Unverified Commit 27a642ee authored by jayd1860's avatar jayd1860 Committed by GitHub
Browse files

Fix SpatialUnit scaling in SD NirsClass (#165) 

* v1.75.0

-- In syncSubmodules.m add option to ignore last revision dates of the parent repo and submodules and instead force the direction of copying changes from parent repo to submodules ('parent2submodules') or submodules to parent repo ('submodules2parent').

* DataTree, v1.9.0, v1.8.3
-- Fix wrong probe scaling converting units in SnirfClass.ProbeClass and NirsClass
-- Add m (meter) to SpatialUnits NirsClass add appropriate scaling. When changing units in SDgui ask iof fixing incorrect units or simply changing units and associated coordinates.

* Utils, v1.4.0, v1.3.5
-- Remove non-class method convert_optodepos_to_circlular_2D_pos.m from ProbeClass to Utils.
-- Add missing function pretty_print_struct.m  used in DataTree to Utils library
-- Fix bug in last commit having to do with the MenuBox radiobutton dialog selction of spatial unit change: either a) correcting them and changing units ONLY  or  b) changing units and coordinates.
-- Add radiobutton selection style option to MenuBox.m
-- Fix some issues with MenuBox.m including issue with MenuBox disappearing outside of screen when run standalone with no parent GUI.

* v1.75.1

-- DataTree, v1.10.0, Fix error in probe registration loading SD file where anchor points are not copied correctly.
parent 4544f60f

DataTree/AcquiredData/Nirs/NirsClass.m

+43 −24
Original line number Diff line number Diff line
@@ -1056,7 +1056,7 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
                'MeasList',[], ...

                'MeasListAct',[], ...

                'SpringList',[], ...

                'AnchorList',[], ...

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

                'SrcMap',[], ...

                'SpatialUnit','', ...

                'xmin',0, ...
@@ -1070,19 +1070,35 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        

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

        function SetProbeSpatialUnit(obj, spatialUnitNew)

        function SetProbeSpatialUnit(obj, spatialUnitNew, scaling)

            % Set scaling based on current units and desired units if they do not match AND

            % scaling was not explcitly specified (i.e., passed in as an argument). 

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

                scaling = 1;

                if strcmpi(spatialUnitNew,'mm')

                    if strcmpi(obj.SD.SpatialUnit,'cm')

                        scaling = 10;

                    elseif strcmpi(obj.SD.SpatialUnit,'m')

                        scaling = 1000;

                    end

                elseif strcmpi(spatialUnitNew,'cm')

                    if strcmpi(obj.SD.SpatialUnit,'mm')

                        scaling = 1/10;

                    elseif strcmpi(obj.SD.SpatialUnit,'m')

                        scaling = 100;

                    end

                elseif strcmpi(spatialUnitNew,'m')

                    if strcmpi(obj.SD.SpatialUnit,'mm')

                        scaling = 1/1000;

                    elseif strcmpi(obj.SD.SpatialUnit,'cm')

                        scaling = 1/100;

                    end

                else

                    spatialUnitNew = '';

                end

            end 

            

            

            obj.SD.SpatialUnit = spatialUnitNew;

            obj.SD.SrcPos = obj.SD.SrcPos * scaling;

            obj.SD.DetPos = obj.SD.DetPos * scaling;
@@ -1102,22 +1118,25 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        function FixProbeSpatialUnit(obj)        

            if isempty(obj.SD.SpatialUnit)

                q = MenuBox('Spatial units not provided in probe data. Please specify spatial units of the optode coordinates?', ...

                    {'mm','cm',sprintf('do not know')});

                    {'mm','cm','m'});

                if q==1

                    obj.SD.SpatialUnit = 'mm';

                elseif q==2

                    obj.SD.SpatialUnit = 'cm';

                elseif q==3

                    obj.SD.SpatialUnit = '';

                end

            end

            if ~strcmpi(obj.SD.SpatialUnit,'mm')

                q = MenuBox(sprintf('This probe uses ''%s'' units for probe coordinates. We recommend converting to ''mm'' units, to be consistent with Homer. Do you want to convert probe coordinates from %s to mm?', ...

                    obj.SD.SpatialUnit), {'YES','NO'}, 'upperleft');

                if q==1

                    obj.SetProbeSpatialUnit('mm')       

                    obj.SD.SpatialUnit = 'm';

                end

            end

            % We don't need to force anything on the user since homer and AV do internal conversions to 'mm'

            %

            %             if ~strcmpi(obj.SD.SpatialUnit,'mm')

            %                 q = MenuBox(sprintf('This probe uses ''%s'' units for probe coordinates. We recommend converting to ''mm'' units, to be consistent with Homer. Do you want to convert probe coordinates from %s to mm?', ...

