sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cae19fbc4e2ed662aa6280ee991be80ba563a01ff60df249a13e3576249c57fb | Python | 15,565 | 425 | from __future__ import annotations
from dataclasses import InitVar, dataclass, field
import numpy as np
from lifelines import KaplanMeierFitter
from SurvivalEVAL.nonparametric_estimator.util import (
infer_survival_probabilities,
)
def create_support_intervals(tau: np.ndarray, exact_times: np.ndarray) -> np.nd... |
b27bc743656df53bf0de890ea34c88a9a844de91f08bd14d8882d2910306b13e | Python | 15,566 | 342 | import h5py
import numpy as np
import torch
import random # Add this import
from torch.utils.data import DataLoader, TensorDataset
import torch.nn as nn
import torch.optim as optim
import h5py as h5
import matplotlib
# matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
# from torchsummary import summary
from auto... |
f59a0e596b9c15fade7122bc336d0260ee1a26f2979c3a72d5d7711fc63ea118 | Python | 15,566 | 378 | # multio - a multi input/output multi file multi channel multi format module
import os
from multiprocessing import Process
try:
import tkFileDialog
except:
pass
import numpy as np
import pyclamp.gui.lbwgui as lbw
from pyclamp.dsp.abf import ABF
from pyclamp.dsp.tdf import TDF
from pyclamp.dsp.ses import SES
from p... |
75e7f9f62897ba40026bba7223160e8d4f2d800bc7a73fb965c98d1625c16f85 | Python | 15,569 | 400 | # -*- coding: utf-8 -*-
"""
Created on Sat Dec 10 10:20:49 2022
@author: Dustin Garner
"""
import os
import collections
import itertools
from enum import Enum
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import bokeh
import holoviews as hv
import hvplot.pandas
import b... |
83e6b47cde532351a13c5ab99014d8f4ecbe1a46a95171eb3dbc2e20fa155321 | Python | 15,574 | 283 | import random
import copy
import numpy as np
import string
import matplotlib.pyplot as plt
import bz2
import _pickle as cPickle
import os
random.seed(1)
def wordlist_to_orth(wordlist):
# takes in list of K words, outputs a 104 x K "spelling" array
alphabet = string.ascii_lowercase
word... |
723c601896996b5c7c8a97a66e5589c894741c102bd1359a295eeaa1c64a79b6 | Python | 15,577 | 475 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
b31d5672f5e0c61b3c7f9ba51b80edc1ceb4e6d38e61ec306acfd4ea4af4c94a | Python | 15,585 | 418 | # -*- coding: utf-8 -*-
import tensorflow as tf
from pinn.layers import (
CellListNL,
CutoffFunc,
PolynomialBasis,
GaussianBasis,
AtomicOnehot,
ANNOutput,
)
class FFLayer(tf.keras.layers.Layer):
R"""`FFLayer` is a shortcut to create a multi-layer perceptron (MLP) or a
feed-forward net... |
e0088751d0b1902892634f9f48e6e3c384a30b35c467230b063e4e76ff9c6bf2 | Python | 15,585 | 378 | """The built-in functions to validate known attributes.
Template for the functions:
All attribute validation functions should follow this signature:
``attribute_checker_template(hed_schema, tag_entry, attribute_name)``
Parameters:
- ``hed_schema (HedSchema)``: The schema to use for validation.
- ``tag_entry (H... |
031779597c5206b8c088e35baef01d7dea933c499b92a6cdf07648290f86983b | Python | 15,590 | 397 | # Copyright (c) OpenBII
# Copyright (c) Lynxi Technologies Co., Ltd. All rights reserved.
# Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os,time
import warnings
import mmcv
import numpy as np
import torch
from mmcv import DictAction
from mmcv.parallel import MMDataParallel, MMDistributedDataPa... |
d2d5b32266004382ac5b29c9f8c589f5d26501d0a0e3f5f71fe42aaa64b18a5d | Python | 15,591 | 325 | #!/usr/bin/env python
# Copyright (c) 2018-2020 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
Follow leading vehicle scenario:
The scenario realizes a common driving behavior, in which the
user-controlled ego vehicle follo... |
efd0c79eb2a2bd31160af3c774997586dfb958512d14c6015923e0add87ffdaa | Python | 15,591 | 449 | import os
import collections
from keras_applications import imagenet_utils
from classification_models import get_submodules_from_kwargs
from ._common_blocks import GroupConv2D, ChannelSE
from ..weights import load_model_weights
backend = None
layers = None
models = None
keras_utils = None
ModelParams = collections.... |
b3e88349eee6805e67d7c177466609ee157e070f232aba555f2dbd491577c87e | Python | 15,597 | 462 | '''
### 코드 로직
1. .npz 파일에서 geometry, gradient 값 read
1. iter = 1 이라면 geometry 생성
2. geometry, gradient 값을 array 저장
3. geometry 값에 gradient * n 만큼 +
4. f0, djdu = opt()
5. f0 값 저장
1. fom.txt 파일 읽어와서 맨 마지막 줄에 값 저장
6. 업데이트 된 geometry, 업데이트 된 구조의 adjoint gradient를 .npz로 저장
→ 모델에 넣고 값 출력해서 1번부터 반복
'''
"""
0... |
4f6954fb977c44da6e4630343eae23c284c0798a28ec95c21da818dfb3119aec | Python | 15,599 | 357 | """Save / load / autosave behaviours for the viewer, packaged as a
mixin so the persistence surface lives in its own file.
