LUMO Toolbox: Introducing a loading function for 2D layouts and Improving Graph Responsiveness

LUMO_toolbox/DOTHUB_LUMOcomputeRotations.m

@@ -0,0 +1,98 @@
+function angle_deg = DOTHUB_LUMOcomputeRotations(xy_original, xy_rotated, plotFlag)
+% This function estimates the rotation of source A from the loaded 2D coordinates
+% after comparing the 2D coordinates of the original (fixed position) and rotated (loaded) tiles. 
+% The function does the following:
+%   1. Find the centroid for the original and rotated sources (A,B,C),
+%      treating them as triangles.
+%   2. Calculate the vector length from the centroid to the reference
+%      vertex (source A) for both triangles.
+%   3. Compute the cosine of the angle between the two vectors, return the
+%      angle in radians and convert it into degrees. 
+%
+% ######################## INPUTS #########################################
+%
+% xy_original        :   The 2D coordinates of the original ABC sources,
+%                        making a triangle.
+% xy_rotaded         :   The 2D coordinates of the rotated (loaded) ABC 
+%                        sources, making a triangle.
+% plotFlag           :   A boolean value to enable a visualisation of the
+%                        original and rotated vectors
+%
+% ####################### OUTPUTS #########################################
+% angle_deg          :   The estimated degree of rotation
+%
+% ####################### Dependencies ####################################
+%
+% #########################################################################
+% GL, UCL, April 2024
+
+% #########################################################################    
+
+    % extract x, y original and rotated
+    x_original = xy_original(:, 1);
+    y_original = xy_original(:, 2);
+    x_rotated = xy_rotated(:, 1);
+    y_rotated = xy_rotated(:, 2);
+
+    % Find centroid for original and rotated coordinates
+    xor_centroid = mean(x_original);
+    yor_centroid = mean(y_original);
+    xrot_centroid = mean(x_rotated);
+    yrot_centroid = mean(y_rotated);
+
+    % Calculate vector components from centroid to source 1 (reference source)
+    vx_original = x_original(1) - xrot_centroid;
+    vy_original = y_original(1) - yrot_centroid;
+    vx_rotated = x_rotated(1) - xrot_centroid;
+    vy_rotated = y_rotated(1) - yrot_centroid;
+
+    %% Plot
+    if plotFlag
+        figure(1)
+        scatter(x_original, y_original, 'r');
+        hold on
+        scatter(xor_centroid, yor_centroid, 'black');
+        % Plot the vector from centroid to source 1
+        quiver(xor_centroid, yor_centroid, vx_original, vy_original, 0, 'red', 'LineWidth', 2);
+        hold on
+        % Overlay the rotated triangle
+        scatter(x_rotated, y_rotated, 'blue');
+        hold on
+        scatter(xrot_centroid, yrot_centroid, 'blue');
+        % Plot the vector from centroid to rotated source
+        quiver(xrot_centroid, yrot_centroid, vx_rotated, vy_rotated, 0, 'blue', 'LineWidth', 2);
+        hold off
+    end
+
+    %%
+    % Compute the dot product of vectors v1 and v2
+    dot_product = dot([vx_original, vy_original], [vx_rotated, vy_rotated]);
+
+    % Establish if rotation is clockwise or anti-clockwise
+    if vx_rotated < vx_original
+       % counter-clockwise rotation
+       rotation_direction = 'left-side';
+    elseif vx_rotated > vx_original
+        % clockwise rotation
+        rotation_direction = 'right-side';
+    else
+        rotation_direction = '180';
+    end 
+
+    % Compute the magnitudes of vectors v1 and v2
+    magnitude_v1 = norm([vx_original, vy_original]);
+    magnitude_v2 = norm([vx_rotated, vy_rotated]);
+
+    % Compute the cosine of the angle between v1 and v2
+    cos_angle = dot_product / (magnitude_v1 * magnitude_v2);
+
+    % Compute the angle in radians
+    angle_rad = acos(cos_angle);
+
+    % Convert the angle from radians to degrees
+    angle_deg = rad2deg(angle_rad);
+
+    % Adjust for rotation on the right-side of original vector
+    if strcmp(rotation_direction, 'right-side')
+        angle_deg = 360 - angle_deg;
+    end 

