Updated code to use new version of progress_bar_object.m

Author: adamltaylor

build_full_trees_as_named_tree_mats.m

@@ -75,7 +75,7 @@
         tree_mat_file_name = sprintf('%s.mat', tree_name) ;
         tree_mat_file_path = fullfile(output_folder_path, tree_mat_file_name);
         does_output_exist_from_processing_index(processing_index) = logical(exist(tree_mat_file_path, 'file')) ;
-        progress_bar.update(processing_index) ;
+        progress_bar.update() ;
     end    
 end
 component_id_from_will_process_index = component_id_from_processing_index(~does_output_exist_from_processing_index) ;
@@ -180,7 +180,7 @@
     end
 
     % Update the progress bar
-    pbo.update() ;
+    pbo.update() ;  %#ok<PFBNS>
 end    
 %pbo = progress_bar_object(0) ;
 

build_full_trees_as_named_tree_mats_function.m

@@ -92,7 +92,7 @@ function build_full_trees_as_named_tree_mats_function(sample_date, ...
             tree_mat_file_name = sprintf('%s.mat', tree_name) ;
             tree_mat_file_path = fullfile(output_folder_path, tree_mat_file_name);
             does_output_exist_from_processing_index(processing_index) = logical(exist(tree_mat_file_path, 'file')) ;
-            progress_bar.update(processing_index) ;
+            progress_bar.update() ;
         end    
     end
     component_id_from_will_process_index = component_id_from_processing_index(~does_output_exist_from_processing_index) ;

clean_up_skeleton_graph.m

@@ -87,7 +87,7 @@ function clean_up_skeleton_graph(skeleton_graph, ...
             tree_mat_file_name = sprintf('%s.mat', tree_name) ;
             tree_mat_file_path = fullfile(output_folder_path, tree_mat_file_name);
             does_output_exist_from_processing_index(processing_index) = logical(exist(tree_mat_file_path, 'file')) ;
-            progress_bar.update(processing_index) ;
+            progress_bar.update() ;
         end    
     end
     component_id_from_will_process_index = component_id_from_processing_index(~does_output_exist_from_processing_index) ;
@@ -192,7 +192,7 @@ function clean_up_skeleton_graph(skeleton_graph, ...
         end
 
         % Update the progress bar
-        pbo.update() ;
+        pbo.update() ;  %#ok<PFBNS>
     end    
     %pbo = progress_bar_object(0) ;
 

collect_fragments_into_single_mat_file.m

@@ -19,7 +19,7 @@ function collect_fragments_into_single_mat_file(sample_date)
         frag_mat_file_name = frag_mat_file_names{tree_index} ;
         frag_mat_file_path = fullfile(input_folder_path, frag_mat_file_name) ;
         fragments_from_tree_id{tree_index} = load_anonymous(frag_mat_file_path) ;
-        pbo.update() ;
+        pbo.update() ; %#ok<PFBNS>
     end
     %pbo = progress_bar_object(0) ;
     %elapsed_time = toc(tic_id) ;

convert_full_named_trees_as_mat_to_swc.m

@@ -19,7 +19,7 @@ function convert_full_named_trees_as_mat_to_swc(trees_as_swc_folder_path, trees_
             named_tree = mat_contents.named_tree ;
             save_named_tree_as_swc(swc_file_path, named_tree) ;
         end
-        pbo.update() ;
+        pbo.update() ; %#ok<PFBNS>
     end
     %pbo = progress_bar_object(0) ;
     elapsed_time = toc(tic_id) ;

extract_tiles_near_tile.m

@@ -9,27 +9,65 @@
             relative_path_from_full_tile_index, ...
             center_tile_relative_path) 
 