The consuming class declares these attributes in ``__init__`` before
any mixin method runs:
* ``annotation``, ``brain``, ``current_slice``, ``n_slices``
* ``slice_states``, ``_history``, `... |
1d83b74d71e6e642c64ac21d7fdcad54b602cd4a5d2d032de0977634deddbb34 | Python | 15,601 | 400 | """distutils.unixccompiler
Contains the UnixCCompiler class, a subclass of CCompiler that handles
the "typical" Unix-style command-line C compiler:
* macros defined with -Dname[=value]
* macros undefined with -Uname
* include search directories specified with -Idir
* libraries specified with -lllib
* library... |
9baaa30500c9fb734c779d728a1c8a73eea334c455fe47c344627abeab1bf262 | Python | 15,610 | 360 | """Tests for query_util module, particularly SearchResult class.
SearchResult represents a query match result consisting of:
- group: The containing HedGroup where matches were found
- children: The specific matched elements (tags/groups) within that group
(NOT all children - only the ones that satisfied ... |
a53dfcc9f507af466097228f058578f4016d8b89636f0a8ea57bfd09d3f42d8d | Python | 15,615 | 692 | from __future__ import annotations
from pathlib import Path
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from mpl_toolkits.axes_grid1 import make_axes_locatable
# ======================================================================
# INTERNAL STYLE HEL... |
fb00cbfcc32af6f2ee0db9c92faf81291f198728f061c234937eb06c212c0fca | Python | 15,625 | 390 | import numpy as np
from ..constants import hartree2ev
from ..utils.math import kgrid_with_tr, make_kkmap, kGsphere
from ..utils.misc import set_range, mytqdm, VKBGData, atom_number2name
from ..utils.mpi import is_master
from ..io.aodata import AOData, calc_FT_kg_orb_spcs
from ..io.bgwio import bgw_vsc, bgw_vkb
from ..... |
e6c743ceb9276ac103460177a3d10849d98891e050ae81dcdf5078e45edcc079 | Python | 15,630 | 317 | import numpy as np
import tensorflow as tf
import tensorflow.contrib.slim as slim
from RNNs import recurrent_networks
import sys, os
####################################################################################
#Used to initialize weights for policy and value output layers
def normalized_columns_initializer(std... |
3d523c203e144a3ab3273e97323eb4237d37661630550b9561b63ea3c978c91f | Python | 15,632 | 503 | #!/usr/bin/env python3
"""
MPRAGEise_yan.py
Compatibility version of MPRAGEise for environments where only AFNI's
`3dUnifize` is available. This variant adds safer defaults for United Imaging
5T eT1W/UNI data by:
1. Optionally applying the vendor-recommended UNI rescaling internally
(equivalent to: fslmaths UNI -a... |
35e40b6438c243fffa8d8b5369023ecf834098628071b9d5a22359c446a5e46f | Python | 15,638 | 465 | """Tests for HDL generator abstraction layer.
This module tests the unified interface for VHDL and Verilog code generation,
ensuring that both implementations work correctly and produce valid HDL code.
"""
import pytest
from elasticai.creator.hdl_generator import HDLLanguage, create_generator
from elasticai.creator.... |
6251176d68420c1e3d6bbebb84b9675f787b16b2debbbef5a7ebce96645a5782 | Python | 15,644 | 445 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
6c53a9346d172fbd73e7d5208e89a4b8302aa07a98b783b2b17fde84e1e80fcf | Python | 15,653 | 540 | #@File (label = "Image to analyze") filename
#@float (label = "Minimum branch length") minBranchLength
#@float (label = "Maximum branch width") maxBranchWidth
#@boolean (label = "Define a region of interest") setRoi
#@boolean (label = "Manually update soma mask") updateSomaMask
#@boolean (label = "Use ... |
8d908e84764239c8ebec20dac631ec1ebc3181b31f83b7b4b7f3cced90f8638f | Python | 15,654 | 446 | import pickle
import numpy as np
import argparse
import math
def area2d_voc(b):
"""Compute the areas for a set of 2D boxes"""
return (b[:, 2] - b[:, 0]) * (b[:, 3] - b[:, 1])
def overlap2d_voc(b1, b2):
"""Compute the overlaps between a set of boxes b1 and one box b2"""
xmin = np.maximum(b1[:, 0], b2[:... |
f9caa43b0d312bb4f9abd92c82ed3219e2899657aa3e5c51b6e2e8857f4bc0b9 | Python | 15,656 | 357 | import pandas as pd
import numpy as np
from scipy.stats import kstwobign, pearsonr
from numpy import random
import statsmodels.api as sm
import matplotlib
import matplotlib.pyplot as plt
import pingouin as pg
from scipy.stats import f
import sys
from IPython.display import display, HTML
#"""""""""""""""""""""""""""""... |
de401077db109cab89faf63d152095c8b5a2004a1a10e9e7d28598f6531d7075 | Python | 15,659 | 441 | import math
import numpy as np
import torch
atom_name_vocab = {
"C": 0, "CA": 1, "CB": 2, "CD": 3, "CD1": 4, "CD2": 5, "CE": 6, "CE1": 7, "CE2": 8,
"CE3": 9, "CG": 10, "CG1": 11, "CG2": 12, "CH2": 13, "CZ": 14, "CZ2": 15, "CZ3": 16,
"N": 17, "ND1": 18, "ND2": 19, "NE": 20, "NE1": 21, "NE2": 22, "NH1": 23... |
17beae7901e7cd00f6da669ca5ab85f999e34485eea2f05912a383f115108b00 | Python | 15,666 | 330 | """Qt side of the plugin system: event hub, panel context, parameter forms and the dock workspace.
