[ImageJ-devel] IJ2 work/Histogram

Fri Aug 10 17:11:23 CDT 2012

Here is a discussion of changes I propose for dealing with histograms in 
IJ2.  Sorry it's so length, let me know if something is unclear and 
please comment if you have an interest in histograms; I do have some 
specific questions for the group (*/in bold italics/*):

1)  First of all I would create some helper methods like the following 
(could just be static methods somewhere)...

// maps a value to a bin index, given the range min...max and the number 
of bins
int valueToBin(int bins, double min, double max, double value);

// returns array of edge values
double[] getEdgeValues(int bins, double min, double max);

// returns array of center values
double[] getCenterValues(int bins, double min, double max);

...and equivalent set for integer values.

Note that these methods would be used for both computing histograms and 
assigning colors from a LUT.  It's nice to use exactly the same code for 
both.  You can characterize a histogram bin or LUT color by the starting 
or edge value or by the center value, I've seen it both ways so I 
included both flavors.

Having these common methods would also avoid bugs:

i) One bug I saw in several places is to compute (value - min) / (max - 
min) and get a value from 0.0 to 1.0, but multiply that by 255.  The 
problem with that is the only way you get bin 255 is if value == min.  
Ideally each bin should represent a range of values; if the data set is 
uniformly distributed the size of the range of values per bin would be 
about the same.

ii) Another bug was to compute width = max - min + 1.  That's certainly 
the way you do it for integer arithmetic but it doesn't work in floating 
point!

I'd rather fix these bugs by refactoring to call the common helper methods.

2)  Regarding the "ImageStatistics" class idea that Curtis mentioned:

For example it might include methods:

// request certain things ahead of time
doMinMax();
doHistogram(int bins);
doHistogram(int bins, double min, double max);
doMean();

// do minimal number of passes through the image
process();

// get accumulated results
double[] getMinMax();
long[] getHistogram();
double getMean;

Here if you don't specify a min/max for doHistogram the code has to take 
an initial pass to get min/max then another to build the histogram using 
that min/max.

3) Discussion of  net.imglib2.script.analysis.Histogram:

Both of these ImgLib2 histogram methods combine a single pass through 
the image with generating histogram statistics.

This code exhibits bug (i).

I'm not sure that this handles integral values as well as floating point.

The mapping of values to histogram bins counts values that are less than 
the min in the first bin and values that are greater than the max in the 
last bin. */Is this really desirable behavior?/ * In my usage of 
histograms I specifically don't want to count under- and over-range 
values.  Similarly when using a LUT I like under- and over-range values 
to appear black. Of course if we need it work both ways we can provide a 
switch.

The output of this code is actually a JFreeChart image, there's no way 
to get the raw histogram count array.

FYI, uses TreeMap<Double, Long> as an internal representation of the 
histogram count array.  Note that this combines what I am calling the 
edge values with the histogram counts.

4) Discussion of net.imglib2.algorithm.stats.Histogram:

This has a HistogramBinMapper base class with RealBinMapper and 
IntBinMapper so it's meant to handle real and integral values. The 
mapper is passed in as a parameter; I think it could be inferred from 
the cursor type T.

Here the RealBinMapper class exhibits bug (ii) when calculating binWidth 
in the constructor.

IntBinMapper doesn't let you specify a bin count, but assumes numBins = 
max - min + 1.  In other words, each bin will track a given integer 
value.  I haven't actually worked with any histograms of integral valued 
images but I thought they should work the same way as floating point, 
that is you could count a range of values in a single histogram bin. 
/*Is there any reason bins and values should always be 1:1 for integral 
valued images?*/  This is so in IJ1 for 8-bit and RGB images.

You pass in the minimum and maximum values when you create a 
HistogramBinMapper, but these are described as bin center values. My 
concept of the minimum and maximum values has been the minimum is the 
lowest value that maps to the first histogram bin and the maximum is the 
highest value that maps to the last histogram bin. If we specify min/max 
as centers some values slightly below minimum and slightly above maximum 
will map to the first and last histogram bins respectively. /*Do we need 
to specify min/max as bin center values?*/

Thanks!
Aivar

On 8/10/12 2:44 PM, Curtis Rueden wrote:
> Hi all,
>
> Aivar & I also discussed histograms, and our plan for those is a bit 
> more nebulous. Aivar is going to investigate improving Larry's 
> histogram API in net.imglib2.algorithms.stats.
>
> The general idea is that computing min/max, computing histograms, and 
> computing other statistics are intrinsically related, and for 
> performance reasons it is nice to minimize the number of passes 
> through the image when computing these. So we would like to create a 
> unified ImageStatistics class (sound familiar? ;-) that can compute 
> one or more of these in an intelligent way, then return the results on 
> demand.
>
> None of this is reconciled with the net.imglib2.script.analysis 
> package (Histogram, ImgMax, ImgMean, etc.), but perhaps in the future 
> the net.imglib2.script stuff can take more direct advantage of it.
>
> Regards,
> Curtis
>
>
> On Tue, Aug 7, 2012 at 4:45 PM, Aivar Grislis <grislis at wisc.edu 
> <mailto:grislis at wisc.edu>> wrote:
>
>     I'd also be interested in working on the histogram code.  Mostly
>     the code that generates histogram data, also their display,
>     perhaps the histogram tool itself.
>
>     SLIM Plugin uses histograms in a very dynamic way, as they are
>     updated periodically during the fit process.  You can change the
>     minimum and maximum values interactively.  So I might be an
>     interested consumer of any common histogram code.
>
>     (I looked at the histogram code in the AutoContrast plugin,
>     net.imglib2.algorithm.stats.Histogram, and
>     net.imglib2.script.analysis.Histogram and found bugs in all of
>     them when binning up the histogram values.)
>
>     Aivar
>
>

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