redirect to imageID

[Tony Collins-4]

Hi,

I'm duplicating an image, then using this to create a binary/watershed mask to "analyze particles" with the measurements redirected to the original.

This works well but I'd like to batch process a folder of these images. Is there a way to "redirect to" an image ID rather than image name?

Thanks,

Tony

 
Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[hidden email]     www.macbiophotonics.ca

[Michael Schmid]

Hi Tony,

sorry, no way to have an ImageID for the Analyze>Set Measurements  
redirect target in a macro.
In the inner works of ImageJ, it is an ImageID, but you cannot access  
it from a macro. You can only find out whether you have one, by using  
call("ij.plugin.filter.Analyzer.isRedirectImage"):
   http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Analyzer.java

You have to use
   sourceTitle = getTitle();
on the input image and set the measurement options, e.g.
   run("Set Measurements...", "area mean min redirect=["+ sourceTitle  
+"] decimal=4");

This will fail if you have two open images with the same name.

Michael
________________________________________________________________

On 5 May 2009, at 17:13, Tony Collins wrote:

> Hi,
>
> I'm duplicating an image, then using this to create a binary/
> watershed mask to "analyze particles" with the measurements  
> redirected to the original.
>
> This works well but I'd like to batch process a folder of these  
> images. Is there a way to "redirect to" an image ID rather than  
> image name?
>
> Thanks,
>
> Tony

[Le, Thai (NIH/NCI) [C]]

Hi,

I'm new to ImageJ.
I'm trying to execute an ImageJ menu command (Import->Image Sequence)
from another application. Can I run it as a command line to start ImageJ
and execute the menu command?

Thanks,
Thai

[Du, Guanghua]

Hello, Tony,
this is exactly what I have done before, you can change the title of the
original image to filename+something to avoid conflict. and then use the
newname for redirection in the measurement.

here is a part of the code I am using.

.....................................................................

                ....................

                measuredImageTitle="IMG"+(i+1)+"Step_"+(j+1);
                rename(measuredImageTitle);
                .......................


                        // 1:  First duplicate the image, set threshold to get pixels above
the minimum intensity value (i.e. > minIntensity)
                        // 2: at the same time hen using the "find maxima" on original
subtracted image to segment the image to recognize objects (i.e.  peak
height > tolerence)
                        // 3: Then using the AND operation (threshold image AND segmented
image) to get image for object analysis such as intensity, area, center,
number. (both > minIntensity AND peak height > tolerence)
                        // 4: Finally, run the measurement (redirect the measuring image to
the original subtracted image)

                        //    ****1**** //
                        //duplicate the image,
                        selectImage(subtractedimageID);
                        duplicateIMGTitle="duplicate-0";
                        run("Duplicate...", "title="+duplicateIMGTitle);
                        duplicatesubIMGID=getImageID();
               
                        //convert the duplicated image to threshold mask
                        setThreshold(minIntensity, PixelValueMaximum);
                        run("Convert to Mask");
                        thresholdImageID=getImageID();
                        thresholdImageTitle="Threshold_"+minIntensity;
                        rename(thresholdImageTitle);
               

                        // **** 2 **** //

                               
                        //using "Find Maxima" function to segment objects,
               
                        selectImage(subtractedimageID);
                        run("Find Maxima...", "noise="+tolerencevalue+" output=[Segmented
Particles]");
                        segmentedImageID=getImageID();
                        segmentedImageTitle="Segmented_"+tolerencevalue;
                        rename(segmentedImageTitle);
               
                        // **** 3 ****//
                        imageCalculator("AND create", segmentedImageTitle,thresholdImageTitle);
                        objectImageID=getImageID();
                        objectImageTitle="IMG01_min"+minIntensity+"_PT"+tolerencevalue;
                        rename(objectImageTitle);
                       
                        // **** 4 ****//
                        //measure the area, mean gray value, max intensity, standard
deviation of the objects
                        setAutoThreshold();
                        run("Set Measurements...", "area mean center limit display
redirect="+measuredImageTitle+" decimal=2");
                        lastEntryNumber=nResults;
                        if (lastEntryNumber<0){ lastEntryNumber=0;}
                        run("Analyze Particles...", "size="+minObjectSize+"-Infinity
circularity=0.00-1.00 show=Nothing display");
                        updateResults();