Panels are ComponentSpecs of category "ui_panel" (plugin_api.PluginRegistrar.panel). Their
factory(context) runs on the GUI thread and returns a QWidget. Panels receive events through
context.subscribe(); delivery is alw... |
49fdba2db1938ed6876a0411ea54e300e20f573184230af5c031ac9b63727b85 | Python | 15,670 | 408 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2021 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : morphology_pdist.py
# Author : Yufeng Liu
# Date : 2021-07-22
# Description :
#
#==============... |
b8fef608d400931050e0f6f61d32aad35d54957a89c93e5b71beb0080d6619eb | Python | 15,671 | 397 | """
Script for reconstructing particles RELION compatible from full reconstructed tomograms
Modification for re-reconstructing the synaptic particles
Input: - STAR file with next columns:
'_rlnMicrographName': tomogram that will be used for reconstruction
'_rlnImageName': ... |
2284a18c203040a263fcf452081e32e8d5cf3665f23ef1df87d8fe295fefa9eb | Python | 15,674 | 398 | """A HED string with its schema and definitions."""
from __future__ import annotations
import copy
from hed.models.hed_group import HedGroup
from hed.models.hed_tag import HedTag
from hed.models.model_constants import DefTagNames, TopTagReturnType
class HedString(HedGroup):
"""A HED string with its schema and ... |
2758ac620ec18f4c819636df3f69b4de415972c57faeac50a41f7359863fa2ed | Python | 15,674 | 446 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
53f91986b56fefb9f64388840a5d002dd88423ea56e4156469e121c884322da0 | Python | 15,685 | 442 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
98c57494e1b9a438cf267204e69c2d89a321a3128c238b7081d9b35aeeac0ea7 | Python | 15,691 | 323 | import os, argparse
import random
import numpy as np
import torch
from tqdm import tqdm
import wandb
from dataset import Edinb_SE_TestDataset #, collate_batch_coherence_net
from model.coherence_net.model import CoherenceNet
from model.coherence_net.loss import CoherenceNetLoss
from utils.checkpoint_saver import Checkp... |
966b2718d889f02e03fcf7fd3db334aa06d9bc3f64981f65a590505196b747f6 | Python | 15,699 | 487 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
import logging
import platform
import sys
import sysconfig
from importlib.machinery import EXTENSION_SUFFIXES
from typing import (
Dict... |
da41bf23ad90ee6ccf7de3255b72eb36992c72d8805dabdfafe8be3e98691029 | Python | 15,700 | 491 | #!/usr/bin/env python
# coding: utf-8
# # LIT-PCBA
# this dataset is a proposed "more difficult" test than DUD-E. I used a 75/25 (sklearn default) stratified split. The dataset is heavily imbalanced, like DUD-E.
#
# - UPDATE: I'm using the AVE split now
# In[1]:
import pickle
from sklearn.metrics import roc_auc_s... |
216ba9f0ff275b293f8efbeb9f0fb3898b099a373f1b6ae601e46e9a9f3dc630 | Python | 15,702 | 335 | def update_param(name, param):
if name == 'distribution':
param['values'].remove('custom')
return param
return None # param untouched
extensions = dict(
validate_params="""
# if (!is.null(beta_constraints)) {
# if (!inherits(beta_constraints, 'data.frame') && !is.H2OFrame(beta_constra... |
98776b130d48eb9b550f2a21cfe7a9ebb0841ed0f806ab828a98da2ed247809b | Python | 15,702 | 378 | """Unit tests for the tissue_masking tool.
