ChangeLog

2013-04-01  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Passing a filename to the -i switch when generating
	random function streams now correctly uses data from that file.

2013-03-27  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* src/Makefile.am: Made single library out of the base libraries,
	which makes sense since the libraries have some interdependencies.

2013-03-26  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* scripts/randfunc/multifunc_mean.sh: Output combination of
	methods into a single large org table for all alpha.

2013-03-25  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* scripts/randfunc: Scripts to calculate values for t-tests on
	random functions. Able to aggregate data from all functions for
	the same estimators and perform t-tests on those rather than on
	individual functions. Improved generation and stuttering functions
	by abstracting data out to the top of scripts for easier
	modification. Script to calculate the mean of a column of values
	from the extracted results. Allows fast calculation of the mean
	and standard deviation of different methods for different alpha
	values.


2013-03-22  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* scripts/extract_results.sh: Script adds 0. onto the front of the
	folder numbers (005 01 03, etc) provided at the top of the
	script. This allows the correct values of alpha to be put into
	output files.

2013-03-21  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Minor additions to homogeneous Poisson generator to
	use for examples later

	* estimator_delta.c: Verbose flags on printlines, obsolete code
	removed.

2013-03-18  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* math_util.c: Fixed midpoint calculation where abs was being used
	instead of fabs, which resulted in incorrect calculations.

	* general_util.c: Estimate at point function returns zero if
	function is < 0 at the given point to avoid issues later on.

	* experimenter.c: Compare stuttered bins function modified
	slightly so sums are calculated before entering the pdf
	calculation loop.

	* generator.c: Gaussian generator takes into account the output
	type requested.

2013-03-17  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_IWLS.c: Fixed soul-destroyingly massive bug where beta
	estimates were not being done properly due to commented line.

	* generator.c: Random generator seeding moved to places where it
	does not reseed when multiple functions are generated in the same
	call.

	* scripts: Improvements to scripts for automatic running of random
	function experiments.  More use of arrays to make modifications
	simpler - only need to modify stuff at the top of the script. More
	usage of variables defined at the top of scripts to control
	behaviour and specify input and output files.

	* scripts/randfunc/extract_results.sh: Fixed issue where output
	files were not correctly created based on the function number.

	* scripts/get_goodness.sh: Arrays used for storing values, loop
	order modified so that data files can be overwritten.

	* scripts/randfunc/runexp_batch.sh: Correction of loops, directory
	creation, correct launcher call.

	* scripts/randfunc/runtd_exp.sh: Modified to match needs of the
	time delay experiments, abstraction of variables, directory
	creation.

2013-03-13  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* scripts: Added scripts to automatically run experiments, most
	are still works in progress but have the basic functionality
	required.

2013-03-12  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Minor improvement to file copying.

	* math_util.c: Fix to double precision issue with gauss_transform
	function which caused incorrect data to be output.

	* experimenter.c: Experiment numbers are output based on the
	experiment that is running, not the overall count.

2013-03-11  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.c: Added the -u switch, updated information to detail
	its usage.

	* file_util.c: Function for copying files, and a function
	specifically for copying the set of functions generated by the
	gaussian random function generator in order to allow for the
	generation of multiple sets of streams from a single function.

	* generator.c: Now possible to generate multiple streams from the
	same random function by using the -u switch.

2013-03-10  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Check that the number of streams sent to the
	generator is not greater than the number of timedelta values that
	exist in the parameter file. Pre-generating raw files is no longer
	necessary. Using a command like ./deltastream -g data/params.txt
	-f rand -t 3 -n 2 -c 5 will automatically generate the number of
	random functions required and output the data to the current
	directory, and then read from the freshly generated files to
	generate streams.

	* estimator_delta.c: PMF estimator no longer normalises the values
	received from combining functions - these values are normalised by
	the function combination done prior to the pmf checks.

	* math_util.c: Implemented a function for checking that a double
	is less than or equal to another with some precision.

	* combinefunction.c: Fixed error with combining functions where
	the functions would be combined one step shorter than necessary
	due to double precision issues. Using the new function in
	math_util to make sure this does not happen.

	* experimenter.c: Error for each stream is calculated and output
	to results file.

2013-03-09  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* experimenter.c: Fixed issue where the last interval to be
	stuttered would not be correctly taken into account.

	* file_util.c: Fixed issue where parameter lists were not being
	output correctly to file due to length being updated at each call.

	* generator.c: Generator outputs the parameters used to generate
	the streams to the current directory if the number of functions
	generated is greater than 1.

	* src/Makefile.am: Renamed launcher to deltastream.

	* combinefunction.c: Fixed issue where combination was not
	correctly using the normaliser when combining gaussian
	vectors. Fixed issue where negative memory was being allocated to
	double arrays for data storage.

2013-03-08  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_gaussian.c: Both functions take a parameter to
	indicate whether to normalise the function being output to
	file. This is the only place that it can be done before the file
	is output - the normaliser cannot be passed in as a function
	estimate is required to compute it.

	* experimenter.c: Stuttering function takes into consideration the
	-r switch.  If on, the random function filename will be used to
	attempt to read files to stutter.

	* generator.c: Modified old generator code so that it returns a
	double_arr struct rather than messing around with
	pointers. Function data is output independently of event
	generation so that the graph is not jagged. When generating with
	the muparser generator, function output step and interval are
	defined by output_step and output_interval in the default
	parameter file.

	* estimator.c: The estimation functions now take a flag which sets
	how they construct file names to read from. If the -r switch is
	passed, the function_outfile parameter will be used in the
	filename. Otherwise, the expression_outfile parameter will be
	used.  This allows the estimators to read from files generated by
	both types of generators.  Estimator now takes normalisation
	flag. Returned data is normalised if it is nonzero.

2013-03-06  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Muparser generation code can now generate multiple
	sets of streams from the same expression by passing a number to
	the -c switch. Now uses an updated output file style to match the
	one used by the random function generator.

2013-03-03  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* file_util.c: Fixed memory leak caused by lost pointer references
	in the get_event_data_interval function. Fixed issue where
	experimenter would not be able to open more files because file
	descriptors of directories were not being freed correctly.

	* experimenter.c: Goodness values averaged over each function in
	the experiment to get a representative value for each
	experiment. These values are output to file.  Function for
	stuttering streams modified to read data from the default
	parameter file which should be available whenever it is called. It
	now uses the interval time for generation to get the actual number
	of array locations it needs to store all the intervals that will
	be calculated. The best parameter settings for individual
	functions are now output to the top level of each experiment
	directory.

2013-03-02  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* experimenter.c: Function estimation experiments now output
	correctly to files.  Stuttering functions simplified so that two
	separate versions are not necessary.  Intervals for uniform
	stuttering are computed and then passed to a function which
	operates on double_arr structs. Non-uniform stuttering intervals
	are already specified, so no additional computation is
	necessary. "Goodness" calculation based on difference between bin
	counts from function estimated from stuttered data and the actual
	function.

	* launcher.c: Fixed some memory leaks caused by changes to return
	types.

	* estimator.c: _estimate function return value changed to void* so
	that gaussian vectors can also be returned. Single stream
	estimation when input file is null correctly grabs data from file
	with the new naming convention. Fixed some memory leaks resulting
	from changes.

2013-03-01  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.c: Added a way to create a default experiment params
	file. Use something like ./launcher -x a -d paramfile to
	create. -x switch requires a parameter, so pass something random
	to it. It will not be used.

	* experimenter.c: Added a function for removing certain intervals
	from stream data in order to do model selection. Call with the
	same parameters as the experimenter, but add the -s switch. This
	creates stuttered files in the input directory. Uniform method and
	method where the intervals are specified implemented.

2013-02-27  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* math_util.c: RMS and MSE error functions, function to shift an
	array so that none of the values it contains are negative.

	* combinefunction.c: Gaussian vector combination now normalises
	the values calculated based on the normalisation constant which is
	passed in.

	* estimator.c: Time delay estimates which use gaussians as the
	estimation method return normalised combined functions.

2013-02-26  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* math_util.c: Added some functions for computing the RSS,ESS,TSS,
	but not sure if they calculate what they are supposed to.

	* estimator_gaussian.c: Fixed memory leak due to incorrect free
	function usage.

	* experimenter.c: Basic analysis of experiment results is
	performed, and the results are output to a file in the directory
	for that experiment, currently only for the time delay estimation
	experiments.

	* estimator.c: New struct for storing data output by the
	multi_estimate function so that it can be analysed during
	experimentation.

2013-02-25  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_gaussian.c: Added output switch parameter to the
	estimator functions.  Outputting the contribution of each gaussian
	takes extremely long, so if it is not necessary it should be
	done. The standard output is just the sum of gaussians if using
	the non-raw estimator. To output the contributions as well, a
	value of 3 should be passed to the -t switch.

	* experimenter.c: The number of functions and number of streams to
	work on for each function are defined in the experiment file and
	passed to the estimators for each experiment. Data for each
	experiment is output to a separate directory and each filename can
	be used to identify which of the input functions was used to
	generate that data. A parameter file is output to each experiment
	directory so that the settings used for that experiment can be
	checked later.  Correct file is now passed to the single stream
	estimator.

	* combinefunction.c: Fixed memory access issue caused by
	allocation of arrays too small to hold data in cases where the
	interval length was a round number.

	* general_util.c: Finally fixed event subinterval function causing
	errors to show up in valgrind.

	* estimator_IWLS.c: More fixes to situations which result in -nan
	values being produced. Beta estimate function returns zero if the
	denominator is zero to prevent nan results.

2013-02-24  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* file_util.c: Functions for creating and checking for existence
	of directories.

	* general_util.c: Functions for freeing experiment structs.

	* struct.h: Experiment structs added.

	* estimator_IWLS.c: Lambda estimates can no longer go below
	zero. Any value < 0 is replaced with a zero, representing the fact
	that it is not possible to have a negative rate. The weight update
	also ignores values < 0 as an additional precaution.

	* launcher.c: Added -c switch to specify the number of functions
	to generate or estimate from. Modified description of -n in the
	help information, since it is now only used to specify the number
	of streams to generate or estimate.

	* estimator.c: Estimating time delays can now be done on multiple
	functions in a directory by using the -c switch to pass in the
	number of functions to estimate, and providing the directory to
	read from using the -i switch. Single function estimates are done
	as before by simply ignoring the -c and -i switches. The file
	containing the function is assumed to be inside the directory from
	which the script is being run.

	* generator.c: Generating streams from functions can now be
	performed on multiple functions by using the -c switch to specify
	a number of functions. The functions must have already been
	generated and follow a specific naming pattern - the
	function_outfile parameter in the parameter file followed by
	"_n.dat", where n refers to the number of the function. The output
	filename contains the original filename, which is generated by
	truncating the input filename and prepending it to the output file
	used for streams. This makes the assumption that the filename ends
	with .dat.

	* experimenter.c: Now takes input and output directories as
	parameters, or reads them from the parameter file if they are not
	specified when the script is called.  The input directory is
	expected to contain stream data for all the streams that are to be
	experimented on. Results will be output to the output directory,
	with subdirectories for each experiment to reduce clutter. Reduced
	code duplication.

2013-02-23  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_piecewise.c: Event file is read before any calls are
	made to the IWLS estimator. This significantly reduces the file
	accesses that IWLS needs to make during piecewise estimation.

	* estimator_IWLS.c: Modified the weight update function to deal
	with lambda values of zero. Previously had errors with division by
	zero, but modified the function to set weights of the points with
	zero value to zero, rather than getting values of
	infinity. Estimator can now take an array of doubles containing
	event data as a parameter so that it does not have to read files
	multiple times when being called more than once.

	* file_util.c: Fixed reallocation on incorrect pointer in
	get_event_data_interval.

	* experimenter.c: Experiment required parameters are generated
	from a list of experiment names in the parameter file - this
	should make it possible to add new experiments without having to
	modify the internals of the system. Can also specify the type of
	estimator used by each experiment.

2013-02-21  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* experimenter.c: Added structs for storing experimental data in a
	structured way.  Data from the experiment parameter file is loaded
	into the exp_set struct.

2013-02-20  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* tests: Tests updated to deal with the changes to return types
	and parameters of functions caused by the modification of the
	event functions.

	* file_util.c: Modified the get_event_data functions to return a
	double array instead of a double pointer with the length in the
	first location. This has changed a few functions in other places
	which read event data, but only small changes were required to get
	things working.

	* estimator_piecewise.c: Fixed bug where when the interval being
	extended into had no events in it the estimator would crash.


2013-02-18  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Old generator functions updated to use the output
	switch system.

	* launcher.h: Modified usage output to detail the -t switch usage
	in more depth.  Each output type is listed for all things which
	use the data passed to the switch.

	* estimator_delta.c: The -t switch now affects what files are
	output by the delta estimators. 0 outputs nothing, 1 outputs the
	value computed by the function for each guess at delta, 2 outputs
	lambda and bin data. The hierarchical estimate outputs its data to
	files with "hier" in the name.

2013-02-17  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator.c, general_util.c: Removed duplicated parameter
	checking function from estimator and made the one in general util
	work.

	* estimator_gaussian.c: Estimators check that the parameter list
	they receive contains the parameters that they require.

	* estimator_delta.c: Restructured delay estimators. Each now has a
	function which extracts parameters from the parameter file and
	then calls the main function which does the calculations. Also
	added the ability to searching for an estimate in a hierarchical
	fashion, first making a coarse pass over the array and then
	refining the estimate. Functions now also check to make sure that
	the parameter list contains the parameters they
	require. Estimators output relevant data to files with names which
	make sense.

	* math_util.c: Implemented a function to check whether a double is
	less than another with a certain precision value. This is now used
	in the array interval summing function, which should work properly
	for most cases.

2013-02-16  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_delta.c: pmf estimator now takes two double_arr
	structs containing event data as parameters - this means that
	files do not have to be read multiple times unnecessarily. Also
	fixed a bug which would mean that only the same two files would be
	read regardless of the number of streams. Normalisation constant
	function split into two functions to make calling it easier. Also
	removed the calculation from inside the pmf estimator and made it
	a parameter. There is no point calculating it multiple times since
	it will be pretty much the same for all functions generated from
	gaussians which use the same standard deviation.

	* estimator_gaussian.c: Changed structure to reduce code
	duplication slightly, output files are now generated depending on
	whether a file name is received or not.

	* math_util.c: Fixed memory leak from gauss_transform function.

	* file_util.c: Fixed memory leak in read_gauss_vector function.

	* general_util.c: Fixed freeing string_arr structs.

2013-02-15  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* check_combinefunction.c: Test for combination of gauss vectors.

	* check_math_util.c: Tests for new mathematical functions.

	* estimator_delta.c: Fixed memory leaks and errors.

	* launcher.c: Combined separate multi estimate functions for gauss
	and baseline estimates into a single one - lots of unnecessary
	code duplication. Fixed memory leaks and errors.

2013-02-14  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimate_delta.c: Fixed issues where baseline pmf calculations
	were not being done correctly due to issues with math functions.

	* math_util.c: When summing pmfs, points at which lambda is zero
	caused -nan to be returned, even if there was only a single point
	at which there was a zero.  This led to bad behaviour, so the
	calculation is now done with a very small lambda value which
	should be better than ignoring those values entirely.  Array
	interval summing now sums values in the right-closed interval
	(start,end]

2013-02-13  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* tests: Fixed some tests which were broken by minor modifications
	to functions.

	* generator.c: Generation stops if the time exceeds the end time
	when the homogeneous lambda value is added to the base time. Would
	previously have a small number of events that exceeded the
	threshold.

	* estimate_delta.c: Implemented a pmf estimator which sums the
	pmfs from both streams being compared. Previous version used only
	one of the streams to check whether the combined function was
	representative of the bin counts, which was sub-optimal. pmf
	estimation now gives good results. Area estimator uses normalised
	start and end points, between which both functions have data at
	all of the delays that are being attempted. The same applies for
	the pmf estimator as well.

	* math_util.c: Fixed array interval summing issue which was
	causing pmf delay estimator to work sub-optimally.

2013-02-12  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* general_util.c, defparams.h: Added parameters for delta
	estimation to default file. Added comments to some existing
	parameters. More headings in the file, as well as some more
	separation for delta estimation parameters.  Each of the area and
	pmf methods has its own start and interval times and
	resolutions. Also added separate start and interval times for
	estimation and generation. Not sure if all places where this is
	used have been found.

	* estimate_delta.c: Functions now use parameters from parameter
	file.

2013-02-11  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimate_delta.c: More progress on the pmf estimator. Looping
	over the different delay values again, as the underlying logic
	seems to work reasonably well. Need to work out how to get the
	pmfs to come out correctly for different interval lengths, as the
	estimates are not as good as expected. Calculating only based on
	the interval in which functions overlaps seems like a good idea,
	but if this is to be implemented it needs to be normalised
	somehow, which is probably quite difficult. Delays with shorter
	overlaps always come out with the highest pmf because there are
	fewer elements to sum. Maybe incur some fixed penalty for points
	at which the combined function is zero? Perhaps using more than 10
	intervals would work better.

	* combinefunctions.c: Expected structure of time delay matches the
	current scheme. Minor fix where the gauss vector function would
	not find the correct maximum delay value if it was in the last
	array position.

	* launcher.c: Fixed time delay arrays to match the scheme. Decided
	to use a value to represent the delay of each individual stream
	rather than delays between streams. The delays will still be
	relative to the first function, but there will be n delay values
	rather than n-1 as was the case previously. This makes things more
	compatible with the generator setup. The two multi-estimate
	functions duplicate a lot of code. Should put them together to
	make things cleaner.

2013-02-10  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* math_util.c: Function for finding the sum of the log of
	probability mass functions, which takes a normalisation
	constant. Takes an array of counts and an array of lambda values
	and finds the pmf for each, summing as it goes.  The normalisation
	constant ensures that the lambda values correspond to the bin
	counts so that a true value can be found. Function for summing
	values in a specified interval given time values and data
	values. Function for summing gaussians at the specified points by
	passing an array of desired sample points. Function to find the
	largest value in the array, positive or negative.

	* general_util.c: Functions for initialising array structs with
	specified lengths, function for finding a series of values from an
	est_arr struct.

	* estimator_delta.c: Prototype of pmf estimator improved and
	almost working.  Function combination needs to be completed to a
	satisfactory level before it can be finished. Implemented a
	function to find the normalisation constant required to get
	gaussians to correspond to differing numbers of bins when doing
	the delta estimation. The normalisation constant required depends
	on the standard deviation of the gaussians used to estimate the
	function.

	* combinefunction.c: Fixed function combination. Required an array
	containing a delay for the first function as well, but since that
	is taken as a base with no delay, it is unneeded. The function now
	takes an array containing delays between the base and subsequent
	functions. This will lead to the function combination breaking
	when the time delta is read from the parameter file, as there the
	base time is specified as zero. Changing the value in the
	parameter file also affects the generator. Decide which one is
	better and fix this!

2013-02-09  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_delta.c: Untested prototype of the pmf estimator
	implemented.

