Commit a3ddc0dd authored by Jay Dubb's avatar Jay Dubb
Browse files

v1.28.8 

-- Change when loading data set that for which the derived data in groupResults doesn't match the directory/file structure of the group folder (because the user has modified folder or file names after the groupResults file was generated) then fix any obstacles to loading and any errors that were generated but print warning and if the new "Group Data Loading Warnings" config parameter is set to "ask every time" then prompt user to select whether to continue loading or quit loading the suspect data set.

-- Add optional argument for "don't ask again" options to MenuBox.m

-- Force add newline to string in Logger.Write method IF it doesn't exist already.

-- Add print debug messages when loading data set to SubjClass and RunClass so that user has clear picture of what the data tree looks in the log file.
parent 859a9f47

AppSettings.cfg

+3 −0
Original line number Original line Diff line number Diff line
@@ -26,4 +26,7 @@ files 
% Auto Save Acquisition Files

% Auto Save Acquisition Files

No

No





% Group Data Loading Warnings

ask every time



% END
 
% END

DataTree/GroupClass.m

+14 −14
Original line number Original line Diff line number Diff line
@@ -4,7 +4,6 @@ classdef GroupClass < TreeNodeClass 
        version;

        version;

        versionStr;

        versionStr;

        subjs;

        subjs;

        logger

    end

    end

    

    

    properties % (Access = private)

    properties % (Access = private)
@@ -19,10 +18,8 @@ classdef GroupClass < TreeNodeClass 
        

        

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

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

        function obj = GroupClass(varargin)

        function obj = GroupClass(varargin)

            global logger



            obj@TreeNodeClass(varargin);

            obj@TreeNodeClass(varargin);

            obj.logger = InitLogger(logger);



            obj.InitVersion();

            obj.InitVersion();





            if nargin<3 || ~strcmp(varargin{3}, 'noprint')

            if nargin<3 || ~strcmp(varargin{3}, 'noprint')
@@ -205,17 +202,20 @@ classdef GroupClass < TreeNodeClass 
            % 

            % 

            % Conversly unconditional copy copies all properties in the runs under this group

            % Conversly unconditional copy copies all properties in the runs under this group

            if nargin==3 && strcmp(conditional, 'conditional')

            if nargin==3 && strcmp(conditional, 'conditional')

                if strcmp(obj.name,obj2.name)

                if obj.Mismatch(obj2)

                    return

                end

                for i = 1:length(obj.subjs)

                for i = 1:length(obj.subjs)

                    j = obj.existSubj(i,obj2);

                    j = obj.existSubj(i,obj2);

                        if (j>0)

                    if j>0

                        obj.subjs(i).Copy(obj2.subjs(j), 'conditional');

                        obj.subjs(i).Copy(obj2.subjs(j), 'conditional');

                    elseif i<=length(obj2.subjs)

                        obj.subjs(i).Copy(obj2.subjs(i), 'conditional');

                    else

                        obj.subjs(i).Mismatch();

                    end

                    end

                end                

                end                

                    if obj == obj2

                obj.Copy@TreeNodeClass(obj2, 'conditional');

                obj.Copy@TreeNodeClass(obj2, 'conditional');

                    end

                end

            else

            else

                for i=1:length(obj2.subjs)

                for i=1:length(obj2.subjs)

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

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

DataTree/RunClass.m

+13 −11
Original line number Original line Diff line number Diff line
@@ -20,6 +20,7 @@ classdef RunClass < TreeNodeClass 
            %   run1copy = RunClass(run1);

            %   run1copy = RunClass(run1);

            %           

            %           

            obj@TreeNodeClass(varargin);            

            obj@TreeNodeClass(varargin);            

            

            obj.type  = 'run';

            obj.type  = 'run';

            if nargin==0

            if nargin==0

                obj.name  = '';

                obj.name  = '';
@@ -121,7 +122,7 @@ classdef RunClass < TreeNodeClass 
            end

            end

            

            

            if obj.acquired.Error() > 0

            if obj.acquired.Error() > 0

                fprintf('     **** Warning: %s failed to load.\n', obj.name);

                obj.logger.Write(sprintf('     **** Warning: %s failed to load.\n', obj.name));

                return;

                return;

            else

            else

                %fprintf('    Loaded file %s to run.\n', obj.name);                

                %fprintf('    Loaded file %s to run.\n', obj.name);
@@ -159,7 +160,7 @@ classdef RunClass < TreeNodeClass 
        function b = AcquiredDataModified(obj)

        function b = AcquiredDataModified(obj)

            b = obj.procStream.AcquiredDataModified();

            b = obj.procStream.AcquiredDataModified();

            if b

            if b

                fprintf('Acquisition data for run %s has been modified\n', obj.name);

                obj.logger.Write(sprintf('Acquisition data for run %s has been modified\n', obj.name));

            end

            end

        end

        end
@@ -168,13 +169,14 @@ classdef RunClass < TreeNodeClass 
        % Copy processing params (procInut and procResult) from