LUMO_toolbox/DOTHUB_LUMOcreate2DSD.m

@@ -11,6 +11,7 @@
     tmp = inputdlg('Enter number of LUMO tiles...','Tile number');
     nTiles = str2num(tmp{1});
 end
+
 xspace = 17.5;
 yspace = 15.1505;
 ng = 12;
@@ -49,9 +50,9 @@
 uit.ColumnWidth = {60,60,60};
 uit.ColumnEditable = true;
 uit.CellEditCallback = @updatePlot;
-uit.Position = [0.05*ss(1) 0.05*ss(2) 0.15*ss(1) 0.75*ss(2)];
+uit.Position = [0.025*ss(1) 0.05*ss(2) 0.15*ss(1) 0.85*ss(2)];
 ax = uiaxes(fig);
-ax.Position = [0.25*ss(1) 0.25*ss(2) 0.7*ss(1) 0.60*ss(2)];
+ax.Position = [0.25*ss(1) 0.25*ss(2) 0.7*ss(1) 0.60*ss(2)]; % position of the Grid
 bt = uibutton(fig,'Text','FINISHED');
 bt.Position = [0.85*ss(1) 0.05*ss(2) 0.1*ss(1) 0.075*ss(2)];
 bt.ButtonPushedFcn = @SaveandQuit;
@@ -60,6 +61,11 @@
 bt2.Position = [0.25*ss(1) 0.05*ss(2) 0.1*ss(1) 0.075*ss(2)];
 bt2.ButtonPushedFcn = @RotateGrid;
 
+% Add button to load 2D layout from existing file
+bt3 = uibutton(fig, 'Text', 'Load');
+bt3.Position = [0.35*ss(1) 0.05*ss(2) 0.1*ss(1) 0.075*ss(2)];
+bt3.ButtonPushedFcn = @Load2Dfile;
+
 [source_array, detector_array] = getTileOptodePos_Callback;
 
 
@@ -117,6 +123,8 @@ function updatePlot(ssrc,event)
         uit.Data(:,1:2) = centers(:,1:2);
         uit.Data(:,3) = orientations;
         [source_array, detector_array] = getTileOptodePos_Callback;
+
+        ax.Position = [0.2*ss(1) 0.2*ss(2) 0.8*ss(1) 0.75*ss(2)]; % position of the Grid
     end
 
     function [source_array, detector_array] = getTileOptodePos_Callback
@@ -148,21 +156,33 @@ function updatePlot(ssrc,event)
         hold(ax,'on');
 
         %plot grid
-        plot(ax,grid(:,1),grid(:,2),'k.','markersize',10);hold on;
+        plot(ax,grid(:,1),grid(:,2),'.','markersize',10, 'Color', [.7 .7 .7]);
+        hold on;
         %plot array
-        plot(ax,source_array(:,1),source_array(:,2),'r.','markersize',30);
-        plot(ax,detector_array(:,1),detector_array(:,2),'b.','markersize',30);
-        for i = 1:size(source_array,1)
-            text(ax,source_array(i,1)+3,source_array(i,2),['S' num2str(i)],'color','r','FontSize',8);
-        end
-        for i = 1:size(detector_array,1)
-            text(ax,detector_array(i,1)+3,detector_array(i,2),['D' num2str(i)],'color','b','FontSize',8);
-        end
+        plot(ax,source_array(:,1),source_array(:,2),'r.','markersize',25);
+        plot(ax,detector_array(:,1),detector_array(:,2), 'b.','markersize',25);
+
+%         for i = 1:size(source_array,1)
+%             text(ax,source_array(i,1)+3,source_array(i,2),['S' num2str(i)],'color','r','FontSize',8);
+%         end
+
+        % add the number of tile anchored to Source3
+        source_counter = 1;
+        for n_source=3:3:size(source_array,1)
+            text(ax,source_array(n_source,1),source_array(n_source,2)+4,['T' num2str(source_counter)],'color','k','FontSize', 15);
+            source_counter = source_counter + 1;
+        end 
+
+        % remove text of detectors
+%         for i = 1:size(detector_array,1)
+%             text(ax,detector_array(i,1)+3,detector_array(i,2),['D' num2str(i)],'color','b','FontSize',8);
+%         end
         linend = source_array(1:3:end,[1 2]);
         linstart = detector_array(3:4:end,[1 2]);
+
         for i = 1:size(linend,1);
-            line(ax,[linstart(i,1) linend(i,1)],[linstart(i,2) linend(i,2)],'color','g','LineWidth',2);hold on;
-            plot(ax,linstart(i,1),linstart(i,2),'g.','MarkerSize',20);
+            line(ax,[linstart(i,1) linend(i,1)],[linstart(i,2) linend(i,2)],'color','#00DB4C','LineWidth',3);hold on;
+%             plot(ax,linstart(i,1),linstart(i,2),'g.','MarkerSize',20);
         end
 
         tmp = [source_array(:,1); detector_array(:,1)];
@@ -196,6 +216,56 @@ function RotateGrid(~,~)
         getTileOptodePos_Callback;
     end
 
