How to get the bin start values

[Avital Steinberg]

Hi,
When I select a ROI and choose analyze, histogram, I get a histogram for
the selection. I am doing this for a 16 bit image. Below the histogram, I
see the values Min and Max. (among other values)

In a macro, I can use:

roiManager("Select", 0);
getHistogram(0, counts, 256);

To select a ROI and get the histogram. How would I find the Min and Max
values that are listed below the histogram in a macro? How are these values
calculated?

In other words: how can I get the x-values for the histogram and not just
the counts?

Thanks,
Avital

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

> On Jul 7, 2015, at 8:41 AM, Avital Steinberg <[hidden email]> wrote:
>
> Hi,
> When I select a ROI and choose analyze, histogram, I get a histogram for
> the selection. I am doing this for a 16 bit image. Below the histogram, I
> see the values Min and Max. (among other values)
>
> In a macro, I can use:
>
> roiManager("Select", 0);
> getHistogram(0, counts, 256);
>
> To select a ROI and get the histogram. How would I find the Min and Max
> values that are listed below the histogram in a macro? How are these values
> calculated?
>
> In other words: how can I get the x-values for the histogram and not just
> the counts?

The getHistogram() macro function returns the x-values in the first argument. The following macro displays a histogram plot based on the values returned by getHistogram() and getRawStatistics().

-wayne

  run("M51 Galaxy (177K, 16-bits)");
  bins = 256;
  getHistogram(values, counts, bins);
  getRawStatistics(count, mean, min, max, std);
  binWidth = (max-min)/bins;
  Plot.create("Histogram", "Value", "Count", values, counts);
  Plot.addText("Count: "+count, 0.3, 0.2);
  Plot.addText("Mean: "+mean, 0.3, 0.3);
  Plot.addText("StdDev: "+std, 0.3, 0.4);
  Plot.addText("Bins: "+bins, 0.3, 0.5);
  Plot.addText("Min: "+min, 0.3, 0.6);
  Plot.addText("Max: "+max, 0.3, 0.7);
  Plot.addText("Bin Width: "+ binWidth, 0.3, 0.8);

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[Avital Steinberg]

Hi Wayne,
Now I understand - my mistake was using 0 instead of values, so I didn't
have access to the x-values.

Thanks a lot,
Avital

On Wed, Jul 8, 2015 at 6:40 AM, Rasband, Wayne (NIH/NIMH) [E] <
[hidden email]> wrote:

> > On Jul 7, 2015, at 8:41 AM, Avital Steinberg <[hidden email]>
> wrote:
> >
> > Hi,
> > When I select a ROI and choose analyze, histogram, I get a histogram for
> > the selection. I am doing this for a 16 bit image. Below the histogram, I
> > see the values Min and Max. (among other values)
> >
> > In a macro, I can use:
> >
> > roiManager("Select", 0);
> > getHistogram(0, counts, 256);
> >
> > To select a ROI and get the histogram. How would I find the Min and Max
> > values that are listed below the histogram in a macro? How are these
> values
> > calculated?
> >
> > In other words: how can I get the x-values for the histogram and not just
> > the counts?
>
> The getHistogram() macro function returns the x-values in the first
> argument. The following macro displays a histogram plot based on the values
> returned by getHistogram() and getRawStatistics().
>
> -wayne
>
>   run("M51 Galaxy (177K, 16-bits)");
>   bins = 256;
>   getHistogram(values, counts, bins);
>   getRawStatistics(count, mean, min, max, std);
>   binWidth = (max-min)/bins;
>   Plot.create("Histogram", "Value", "Count", values, counts);
>   Plot.addText("Count: "+count, 0.3, 0.2);
>   Plot.addText("Mean: "+mean, 0.3, 0.3);
>   Plot.addText("StdDev: "+std, 0.3, 0.4);
>   Plot.addText("Bins: "+bins, 0.3, 0.5);
>   Plot.addText("Min: "+min, 0.3, 0.6);
>   Plot.addText("Max: "+max, 0.3, 0.7);
>   Plot.addText("Bin Width: "+ binWidth, 0.3, 0.8);
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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