Commit 5ce45ea8 authored by jayd1860's avatar jayd1860
Browse files

v1.12.22 

-- Add manual exclusion of time and stims in MainGUI.
-- Add Motion Artifacts panel.
-- Fix small bug in help_local
-- Rebuild windows installation file
parent 05cc2eb9

DataTree/AcquiredData/Snirf/SnirfClass.m

+22 −10
Original line number Diff line number Diff line
@@ -593,18 +593,26 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 


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

        function t = GetTime(obj, iBlk)

            t = [];

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk=1;

            end

            if iBlk>length(obj.data)

                return;

            end

            t = obj.data(iBlk).GetTime();

        end

        

        

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

        function datamat = GetDataMatrix(obj, iBlk)

            datamat = [];

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk=1;

            end

            if iBlk>length(obj.data)

                return;

            end

            datamat = obj.data(iBlk).GetDataMatrix();

        end
@@ -640,9 +648,13 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

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

        function ml = GetMeasList(obj, iBlk)

            ml = [];

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk=1;

            end

            if iBlk>length(obj.data)

                return;

            end

            ml = obj.data(iBlk).GetMeasList();

        end
@@ -794,12 +806,12 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        % ----------------------------------------------------------------------------------

        function d = Get_d(obj, iBlk)

            d = [];

            if isempty(obj.data)

                return;

            end

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

            end

            if iBlk>length(obj.data)

                return;

            end

            d = obj.data(iBlk).GetDataMatrix();

        end
@@ -807,12 +819,12 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        % ----------------------------------------------------------------------------------

        function t = Get_t(obj, iBlk)

            t = [];

            if isempty(obj.data)

                return;

            end

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

            end

            if iBlk>length(obj.data)

                return;

            end

            t = obj.data(iBlk).GetTime();

        end
@@ -823,12 +835,12 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            if isempty(obj.probe)

                return;

            end

            if isempty(obj.data)

                return;

            end

            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

            end

            if iBlk>length(obj.data)

                return;

            end

            SD.Lambda   = obj.probe.GetWls();

            SD.SrcPos   = obj.probe.GetSrcPos();

            SD.DetPos   = obj.probe.GetDetPos();
@@ -852,7 +864,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            if ~exist('iBlk','var') || isempty(iBlk)

                iBlk = 1;

            end

            if isempty(obj.data)

            if iBlk>length(obj.data)

                return;

            end

            t = obj.data(iBlk).GetTime();

DataTree/ProcStream/ProcInputClass.m

+60 −10
Original line number Diff line number Diff line
@@ -42,7 +42,9 @@ classdef ProcInputClass < handle 
            if isempty(obj)

                obj = ProcInputClass();

            end

            if ~isempty(obj2.tIncMan)

                obj.tIncMan = obj2.tIncMan;

            end

            

            fields = properties(obj.misc);

            for ii=1:length(fields)
@@ -127,19 +129,22 @@ classdef ProcInputClass < handle 
        

        

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

        function SetTincMan(obj, val)

            obj.tIncMan = val;

        function SetTincMan(obj, val, iBlk)

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

                iBlk=1;

            end

            obj.tIncMan{iBlk} = val;

        end

        

        

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

        function tIncMan = GetTincMan(obj, iBlk)

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

                iBlk=1;

        function val = GetTincMan(obj, iBlk)

            val = {};

            if ~exist('iBlk','var') || isempty(iBlk)

                val = obj.tIncMan;

            elseif ~isempty(obj.tIncMan)

                val = obj.tIncMan{iBlk};

            end

            

            % TBD: need to implement this

            tIncMan = obj.tIncMan;

        end
@@ -276,6 +281,51 @@ classdef ProcInputClass < handle 
        end

        

        

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

        function SetStims_MatInput(obj, s, t, CondNames)

            obj.acquiredEditable.SetStims_MatInput(s, t);

        end

        

        

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

        function StimReject(obj, t, iBlk)

            tRange = [-2, 10];

            

            s = obj.acquiredEditable.GetStims(t);

            dt = (t(end)-t(1))/length(t);

            tRangeIdx = floor(tRange(1)/dt):ceil(tRange(2)/dt);

            smax = max(s,[],2);

            lstS = find(smax==1);

            for iS = 1:size(lstS,1)

                lst = round(min(max(lstS(iS) + tRangeIdx,1),length(t)));

                if ~isempty(obj.tIncMan{iBlk}) && min(obj.tIncMan{iBlk}(lst))==0

                    s(lstS(iS),:) = -1*abs(s(lstS(iS),:));

                end

            end

            obj.acquiredEditable.SetStims_MatInput(s, t);

        end

        

