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Re: Displaying raw image and annotated ROI

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Harry Parker

Re: Displaying raw image and annotated ROI

I don't know of a plugin that does what you need, but these are easily accomplished via a short macro you can easily write yourself to do exactly what you want.

It's not hard to do. Just select the menu, Help->Macro Language..., to get started learning how.

Macro functions exist to
read the coordinates of ROI: getSelectionBounds(x, y, width, height)
and display text in a text window or save it in a file: print(string) and print(file, string) .

--
Harry Parker
Senior Systems Engineer
Digital Imaging Systems, Inc.

----- Original Message ----
From: subhendu seth <[hidden email]>
To: [hidden email]
Sent: Tuesday, March 4, 2008 5:09:30 AM
Subject: Re: Antwort: Displaying raw image and annotated ROI

Thanks for your previous help. It helps me a lot. Now I am stuck t
Hi,

Thanks for your previous help. It helps me a lot. Now I am stuck to other problems.

(1) Is there any plugin that will save the starting and finishing co-ordinates of the selected ROI rectangle(ROI will be selected by mouse action)?
(2) Also the plugin should be capable of storing one pair of selected co-ordinates (starting and ending point of the selected rectangle) and a text window at a time inside a single container window.
(3) All together they should be saved separately from the original image.

Please help me finding out the problem. If any plugin is available please send me.

With warm regards
Subhendu Seth.

----- Original Message ----
From: Emilio Miguelanez Martin <[hidden email]>
To: [hidden email]
Sent: Tuesday, 12 February, 2008 4:24:24 PM
Subject: Re: Antwort: Displaying raw image and annotated ROI

Hi Seth,

This plugin (http://rsb.info.nih.gov/ij/plugins/roi-importer.html) may
help you. This plugin imports a two column text file, such as those
created by File/Save As/XY Coordinates, as a polygon selection. The
selection is displayed in the current image or, if the current image is
too small, in a new blank image.

Cheers,
Emilio

On Tue, 2008-02-12 at 16:01 +0530, subhendu seth wrote:

> Hi Joachim,
> You hit the right point. Yes I need the overlay graphics of ROI information (ROI image and its annotation) on the original data. But provided the original data should not be affected. And regarding the file format I am dealing with dicom images. And the subject of this topic will be "Overlaying raw image and annotated ROI ".
> With warm
> Subhendu Seth.
> JRF & MS student, dept. E&ECE
> IIT, Kharagpur.
>
>
>
>
>
>
> ----- Original Message ----
> From: Joachim Wesner <[hidden email]>
> To: [hidden email]
> Sent: Monday, 11 February, 2008 11:37:22 PM
> Subject: Antwort: Displaying raw image and annotated ROI
>
> Hi Seth
>
>
> ImageJ Interest Group <[hidden email]> schrieb am 10.02.2008 15:36:09:
>
> > I have some mammogram (breast x-ray) data. For each of those data I have
> > some region of interest and its corresponding description.
> >
> > I need a plug-in that will arrange the image and its corresponding ROI
> > information. Along with the raw images corresponding ROI information (ROI
>
> > and its annotation) will be displayed.
> >
>
> What do you mean by "arrange" and "along with"? In an extra windows? As
> overlay graphics on the original data?
> What means "displayed"? You will also need to print that info as it´s shown
> on screne? You want to generate a new "non-raw"
> image that has the overlay info included in a regular .JPG,.TIF or
> whatever?
>
> Joachim
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>
>
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--
Emilio Migueláñez Martín, PhD
Research Associate
Electrical, Electronic and Computing Engineering
School of Engineering and Physical Sciences
Heriot-Watt University
Riccarton
Edinburgh EH14 4AS

t: +44 (0) 131 4513357

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Emilio Miguelanez Martin

Re: Displaying raw image and annotated ROI

Hi,

It may be helpful to you to have a look at the ROI importer plugin http://rsb.info.nih.gov/ij/plugins/roi-importer.html

Cheers,
Emilio

--
Emilio Migueláñez Martín, PhD
Research Associate

Ocean Systems Laboratory
School of Eng. & Phy. Sciences
Heriot-Watt University, Edinburgh,
Scotland, UK, EH14 4AS

[hidden email]
Tel : +44 (0)131 451 3506
Fax : +44 (0)131 451 3357

-----Original Message-----
From: ImageJ Interest Group on behalf of Harry Parker
Sent: Wed 3/5/2008 2:51 PM
To: [hidden email]
Subject: Re: Displaying raw image and annotated ROI

I don't know of a plugin that does what you need, but these are easily accomplished via a short macro you can easily write yourself to do exactly what you want.

It's not hard to do. Just select the menu, Help->Macro Language..., to get started learning how.

Macro functions exist to
read the coordinates of ROI: getSelectionBounds(x, y, width, height)
and display text in a text window or save it in a file: print(string) and print(file, string) .

--
Harry Parker
Senior Systems Engineer
Digital Imaging Systems, Inc.

