Unverified Commit de02dd76 authored by jayd1860's avatar jayd1860 Committed by GitHub
Browse files

v1.79.1 -- Fix Homer3 displaying probe in 3D rather than 2D. (#177) 

v1.79.0

* DataTree, v1.14.0
-- Fix Homer3 displaying probe in 3D rather than 2D. Back out changes that default to 3D in ProbeClass and NirsClass GetSrcPos and GetDetPos for ALL cases. The way it's supposed to work is probe is supposed to use 2D coordinates ONLY when being displayed in Homer3. Rest of the time default to 3D if it exists. Reason for original change is misunderstanding of what the purpose of 2D coord was which is ONLY for display

* Utils, v1.5.1
-- Add ability to simulate full dataset (generateSimData.m, simulateDataTimeSeries.m)  to be able to eventually do workflow unit and system tests
parent b69f6e6f

DataTree/AcquiredData/Nirs/NirsClass.m

+55 −9
Original line number Diff line number Diff line
@@ -794,14 +794,45 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function srcpos = GetSrcPos(obj, ~)

        function srcpos = GetSrcPos(obj, options) %#ok<*INUSD>

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

                options = '';

            end

            if optionExists(options,'2D')

                if ~isempty(obj.SD.SrcPos)

            srcpos = obj.SD.SrcPos;

                else

                    srcpos = obj.SD.SrcPos3D;

                end

            else

                if ~isempty(obj.SD.SrcPos3D)

                    srcpos = obj.SD.SrcPos3D;

                else

                    srcpos = obj.SD.SrcPos;

                end

            end

        end

        

        

        

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

        function detpos = GetDetPos(obj, ~)

        function detpos = GetDetPos(obj, options)

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

                options = '';

            end

            if optionExists(options,'2D')

                if ~isempty(obj.SD.DetPos)

                    detpos = obj.SD.DetPos;

                else

                    detpos = obj.SD.DetPos3D;

                end

            else

                if ~isempty(obj.SD.DetPos3D)

                    detpos = obj.SD.DetPos3D;

                else

                    detpos = obj.SD.DetPos;

                end

            end

        end
@@ -1048,12 +1079,27 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SD = InitProbe(obj)

        function SD = InitProbe(obj, srcpos, detpos, ml, lambda, dummypos)

            if nargin<2

                srcpos = [];

            end

            if nargin<3

                detpos = [];

            end

            if nargin<4

                ml = [];

            end

            if nargin<5

                lambda = [];

            end

            if nargin<6

                dummypos = [];

            end

            SD = struct(...

                'Lambda',[], ...

                'SrcPos',[], ...

                'DetPos',[], ...

                'DummyPos',[], ...

                'Lambda',lambda, ...

                'SrcPos',srcpos, ...

                'DetPos',detpos, ...

                'DummyPos',dummypos, ...

                'SrcPos3D',[], ...

                'DetPos3D',[], ...

                'DummyPos3D',[], ...
@@ -1069,7 +1115,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
                'Landmarks',obj.InitLandmarks(), ...

                'Landmarks2D',obj.InitLandmarks(), ...

                'Landmarks3D',obj.InitLandmarks(), ...

                'MeasList',[], ...

                'MeasList',ml, ...

                'MeasListAct',[], ...

                'SpringList',[], ...

                'AnchorList',{{}}, ...

DataTree/AcquiredData/Snirf/ProbeClass.m

+37 −11
Original line number Diff line number Diff line
@@ -386,23 +386,47 @@ classdef ProbeClass < FileLoadSaveClass 
        

        

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

        function srcpos = GetSrcPos(obj, ~)

        function srcpos = GetSrcPos(obj, options) %#ok<*INUSD>

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

                options = '';

            end

            if optionExists(options,'2D')

                if ~isempty(obj.sourcePos2D)

                    srcpos = obj.sourcePos2D;

                else

                    srcpos = obj.sourcePos3D;

                end

            else

                if ~isempty(obj.sourcePos3D)

                    srcpos = obj.sourcePos3D;

                else

                    srcpos = obj.sourcePos2D;

                end

            end

        end

        

        

        

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

        function detpos = GetDetPos(obj, ~)

        function detpos = GetDetPos(obj, options)

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

                options = '';

            end

            if optionExists(options,'2D')

                if ~isempty(obj.detectorPos2D)

                    detpos = obj.detectorPos2D;

                else

                    detpos = obj.detectorPos3D;

                end

            else

	            if ~isempty(obj.detectorPos3D)

	                detpos = obj.detectorPos3D;

	            else

	                detpos = obj.detectorPos2D;

	            end

	        end

        end

        

        

        

        % -------------------------------------------------------
@@ -418,7 +442,6 @@ classdef ProbeClass < FileLoadSaveClass 
                return;

            end

            if isempty(obj) && isempty(obj2)

                b = true;

                return;

            end

            if ~all(obj.wavelengths(:)==obj2.wavelengths(:))
@@ -477,6 +500,7 @@ classdef ProbeClass < FileLoadSaveClass 
        end

        

        

        

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

        function nbytes = MemoryRequired(obj)

            nbytes = 0;
@@ -487,6 +511,7 @@ classdef ProbeClass < FileLoadSaveClass 
        end

        

        

        

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

        function b = IsEmpty(obj)

            b = true;
@@ -501,6 +526,7 @@ classdef ProbeClass < FileLoadSaveClass 
        end



        

        

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

        function b = IsValid(obj)

            b = false;

DataTree/AcquiredData/Snirf/SnirfClass.m

+8 −10
Original line number Diff line number Diff line
@@ -1339,22 +1339,20 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function srcpos = GetSrcPos(obj,option)

            if exist('option','var')

                srcpos = obj.probe.GetSrcPos(option);

            else

                srcpos = obj.probe.GetSrcPos();

        function srcpos = GetSrcPos(obj, options)

            if exist(options,'var')

                options = '';

            end

            srcpos = obj.probe.GetSrcPos(options);

        end

        

        

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

        function detpos = GetDetPos(obj,option)

            if exist('option','var')

                detpos = obj.probe.GetDetPos(option);

            else

                detpos = obj.probe.GetDetPos();

        function detpos = GetDetPos(obj, options)

            if exist(options,'var')

                options = '';

            end

            detpos = obj.probe.GetDetPos(options);

        end

DataTree/SessClass.m

+1 −26
Original line number Diff line number Diff line
@@ -452,13 +452,8 @@ classdef SessClass < TreeNodeClass 
        

        

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

        function probe = GetProbe(obj, option)

        function probe = GetProbe(obj, ~)

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

%             for run = obj.runs

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

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

%                end

%             end

        end
@@ -472,26 +467,6 @@ classdef SessClass < TreeNodeClass 
        end

        

        

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

        function srcpos = GetSrcPos(obj,option)

            if exist('option','var')

                srcpos = obj.runs(1).GetSrcPos(option);

            else

                srcpos = obj.runs(1).GetSrcPos();

            end

        end

        

        

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

        function detpos = GetDetPos(obj,option)

            if exist('option','var')

                detpos = obj.runs(1).GetDetPos(option);

            else

                detpos = obj.runs(1).GetDetPos();

            end

        end

        

        

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

        function bbox = GetSdgBbox(obj)

            bbox = obj.runs(1).GetSdgBbox();

DataTree/SubjClass.m

+0 −27
Original line number Diff line number Diff line
@@ -518,26 +518,6 @@ classdef SubjClass < TreeNodeClass 
        end

        

        

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

        function srcpos = GetSrcPos(obj,option)

            if exist('option','var')

                srcpos = obj.sess(1).GetSrcPos(option);

            else

                srcpos = obj.sess(1).GetSrcPos();

            end

        end

        

        

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

        function detpos = GetDetPos(obj,option)

            if exist('option','var')

                detpos = obj.sess(1).GetDetPos(option);

            else

                detpos = obj.sess(1).GetDetPos();

            end

        end

        

        

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

        function bbox = GetSdgBbox(obj)

            bbox = obj.sess(1).GetSdgBbox();
@@ -547,13 +527,6 @@ classdef SubjClass < TreeNodeClass 
        % ----------------------------------------------------------------------------------

        function probe = GetProbe(obj)

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

%             for sess = obj.sess

%                for run = sess.runs

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

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

%                     end

%                end   

%            end

        end

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