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import logging
import os
import re
from typing import Sequence, Union
logger = logging.getLogger(__name__)
def format_output_path(
file_path,
save_dir: str = None,
base_dirs: Sequence[str] = None,
file_name: Sequence[str] = None,
):
"""Format output path for a given file.
Args:
file_path (str): File path.
save_dir (str, optional): Save directory. Defaults to None.
base_dirs (Sequence[str], optional): Base directories. Defaults to None.
file_name (Sequence[str], optional): File name. Defaults to None.
Returns:
str: Output path.
"""
dirname = os.path.dirname(file_path) if not save_dir else save_dir
if save_dir and base_dirs:
dirname: str = os.path.dirname(file_path)
relative_dir = [
dirname.split(bdir, 1)[1] for bdir in base_dirs if dirname.startswith(bdir)
][0]
# Trim path separator from the path
relative_dir = relative_dir.lstrip(os.path.sep)
dirname = os.path.join(save_dir, relative_dir)
if file_name is not None:
return os.path.join(
dirname,
"{}.h5".format(file_name),
)
return os.path.join(
dirname,
"{}.h5".format(os.path.splitext(os.path.basename(file_path))[0]),
)
# Function the returns a list of file names exluding
# the extention from the list of file paths
def get_file_names(files):
"""Get file names from a list of file paths.
Args:
files (list): List of file paths.
Returns:
list: List of file names.
"""
file_names = []
for file in files:
file_name = os.path.splitext(os.path.basename(file))[0]
file_names.append(file_name)
return file_names
def find_files(
root_dirs: Union[str, Sequence[str]],
max_depth: int = None,
exist_ok: bool = False,
pattern: str = None,
):
"""Recursively search for files.
To avoid recomputing experiments with results, set `exist_ok=False`.
Results will be searched for in `PREFERENCES.OUTPUT_DIR` (if non-empty).
Args:
root_dirs (`str(s)`): Root folder(s) to search.
max_depth (int, optional): Maximum depth to search.
exist_ok (bool, optional): If `True`, recompute results for
scans.
pattern (str, optional): If specified, looks for files with names
matching the pattern.
Return:
List[str]: Experiment directories to test.
"""
def _get_files(depth: int, dir_name: str):
if dir_name is None or not os.path.isdir(dir_name):
return []
if max_depth is not None and depth > max_depth:
return []
files = os.listdir(dir_name)
ret_files = []
for file in files:
possible_dir = os.path.join(dir_name, file)
if os.path.isdir(possible_dir):
subfiles = _get_files(depth + 1, possible_dir)
ret_files.extend(subfiles)
elif os.path.isfile(possible_dir):
if pattern and not re.match(pattern, possible_dir):
continue
output_path = format_output_path(possible_dir)
if not exist_ok and os.path.isfile(output_path):
logger.info(
"Skipping {} - results exist at {}".format(
possible_dir, output_path
)
)
continue
ret_files.append(possible_dir)
return ret_files
out_files = []
if isinstance(root_dirs, str):
root_dirs = [root_dirs]
for d in root_dirs:
out_files.extend(_get_files(0, d))
return sorted(set(out_files))
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