update on WIP BSM class
This commit is contained in:
p147685
parent
20b2d4f22b
commit
3440e5b6d8
@ -12,14 +12,14 @@ classdef BSM<handle
|
||||
ActiveColumns %store the columns to be analized
|
||||
U_orig %store the U field of SPM
|
||||
TargetFolder %target folder
|
||||
% option below obsolete?
|
||||
% option below obsolete?
|
||||
BSMToolboxPath%store path to BSMToolbox
|
||||
SPMPath;%store path to SPM folder
|
||||
SPMIndexList=[];
|
||||
end
|
||||
properties (Dependent) %dependent properties
|
||||
NumSPMs% number of SPM.mat files to process
|
||||
|
||||
|
||||
end
|
||||
properties %constants
|
||||
BSMMethod={'Traditional BSM Rissman et al', 'Adapted BSM Rissman et al', 'Fast approach (Mumford et al)', 'Adapted fast approach','none'};
|
||||
@ -32,7 +32,7 @@ classdef BSM<handle
|
||||
% obj.calc([1 3 6]) to indicate which SPM.mat file to calculate
|
||||
|
||||
|
||||
SPMidx=[];% will contain the index to the SPMs to work on
|
||||
SPMidx=[];% will contain the index to the SPMs to work on
|
||||
if logical(numel(varargin))
|
||||
SPMidx=varargin{1};
|
||||
end
|
||||
@ -52,20 +52,30 @@ classdef BSM<handle
|
||||
if numel(SPMidx)>1
|
||||
obj.SPMIndexList=SPMidx;
|
||||
SPMidx=obj.SPMIndexList(end);
|
||||
try
|
||||
obj.Calc(SPMidx); %handle the single case
|
||||
catch ME
|
||||
%if the identifier matches, just continue with next SPM
|
||||
if ~any(strcmpi(ME.identifier,...
|
||||
{'BSM:CoreCalc:SPMxBFOrder:invalid'...
|
||||
,'BSM:CoreCalc:SPMSess:invalid'...
|
||||
}))
|
||||
rethrow(ME)
|
||||
else
|
||||
disp(ME.message);
|
||||
end
|
||||
end
|
||||
obj.SPMIndexList=obj.SPMIndexList(1:end-1);
|
||||
if isempty(obj.SPMIndexList)
|
||||
return;
|
||||
else
|
||||
obj.Calc(obj.SPMIndexList);% recursively run the rest of the list
|
||||
end
|
||||
else % deal with single entry
|
||||
obj.CoreCalc(SPMidx)
|
||||
end
|
||||
%% start dealing with val is a single entry
|
||||
%% do the calculation
|
||||
%% clean up
|
||||
%% make SPMIndexList one shorter, return if not possible
|
||||
%% next recursion loop.
|
||||
warning('OFF', 'MATLAB:MKDIR:DirectoryExists');
|
||||
%this try catch block will handle any errors that might ocure
|
||||
%warning will not remain off by accident
|
||||
try
|
||||
catch ME
|
||||
warning('ON', 'MATLAB:MKDIR:DirectoryExists');
|
||||
rethrow(ME);
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
end
|
||||
methods %constructor and set/get methods
|
||||
@ -82,7 +92,7 @@ classdef BSM<handle
|
||||
[val,TF]=obj.MyGetVal('Acfl',varargin);if TF;obj.Acfl=val;end
|
||||
end
|
||||
% initialize spm job enviourment
|
||||
spm_jobman('initcfg');
|
||||
spm_jobman('initcfg');
|
||||
end
|
||||
function val=get.NumSPMs(obj)
|
||||
val=numel(obj.SPMs);
|
||||
@ -97,7 +107,7 @@ classdef BSM<handle
|
||||
obj.Type=val;
|
||||
end
|
||||
function set.Acfl(obj,val)
|
||||
%allow clearing
|
||||
%allow clearing
|
||||
if isempty(val)
|
||||
obj.Acfl=[];
|
||||
end
|
||||
@ -140,12 +150,111 @@ classdef BSM<handle
|
||||
if any(not(TF))
|
||||
id='BSM:SetSPMs:FileNotFound';
|
||||
msg=sprintf('file not found\t%s\n',val{not(TF)});
|
||||
throw(MException(id,msg));
|
||||
throw(MException(id,msg));
|
||||
end
|
||||
obj.SPMs=val;
|
||||
end
|
||||
end
|
||||
methods %private functions
|
||||
function CoreCalc(obj,idx)
|
||||
fprintf('working on :%d: %s\n',idx,obj.SPMs{idx});
|
||||
% how to store the current status of warning and restore curent
|
||||
WarnStat=warning;
|
||||
warning('OFF', 'MATLAB:MKDIR:DirectoryExists');
|
||||
%this try catch block will handle any errors that might ocure
|
||||
%warning will not remain off by accident
|
||||
try
|
||||
SpmFile=obj.SPMs{idx};
|
||||
load(SpmFile); %#ok<LOAD>
|
||||
%% exception block
|
||||
%NB these exception has not been tested properly by the
|
||||
if (SPM.xBF.order ~=1 )
|
||||
%TestBSMClass program
|
||||
%throw an error. The calling function should properly
|
||||
%handle the error.
|
||||
id='BSM:CoreCalc:SPMxBFOrder:invalid';
|
||||
msg=sprintf('%s\n','Problem found', ...
|
||||
'No canonical HRF was used to model the data', ...
|
||||
'Current file will be skipped');
|
||||
throw(MException(id,msg));
|
||||
end
|
||||
if (length(SPM.Sess) > 1 )
|
||||
id='BSM:CoreCalc:SPMSess:invalid';
|
||||
msg=sprintf('%s\n',...
|
||||
'Problem found', ...
|
||||
'Multiple sessions in one SPM.mat not supported', ...
|
||||
'Current file will be skipped');
|
||||
throw(MException(id,msg));
|
||||
end
|
||||
% end exception block
|
||||
%% set local variables
|
||||
SPMOrig = SPM;
|
||||
UOrig = SPM.Sess(1).U;
|
||||
[ActCol,PasCol,AllCol]=obj.GetColDef(UOrig);
|
||||
LocalTargetFolder = fullfile(fileparts(SpmFile),'BSM');%RR replace BSM by a obj.BSMDir so user can modify this
|
||||
%% create directory
|
||||
mkdir(LocalTargetFolder);
|
||||
% loop over ActCol
|
||||
for c=1:length(ActCol)
|
||||
% get current col, get other col
|
||||
CurCol=ActCol(c);
|
||||
OthCol=setdiff(1:length(ActCol),CurCol);
|
||||
TargetFolderCurCol=fullfile(LocalTargetFolder,sprintf('col_%04d', CurCol));
|
||||
for e=1:numel(UOrig(CurCol).ons)% loop over events
|
||||
U=obj.GetU(UOrig,e,c)%build U
|
||||
% build SPM
|
||||
% process SPM
|
||||
% Cleanup
|
||||
end% end loop
|
||||
% pack per event result
|
||||
% Cleanup
|
||||
|
||||
end % end loop act. col
|
||||
% restore warning status
|
||||
warning(WarnStat);
|
||||
catch ME %turn matlab warning back on
|
||||
warning(WarnStat);
|
||||
rethrow(ME);
|
||||
end
|
||||
end
|
||||
function U=GetU(obj,UOrig,Event,Col)
|
||||
U=struct('name',{},'ons', [], 'dur',[], 'P',[], 'dt', [], 'u', [],'pst',[]);
|
||||
idx=1;
|
||||
%split out current event as first condition
|
||||
U(idx).name{1} = sprintf('%s_%d',UOrig(Col).name{1},Event);
|
||||
U(idx).ons = UOrig(Col).ons(Event);
|
||||
U(idx).dur = UOrig(Col).dur(Event);
|
||||
U(idx).P = UOrig(Col).P;
|
||||
U(idx).dt = UOrig(Col).dt;
|
||||
%optional add all other events as the next condition
|
||||
switch obj.Type
|
||||
case {1,2}
|
||||
idx = idx +1;
|
||||
OtherTrials=setdiff(1:numel(UOrig(Col).ons),Event);
|
||||
U(idx).name{1} = sprintf('%s_oe',UOrig(Col).name{1});
|
||||
U(idx).ons = UOrig(Col).ons(OtherTrials);
|
||||
U(idx).dur = UOrig(Col).dur(OtherTrials);
|
||||
U(idx).P = UOrig(Col).P;
|
||||
U(idx).dt = UOrig(Col).dt;
|
||||
case {3,4}
|
||||
otherwise
|
||||
end
|
||||
% deal with other conditions
|
||||
switch obj.Type
|
||||
case {1,4} %put all other conditions in one column
|
||||
case {2,3} %keep other conditions each in their own column
|
||||
otherwise
|
||||
end
|
||||
end
|
||||
function [ActCol,PasCol,AllCol]=GetColDef(obj,U)
|
||||
AllCol=1:length(U);
|
||||
if ~isempty(obj.Acfl)
|
||||
PasCol = AllCol(obj.Acfl); %cf line 53 in spm_bsm.m
|
||||
else
|
||||
PasCol = [];
|
||||
end
|
||||
ActCol = setdiff(AllCol,PasCol);
|
||||
end
|
||||
function set.SPMPath(obj,~)
|
||||
SPMFound=which('spm'); %check if SPM in searchpath
|
||||
if isempty(SPMFound) %SPM not found
|
||||
|
||||
@ -1,4 +1,6 @@
|
||||
%% This code will check the BSM class code in a very basic way.
|
||||
%% BSM code validity check.
|
||||
% This code will check the BSM class code in a very basic way.
|
||||
%
|
||||
%% create an instance
|
||||
B=BSM;
|
||||
%%
|
||||
@ -91,4 +93,6 @@ catch ME
|
||||
end
|
||||
end
|
||||
%%
|
||||
B.Acfl=[];
|
||||
B.Acfl=[];
|
||||
%% Test Calc routine
|
||||
B.Calc
|
||||
Loading…
x
Reference in New Issue
Block a user