Posted by
Rotella, Anthony M. (GRC)[] on
Aug 08, 2007; 9:43pm
URL: http://imagej.273.s1.nabble.com/tube-diameter-tp3698688p3698694.html
Paxton,
If you don't mind some kind of user input, one silly idea would be to
write something where the macro does each tube one by one, using a user
selection to outline the tube in question. You could select the tube,
click a continue button (there is a "Wait for User" plug-in), have it do
something like the macro I wrote previously, except it gets the loop
bounds from the selection paramteres, and keep doing that until you've
analyzed all the tubes. Of course, if there are hundreds of tubes or
images, you will have to find something better.
For instance:
function getRadius(numTubes){
radius = -1;
for(n = 0; n < numTubes; n++){
run("Wait For User..."); //draw a square
getSelectionBounds(x, y, w, h);
for(c = x; c < x + w; c++){
for(r = y; r < y + h; r++){
if (getPixel(c,r) > radius)
radius = getPixel(c,r) }
}
print(radius);
}
}
It may also be possible to outline them all one by one using the ROI
Manager and to just loop them all at once.
Regards,
Tony
>-----Original Message-----
>From: ImageJ Interest Group [mailto:
[hidden email]] On
>Behalf Of Paxton Provitera
>Sent: Wednesday, August 08, 2007 4:18 PM
>To:
[hidden email]
>Subject: Re: tube diameter
>
>I neglected to mention that there are many fibers of slightly
>varying radii in each image.
>
>On 8/8/07, Rotella, Anthony M. (GRC)[]
><
[hidden email]> wrote:
>>
>> Paxton,
>>
>> I must be confused about your problem. If you know that the
>> radius value will be the biggest value in the map, then doesn't this
>> work :
>>
>> function findRadius(){
>> radius = -1;
>> for(c = 0; c < getWidth(); c++)
>> for(r = 0; r < getHeight(); r++){
>> if (getPixel(c,r) > radius)
>> radius = getPixel(c,r); }
>> return radius;
>> }
>>
>> Tony
>>
>>
>> >-----Original Message-----
>> >From: ImageJ Interest Group [mailto:
[hidden email]] On
>Behalf Of
>> >Paxton Provitera
>> >Sent: Wednesday, August 08, 2007 3:46 PM
>> >To:
[hidden email]
>> >Subject: tube diameter
>> >
>> >Hi.
>> >I have images that I have thresholded and then run through
>> >Process>Binary>Distance Map.
>> >
>> >The images are of tubes in which I would like to extract the radius
>> >value (or the largest and center value given by the distance map).
>> >
>> >The images vary in size but are mostly 640x480.
>> >From the following example pixel values I want to extract only the
>> >value of
>> >6:
>> >
>> >
>> >Sample pixel values from a distance map image:
>> >
>> >0 0 0 0 0 0 1 2 3 4 5 6 6 5 4 3 2 1 0 0 0 0 0 0 0 0 0 0 1 2 3
>> >4 5 6 6 5 4 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 4 5 6 6 5 4 3
>> >2 1 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 4 5 6 6 5 4 3 2 1 0 0 0 0
>0 0 0 0 0
>> >0 0 0 1 2 3 4 5 6 6 5 4 3 2 1 0 0 0
>> >
>> >I've been stuck on some algorithm to extract the relevant
>information.
>> >Thanks for any help on this.
>> >
>> >-Paxton
>> >
>>
>