----- Original Message ----
From: subhendu seth <[hidden email]>
To: [hidden email]
Sent: Tuesday, March 4, 2008 5:09:30 AM
Subject: Re: Antwort: Displaying raw image and annotated ROI

Thanks for your previous help. It helps me a lot. Now I am stuck t
Hi,

Thanks for your previous help. It helps me a lot. Now I am stuck to other problems.

(1) Is there any plugin that will save the starting and finishing co-ordinates of the selected ROI rectangle(ROI will be selected by mouse action)?
(2) Also the plugin should be capable of storing one pair of selected co-ordinates (starting and ending point of the selected rectangle) and a text window at a time inside a single container window.
(3) All together they should be saved separately from the original image.

Please help me finding out the problem. If any plugin is available please send me.

With warm regards
Subhendu Seth.

----- Original Message ----
From: Emilio Miguelanez Martin <[hidden email]>
To: [hidden email]
Sent: Tuesday, 12 February, 2008 4:24:24 PM
Subject: Re: Antwort: Displaying raw image and annotated ROI

Hi Seth,

This plugin (http://rsb.info.nih.gov/ij/plugins/roi-importer.html) may
help you. This plugin imports a two column text file, such as those
created by File/Save As/XY Coordinates, as a polygon selection. The
selection is displayed in the current image or, if the current image is
too small, in a new blank image.

Cheers,
Emilio

On Tue, 2008-02-12 at 16:01 +0530, subhendu seth wrote:

Emilio Miguelanez Martin

Placing image on the screen

In reply to this post by Harry Parker

Hi,

When a new image is open, it is always been placed in the center of the monitor screen. However, I need to place it on the right hand-side of the screen. Any idea how?

I have noticed that the IJ_Prefs.txt file holds some preferential information, such as the location of the toolbar (IJ.x & IJ.y). I was wondering if it is possible to store the default location of the image window in this size.
Any help is appreciated.

Cheers,
Emilio

Albert Cardona

Re: Placing image on the screen

Hi Emilio,

You can customize ImageJ to do it for you.
What you need:
- a plugin that implements an ImageListener
- a macro that launches the plugin at startup

The macro: edit macros/StartupMacros.txt, add the following
(or set into an existing AutoRun macro, if any):

macro "AutoRun" {
run("ImageWindow_Position");
}

The plugin, in its simplest form:
(just place into ImageJ plugins folder or subfolder, and call
"Compile and run" on it - then restart ImageJ)
(Be sure to copy this into a file named ImageWindow_Position.java )

import ij.*;
import ij.plugin.PlugIn;
import java.awt.*;

public class ImageWindow_Position implements PlugIn, ImageListener {
public void run(String arg) {
ImagePlus.addImageListener(this);
}
public void imageOpened(ImagePlus imp) {
ImageWindow win = imp.getWindow();
if (null == win) return;
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
Rectangle box = win.getBounds();
win.setLocation(screen.width - box.width,
(screen.height - box.height) / 2);
}
public void imageUpdated(ImagePlus imp) {}
public void imageClosed(ImagePlus imp) {}
}

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

Emilio Miguelanez Martin

Re: Placing image on the screen

Albert,

Thanks for your valuable input. Your suggestion fits even better, considering that the images were opening from a plugin, and I didn't know how to set the location of the image window.

Cheers,
Emilio

-----Original Message-----
From: ImageJ Interest Group on behalf of Albert Cardona
Sent: Fri 3/7/2008 8:23 PM
To: [hidden email]
Subject: Re: Placing image on the screen

Hi Emilio,

You can customize ImageJ to do it for you.
What you need:
- a plugin that implements an ImageListener
- a macro that launches the plugin at startup

The macro: edit macros/StartupMacros.txt, add the following
(or set into an existing AutoRun macro, if any):

macro "AutoRun" {
run("ImageWindow_Position");
}

The plugin, in its simplest form:
(just place into ImageJ plugins folder or subfolder, and call
"Compile and run" on it - then restart ImageJ)
(Be sure to copy this into a file named ImageWindow_Position.java )

import ij.*;
import ij.plugin.PlugIn;
import java.awt.*;

public class ImageWindow_Position implements PlugIn, ImageListener {
public void run(String arg) {
ImagePlus.addImageListener(this);
}
public void imageOpened(ImagePlus imp) {
ImageWindow win = imp.getWindow();
if (null == win) return;
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
Rectangle box = win.getBounds();
win.setLocation(screen.width - box.width,
(screen.height - box.height) / 2);
}
public void imageUpdated(ImagePlus imp) {}
public void imageClosed(ImagePlus imp) {}
}

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

Albert Cardona

Re: Placing image on the screen

> Albert,
>
> Thanks for your valuable input. Your suggestion fits even better, considering that the images were opening from a plugin, and I didn't know how to set the location of the image window.
>
> Cheers,
> Emilio
>

Glad it helped. I've placed it in my doodle programming page, for your
reference:

http://www.mcdb.ucla.edu/research/hartenstein/acardona/doodle_programming.html#9

There is also a collection of small plugins at the bottom of the
software page, which may provide you with related examples (for example,
the Zoom_Exact comes to mind, which manipulates the ImageCanvas):

http://www.mcdb.ucla.edu/research/hartenstein/acardona/software.html

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona