Got rid of parfor_progress(), which didn't work well for multiple simultaneous jobs

Author: adamltaylor

build_full_trees_as_named_tree_mats.m

@@ -99,7 +99,7 @@
 components_to_process_in_parallel_count = length(component_id_from_parallel_will_process_index) ;
 
 fprintf('Starting the serial for loop, going to process %d components...\n', components_to_process_serially_count) ;
-parfor_progress(components_to_process_serially_count) ;
+pbo = progress_bar_object(components_to_process_serially_count) ;
 
 % Do the big ones in a regular for loop, since each requires a lot of
 % memory    
@@ -134,16 +134,16 @@
     end
 
     % Update the progress bar
-    parfor_progress() ;
+    pbo.update() ;
 end
-parfor_progress(0) ;
+%pbo = progress_bar_object(0) ;
 
 
 % Do the small ones in a parfor loop, since memory is less of an issue
 % for them    
 fprintf('Starting the parallel for loop, will process %d components...\n', components_to_process_in_parallel_count) ;
 use_this_many_cores(maximum_core_count_desired) ;
-parfor_progress(components_to_process_in_parallel_count) ;
+pbo = progress_bar_object(components_to_process_in_parallel_count) ;
 component_from_component_id_as_parpool_constant = parallel.pool.Constant(component_from_component_id) ;
 skeleton_xyzs_as_parpool_constant = parallel.pool.Constant(skeleton_xyzs) ;
 A_as_parpool_constant = parallel.pool.Constant(A) ;
@@ -180,8 +180,8 @@
     end
 
     % Update the progress bar
-    parfor_progress() ;
+    pbo.update() ;
 end    
-parfor_progress(0) ;
+%pbo = progress_bar_object(0) ;
 
 toc(runtic) ;

build_full_trees_as_named_tree_mats_function.m

@@ -116,7 +116,7 @@ function build_full_trees_as_named_tree_mats_function(sample_date, ...
     components_to_process_in_parallel_count = length(component_id_from_parallel_will_process_index) ;
 
     fprintf('Starting the serial for loop, going to process %d components...\n', components_to_process_serially_count) ;
-    parfor_progress(components_to_process_serially_count) ;
+    pbo = progress_bar_object(components_to_process_serially_count) ;
 
     % Do the big ones in a regular for loop, since each requires a lot of
     % memory    
@@ -151,16 +151,16 @@ function build_full_trees_as_named_tree_mats_function(sample_date, ...
         end
 
         % Update the progress bar
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
 
 
     % Do the small ones in a parfor loop, since memory is less of an issue
     % for them    
     fprintf('Starting the parallel for loop, will process %d components...\n', components_to_process_in_parallel_count) ;
     use_this_many_cores(maximum_core_count_desired) ;
-    parfor_progress(components_to_process_in_parallel_count) ;
+    pbo = progress_bar_object(components_to_process_in_parallel_count) ;
     component_from_component_id_as_parpool_constant = parallel.pool.Constant(component_from_component_id) ;
     skeleton_xyzs_as_parpool_constant = parallel.pool.Constant(skeleton_xyzs) ;
     A_as_parpool_constant = parallel.pool.Constant(A) ;
@@ -197,9 +197,9 @@ function build_full_trees_as_named_tree_mats_function(sample_date, ...
         end
 
         % Update the progress bar
-        parfor_progress() ;
+        pbo.update() ;
     end    
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
 
     toc(runtic) ;
 

clean_up_skeleton_graph.m

@@ -111,7 +111,7 @@ function clean_up_skeleton_graph(skeleton_graph, ...
     components_to_process_in_parallel_count = length(component_id_from_parallel_will_process_index) ;
 
     fprintf('Starting the serial for loop, going to process %d components...\n', components_to_process_serially_count) ;
-    parfor_progress(components_to_process_serially_count) ;
+    pbo = progress_bar_object(components_to_process_serially_count) ;
 
     % Do the big ones in a regular for loop, since each requires a lot of
     % memory    
@@ -146,16 +146,16 @@ function clean_up_skeleton_graph(skeleton_graph, ...
         end
 