            %                     obj.SD.SpatialUnit), {'YES','NO'}, 'upperleft');

            %                 if q==1

            %                     obj.SetProbeSpatialUnit('mm')

            %                 end

            %             end

            %

        end

DataTree/AcquiredData/Snirf/DataClass.m

+32 −2
Original line number Diff line number Diff line
@@ -1040,8 +1040,29 @@ classdef DataClass < FileLoadSaveClass 
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    methods

        

        

        

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

        function Copy(obj, obj2)

            if isempty(obj)

                obj = DataClass();

            end

            if isempty(obj2)

                obj = DataClass();

                return;

            end

            if ~isa(obj2, 'DataClass')

                return;

            end

            obj.CopyMeasurementList(obj2);

            obj.dataTimeSeries = obj2.dataTimeSeries;

            obj.time = obj2.time;

        end

        

        

        

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

        function CopyMeasurementList(obj, obj2)

            if isempty(obj)

                obj = DataClass();

            end
@@ -1055,11 +1076,10 @@ classdef DataClass < FileLoadSaveClass 
            for ii=1:length(obj2.measurementList)

                obj.measurementList(ii) = obj2.measurementList(ii).copy();      % shallow copy ok because MeasListClass has no handle properties

            end

            obj.dataTimeSeries = obj2.dataTimeSeries;

            obj.time = obj2.time;

        end

        

        

        

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

        function B = eq(obj, obj2)

            B = false;
@@ -1081,6 +1101,16 @@ classdef DataClass < FileLoadSaveClass 
            if length(obj.measurementList)~=length(obj2.measurementList)

                return;

            end

            if ~obj.EqualMeasurementLists(obj2)

                return;

            end

            B = true;

        end

        

        

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

        function B = EqualMeasurementLists(obj, obj2)

            B = false;

            for ii=1:length(obj.measurementList)

                if obj.measurementList(ii)~=obj2.measurementList(ii)

                    return;

DataTree/AcquiredData/Snirf/MetaDataTagsClass.m

+10 −0
Original line number Diff line number Diff line
@@ -191,6 +191,16 @@ classdef MetaDataTagsClass < FileLoadSaveClass 
        end

        

        

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

        function val = GetLengthUnit(obj)

            val = '';

            if isempty(obj)

                return

            end

            val = obj.tags.LengthUnit;

        end

        

        

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

        function nbytes = MemoryRequired(obj)

            nbytes = 0;

DataTree/AcquiredData/Snirf/ProbeClass.m

+10 −22
Original line number Diff line number Diff line
@@ -41,22 +41,22 @@ classdef ProbeClass < FileLoadSaveClass 
                    SD = n.SD;

                    obj.wavelengths = SD.Lambda;

                    obj.wavelengthsEmission  = [];

                    if isfield(SD,'SrcPos2D') &  ~isempty(SD.SrcPos2D)

                    if isfield(SD,'SrcPos2D') &&  ~isempty(SD.SrcPos2D)

                        obj.sourcePos2D  = SD.SrcPos2D;

                    else

                        obj.sourcePos2D  = SD.SrcPos;

                    end

                    if isfield(SD,'DetPos2D') & ~isempty(SD.DetPos2D)

                    if isfield(SD,'DetPos2D') && ~isempty(SD.DetPos2D)

                        obj.detectorPos2D  = SD.DetPos2D;

                    else

                        obj.detectorPos2D  = SD.DetPos;

                    end

                    if isfield(SD,'SrcPos3D') & ~isempty(SD.SrcPos3D)

                    if isfield(SD,'SrcPos3D') && ~isempty(SD.SrcPos3D)

                        obj.sourcePos3D  = SD.SrcPos3D;

                    else

                        obj.sourcePos3D  = SD.SrcPos;

                    end

                    if isfield(SD,'DetPos3D') & ~isempty(SD.DetPos3D)

                    if isfield(SD,'DetPos3D') && ~isempty(SD.DetPos3D)

                        obj.detectorPos3D  = SD.DetPos3D;

                    else

                        obj.detectorPos3D  = SD.DetPos;
@@ -132,19 +132,6 @@ classdef ProbeClass < FileLoadSaveClass 
            end

        end

        

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

        function xy = convert_optodepos_to_circlular_2D_pos(obj, pos, T, norm_factor)

            pos = [pos ones(size(pos,1),1)];

            pos_unit_sphere = pos*T;

            pos_unit_sphere_norm = sqrt(sum(pos_unit_sphere.^2,2));

            pos_unit_sphere = pos_unit_sphere./pos_unit_sphere_norm ;



            [azimuth,elevation,r] = cart2sph(pos_unit_sphere(:,1),pos_unit_sphere(:,2),pos_unit_sphere(:,3));

            elevation = pi/2-elevation;

            [x,y] = pol2cart(azimuth,elevation);      % get plane coordinates

            xy = [x y];

            xy = xy/norm_factor;               % set maximum to unit length

        end

        

        

        % ----------------------------------------------
@@ -161,9 +148,10 @@ classdef ProbeClass < FileLoadSaveClass 
            end 

        end



        

        

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

        function Project_3D_to_2D(obj)             

            

            if isempty(obj.sourcePos2D) && isempty(obj.detectorPos2D)

                if isempty(obj.landmarkPos3D) || ~obj.isValidLandmarkLabels()

                    nSource = size(obj.sourcePos3D,1);
@@ -230,8 +218,8 @@ classdef ProbeClass < FileLoadSaveClass 
                        obj.landmarkPos2D = refpts_2D.pos;



                        %

                        obj.sourcePos2D = convert_optodepos_to_circlular_2D_pos(obj, obj.sourcePos3D, T, norm_factor);

                        obj.detectorPos2D = convert_optodepos_to_circlular_2D_pos(obj, obj.detectorPos3D, T, norm_factor);

                        obj.sourcePos2D = convert_optodepos_to_circlular_2D_pos(obj.sourcePos3D, T, norm_factor);

                        obj.detectorPos2D = convert_optodepos_to_circlular_2D_pos(obj.detectorPos3D, T, norm_factor);

                    end

                end

            end
@@ -259,7 +247,7 @@ classdef ProbeClass < FileLoadSaveClass 
            if exist('LengthUnit','var')

                % Figure out the scaling factor to multiple by to get the coorinates to be in mm units

                if strcmpi(LengthUnit,'m')  % meter units

                    obj.scaling = 100;

                    obj.scaling = 1000;

                elseif strcmpi(LengthUnit,'cm')  % centimeter units

                    obj.scaling = 10;

                end

DataTree/AcquiredData/Snirf/SnirfClass.m

+73 −0
Original line number Diff line number Diff line
@@ -1794,6 +1794,79 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass 
            

        end

        

        

        

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

        function [md2d, md3d] = GetChannelsMeanDistance(obj)

            ml = obj.data(1).GetMeasListSrcDetPairs();

            d1 = zeros(size(ml,1),1);

            for ii = 1:length(d1)

                d1(ii) = dist3(obj.probe.sourcePos2D(ml(ii,1),:), obj.probe.detectorPos2D(ml(ii,2),:)); 

                d2(ii) = dist3(obj.probe.sourcePos3D(ml(ii,1),:), obj.probe.detectorPos3D(ml(ii,2),:)); 

            end

            md2d = mean(d1);

            md3d = mean(d2);

        end

        

        

        

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

        function err = ErrorCheckSpatialUnits(obj)

            err = 0;

            msg = [];

            [md2d, md3d] = obj.GetChannelsMeanDistance();

            LengthUnitDeclared = obj.metaDataTags.GetLengthUnit();            

            magnitudeMm = log10(30);

            magnitudeCm = log10(3);

            magnitudeM  = log10(.03);

            

            % 2D coordinates

            diffMm = abs(magnitudeMm - log10(md2d));

            diffCm = abs(magnitudeCm - log10(md2d));

            diffM = abs(magnitudeM - log10(md2d));

            [~, idx] =  min([diffMm, diffCm, diffM]);

            if idx == 1

                LengthUnitActual2D = 'mm';

            elseif idx == 2

                LengthUnitActual2D = 'cm';

            elseif idx == 3

                LengthUnitActual2D = 'm';

            end

            if ~strcmpi(LengthUnitDeclared, LengthUnitActual2D)

                msg{1} = sprintf('WARNING: Declared LengthUnit (%s) might not match the likely actual units (%s) of the 2D coordinates\n', ...

                    LengthUnitDeclared, LengthUnitActual2D);

            end

            

            % 2D coordinates

            diffMm = abs(magnitudeMm - log10(md3d));

            diffCm = abs(magnitudeCm - log10(md3d));

            diffM = abs(magnitudeM - log10(md3d));

            [~, idx] =  min([diffMm, diffCm, diffM]);

            if idx == 1

                LengthUnitActual3D = 'mm';

            elseif idx == 2

                LengthUnitActual3D = 'cm';

            elseif idx == 3

                LengthUnitActual3D = 'm';

            end

            if ~strcmpi(LengthUnitDeclared, LengthUnitActual3D)

                msg{2} = sprintf('WARNING: Declared LengthUnit (%s) might not match the likely actual units (%s) of the 3D coordinates\n\n', ...

                    LengthUnitDeclared, LengthUnitActual3D);

            end

            

            % Compare 2D units with 3D units

            if ~strcmpi(LengthUnitActual2D, LengthUnitActual3D)

                msg{3} = sprintf('WARNING: The likely actual units of the 2D coordinates (%s) might not match the like actual units of the 3D coordinates (%s)\n\n', ...

                    LengthUnitActual3D, LengthUnitActual3D);

            end

            

            if ~isempty(msg)

                MenuBox(msg);

            end

        end

        

        

        

    end

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