Re: Radial profile ext to work with Macros

Posted by JimmiB on Feb 12, 2014; 11:36pm
URL: http://imagej.273.s1.nabble.com/Radial-profile-ext-to-work-with-Macros-tp5005598p5006508.html

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
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

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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