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Selecting image windows as a menu in ijm.

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Ethan Cohen

Selecting image windows as a menu in ijm.

I am looking for a way to manually select a stack window (either as a menu, or user input) to an ImageJ Macro.

Anybody know of a way to do this?

selectWindow("Get User Selection"); //select Stack window

.......

Ethan Cohen, Ph.D.
FDA Center for Devices and Radiological Health
Office: Rm 1204 WO62
White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993

Senseney, Justin (NIH/CIT) [E]

Re: Selecting image windows as a menu in ijm.

Ethan,

Will selectWindow(getTitle()); work for you? That returns the window of the current image. Johannes also provided a nice example of selecting images by id:

https://list.nih.gov/cgi-bin/wa.exe?A2=ind1108&L=IMAGEJ&D=0&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=145848

-Justin

BIRSS/ISL/DCB/CIT/NIH
Building 12A/2015

-----Original Message-----
From: Cohen, Ethan D (FDA/CDRH)
Sent: Monday, April 16, 2012 8:59 PM
To: List IMAGEJ
Subject: Selecting image windows as a menu in ijm.

I am looking for a way to manually select a stack window (either as a menu, or user input) to an ImageJ Macro.

Anybody know of a way to do this?

selectWindow("Get User Selection"); //select Stack window

.......

Ethan Cohen, Ph.D.
FDA Center for Devices and Radiological Health
Office: Rm 1204 WO62
White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993

Michael Schmid

Re: Selecting image windows as a menu in ijm.

In reply to this post by Ethan Cohen

Hi Ethan,

the easiest would be
waitForUser("Select the window of the stack that you want to study");

A longer version:
setBatchMode(true); //unless you have that somewhere
allStackTitles=newArray(nImages);
nStacks=0;
for (i=1; i<=nImages; i++) {
selectImage(i);
if (nSlices>1) {
allStackTitles[nStacks]=getTitle();
nStacks++;
}
}
if (nStacks <1) exit("No Stack Window Open");
Dialog.create("Select input");
Dialog.addChoice("Name", allStackTitles);
Dialog.show();
setBatchMode(false); //if you don't continue in BatchMode
selectWindow(Dialog.getChoice());

Michael
________________________________________________________________
On Apr 17, 2012, at 02:59, Cohen, Ethan D wrote:

> I am looking for a way to manually select a stack window (either as a menu, or user input) to an ImageJ Macro.
>
> Anybody know of a way to do this?
>
> selectWindow("Get User Selection"); //select Stack window
>
> .......
>
>
> Ethan Cohen, Ph.D.
> FDA Center for Devices and Radiological Health
> Office: Rm 1204 WO62
> White Oak Federal Res Ctr.
> 10903 New Hampshire Ave.
> Silver Spring, MD 20993

Ethan Cohen

Re: Selecting image windows as a menu in ijm.

In reply to this post by Senseney, Justin (NIH/CIT) [E]

Justin:

Could you say something like this? (but this does not work).

StackTitle = selectWindow(getTitle());

waitForUser( "Selected Stack: ESC to abort", StackTitle);

I do not want to manually select writte image files.

I want to pick an image stack from those opened in ImageJ.

list = getList("window.titles"); // But then how to pick in a menu?

Ethan

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Senseney, Justin (NIH/CIT) [E]
Sent: Tuesday, April 17, 2012 8:08 AM
To: [hidden email]
Subject: Re: Selecting image windows as a menu in ijm.

Ethan,

Will selectWindow(getTitle()); work for you? That returns the window of the current image. Johannes also provided a nice example of selecting images by id:

https://list.nih.gov/cgi-bin/wa.exe?A2=ind1108&L=IMAGEJ&D=0&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=145848

-Justin

BIRSS/ISL/DCB/CIT/NIH
Building 12A/2015

-----Original Message-----
From: Cohen, Ethan D (FDA/CDRH)
Sent: Monday, April 16, 2012 8:59 PM
To: List IMAGEJ
Subject: Selecting image windows as a menu in ijm.

I am looking for a way to manually select a stack window (either as a menu, or user input) to an ImageJ Macro.

Anybody know of a way to do this?

selectWindow("Get User Selection"); //select Stack window

.......

Ethan Cohen, Ph.D.
FDA Center for Devices and Radiological Health
Office: Rm 1204 WO62
White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993

Senseney, Justin (NIH/CIT) [E]

Re: Selecting image windows as a menu in ijm.

Hi Ethan,

selectWindow() just activates the image, it's getTitle() that returns the name, try:

StackTitle = getTitle();
selectWindow(StackTitle);

Another useful one: getImageID().

The ImageJ website has a nice list of all available macro functions. Post here if you have trouble using any of them: http://rsbweb.nih.gov/ij/developer/macro/functions.html

-Justin

-----Original Message-----
From: Cohen, Ethan D (FDA/CDRH)
Sent: Thursday, April 19, 2012 3:36 AM
To: List IMAGEJ
Subject: Re: Selecting image windows as a menu in ijm.

Justin:

Could you say something like this? (but this does not work).

StackTitle = selectWindow(getTitle());

waitForUser( "Selected Stack: ESC to abort", StackTitle);

I do not want to manually select writte image files.

I want to pick an image stack from those opened in ImageJ.

list = getList("window.titles"); // But then how to pick in a menu?

