Added Data Analysis tool files from May 16-30's repository

controls/DataAnalysisTool/SupportFiles/cam_sys_data_load.m

+function [] = cam_sys_data_load( varargin )
+%cam_sys_data_load(...)
+%
+% USE: 
+%
+% Produces a structure containing the time data, x axis position, y axis
+% position, z axis position, roll Euler angle, pitch Euler angle, and yaw
+% Euler angle for each CSV file produced by Optitrack Tracking Tools 
+% contained in a given directory. 
+%
+% SYNTAX: 
+%   
+% cam_sys_data_load( path )
+%  
+% Optional Inputs: 
+%
+%   path is a string containing the name of the directory containing the 
+%   CSV files to be read in. If this argument is not included, the user
+%   will be prompted to choose a director through a GUI menu. 
+%
+% Outputs: 
+%
+%   One or more instances of a structure containing vectors for time, 
+%   position and orientation. For an output structure called data: 
+%       data.t (time stamp vector)
+%       data.x (x axis position vector)
+%       data.y (y axis position vector) 
+%       data.z (z axis position vector)
+%       data.phi (roll Euler angle vector)
+%       data.theta (pitch Euler angle vector)
+%       data.psi (yaw Euler angle vector) 
+%
+%       ***The structure names will generally be the same as the CSV file
+%       names, unless the file name is not a valid MATLAB variable name in
+%       which case it will be renamed data#, where # will be the index
+%       where the file would appear in the result of a dir or ls command. 
+%
+% AUTHOR(s): 
+%
+%   Matt Rich 
+%   Graduate Student 
+%   Electrical and Computer Engineering Department
+%   Iowa State University 
+%   m87rich@iastate.edu
+%
+% LAST MODIFIED: 
+%   
+%   13-Mar-2012 (Matt Rich) : initial creation
+%
+%
+
+if isempty(varargin)
+    path = uigetdir('.','Choose a directory containing the Optitrack CSV files you want to load.');
+else
+    path = varargin{end}; 
+end
+
+files = dir(path);
+
+fileIndex = find(~[files.isdir]);
+
+for k = 1:length(fileIndex)
+    fileName = files(fileIndex(k)).name;
+    
+    if strcmpi('.csv',fileName(end-3:end))
+        if isvarname(fileName(1:end-4)) 
+            assignin('base',fileName(1:end-4),cam_sys_data_read([path,'\',fileName])); 
+        else
+            assignin('base',['data',num2str(k)],cam_sys_data_read([path,'\',fileName])); 
+            disp([fileName(1:end-4),' has been renamed data',num2str(k),...
+            ' in order to be a valid MATLAB variable name.']); 
+        end
+    else
+        disp([fileName,' not loaded since it is not a CSV file.']); 
+    end
+end
+
+end
+

controls/DataAnalysisTool/SupportFiles/cam_sys_data_read.m

+function data = cam_sys_data_read(filename)
+%cam_sys_data_read(...)
+%
+% USE: 
+%
+% Produces a structure containing the time data, x axis position, y axis
+% position, z axis position, roll Euler angle, pitch Euler angle, and yaw
+% Euler angle from a CSV file produced by Optitrack Tracking Tools. 
+%
+% SYNTAX: 
+%   
+% data = cam_sys_data_read(filename)
+%  
+% Inputs: 
+%
+%   filename is a string containing the name of the CSV file to be read in
+%
+% Outputs: 
+%
+%   data is a structure containing vectors for time, position and
+%   orientation: 
+%       data.t (time stamp)
+%       data.x (x axis position)
+%       data.y (y axis position) 
+%       data.z (z axis position)
+%       data.phi (roll Euler angle *(as reported by Tracking Tools)) 
+%       data.theta (pitch Euler angle *(as reported by Tracking Tools)) 
+%       data.psi (yaw Euler angle *(as reported by Tracking Tools)) 
+%       data.qx = 1st quaternion component  
+%       data.qy = 1st quaternion component
+%       data.qz = 1st quaternion component
+%       data.qw = 1st quaternion component
+%
+%       *The Euler Angles reported by Tracking Tools may be incorrect
+%       depending on the setup of the axes. As of 3-14-13, they are
+%       incorrect since the axes are set up to provide the correct
+%       information for the VRPN decoding of the MicroCART base station
+%       software, which assumes a Yaw-Pitch-Roll sequence of rotations.
+%       The quaternions can be used to obtain the correct Euler angles if
+%       the rotation sequence is known. 
+%  
+%
+% AUTHOR(s): 
+%
+%   Matt Rich 
+%   Graduate Student 
+%   Electrical and Computer Engineering Department
+%   Iowa State University 
+%   m87rich@iastate.edu
+%
+% LAST MODIFIED: 
+%   
+%   13-Mar-2012 (Matt Rich) : initial creation
+%   14-Mar-2013 (Matt Rich) : added quaternion extraction 
+%
+%
+
+[num,txt,raw] = xlsread(filename);
+
+data.t = raw(45:end,3); data.t = [data.t{1:2:end}]; 
+
+data.x = raw(45:end,6); data.x = [data.x{1:2:end}];
+data.y = raw(45:end,7); data.y = [data.y{1:2:end}];
+data.z = raw(45:end,8); data.z = [data.z{1:2:end}];
+
+data.psi = raw(45:end,13); data.psi = [data.psi{1:2:end}]; 
+data.theta = raw(45:end,14); data.theta = [data.theta{1:2:end}]; 
+data.phi = raw(45:end,15); data.phi = [data.phi{1:2:end}]; 
+
+data.qx = raw(45:end,9); data.qx = [data.qx{1:2:end}];
+data.qy = raw(45:end,10); data.qy = [data.qy{1:2:end}];
+data.qz = raw(45:end,11); data.qz = [data.qz{1:2:end}];
+data.qw = raw(45:end,12); data.qw = [data.qw{1:2:end}];
+
+end

controls/DataAnalysisTool/SupportFiles/sampleLogFile2.txt

+#
+#**********************************************
+#Custom Header:::::
+#Settings: x y z
+#Constants: 1 2 3
+#Contents will be printed to MATLAB terminal
+#**********************************************
+#
+#▼▼▼▼ - Time must be included for parser to work properly needs to be exactly the following string: 'Time'
+%Time	Header1 Header2	Header3	Header4	b
+&sec    Unit1   Unit2   Unit3   Unit4   b
+1	1	1	100	0	0
+2	1	2	80	.5	-1
+3	1	3	60	1	1
+4	1	4	40	.5	-.5
+5	1	5   20	0	0

controls/DataAnalysisTool/Tool/DataAnalysis.m

+%% ANALYSIS CONFIGURATION OPTIONS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Modify your analysis configuration options here
+
+% FNAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% if you know the name of the log file that you want to parse, set the it
+% here only if it is in the working directory. Otherwise, you may leave it
+% blank. You will be able to choose the file to parse through an explorer
+% window.
+%
+%fname = 'sampleLogFileWithMarker.txt';  
+fname = 'testies_v2.txt';  
+
+% PLOTTING SWITCHES - set them to 0 or 1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+plot            = 1;    % to choose plotting
+separatePlot    = 1;    % to generate separatePlots
+multiPlot       = 1;    % to generate multiPlot
+subPlot         = 0;    % to generate subPlots
+clearFigs       = 0;    % to close all the plots (needed only by the GUI)
+
+% DATA TO PLOT %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+% SEPARATEDATA 
+% write names of the data headers that you want to plot using
+% seperatePlots. If this is empty but "plot" switch is 1, all the columns
+% will be plotted using seperatePlots.
+%
+separateData = {'PID_roll_vel'};
+                                                
+% MULTIDATA
+% write names of the data headers that you want to plot using multiPlots.
+% If this is empty but "plot" switch is 1, the data headers in separateData
+% will be plotted using multiPlots.
+%
+multiData = {}; 
+
+% SUBDATA
+% write names of the data headers that you want to plot using subPlots.
+% If this is empty but "plot" switch is 1, the data headers in multiData
+% will be plotted using subPlots.
+%
+subData = {};
+
+% COLOR FOR PLOTTING %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%
+color       = 'r';      % one character for color of the plotting line
+marker      = '';       % one character for the marker of the plotting line
+style       = ':';      % one character for the style of the plotting line
+backgnd     = [1 1 1];  % rgb array for background color of the plot
+
+
+%% DO NOT MODIFY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+fpath = '';
+if(isempty(fname))
+    [fname, fpath] = uigetfile('.txt','Select log file');
+end
+
+% storing file options in the structure
+params.file.name = fname;               % file name only
+params.file.path = fpath;               % file path only
+params.file.pathName = [fpath fname];   % file path with file name
+
+
+% storing plotting parameters in the structure
+params.plotting.plot = plot;               
+params.plotting.separatePlot = separatePlot;           
+params.plotting.multiPlot = multiPlot;              
+params.plotting.subPlot = subPlot;
+params.plotting.clearFigs = clearFigs;
+
+% storing plotting data in the structure
+params.plotting.separateData = separateData;                
+params.plotting.multiData = multiData;         
+params.plotting.subData = subData;
+
+% storing colors for plotting in the struture
+params.plotting.color = color; 
+params.plotting.marker = marker; 
+params.plotting.style = style; 
+params.plotting.backgnd = backgnd;
+
+% saving params into a file
+%save params params;
+
+% DO NOT MODIFY - END
+%% parsing the log file specified %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% parse the log and instantiate the data structure, expData
+%
+expData = parse_log(params.file.pathName, params); 
+
+%save expData expData;
+
+%% plotting routines %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% plot the data accoriding to the plotting parameters set
+%
+plot_data(expData, params.plotting);
+
+%% creating the main structure to be stored in the workspace %%%%%%%%%%%%%
+%
+main.params     = params;
+main.expData    = expData;
+clearvars -except main;
+save main main;
\ No newline at end of file

controls/DataAnalysisTool/Tool/buildPlotCharString.m

+function plotCharStr = buildPlotCharString(plotParams)
+%buildPlotCharString builds a character string for plotting using the
+%plotParams input structure
+%   plotParams : structure that contains the plotting style parameters.
+%       fields of plotParams:
+%           plotParams.plot
+%           plotParams.style
+%           plotParams.color
+%           plotParams.marker
+%           plotParams.backgnd
+%           
+
+% keeps track of the index in the string
+i = 1;
+
+% color
+if(~isempty(plotParams.color))
+    plotCharStr(i) = plotParams.color;
+    i = i + 1;
+end
+
+% marker
+if(~isempty(plotParams.marker))
+    plotCharStr(i) = plotParams.marker;
+    i = i + 1;
+end
+
+% style
+if(~isempty(plotParams.style))
+    plotCharStr(i) = plotParams.style;
+    i = i + 1;
+end
+
+% sanity check for the string
+if(~isPlotCharString(plotCharStr))
+    error('Wrong plot style formatting options, please use allowed values only');
+end
+
+end
+

controls/DataAnalysisTool/Tool/haveDiffPlotStyles.m

+function y = haveDiffPlotStyles(data,headers)
+%   haveDiffPlotStyles checks to see if the headers in the data structure
+%   have different plotting parameters
+%
+%   This function ONLY compares the color, marker and style fields of the
+%   params structure.
+
+% initialize to true
+y = 1;
+
+% return 1 if only one
+if(length(headers) == 1)
+    y = 1;
+    return
+end
+
+% obtaining the plotting params structure from each header
+j = 0;
+for i = 1:length(headers)
+    
+    entity = headers{i};
+    headerPlotParams(i) = eval(['data.' entity '.params']);
+
+end
+
+% check if there are more than two defaults
+numOfDefaults = 0;
+for i = 1:length(headerPlotParams)
+    if(isDefaultPlotCharString(headerPlotParams(i)))
+        numOfDefaults = numOfDefaults + 1;
+        if(numOfDefaults >= 2)
+            y = 0;
+            return
+        end
+    else
+    end
+end
+
+% checking for equality between the plotting parameters
+colorEqual = 0;
+markerEqual = 0;
+styleEqual = 0;
+for i = 1:length(headerPlotParams)
+    for j = 1:length(headerPlotParams)
+       if(i == j)
+           continue;
+       else
+           if(strcmp(headerPlotParams(i).color, headerPlotParams(j).color) == 1)
+               colorEqual = 1;
+           end
+           if(strcmp(headerPlotParams(i).marker, headerPlotParams(j).marker) == 1)
+               markerEqual = 1;
+           end
+           if(strcmp(headerPlotParams(i).marker, headerPlotParams(j).marker) == 1)
+               styleEqual = 1;
+           end
+           
+           if(colorEqual && markerEqual && styleEqual)
+               y = 0;
+               return;
+           end
+           colorEqual = 0;
+           markerEqual = 0;
+           styleEqual = 0;
+       end 
+    end
+end
+
+end
+

controls/DataAnalysisTool/Tool/isDefaultPlotCharString.m

+function y = isDefaultPlotCharString(plotParams)
+%isDefaultPlotCharString Compares the input plotParams structure to the
+%default plotting format:
+%       color   b
+%       marker  (none)
+%       style   -
+%   Return 1 if it is the default plotting style. Returns 0 otherwise
+
+defaultColor = 0;
+defaultMarker = 0;
+defaultStyle = 0;
+
+% checking plotting color
+if(plotParams.color == 'b' || isempty(plotParams.color))
+    defaultColor = 1;
+end
+
+% checking plotting marker
+if(isempty(plotParams.marker))
+    defaultMarker = 1;
+end
+
+% checking plotting style
+if(plotParams.style == '-' || isempty(plotParams.style))
+    defaultStyle = 1;
+end
+
+% final check
+if(defaultColor && defaultMarker && defaultStyle)
+    y = 1;
+else
+    y = 0;
+end
+
+end
+

controls/DataAnalysisTool/Tool/isPlotCharString.m

+function y = isPlotCharString(str)
+% isPlotCharString sees if the str is composed of characeters that are used
+% in making up a plot formatting string.
+%   str - string to check
+
+if (length(str) <= 4)
+    
+    % if the input string is empty, it is a valid plot formatting character
+    % string
+    if(length(str) == 0)
+        y = 1;
+        return
+    end
+    
+    % list of possible characters allowed in the string
+    plotTypeChars = ['bgrcmykw.ox+*sdv^<>ph-:.'];
+    
+    for i = 1:length(str)
+        if (ismember(str(i),plotTypeChars))
+            y = 1;
+            continue
+        else
+            y = 0;
+            break;
+        end
+    end
+    
+else
+    y = 0;
+end
+
+end
\ No newline at end of file

controls/DataAnalysisTool/Tool/parse_camera_log.m

+function trackableData = parse_camera_log(filepath)
+%loads position, quaternion orientation and euler angles from rigidbody
+%trajectories exported to csv in Motive 1.5.1 and returns them in the
+%array of structs
+%tested for one and three rigid bodies
+%license: GPL, author Frieder Wittmann, email frieder.wittmann@gmail.com
+
+openedFile = fopen(filepath,'r');
+
+currentLineNo = 0;
+
+%go through the first lines which dont contain data of interest
+for lineIndex = 1:41                                                        % edited by RZ: to match the OptiTrack Tools software used by the Controls Lab at Iowa State University
+    readNextLine(openedFile);
+    currentLineNo = currentLineNo +1;
+end
+
+commaSeperatedValues = csvStringFromOpenedFile(openedFile);
+numberOfFrames = str2num(commaSeperatedValues{3})
+
+commaSeperatedValues = csvStringFromOpenedFile(openedFile);
+numberOfRidgidBodies = str2num(commaSeperatedValues{3})
+
+%create container of size numberOfRidgidBodies for the output data
+RigidBodies = repmat(struct(...
+    'Name', 'empty_name', ...                                               % added by RZ: name of the trackable
+    'T', NaN(numberOfFrames,1), ...
+    'P', NaN(numberOfFrames,3), ...
+    'Q', NaN(numberOfFrames,4), ...
+    'Euler', NaN(numberOfFrames,3)),numberOfRidgidBodies,1);
+
+%the next lines contain information about the markerpositions on the ridigd bodies. we ignore this infrmation
+for i = 1:numberOfRidgidBodies 
+    commaSeparatedValues = csvStringFromOpenedFile(openedFile);
+    name = commaSeparatedValues{2};
+    if(isequal(name(1),'"'))    % taking care of this issue. Occurs sometimes only.
+        name(1) = '';
+        name(end) = '';
+    end
+    RigidBodies(i).Name = name;
+end
+
+
+frameIndex = 0; %every nth (numberOfRidgidBodies+1) contains the ridgidbody information of a frame/timestamp
+numberOfLinesUntilNextFrameLine = numberOfRidgidBodies+1;
+
+for lineIndex = 1:numberOfFrames*numberOfLinesUntilNextFrameLine 
+%there is always a frame line and then one line per rigid body with details which are not of interest to us here  
+    
+    currentLineContent = readNextLine(openedFile);
+    
+    %if current line is a line with frame information  
+    if( mod(lineIndex,numberOfLinesUntilNextFrameLine) == 1)     
+        frameIndex = frameIndex+1; %we're at the next frame
+        frameLine = currentLineContent;
+        commaSeperatedValues = regexp(frameLine, ',', 'split');
+
+        frameIndexFromFile = str2num(commaSeperatedValues{2});
+        timestamp = str2num(commaSeperatedValues{3});
+        %check how many ridig bodies were tracked, sometimes so are out of
+        %sight and hence not tracked
+        numberOFTrackedRidigdBodiesInThisFrame = str2num(commaSeperatedValues{4});
+        currentCSVIndex = 4;
+        
+        if (numberOFTrackedRidigdBodiesInThisFrame > 0)
+            currentCSVIndex = currentCSVIndex+1;
+            currentRidgidBodyID = str2num(commaSeperatedValues{currentCSVIndex});
+            
+            for(expectedRidigbBodyID = 1:numberOfRidgidBodies + 1)   
+                if (expectedRidigbBodyID ~= currentRidgidBodyID)
+                    break %go to next 
+                end
+                currentCSVIndex = currentCSVIndex+1;
+                [p, q, euler ] = readPQEulerStartingAtIndex(currentCSVIndex, commaSeperatedValues);              
+                RigidBodies(currentRidgidBodyID).T(frameIndex,:) = timestamp;
+                RigidBodies(currentRidgidBodyID).P(frameIndex,:) = p;
+                RigidBodies(currentRidgidBodyID).Q(frameIndex,:) = q; 
+                RigidBodies(currentRidgidBodyID).Euler(frameIndex,:) = euler;
+                currentCSVIndex = currentCSVIndex+10; %the ten values are p(3),q(4)euler(3)=10
+                if (currentCSVIndex + 11 < length(commaSeperatedValues))
+                    currentRidgidBodyID = str2num(commaSeperatedValues{currentCSVIndex}); %get next ridgid body id
+                else
+                    break;
+                end
+            end
+        end           
+    end
+end
+
+% added by RZ: to output the structure in readable format
+trackableData.numOfTrackables = length(RigidBodies);
+for i=1:trackableData.numOfTrackables
+    eval(['trackableData.' RigidBodies(i).Name ' = RigidBodies(i);']);
+end
+
+end
+
+function lineContent = readNextLine(openedFile)
+    lineContent = fgetl(openedFile);
+end
+
+function csvString = csvStringFromOpenedFile(openedFile)
+    lineContent = readNextLine(openedFile);
+    csvString = regexp(lineContent, ',', 'split');
+end
+
+function [p, q, euler] = readPQEulerStartingAtIndex(index, commaSeperatedValues)
+                positionX = str2double(commaSeperatedValues{index});
+                positionY = str2double(commaSeperatedValues{index+1});
+                positionZ = str2double(commaSeperatedValues{index+2});
+
+                p = [positionX, positionY, positionZ];
+
+                QuaternionX = str2double(commaSeperatedValues{index+3});
+                QuaternionY = str2double(commaSeperatedValues{index+4});
+                QuaternionZ = str2double(commaSeperatedValues{index+5});
+                QuaternionW =  str2double(commaSeperatedValues{index+6});
+
+                q = [QuaternionX, QuaternionY, QuaternionZ, QuaternionW];
+                
+                EulerX = str2double(commaSeperatedValues{index+7});
+                EulerY = str2double(commaSeperatedValues{index+8});
+                EulerZ = str2double(commaSeperatedValues{index+9});
+                
+                euler = [EulerX, EulerY, EulerZ];
+end
\ No newline at end of file

