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Radial profile ext to work with Macros

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madtrick

Radial profile ext to work with Macros

Hi,

I have very limited experience with Java and I was wondering if someone had updated the Radial profile EXT plugin to enable macros to work with it? More specifically, its the Radial profile angle plugin, which was posted in 2006 and hasn't been updated since. Radial Profile Ext

I found this page Link here - Go to Chapter 11 which describes writing plugins with macro compatibility, but I don't really understand what needs changing.

Many thanks for your time, Matt

madtrick

Re: Radial profile ext to work with Macros

Any ideas?

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

Dear madtrick,
I'm the author of the Radial profile ext plugin (quite some years ago).
What are you trying to do within a macro?
Just launch the plugin or more?
Best regards,
Philippe

On Donderdag 28 November 2013 17:51 CET, madtrick <[hidden email]> wrote:

> Any ideas?
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macros-tp5005598p5005737.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Jan Eglinger

Re: Radial profile ext to work with Macros

In reply to this post by madtrick

Dear Matt,

> Any ideas?
>

your original post was not accepted by the mailing list [1], presumably
because you didn't confirm it. That might be a reason why you didn't get
an answer for a little while.

I am copying some of your original question here for the convenience of
readers joining the discussion at a later point.

> I have very limited experience with Java and I was wondering if
> someone had updated the Radial profile EXT plugin to enable macros to
> work with it? More specifically, its the Radial profile angle plugin,
> which was posted in 2006 and hasn't been updated since.
> http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html

Since the plugin makes use of ImageJ's GenericDialog in a non-standard
way to create its own user interface (thereby preventing the built-in
recordability of the command), you have to resort to one of the more
powerful scripting languages like Javascript [2] or Python [3] to
interact with the plugin from within a macro.

In addition the Radial_Profile_Angle_Ext class tightly couples parameter
initialization with the display of its dialog. I'd suggest to add a
helper method setParameters(Sa, Ia, X0, Y0, mR) to the plugin, such as:

public void setParameters(int mSa, int mIa, Double mX0, Double mY0,
Double mmR) {
Sa = mSa;
Ia = mIa;
X0 = mX0;
Y0 = mY0;
mR = mmR;
setCosSin();
}

(mind the line breaks introduced by the mailer)

After adding the above code and compiling the java file via "Compile and
Run", you should be able to execute the following javascript (with an
image open and any active selection):

importClass(Packages.Radial_Profile_Angle_Ext);

rp = new Radial_Profile_Angle_Ext();
imp = IJ.getImage();
ip = imp.getProcessor();
rp.setup("", imp);
rp.setParameters(180, 40, 77.5, 108.5, 57.5);
rp.doRadialDistribution(ip);

and you should see a profile plot without any dialog showing up.

Hope that helps,
Jan

[1]:
http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macros-td5005598.html
[2]: http://fiji.sc/Javascript_Scripting
[3]: http://fiji.sc/Jython_Scripting

On 28.11.2013, 5:51 PM, madtrick wrote:

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Kota Miura

Re: Radial profile ext to work with Macros

Hi Matt, Carl, Jan & all,

On Mon, Dec 2, 2013 at 1:02 PM, Jan Eglinger <[hidden email]> wrote:

> Dear Matt,
>
> > Any ideas?
> >
>
> your original post was not accepted by the mailing list [1], presumably
> because you didn't confirm it. That might be a reason why you didn't get an
> answer for a little while.
>
> I am copying some of your original question here for the convenience of
> readers joining the discussion at a later point.
>
> > I have very limited experience with Java and I was wondering if
> > someone had updated the Radial profile EXT plugin to enable macros to
> > work with it? More specifically, its the Radial profile angle plugin,
> > which was posted in 2006 and hasn't been updated since.
> > http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html
>
> Since the plugin makes use of ImageJ's GenericDialog in a non-standard way
> to create its own user interface (thereby preventing the built-in
> recordability of the command), you have to resort to one of the more
> powerful scripting languages like Javascript [2] or Python [3] to interact
> with the plugin from within a macro.
>
> In addition the Radial_Profile_Angle_Ext class tightly couples parameter
> initialization with the display of its dialog. I'd suggest to add a helper
> method setParameters(Sa, Ia, X0, Y0, mR) to the plugin, such as:
>
> public void setParameters(int mSa, int mIa, Double mX0, Double
> mY0, Double mmR) {
> Sa = mSa;
> Ia = mIa;
> X0 = mX0;
> Y0 = mY0;
> mR = mmR;
> setCosSin();
> }
>
> (mind the line breaks introduced by the mailer)
>
> After adding the above code and compiling the java file via "Compile and
> Run", you should be able to execute the following javascript (with an image
> open and any active selection):
>
> importClass(Packages.Radial_Profile_Angle_Ext);
>
> rp = new Radial_Profile_Angle_Ext();
> imp = IJ.getImage();
> ip = imp.getProcessor();
> rp.setup("", imp);
> rp.setParameters(180, 40, 77.5, 108.5, 57.5);
> rp.doRadialDistribution(ip);
>
> and you should see a profile plot without any dialog showing up.
>
> Hope that helps,
> Jan
>
>
>
>
> [1]: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-
> work-with-Macros-td5005598.html
> [2]: http://fiji.sc/Javascript_Scripting
> [3]: http://fiji.sc/Jython_Scripting
>
>

here is another upgraded version of the Radial Profile plugin,

https://github.com/cmci/RadialProfileV2/tree/master/target

that allows having options to the macro command e.g.

run("Radial Profile", "x=148 y=125 radius=80");

Original version had some bug in the measurement for the value in the last
index of the profile, and this is fixed in my version as well.

Maybe Carl's extended version could be merged at some point.

Cheers,

Kota

>
> On 28.11.2013, 5:51 PM, madtrick wrote:
>
>> Any ideas?
>>
>>
>>
>> --
>> View this message in context: http://imagej.1557.x6.nabble.
>> com/Radial-profile-ext-to-work-with-Macros-tp5005598p5005737.html
>> Sent from the ImageJ mailing list archive at Nabble.com.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

-------------------------------------------------------------*Dr. Kota Miura*

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging,
European Molecular Biology Laboratory
Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel +49 6221 387 404

Mobile +49 160 95001177

Fax +49 6221 387 512

http://cmci.embl.de
-------------------------------------------------------------

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

Dear all,
To say the truth the "Radial profile ext" was actually the very first plugin I had ever written under ImageJ, in what seems to me now to be almost an eternity ago.
And in this times I absolutely needed such a sharp tool in order to quantify some RICM pictures in a certain way for generating a part of a publication.
Also I had indeed not written the plugin for a macro (I even didn't know how to program macros at this time) use and the code may probably be quite improved.
So what I can propose is to look over the code in general to try to improve it, extend its capabilities for macros, look for the bug correction Kota made (this bug is quite probably as well within the "Radial profile ext" plugin) and then post this new plugin on a site for you guys to download and try it.
And if everybody agrees on the update we can then contact Wayne for him to update the posted code on the ImageJ website.
Thus please allow me a couple days (= 2-3) for doing this.
Also I would like to ask whether the new plugin update and evaluation discussion should rather be continued within the ImageJ list or rather outside, in private, until a new updated plugin is available?
Best regards,
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Kota Miura
Envoyé : lundi 2 décembre 2013 13:42
À : [hidden email]
Objet : Re: Radial profile ext to work with Macros

Hi Matt, Carl, Jan & all,

On Mon, Dec 2, 2013 at 1:02 PM, Jan Eglinger <[hidden email]> wrote:

> Dear Matt,
>
> > Any ideas?
> >
>
> your original post was not accepted by the mailing list [1],
> presumably because you didn't confirm it. That might be a reason why
> you didn't get an answer for a little while.
>
> I am copying some of your original question here for the convenience
> of readers joining the discussion at a later point.
>
> > I have very limited experience with Java and I was wondering if
> > someone had updated the Radial profile EXT plugin to enable macros
> > to work with it? More specifically, its the Radial profile angle
> > plugin, which was posted in 2006 and hasn't been updated since.
> > http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html
>
> Since the plugin makes use of ImageJ's GenericDialog in a non-standard
> way to create its own user interface (thereby preventing the built-in
> recordability of the command), you have to resort to one of the more
> powerful scripting languages like Javascript [2] or Python [3] to
> interact with the plugin from within a macro.
>
> In addition the Radial_Profile_Angle_Ext class tightly couples
> parameter initialization with the display of its dialog. I'd suggest
> to add a helper method setParameters(Sa, Ia, X0, Y0, mR) to the plugin, such as:
>
> public void setParameters(int mSa, int mIa, Double mX0, Double
> mY0, Double mmR) {
> Sa = mSa;
> Ia = mIa;
> X0 = mX0;
> Y0 = mY0;
> mR = mmR;
> setCosSin();
> }
>
> (mind the line breaks introduced by the mailer)
>
> After adding the above code and compiling the java file via "Compile
> and Run", you should be able to execute the following javascript (with
> an image open and any active selection):
>
> importClass(Packages.Radial_Profile_Angle_Ext);
>
> rp = new Radial_Profile_Angle_Ext();
> imp = IJ.getImage();
> ip = imp.getProcessor();
> rp.setup("", imp);
> rp.setParameters(180, 40, 77.5, 108.5, 57.5);
> rp.doRadialDistribution(ip);
>
> and you should see a profile plot without any dialog showing up.
>
> Hope that helps,
> Jan
>
>
>
>
> [1]: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-
> work-with-Macros-td5005598.html
> [2]: http://fiji.sc/Javascript_Scripting
> [3]: http://fiji.sc/Jython_Scripting
>
>

here is another upgraded version of the Radial Profile plugin,

https://github.com/cmci/RadialProfileV2/tree/master/target

that allows having options to the macro command e.g.

run("Radial Profile", "x=148 y=125 radius=80");

Original version had some bug in the measurement for the value in the last index of the profile, and this is fixed in my version as well.

Maybe Carl's extended version could be merged at some point.

Cheers,

Kota

--

-------------------------------------------------------------*Dr. Kota Miura*

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel +49 6221 387 404

Mobile +49 160 95001177

Fax +49 6221 387 512

http://cmci.embl.de
-------------------------------------------------------------

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Jan Eglinger

Re: Radial profile ext to work with Macros

In reply to this post by Kota Miura

Dear Philippe, Kota and all,

On 03.12.2013, 9:47 AM, Philippe CARL wrote:
> Dear all,
> To say the truth the "Radial profile ext" was actually the very first plugin I had ever written under ImageJ, in what seems to me now to be almost an eternity ago.
> And in this times I absolutely needed such a sharp tool in order to quantify some RICM pictures in a certain way for generating a part of a publication.
> Also I had indeed not written the plugin for a macro (I even didn't know how to program macros at this time) use and the code may probably be quite improved.
> So what I can propose is to look over the code in general to try to improve it, extend its capabilities for macros, look for the bug correction Kota made (this bug is quite probably as well within the "Radial profile ext" plugin) and then post this new plugin on a site for you guys to download and try it.
> And if everybody agrees on the update we can then contact Wayne for him to update the posted code on the ImageJ website.
> Thus please allow me a couple days (= 2-3) for doing this.

Since Kota has made his plugin so nicely available via github, I would
suggest that you fork that project and open a pull request with your
changes [*1*]. (Since recently, you can even edit the files online,
making it very easy to contribute.)
That will also permit others (devlopers but also advanced users of the
plugin) to contribute small changes if necessary.

> Also I would like to ask whether the new plugin update and evaluation discussion should rather be continued within the ImageJ list or rather outside, in private, until a new updated plugin is available?

After all, the plugin is made for its users, so I suggest that the
discussion about possible enhancements stays on this list.

Cheers,
Jan

[*1*]: https://help.github.com/articles/using-pull-requests

> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de Kota Miura
> Envoyé : lundi 2 décembre 2013 13:42
> À : [hidden email]
> Objet : Re: Radial profile ext to work with Macros
>
> Hi Matt, Carl, Jan & all,
>
>
>
> On Mon, Dec 2, 2013 at 1:02 PM, Jan Eglinger <[hidden email]> wrote:
>
>> Dear Matt,
>>
>>> Any ideas?
>>>
>>
>> your original post was not accepted by the mailing list [1],
>> presumably because you didn't confirm it. That might be a reason why
>> you didn't get an answer for a little while.
>>
>> I am copying some of your original question here for the convenience
>> of readers joining the discussion at a later point.
>>
>>> I have very limited experience with Java and I was wondering if
>>> someone had updated the Radial profile EXT plugin to enable macros
>>> to work with it? More specifically, its the Radial profile angle
>>> plugin, which was posted in 2006 and hasn't been updated since.
>>> http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html
>>
>> Since the plugin makes use of ImageJ's GenericDialog in a non-standard
>> way to create its own user interface (thereby preventing the built-in
>> recordability of the command), you have to resort to one of the more
>> powerful scripting languages like Javascript [2] or Python [3] to
>> interact with the plugin from within a macro.
>>
>> In addition the Radial_Profile_Angle_Ext class tightly couples
>> parameter initialization with the display of its dialog. I'd suggest
>> to add a helper method setParameters(Sa, Ia, X0, Y0, mR) to the plugin, such as:
>>
>> public void setParameters(int mSa, int mIa, Double mX0, Double
>> mY0, Double mmR) {
>> Sa = mSa;
>> Ia = mIa;
>> X0 = mX0;
>> Y0 = mY0;
>> mR = mmR;
>> setCosSin();
>> }
>>
>> (mind the line breaks introduced by the mailer)
>>
>> After adding the above code and compiling the java file via "Compile
>> and Run", you should be able to execute the following javascript (with
>> an image open and any active selection):
>>
>> importClass(Packages.Radial_Profile_Angle_Ext);
>>
>> rp = new Radial_Profile_Angle_Ext();
>> imp = IJ.getImage();
>> ip = imp.getProcessor();
>> rp.setup("", imp);
>> rp.setParameters(180, 40, 77.5, 108.5, 57.5);
>> rp.doRadialDistribution(ip);
>>
>> and you should see a profile plot without any dialog showing up.
>>
>> Hope that helps,
>> Jan
>>
>>
>>
>>
>> [1]: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-
>> work-with-Macros-td5005598.html
>> [2]: http://fiji.sc/Javascript_Scripting
>> [3]: http://fiji.sc/Jython_Scripting
>>
>>
>
> here is another upgraded version of the Radial Profile plugin,
>
> https://github.com/cmci/RadialProfileV2/tree/master/target
>
>
> that allows having options to the macro command e.g.
>
> run("Radial Profile", "x=148 y=125 radius=80");
>
> Original version had some bug in the measurement for the value in the last index of the profile, and this is fixed in my version as well.
>
> Maybe Carl's extended version could be merged at some point.
>
> Cheers,
>
> Kota
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

madtrick

Re: Radial profile ext to work with Macros

In reply to this post by CARL Philippe (LBP)

That would be fantastic! Thank you :)

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

In reply to this post by Jan Eglinger

Dear all,
Following the request of macro integration of the "Radial profile ext" plugin, I tried to move forward.
Thus up to the following document:
http://rsb.info.nih.gov/ij/docs/macro_reference_guide.pdf
in order to have easily access to the built-in macro command recorder, the plugin should be using the ij.gui.GenericDialog class (I'm very happy to be aware of this now since I used already this knowledge for another project...).
In the "Radial profile ext" plugin I haven't used this class but the GenericRecallableDialog class developped in the Contour_Plotter routine by Walter O'Dell PhD.
And I used this class since with this class the window is non blocking (can actually be solved by using the NonBlockingGenericDialog class developed by Johannes Schindelin) but as well since it is possible to add more buttons in the window (the "Radial profile ext" plugin has 6 buttons) which seems can't be done with the NonBlockingGenericDialog class.
Thus is there a way to use the NonBlockingGenericDialog class and implement more than 2 (= 6 in my case) buttons with it?
Alternatively I need to stick with the GenericRecallableDialog class and thus implement calls to public static methods like described at the page 17 and 18 of the http://rsb.info.nih.gov/ij/docs/macro_reference_guide.pdf file.
Unfortunately with the data indicated in this document I'm not able to move forward (for example where and how should the "Recorder.record" command be used?).
Could some examples of such implementation be found somewhere for better understanding?
I thank you very much in advance.
Best regards,
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael Schmid

Re: Radial profile ext to work with Macros

Hi Philippe,

when recording, a GenericDialog records the values (including checkbox settings, Choice menu settings) after the user has pressed the 'OK' button.
When running the macro, it fills in the values and behaves as if the user had pressed 'OK'.

So it won't record pressing any other buttons, and when running the macro it won't simulate pressing any buttons.

If this is ok for you, you can add a Panel with an arbitrary number of buttons to the GenericDialog. You have to add your class as an ActionListener for all the buttons and have an actionPerformed method that detects which button was pressed and reacts accordingly. The actionPerformed methods may modify input fields of the GenericDialog, e.g. change the numbers in the numeric fields (getText, setText).

If your plugin implements ExtendedPlugInFilter and DialogListener you may also have a 'preview' checkbox. With preview on, you could e.g. show what a selection with given center coordinates would look like on the image (set a roi or overlay in the run(ip) method).

Michael
________________________________________________________________
On Dec 18, 2013, at 15:05, Philippe CARL wrote:

> Dear all,
> Following the request of macro integration of the "Radial profile ext" plugin, I tried to move forward.
> Thus up to the following document:
> http://rsb.info.nih.gov/ij/docs/macro_reference_guide.pdf
> in order to have easily access to the built-in macro command recorder, the plugin should be using the ij.gui.GenericDialog class (I'm very happy to be aware of this now since I used already this knowledge for another project...).
> In the "Radial profile ext" plugin I haven't used this class but the GenericRecallableDialog class developped in the Contour_Plotter routine by Walter O'Dell PhD.
> And I used this class since with this class the window is non blocking (can actually be solved by using the NonBlockingGenericDialog class developed by Johannes Schindelin) but as well since it is possible to add more buttons in the window (the "Radial profile ext" plugin has 6 buttons) which seems can't be done with the NonBlockingGenericDialog class.
> Thus is there a way to use the NonBlockingGenericDialog class and implement more than 2 (= 6 in my case) buttons with it?
> Alternatively I need to stick with the GenericRecallableDialog class and thus implement calls to public static methods like described at the page 17 and 18 of the http://rsb.info.nih.gov/ij/docs/macro_reference_guide.pdf file.
> Unfortunately with the data indicated in this document I'm not able to move forward (for example where and how should the "Recorder.record" command be used?).
> Could some examples of such implementation be found somewhere for better understanding?
> I thank you very much in advance.
> Best regards,
> Philippe
>
> Philippe CARL
> Laboratoire de Biophotonique et Pharmacologie
> UMR 7213 CNRS - Université de Strasbourg
> Faculté de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : +33(0)3 68 85 41 84
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

Dear Michael,

> when recording, a GenericDialog records the values (including checkbox
settings, Choice menu settings) after the user has pressed the 'OK' button.
> When running the macro, it fills in the values and behaves as if the user
had pressed 'OK'.
> So it won't record pressing any other buttons, and when running the macro
it won't simulate pressing any buttons.
> If this is ok for you, you can add a Panel with an arbitrary number of
buttons to the GenericDialog.

This could actually be fine and work (= code already implemented and
working)....

> The actionPerformed methods may modify input fields of the GenericDialog,
e.g. change the numbers in the numeric fields (getText, setText).

This is actually my next problem: how am I doing this?
Let's say I have the following code defining the window:
NonBlockingGenericDialog gd = new NonBlockingGenericDialog("Radial Profile
Angle...");
gd.addStringField("Title: ", title);
gd.addNumericField("Width: ", width, 0);
gd.addNumericField("Height: ", height, 0);
How can I then upon an action performed with a button defined by an added
Panel change the value shown up in either the "Width: " or "Height: "
NumericField?

I thank you very much in advance for your answer and wish you a merry
Christmas and happy NEW Year!!!.

Best regards,

Philippe

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Michael Schmid

Re: Radial profile ext to work with Macros

Hi Philippe,

you can get a Vector of the TextFields used for number input with
Vector numericFields = gd.getNumericFields();

Assuming that you want a reference to the first numeric field:
TextField tf0 = (TextField)(numericFields.elementAt(0));

Assuming that it should contain the variable 'width' you can use
tf0.setText(Integer.toString(width));

[if 'width' is double, use one of the IJ.d2s functions to convert it to a String]

Note that there is a nasty bug with Java on Mac computers (at least for modal dialogs, probably the same for the NonBlockingGenericDialog): If you do several changes at the same time (within a few milliseconds), only the first one will be shown, the other fields are not updated until the next change. [TextField.getText() correctly shows the new data. This bug does not only affect TextFields but also Checkboxes, etc. Mac users may have noticed that the 'preview' and 'wait' of some ImageJ functions with preview is sometimes displayed incorrectly due to this bug.]

As a workaround, if you want to modify the contents of several TextFields at once, it is advisable to add an 'IJ.wait(100)' statement before the last modification.

Enjoy Christmas time and best wishes for a good New Year!

Michael
________________________________________________________________
On Dec 20, 2013, at 14:26, Philippe CARL wrote:

> Dear Michael,
>
>> when recording, a GenericDialog records the values (including checkbox
>> settings, Choice menu settings) after the user has pressed the 'OK' button.
>> When running the macro, it fills in the values and behaves as if the user
>> had pressed 'OK'.
>> So it won't record pressing any other buttons, and when running the macro
>> it won't simulate pressing any buttons.
>> If this is ok for you, you can add a Panel with an arbitrary number of
>> buttons to the GenericDialog.
>>
> This could actually be fine and work (= code already implemented and
> working)....
>
>> The actionPerformed methods may modify input fields of the GenericDialog,
>> e.g. change the numbers in the numeric fields (getText, setText).
>>
> This is actually my next problem: how am I doing this?
> Let's say I have the following code defining the window:
> NonBlockingGenericDialog gd = new NonBlockingGenericDialog("Radial Profile
> Angle...");
> gd.addStringField("Title: ", title);
> gd.addNumericField("Width: ", width, 0);
> gd.addNumericField("Height: ", height, 0);
> How can I then upon an action performed with a button defined by an added
> Panel change the value shown up in either the "Width: " or "Height: "
> NumericField?
>
> I thank you very much in advance for your answer and wish you a merry
> Christmas and happy NEW Year!!!.
>
> Best regards,
>
> Philippe
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

In reply to this post by Jan Eglinger

Dear all,
You will find an updated version of the Radial profile ext plugin implementing Macros recording and use under the following link:
http://punias.free.fr/Radial_Profile_Angle_Ext.jar
Please feel free to test it and give me feedback about it before I contact Wayne for an update on the ImageJ website.
Also there is a small bug within the code I don't really know how to solve concerning the plotting of the integration area by using the "b" hotkey in opposition to the associated button. Since by using the "b" hotkey the cone of the integration angle calculation is unwantedly drawn as by using the same code with the button it isn't drawn and thus the code behaves normally.
Dear Kota,
Could you please indicate me in what consist your bug correction on the original radial profile plugin?
Your plugin is quite different from the original one and thus it is difficult to track your correction.
I wish you all a happy New Year 2014!!!
My best regards,
Philippe

Le Mardi 3 Décembre 2013 12:12 CET, Jan Eglinger <[hidden email]> a écrit:

> Dear Philippe, Kota and all,
>
> On 03.12.2013, 9:47 AM, Philippe CARL wrote:
> > Dear all,
> > To say the truth the "Radial profile ext" was actually the very first plugin I had ever written under ImageJ, in what seems to me now to be almost an eternity ago.
> > And in this times I absolutely needed such a sharp tool in order to quantify some RICM pictures in a certain way for generating a part of a publication.
> > Also I had indeed not written the plugin for a macro (I even didn't know how to program macros at this time) use and the code may probably be quite improved.
> > So what I can propose is to look over the code in general to try to improve it, extend its capabilities for macros, look for the bug correction Kota made (this bug is quite probably as well within the "Radial profile ext" plugin) and then post this new plugin on a site for you guys to download and try it.
> > And if everybody agrees on the update we can then contact Wayne for him to update the posted code on the ImageJ website.
> > Thus please allow me a couple days (= 2-3) for doing this.
>
> Since Kota has made his plugin so nicely available via github, I would
> suggest that you fork that project and open a pull request with your
> changes [*1*]. (Since recently, you can even edit the files online,

> making it very easy to contribute.)
> That will also permit others (devlopers but also advanced users of the
> plugin) to contribute small changes if necessary.
>
> > Also I would like to ask whether the new plugin update and evaluation discussion should rather be continued within the ImageJ list or rather outside, in private, until a new updated plugin is available?
>
> After all, the plugin is made for its users, so I suggest that the
> discussion about possible enhancements stays on this list.
>
> Cheers,
> Jan
>
> [*1*]: https://help.github.com/articles/using-pull-requests
>
> > -----Message d'origine-----
> > De : ImageJ Interest Group [mailto:[hidden email]] De la part de Kota Miura
> > Envoyé : lundi 2 décembre 2013 13:42
> > À : [hidden email]
> > Objet : Re: Radial profile ext to work with Macros
> >
> > Hi Matt, Carl, Jan & all,
> >
> >
> >
> > On Mon, Dec 2, 2013 at 1:02 PM, Jan Eglinger <[hidden email]> wrote:
> >
> >> Dear Matt,
> >>
> >>> Any ideas?
> >>>
> >>
> >> your original post was not accepted by the mailing list [1],
> >> presumably because you didn't confirm it. That might be a reason why
> >> you didn't get an answer for a little while.
> >>
> >> I am copying some of your original question here for the convenience
> >> of readers joining the discussion at a later point.
> >>
> >>> I have very limited experience with Java and I was wondering if
> >>> someone had updated the Radial profile EXT plugin to enable macros
> >>> to work with it? More specifically, its the Radial profile angle

> >>> plugin, which was posted in 2006 and hasn't been updated since.
> >>> http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html
> >>
> >> Since the plugin makes use of ImageJ's GenericDialog in a non-standard
> >> way to create its own user interface (thereby preventing the built-in
> >> recordability of the command), you have to resort to one of the more
> >> powerful scripting languages like Javascript [2] or Python [3] to

> >> interact with the plugin from within a macro.
> >>
> >> In addition the Radial_Profile_Angle_Ext class tightly couples
> >> parameter initialization with the display of its dialog. I'd suggest
> >> to add a helper method setParameters(Sa, Ia, X0, Y0, mR) to the plugin, such as:
> >>
> >> public void setParameters(int mSa, int mIa, Double mX0, Double
> >> mY0, Double mmR) {
> >> Sa = mSa;
> >> Ia = mIa;
> >> X0 = mX0;
> >> Y0 = mY0;
> >> mR = mmR;
> >> setCosSin();
> >> }
> >>
> >> (mind the line breaks introduced by the mailer)
> >>
> >> After adding the above code and compiling the java file via "Compile
> >> and Run", you should be able to execute the following javascript (with
> >> an image open and any active selection):
> >>
> >> importClass(Packages.Radial_Profile_Angle_Ext);
> >>
> >> rp = new Radial_Profile_Angle_Ext();
> >> imp = IJ.getImage();
> >> ip = imp.getProcessor();
> >> rp.setup("", imp);
> >> rp.setParameters(180, 40, 77.5, 108.5, 57.5);
> >> rp.doRadialDistribution(ip);
> >>
> >> and you should see a profile plot without any dialog showing up.
> >>
> >> Hope that helps,
> >> Jan
> >>
> >>
> >>
> >>
> >> [1]: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-
> >> work-with-Macros-td5005598.html
> >> [2]: http://fiji.sc/Javascript_Scripting
> >> [3]: http://fiji.sc/Jython_Scripting
> >>
> >>
> >
> > here is another upgraded version of the Radial Profile plugin,
> >
> > https://github.com/cmci/RadialProfileV2/tree/master/target
> >
> >
> > that allows having options to the macro command e.g.
> >
> > run("Radial Profile", "x=148 y=125 radius=80");
> >
> > Original version had some bug in the measurement for the value in the last index of the profile, and this is fixed in my version as well.

> >
> > Maybe Carl's extended version could be merged at some point.
> >
> > Cheers,
> >
> > Kota
> >
> >

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Kota Miura

Re: Radial profile ext to work with Macros

Hi Philippe,

I apologize for being too lazy to respond.
The large difference is not really a big difference. I converted the
original plugin to separate plugin implementation and the core processing
part to ease the use of the plugin from scripts, and also fixed a bug. I
will find time to see your code to do the same thing, and it probably then
will be the merge of two works, mine and yours.

... and I wish for a Happy New Year to you as well, including all the
subscribers of this list. It's only another 30 minutes left for this year n
Japan, where I am now staying.

a+ and Cheers,
Kota

On Tue, Dec 31, 2013 at 8:24 AM, CARL Philippe (PHA) <
[hidden email]> wrote:

> Dear all,
> You will find an updated version of the Radial profile ext plugin
> implementing Macros recording and use under the following link:
> http://punias.free.fr/Radial_Profile_Angle_Ext.jar
> Please feel free to test it and give me feedback about it before I contact
> Wayne for an update on the ImageJ website.
> Also there is a small bug within the code I don't really know how to solve
> concerning the plotting of the integration area by using the "b" hotkey in
> opposition to the associated button. Since by using the "b" hotkey the cone
> of the integration angle calculation is unwantedly drawn as by using the
> same code with the button it isn't drawn and thus the code behaves normally.
> Dear Kota,
> Could you please indicate me in what consist your bug correction on the
> original radial profile plugin?
> Your plugin is quite different from the original one and thus it is
> difficult to track your correction.
> I wish you all a happy New Year 2014!!!
> My best regards,
> Philippe
>
> Le Mardi 3 Décembre 2013 12:12 CET, Jan Eglinger <[hidden email]>
> a écrit:
>
> > Dear Philippe, Kota and all,
> >
> > On 03.12.2013, 9:47 AM, Philippe CARL wrote:
> > > Dear all,
> > > To say the truth the "Radial profile ext" was actually the very first
> plugin I had ever written under ImageJ, in what seems to me now to be
> almost an eternity ago.
> > > And in this times I absolutely needed such a sharp tool in order to
> quantify some RICM pictures in a certain way for generating a part of a
> publication.
> > > Also I had indeed not written the plugin for a macro (I even didn't
> know how to program macros at this time) use and the code may probably be
> quite improved.
> > > So what I can propose is to look over the code in general to try to
> improve it, extend its capabilities for macros, look for the bug correction
> Kota made (this bug is quite probably as well within the "Radial profile
> ext" plugin) and then post this new plugin on a site for you guys to
> download and try it.
> > > And if everybody agrees on the update we can then contact Wayne for
> him to update the posted code on the ImageJ website.
> > > Thus please allow me a couple days (= 2-3) for doing this.
> >
> > Since Kota has made his plugin so nicely available via github, I would
> > suggest that you fork that project and open a pull request with your
> > changes [*1*]. (Since recently, you can even edit the files online,
>
> > making it very easy to contribute.)
> > That will also permit others (devlopers but also advanced users of the
> > plugin) to contribute small changes if necessary.
> >
> > > Also I would like to ask whether the new plugin update and evaluation
> discussion should rather be continued within the ImageJ list or rather
> outside, in private, until a new updated plugin is available?
> >
> > After all, the plugin is made for its users, so I suggest that the
> > discussion about possible enhancements stays on this list.
> >
> > Cheers,
> > Jan
> >
> > [*1*]: https://help.github.com/articles/using-pull-requests
> >
> > > -----Message d'origine-----
> > > De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Kota Miura
> > > Envoyé : lundi 2 décembre 2013 13:42
> > > À : [hidden email]
> > > Objet : Re: Radial profile ext to work with Macros
> > >
> > > Hi Matt, Carl, Jan & all,
> > >
> > >
> > >
> > > On Mon, Dec 2, 2013 at 1:02 PM, Jan Eglinger <[hidden email]>
> wrote:
> > >
> > >> Dear Matt,
> > >>
> > >>> Any ideas?
> > >>>
> > >>
> > >> your original post was not accepted by the mailing list [1],
> > >> presumably because you didn't confirm it. That might be a reason why
> > >> you didn't get an answer for a little while.
> > >>
> > >> I am copying some of your original question here for the convenience
> > >> of readers joining the discussion at a later point.
> > >>
> > >>> I have very limited experience with Java and I was wondering if
> > >>> someone had updated the Radial profile EXT plugin to enable macros
> > >>> to work with it? More specifically, its the Radial profile angle
>
> > >>> plugin, which was posted in 2006 and hasn't been updated since.
> > >>> http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html
> > >>
> > >> Since the plugin makes use of ImageJ's GenericDialog in a non-standard
> > >> way to create its own user interface (thereby preventing the built-in
> > >> recordability of the command), you have to resort to one of the more
> > >> powerful scripting languages like Javascript [2] or Python [3] to
>
> > >> interact with the plugin from within a macro.
> > >>
> > >> In addition the Radial_Profile_Angle_Ext class tightly couples
> > >> parameter initialization with the display of its dialog. I'd suggest
> > >> to add a helper method setParameters(Sa, Ia, X0, Y0, mR) to the
> plugin, such as:
> > >>
> > >> public void setParameters(int mSa, int mIa, Double mX0,
> Double
> > >> mY0, Double mmR) {
> > >> Sa = mSa;
> > >> Ia = mIa;
> > >> X0 = mX0;
> > >> Y0 = mY0;
> > >> mR = mmR;
> > >> setCosSin();
> > >> }
> > >>
> > >> (mind the line breaks introduced by the mailer)
> > >>
> > >> After adding the above code and compiling the java file via "Compile
> > >> and Run", you should be able to execute the following javascript (with
> > >> an image open and any active selection):
> > >>
> > >> importClass(Packages.Radial_Profile_Angle_Ext);
> > >>
> > >> rp = new Radial_Profile_Angle_Ext();
> > >> imp = IJ.getImage();
> > >> ip = imp.getProcessor();
> > >> rp.setup("", imp);
> > >> rp.setParameters(180, 40, 77.5, 108.5, 57.5);
> > >> rp.doRadialDistribution(ip);
> > >>
> > >> and you should see a profile plot without any dialog showing up.
> > >>
> > >> Hope that helps,
> > >> Jan
> > >>
> > >>
> > >>
> > >>
> > >> [1]: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-
> > >> work-with-Macros-td5005598.html
> > >> [2]: http://fiji.sc/Javascript_Scripting
> > >> [3]: http://fiji.sc/Jython_Scripting
> > >>
> > >>
> > >
> > > here is another upgraded version of the Radial Profile plugin,
> > >
> > > https://github.com/cmci/RadialProfileV2/tree/master/target
> > >
> > >
> > > that allows having options to the macro command e.g.
> > >
> > > run("Radial Profile", "x=148 y=125 radius=80");
> > >
> > > Original version had some bug in the measurement for the value in the
> last index of the profile, and this is fixed in my version as well.
>
> > >
> > > Maybe Carl's extended version could be merged at some point.
> > >
> > > Cheers,
> > >
> > > Kota
> > >
> > >
>
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

In reply to this post by Jan Eglinger

Dear all,
Following the request a couple of months ago of macros implementation of the Radial profile ext plugin, I have submitted a version to Wayne who has updated it on the ImageJ website.
http://imagej.nih.gov/ij/plugins/radial-profile-ext.html
This version takes into account the bug correction found and discussed by Kota Miura.
It also and especially introduces several new functionalities which are the results of some fruitful back and forth discussions with Michael Schmid which lasted over several days and from which I learned really a lot.
Thus I would like to specially thank him here.
Thus enjoy and feel free to contact me again about this plugin or other purposes.
Best regards
Philippe

Philippe CARL
Laboratoire de Biophotonique et Pharmacologie
UMR 7213 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 41 84

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de Jan Eglinger
Envoyé : mardi 3 décembre 2013 12:12
À : [hidden email]
Objet : Re: Radial profile ext to work with Macros

Dear Philippe, Kota and all,

On 03.12.2013, 9:47 AM, Philippe CARL wrote:
> Dear all,
> To say the truth the "Radial profile ext" was actually the very first plugin I had ever written under ImageJ, in what seems to me now to be almost an eternity ago.
> And in this times I absolutely needed such a sharp tool in order to quantify some RICM pictures in a certain way for generating a part of a publication.
> Also I had indeed not written the plugin for a macro (I even didn't know how to program macros at this time) use and the code may probably be quite improved.
> So what I can propose is to look over the code in general to try to improve it, extend its capabilities for macros, look for the bug correction Kota made (this bug is quite probably as well within the "Radial profile ext" plugin) and then post this new plugin on a site for you guys to download and try it.
> And if everybody agrees on the update we can then contact Wayne for him to update the posted code on the ImageJ website.
> Thus please allow me a couple days (= 2-3) for doing this.

Since Kota has made his plugin so nicely available via github, I would suggest that you fork that project and open a pull request with your changes [*1*]. (Since recently, you can even edit the files online, making it very easy to contribute.) That will also permit others (devlopers but also advanced users of the
plugin) to contribute small changes if necessary.

> Also I would like to ask whether the new plugin update and evaluation discussion should rather be continued within the ImageJ list or rather outside, in private, until a new updated plugin is available?

After all, the plugin is made for its users, so I suggest that the discussion about possible enhancements stays on this list.

Cheers,
Jan

[*1*]: https://help.github.com/articles/using-pull-requests

> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Kota Miura Envoyé : lundi 2 décembre 2013 13:42 À :
> [hidden email] Objet : Re: Radial profile ext to work with Macros
>
> Hi Matt, Carl, Jan & all,
>
>
>
> On Mon, Dec 2, 2013 at 1:02 PM, Jan Eglinger <[hidden email]> wrote:
>
>> Dear Matt,
>>
>>> Any ideas?
>>>
>>
>> your original post was not accepted by the mailing list [1],
>> presumably because you didn't confirm it. That might be a reason why
>> you didn't get an answer for a little while.
>>
>> I am copying some of your original question here for the convenience
>> of readers joining the discussion at a later point.
>>
>>> I have very limited experience with Java and I was wondering if
>>> someone had updated the Radial profile EXT plugin to enable macros
>>> to work with it? More specifically, its the Radial profile angle
>>> plugin, which was posted in 2006 and hasn't been updated since.
>>> http://rsb.info.nih.gov/ij/plugins/radial-profile-ext.html
>>
>> Since the plugin makes use of ImageJ's GenericDialog in a
>> non-standard way to create its own user interface (thereby preventing
>> the built-in recordability of the command), you have to resort to one
>> of the more powerful scripting languages like Javascript [2] or
>> Python [3] to interact with the plugin from within a macro.
>>
>> In addition the Radial_Profile_Angle_Ext class tightly couples
>> parameter initialization with the display of its dialog. I'd suggest
>> to add a helper method setParameters(Sa, Ia, X0, Y0, mR) to the plugin, such as:
>>
>> public void setParameters(int mSa, int mIa, Double mX0,
>> Double mY0, Double mmR) {
>> Sa = mSa;
>> Ia = mIa;
>> X0 = mX0;
>> Y0 = mY0;
>> mR = mmR;
>> setCosSin();
>> }
>>
>> (mind the line breaks introduced by the mailer)
>>
>> After adding the above code and compiling the java file via "Compile
>> and Run", you should be able to execute the following javascript
>> (with an image open and any active selection):
>>
>> importClass(Packages.Radial_Profile_Angle_Ext);
>>
>> rp = new Radial_Profile_Angle_Ext();
>> imp = IJ.getImage();
>> ip = imp.getProcessor();
>> rp.setup("", imp);
>> rp.setParameters(180, 40, 77.5, 108.5, 57.5);
>> rp.doRadialDistribution(ip);
>>
>> and you should see a profile plot without any dialog showing up.
>>
>> Hope that helps,
>> Jan
>>
>>
>>
>>
>> [1]: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-
>> work-with-Macros-td5005598.html
>> [2]: http://fiji.sc/Javascript_Scripting
>> [3]: http://fiji.sc/Jython_Scripting
>>
>>
>
> here is another upgraded version of the Radial Profile plugin,
>
> https://github.com/cmci/RadialProfileV2/tree/master/target
>
>
> that allows having options to the macro command e.g.
>
> run("Radial Profile", "x=148 y=125 radius=80");
>
> Original version had some bug in the measurement for the value in the last index of the profile, and this is fixed in my version as well.
>
> Maybe Carl's extended version could be merged at some point.
>
> Cheers,
>
> Kota
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

JimmiB

Re: Radial profile ext to work with Macros

Dear Philippe,
Thanks for the update to radial-profile-ext. I came across your earlier version several years ago, but was unable to employ it as desired due to the lack of macro compatibility. I have tested the new version in a few basic macros and it is great.
As a suggestion, for time/stack measurements, it would be nice to have the option to output the plot as intensity vs time rather than an individual plot at each time point. eg.
+++-

Secondly, I can't work out how to access the data through a macro. Any suggestions here?

What I am trying to develop is a macro that will take a list of co-ordinates and measure the radial profile at each given point outputting the data to a single updated results file.

Cheers,

James

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

Dear James,
I'm happy that you like the work that has been implemented in the new
version of the radial-profile-ext plugin.
Following your request, please download an even newer version (from this
morning) under the following link:
http://punias.free.fr/Radial_Profile_Angle_Ext.jar
In this version I have now added MacroExtension features which are
illustrated in the following macro:
run("Radial Profile Angle", "x_center=200 y_center=200 radius=200
starting_angle=0 integration_angle=180 use_spatial_calibration");
print(Ext.getBinSize);
print(Ext.getStackSize);
print(Ext.getXValue(0)); // XValue
[Ext.getBinSize]
print(Ext.getYValue(0, 0)); //
YValue[Ext.getStackSize][Ext.getBinSize]
Is this newer version completely answering your issue or do you need
additional methods?
In the case you validate this version I will then ask Wayne to make a new
update on the ImageJ Website.
My best regards,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de JimmiB
Envoyé : mardi 11 février 2014 01:15
À : [hidden email]
Objet : Re: Radial profile ext to work with Macros

Dear Philippe,
Thanks for the update to radial-profile-ext. I came across your earlier
version several years ago, but was unable to employ it as desired due to the
lack of macro compatibility. I have tested the new version in a few basic
macros and it is great.
As a suggestion, for time/stack measurements, it would be nice to have the
option to output the plot as intensity vs time rather than an individual
plot at each time point. eg.
+++-
+++<http://imagej.1557.x6.nabble.com/file/n5006479/Radial_Plot_IvT.jpg>
vs
<http://imagej.1557.x6.nabble.com/file/n5006479/Profile_Plot_Fvt.png>

Secondly, I can't work out how to access the data through a macro. Any
suggestions here?

What I am trying to develop is a macro that will take a list of co-ordinates
and measure the radial profile at each given point outputting the data to a
single updated results file.

Cheers,

James

--
View this message in context:
http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macros-tp50
05598p5006479.html
Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

Hi again,
I guess by having "the option to output the plot as intensity vs time rather
than an individual plot at each time point" you probably wanted something
similar to what can now be done with the following macro, isn't it?:
run("Radial Profile Angle", "x_center=200 y_center=200 radius=200
starting_angle=0 integration_angle=180 use_spatial_calibration
calculate_radial_profile_on_stack");
run("Clear Results");
for(i = 0; i != Ext.getStackSize; i++)
{
setResult("Time", i, i);
for(j = 0; j != Ext.getBinSize; j++)
setResult(Ext.getXValue(j), i, Ext.getYValue(i, j));
}
updateResults();
My best regards,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de
Philippe CARL Envoyé : mardi 11 février 2014 13:34 À : [hidden email]
Objet : Re: Radial profile ext to work with Macros

Dear James,
I'm happy that you like the work that has been implemented in the new
version of the radial-profile-ext plugin.
Following your request, please download an even newer version (from this
morning) under the following link:
http://punias.free.fr/Radial_Profile_Angle_Ext.jar
In this version I have now added MacroExtension features which are
illustrated in the following macro:
run("Radial Profile Angle", "x_center=200 y_center=200 radius=200
starting_angle=0 integration_angle=180 use_spatial_calibration");
print(Ext.getBinSize);
print(Ext.getStackSize);
print(Ext.getXValue(0)); // XValue
[Ext.getBinSize]
print(Ext.getYValue(0, 0)); //
YValue[Ext.getStackSize][Ext.getBinSize]
Is this newer version completely answering your issue or do you need
additional methods?
In the case you validate this version I will then ask Wayne to make a new
update on the ImageJ Website.
My best regards,
Philippe

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de JimmiB
Envoyé : mardi 11 février 2014 01:15 À : [hidden email] Objet : Re:
Radial profile ext to work with Macros

Dear Philippe,
Thanks for the update to radial-profile-ext. I came across your earlier
version several years ago, but was unable to employ it as desired due to the
lack of macro compatibility. I have tested the new version in a few basic
macros and it is great.
As a suggestion, for time/stack measurements, it would be nice to have the
option to output the plot as intensity vs time rather than an individual
plot at each time point. eg.
+++-
+++<http://imagej.1557.x6.nabble.com/file/n5006479/Radial_Plot_IvT.jpg>
vs
<http://imagej.1557.x6.nabble.com/file/n5006479/Profile_Plot_Fvt.png>

Secondly, I can't work out how to access the data through a macro. Any
suggestions here?

What I am trying to develop is a macro that will take a list of co-ordinates
and measure the radial profile at each given point outputting the data to a
single updated results file.

