getPixel() for loop

[Weller Andrew Francis]

Dear all,

I am trying to determine the normalised variance of an image. For this I
need to minus the grey-level mean from each pixel's grey-level and
square this value. I figure the best way to do this is to determine each
pixel value by using getPixel() in a for loop.

My first question: is the initial (origin) pixel getPixel(0,0) or
getPixel(1,1)?

My second question: if I need to sum these values, how can I keep an
'updater' variable in my for-loop?

So for example, I have:

W = getWidth();
H = getHeight();
for (i=0; i<=H-1; i++) { // Presuming that the origin is 0,0
                                // else I guess for (i=1; i<=H; i++)?
        for (i=0; i<=W; i++) {
                p = getPixel(W,H);
                b = (p-mean)^2;
                SOME UPDATER HERE TO A SUM OF b
                }
        }
Once out of the loop, I can do things to the total.

Cheers, Andy

[Agnès Sauleda Brossa]

Hi,

First, yes, the origin is (0,0). And second, if you mean that you need to
have a sum of all b values for all the pixels you just have to add it to the
same variable as:

double b=0;
W = getWidth();
H = getHeight();
for (i=0; i<H; i++) {
        for (j=0; j<W; j++) {  //you need to define another variable here
                p = getPixel(i,j);    //you need a loop to all the pair of
coordinates i,j
                b += (p-mean)*(p-mean);   //adds the value to the variable
b. At the end of the loop you'll have
        }                                            // the sum of all
(p-mean)*(p-mean)
}

Anyway, I think that there is a way of asking for that value with some
method, but I'm sorry to say that I don't know how.

Hope it helps,

Agnès

On 27/06/06, Andy Weller <[hidden email]> wrote:

>
> Dear all,
>
> I am trying to determine the normalised variance of an image. For this I
> need to minus the grey-level mean from each pixel's grey-level and
> square this value. I figure the best way to do this is to determine each
> pixel value by using getPixel() in a for loop.
>
> My first question: is the initial (origin) pixel getPixel(0,0) or
> getPixel(1,1)?
>
> My second question: if I need to sum these values, how can I keep an
> 'updater' variable in my for-loop?
>
> So for example, I have:
>
> W = getWidth();
> H = getHeight();
> for (i=0; i<=H-1; i++) {        // Presuming that the origin is 0,0
>                                 // else I guess for (i=1; i<=H; i++)?
>         for (i=0; i<=W; i++) {
>                 p = getPixel(W,H);
>                 b = (p-mean)^2;
>                 SOME UPDATER HERE TO A SUM OF b
>                 }
>         }
> Once out of the loop, I can do things to the total.
>
> Cheers, Andy
>

[Martin du Saire]

Is the grey-level mean for the entire image or a ROI?  Would it be
more efficient to use the image calculator?

M

At 08:47 AM 6/27/2006, you wrote:

>Dear all,
>
>I am trying to determine the normalised variance of an image. For this I
>need to minus the grey-level mean from each pixel's grey-level and
>square this value. I figure the best way to do this is to determine each
>pixel value by using getPixel() in a for loop.
>
>My first question: is the initial (origin) pixel getPixel(0,0) or
>getPixel(1,1)?
>
>My second question: if I need to sum these values, how can I keep an
>'updater' variable in my for-loop?
>
>So for example, I have:
>
>W = getWidth();
>H = getHeight();
>for (i=0; i<=H-1; i++) {        // Presuming that the origin is 0,0
>                                 // else I guess for (i=1; i<=H; i++)?
>         for (i=0; i<=W; i++) {
>                 p = getPixel(W,H);
>                 b = (p-mean)^2;
>                 SOME UPDATER HERE TO A SUM OF b
>                 }
>         }
>Once out of the loop, I can do things to the total.
>
>Cheers, Andy

[Gary Chinga]

You can get the standard deviation directly from the Analyze/Measure  
command in imageJ. The statistics you want can be defined in Analyze/
Set Measurements...

Try the following macro which measures several statistics for a  
series of images in a stack. The results are included in a result  
table which can be imported into e.g. excel.


run("Set Measurements...", "  mean standard modal min median skewness  
kurtosis slice redirect=None decimal=3");
run("Clear Results");
for (i=1; i<=nSlices;i++){
        setSlice(i);
        run("Measure");
}

Gary.



