ShihChengChangeLog.txt

September 20, 2001
ContoursPlotUnleavedSpikes: Changed if statements to compare target 
	string directly instead of setting a flag.
ContoursNeuCalPSTH: New function.

September 24, 2001
ContoursNeuCalPSTH: Uses duration field in newly modified unleaved 
	spikes structure to set up timebins for histogram. Timebins	are also
	saved for use by ContoursNeuPlotPSTH.
ContoursNeuPlotPSTH: New function. Plots PSTH according to salience 
	conditions.	Uses same format as ContoursPlotUnleavedSpikes.
ContoursUnleaveSpikes: Added duration to unleaved spikes structure to 
	make it easy for ContoursNeuCalPSTH to compute max duration.

October 17, 2001
Contents: Fixed typo in ContoursPlotResult.
ContoursUnleaveSpikes: Fixed omissions in help comments.
ContoursUnleaveSignals: New function.
ContoursPlotUnleavedSignals: New function.
ContoursNeuPlotPSTH: Moved axis adjustment out of the if loop since it 
	is common to both conditions.

October 19, 2001
ContoursReadIniFile: Consolidated return arguments into SESINFO. 
ContoursUnleaveSequence: Updated to use SESINFO.
ContoursUnleaveSignals: Updated to use SESINFO and also now takes the
	signal name as an argument.

October 23, 2001
ContoursUnleaveSpikes: Updated to use SESINFO.

October 24, 2001
ContoursUnleaveMarkers: Updated to use SESINFO.
ContoursPlotUnleavedSignals: Changed catch argument to argcatch to
	prevent conflict with builtin catch argument.
ContoursPlotUnleavedMarkers: Added argcatch argument and code to plot 
	markers from catch trials.

October 25, 2001
ContoursPlotUnleavedSpikes: Updated help comments. Fixed bug in
	determining salience steps and repetitions. Added 'allcatch'
	argument to plot all catch trials.
ContoursPlotResultSpikes: New function.
ContoursNeuCalPSTH: Added allcatch field in structure.
ContoursNeuPlotPSTH: Added 'allcatch' as argument which will plot all
	catch trials instead of subdividing into locations.
ContoursBehGetResults: Updated to use SESINFO. 

October 26, 2001
ContoursPlotUnleavedSpikes: Now plots dividing line before plotting 
	allcatch trials. Updated so this function can be used to plot 
	unleaved spikes as well as result spikes. 
ContoursNeuPlotPSTH: Reverse plot orders so it matches raster plots. 
	Renamed to ContoursPlotPSTH.
ContoursNeuCalPSTH: Renamed to ContoursCalPSTH.
ContoursGetResultSpikes: New function to sort unleaved spikes into 
	correct and incorrect trials.
ContoursPlotResultSpikes: Function replaced by ContoursGetResultSpikes 
	and ContoursPlotUnleavedSpikes.
					
October 28, 2001
ContoursPlotUnleavedMarkers: Renamed to ContoursPlotMarkers.
ContoursPlotUnleavedSpikes: Renamed to ContoursPlotSpikes.
ContoursPlotUnleavedSignals: Renamed to ContoursPlotSignals.
ContoursGetSessionInfo: Updated to get min duration using the updated
	nptReadSorterHdr.
				
October 29, 2001
ContoursPlotSignals: Fixed bug with saliencesteps. Updated to use 
	'allcatch' argument. Now will check for reps before plotting so as 
	to be compatible with all signals or results signals. Added	check for
	allcatch field to plot signals for all catch trials together.
ContoursGetResultSignals: New function. Added allcatch field to group the
	signals for all the catch trials together. Added sampling_rate to the 
	data structure.
ContoursUnleaveSignals: Added sampling_rate argument to allow for 
	subsampled data to be processed properly. Added sampling_rate to the 
	data structure.
ContoursGetResultSpikes: Added allcatch field to store spikes from all 
	catch trials regardless of the result of the trial.
ContoursPlotSpikes: Added check for allcatch field to see if we are 
	plotting spikes or results spikes. Now plots all catch trials 
	regardless or result if 'allcatch' argument is used.
ContoursCalPSTH: Now checks for existence of allcatch field and computes 
	psth for all the catch trials.
ContoursAverageSignals: New function to average signals for all salience 
	conditions. Uses similar data structure to signals so we can use 
	ContoursPlotSignals to look at the data.
ContoursGetResultMarkers: New function to arrange markers according to 
	result of the trial.
ContoursPlotMarkers: Added 'allcatch' argument. Now uses reps in data 
	structure so we can use this function to plot markers and result 
	markers. Removed clf to allow more flexible plotting.
				
October 30, 2001
ContoursCombineSpikes: New function to combine spikes from multiple 
	sessions. (Incomplete).
ContoursInspectEyes: New function to inspect eye movements.
ContoursPlotSpikes: Removed clf call to allow for more flexible plotting.
ContoursUnleaveSequence: Updated to use SESINFO.
ContoursGetResultSequence: New function to return sequence sorted by 
	result of the trial and salience conditions.
ContoursExtractSpikeTimes: Extract the times of the first spike after a 
	specified latency.
ContoursExtractEyeData: Extract the eye position for a range of times.

November 1, 2001
ContoursPlotPSTH: Removed clf to allow more flexible plotting.
ContoursPlotSignals: Removed clf to allow more flexible plotting.
ContoursCalOriTuning: New function to calculate orientation tuning 
	functions.

November 8, 2001
ContoursGetResultSpikes: Now checks for catch trials before trying to
	access catch trial data.
ContoursGetResultSignals: Now checks for catch trials before trying to
	access catch trial data.
ContoursAverageSignals: Now checks for catch trials before trying to
	access catch trial data.
ContoursGetResultMarkers: Now checks for catch trials before trying to
	access catch trial data.

January 29, 2002
@sesinfo: New class that reads INI file and instantiates SESINFO object.
@sesinfo/sesinfo: Constructor function for SESINFO object.
@sesinfo/display: Display method for SESINFO object.
@sesinfo/subsref: Indexing method for SESINFO object.
@sesinfo/private/ContoursReadIniFile: Function that is now a private
	function since this is used only by the constructor function.
@markers: New class that reads MRK file and instantiates MARKERS object.
@markers/markers: Constructor function for unleaved MARKERS object.
@markers/display: Display method for MARKERS object.
@markers/plot: Used to be ContoursPlotMarkers. Now draws lines between
	stimulus conditions and modifies the tick marks accordingly.
@markers/private/unleave: Used to be ContoursUnleaveMarkers. Now uses 
	SESINFO object to get sequence.
@markers/private/ContoursReadMarkerFile: Function is now private since
	it is used only by the constructor.
@markers/private/ContoursMarkersToTrials: Function is now private since
	it is used only by the constructor.
	
January 30, 2002
@sesinfo/sesinfo: Added help comments. Changed call to 
	ContoursReadIniFile to ReadIniFile.
@sesinfo/private/ReadIniFile: Renamed from ContoursReadIniFile.
@markers/markers: Changed call to ContoursReadMarkerFile to 
	ReadMarkerFile and ContoursMarkersToTrials to MarkersToTrials. Added
	session field.
@markers/private/ReadMarkerFile: Renamed from ContoursReadMarkerFile.
@markers/private/MarkerToTrials: Renamed from ContoursMarkersToTrials.
@markers/subsref: New method to index data in MARKERS object. Added 
	access to session field.
@markers/display: Added session field.
@performance: New class that computes and store the mean and sd for 
	different stimulus conditions.
@performance/performance: Constructor function for PERFORMANCE object.
@performance/display: Display function for PERFORMANCE object.
@performance/subsref: Indexing method for PERFORMANCE object.

January 31, 2002
@sesinfo/subsref: Added access to stim_p field.
@sesinfo/diff: New function to list differences between SESINFO objects.
@performance/plus: New function to combine PERFORMANCE objects.
@performance/private/MarkersToPerformance: Moved calculation of 
	population statistics to ComputeMeanStdev function.
@performance/private/ComputeMeanStdev: New private function to compute 
	population statistics which can be called by other functions like 
	plus.

February 4, 2002
@performance/plot: New function to plot performance curves.
Contents: Updated to list new classes and functions.

February 6, 2002
@sesinfo/private/ReadIniFile: Renamed sequence field to isequence.
@sesinfo/sesinfo: Added call to unleave function. This way unleave is 
	only done in one function instead of being scattered throughout.
@sesinfo/private/unleave: New function that unleaves the trial sequence 
	and stores it in the sequence field.
@sesinfo/display: Updated to indicate new sequence access.
@sesinfo/subsref: Updated to return trial number given salience condition
	and repetition number.

February 7, 2002
@performance/plot: Added hold off at the end of the function.
@sesinfo/ReadIniFile: Fixed typo in transient field.
@sesinfo/diff: Changed display calls to fprintf to improve formatting.

March 4, 2002
@sesinfo/private/ReadIniFile: Now calls ReadIniGabor, ReadIniTiming, and 
	ReadIniSequence	to read the appropriate sections. Also passes empty
	string to the these functions so that the right structure is returned 
	in the case when the null constructor is called.
@sesinfo/private/ReadIniGabor: Now checks version information to figure 
	out	what needs to be read in. Added some reordering in order to keep 
	the field order the same for different versions. Also returns empty 
	data structure when -1 is passed as the fid.
@sesinfo/private/ReadIniTiming: Now checks version information to figure 
	out	what needs to be read in. Added some reordering in order to keep 
	the field order the same for different versions. Also returns empty 
	data structure when -1 is passed as the fid.
@sesinfo/private/ReadIniSequence: Now checks version information to 
	figure out what needs to be read in. Depending on the verion, 
	different unleave functions are called. Also, if contourtype is not 
	interpolated i.e. probably a psychophysical session, unleavePsych is 
	called. Also returns empty data structure when -1 is passed as the 
	fid.
@sesinfo/private/unleave: Updated to new object structure that supports
	stimulus repetitions, which means that repetition is now a member of 
	stimlus, which is a member of contour/control/catchcontour/catchcontrol.
	Also unleaves tuning stimuli if present.
@sesinfo/private/unleave1: New function to read and unleave stimulus 
	sequence version 1.
@sesinfo/private/unleavePsych: New function to read and unleave stimulus
	sequence for non-interpolated contours, i.e. probably for 
	psychophysics.
@sesinfo/sesinfo: Now calls ReadIniFile to read and unleave stimulus. 
	Also passes empty string to ReadIniFile when the null constructor is 
	called.
@sesinfo/subsref: Updated to handle new data structure.
@sesinfo/diff: Updated to handle new data structure.
@sesinfo/display: Updated to handle new data structure.
@markers/subsref: Updated handle new sesinfo structure. Removed need to 
	reference catchcontour/catchcontrol with salience value of 1.
@markers/plot: Updated to handle new sesinfo structure.
@markers/private/unleave: Updated to handle new sesinfo structure.
@performance/private/MarkersToPerformance: Updated to handle new sesinfo 
	structure.

March 12, 2002
@sesinfo/private/ReadIniFile: Added presenterversion field to sesinfo as 
	well as code to read the field from INI file.
@sesinfo/display: Added presenterversion.
@sesinfo/subsref: Added presenterversion.
@sesinfo/diff: Added presenterversion.

March 15, 2002
@markers/plot: Added code to check for presence of control trials so
	we can use with psychophysical sessions.
@markers/private/unleave: Added code to check for presence of control 
	trials so we can use with psychophysical sessions.
@performance/performance: Modified structure to allow storage of multiple
	sessions. 
@performance/private/MarkersToPerformance: Updated to new structure with
	multiple sessions. Now totals results before calling 
	ComputeMeanStdev. Now checks for control trials so we can use with 
	psychophysical sessions.
@performance/private/ComputeMeanStdev: Updated to new structure with
	multiple sessions. Now just computes mean and stdev. Also checks for 
	control trials so we can use with psychophysical sessions.
@performance/display: Updated for new data structure.
@performance/plot: Added code to check for presence of control trials so 
	we can use with psychophysical sessions. Added code to adjust the 
	axis so that the plot is centered on the graph.
@performance/plus: Added code to check for presence of control trials so 
	we can use with psychophysical sessions. Also totals up results 
	before calling ComputeMeanStdev. Removed addition of daysessions 
	field.
@performance/subsref: Modified code to be more efficient and readable.
@sesinfo/subsref: Modified code to be more efficient and readable.

April 25, 2002
ContoursCheckPresenterTiming: New function to scan and extract problems
	identified in the syncs and scanlines files.

August 5, 2002
@sesinfo/private/ReadIniGabor: Now checks entries representing checkboxes
	and sets any disabled entries controlled by checkboxes to default values.
@sesinfo/private/unleavePsych: Added code to handle repeats.

August 16, 2002
@markers/plot: Fixed bug in getting repetition value in control section
	of the code. Added code to generate appropriate legend.
@performance/plot: Added code to generate legend when plotting results 
	from neural sessions.

August 27, 2002
@sesinfo/private/ReadIniFile: Changed .INI to .ini to work better with 
	unix. We have tolower script that converts uppercase names to lowercase
	so everything should be lowercase.

October 6, 2002
@sesinfo/ReadIniSequence: Put sequence found in INI file into isequence for
	use by view functions in NPT.
@sesinfo/subsref: Added function to access isequence field. Changed 'session'
	field to 'sessionname'.
@sesinfo/display: Changed 'session' to 'sessionname' and added 'isequence'.
@eyestarget/eyestarget: New class to inspect eye traces along with target 
	locations.
@eyestarget/display: New function.
@eyestarget/plot: New function.
@eyestarget/subsref: New function.
@eyetarget/private/GetTargetLocation: Function to read target location 
	from stimulus file.

October 9, 2002
GetTargetLocation: Added comments.

October 13, 2002
ContoursPresenterTiming: Renamed from ContoursCheckPresenterTiming. Removed
	session name argument. Now gets session name from the files in the 
	current directory.
@sesinfo/sesinfo: Removed session name argument. Now gets the session name
	from files in the current directory.
@eyestarget/eyestarget: Updated comments.

October 15, 2002
@eyestarget/eyestarget: Now loads timing.mat as well to get stimulus onsets.
@eyestarget/plot: Modified title to get rid of subscripting problem. Now 
	includes analysis of eye positions.

October 16, 2002
ContoursTrialResultTiming: New function that computes outcome of trial
	as well as timing events.
@eyestarget/plot: Now calls ContoursTrialResult and prints output from
	the function to the command window.
@sesinfo/sesinfo: Replaced strfind command with findstr since strfind 
	does not exist in Matlab 5.3.
ContoursSessionsDiff: New function to compare sessions on CDs.

October 17, 2002
isEyeCal: New function to check to see if ini file in current directory
	is an eye calibration session. Uses system('grep ...') so will only
	work on UNIX right now.
ContoursSessionsDiff: Modified to use isEyeCal. Run from /Volumes 
	directory which means it might only run in OS X, but might run fine
	on other UNIX as well.

October 18, 2002
@sesinfo/private/ReadIniFile: Modified to take filename instead of 
	appending suffix in the function. This will allow analysis of 
	INI files that did not have their names changed to lowercase.

October 19, 2002
@sesinfo/sesinfo: Fixed bug that failed to pass full filename to 
	ReadIniFile.

October 21, 2002
ContoursMoveEyesFiles: Move files in Eyes directory session by session
	when the number of files in the Eyes directory exceeds limits of mv.

October 23,2002
ContoursCopyDescriptors: New function to copy descriptor files to
	days without descriptor files.

October 24, 2002
@eyestarget/subsref: Now passes unknown fields to parent object.

October 25, 2002
@eyestarget/eyestarget: Turned off holdaxis property in nptdata parent 
	object.
isEyeCal: Added optional arguments in case ini suffix is not lowercase.
ContoursSessionsDiff: Added code to handle old data hierarchy. Also calls
	isEyeCal now with filename of ini file.

October 28, 2002
ContoursMoveEyesFiles: Added day string to move command so files that
	don't have a period immediately following the session numbers will
	be moved as well.

October 29, 2002
ContoursCopyDescriptors: Modified to take list of directories to work on.

October 30, 2002
ContoursRenameSession: New function to rename files from disco080202 which
	had an extra 0 in the session name: disco080202001, etc. 

October 31, 2002
@sesinfo/sesinfo: Added 'CaseInsensitive' to nptDir call.
@eyestarget/eyestarget: Fixed bug that failed to instantiate eyes object
	using 'pixels' as units.

November 14, 2002
@sesinfo/private/ReadIniTiming.m: Fixed order of fixlimit field when
	ini_fid == -1.
@sesinfo/sesinfo: Now uses grep to make sure INI file is for a
	Gabor session.
@eyestarget/ProcessSession: New method for batch processing whole 
	session.
@eyestarget/ProcessTrial: New method called by ProcessSession to
	return data for each trial.

December 4, 2002
ContoursReadTargetLocations: New function that reads all target 
	locations from stimuli file.

January 27, 2003
@eyestarget/eyestarget: Modified to use ContoursReadTargetLocations.
@eyestarget/display: Modified to show correct fields.
@eyestarget/plot: Modified to use targets returned by 
	ContoursReadTargetLocations.
@sesinfo/sesinfo: Modified grep call to use -s to suppress error
	about directories.
@markers/private: Deleted ReadMarkerFiles and MarkersToTrials. Will
	now use npt/scripts/read_files/ReadMarkerFiles and 
	Contours/ContoursMarkersToTrials, which are more generally 
	accessible.
@markers/markers: Modified to use ReadMarkerFiles and
	ContoursMarkersToTrials.
ContoursMarkersToTrials: Fixed bug in signal numbers in case 
	statements. Now stores time of correct or incorrect marker as well.
@eyestarget/ProcessTrial: Modified to use targets returned by 
	ContoursReadTargetLocations.

January 28, 2003
@eyestarget/ProcessTrial: Fixed bug that used et instead of obj as name
	of object. Now also returns markers as part of data. 

January 30, 2003
@sesinfo/sesinfo: Added isequence and ulsequence.
@sesinfo/display: Added ulsequence field.
@sesinfo/ReadIniSequence: Added ulsequence and added comments about
	stim_info.sequence being filled by unleave functions.
@sesinfo/private/unleave: Now uses ulsequence instead of isequence.
@sesinfo/private/unleave1: Now uses ulsequence instead of isequence.
@sesinfo/private/unleavePsych: Now uses ulsequence instead of isequence.
@sesinfo/subsref: Added code to access ulsequence.

February 3, 2003
@eyestarget/eyestarget: Added code to check for batch argument.
	New fields added and initialized by default. Targets field is now 
	unleaved.
@eyestarget/ProcessTrial: Added code to store calculated values in
	object. Now returns object as well as calculated values. Now uses
	unleaved targets field.
@eyestarget/ProcessAllTrials: New function to compute data for all
	trials. Visual feedback while in loop added.
@eyestarget/ProcessSession: Modified to accomodate changes in
	return types in ProcessTrial.
@eyestarget/display: New fields added.
@eyestarget/subsref: Modified to support new fields. Now returns 
	error status to allow support for passing subsref to parent
	objects when multiple inheritance is involved.
@eyestarget/plot: Now uses unleaved targets field.
@eyestarget/display: Function removed.
@eyestarget/displayfields: New overloaded function that displays
	fields from parent objects in addition to those created in this
	object.
@sesinfo/sesinfo: Changed name of session field in comment to 
	sessionname.
@sesinfo/private/ReadIniFile: Changed name of session field to
	sessionname to be consistent with nptdata.
@sesinfo/subsref: Now returns error status when called by other
	functions and prints error only when called directly to support
	multiple inheritance. Field name changed from session to 
	sessionname.
@sesinfo/display: This function is now inherited by all children
	objects and it is the displayfields that is overloaded.
@sesinfo/displayfields: New function that is called by display and is
	overloaded for child objects.
@performance/performance: Added code to process eyestarget object.

February 4, 2003
@performance/private/EyesTargetToPerformance: New function to create
	performance object from eyestarget object.
@sesinfo/subsref: Modified to return stim steps for contour, control,
	catchcontour, and catchcontrol. 
@eyestarget/subsref: Moved length command outside loop
	to reduce redundency.

February 5, 2003
@sesinfo/subsref: Modified to return unleaved sequences for contour, 
	control, catchcontour, and catchcontrol. Will also return portions
	of sequences within these categories.
@eyestarget/subsref: Modified to return results for contour, control,
	catchcontour, and catchcontrol. 
@eyestarget/ProcessTrial: Now stores data in column vectors instead
	of row vectors to make it more readable.
@eyestarget/eyestarget: Added code to check local directory and parent
	directory for INI files if called without arguments. Moved 
	repeated code to internal function ReadStimuliMarkersTargets.
	
February 6, 2003
@performance/plus: Fixed code that adds session structure.
@timing: New class for computing reaction times.
@timing/timing: Constructor for new timing class.
@timing/private/EyesTargetToTiming: New function to extract timing data
	from eyestarget object.

February 7, 2003
@timing/subsref: Subsref function for new timing class.
@timing/private/EyesTargetToTiming: Added median and quartiles for each
	session.
@timing/timing: Added median and quartiles fields to each session.
@timing/display: Display function for new timing class.

February 9, 2003
@eyestarget/eyestarget: Changed default to process all trials. The
	optional argument is now 'nobatch'.

February 10, 2003
@timing/plot: New function that plots timing data for new timing class.
@timing/timing: Timing class now derived from eyetarget class so timing
	class has access to sesinfo.
@timing/displayfields: Overloaded function that displays unique class
	fields.
@timing/display: Removed.
@timing/subsref: Now passes unknown arguments to eyestarget class. Added
	output argument to indicate error state.
@performance/performance: Now derived from eyestarget class so performance
	class has access to sesinfo. Removed code to create performance object
	from markers object.
@performance/displayfields: Overloaded function that displays unique class
	fields.
@performance/display: Removed.
@performance/subsref: Now passes unknown arguments to eyestarget class.
	Added output argument to indicate error state.
@performance/private/MarkersToPerformance: Removed.
@performance/plot: Now uses stim_p from data structure inherited from
	eyestarget object. Added x- and y-labels. Modified x ticks to match
	stim_p. Now takes input argument for session to plot.
@timing/EyesTargetToTiming: Fixed bugs in the storage of catch trial data.
	Added code to check for conditions with no successful trials.
@performance/plus: Added code to check similarity of objects before
	merging them.
@timing/plus: New function to merge timing objects.

February 11, 2003
@performance/private/ComputeMeanStdev: Added code to compute mean and std
	for combined objects.
@performance/performance: Added code to set Number and HoldAxis properties
	in nptdata parent object.
@performance/plus: Added code to update Number property in nptdata parent
	object.
@performance/ProcessSession: Modified to check for saved eyestarget and
	performance objects.

February 12, 2003
@performance/plus: Added check for empty objects.
@performance/performance: Added code to explicitly create empty object.
	Moved creation of empty object to separate function. Added code to 
	create empty peformance object if eyestarget is empty.
@performance/ProcessSession: Added code to check for fake eye calibration
	sessions. Now uses new function ispresent instead of exist. Now
	returns empty object if skip.txt or marker file exists.
@performance/plot: Added code to process optional arguments. Improved
	code to handle legends. Now can plot overall data as well as session
	data. User can now specify which data to plot.
@eyestarget/eyestarget: Added code to explicitly create empty object using
	null argument. Moved creation of empty object to separate function.
@sesinfo/private/ReadIniSequence: Fixed order of fields in when creating
	empty object.

February 13, 2003
@performance/plot: Fixed legend strings for overall plots. Added cla 
	command to clear plots before hold on command.
@eyestarget/eyestarget: Added code to check for empty sesinfo object
	before trying to create eyes object.
@performance/ProcessSession: Added code to check for empty eyestarget
	objects returned from eye calibration sessions.
@sesinfo/isempty: New function to check for empty object.
@eyestarget/isempty: New function to check for empty object.

February 17, 2003
@sesinfo/display: Removed extraenous "trials" in printout message.

February 19, 2003
@performance/ProcessSession: Added 'reuseeyestarget' optional argument.

February 20, 2003
ContoursTrialResultTiming: Added some comments to remind myself that
	this function works with data that might be missing end data.
@performance/subsref: Added access to .session(1).sessionname.
@performance/useProcessedMarker: New function to indicate that this
	class does not use a processed marker file.
@performance/ProcessSession: Modified to use checkMarkers and
	createProcessedMarker.

February 27, 2003
@performance/plot: Updated help comments to explain new options.

February 28,, 2003
@eyestarget/diffResults: New function to return differences in marker
	results versus eyes results.
@eyestarget/eyestarget: Modifed to check for presence of marker file.	
@eyestarget/ProcessTrial: Modified to check for empty tmarkers field
	in the event that there was no marker file.
@performance/ProcessSession: Modified to call eyestarget/diffResults.
	Added CaseInsensitive argument to ispresent when checking for
	presence of eye directory.

March 1, 2003
@performance/plotGroups: New function to plot grouped performance data.

March 3, 2003
@sesinfo/sesinfo: Modified to create empty object when there are no
	arguments so load will work properly. Now uses 'auto' argument
	when we want it to figure out the session name. Also uses ispresent.
@eyestarget/eyestarget: Modified to create empty object when there are no
	arguments so load will work properly. Now uses 'auto' argument
	when we want it to try to create sesinfo and eyes objects.
@eyestarget/ProcessSession: Updated to new format using checkMarkers and
	createProcessedMarker.
@performance/performance: Modified to create empty object when there are 
	no arguments so load will work properly. Now uses 'auto' argument
	when we want it to try to create the object automatically.
@performance/ProcessSession: Updated to use new constructor.

March 10, 2003
@sesinfo/sesinfo: Now checks for sesinfo.mat and loads it when present
	with the 'auto' option. Added save and redo options to save newly
	created objects and to recreate object even if sesinfo.mat is
	present.

March 11, 2003
@sesinfo/sesinfo: Now checks for 'redolevels', 'savelevels', 'redo',
	and 'save' optional arguments.
@eyestarget/eyestarget: Now checks for 'redolevels','savelevels','redo',
	and 'save' optional arguments. Now creates sesinfo object only in the
	parent directory and checks to see if it is empty before trying to
	create eyestarget object. Now passes remaining varargin to sesinfo
	when creating sesinfo object.
@eyestarget/ProcessSession: Updated to work with new constructor. Now
	only checks to see if there is a skip file in the session directory.
@eyestarget/plus: New function that attempts to return non-empty object
	just so we can use batch functions with eyestarget class.
@performance/performance: Now checks for 'redolevels','savelevels','redo',
	and 'save' optional arguments. Now passes remaining varargin to 
	eyestarget when creating eyestarget object.
@performance/ProcessSession: Updated to work with new constructor. Now
	only checks to see if there is a skip file in the session directory.
@timing/timing: Now checks for 'redolevels','savelevels','redo',
	and 'save' optional arguments. Now passes remaining varargin to 
	eyestarget when creating eyestarget object.
@timing/ProcessSession: Updated to work with new constructor. Now
	only checks to see if there is a skip file in the session directory.
@timing/private/EyesTargetToTiming: Corrected "Dependencies" in help
	comments to "None".

March 12, 2003
@performance/plus: Now uses sessions field of input objects instead of 
	calling size.
@timing/timing: Removed daysessions field. Rearranged object fields so
	most of the data falls under the data field in order to simplify
	initialization of empty objects. 
@timing/subsref: Removed references to daysessions field.
@timing/EyesTargetToTiming: Removed daysessions field. Now stores timing
	in 1 array instead of in separate sessions. Added indexses field to
	keep track of which values are associated with each session. Added 
	fields to store medians and quartiles for each session. Now stores
	quartiles using 3 dimension arrays to simplify access.
@timing/plus: Makes use of the new way of storing reaction times to
	simplify calculating overall stats for merged data.

March 13, 2003
@timing/EyesTargetToTiming: Changed overall quartiles to 2D array
	of 3D since we don't need 3D at all.
@timing/plus: Modified to use 2D array in overall quartiles.
@timing/subsref: New function access timing object.
@timing/displayfields: New function that displays the fields accessible
	via subsref.

March 14, 2003
@performance/plot: Added catchstep optional argument. Updated help 
	comments to add catch step argument. Added ischar check to 
	optional arguments and removed redundant index arithmetic.
@timing/EyesTargetToTiming: Now saves median-quartile25 and
	quartile75-median instead.
@timing/plus: Now saves median-quartile25 and quartile75-median instead.
	Now checks for empty objects and updates the Number field in 
	nptdata.

March 17, 2003
@timing/plus: Fixed bug that left out semi-colons after some lines.
	Fixed bug in merging indexes.
@timing/plot: New function that plots timing data.
@timing/timing: Turned HoldAxis off by default. Fixed bug that 
	failed to save object. Changed name of output variable so it is 
	consistent with saved object name.
@eyestarget/eyestarget: Fixed bug that failed to save object in all
	but 1 case. Added code to change directory into the eye sub-dir
	if we are not there initially and to change back when we are 
	done so that batch programs will still work as expected. Changed
	name of output variable so it is consistent with saved object
	name.
@peformance/performance: Fixed bug that failed to save object. Changed
	name of output variable so it is consistent with saved object
	name.

March 18, 2003
@eyestarget/eyestarget: Now prints out class name when loading or
	saving objects. Added call to diffResults when a new eyestarget
	object is created.
@eyestarget/plot: Added check for sessions with no marker files.
@sesinfo/sesinfo: Now prints out class name when loading or saving 
	objects. Fixed bug that failed to save object in some cases.
@performance/performance: Now prints out class name when loading or saving 
	objects.
@timing/timing: Now prints out class name when loading or saving objects.
@timing/plotGroups: New function that plots contour reaction times
	versus reaction times for case with no background and for case
	with just a dot.

March 19, 2003
@timing/plot: Added title to plots when plotting session data.
@timing/plotGroups: Now plots legend in the bottom right corner, labels
	the XTicks properly, and turns hold off at the end.
@timing/plus: Fixed bug that omitted 's' argument in input function 
	call.
@eyestarget/eyestarget: Added 'CaseInsensitive' argument to ispresent
	call to handle eye directories that are capitalized. Added 
	'CaseInsensitiveSuffix' to ispresent call to check for presence
	of marker file.
@performance/plus: Fixed bug that omitted 's' argument in input 
	function call.

March 22, 2003
@performance/plot: Fixed bug in processing optional arguments. Added
	'sessionmeans' optional argument to plot means of individual
	sessions.
	
March 23, 2003
@performance/subsref: Added .contourmean.sessions option to obtain 
	session means. Also works for all other mean values.

March 24, 2003
@performance/plotDist: New function that plots distribution of session
	means.

March 25, 2003
@performance/plotGroups: Switched placement of open and closed plots.
	Added hold off at the end of each subplot.
@performance/plot: Added help comment for 'sessionmeans' option. Added
	missing N argument in help comments.
@timing/plot: Added help comments.

March 26, 2003
@timing/plot: Changed colors of plots of medians and quartiles to
	make them more visible. Fixed bug in parsing optional arguments.
	Fixed typo in plotting catch data.
@timing/plotDiff: Renamed from plotGroups.
@timing/plotGroups: New function that plots reaction times for different
	stimulus conditions.

March 27, 2003
@sesinfo/sesinfo: Added fixx and fixy fields to help comments.
@sesinfo/displayfields: Added fixx and fixy fields.
@sesinfo/subsref: Added access to fixx and fixy fields.

March 28, 2003
@timing/plus: Updated help comments.
@bias: New class to look at angular biases.
@bias/bias: Constructor for new bias class.
@bias/private/EyesTargetToBias: New function to create bias object 
	from eyestarget	object.
@bias/plot: Plot function for new bias class.
@bias/plus: Plus function for new bias class.
@bias/subsref: Subsref function for new bias class.
@eyestarget/eyestarget: Updated help comments to better explain what
	happens in the 'auto' mode.

April 02, 2003
@bias/EyesTargetToBias: Changed internal data structure to more easily
	compute reaction times as well as performance for selected salience
	conditions.
@bias/plus: Updated to use new internal data structure.
@bias/plot: Updated to use new internal data structure. Added options	
	to plot reaction times, as well as selected salience conditions.
@bias/subsref: Updated to use new internal structure.
@bias/bias: Now calls EyesTargetToBias to create empty object when
	called with no arguments. Now renames object before saving.
@bias/displayfields: Displayfields function for new bias object.
@bias/ProcessSession: ProcessSession function for new bias object.
@bias/useProcessedMarker: Function for new bias object.

April 03, 2003
@bias/plot: Added 'flat' optional argument to display data using
	plot instead of polar. 

April 04, 2003
@bias/plot: Added optional argument to change plot symbols and colors. 
	Updated help comments.
@bias/plus: Added 'ignorediff' optional argument so that the function
	will continue running even if there are differences.

April 08, 2003
@bias/plot: Changed default color for session data to magenta and 
	black for overall data.

April 09, 2003
@bias/plot: Defined names for constants and plot symbols to make changes
	easier. Changed values used in nopolar plots for correct and incorrect 
	trials to make them clearer. Changed colors for correct and incorrect
	data points to cyan and magenta. Changed colors for session and overall
	data to blue and red.

April 29, 2003
@sesinfo/sesinfo: Added code to run grep on PC's.

April 30, 2003
@bias/plus: Updated help comments to include 'ignorediff' argument. Now
	also prints out warning when 'ignorediff' argument is used.
@performance/plus: Added 'ignorediff' optional argument.
@timing/plus: Added 'ignorediff' optional argument.

May 2, 2003
@timing/private/EyesTargetToTiming: Fixed typo that initialized 
	contour.indexes	instead of control.indexes.
@bias/plus: Fixed typo in fprintf command.
@performance/plus: Fixed typo in fprintf command.
@timing/plus: Fixed typo in fprintf command. Now sets medians and
	quartiles to 0 when there are no entries.

May 6, 2003
@timing/timing: Added 'CaseInsensitive' option to ispresent call.
@sesinfo/sesinfo: Added 'CaseInsensitive' option to ispresent calls.
@performance/performance: Added 'CaseInsensitive' option to ispresent calls.
@eyestarget/eyestarget: Added 'CaseInsensitive' option to ispresent calls.
@bias/bias: Added 'CaseInsensitive' option to ispresent call.

May 7, 2003
@eyestarget/ProcessTrial: Now passes match limit and eye tracker fixation
	duration to ContoursTrialResultTiming in case we are not using
	default values.
@sesinfo/subsref: Added access to matchlimit and etfix values.
@sesinfo/displayfields: Updated to reflect accessible fields.

May 11, 2003
@bias/subsref: Fixed missing close parentheses.

July 2, 2003
@eyestarget/plot: Updated to use match time limit and fixation criteria 
	to compute result of trial.

October 3, 2003
@performance/plot: Fixed error when plotting interpolated data without 
	catch trials.
@timing/plot: Fixed error when there are no correct trials, and hence
	no reaction times, in the first salience condition.

January 14, 2004
@sesinfo/private/ReadIniGabor: Added controlangle field from version
	3 of Gabor Contours Info from Presenter 1.53.
@sesinfo/diff.m: Now uses data structure to store fields so we 
	don't have to keep changing the object when new fields are added.
@sesinfo/display.m: Now uses data structure to store fields.
@sesinfo/isempty.m: Now uses data structure to store fields.
@sesinfo/subsref.m: Now uses data structure to store fields.
@sesinfo/private/ReadIniFile.m: Now uses data structure to store fields.
@sesinfo/private/ReadIniGabor.m: Now uses data structure to store 
	fields. Added controlangle field from version 3 of Gabor Contours 
	Info from Presenter 1.53.
@sesinfo/private/ReadIniSequence.m: Now uses data structure to store 
	fields.
@sesinfo/private/ReadIniTiming.m: Now uses data structure to store 
	fields. Added incorpenalty, incorpenaltymax, and rincorpenalty
	fields added in version 2 of timing section in Presenter 1.53.
@sesinfo/private/unleave.m: Now uses data structure to store fields.
@sesinfo/private/unleave1.m: Now uses data structure to store fields.
@sesinfo/private/unleavePsych.m: Now uses data structure to store 
	fields.

January 15, 2004
russ.m: Added script for Russ to easily check data. Updated to use
	cygwin to move files in ProcessDay and simplified to copy 
	descriptor files.
plottargets: New function to plot contour targets from stimulus.bin
	file.

January 20, 2004
@bias/plot: Added titles to plot.
russ.m: Updated scripts to save objects and to plot bias object by
	salience level.

January 26, 2004
@performance/plot: Modified sessionmeans option to plot session
	data using colors from the cool colormap while overall data is 
	plotted in black.

February 12, 2004
@timing/plot: Fixed bug in code drawing dividers between salience 
	conditions for trials where the target appeared in the control
	location.
@bias/private/EyesTargetToBias: Modified so it will also work with 
	sessions with interpolated contours.

February 16, 2004
@bias/plot: Added code to plot data from sessions with intepolated
	contours. Fixed bug that changed the axis limits and labeled the
	axis for 'flat' plots only if overall data is plotted.
@sesinfo/sesinfo: Now searches for the word Contour instead of Gabor
	since Gabor also now appears in the .seq file created by Sparse
	Noise. Now searches only *.ini and *.INI files instead of all
	files in directory.

February 18, 2004
@performance/plot: Modified code to fix bug in dealing with cx in 
	plotting data from interpolated contours. Code is also now more
	streamlined.

February 19, 2004
@sesinfo/loadobj: New function that converts old saved objects to
	the current object data structure and saves the new object.
@sesinfo/updateDataStructure: New function that is called by
	loadobj to do conversion from data structures of old objects
	to the current data structure.

February 20, 2004
@sesinfo/loadobj: Removed code to automatically save converted
	object since the function could be called while loading another
	object that contains an old sesinfo object and we might not be
	in the right directory to save the converted sesinfo object.

February 24, 2004
@bias/plot: Now uses actual match limit from sesinfo object stored
	in eyestarget object. Fixed bug that labeled the y-axis of both 
	types of flat plots as 'Performance'.

February 25, 2004
@bias/plot: Modified binsc so it drops the last value of bins before
	shifting by half the bin size to get center of bins. Added code to
	plot different salience levels in different colors. Added code
	so we use the same color when plotting one salience level and 
	plotting all salience levels. Now makes sure bins is a column 
	vector. 
@bias/plot0: Renamed old plot function.
russ: Modified to use new capabilities of nptdata to plot individual 
	sessions.
russ0.m: Renamed old russ function.

March 2, 2004
@eyestarget/plot: Added code to display data in 2D.
@sesinfo/subsref: Added access to width and height fields for use
	with @eyestarget/plot.
@sesinfo/displayfields: Added width and height fields.

March 5, 2004
@bias/name2index: New function that returns session index when given
	session name or part of session name.
@performance/name2index: New function that returns session index when 
	given session name or part of session name.
@performance/plot: Now checks for presence of control data and sets
	plotcontrol and plotcombined to 0 when no control data are found.
@timing/name2index: New function that returns session index when 
	given session name or part of session name.
@timing/timing: Updated description of internal data structure in help 
	comments.

March 8, 2004
@eyestarget/eyestarget: Added onsetsMS field to store presenter 
	trigger onsets in milliseconds.
@eyestarget/ProcessTrial: Modified so that onsetsMS is used rather
	than trying to convert from datapoint to time assuming a 30 kHz
	sampling rate.
@eyestarget/plot: Modified so that onsetsMS is used rather than 
	trying to convert from datapoint to time assuming a 30 kHz
	sampling rate.
@eyestarget/loadobj: New function to convert from old eyestarget
	objects to new object containing onsetsMS. This function tries
	to find a raw streamer file in order to obtain the sampling rate.

March 9, 2004
@eyestarget/loadobj: Now adds data fields in proper order and inherits
	properly from sesinfo and eyes objects.
salienceSpikes: New script to plot spike trains according to salience
	condition.

March 16, 2004
@eyestarget/plot: Added option to plot rasters given ispikes objects.

March 18, 2004
@eyestarget/plotEyeJitter: New function that plots the mean and 
	std of the eye positions for multiple trials.
@eyestarget/plotSalienceSpikes: Moved code to plot spike trains 
	according to salience condition into separate function.
@eyestarget/plot: Moved code for 'iSpikes' option to separate function.
	Added 'EyeJitter' option that calls plotEyeJitter. Rearranged
	help comments to clarify the three different kinds of plots that
	can be created. Renamed 'Data2D' option to 'XY' and added 
	'FixZoom' option. 

March 23, 2004
plotTargets: Added help comments.
@eyestarget/subsref: Added access to onsetsMS field.

March 31, 2004
ReadContourStimuli: New function that returns both target window and
	properties of gabor elements.
@sesinfo/subsref: Now computes and returns nTotalStimuli, 
	nContourStimuli, nControlStimuli.
@sesinfo/displayfields: Added nTotalStimuli, nContourStimuli,
	nControlStimuli.
@gaborcontours/gaborcontours: Constructor for new class used to display
	receptive fields along with gabor contours.
@gaborcontours/plot: Plot function for new gaborcontours class.
AnalysisClasses.graffle: First attempt at creating UML diagram for npt
	and Contours classes.

May 27, 2004
@eyestarget/plot: Made second argument optional so number argument no
	longer necessary for plot options that don't use it.

June 4, 2004
@eyestarget/plotEyeJitter: Now includes help comments and parsing of 
	optional input arguments previously in main plot function. Added
	option to create RepsonseWeighted plots. Now calls eyejitter object
	to do most of the work.
@eyestarget/plot: Moved help comments for EyeJitter to plotEyeJitter
	function. Moved parsing of optional input arguments for EyeJitter to
	plotEyeJitter function.
@eyestarget/plotSalienceSpikes: Started to add code to plot histograms 
	(unfinished).
@sesinfo/subsref: Now takes advantage of the .data structure to greatly
	simplify subsref function. The remaining code is being kept for
	backward compatability.

June 16, 2004
@gaborcontours/plot: Made second argument optional. Now looks for 
	optional numeric argument to use for selecting which stimuli
	to plot.

June 29, 2004
@eyestarget/examples.txt: New file to illustrate use of eyestarget 
	objects. Currently contains code for creating plot for included 
	trials.
@eyestarget/getTrialsInFields.m: New function that figures out which 
	trials have stable eye positions within the limits of receptive 
	fields.
@gaborcontours/subsref.m: New function to access gaborcontours objects.
@eyestarget/plot.m: Added 'InFields' option which calls the 
	getTrialsInFields function.
@gaborcontours/gaborcontours.m: Now stores gabor size in data structure.
@gaborcontours/plot.m: Now uses rectangle to draw gabors with the 
	correct	size.

June 30, 2004
@eyestarget/getTrialsInFields.m: Now uses Arg.FieldMark instead to
	determine which fields should be used in computing limits. Function
	moved to npt/scripts/view/@eyejitter class since it does not contain
	any code specific to contour sessions now that FieldMark is an
	optional input argument and defaults to 0.
@eyestarget/plot.m: Removed 'InFields' option since getTrialsInFields
	has been moved to the eyejitter class. Moved argument parsing for
	'iSpikes' option into plotSalienceSpikes. Now removes 'EyeJitter'
	from varargin before passing it on to either plotEyeJitter or
	plotSalienceSpikes.
@eyestarget/plotEyeJitter: Replaced plot with plotEyeJitter in help
	comments. Updated optional input arguments in help comments. Added
	description of ResponseWeighted optional input argument. Changed 
	default group directory to group0001 instead of group001 to match
	new data hierarchy.
@eyestarget/plotSalienceSpikes: Added input	argument parsing code from 
	eyestarget/plot. Added code to plot psth for different salience
	conditions.

July 5, 2004
@gaborcontours/plot: Fixed bug that failed to set n when a numeric 
	argument was present (e.g. when using InspectGUI(gc)).
@eyestarget/examples: Removed code used to generate trials in fields.
	This functionality now exists in the eyejitter class in the method
	getTrialsInFields.m. Added example of using 'XY' option in
	@eyestarget/plot.m with InspectGUI.
@eyestarget/plotSalienceSpikes: Added code to use 
	@eyejitter/getTrialsInFields to get excluded points before 
	calculating mean and standard deviation. Added code to label axes
	and generate legend. Now only plots all the salience conditions at
	the contour target, the highest salience condition for the control
	target and the catch trials at the contour target. These are the
	trials where the stimulus in the receptive field is always the 
	optimal	orientation. If there are multiple iSpikes objects present,
	the subplots are now arranged in rows instead of in columns.

July 6, 2004
@contoursPSTH: New class that computes the PSTH of contour sessions.
@contoursPSTH/contoursPSTH.m: Constructor for new contoursPSTH class.
@contoursPSTH/plot.m: Plot function for new contoursPSTH class.

July 8, 2004
@contoursPSTH/contoursPSTH.m: Moved code that calculates the mean and
	standard deviation to @contours/private/getContoursPSTH.m so it can
	also be called by plot when the parameters do not match the ones
	used in the creation of the object.
@contoursPSTH/private/getContoursPSTH.m: New function that calculates the
	mean and standard deviations of the PSTH.
@contoursPSTH/plot: Added option to check if specified parameters match
	those used in creating the object and performs recalculation when
	there is a mismatch.
@contoursPSTH/subsref: New function to access contoursPSTH objects.

July 12, 2004
@contoursPSTH/private/getContoursPSTH.m: Now returns error status
	if there is a problem so that contoursPSTH.m can create empty
	object. Removed code that attempted to call createEmptyObject,
	which is only accessible from within the constructor.
@contoursPSTH/contoursPSTH.m: Now checks error status from 
	getContoursPSTH.m and creates empty object if necessary.
@contoursPSTH/plot.m: Added comment about ignoring the new error status
	from getContoursPSTH.m.
ContoursCmds.m: New file to list sequence of commands used to look at
	contour data.

July 19, 2004
@contoursPSTH/contoursPSTH.m: Fixed bug that was still passing objects
	to getContoursPSTH.
@contoursPSTH/plot.m: Added Recalc option to force recalculation of
	data. 
@contoursPSTH/private/getContoursPSTH.m: Fixed bug that was not taking
	the square root of the variance when computing standard deviation.
@eyestarget/plotSalienceSpikes.m: Now passes varargin during call to
	getTrialsInFields. Now uses separateAxis to setup multiple plots.
	Now computes mean standard deviation using Matlab functions instead
	of computing running sum so we can compare to code in 
	getcontoursPSTH. Now includes the number of trials in each condition
	in the legend.

August 3, 2004
ContoursCmds.m: Added example of running checksystem with sync and
	trigger data. Added example of using 'cygwinmove' in ProcessSession.
@contoursPSTH/contoursPSTH.m: Added directory information when creating
	nptdata object.
@contoursPSTH/plot.m: Added 'EyesTarget' option to call 
	plotSalienceSpikes with ispikes object. Moved x- and y- label
	commands so that different kinds of plots are labelled correctly.
@contoursPSTH/private/getContoursPSTH.m: Now correctly returns empty
	data matrix (which is a required output) when there is an error.
@eyestarget/plotSalienceSpikes.m: Added 'XLimitsEval' option so that we
	can specify limits with respect to stimulus onset. Modified code to
	display spike trains to display trials from all contour trials, plus
	the set of control trials with the highest salience, and the catch 
	trials at the contour location. Now also uses the excluded trials 
	from the eyejitter object. The reaction times are now plotted as
	well.
@timing/private/EyesTargetToTiming.m: Fixed typo in comment.
@performance/plot: Modified to use getOptArgs so it will work with
	npdata/plot which does not pass a numeric argument when calling
	the plot function.

September 7, 2004
ContoursCmds.m: Updated to create diary in the day directory and to
	not run KlustaKwik by default.
ContoursMarkersToTrials.m: Fixed bug that failed to initialize output
	arguments in case input is empty.
@performance/plot.m: Now correctly uses double braces to set the flags
	field in Args.

September 8, 2004
@bias/plot.m: Removed mandatory second input argument so it will work
    with nptdata/plot. Now uses getOptArgs to parse optional input
    arguments. Now lists the sessionname in the title either when
    there is a numeric argument (i.e. individual data set is specified),
    or if there is only 1 data set (i.e. when using nptdata/plot).
    Updated help comments to reflect new changes. Removed Session from
    Args since it is implied when there is a numeric argument.
@timing/plot.m: Removed mandatory second input argument so it will work
    with nptdata/plot. Now uses getOptArgs to parse optional input
    arguments. Updated help comments to reflect new changes.

October 1, 2004
@contourspsth: Changed to lower case so that objects saved in Windows
	will work on non-Windows machines.
@contourspsth/contourspsth.m: Changed case of contourspsth.
@contourspsth/loadobj.m: Changed case of contourspsth.
@contourspsth/plot.m: Changed case of contourspsth.
@contourspsth/subsref.m: Changed case of contourspsth.
@contourspsth/private/getContoursPSTH.m: Changed case of contourspsth.
@contoursxcorr: Changed to lower case so that objects saved in Windows
	will work on non-Windows machines.
@contoursxcorr/contoursxcorr.m: Changed case of contoursxcorr.
@contoursxcorr/get.m: Changed case of contoursxcorr.
@contoursxcorr/plus.m: Changed case of contoursxcorr.
@contoursxcorr/subsref.m: Changed case of contoursxcorr.
ContoursCmds.m: Changed references to contourspsth to lower case.

October 4, 2004
@eyestarget/eyestarget.m: Replaced 'CaseInsensitiveSuffix' option in 
	call to nptDir with 'CaseInsensitive' since the former option is no
	longer available.
@sesinfo/sesinfo.m: Replaced 'CaseInsensitiveSuffix' option in call to 
	nptDir with 'CaseInsensitive' since the former option is no	longer 
	available.