+    % Extracts a 3x3x3 subset of tiles around a given central tile.
+    % Good for running analysis on a small subset of tiles
+    %
+    % The full_tile_index is the index of a tile in the full tile set.
+    % The tile_index is the index of a tile withing the extracted subset.
+    % Currently the extracted subset is always a 3x3x3 cuboid of tiles.
+    
+    % Get the full tile index of the center tile
     is_center_tile_from_full_tile_index = strcmp(center_tile_relative_path, relative_path_from_full_tile_index) ;
     center_tile_full_index = find(is_center_tile_from_full_tile_index) ;
-    center_tile_full_ijk1 = full_tile_ijk1_from_full_tile_index(center_tile_full_index, :) ;  %#ok<FNDSB>
-    is_in_hood_from_full_tile_ijk1 = false(size(full_tile_index_from_full_tile_ijk1)) ;  % "hood" == "neighborhood" b/c I'm *very* street
-    is_in_hood_from_full_tile_ijk1(center_tile_full_ijk1(1)-1:center_tile_full_ijk1(1)+1, ...
-                                   center_tile_full_ijk1(2)-1:center_tile_full_ijk1(2)+1, ...
-                                   center_tile_full_ijk1(3)-1:center_tile_full_ijk1(3)+1) = true ;
 
+    % Get the one-based ijk (integral xyz) coordinates of the center tile
+    % within the full tile block
+    center_tile_full_ijk1 = full_tile_ijk1_from_full_tile_index(center_tile_full_index, :) ;  %#ok<FNDSB>
 
-    full_tile_index_from_tile_ijk1 = full_tile_index_from_full_tile_ijk1(is_in_hood_from_full_tile_ijk1) ;
-    full_tile_index_from_tile_index = full_tile_index_from_tile_ijk1(:) ;
+    % Get the 3x3x3 array of file tile indices around the central tile
+    full_tile_index_from_tile_ijk1 = ...
+        full_tile_index_from_full_tile_ijk1(center_tile_full_ijk1(1)-1:center_tile_full_ijk1(1)+1, ...
+                                            center_tile_full_ijk1(2)-1:center_tile_full_ijk1(2)+1, ...
+                                            center_tile_full_ijk1(3)-1:center_tile_full_ijk1(3)+1) ;
+                                        
+    % The raw tile index is the index of each tile within the 3x3x3 block.
+    % The actual tile index may differ because some tiles may be missing.
+    % Missing tiles in full_tile_index_from_full_tile_ijk1 are represented by
+    % nans.    
+    
+    % Get the array that maps from raw tile indices to full tile indices
+    full_tile_index_from_raw_tile_index = full_tile_index_from_tile_ijk1(:) ;  % may have nans for missing tiles
+    
+    % Get the mapping from tile indices to raw tile indices
+    raw_tile_count = length(full_tile_index_from_raw_tile_index) ;  % Should be 27, always
+    assert(raw_tile_count==27) ;
+    raw_tile_index_from_raw_tile_index = (1:raw_tile_count)' ;
+    is_present_from_raw_tile_index = isfinite(full_tile_index_from_raw_tile_index) ;
+    raw_tile_index_from_tile_index = raw_tile_index_from_raw_tile_index(is_present_from_raw_tile_index) ;  
+    assert(all(isfinite(raw_tile_index_from_tile_index))) ;  % There shouldn't be any nans in raw_tile_index_from_tile_index
 
-    full_tile_count  = length(relative_path_from_full_tile_index) ;
-    tile_index_from_full_tile_index = invert_map_array(full_tile_index_from_tile_index, full_tile_count) ;
-    tile_index_from_tile_ijk1 = tile_index_from_full_tile_index(full_tile_index_from_tile_ijk1) ;
+    % Get the mapping from tile indices to full tile indices
+    full_tile_index_from_tile_index = full_tile_index_from_raw_tile_index(is_present_from_raw_tile_index) ;
 
+    % Invert raw_tile_index_from_tile_index
+    tile_indexoid_from_raw_tile_index = invert_map_array(raw_tile_index_from_tile_index, raw_tile_count) ;    
+    % tile_indexoid_from_raw_tile_index has zeros for missing raw tile indices,
+    % want those to be nan's
+    tile_index_from_raw_tile_index = tile_indexoid_from_raw_tile_index ;
+    tile_index_from_raw_tile_index(tile_indexoid_from_raw_tile_index==0) = nan ;
 