Covers:
- compute_tissue_mask (synthetic blob, hole preservation, degenerate)
- process_group (shared mask across channels)
- background spec drop (the user-identified property)
- discover_channels (folder discovery + grouping)
- round-trip writes ... |
6cce2bfff3b5e59ab21d31213fa360cff5163a051cad3cf1ef8583ad6dce7b78 | Python | 15,703 | 323 | import numpy as np
import pandas as pd
import math
import os
import pickle as pkl
import re
import traceback
from copy import deepcopy
from src.utils import parse_config, logger, contain_substr
def preprocess_appear(appear_csv):
appear_df = pd.read_csv(appear_csv, index_col='frame')
for c in appear_df.columns... |
2954a6473cffbea582bb21138cc24197512a41cca3fb0d7aaa782f1171d54ede | Python | 15,705 | 318 | import os
import unittest
from hed import schema
# from hed import
from hed.errors import ErrorContext, ErrorSeverity
from hed.models import HedString, Sidecar, SpreadsheetInput, TabularInput
from hed.validator import HedValidator
# todo: redo all this so we
class Test(unittest.TestCase):
@classmethod
def s... |
a0697838d09f3c6e55b0a59fa72bad2043a096e42552744461ef4c89dc6eedb6 | Python | 15,705 | 306 | import numpy as np
import os
from shutil import copy,rmtree
import pickle
from webbrowser import open_new
import tkinter as tk
from tkinter import filedialog,messagebox
from PIL import Image,ImageTk
import run,excel,settings # pupillometry code
class App(tk.Tk): # main window
def __init__(self): # set ... |
cdc1e2936d81561964643655c894b2424634864b85b331f683d3bcd6509d7faf | Python | 15,705 | 493 | import sys
import os
import warnings
CWDIR = os.getcwd()
GENDIR = CWDIR + '/../gen/'
sys.path.append(GENDIR)
import numpy as np
import scipy.stats as stats
from pyclamp.dsp.wffunc import *
from pyclamp.dsp.wfprot import *
from pyclamp.dsp.fpfunc import *
from pyclamp.dsp.fpanal import *
if SHOWFITS: import matplotlib.... |
23231c34b2f04df63c4e25d284cc1cf46d31aae018f7e4dbdb0aa94bc22185bf | Python | 15,710 | 480 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
b5ad2d693eea2bcbbf7eb152cb878a3b625b4a24c36a56615c5f5037cf573efe | Python | 15,710 | 397 | """
m6A_calling.py
Author: Anupama Jha <anupamaj@uw.edu>
Training and data generator code adapted from bpnet-lite (https://github.com/jmschrei/bpnet-lite)
This module contains a reference implementation of a CNN model for m6A calling.
GS hackathon participants: you can start with this code to develop your own
models f... |
2861566894015e39bab4443448bab64df97e102b343c83e807b2e17b6799f3b7 | Python | 15,711 | 345 | #!/usr/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import numpy as np
import pandas as pd
from logP_analysis import mae, rmse, barplot_with_CI_errorbars
from log... |
5567e05fd6d8cd2f7ad8ead23aac5e5446e7ab0252ecb6ebf02f9c8858a4251e | Python | 15,713 | 456 | """Widget with general information about the dataset."""
from datetime import timedelta
from functools import partial
from logging import getLogger
from os.path import basename, dirname, splitext
from PyQt5.QtCore import QSettings, Qt
from PyQt5.QtGui import QIcon, QKeySequence
from PyQt5.QtWidgets import (QAbstractIt... |
fec7615d3c90c9bb2665be400ad3649566504a87accbcab5bbb81996177a18a3 | Python | 15,717 | 384 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
2167956312ad20d8dd98e654e7c89df567748cb2437251e5d3bead72e55f4d3b | Python | 15,737 | 416 | #!/usr/bin/env python
import gzip
import io
import os
from collections import defaultdict
import requests
from pysam import AlignmentFile, idxstats, index
from irescue.misc import getlen, run_shell_cmd, testGz, unGzip, writerr
def checkIndex(bamFile, verbose):
"""Check if BAM file is indexed. If not, attempt t... |
3d22fb9e11bd59593f0091a14ddfdcd622e98a6bf7c3134f910949b0926f9fea | Python | 15,746 | 444 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2021 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : morphology.py
# Author : Yufeng Liu
# Date : 2021-07-16
# Description : The script is responsibl... |
4b8ac9112dc9e50fa5a349131833a0b955df5618fddcf446bbe9f2f81a4ab933 | Python | 15,749 | 443 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
5ef06a5364b4906f637b74f8b1deda1301014362962e18f07800fcbf1797e5d0 | Python | 15,749 | 418 | from __future__ import annotations
import warnings
from dataclasses import InitVar, dataclass, field
from typing import Literal
import numpy as np
from scipy.integrate import trapezoid
from SurvivalEVAL.nonparametric_estimator.util import (
_compute_event_counts,
_predict_step,
infer_survival_probabiliti... |
89bd8784ed6aae355c8dc604cecfa46dffda2dfd420228b8fa32907a51fbddd6 | Python | 15,751 | 403 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
48559c8c54c2d5e2acd41db740fb9c1bcf6fbd4a273400d7f470a3485b901f25 | Python | 15,759 | 382 | """Pipeline-side analysis figures for the registration report (matplotlib, Agg, colorblind-safe).
