id int64 0 458k | file_name stringlengths 4 119 | file_path stringlengths 14 227 | content stringlengths 24 9.96M | size int64 24 9.96M | language stringclasses 1
value | extension stringclasses 14
values | total_lines int64 1 219k | avg_line_length float64 2.52 4.63M | max_line_length int64 5 9.91M | alphanum_fraction float64 0 1 | repo_name stringlengths 7 101 | repo_stars int64 100 139k | repo_forks int64 0 26.4k | repo_open_issues int64 0 2.27k | repo_license stringclasses 12
values | repo_extraction_date stringclasses 433
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2,285,300 | test_TreeBoxes.py | weecology_MillionTrees/tests/test_TreeBoxes.py | from milliontrees.datasets.TreeBoxes import TreeBoxesDataset
from milliontrees.common.data_loaders import get_train_loader, get_eval_loader
import torch
import pytest
import os
import pandas as pd
import numpy as np
# Check if running on hipergator
if os.path.exists("/orange"):
on_hipergator = True
else:
on_h... | 4,663 | Python | .py | 107 | 36.607477 | 98 | 0.646018 | weecology/MillionTrees | 8 | 2 | 7 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,301 | test_TreePoints.py | weecology_MillionTrees/tests/test_TreePoints.py | from milliontrees.datasets.TreePoints import TreePointsDataset
import os
import pytest
import torchvision.transforms.v2 as transforms
# Check if running on hipergator
if os.path.exists("/orange"):
on_hipergator = True
else:
on_hipergator = False
# Test structure without real annotation data to ensure format i... | 2,391 | Python | .py | 58 | 34.87931 | 124 | 0.694444 | weecology/MillionTrees | 8 | 2 | 7 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,302 | CVE-2023-22518.py | davidfortytwo_CVE-2023-22518/CVE-2023-22518.py | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Author: David Espejo (Fortytwo Security)
import os
import json
import argparse
import requests
import logging
from rich import print
from alive_progress import alive_bar
HEADERS = {
"X-Atlassian-Token": "no-check",
"User-Agent": "Mozilla/5.0 (Linux; U; Android ... | 7,881 | Python | .py | 161 | 40.086957 | 212 | 0.657381 | davidfortytwo/CVE-2023-22518 | 8 | 2 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,303 | decorator.py | Aues6uen11Z_Zafkiel/zafkiel/decorator.py | from typing import Callable, Generic, TypeVar
T = TypeVar("T")
def run_once(f):
"""
From https://github.com/LmeSzinc/StarRailCopilot/blob/master/module/base/decorator.py
Run a function only once, no matter how many times it has been called.
Examples:
@run_once
def my_function(foo, ba... | 1,946 | Python | .py | 58 | 25.517241 | 94 | 0.604925 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,304 | config.py | Aues6uen11Z_Zafkiel/zafkiel/config.py | from airtest.core.settings import Settings
class Config:
ST = Settings
ST.CVSTRATEGY = ["tpl", "akaze"]
ST.THRESHOLD = 0.8
| 137 | Python | .py | 5 | 23.6 | 42 | 0.7 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,305 | exception.py | Aues6uen11Z_Zafkiel/zafkiel/exception.py | class NotRunningError(Exception):
pass
class PageUnknownError(Exception):
pass
class ScriptError(Exception):
pass
class LoopError(Exception):
pass
| 168 | Python | .py | 8 | 17.375 | 34 | 0.793548 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,306 | report.py | Aues6uen11Z_Zafkiel/zafkiel/report.py | import os
import shutil
import traceback
from PIL import Image
from airtest.aircv import imread, FileNotExistError, get_resolution
from airtest.report.report import LogToHtml, LOGGING, HTML_FILE, DEFAULT_LOG_DIR, DEFAULT_LOG_FILE, HTML_TPL
from airtest.utils.compat import script_dir_name
from zafkiel.config import C... | 3,786 | Python | .py | 83 | 33.686747 | 120 | 0.579846 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,307 | utils.py | Aues6uen11Z_Zafkiel/zafkiel/utils.py | import cv2
import numpy as np
from PIL import Image
def random_rectangle_point(center, h, w, n=3):
"""
From https://github.com/LmeSzinc/StarRailCopilot/blob/master/module/base/utils/utils.py
Choose a random point in an area.
Args:
center: coordinate of the area center
h: height of the... | 4,133 | Python | .py | 99 | 35.737374 | 110 | 0.666001 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,308 | __init__.py | Aues6uen11Z_Zafkiel/zafkiel/__init__.py | from airtest.core.helper import G
from zafkiel.config import Config
from zafkiel.device.api import *
from zafkiel.device.template import Template
from zafkiel.device.win import WindowsPlatform
from zafkiel.timer import Timer
from zafkiel.report import simple_report
from zafkiel.logger import logger
__version__ = '0.2... | 368 | Python | .py | 10 | 35.4 | 46 | 0.847458 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,309 | logger.py | Aues6uen11Z_Zafkiel/zafkiel/logger.py | import logging
import sys
from loguru import logger
airtest_logger = logging.getLogger("airtest")
airtest_logger.setLevel(logging.ERROR)
logger.remove()
logger.add(sys.stdout, format="<green>{time:YYYY-MM-DD HH:mm:ss.SSS}</green> | "
"<level>{level: <7}</level> | "
... | 372 | Python | .py | 10 | 28.6 | 80 | 0.596639 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,310 | timer.py | Aues6uen11Z_Zafkiel/zafkiel/timer.py | import time
from zafkiel import logger
class Timer:
def __init__(self, limit, count=0):
"""
From https://github.com/LmeSzinc/StarRailCopilot/blob/master/module/base/timer.py
Args:
limit (int, float): Timer limit
count (int): Timer reach confirm count. Default to 0... | 2,503 | Python | .py | 79 | 21.632911 | 110 | 0.529314 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,311 | ui.py | Aues6uen11Z_Zafkiel/zafkiel/ui/ui.py | from zafkiel import exists, Template, app_is_running, touch, screenshot
from zafkiel.logger import logger
from zafkiel.ocr.ocr import Ocr
from zafkiel.ui.page import Page
from zafkiel.decorator import run_once
from zafkiel.exception import NotRunningError, PageUnknownError, ScriptError
from zafkiel.timer import Timer
f... | 9,036 | Python | .py | 243 | 24.666667 | 112 | 0.529728 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,312 | page.py | Aues6uen11Z_Zafkiel/zafkiel/ui/page.py | from __future__ import annotations
import traceback
from zafkiel.device.template import ImageTemplate as Template
from zafkiel.ui.switch import Switch
class Page:
"""
Main code comes from https://github.com/LmeSzinc/StarRailCopilot/blob/master/tasks/base/page.py
"""
# Key: str, page name like "page_... | 2,391 | Python | .py | 66 | 26.80303 | 99 | 0.582936 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,313 | switch.py | Aues6uen11Z_Zafkiel/zafkiel/ui/switch.py | from zafkiel.device.template import ImageTemplate as Template
from zafkiel.exception import ScriptError
class Switch:
"""
A wrapper to handle switches in game, switch among states with retries.
Main code comes from https://github.com/LmeSzinc/StarRailCopilot/blob/master/module/ui/switch.py
Examples:
... | 2,118 | Python | .py | 54 | 29.703704 | 104 | 0.584308 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,314 | __init__.py | Aues6uen11Z_Zafkiel/zafkiel/ui/__init__.py | from zafkiel.ui.page import Page
from zafkiel.ui.switch import Switch
from zafkiel.ui.ui import UI
| 99 | Python | .py | 3 | 32 | 36 | 0.84375 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,315 | template.py | Aues6uen11Z_Zafkiel/zafkiel/device/template.py | import os
import types
from functools import cached_property
from pathlib import Path
import cv2
from airtest.core.cv import Template, MATCHING_METHODS
from airtest.core.error import InvalidMatchingMethodError
from airtest.core.helper import G, logwrap
from airtest.utils.transform import TargetPos
from numpy import nd... | 7,563 | Python | .py | 160 | 36.88125 | 133 | 0.60456 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,316 | api.py | Aues6uen11Z_Zafkiel/zafkiel/device/api.py | from typing import Optional, Tuple, Type, Callable, Union, List
from airtest.core.api import *
from airtest.core.cv import try_log_screen
from airtest.core.error import TargetNotFoundError
from airtest.core.helper import G, logwrap, delay_after_operation, set_logdir
from airtest.core.settings import Settings as ST
fro... | 13,483 | Python | .py | 326 | 33.521472 | 118 | 0.637447 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,317 | win.py | Aues6uen11Z_Zafkiel/zafkiel/device/win.py | from typing import Tuple
from airtest.core.win import Windows
from pyautogui import dragTo, moveTo
from pytweening import easeOutQuad
import win32gui
class WindowsPlatform(Windows):
def app_is_running(self) -> bool:
state = self.app.is_process_running()
return state
def stop_app(self, pid: ... | 1,386 | Python | .py | 37 | 28.918919 | 103 | 0.609118 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,318 | cv.py | Aues6uen11Z_Zafkiel/zafkiel/device/cv.py | import time
from airtest.core.cv import try_log_screen
from airtest.core.error import TargetNotFoundError
from airtest.core.helper import logwrap, G
from airtest.core.settings import Settings as ST
from zafkiel.logger import logger
from zafkiel.ocr.ocr import Ocr
from zafkiel.utils import is_color_similar, crop
@lo... | 3,014 | Python | .py | 68 | 33.735294 | 118 | 0.618609 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,319 | models.py | Aues6uen11Z_Zafkiel/zafkiel/ocr/models.py | from pponnxcr import TextSystem as TextSystem_
from zafkiel.decorator import cached_property
from zafkiel.exception import ScriptError
DIC_LANG_TO_MODEL = {
'cn': 'zhs',
'en': 'en',
'jp': 'ja',
'tw': 'zht',
}
def lang2model(lang: str) -> str:
"""
Args:
lang: In-game language name, de... | 1,731 | Python | .py | 57 | 23.842105 | 79 | 0.621148 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,320 | ocr.py | Aues6uen11Z_Zafkiel/zafkiel/ocr/ocr.py | import re
import time
from datetime import timedelta
from difflib import SequenceMatcher
from typing import Optional
from pponnxcr.predict_system import BoxedResult
from zafkiel.logger import logger
from zafkiel.config import Config
from zafkiel.decorator import cached_property
from zafkiel.device.template import Ima... | 12,938 | Python | .py | 338 | 28.14497 | 115 | 0.575561 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,321 | keyword.py | Aues6uen11Z_Zafkiel/zafkiel/ocr/keyword.py | import re
from dataclasses import dataclass
from functools import cached_property
from typing import ClassVar
from zafkiel.config import Config
from zafkiel.exception import ScriptError
REGEX_PUNCTUATION = re.compile(r'[ ,.\'"“”，。:：!！?？·•\-—/\\\n\t()\[\]（）「」『』【】《》［］]')
def parse_name(n):
n = REGEX_PUNCTUATION.s... | 4,613 | Python | .py | 139 | 23.071942 | 101 | 0.541676 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,322 | utils.py | Aues6uen11Z_Zafkiel/zafkiel/ocr/utils.py | import itertools
import numpy as np
from pponnxcr.predict_system import BoxedResult
def area_cross_area(area1, area2, thres_x=20, thres_y=20):
"""
Args:
area1: (upper_left_x, upper_left_y, bottom_right_x, bottom_right_y).
area2: (upper_left_x, upper_left_y, bottom_right_x, bottom_right_y).
... | 5,507 | Python | .py | 139 | 32.827338 | 93 | 0.633189 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,323 | __init__.py | Aues6uen11Z_Zafkiel/zafkiel/ocr/__init__.py | """
This OCR module is from https://github.com/LmeSzinc/StarRailCopilot/tree/master/module/ocr,
only modified to fit the project and:
delete some methods
add Ocr.ocr_match_keyword()
"""
from zafkiel.ocr.keyword import Keyword
from zafkiel.ocr.ocr import Ocr, Digit, DigitCounter, Duration, OcrResultButton
| 306 | Python | .py | 8 | 37.25 | 91 | 0.815436 | Aues6uen11Z/Zafkiel | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,324 | main.py | usexhs_xhs-link/src/main.py | import os
import re
import logging
from flask import Flask, redirect, request, send_file, render_template
from urllib.parse import unquote
import requests
from requests.adapters import HTTPAdapter
from requests.packages.urllib3.util.retry import Retry
# import lib.redis_handler # WIP
from lib import sql_handler
... | 7,049 | Python | .py | 152 | 41.072368 | 108 | 0.692342 | usexhs/xhs-link | 8 | 0 | 0 | AGPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,325 | sql_handler.py | usexhs_xhs-link/src/lib/sql_handler.py | import os
import psycopg2
# from datetime import datetime
# Set up PostgreSQL
pg_host = os.environ.get('POSTGRES_HOST', 'postgres')
pg_port = os.environ.get('POSTGRES_PORT', '5432')
pg_user = os.environ.get('POSTGRES_USER', 'xhslink')
pg_password = os.environ.get('POSTGRES_PASSWORD', 'xhslink-password')
# pg_database ... | 1,882 | Python | .py | 57 | 26.701754 | 91 | 0.645465 | usexhs/xhs-link | 8 | 0 | 0 | AGPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,326 | main.py | activate-sh_Rubika-Group-Management/main.py | from rubpy import Client, Message, handlers
from rubpy import models, methods, exceptions
from rich.console import Console
from datetime import datetime
from asyncio import run
admins = [] # No need to edit this list
groups = [
'', # group one
'', # group two
# and...
]
filters = [
'@',
'joinc',
... | 19,614 | Python | .py | 370 | 27.035135 | 104 | 0.40988 | activate-sh/Rubika-Group-Management | 8 | 0 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,327 | dlc2adpt.py | tangguoling_ADPT/data/dlc2adpt.py | # -*- coding: utf-8 -*-
"""
Created on Wed Nov 16 10:36:10 2022
@author: tang
"""
import cv2
import glob
import pandas as pd
import json
import h5py
csvs = glob.glob('D:/ADPT/data/mouse/labeled-data/*/CollectedData_*.csv')
f = open('mouse.json','w')
all_data = []
for csv in csvs:
data = pd.read_cs... | 1,456 | Python | .py | 46 | 22.478261 | 74 | 0.51787 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,328 | predict.py | tangguoling_ADPT/code/predict.py | # -*- coding: utf-8 -*-
"""
Created on Mon Jan 8 18:49:52 2024
@author: tang
"""
import warnings
warnings.filterwarnings('ignore')
from core.predict import predict
import yaml
from config.config_training import configuration
from config.config_predicting import configuration_predict
if __name__ == '__ma... | 1,881 | Python | .py | 31 | 54.741935 | 339 | 0.700883 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,329 | train.py | tangguoling_ADPT/code/train.py | # -*- coding: utf-8 -*-
"""
Created on Mon Jan 8 18:49:52 2024
@author: tang
"""
import warnings
warnings.filterwarnings('ignore')
from core.train import train
from core.data_aug import data_augmentation
import yaml
from config.config_training import configuration
if __name__ == '__main__':
print('... | 1,637 | Python | .py | 27 | 55.296296 | 367 | 0.701511 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,330 | config_predicting.py | tangguoling_ADPT/code/config/config_predicting.py | # -*- coding: utf-8 -*-
"""
Created on Tue Jan 2 21:45:08 2024
@author: tang
"""
import glob
def configuration_predict(result_predict):
videos = glob.glob(result_predict['Video_path']+ '/*.' + result_predict['Video_type'])
save_video = result_predict['save_predicted_video']
# shuffle_num = 1... | 534 | Python | .py | 14 | 33.857143 | 91 | 0.679612 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,331 | config_training.py | tangguoling_ADPT/code/config/config_training.py | # -*- coding: utf-8 -*-
"""
Created on Mon Jan 8 16:21:36 2024
@author: tang
"""
import glob
from matplotlib import pyplot as plt
import yaml
def configuration(result):
IMG_DIR = result['IMG_DIR']
JSON = result['JSON']
IMG_SIZE_H_ori, IMG_SIZE_W_ori = result['IMG_SIZE_H_ori'],result['IMG_SIZ... | 1,660 | Python | .py | 33 | 44.424242 | 304 | 0.676286 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,332 | predict.cp39-win_amd64.pyd | tangguoling_ADPT/code/core/predict.cp39-win_amd64.pyd | MZ� ÿÿ ¸ @ º ´ Í!¸LÍ!This program cannot be run in DOS mode.
$ ÖIÊ4’(¤g’(¤g’(¤g›P7g�(¤g”©¥f�(¤gÙP¥f�(¤g”©¡fŸ(¤g”© fš(¤g”©§f–(¤g1A¥f‘(¤g’(¥g!(¤gÿ©¬f“(¤gÿ©¤f“(¤gÿ©[g“(¤gÿ©¦f“(¤gRich’(¤g PE d† R”ªe ğ " & ü p \ÿ € ... | 154,624 | Python | .py | 326 | 473.251534 | 5,589 | 0.421503 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,333 | train.cp39-win_amd64.pyd | tangguoling_ADPT/code/core/train.cp39-win_amd64.pyd | MZ� ÿÿ ¸ @ º ´ Í!¸LÍ!This program cannot be run in DOS mode.
$ ÎIÈ4Š(¦gŠ(¦gŠ(¦gƒP5gˆ(¦gŒ©§fˆ(¦gÁP§fˆ(¦gŒ©£f‡(¦gŒ©¢f‚(¦gŒ©¥f�(¦g)A§f‰(¦gŠ(§gK(¦gç©®f‹(¦g穦f‹(¦gç©Yg‹(¦g穤f‹(¦gRichŠ(¦g PE d† E”ªe ğ " & � š l‘ € ... | 265,216 | Python | .py | 528 | 501.255682 | 8,110 | 0.422905 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,334 | data_aug.py | tangguoling_ADPT/code/core/data_aug.py | # -*- coding: utf-8 -*-
"""
Created on Tue Jan 9 03:29:02 2024
@author: tang
"""
import imgaug.augmenters as iaa
def data_augmentation():
aug = iaa.Sequential(
[
iaa.Sometimes(0.5, iaa.Affine(rotate=(-25, 25))),
iaa.Sometimes(0.33, iaa.Affine(translate_percent={... | 1,934 | Python | .py | 34 | 43.558824 | 105 | 0.53611 | tangguoling/ADPT | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,335 | setup.py | aashishsec_httpAlive/setup.py | from setuptools import setup, find_packages
setup(
name='httpAlive',
version='1.0.2',
description='HttpAlive is a web probing tool designed for discovering alive subdomains and URLs.',
author='Bande Aashish',
url='https://github.com/aashishsec/httpAlive',
packages=find_packages(),
install_r... | 571 | Python | .py | 22 | 20 | 102 | 0.613139 | aashishsec/httpAlive | 8 | 1 | 2 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,336 | httpAlive.py | aashishsec_httpAlive/httpAlive/httpAlive.py | #!/usr/bin/python3
import requests
import colorama
import random
import argparse
import concurrent.futures
import httpx
from datetime import datetime
from colorama import Fore, Style
colorama.init(autoreset=True)
green = Fore.GREEN
magenta = Fore.MAGENTA
cyan = Fore.CYAN
mixed = Fore.RED + Fore.BLUE
red =... | 8,745 | Python | .py | 143 | 49.202797 | 228 | 0.618388 | aashishsec/httpAlive | 8 | 1 | 2 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,337 | applepy.iml | Cypheriel_applepy/.idea/applepy.iml | <?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" />
<orderEntry type="jdk" jdkName="Poetry (applepy)" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
</modu... | 323 | Python | .py | 8 | 37.5 | 77 | 0.686709 | Cypheriel/applepy | 8 | 1 | 0 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,338 | 10_Contour_Map.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/10_Contour_Map.py | #!/usr/bin/env python
# coding: utf-8
# ## 0 Loading
# ### 0.0 Import Libs
# In[2]:
import pythreejs, ipywidgets
import cupy as cp
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import scipy.signal
import sklearn.neighbors
from sklearn.neighbors import KDTree
from scipy.sp... | 6,377 | Python | .py | 158 | 35.088608 | 128 | 0.655749 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,339 | plot_contour_map_with_Prot_top.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/plot_contour_map_with_Prot_top.py | import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
# Define the path to your data files
file1 = 'smoothed_x_points.cor'
file2 = 'scaled_prot.cor'
# Define the X range (minimum and maximum X values)
x_min_map = 20 # Change this to your desired minimum X
x_min_prot = 50 # Chan... | 3,045 | Python | .py | 63 | 46.968254 | 116 | 0.733738 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,340 | 21_Replace_PO4_to_Lipids.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/21_Replace_PO4_to_Lipids.py | #!/usr/bin/env python
# coding: utf-8
# In[723]:
import os
import numpy as np
def load_coords(path):
data_list = []
with open(path, 'r') as f:
lines = f.readlines()
matrix = []
for line in lines:
x, y, z = map(float, line.strip().split(","))
ma... | 5,186 | Python | .py | 123 | 33.495935 | 224 | 0.576743 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,341 | find_surf.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/find_surf.py | def read_points_from_file(filename):
points = []
with open(filename, 'r') as file:
for line in file:
parts = line.strip().split()
if len(parts) == 3:
x, y, z = map(float, parts)
points.append((x, y, z))
return points
def filter_largest_x(point... | 1,337 | Python | .py | 30 | 35.966667 | 92 | 0.617089 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,342 | smooth_x_value.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/smooth_x_value.py | import numpy as np
# Define the valid range for y and z coordinates
y_min, y_max = 0, 600
z_min, z_max = 0, 600
# Read points from the file
points = []
try:
with open('edge_removed.cor', 'r') as file:
for line in file:
x, y, z = map(float, line.strip().split())
# Check if y and z c... | 2,345 | Python | .py | 57 | 35.157895 | 105 | 0.605888 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,343 | remove_edge.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/remove_edge.py | import numpy as np
import matplotlib.pyplot as plt
from scipy.spatial import ConvexHull
# Step 1: Read 3D points from a file (replace 'your_points_file.txt' with your file path)
points_3d = np.loadtxt('surface.cor')
# Define the number of iterations (N)
N = 95 # Change this to the desired number of iterations
for i... | 2,161 | Python | .py | 41 | 49.512195 | 97 | 0.732636 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,344 | mmbr.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/mmbr.py | #!/usr/bin/env python
# coding: utf-8
# In[1]:
!pip install matplotlib plotly mayavi
# In[11]:
# Import necessary libraries
import numpy as np
import pandas as pd
from sklearn.preprocessing import PolynomialFeatures
from sklearn.linear_model import LinearRegression
from sklearn.pipeline import m... | 4,959 | Python | .py | 119 | 36.403361 | 169 | 0.65864 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,345 | scale_up_points_map_pixel_size.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/scale_up_points_map_pixel_size.py | scale = 1.17
import numpy as np
points_file_path = 'prot.cor'
with open(points_file_path, 'r') as points_file:
points_lines = points_file.readlines()
scaled_up_coor = []
for line in points_lines:
xyz = list(line.strip().split())
scaled_xyz = [(float(i) * scale) for i in xyz ]
scaled_up_coor.append(sc... | 579 | Python | .py | 17 | 31.176471 | 64 | 0.682796 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,346 | mmbr_homogenized_cpu.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/mmbr_homogenized_cpu.py | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import sklearn.neighbors
from sklearn.neighbors import KDTree
from mpl_toolkits.mplot3d import Axes3D
from ipywidgets import interactive
from scipy.spatial import distance_matrix
def parse_pdb(pdb_file):
"""
Parse a PDB file and return a di... | 7,841 | Python | .py | 164 | 39.268293 | 185 | 0.638786 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,347 | 20_Prepare_For_Replace_P2lipids.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/20_Prepare_For_Replace_P2lipids.py | #!/usr/bin/env python
# coding: utf-8
# ## Load un-curved mmbr
# In[17]:
import os
import numpy as np
p_coordinates = []
with open("/home/boyuan/Desktop/mmbr_fit/input/double_mmbr_square.pdb", "r") as file:
contents = file.readlines()
p_lines = [line for line in contents if line[0:6]=="HE... | 2,572 | Python | .py | 70 | 32.771429 | 110 | 0.673394 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,348 | generate_points_insideProt_Map.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/generate_points_insideProt_Map.py | import mrcfile
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
# Define the MRC file path and the subsampling factor
mrc_file_path = 'protein_ongrid.mrc'
subsample_factor = 4 # Adjust as needed
# Read the MRC file
with mrcfile.open(mrc_file_path, mode='r') as mrc:
densi... | 1,902 | Python | .py | 53 | 32.754717 | 111 | 0.683696 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,349 | generate_points_insideMembrane.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/generate_points_insideMembrane.py | import mrcfile
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
# Define the MRC file path and the subsampling factor
mrc_file_path = 'typeO_membrane.mrc'
subsample_factor = 2 # Adjust as needed
# Read the MRC file
with mrcfile.open(mrc_file_path, mode='r') as mrc:
densi... | 1,901 | Python | .py | 53 | 32.735849 | 111 | 0.683524 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,350 | 00_Rotation_Memebrane.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/00_Rotation_Memebrane.py | #!/usr/bin/env python
# coding: utf-8
# ## Import Libs
# In[ ]:
import pythreejs, ipywidgets
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import scipy.signal
import sklearn.neighbors
from sklearn.neighbors import KDTree
from scipy.spatial.distance import cdist
from scipy.... | 6,538 | Python | .py | 168 | 33.75 | 121 | 0.665267 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,351 | 30_Analytical_Equations.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/30_Analytical_Equations.py | #!/usr/bin/env python
# coding: utf-8
# # try to find analytical equations
# In[ ]:
import numpy as np
from sklearn.linear_model import ElasticNet, BayesianRidge
from sklearn.preprocessing import PolynomialFeatures
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScal... | 2,021 | Python | .py | 59 | 29.525424 | 94 | 0.677778 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,352 | 01_optional_pdb_clean_up.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/01_optional_pdb_clean_up.py | #!/usr/bin/env python
# coding: utf-8
# # Lipids Clean-Up
# This script can be used after discarding lipids occupied protein's position.
# To discard lipids, use select zone command in Chimearx and set the discarding range as u like.
# In[117]:
# Load original coords
import pandas as pd
def parse_pd... | 5,243 | Python | .py | 122 | 33.311475 | 150 | 0.560135 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,353 | sample_map_build_lipids_v1.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/sample_map_build_lipids_v1.py | import os
import sys
import mrcfile
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import math
import warnings
import coot
# import cupy as cp # uncomment it when you have GPU
from scipy.interpolate import griddata
from scipy.ndimage import gaussian_filter
from scipy.spatial.distance import cdis... | 30,778 | Python | .py | 671 | 37.479881 | 158 | 0.608499 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,354 | mmbr_homogenized_gpu.py | JackZhang-Lab_Cryo-MEM/Mem_modeling/mmbr_homogenized_gpu.py | import cupy as cp
import pandas as pd
import matplotlib.pyplot as plt
import sklearn.neighbors
from sklearn.neighbors import KDTree
from mpl_toolkits.mplot3d import Axes3D
from ipywidgets import interactive
from scipy.spatial import distance_matrix
def parse_pdb(pdb_file):
with open(pdb_file, 'r') as f:
li... | 7,191 | Python | .py | 128 | 46.429688 | 188 | 0.631616 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,355 | setup.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/setup.py | from setuptools import setup, find_packages
setup(
name='MemXTerminator',
version='1.0.0',
packages=find_packages(where='src'),
package_dir={'': 'src'},
author='Zhen Huang',
author_email='zhen.victor.huang@gmail.com',
description='A software for membrane analysis and subtraction in cryo-EM'... | 1,248 | Python | .py | 40 | 24.575 | 78 | 0.583264 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,356 | __init__.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/__init__.py | __author__ = 'Zhen Huang'
__email__ = 'zhen.victor.huang@gmail.com'
__version__ = '1.0.0'
| 90 | Python | .py | 3 | 29 | 41 | 0.609195 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,357 | membrane_analysis-main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/bin/membrane_analysis-main.py | import numpy as np
import cupy as cp
from ..lib._utils import *
from ..lib.radonanalyser import *
from ..lib.template_centerfitting import *
from ..lib.calculate_curve import *
from ..lib.generate_membrane_mask import *
from ..lib.mem_average import *
# from mem_subtract_old import *
from cupyx.scipy.ndimage import zoo... | 8,024 | Python | .py | 119 | 64.361345 | 364 | 0.740975 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,358 | micrograph_mem_subtraction.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/bin/micrograph_mem_subtraction.py | import numpy as np
import cupy as cp
import mrcfile
import starfile
import matplotlib.pyplot as plt
import os
import argparse
import multiprocessing
from multiprocessing import Pool
import time
if __name__ == '__main__':
class MicrographMembraneSubtract:
def __init__(self, particles_selected_filename):
... | 13,306 | Python | .py | 184 | 60.538043 | 197 | 0.627075 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,359 | membrane_subtract-main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/bin/membrane_subtract-main.py | import numpy as np
import cupy as cp
import starfile
from ..lib._utils import *
from ..lib.mem_subtract import *
import argparse
import os
from multiprocessing import Pool
import multiprocessing
import time
if __name__ == '__main__':
class MembraneSubtract:
def __init__(self, particles_selected_filename, ... | 12,153 | Python | .py | 170 | 59.323529 | 274 | 0.638975 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,360 | calculate_curve.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/calculate_curve.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from ._utils import *
from .template_centerfitting import *
from .radonanalyser import *
from .circle_mask_generator import *
from cupyx.scipy.ndimage import zoom
from cupyx.scipy.signal import correlate2d
class Curve:
def __init__(self, output_f... | 7,054 | Python | .py | 149 | 38.436242 | 132 | 0.605534 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,361 | circle_mask_generator.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/circle_mask_generator.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from ._utils import *
class circle_mask:
def __init__(self, image_array, x0, y0, radius, sigma):
self.image = image_array
self.image_size = self.image.shape[0]
self.x0 = x0
self.y0 = y0
self.radius = radius... | 2,266 | Python | .py | 50 | 39.06 | 118 | 0.603705 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,362 | mem_subtract.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/mem_subtract.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from cupyx.scipy.ndimage import rotate, shift, zoom
from cupyx.scipy.signal import correlate2d, convolve
from ._utils import *
from .mem_average import *
from .circle_mask_generator import *
import time
class Get2Raw:
def __init__(self, mem_anal... | 12,210 | Python | .py | 213 | 48.41784 | 246 | 0.611666 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,363 | get_particles_info.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/get_particles_info.py | import pandas as pd
import numpy as np
import cupy as cp
import starfile
import mrcfile
from ._utils import *
from cupyx.scipy.ndimage import zoom
# from mem_subtract_old import *
df_membrane_analysis_star = starfile.read('mem_analysis.star')
average_raw_series = df_membrane_analysis_star['rln2DAverageimageName'].appl... | 3,032 | Python | .py | 58 | 50.793103 | 247 | 0.685185 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,364 | generate_gaussian_template.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/generate_gaussian_template.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from scipy.stats import norm
from ._utils import *
def gaussian_pdf(x, mean, std):
coefficient = 1.0 / (std * cp.sqrt(2 * cp.pi))
exponential = cp.exp(- (x - mean) ** 2 / (2 * std ** 2))
return coefficient * exponential
def gaussian2(x, ... | 2,563 | Python | .py | 74 | 26.635135 | 79 | 0.537253 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,365 | radonanalyser.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/radonanalyser.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from skimage.transform import radon
from cupyx.scipy.ndimage import maximum_filter
# from cupyx.scipy.signal import convolve
from ._utils import *
from .circle_mask_generator import *
class RadonAnalyzer:
def __init__(self, output_filename, i, im... | 6,764 | Python | .py | 134 | 41.186567 | 129 | 0.582687 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,366 | lpfilter.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/lpfilter.py | import numpy as np
import matplotlib.pyplot as plt
from ._utils import *
def create_gaussian_low_pass_filter(image, cutoff_frequency):
shape = image.shape
rows, cols = shape
crow, ccol = rows // 2, cols // 2
y, x = np.ogrid[-crow:rows-crow, -ccol:cols-ccol]
distance = np.sqrt(x*x + y*y)
mask = ... | 1,552 | Python | .py | 38 | 35.973684 | 135 | 0.699789 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,367 | mem_average.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/mem_average.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from ._utils import *
from .template_centerfitting import *
from .radonanalyser import *
from .calculate_curve import *
from .generate_membrane_mask import *
from scipy.interpolate import interp1d
from cupyx.scipy.ndimage import zoom
class average_me... | 6,570 | Python | .py | 106 | 53.537736 | 147 | 0.666201 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,368 | generate_membrane_mask.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/generate_membrane_mask.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from ._utils import *
from .template_centerfitting import *
from .radonanalyser import *
from .calculate_curve import *
from cupyx.scipy.ndimage import zoom
class mem_mask:
def __init__(self,output_filename, i, image, edge_sigma):
# fit_c... | 4,135 | Python | .py | 82 | 43.792683 | 134 | 0.630462 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,369 | _utils.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/_utils.py | import mrcfile
import starfile
import numpy as np
import cupy as cp
import pandas as pd
import matplotlib.pyplot as plt
from cupyx.scipy.ndimage import convolve
def readmrc(filename, section=0, mode='cpu'):
image = mrcfile.open(filename)
if len(image.data.shape) == 2:
gray_image = image.data.copy()
... | 3,723 | Python | .py | 83 | 41.108434 | 209 | 0.662621 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,370 | template_centerfitting.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/radonfit/lib/template_centerfitting.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from cupyx.scipy.signal import correlate2d
from .generate_gaussian_template import *
from ._utils import *
from .radonanalyser import *
from cupyx.scipy.ndimage import zoom
class Template_centerfitting:
def __init__(self, output_filename, i, sigm... | 7,665 | Python | .py | 145 | 44.524138 | 146 | 0.643657 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,371 | micrograph_mem_subtract_main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/bin/micrograph_mem_subtract_main.py | import numpy as np
import cupy as cp
import mrcfile
import starfile
import matplotlib.pyplot as plt
import os
import argparse
import multiprocessing
from multiprocessing import Pool
import time
if __name__ == '__main__':
class MicrographMembraneSubtract:
def __init__(self, particles_selected_filename):
... | 9,136 | Python | .py | 139 | 52.705036 | 195 | 0.625642 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,372 | mem_subtract_main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/bin/mem_subtract_main.py | from cryosparc.dataset import Dataset
import numpy as np
import cupy as cp
from cupyx.scipy.ndimage import zoom
import glob
import json
import os
import mrcfile
import time
import multiprocessing
