io_utils module

class io_utils.FileConfig(cfg, sample: str, pipeline: str = 'fast', origaim_separate: bool = True)

Bases: object

__dict__ = mappingproxy({'__module__': 'io_utils', '__init__': <function FileConfig.__init__>, 'file_bmd': <property object>, 'file_gray': <property object>, 'raw_name': <property object>, 'bmd_name': <property object>, 'boundary_conditions': <property object>, 'file_mask': <property object>, 'mask_name': <property object>, 'file_mask_cort': <property object>, 'file_mask_trab': <property object>, 'file_seg': <property object>, 'cort_mask_name': <property object>, 'trab_mask_name': <property object>, 'seg_name': <property object>, 'inp_name': <property object>, 'vtk_name': <property object>, 'sum_name': <property object>, 'ver_bpv_name': <property object>, 'set_filenames': <function FileConfig.set_filenames>, '__dict__': <attribute '__dict__' of 'FileConfig' objects>, '__weakref__': <attribute '__weakref__' of 'FileConfig' objects>, '__doc__': None, '__annotations__': {}})

__init__(cfg, sample: str, pipeline: str = 'fast', origaim_separate: bool = True)

__module__ = 'io_utils'

__weakref__

list of weak references to the object (if defined)

property bmd_name: Path

property boundary_conditions: str

property cort_mask_name: Path

property file_bmd: Path

property file_gray: Path

property file_mask: Path

property file_mask_cort: Path

property file_mask_trab: Path

property file_seg: Path

property inp_name: Path

property mask_name: Path

property raw_name: Path

property seg_name: Path

set_filenames()

property sum_name: Path

property trab_mask_name: Path

property ver_bpv_name: Path

property vtk_name: Path

io_utils.ext(filename, new_ext)

Changes the file extension.

io_utils.hydra_update_cfg_key(cfg, key, value)

io_utils.log_append_processingtime(filename, time)

io_utils.log_summary(bone, config, filenames, var)

io_utils.print_mem_usage()

io_utils.set_filenames(cfg, sample, pipeline='fast', origaim_separate=True)

Set filenames for each grayscale file. Filenames depend on pipeline (fast/accurate). Always: - native image for header - BMD or Native image croppped to ROI additional for fast pipeline: - periosteal mask additional for accurate pipeline: - trabecular mask - cortical mask - two-phase segmentation

io_utils.timeit(method)

io_utils.write_timing_summary(cfg, sample: str, time: dict)

Writes a summary of processing times for all samples in config to summaries folder. :param path path to store (summaries): :param time dict with full processing time and simulation processing time:

Return type:

writes txt file