         % Update the progress bar
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
 
 
     % Do the small ones in a parfor loop, since memory is less of an issue
     % for them    
     fprintf('Starting the parallel for loop, will process %d components...\n', components_to_process_in_parallel_count) ;
     use_this_many_cores(maximum_core_count_desired) ;
-    parfor_progress(components_to_process_in_parallel_count) ;
+    pbo = progress_bar_object(components_to_process_in_parallel_count) ;
     component_from_component_id_as_parpool_constant = parallel.pool.Constant(component_from_component_id) ;
     skeleton_xyzs_as_parpool_constant = parallel.pool.Constant(skeleton_xyzs) ;
     A_as_parpool_constant = parallel.pool.Constant(A) ;
@@ -192,9 +192,9 @@ function clean_up_skeleton_graph(skeleton_graph, ...
         end
 
         % Update the progress bar
-        parfor_progress() ;
+        pbo.update() ;
     end    
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
 
     toc(runtic) ;
 end

collect_fragments_into_single_mat_file.m

@@ -14,14 +14,14 @@ function collect_fragments_into_single_mat_file(sample_date)
     tree_count = length(frag_mat_file_names) ;
     fragments_from_tree_id = cell(1, tree_count) ;
     %tic_id = tic() ;
-    parfor_progress(tree_count) ;
+    pbo = progress_bar_object(tree_count) ;
     parfor tree_index = 1 : tree_count ,
         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) ;
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
     %elapsed_time = toc(tic_id) ;
     %fprintf('Elapsed time to read in all fragment .mats was %g seconds\n', elapsed_time) ;
 

convert_full_named_trees_as_mat_to_swc.m

@@ -7,7 +7,7 @@ function convert_full_named_trees_as_mat_to_swc(trees_as_swc_folder_path, trees_
     file_count = length(mat_file_names) ;
 
     fprintf('Converting %d trees as .mat to .swc...\n', file_count) ;
-    parfor_progress(file_count) ;
+    pbo = progress_bar_object(file_count) ;
     parfor i = 1 : file_count ,
         mat_file_name = mat_file_names{i} ;
         swc_base_name = base_name_from_file_name(mat_file_name) ;
@@ -19,9 +19,9 @@ 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
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
     elapsed_time = toc(tic_id) ;
     fprintf('Elapsed time for convert_full_named_trees_as_mat_to_swc() was %g seconds\n', elapsed_time) ;
 end

generate_fragments.m

@@ -24,7 +24,7 @@ function generate_fragments(input_folder_path, ...
     full_trees_to_process_count = length(full_tree_file_names) ;
     %tic_id = tic() ;
     fprintf('Starting the fragment generation outer for loop, going to process %d full trees...\n', full_trees_to_process_count) ;
-    %parfor_progress(full_trees_to_process_count) ;
+    %pbo = progress_bar_object(full_trees_to_process_count) ;
     pbo = progress_bar_object(full_trees_to_process_count) ;
     for full_tree_index = 1 : full_trees_to_process_count ,
     %for full_tree_index = full_trees_to_process_count : -1 : 1 ,  % good for debugging, process small ones first to make sure loop body runs
@@ -40,9 +40,9 @@ function generate_fragments(input_folder_path, ...
 
         % Update the progress bar
         pbo.update(full_tree_index) ;
-        %parfor_progress() ;
+        %pbo.update() ;
     end
     pbo.finish_up() ;    
-    %parfor_progress(0) ;
+    %%pbo = progress_bar_object(0) ;
     %toc(tic_id) ;
 end

generate_fragments_as_one_mat_per_tree.m

@@ -13,7 +13,7 @@ function generate_fragments_as_one_mat_per_tree(input_folder_path, ...
     full_trees_to_process_count = length(full_tree_file_names) ;
     tic_id = tic() ;
     fprintf('Starting the big parfor loop, going to process %d full trees...\n', full_trees_to_process_count) ;
-    parfor_progress(full_trees_to_process_count) ;
+    pbo = progress_bar_object(full_trees_to_process_count) ;
     parfor full_tree_index = 1 : full_trees_to_process_count ,
         full_tree_file_name = full_tree_file_names{full_tree_index} ;
         full_tree_mat_file_path = fullfile(input_folder_path, full_tree_file_name) ;
@@ -25,8 +25,8 @@ function generate_fragments_as_one_mat_per_tree(input_folder_path, ...
                                                  bounding_box_high_corner_xyz) ;
 
