sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cb8fd0dded8af83d1cfb11d920e66ed8301c5e7b174e44e29bd28e895386c622 | Python | 14,367 | 298 | from collections import defaultdict
from .utils import fix_dataclass_init_docs
from .sim import SimGrid
from .typing import Optional, Callable, Union, List, Tuple, Dict
import jax
import jax.numpy as jnp
from jax.config import config
from jax.example_libraries.optimizers import adam
import numpy as np
import dataclas... |
2d675a80928b4e96c6c3f5add3b9a7b28ffbc36eedbc488e87165161e8b8a3db | Python | 14,385 | 336 | #!/usr/bin/env python3
# Copyright (c) 2026 Computer Vision Center (CVC) at the Universitat Autonoma de
# Barcelona (UAB).
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
Runs two independent, asynchronous weather cycles against a live CARLA s... |
05bee663055614d66045b918635a24b0b8d4ffb107fb362205138ed38615e89b | Python | 14,387 | 401 | #!/usr/bin/env python
"""
Convert DICOM neuroimaging data into a BIDS dataset with validation
Authors
----
Mike Tyszka, Caltech Brain Imaging Center
Remya Nair, Caltech Brain Imaging Center
Julien Dubois, Caltech and Cedars Sinai Medical Center
MIT License
Copyright (c) 2017-2019 Mike Tyszka
Permission is hereby gr... |
fafaf3da7a67b258ccc16ae87be50af80f8ad4a9062d1320b44847cc34a43c36 | Python | 14,390 | 403 | # coding=utf-8
# Copyright 2020 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... |
5ec16b2d408829ca0a2db404fd2965156eef7d1dede2b49975dda5a00c3e29a7 | Python | 14,393 | 378 |
# System imports
import os
import copy
# Blender imports
import bpy
# Internal imports
import vmv
import vmv.consts
import vmv.enums
import vmv.interface
import vmv.skeleton
import vmv.bbox
import vmv.rendering
####################################################################################################
# @... |
ace9e4486ea6d8f8c52310a8ddf27212022136eda719c12d8204fab1bfcfdc67 | Python | 14,396 | 360 | import torch
from torch import nn
from torch.nn.init import xavier_uniform_
from torch.nn.init import constant_
from torch.nn.init import xavier_normal_
import math
import torch.nn.functional as F
from enum import IntEnum
import numpy as np
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
class ... |
a884eba304df57ae49614b11ae5be4fa918412354a43cfd894c9af81123d1cd0 | Python | 14,398 | 300 | import os
import json
import time
import argparse
import pandas as pd
from drugex.data.corpus.corpus import SequenceCorpus, ScaffoldGraphCorpus, ScaffoldSequenceCorpus
from drugex.data.processing import Standardization, CorpusEncoder, RandomTrainTestSplitter
from drugex.data.datasets import SmilesDataSet, SmilesFragD... |
7ea0814b1cf1c9e0119bdaa96f5bacaf9d12092dfae86f34a7d030c78cc15fee | Python | 14,401 | 406 | from abc import ABC, abstractmethod
from typing import List
import torch
from torch import nn
class Embedding(nn.Module, ABC):
def __init__(self):
super().__init__()
@property
@abstractmethod
def out_channels(self):
pass
class GridEmbedding2D(Embedding):
"""GridEmbedding2D appl... |
7574b8dddb0504b2ec2fd59f626929d0bf5d29ba2d2f72bc64d227b7b5701836 | Python | 14,403 | 265 | """Cosmos Transfer 2.5-2B general worker (``Control2WorldInference`` in a torchrun rank group).
Runs inside the ``transfer25`` venv (cosmos-transfer2.5 v1.5.x, torch cu130).
