Utils

The utils module define functions (or class) that can be used in several other modules, needed by the core of biom3d or not numerous enough to constitute a new module.

Note

Altough we present submoduls, you don’t need to specify them when importing :

from biom3d.utils.data_handler_abstract import DataHandler
# Is the same thing as
from biom3d.utils import DataHandler

Only some functions/classes cannot be imported directly with utils.

Utils

• DataHandler
  • Instanciating a DathaHandler with the DataHandlerFactory
  • The DataHandler contract
  • OutputType
  • Adding a new dataset format
  • Adding a new image format
• Config
  • AttrDict
  • adaptive_load_config()
  • compat_old_config()
  • config_to_type()
  • load_python_config()
  • load_yaml_config()
  • nested_dict_change_value()
  • nested_dict_change_value_case_insensitive()
  • nested_dict_pairs_iterator()
  • recursive_rename_key()
  • replace_line_multiple()
  • replace_line_single()
  • save_python_config()
  • save_yaml_config()
• Sampling & Data augmentation
  • SmartPatch
  • centered_pad()
• Image visualisation & resizing
  • display_mesh()
  • display_voxels()
  • napari_viewer()
  • resize_3d()
  • resize_segmentation()
• Filtering & thresholding
  • center()
  • closest()
  • compute_otsu_criteria()
  • dist_vec()
  • keep_big_volumes()
  • keep_biggest_volume_centered()
  • keep_center_only()
  • otsu_thresholding()
  • volumes()
• Encoding
  • one_hot()
  • one_hot_fast()
  • one_hot_fast_v1()
• Testing
• Decorator
  • deprecated()
• Folds
  • get_folds_df()
  • get_folds_train_test_df()
  • get_splits_train_val_test()
  • get_splits_train_val_test_overlapping()
  • get_train_test_df()
• Neural network
  • convert_num_pools()
• Files & directories
  • abs_listdir()
  • abs_path()
  • create_save_dirs()
• Time
  • Time