2

I have limited experience with programming and Linux and I need your help.

The situation I am in is that I have a stack of black and white .tiff images (approx. 400 of 10 Mb each one) which I need to convert into xyz coordinates plus grayscale values and to compile all those in ONLY a single text file with x,y,z,grayscale (the z coordinates, this way: first image of the folder z=0000, second image 0001...as many z coordinates as images in the folder).

I have a script (that I am pretty unfamiliar with, but I think it is done with Image Magick) which can do it but only for a single image at a time, and adds only the x, y coordinates and a value in grayscale, but no z.

The script is:

The exact format of the TXT image is defined by the convert command, then 'tail' is used to junk the header, 'tr' to character replace every non-number character with a single space, so that the later 'while' can read it easily, junking any comment numbers that may have been left.

convert -depth 8 -colorspace RGB $1 txt:- | tail -n +2 | tr -cs '0-9.\n' ' ' | while read x y Gray junk; do if [ "$Gray" -eq 0 ]; then echo "$x,$y $Gray" done

To run it I put in the Linux terminal:

chmod +x img.sh

And after that (I selected the same name as the image but with .txt as filename):

./img.sh pic0000.tif > pic0000.txt

Also I tried to change it to do it all at once, replacing the line convert -depth 8 -colorspace RGB $1 txt:- |

with

convert -depth 8 -colorspace RGB $* txt:- |

and putting this in the terminal

chmod +x ./img.sh ./img.sh *.tif > *.txt

And now it puts all the files in one with x y Grayscale, but I cannot add the z values.

By the way,it takes a long time to create the txt file.

The first lines of the final XYZ file must be, for example:

0 0 0 value in greyscale 1 0 0 value in greyscale `

and the last:

3095 2951 400 value in greyscale

Would you give me any clues, ideas or solutions to do it? Any help would be sincerely appreciated.

2

I'd use a simpler script in ImageMagick and then sed the output. The problem lies in determining your Z images.

Let's say that the image at Z=27 is DCM0027.tif and that you have images from 1 to 420.

Then you need to generate the filename from the number, and parse the file itself. For ease of use, the XYZ.txt file is generated incrementally:

 #!/bin/sh

 rm -f XYZ.txt
 for i in $( seq 1 420 ); do
      FILE=$( printf "DCM%04d.tif" )
      convert -depth 8 -colorspace gray $FILE txt:- \
         | sed -e "s/^\\([0-9]*\\),\\([0-9]*\\):.*gray(\\([0-9]*\\))/\1,\2,$i,\3/g' >> XYZ.txt
 done

The above must be run as a script (saved into img.sh and so on). If you need the numbers 1 and 420 to be parameterized, you can do so by replacing them with $1 and $2. Then you would run img.sh 1 420.

Another possibility is to redirect the script itself:

 #!/bin/sh
 for i in $( seq $1 $2 ); do
      FILE=$( printf $3 )
      convert -depth 8 -colorspace gray $FILE txt:- \
         | sed -e "s/^\\([0-9]*\\),\\([0-9]*\\):.*gray(\\([0-9]*\\))/\1,\2,$i,\3/g'
 done

The above would require both numbers and the filename structure, and redirection to save data:

 img.sh 1 500 "DCM%04d.tif" > XYZ.txt

"%04d" means "four digits, zero padded". So 0001, 0002, 0003. If the numbers are instead, say, DCM1FILE.tif, DCM9FILE.tif, DCM10FILE.tif etc, you would use "DCM%dFILE.tif" as a file pattern.

Finally, if you need the number of .tif files in a folder, you can use $( ls *.tif | wc -l ) (probably some easier way exists):

 img.sh 1 $( ls DCM*.tif | wc -l) "DCM%04d.tif" > XYZ.txt
0

Thank you @Iserni, I appreciate your effort, but I think that I don't understand your script.

By the way, In the end I solved the problem, I will post it here, maybe it will be useful to someone.

From .tiff grayscale to .txt in one file, with z coordinates, like this:

x y z Gray (always zero)

To know when one pic ends and another begins, see that the "z" value changes. To compile it: chmod +x ./script.sh and then:

./script.sh>xyzfile.txt

Don't forget to have in the folder ONLY the pictures and the script.

#!/bin/bash 
z=0 
for i in pic*; do
 z=$[$z+1] 
convert -depth 8 -colorspace Gray $i txt:- |
 tail -n +2 | tr -cs '0-9.\n' ' ' |
 while read x y Gray junk;
 do if [ "$Gray" -eq 0 ]; then 
echo "$x $y $z $Gray"
 fi
 done
 done 

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