Inclided function to copy an entired h5 file in a group. Useful when integrating h5 files into new ones.

src/g5505_file_reader.py

@@ -10,6 +10,9 @@ from igor2.binarywave import load as loadibw
 import os
 import tempfile
 import shutil
+import h5py
+
+ROOT_DIR = os.path.abspath(os.curdir)
 
 def read_xps_ibw_file_as_dict(filename):
 
@@ -48,6 +51,24 @@ def read_xps_ibw_file_as_dict(filename):
 
     return file_dict
 
+def copy_file_in_group(source_file_path, dest_file_obj : h5py.File, dest_group_name):
+    # Create copy of original file to avoid possible file corruption and work with it.
+
+    pathtail, filename = os.path.split(source_file_path)
+    backup_filename = 'backup_'+ filename
+    # Path                     
+    ROOT_DIR = os.path.abspath(os.curdir)
+
+    tmp_dirpath = os.path.join(ROOT_DIR,'tmp_files')
+    if not os.path.exists(tmp_dirpath):
+        os.mkdir(tmp_dirpath)
+
+    shutil.copy(source_file_path, os.path.join(tmp_dirpath,backup_filename))
+    # Open backup h5 file and copy complet filesystem directory onto a group in h5file
+    with h5py.File(os.path.join(tmp_dirpath,backup_filename),'r') as src_file:
+        dest_file_obj.copy(source= src_file['/'], dest= dest_group_name +'/'+filename)
+
+
 
 
 def main():