Images to stack in batch mode

[remi-2-3]

Hello,

I am currently trying to do some image analysis with an imageJ macro
that I launch in batch mode from the command line (-batch option and
setBatch(true)). After generating 68 images I would like to run the
'Images to Stack' command, to 'compile' them. Unfortunately, the stack
is never generated.
Any idea? Advice? Other way to do it? Anything would be greatly
appreciated.

Thank you,

Rémi P.

[David Webster]

Remi,

I don't know if this is the same thing, but I recently had a problem with
images created in batch mode, not being there when I exited (see my email
"Batch Mode/Active Image Ambiguity" and Wayne's reply. I did an experiment
using the macro shown below:

setBatchMode(true);
newImage("1", "8-bit Black", 100, 100, 1);
newImage("2", "8-bit Black", 100, 100, 1);
newImage("3", "8-bit Black", 100, 100, 1);
// Point 1
//setBatchMode(false);
// Point 2
run("Images to Stack");
//setBatchMode(false);

If I uncomment the first "setBatchMode(false)" then images 1 and 2 aren't
seen and I get the error message "There must be two images open" (image 3 is
open). If I recomment that statement and uncomment the second
"setBatchMode(false)", then I egt a stack with no problems. I hope this
helps.

David Webster


On Thu, Mar 19, 2009 at 9:24 AM, Remi <[hidden email]> wrote:

> Hello,
>
> I am currently trying to do some image analysis with an imageJ macro that I
> launch in batch mode from the command line (-batch option and
> setBatch(true)). After generating 68 images I would like to run the 'Images
> to Stack' command, to 'compile' them. Unfortunately, the stack is never
> generated.
> Any idea? Advice? Other way to do it? Anything would be greatly
> appreciated.
>
> Thank you,
>
> Rémi P.
>

[Gabriel Landini]

On Friday 20 March 2009 01:25:15 David Webster wrote:

> setBatchMode(true);
> newImage("1", "8-bit Black", 100, 100, 1);
> newImage("2", "8-bit Black", 100, 100, 1);
> newImage("3", "8-bit Black", 100, 100, 1);
> // Point 1
> //setBatchMode(false);
> // Point 2
> run("Images to Stack");
> //setBatchMode(false);
>
> If I uncomment the first "setBatchMode(false)" then images 1 and 2 aren't
> seen and I get the error message "There must be two images open" (image 3
> is open).

But that is correct. The documentation states that when you exit batch mode
with "false", only the last selected image is shown, the others are closed.

> > I am currently trying to do some image analysis with an imageJ macro that
> > I launch in batch mode from the command line (-batch option and
> > setBatch(true)). After generating 68 images I would like to run the
> > 'Images to Stack' command, to 'compile' them. Unfortunately, the stack is
> > never generated.

Does it run without the batchmode?
Do you by any chance have different types of images, or different sizes?

cheers,
G.

[remi-2-3]

Gabriel Landini wrote:

> On Friday 20 March 2009 01:25:15 David Webster wrote:
>  
>> setBatchMode(true);
>> newImage("1", "8-bit Black", 100, 100, 1);
>> newImage("2", "8-bit Black", 100, 100, 1);
>> newImage("3", "8-bit Black", 100, 100, 1);
>> // Point 1
>> //setBatchMode(false);
>> // Point 2
>> run("Images to Stack");
>> //setBatchMode(false);
>>
>> If I uncomment the first "setBatchMode(false)" then images 1 and 2 aren't
>> seen and I get the error message "There must be two images open" (image 3
>> is open).
>>    
>
> But that is correct. The documentation states that when you exit batch mode
> with "false", only the last selected image is shown, the others are closed.
>
>  
>>> I am currently trying to do some image analysis with an imageJ macro that
>>> I launch in batch mode from the command line (-batch option and
>>> setBatch(true)). After generating 68 images I would like to run the
>>> 'Images to Stack' command, to 'compile' them. Unfortunately, the stack is
>>> never generated.
>>>      
>
> Does it run without the batchmode?
> Do you by any chance have different types of images, or different sizes?
>
> cheers,
> G.
>  

It does run without the batch mode. I think the problem is that I
generate Z-axis profiles to get mean intensity values and that I can't
close the graph in batch mode. So, at the end I do have different types
of images: 68 I want to make a stack with and 2 Z-axis plot I can't
close, even with a close(); just after their generation...