controls/DataAnalysisTool/Tool/parse_log.m

+function [loggedData] = parse_log(filename, params, expData)
+%parse_log This independent function parses the data stored in the file and
+%returns a structure containing the data
+%   filename    - this is the complete path of the file with the filename
+%   params      - this is the params structure which holds the analysis
+%                 configuration options
+
+% Check if file exists
+if (~exist(filename,'file'))
+    error(strcat(filename, ' does not exist'));
+end
+
+% Open file
+FileID = fopen(filename, 'r');
+
+% Gets the first line of the file
+string = fgetl(FileID);
+
+% Test first line, if not formatted correctly, reject
+if(size(regexp(string, '^#')) == 0)
+    error(strcat(filename, ' is not properly formatted, and does not contain "#" headers'));
+end
+
+% Loop through header lines
+while( regexp(string, '^#') == 1 )
+    
+    %Print out string and move on
+    disp(string)
+    old = string;
+    string = fgetl(FileID);
+    
+end
+
+% Two possibilities for the next two lines:
+%   1) line of headers
+%   2) line of units
+foundHeaders = 0;
+foundUnits = 0;
+
+% Checking current line's type:
+identifier = string(1);
+
+if (regexp(identifier,'%'))
+    foundHeaders = 1;
+    % this is a line of headers; extract headers:
+    headers = strsplit(string);
+    headers{1} = strrep(headers{1},'%', '');
+    numOfHeaders = length(headers);
+else
+    if (regexp(identifier,'&'))
+        foundUnits = 1;
+        % this is a line of units; extract units:
+        units = strsplit(string);
+        units{1} = strrep(units{1},'&','');
+    else
+         error(strcat(filename, ' is not properly formatted, contains undefined line identifier.'));
+    end
+end
+
+% Obtaining the next line
+string = fgetl(FileID); 
+identifier = string(1);
+
+if(foundHeaders)
+    if(regexp(identifier,'&'))
+        foundUnits = 1;
+        % this is a line of units; extract units:
+        units = strsplit(string);
+        units{1} = strrep(units{1},'&','');
+    else
+        error(strcat(filename, ' is not properly formatted, contains or undefined/excessive line identifiers.'));
+    end
+else
+    if(foundUnits)
+        if(regexp(identifier,'%'))
+            % this is a line of headers; extract headers:
+            headers = strsplit(string);
+            headers{1} = strrep(headers{1},'%', '');
+            numOfHeaders = length(headers);
+        end
+    else
+        error('Should never be able to get here');
+    end
+end
+
+% sanity check and clean up
+if(numOfHeaders ~= length(units))
+    error(strcat(filename, ' is not properly formatted, contains unmatched number of units and headers'));
+end
+clear foundHeaders foundUnits;
+
+% Get all data into a single matrix called "log"
+log = [];
+line = zeros(1,numOfHeaders);
+while ~feof(FileID)
+    line = textscan(FileID, '%f', numOfHeaders);
+    line = transpose(cell2mat(line));
+    log = [log;line];
+end
+
+% Converting the log matrix into a expData structure.
+for i = 1:numOfHeaders
+    
+    eval(['loggedData.' headers{i} '.data = log(:,i);']);           % adding data
+    eval(['loggedData.' headers{i} '.unit = cell2mat(units(i));']);           % adding unit
+    eval(['loggedData.' headers{i} '.params.plot = 0;']);           % adding params.plot
+    eval(['loggedData.' headers{i} '.params.style = ''-'';']);      % adding params.style
+    eval(['loggedData.' headers{i} '.params.color = ''b'';']);      % adding params.color
+    eval(['loggedData.' headers{i} '.params.marker = '''';']);      % adding params.marker
+    eval(['loggedData.' headers{i} '.params.backgnd = [1 1 1];']);  % adding params.backgnd
+    
+end
+
+% data types are set
+if exist('params', 'var')
+    
+    % setting the value of <header-name>.params.plot value
+    if(params.plotting.plot == 1)
+        
+        if(params.plotting.subPlot == 1)
+            if(isempty(params.plotting.subData))
+                if(isempty(params.plotting.multiData))
+                    if(isempty(params.plotting.separateData))
+                        for i = 1:numOfHeaders
+                            eval(['loggedData.' headers{i} '.params.plot = 1;']);
+                        end
+                    else
+                        for i = 1:length(params.plotting.separateData)
+                            eval(['loggedData.' params.plotting.separateData{i} '.params.plot = 1;']);
+                        end
+                    end
+                    
+                else
+                    for i = 1:length(params.plotting.multiData)
+                        eval(['loggedData.' params.plotting.multiData{i} '.params.plot = 1;']);
+                    end
+                end
+            else
+                for i = 1:length(params.plotting.subData)
+                    eval(['loggedData.' params.plotting.subData{i} '.params.plot = 1;']);
+                end
+            end
+        end
+        
+        if(params.plotting.multiPlot == 1)
+            if(isempty(params.plotting.multiData))
+                if(isempty(params.plotting.separateData))
+                    for i = 1:numOfHeaders
+                        eval(['loggedData.' headers{i} '.params.plot = 1;']);
+                    end
+                else
+                    for i = 1:length(params.plotting.separateData)
+                        eval(['loggedData.' params.plotting.separateData{i} '.params.plot = 1;']);
+                    end
+                end
+            else
+                for i = 1:length(params.plotting.multiData)
+                    eval(['loggedData.' params.plotting.multiData{i} '.params.plot = 1;']);
+                end
+            end
+        end
+        
+        if(params.plotting.separatePlot == 1)
+            if(isempty(params.plotting.separateData))
+                for i = 1:numOfHeaders
+                    eval(['loggedData.' headers{i} '.params.plot = 1;']);
+                end
+            else
+                for i = 1:length(params.plotting.separateData)
+                    eval(['loggedData.' params.plotting.separateData{i} '.params.plot = 1;']);
+                end
+            end
+        end
+        
+        
+    else
+        % nothing really needed to do here since the default value of
+        % <header-name>.params.plot is 0
+    end 
+    
+    % setting the following values to those set in DataAnalysis.m
+    % 1) <header-name>.params.style
+    % 2) <header-name>.params.color
+    % 3) <header-name>.params.marker
+    % 4) <header-name>.params.backgnd
+    for i = 1:numOfHeaders
+        
+        eval(['loggedData.' headers{i} '.params.style = params.plotting.style;']);
+        eval(['loggedData.' headers{i} '.params.color = params.plotting.color;']);
+        eval(['loggedData.' headers{i} '.params.marker = params.plotting.marker;']);
+        eval(['loggedData.' headers{i} '.params.backgnd = params.plotting.backgnd;']);
+        
+    end
+end
+
+% converting time to relative time
+loggedData.Time.data = loggedData.Time.data - loggedData.Time.data(1);
+
+% this is to parse the Marker field, if it exists
+if (isfield(loggedData,'Marker'))
+    
+    c = zeros(numel(loggedData.Marker.data),1);
+    
+    for i = 2: numel(loggedData.Marker.data)
+         if (loggedData.Marker.data(i)>loggedData.Marker.data(i-1))
+             c(i) = loggedData.Marker.data(i);
+         end
+    end
+    
+    loggedData.Marker.data = c;
+     
+end
+
+% if expData was sent in as a variable, then update the plotting parameters
+% of loggedData to be the same as that in the existing data structure
+if (exist('expData','var'))
+    if(isempty(setdiff(headers,expData.datafields)))
+    for i = 1:numOfHeaders
+        
+        eval(['loggedData.' headers{i} '.params.style = expData.' headers{i} '.params.style;']);
+        eval(['loggedData.' headers{i} '.params.color = expData.' headers{i} '.params.color;']);
+        eval(['loggedData.' headers{i} '.params.marker = expData.' headers{i} '.params.marker;']);
+        eval(['loggedData.' headers{i} '.params.backgnd = expData.' headers{i} '.params.backgnd;']);
+        
+    end
+    end
+end
+
+end
+

controls/DataAnalysisTool/Tool/plot_data.m

+function plot_data(expData, plotParams)
+%PLOT_DATA This function plots the data according to the parameters mentioned in params
+%   expData     - structure that contains the data to be plotted
+%   plotParams  - structure that contains the plotting options
+
+% check plotting switch
+if (~plotParams.plot) 
+    disp('No plotting');
+else
+    %% check separate plotting switch
+    if(plotParams.separatePlot)
+        
+        % bulding the plot_separate statement that will be executed
+        plot_separateString = 'plot_separate(expData,0,''';
+        
+        % extracting data headers to plot
+        if(isempty(plotParams.separateData))
+            headers = fieldnames(expData);  % if none mentioned, use all of the headers
+            headers = headers(2:end);       % except Time :)
+        else
+            headers = plotParams.separateData;
+        end
+        
+        % adding the headers to the plot_separate statement
+        for i = 1:length(headers)
+            if(i==length(headers))
+                plot_separateString = strcat(plot_separateString,headers{i},''');');
+            else
+                plot_separateString = strcat(plot_separateString,headers{i},''',''');
+            end
+        end
+        
+        % executing the plot_separate statement
+        eval(plot_separateString);
+    end
+    
+    %% check multi plotting switch
+    if(plotParams.multiPlot)
+        
+        % building the plot_multi statement that will be executed
+        plot_multiString = 'plot_multi(expData,0,''';
+        
+        % extracting data headers to plot
+        if(isempty(plotParams.multiData)) % if none mentioned, use headers for separate plotting
+            if(isempty(plotParams.separateData))
+                headers = fieldnames(expData); % if no headers mentioned for separate plotting, use all of the headers
+            else
+                headers = plotParams.separateData;
+            end
+        else
+            headers = plotParams.multiData;
+        end
+        
+        % adding the headers to the plot_multi statement
+        for i = 1:length(headers)
+            if(i==length(headers))
+                plot_multiString = strcat(plot_multiString,headers{i},''');');
+            else
+                plot_multiString = strcat(plot_multiString,headers{i},''',''');
+            end
+        end
+        
+        % executing the plot_multi statement
+        eval(plot_multiString);
+    end
+    
+    %% check sub plotting switch
+    if(plotParams.subPlot)
+        
+        % building the plot_sub statement that will be executed
+        plot_subString = 'plot_sub(expData,0,''';
+        
+        % extracting data headers to plot
+        if(isempty(plotParams.subData)) % if none mentioned, use headers mentioned for multi plotting
+            if(isempty(plotParams.multiData)) % if no headers mentioned for multi plotting, use headers mentioned for separate plotting
+                if(isempty(plotParams.separateData)) % if no headers mentioned for separate plotting, use all of the headers
+                    headers = fieldNames(expData);
+                else
+                    headers = plotParams.separateData;
+                end
+            else
+                headers = plotParams.multiData;
+            end
+        else
+            headers = plotParams.subData;
+        end
+        
+        % adding the headers to the plot_sub statement
+        for i = 1:length(headers)
+            if(i==length(headers))
+                plot_subString = strcat(plot_subString,headers{i},''');');
+            else
+                plot_subString = strcat(plot_subString,headers{i},''',''');
+            end
+        end
+        
+        % executing the plot_sub statement
+        eval(plot_subString);
+    end
+    
+end
+
+
+end
+

controls/DataAnalysisTool/Tool/plot_multi.m

+function plot_multi(expData, useMarker, varargin)
+%PLOT_MULTI This function is used to plot multiple headers on the same plot 
+%   expData - structure that stores all of the data
+%   useMarker   - flag to indicated whether or not to plot vertical lines
+%                 at the marker locations
+%   varargin - the header names and corresponding plotting parameters
+%
+%   Example of varargin: 'Pitch','r-','Roll','Yaw','go' 
+%   This means that Pitch will be plotted in red solids, Roll with no
+%   special formatting and Yaw in green circles.
+
+% calculating number of headers
+numOfHeaders = 0;
+headers = {};
+for i = 1:length(varargin)
+    if(~isPlotCharString(varargin{i}))
+        numOfHeaders = numOfHeaders + 1;
+        headers{numOfHeaders} = varargin{i};
+    end
+end
+
+% checking to see validity of varargin
+if (length(varargin) > (numOfHeaders*2))
+    error('Too many arguments entered');
+end
+
+% if the plotting style params for each header are different, diffPlotStyles = 1
+diffPlotStyles = haveDiffPlotStyles(expData,headers);
+
+% extracting time structure
+time = expData.Time;
+
+% extract markerlocations, if any
+markerLocations = [];
+if(useMarker)
+    if(~isfield(expData,'Marker'))
+        error('Error! Attempting to plot markers without Marker field');
+    else
+        markerLocations = find(expData.Marker.data);
+    end
+end
+
+% initiliazing final plot statement to be executed
+plotString = ['plot(time.data,expData.'];
+
+% building the plot statement to be executed
+for i = 1:length(varargin)
+    entity = varargin{i};
+    
+    plotString = strcat(plotString,entity);
+        
+    if (i~=length(varargin))
+        % adding plot style character string
+        if (isPlotCharString(entity))
+            % entity is a plot character string here
+            plotString = strcat(plotString,''',time.data,expData.');
+        else
+            % entity is a header here
+            
+            plotString = strcat(plotString,'.data,');
+            
+            % extracting next entity 
+            nextEntity = varargin{i+1};
+            
+            % checking to see if next entity is a plot character string
+            if (isPlotCharString(nextEntity))
+                % if yes, add the required inverted commas
+                plotString = strcat(plotString,'''');
+            else
+                % if not, add the plot character string from header's params
+                if(diffPlotStyles)
+                    % if the headers have different plotting style params
+                    if(isDefaultPlotCharString(eval(['expData.' entity '.params'])))
+                        % if the plotting params are default, don't bother
+                        plotString = strcat(plotString,'time.data,expData.');
+                    else
+                        % else, construct a plot char string and append
+                        plotCharString = buildPlotCharString(eval(['expData.' entity '.params']));
+                        plotString = strcat(plotString,'''');
+                        plotString = strcat(plotString,plotCharString);
+                        plotString = strcat(plotString,''',');
+                        plotString = strcat(plotString,'time.data,expData.');
+                    end
+                else
+                    % if two or more headers have the same plotting style
+                    % params, don't construct their plot char strings  
+                    plotString = strcat(plotString,'time.data,expData.');                    
+                end
+            end
+            
+        end
+    else
+        % this is the last entity in the varargin cell array
+        
+        if(isPlotCharString(entity))
+             % if a plot character string, add the ending inverted comma
+            plotString = strcat(plotString,''');');
+        else
+            % if not, add the header's data to the plotString
+            plotString = strcat(plotString,'.data');
+            % and also add the plot character string from its params
+            if(diffPlotStyles)
+                 % if the headers have different plotting style params
+                if (isDefaultPlotCharString(eval(['expData.' entity '.params'])))
+                    % if the plotting params are default, don't worry
+                    plotString = strcat(plotString,');');
+                else
+                    % else, construct a plot char string and append
+                    plotCharString = buildPlotCharString(eval(['expData.' entity '.params']));
+                    plotString = strcat(plotString,',''');
+                    plotString = strcat(plotString,plotCharString);
+                    plotString = strcat(plotString,''');');
+                end
+            else
+                % if two or more headers have the same plotting style
+                % params, don't construct their plot char strings  
+                plotString = strcat(plotString,');');
+            end
+        end
+    end
+   
+end
+
+%% plotting stuff
+figure;                 % opening a new figure
+whitebg(gcf,[1 1 1]);   % making sure the background is set to white
+eval(plotString);       % plotting
+grid ON;                % plotting grid lines
+xlim([0,time.data(end)]); % setting x-axis limits
+xlabel(['Time (' time.unit ')']);       % setting x-axis label
+
+%constructing yAxisLabel
+yAxisLabel = [];
+for i = 1:numOfHeaders
+    if i == numOfHeaders
+        yAxisLabel = strcat(yAxisLabel,headers{i});
+        if(eval(['isempty(expData.' headers{1} '.unit)']))
+            break;
+        else
+            yAxisLabel = strcat(yAxisLabel,'(', eval(['expData.' headers{1} '.unit']),')');
+        end
+    else
+        yAxisLabel = strcat(yAxisLabel,headers{i},',');
+    end
+end
+
+ylabel(yAxisLabel);
+
+% constructing statement for inserting the legend
+legendString = ['legend('''];
+for i = 1:numOfHeaders
+    if(i == numOfHeaders)
+        legendString = strcat(legendString,headers{i},''',''Location'',''NorthWest'');');
+    else
+        legendString = strcat(legendString,headers{i},''',''');
+    end
+end
+
+eval(legendString);
+
+% plotting markers, if any
+for i = 1:numel(markerLocations)
+    %hx = graph2d.constantline(time.data(markerLocations(i)),'Linestyle','--', 'Color', [0.7 0.7 0.7]);
+    %changedependvar(hx,'x');
+    text(time.data(markerLocations(i)),(min(ylim)+max(ylim))/2,num2str(i));
+end
+    
+end
+