Ethan

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Senseney, Justin (NIH/CIT) [E]
Sent: Tuesday, April 17, 2012 8:08 AM
To: [hidden email]
Subject: Re: Selecting image windows as a menu in ijm.

Ethan,

Will selectWindow(getTitle()); work for you? That returns the window of the current image. Johannes also provided a nice example of selecting images by id:

https://list.nih.gov/cgi-bin/wa.exe?A2=ind1108&L=IMAGEJ&D=0&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=145848

-Justin

BIRSS/ISL/DCB/CIT/NIH
Building 12A/2015

-----Original Message-----
From: Cohen, Ethan D (FDA/CDRH)
Sent: Monday, April 16, 2012 8:59 PM
To: List IMAGEJ
Subject: Selecting image windows as a menu in ijm.

I am looking for a way to manually select a stack window (either as a menu, or user input) to an ImageJ Macro.

Anybody know of a way to do this?

selectWindow("Get User Selection"); //select Stack window

.......

Ethan Cohen, Ph.D.
FDA Center for Devices and Radiological Health
Office: Rm 1204 WO62
White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993

Ethan Cohen

Re: Selecting image windows as a menu in ijm.

Justin:

Ok, I opened a bunch of images and a stack series in ImageJ.
But your code does not allow me to pick the active (selectWindow).....It just blows right past this "getTitle(); to my waitForUser("pause statement.

I am looking for some sort of a menu like structure to pick the active window and pass it to the program.

StackTitle = getTitle();
selectWindow(StackTitle);//select Stack window

run("Rotate 90 Degrees Right");// rotate vertically
waitForUser( "Pause","Get cross-sectional profile.\nDraw square ROI. \nMake sure object is \nvertically oriented.");// Enter square ROI

I want something more like pickTitle();

Ethan
-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Senseney, Justin (NIH/CIT) [E]
Sent: Thursday, April 19, 2012 1:52 PM
To: [hidden email]
Subject: Re: Selecting image windows as a menu in ijm.

Hi Ethan,

selectWindow() just activates the image, it's getTitle() that returns the name, try:

StackTitle = getTitle();
selectWindow(StackTitle);

Another useful one: getImageID().

The ImageJ website has a nice list of all available macro functions. Post here if you have trouble using any of them: http://rsbweb.nih.gov/ij/developer/macro/functions.html

-Justin

-----Original Message-----
From: Cohen, Ethan D (FDA/CDRH)
Sent: Thursday, April 19, 2012 3:36 AM
To: List IMAGEJ
Subject: Re: Selecting image windows as a menu in ijm.

Justin:

Could you say something like this? (but this does not work).

StackTitle = selectWindow(getTitle());

waitForUser( "Selected Stack: ESC to abort", StackTitle);

I do not want to manually select writte image files.

I want to pick an image stack from those opened in ImageJ.

list = getList("window.titles"); // But then how to pick in a menu?

Ethan

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Senseney, Justin (NIH/CIT) [E]
Sent: Tuesday, April 17, 2012 8:08 AM
To: [hidden email]
Subject: Re: Selecting image windows as a menu in ijm.

Ethan,

Will selectWindow(getTitle()); work for you? That returns the window of the current image. Johannes also provided a nice example of selecting images by id:

https://list.nih.gov/cgi-bin/wa.exe?A2=ind1108&L=IMAGEJ&D=0&1=IMAGEJ&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=145848

-Justin

BIRSS/ISL/DCB/CIT/NIH
Building 12A/2015

-----Original Message-----
From: Cohen, Ethan D (FDA/CDRH)
Sent: Monday, April 16, 2012 8:59 PM
To: List IMAGEJ
Subject: Selecting image windows as a menu in ijm.

I am looking for a way to manually select a stack window (either as a menu, or user input) to an ImageJ Macro.

Anybody know of a way to do this?

selectWindow("Get User Selection"); //select Stack window

.......

Ethan Cohen, Ph.D.
FDA Center for Devices and Radiological Health
Office: Rm 1204 WO62
White Oak Federal Res Ctr.
10903 New Hampshire Ave.
Silver Spring, MD 20993

Ethan Cohen

Re: Selecting image windows as a menu in ijm.

In reply to this post by Michael Schmid

Thanks, Michael.

That was very useful.
I would not of figured that out.

Ethan.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Michael Schmid
Sent: Tuesday, April 17, 2012 9:39 AM
To: [hidden email]
Subject: Re: Selecting image windows as a menu in ijm.

Hi Ethan,

the easiest would be
waitForUser("Select the window of the stack that you want to study");

A longer version:
setBatchMode(true); //unless you have that somewhere
allStackTitles=newArray(nImages);
nStacks=0;
for (i=1; i<=nImages; i++) {
selectImage(i);
if (nSlices>1) {
allStackTitles[nStacks]=getTitle();
nStacks++;
}
}
if (nStacks <1) exit("No Stack Window Open");
Dialog.create("Select input");
Dialog.addChoice("Name", allStackTitles);
Dialog.show();
setBatchMode(false); //if you don't continue in BatchMode
selectWindow(Dialog.getChoice());

Michael
________________________________________________________________
On Apr 17, 2012, at 02:59, Cohen, Ethan D wrote: