Commit 975ff157 authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.21.3 

-- -- Step 2 of changing the way Homer3 stores the group data in memory, how it saves processed data and loads processed and acquired data. Clean up and simplify Calc() method code for generating tHRF_Common in GroupClass and SubjClass.

-- Update Homer3 to preserve capability of handling .nirs files and generating group level processing output.

-- Change the way unit test code modifies AppSettings config file and then restores it to original, in order not to have to revert change for AppSettings.cfg every time after running unit test.  Add userInterrupt function to be able to interrupt a long-running unit test with a Ctrl-C and have it automatically revert to original AppSettings.
parent 1c35139c

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+1 −1
Original line number Diff line number Diff line
@@ -38,7 +38,7 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable 
                        

            switch(lower(format))

                case obj.supportedFomats.matlab

                    if ismethod(obj, 'LoadMat', params)

                    if ismethod(obj, 'LoadMat')

                        obj.LoadMat(filename);

                    end

                case obj.supportedFomats.hdf5

DataTree/AcquiredData/Nirs/NirsClass.m

+11 −1
Original line number Diff line number Diff line
@@ -256,7 +256,17 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        end

        

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

        function val = GetDataTimeSeries(obj)

        function val = GetDataTimeSeries(obj, options, iBlk)

            val = [];

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

                options = '';

            end

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

                iBlk=1;

            end

            if iBlk>1

            	return

            end

            val = obj.d;

        end

DataTree/GroupClass.m

+31 −32
Original line number Diff line number Diff line
@@ -396,6 +396,26 @@ classdef GroupClass < TreeNodeClass 
        

        

        

        

        

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

        function LoadVars(obj, s, tHRF_common)

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

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

            s.procStream.output.SettHRFCommon(tHRF_common, s.name, s.type);

            

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

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

            obj.outputVars.dcAvgSubjs{s.iSubj}     = s.procStream.output.GetVar('dcAvg');

            obj.outputVars.dcAvgStdSubjs{s.iSubj}  = s.procStream.output.GetVar('dcAvgStd');

            obj.outputVars.tHRFSubjs{s.iSubj}      = s.procStream.output.GetTHRF();

            obj.outputVars.nTrialsSubjs{s.iSubj}   = s.procStream.output.GetVar('nTrials');

            obj.outputVars.SDSubjs{s.iSubj}        = s.GetMeasList();

        end

            

            

            

            

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

        function Calc(obj, options)           

            if ~exist('options','var') || isempty(options)
@@ -413,44 +433,23 @@ classdef GroupClass < TreeNodeClass 
            

            % Calculate all subjs in this session

            s = obj.subjs;

            nSubj = length(s);

            nDataBlks = s(1).GetDataBlocksNum();

            tHRF_common = cell(nDataBlks,1);

            for iSubj = 1:nSubj

            tHRF_common = {};

            for iSubj = 1:length(s)

                s(iSubj).Calc();

                

                % Find smallest tHRF among the subjs. We should make this the common one.

                for iBlk = 1:nDataBlks

                    if isempty(tHRF_common{iBlk})

                        tHRF_common{iBlk} = s(iSubj).procStream.output.GetTHRF(iBlk);

                    elseif length(s(iSubj).procStream.output.GetTHRF(iBlk)) < length(tHRF_common{iBlk})

                        tHRF_common{iBlk} = s(iSubj).procStream.output.GetTHRF(iBlk);

                    end

                end

                % Find smallest tHRF among the subjs and make this the common one.

                tHRF_common = s(iSubj).procStream.output.GeneratetHRFCommon(tHRF_common);

            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 iBlk = 1:length(tHRF_common)

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

                end



                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');

                vars.dcAvgStdSubjs{iSubj}  = s(iSubj).procStream.output.GetVar('dcAvgStd');

                vars.tHRFSubjs{iSubj}      = s(iSubj).procStream.output.GetTHRF();

                vars.nTrialsSubjs{iSubj}   = s(iSubj).procStream.output.GetVar('nTrials');

                vars.SDSubjs{iSubj}        = s(iSubj).GetMeasList();

            % Load all the output valiraibles that might be needed by procStream.Calc() to calculate proc stream for this group

            obj.outputVars = [];

            for iSubj = 1:length(s)

                obj.LoadVars(s(iSubj), tHRF_common); 

            end

            

            % Make variables in this group available to processing stream input

            obj.procStream.input.LoadVars(vars);

            obj.procStream.input.LoadVars(obj.outputVars);



            % Calculate processing stream

            obj.procStream.Calc();

DataTree/ProcStream/ProcResultClass.m

+112 −72
Original line number Diff line number Diff line
@@ -40,16 +40,37 @@ classdef ProcResultClass < handle 
        end

        

        

        

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

        function SettHRFCommon(obj, tHRF_common, name, type, iBlk)

            if size(tHRF_common,2)<size(tHRF_common,1)

                tHRF_common = tHRF_common';

        function tHRF_common = GeneratetHRFCommon(obj, tHRF_common)

            nDataBlks = obj.GetDataBlocksNum();

            if isempty(tHRF_common)

                tHRF_common = cell(nDataBlks,1);

            end

            

            % Find smallest tHRF among the runs. We should make this the common one.

            for iBlk = 1:nDataBlks

                if isempty(tHRF_common{iBlk})

                    tHRF_common{iBlk} = obj.GetTHRF(iBlk);

                elseif length(obj.GetTHRF(iBlk)) < length(tHRF_common{iBlk})

                    tHRF_common{iBlk} = obj.GetTHRF(iBlk);

                end

            end

        end

        

        

        

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

        function SettHRFCommon(obj, tHRF_common, name, type)

            for iBlk = 1:length(tHRF_common)

                if size(tHRF_common{iBlk},2)<size(tHRF_common{iBlk},1)

                    tHRF_common{iBlk} = tHRF_common{iBlk}';

                end

                t = obj.GetTHRF(iBlk);

                if isempty(t)

                    return;

                end

            n = length(tHRF_common);

                n = length(tHRF_common{iBlk});

                m = length(t);

                d = n-m;

                if d<0
@@ -97,10 +118,12 @@ classdef ProcResultClass < handle 
                        end

                    end

                end

            obj.tHRF = tHRF_common;

                obj.tHRF = tHRF_common{iBlk};

            end

        end

        

        

        

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

        function var = GetVar(obj, varname, iBlk)

            var = [];
@@ -467,16 +490,33 @@ classdef ProcResultClass < handle 
        % ----------------------------------------------------------------------------------

        function n = GetDataBlocksNum(obj)

            n = 0;

                

            if ~isempty(obj.dcAvg)

                if isnumeric(obj.dcAvg)

                    n = 1;

                else

                    n = length(obj.dcAvg);

                end

            elseif ~isempty(obj.dodAvg)

                if isnumeric(obj.dodAvg)

                    n = 1;

                else

                    n = length(obj.dodAvg);

                end

            elseif ~isempty(obj.dc)

                if isnumeric(obj.dc)

                    n = 1;

                else

                    n = length(obj.dc);

                end

            elseif ~isempty(obj.dod)

                if isnumeric(obj.dod)

                    n = 1;

                else

                    n = length(obj.dod);

                end

            end

        end

        

    end

DataTree/ProcStream/ProcStreamClass.m

+8 −3
Original line number Diff line number Diff line
@@ -21,6 +21,7 @@ classdef ProcStreamClass < handle 
            obj.config = struct('procStreamCfgFile','', 'defaultProcStream','','suffix','');

            cfg = ConfigFileClass();

            obj.config.procStreamCfgFile    = cfg.GetValue('Processing Stream Config File');

            obj.config.regressionTestActive = cfg.GetValue('Regression Test Active');

            copyOptions = '';

            if strcmpi(obj.getDefaultProcStream(), '_nirs')

                copyOptions = 'extended';
@@ -206,9 +207,13 @@ classdef ProcStreamClass < handle 
                    eval( fcall );

                catch ME

                    msg = sprintf('Function %s generated error at line %d: %s', obj.fcalls(iFcall).name, ME.stack(1).line, ME.message);

                    menu(msg,'OK');

                    if strcmp(obj.config.regressionTestActive, 'false')

                        MessageBox(msg);

                    elseif strcmp(obj.config.regressionTestActive, 'false')

                        fprintf('%s\n', msg);

                    end

                    close(hwait);

                    assert(false, msg);

                    rethrow(ME)

                end

                

                %%%% Parse output parameters

CRA Git | Maintained and supported by SUSTech CRA and CCSE