Commit bc725bf4 authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.21.1 

-- Step 1 of changing the way Homer3 stores the group data in memory, how it saves processed data and loads processed and acquired data. It currently loads entire data from derived and acquired files into memory. The goal is to save the output of processing to files instead of storing it in memory and to load the derived output and acquired data only of the current element. In this way Homer3 will be able to handle arbitrarily large data sets.
-- In this step get rid of the half-measure used previously to handle large data sets by not storing dc and dod and calculating them automatically when Homer3 starts up by sensing that there's derived data that was previously calculated in groupResults.mat
parent 2a960899

DataTree/AcquiredData/Snirf/AuxClass.m

+4 −0
Original line number Diff line number Diff line
@@ -170,6 +170,10 @@ classdef AuxClass < FileLoadSaveClass 
        

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

        function nbytes = MemoryRequired(obj)

            nbytes = 0;

            if isempty(obj)

                return

            end

            nbytes = sizeof(obj.name) + sizeof(obj.dataTimeSeries) + sizeof(obj.time) + sizeof(obj.timeOffset);

        end

DataTree/AcquiredData/Snirf/DataClass.m

+4 −0
Original line number Diff line number Diff line
@@ -611,6 +611,10 @@ classdef DataClass < FileLoadSaveClass 
        

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

        function nbytes = MemoryRequired(obj)

            nbytes = 0;

            if isempty(obj)

                return

            end

            nbytes = sizeof(obj.dataTimeSeries) + sizeof(obj.time);

            for ii=1:length(obj.measurementList)

                nbytes = nbytes + obj.measurementList(ii).MemoryRequired();

DataTree/AcquiredData/Snirf/StimClass.m

+4 −0
Original line number Diff line number Diff line
@@ -425,6 +425,10 @@ classdef StimClass < FileLoadSaveClass 
                

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

        function nbytes = MemoryRequired(obj)

            nbytes = 0;

            if isempty(obj)

                return

            end

            nbytes = sizeof(obj.name) + sizeof(obj.data) + sizeof(obj.filename) + sizeof(obj.fileformat) + sizeof(obj.supportedFomats) + 8;

        end

DataTree/GroupClass.m

+1 −8
Original line number Diff line number Diff line
@@ -4,7 +4,6 @@ classdef GroupClass < TreeNodeClass 
        version;

        versionStr;

        subjs;

        spacesaver;

        logger

    end
@@ -33,7 +32,6 @@ classdef GroupClass < TreeNodeClass 
            

            obj.type    = 'group';

            obj.subjs   = SubjClass().empty;

            obj.spacesaver = false;

            

            if nargin==0

                return;
@@ -218,13 +216,8 @@ classdef GroupClass < TreeNodeClass 
                    end

                end

            else

                if obj.spacesaver

                    option = 'spacesaver';

                else

                    option = 'saveall';

                end

                for i=1:length(obj2.subjs)

                    obj.subjs(i) = SubjClass(obj2.subjs(i), option);

                    obj.subjs(i) = SubjClass(obj2.subjs(i));

                end

                obj.Copy@TreeNodeClass(obj2);

            end

DataTree/ProcStream/ProcResultClass.m

+27 −9
Original line number Diff line number Diff line
@@ -122,6 +122,29 @@ classdef ProcResultClass < handle 
        end

        



        

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

        function AddVars(obj, vars, filename)

            output = obj;

            props = propnames(vars);

            for ii=1:length(props)

                if eval( sprintf('isproperty(output, ''%s'');', props{ii}) )

                    eval( sprintf('output.%s = vars.%s;', props{ii}, props{ii}) );

                else

                    eval( sprintf('output.misc.%s = vars.%s;', props{ii}, props{ii}) );

                end

            end

            if ~isempty(filename)

                [~, ~, ext] = fileparts(filename);

                if isempty(ext)

                    filename = [filename, '.mat']; 

                end

                save(filename, '-mat', 'output');

            end

        end

            



        

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

        function Flush(obj)

            obj.Initialize();
@@ -448,22 +471,17 @@ classdef ProcResultClass < handle 
    methods

        

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

        function Copy(obj, obj2, option)

        function Copy(obj, obj2, filename)

            if ~isa(obj, 'ProcResultClass')

                return;

            end

            if nargin==2

                option = '';

            end

            

            % Ok to shallow copy since ProcResult objects are read only

            % Also we don't want to transfer space hogging time course

            % data dc and dod

            

            if ~strcmp(option, 'spacesaver')

            obj.dod = obj2.dod;

            obj.dc = obj2.dc;

            end

            obj.dodAvg = obj2.dodAvg;

            obj.dcAvg = obj2.dcAvg;

            obj.dodAvgStd = obj2.dodAvgStd;
@@ -543,7 +561,7 @@ classdef ProcResultClass < handle 
            nbytes = zeros(length(fields),1);

            for ii = 1:length(fields)

                fieldstr = sprintf('obj.%s', fields{ii});

                if ~eval('isempty(fieldstr)')

                if ~isempty(fieldstr)

                    if isa(eval(fieldstr), 'DataClass')

                        nbytes(ii) =  eval(sprintf('%s.MemoryRequired();', fieldstr));

                    else

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