Commit 193cfd2c authored by jayd1860's avatar jayd1860
Browse files

v1.42.0 

-- Fix issue with probe.snirf or any other snirf files with no data or intentionally corrupt data being accepted as valid.
-- Fix Nirs2Snirf not working for some some .nirs datasets which do not have CondNames. Add default CondNames to NirsClass.ErrorCheck()
-- Fix display of mlAct in MainGUI broken after the measurement list order issue.
-- For diagnostic purposes save error code in err field of all the SnirfClass sub-classes
-- Add back to MainGUI making channels invisible by mouse right-clicking on them.
parent 1fb30baa

DataTree/AcquiredData/DataFiles/DataFilesClass.m

+5 −2
Original line number Diff line number Diff line
@@ -477,7 +477,10 @@ classdef DataFilesClass < handle 
                if  o.GetError() < 0

                    obj.logger.Write('DataFilesClass.ErrorCheck:   FAILED error check - %s will not be added to data set\n', filename);

                    errorIdxs = [errorIdxs, ii]; %#ok<AGROW>

                elseif  contains(o.GetErrorMsg(), 'WARNING: ''data'' corrupt and unusable')                    

                elseif  contains(o.GetErrorMsg(), '''data'' corrupt and unusable')                    

                    obj.logger.Write('DataFilesClass.ErrorCheck:   WARNING data is unusable - %s will not be added to data set\n', filename);

                    errorIdxs = [errorIdxs, ii]; %#ok<AGROW>

                elseif  contains(o.GetErrorMsg(), '''data'' is invalid')                    

                    obj.logger.Write('DataFilesClass.ErrorCheck:   WARNING data is unusable - %s will not be added to data set\n', filename);

                    errorIdxs = [errorIdxs, ii]; %#ok<AGROW>

                else

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+5 −0
Original line number Diff line number Diff line
@@ -142,6 +142,11 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable 
        

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

        function err = GetError(obj)

            err = [];

            if isempty(obj)

                fprintf('Warning: object is empty.')

                return

            end

            err = obj.err;

        end

DataTree/AcquiredData/Nirs/NirsClass.m

+30 −17
Original line number Diff line number Diff line
@@ -650,17 +650,28 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SD = GetSDG(obj, option)

        function SD = GetSDG(obj, ~)

            SD = obj.SD;

        end

        

        

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

        function ml = GetMeasList(obj, iBlk)

        function ml = GetMeasList(obj, ~)

            ml = obj.SD.MeasList;

        end

        

        

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

        function ml = GetMeasurementList(obj, ~)

            ml = MeasListClass();

            for ii = 1:size(obj.SD.MeasList,1)

                ml(ii).sourceIndex = obj.SD.MeasList(ii,1);

                ml(ii).detectorIndex = obj.SD.MeasList(ii,2);

                ml(ii).wavelengthIndex = obj.SD.MeasList(ii,4);

            end

        end

        

        

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

        function wls = GetWls(obj)

            wls = obj.SD.Lambda;
@@ -668,7 +679,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SetStims_MatInput(obj,s,t,CondNames)

        function SetStims_MatInput(obj, s, ~, ~)

            obj.s = s;

        end
@@ -703,13 +714,13 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function srcpos = GetSrcPos(obj,option)

        function srcpos = GetSrcPos(obj, ~)

            srcpos = obj.SD.SrcPos;

        end

        

        

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

        function detpos = GetDetPos(obj,option)

        function detpos = GetDetPos(obj, ~)

            detpos = obj.SD.DetPos;

        end
@@ -728,13 +739,13 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function n = GetDataBlocksNum(obj)

        function n = GetDataBlocksNum(~)

            n = 1;

        end

        

        

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

        function [iDataBlks, ich] = GetDataBlocksIdxs(obj, ich)

        function [iDataBlks, ich] = GetDataBlocksIdxs(~, ich)

            iDataBlks = 1;

            ich={ich};

        end
@@ -882,30 +893,30 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SetStimTpts(obj, icond, tpts)

        function SetStimTpts(~, ~, ~)

            return;

        end

        

        

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

        function tpts = GetStimTpts(obj, icond)

        function tpts = GetStimTpts(~, ~)

            tpts = [];

        end

        

        

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

        function SetStimDuration(obj, icond, duration)

        function SetStimDuration(~, ~, ~)

            return;

        end

        

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

        function duration = GetStimDuration(obj, icond)

        function duration = GetStimDuration(~, ~)

            duration = [];

        end

        

        

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

        function SetStimAmplitudes(obj, icond, vals)

        function SetStimAmplitudes(~, ~, ~)

            return;

        end
@@ -1127,36 +1138,38 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
                    obj.SD.SrcGrommetType{ii} = 'none';

                end

            end

            

            if isempty(obj.SD.DetGrommetType)

                for ii = 1:size(obj.SD.DetPos,1)

                    obj.SD.DetGrommetType{ii} = 'none';

                end

            end

            

            if isempty(obj.SD.DummyGrommetType)

                for ii = 1:size(obj.SD.DummyPos,1)

                    obj.SD.DummyGrommetType{ii} = 'none';

                end

            end

            

            if isempty(obj.SD.SrcGrommetRot)

                for ii = 1:size(obj.SD.SrcPos,1)

                    obj.SD.SrcGrommetRot(ii) = 0;

                end

            end

            

            if isempty(obj.SD.DetGrommetRot)

                for ii = 1:size(obj.SD.DetPos,1)

                    obj.SD.DetGrommetRot(ii) = 0;

                end

            end

            

            if isempty(obj.SD.DummyGrommetRot)

                for ii = 1:size(obj.SD.DummyPos,1)

                    obj.SD.DummyGrommetRot(ii) = 0;

                end

            end

            if isempty(obj.CondNames)

                for ii = 1:size(obj.s,2)

                    if length(obj.s(:,ii)) == length(obj.t)

                        obj.CondNames{ii} = num2str(ii);

                    end

                end

            end

            

        end

DataTree/AcquiredData/Snirf/AuxClass.m

+2 −0
Original line number Diff line number Diff line
@@ -110,6 +110,8 @@ classdef AuxClass < FileLoadSaveClass 
                end

                

            end

            

            obj.SetError(err); 

        end

DataTree/AcquiredData/Snirf/DataClass.m

+1 −0
Original line number Diff line number Diff line
@@ -173,6 +173,7 @@ classdef DataClass < FileLoadSaveClass 
            end

            

            err = ErrorCheck(obj, err);

            obj.SetError(err); 

        end

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