diff --git a/instruments/readers/hdf5_file_reader.py b/instruments/readers/hdf5_file_reader.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ba639850b4d073dd47b6629b1f57476bde16257
--- /dev/null
+++ b/instruments/readers/hdf5_file_reader.py
@@ -0,0 +1,79 @@
+import sys
+import os
+
+try:
+ thisFilePath = os.path.abspath(__file__)
+except NameError:
+ print("Error: __file__ is not available. Ensure the script is being run from a file.")
+ print("[Notice] Path to DIMA package may not be resolved properly.")
+ thisFilePath = os.getcwd() # Use current directory or specify a default
+
+dimaPath = os.path.normpath(os.path.join(thisFilePath, "..",'..','..')) # Move up to project root
+
+if dimaPath not in sys.path: # Avoid duplicate entries
+ sys.path.insert(0,dimaPath)
+
+import pandas as pd
+import collections
+import yaml
+import h5py
+import argparse
+import logging
+import utils.g5505_utils as utils
+import src.hdf5_ops as hdf5_ops
+import instruments.filereader_registry as filereader_registry
+
+
+
+
+def hdf5_file_reader(dest_file_obj_or_path, src_file_path=None, dest_group_name=None, work_with_copy: bool = True):
+ """
+ Reads an HDF5 file and copies its contents to a destination group.
+ If an HDF5 file object is provided, it skips reading from a file path.
+ """
+ # Determine if dest_file_obj_or_path is a file path or an HDF5 file object
+ if isinstance(dest_file_obj_or_path, h5py.File):
+ dest_file_obj = dest_file_obj_or_path
+ else:
+ dest_file_obj = h5py.File(dest_file_obj_or_path, mode='r+', track_order=True)
+
+ try:
+ if work_with_copy:
+ tmp_src_file_path = utils.make_file_copy(src_file_path)
+ else:
+ tmp_src_file_path = src_file_path
+
+ # Open source HDF5 file
+ with h5py.File(tmp_src_file_path, 'r') as src_file:
+ dest_file_obj.copy(source=src_file['/'], dest=dest_group_name)
+
+ # Remove temporary file if created
+ if 'tmp_files' in tmp_src_file_path:
+ os.remove(tmp_src_file_path)
+
+ print(f'Completed transfer for /{dest_group_name}')
+
+ finally:
+ if not isinstance(dest_file_obj_or_path, h5py.File):
+ dest_file_obj.close()
+
+ return 0
+
+if __name__ == "__main__":
+
+ # Set up argument parsing
+ parser = argparse.ArgumentParser(description="Data ingestion process to HDF5 files.")
+ parser.add_argument('dst_file_path', type=str, help="Path to the target HDF5 file.")
+ parser.add_argument('src_file_path', type=str, help="Path to source HDF5 file to be saved to target HDF5 file.")
+ parser.add_argument('dst_group_name', type=str, help="Group name '/instFolder/[category]/fileName' in the target HDF5 file.")
+
+ args = parser.parse_args()
+
+ dst_file_path = args.dst_file_path
+ src_file_path = args.src_file_path
+ dst_group_name = args.dst_group_name
+ default_mode = 'r+'
+
+ status = hdf5_file_reader(dst_file_path, src_file_path, dst_group_name)
+
+ print('Return status: {status}')
diff --git a/instruments/registry.yaml b/instruments/registry.yaml
index 797226cfd4bdba8834d0b40f7450e079a9db5b94..95557ea06c64f99113ea564dc7536ba18214ee63 100644
--- a/instruments/registry.yaml
+++ b/instruments/registry.yaml
@@ -6,7 +6,7 @@ instruments:
- instrumentFolderName: NEXAFS
fileExtension: h5
- fileReaderPath: null
+ fileReaderPath: instruments/readers/hdf5_file_reader.py
InstrumentDictionaryPath: null
- instrumentFolderName: SES
diff --git a/src/hdf5_writer.py b/src/hdf5_writer.py
index 30e3ae2cce47f3826dc308df9425e5a3a09ce712..175d288b7c8fd820fb1c44833cb0163348290086 100644
--- a/src/hdf5_writer.py
+++ b/src/hdf5_writer.py
@@ -22,27 +22,6 @@ import instruments.filereader_registry as filereader_registry
-def __copy_file_in_group(path_to_output_file, source_file_path, dest_group_name, work_with_copy : bool = True):
-
- # Create copy of original file to avoid possible file corruption and work with it.
