import os
import shutil
import re
import numpy as np
[docs]
def natural_sort(list_to_sort):
"""
Sorts a list of strings in natural order, where numerical values are ordered as numbers,
not as individual characters.
Args:
list_to_sort (list of str): The list of strings to be sorted.
Returns:
list of str: A new list sorted in natural order.
Example:
natural_sort(['file2.txt', 'file10.txt', 'file1.txt'])
-> ['file1.txt', 'file2.txt', 'file10.txt']
"""
def _natural_keys(text):
# Split text into components: numbers are converted to integers, others remain as strings
def _atoi(text):
return int(text) if text.isdigit() else text
return [_atoi(c) for c in re.split(r"(\d+)", text)]
# Sort the list using the natural key function
return sorted(list_to_sort, key=_natural_keys)
[docs]
def get_tile_yx(n_tile_y, n_tile_x, scan_type):
"""
Generates a list of (y, x) coordinates for tiles scanned according to a
specified pattern.
Args:
n_tile_y (int): The number of tiles in the y direction.
n_tile_x (int): The number of tiles in the x direction.
scan_type (str): The scanning pattern type, e.g., "snake_up_right" or
"snake_right_down".
Returns:
list of tuple: A list of (y, x) coordinates for each tile.
Raises:
ValueError: If the scan_type is not supported.
"""
# Horizontal snake
if scan_type == "snake_right_down":
tile_x = [np.arange(n_tile_x) if i % 2 == 0 else np.arange(
n_tile_x)[::-1] for i in range(n_tile_y)]
tile_y = np.repeat(np.arange(n_tile_y), n_tile_x)
elif scan_type == "snake_left_down":
tile_x = [np.arange(n_tile_x)[::-1] if i % 2 ==
0 else np.arange(n_tile_x) for i in range(n_tile_y)]
tile_y = np.repeat(np.arange(n_tile_y), n_tile_x)
elif scan_type == "snake_right_up":
tile_x = [np.arange(n_tile_x) if i % 2 == 0 else np.arange(
n_tile_x)[::-1] for i in range(n_tile_y)]
tile_y = np.repeat(np.arange(n_tile_y)[::-1], n_tile_x)
elif scan_type == "snake_left_up":
tile_x = [np.arange(n_tile_x)[::-1] if i % 2 ==
0 else np.arange(n_tile_x) for i in range(n_tile_y)]
tile_y = np.repeat(np.arange(n_tile_y)[::-1], n_tile_x)
# Vertical snake
elif scan_type == "snake_up_right":
tile_y = [np.arange(n_tile_y)[::-1] if i % 2 ==
0 else np.arange(n_tile_y) for i in range(n_tile_x)]
tile_x = np.repeat(np.arange(n_tile_x), n_tile_y)
elif scan_type == "snake_up_left":
tile_y = [np.arange(n_tile_y)[::-1] if i % 2 ==
0 else np.arange(n_tile_y) for i in range(n_tile_x)]
tile_x = np.repeat(np.arange(n_tile_x)[::-1], n_tile_y)
elif scan_type == "snake_down_right":
tile_y = [np.arange(n_tile_y) if i % 2 == 0 else np.arange(
n_tile_y)[::-1] for i in range(n_tile_x)]
tile_x = np.repeat(np.arange(n_tile_x), n_tile_y)
elif scan_type == "snake_down_left":
tile_y = [np.arange(n_tile_y) if i % 2 == 0 else np.arange(
n_tile_y)[::-1] for i in range(n_tile_x)]
tile_x = np.repeat(np.arange(n_tile_x)[::-1], n_tile_y)
# Row scan
elif scan_type == "row_right_down":
tile_x = np.tile(np.arange(n_tile_x), n_tile_y)
tile_y = np.repeat(np.arange(n_tile_y), n_tile_x)
elif scan_type == "row_left_down":
tile_x = np.tile(np.arange(n_tile_x)[::-1], n_tile_y)
tile_y = np.repeat(np.arange(n_tile_y), n_tile_x)
elif scan_type == "row_right_up":
tile_x = np.tile(np.arange(n_tile_x), n_tile_y)
tile_y = np.repeat(np.arange(n_tile_y)[::-1], n_tile_x)
elif scan_type == "row_left_up":
tile_x = np.tile(np.arange(n_tile_x)[::-1], n_tile_y)
tile_y = np.repeat(np.arange(n_tile_y)[::-1], n_tile_x)
# Column scan
elif scan_type == "column_down_right":
tile_y = np.tile(np.arange(n_tile_y), n_tile_x)
tile_x = np.repeat(np.arange(n_tile_x), n_tile_y)
elif scan_type == "column_down_left":
tile_y = np.tile(np.arange(n_tile_y), n_tile_x)
tile_x = np.repeat(np.arange(n_tile_x)[::-1], n_tile_y)
elif scan_type == "column_up_right":
tile_y = np.tile(np.arange(n_tile_y)[::-1], n_tile_x)
tile_x = np.repeat(np.arange(n_tile_x), n_tile_y)
elif scan_type == "column_up_left":
tile_y = np.tile(np.arange(n_tile_y)[::-1], n_tile_x)
tile_x = np.repeat(np.arange(n_tile_x)[::-1], n_tile_y)
else:
raise ValueError("Unsupported scan_type")
# Flatten the lists if they were created with list comprehensions
if isinstance(tile_y, list):
tile_y = np.concatenate(tile_y)
if isinstance(tile_x, list):
tile_x = np.concatenate(tile_x)
return list(zip(tile_y, tile_x))
[docs]
def get_round_cycle(n_round, n_cycle):
"""
Generates a list of (round, cycle) pairs for each round and cycle.
Args:
n_round (int): The number of rounds.
n_cycle (int): The number of cycles.
Returns:
list of tuple: A list of (round, cycle) pairs for each round and cycle.
"""
return [(round_, cycle) for round_ in range(n_round) for cycle in range(n_cycle)]
[docs]
def copy_groups(src_dir, zarr_path, groups):
for group in groups:
print("Copying: " + group)
sample_name = os.path.splitext(os.path.basename(zarr_path))[0]
src_path = os.path.join(src_dir, sample_name + ".zarr", group)
dst_path = os.path.join(zarr_path, group)
shutil.copytree(src_path, dst_path)