+    function Load2Dfile(~,~)
+        % choose a file using a graphical file picker window
+        [file, path] = uigetfile('*.*', 'Select a file');
+        fname = fullfile(path, file);
+        layout_2D = load(fname, "-mat"); % the loaded structure
+
+        % Warning if the loaded file contains a different number from
+        % intended nTiles
+        loaded_nTiles = size(layout_2D.SD.DetPos, 1)/4; 
+        if loaded_nTiles ~= nTiles
+            warning_msg = sprintf('The loaded SD files contains %d tiles. Initial nTiles input was %d', loaded_nTiles, nTiles);
+            uiwait(warndlg(warning_msg));
+
+            quest = {'Do you want to continue?'};
+            dlgtitle = 'Warning';
+            fieldsize = [1 45];
+            answer = questdlg(quest, dlgtitle, 'Yes', 'No', 'Cancel');
+
+            switch answer
+                case 'No'
+                    error_msg = 'The number of loaded tiles does not match the initial nTiles input';
+                    uiwait(errordlg(error_msg));
+                    error('The number of loaded tiles does not match the initial nTiles input');
+            end
+        end 
+
+        % extract the x, y values every 3 row (corresponding to the central
+        % detector
+        detCounter = 1;
+        for i = 3:4:size(detector_array, 1)
+            uit.Data(detCounter, 1:2) = layout_2D.SD.DetPos(i, 1:2);
+
+            detCounter = detCounter + 1; 
+        end
+        updatePlot; % update the plot
+
+        srcCounter = 1;
+        for i=3:3:size(source_array,1)
+            source_original = source_array(i-2:i, :);
+            source_rotated = layout_2D.SD.SrcPos(i-2:i, :);
+            % Extract the degree of the rotated angle
+            angle_deg = DOTHUB_LUMOcomputeRotations(source_original, source_rotated, 0);
+            % update the data and the plot
+            uit.Data(srcCounter, 3) = angle_deg;
+            srcCounter = srcCounter + 1; 
+        end
+        updatePlot;
+
+    end
+
     function SaveandQuit(~,~)
 
         SD_2Dtmp.SrcPos = source_array;

LUMO_toolbox/DOTHUB_LUMOpolhemus2SD3D.m

@@ -41,34 +41,62 @@
 
 %Manage Inputs ###########################################################
 %#########################################################################
+
+% Variables
+slg_Flag = -1;              % flag to determine whether the user has selected SLGs
+LG_length_Flag = 0;         % flag to determine if the user uses fixed LGs
+FLG_infant = 12.94;         % TOTAL offset of the infant fixed light guide used when offsetting the Polhemus values
+FLG_adult = 18.75;          % TOTAL offset of the adult fixed light guide used when offsetting the Polhemus values
+
+% Physical length of the movable light guide component. DO NOT CHANGE. 
+short_SLG_full_l = 3.2; % fully extended movable light guide for a short SLG
+medium_SLG_full_l = 5.24; 
+long_SLG_full_l = 9.13;
+
+% The compression value (compression in % / 100)
+% Note: These values correspond to the average compression values
+% obtained across subjects (N=3). 
+short_SLG_compression = 0.32; 
+medium_SLG_compression = 0.14;
+long_SLG_compression = 0.14;
+
+% Length of the movable light guide(in mm) after being compressed
+short_SLG_compression_l = short_SLG_compression * short_SLG_full_l; 
+medium_SLG_compression_l = medium_SLG_compression * medium_SLG_full_l;
+long_SLG_compression_l = long_SLG_compression * long_SLG_full_l;
+
+% Calculate the SLGs offset 
+%   offset = fully extended movable light guide - compression length
+short_SLG_offset = short_SLG_full_l - short_SLG_compression_l;     
+medium_SLG_offset = medium_SLG_full_l - medium_SLG_compression_l;   
+long_SLG_offset = long_SLG_full_l - long_SLG_compression_l;      
+
 if ~exist('posCSVFileName','var')
     [file,path] = uigetfile('*.csv','Select Polhemus data set (.csv)','MultiSelect','on');
     posCSVFileName = fullfile(path,file);
 end
 
