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284
resources/BSM_Class/BSM.m
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284
resources/BSM_Class/BSM.m
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classdef BSM<handle
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%BSM Summary of this class goes here
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% Detailed explanation goes here
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properties %public properties
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SPMs={}; %field to contain the full path of all SPM.mat files to be analysed
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Acfl %columns in SPM.xX.X to ignore
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Type=1; %BSM type 1..4 5: none
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end
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properties %private properties
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SPM_orig %temporary storage for SPM.mat file
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ActiveColumns %store the columns to be analized
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U_orig %store the U field of SPM
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TargetFolder %target folder
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% option below obsolete?
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BSMToolboxPath%store path to BSMToolbox
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SPMPath;%store path to SPM folder
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SPMIndexList=[];
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end
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properties (Dependent) %dependent properties
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NumSPMs% number of SPM.mat files to process
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end
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properties %constants
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BSMMethod={'Traditional BSM Rissman et al', 'Adapted BSM Rissman et al', 'Fast approach (Mumford et al)', 'Adapted fast approach','none'};
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end
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methods %user callable methods
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function Calc(obj,varargin)
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% obj.calc to apply calculate to all SPM.mat files
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% obj.calc(n) to calculated the nth SPM.mat file
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% obj.calc([1 3 6]) to indicate which SPM.mat file to calculate
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SPMidx=[];% will contain the index to the SPMs to work on
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if logical(numel(varargin))
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SPMidx=varargin{1};
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end
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%check number of input arguments
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if ~logical(obj.NumSPMs)%nothing to do
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fprintf('== == == Nothing to do: done == == ==\n')
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return;
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end
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if isempty(SPMidx)
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SPMidx=1:obj.NumSPMs;
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end
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if ~isnumeric(SPMidx)||~all(isfinite(SPMidx))||min(SPMidx)<1||max(SPMidx)>obj.NumSPMs
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id='BSM:Calc:InvalidIndex';
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msg='Invalid Index';
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throw(MException(id,msg));
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end
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if numel(SPMidx)>1
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obj.SPMIndexList=SPMidx;
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SPMidx=obj.SPMIndexList(end);
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try
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obj.Calc(SPMidx); %handle the single case
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catch ME
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%if the identifier matches, just continue with next SPM
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if ~any(strcmpi(ME.identifier,...
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{'BSM:CoreCalc:SPMxBFOrder:invalid'...
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,'BSM:CoreCalc:SPMSess:invalid'...
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}))
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rethrow(ME)
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else
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disp(ME.message);
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end
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end
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obj.SPMIndexList=obj.SPMIndexList(1:end-1);
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if isempty(obj.SPMIndexList)
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return;
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else
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obj.Calc(obj.SPMIndexList);% recursively run the rest of the list
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end
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else % deal with single entry
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obj.CoreCalc(SPMidx)
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end
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end
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end
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methods %constructor and set/get methods
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function obj = BSM(varargin)
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%BSM Construct an instance of this class
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%option: parse the info of a matlab batch file? see
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%tbx_cf_bsm?
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%TODO:
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% set default values
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obj.SPMPath=[]; %get the SPM path
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if nargin>0
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[val,TF]=obj.MyGetVal('SPMs',varargin);if TF;obj.SPMs=val;end
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[val,TF]=obj.MyGetVal('Type',varargin);if TF;obj.Type=val;end
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[val,TF]=obj.MyGetVal('Acfl',varargin);if TF;obj.Acfl=val;end
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end
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% initialize spm job enviourment
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spm_jobman('initcfg');
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end
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function val=get.NumSPMs(obj)
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val=numel(obj.SPMs);
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end
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function set.Type(obj,val)
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%check allowed input
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if ~isnumeric(val)|| any(~ismember(val,1:5))
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id='BSM:Type:invalid';
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msg='use a value in the range 1..5';
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throw(MException(id,msg));
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end
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obj.Type=val;
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end
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function set.Acfl(obj,val)
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%allow clearing
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if isempty(val)
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obj.Acfl=[];
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end
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if ~isnumeric(val) || any(val<1) || any(~isfinite(val))
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id='BSM:Acfl:invalid';
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msg='set an array of positive integer values to the Acfl field';
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throw(MException(id,msg));
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end
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obj.Acfl=val;
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end
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function set.SPMs(obj,val)
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%set the SPMs to be analysed
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%obj.SPMs=<val>
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%possible values for <val>
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% {} : clear the SPMs field
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% {'ui'} : ask user input
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if ~iscell(val)
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fprintf('%s\n',...
