Reimplemented file filtering, first file extension contraints are imposed and then file keyword contraints.

src/hdf5_lib.py

@@ -268,24 +268,23 @@ def create_hdf5_file_from_filesystem_path(config_param : dict ,
         raise  ValueError('input_file_system_path needs to be specified using forward slashes "/".' )
     
     for i, keyword in enumerate(select_dir_keywords):
-        select_dir_keywords[i] = keyword.replace('/',os.sep)
+        select_dir_keywords[i] = keyword.replace('/',os.sep)          
 
+    # Visit each subdirectory from top to bottom, root directory defined by input_file_sytem_path to the lower
+    # level directories.
 
-    with h5py.File(output_filename, 'w') as h5file:        
+    # Constrain walkable paths on the specified directory tree by allowing walks that start from root
+    # through subdirectories specified by dir_keywords. This improves efficiency especially, in deep
+    # directory trees with many leaves.
+    paths = []
+    if top_sub_dir_mask:
+        for item in os.listdir(input_file_system_path):
+            if any([item in keyword for keyword in select_dir_keywords]):
+                paths.append(os.path.join(input_file_system_path,item))
+    else:
+        paths.append(input_file_system_path)
 
-        # Visit each subdirectory from top to bottom, root directory defined by input_file_sytem_path to the lower
+    with h5py.File(output_filename, 'w') as h5file:
-        # level directories.
-
-        # Constrain walkable paths on the specified directory tree by allowing walks that start from root
-        # through subdirectories specified by dir_keywords. This improves efficiency especially, in deep
-        # directory trees with many leaves.
-        paths = []
-        if top_sub_dir_mask:
-            for item in os.listdir(input_file_system_path):
-                if any([item in keyword for keyword in select_dir_keywords]):
-                    paths.append(os.path.join(input_file_system_path,item))
-        else:
-            paths.append(input_file_system_path)
 
         for item in paths:
 
@@ -294,23 +293,34 @@ def create_hdf5_file_from_filesystem_path(config_param : dict ,
             # Create dictionary with directory-files pairs where files satisfy keyword and admisible type contraints
             # It requires an extra pass over directory three and additional memory for dictionary, but it may be useful
             # to speed up subsequent step and prune resulting directory tree.
-            file_paths_dict = {}
-            if select_file_keywords:                
-                for dirpath, _, filenames_list in os.walk(item,topdown=False):
-                    file_paths_dict[dirpath] = []
-                    for filename in filenames_list:
 
-                        if not any([ext in filename for ext in admissible_file_ext_list]):
+            # For each directory and/or subdirectory, keep files that satisfy file_keyword constraints, and store
-                            continue
+            # (directory_path, suitable files) relationships in a dictionary. 
+            file_paths_dict = {}  
 
+            check_file_ext = lambda filename: any([ext in filename for ext in admissible_file_ext_list])
+
+            for dirpath, _, filenames in os.walk(item,topdown=False):
+                file_paths_dict[dirpath] = []
+
+                # Check files that have an admissible extension and store them in admissible_filenames list
+                admissible_filenames = []
+                for fn in filenames:
+                    if check_file_ext(fn):
+                        admissible_filenames.append(fn)
+
+                if select_file_keywords:  # when select_file_keywords = [], all files are considered    
+                    for filename in admissible_filenames:                        
+                        # Do not consider files with types for which there is still no file_reader. TODO: extend file_reader library.
+                        #if not any([ext in filename for ext in admissible_file_ext_list]):
+                        #    continue
+
+                        # Add files with name, that contains any of the file_keywords
                         if any([keyword in filename for keyword in select_file_keywords]):
                                 file_paths_dict[dirpath].append(filename)
-
+                else:
-            #admissible_file_ext_list = list(config_file.ext_to_reader_dict.keys())
+                    file_paths_dict[dirpath] = admissible_filenames 
-            #for filename in filtered_filename_list.copy():
+    
-            #    if not any([ext in filename for ext in admissible_file_ext_list]):
-            #        filtered_filename_list.remove(filename)
-
             for node_number, node in enumerate(os.walk(item, topdown=True)):
 
                 dirpath, dirnames, filenames_list = node