Cheers,

Rémi.

[remi-2-3]

Gabriel Landini wrote:

> On Friday 20 March 2009 01:25:15 David Webster wrote:
>  
>> setBatchMode(true);
>> newImage("1", "8-bit Black", 100, 100, 1);
>> newImage("2", "8-bit Black", 100, 100, 1);
>> newImage("3", "8-bit Black", 100, 100, 1);
>> // Point 1
>> //setBatchMode(false);
>> // Point 2
>> run("Images to Stack");
>> //setBatchMode(false);
>>
>> If I uncomment the first "setBatchMode(false)" then images 1 and 2 aren't
>> seen and I get the error message "There must be two images open" (image 3
>> is open).
>>    
>
> But that is correct. The documentation states that when you exit batch mode
> with "false", only the last selected image is shown, the others are closed.
>
>  
>>> I am currently trying to do some image analysis with an imageJ macro that
>>> I launch in batch mode from the command line (-batch option and
>>> setBatch(true)). After generating 68 images I would like to run the
>>> 'Images to Stack' command, to 'compile' them. Unfortunately, the stack is
>>> never generated.
>>>      
>
> Does it run without the batchmode?
> Do you by any chance have different types of images, or different sizes?
>
> cheers,
> G.
>  

This code, with a Z-axis plot doesn't work

setBatchMode(true);

//Setting the autoclose options
run("Profile Plot Options...", "width=450 height=200 minimum=0 maximum=0
do auto-close interpolate draw")

//Creating three pictures
newImage("1", "8-bit White", 500, 500, 1);
newImage("2", "8-bit White", 500, 500, 1);
newImage("3", "8-bit White", 500, 500, 1);

//Making a stack
run("Images to Stack");

print("nImages: "+nImages);
print("title: "+getTitle);
print("stack size: "+nSlices);

//Doing some analysis
run("Plot Z-axis Profile");
close(); //On ferme le plot généré par le Z-axis Profile-A

//Closing the stack
selectWindow("Stack");
close();

print("nImages: "+nImages);
print("title: "+getTitle);
print("stack size: "+nSlices);


//Creating three pictures
newImage("1", "8-bit White", 500, 500, 1);
newImage("2", "8-bit White", 500, 500, 1);
newImage("3", "8-bit White", 500, 500, 1);

//    ---> Impossible to make this stack  <---
run("Images to Stack"); //   <--

[Gabriel Landini]

On Friday 20 March 2009 09:19:28 Remi wrote:
> It does run without the batch mode. I think the problem is that I
> generate Z-axis profiles to get mean intensity values and that I can't
> close the graph in batch mode.

You should be able to get the title or id just after z profile creation and
close() it.

> So, at the end I do have different types of images: 68 I want to make a
> stack with and 2 Z-axis plot I can't  close, even with a close(); just after
> their generation...

Check that you got the name right *and* select it with selectImage(). You
should be able to close it.

I hope it helps

G.

[Wayne Rasband]

This bug is fixed in the ImageJ 1.42l daily build. The
Image>Stacks>Plot Z-axis profile command was not working correctly in
batch mode macros.

-wayne

On Mar 20, 2009, at 5:39 AM, Remi wrote:

> Gabriel Landini wrote:
>> On Friday 20 March 2009 01:25:15 David Webster wrote:
>>
>>> setBatchMode(true);
>>> newImage("1", "8-bit Black", 100, 100, 1);
>>> newImage("2", "8-bit Black", 100, 100, 1);
>>> newImage("3", "8-bit Black", 100, 100, 1);
>>> // Point 1
>>> //setBatchMode(false);
>>> // Point 2
>>> run("Images to Stack");
>>> //setBatchMode(false);
>>>
>>> If I uncomment the first "setBatchMode(false)" then images 1 and 2
>>> aren't
>>> seen and I get the error message "There must be two images open"
>>> (image 3
>>> is open).
>>>
>>
>> But that is correct. The documentation states that when you exit
>> batch mode with "false", only the last selected image is shown, the
>> others are closed.
>>
>>
>>>> I am currently trying to do some image analysis with an imageJ
>>>> macro that
>>>> I launch in batch mode from the command line (-batch option and
>>>> setBatch(true)). After generating 68 images I would like to run the
>>>> 'Images to Stack' command, to 'compile' them. Unfortunately, the
>>>> stack is
>>>> never generated.
>>>>
>>
>> Does it run without the batchmode?
>> Do you by any chance have different types of images, or different
>> sizes?
>>
>> cheers,
>> G.
>>
>
> This code, with a Z-axis plot doesn't work
>
> setBatchMode(true);
>
> //Setting the autoclose options
> run("Profile Plot Options...", "width=450 height=200 minimum=0
> maximum=0 do auto-close interpolate draw")
>
> //Creating three pictures
> newImage("1", "8-bit White", 500, 500, 1);
> newImage("2", "8-bit White", 500, 500, 1);
> newImage("3", "8-bit White", 500, 500, 1);
>
> //Making a stack
> run("Images to Stack");
>
> print("nImages: "+nImages);
> print("title: "+getTitle);
> print("stack size: "+nSlices);
>
> //Doing some analysis
> run("Plot Z-axis Profile");
> close(); //On ferme le plot généré par le Z-axis Profile-A
>
> //Closing the stack
> selectWindow("Stack");
> close();
>
> print("nImages: "+nImages);
> print("title: "+getTitle);
> print("stack size: "+nSlices);
>
>
> //Creating three pictures
> newImage("1", "8-bit White", 500, 500, 1);
> newImage("2", "8-bit White", 500, 500, 1);
> newImage("3", "8-bit White", 500, 500, 1);
>
> //    ---> Impossible to make this stack  <---
> run("Images to Stack"); //   <--
>

[Joachim Wesner]

Hi list,

I seem to remember there were related entries in the list (archives) here,
but it seems I cannot find the right entries/keyword in the moment....

I´m working on a plugin that seems to show erratic behaviour on my new fast
dual core system. I think I "nailed" the problem down to the
point where I call an external plugin to do some extra processing on an
internal image that I create (and usually close again after).

The task here is to create a circular ROI from interferometer mask data +
some hole filling
.
.
.
            bProc.dilate(); bProc.dilate();
            bProc.erode(); bProc.erode();
            ImagePlus impb = new ImagePlus("Zygo phase mask - "+file,
bProc);
            impb.updateAndRepaintWindow();
            impb.show();
//          IJ.wait(200);
            createSelectionFromMask(bProc);
.
.
.
.
      void createSelectionFromMask(ImageProcessor ip) {
            ip.setThreshold(0, 0, ImageProcessor.NO_LUT_UPDATE);
            IJ.runPlugIn("ij.plugin.filter.ThresholdToSelection", "");
      }


It only works if I really shortly "show" the ImagePlus impb before calling
createSelectionFromMask,, OK, I can accept that, as it´s another
plugin, that I use.

HOWEVER,

Without the added IJ.wait it seems that often on the new fast, dual core
system, the other plugin already runs *BEFORE* the image is "shown", so it
will cease to work.
Inserting the short delay of 200-500 ms seems to cure the problem for the
moment, but I wonder if there is a better solution!?


