save the data from Oval Profile Plot

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

save the data from Oval Profile Plot

foxtango
Hi,

I can use the Oval Profile Plot and download the list interactively. But I
do not know how to do in a macro. getProfile() seems to require a
rectangular selection or a straight line.

thank you, Thomas



-----
Thomas
--
Sent from: http://imagej.1557.x6.nabble.com/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Thomas
Reply | Threaded
Open this post in threaded view
|

Re: save the data from Oval Profile Plot

Herbie
Good day Thomas,

this is in fact strange...

Usually
"
*Plot.getValues(xpoints, ypoints)*
Returns the values displayed by clicking on "List" in a plot or
histogram window (example).
"
should do what you want.

In case of the plot in question this doesn't work.
I've briefly inspected the source code and it contains the usual plot
calls* but I can't find the axis labels in the source code. Not sure
what's going on.

Perhaps someone else is able to lift the veil of secrecy.

Regards

Herbie
___________
*
void createPlot()
{
           String xLabel = "";
           if(mode == 3) xLabel = "Circumference";
           else xLabel = "Degrees";
           Plot plot = new Plot(modes[mode], xLabel, "Gray Value",
xValues, profile);
           plot.setLimits(getMin(xValues), getMax(xValues),
getMin(profile), getMax(profile));
           plot.setColor(Color.black);
           plot.show();
}

In fact the actual y-label reads "Normalized Integrated Intensity" a
string I can't find in the source code.
Consequently, there must be another plot method.

::::::::::::::::::::::::::::::::::::::
Am 20.06.20 um 23:18 schrieb foxtango:

> Hi,
>
> I can use the Oval Profile Plot and download the list interactively. But I
> do not know how to do in a macro. getProfile() seems to require a
> rectangular selection or a straight line.
>
> thank you, Thomas
>
>
>
> -----
> Thomas
> --
> Sent from: http://imagej.1557.x6.nabble.com/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: save the data from Oval Profile Plot

Wayne Rasband-2
In reply to this post by foxtango
>
> I can use the Oval Profile Plot and download the list interactively. But I
> do not know how to do in a macro. getProfile() seems to require a
> rectangular selection or a straight line.

Plot.getValues works for me. Here is a runnable example:

  run("Blobs (25K)");
  makeOval(77, 61, 123, 122);
  run("Oval Profile", "number=30 analysis=[Maximum Intensity]");
  selectWindow("Maximum Intensity");
  Plot.getValues(xpoints, ypoints);
  Array.show(xpoints,ypoints);

The Oval Profile Plot plugin is available at

    https://imagej.nih.gov/ij/plugins/oval-profile.html

-wayne

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: save the data from Oval Profile Plot

Herbie
Dear Wayne,

thanks for testing and you are right!

I was applying "Radial_Profile_Angle_Ext.jar":
<https://imagej.nih.gov/ij/plugins/radial-profile-ext.html>

Mea culpa!

The data of the resulting plot can't be accessed because the plugin uses
a special "multi_plot"-class.

//
run("Blobs (25K)");
makeOval(77, 61, 123, 122);
run("Radial Profile Angle", "x_center=128 y_center=127 radius=127.50
starting_angle=0 integration_angle=180");
Plot.getValues(xpoints, ypoints);
Array.show(xpoints,ypoints);
//

Sorry for the confusion!

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 22.06.20 um 03:39 schrieb Wayne Rasband:

>> I can use the Oval Profile Plot and download the list interactively. But I
>> do not know how to do in a macro. getProfile() seems to require a
>> rectangular selection or a straight line.
>
> Plot.getValues works for me. Here is a runnable example:
>
>    run("Blobs (25K)");
>    makeOval(77, 61, 123, 122);
>    run("Oval Profile", "number=30 analysis=[Maximum Intensity]");
>    selectWindow("Maximum Intensity");
>    Plot.getValues(xpoints, ypoints);
>    Array.show(xpoints,ypoints);
>
> The Oval Profile Plot plugin is available at
>
>      https://imagej.nih.gov/ij/plugins/oval-profile.html
>
> -wayne
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Fwd: save the data from Oval Profile Plot

CARL Philippe (LBP)
Dear Herbie,
I'm the author of the "Radial_Profile_Angle_Ext" plugin.
And it's first versions indeed implemented a special "multi_plot"-class since at that time multi-plotting wasn't implemented within the native Plot class.
But since then the native ImageJ Plot class has really evolved and became even way more powerful than the "multi_plot"-class I was using within the plugin.
So I have modified the plugin so that it is using the native ImageJ Plot class.
Thus all what you have to do is to update your "Radial_Profile_Angle_Ext" plugin to it's last version and you should be all set.
Kindest regards,
Philippe

Philippe CARL
Laboratoire de Bioimagerie et Pathologies
UMR 7021 CNRS - Université de Strasbourg
Faculté de Pharmacie
74 route du Rhin
67401 ILLKIRCH
Tel : +33(0)3 68 85 42 89

----- Mail original -----
De: "l16" <[hidden email]>
À: "imagej" <[hidden email]>
Envoyé: Lundi 22 Juin 2020 10:40:22
Objet: Re: save the data from Oval Profile Plot

Dear Wayne,

thanks for testing and you are right!

