save summary file

[Colin Sturm]

ImageJ List,

I am trying to analyze the number of particles in a group of images.
I have a macro to cycle through the directories, open the correct image,
and threshold.
I run the analyze particles:
    run("Analyze Particles...", "size=7-Infinity circularity=0.75-1.00
show=Nothing clear summarize");
which gives me a summary of particle count.
I then want to save the summary:
    run("Text...", "save="+listdirect+"bead_count.txt");    // saves
results  

This works fine for a few directories but then stops with an error:
"This command requires a TextWindow such as the "Log" window or an "Info
for..." window."

I assumed this was because the analyze particles hadn't finished and the
summary window wasn't up yet.  I put in a wait(3000) before saving but
still got the error.  Even with a wait(10000) the error arose.

Is there a way to wait until processing of analyze particles is done?  
Or even better is there a way to directly send the summary of analyze
particles to a text file?

Thanks for any help.
I've included my code below if needed.

Colin Sturm



fitdirectory = getDirectory("Select a Directory")    // prompts what
directory to take images from for processing
setBatchMode(true);
for (i = 1; i <=40; i++) {            // changes directory
    if (i<=9){
        listdirect = fitdirectory+"0"+i+"/";    // sets directory
    }
    if (i>9){
        listdirect = fitdirectory+i+"/";    // sets directory
    }
    list = getFileList(listdirect);        // gets list of files for
working directory
    if (list.length==0){        // checks if no files found
        print("Stopped at directory "+listdirect);
        exit        // stops code
    }
    open(listdirect+"bandpass_fitc.tif");        // open fitc image
    setThreshold(0, 60000);                // sets threshold of 16-bit image
    run("Convert to Mask");                // removes everything that
isn't thresholded
    setThreshold(0, 254);                // sets threshold so particles
can be analyzed
    run("Analyze Particles...", "size=7-Infinity circularity=0.75-1.00
show=Nothing clear summarize");
    close();
    wait(3000);                  
    run("Text...",
"save="+listdirect+"bandpass_fitc_bead_count.txt");    // saves results  
    run("Close");                    // closes results
    open(listdirect+"bandpass_tritc.tif");        // open tritc image
    setThreshold(0, 60000);                // same as above except for
tritc image
    run("Convert to Mask");
    setThreshold(0, 254);
    run("Analyze Particles...", "size=7-Infinity circularity=0.5-1.00
show=Nothing clear summarize");
    close();
    wait(3000);
    run("Text...", "save="+listdirect+"bandpass_tritc_bead_count.txt");
    run("Close");
}
setBatchMode(false);

[Gabriel Landini]

On Monday 02 April 2007 16:17:32 Colin Sturm wrote:
> This works fine for a few directories but then stops with an error:
> "This command requires a TextWindow such as the "Log" window or an "Info
> for..." window."

You could test whether the Results window is open, if so, save it and close
it, otherwise wait:

isOpen("Title")
 Returns true if the window with the specified title is open.

Cheers,

G.

[Colin Sturm]

Is there a way to continue to the next iteration of a for loop if a
criteria is met?
I tried using continue; but didn't work.

Ex:
for (i=1; i<=8; i++){
    if(i==5)
          continue;
    print(i);
}

So the desired output would be:
1
2
3
4
6
7
8

Thanks

[Bill Christens-Barry]

Chris,

You can do this:

for (i=1; i<=8; i++){
    if(i<>5)
        print(i);
}

Bill Christens-Barry


On Mon, 2 Apr 2007 15:54:45 -0400, Colin Sturm <[hidden email]> wrote:

>Is there a way to continue to the next iteration of a for loop if a
>criteria is met?
>I tried using continue; but didn't work.
>
>Ex:
>for (i=1; i<=8; i++){
>    if(i==5)
>          continue;
>    print(i);
>}

[Lelli Thomas]

Hi
I think you have to save it like this:
saveAs("Measurements",listdirect+"bandpass_tritc_bead_count");
or saveAs("Measurements",listdirect+"bandpass_tritc_bead_count.xls");

Thomas
Colin Sturm a écrit :

> ImageJ List,
>
> I am trying to analyze the number of particles in a group of images.
> I have a macro to cycle through the directories, open the correct
> image, and threshold.
> I run the analyze particles:
>    run("Analyze Particles...", "size=7-Infinity circularity=0.75-1.00
> show=Nothing clear summarize");
> which gives me a summary of particle count.
> I then want to save the summary:
>    run("Text...", "save="+listdirect+"bead_count.txt");    // saves
> results  
> This works fine for a few directories but then stops with an error:
> "This command requires a TextWindow such as the "Log" window or an
> "Info for..." window."
>
> I assumed this was because the analyze particles hadn't finished and
> the summary window wasn't up yet.  I put in a wait(3000) before saving
> but still got the error.  Even with a wait(10000) the error arose.
>
> Is there a way to wait until processing of analyze particles is done?  
> Or even better is there a way to directly send the summary of analyze
> particles to a text file?
>
> Thanks for any help.
> I've included my code below if needed.
>
> Colin Sturm
>
>
>
> fitdirectory = getDirectory("Select a Directory")    // prompts what
> directory to take images from for processing
> setBatchMode(true);
> for (i = 1; i <=40; i++) {            // changes directory
>    if (i<=9){
>        listdirect = fitdirectory+"0"+i+"/";    // sets directory
>    }
>    if (i>9){
>        listdirect = fitdirectory+i+"/";    // sets directory
>    }
>    list = getFileList(listdirect);        // gets list of files for
> working directory
>    if (list.length==0){        // checks if no files found
>        print("Stopped at directory "+listdirect);
>        exit        // stops code
>    }
>    open(listdirect+"bandpass_fitc.tif");        // open fitc image
>    setThreshold(0, 60000);                // sets threshold of 16-bit
> image
>    run("Convert to Mask");                // removes everything that
> isn't thresholded
>    setThreshold(0, 254);                // sets threshold so particles
> can be analyzed
>    run("Analyze Particles...", "size=7-Infinity circularity=0.75-1.00
> show=Nothing clear summarize");
>    close();
>    wait(3000);                      run("Text...",
> "save="+listdirect+"bandpass_fitc_bead_count.txt");    // saves
> results      run("Close");                    // closes results
>    open(listdirect+"bandpass_tritc.tif");        // open tritc image
>    setThreshold(0, 60000);                // same as above except for
> tritc image
>    run("Convert to Mask");
>    setThreshold(0, 254);
>    run("Analyze Particles...", "size=7-Infinity circularity=0.5-1.00
> show=Nothing clear summarize");
>    close();
>    wait(3000);
>    run("Text...", "save="+listdirect+"bandpass_tritc_bead_count.txt");
>    run("Close");
> }
> setBatchMode(false);
>

[Reisak]

i did this and it works .:)

selectWindow("Summary");
saveAs("Text", dir2+excel);

Dir 2 ist defined as in the beginning of the macro.
dir2 = getDirectory("Choose Destination Directory ");