-
Notifications
You must be signed in to change notification settings - Fork 10
/
tutorial3_script.m
172 lines (156 loc) · 7.02 KB
/
tutorial3_script.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% The ROC Toolbox is the proprietary property of The Regents of the
% University of California (“The Regents.”)
%
% Copyright © 2014 The Regents of the University of California, Davis
% campus. All Rights Reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted by nonprofit, research institutions for
% research use only, provided that the following conditions are met:
%
% • Redistributions of source code must retain the above copyright
% notice, this list of conditions and the following disclaimer.
%
% • Redistributions in binary form must reproduce the above copyright
% notice, this list of conditions and the following disclaimer in the
% documentation and/or other materials provided with the distribution.
%
% • The name of The Regents may not be used to endorse or promote
% products derived from this software without specific prior written
% permission.
%
% The end-user understands that the program was developed for research
% purposes and is advised not to rely exclusively on the program for any
% reason.
%
% THE SOFTWARE PROVIDED IS ON AN "AS IS" BASIS, AND THE REGENTS HAVE NO
% OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR
% MODIFICATIONS. THE REGENTS SPECIFICALLY DISCLAIM ANY EXPRESS OR IMPLIED
% WARRANTIES, INCLUDING BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
% MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
% IN NO EVENT SHALL THE REGENTS BE LIABLE TO ANY PARTY FOR DIRECT,
% INDIRECT, SPECIAL, INCIDENTAL, EXEMPLARY OR CONSEQUENTIAL DAMAGES,
% INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR
% SERVICES, LOSS OF USE, DATA OR PROFITS, OR BUSINESS INTERRUPTION,
% HOWEVER CAUSED AND UNDER ANY THEORY OF LIABILITY WHETHER IN CONTRACT,
% STRICT LIABILITY OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN
% ANY WAY OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
% ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
%
% If you do not agree to these terms, do not download or use the software.
% This license may be modified only in a writing signed by authorized
% signatory of both parties.
%
% For commercial license information please contact
% copyright@ucdavis.edu.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% This is the code that accompanies tutorial 3. The objectives of this
% tutorial are:
% 1) Use the roc_import_data function
% 2) Extract group data by using the get_group_data function
%
% In total, four models will be fit to the data. The models that will be
% fit to the data include the EVSD model, the UVSD model, the standard DPSD
% model (Ro and F parmaeters estimated), and the MSD model with the
% lambda_targ and Dprime1_targ parameters estimated.
%% Clear workspace and command window
clear all;
clc;
%% Define the directory to save the data to, and a variable to store file names
% This will be the examples directory of the toolbox
saveDir = fullfile(fileparts(which('tutorial3_data.csv')),'tutorial3');
mkdir(saveDir);
%% Import the data from tutorial3_data.csv
rawData = roc_import_data('tutorial3_data.csv');
% Note that rawData is a cell array of structures with the fields
% condLabels, subID, groupID, targf, and luref.
%% Define some information about the design based on the first subject
[nConds,nBins] = size(rawData{1}.targf); % Number of conditions and rating bins
nSubs = length(rawData); % Number of subjects
fitStat = '-LL'; % The two options are '-LL' and 'SSE'
%% Fit the models to each subjects data, and save the rodData structure
subFiles = {};
for i = 1:length(rawData)
% Initialize rocData anew for each subject
rocData = [];
% Fit the UVSD model to the data
model = 'uvsd';
modelID = 'evsd_model';
parNames = {'Dprime'};
[x0, LB, UB] = gen_pars(model,nBins,nConds,parNames);
rocData = roc_solver(rawData{i}.targf,rawData{i}.luref, ...
model,fitStat,x0,LB,UB, ...
'subID',rawData{i}.subID, ...
'groupID',rawData{i}.groupID, ...
'condLabels',rawData{i}.condLabels, ...
'modelID',modelID, ...
'saveFig',saveDir, ...
'figTimeout',2, ...
'append',rocData);
% Fit the UVSD model to the data
model = 'uvsd';
modelID = 'uvsd_model';
parNames = {'Dprime' 'Vo'};
[x0, LB, UB] = gen_pars(model,nBins,nConds,parNames);
rocData = roc_solver(rawData{i}.targf,rawData{i}.luref, ...
model,fitStat,x0,LB,UB, ...
'subID',rawData{i}.subID, ...
'groupID',rawData{i}.groupID, ...
'condLabels',rawData{i}.condLabels, ...
'modelID',modelID, ...
'saveFig',saveDir, ...
'figTimeout',2, ...
'append',rocData);
% Fit the DPSD model to the data
model = 'dpsd';
modelID = 'dpsd_model';
parNames = {'Ro' 'F'};
[x0, LB, UB] = gen_pars(model,nBins,nConds,parNames);
rocData = roc_solver(rawData{i}.targf,rawData{i}.luref, ...
model,fitStat,x0,LB,UB, ...
'subID',rawData{i}.subID, ...
'groupID',rawData{i}.groupID, ...
'condLabels',rawData{i}.condLabels, ...
'modelID',modelID, ...
'saveFig',saveDir, ...
'figTimeout',2, ...
'append',rocData);
% Fit the MSD model to the data (version 1)
model = 'msd';
modelID = 'msd_model';
parNames = {'lambda_targ' 'Dprime1_targ'};
[x0, LB, UB] = gen_pars(model,nBins,nConds,parNames);
rocData = roc_solver(rawData{i}.targf,rawData{i}.luref, ...
model,fitStat,x0,LB,UB, ...
'subID',rawData{i}.subID, ...
'groupID',rawData{i}.groupID, ...
'condLabels',rawData{i}.condLabels, ...
'modelID',modelID, ...
'saveFig',saveDir, ...
'figTimeout',2, ...
'append',rocData);
% Save rocData to a .mat file for the current subject
matFile = fullfile(saveDir,strcat(rawData{i}.subID,'_rocData.mat'));
subFiles{i} = matFile;
save(matFile,'rocData');
end
%% Extract the group data for each model and save to a .mat and .csv file
% Extract the EVSD data
evsdPrefix = fullfile(saveDir,'evsd_group_data');
evsdData = get_group_data(subFiles,'uvsd',1,'rocData','saveCSV',evsdPrefix);
% Note that the model input here is the same as the model used with the
% roc_solver function. The input following the model is the index, which
% indicates what element of the structure array to extract the data from.
% Extract the UVSD data
uvsdPrefix = fullfile(saveDir,'uvsd_group_data');
uvsdData = get_group_data(subFiles,'uvsd',2,'rocData','saveCSV',uvsdPrefix);
% Extract the DPSD data
dpsdPrefix = fullfile(saveDir,'dpsd_group_data');
dpsdData = get_group_data(subFiles,'dpsd',1,'rocData','saveCSV',dpsdPrefix);
% Extract the MSD data
msdPrefix = fullfile(saveDir,'msd_group_data');
msdData = get_group_data(subFiles,'msd',1,'rocData','saveCSV',msdPrefix);
% Save the group data structures to a .mat file
save(fullfile(saveDir,'all_group_data.mat'),'evsdData','uvsdData', ...
'dpsdData','msdData');