Major update. Remove file filtering option and outputname input arg. The output name is now the same as the path_to_input_dir + .h5. By default, the hdf5 writer preserves second level subdirectories and the rest are flattend. dir filtering is outsource to copy_dir_with_constraints from utils-

src/hdf5_lib.py

@@ -238,11 +238,9 @@ def copy_file_in_group(source_file_path, dest_file_obj : h5py.File, dest_group_n
     if 'tmp_files' in tmp_file_path:
         os.remove(tmp_file_path)
 
-def create_hdf5_file_from_filesystem_path(output_filename : str, 
-                                          path_to_input_directory: str, 
-                                          select_dir_keywords = [], 
-                                          select_file_keywords =[], 
-                                          top_sub_dir_mask : bool = True,
+def create_hdf5_file_from_filesystem_path(path_to_input_directory: str, 
+                                          path_to_filenames_dict: dict = None,
+                                          select_dir_keywords : list = [],
                                           root_metadata_dict : dict = {}):
 
     """
@@ -257,17 +255,17 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
     ----------
     output_filename : str
         Name of the output HDF5 file.
-    path_to_input_directory: str
+    path_to_input_directory : str
         Path to root directory, specified with forward slashes, e.g., path/to/root.
+
+    path_to_filenames_dict : dict, optional
+        A pre-processed dictionary where keys are directory paths on the input directory's tree and values are lists of files.
+        If provided, 'input_file_system_path' is ignored.
+
     select_dir_keywords : list
         List of string elements to consider or select only directory paths that contain
                                 a word in 'select_dir_keywords'. When empty, all directory paths are considered
                                 to be included in the HDF5 file group hierarchy.
-    select_file_keywords : list
-        List of string elements to consider or select only files that contain a word in
-                                 'select_file_keywords'. When empty, all files are considered to be stored in the HDF5 file.
-    top_sub_dir_mask : bool
-        Mask for top-level subdirectories.
     root_metadata_dict : dict
         Metadata to include at the root level of the HDF5 file.
 
@@ -277,7 +275,9 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
         Path to the created HDF5 file.
     """
 
-    allowed_file_extensions = filereader_registry.file_extensions 
+    output_filename = path_to_input_directory + '.h5'
+    
+
     if '/' in path_to_input_directory:
         path_to_input_directory= path_to_input_directory.replace('/',os.sep)
     else:
@@ -287,12 +287,12 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
         select_dir_keywords[i] = keyword.replace('/',os.sep)          
 
     # Copy input_directory into the output_dir_path, and work with it from now on
-    output_dir_path = os.path.splitext(output_filename)[0].replace('/',os.sep)
-    path_to_filenames_dict = utils.copy_directory_with_contraints(path_to_input_directory, 
-                                                                        output_dir_path, 
-                                                                        select_dir_keywords, 
-                                                                        select_file_keywords,
-                                                                        allowed_file_extensions)
+    output_dir_path = os.path.splitext(output_filename)[0].replace('/',os.sep)    
+
+    if not path_to_filenames_dict:
+        path_to_filenames_dict = utils.copy_directory_with_contraints(path_to_input_directory, 
+                                                                      output_dir_path,
+                                                                      dry_run=True)
     # Set input_directory as copied input directory
     root_dir = output_dir_path
     
@@ -307,10 +307,7 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
             # Print and log the start message
             print(start_message)
             logging.info(start_message)
-
-            # Check if dirpath is valid. TODO: This is perhaps redundant by design of path_to_filenames_dict. 
-            if not is_valid_directory_path(dirpath,select_dir_keywords):
-                continue                
+         
             # Check if filtered_filenames_list is nonempty. TODO: This is perhaps redundant by design of path_to_filenames_dict. 
             if not filtered_filenames_list:
                 continue
@@ -319,7 +316,10 @@ def create_hdf5_file_from_filesystem_path(output_filename : str,
             group_name = group_name.replace(root_dir.replace(os.sep,'/') + '/', '/')
 
             # Flatten group name to one level
-            offset = sum([len(i.split(os.sep)) if i in dirpath else 0 for i in select_dir_keywords])
+            if select_dir_keywords:
+                offset = sum([len(i.split(os.sep)) if i in dirpath else 0 for i in select_dir_keywords])
+            else:
+                offset = 1
             tmp_list = group_name.split('/')
             if len(tmp_list) > offset+1:
                 group_name = '/'.join([tmp_list[i] for i in range(offset+1)])