Sincerely

Joachim


Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis


______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________

[Wayne Rasband]

Images are displayed in a thread separate from the thread used to run
plugins, so it would be better not to display the image until you have
finished processing it. With macros, you can easily do this by running
in batch mode. JavaScripts and plugins can run plugins or commands on
images that are not displayed using

    IJ.runPlugIn(ImagePlus, className, arg)

or

    IJ.run(ImagePlus, command, options)

Here is and updated version of your example that does not display the
image until it has finished:

    bProc.dilate(); bProc.dilate();
    bProc.erode(); bProc.erode();
    ImagePlus impb = new ImagePlus("Zygo phase mask - "+file, bProc);
    createSelectionFromMask(impb);
    impb.show();
    .
    .
    .
    void createSelectionFromMask(ImagePlus imp) {
       ImageProcessor ip = imp.getProcessor();
       ip.setThreshold(0, 0, ImageProcessor.NO_LUT_UPDATE);
       IJ.runPlugIn(imp, "ij.plugin.filter.ThresholdToSelection", "");
    }

-wayne

On Mar 20, 2009, at 11:15 AM, Joachim Wesner wrote:

> Hi list,
>
> I seem to remember there were related entries in the list (archives)
> here,
> but it seems I cannot find the right entries/keyword in the moment....
>
> I´m working on a plugin that seems to show erratic behaviour on my new
> fast
> dual core system. I think I "nailed" the problem down to the
> point where I call an external plugin to do some extra processing on an
> internal image that I create (and usually close again after).
>
> The task here is to create a circular ROI from interferometer mask
> data +
> some hole filling
> .
> .
> .
>             bProc.dilate(); bProc.dilate();
>             bProc.erode(); bProc.erode();
>             ImagePlus impb = new ImagePlus("Zygo phase mask - "+file,
> bProc);
>             impb.updateAndRepaintWindow();
>             impb.show();
> //          IJ.wait(200);
>             createSelectionFromMask(bProc);
> .
> .
> .
> .
>       void createSelectionFromMask(ImageProcessor ip) {
>             ip.setThreshold(0, 0, ImageProcessor.NO_LUT_UPDATE);
>             IJ.runPlugIn("ij.plugin.filter.ThresholdToSelection", "");
>       }
>
>
> It only works if I really shortly "show" the ImagePlus impb before
> calling
> createSelectionFromMask,, OK, I can accept that, as it´s another
> plugin, that I use.
>
> HOWEVER,
>
> Without the added IJ.wait it seems that often on the new fast, dual
> core
> system, the other plugin already runs *BEFORE* the image is "shown",
> so it
> will cease to work.
> Inserting the short delay of 200-500 ms seems to cure the problem for
> the
> moment, but I wonder if there is a better solution!?
>
>
> Sincerely
>
> Joachim
>
>
> Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
> Wetzlar  HRB 2432
> Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr.
> David Roy
> Martyr | Colin Davis
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>

[Joachim Wesner]

Thanks Wayne,

again, extremely fast and exactly on the point!!

Actually, I did not really want to display that temporary ImagePlus at all,
but was forced to do so for the other plugin to work,
as I overlooked the alternative method you mention!

I changed my code and left the display of that mask window as a debug
option, works great now!

Thanks again!

Cheers

Joachim

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis


ImageJ Interest Group <[hidden email]> schrieb am 20.03.2009 17:08:54:

> Images are displayed in a thread separate from the thread used to run
> plugins, so it would be better not to display the image until you have
> finished processing it. With macros, you can easily do this by running
> in batch mode. JavaScripts and plugins can run plugins or commands on
> images that are not displayed using
>
>     IJ.runPlugIn(ImagePlus, className, arg)
>
> or
>
>     IJ.run(ImagePlus, command, options)
>
> Here is and updated version of your example that does not display the
> image until it has finished:
>
>     bProc.dilate(); bProc.dilate();
>     bProc.erode(); bProc.erode();
>     ImagePlus impb = new ImagePlus("Zygo phase mask - "+file, bProc);
>     createSelectionFromMask(impb);
>     impb.show();
>     .
>     .
>     .
>     void createSelectionFromMask(ImagePlus imp) {
>        ImageProcessor ip = imp.getProcessor();
>        ip.setThreshold(0, 0, ImageProcessor.NO_LUT_UPDATE);
>        IJ.runPlugIn(imp, "ij.plugin.filter.ThresholdToSelection", "");
>     }
>
> -wayne
>

______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________