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""" |
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Module for IO of files in relation to |
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data loading. |
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""" |
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import glob |
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import itertools as it |
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import os |
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import random |
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from typing import List, Tuple, Union |
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import h5py |
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def get_h5_sorted_keys(filename: str) -> List[str]: |
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""" |
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Function to get sorted keys from filename |
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:param filename: h5 file. |
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:return: sorted keys of h5 file. |
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""" |
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with h5py.File(filename, "r") as h5_file: |
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return sorted(h5_file.keys()) |
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def get_sorted_file_paths_in_dir_with_suffix( |
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dir_path: str, suffix: Union[str, List[str]] |
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) -> List[Tuple[str, ...]]: |
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""" |
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Return the path of all files under the given directory. |
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:param dir_path: path of the directory |
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:param suffix: suffix of file names like h5, nii.gz, nii, should not start with . |
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:return: list of relative file path, each element is (file_path, suffix) |
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assuming the full path of the file is dir_path/file_path.suffix |
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""" |
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if isinstance(suffix, str): |
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suffix = [suffix] |
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paths = [] |
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for suffix_i in suffix: |
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# full_path is dir_path/file_path.suffix |
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full_paths = glob.glob( |
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os.path.join(dir_path, "**", "*." + suffix_i), recursive=True |
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) |
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file_paths = [ |
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os.path.relpath(path=p, start=dir_path)[: -(len(suffix_i) + 1)] |
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for p in full_paths |
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] |
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paths += [(p, suffix_i) for p in file_paths] |
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return sorted(paths) |
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def check_difference_between_two_lists(list1: list, list2: list, name: str): |
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""" |
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Raise error if two lists are not identical |
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:param list1: list |
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:param list2: list |
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:param name: name to be printed in case of difference |
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""" |
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diff = [(x, y) for x, y in it.zip_longest(list1, list2) if x != y] |
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if len(diff) > 0: |
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raise ValueError(f"{name} are not identical\n" f"difference are {diff}\n") |
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def get_label_indices(num_labels: int, sample_label: str) -> list: |
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""" |
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Function to get sample label indices for a given number |
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of labels and a sampling policy |
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:param num_labels: int number of labels |
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:param sample_label: method for sampling the labels |
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:return: list of labels defined by the sampling method. |
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""" |
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if sample_label == "sample": # sample a random label |
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return [random.randrange(num_labels)] |
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elif sample_label == "all": # use all labels |
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return list(range(num_labels)) |
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else: |
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raise ValueError("Unknown label sampling policy %s" % sample_label) |
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DeepRegNet /
DeepReg