+    % Get mapping from tile_ijk1 to the tile index
+    raw_tile_index_from_tile_ijk1 = reshape(raw_tile_index_from_raw_tile_index, [3 3 3]) ;
+    tile_index_from_tile_ijk1 = tile_index_from_raw_tile_index(raw_tile_index_from_tile_ijk1) ;
+    
+    % Get the mapping from tile index to tile ijk1 (within the subset)
     full_tile_ijk1_from_tile_index = full_tile_ijk1_from_full_tile_index(full_tile_index_from_tile_index, :) ;
     offset_ijk = min(full_tile_ijk1_from_tile_index, [] , 1) ;
     tile_ijk1_from_tile_index = full_tile_ijk1_from_tile_index - offset_ijk + 1 ;
-    
+
+    % Get the xyz coordinate of each tile in the subset
     xyz_from_tile_index = xyz_from_full_tile_index(full_tile_index_from_tile_index,:) ;
+    
+    % Get the relative path of each tile in the subset
     relative_path_from_tile_index = relative_path_from_full_tile_index(full_tile_index_from_tile_index) ;
 end

generate_fragments.m

@@ -39,8 +39,7 @@ function generate_fragments(input_folder_path, ...
                                            bounding_box_high_corner_xyz) ;
 
         % Update the progress bar
-        pbo.update(full_tree_index) ;
-        %pbo.update() ;
+        pbo.update() ;
     end
     pbo.finish_up() ;    
     %%pbo = progress_bar_object(0) ;

generate_fragments_as_one_mat_per_tree.m

@@ -25,7 +25,7 @@ function generate_fragments_as_one_mat_per_tree(input_folder_path, ...
                                                  bounding_box_high_corner_xyz) ;
 
         % Update the progress bar
-        pbo.update() ;
+        pbo.update() ;  %#ok<PFBNS>
     end
     %pbo = progress_bar_object(0) ;
     toc(tic_id) ;

run_some_tiles_through_1234_stages.m

@@ -72,7 +72,7 @@
 
 % Create the bqueue
 if do_use_bsub ,
-    fprintf('Queueing LPL on %d tiles...\n', tile_to_be_run_count) ;
+    fprintf('Queueing LPL jobs for %d tiles...\n', tile_to_be_run_count) ;
     bqueue = bqueue_type(do_actually_submit, max_running_slot_count) ;
     pbo = progress_bar_object(tile_to_be_run_count) ;
     for tile_to_be_run_index = 1 : tile_to_be_run_count ,
@@ -93,15 +93,15 @@
         pbo.update() ;
     end
     %pbo = progress_bar_object(0) ;
-    fprintf('Done queueing LPL on %d tiles.\n\n', tile_to_be_run_count) ;
+    fprintf('Done queueing LPL jobs for %d tiles.\n\n', tile_to_be_run_count) ;
 
-    fprintf('LPLing queue on %d tiles...\n', length(bqueue.job_ids)) ;
+    fprintf('Running queued LPL jobs for %d tiles...\n', length(bqueue.job_ids)) ;
     maximum_wait_time = inf ;
     do_show_progress_bar = true ;
     tic_id = tic() ;
     job_statuses = bqueue.run(maximum_wait_time, do_show_progress_bar) ;
     toc(tic_id)
-    fprintf('Done LPLing queue on %d tiles.\n', length(bqueue.job_ids)) ;
+    fprintf('Done running queued LPL jobs for %d tiles.\n', length(bqueue.job_ids)) ;
     job_statuses
     successful_job_count = sum(job_statuses==1)
 else

sample_rendered_data.m

@@ -17,7 +17,7 @@
             sample_stack = get_mouselight_rendered_substack(sample_folder_path, 0, sample_offset, sample_shape) ;
             sample_index = last_sample_index + 1 ;
             sample_stacks(:,:,:,sample_index) = sample_stack ;
-            pbo.update(sample_index) ;
+            pbo.update() ;
             last_sample_index = sample_index ;
         catch err
             if isequal(err.identifier, 'mouselight:stackMustBeInOneChunk') ,