http://imagej.273.s1.nabble.com/Why-is-the-median-value-zero-tp5017632p5017639.html
The bad news is that this issue applies not only to the median but also for
some other ImageStatistics fields. (for example, the xCentroid and
> Thanks Herbie, Gabriel, Aryeh and especially Jan for your help. Now I
> understand what's going on because I knew that my script used to work and
> suddenly stopped working. Now I know how to fix it,
>
> Avital
>
> On Sun, Nov 27, 2016 at 8:32 PM, Jan Eglinger <
[hidden email]>
> wrote:
>
>> Dear all,
>>
>> the Median calculation was recently removed from both ImagePlus [1] and
>> ImageStatistics [2] by Wayne in reaction to a related bug report [3].
>>
>> I guess that from v1.51i on, you'll have to use .getAllStatistics()
>> introduced with v1.51i2 [4] instead of .getStatistics().
>>
>> This is a backwards-incompatible change, but as mentioned in the github
>> issue, this improved the performance of the Brightness&Contrast dialog.
>>
>> Hope that helps,
>> Jan
>>
>>
>> [1]:
https://github.com/imagej/imagej1/commit/6e74324174a6c5c87bd>> 01c1a9ffb5568de8b1dce
>> [2]:
https://github.com/imagej/imagej1/commit/354b0d50a9f4c34908c>> 0cb573d05ecde69ad5052
>> [3]:
https://github.com/imagej/imagej1/issues/25#issuecomment-261691787>> [4]:
https://github.com/imagej/imagej1/commit/6e74324174a6c5c87bd>> 01c1a9ffb5568de8b1dce
>>
>>
>>
>> On 27.11.16 17:10, Aryeh Weiss wrote:
>>
>>> I can reproduce it, but I dont think that it is a bug.
>>>
>>> ip.getStatistics() does nto claim to return the median.
>>> Here is the API doc:
>>> Calculates and returns statistics (area, mean, std-dev, mode, min, max,
>>> centroid, center of mass, 256 bin histogram) for this image or ROI.
>>>
>>> ImageStatistics.getStatistics() is:
>>>
>>> public staticImageStatistics
>>> <
https://imagej.nih.gov/ij/developer/api/ij/process/ImageStatistics.html>>> >
>>> getStatistics(ImageProcessor
>>> <
https://imagej.nih.gov/ij/developer/api/ij/process/ImageProcessor.html>
>>> ip,
>>>
>>> int mOptions,
>>> Calibration
>>> <
https://imagej.nih.gov/ij/developer/api/ij/measure/Calibration.html>
>>> cal)
>>>
>>>
>>> If you set mOptions, you can get it to return many other things
>>> (including median), but I dont know how to set mOptions.
>>> Where is that documented?
>>>
>>> I think if you use the ImageStatistics.getStatistics()
>>> with the correct mOptions, you will get the median.
>>>
>>> --aryeh
>>>
>>> On 27/11/2016 17:57, Herbie wrote:
>>>
>>>> Good afternoon Avital,
>>>>
>>>> I've just upgraded ImageJ to the daily build 1.51i and now I can
>>>> confirm median = 0.
>>>>
>>>> This seems to be a case for Wayne...
>>>>
>>>> Best
>>>>
>>>> Herbie
>>>>
>>>> :::::::::::::::::::::::::::::::::::::::::::::
>>>> Am 27.11.16 um 16:35 schrieb Avital Steinberg:
>>>>
>>>>> Thanks, Herbie - when I run it with Fiji on my Linux machine, which has
>>>>> ImageJ 1.51a13 with Java 1.6.0_24, there is no bug like you said. But
>>>>> when
>>>>> I run it on Fiji with my 10.9.5 mac OsX, I get a value of zero.
>>>>>
>>>>> Can anyone else reproduce the bug?
>>>>> Thanks,
>>>>> Avital
>>>>>
>>>>> On Sun, Nov 27, 2016 at 5:20 PM, Herbie <
[hidden email]> wrote:
>>>>>
>>>>> Good day Avital
>>>>>>
>>>>>> when running your script entered to a window from "Plugins > New >
>>>>>> JavaScript" I get in the Log-window:
>>>>>>
>>>>>> "The median is: 71"
>>>>>>
>>>>>> ImageJ 1.51h, OSX 10.11.6, 64bit Java 1.6.0_65.
>>>>>>
>>>>>> HTH
>>>>>>
>>>>>> Herbie
>>>>>>
>>>>>> ::::::::::::::::::::::::::::::::::::::::::::::
>>>>>> Am 27.11.16 um 15:57 schrieb Avital Steinberg:
>>>>>>
>>>>>> importClass(Packages.ij.IJ);
>>>>>>> importClass(Packages.ij.plugin.frame.RoiManager);
>>>>>>> importClass(Packages.ij.ImagePlus);
>>>>>>> importClass(Packages.ij.process.ImageProcessor);
>>>>>>> importClass(Packages.ij.gui.Roi);
>>>>>>> importClass(Packages.ij.gui.OvalRoi);
>>>>>>> importClass(Packages.ij.process.ImageStatistics);
>>>>>>>
>>>>>>> rm = RoiManager.getInstance();
>>>>>>> if (rm==null) rm = new RoiManager();
>>>>>>>
>>>>>>> imp = IJ.createImage("randRamp", "8-bit ramp", 2000, 2048, 1);
>>>>>>> imp.setRoi(new OvalRoi(471,273,177,180));
>>>>>>> imp.show();
>>>>>>> IJ.run("ROI Manager...", "");
>>>>>>> rm.addRoi(imp.getRoi());
>>>>>>> rm.select(0);
>>>>>>> ip = imp.getProcessor();
>>>>>>> selROI = rm.getRoi(0);
>>>>>>> imp.setRoi(selROI, false);
>>>>>>> ip.setRoi(selROI);
>>>>>>> stats = ip.getStatistics();
>>>>>>> median = stats.median; // Adjusted median
>>>>>>> IJ.log("The median is: " + median);
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>>>
>>>>>>
>>>>> --
>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>>
>>>>>
>>>> --
>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>
>>>>
>>>
>>>
>