At start-up it launches one rank per GPU given to the worker (``torchrun
--nproc_per_node N -m cosmos_workers.transfer25.ranks --context-parallel... |
1359d1a7d73348a70c27088c84429c0b26a8e5b457d39a4324154dd7875a96d5 | Python | 14,415 | 342 | import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, normal_init
from mmcv.ops import DeformConv2d
from mmdet.core import multi_apply, multiclass_nms
from ..builder import HEADS
from .anchor_free_head import AnchorFreeHead
INF = 1e8
class FeatureAlign(nn.Module):
def __init__(self,
... |
354d2041b228f761943496f2ec5045bc6e2d8569eedf92b9fc50def559e0beb6 | Python | 14,422 | 355 | import sys
sys.path.insert(0, '.')
import loadData as ld
import os
import os.path as osp
import torch
import numpy as np
from torch.autograd import Variable
import torch.backends.cudnn as cudnn
import transforms as myTransforms
import dataset as myDataLoader
import time
from argparse import ArgumentParser
from IOUEval ... |
a73665aff3571a6b90bcdd53547b550f7d239966aa604e19cf4d384137599723 | Python | 14,439 | 552 | #%%
import os
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.lines import Line2D
from graspologic.utils import binarize
from src.data import load_metagraph
from src.io import savefig
from src.utils import get_paired_inds
from src.v... |
6acd527c9f40da01b1392239c5b73fc14032fb8bbecb4b0a43a35ca2ce71c271 | Python | 14,448 | 561 | # %% [markdown]
# ##
import os
import time
import warnings
from itertools import chain
import colorcet as cc
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from anytree import LevelOr... |
c2213c009dff535ef33b271fba86a2651d2825cef9ec37025a7909e364c43066 | Python | 14,450 | 319 | import logging
from collections import defaultdict
from copy import deepcopy
from typing import List, Iterator, Tuple, Collection, TextIO
from oaklib.datamodels.taxon_constraints import SubjectTerm, TaxonConstraint, Taxon
from oaklib.datamodels.vocabulary import IS_A, NEVER_IN_TAXON, ONLY_IN_TAXON, IN_TAXON, PRESENT_I... |
2a6cb2cf5df9344e31488830dda380f8382d3884aa40b7f0428b18e940d66b3d | Python | 14,454 | 382 | ####################################################################################################
# Copyright (c) 2019 - 2023, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
14f8b55bdc572715212ef0ebc165b02205a1ff130b35b8a30d1dd6fc0922da27 | Python | 14,460 | 375 | """
-----------------------------------------------------------------------
Author: Brin Rosenthal (sbrosenthal@ucsd.edu)
-----------------------------------------------------------------------
"""
#import matplotlib.pyplot as plt
#import seaborn
import networkx as nx
import pandas as pd
import random
import nump... |
eb020777b37d471513a7a249b03d85a7f572df3e5e41da52b38443713c332106 | Python | 14,463 | 487 | # %% [markdown]
# ##
import os
import warnings
from itertools import chain
import matplotlib as mpl
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd
import seaborn as sns
from joblib import Parallel, delayed
from sc... |
a8e951f7bb2ec3711e55b5a15c24e091f9e36100b3a50d644017b3d8745bfe3a | Python | 14,468 | 361 | """Static-obstacle export: what the level bounding boxes are allowed to become.
No CARLA server - only ``carla``'s value types (``BoundingBox``, ``Location``) plus a stub world
whose ``get_level_bbs`` returns whatever the test wants.
"""
import types
import numpy as np
import pytest
import carla
from carla_cosmos.... |
c11394f000654309bfa7b49beeef6be8fe2c0ecf60f49305440e5e1a283d976f | Python | 14,487 | 244 | import os
import numpy as np
import pandas as pd
from datetime import datetime
import pytorch_lightning as pl
import wandb
import torch
from constants.constants import*
from torch.utils.data import DataLoader
from lab.training_tools import TrainingToolsFactory
from utils.nilm_reporting import save_appliance_report
fro... |
ecaa7accaa4153dbce0e3215f132d9adff6eba436edf5cd85c328d42b5382888 | Python | 14,495 | 394 | ## 2021/10/13
# Gene Regulatory Network Simulation Using Simple Multivariate Gaussian
## System
import os
import shutil
## Plots
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib import offsetbox
from matplotlib import cm
impor... |
796f1e2c03031b5c4347e25fdee60a636d9eb15082f1d250721c8aae4285d52d | Python | 14,500 | 467 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""
Variant of the resnet module that takes cfg as an argument.
