pixel by pixel intensity in a time lapase series

[Runa Hamid]

Dear Image J users,

Can someone help me to modify this macro to get pixel by pixel intensity of
a selected circular ROI in all the frames in time lapse series.This macro is
working perfectly fine for a single frame. If this can be modified for a
time lapse series, it will save lot of time running the macro for each
frame.

// list pixels values inside a selection
w=getWidth();h=getHeight();
getSelectionBounds(xmin, ymin, selwidth, selheight);
run("Create Mask");
m=newArray(w*h);
for(x=0;x<w;x++){
       for(y=0;y<h;y++){
               m[y*w+x]=getPixel(x,y);
       }
}
close(); //close mask
for(x=xmin;(x<=xmin+selwidth);x++){
       for(y=ymin;(y<=ymin+selheight);y++){
               if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
       }
}

Thanks in advance,

Runa

[Gabriel Lapointe]

Hello Runa,
I didn't tested it but adding a loop should make it work.

Good luck
Gabriel Lapointe

for (slice=1, slice<=nSlices(); slice++){
setSlice(slice);
// list pixels values inside a selection
    w=getWidth();h=getHeight();
    getSelectionBounds(xmin, ymin, selwidth, selheight);
    run("Create Mask");
    m=newArray(w*h);
    for(x=0;x<w;x++){
           for(y=0;y<h;y++){
                   m[y*w+x]=getPixel(x,y);
           }
    }
    close(); //close mask
    for(x=xmin;(x<=xmin+selwidth);x++){
           for(y=ymin;(y<=ymin+selheight);y++){
                   if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
           }
    }
}

Runa Hamid wrote:

> Dear Image J users,
>
> Can someone help me to modify this macro to get pixel by pixel intensity of
> a selected circular ROI in all the frames in time lapse series.This macro is
> working perfectly fine for a single frame. If this can be modified for a
> time lapse series, it will save lot of time running the macro for each
> frame.
>
> // list pixels values inside a selection
> w=getWidth();h=getHeight();
> getSelectionBounds(xmin, ymin, selwidth, selheight);
> run("Create Mask");
> m=newArray(w*h);
> for(x=0;x<w;x++){
>        for(y=0;y<h;y++){
>                m[y*w+x]=getPixel(x,y);
>        }
> }
> close(); //close mask
> for(x=xmin;(x<=xmin+selwidth);x++){
>        for(y=ymin;(y<=ymin+selheight);y++){
>                if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
>        }
> }
>
> Thanks in advance,
>
> Runa
>
>  

[Runa Hamid]

Hi Gabriel,

Thankyou very much. After removing few syntax errors, the macro is running
perfectly fine now.


Runa
On Tue, Jun 2, 2009 at 4:53 PM, Gabriel Lapointe <
[hidden email]> wrote:

> Hello Runa,
> I didn't tested it but adding a loop should make it work.
>
> Good luck
> Gabriel Lapointe
>
> for (slice=1, slice<=nSlices(); slice++){
> setSlice(slice);
> // list pixels values inside a selection
>    w=getWidth();h=getHeight();
>    getSelectionBounds(xmin, ymin, selwidth, selheight);
>    run("Create Mask");
>    m=newArray(w*h);
>    for(x=0;x<w;x++){
>           for(y=0;y<h;y++){
>                   m[y*w+x]=getPixel(x,y);
>           }
>    }
>    close(); //close mask
>    for(x=xmin;(x<=xmin+selwidth);x++){
>           for(y=ymin;(y<=ymin+selheight);y++){
>                   if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
>           }
>    }
> }
>
>  Runa Hamid wrote:
> > Dear Image J users,
> >
> > Can someone help me to modify this macro to get pixel by pixel intensity
> of
> > a selected circular ROI in all the frames in time lapse series.This macro
> is
> > working perfectly fine for a single frame. If this can be modified for a
> > time lapse series, it will save lot of time running the macro for each
> > frame.
> >
> > // list pixels values inside a selection
> > w=getWidth();h=getHeight();
> > getSelectionBounds(xmin, ymin, selwidth, selheight);
> > run("Create Mask");
> > m=newArray(w*h);
> > for(x=0;x<w;x++){
> >        for(y=0;y<h;y++){
> >                m[y*w+x]=getPixel(x,y);
> >        }
> > }
> > close(); //close mask
> > for(x=xmin;(x<=xmin+selwidth);x++){
> >        for(y=ymin;(y<=ymin+selheight);y++){
> >                if (m[y*w+x]!=0) print (x,y,getPixel(x,y));
> >        }
> > }
> >
> > Thanks in advance,
> >
> > Runa
> >
> >
>