Commit 1c35139c authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.21.2 

-- Step 2 of changing the way Homer3 stores the group data in memory, how it saves processed data and loads processed and acquired data. Finish getting rid of all remaining code related to the previous solution to the problem of loading and keeping a large data set in memory; a half-measure which calculated dc and dod automatically when Homer3 starts up by sensing that there's derived data that was previously calculated in groupResults.mat.

-- Clean up Calc() method a little bit in preparation for new solution to the above-described problem

-- Add foolproof functionality to ConfigFileClass to be able to restore original config file instead of rewriting AppSettings with same parameters simply make a backup copy whenever you save the config  file and use the new Restore method to get back to original version. That way whenever we run the unit test version control will not show that the file changed even though the substance is same as original.

-- Add code to unit test to be able to call clean up when user interrupts it.

-- Make version2string - converting version cell array return by getVernum to string - a simpler and more robust function.

-- Add DesignNotes.odp OpenOffice version and add 2 diagrams if how the dataTree works
parent 2c1aad11

DataTree/GroupClass.m

+6 −19
Original line number Diff line number Diff line
@@ -427,21 +427,19 @@ classdef GroupClass < TreeNodeClass 
                        tHRF_common{iBlk} = s(iSubj).procStream.output.GetTHRF(iBlk);

                    end

                end

                

            end

           

            

            % Instantiate all the variables that might be needed by

            % procStream.Calc() to calculate proc stream for this group

            vars = [];

            for iSubj = 1:nSubj

                % Set common tHRF: make sure size of tHRF, dcAvg and dcAvg is same for

                % all subjs. Use smallest tHRF as the common one.

            for iSubj = 1:nSubj

                for iBlk = 1:length(tHRF_common)

                    s(iSubj).procStream.output.SettHRFCommon(tHRF_common{iBlk}, s(iSubj).name, s(iSubj).type, iBlk);

                end

            end



            % Instantiate all the variables that might be needed by

            % procStream.Calc() to calculate proc stream for this group

            vars = [];

            for iSubj = 1:nSubj

                vars.dodAvgSubjs{iSubj}    = s(iSubj).procStream.output.GetVar('dodAvg');

                vars.dodAvgStdSubjs{iSubj} = s(iSubj).procStream.output.GetVar('dodAvgStd');

                vars.dcAvgSubjs{iSubj}     = s(iSubj).procStream.output.GetVar('dcAvg');
@@ -474,17 +472,6 @@ classdef GroupClass < TreeNodeClass 
        

        

        

        % ----------------------------------------------------------------------------------

        function CalcRunLevelTimeCourse(obj)

            % Calculate all subjs in this session

            s = obj.subjs;

            nSubj = length(s);

            for iSubj = 1:nSubj

                s(iSubj).CalcRunLevelTimeCourse();

            end

        end

        



        % ----------------------------------------------------------------------------------

        function Print(obj, indent)

            if ~exist('indent', 'var')

DataTree/ProcStream/ProcResultClass.m

+59 −40
Original line number Diff line number Diff line
@@ -121,10 +121,28 @@ classdef ProcResultClass < handle 
            end

        end

        

    end

        

        

    methods

        

        % ----------------------------------------------------------------------------------

        function AddVars(obj, vars, filename)

        function SetFilename(obj, filename)

            if isempty(filename)

                return;

            end

            [pname, fname] = fileparts(filename);

            if isempty(pname)

                pname = '.';

            end

            obj.filename = [pname, '/', fname, '.mat'];

        end

        

        

        % ----------------------------------------------------------------------------------

        function Save(obj, vars, filename)            

            obj.SetFilename(filename)



            output = obj;

            props = propnames(vars);

            for ii=1:length(props)
@@ -175,7 +193,6 @@ classdef ProcResultClass < handle 
        

        % ----------------------------------------------------------------------------------

        function t = GetTHRF(obj, iBlk)

            t = [];

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

            end
@@ -235,7 +252,7 @@ classdef ProcResultClass < handle 
        

        

        % ----------------------------------------------------------------------------------

        function yavg = GetDodAvg(obj, type, condition, iBlk)

        function yavg = GetDodAvg(obj, type, condition, iBlk) %#ok<*INUSL>

            yavg = [];

