Calling Make Binary from within a macro brings up a pop-up

[Dan McDonald]

Dear List,

 

I am running ImageJ 1.45l under Ubuntu 11.04.

 

I am using the macro function run("Make Binary") in a macro that worked
properly in early July.  When I run the macro now a new pop-up window
appears with the Title "Make Binary" and with three checkboxes.  I assumed
there was an enhancement to the Make Binary function and that I would have
to run the macro recorder to see the new required formats to the command.
But the recorder does not give me any indication that the Make Binary
function can be sent arguments.

 

My macro processes a directory full of files automatically.  Having to
interact with the program whenever the run("Make Binary") command is
executed is not a good option.

 

Has anyone else run into this?  Can anyone suggest a work around?

 

Regards,

 

Dan

 

 

Daniel W. McDonald, President

Phenotype Screening Corporation

4028 Papermill Rd, Suite 10

Knoxville, TN 37909

[phone]

 

Our product, RootViz FS, was a 2007 R&D100 Award Winner. Rated as one of the
100 most technologically significant products introduced into the
marketplace in the prior year.

 

[Gabriel Landini]

On Sunday 07 Aug 2011, you wrote:
> I am using the macro function run("Make Binary") in a macro that worked
> properly in early July.  When I run the macro now a new pop-up window
> appears with the Title "Make Binary" and with three checkboxes.  

I only see 2 check boxes, not 3, but that happens if I try to binarise a
stack.
What are do the 3 checkboxes say?
I am using the daily build.
Cheers

Gabriel

[Dan McDonald]

Gabriel,

This particular macro does not process a stack.  It is processing a "mask"
image from a previous "Analyze Particles" and saved as a Tiff file.

The three checkboxes in the pop-up window are all checked as the default
response.  They are:
Thresholded pixels to foreground color
Remaining pixels to background color
Black foreground, white background

Regards,

Dan

Daniel W. McDonald, President
Phenotype Screening Corporation
4028 Papermill Rd, Suite 10
Knoxville, TN 37909
[phone]
 
Our product, RootViz FS, was a 2007 R&D100 Award Winner. Rated as one of the
100 most technologically significant products introduced into the
marketplace in the prior year.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: Sunday, August 07, 2011 1:50 PM
To: [hidden email]
Subject: Re: Calling Make Binary from within a macro brings up a pop-up

On Sunday 07 Aug 2011, you wrote:
> I am using the macro function run("Make Binary") in a macro that worked
> properly in early July.  When I run the macro now a new pop-up window
> appears with the Title "Make Binary" and with three checkboxes.  

I only see 2 check boxes, not 3, but that happens if I try to binarise a
stack.
What are do the 3 checkboxes say?
I am using the daily build.
Cheers

Gabriel

[Gabriel Landini]

On Sunday 07 Aug 2011 19:09:18 you wrote:
> This particular macro does not process a stack.  It is processing a "mask"
> image from a previous "Analyze Particles" and saved as a Tiff file.

First thing to try: Does your macro set a threshold before calling the Make
Binary command? If not try setting one.

If that does not make a difference, what happens if before running the macro
you make a dummy image and run these macro commands:

setThreshold(127, 255);
run("Threshold", "thresholded remaining");

Then close that dummy image and try your macro again. Does the dialog still
appear?
I seem to remember something like this happening. I have a custom
startupmacros file where I set a number of defaults and those 2 command above
are in my file.

Cheers
Gabriel

[Dan McDonald]

Gabriel,

When I create and run a simple macro with the Make Binary command on my
machine I do not get the pop-up window.  The problematic macro has several
hundred lines of code.  I must be doing something within my macro that is
not correct.  I had assumed the bad line of code causing the Make Binary
window to pop-up was when I ran Make Binary.  That might not be the case.
Let me try to parse the problem up and isolate it.  I'll let you know what I
find out.

Dan

Daniel W. McDonald, President
Phenotype Screening Corporation
4028 Papermill Rd, Suite 10
Knoxville, TN 37909
[phone]
 
Our product, RootViz FS, was a 2007 R&D100 Award Winner. Rated as one of the
100 most technologically significant products introduced into the
marketplace in the prior year.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: Sunday, August 07, 2011 4:04 PM
To: [hidden email]
Subject: Re: Calling Make Binary from within a macro brings up a pop-up

On Sunday 07 Aug 2011 19:09:18 you wrote:
> This particular macro does not process a stack.  It is processing a "mask"
> image from a previous "Analyze Particles" and saved as a Tiff file.

First thing to try: Does your macro set a threshold before calling the Make
Binary command? If not try setting one.

If that does not make a difference, what happens if before running the macro

you make a dummy image and run these macro commands:

setThreshold(127, 255);
run("Threshold", "thresholded remaining");

Then close that dummy image and try your macro again. Does the dialog still
appear?
I seem to remember something like this happening. I have a custom
startupmacros file where I set a number of defaults and those 2 command
above
are in my file.

Cheers
Gabriel