Re: Radial profile ext to work with Macros

Posted by JimmiB on
URL: http://imagej.273.s1.nabble.com/Radial-profile-ext-to-work-with-Macros-tp5005598p5006496.html

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:[phone]
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
>
>
>
>
>
>
> --
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> 05598p5006479.html
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>
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