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--particle', type=str, default='./particles_select... | 4,967 | Python | .py | 97 | 46.793814 | 171 | 0.734656 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,373 | mem_analyze_main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/bin/mem_analyze_main.py | from cryosparc.dataset import Dataset
import numpy as np
import cupy as cp
from cupyx.scipy.ndimage import zoom
import mrcfile
from ..lib.bezierfit import Coarsefit, GA_Refine
import json
import argparse
import multiprocessing
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('-... | 3,220 | Python | .py | 54 | 53.481481 | 177 | 0.70981 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,374 | pickpoints.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/lib/pickpoints.py | import numpy as np
import cupy as cp
import mrcfile
from cupyx.scipy.ndimage import maximum_filter as maximum_filter_gpu
def max_filter(image):
image = cp.array(image)
max_filtered_image = maximum_filter_gpu(image, size=9, mode='constant')
threshold = cp.sum(max_filtered_image) / cp.sum(max_filtered_image ... | 1,293 | Python | .py | 29 | 38.034483 | 113 | 0.669348 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,375 | bezierfit.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/lib/bezierfit.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from deap import base, creator, tools, algorithms
from scipy.interpolate import griddata
from scipy.interpolate import interp1d
from scipy.special import comb
import mrcfile
from .pickpoints import generate_data_points
from cupyx.scipy.signal import c... | 16,424 | Python | .py | 315 | 45.155556 | 193 | 0.641265 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,376 | visualize_fitting_result.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/lib/visualize_fitting_result.py | import numpy as np
import matplotlib.pyplot as plt
import json
import mrcfile
from cryosparc.dataset import Dataset
from .bezierfit import generate_curve_within_boundaries
from scipy.ndimage import zoom
def getzoomfactor(template_csfile, particle_csfile):
template_dset = Dataset.load(template_csfile)
particle_... | 2,634 | Python | .py | 49 | 48.510204 | 145 | 0.72685 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,377 | subtraction.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/bezierfit/lib/subtraction.py | import numpy as np
import cupy as cp
import cupyx.scipy.ndimage
import matplotlib.pyplot as plt
from scipy.interpolate import griddata
import mrcfile
from cupyx.scipy.signal import convolve2d
from .bezierfit import points_along_normal, generate_curve_within_boundaries, cupy_cdist
import time
def bilinear_interpolatio... | 17,292 | Python | .py | 319 | 46.373041 | 189 | 0.610245 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,378 | radonfit_cli.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/cli/radonfit_cli.py | from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtWidgets import QMainWindow, QFileDialog, QMessageBox, QApplication, QDialog
from memxterminator.GUI.radon_gui import Ui_Form
from memxterminator.GUI.radonfit_membrane_analyzer_gui import Ui_MembraneAnalyzer
from memxterminator.GUI.radonfit_membrane_subtraction_gui... | 20,326 | Python | .py | 375 | 42.293333 | 194 | 0.623715 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,379 | main_cli.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/cli/main_cli.py | import sys
from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtWidgets import QMainWindow, QFileDialog, QMessageBox, QApplication, QDialog
from memxterminator.GUI.mainwindow_gui import Ui_MainWindow
from .radonfit_cli import RadonApp, MembraneAnalyzerApp, MembraneSubtractionApp, MicrographMembraneSubtraction_Radon_... | 4,283 | Python | .py | 59 | 64.79661 | 277 | 0.754928 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,380 | bezierfit_cli.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/cli/bezierfit_cli.py | from PyQt5 import QtCore, QtGui, QtWidgets
from PyQt5.QtWidgets import QMainWindow, QFileDialog, QMessageBox, QApplication, QDialog
from memxterminator.GUI.MembraneAnalyzer_Bezierfit import Ui_MembraneAnalyzer_Bezierfit
from memxterminator.GUI.particle_membrane_subtraction_bezierfit import Ui_ParticleMembraneSubtractio... | 13,981 | Python | .py | 266 | 41.101504 | 172 | 0.62893 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,381 | MicrographMembraneSubtraction_Bezierfit.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/MicrographMembraneSubtraction_Bezierfit.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'MicrographMembraneSubtraction_Bezierfit.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
... | 6,125 | Python | .py | 82 | 66.585366 | 181 | 0.760106 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,382 | particle_membrane_subtraction_bezierfit.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/particle_membrane_subtraction_bezierfit.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'particle_membrane_subtraction_bezierfit.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
... | 8,215 | Python | .py | 109 | 67.036697 | 176 | 0.756884 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,383 | MicrographMembraneSubtraction_Radonfit.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/MicrographMembraneSubtraction_Radonfit.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'MicrographMembraneSubtraction_Radonfit.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
... | 6,256 | Python | .py | 82 | 68.182927 | 178 | 0.770391 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,384 | mainwindow_gui.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/mainwindow_gui.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'mainwindow.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import QtCore, Q... | 6,192 | Python | .py | 92 | 59.097826 | 132 | 0.752667 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,385 | MembraneAnalyzer_Bezierfit.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/MembraneAnalyzer_Bezierfit.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'MembraneAnalyzer_Bezierfit.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 ... | 13,715 | Python | .py | 182 | 66.758242 | 141 | 0.741831 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,386 | radon_gui.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/radon_gui.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'radon_gui.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import QtCore, Qt... | 7,845 | Python | .py | 125 | 54.344 | 118 | 0.733696 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,387 | radonfit_membrane_subtraction_gui.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/radonfit_membrane_subtraction_gui.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'membrane_subtraction_gui.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 im... | 10,304 | Python | .py | 145 | 62.565517 | 139 | 0.73355 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,388 | radonfit_membrane_analyzer_gui.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/build/lib/memxterminator/GUI/radonfit_membrane_analyzer_gui.py | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'membrane_analyzer.ui'
#
# Created by: PyQt5 UI code generator 5.15.7
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import Qt... | 42,007 | Python | .py | 662 | 58.734139 | 109 | 0.69504 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,389 | test_bezier_mem_analyze.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/test/test_bezier_mem_analyze.py | from memxterminator.bezierfit.bin import mem_analyze_main
from cryosparc.dataset import Dataset
import numpy as np
particle_csfile = '/data2/J729/particles_selected.cs'
passthrough_csfile = '/data3/Zhen/VSV/membrane_subtraction/VSV/J419/J419_passthrough_particles_selected.cs'
particle_dset = Dataset.load(particle_cs... | 1,028 | Python | .py | 20 | 50.2 | 135 | 0.790837 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,390 | __init__.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/__init__.py | __author__ = 'Zhen Huang'
__email__ = 'zhen.victor.huang@gmail.com'
__version__ = '1.0.0'
| 90 | Python | .py | 3 | 29 | 41 | 0.609195 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,391 | membrane_analysis-main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/bin/membrane_analysis-main.py | import numpy as np
import cupy as cp
from ..lib._utils import *
from ..lib.radonanalyser import *
from ..lib.template_centerfitting import *
from ..lib.calculate_curve import *
from ..lib.generate_membrane_mask import *
from ..lib.mem_average import *
# from mem_subtract_old import *
from cupyx.scipy.ndimage import zoo... | 8,024 | Python | .py | 119 | 64.361345 | 364 | 0.740975 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,392 | micrograph_mem_subtraction.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/bin/micrograph_mem_subtraction.py | import numpy as np
import cupy as cp
import mrcfile
import starfile
import matplotlib.pyplot as plt
import os
import argparse
import multiprocessing
from multiprocessing import Pool
import time
if __name__ == '__main__':
class MicrographMembraneSubtract:
def __init__(self, particles_selected_filename):
... | 13,306 | Python | .py | 184 | 60.538043 | 197 | 0.627075 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,393 | membrane_subtract-main.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/bin/membrane_subtract-main.py | import numpy as np
import cupy as cp
import starfile
from ..lib._utils import *
from ..lib.mem_subtract import *
import argparse
import os
from multiprocessing import Pool
import multiprocessing
import time
if __name__ == '__main__':
class MembraneSubtract:
def __init__(self, particles_selected_filename, ... | 12,153 | Python | .py | 170 | 59.323529 | 274 | 0.638975 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,394 | calculate_curve.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/lib/calculate_curve.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from ._utils import *
from .template_centerfitting import *
from .radonanalyser import *
from .circle_mask_generator import *
from cupyx.scipy.ndimage import zoom
from cupyx.scipy.signal import correlate2d
class Curve:
def __init__(self, output_f... | 7,054 | Python | .py | 149 | 38.436242 | 132 | 0.605534 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,395 | circle_mask_generator.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/lib/circle_mask_generator.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from ._utils import *
class circle_mask:
def __init__(self, image_array, x0, y0, radius, sigma):
self.image = image_array
self.image_size = self.image.shape[0]
self.x0 = x0
self.y0 = y0
self.radius = radius... | 2,266 | Python | .py | 50 | 39.06 | 118 | 0.603705 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,396 | mem_subtract.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/lib/mem_subtract.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from cupyx.scipy.ndimage import rotate, shift, zoom
from cupyx.scipy.signal import correlate2d, convolve
from ._utils import *
from .mem_average import *
from .circle_mask_generator import *
import time
class Get2Raw:
def __init__(self, mem_anal... | 12,210 | Python | .py | 213 | 48.41784 | 246 | 0.611666 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,397 | get_particles_info.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/lib/get_particles_info.py | import pandas as pd
import numpy as np
import cupy as cp
import starfile
import mrcfile
from ._utils import *
from cupyx.scipy.ndimage import zoom
# from mem_subtract_old import *
df_membrane_analysis_star = starfile.read('mem_analysis.star')
average_raw_series = df_membrane_analysis_star['rln2DAverageimageName'].appl... | 3,032 | Python | .py | 58 | 50.793103 | 247 | 0.685185 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,398 | generate_gaussian_template.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/lib/generate_gaussian_template.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from scipy.stats import norm
from ._utils import *
def gaussian_pdf(x, mean, std):
coefficient = 1.0 / (std * cp.sqrt(2 * cp.pi))
exponential = cp.exp(- (x - mean) ** 2 / (2 * std ** 2))
return coefficient * exponential
def gaussian2(x, ... | 2,563 | Python | .py | 74 | 26.635135 | 79 | 0.537253 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |
2,285,399 | radonanalyser.py | JackZhang-Lab_Cryo-MEM/Mem_subtraction/src/memxterminator/radonfit/lib/radonanalyser.py | import numpy as np
import cupy as cp
import matplotlib.pyplot as plt
from skimage.transform import radon
from cupyx.scipy.ndimage import maximum_filter
# from cupyx.scipy.signal import convolve
from ._utils import *
from .circle_mask_generator import *
class RadonAnalyzer:
def __init__(self, output_filename, i, im... | 6,764 | Python | .py | 134 | 41.186567 | 129 | 0.582687 | JackZhang-Lab/Cryo-MEM | 8 | 0 | 1 | GPL-3.0 | 9/5/2024, 10:47:52 PM (Europe/Amsterdam) |