         % Update the progress bar
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
     toc(tic_id) ;
 end

generate_fragments_as_swcs.m

@@ -15,7 +15,7 @@ function generate_fragments_as_swcs(input_folder_path, ...
     full_trees_to_process_count = length(full_tree_file_names) ;
     tic_id = tic() ;
     fprintf('Starting the big parfor loop, going to process %d full trees...\n', full_trees_to_process_count) ;
-    parfor_progress(full_trees_to_process_count) ;
+    pbo = progress_bar_object(full_trees_to_process_count) ;
     for full_tree_index = 1 : full_trees_to_process_count ,
         full_tree_file_name = full_tree_file_names{full_tree_index} ;
         full_tree_mat_file_path = fullfile(input_folder_path, full_tree_file_name) ;
@@ -27,8 +27,8 @@ function generate_fragments_as_swcs(input_folder_path, ...
                                                    bounding_box_high_corner_xyz) ;
 
         % Update the progress bar
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
     toc(tic_id) ;
 end

landmark-matching/landmark_match_all_tiles_in_z.m

@@ -73,7 +73,7 @@ function landmark_match_all_tiles_in_z( ...
         is_to_be_matched_from_pair_index = true(pair_count, 1) ;
     else
         is_to_be_matched_from_pair_index = true(pair_count,1) ;
-        parfor_progress(pair_count) ;
+        pbo = progress_bar_object(pair_count) ;
         parfor pair_index = 1 : pair_count
             central_tile_relative_path = central_tile_relative_path_from_pair_index{pair_index} ;
             channel_0_tile_file_name = sprintf('channel-%d-match-Z.mat', 0) ;
@@ -83,9 +83,9 @@ function landmark_match_all_tiles_in_z( ...
             is_to_be_matched = ...
                 ~(exist(channel_0_tile_file_path, 'file') && exist(channel_1_tile_file_path, 'file')) ;
             is_to_be_matched_from_pair_index(pair_index) = is_to_be_matched ;
-            parfor_progress() ;
+            pbo.update() ;
         end
-        parfor_progress(0) ;
+        %pbo = progress_bar_object(0) ;
     end
     fprintf('Done determining which of the %d eligible tiles need to be landmark-matched.\n', pair_count) ;
     pair_index_from_tile_to_be_matched_index = find(is_to_be_matched_from_pair_index) ;
@@ -97,7 +97,7 @@ function landmark_match_all_tiles_in_z( ...
 
     % Run z point match on all tiles
     fprintf('Running z-point-matching on %d tile pairs...\n', tile_to_be_matched_count) ;
-    parfor_progress(tile_to_be_matched_count) ;
+    pbo = progress_bar_object(tile_to_be_matched_count) ;
     parfor tile_to_be_matched_index = 1 : tile_to_be_matched_count ,
         center_tile_relative_path = central_tile_relative_path_from_tile_to_be_matched_index{tile_to_be_matched_index} ;
         other_tile_relative_path = other_tile_relative_path_from_tile_to_be_matched_index{tile_to_be_matched_index} ;
@@ -108,9 +108,9 @@ function landmark_match_all_tiles_in_z( ...
                                       center_tile_relative_path, ...
                                       central_tile_ijk1, ...
                                       other_tile_relative_path)
-        parfor_progress() ;
+        pbo.update() ;
     end
-    parfor_progress(0) ;
+    %pbo = progress_bar_object(0) ;
 
     % Declare victory
     fprintf('Done running z-point-match for all tiles.\n') ;

landmark-matching/pointmatch_all_pairs_2021_11_26.m

@@ -49,7 +49,7 @@
 
 % Run z point match on all tiles
 fprintf('Running z-point-matching on %d valid tile pairs...\n', pair_count) ;
-parfor_progress(pair_count) ;
+pbo = progress_bar_object(pair_count) ;
 parfor pair_index = 1 : pair_count ,
     center_tile_relative_path = central_tile_relative_path_from_pair_index{pair_index} ;
     other_tile_relative_path = other_tile_relative_path_from_pair_index{pair_index} ;
@@ -60,9 +60,9 @@
                                   center_tile_relative_path, ...
                                   central_tile_ijk1, ...
                                   other_tile_relative_path)
-    parfor_progress() ;
+    pbo.update() ;
 end
-parfor_progress(0) ;
+%pbo = progress_bar_object(0) ;
 
 % Declare victory
 fprintf('Done running z-point-match for all tiles.\n') ;