Cheers,

James

--
View this message in context:
http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macros-tp50
05598p5006479.html
Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
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JimmiB

Re: Radial profile ext to work with Macros

In reply to this post by JimmiB

Dear Phillipe,
Thankyou for your help and prompt response. I am in the process of testing
the new update and will get back to you ASAP.
re:

> run("Radial Profile Angle", "x_center=200 y_center=200 radius=200
> starting_angle=0 integration_angle=180 use_spatial_calibration
>
calculate_radial_profile_on_stack");
> run("Clear Results");
> for(i = 0; i != Ext.getStackSize; i++)
> {
> setResult("Time", i, i);
> for(j = 0; j != Ext.getBinSize; j++)
> setResult(Ext.getXValue(j), i, Ext.getYValue(i,
> j));
> }
> updateResults();

When I run this I get a results list with Time = Slice# and The intensity
of the first radius.
This looks good. How do i get this to plot, or add the other radius.
Apologies, I have no experience with the Ext. commands.
I was also wondering if you could clarify exactly what the
starting angle (*seems pretty self explanatory)*
and
integration angle - (*Does this define the number of sections the
measurements are broken down into? each half of the ROI is analysed and
then averaged to give the final result?)*
are.

Also, What defines the size and number of the radii
Cheers,
James

*Dr James Burchfield*
The Garvan Institute of Medical Research
384 Victoria Street
Darlinghurst, NSW, 2010
Australia

Email: [hidden email]
Phone:+61 2 92958229
Web: *www.garvan.org.au <http://www.garvan.org.au>*

On Wed, Feb 12, 2014 at 12:23 AM, Philippe CARL <[hidden email]>wrote:

> Hi again,
> I guess by having "the option to output the plot as intensity vs time
> rather
> than an individual plot at each time point" you probably wanted something
> similar to what can now be done with the following macro, isn't it?:
> run("Radial Profile Angle", "x_center=200 y_center=200 radius=200
> starting_angle=0 integration_angle=180 use_spatial_calibration
> calculate_radial_profile_on_stack");
> run("Clear Results");
> for(i = 0; i != Ext.getStackSize; i++)
> {
> setResult("Time", i, i);
> for(j = 0; j != Ext.getBinSize; j++)
> setResult(Ext.getXValue(j), i, Ext.getYValue(i,
> j));
> }
> updateResults();
> My best regards,
> Philippe
>
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> Philippe CARL Envoyé : mardi 11 février 2014 13:34 À : [hidden email]
> Objet : Re: Radial profile ext to work with Macros
>
> Dear James,
> I'm happy that you like the work that has been implemented in the new
> version of the radial-profile-ext plugin.
> Following your request, please download an even newer version (from this
> morning) under the following link:
> http://punias.free.fr/Radial_Profile_Angle_Ext.jar
> In this version I have now added MacroExtension features which are
> illustrated in the following macro:
> run("Radial Profile Angle", "x_center=200 y_center=200 radius=200
> starting_angle=0 integration_angle=180 use_spatial_calibration");
> print(Ext.getBinSize);
> print(Ext.getStackSize);
> print(Ext.getXValue(0)); // XValue
> [Ext.getBinSize]
> print(Ext.getYValue(0, 0)); //
> YValue[Ext.getStackSize][Ext.getBinSize]
> Is this newer version completely answering your issue or do you need
> additional methods?
> In the case you validate this version I will then ask Wayne to make a new
> update on the ImageJ Website.
> My best regards,
> Philippe
>
> -----Message d'origine-----
> De : ImageJ Interest Group [mailto:[hidden email]] De la part de
> JimmiB
> Envoyé : mardi 11 février 2014 01:15 À : [hidden email] Objet : Re:
> Radial profile ext to work with Macros
>
> Dear Philippe,
> Thanks for the update to radial-profile-ext. I came across your earlier
> version several years ago, but was unable to employ it as desired due to
> the
> lack of macro compatibility. I have tested the new version in a few basic
> macros and it is great.
> As a suggestion, for time/stack measurements, it would be nice to have the
> option to output the plot as intensity vs time rather than an individual
> plot at each time point. eg.
> +++-
> +++<http://imagej.1557.x6.nabble.com/file/n5006479/Radial_Plot_IvT.jpg>
> vs
> <http://imagej.1557.x6.nabble.com/file/n5006479/Profile_Plot_Fvt.png>
>
> Secondly, I can't work out how to access the data through a macro. Any
> suggestions here?
>
> What I am trying to develop is a macro that will take a list of
> co-ordinates
> and measure the radial profile at each given point outputting the data to a
> single updated results file.
>
> Cheers,
>
> James
>
>
>
>
>
>
> --
> View this message in context:
>
> http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macros-tp50
> 05598p5006479.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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CARL Philippe (LBP)

Re: Radial profile ext to work with Macros

Dear James

> When I run this I get a results list with Time = Slice# and The intensity
of the first radius.
> This looks good.

Ok good...

> How do i get this to plot, or add the other radius.

Getting the data in a result table or plot is not very different in terms of
use of the "Ext." methods ; nevertheless, the following macro will do the
job you are looking for:

for(rad = 200; rad <= 210; rad += 10)
raduisPlot(rad);

function raduisPlot(radius)
{
selectWindow("confocal-series.tif");
run("Radial Profile Angle", "x_center=200 y_center=200 radius=" +
radius + " starting_angle=0 integration_angle=180 use_spatial_calibration
calculate_radial_profile_on_stack");
color = newArray("black", "blue", "cyan", "darkGray", "gray",
"green", "lightGray", "magenta", "orange", "pink", "red", "yellow");
xValues = newArray(Ext.getStackSize);
yValues = newArray(Ext.getStackSize);
Plot.create("Radius = " + radius, "Time", "Fluorescence (A.U.)",
xValues, yValues);
Plot.setLimits(0, Ext.getStackSize, 0, 150);
for(j = 0; j != Ext.getBinSize; j++)
{
for(i = 0; i != Ext.getStackSize; i++)
{
xValues[i] = i;
yValues[i] = Ext.getYValue(i, j);
}
Plot.add("line", xValues, yValues);
Plot.setColor(color[j % 12]);
}
Plot.show();
}

> I was also wondering if you could clarify exactly what the starting angle
(*seems pretty self explanatory)* and integration angle - (*Does this
define the number of sections the measurements are broken down into?
> each half of the ROI is analysed and then averaged to give the final
result?)* are.

I have added an "Application" tab at the bottom of the plugin Website that
can be found under the following link:
http://punias.free.fr/radial-profile-ext.html
is this new addition answering clearly your questions now or do you still
have some doubts or misunderstanding?

> Also, What defines the size and number of the radii Cheers, James

I'm afraid that I don't understand this question.
Do you want to know what the values of "Ext.getStackSize" and
"Ext.getBinSize" are or something else?

Best regards,

Philippe

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