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'Use any of the following options',...
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'obj.SPMs={}',...
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'obj.SPMs={''ui''}',...
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'obj.SPMs={<Ful path to SPM.mat>}');
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return
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end
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if isempty(val) %allow empty input
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return;
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end
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if strcmpi(val{1},'ui')
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[P,sts]=spm_select([1 Inf],'mat','select the SPM.mat files',obj.SPMs,pwd,'^SPM.mat');
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if ~logical(sts);return;end
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if iscell(P)
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val=P;
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else
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val=cellstr(P);
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end
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end
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% capture file not found somewhat clever
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TF=cellfun(@exist,val);
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if any(not(TF))
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id='BSM:SetSPMs:FileNotFound';
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msg=sprintf('file not found\t%s\n',val{not(TF)});
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throw(MException(id,msg));
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end
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obj.SPMs=val;
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end
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end
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methods %private functions
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function CoreCalc(obj,idx)
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fprintf('working on :%d: %s\n',idx,obj.SPMs{idx});
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% how to store the current status of warning and restore curent
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WarnStat=warning;
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warning('OFF', 'MATLAB:MKDIR:DirectoryExists');
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%this try catch block will handle any errors that might ocure
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%warning will not remain off by accident
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try
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SpmFile=obj.SPMs{idx};
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load(SpmFile); %#ok<LOAD>
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%% exception block
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%NB these exception has not been tested properly by the
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if (SPM.xBF.order ~=1 )
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%TestBSMClass program
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%throw an error. The calling function should properly
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%handle the error.
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id='BSM:CoreCalc:SPMxBFOrder:invalid';
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msg=sprintf('%s\n','Problem found', ...
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'No canonical HRF was used to model the data', ...
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'Current file will be skipped');
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throw(MException(id,msg));
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end
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if (length(SPM.Sess) > 1 )
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id='BSM:CoreCalc:SPMSess:invalid';
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msg=sprintf('%s\n',...
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'Problem found', ...
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'Multiple sessions in one SPM.mat not supported', ...
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'Current file will be skipped');
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throw(MException(id,msg));
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end
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% end exception block
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%% set local variables
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SPMOrig = SPM;
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UOrig = SPM.Sess(1).U;
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[ActCol,PasCol,AllCol]=obj.GetColDef(UOrig);
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LocalTargetFolder = fullfile(fileparts(SpmFile),'BSM');%RR replace BSM by a obj.BSMDir so user can modify this
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%% create directory
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mkdir(LocalTargetFolder);
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% loop over ActCol
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for c=1:length(ActCol)
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% get current col, get other col
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CurCol=ActCol(c);
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OthCol=setdiff(1:length(ActCol),CurCol);
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TargetFolderCurCol=fullfile(LocalTargetFolder,sprintf('col_%04d', CurCol));
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for e=1:numel(UOrig(CurCol).ons)% loop over events
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U=obj.GetU(UOrig,e,c)%build U
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% build SPM
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% process SPM
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% Cleanup
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end% end loop
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% pack per event result
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% Cleanup
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end % end loop act. col
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% restore warning status
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warning(WarnStat);
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catch ME %turn matlab warning back on
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warning(WarnStat);
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rethrow(ME);
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end
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end
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function U=GetU(obj,UOrig,Event,Col)
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U=struct('name',{},'ons', [], 'dur',[], 'P',[], 'dt', [], 'u', [],'pst',[]);
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idx=1;
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%split out current event as first condition
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U(idx).name{1} = sprintf('%s_%d',UOrig(Col).name{1},Event);
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U(idx).ons = UOrig(Col).ons(Event);
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U(idx).dur = UOrig(Col).dur(Event);
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U(idx).P = UOrig(Col).P;
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U(idx).dt = UOrig(Col).dt;
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%optional add all other events as the next condition
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switch obj.Type
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case {1,2}
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idx = idx +1;
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OtherTrials=setdiff(1:numel(UOrig(Col).ons),Event);
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U(idx).name{1} = sprintf('%s_oe',UOrig(Col).name{1});
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U(idx).ons = UOrig(Col).ons(OtherTrials);
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U(idx).dur = UOrig(Col).dur(OtherTrials);