        % Copy processing params (procInut and procResult) from

        % N2 to N1 if N1 and N2 are same nodes

        % N2 to N1 if N1 and N2 are same nodes

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

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

        function Copy(obj, R, conditional)

        function Copy(obj, obj2, conditional)

            if nargin==3 && strcmp(conditional, 'conditional')

            if nargin==3 && strcmp(conditional, 'conditional')

                if obj == R

                if obj.Mismatch(obj2)

                    obj.Copy@TreeNodeClass(R, 'conditional');

                    return

                end

                end

                obj.Copy@TreeNodeClass(obj2, 'conditional');

            else

            else

                obj.Copy@TreeNodeClass(R);

                obj.Copy@TreeNodeClass(obj2);

                if isempty(obj.acquired)

                if isempty(obj.acquired)

                    if obj.IsNirs()

                    if obj.IsNirs()

                        obj.acquired = NirsClass();

                        obj.acquired = NirsClass();
@@ -182,7 +184,7 @@ classdef RunClass < TreeNodeClass 
                        obj.acquired = SnirfClass();

                        obj.acquired = SnirfClass();

                    end

                    end

                end

                end

                obj.acquired.Copy(R.acquired);

                obj.acquired.Copy(obj2.acquired);

            end

            end

        end

        end
@@ -299,8 +301,8 @@ classdef RunClass < TreeNodeClass 
            obj.procStream.Calc(obj.GetFilename);

            obj.procStream.Calc(obj.GetFilename);





            if obj.DEBUG

            if obj.DEBUG

                fprintf('Completed processing stream for group %d, subject %d, run %d\n', obj.iGroup, obj.iSubj, obj.iRun);

                obj.logger.Write(sprintf('Completed processing stream for group %d, subject %d, run %d\n', obj.iGroup, obj.iSubj, obj.iRun));

                fprintf('\n')

                obj.logger.Write('\n')

            end            

            end            

        end

        end

DataTree/SubjClass.m

+19 −15
Original line number Original line Diff line number Diff line
@@ -4,6 +4,7 @@ classdef SubjClass < TreeNodeClass 
        runs;

        runs;

    end

    end

       

       

    

    methods

    methods

                

                

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

        % ----------------------------------------------------------------------------------
@@ -57,32 +58,35 @@ classdef SubjClass < TreeNodeClass 
        % Copy processing params (procInut and procResult) from

        % Copy processing params (procInut and procResult) from

        % S to obj if obj and S are equivalent nodes

        % S to obj if obj and S are equivalent nodes

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

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

        function Copy(obj, S, conditional)

        function Copy(obj, obj2, conditional)

            % Copy SubjClass object obj2 to SubjClass object obj. Conditional option applies 

            % Copy SubjClass object obj2 to SubjClass object obj. Conditional option applies 

            % only to all the runs under this group. If == 'conditional' ONLY derived data, 

            % only to all the runs under this group. If == 'conditional' ONLY derived data, 

            % that is, only from procStream but NOT from acquired data is copied for all the runs. 

            % that is, only from procStream but NOT from acquired data is copied for all the runs. 

            % 

            % 

            % Conversly unconditional copy copies all properties in the runs under this subject

            % Conversly unconditional copy copies all properties in the runs under this subject

            if nargin==3 && strcmp(conditional, 'conditional')

            if nargin==3 && strcmp(conditional, 'conditional')

                if strcmp(obj.name, S.name)

                if obj.Mismatch(obj2)

                    return

                end

                for i = 1:length(obj.runs)

                for i = 1:length(obj.runs)

                        j = obj.existRun(i,S);

                    j = obj.existRun(i,obj2);

                    if (j>0)

                    if (j>0)

                            obj.runs(i).Copy(S.runs(j), 'conditional');

                        obj.runs(i).Copy(obj2.runs(j), 'conditional');

                        end

                    elseif i<=length(obj2.runs)

                    end

                        obj.runs(i).Copy(obj2.runs(i), 'conditional');

                    if obj == S

                    else

                        obj.Copy@TreeNodeClass(S, 'conditional');

                        obj.Mismatch();

                    end

                    end

                end

                end

                obj.Copy@TreeNodeClass(obj2, 'conditional');

            else

            else

                if nargin<3

                if nargin<3

                    conditional = '';

                    conditional = '';

                end

                end

                for i=1:length(S.runs)

                for i=1:length(obj2.runs)

                    obj.runs(i) = RunClass(S.runs(i), conditional);

                    obj.runs(i) = RunClass(obj2.runs(i), conditional);

                end

                end

                obj.Copy@TreeNodeClass(S);

                obj.Copy@TreeNodeClass(obj2);

            end

            end

        end

        end
@@ -165,7 +169,7 @@ classdef SubjClass < TreeNodeClass 
                jj = length(obj.runs)+1;

                jj = length(obj.runs)+1;

                run.SetIndexID(obj.iGroup, obj.iSubj, jj);

                run.SetIndexID(obj.iGroup, obj.iSubj, jj);

                obj.runs(jj) = run;

                obj.runs(jj) = run;

                fprintf('     Added run %s to subject %s.\n', obj.runs(jj).GetFileName, obj.GetName);

                obj.logger.Write(sprintf('     Added run %s to subject %s.\n', obj.runs(jj).GetFileName, obj.GetName));

            end

            end

            

            

            % If subject has only one run AND the run file name is not formatted according to the standard Homer 

            % If subject has only one run AND the run file name is not formatted according to the standard Homer
@@ -265,7 +269,7 @@ classdef SubjClass < TreeNodeClass 
            end

            end

                        

                        

            if obj.DEBUG

            if obj.DEBUG

                fprintf('Calculating processing stream for group %d, subject %d\n', obj.iGroup, obj.iSubj)

                obj.logger.Write(sprintf('Calculating processing stream for group %d, subject %d\n', obj.iGroup, obj.iSubj));

            end

            end

            

            

            % Calculate all runs in this session and generate common tHRF

            % Calculate all runs in this session and generate common tHRF

DataTree/TreeNodeClass.m

+74 −11
Original line number Original line Diff line number Diff line
@@ -17,13 +17,17 @@ classdef TreeNodeClass < handle 
        outputVars

        outputVars

        DEBUG

        DEBUG

        path

        path

        logger

    end

    end

    

    

    methods        

    methods        

        

        

        

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

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

        function obj = TreeNodeClass(arg)

        function obj = TreeNodeClass(arg)

            global logger



            obj.logger = InitLogger(logger);



            obj.DEBUG = 0;

            obj.DEBUG = 0;

            

            

            obj.name = '';

            obj.name = '';
@@ -36,7 +40,6 @@ classdef TreeNodeClass < handle 
            obj.CondNames = {};

            obj.CondNames = {};

            obj.path = filesepStandard(pwd);            

            obj.path = filesepStandard(pwd);            

                        

                        

            

            obj.InitParentAppFunc();

            obj.InitParentAppFunc();

            

            

            % If this constructor is called from this class' copy method,

            % If this constructor is called from this class' copy method,
@@ -56,7 +59,7 @@ classdef TreeNodeClass < handle 
                end

                end

            end

            end

            obj.CondColTbl('init');

            obj.CondColTbl('init');

                                   

            obj.GroupDataLoadWarnings();            

        end

        end

        

        

    end

    end
@@ -174,7 +177,7 @@ classdef TreeNodeClass < handle 
        % ----------------------------------------------------------------------------------

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

        function InitParentAppFunc(obj)

        function InitParentAppFunc(obj)

            global maingui

            global maingui

            if ~isempty(maingui)

            if isfield(maingui, 'Update')

                obj.updateParentGui = maingui.Update;

                obj.updateParentGui = maingui.Update;

            end

            end

        end

        end
@@ -660,6 +663,53 @@ classdef TreeNodeClass < handle 
        end

        end

        

        

        

        

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

        function status = Mismatch(obj, obj2)

            status = 0;

            if exist('obj2','var')                

                if obj == obj2

                    return

                end

            end

            status = 1;

                        

            configFileOptions =  MenuBox('',{},[],[], 'dontaskagain');

            choices = { ...

                sprintf('Continue Loading'); ...

                sprintf('Quit Loading'); ...

            };

        

            if exist('obj2','var')

                msg{1} = sprintf('WARNING: Saved data for %s "%s" does not match this group folder. ', obj.type, obj.name);

                msg{2} = sprintf('Are you sure this saved data belongs to this group folder?');

            else

                msg{1} = sprintf('WARNING: The %s "%s" does not match the saved group data. ', obj.type, obj.name);

                msg{2} = sprintf('Are you sure the saved data belongs to this group folder?');

            end

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

            if strcmp(obj.GroupDataLoadWarnings, configFileOptions{1})

                status = 0;

                return;

            end

            selection = MenuBox([msg{:}], choices, [], [], 'dontaskagain');

            if selection(1)==1

                status = 0;

            end

            

            % Find out if config value does not equal current selection. If

            % not then reset config value

            if selection(2)>0

                if ~strcmp(obj.GroupDataLoadWarnings, configFileOptions{selection(2)})

                    % Overwrite config value

                    cfg = ConfigFileClass();

                    cfg.SetValue('Group Data Loading Warnings', configFileOptions{selection(2)});

                    cfg.Save();

                    obj.GroupDataLoadWarnings()

                end

            end

                        

        end

                

    end

    end
@@ -710,6 +760,19 @@ classdef TreeNodeClass < handle 
        end

        end

   

   

                

                

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

        function out = GroupDataLoadWarnings()

            persistent v;

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

                cfg = ConfigFileClass();

                v = cfg.GetValue('Group Data Loading Warnings');

            elseif exist('arg','var')

                v = arg;

            end

            out = v;

        end

        

        

    end

    end

    

    

end

end

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