Every generator is best-effort and NEVER raises: on any error it returns [] / writes nothing, so a
plotting failure can never fail a registration run. The report embeds whatever PNGs land."""
import os
def _agg()... |
943d0998b4a38de6321323c149a743eb740635584bd1e152db4dfad3c48b0550 | Python | 15,759 | 442 | import numpy as np
import pandas as pd
import rdkit
import rdkit.Chem as Chem
import networkx as nx
import torch
import os
from tqdm import tqdm
from torch_geometric.loader import DataLoader
from build_vocab import WordVocab
from utils import *
from dataset import DTADataset
from sklearn.model_selection import KFold
... |
0aa554f0fb4310d280f49a6c101e3b8110f9bea00ddc18ede61606bea67c2309 | Python | 15,762 | 410 | """Axis alignment utilities for brain volume orientation.
Provides functions for detecting the longitudinal fissure,
fitting rotation/flip transforms via SVD, and aligning brain
volumes to the Allen CCF orientation.
"""
import math
import os
import numpy as np
import cv2
from scipy.spatial.transform import... |
7ea6678a1868352ab2356d51d918c57f9fe79858be4bb4ddd233a2fc7d8242f6 | Python | 15,762 | 400 | '''
Edited utils file with helper functions for diffdock docking.
'''
import os
import torch
from Bio.PDB import PDBParser
from esm import FastaBatchedDataset, pretrained
from rdkit import Chem # Extra import
from rdkit.Geometry import Point3D # Extra import
from rdkit.Chem import AddHs, MolFromSmiles
from torch_geome... |
b6bbdfe9fdca70bb65993674b5e47a11365440ae6aabd66c6f70aebf57614adf | Python | 15,764 | 392 | import numpy as np
import torch
from torch import nn
from typing import Any, Optional, Union
from lightning.pytorch import LightningModule
from torchinfo import summary
from .components import \
activation_from_str, \
GUNet, \
get_unet_input_size, \
TemporalDenoiser
from .denoising_model import Deno... |
b9b0ef204f96d4311150d1e583a6fb146022499148c5532417057dbaddb3a991 | Python | 15,764 | 495 | import torch
from torch import nn
import numpy as np
from collections import OrderedDict
import math
import ConditionalNeuralField.cnf.initialization as init
########################
# define all activation functions that are not in pytorch library.
########################
class Swish(nn.Module):
def __init__(self... |
3fe04ace8b1dd28d8d69051f2205d839ec355e6305301a3ebb4c27b825beac69 | Python | 15,766 | 371 | """
Generates a ListTomoParticle object from a input STAR file
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import numpy as np
import scipy as sp
import ... |
5f10662a6917710d9999df1eb12945413843a154f9fc5293b8497b66de2b3fcf | Python | 15,770 | 381 | #!/usr/bin/env python
# Copyright (c) 2019 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides the key configuration parameters for a scenario based on OpenSCENARIO
"""
import logging
import os
import xml.et... |
d7f708cc273bb84de8e5c25ae8ae0aad986bf50dd05a5db73e0e5fa04d9e04dd | Python | 15,772 | 364 | """
DeepLabCut2.0 Toolbox (deeplabcut.org)
copyright A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
Loader structure adapted from DeeperCut by Eldar Insafutdi... |
368fe643c96fc9b44a2dd3241c79dd508ff36a812ea6148a1f910913b62b35fe | Python | 15,774 | 436 | #%%
import tensorly as tl
import numpy as np
import warnings
from scipy.optimize import brentq
from collections.abc import Iterable
from tensorly.tenalg import svd_interface, multi_mode_dot
from tensorly import unfold
from tensorly.tenalg.proximal import hals_nnls
from tensorly.tucker_tensor import tucker_to_tensor, Tu... |
8691d909ffd17bca3e169e949a24e9da04c1ffe7404f3d5b241723d81279638b | Python | 15,779 | 418 | '''
Description:
Utility functions for extrapolating multiple timepoints.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import numpy as np
import scanpy
import pandas as pd
import natsort
import torch
import torch.distributions as dist
from optim.evaluation import _ot
# --------------------------------
de... |
e05f57c0647731083126fe4df071911da5e13af090f19ea0ceb1855418f23e73 | Python | 15,780 | 397 | import math, torch
