nxtomomill.io.config.hdf5config.TomoHDF5Config#

class nxtomomill.io.config.hdf5config.TomoHDF5Config[source]#

Bases: ConfigBase

Configuration class to provide to the convert from h5 to nx

__init__()[source]#

Methods

`__init__`()
`clear_entries_and_subentries`()	clear entries and sub_entries_to_ignore
`clear_titles`()	set all titles to empty tuple
`dict_to_cfg`(file_path, dict_)
`from_cfg_file`(file_path[, encoding])
`from_dict`(dict_)	Create a HDF5Config object and set it from values contained in the dictionary :param_: settings dictionary :return: HDF5Config
`get_comments`(key)
`get_extra_params_default_unit`(key)	return the default unit for the extra parameters that can be defined by the user
`load_entries_titles_section`(dict_)
`load_extra_params_section`(dict_)
`load_frame_type_section`(dict_)
`load_from_dict`(dict_)	Load the configuration from a dictionary
`load_general_section`(dict_)
`load_keys_section`(dict_)
`load_pcotomo_section`(dict_)
`to_cfg_file`(file_path)
`to_dict`()	convert the configuration to a dictionary

Attributes

`ACQUISITION_EXPO_TIME_KEYS_DK`
`ALIGNMENT_TITLES_DK`
`COMMENTS`
`COMMENTS_ENTRIES_TITLES_SECTION`
`COMMENTS_EXTRA_PARAMS_SECTION`
`COMMENTS_FRAME_TYPE_SECTION`
`COMMENTS_GENERAL_SECTION`
`COMMENTS_KEYS_SECTION`
`COMMENTS_PCOTOMO_SECTION`
`DARK_TITLES_DK`
`DATA_DK`
`DEFAULT_DATA_COPY_DK`
`DIODE_KEYS_DK`
`ENTRIES_AND_TITLES_SECTION_DK`
`ENTRIES_DK`
`EXTRA_PARAMS_ALIASES`
`EXTRA_PARAMS_DEFAULT_VALID_KEYS`
`EXTRA_PARAMS_ENERGY_DK`
`EXTRA_PARAMS_ENERGY_DK_ALIASES`
`EXTRA_PARAMS_SAMPLE_DETECTOR_DISTANCE`
`EXTRA_PARAMS_SAMPLE_DETECTOR_DISTANCE_ALIASES`
`EXTRA_PARAMS_SECTION_DK`
`EXTRA_PARAMS_SOURCE_SAMPLE_DISTANCE`
`EXTRA_PARAMS_SOURCE_SAMPLE_DISTANCE_ALIASES`
`EXTRA_PARAMS_VALID_KEYS`
`EXTRA_PARAMS_X_PIXEL_SIZE_DK`
`EXTRA_PARAMS_X_PIXEL_SIZE_DK_ALIASES`
`EXTRA_PARAMS_Y_PIXEL_SIZE_DK`
`EXTRA_PARAMS_Y_PIXEL_SIZE_DK_ALIASES`
`FIELD_OF_VIEW_DK`
`FILE_EXTENSION_DK`
`FLAT_TILES_ALIASES`
`FLAT_TITLES_DK`
`FRAME_TYPE_SECTION_DK`
`GENERAL_SECTION_DK`
`HANDLE_MACHINE_CURRENT`
`IGNORE_BLISS_TOMO_CONFIG`
`INIT_TITLES_DK`
`INPUT_FILE_DK`
`INPUT_FORMAT_DK`
`KEYS_SECTION_DK`
`LOG_LEVEL_DK`
`NO_INPUT_DK`
`NO_MASTER_FILE_DK`
`OUTPUT_FILE_DK`
`OVERWRITE_DK`
`PCOTOMO_N_NXTOMO_DK`
`PCOTOMO_SCAN_RANGE_DK`
`PCOTOMO_SECTION_DK`
`PCOTOMO_SHIFT_ANGLES_DK`
`PCOTOMO_START_ANGLE_OFFSET_DK`
`PROJ_TITLES_DK`
`RAISES_ERROR_DK`
`ROT_ANGLE_DK`
`SAMPLE_DETECTOR_DISTANCE_DK`
`SAMPLE_X_KEYS_DK`
`SAMPLE_Y_KEYS_DK`
`SINGLE_FILE_DK`
`SOURCE_SAMPLE_DISTANCE_DK`
`SUB_ENTRIES_TO_IGNORE`
`TRANSLATION_Y_KEYS_DK`
`TRANSLATION_Z_KEYS_DK`
`VALID_CAMERA_DK`
`X_PIXEL_SIZE_KEYS_DK`
`Y_PIXEL_SIZE_KEYS_DK`
`ZSERIE_INIT_TITLES_DK`
`alignment_titles`
`bam_single_file`
`check_tomo_n`
`dark_titles`
`data_frame_grps`	rtype `tuple`
`default_copy_behavior`	rtype `bool`
`diode_keys`	rtype `Iterable`
`entries`
`exposition_time_keys`	rtype `Iterable`
`field_of_view`
`file_extension`	rtype `FileExtension`
`flat_titles`
`handle_machine_current`
`ignore_bliss_tomo_config`	rtype `bool`
`init_titles`
`input_file`
`is_using_titles`	rtype `bool`
`is_using_urls`	Return true if we want to use urls for darks, flats, projections instead of titles
`log_level`
`machine_electric_current_keys`	rtype `Iterable`
`no_input`
`no_master_file`	Option to avoid creating a master file at the end of the conversion
`output_file`
`overwrite`	rtype `bool`
`param_already_defined`	rtype `dict`
`pcotomo_init_titles`
`pcotomo_n_nxtomo`	rtype `int`
`pcotomo_scan_range`	if we want to take a subset of the NXtomo for the pcotomo we can define an interval.
`pcotomo_shift_angles`	rtype `bool`
`pcotomo_start_angle_offset`	If provided then nb_loop and nb_turn values will be ignored and splitting will be done as follow:
`projections_titles`
`raises_error`
`request_input`	rtype `bool`
`rotation_angle_keys`	rtype `Iterable`
`sample_detector_distance_paths`
`sample_x_keys`	rtype `Iterable`
`sample_y_keys`	rtype `Iterable`
`single_file`
`source_sample_distance_paths`
`sub_entries_to_ignore`
`translation_y_keys`	rtype `str`
`translation_z_keys`	rtype `Iterable`
`valid_camera_names`
`x_pixel_size_paths`	rtype `Iterable`
`y_pixel_size_paths`	rtype `Iterable`
`zserie_init_titles`

