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Robustified definition of path_to_input_dir arg or parameter by ensuring is always defined using forward slashes and then is normalized to the os specification. Improved dry run = True of copy directory func.

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florez_j
2024-09-25 15:12:19 +02:00
parent 0dbec94374
commit 1e1499c28a
1 changed files with 13 additions and 12 deletions
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25
src/hdf5_lib.py
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@ -275,28 +275,29 @@ def create_hdf5_file_from_filesystem_path(path_to_input_directory: str,
Path to the created HDF5 file.
"""
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:
if not '/' in path_to_input_directory:
raise ValueError('path_to_input_directory needs to be specified using forward slashes "/".' )
#path_to_output_directory = os.path.join(path_to_input_directory,'..')
path_to_input_directory = os.path.normpath(path_to_input_directory).strip(os.sep)
for i, keyword in enumerate(select_dir_keywords):
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)
if not path_to_filenames_dict:
# On dry_run=True, returns path to files dictionary of the output directory without making a actual copy of the input directory
path_to_output_directory = os.path.join(path_to_input_directory,'..')
path_to_filenames_dict = utils.copy_directory_with_contraints(path_to_input_directory,
output_dir_path,
path_to_output_directory,
dry_run=True)
# Set input_directory as copied input directory
root_dir = output_dir_path
root_dir = path_to_input_directory
path_to_output_file = path_to_input_directory.rstrip(os.path.sep) + '.h5'
with h5py.File(output_filename, mode='w', track_order=True) as h5file:
with h5py.File(path_to_output_file, mode='w', track_order=True) as h5file:
number_of_dirs = len(path_to_filenames_dict.keys())
dir_number = 1
@ -372,7 +373,7 @@ def create_hdf5_file_from_filesystem_path(path_to_input_directory: str,
#output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(output_filename)
return output_filename #, output_yml_filename_path
return path_to_output_file #, output_yml_filename_path
def save_processed_dataframe_to_hdf5(df, annotator, output_filename): # src_hdf5_path, script_date, script_name):
"""