Unverified Commit 758aa4fa authored by stephen scott tucker's avatar stephen scott tucker Committed by GitHub
Browse files

Export current element to SNIRF (#118) 

* Bug in StimEditGUI in no stim conditions

* Removed export to script, add export to SNIRF option in File menu

* added *.asv to gitignore

* GetAllData method for proc result class returns non-empty DataClass properties

* GetAllData returns misc contents

* Don't call save on nonexistant Snirf subobjects

* Remove 'SnirfDraft = '3'' from mdt defaults

* ;

* Add GetProbe interface. TODO add warnings. Remove faulty setter.

* ExportSnirfGUI

* Update ExportSnirfGUI.m

* Avoid crash on empty misc
parent 4cbc6e00

.gitignore

+1 −0
Original line number Diff line number Diff line
@@ -2,3 +2,4 @@ 
LastCheckForUpdates.dat

FuncRegistry/UserFunctions/Registry.mat

*.snirf

*.asv
 
 No newline at end of file

DataTree/AcquiredData/Snirf/MetaDataTagsClass.m

+0 −1
Original line number Diff line number Diff line
@@ -18,7 +18,6 @@ classdef MetaDataTagsClass < FileLoadSaveClass 
            obj.tags.TimeUnit = 'unknown';

            obj.tags.FrequencyUnit = 'unknown';

            obj.tags.AppName  = 'snirf-homer3';

            obj.tags.SnirfDraft = '3';

            

            if nargin==1

                obj.SetFilename(varargin{1});

DataTree/AcquiredData/Snirf/SnirfClass.m

+12 −2
Original line number Diff line number Diff line
@@ -424,6 +424,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

        

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

        function err = LoadStim(obj, fileobj)

            err = 0;
@@ -596,8 +597,10 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

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

        function SaveMetaDataTags(obj, fileobj)

            if ~isempty(obj.metaDataTags)

                obj.metaDataTags.SaveHdf5(fileobj, [obj.location, '/metaDataTags']);

            end

        end
@@ -627,8 +630,10 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

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

        function SaveProbe(obj, fileobj)

            if ~isempty(obj.probe)

                obj.probe.SaveHdf5(fileobj, [obj.location, '/probe']);

            end

        end

        

        

        % -------------------------------------------------------
@@ -1122,6 +1127,11 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        end

        

        

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

        function probe = GetProbe(obj)

           probe = obj.probe; 

        end

        

        

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

        function SD = GetSDG(obj,option)

DataTree/GroupClass.m

+15 −0
Original line number Diff line number Diff line
@@ -831,6 +831,21 @@ classdef GroupClass < TreeNodeClass 
    methods

        

        

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

        function probe = GetProbe(obj)

            probe = obj.subjs(1).GetProbe();

%             for subj = obj.subjs

%                 for sess = subj.sess

%                    for run = sess.runs

%                         if ~(probe == run.GetProbe()) 

%                             warning(['Probe ', run.name, ' differs from ', obj.subjs(1).sess(1).runs(1).name]) 

%                         end

%                    end   

%                 end

%             end

        end

        

        

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

        function SD = GetSDG(obj,option)

            if exist('option','var')

DataTree/ProcStream/ProcResultClass.m

+32 −0
Original line number Diff line number Diff line
@@ -362,6 +362,38 @@ classdef ProcResultClass < handle 
    

    methods



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

        function [keys, values] = GetAllData(obj)

            % Returns names and references to all non-empty DataClass objects available as

            % properties of the ProcResultClass instance or of the misc list

            props = properties(obj);

            keys = {};

            values = {};

            for i = 1:length(props)

                val = eval(sprintf('obj.%s', props{i}));

                if isa(val, 'DataClass')

                    if ~isempty(val.dataTimeSeries) && ~isempty(val.time) && ~isempty(val.measurementList)

                        keys{end + 1} = props{i}; %#ok<AGROW>

                        values{end + 1} = val; %#ok<AGROW>

                    end

                end

            end

            try

                miscnames = fields(obj.misc);

            catch

                return

            end

            for i = 1:length(miscnames)

                val = eval(sprintf('obj.misc.%s', miscnames{i}));

                if isa(val, 'DataClass')

                    if ~isempty(val.dataTimeSeries) && ~isempty(val.time) && ~isempty(val.measurementList)

                        keys{end + 1} = miscnames{i}; %#ok<AGROW>

                        values{end + 1} = val; %#ok<AGROW>

                    end

                end

            end

        end

        

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

        function SetTHRF(obj, t)

            obj.tHRF = t;

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