User-defined tasks then save results

[hydranassa]

Hi,
I'm really new to ImageJ and macros in general. My goal is to have research assistants be able to open the first image in a folder manually, measure RGB for three set locations that they have to select with a rectangle, then have it automatically save the results and possibly close the file and open the next image in the folder.
Right now I have the first part:

setTool("rectangle");
run("Select None");
waitForUser("Select areas","Select the area to analyze and click 'OK'");
getSelectionBounds(x,y,width,height);
run("Measure RGB");
run("Select None");
waitForUser("Select areas","Select the area to analyze and click 'OK'");
getSelectionBounds(x,y,width,height);
run("Measure RGB");
run("Select None");
waitForUser("Select areas","Select the area to analyze and click 'OK'");
getSelectionBounds(x,y,width,height);
run("Measure RGB");

I'm just not sure how to save the results window.
Any help you can give would be greatly appreciated.

[Michael Schmid]

Hi Hydranassa,

to save the results in a macro, first select the Results Window
  selectWindow("Results");
Then use
  saveAs("txt", pathAndFileName);
Here, pathAndFileName is where you want to save it. If you want to save it in the same directory as the image, you can have, e.g.
  pathAndFileName = getInfo("image.directory")+getTitle()+"_RGBvalues.txt";

See
  http://rsb.info.nih.gov/ij/developer/macro/functions.html#selectWindow
  http://rsb.info.nih.gov/ij/developer/macro/functions.html#saveAs

Michael
________________________________________________________________

On Nov 14, 2012, at 01:42, hydranassa wrote:

> Hi,
> I'm really new to ImageJ and macros in general. My goal is to have research
> assistants be able to open the first image in a folder manually, measure RGB
> for three set locations that they have to select with a rectangle, then have
> it automatically save the results and possibly close the file and open the
> next image in the folder.
> Right now I have the first part:
>
> setTool("rectangle");
> run("Select None");
> waitForUser("Select areas","Select the area to analyze and click 'OK'");
> getSelectionBounds(x,y,width,height);
> run("Measure RGB");
> run("Select None");
> waitForUser("Select areas","Select the area to analyze and click 'OK'");
> getSelectionBounds(x,y,width,height);
> run("Measure RGB");
> run("Select None");
> waitForUser("Select areas","Select the area to analyze and click 'OK'");
> getSelectionBounds(x,y,width,height);
> run("Measure RGB");
>
> I'm just not sure how to save the results window.
> Any help you can give would be greatly appreciated.

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[Krs5]

Dear Hydranassa,

What do you try to do? Make a selection of 3 ROIs in the first image in a directory and analyse all other images using these selections or do you want the user to draw 3 ROIs on each image in the directory?

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of hydranassa
Sent: 14 November 2012 00:43
To: [hidden email]
Subject: User-defined tasks then save results

Hi,
I'm really new to ImageJ and macros in general. My goal is to have research
assistants be able to open the first image in a folder manually, measure RGB
for three set locations that they have to select with a rectangle, then have
it automatically save the results and possibly close the file and open the
next image in the folder.
Right now I have the first part:

setTool("rectangle");
run("Select None");
waitForUser("Select areas","Select the area to analyze and click 'OK'");
getSelectionBounds(x,y,width,height);
run("Measure RGB");
run("Select None");
waitForUser("Select areas","Select the area to analyze and click 'OK'");
getSelectionBounds(x,y,width,height);
run("Measure RGB");
run("Select None");
waitForUser("Select areas","Select the area to analyze and click 'OK'");
getSelectionBounds(x,y,width,height);
run("Measure RGB");

I'm just not sure how to save the results window.
Any help you can give would be greatly appreciated.





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[hydranassa]

Hi Kees,
I want the user to draw 3 ROIs on each image. I am analyzing animal patterns and the animals aren't always in the exact same spot in the photograph.
Thanks,
Hydranassa

[Krs5]

Hi Hydranassa,

The macro below might do what you have in mind. It will ask the user for the directory with images and will open each image indvidually. Results per image are stored in a subdirectory "results".

At the momentthe function getSelectionBounds(x,y,width,height); is not used for anything.

dir1 = getDirectory("Choose file directory ");
File.makeDirectory(dir1+File.separator+"results");
dir2 = dir1+"results";
setTool("rectangle");
list = getFileList(dir1);
for (i=0; i<list.length; i++) {
     if (File.isDirectory(dir1+list[i])){}
    else{
        path = dir1+list[i];
        open(path);
        title1=getTitle;
        title2=File.nameWithoutExtension;
        for (j=1;j<4;j++){
          waitForUser("Select areas","Select the area to analyze and click 'OK'");
          getSelectionBounds(x,y,width,height);
          run("Measure RGB");
          run("Select None");
       }
       selectWindow(title1);
       close();
       selectWindow("Results");
       saveAs("txt", dir2+File.separator+"Results"+title2);
       run("Close");
    }
}

Best wishes

Kees
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of hydranassa [[hidden email]]
Sent: 14 November 2012 18:02
To: [hidden email]
Subject: Re: User-defined tasks then save results

Hi Kees,
I want the user to draw 3 ROIs on each image. I am analyzing animal patterns
and the animals aren't always in the exact same spot in the photograph.
Thanks,
Hydranassa



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