naive question involving a macro to apply misc. (contrast, scale bar, convert image) to multiple files

Posted by William Jeffrey Triffo on Feb 11, 2008; 8:18am
URL: http://imagej.273.s1.nabble.com/naive-question-involving-a-macro-to-apply-misc-contrast-scale-bar-convert-image-to-multiple-files-tp3697222.html

hello,

I am trying to write a simple macro file to open a bunch of images,
'auto set' the contrast, add a scalebar, and then save the image as a
jpeg. In the text below, I have edited an example I found for converting
BioRad to TIFF (can't remember where), that I appended commands to based
on the output of the "record macro" function in ImageJ. To the author of
that macro, thanks.

regarding the scalebar, I am using the .DM3 reader plug-in which
(nicely) sets the scale for me for each image using the .DM3 header.

The macro appears to convert all the images in a directory to .jpg, but
the scalebar (and presumably the 'auto contrast' line) only appear to
effect the last file in the series. As you can see, I have done some
very crude debugging using 'wait', to see if the commands were running
over each other (I would not know).

at any rate, any help would be appreciated; I tried searching the
archive for "scale bar batch", etc, but did not find a post dealing with
this (although it seems like a frequent operation to me, so I may have
mis-used the search function on the listserv homepage).

thanks much,

-Jeff

//
// the macro also assumes that you have the biorad plugin install
// (Biorad_Reader.class) as well as the file handler for other
// file types (HandleExtraFileTypes.class)
//
// gma - 28 mar 05
//

  macro "Batch Convert Image to JPEG with Contrast and Scalebar" {convert("jpeg");}

  function convert(format) {
      requires("1.33s");
      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]);
          wait(1000);
        //  run("Enhance Contrast", "saturated=0.5");
          wait(1000);
          run("Scale Bar...", "width=0.10 height=12 font=42 color=White background=None location=[Lower Right] hide");
          wait(1000);
          saveAs(format, dir2+list[i]);
          close();
      }
  }