            

            % Check type argument
@@ -243,7 +260,7 @@ classdef ProcResultClass < handle 
                type = 'dodAvg';

            end

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

                iBlk = 1; %#ok<NASGU>

            end

            

            if ~ischar(type)
@@ -292,7 +309,7 @@ classdef ProcResultClass < handle 
                type = 'dcAvg';

            end

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

                iBlk = 1; %#ok<NASGU>

            end

            

            if ~ischar(type)
@@ -334,14 +351,14 @@ classdef ProcResultClass < handle 
        % ----------------------------------------------------------------------------------

        function y = GetDataTimeCourse(obj, type, iBlk)

            y = [];

            options = '';

            options = ''; %#ok<NASGU>

            

            % Check type argument

            if ~exist('type','var') || isempty(type)

                type = 'dcAvg';

            end

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

                iBlk = 1; %#ok<NASGU>

            end

            

            if ~ischar(type)
@@ -353,7 +370,7 @@ classdef ProcResultClass < handle 
                    return;

                end

                if strcmp(type, 'dc') || strcmp(type, 'dcAvg') || strcmp(type, 'dodAvg')

                    options = 'reshape';

                    options = 'reshape'; %#ok<NASGU>

                end

                y = eval(sprintf('obj.%s(iBlk).GetDataTimeSeries(options)', type));

            else
@@ -439,7 +456,6 @@ classdef ProcResultClass < handle 
        

        % ----------------------------------------------------------------------------------

        function mlActAuto = GetMeasListActAuto(obj, iBlk)

            mlActAuto = {};

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk=1;

            end
@@ -471,7 +487,7 @@ classdef ProcResultClass < handle 
    methods

        

        % ----------------------------------------------------------------------------------

        function Copy(obj, obj2, filename)

        function Copy(obj, obj2)

            if ~isa(obj, 'ProcResultClass')

                return;

            end
@@ -501,45 +517,48 @@ classdef ProcResultClass < handle 
        

        

        % ----------------------------------------------------------------------------------

        function b = HaveBlockAvgOutput(obj)

            b=0;

        function b = IsEmpty(obj)

            b = false;

            if isempty(obj)

                return;

                return

            end

            if ~isempty(obj.dcAvg)

                b=1;

            if ~isempty(obj.dod)

                return

            end

            if ~isempty(obj.dc)

                return

            end

            if ~isempty(obj.dodAvg)

                b=1;

                return

            end

            if ~isempty(obj.dcAvg)

                return

        	end

        

        

        % ----------------------------------------------------------------------------------

        function b = HaveTimeCourseOutput(obj)

            b=0;

            if isempty(obj)

                return;

            if ~isempty(obj.dodAvgStd)

                return

            end

            if ~isempty(obj.dc)

                b=1;

            if ~isempty(obj.dcAvgStd)

                return

            end

            if ~isempty(obj.dod)

                b=1;

            if ~isempty(obj.dodSum2)

                return

            end

            if ~isempty(obj.dcSum2)

                return

            end

        

        

        % ----------------------------------------------------------------------------------

        function b = IsEmpty(obj)

            b=0;

            if obj.HaveTimeCourseOutput()

                return;

            if ~isempty(obj.tHRF)

                return

            end

            if obj.HaveBlockAvgOutput()

                return;

            if ~isempty(obj.nTrials)

                return

        	end

            if ~isempty(obj.grpAvgPass)

                return

            end

            if ~isempty(obj.misc)

                return

            end

            b=1;

            b = false;

        end

DataTree/ProcStream/ProcStreamClass.m

+3 −53
Original line number Diff line number Diff line
@@ -62,7 +62,7 @@ classdef ProcStreamClass < handle 
            obj.fcalls(ii+1:end) = [];

            

            obj.input.Copy(obj2.input);

            obj.output.Copy(obj2.output, filename);

            obj.output.Copy(obj2.output);

        end
@@ -239,11 +239,10 @@ classdef ProcStreamClass < handle 
            for ii=1:length(paramOut)

                eval( sprintf('paramsOutStruct.%s = %s;', paramOut{ii}, paramOut{ii}) );

            end            

            obj.output.AddVars(paramsOutStruct, filename);

            obj.output.Save(paramsOutStruct, filename);

            

            obj.input.misc = [];

            close(hwait);

                        

        end
@@ -259,27 +258,6 @@ classdef ProcStreamClass < handle 
        

        

        

        % ----------------------------------------------------------------------------------

        function FcallsIdxsTimeCourses(obj)

            if ~obj.output.HaveBlockAvgOutput()

                return;

            end

            idxs = zeros(1, length(obj.fcalls));

            for ii=1:length(obj.fcalls)

                sargout = ParseOutputArgs(obj, ii);

                if strfind('dod', sargout) %#ok<*STRIFCND>

                    idxs(ii) = 1;

                end

                if strfind('dc', sargout)

                    idxs(ii) = 1;

                end

            end

            k = find(idxs==1);

            obj.fcallsIdxs=1:k(end);

        end

                

        

        

        % ----------------------------------------------------------------------------------

        function FcallsIdxsReset(obj)

            obj.fcallsIdxs=[];
@@ -316,34 +294,6 @@ classdef ProcStreamClass < handle 
            end

        end

        

        

        

        % ----------------------------------------------------------------------------------

        function b = HaveBlockAvgOutput(obj)

            b=0;

            if isempty(obj)

                return;

            end

            if isempty(obj.output)

                return;

            end

            b = obj.output.HaveBlockAvgOutput();

        end

        

        

        

        % ----------------------------------------------------------------------------------

        function b = HaveTimeCourseOutput(obj)

            b=0;

            if isempty(obj)

                return;

            end

            if isempty(obj.output)

                return;

            end

            b = obj.output.HaveTimeCourseOutput();

        end

                

    end

DataTree/RunClass.m

+0 −12
Original line number Diff line number Diff line
@@ -217,18 +217,6 @@ classdef RunClass < TreeNodeClass 




        

        % ----------------------------------------------------------------------------------

        function CalcTimeCourses(obj)

            if obj.procStream.HaveTimeCourseOutput()

                return;

            end

            obj.procStream.FcallsIdxsTimeCourses();

            obj.Calc('keepexisting');

            obj.procStream.FcallsIdxsReset();

        end

        

        

        

        % ----------------------------------------------------------------------------------

        function Print(obj, indent)

            if ~exist('indent', 'var')

DataTree/SubjClass.m

+6 −18
Original line number Diff line number Diff line
@@ -196,18 +196,17 @@ classdef SubjClass < TreeNodeClass 
                end

            end

            

            

            % Instantiate all the variables that might be needed by

            % procStream.Calc() to calculate proc stream for this subject

            vars = [];

            for iRun = 1:nRun

                % Set common tHRF: make sure size of tHRF, dcAvg and dcAvg is same for

                % all runs. Use smallest tHRF as the common one.

            for iRun = 1:nRun

                for iBlk = 1:length(tHRF_common)

                    r(iRun).procStream.output.SettHRFCommon(tHRF_common{iBlk}, r(iRun).name, r(iRun).type, iBlk);

                end

            end            



            % Instantiate all the variables that might be needed by

            % procStream.Calc() to calculate proc stream for this subject

            vars = [];

            for iRun = 1:nRun

                vars.dodAvgRuns{iRun}    = r(iRun).procStream.output.GetVar('dodAvg');

                vars.dodAvgStdRuns{iRun} = r(iRun).procStream.output.GetVar('dodAvgStd');

                vars.dodSum2Runs{iRun}   = r(iRun).procStream.output.GetVar('dodSum2');
@@ -245,17 +244,6 @@ classdef SubjClass < TreeNodeClass 
        end

                

        

        % ----------------------------------------------------------------------------------

        function CalcRunLevelTimeCourse(obj)

            r = obj.runs;

            nRun = length(r);

            for iRun = 1:nRun

                r(iRun).CalcTimeCourses();

            end

        end

        

        



        % ----------------------------------------------------------------------------------

        function Print(obj, indent)

            if ~exist('indent', 'var')

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