Fix reco size. Add missing angle interpolation.

matlab/astra/astra_parallel3D.m

@@ -65,17 +65,40 @@
 gpu_index = assign_from_struct( tomo, 'astra_gpu_index', [] );
 link_data = assign_from_struct( tomo, 'astra_link_data', 0 );
 offset_shift = assign_from_struct( tomo, 'offset_shift', 0 );
+interpolate_missing_angles = assign_from_struct( tomo, 'interpolate_missing_angles', 0 );
 
-
 %% Main %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-
 rotation_axis_offset = rotation_axis_offset + offset_shift;
 
-
 angles = double( angles );
 %rotation_axis_offset = double( rotation_axis_offset );
 
+if interpolate_missing_angles
+    angles0 = angles; % orginal range
+    da = angles(2) - angles(1); % angle increment
+    a0 = angles(1); % First angle
+    a1 = angles(end); % last original angle
+    a2 = ceil( a1 / pi ) * pi; % supposed to be final angle plus one inc
+    angles_missing = (a1+da:da:a2)';
+
+    % Interpolation
+    angles_query = [a1, a2 + a0];
+    [X1, X2, X3] = meshgrid( angles_query, 1:size( sino, 1), 1:size( sino, 3) );    
+    [X1q, X2q, X3q] = meshgrid( angles_missing, 1:size( sino, 1), 1:size( sino, 3) );
+    V = cat(2, sino(:,end,:), sino(:,1,:));
+    switch ndims( sino )
+        case 2
+            sino_missing = interp2(X1,X2,V,X1q,X2q);
+        case 3
+            sino_missing = interp3(X1,X2,X3,V,X1q,X2q,X3q);
+    end    
+
+    % Concatenation
+    angles = cat(1, angles0, angles_missing); % new angle range
+    sino = cat(2, sino, sino_missing);    
+end
+
 % GPU
 if isempty( gpu_index )
     astra_mex('set_gpu_index', 0:gpuDeviceCount - 1);

matlab/experiments/p05/p05_create_reco_loop.m

@@ -130,8 +130,13 @@ function p05_create_reco_loop( raw_path, scan_name_pattern, out_path, name)
 % Write Data Sets
 fprintf(fid, '\nraw_path = ''%s/'';', raw_path);
 for nn = 1:numel( folders )
+    fn = folders{nn};
+    % Skip non tomo folders from in situ measurements
+    if numel( fn ) > 7 && strcmp( fn(end-7:end), 'setforce')
+        continue
+    end
     fprintf(fid, '\n' );
-    fprintf(fid, '\npar.scan_path = [raw_path ''%s'']; ADD', folders{nn});    
+    fprintf(fid, '\npar.scan_path = [raw_path ''%s'']; ADD', fn );    
 end
 
 % Write bottom: call reco loop

matlab/experiments/p05/p05_reco.m

@@ -34,21 +34,22 @@ function p05_reco( external_parameter )
 % !!! OVERWRITES PARAMETERS BELOW QUICK SWITCH SECTION !!!
 % Just copy parameter and set quick switch to 1
 par.quick_switch = 1;
-par.raw_bin = 10;
-par.raw_roi = [0.2 0.8];
-par.proj_range = 8;
-par.ref_range = 10;
+par.raw_bin = 3;
+par.raw_roi = [];
+par.proj_range = 1;
+par.ref_range = 1;
 par.ref_path = {};
 phase_retrieval.apply = 0;
-write.to_scratch = 0;
-tomo.rot_axis_offset = [];%-9.95 * 2 / par.raw_bin;
+write.to_scratch = 1;
+tomo.rot_axis_offset = 2 * 3 / par.raw_bin;
 tomo.rot_axis_tilt_camera = [];
-image_correlation.method = 'median';
+image_correlation.num_flats = 19;
+%image_correlation.method = 'median';
 interactive_mode.rot_axis_pos = 1;
 interactive_mode.rot_axis_tilt = 0; 
 interactive_mode.phase_retrieval = 0;
-%write.subfolder_reco = 'tilt-0p001';
-%par.pixel_scaling = 0.9985;
+tomo.interpolate_missing_angles = 1;
+%write.subfolder_reco = 'interpolate_missing_angles';
 % END OF QUICK SWITCH TO ALTERNATIVE SET OF PARAMETERS %%%%%%%%%%%%%%%%%%%%
 
 pp_parameter_switch % DO NOT DELETE THIS LINE
@@ -227,7 +228,7 @@ function p05_reco( external_parameter )
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 weblink_url = 'https://github.com/moosmann/matlab';
-weblink_name = sprintf( 'code reposiory on github: %s', weblink_url );
+weblink_name = sprintf( 'code repository on github: %s', weblink_url );
 weblink = sprintf('<a href = "%s">%s</a>\n', weblink_url, weblink_name);
 fprintf( weblink );
 
@@ -360,6 +361,7 @@ function p05_reco( external_parameter )
 assign_default( 'tomo.angle_scaling', 1 );
 assign_default( 'tomo.MinConstraint', [])
 assign_default( 'tomo.MaxConstraint', [])
+assign_default( 'tomo.interpolate_missing_angles', 0)
 assign_default( 'write.path', '' )
 assign_default( 'write.parfolder', '' )
 assign_default( 'write.subfolder_reco', '' )
@@ -889,7 +891,7 @@ function p05_reco( external_parameter )
                     otherwise
                         vert_shift_micron = s_stage_z.value( 1:num_proj_found );
                 end
-                if std( vert_shift_micron )
+                if abs(std( SubtractMean( vert_shift_micron ) )) > 1e-3
                     vert_shift_micron = vert_shift_micron(par.proj_range);
 
                     % Check

matlab/experiments/p07/mgsafe_p07_11012079.m

@@ -246,6 +246,7 @@ function mgsafe_p07_11012079( SUBSETS, RUN_RECO, PRINT_PARAMETERS)
 write.to_scratch = 0;
 tomo.rot_axis_offset = 2 * 3 / par.raw_bin;
 tomo.rot_axis_tilt_camera = [];
+tomo.interpolate_missing_angles = 1;
 interactive_mode.rot_axis_pos = 0;
 interactive_mode.rot_axis_tilt = 0; 
 %tomo.vol_size = [-1.1 1.1 -1.1 1.1 -0.5 0.5];