- with h5py.File(path_to_output_file, mode='r+', track_order=True) as dest_file_obj:
-
- if work_with_copy:
- tmp_file_path = utils.make_file_copy(source_file_path)
- else:
- tmp_file_path = source_file_path
-
- # Open backup h5 file and copy complet filesystem directory onto a group in h5file
- with h5py.File(tmp_file_path,'r') as src_file:
- dest_file_obj.copy(source= src_file['/'], dest= dest_group_name)
-
- if 'tmp_files' in tmp_file_path:
- os.remove(tmp_file_path)
-
- stdout = f'Completed transfer for /{dest_group_name}'
-
- return stdout
-
def create_hdf5_file_from_filesystem_path(path_to_input_directory: str,
path_to_filenames_dict: dict = None,
select_dir_keywords : list = [],
@@ -178,20 +157,18 @@ def create_hdf5_file_from_filesystem_path(path_to_input_directory: str,
# hdf5 path to filename group
dest_group_name = f'{group_name}/{filename}'
source_file_path = os.path.join(dirpath,filename)
-
+ dest_file_obj = h5file
if not 'h5' in filename:
#file_dict = config_file.select_file_readers(group_id)[file_ext](os.path.join(dirpath,filename))
#file_dict = ext_to_reader_dict[file_ext](os.path.join(dirpath,filename))
file_dict = filereader_registry.select_file_reader(dest_group_name)(source_file_path)
- stdout = hdf5_ops.save_file_dict_to_hdf5(h5file, group_name, file_dict)
+ stdout = hdf5_ops.save_file_dict_to_hdf5(dest_file_obj, group_name, file_dict)
else:
- dest_file_obj = h5file
- #group_name +'/'+filename
- #ext_to_reader_dict[file_ext](source_file_path, dest_file_obj, dest_group_name)
- #g5505f_reader.select_file_reader(dest_group_name)(source_file_path, dest_file_obj, dest_group_name)
- stdout = __copy_file_in_group(source_file_path, dest_file_obj, dest_group_name, False)
+ from instruments.readers.hdf5_file_reader import hdf5_file_reader
+ stdout = hdf5_file_reader(dest_file_obj, source_file_path, dest_group_name)
+ #stdout = __copy_file_in_group(source_file_path, dest_file_obj, dest_group_name, False)
# Update the progress bar and log the end message
instFoldermsdEnd = f'\nCompleted data transfer for instFolder: {group_name}\n'
@@ -353,7 +330,7 @@ def create_hdf5_file_from_filesystem_path_new(path_to_input_directory: str,
filereader_registry.run_reader(path_to_output_file, source_file_path, dest_group_name)
else:
-
+ from instruments.readers.hdf5_file_reader import hdf5_file_reader
#try:
# # Create group if it does not exist
# if dest_group_name not in dest_file_obj:
@@ -370,7 +347,7 @@ def create_hdf5_file_from_filesystem_path_new(path_to_input_directory: str,
#group_name +'/'+filename
#ext_to_reader_dict[file_ext](source_file_path, dest_file_obj, dest_group_name)
#g5505f_reader.select_file_reader(dest_group_name)(source_file_path, dest_file_obj, dest_group_name)
- stdout = __copy_file_in_group(path_to_output_file, source_file_path, dest_group_name, False)
+ stdout = hdf5_file_reader(path_to_output_file, source_file_path, dest_group_name, False)
# Update the progress bar and log the end message
instFoldermsdEnd = f'\nCompleted data transfer for instFolder: {group_name}\n'