Batch processing Z stacks + labelling them

Posted by Andy Gotz-2 on Mar 10, 2006; 9:49am
URL: http://imagej.273.s1.nabble.com/Batch-processing-Z-stacks-labelling-them-tp3703431.html

Hi,

I am a beginner user of ImageJ and would like to know if anyone can help
me with the following questions about z stacks :

(1) I would like to build a stack of a set of raw images from the
command line i.e. without the gui. I tried to use the RunMacro java
program and the following macro :

macro 'EdfMovie' {
/*
#       EdfMovie - make a movie of a series of EDF and write it out as
an AVI file
#
#       author - [hidden email]
#
#       date - 7 March 2006
#
#       version - 1.0
#
#       input arguments : directory,start,stop,step,width,height
#
#       example : /data/opid11/external/me1015/D30_30_,0,490,10,512,512
#
#       running : to run this macro from the command line use
#
#               run("EdfMovie",
"/data/opid11/external/me1015/D30_30_,0,490,10,512,512")
#
*/

       /* split arg to find directory, start, stop, step */
       parameters = getArgument();
       if (parameters!="") {
               parm_index = 0;
               comma_index = indexOf(parameters,",",parm_index);
               parm1 = substring(parameters,parm_index,comma_index);
               print("directory = ",parm1);
               parm_index = comma_index+1;
               comma_index = indexOf(parameters,",",comma_index+1);
               parm2 = substring(parameters,parm_index,comma_index);
               print("start = ",parm2);
               parm_index = comma_index+1;
               comma_index = indexOf(parameters,",",comma_index+1);
               parm3 = substring(parameters,parm_index,comma_index);
               print("stop = ",parm3);
               parm_index = comma_index+1;
               comma_index = indexOf(parameters,",",comma_index+1);
               parm4 = substring(parameters,parm_index,comma_index);
               print("step = ",parm4);
               parm_index = comma_index+1;
               comma_index = indexOf(parameters,",",comma_index+1);
               parm5 = substring(parameters,parm_index,comma_index);
               print("width = ",parm5);
               parm_index = comma_index+1;
               parm6 =
substring(parameters,parm_index,lengthOf(parameters));
               print("height = ",parm6);
       }
       else {
               exit();
       }
       directory=parm1;
       directory=substring(directory, 0 , lengthOf(directory)-1);
       stem = substring(directory, lastIndexOf(directory,"/"),
lengthOf(directory));
       movie_start = parseInt(parm2);
       movie_stop =  parseInt(parm3);
       movie_step =  parseInt(parm4);
       movie_width =  parseInt(parm5);
       movie_height =  parseInt(parm6);
       if (movie_step < 1) {
               movie_step = 1
       }
       for (i = movie_start; i < movie_stop; i = i+movie_step) {
               if (i < 10 )  {
                       z = "000";
               }
               if (i >= 10 && i < 100) {
                       z="00";
               }
               if (i >= 100 && i < 1000) {
                       z = "0";
               }
               if (i >= 1000) {
                       z = "";
               }
               file = directory+"/"+stem+z+i+".edf";
               run("EDF Reader", "open="+file);
               run("Size...", "width="+movie_width+"
height="+movie_height+" interpolate");
       }
       print("convert images to stack");
       run("Convert Images to Stack");
       run("Fire");
       setMinAndMax(1000, 1500);
       movie_file = directory+stem+parm2+"_"+parm3+"_"+parm4;
       print("save stack as ",movie_file);
       saveAs("AVI... ", movie_file);
       close();
}


But when I run it with RunMacro the images get opened but not converted
to a stack. The command run("Convert Images to Stack") complains there
are no images open. How can I add images to a stack without displaying
them?

(1) how to label the z axis? I would like to label the z axes with a
floating point value. Is there a way of doing this via the z axis
directly or should I add a label to the picture? Again can I do this if
I am running the macro without displaying the image?

Thanks for any help or pointers to existing solutions.

By the way congratulations on a great piece of software !

Andy