# coding: utf-8
from __future__ import annotations
from pydantic import BaseModel, ConfigDict
from configparser import ConfigParser
from ..base.NestedModelBase import NestedModelBase
from ..base.FrmFlatToNestedBase import FrmFlatToNestedBase
from ..base.instrument_section import InstrumentSection
from .general_section import GeneralSection
from .keys_section import KeysSection
from .entries_and_title_section import EntriesAndTitlesSection
from .frame_type_section import FrameTypeSection
from .multitomo_section import MultiTomoSection
from .extra_params_section import ExtraParamsSection
from nxtomomill.utils.io import deprecated_warning, deprecated
__all__ = [
"H52nxModel",
"generate_default_h5_config",
]
[docs]class H52nxModel(
FrmFlatToNestedBase,
GeneralSection,
KeysSection,
EntriesAndTitlesSection,
FrameTypeSection,
MultiTomoSection,
ExtraParamsSection,
InstrumentSection,
):
"""Configuration file to run a conversion from bliss-hdf5 file to NXtomo format"""
model_config: ConfigDict = ConfigDict(validate_assignment=True)
def to_nested_model(self) -> _NestedTomoHDF5Config:
return _NestedTomoHDF5Config(
general_section=GeneralSection(
output_file=self.output_file,
overwrite=self.overwrite,
log_level=self.log_level,
input_file=self.input_file,
file_extension=self.file_extension,
raises_error=self.raises_error,
no_input=self.no_input,
single_file=self.single_file,
no_master_file=self.no_master_file,
ignore_bliss_tomo_config=self.ignore_bliss_tomo_config,
field_of_view=self.field_of_view,
rotation_is_clockwise=self.rotation_is_clockwise,
create_control_data=self.create_control_data,
check_tomo_n=self.check_tomo_n,
mechanical_lr_flip=self.mechanical_lr_flip,
mechanical_ud_flip=self.mechanical_ud_flip,
),
keys_section=KeysSection(
valid_camera_names=self.valid_camera_names,
rotation_angle_keys=self.rotation_angle_keys,
sample_x_keys=self.sample_x_keys,
sample_y_keys=self.sample_y_keys,
translation_y_keys=self.translation_y_keys,
translation_z_keys=self.translation_z_keys,
diode_keys=self.diode_keys,
exposure_time_keys=self.exposure_time_keys,
sample_x_pixel_size_keys=self.sample_x_pixel_size_keys,
sample_y_pixel_size_keys=self.sample_y_pixel_size_keys,
detector_x_pixel_size_keys=self.detector_x_pixel_size_keys,
detector_y_pixel_size_keys=self.detector_y_pixel_size_keys,
sample_detector_distance_keys=self.sample_detector_distance_keys,
source_sample_distance_keys=self.source_sample_distance_keys,
machine_current_keys=self.machine_current_keys,
),
entries_and_titles_section=EntriesAndTitlesSection(
entries=self.entries,
sub_entries_to_ignore=self.sub_entries_to_ignore,
init_titles=self.init_titles,
zseries_init_titles=self.zseries_init_titles,
multitomo_init_titles=self.multitomo_init_titles,
dark_titles=self.dark_titles,
flat_titles=self.flat_titles,
projection_titles=self.projection_titles,
alignment_titles=self.alignment_titles,
back_and_forth_init_titles=self.back_and_forth_init_titles,
),
frame_type_section=FrameTypeSection(
data_scans=self.data_scans,
default_data_copy=self.default_data_copy,
),
multitomo_section=MultiTomoSection(
start_angle_offset_in_degree=self.start_angle_offset_in_degree,
n_nxtomo=self.n_nxtomo,
angle_interval_in_degree=self.angle_interval_in_degree,
shift_angles=self.shift_angles,
),
extra_params_section=ExtraParamsSection(
energy_kev=self.energy_kev,
x_sample_pixel_size_m=self.x_sample_pixel_size_m,
y_sample_pixel_size_m=self.y_sample_pixel_size_m,
x_detector_pixel_size_m=self.x_detector_pixel_size_m,
y_detector_pixel_size_m=self.y_detector_pixel_size_m,
detector_sample_distance_m=self.detector_sample_distance_m,
source_sample_distance_m=self.source_sample_distance_m,
),
)
@property
def is_using_titles(self) -> bool:
return len(self.data_scans) == 0
@property
def is_using_urls(self) -> bool:
"""
Return true if we want to use urls for darks, flats, projections
instead of titles
"""
return len(self.data_scans) > 0
def clear_entries_and_subentries(self):
self.entries = ()
self.sub_entries_to_ignore = ()
@classmethod
def from_cfg_file(cls, file_path: str) -> H52nxModel:
txt_parser = ConfigParser(allow_no_value=True)
txt_parser.read(file_path)
def get_section(name, default={}):
if txt_parser.has_section(name):
return txt_parser[name]
else:
return default
return _NestedTomoHDF5Config(
general_section=GeneralSection(**get_section("GENERAL_SECTION")),
entries_and_titles_section=EntriesAndTitlesSection(
**get_section("ENTRIES_AND_TITLES_SECTION")
),
extra_params_section=ExtraParamsSection(
**get_section("EXTRA_PARAMS_SECTION")
),
frame_type_section=FrameTypeSection(**get_section("FRAME_TYPE_SECTION")),
multitomo_section=MultiTomoSection(**get_section("MULTITOMO_SECTION")),
keys_section=KeysSection(**get_section("KEYS_SECTION")),
).to_flatten_config()
# deprecated function / properties from version 1
[docs] @staticmethod
def from_dict(dict_: dict) -> None:
deprecated_warning(
type_="function",
name="from_dict",
reason="replaced by pydantic 'model_dump' function",
replacement="model_dump",
since_version="2.0",
)
dict_ = {key.lower(): value for key, value in dict_.items()}
config = _NestedTomoHDF5Config(**dict_)
return config.to_flatten_config()
@property
@deprecated(since_version="2.0", reason="removed", replacement="")
def bam_single_file(self):
"""This option has been removed. Usage of 'single_file' should be enough"""
pass
@bam_single_file.setter
@deprecated(since_version="2.0", reason="removed", replacement="")
def bam_single_file(self, bam: bool):
"""This option has been removed. Usage of 'single_file' should be enough"""
pass
class _NestedTomoHDF5Config(BaseModel, NestedModelBase):
"""
Nested model to dump the model to .cfg.
It has historically sections when the model (config class is flat). But the parameters are the same
"""
model_config = ConfigDict(str_to_upper=True)
general_section: GeneralSection = GeneralSection()
keys_section: KeysSection = KeysSection()
entries_and_titles_section: EntriesAndTitlesSection = EntriesAndTitlesSection()
frame_type_section: FrameTypeSection = FrameTypeSection()
multitomo_section: MultiTomoSection = MultiTomoSection()
extra_params_section: ExtraParamsSection = ExtraParamsSection()
def to_flatten_config(self) -> H52nxModel:
return H52nxModel(
**self.general_section.model_dump(),
**self.keys_section.model_dump(),
**self.entries_and_titles_section.model_dump(),
**self.frame_type_section.model_dump(),
**self.multitomo_section.model_dump(),
**self.extra_params_section.model_dump(),
)
[docs]def generate_default_h5_config() -> dict:
"""generate a default configuration for converting hdf5 to nx"""
config = H52nxModel().to_nested_model()
return {key.upper(): value for key, value in config.model_dump().items()}
