====== Smooth Histogram ======


===== Description =====

If an arbitrary number of bins is used to generate a histogram from an integer data-type image, spikes can arise due to an uneven number of integer values within each bin. This utility converts images to floating point and adds random noise with values between 0 and 1 before calculating the histogram 

===== Author =====

Jonathan Jackson (jjackson a.t familyjackson dot net)

===== Change List =====

  * 2008-12-04: First uploaded to ImageJ Wiki 

===== Usage =====
<code>

Usage: histogram [options] image

Purpose:  Generates smooth histograms with a user-specified number of bins.

Options:
  -a<n>         set min and max automatically (mean +- 2*sd)
                n is an optional parameter to change the number of sd's
  -l <hMin>     histogram min (lower) value
  -m            set min and max to the min and max values in the image
  -n <nBins>    number of bins in histogram (default=256)
                if n <= 1 then the bin width is set to 1 (ie. nBins = max-min)
  -u <hMax>     histogram max (upper) value
  -z            include pixels with values <= 0

Advanced Options:
  -s            don't add 0-1 random noise for smoother histogram
                (this eliminates spikes and is on by default when bin width != 1)

Input files may be in Analyze, NIFTI, DICOM or UNC format
The output has three columns: 'Bin number' 'Bin start' 'Number of Pixels'
</code>

===== Installation =====

  * Download {{:diverse:commandline:smooth_histogram.class|}} to the ImageJ plugins folder
  * Source code: {{:diverse:commandline:smooth_histogram.java|}}

Dependencies:
  * Download [[http://www.urbanophile.com/arenn/hacking/download.html|java-getopt.jar]] (to ImageJ/plugins/jars)
  * Save [[diverse:commandline:estimatemem|estimate_mem]] (to ImageJ/bin)
  * Install the [[http://rsb.info.nih.gov/ij/plugins/unc.html|UNC plugin]] if UNC image support is required
  * Install the [[http://rsb.info.nih.gov/ij/plugins/nifti.html|NIFTI plugin]] if Analyze/Nifti image support is required

Finally, save the wrapper script (to ImageJ/bin/histogram), make the file executable and edit paths as appropriate:
<code bash>
#!/bin/bash

class="Smooth_Histogram"

ij_path="/usr/local/ImageJ/"
ij_plugins="${ij_path}plugins"

java_path="/usr/java/jdk1.5/bin/"

CLASSPATH="${ij_path}ij.jar"
CLASSPATH="${CLASSPATH}:${ij_plugins}/Histogram/"
CLASSPATH="${CLASSPATH}:${ij_plugins}/jars/getopt.jar"
export CLASSPATH

shopt -s xpg_echo
RED='\e[1;31m'
NC='\e[0m' # no color
if [[ -z "$DISPLAY" ]] ; then
    echo "${RED}$(basename $0) may fail because the DISPLAY variable is not set properly${NC}" 1>&2
    echo "Try using 'ssh -Y' when you log in to a remote machine" 1>&2
fi

shopt -s extglob
eval im_file='${'$#'}'  # last argument should be the image file
mem=$(${ij_path}bin/estimate_mem -m 4 -b 32 $im_file) # need space for image in 32bit, so possible 4x 8bit -> 32 bit conversion

${java_path}java -mx${mem}m -Dplugins.dir=${ij_path} -Dscript.name=`basename $0`  $class $@
exit $?
</code>