Remove the time offset of the first slice from slice times.
Fixed a bug in the creation of the KTTimeFrequency part of the KTWaterfallCandidate data in KTMultiSliceClustering.
Improved the the printing as data is created in KTMultiSliceClustering.
Minor, but important fix to the time-dimension of clustering.
Removed the ability to change the time separation clustering criterion.
Minor change to some debug printing in KTEggReaderMonarch
Fixing the setting of the frequency range of candidates in candidate histograms
Created Matlab File Reader Placeholders

Created placeholder files for a matlab file reader (meant to read the
RSA MAT files).  The placeholder files don’t do anything but are
compilable in Katydid and are based on the KTProcessorTemplate files
(but had to be extensively modified to be compiled).
Removed KTRSAMatProcessor

We decided to use the existing KTEggProcessor to handle the processing
of matlab files; it will simply call a different reader.  Accordingly,
we have deleted the KTRSAMatProcessor cc and hh files
Created KTRSAMatReader

Created functions to be used by the KTEggProcessor to read mat files
Added support to Matlab libraries

We added support to the Matlab Compiler Runtime libraries, which allow
us to read mat files.
KTEggProcessor uses KTRSAMatReader

Modified KTEggProcessor to use the functions from KTRSAMatReader  for
matlab files (BreakEgg, HatchNextSlice, etc…)
CMakeLists comment about Matlab Compiler Runtime

Modified the comment on CMakeLists to indicate that we need the path to
Matlab Compiler Runtime R2012b
BreakEgg in KTRSAMatReader

We wrote out the BreakEgg function in KTRSAMatReader; it can open the
matlab file, read its contents (both the data and the XML configuration
string), parse the XML and write the configuration to the KTEggHeader
variable
Partial work fixing the logger
KTEggProcessor handling of normalized time series

KTEggProcessor has been modified to handle the case in which
HatchNextSlice returns data either in TSRawTimeSeries (raw data) or
TSTimeSeries (normalized data).  If it is already normalized, then it
skips the NormalizeData function.  This is necessary because the RSA
stores the data already in voltage (that is, normalized), so that
RSAMATReader creates only TSTimeSeries and not TSRawTimeSeries.
KTEggProcessor.hh documents egg-reader options

KTEggProcessor.hh comments have been modified to explain the options
for the “egg-reader” input.  It explains the special case for reading
RSA matlab files, using the option “rsamat”.
KTEggProcessor.cc with pre-normalized time series

I had forgotten to add KTTimeSeriesData.hh to the include list.
Working version of logging, using what was previously the fallback logging.  log4cxx and the closest-to-functional boost::log versions still there, but not in use.
Removed log4cxx dependence from the top-level CMakeLists.txt.
Removed commented-out logger implementations.
Verified functionality.
SliceHeader in KTRSAMATReader

Added the code to set the sliceHeader variables in
KTRSAMatReader::HatchNextSlice()
Further removal of log4cxx from CMakeLists, and removal of the Utility/log4cxx directory.