Unverified Commit 5171011a authored by David Boas's avatar David Boas Committed by GitHub
Browse files

Merge 2d and 3d positions (#35) 

* initial changes to add 2D option to classes and otherwise use 3D position

* added exist('opton','var')

* fixed typoes in previous commit

* Update hmrR_PruneChannels.m

removed reset option since it was not used

* Update NirsClass.m

added the option into GetSDG, GetSrcPos, and GetDetPos to be consistent with other classes even though it is not used in this class
parent 578a8a59

DataTree/AcquiredData/AcqDataClass.m

+4 −4
Original line number Diff line number Diff line
@@ -22,13 +22,13 @@ classdef AcqDataClass < matlab.mixin.Copyable 
        datamat   = GetDataTimeSeries(obj, options, iBlk)

        

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

        SD        = GetSDG(obj)

        SD        = GetSDG(obj,option)



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

        srcpos    = GetSrcPos(obj)

        srcpos    = GetSrcPos(obj,option)



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

        detpos    = GetDetPos(obj)

        detpos    = GetDetPos(obj,option)

        

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

        ml        = GetMeasList(obj, iBlk)
@@ -106,7 +106,7 @@ classdef AcqDataClass < matlab.mixin.Copyable 
        

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

        function bbox = GetSdgBbox(obj)

            optpos = [obj.GetSrcPos(); obj.GetDetPos()];

            optpos = [obj.GetSrcPos('2D'); obj.GetDetPos('2D')];

            

            xmax = max(optpos(:,1));

            ymax = max(optpos(:,2));

DataTree/AcquiredData/Nirs/NirsClass.m

+3 −3
Original line number Diff line number Diff line
@@ -439,7 +439,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
               

        

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

        function SD = GetSDG(obj)

        function SD = GetSDG(obj, option)

            SD = obj.SD;

        end
@@ -498,13 +498,13 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
                

        

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

        function srcpos = GetSrcPos(obj)

        function srcpos = GetSrcPos(obj,option)

            srcpos = obj.SD.SrcPos;

        end

        

        

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

        function detpos = GetDetPos(obj)

        function detpos = GetDetPos(obj,option)

            detpos = obj.SD.DetPos;

        end

DataTree/AcquiredData/Snirf/ProbeClass.m

+45 −8
Original line number Diff line number Diff line
@@ -35,8 +35,8 @@ classdef ProbeClass < FileLoadSaveClass 
                    obj.wavelengthsEmission  = [];

                    obj.sourcePos2D  = SD.SrcPos;

                    obj.detectorPos2D  = SD.DetPos;

                    obj.sourcePos3D  = [];

                    obj.detectorPos3D  = [];

                    obj.sourcePos3D  = SD.SrcPos;

                    obj.detectorPos3D  = SD.DetPos;

                    obj.frequencies  = 1;

                    obj.timeDelays  = 0;

                    obj.timeDelayWidths  = 0;
@@ -137,8 +137,8 @@ classdef ProbeClass < FileLoadSaveClass 
                obj.sourcePos2D               = HDF5_DatasetLoad(gid, 'sourcePos2D', [], '2D');

                obj.detectorPos2D             = HDF5_DatasetLoad(gid, 'detectorPos2D', [], '2D');

                obj.landmarkPos2D             = HDF5_DatasetLoad(gid, 'landmarkPos2D', [], '2D');

                obj.sourcePos3D               = HDF5_DatasetLoad(gid, 'sourcePos3D', [], '2D');

                obj.detectorPos3D             = HDF5_DatasetLoad(gid, 'detectorPos3D', [], '2D');

                obj.sourcePos3D               = HDF5_DatasetLoad(gid, 'sourcePos3D', [], '3D');

                obj.detectorPos3D             = HDF5_DatasetLoad(gid, 'detectorPos3D', [], '3D');

                obj.frequencies               = HDF5_DatasetLoad(gid, 'frequencies');

                obj.timeDelays                 = HDF5_DatasetLoad(gid, 'timeDelays');

                obj.timeDelayWidths            = HDF5_DatasetLoad(gid, 'timeDelayWidths');
@@ -163,6 +163,21 @@ classdef ProbeClass < FileLoadSaveClass 
            % SNIRF data to Homer3 compatible structure

            obj.ForwardCompatibility();

            

