>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.
I totally forgot, actually thats how IJ1 works: it does assign
under-range values to the first color and over-range values to the last
color.
For my purposes, I had to kludge up the first and last colors of the LUT
to be black and fiddle with the min/max values to make it all work.
On 8/10/12 5:11 PM, Aivar Grislis wrote:
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 <[email protected]
<mailto:[email protected]>> 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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