update on WIP BSM class
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p147685
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3440e5b6d8
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@ -12,14 +12,14 @@ classdef BSM<handle
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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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% 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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@ -32,7 +32,7 @@ classdef BSM<handle
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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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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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@ -52,20 +52,30 @@ classdef BSM<handle
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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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%% start dealing with val is a single entry
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%% do the calculation
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%% clean up
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%% make SPMIndexList one shorter, return if not possible
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%% next recursion loop.
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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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catch ME
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warning('ON', 'MATLAB:MKDIR:DirectoryExists');
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rethrow(ME);
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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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@ -82,7 +92,7 @@ classdef BSM<handle
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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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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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@ -97,7 +107,7 @@ classdef BSM<handle
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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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%allow clearing
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if isempty(val)
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obj.Acfl=[];
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end
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@ -140,12 +150,111 @@ classdef BSM<handle
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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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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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@ -1,4 +1,6 @@
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%% This code will check the BSM class code in a very basic way.
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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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@ -91,4 +93,6 @@ catch 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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B.Acfl=[];
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%% Test Calc routine
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B.Calc
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