Commit 344f659e authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.21.7 

-- Step 5 of changing the way Homer3 stores the group data in memory, how it saves processed data and loads processed and acquired data. Implemented loading and freeing of acquired data.

-- Removed old code to quickly calculate memory required and check for enough disk space. The rationale for getting rid of this code is that I'm not sure this is a big problem people are encountering and woth complicating already intricate code which we want to keep as simple as possible. The distributed storage scheme should take care of the issue of limited max size of a single file (groupResults.mat). If running out of disk space proves a widespread issue we can re-introduce that code.

-- Returned original slow-running implementation of MemoryRequired for diagnostic purposes but not meant to be run during a user session of Homer3.

-- Change MainGUI.GetWl.m to get selected wavelength ONLY from GUI
parent 8adef79b

AppSettings.cfg

+1 −1
Original line number Diff line number Diff line
@@ -21,6 +21,6 @@ On 
on



% Data Storage Scheme

memory

disk



% END

DataTree/AcquiredData/AcqDataClass.m

+14 −5
Original line number Diff line number Diff line
@@ -69,6 +69,18 @@ classdef AcqDataClass < matlab.mixin.Copyable 
    

    methods

        

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

        function b = Error(obj)

            if obj.err<0

                b = true;

            elseif obj.err==0

                b = false;

            else

                b = true;

            end

        end

        

        

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

        function FreeMemory(obj, filename)

            if ~exist('filename','var')
@@ -77,10 +89,7 @@ classdef AcqDataClass < matlab.mixin.Copyable 
            if isempty(filename)

                return;

            end            

            

            % TBD: Tight now we only save processed output and free memory 

            % associated with it. Need to do the same for acquired data

            % obj.Initialize();  

            obj.Initialize();

        end

DataTree/AcquiredData/Nirs/NirsClass.m

+8 −1
Original line number Diff line number Diff line
@@ -104,11 +104,18 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
            else

                fname = obj.filename;

            end

            if isempty(fname)

            if exist(fname, 'file') ~= 2

               err=-1;

               return;

            end

            

            % Don't reload if not empty

            if ~obj.IsEmpty()

               return;

            end

            

            

                        

            warning('off', 'MATLAB:load:variableNotFound');

            fdata = load(fname,'-mat', 'SD','t','d','s','aux','CondNames');

            if isproperty(fdata,'d')

DataTree/AcquiredData/Snirf/SnirfClass.m

+6 −1
Original line number Diff line number Diff line
@@ -383,6 +383,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
               return;

            end

            

            % Don't reload if not empty

            if ~obj.IsEmpty()

               return;

            end

            

            

            %%%%%%%%%%%% Ready to load from file

DataTree/DataTreeClass.m

+12 −63
Original line number Diff line number Diff line
@@ -305,7 +305,7 @@ classdef DataTreeClass < handle 
                % (We do not reset current subject or group because they can contain multiple 

                % nodes and they cannot be empty once they've been initialized once whereas run 

                % can be if it fails to load a data file. 

                if ~runCurr.IsEmpty()

                if ~runCurr.Error()

                    obj.Add(groupCurr, subjCurr, runCurr);

                    runCurr = RunClass().empty();

                end
@@ -426,73 +426,22 @@ classdef DataTreeClass < handle 




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

        function nbytes = MemoryRequired(obj, option)

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

                option = 'memory';

            end

        function nbytes = MemoryRequired(obj)

            nbytes = 0;

            if isempty(obj)

                return;

            end                        

            

            nbytes = [0,0,0];

            kg = find(obj.groups.GroupsProcFlags==1);

            ks = find(obj.groups.SubjsProcFlags==1);

            kr = find(obj.groups.RunsProcFlags==1);

            

            % We assume for practcal purposes that unprocessed nodes take up zero bytes 

            if ~isempty(kg)

                nbytes(1) = length(kg) * obj.groups(kg(1)).MemoryRequired();

            end

            if ~isempty(ks)

                [iG,iS] = ind2sub(size(obj.groups.SubjsProcFlags), ks);

                nbytes(2) = length(ks) * obj.groups(iG(1)).subjs(iS(1)).MemoryRequired();

            for ii = 1:length(obj.groups)

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

            end

            if ~isempty(kr)

                [iG,iS,iR] = ind2sub(size(obj.groups.RunsProcFlags), kr);

                nbytes(3) = length(kr) * obj.groups(iG(1)).subjs(iS(1)).runs(iR(1)).MemoryRequired(option);

        end

        

            % Add up the bytes. 

            nbytes = sum(nbytes);

        end

        

        

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

        function diskspaceToSpare = CheckAvailableDiskSpace(obj, hwait)

            if ishandle(hwait)

                obj.logger.Write(sprintf('Estimating disk space required to save processing results ...\n'), obj.logger.ProgressBar(), hwait);

            end

            

            % Calculate the amount of disk space already used by groupResults. Add that to free disk space because

            % groupResults will be overwritten 

            freeDiskSpace = 0;

            for ii = 1:length(obj.groups)

                freeDiskSpace = freeDiskSpace + GetFileSize([obj.groups(ii).pathOutput, 'groupResults.mat']);

            end

            

            memRequired = obj.MemoryRequired('disk');

            freeDiskSpace = getFreeDiskSpace() + freeDiskSpace;

            

            diskspaceToSpare = (freeDiskSpace - memRequired);   % Disk space to spare in megabytes

            diskspacePercentRemaining = 100 * diskspaceToSpare/memRequired;

            msg = {};

            obj.logger.Write(sprintf('CheckAvailableDiskSpace:    disk space available = %0.1f MB,    required disk space estimate = %0.1f MB\n', freeDiskSpace/1e6, memRequired/1e6));

            if diskspaceToSpare < 0

                msg{1} = sprintf('ERROR: Cannot save processing results requiring ~%0.1f MB of disk space on current drive with only %0.1f MB of free space available.\n', ...

                                  memRequired/1e6, freeDiskSpace/1e6);

                obj.warningflag = 0;

            elseif diskspacePercentRemaining < 200                

                msg{1} = sprintf('WARNING: Available disk space on the current drive is low (%0.1f MB). This may cause problems saving processing results in the future.', ...

                                  freeDiskSpace/1e6);

                msg{2} = sprintf('Consider moving your data set to a drive with more free space\n');

            end            

            if ~isempty(msg)

                if ~obj.warningflag

                    MessageBox([msg{:}]);

                    obj.warningflag = 1;

                end

                obj.logger.Write([msg{:}]);

            end            

            diskspaceToSpare = getFreeDiskSpace();   % Disk space to spare in megabytes

            %diskspaceToSpare = (getFreeDiskSpace() - obj.MemoryRequired());   % Disk space to spare in megabytes

        end
@@ -506,7 +455,7 @@ classdef DataTreeClass < handle 
            % Check that there is anough disk space. NOTE: for now we

            % assume that all groups are on the same drive. This should be 

            % changed but for now we simplify. 

            if obj.CheckAvailableDiskSpace(hwait) < 0

            if obj.CheckAvailableDiskSpace(hwait) <= 0

                return;

            end

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