        

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

        function StimInclude(obj, t, iBlk)

            tRange = [-2, 10];

            

            s = obj.acquiredEditable.GetStims(t);

            dt = (t(end)-t(1))/length(t);

            tRangeIdx = floor(tRange(1)/dt):ceil(tRange(2)/dt);

            for iC = 1:size(s,2)

                lstS = find(s(:,iC)<0);

                for iS = 1:size(lstS,1)

                    lst = round(min(max(lstS(iS) + tRangeIdx,1),length(t)));

                    if ~isempty(obj.tIncMan{iBlk}) && min(obj.tIncMan{iBlk}(lst))==1

                        s(lstS(iS),iC) = 1;

                    end

                end

            end

            obj.acquiredEditable.SetStims_MatInput(s, t);

        end

        

        

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

        function RenameCondition(obj, oldname, newname)

            % Function to rename a condition. Important to remeber that changing the

DataTree/ProcStream/ProcStreamClass.m

+27 −0
Original line number Diff line number Diff line
@@ -1200,6 +1200,15 @@ classdef ProcStreamClass < handle 
        end

        

        

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

        function SetTincMan(obj, val, iBlk)

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

                iBlk = [];

            end

            obj.input.SetTincMan(val, iBlk);

        end

        



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

        function tIncMan = GetTincMan(obj, iBlk)

            if ~exist('iBlk','var')
@@ -1366,6 +1375,24 @@ classdef ProcStreamClass < handle 
        end

        

        

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

        function SetStims_MatInput(obj, s, t, CondNames)

            obj.input.SetStims_MatInput(s, t, CondNames);

        end

        

        

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

        function StimReject(obj, t, iBlk)

            obj.input.StimReject(t, iBlk)

        end

        

        

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

        function StimInclude(obj, t, iBlk)

            obj.input.StimInclude(t, iBlk);

        end

        

        

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

        function RenameCondition(obj, oldname, newname)

            % Function to rename a condition. Important to remeber that changing the

DataTree/RunClass.m

+51 −6
Original line number Diff line number Diff line
@@ -48,7 +48,7 @@ classdef RunClass < TreeNodeClass 
                return;

            end

            obj.procStream = ProcStreamClass(obj.acquired);



            obj.InitTincMan();

            if isa(varargin{1}, 'FileClass')

                varargin{1}.Loaded();

            end
@@ -430,6 +430,38 @@ classdef RunClass < TreeNodeClass 
        end

        

        

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

        function SetTincMan(obj, idxs, iBlk, excl_incl)

            if nargin<2

                return

            end

            if nargin<4

                excl_incl = 'exclude';

            end

            tIncMan = obj.procStream.GetTincMan(iBlk);

            if strcmp(excl_incl, 'exclude')

                tIncMan(idxs) = 0; 

            elseif strcmp(excl_incl, 'include')

                tIncMan(idxs) = 1; 

            end

            obj.procStream.SetTincMan(tIncMan, iBlk);

        end

        

        

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

        function InitTincMan(obj)

            iBlk = 1;

            while 1

                t = obj.acquired.GetTime(iBlk);

                if isempty(t)

                    break

                end

                tIncMan = ones(length(t),1);

                obj.procStream.SetTincMan(tIncMan, iBlk);

                iBlk = iBlk+1;

            end

        end

                

    end        % Public Set/Get methods
@@ -555,6 +587,19 @@ classdef RunClass < TreeNodeClass 
        end

        

        

        

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

        function StimReject(obj, t, iBlk)

            obj.procStream.StimReject(t, iBlk);

        end

        

        

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

        function StimInclude(obj, t, iBlk)

            obj.procStream.StimInclude(t, iBlk);

        end

        

        

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

        function vals = GetStimValSettings(obj)

            vals = obj.procStream.input.GetStimValSettings();

DataTree/TreeNodeClass.m

+6 −0
Original line number Diff line number Diff line
@@ -567,6 +567,12 @@ classdef TreeNodeClass < handle 
        end



        

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

        function SetTincMan(obj, idxs, iBlk, excl_incl)

            ;

        end

        

        

    end

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