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U(idx).P = UOrig(Col).P;
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U(idx).dt = UOrig(Col).dt;
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case {3,4}
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otherwise
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end
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% deal with other conditions
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switch obj.Type
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case {1,4} %put all other conditions in one column
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case {2,3} %keep other conditions each in their own column
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otherwise
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end
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end
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function [ActCol,PasCol,AllCol]=GetColDef(obj,U)
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AllCol=1:length(U);
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if ~isempty(obj.Acfl)
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PasCol = AllCol(obj.Acfl); %cf line 53 in spm_bsm.m
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else
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PasCol = [];
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end
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ActCol = setdiff(AllCol,PasCol);
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end
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function set.SPMPath(obj,~)
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SPMFound=which('spm'); %check if SPM in searchpath
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if isempty(SPMFound) %SPM not found
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error('please add SPM to your path before trying to run BSM');
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%to do add a check on spm version
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end
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obj.SPMPath=fileparts(SPMFound);
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end
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function[val,TF]=MyGetVal(~,selector,List)
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TF=strcmpi(selector,List);
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if any(TF) %spmpath is set as option
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k=find(TF, 1 );%find the first instance
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if (k+1)>numel(List)
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id='BSM:getval:ReadBeyondEndInput';
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msg=sprintf('use name value pairs\nlast entry is a name');
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throw(MException(id,msg));
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end
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val=List{k+1};
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TF=true;
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else
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val=false;
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TF=false;
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end
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end
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end
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end
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98
resources/BSM_Class/TestBSMClass.m
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98
resources/BSM_Class/TestBSMClass.m
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@ -0,0 +1,98 @@
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%% BSM code validity check.
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% This code will check the BSM class code in a very basic way.
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%
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%% create an instance
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B=BSM;
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%%
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clear B
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try
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B=BSM('type',3,'Acfl',[],'SPMs'); %#ok<*NASGU> %will create an error
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catch ME
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if strcmpi(ME.identifier,'BSM:getval:ReadBeyondEndInput')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME);
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end
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end
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%%
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clear B
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B=BSM('type',1,'Acfl',[],'SPMs',{});
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%% set SPMs validity check
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B.SPMs=''; %should produce instructions on how to set SPMs
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B.SPMs={'ui'}; %get input from the user
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tmp=B.SPMs; %store for future use
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%B.SPMs={'ui'}; %calling it again will allow me to edit the list
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B.SPMs={}; %clear out SPMs
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try
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B.SPMs={'SPM.mat';'onzin.mat'}; %provides an error if file does not exist
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catch ME
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if strcmpi(ME.identifier,'BSM:SetSPMs:FileNotFound')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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B.SPMs=tmp;
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%% set Type check
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try
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B.Type='onzin'; %gives an error
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catch ME
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if strcmpi(ME.identifier,'BSM:Type:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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try
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B.Type=0; %gives an error
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catch ME
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if strcmpi(ME.identifier,'BSM:Type:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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B.Type=1; % correct call
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%% set Acfl check
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try
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B.Acfl=0;
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catch ME
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if strcmpi(ME.identifier,'BSM:Acfl:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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try
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B.Acfl=-5;
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catch ME
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if strcmpi(ME.identifier,'BSM:Acfl:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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try
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B.Acfl='test';
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catch ME
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if strcmpi(ME.identifier,'BSM:Acfl:invalid')
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disp('error properly handled')
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disp(ME);
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else
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rethrow(ME)
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end
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end
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%%
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B.Acfl=[];
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%% Test Calc routine
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B.Calc
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