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some refactoring
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ian committed Jun 10, 2014
1 parent 770fa5f commit dd6cd2d
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Showing 4 changed files with 176 additions and 195 deletions.
41 changes: 21 additions & 20 deletions omniplex/LFPAnalysis.m
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,7 @@ function getFiles(ego, force)
return
end
end
checkPaths(ego);
end

% ===================================================================
Expand Down Expand Up @@ -151,6 +152,26 @@ function parse(ego)
plot(ego,'normal');
end

% ===================================================================
%> @brief reparse data after an initial parse
%>
%> @param
%> @return
% ===================================================================
function reparse(ego)
if isempty(ego.lfpfile) %we obviously haven't done an initial parse
parse(ego);
return
end
ego.ft = struct();
ego.results = struct();
parseEvents(ego.p);
parseLFPs(ego);
select(ego);
selectTrials(ego);
getFieldTripLFPs(ego);
end

% ===================================================================
%> @brief reparse data after an initial parse
%>
Expand All @@ -172,26 +193,6 @@ function toggleSaccadeRealign(ego)
disp('Saccade Realign is now DISABLED...')
end
end
% ===================================================================
%> @brief reparse data after an initial parse
%>
%> @param
%> @return
% ===================================================================
function reparse(ego)
if isempty(ego.lfpfile) %we obviously haven't done an initial parse
parse(ego);
return
end
ego.ft = struct();
ego.results = struct();
parseEvents(ego.p);
parseLFPs(ego);
select(ego);
selectTrials(ego);
getFieldTripLFPs(ego);
plot(ego,'normal');
end

% ===================================================================
%> @brief
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74 changes: 19 additions & 55 deletions omniplex/analysisCore.m
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@
measureRange@double = [0.1 0.2]
%> default range to plot
plotRange@double = [-0.2 0.4]
%> root directory to check for data if files can't be found
rootDirectory@char = ''
end

%--------------------ABSTRACT PROPERTIES----------%
Expand Down Expand Up @@ -101,6 +103,12 @@ function checkPaths(ego)
warning('Can''t find valid source directory')
end
end
if ~isempty(regexpi(ego.dir,'^/Users/'))
re = regexpi(ego.dir,'^(?<us>/Users/[^/]+)(?<rd>.+)','names');
if ~isempty(re.rd)
ego.dir = ['~' re.rd];
end
end
end
if isprop(ego,'p') && isa(ego.p,'plxReader')
ego.p.dir = ego.dir;
Expand Down Expand Up @@ -605,7 +613,7 @@ function initialiseStats(ego)
end

% ===================================================================
%> @brief format for ROC
%> @brief format data for ROC
%>
%> @param dp scores for "signal" distribution
%> @param dn scores for "noise" distribution
Expand All @@ -622,7 +630,7 @@ function initialiseStats(ego)
end

% ===================================================================
%> @brief ROC
%> @brief ROC see http://www.subcortex.net/research/code/area_under_roc_curve
%>
%> @param data - [class , score] matrix
%> @return tp - true positive rate
Expand Down Expand Up @@ -660,60 +668,16 @@ function initialiseStats(ego)
% ===================================================================
%> @brief Area under ROC
%>
% ===================================================================
function [A,Aci] = auc(ego,data,alpha,flag,nboot,varargin);
% [A,Aci] = auc(data,alpha,flag,nboot,varargin);
%
% INPUTS
% data - Nx2 matrix [t , y], where
% t - a vector indicating class value (>0 positive class, <=0 negative)
% y - score value for each instance
%
% OPTIONAL
% alpha - level for confidence intervals (eg., enter 0.05 if you want 95% CIs)
% flag - 'hanley' yields Hanley-McNeil (1982) asymptotic CI
% 'maxvar' yields maximum variance CI
% 'mann-whitney'
% 'logit'
% 'boot' yields bootstrapped CI (DEFAULT)
% nboot - if 'boot' is set, specifies # of resamples, default=1000
% varargin - additional arguments to pass to BOOTCI, only valid for 'boot'
% this assumes you have the STATs toolbox, otherwise it's
% ignored and a crude percentile bootstrap is estimated.
%
% OUTPUTS
% A - area under ROC
% Aci - confidence intervals
%
% EXAMPLES
% % Classic binormal ROC. 100 samples from each class, with a unit mean separation
% % between the classes.
% >> mu = 1;
% >> y = [randn(100,1)+mu ; randn(100,1)];
% >> t = [ones(100,1) ; zeros(100,1)];
% >> [A,Aci] = auc([t,y])
% >> trueA = normcdf(mu/sqrt(1+1^2))
%
% REFERENCE
% Gengsheng Qin & Lejla Hotilovac. Comparison of non-parametric
% confidence intervals for the area under the ROC curve of a continuous
% scale diagnostic test.
% Stat Methods Med Res 17:207, 2008

%> @param data - [class , score] matrix
%> @param alpha - level for confidence intervals (eg., enter 0.05 if you want 95% CIs)
%> @param flag - 'hanley' yields Hanley-McNeil (1982) asymptotic CI; 'maxvar' yields maximum variance CI;'mann-whitney';'logit';'boot' yields bootstrapped CI (DEFAULT)
%> @param nboot - if 'boot' is set, specifies # of resamples, default=1000
%> @param varargin - additional arguments to pass to BOOTCI, only valid for 'boot' this assumes you have the STATs toolbox, otherwise it's ignored and a crude percentile bootstrap is estimated.
%> @return A - area under ROC
%> @return Aci - confidence intervals
% ===================================================================
function [A,Aci] = auc(ego,data,alpha,flag,nboot,varargin)
% $ Copyright (C) 2011 Brian Lau http://www.subcortex.net/ $
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
if size(data,2) ~= 2
error('Incorrect input size in AUC!');
end
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