Re: Radial profile ext to work with Macros

Posted by CARL Philippe (LBP) on Feb 13, 2014; 8:40am
URL: http://imagej.273.s1.nabble.com/Radial-profile-ext-to-work-with-Macros-tp5005598p5006514.html

Dear James,
The "incremental increase in radius from the centre" is actually part of the
native radial profile plugin (i.e. I haven't written this code).
Nevertheless here is how it is calculated:

for (i = 0; i < nBins; i++)
        dataX[i] = (float) (cal.pixelWidth * mR * ((double)(i + 1) /
nBins));
with:
        mR the radius
        nBins = (int) (3*mR/4);
        cal.pixelWidth is the set calibration parameter in the case you
activate the "Use Spatial Calibration" option and is equal to 1 otherwise

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 : [phone]

-----Message d'origine-----
De : ImageJ Interest Group [mailto:[hidden email]] De la part de JimmiB
Envoyé : jeudi 13 février 2014 00:37
À : [hidden email]
Objet : Re: Radial profile ext to work with Macros

Dear Philippe,
Thanks again for your help and patience.

The macro you posted is exactly what i was after.

*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
> <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?  *


This is a great addition.

*What defines the size and number of the radii *


My question here was about what defines the incremental increase in radius
from the centre. ie if the radius is set to 6.0 pixels 4 results are
returned at a radius of 1.5, 3, 4.5, 6.

Thanks again
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 Thu, Feb 13, 2014 at 12:07 AM, Philippe CARL [via ImageJ] <
[hidden email]> wrote:

> 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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