Added code for doing line-shifting in-place

Author: adamltaylor

.gitignore

@@ -8,4 +8,5 @@ parfor_progress.txt
 *.stdouterr
 foreground-classifiers/data/
 foreground-classifiers/2021-03-17/
+RESTORED/
 

build_tile_index_dirwalk_callback.m

@@ -13,7 +13,8 @@
         [~,file_base_name] = fileparts2(current_folder_relative_path) ;
         acquisition_file_name = [file_base_name '-ngc.acquisition'] ;
         acquisition_file_path = fullfile(root_folder_absolute_path, current_folder_relative_path, acquisition_file_name) ;
-        if exist(acquisition_file_path, 'file') ,
+        if ismember(acquisition_file_name, file_names) ,
+        %if exist(acquisition_file_path, 'file') ,  % don't hit the FS again
             [ijk1, xyz] = read_lattice_position_from_acquisition_file(acquisition_file_path) ;
             updated_state = struct() ;
             updated_state.ijk1_from_tile_index = [state.ijk1_from_tile_index ; ijk1] ;

check_tiles/check_classifier_tile.m renamed to check-tiles/check_classifier_tile.m

@@ -27,19 +27,19 @@ function copy_raw_tile_neighborhood(hood_raw_tile_root_folder_path, ...
                                 center_tile_relative_path) ; %#ok<ASGLU>
     tile_count = length(relative_path_from_tile_index) ;
 
-    % For each relative path, make a link
+    % For each relative path, make a copy
     for tile_index = 1 : tile_count ,
         tile_relative_path = relative_path_from_tile_index{tile_index} ;
         destination_path = fullfile(hood_raw_tile_root_folder_path, tile_relative_path) ;
         source_path = fullfile(raw_tile_root_folder_path, tile_relative_path) ;
         destination_parent_path = fileparts(destination_path) ;
         ensure_folder_exists(destination_parent_path) ;
-        system_from_list_with_error_handling({'ln', '-s', '-T', source_path, destination_path}) ;
+        system_from_list_with_error_handling({'cp', '-R', '-T', source_path, destination_path}) ;
     end
 
-    % Make links for the metadata, etc
+    % Make copies for the metadata, etc
     file_name = 'sample-metadata.txt' ;
     source_path = fullfile(raw_tile_root_folder_path, file_name) ;
     destination_path = fullfile(hood_raw_tile_root_folder_path, file_name) ;
-    system_from_list_with_error_handling({'ln', '-s', '-T', source_path, destination_path}) ;    
+    system_from_list_with_error_handling({'cp', '-T', source_path, destination_path}) ;    
 end

check_tiles/check_raw_tile.m renamed to check-tiles/check_raw_tile.m

@@ -0,0 +1,45 @@
+function copy_raw_tile_neighborhood_as_links(hood_raw_tile_root_folder_path, ...
+                                             raw_tile_root_folder_path, ...
+                                             center_tile_relative_path, ...
+                                             sample_memo_folder_path, ...
+                                             do_force_computation)
+    % Build the full tile index
+    raw_tile_index = compute_or_read_from_memo(sample_memo_folder_path, ...
+                                               'raw-tile-index', ...
+                                               @()(build_raw_tile_index(raw_tile_root_folder_path)), ...
+                                               do_force_computation) ;
+    full_tile_index_from_full_tile_ijk1 = raw_tile_index.tile_index_from_tile_ijk1 ;
+    full_tile_ijk1_from_full_tile_index = raw_tile_index.ijk1_from_tile_index ;
+    xyz_from_full_tile_index = raw_tile_index.xyz_from_tile_index ;
+    relative_path_from_full_tile_index = raw_tile_index.relative_path_from_tile_index ;
+    %full_tile_grid_shape = size(full_tile_index_from_full_tile_ijk1)
+    %full_tile_count = length(relative_path_from_full_tile_index) 
+
+    % Get out just the tiles around the center_tile
+    [tile_index_from_tile_ijk1, ...
+     tile_ijk1_from_tile_index, ...
+     xyz_from_tile_index, ...
+     relative_path_from_tile_index] = ...
+        extract_tiles_near_tile(full_tile_index_from_full_tile_ijk1, ...
+                                full_tile_ijk1_from_full_tile_index, ...
+                                xyz_from_full_tile_index, ...
+                                relative_path_from_full_tile_index, ...
+                                center_tile_relative_path) ; %#ok<ASGLU>
+    tile_count = length(relative_path_from_tile_index) ;
+
+    % For each relative path, make a link
+    for tile_index = 1 : tile_count ,
+        tile_relative_path = relative_path_from_tile_index{tile_index} ;
+        destination_path = fullfile(hood_raw_tile_root_folder_path, tile_relative_path) ;
+        source_path = fullfile(raw_tile_root_folder_path, tile_relative_path) ;
+        destination_parent_path = fileparts(destination_path) ;
+        ensure_folder_exists(destination_parent_path) ;
+        system_from_list_with_error_handling({'ln', '-s', '-T', source_path, destination_path}) ;
+    end
+    
+    % Make links for the metadata, etc
+    file_name = 'sample-metadata.txt' ;
+    source_path = fullfile(raw_tile_root_folder_path, file_name) ;
+    destination_path = fullfile(hood_raw_tile_root_folder_path, file_name) ;
+    system_from_list_with_error_handling({'ln', '-s', '-T', source_path, destination_path}) ;    
+end

check_tiles/check_tiles.m renamed to check-tiles/check_tiles.m

@@ -0,0 +1,26 @@
+function flip_metadata = get_tile_flip_state(tile_path, sample_metadata)
+    if sample_metadata.sample_metadata_version<=1 ,
+        flip_metadata = struct() ;
+        flip_metadata.is_x_flipped = sample_metadata.is_x_flipped ;
+        flip_metadata.is_y_flipped = sample_metadata.is_y_flipped ;
+    elseif sample_metadata.sample_metadata_version==2 ,
+        xlineshift_file_path = fullfile(tile_path, 'Xlineshift.txt') ;
+        if exist(xlineshift_file_path, 'file') ,
+            % Tile is already line-shifted, which means it's also flipped on both axes
+            flip_metadata = struct() ;
+            flip_metadata.is_x_flipped = true ;
+            flip_metadata.is_y_flipped = true ;
+        else
+            % Tile has not been line-shifted, so use the value from the sample metadata
+            flip_metadata = struct() ;
+            flip_metadata.is_x_flipped = sample_metadata.is_x_flipped ;
+            flip_metadata.is_y_flipped = sample_metadata.is_y_flipped ;
+        end
+    else
+        tile_metadata = read_tile_metadata(tile_path) ;
+        flip_metadata = struct() ;
+        flip_metadata.is_x_flipped = tile_metadata.is_x_flipped ;
+        flip_metadata.is_y_flipped = tile_metadata.is_y_flipped ;        
+    end        
+end
+