October 13, 2004
Removed directories @contoursPSTH and @contoursXCorr on CVS server by
	hand since SmartCVS on Windows is unable to distinguish	lowercase
	and uppercase.

November 9, 2004
ContoursCmds.m: Added additional braces for Objects argument.
@contourspsth/contourspsth.m: Changed case of getContoursPSTH.

November 11, 2004
ContoursTrialResultTiming.m: Added optional additional argument that
	contains saccade data from fvtGenerateSessionEyeMovements. Added
	code to create markers using saccade data.
@eyestarget/ProcessTrial.m: Added code to use saccade data to compute
	reaction times.
@eyestarget/private/ProcessAllTrials.m: Added 'EyeMovements' optional
	inpout argument to use saccade data in eyemovements object to 
	compute reaction times. Optional input arguments to eyemovements 
	are also now passed along properly.
@eyestarget/eyestarget.m: Now uses getOptArgs to parse optional input
	arguments. Now passes modified varargin to ProcessAllTrials so
	optional input arguments to fvtGenerateSessionEyeMovements can
	be passed to eyemovements object which is called in 
	ProcessAllTrials.
@eyestarget/plot.m: Now uses data stored in object instead of calling
	ContoursTrialResultTiming again.

November 15, 2004
@bias/plot.m: Fixed typo in spelling of catch data in code that plots
	data for individual salience levels.

November 17, 2004
ContoursCmds.m: Removed unnecessary {} in call to nptdata/plot.
@eyestarget/eyestarget.m: Fixed bug that was using redo instead of
	Args.RedoLevels.
@sesinfo/private/unleave1.m: Broke up long lines into shorter lines.

November 18, 2004
ContoursCmds.m: Added new line at the end of the file.
@eyestarget/eyestarget.m: Now calls dirLevel to move to eye
	directory before trying to instantiate object. This way other
	objects don't have to worry about changing directories before 
	instantiating the object.
@sesinfo/sesinfo.m: Added comments to describe isequence, ulsequence,
	and sequence fields.
@sesinfo/private/unleave1.m: Now correctly gathers the trial numbers
	for the tuning stimuli.
@contourstuning: New class to compute orientation tuning curves.
@contourstuning/contourstuning.m: Constructor function for new 
	contourstuning class.
@contourstuning/plot.m: Plot function for new contourstuning class.
@contourstuning/plus.m: Plus function for new contourstuning class.
@contourstuning/subsref.m: Subsref function for new contourstuning 
	class.
@sesinfo/getTuningTrials.m: New function to return the trial numbers
	corresponding to the different orientation tuning stimuli.

November 19, 2004
@contourstuning/subsasgn.m: New function to modify object fields.
@contourstuning/contourstuning.m: Removed optional input arguments in
	call to ispikes since we don't really want to regenerate the ispikes
	object. Now checks for sessions with no tuning stimuli and correctly
	creates empty data matrices and the proper setIndex. Now stores
	spike counts instead of mean and std so we can plot the distribution
	of the values using boxplot.
@contourstuning/plus.m: Modified to concatenate spike counts instead of
	mean and std and increments setIndex accordingly.
@contourstuning/contourstuning.m: Added option to do boxplots. Now 
	computes mean and std on the fly to create default plot.
ContoursCmds.m: Added example of computing contourstuning object.
@contourstuning/plot.m: Now creates boxplots by default. Added option to
	create imagesc and line plots of histogram data.

November 22, 2004
@eyestarget/private/ProcessAllTrials.m: Added option to take 
	eyemovements object as optional input argument so it does not have
	to be recalculated.

January 21, 2005
russ.m: Modified the path to the template descriptor file to a fully
	qualified path so this script will now work from any day directory.

January 24, 2005
@eyestarget/eyestarget.m: Put back code from old version on cvs that
	changes directory to the eye directory in cases dirLevel does not
	work (i.e. the data hierarchy has not been updated to the latest
	format).
ContoursTrialResultTiming.m: Fixed bug that was not computing result
	when not using eyemovement data.
russ.m: Updated call to nptdata/plot to use proper embedding of cell
	arrays for objects and plot options.
@bias/plot.m: Now correctly checks for sessions with on incorrect
	trials. Now plots incorrect trials with a different symbol.

January 25, 2005
russ.m: Modified to work with session directories named session01 etc.

April-18-2005
ChangeLog.txt: Renamed to ShihChengChangeLog.txt so cvsci will work. 
@eyestarget/eyestarget.m: Replaced calls to dirLevel with getDataDirs. 
@contoursxcorr/contoursxcorr.m: Replaced calls to dirLevel with 
	getDataDirs. 
@contourstuning/plot.m: Replaced calls to dirLevel with getDataDirs. 

May-17-2005
ShihChengChangeLog.txt: Removed cvs watch from the Contours directory and 
	added Contours directory to CVSROOT/loginfo so that changes to the 
	Contours project are emailed to Rodrigo and Michael.
@eyestarget/plotSalienceSpikes.m: Added hack to handle incomplete sessions. 
@eyestarget/eyestarget.m: Removed hack to find timing.mat files created by 
	ProcessSession since it might find timing.mat files created by the 
	timing object. 

June-07-2005
@eyestarget/eyestarget.m: Removed commands to change directories before 
	instantiating sesinfo object since the sesinfo object now uses 
	getDataDirs to get itself to the right directory. 
@sesinfo/sesinfo.m: Updated to use getOptArgs to process optional input 
	arguments and the style in npt/scipts/view/dirfiles. Now uses 
	getDataDirs to move to appropriate directory before trying to read ini 
	file. 

June-08-2005
@sesinfo/sesinfo.m: Now correctly changes directory back to the original 
	directory if needed. 
@eyestarget/eyestarget.m: Removed code that was unnecessarily changing 
	directories. Removed command that attempted to load a file with name 
	stored in aname(1).name. 

June-14-2005
@sesinfo/sesinfo.m: Addded code to check for incomplete sessions 
	(commented out for now as we try another method).
@timing/private/EyesTargetToTiming.m: Now checks for incomplete sessions 
	and pads the data in the eyestarget object with nans. 
@performance/private/EyesTargetToPerformance.m: Now checks for incomplete 
	sessions and pads the data in the eyestarget object with nans. 
	Replaced calls to sum with nansum and length with sum(~isnan()) so 
	that data with nan's are calculated correctly. 
@sesinfo/subsref.m: Now returns the trials field, which is used to 
	determine if a session is incomplete. 
@sesinfo/private/ReadIniSequence.m: Added code to check for incomplete 
	sessions (commented out for now as we try another method). 
@eyestarget/subsasgn.m: New function to change data in eyestarget objects. 
	This allows us to pad the data for incomplete sessions so other 
	objects can index normally into the eyestarget object without having 
	to modify the indices for incomplete sessions. 

June-15-2005
@eyestarget/plot.m: Now plots both target windows with the correct window 
	plotted in red and the other plotted in black. 