-mixedFlag = 0;
-if ~exist('infantFlag','var')
-    answer = questdlg('Which light-guides were used in this array?','Select light guide type','ADULT','INFANT','MIXED','ADULT');
-    if strcmp(answer,'INFANT')
-        infantFlag = 1;
-    elseif strcmp(answer,'ADULT')
-        infantFlag = 0;
-    elseif  strcmp(answer,'MIXED')
-        mixedFlag = 1;
-    else
-        return
+    answer = questdlg('Which light-guides were used in this array?','Select light guide type','ADULT','INFANT','SLGs','ADULT');
+    switch answer
+        case 'INFANT'
+            LG_length_Flag = 0;
+        case 'ADULT'
+            LG_length_Flag = 1;
+        case 'SLGs'
+            LG_length_Flag = 2;
     end
-elseif isempty(infantFlag)
-    answer = questdlg('Which light-guides were used in this array?','Select light guide type','ADULT','INFANT','MIXED','ADULT');
-    if strcmp(answer,'INFANT')
-        infantFlag = 1;
-    elseif strcmp(answer,'ADULT')
-        infantFlag = 0;
-    elseif  strcmp(answer,'MIXED')
-        mixedFlag = 1;
-    else
-        return
-    end   
+
+% SLG selection
+if LG_length_Flag == 2
+   answer = questdlg('What length of SLGs did you use?', 'Select SLG Length', 'SHORT', 'MEDIUM', 'LONG', 'MEDIUM');
+   switch answer
+       case 'SHORT'
+           slg_Flag = 0;
+       case 'MEDIUM'
+           slg_Flag = 1;
+       case 'LONG'
+           slg_Flag = 2;
+   end
 end
 
 if ~exist('saveFlag','var')
@@ -84,7 +112,7 @@
     ext = '.csv';
 end
 posCSVFileName = fullfile(path,[name ext]);
-SD3DFileName = fullfile(path,[name '.SD3D']);
+SD3DFileName = fullfile(path,[(strcat(name, '_', answer)) '.SD3D']);
 
 %Wavelengths
 wavelength1 = 735;
@@ -118,27 +146,24 @@
     nTiles = size(PolPoints,1)/3;
 end
 
-%Define offsets vector
-if mixedFlag
-    prompt = 'Enter nTile space-separated values of 1 (Adult) and 0 (Infant)';
-    dlgtitle = 'Light guide specification';
-    dims = [1 45];
-    answer = inputdlg(prompt,dlgtitle,dims);
-    answer = str2num(cell2mat(answer));
-    if isempty(answer)
-        error('No light guide specification provided')
-    else
-        offset = zeros(nTiles,1);
-        offset(answer==1) = 18.75;
-        offset(answer==0) = 12.94;
-        if any(offset==0)
-            error('Error in light guide specification')
-        end
-    end      
-elseif infantFlag==1
-    offset = ones(nTiles,1)*12.94; %Infant offset length (mm)
-elseif infantFlag==0
-    offset = ones(nTiles,1)*18.75; %Adult offset length (mm)
+%Define the offsets vector
+if LG_length_Flag==2 % 2=SLG
+
+    switch slg_Flag
+        case 0
+            offset = ones(nTiles,1)*(FLG_adult + short_SLG_offset);     %short SLG offset (mm)
+        case 1
+            offset = ones(nTiles,1)*(FLG_adult + medium_SLG_offset);     %medium SLG offset (mm)
+        case 2
+            offset = ones(nTiles,1)*(FLG_adult + long_SLG_offset);     %long SLG offset (mm)
+    end
+else 
+    switch  LG_length_Flag
+        case 0
+            offset = ones(nTiles,1)*FLG_infant; %Infant offset length (mm)
+        case 1
+            offset = ones(nTiles,1)*FLG_adult; %Adult offset length (mm)
+    end
 end
 
 %Translate and Rotate so that Iz is at 0 0 0, Nz is at 0 y 0, Ar and Al have same z

resources/project/-RzJnnIsB2A391lUjvySEOkWAmU/4jGMX_vDpcTofGPgf7QfpEqdH0Id.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info />

resources/project/-RzJnnIsB2A391lUjvySEOkWAmU/4jGMX_vDpcTofGPgf7QfpEqdH0Ip.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="lumo.log" type="File" />

resources/project/-RzJnnIsB2A391lUjvySEOkWAmU/601AbEO1I8xArzaDVRxS96newoYd.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info />

resources/project/-RzJnnIsB2A391lUjvySEOkWAmU/601AbEO1I8xArzaDVRxS96newoYp.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<Info location="recordingdata.toml" type="File" />