Problem calling an Installed Macro

[Paul Grimm-2]

I hope the smart people on this forum can help me. I have been  
lurking on this site for a few years and using ImageJ and before  
that, NIH Image for a decade.

I have a problem with calling a macro.
I have a pretty complicated image processing macro for processing a  
folder full of images and using the setbatchmode function.

when I call the macro directly from an open text window (Macros-Run  
Macro or Apple-R) it runs perfectly, even on a folder full of images.
When I call the identical macro after loading it into the macros menu  
(Plugins->Macros->Install-> MyMacro, then going directly to it in the  
menu (Plugins->Macros-> MyMacro) or  accessing a keyboard shortcut  
(lowercase), it fails.

It starts and processes the images fine, but it fails during the  
saving portion at the end
somewhere around here

...
selectWindow("tempTotalImage.tif");
close();
close();
close();


call("java.lang.System.gc");
         }
     }
  call("java.lang.System.gc");
}

savepath = "/Users/Paul/Desktop/macroresults/" + "512PixWhite  
analysis" + ".xls";
saveAs("Measurements", savepath);
print(savepath);
run("Clear Results");
call("java.lang.System.gc");

...
Any suggestions why that might be happening?

I will attach the whole macro after my signature.
I am using the latest Image J build (1.41M) on a MacBook, the memory  
monitor shows lots of free memory..

Thanks so much.
--




--


Paul C. Grimm
Professor of Pediatrics
Dept of Pediatric Nephrology
Lucile Packard Children's Hospital
Stanford University School of Medicine
G306, MC 5208
300 Pasteur Drive
Stanford, CA 94305-5208
USA

phone   [phone]
fax       [phone]



"Obstacles are those frightful things you see when you take your eyes  
off your goal"
Henry Ford

------------

THE WHOLE MACRO
macro "Tissue area for GN8 Polarized [b]" {
     requires("1.34n");
        title = "untitled";
     dir = getDirectory("Choose a Directory ");
     list = getFileList(dir);
     start = getTime();
//run("Set Measurements...", "area display redirect=None decimal=3");

     //for (i=0; i<1; i++) {
     for (i=0; i<list.length; i++) {
         path = dir+list[i];
         showProgress(i, list.length);
         if (!endsWith(path,"/")) open(path);
         if (nImages>=1) {



   run("Options...", "iterations=1 count=1");
run("Colors...", "foreground=black background=white selection=yellow");
//this next line gets the name of the image, and is used later to  
label the result in the table
        title =getTitle();
  run("Size...", "width=512 height=512 constrain interpolate");
     setLocation(515, 100);
setBatchMode(true); // runs up to 6 times faster

selectWindow(title);
run("Duplicate...", "title=title2");
run("Duplicate...", "title=matrixtemp");
selectWindow("title2");


// here is the total tissue part
   run("Options...", "iterations=1 count=1");
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
run("Duplicate...", "title=Hue2");


selectWindow("Hue");
   setThreshold(0, 57);
run("Convert to Mask");


selectWindow("Hue2");
   setThreshold(203, 255);
run("Convert to Mask");


selectWindow("Saturation");
   setThreshold(20, 255);
run("Convert to Mask");


selectWindow("Brightness");
close();


imageCalculator("OR create", "Hue","Hue2");
//run("Make Binary", "thresholded remaining black");
//selectWindow("Result of Hue");
     setLocation(0, 200);

imageCalculator("AND create", "Saturation","Result of Hue");
//run("Make Binary", "thresholded remaining black");
//selectWindow("Result of Saturation");
//now we do a dilation to fill in the spaces then do an analyze  
particles to fill in the holes
run("Dilate");
run("Dilate");
run("Analyze Particles...", "size=50-Infinity circularity=0.00-1.00  
show=Masks include");


rename("TotalTissue");
// was tubuli

selectWindow("Saturation");
close();
selectWindow("Result of Hue");
close();
selectWindow("Hue");
close();
selectWindow("Hue2");
close();


//next we add the Matrix part

selectWindow("matrixtemp");
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
setThreshold(200, 255);
run("Convert to Mask");

selectWindow("Saturation");
   setThreshold(63, 255);
run("Convert to Mask");

selectWindow("Brightness");
  close();


imageCalculator("AND create", "Hue","Saturation");

selectWindow("Result of Hue");
rename("Matrix");

//run("Make Binary", "thresholded remaining black");
selectWindow("Saturation");
close();

selectWindow("Hue");
close();



//this next line renames the TotalTissue result window so the result  
is copied to the table with a name
selectWindow("TotalTissue");
rename("White Total - " +title);
setThreshold(250, 255);

run("Make Binary", "thresholded remaining black");
run("Set Measurements...", "area limit display redirect=None  
decimal=1");
run("Measure");

//here we save the image to the hard drive so we can get to it after  
the batchmode is turned off
saveAs("Tiff", "/Users/Paul/Desktop/macroresults/tempTotalImage.tif");

//this next line renames the Matrix result window so the result is  
copied to the table with a name
selectWindow("Matrix");
rename("White Matrix - " +title);
setThreshold(250, 255);
     setBatchMode(false);
run("Make Binary", "thresholded remaining black");
run("Set Measurements...", "area limit display redirect=None  
decimal=1");
run("Measure");
setLocation(1030, 100);
open("/Users/Paul/Desktop/macroresults/tempTotalImage.tif");
setLocation(0, 100);

wait(2000);
selectWindow("tempTotalImage.tif");
close();
close();
close();


call("java.lang.System.gc");
         }
     }
  call("java.lang.System.gc");
}

savepath = "/Users/Paul/Desktop/macroresults/" + "512PixWhite  
analysis" + ".xls";
saveAs("Measurements", savepath);
print(savepath);
run("Clear Results");
call("java.lang.System.gc");

[Gabriel Landini]

On Sunday 21 September 2008, Paul Grimm wrote:
> When I call the identical macro after loading it into the macros menu
> (Plugins->Macros->Install-> MyMacro, then going directly to it in the
> menu (Plugins->Macros-> MyMacro) or  accessing a keyboard shortcut
> (lowercase), it fails.
>
> It starts and processes the images fine, but it fails during the
> saving portion at the end
> somewhere around here

Hi,
What is the error that you get?

G

[Paul Grimm-2]

Sorry, I should have stated that.
When I run the macro after installing it into the plugins menu or  
from an open text window the entire macro processes correctly.
When I run it from a keyboard shortcut or after installing it into  
the macros menu the images are processed, the results go to the  
results window, but the file is not saved to the hard drive. The last  
instructions are simply ignored by the macro  which seems to just  
close. No error messages appear.



--

Paul C. Grimm



"The first rule is to keep an untroubled spirit.  The second is to look
things in the face and know them for what they are."
Marcus Aurelius, Roman Emperor


On Sep 21, 2008, at 1:00 AM, Gabriel Landini wrote:

> On Sunday 21 September 2008, Paul Grimm wrote:
>> When I call the identical macro after loading it into the macros menu
>> (Plugins->Macros->Install-> MyMacro, then going directly to it in the
>> menu (Plugins->Macros-> MyMacro) or  accessing a keyboard shortcut
>> (lowercase), it fails.
>>
>> It starts and processes the images fine, but it fails during the
>> saving portion at the end
>> somewhere around here
>
> Hi,
> What is the error that you get?
>
> G

[Ben Tupper]

On Sep 22, 2008, at 10:48 AM, Paul Grimm wrote:

> Sorry, I should have stated that.
> When I run the macro after installing it into the plugins menu or  
> from an open text window the entire macro processes correctly.
> When I run it from a keyboard shortcut or after installing it into  
> the macros menu the images are processed, the results go to the  
> results window, but the file is not saved to the hard drive. The  
> last instructions are simply ignored by the macro  which seems to  
> just close. No error messages appear.
>
>>

Hi Paul,

I don't think you are providing sufficient information.  Can you  
create a very simple macro that shows the errant behavior and post  
that to this list?

Cheers,
Ben

[Paul Grimm-2]

That fixed it!!!!
Thank you so much.

Paul
--  



On Sep 22, 2008, at 9:08 AM, Wayne Rasband wrote:

>
> Your macro may be failing because a "}" is in the wrong place. I  
> suspect that the "}" just before
>
>     savepath = "/Users/Paul/Desktop/macroresults/" + "512PixWhite  
> analysis" + ".xls";
>
> should instead be added the end of the macro.
>
> Sincerely,
>
> -wayne

[Florian Blaschke]

Could you please take me from the list.
Thanks a lot!
 
Florian Blaschke
E-mail: [hidden email]

________________________________

From: ImageJ Interest Group on behalf of Paul Grimm
Sent: Tue 9/23/2008 5:18 AM
To: [hidden email]
Subject: Re: Problem calling an Installed Macro



That fixed it!!!!
Thank you so much.

Paul
--



On Sep 22, 2008, at 9:08 AM, Wayne Rasband wrote:

>
> Your macro may be failing because a "}" is in the wrong place. I
> suspect that the "}" just before
>
>     savepath = "/Users/Paul/Desktop/macroresults/" + "512PixWhite
> analysis" + ".xls";
>
> should instead be added the end of the macro.
>
> Sincerely,
>
> -wayne