Re: Handling signed and unsigned 16-bit images

Posted by Michael Schmid on Mar 25, 2009; 1:19pm
URL: http://imagej.273.s1.nabble.com/Handling-signed-and-unsigned-16-bit-images-tp3693185p3693189.html

Hi Mike,

just two remarks:

getPixelValue is float, not int. It is the most convenient way of  
accessing calibrated values.

Accessing the pixels array is faster than getPixelValue, but you  
won't feel much of a difference unless you access each pixel many  
times (as, e.g., in a filter operation, where the output for each  
pixel is computed from the values of all of its neighbors).

Michael
________________________________________________________________

On 24 Mar 2009, at 18:47, Michael Doube wrote:

> Thanks Michael,
>
> This is helpful.  I am comparing a pixel value to min/max cutoffs  
> and also applying a pixel value -> apparent density calibration and  
> getting thoroughly confused about the actual values that are being  
> compared and converted.
>
> While accessing pixel values directly from an array should be faster:
>
> short[] pixels = (short[])ImageStack.getPixels(sliceNumber);
> int value32bit = pixels[pixelPointer]&0xffff;
>
> Perhaps using
> ImageProcessor sliceProcessor = ImageStack.getProcessor(sliceNumber);
> int value32bit = sliceProcessor.getPixelValue(x,y);
>
> Would be more convenient, since value32bit will be a calibrated value?
>
> Mike
>
> Michael Schmid wrote:
>> Hi Mike,
>> it depends what you want.
>> In ImageJ, 16-bit images are taken as unsigned by default; thus  
>> all  reading of pixel data requires code like this:
>>    int value32bit = pixels[pixelPointer]&0xffff;
>> where
>>    short[] pixels = (short[])ImageProcessor.getPixels();
>> Signed 16-bit images are simply unsigned data with a calibration  
>> table that maps pixel value 0 to -32768 and
>> 32768 to 0. To simplify the code, actually any calibration table  
>> that  maps 0 to -32768 (irrespective of the further values) is  
>> taken as an  indication of signed 16-bit data.
>> For most filter operations, it makes no difference whether the  
>> data  are signed or unsigned.
>> For math operations such as multiply, the operation depends on  
>> the  calibration table as stated above.
>> For analysis of pixel values, you can use  
>> ImageProcessor.getPixelValue; it gives the calibrated values and  
>> thus  you get the correct values for signed data. Also  
>> ImageProcessor.putPixelValue works with both signed and unsigned  
>> 16- bit images.
>> When writing a PluginFilter, ImageJ will automatically take care  
>> that  an ImageProcessor gets the correct calibration from its  
>> ImagePlus. In  a Plugin, you may have to care about this  
>> separately, especially when  processing stacks.
>> The CONVERT_TO_FLOAT flag of a PlugInFilter does not take  
>> calibration  into account; thus it always takes the data as  
>> unsigned 16 bit.
>> Hope this helps,
>> Michael
>> ________________________________________________________________
>> On 24 Mar 2009, at 14:01, Burger Wilhelm wrote:
>>> Right, Java has no unsigned types - but it is only a matter of a  
>>> few bit operations to treat 16-bit words as either signed  
>>> (default)  or unsigned. However, I don't think there is any way  
>>> to mark a  ShortProcessor as "signed", so a plugin cannot  
>>> distinguish between  unsigned and signed images (unless you make  
>>> assumptions).
>>>
>>> --Wilhelm
>>>
>>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: ImageJ Interest Group [mailto:[hidden email]] On
>>>> Behalf Of Reinhard Mayr aka Czerwinski
>>>> Sent: Tuesday, March 24, 2009 1:43 PM
>>>> To: [hidden email]
>>>> Subject: Re: Handling signed and unsigned 16-bit images
>>>>
>>>> Mike,
>>>>
>>>> I once extended the AVIReader for a certain kind of 16bit
>>>> AVIs
>>>> (http://rsb.info.nih.gov/ij/plugins/download/AVI_Reader.java).
>>>>  Maybe you find something useful there.
>>>>
>>>> As far as I remember, the major problem is that Java does not
>>>> know unsigned data types.
>>>>
>>>> Hth & all the best!
>>>>
>>>> Reinhard.
>>>>
>>>> -------- Original-Nachricht --------
>>>>> Datum: Tue, 24 Mar 2009 11:15:15 +0000
>>>>> Von: Michael Doube <[hidden email]>
>>>>> An: [hidden email]
>>>>> Betreff: Handling signed and unsigned 16-bit images
>>>>> Hi all
>>>>>
>>>>> After a bit of googling and hacking and tying myself in
>>>> knots, I have to
>>>>> ask the list how people write plugins that can elegantly
>>>> handle both
>>>>> signed and unsigned 16-bit images?
>>>>>
>>>>> I had a play with
>>>> http://rsbweb.nih.gov/ij/plugins/converter.html, and
>>>>> will continue in this sort of direction unless there's a
>>>> known better
>>>>> way to do it.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Mike
>>>> --
>>>> Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s
>>>> mit allen: http://www.gmx.net/de/go/multimessenger01
>>>>
>
> --
> Dr Michael Doube  BPhil BVSc PhD MRCVS
> Research Associate
> Department of Bioengineering
> Imperial College London
> South Kensington Campus
> London  SW7 2AZ
> United Kingdom
>
> Phone: [phone]
> Fax: [phone]