png
done
IFS=$OLDIFS

Result: