|
a |
|
b/utils/filemanager.py |
|
|
1 |
import os |
|
|
2 |
import sys |
|
|
3 |
import pandas as pd |
|
|
4 |
from glob import glob |
|
|
5 |
from .logger import logger |
|
|
6 |
import re |
|
|
7 |
|
|
|
8 |
def extract_parameter(text): |
|
|
9 |
''' |
|
|
10 |
Extract the parameter number from the text. |
|
|
11 |
|
|
|
12 |
Args: |
|
|
13 |
text ('str'): Text to search for the parameter number. |
|
|
14 |
|
|
|
15 |
Returns: |
|
|
16 |
parameter_number ('str'): Parameter number. |
|
|
17 |
''' |
|
|
18 |
match = re.search(r'Par(\w+)', text) |
|
|
19 |
if match: |
|
|
20 |
return 'Par' + match.group(1) |
|
|
21 |
else: |
|
|
22 |
return None |
|
|
23 |
|
|
|
24 |
|
|
|
25 |
|
|
|
26 |
def get_points_paths(base_path, suffix, num_occurrences = 2): |
|
|
27 |
''' |
|
|
28 |
Get the paths of the transformed points. |
|
|
29 |
|
|
|
30 |
Args: |
|
|
31 |
args ('argparse.Namespace'): Command line arguments. |
|
|
32 |
suffix ('str'): Suffix of the file name. |
|
|
33 |
num_occurrences ('int'): Number of occurrences of the suffix in the path. |
|
|
34 |
|
|
|
35 |
Returns: |
|
|
36 |
paths ('list'): List of paths. |
|
|
37 |
''' |
|
|
38 |
paths = [path.replace('\\', '/') for path in sorted(glob(os.path.join(base_path, *["***"] * num_occurrences , f"*{suffix}.txt"), recursive=True))] |
|
|
39 |
return paths |
|
|
40 |
|
|
|
41 |
def get_paths(args, suffix): |
|
|
42 |
''' |
|
|
43 |
Get the paths of the volumes and segmentations. |
|
|
44 |
|
|
|
45 |
Args: |
|
|
46 |
args ('argparse.Namespace'): Command line arguments. |
|
|
47 |
suffix ('str'): Suffix of the file name. |
|
|
48 |
|
|
|
49 |
Returns: |
|
|
50 |
paths ('list'): List of paths. |
|
|
51 |
''' |
|
|
52 |
paths = [path.replace('\\', '/') for path in sorted(glob(os.path.join(args.dataset_path, "***" , f"*{suffix}.nii.gz"), recursive=True))] |
|
|
53 |
return paths |
|
|
54 |
|
|
|
55 |
def check_paths(args, paths, message): |
|
|
56 |
''' |
|
|
57 |
Check if the paths exist. |
|
|
58 |
|
|
|
59 |
Args: |
|
|
60 |
args ('argparse.Namespace'): Command line arguments. |
|
|
61 |
paths ('list'): List of paths. |
|
|
62 |
message ('str'): Message to display in the logger. |
|
|
63 |
|
|
|
64 |
Returns: |
|
|
65 |
None |
|
|
66 |
''' |
|
|
67 |
if len(paths) == 0: |
|
|
68 |
logger.error(f"No {message} found in {args.dataset_path} directory.") |
|
|
69 |
sys.exit(1) |
|
|
70 |
|
|
|
71 |
|
|
|
72 |
def create_directory_if_not_exists(path): |
|
|
73 |
''' |
|
|
74 |
Create a directory if it does not exist. |
|
|
75 |
|
|
|
76 |
Args: |
|
|
77 |
path ('str'): Directory path. |
|
|
78 |
''' |
|
|
79 |
if not os.path.exists(path): |
|
|
80 |
os.makedirs(path) |
|
|
81 |
|
|
|
82 |
def replace_text_in_file(file_path, search_text, replacement_text): |
|
|
83 |
''' |
|
|
84 |
Replace text in a text file. |
|
|
85 |
|
|
|
86 |
Args: |
|
|
87 |
file_path ('str'): Path to the text file. |
|
|
88 |
search_text ('str'): Text to search for in the file. |
|
|
89 |
replacement_text ('str'): Text to replace the searched text with. |
|
|
90 |
''' |
|
|
91 |
try: |
|
|
92 |
# Read the file |
|
|
93 |
with open(file_path, 'r') as file: |
|
|
94 |
content = file.read() |
|
|
95 |
|
|
|
96 |
# Replace the search_text with replacement_text |
|
|
97 |
modified_content = content.replace(search_text, replacement_text) |
|
|
98 |
|
|
|
99 |
# Write the modified content back to the file |
|
|
100 |
with open(file_path, 'w') as file: |
|
|
101 |
file.write(modified_content) |
|
|
102 |
|
|
|
103 |
# print(f"Text replaced in {file_path} and saved.") |
|
|
104 |
except FileNotFoundError: |
|
|
105 |
print(f"File not found: {file_path}") |
|
|
106 |
# except Exception as e: |
|
|
107 |
# print(f"An error occurred: {e}") |
|
|
108 |
|
|
|
109 |
def add_and_delete_rows(file_path, row1, row2): |
|
|
110 |
# Add two rows at the beginning of the file |
|
|
111 |
with open(file_path, 'r+') as file: |
|
|
112 |
content = file.read() |
|
|
113 |
file.seek(0, 0) |
|
|
114 |
file.write(row1 + '\n' + row2 + '\n' + content) |
|
|
115 |
|
|
|
116 |
def delete_added_rows(file_path): |
|
|
117 |
# Delete the first two rows from the file |
|
|
118 |
with open(file_path, 'r') as file: |
|
|
119 |
lines = file.readlines() |
|
|
120 |
|
|
|
121 |
# Handle different newline characters when writing back to the file |
|
|
122 |
with open(file_path, 'w', newline=os.linesep) as file: |
|
|
123 |
file.writelines(lines[2:]) |
|
|
124 |
|
|
|
125 |
|