need advice on batch macros

[olao4]

Hello,

I have a very basic question, but since I never wrote a macro before I feel
really lost.
I need a simple macro that opens every separate file and that for every file
in a folder calculates its difference with a one specified picture and then
inverts it. I know how to do the difference: process>image calculator>
and how to invert ctrl+shift+i, however I do not know how to make it repeat
the function for every separate file, i.e. I do not know how to refer to my
files while writing the macro.

I would really appreciate your advice!

[Nathaniel Ryckman]

 1) If you have 1 directory with all the files, you can use this:

  head = getDirectory("Choose a directory containing raw image sets.");
  setBatchMode(true);
  children = getFileList(head);
  for(i = 0; i < children.length; i++)
  {
     curChild = curDir + children[i];
     
     // DO STUFF HERE WITH curChild
  }

 2) If you need to recursively search folders:

  head = getDirectory("Choose a directory containing raw image sets.");

  setBatchMode(true);

  focusStacks(head);

  function focusStacks(curDir)
  {
    children = getFileList(curDir);

    for(i = 0; i < children.length; i++)
    {
      curChild = curDir + children[i];
      isDir = File.isDirectory(curChild);
      if(!isDir)
      {
        // DO STUFF HERE WITH curChild
      }
      else
      {
        focusStacks(curChild);
      }
    }
  }

 3) Batchmode doesn't work well....

It should be fine for what you are trying to do, but if you make your macro any more complicated, you might want to consider making a plugin.

[Nathaniel Ryckman]

olao4 wrote

Hello,

I have a very basic question, but since I never wrote a macro before I feel
really lost.
I need a simple macro that opens every separate file and that for every file
in a folder calculates its difference with a one specified picture and then
inverts it. I know how to do the difference: process>image calculator>
and how to invert ctrl+shift+i, however I do not know how to make it repeat
the function for every separate file, i.e. I do not know how to refer to my
files while writing the macro.

I would really appreciate your advice!

Oh, you will definitely need this as well!
     
fileName = File.getName(curDir);
selectWindow(fileName + ".tif");

Once you select a window, you can just run commands like you normally would.

[olao4]

Thanks for a fast reply!

I still have a problem though.
It says that some variable is undefined, I guess it means curDir, even after I added the two lines you posted later...

[Nathaniel Ryckman]

olao4 wrote

Thanks for a fast reply!

I still have a problem though.
It says that some variable is undefined, I guess it means curDir, even after I added the two lines you posted later...

I didn't give you the EXACT code. I only gave you some starting points. Here, I just wrote the following code for you, but I didn't test it out:


// Get image to do subtraction
userImg = File.openDialog("Select Specified File")
open(userImg);
imgName = File.getName(userImg);

// Get file list
head = getDirectory("Choose a directory containing raw image sets.");
children = getFileList(head);

// Set batch mode to true
setBatchMode(true);

// Process each image
for(i = 0; i < children.length; i++)
{
  // Open 2nd image
  curChild = head + children[i];
  open(curChild);
       
  // Subtraction
  imageCalculator("Subtract create", imgName, children[i]);

  // Invert result
  selectWindow("Result of " + imgName);
  run("Invert");

  // Save result
  selectWindow("Result of " + imgName);
  saveAs("Tiff", head + "Result_" + imgName);
  close();  

  // Close 2nd image
  selectWindow(children[i]);
  close();
}

// Close 1st image
selectWindow(imgName);
close();


A few things to note:

1) I didn't know if you are trying to subtract the 1st image from the 2nd or the 2nd from the first.
2) If you want to continue using Macros, you will unfortunately need to learn a little programming. Herre are some resources:

http://rsb.info.nih.gov/ij/developer/macro/macros.html
http://rsbweb.nih.gov/ij/developer/macro/functions.html
Start imageJ and then use Plugins->Macros->Record...

[olao4]

Thanks so much for the reply! Yeah, I don't know much about programing, I will refer to those websites to learn some more, it's so useful.