	* launcher.c: Function combination for gaussians added to the
	multiple estimate process. pmf method now able to be used.

	* general_util.c: Function for initialising double_multi_arr
	structs so that code is cleaner.

	* combinefunction.c: Function for combining gaussians. Takes a set
	of gauss vectors and finds their average. This should probably be
	done on non-normalised gaussians which can be normalised when
	being output to file, or once the normalisation constant has been
	estimated.

2013-02-08  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.c: Estimates delta according to parameters in the
	paramfile.  Perhaps a good idea to add another switch to the
	launcher to specify whether or not to estimate it? Seems a little
	different to the main estimators, so it's probably fine to keep it
	in the parameter file.

	* combinefunction.c: Moved functions for finding the value of an
	estimate at a given point to general_util as it is useful in other
	places as well.

	* general_util.c: Parameters for time delta estimation added to
	default parameter file. estimate_timedelta specifies whether to
	estimate delta or just take it from the
	paramfile. timedelta_est_method specifies which method of
	estimation to use. Parameters for specifying the step, resolution
	and max delta for delta estimation. Modified some of the default
	parameters for the baseline estimator so it performs better by
	default.

	* estimator_delta.c: Function for estimating the time delta based
	on the area between two curves. Works for data from both the
	gaussian and baseline estimators. Single function for both which
	requires the conversion to a void pointer. This is so that there
	is less code duplication - there is essentially only one function
	that has to change in each of the sub-functions.

	* paramlist.c: New function to extract a list of double parameters
	separated by commas (with no spaces).

	* launcher.c, generator.c: Time delta extraction changed to use
	new function in paramlist.

	* combinefunction.c: Function now takes a double_arr struct.

	* check_math_util.c: Tests modified to use new double checking
	function, updated for new gaussian calculation (which was wrong).

	* testmain.h: Added function for checking the equivalence of
	doubles.

2013-02-06  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* general_util.c: Passing a file which already exists to default
	parameter creation asks whether to overwrite.

2013-02-05  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* general_util.c, defparams.h: Added parameters to the files to
	allow for dynamic calculation of the standard deviation based on
	the step between gaussians and a parameter alpha. Specifying the
	standard deviation normally is also possible. The simple_stdev
	parameter decides which is used.  Parameters for gaussian
	generator output modified. One parameter for generating from
	stream data, one for generating from a uniform distribution of
	gaussians.  Files are output with strings appended to show what
	they contain.

	* generator.c: Improved output file handling. Multiple files are
	output depending on the parameter provided to the gaussian
	generator. Fixed erroneous time delta extraction.

2013-02-04  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* develop: Merged gaussians branch as it had pretty much all the
	intended functionality and was working relatively well. Need to
	move on.  Also merged the experiment harness branch. Was getting
	too far behind and there were structural changes in both that and
	the gaussian branch that had some minor conflicts - better to
	merge now than to risk things getting even more disparate and
	difficult to merge later on. Development of the experiment harness
	put on hold for now.


2013-02-03  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_baseline.c: Discovered crashes, but not sure of the
	cause.  Mostly related to estimation of functions generated by the
	random generator, but this implies that there is something to do
	with the shape of the function that causes the crashes.

	* math_util.c: Functions to create gaussian vectors take a
	multiplier which modifies the weights of gaussians. Standard
	weights are ~ N(0,1).  This allows for functions to have larger
	ranges than just -5 to 5 or so.

	* estimator_gaussian.c: Reverted to using the standard system in
	use for everything else rather than kernel density.

	* printf: Some print statements depend on the VERBOSE flag being
	defined.  can do this at compile time by passing -DVERBOSE to
	make.

	* output: Modifications to output filenames for the various
	generators and estimators.

2013-02-02  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.h: Updated help info for switches, -R replaced with -t,
	specify output type.

	* general_util.c: Function for freeing memory allocated for
	double_multi_arr structs. Default parameter file has more files to
	output gaussian data to. Separate ones for raw data and that
	generated from an event file.

