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<div class="moz-cite-prefix">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 (<b><i>in bold italics</i></b>):<br>
<br>
<br>
1) First of all I would create some helper methods like the
following (could just be static methods somewhere)...<br>
<br>
// maps a value to a bin index, given the range min...max and the
number of bins<br>
int valueToBin(int bins, double min, double max, double value);<br>
<br>
// returns array of edge values<br>
double[] getEdgeValues(int bins, double min, double max);<br>
<br>
// returns array of center values<br>
double[] getCenterValues(int bins, double min, double max);<br>
<br>
...and equivalent set for integer values.<br>
<br>
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.<br>
<br>
Having these common methods would also avoid bugs:<br>
<br>
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.<br>
<br>
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!<br>
<br>
I'd rather fix these bugs by refactoring to call the common helper
methods.<br>
<br>
<br>
2) Regarding the "ImageStatistics" class idea that Curtis
mentioned:<br>
<br>
For example it might include methods:<br>
<br>
// request certain things ahead of time<br>
doMinMax();<br>
doHistogram(int bins);<br>
doHistogram(int bins, double min, double max);<br>
doMean();<br>
<br>
// do minimal number of passes through the image<br>
process();<br>
<br>
// get accumulated results<br>
double[] getMinMax();<br>
long[] getHistogram();<br>
double getMean;<br>
<br>
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.<br>
<br>
<br>
3) Discussion of net.imglib2.script.analysis.Histogram:<br>
<br>
Both of these ImgLib2 histogram methods combine a single pass
through the image with generating histogram statistics.<br>
<br>
This code exhibits bug (i).<br>
<br>
I'm not sure that this handles integral values as well as floating
point.<br>
<br>
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. <b><i>Is this really desirable
behavior?</i> </b> 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.<br>
<br>
The output of this code is actually a JFreeChart image, there's no
way to get the raw histogram count array.<br>
<br>
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.<br>
<br>
<br>
4) Discussion of net.imglib2.algorithm.stats.Histogram:<br>
<br>
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.<br>
<br>
Here the RealBinMapper class exhibits bug (ii) when calculating
binWidth in the constructor.<br>
<br>
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. <i><b>Is there any
reason bins and values should always be 1:1 for integral
valued images?</b></i> This is so in IJ1 for 8-bit and RGB
images.<br>
<br>
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. <i><b>Do we need to specify min/max
as bin center values?</b></i><br>
<br>
<br>
Thanks!<br>
Aivar<br>
<br>
<br>
On 8/10/12 2:44 PM, Curtis Rueden wrote:<br>
</div>
<blockquote
cite="mid:CADN69ymmcB1DOPRrxywm9UknHbfx9JNe63Xv3bh8xV9jtTbKyQ@mail.gmail.com"
type="cite">Hi all,
<div><br>
</div>
<div>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.</div>
<div>
<br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
<div><br>
<br>
<div class="gmail_quote">On Tue, Aug 7, 2012 at 4:45 PM, Aivar
Grislis <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:grislis@wisc.edu" target="_blank">grislis@wisc.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">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.<br>
<br>
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.<br>
<br>
(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.)<span
class="HOEnZb"><font color="#888888"><br>
<br>
Aivar<br>
<br>
</font></span></blockquote>
</div>
<br>
</div>
</blockquote>
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