# coding: utf-8
# /*##########################################################################
#
# Copyright (c) 2015-2020 European Synchrotron Radiation Facility
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"""
Utils related to bliss-HDF5
"""
from collections import namedtuple
import os
from pathlib import Path
H5FileKeys = namedtuple(
"H5FileKeys",
[
"acq_expo_time_keys",
"rot_angle_keys",
"valid_camera_names",
"x_trans_keys",
"y_trans_keys",
"z_trans_keys",
"y_rot_key",
"x_pixel_size",
"y_pixel_size",
"diode_keys",
],
)
H5ScanTitles = namedtuple(
"H5ScanTitles",
[
"init_titles",
"init_zserie_titles",
"init_pcotomo_titles",
"dark_titles",
"flat_titles",
"proj_titles",
"align_titles",
],
)
PROCESSED_DATA_DIR_NAME = "PROCESSED_DATA"
RAW_DATA_DIR_NAME = "RAW_DATA"
[docs]def get_default_output_file(input_file: str, output_file_extension: str = ".nx") -> str:
"""
Policy: look for any 'RAW_DATA' in file directory. If find any (before any 'PROCESSED_DATA' directory) replace it "RAW_DATA".
Then replace input_file by the expected file_extension and make sure the output file is different than the input file. Else append _nxtomo to it.
:param str input_file: file to be converted from bliss to NXtomo
:param str output_file_extension:
:return: default output file according to policy
"""
if isinstance(input_file, Path):
input_file = str(input_file)
if not isinstance(input_file, str):
raise TypeError(
f"input_file is expected to be an instance of str. {type(input_file)} provided"
)
if not isinstance(output_file_extension, str):
raise TypeError("output_file_extension is expected to be a str")
if not output_file_extension.startswith("."):
output_file_extension = "." + output_file_extension
input_file = os.path.abspath(input_file)
input_file_no_ext, _ = os.path.splitext(input_file)
def from_raw_data_path_to_process_data_path(file_path: str):
split_path = file_path.split(os.sep)
# reverse it to find the lower level value of '_RAW_DATA_DIR_NAME' if by any 'chance' has several in the path
# in this case this is most likely what we want
split_path = split_path[::-1]
# check if already contain in a "PROCESSED_DATA" directory
try:
index_processed_data = split_path.index(PROCESSED_DATA_DIR_NAME)
except ValueError:
index_processed_data = None
try:
index_raw_data = split_path.index(RAW_DATA_DIR_NAME)
except ValueError:
# if the value is not in the list
pass
else:
if index_processed_data is None or index_raw_data < index_processed_data:
# make sure we are not already in a 'PROCESSED_DATA' directory. Not sure it will never happen but safer
split_path[index_raw_data] = PROCESSED_DATA_DIR_NAME
# reorder path to original
split_path = split_path[::-1]
return os.sep.join(split_path)
output_path = from_raw_data_path_to_process_data_path(input_file_no_ext)
output_file = output_path + output_file_extension
if output_file == input_file:
# to be safer if the default output file is the same as the input file (if the input file has a .nx extension and not in any 'RAw_DATA' directory)
return output_path + "_nxtomo" + output_file_extension
else:
return output_file