	* math_util.c: GSL random number generator is deallocated when the
	program exits using an atexit function. Function for shifting a
	gauss transform so that all points are non-negative

	* generator.c: Generation of event streams from
	gaussians. Generation of functions simplified to a single
	function. Output of contribution of gaussians if the -t 2 switch
	is used.

	* launcher.c: Generation of event streams from gaussians possible
	by passing the -f rand switch to the launcher. If no parameter is
	provided then the default muparser version is used which takes the
	function in the paramfile. Function generation is done using the
	-r switch. Adding -R outputs gaussians in their raw forms, and
	including an input file with one-dimensional data has the program
	centre a gaussian on each point.

2013-02-01  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.c: Added struct to make adding switches easier. Split
	multi-estimate function into gaussian and other estimators since
	return types are different.

	* generator.c: Random functions can now be generated with the -r
	switch. Still untested, but appears to work as intended. Another
	function for gaussians also implemented, but not sure of what
	functionality it should have. One function is required to generate
	random functions for experimenting on, the other is used to
	generate gaussians from event data to use in gaussian estimates?

	* file_util.c: Function for outputting double_multi_arr struct.

	* math_util.c: Fixed cause of crash on fclose when calling the
	gauss_transform function - data was being written to un-malloced
	locations. Changed return type of gaussian transform to struct to
	make it easier to work with. Gaussian transform needs some kind of
	normalisation parameter so that it outputs data int the correct
	range for the function it is being used to estimate. Attempted to
	implement kernel density estimation, but still unsure of how to
	proceed.

	* estimator.c: New file can be run by calling the estimator with
	the -a gauss switch. Multiple stream estimates are also possible.

	* estimator_gaussian.c: New estimator which uses kernel density to
	estimate functions. Prototype functions implemented.

	* makefile.am: Dependencies for new file added.

	* defparams.h: Added gaussian estimation and generation
	parameters.

	* general_util.c: Added writing of gaussian parameters to default
	paramfile.

	* params.txt: Gaussian estimation and generation parameters split.

2013-01-31  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* file_util.c: Extremely weird bug where crash occurs on fclose
	discovered.  Not sure how to solve yet. Functions to read and
	write gaussians with mean, stdev and weight representation, along
	with tests.

	* struct.h: Header file for structs to prevent interdependencies
	causing compilation issues.

	* defparams.h: Default gaussian parameters

	* general_util.c: Gaussian parameters added to default paramfile
	generation.  Functions for printing and freeing gaussian vectors.

	* params.txt: Added gaussian parameters


2013-01-30  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* check_math_util.c: tests for the new functions

	* math_util.c: Function for generating a vector initialised with
	the same values, finding the minimum value in an array, adding a
	constant to an array.

	* launcher.c: Can generate gaussians from the launcher into output
	files.

	* generator.c: Generation functions for gaussians. Output data to
	files.

	* general_util.c: Parameters for gaussians added to default file
	generation.

	* file_util.c: Gauss transform output can be shifted along the y
	axis.

2013-01-29  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* file_util.c: Wondering whether to allow parameters without
	values specified. Makes having to specify loads of parameters in
	the experiment paramfile unnecessary if you just want to run
	experiments on one part of the system.

	* experimenter.c: Function to parse parameters from a string of
	comma separated values. If the string contains a range indicator
	(...), then it will revert to the function to calculate the range.
	Experimenter structure changed. Requires parameters to be defined
	for all the parts of the system you want to experiment
	with. Checks whether these parameters exist in the
	paramfile. Still a work in progress.

	* general_util.c: Function to check whether parameters in a string
	array are present in a paramlist.

2013-01-28  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* general_util.c: Modified split_string function and its tests.

	* experimenter.c: Completed range parsing functions, with tests.
	Experimenter now takes two parameter files to read - one to read
	default parameters, and one for its own use. Checks that some
	required parameters are present.

	* exp_param.txt: Added some parameters that make sense to use.

	* check_file_util.c: Test for create file function.

	* file_util.c: Added function for creating files within
	directories.  Fixed crash when parameter in paramfile does not
	have a value.

2013-01-27  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* math_util.c: Error checking on parameters for some gaussian
	functions

	* check_math_util.c: Added tests for gaussian-related code

	* combinefunction.c: Basic error checking added.

	* tests: Tests for combining functions.

2013-01-26  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* GMP: Removed use of GMP in math library - necessary
	functionality available in GSL.

	* estimator_piecewise.c: Replaced custom probability mass function
	with the function from the GSL.

	* math_util.h: Fixed bug in gaussian transform calculation, split
	some functions to get more control over what goes on.

	* file_util.h: Added functions for outputting gaussians and
	discrete Gaussian transforms to file. Moved includes into header
	file.  Function for writing one of the new structs to file.

	* launcher.c: multi-estimate data should go to specified output
	file.

	* general_util.c: Parameter for step used when going through data
	added

	* general_util.h: Added some structs to make array length storage
	easier.

	* combinefunction.c: Function used to combine functions now works
	as it should, returning an array containing data to use.

2013-01-25  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* generator.c: Changed random number function usage to echo below
	changes.

	* configure.ac: Added checks for GSL library

	* math_util.c: Switched to using GSL to generate random numbers.
	Implemented discrete Gaussian transform with some structs to store
	Gaussians in a clean way. Various functions for initialising
	vectors of gaussians.

2013-01-23  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.c: Updated to reflect changes to functions in
	combinefunction.c

	* combinefunction.c: Implemented a basic function
	combinator. Current implementation is rough and outputs to a file
	specified within the code.

2013-01-20  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* launcher.c: Estimation of multiple streams at once by the
	launcher. Updated switches to allow for this. Some commenting and
	more checking for null values.

	* combinefunction.c: Function skeletons for combining functions.

	* makefile.am: Added new file and dependencies generated by it to
	launcher.

	* scripts: Removed unused plotting scripts. Obsoleted by
	plotmaster.

	* estimators: All now return an est_arr rather than some returning
	est_data.  Easier to integrate with the launcher and other parts
	of the system.

	* memory: Fixed some leaks caused by swath of changes, and some
	old ones.

2013-01-19  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* headers: Moved headers around in some files in src. Launcher
	strings moved into header file.

	* src/makefile.am: No longer includes muparser. Correctly added by
	configure.ac.

	* configure.ac: Checks for correct version of muparser.

	* plotmaster.sh: Plots data from the new plot

	* plots: Gnuplot code for plotting two estimates added


2013-01-13  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* paramlist.c: Added functions for setting the value of parameters
	in the list.

	* file_util.c: Modified file generator to take parameters.

	* generator.c: Added helper function to extract parameters from a
	parameter file.

	* estimator_piecewise.c: Fixed bug with estimation data from the
	first subinterval not being output to file. Minimum length of
	interval now in place for piecewise estimate. Affects the baseline
	estimator as well.

	* defparams.h: New header file containing default parameters for
	estimators and generator.

	* general_util.c: Added a function for generating a default
	parameter file, moved in function for checking parameters in a
	list.

2013-01-11  Michal Staniaszek  <mxs968@cs.bham.ac.uk>

	* estimator_piecewise.c: Removed preprocessor variables and
	modified functions to take additional parameters instead.

	* estimators: Added a helper function to the estimators so that
	you do not have to call them with all the parameters specified if
	it is not necessary.  You can now pass in a parameter list
	containing the relevant parameters, which will be extracted and
	passed into the function.

	* tests/Makefile.am: Tests can now be compiled using `make check`

	* tests/check_estimator.c: Added a basic test for estimator.c

	* tests/testmain.c: Added estimator test suite.

	* AUTHORS: Added name

	* ChangeLog: Put some actual stuff in it.

	* NEWS: Very brief information about releases.

	* README: Added basic information.