Rework the trackmateSpot MATLAB example with ROIs.

scripts/ExampleScript_MATLABImportROIs.m

@@ -1,95 +1,61 @@
+%% Import spot ROIs from a TrackMate file.
+% 
+% This example MATLAB script shows how to use the `trackmateSpot.m`
+% function to open a TrackMate file that contains spots with ROIs (their
+% shape as polygon). They are then painted in a common graph, colored by
+% frame.
+% 
+% The `trackmateSpot.m` does not return the track information, and we
+% cannot retrieve the tracks solely with this function. See the other
+% example `ExampleScript_MATLABImportROIs.m` in this folder for a more
+% involved example that does this.
+%
+% Jean-Yves Tinevez - 2024
 
 close all
 clear 
 clc
 
-% Read movie file
-movie_path = 'c:/Users/tinevez/Desktop/MAX_Merged-1.tif'; 
-I = tiffreadVolume( movie_path );
-w = size(I, 1);
-h = size(I, 2);
-
-% Pixel size is manually specified.
-pixel_size = 0.1984666072986889; % microns
+% Where are the files?
+root_folder = '/Users/tinevez/Google Drive/TrackMate/Applications/MATLABimport/';
+% TrackMate file.
+file_path = fullfile( root_folder, 'MAX_Merged.xml' );
 
 % Read tracks.
-file_path = 'c:/Users/tinevez/Desktop/MAX_Merged.xml';
 [S, idmap, rois] = trackmateSpots( file_path );
 
 n_frames = max(S.FRAME)+1;
 colors = turbo(n_frames);
 
 n_spots = height(S);
 
-%%
-
-F(n_frames) = struct('cdata',[],'colormap',[]);
-
-figure
-hold on
-
-for t = 1 : n_frames
-
-    % Clear axes.
-    cla
-
-    % Image data of current frame.
-    If = I( :, :, t );
-    imshow( If, [], ...
-        'XData', [ 0 pixel_size * h ], ...
-        'YData', [ 0 pixel_size * w ] )
-
-    % Spot data of current frame.
-    frame = t-1;
-    log_index = S.FRAME == frame;
-    Sf = S(log_index, :);
-    index = find( log_index );
-
-    nsf = height( Sf );
-    for i = 1 : nsf
-        x   = Sf.POSITION_X(i);
-        y   = Sf.POSITION_Y(i);
-        roi = rois{ index(i) };
-        roi(:,1) = roi(:,1) + x;
-        roi(:,2) = roi(:,2) + y;
-
-        patch( 'XData', roi(:,1), 'YData', roi(:,2), ...
-            'FaceColor', 'None', ...
-            'EdgeColor', 'r', ...
-            'LineWidth', 2, ...
-            'Marker', 'none')
-
-    end
-    drawnow
-    F(t) = getframe(gca);
-
-end
-
-cla
-movie( F, 10, 3 )
-
-
-
-%% 
+%% Plot the spot contours.
 
 figure
 hold on
 axis square
 
 for i = 1 : n_spots
 
+    % Spot center.
     x   = S.POSITION_X(i);
     y   = S.POSITION_Y(i);
+    % Spot contour (centered on 0).
     roi = rois{i};
+    % Put the contours with respect to the spot center.
     roi(:,1) = roi(:,1) + x;
     roi(:,2) = roi(:,2) + y;
-
+
+    % Color by frame.
     frame = S.FRAME(i)+1;
     col = colors( frame, : );
 
     patch( 'XData', roi(:,1), 'YData', roi(:,2), ...
         'FaceColor', 'None', ... 
         'EdgeColor', col )
-
+    plot( x, y, 'Color', col, 'Marker', 'x' )
 
-end
+end
+xlabel( 'X (um)' )
+ylabel( 'Y (um)' )
+set(gca, 'YDir', 'reverse' )