# coding: utf-8
"""
contains the HDF5ConfigHandler
"""
from __future__ import annotations
import logging
import os
from nxtomomill.utils._os import abspath
from nxtomomill.converter.hdf5.utils import get_default_output_file
from .hdf5config import TomoHDF5Config
_logger = logging.getLogger(__name__)
__all__ = [
"SETTABLE_PARAMETERS_UNITS",
"SETTABLE_PARAMETERS_TYPE",
"SETTABLE_PARAMETERS",
"TomoHDF5ConfigHandler",
]
SETTABLE_PARAMETERS_UNITS = {
"energy": "kev",
"x_pixel_size": "m",
"y_pixel_size": "m",
"detector_sample_distance": "m",
}
SETTABLE_PARAMETERS_TYPE = {
"energy": float,
"x_pixel_size": float,
"y_pixel_size": float,
"detector_sample_distance": float,
}
SETTABLE_PARAMETERS = SETTABLE_PARAMETERS_UNITS.keys()
def _extract_param_value(key_values):
"""extract all the key / values elements from the str_list. Expected
format is `param_1_name param_1_value param_2_name param_2_value ...`
:param str_list: raw input string as `param_1_name param_1_value
param_2_name param_2_value ...`
:return: dict of tuple (param_name, param_value)
"""
if len(key_values) % 2 != 0:
raise ValueError(
"Expect a pair `param_name, param_value` for each " "parameters"
)
def pairwise(it):
it = iter(it)
while True:
try:
yield next(it), next(it)
except StopIteration:
# no more elements in the iterator
return
res = {}
for name, value in pairwise(key_values):
if name not in SETTABLE_PARAMETERS:
raise ValueError(f"parameters {name} is not managed")
if name in SETTABLE_PARAMETERS_TYPE:
type_ = SETTABLE_PARAMETERS_TYPE[name]
if type_ is not None:
res[name] = type_(value)
continue
res[name] = value
return res
[docs]class TomoHDF5ConfigHandler:
"""
Create a TomoHDF5Config from argparse option provided from the CLI.
..warning:: If a configuration file (--config_file) is given then other argparse options will be ignored.
"""
[docs] def __init__(self, argparse_options):
self._argparse_options = argparse_options
self._config = None
self.build_configuration()
@property
def configuration(self) -> TomoHDF5Config | None:
return self._config
@property
def argparse_options(self):
return self._argparse_options
def build_configuration(self):
if self.argparse_options.config_file is not None:
assert isinstance(
self.argparse_options.config_file, str
), f"{self.argparse_options.config_file}, {type(self.argparse_options.config_file)}"
# from the configuration file
_logger.warning(
"A configuration has been given. All other options at the exception of the input and output file will be ignored"
)
config = TomoHDF5Config.from_cfg_file(self.argparse_options.config_file)
if self.argparse_options.input_file is not None:
config.input_file = self.argparse_options.input_file
if self.argparse_options.output_file is not None:
config.output_file = self.argparse_options.output_file
else:
# from argparse
config = TomoHDF5Config()
options = self.argparse_options
# check input and output file
# propagate options defined by the user to the config file.
# policy: all options when not defined have a default value set to None
# So we don't have to set twice the default value from the source code (class and argparse)
for opt_name in (
"input_file",
"output_file",
"file_extension",
"single_file",
"no_master_file",
"overwrite",
"entries",
"sub_entries_to_ignore",
"raises_error",
"field_of_view",
"request_input",
"default_data_copy",
"sample_x_keys",
"sample_y_keys",
"translation_z_keys",
"sample_detector_distance_keys",
"valid_camera_names",
"rotation_angle_keys",
"exposure_time_keys",
"sample_x_pixel_size_keys",
"sample_y_pixel_size_keys",
"init_titles",
"zseries_init_titles",
"multitomo_init_titles",
"back_and_forth_init_titles",
"dark_titles",
"flat_titles",
"projection_titles",
"alignment_titles",
):
opt_value = getattr(options, opt_name)
if opt_value is not None:
setattr(config, opt_name, opt_value)
# handle specific use cases
if options.debug is not None:
config.log_level = logging.DEBUG
if options.set_params is not None:
extra_params = _extract_param_value(options.set_params)
for param, param_value in extra_params.items():
setattr(config, param, param_value)
if config.input_file is None:
raise ValueError("No input file provided")
if not config.output_file:
# Warning: output_file can be None or "" at this stage.
if config.file_extension is None:
raise ValueError(
"If no output file provided you should provide the extension"
)
config.output_file = get_default_output_file(
input_file=config.input_file,
output_file_extension=config.file_extension.value, # pylint: disable=E1101
)
elif os.path.isdir(config.output_file):
# if the output file is only a directory: consider we want the same file basename with default extension
# in this directory
input_file, _ = os.path.splitext(config.input_file)
config.output_file = os.path.join(
abspath(config.output_file),
os.path.basename(input_file)
+ config.file_extension.value, # pylint: disable=E1101
)
self._config = config