I was applying "Radial_Profile_Angle_Ext.jar":
<https://imagej.nih.gov/ij/plugins/radial-profile-ext.html>

Mea culpa!

The data of the resulting plot can't be accessed because the plugin uses
a special "multi_plot"-class.

//
run("Blobs (25K)");
makeOval(77, 61, 123, 122);
run("Radial Profile Angle", "x_center=128 y_center=127 radius=127.50
starting_angle=0 integration_angle=180");
Plot.getValues(xpoints, ypoints);
Array.show(xpoints,ypoints);
//

Sorry for the confusion!

Kind regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 22.06.20 um 03:39 schrieb Wayne Rasband:

>> I can use the Oval Profile Plot and download the list interactively. But I
>> do not know how to do in a macro. getProfile() seems to require a
>> rectangular selection or a straight line.
>
> Plot.getValues works for me. Here is a runnable example:
>
>    run("Blobs (25K)");
>    makeOval(77, 61, 123, 122);
>    run("Oval Profile", "number=30 analysis=[Maximum Intensity]");
>    selectWindow("Maximum Intensity");
>    Plot.getValues(xpoints, ypoints);
>    Array.show(xpoints,ypoints);
>
> The Oval Profile Plot plugin is available at
>
>      https://imagej.nih.gov/ij/plugins/oval-profile.html
>
> -wayne
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
Reply | Threaded
Open this post in threaded view
|

Re: save the data from Oval Profile Plot

foxtango
Hi Herbie and Wayne,

thank you for your help. The two lines work as expected.

Regards, Thomas

Am Mo., 22. Juni 2020 um 11:14 Uhr schrieb CARL Philippe (LBP) <
[hidden email]>:

> Dear Herbie,
> I'm the author of the "Radial_Profile_Angle_Ext" plugin.
> And it's first versions indeed implemented a special "multi_plot"-class
> since at that time multi-plotting wasn't implemented within the native Plot
> class.
> But since then the native ImageJ Plot class has really evolved and became
> even way more powerful than the "multi_plot"-class I was using within the
> plugin.
> So I have modified the plugin so that it is using the native ImageJ Plot
> class.
> Thus all what you have to do is to update your "Radial_Profile_Angle_Ext"
> plugin to it's last version and you should be all set.
> Kindest regards,
> Philippe
>
> Philippe CARL
> Laboratoire de Bioimagerie et Pathologies
> UMR 7021 CNRS - Université de Strasbourg
> Faculté de Pharmacie
> 74 route du Rhin
> 67401 ILLKIRCH
> Tel : +33(0)3 68 85 42 89
>
> ----- Mail original -----
> De: "l16" <[hidden email]>
> À: "imagej" <[hidden email]>
> Envoyé: Lundi 22 Juin 2020 10:40:22
> Objet: Re: save the data from Oval Profile Plot
>
> Dear Wayne,
>
> thanks for testing and you are right!
>
> I was applying "Radial_Profile_Angle_Ext.jar":
> <https://imagej.nih.gov/ij/plugins/radial-profile-ext.html>
>
> Mea culpa!
>
> The data of the resulting plot can't be accessed because the plugin uses
> a special "multi_plot"-class.
>
> //
> run("Blobs (25K)");
> makeOval(77, 61, 123, 122);
> run("Radial Profile Angle", "x_center=128 y_center=127 radius=127.50
> starting_angle=0 integration_angle=180");
> Plot.getValues(xpoints, ypoints);
> Array.show(xpoints,ypoints);
> //
>
> Sorry for the confusion!
>
> Kind regards
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::::
> Am 22.06.20 um 03:39 schrieb Wayne Rasband:
> >> I can use the Oval Profile Plot and download the list interactively.
> But I
> >> do not know how to do in a macro. getProfile() seems to require a
> >> rectangular selection or a straight line.
> >
> > Plot.getValues works for me. Here is a runnable example:
> >
> >    run("Blobs (25K)");
> >    makeOval(77, 61, 123, 122);
> >    run("Oval Profile", "number=30 analysis=[Maximum Intensity]");
> >    selectWindow("Maximum Intensity");
> >    Plot.getValues(xpoints, ypoints);
> >    Array.show(xpoints,ypoints);
> >
> > The Oval Profile Plot plugin is available at
> >
> >      https://imagej.nih.gov/ij/plugins/oval-profile.html
> >
> > -wayne
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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