Image is overwritten in batchmode

[Johannes Breu]

Hello,

I tried to use a macro (that worked if the image was open- a multi tiff
Z-stack) in BatchMode and could not prevent coming in trouble.
I wish to extract the two channels out of a Z-stack for doing some
procedures with them (just for testing if it works I tried to save them
separatly; and this doesn´t work).
Actually I would like to have two distinct images (in this code called
A_zproject_name and B_zproject_name):


      dir1 = getDirectory("Choose Source Directory ");
      dir2 = getDirectory("Choose Destination Directory ");
      list = getFileList(dir1);
      setBatchMode(true);
      for (i=0; i<list.length; i++) {
          showProgress(i+1, list.length);
          open(dir1+list[i]);

          Aid = getImageID();
          run("Z Project...", "start=1 stop=6 projection=[Max Intensity]");
          setAutoThreshold();
          //run("Threshold...");
          run("Convert to Mask");
          A_zproject_name = getTitle();
          saveAs("tiff", dir2+A_zproject_name);


          //This is the image of channel 1

          //restore selection to the first image
          selectImage(Aid);

          //make second projection
          run("Z Project...", "start=7 stop=12 projection=[Max Intensity]");
          run("Subtract...", "value=500");
          setAutoThreshold();
          //run("Threshold...");
          run("Convert to Mask");
          B_zproject_name = getTitle();
          saveAs("tiff", dir2+B_zproject_name);
          //This is the image of channel 2


          close();
          }

So I would like to have two distinct images which I wish to address for
further processing. How does this work?
Thanks
Johannes

[Christine Labno]

Hello Johannes,

Your current macro is not giving each z-projection an
individual name, therefore the first z-projection is being
overwritten by the second.  I modified your code below to
assign the names A_zproject_name and B_zproject_name to
variables t1 and t2. I'm not clear on exactly how your stack
files are saved, or if there are multiple stacks in a folder,
but this should do the trick if there is only one stack per
folder:

dir1 = getDirectory("Choose Source Directory ");
      dir2 = getDirectory("Choose Destination Directory ");
      list = getFileList(dir1);
      setBatchMode(true);
      for (i=0; i<list.length; i++) {
          showProgress(i+1, list.length);
          open(dir1+list[i]);

          Aid = getImageID();
          run("Z Project...", "start=1 stop=6 projection=[Max
Intensity]");
          setAutoThreshold();
          //run("Threshold...");
          run("Convert to Mask");
          t1=dir2+"A_zproject_name";
          saveAs("tiff", t1);


          //This is the image of channel 1

          //restore selection to the first image
          selectImage(Aid);

          //make second projection
          run("Z Project...", "start=7 stop=12 projection=[Max
Intensity]");
          run("Subtract...", "value=500");
          setAutoThreshold();
          //run("Threshold...");
          run("Convert to Mask");
          t2=dir2+"B_zproject_name";
          saveAs("tiff", t2);

          //This is the image of channel 2


          close();
          }


Best,
Christine



---- Original message ----
>Date: Mon, 28 Jul 2008 19:33:57 +0200
>From: Johannes Breu <[hidden email]>  
>Subject: Image is overwritten in batchmode  
>To: [hidden email]
>
>Hello,
>
>I tried to use a macro (that worked if the image was open- a
multi tiff
>Z-stack) in BatchMode and could not prevent coming in trouble.
>I wish to extract the two channels out of a Z-stack for doing
some
>procedures with them (just for testing if it works I tried to
save them
>separatly; and this doesn´t work).
>Actually I would like to have two distinct images (in this
code called

>A_zproject_name and B_zproject_name):
>
>
>      dir1 = getDirectory("Choose Source Directory ");
>      dir2 = getDirectory("Choose Destination Directory ");
>      list = getFileList(dir1);
>      setBatchMode(true);
>      for (i=0; i<list.length; i++) {
>          showProgress(i+1, list.length);
>          open(dir1+list[i]);
>
>          Aid = getImageID();
>          run("Z Project...", "start=1 stop=6 projection=[Max

Intensity]");

>          setAutoThreshold();
>          //run("Threshold...");
>          run("Convert to Mask");
>          A_zproject_name = getTitle();
>          saveAs("tiff", dir2+A_zproject_name);
>
>
>          //This is the image of channel 1
>
>          //restore selection to the first image
>          selectImage(Aid);
>
>          //make second projection
>          run("Z Project...", "start=7 stop=12

projection=[Max Intensity]");

>          run("Subtract...", "value=500");
>          setAutoThreshold();
>          //run("Threshold...");
>          run("Convert to Mask");
>          B_zproject_name = getTitle();
>          saveAs("tiff", dir2+B_zproject_name);
>          //This is the image of channel 2
>
>
>          close();
>          }
>
>So I would like to have two distinct images which I wish to

address for
>further processing. How does this work?
>Thanks
>Johannes
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
Abbott 129
[phone] (phone)