clear_entries_and_subentries()[source]#: clear entries and sub_entries_to_ignore

clear_titles()[source]#: set all titles to empty tuple

static from_dict(dict_)[source]#: Create a HDF5Config object and set it from values contained in the dictionary :param_: settings dictionary :return: HDF5Config

static get_extra_params_default_unit(key)[source]#

return the default unit for the extra parameters that can be defined by the user

Return type: str

property is_using_urls: bool#

Return true if we want to use urls for darks, flats, projections instead of titles

Return type: bool

load_from_dict(dict_)[source]#

Load the configuration from a dictionary

Return type: None

property no_master_file: bool#

Option to avoid creating a master file at the end of the conversion

Return type: bool

property pcotomo_scan_range: float | None#: if we want to take a subset of the NXtomo for the pcotomo we can define an interval. Interval must be in degree. If None we expect to take the full interval.

property pcotomo_start_angle_offset: float#

If provided then nb_loop and nb_turn values will be ignored and splitting will be done as follow:

take a subselection of the NXtomo based on pcotomo_start_angle_offset and tomo_n
split this sub selection to tomo_n NXtomo
shift angle if requested

Angle is expected to be in degree (when set). The offset is always relative to the first projection angle value

Return type: float

to_dict()[source]#

convert the configuration to a dictionary

Return type: dict