On Jun 27, 2006, at 3:47 PM, Andy Weller wrote:

> Dear all,
>
> I am trying to determine the normalised variance of an image. For  
> this I
> need to minus the grey-level mean from each pixel's grey-level and
> square this value. I figure the best way to do this is to determine  
> each
> pixel value by using getPixel() in a for loop.
>
> My first question: is the initial (origin) pixel getPixel(0,0) or
> getPixel(1,1)?
>
> My second question: if I need to sum these values, how can I keep an
> 'updater' variable in my for-loop?
>
> So for example, I have:
>
> W = getWidth();
> H = getHeight();
> for (i=0; i<=H-1; i++) { // Presuming that the origin is 0,0
> // else I guess for (i=1; i<=H; i++)?
> for (i=0; i<=W; i++) {
> p = getPixel(W,H);
> b = (p-mean)^2;
> SOME UPDATER HERE TO A SUM OF b
> }
> }
> Once out of the loop, I can do things to the total.
>
> Cheers, Andy
>
>

[Vincenzo Della Mea]

Il giorno 27/giu/06, alle ore 16:47, Gary Chinga ha scritto:

> You can get the standard deviation directly from the Analyze/
> Measure command in imageJ. The statistics you want can be defined  
> in Analyze/Set Measurements...

by the way, this will be much faster...

Vincenzo

[Thomas Mandl-2]

Hi,

To your questions (if I understand correctly):
(1) getPixel(0,0)
(2) simply declare it and update it (See below)

\begin{macrocode}
SOME_UPDATER=0;
mean=42; //need this so I can test
W = getWidth();
H = getHeight();
for (i=0; i<=H-1; i++) {
        for (j=0; j<=W; j++) { //changed i to j
                p = getPixel(j,i); //changed from p = getPixel(W,H);
                b = (p-mean)^2;

                //SOME UPDATER HERE TO A SUM OF b
                SOME_UPDATER+=b;
                }
        }
print(SOME_UPDATER);
\end{macrocode}


Here's a different version/Approach. I use the calculator instead of a loop
(example image is called  "R^2_pre1" without the quotes)

\begin{macrocode}
        run("Subtract...", "stack value=42"); //subtract
        run("Image Calculator...", "image1=R^2_pre1 operation=Multiply
image2=R^2_pre1 create 32-bit stack"); //square
        run("Measure"); //get the mean (similar to the updater)
\end{macrocode}


Hope it helps!
TeM


-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Andy
Weller
Gesendet: Dienstag, 27. Juni 2006 15:48
An: [hidden email]
Betreff: getPixel() for loop

Dear all,

I am trying to determine the normalised variance of an image. For this I
need to minus the grey-level mean from each pixel's grey-level and
square this value. I figure the best way to do this is to determine each
pixel value by using getPixel() in a for loop.

My first question: is the initial (origin) pixel getPixel(0,0) or
getPixel(1,1)?

My second question: if I need to sum these values, how can I keep an
'updater' variable in my for-loop?

So for example, I have:

W = getWidth();
H = getHeight();
for (i=0; i<=H-1; i++) { // Presuming that the origin is 0,0
                                // else I guess for (i=1; i<=H; i++)?
        for (i=0; i<=W; i++) {
                p = getPixel(W,H);
                b = (p-mean)^2;
                SOME UPDATER HERE TO A SUM OF b
                }
        }
Once out of the loop, I can do things to the total.

Cheers, Andy

[Weller Andrew Francis]

Dear all,

If the 'origin' of getPixel is (0,0), then in the following for-loop,
what should the 'condition' be set to? My feeling is that as the
'initialization' is set to "0" that the 'condition' should be set to
"j<H-1" - is this correct? Or should it be "j<H", "j<=H", etc?

I've also tried in vain to replicate the result I get here with the
Analyze -> Measure command (as previously suggested for speed), but have
been unable to using various equations conatining the mean, standard
deviation, area, etc!? Perhaps I am missing something trivial...?

run("Set Measurements...", "  mean standard redirect=None decimal=5");
run("Measure");
mean = getResult("Mean");
stdev = getResult("StdDev");
W = getWidth();
H = getHeight();
b = 0;
for (j=0; j<H-1; j++) {
   for (i=0; i<W-1; i++) {
      p = getPixel(i,j);
      t = (p-mean)^2;
      b += t;
      }
   }
normVar = b/(H*W*mean);

Cheers, Andy

[Joachim Wesner]

HI,

>If the 'origin' of getPixel is (0,0), then in the following for-loop,
>what should the 'condition' be set to? My feeling is that as the
>'initialization' is set to "0" that the 'condition' should be set to
>"j<H-1" - is this correct? Or should it be "j<H", "j<=H", etc?

If H is the # of elements, and the index j starts from 0, it should be
either j < H
or j <= H-1, which are both equivalent!!

(It is 100 elements going from 0 to 99 inclusive!)

JW


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