from torch.nn.parameter import Parameter
import torch.nn.functional as F
from torch.nn.modules.module import Module
import torch.nn as nn
from opt import *
opt = OptInit().initialize()
device = opt.device
class general_GCN_layer(Module):
def __init__(self):
super(general_GCN... |
f90d666db2b98ce57ffa8d51472fc1e3f08691e3dc2c7a7c54532851da0265bb | Python | 15,781 | 422 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
9baf81cc953b91a8d4741b307492144907de7a61ccd3d164d901a1a0ad2f4194 | Python | 15,783 | 348 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""md_to_pdf.py —— 把 game/docs/TECH-NOTE.md 渲染为学术风格 PDF（stdlib + reportlab）。
用法：python game/tools/md_to_pdf.py game/docs/TECH-NOTE.md game/docs/TECH-NOTE.pdf
支持的 Markdown 子集（按该文件实际用到的语法）：
#/##/### 标题、段落、管道表格（含对齐行）、``` 代码围栏、**粗体**、*斜体*、
~~删除线~~、行内 `code`、- 无序列表、1. 有序列... |
c5a43a290004510fafc79d414a6cd0746059c79ef439d6d5a2b4700c814fd760 | Python | 15,786 | 352 | # -*- coding: utf-8 -*-
"""
Created on Fri Dec 18 20:13:02 2020
@author: asohr
"""
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Pac... |
5965111313b6e26f5096082efe5d1b894261bec00bbc4762c898bd3d8bc48777 | Python | 15,787 | 415 | from __future__ import print_function
import sys
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import torch.backends.cudnn as cudnn
import random
import os
import sys
import argparse
import numpy as np
from InceptionResNetV2 import *
from sklearn.mixture import GaussianM... |
082f3a4623c2f1a0589b90cf473178c42b0815c68bc67b6201d30d1a91467176 | Python | 15,788 | 320 | import os
import re
from typing import Any, Callable, Dict, Tuple, Union
import scipy.io as scio
from torcheeg.io import EEGSignalIO, MetaInfoIO
from ...constants.emotion_recognition.seed_iv import (
SEED_IV_ADJACENCY_MATRIX, SEED_IV_CHANNEL_LOCATION_DICT)
from ..base_dataset import BaseDataset
class SEEDIVDat... |
0bdc2fbc38d2a507a252aa3280bb1631c0c560ca752b83d376c798e8ced0e3e4 | Python | 15,791 | 315 | r"""Functional interface"""
import warnings
import math
import torch
from torch import _VF
from torch._jit_internal import Optional, Tuple
from torch.overrides import has_torch_function, handle_torch_function
from torch.nn.functional import pad, linear, softmax, dropout
Tensor = torch.Tensor
def mult... |
1e3a1cc6c777eb3827322ebf9c9505743acab37270be1c6c8a4e95e7f302b121 | Python | 15,801 | 371 | """
Generates a ListTomoParticle object from a input STAR file
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import numpy as np
import scipy as sp
import ... |
73f764644b309bd3d1ee796694f41ea73a37aeb4ed37c4a6c0e9fa20ae4b928b | Python | 15,801 | 379 | #!/usr/bin/python
# -*- coding:utf-8 -*-
# -*-mode:python ; tab-width:4 -*- ex:set tabstop=4 shiftwidth=4 expandtab: -*-
#
from ctypes import *
import sys
import os
if sys.platform == 'linux2' or sys.platform == 'linux':
if os.path.exists('/usr/lib/libdximageproc.so') :
filepath = '/usr/lib/li... |
15785146d3b1338eb842cf76723937a02e1e43ae8105f2f40bada98568333359 | Python | 15,802 | 414 |
import os
import csv
import numpy as np
import scipy.io as sio
import torch.nn.functional as F
from sklearn.linear_model import RidgeClassifier
from sklearn.feature_selection import RFE
from nilearn import connectome
from scipy.spatial import distance
import SimpleITK as sitk
# Reading and computing the i... |
be801d3efe7bc0a8d8052741bb5b97252e23c2ddfc42350c79132a61b71c19e3 | Python | 15,803 | 338 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
d69884636f12d9519ef9cfd511c27fa3089aea7fdf6db18343c8f12ab1b526e0 | Python | 15,803 | 338 | import xlrd # version 1.2.0
import numpy as np
import networkx as nx
import numpy.random as nr
import matplotlib.pyplot as plt
import seaborn
import matplotlib.patches as ptc
import json
import os
import struct
import math
from eworm.network.detailed_circuit import DetailedCircuit
from eworm.network.point_circuit impo... |
2a57e2946e94e1a5beb99b48faf63c21cdba31548f1646ed8a28126597e0156d | Python | 15,804 | 355 | """Shared mixin for GUI tabs that launch work in an external terminal.
Usage
-----
Inherit from ``_TerminalJobMixin`` alongside ``QWidget`` (or any other Qt
widget base). The hosting class **must** provide:
* ``_toggle_ui(enabled: bool)`` - disable/re-enable all interactive controls
while a job is running.... |
ff0abcffe674d877a4ad2994e76a3ef2426f4891f9a1b5c108b2abe5f45aa7e2 | Python | 15,806 | 413 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 13 10:52:47 2023
@author: emma
"""
import ants
import numpy as np
import SimpleITK as sitk
import os
import random
import pandas as pd
import pickle
random.seed(6)
def load_image(fpath):
# load image in both itk image type and ants image type
... |
56c800764bf81e47db07ed6ca17e8d736d56e63bb5c9fb8ac4517fccbe3b9a39 | Python | 15,814 | 353 | """Baseclass for MEDIAWIKI/XML/JSON/TSV writers"""
from hed.errors.exceptions import HedExceptions, HedFileError
from hed.schema.hed_schema_constants import HedKey, HedSectionKey
from hed.schema.schema_io import df_constants, df_util
class Schema2Base:
"""Template base class for all HED schema serializers (media... |
36239a9b49158c16a08e8bd1098de35373387bf4c3d0eb8e4a44fa14bb0628c6 | Python | 15,816 | 453 | from pathlib import Path
from typing import Annotated, List, Optional
import pytest
from cog import BaseModel, Opaque
from cog import _adt as adt
from cog._inspector import _create_predictor_info, create_predictor
def test_inspector_uses_run_method_for_classes(
tmp_path: Path, monkeypatch: pytest.MonkeyPatch
) ... |
7382b6dcceca847054b7f93a40baa6b5394028209503edef7bfafec289501fb6 | Python | 15,822 | 446 | import gzip
import io
import os
import tempfile
import time
from pathlib import Path
from unittest.mock import Mock, patch
import biotite.database.rcsb as rcsb
import pytest
import requests
from biotite.structure.io import load_structure
import molecularnodes as mn
from molecularnodes.download import (
CACHE_DIR,
... |
97c5c55661e8cf2fc3edfc1e19e7dbbecf495c537d1966f2414bb2f211c3d424 | Python | 15,824 | 247 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
import pandas as pd
import numpy as np
import time
import cv2
from control._def import *
import control.utils as utils
def multipoint_... |
a84c11b8ddb1917e561e325bbd0fcd20284f4acb37313e399e8393b994b18a14 | Python | 15,826 | 248 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
import pandas as pd
import numpy as np
import time
import cv2
from control._def import *
import control.utils as utils
def multipoint_... |
6adf98c0161fc4ffca3d2525ed9855a3fac473f345f8381e1fdc68db6bf1bb6e | Python | 15,829 | 394 | # -*- coding: utf-8 -*-
# File : batchnorm.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import collections
import contextlib
import... |
2d440f2f4c015d5a606bc8adcec0e1a0d4fb7f04d96f2cc97f601875db5aa06a | Python | 15,834 | 362 | """
Script for extracting an analyzing a SynGraphMCF from an oriented pairs of membranes (like a synapse)
Input: - A STAR file with a list of (sub-)tomograms to process:
+ Density map tomogram
+ Segmentation tomogram
- Graph input parameters
Output: - A STAR file with th... |
09d52148804bfc57e5427e7ac26c281b9f64d7c140c139114cd08b92042116ea | Python | 15,843 | 291 | ##### MODEL AND DATA LOADING
import time
start = time.time()
import torch
import torch.utils.data
import torchvision.transforms as transforms
import torchvision.datasets as datasets
from torch.autograd import Variable
import numpy as np
import matplotlib.pyplot as plt
import cv2
from PIL import Image
import re
impor... |
1d43d01badf45ac9d7aaef161bc741efa9b5b5e88cb7bf14fbaf0f29060d45c8 | Python | 15,846 | 496 | from collections import namedtuple
import numpy as np
import string
import random
GROUND_NAME = 'grey'
BLOCK_WIDTH = 2
BLOCK_HEIGHT = BLOCK_WIDTH
GROUND_Y = 0.
SUCTION_HEIGHT = 1.
GRASP = -np.array([0, BLOCK_HEIGHT + SUCTION_HEIGHT/2]) # TODO: side grasps
CARRY_Y = 2*BLOCK_WIDTH+SUCTION_HEIGHT
APPROACH = -np.array([... |
7a21d825fb5e27ccc625a898345271c68c2601740157ad9ab26da3177a74ef62 | Python | 15,846 | 307 | import torch
import torch.nn as nn
from torch.utils.data import Dataset
from typing import Callable, Optional, Union, List
import numpy as np
from tqdm import tqdm
from mnp.utils.scripting import (train_model, choose_criterion_from_model,
effective_epochs_to_epochs, get_subset_metadatas... |
a5d65847d7789cf6714b578da73900930cacdecff4d57b70cfe4a72847da8703 | Python | 15,854 | 391 | """Symmetric-annotation variant + per-hemisphere counting.
Covers the deterministic parts without the (already-installed) Allen data:
* build_symmetric_annotation: ML-axis detection + provable mirror symmetry
* registry / config-menu wiring of the allen_ccf_symmetric variant
* the both-files install gate th... |
149e78f5059ad7e54693ee42e6b1ff71d500bf684c466eff9230cd5fb2600708 | Python | 15,855 | 381 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
391bba8fc48f92600e3727de6f087ea6fab10ab8a6e63c46ff0baafb32829e40 | Python | 15,855 | 392 | """Acquisition Control Class."""
import copy
import functools
import logging
import logging.config
import time
from collections.abc import Callable
from datetime import datetime
from pathlib import Path
from typing import cast
import matplotlib as mpl
import numpy as np
from pypulseq import Opts
from console.interfa... |
8edc45af315461e6f551514f2f19e8c23decdacb9e66966abbff8bd168f4818e | Python | 15,855 | 517 | import os
import pandas as pd
from tqdm import tqdm
import matplotlib as mpl
import matplotlib.pyplot as plt
import seaborn as sns
from language import load_input_language
from measures import production_similarity, generalization_score
from learning_experiment import scenes
from tqdm import tqdm
from stats import c... |
99231a7b9b816dab2e0bcb78a3ba2a79ebbcdb6ad6f8449230161a3168768216 | Python | 15,859 | 359 | #!/usr/bin/env python
# -*- encoding: utf-8 -*-
from collections import OrderedDict as odict
from copy import deepcopy
from functools import partial
import bindings as bi
from custom import get_customizations_for, reformat_block
str_type = str
get_customizations_for = partial(get_customizations_for, 'R')
def get_cu... |
c483a560a7ad3b2a9df4de49f1c667a585250841d4add701bc303483f7a1e52c | Python | 15,861 | 552 | from collections.abc import Sequence
from json import load
from typing import Literal
from warnings import catch_warnings, simplefilter
import numpy as np
import pandas as pd
from MDAnalysis import Universe
from MDAnalysis.analysis import distances
from numpy.typing import NDArray
from openmm import app, unit
from sci... |
9524d0905c88b4cfa9965aeb2a055c285f0c811972ce6bc6b5b0122098d6731a | Python | 15,865 | 532 | import torch
import torch.nn as nn
import torch.optim as optim
import numpy as np
import matplotlib
import shutil
import os
import glob
from scripts.convert_to_gpu import gpu
from scripts.convert_to_gpu_and_tensor import gpu_t
from scripts.convert_to_gpu_scalar import gpu_ts
from scripts.convert_to_cpu import cpu
impor... |
8c9e1cd952fcb701e5f5a77954f65f75eef5d8f71802af239796a9669fa0b92e | Python | 15,884 | 342 | #!/usr/bin/env python
import sys, os, subprocess, platform, argparse
from argparse import RawTextHelpFormatter
from glob import glob
from utils import execute
from os.path import expanduser, join
class BuildPython:
""" Base class to set paths to pybioshell compilation
Use BuildPythonXY.py to complile PyBioShe... |
43147a54f472286f868ddca767d4f9a1daa36fa507bd4befa4b91639b6fb7833 | Python | 15,885 | 369 | import os
import sys
import json
import h5py
import pickle
import tensorflow as tf
import numpy as np
import google.protobuf.json_format
import util_signal
import util
def _bytes_feature(value):
"""
Returns a bytes_list from a string / byte.
"""
if isinstance(value, type(tf.constant(0))):
val... |
27075868c935cfc516ab3d5b573b186d2d906e7877ef36a105b6aeb5e905aaa1 | Python | 15,886 | 343 | import argparse
import schnetpack as spk
import torch
from torch.utils.data.sampler import RandomSampler
from torch.optim import Adam
import os
import shutil
from schnarc.schnarc import get_energy, get_gradient, get_dipoles, get_nacs, get_schnarc
from schnarc.model import MultiEnergy,MultiDipole,MultiNac,CombinePropert... |
c8bb4d13de4dc8d202953a6856c4672dd8610277a8de32f7d224b8225161d489 | Python | 15,901 | 518 | import pickle
import cv2
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from PIL import Image
import os, sys
from tensorflow.keras.applications.vgg19 import preprocess_input
from numpy.random import randint
from random import randrange
def load_dataset(filename):
"""
load image and l... |
9116276cb05974a66d1df33885e7759d78d02cbf74d31e6f335f7613c7f8a6d7 | Python | 15,907 | 338 | # Identify best unified model and save data from larger unified model search
from os.path import join
from get_paths import *
import pickle
import matplotlib.pyplot as plt
import numpy as np
from os.path import join
import objective
## Load data
# Load simulation results
fname = "data_unified_model_sear... |
346f9b6935a6a55e75a86c91540d4d6ad146fca6f8df072c68b0a7813a16f5df | Python | 15,915 | 399 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.addition import Addition
from elasticai.creator.nn.integer.concatenate import Concatenate
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.hadamardproduct import HadamardProduct
from... |
84761281f0d820f2a2862b97f9aaf4fe94873c5b318c6beb50093a01210aaf64 | Python | 15,917 | 405 | '''
Description:
Utility functions for benchmarking.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import numpy as np
import scanpy
import pandas as pd
import natsort
import torch
import torch.distributions as dist
from optim.evaluation import _ot
# --------------------------------
# Load scRNA-seq dataset... |
b287c34bb384ece02f1760ed3db43371160e4f6af24daee4aa0f67451c86df4e | Python | 15,917 | 357 | # Copyright 2022 HYBRID Team INCIA, UMR5287, CNRS, Université de Bordeaux
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required b... |
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