            % for Homer3 usage, add 3D positions if they are empty

            if isempty(obj.sourcePos3D)

                obj.sourcePos3D = obj.sourcePos2D;

                if size(obj.sourcePos3D,2)<3

                    obj.sourcePos3D(:,3) = 0;

                end

            end

            

            if isempty(obj.detectorPos3D)

                obj.detectorPos3D = obj.detectorPos2D;

                if size(obj.detectorPos3D,2)<3

                    obj.detectorPos3D(:,3) = 0;

                end

            end

            

        end
@@ -189,6 +204,8 @@ classdef ProbeClass < FileLoadSaveClass 
            hdf5write_safe(fileobj, [location, '/wavelengthsEmission'], obj.wavelengthsEmission);

            hdf5write_safe(fileobj, [location, '/sourcePos2D'], obj.sourcePos2D(:,1:2), 'rw:2D');

            hdf5write_safe(fileobj, [location, '/detectorPos2D'], obj.detectorPos2D(:,1:2), 'rw:2D');

            hdf5write_safe(fileobj, [location, '/sourcePos3D'], obj.sourcePos3D, 'rw:3D');

            hdf5write_safe(fileobj, [location, '/detectorPos3D'], obj.detectorPos3D, 'rw:3D');

            hdf5write_safe(fileobj, [location, '/frequencies'], obj.frequencies);

            hdf5write_safe(fileobj, [location, '/timeDelays'], obj.timeDelays);

            hdf5write_safe(fileobj, [location, '/timeDelayWidths'], obj.timeDelayWidths);
@@ -209,15 +226,29 @@ classdef ProbeClass < FileLoadSaveClass 
        

        

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

        function srcpos = GetSrcPos(obj)

        function srcpos = GetSrcPos(obj,flag2d)

            if ~exist('flag2d','var')

                flag2d = 0;

            end

            if flag2d==0

                srcpos = obj.sourcePos3D;

            else

                srcpos = obj.sourcePos2D;

            end                

        end

        

        

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

        function detpos = GetDetPos(obj)

        function detpos = GetDetPos(obj,flag2d)

            if ~exist('flag2d','var')

                flag2d = 0;

            end

            if flag2d==0

                detpos = obj.detectorPos3D;

            else

                detpos = obj.detectorPos2D;

            end                

        end

        

        

        % -------------------------------------------------------
@@ -248,6 +279,12 @@ classdef ProbeClass < FileLoadSaveClass 
            if ~all(obj.detectorPos2D(:)==obj2.detectorPos2D(:))

                return;

            end

            if ~all(obj.sourcePos3D(:)==obj2.sourcePos3D(:))

                return;

            end

            if ~all(obj.detectorPos3D(:)==obj2.detectorPos3D(:))

                return;

            end

            if ~all(obj.frequencies(:)==obj2.frequencies(:))

                return;

            end

DataTree/AcquiredData/Snirf/SnirfClass.m

+29 −11
Original line number Diff line number Diff line
@@ -1020,7 +1020,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SD = GetSDG(obj)

        function SD = GetSDG(obj,option)

            SD = [];

            if isempty(obj)

                return;
@@ -1029,21 +1029,34 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                return;

            end

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

            if exist('option','var')

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

                SD.DetPos = obj.probe.GetDetPos(option);

            else

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

                SD.DetPos = obj.probe.GetDetPos();

            end

        end

        

        

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

        function srcpos = GetSrcPos(obj)

        function srcpos = GetSrcPos(obj,option)

            if exist('option','var')

                srcpos = obj.probe.GetSrcPos(option);

            else

                srcpos = obj.probe.GetSrcPos();

            end

        end

        

        

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

        function detpos = GetDetPos(obj)

        function detpos = GetDetPos(obj,option)

            if exist('option','var')

                detpos = obj.probe.GetDetPos(option);

            else

                detpos = obj.probe.GetDetPos();

            end

        end

        

        

        % ----------------------------------------------------------------------------------
@@ -1128,7 +1141,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SD = Get_SD(obj, iBlk)

        function SD = Get_SD(obj, iBlk, option)

            SD = [];

            if isempty(obj.probe)

                return;
@@ -1140,8 +1153,13 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
                return;

            end

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

            if exist('option','var')

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

                SD.DetPos   = obj.probe.GetDetPos(option);

            else

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

                SD.DetPos   = obj.probe.GetDetPos();

            end

            SD.MeasList = obj.data(iBlk).GetMeasList();

            SD.MeasListAct = ones(size(SD.MeasList,1),1);

        end
@@ -1435,7 +1453,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            % Load probe and extract .nirs-style SD structure

            %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

            fprintf('    Probe (.nirs-style display):\n');

            SD = obj.GetSDG();

            SD = obj.GetSDG('2D');

            pretty_print_struct(SD, 8, 1);

            fprintf('\n');

DataTree/GroupClass.m

+6 −2
Original line number Diff line number Diff line
@@ -746,9 +746,13 @@ classdef GroupClass < TreeNodeClass 
        

        

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

        function SD = GetSDG(obj)

        function SD = GetSDG(obj,option)

            if exist('option','var')

                SD = obj.subjs(1).GetSDG(option);

            else

                SD = obj.subjs(1).GetSDG();

            end

        end

        

        

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

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