       

Tony Collins wrote:

> Hi,
>
> I'm duplicating an image, then using this to create a binary/watershed mask to "analyze particles" with the measurements redirected to the original.
>
> This works well but I'd like to batch process a folder of these images. Is there a way to "redirect to" an image ID rather than image name?
>
> Thanks,
>
> Tony
>
>  
> Tony J. Collins, Ph.D.
> McMaster Biophotonics Facility
> Dept. Biochemistry and Biomedical Sciences HSC 4H21A
> McMaster University, Hamilton, ON, L8N 3Z5
> [hidden email]     www.macbiophotonics.ca

--
best wishes!
**************************************
Guanghua Du, PhD
James-Franck Str. 1
Physik Dept, E12, TUM
85748, Garching b. Muenchen
Germany

Tel:[phone]
E-mail: [hidden email]
**************************************

[Tony Collins-4]

Hi Michael, (and thanks to Guanghua too),

Thanks for the solutions. Using the image title is a good workaround  - until, as you say, you have two images open of the same name. I was hoping to avoid this as in the past I'd had trouble using titles with the image calculator menu command  - but this was updated to something that could cope with Image IDs.

Looking at the source code now I guess the image calculator was easier to make macro/imageID friendly...

Cheers,

Tony
 
Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[hidden email]     www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Michael Schmid
> Sent: May 5, 2009 12:13 PM
> To: [hidden email]
> Subject: Re: redirect to imageID
>
> Hi Tony,
>
> sorry, no way to have an ImageID for the Analyze>Set Measurements
> redirect target in a macro.
> In the inner works of ImageJ, it is an ImageID, but you cannot access
> it from a macro. You can only find out whether you have one, by using
> call("ij.plugin.filter.Analyzer.isRedirectImage"):
>    http://rsb.info.nih.gov/ij/source/ij/plugin/filter/Analyzer.java
>
> You have to use
>    sourceTitle = getTitle();
> on the input image and set the measurement options, e.g.
>    run("Set Measurements...", "area mean min redirect=["+ sourceTitle
> +"] decimal=4");
>
> This will fail if you have two open images with the same name.
>
> Michael
> ________________________________________________________________
>
> On 5 May 2009, at 17:13, Tony Collins wrote:
>
> > Hi,
> >
> > I'm duplicating an image, then using this to create a binary/
> > watershed mask to "analyze particles" with the measurements
> > redirected to the original.
> >
> > This works well but I'd like to batch process a folder of these
> > images. Is there a way to "redirect to" an image ID rather than
> > image name?
> >
> > Thanks,
> >
> > Tony

[Wayne Rasband]

> Hi,
>
> I'm new to ImageJ.
> I'm trying to execute an ImageJ menu command (Import->Image Sequence)
> from another application. Can I run it as a command line to start
> ImageJ
> and execute the menu command?

1. Create a one line macro by running Import>Image Sequence with the
recorder running
2. Save the macro in the ImageJ/macros folder as, say, "import.txt"
3. Run it from the command line using a command something like:

     java -jar /path/to/ij.jar -ijpath /path/to/ImageJ -macro import

-wayne

[Le, Thai (NIH/NCI) [C]]

Thank you!

-Thai

-----Original Message-----
From: Rasband, Wayne (NIH/NIMH) [E]
Sent: Tuesday, May 05, 2009 5:36 PM
To: List IMAGEJ
Subject: Re: Integration with other software

> Hi,
>
> I'm new to ImageJ.
> I'm trying to execute an ImageJ menu command (Import->Image Sequence)
> from another application. Can I run it as a command line to start
> ImageJ and execute the menu command?

1. Create a one line macro by running Import>Image Sequence with the
recorder running 2. Save the macro in the ImageJ/macros folder as, say,
"import.txt"
3. Run it from the command line using a command something like:

     java -jar /path/to/ij.jar -ijpath /path/to/ImageJ -macro import

-wayne