Problem with StackStatistics function (Histogram)

[damien.schnebelen]

Hi everybody,
I've loaded stacks in Fiji and I used the StackStatistics function applied on these stacks. One output of this function is the histogram.
Nonetheless, severals tests make me wondering that the range of value for the x-axis is [0, max] instead of [0,255] where max is defined by the maximum pixel value (max = 100 for example for a stack filled with pixels valued  0 or 100).
The main problem is that in this range of values, the histogram function gives us 256 values too and not 'max+1'!
Do you know how one can face this issue ? Is there an option in the StatckStatistics function which allows us to set the range automatically?
Thank you by advance.

You will find below one of the test I have done.

Script:
Im_green = ImagePlus("Green", green) #Stack Loaded
green = Im_green.getStack()        

for i in range(1, Im_green.getNSlices()+1):    #Initialize all slices with pixels whose value is 0
        ip = green.getProcessor(i)
        rect = Roi(0, 0, Im_crop.width,Im_crop.height)
        ip.setRoi(rect)
        ip.setValue(0)
        ip.fill()

        #Im_green.show()
        stats_before = StackStatistics(Im_green)   #Calculating the histogram of the stack
        hist_before = stats_before.histogram   #Store the histogram

        p = 1
        ip = green.getProcessor(p)
        rect = Roi(0, 0, Im_crop.width,Im_crop.height) # Fill the first slice with pixels whose value is 100
        ip.setRoi(rect)
        ip.setValue(100)
        ip.fill()
       
        stats_after = StackStatistics(Im_green) #Calculate the histogram of the stack after this shift
        hist_after = stats_after.histogram
       
       
        print " Green Hist Values Before " + " : \n" + str(hist_before) + "\n"   #Compare the results
        print " Green Hist Values After " + " : \n" + str(hist_after) + "\n"

Results
Green Hist Values Before  :
array('i', [530063160, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])

 Green Hist Values After  :
array('i', [528401520, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1661640])

Here you can see that the max value is 1661640, which fit with the area of one slice. But this values correspond to a pixel value of 100 and not 255...

[Rasband, Wayne (NIH/NIMH) [E]]

> On Jul 2, 2015, at 8:39 PM, damien.schnebelen <[hidden email]> wrote:
>
> Hi everybody,
> I've loaded stacks in Fiji and I used the StackStatistics function applied
> on these stacks. One output of this function is the histogram.
> Nonetheless, severals tests make me wondering that the range of value for
> the x-axis is [0, max] instead of [0,255] where max is defined by the
> maximum pixel value (max = 100 for example for a stack filled with pixels
> valued  0 or 100).

There is a StackStatistics constructor that allows you to specify the number of bins and the x-axis (pixel value) histogram range. The following JavaScript example generates a histogram of the T1 Head sample stack that uses 200 bins and a x-axis range of 0-400. The StackStatistics constructor with only an ImagePlus argument defaults to  256 bins and an x-axis range of min-max for 16-bit stacks and 0-255 for 8-bit stacks, where ‘min’ and ‘max’ are the minimum and maximum stack pixel values.

-wayne

  imp = IJ.openImage("http://imagej.nih.gov/ij/images/t1-head.zip");
  bins = 200;
  xmin = 0;
  xmax = 400;
  binSize = xmax/bins;
  stats = new StackStatistics(imp, bins, xmin, xmax);
  plot = new Plot("Histogram", "Pixel Value", "Count");
  n = stats.histogram.length;
  x = new Array(n);
  y = new Array(n);
  for (i=0; i<n; i++) {
    x[i] = i*binSize;
    y[i] = stats.histogram[i];
  }
  plot.setLimits(0, n*binSize, 0, 20000);
  plot.add("line", x, y);
  plot.show();

>  
> The main problem is that in this range of values, the histogram function
> gives us 256 values too and not 'max+1'!
> Do you know how one can face this issue ? Is there an option in the
> StatckStatistics function which allows us to set the range automatically?
> Thank you by advance.
>
> You will find below one of the test I have done.
>
> *Script: *
> Im_green = ImagePlus("Green", green) #Stack Loaded
> green = Im_green.getStack()        
>
> for i in range(1, Im_green.getNSlices()+1):    #Initialize all slices with
> pixels whose value is 0
> ip = green.getProcessor(i)
> rect = Roi(0, 0, Im_crop.width,Im_crop.height)
> ip.setRoi(rect)
> ip.setValue(0)
> ip.fill()
>
> #Im_green.show()
> stats_before = StackStatistics(Im_green)   #Calculating the histogram of
> the stack
> hist_before = stats_before.histogram   #Store the histogram
>
> p = 1
> ip = green.getProcessor(p)
> rect = Roi(0, 0, Im_crop.width,Im_crop.height) # Fill the first slice with
> pixels whose value is 100
> ip.setRoi(rect)
> ip.setValue(100)
> ip.fill()
>
> stats_after = StackStatistics(Im_green) #Calculate the histogram of the
> stack after this shift
> hist_after = stats_after.histogram
>
>
> print " Green Hist Values Before " + " : \n" + str(hist_before) + "\n"  
> #Compare the results
> print " Green Hist Values After " + " : \n" + str(hist_after) + "\n"
>
> *Results*
> Green Hist Values Before  :
> array('i', [530063160, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
>
> Green Hist Values After  :
> array('i', [528401520, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1661640])
>
> Here you can see that the max value is 1661640, which fit with the area of
> one slice. But this values correspond to a pixel value of 100 and not 255...
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Problem-with-StackStatistics-function-Histogram-tp5013403.html
> Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[damien.schnebelen]

Thank you very much, it works perfectly ! =)