June-20-2005
checkStimOri.m: New function to check the orientation of the stimulus with 
	the results of the unleave function. 
@contourspsth/private/getContoursPSTH.m: Now uses the sequence field 
	instead of the ulsequence field in the sesinfo object that is part of 
	the eyestarget object. This allows incomplete sessions to be handled 
	transparently. 
@sesinfo/private/ReadIniSequence.m: Now checks for the presence of 
	incomplete sessions, including for empty last trials, before calling 
	the unleave functions. Now calls the unleave functions with the number 
	of complete trials so those functions don't have to recompute it. 
@gaborcontours/gaborcontours.m: Now removes GaborPixels from varargin and 
	renames it varargin2. The variable varargin2 is then passed on to other 
	objects that are used in the creation of this object. 
@sesinfo/displayfields.m: Removed ulsequence.contour and other similar 
	entries since we should be using sequence.contour and so on from now 
	on. 
salienceSpikes.m: Now uses the sequence field instead of the ulsequence 
	field in the sesinfo object that is part of the eyestarget object. This 
	allows incomplete sessions to be handled transparently. 
@sesinfo/private/unleavePsych.m: Rewritten to use histc to more efficiently 
	unleave the stimulus sequence. Now handles incomplete sessions properly 
	as well. 
@eyestarget/subsref.m: Now uses the sequence field instead of the 
	ulsequence field when calling the subsref function for the sesinfo 
	object. This allows incomplete sessions to be handled transparently. 
@sesinfo/subsref.m: Now returns value of inlcludetuning field. Now returns 
	the list of completed trials for each salience condition when for 
	example sequence.contour(1) is used. This allows incomplete sessions 
	to be handles transparently by other objects. Removed code that parsed 
	the sequence into stimulus and repetitions since that was not being 
	used. Now returns lists of trials corresponding to the different tuning 
	stimuli using the sequence.tuning format so incomplete sessions will be 
	handled transparently. 
@eyestarget/plotSalienceSpikes.m: Now uses the sequence field instead of 
	the ulsequence field in the sesinfo object that is part of the 
	eyestarget object. This allows incomplete sessions to be handled 
	transparently. 
@eyestarget/plotEyeJitter.m: Now uses the sequence field instead of the 
	ulsequence field in the sesinfo object that is part of the eyestarget 
	object. This allows incomplete sessions to be handled transparently. 
@sesinfo/private/unleave1.m: Rewritten to use histc to more efficiently 
	unleave the stimulus sequence. Now handles incomplete sessions properly 
	as well. 
@eyestarget/diffResults.m: Now prints out the number of trials in the 
	marker file and in the eye files when printing out the mismatch error. 
@bias/private/EyesTargetToBias.m: Now uses the sequence field instead of 
	the ulsequence field in the sesinfo object that is part of the 
	eyestarget object. This allows incomplete sessions to be handled 
	transparently. Now uses the new concat function to concatenate 
	multiple numeric vectors together. 
@performance/private/EyesTargetToPerformance.m: Removed code that checks 
	for incomplete sessions since this is now taken care of by the unleave 
	functions in the sesinfo class. 
@timing/private/EyesTargetToTiming.m: Removed code that checks for 
	incomplete sessions since this is now taken care of by the unleave 
	functions in the sesinfo class. 
@eyestarget/subsasgn.m: Now uses the sequence field instead of the 
	ulsequence field when calling the subsref function for the sesinfo 
	object. This allows incomplete sessions to be handled transparently. 
@contourspsth/plot.m: Added a XLim optional input argument so we can line 
	up the PSTH with the raster plot created by plotSalienceSpikes. 
@sesinfo/private/unleave.m: Rewritten to use histc to more efficiently 
	unleave the stimulus sequence. Now handles incomplete sessions properly 
	as well. 

June-21-2005
@sesinfo/sesinfo.m: Now removes the newline character from the filename 
	string since Matlab 7 does not seem to be able to find the file with 
	the newline character present in the filename. 
@eyestarget/plotSalienceSpikes.m: Removed hack to deal with incomplete 
	sessions since sesinfo now handles incomplete sessions properly. 
@gaborcontours/gaborcontours.m: Added call to getDataDirs to change to the 
	proper directory before looking for saved object. 
@gaborcontours/subsref.m: Now correctly calls mapfields/subsref instead of 
	nptdata/subsref when the index arguments are unknown. 
@gaborcontours/plot.m: Now changes to the proper directory before trying 
	to read the stimulus file. 

June-23-2005
@performance/plot.m: Modified to work around change in errorbar function 
	in Matlab 7 that returns only 1 handle instead of the 2 handles 
	returned by Matlab 6.5. Now works for both Matlab 6.5 and Matlab 7. 
@timing/plotDiff.m: Modified to work around change in errorbar function in 
	Matlab 7 that returns only 1 handle instead of the 2 handles returned 
	by Matlab 6.5. Now works for both Matlab 6.5 and Matlab 7. 
@timing/plot.m: Modified to work around change in errorbar function in 
	Matlab 7 that returns only 1 handle instead of the 2 handles returned 
	by Matlab 6.5. Now works for both Matlab 6.5 and Matlab 7. 
@timing/plotGroups.m: Modified to work around change in errorbar function 
	in Matlab 7 that returns only 1 handle instead of the 2 handles 
	returned by Matlab 6.5. Now works for both Matlab 6.5 and Matlab 7. 
@performance/plotGroups.m: Modified to work around change in errorbar 
	function in Matlab 7 that returns only 1 handle instead of the 2 
	handles returned by Matlab 6.5. Now works for both Matlab 6.5 and 
	Matlab 7. 
@contourstuning/plot.m: Updated call to getDataDirs to shorten names by 
	adding 'DirString'. 

June-27-2005
@eyestarget/ProcessTrial.m: Now correctly transposes SacData so that 
	trials with more than one saccade are rejected correctly. 

June-30-2005
@eyestarget/plotSalienceSpikes.m: Now just draws lines between salience 
	conditions instead of using patch object, which made the spikes harder 
	to see. 
ContoursTrialResultTiming.m: Now saves the reaction times for all trials. 
	Now returns result values other than 0 and 1 to distinguish between the 
	different possible results. Now properly differentiates between trials 
	with no saccades identified by the eye movement analysis and trials 
	where eye movement analysis are not used. 
@eyestarget/ProcessTrial.m: Now sets the default value of SaccadeData to 
	nan to correctly distinguish between trials with no saccades identified 
	by the eye movement object (eyemvt) from trials where the eyemvt object 
	was not used. 
@sesinfo/getTuningTrials.m: Now uses the sequence.tuning field in sesinfo 
	objects to return the trial numbers for the different tuning stimuli. 
	The 0's returned by the sesinfo object are replaced with nan so that 
	when the mean and standard error are computed in the contourstuning 
	object, values of 0, which indicate trials missing from incomplete 
	sessions, are not confounded with complete trials with 0 spikes. 
@contourspsth/plot.m: Turned off the legend as it was obscuring the plots. 
	Need to find way to reduce size of legend and perhaps to automatically 
	place it in the least intrusive place. 
checkStimOri.m: Removed the redo option to sesinfo. 
@performance/performance.m: Now correctly changes to the proper directory 
	before checking for saved performance objects. 
@contourstuning/plot.m: Now plots the mean and standard error by default 
	instead of box plots, which is now an optional plot. Added code to 
	handle LabelsOff and Color so this function can be used with 
	nptgroup/plot. Now uses the short form of the directory in the title 
	when plotting just one cell instead of "... data for 1 cells". Added 
	code to check for empty data, which might no longer be necessary since 
	we no longer save objects with no tuning trials. Now checks to make 
	sure the histograms are not empty before trying to plot them. 
@gaborcontours/plot.m: Added options to control the X and Y axes limits. 
@contourstuning/contourstuning.m: Now correctly returns empty object when 
	there are no tuning trials. Now uses nanindex to properly handle 
	incomplete sessions. 
@sesinfo/getTuningTrials.m: Moved code that replaced 0's for incomplete 
	sessions with nan to contourstuning since it is more relevant there. 
	Removed commented code that was made redundant with the use of the 
	sequence field in the sesinfo objects. 
@contourstuning/contourstuning.m: Moved code that used to be in 
	getTuningTrials that replaced 0's in the trial numbers with nan's to 
	this function since it is more relevant here. 
@contourstuning/contourstuning.m: Now allows creation of objects with no 
	tuning data so that we can indicate that there are no tuning trials in 
	the title instead of having it be blank. Now computes spike counts only 
	when there are valid tuning trials. 
@contourstuning/plot.m: Added Normalized option to plot normalized spike 
	counts so that we can plot tuning curves for different cells on the 
	same axis (e.g. using nptgroup objects). Now checks for objects with no 
	tuning data at the beginning so we don't have to have code in every 
	option checking for sessions with no tuning data. Modified code to set 
	the colors of the errorbars so that it will work with both Matlab 6 and 
	7. Added code to add x and y axis labels. Now checks to make sure that 
	the maximum spike count is not 0 when computing the normalized spike 
	count. 
@eyestarget/plot.m: Now includes the result of the trial in the title. 
ContoursMarkersToTrials.m: Fixed bug that was interpreting 1 and 2 as 
	results of the trial when they are actually the stimulus onset and 
	fixation offset times. Now correctly returns the result of the trial 
	according to Control. 

July-01-2005
@performance/private/EyesTargetToPerformance.m: Modified to handle the 
	various different results now returned by the eyestarget object. 

July-12-2005
@eyestarget/eyestarget.m: Modified to work with marker files with upper-
	case suffixes. 


June-04-2006
@gaborcontours/gaborcontours.m: Committing some changes that were made some 
	time ago but for some reason was not committed. 

June-05-2006
@gaborcontours/plot.m: Fixed typo in comments. 

October-09-2006
ContoursCmds.m: Fixed typo in spelling of eyestarget. 

January-03-2007
@sesinfo/sesinfo.m: Now returns empty object it no ini files are found. 
@performance/ProcessSession.m: Now returns additional output argument to 
	make it compatible with nptdata/ProcessDay.