Fix deprecated avifile/addframe API and timeseries_extract_slice returning all zeros (#70)

* Initial plan

* Fix deprecated avifile/addframe and all-zeros timeseries_extract_slice

Co-authored-by: torwager <6262700+torwager@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: torwager <6262700+torwager@users.noreply.github.com>
Co-authored-by: Tor Wager <torwager@gmail.com>

Author: Copilot

CanlabCore/Data_extraction/timeseries_extract_slice.m

@@ -6,22 +6,25 @@
 % :Usage:
 % ::
 %
-%     function sl = timeseries_extract_slice(V,sliceno)
+%     function sl = timeseries_extract_slice(V, sliceno, orientation)
+%
+% :Inputs:
+%
+%   **V:**
+%        image filenames (char) or spm_vol memory-mapped volumes
+%
+%   **sliceno:**
+%        slice number (voxel index) to extract
+%
+%   **orientation:**
+%        'axial' (default), 'sagittal', or 'coronal'
+%
+% :Output:
+%
+%   **sl:**
+%        X x Y x time matrix of slice data
 %
 
-    global defaults
-    
-    % defaults
-    switch spm('Ver')
-        case 'SPM2'
-            % SPM2: spm_defaults is a script, not callable here
-            disp('WARNING: spm defaults not set for spm2. Make sure your defaults are set correctly');
-        otherwise
-            % SPM5+, including any future versions
-            spm_defaults()
-    end
-
-    
     if ischar(V)
         V = spm_vol(V);
     end
@@ -32,16 +35,29 @@
 
     switch(orientation)
         case 'axial'
-            get_slice = @get_ax_slice;
+            % Map output pixel (x,y) -> voxel (x, y, sliceno)
+            mat = spm_matrix([0 0 sliceno]);
+            for i = 1:length(V)
+                sl(:,:,i) = spm_slice_vol(V(i), mat, V(i).dim(1:2), 0);
+            end
+
         case 'sagittal'
-            get_slice = @get_sag_slice;
+            % Map output pixel (x,y) -> voxel (sliceno, x, y)
+            % Matrix maps: x_vox=sliceno (const), y_vox=x_pix, z_vox=y_pix
+            mat = [0 0 0 sliceno; 1 0 0 0; 0 1 0 0; 0 0 0 1];
+            for i = 1:length(V)
+                sl(:,:,i) = spm_slice_vol(V(i), mat, V(i).dim(2:3), 0);
+            end
+
         case 'coronal'
-            get_slice = @get_cor_slice;
+            % Map output pixel (x,y) -> voxel (x, sliceno, y)
+            % Matrix maps: x_vox=x_pix, y_vox=sliceno (const), z_vox=y_pix
+            mat = [1 0 0 0; 0 0 0 sliceno; 0 1 0 0; 0 0 0 1];
+            for i = 1:length(V)
+                sl(:,:,i) = spm_slice_vol(V(i), mat, [V(i).dim(1) V(i).dim(3)], 0);
+            end
+
         otherwise
             error('Unknown orientation: %s\n', orientation);
     end
-
-    for i = 1:length(V)
-        sl(:,:,i) = get_slice(V(i), sliceno);
-    end
 end

CanlabCore/Visualization_functions/Support/movie_tools.m

@@ -393,7 +393,10 @@
 switch(FRAMESTYLE)
     case 'avi' % write to avi format directly
         if isempty(mov)
-            mov = avifile('mymovie.avi','Quality',75,'Compression','None','Fps',fps);
+            mov = VideoWriter('mymovie.avi');
+            mov.Quality = 75;
+            mov.FrameRate = fps;
+            open(mov);
         end
 
     case 'matlab' % matlab movie format
@@ -425,7 +428,8 @@
         drawnow
 
         try
-            mov = addframe(mov,H);
+            frame = getframe(H);
+            writeVideo(mov, frame);
         catch
             disp('Cannot write frame.  Failed to set stream format??')
             mov = close(mov);

CanlabCore/Visualization_functions/movie_of_slice_timeseries.m

@@ -56,7 +56,8 @@ function movie_of_slice_timeseries(imgs, slicenumber, moviename, orientation)
         title(sprintf('Image %3.0f: %s', i, ff), 'FontSize', 24)
 
         % mov = add_a_frame(mov, H);
-        writeVideo(mov, H);
+        frame = getframe(H);
+        writeVideo(mov, frame);
     end
 
     tmp = close(mov); %#ok;
@@ -77,7 +78,7 @@ function movie_of_slice_timeseries(imgs, slicenumber, moviename, orientation)
 
 %         frame_rate = 1/tr;
         mov = VideoWriter(moviename);
-        mov.Quality
+        mov.Quality = 75;
         mov.FrameRate = fps;
         open(mov);
 
@@ -96,7 +97,8 @@ function movie_of_slice_timeseries(imgs, slicenumber, moviename, orientation)
 
     lightRestoreSingle(H);
     try
-        mov = addframe(mov, H);
+        frame = getframe(H);
+        writeVideo(mov, frame);
     catch
         disp('Cannot write frame.  Failed to set stream format??')
         mov = close(mov);

CanlabCore/hewma_utility/get_ax_slice.m

@@ -39,16 +39,10 @@
 
     % Transverse slice
     %==========================================================
-    C = [1 0 0 0;0 1 0 0;0 0 1 0;0 0 0 1];
-    DIM = V(1).dim(1:2);
+    mat = spm_matrix([0 0 slice_num]);
 
-    C(3,4) = slice_num;
-    %C(3,4)=-p;
-
-    % img = rot90(spm_slice_vol(V,C,DIM,0));
-    % img = spm_slice_vol(V,inv(C),DIM,0);
     for i=1:length(V)
-        slice_data(:,:,i) = spm_slice_vol(V(i), C, DIM, 0);
+        slice_data(:,:,i) = spm_slice_vol(V(i), mat, V(i).dim(1:2), 0);
     end
 
     slice_data = squeeze(slice_data);