Example usage. Strings may be specified in the config file.
model = ResNet(
"StemWithFixedBatchNorm",
"BottleneckWithFixedBatchNorm",
"ResNet50StagesTo4",
... |
97bf0c5d44c82bc008fe492ae7f08db54418b624908a7f0b53bf6e7473f90f94 | Python | 14,504 | 319 | # Copyright (c) # Copyright (c) 2018-2020 CVC.
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
""" This module implements an agent that roams around a track following random
waypoints and avoiding other vehicles. The agent also responds to traffic... |
cf1894e58ec97f227664bc9a1aee9806f9ba878f7907658ebe35d33ca71be00b | Python | 14,517 | 412 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Statistical Parametric Mapping"""
from operator import mul
import numpy as np
from .. import _info, fmtxt
from .._data_obj import Dataset, Factor, Var, NDVar, Case, asmodel, asndvar, assub, combine, dataobj_repr
from .._exceptions import DimensionMismatchErr... |
d2cefc90bcceeb79377ffa9f0f4d2600f292048edfc998b78802f81b6a149846 | Python | 14,517 | 335 | # Copyright 2020 Huawei Technologies Co., Ltd
#
# 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 applicable law or agreed to... |
bfe6420aba3707658c8feefe52e88612f18f36ade389ace3b42903d82644f2a2 | Python | 14,520 | 360 | #%%
import os
import sys
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
from pymaid_creds import url, name, password, token
import pymaid
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
# allows text... |
142e512a59f4d41f7f0715bef02cd634cf6ac53ead2a4844ec953845723eb3de | Python | 14,527 | 414 | import numpy as np
import jax.numpy as jnp
from jax import jit, lax
from jax.ops import index,index_update
from jax.random import split,uniform,PRNGKey
from functools import partial
from matplotlib import pyplot as plt
from .figures import panels, performance, plot_dXs, compare_pfc_dysfunction
dms_ctx_gain = .4
pfc_... |
660ed80d7dcfd711106e54bc11227d89cb0a79b99318c61096f52a89e5cd14bc | Python | 14,534 | 455 | from itertools import starmap
import numpy as np
import torch
import torchvision
class PermuteSequenceChannels(torch.nn.Module):
"""
Permute channels of retrieved encoded DNA sequence.
Permutes axes of `np.array` of shape `(sequence_length, alphabet_size)` to
obtain `np.array` of shape `(alphabet_si... |
903c8a18eb3e917c97267f3a979e755db3b0313499b72f3af855fea0795fa163 | Python | 14,536 | 386 | """
Copyright 2020 - by Jerome Tubiana (jertubiana@gmail.com)
All rights reserved
Permission is granted for anyone to copy, use, or modify this
software for any uncommercial purposes, provided this copyright
notice is retained, and note is made of any changes that have
been made. This softwar... |
0c732d6b3a919eeac04b27e52edced9be768b1d0967b8dcb09c0736776ba09dc | Python | 14,541 | 377 | """
This class contains methods to query a file of genomic coordinates,
where each row of [start, end) coordinates corresponds to a genomic feature
in the sequence.
It accepts the path to a tabix-indexed .bed.gz file of genomic coordinates.
This .tsv/.bed file must contain the following columns, in order:
chrom (... |
15dd5eb6e9fab62dc278784c4795fd5181ccdae1da832b161d82b4f721ce01e0 | Python | 14,545 | 260 | # basic imports
import numpy as np
import pickle
import matplotlib.pyplot as plt
def load_data() -> dict:
'''
This function loads simulation data and prepares it.
Parameters
----------
None
Returns
----------
data : The prepared simulation data.
... |
dd75700cd14c8993eb44352e7064b132ab7edd3db8a20eeccfd1cb5d1e034b9a | Python | 14,547 | 418 | from abc import ABCMeta, abstractmethod
import torch
from neuralop.training.patching import MultigridPatching2D
import torch
from neuralop.training.patching import MultigridPatching2D
class DataProcessor(torch.nn.Module, metaclass=ABCMeta):
def __init__(self):
"""
DataProcessor exposes fun... |
f2674b1b3d78c3785a434084ad12a8017e9e5110accb585505e7d930b4c09816 | Python | 14,554 | 518 | #!/usr/bin/env python
"""
subpixel.py -- localize PSFs to subpixel resolution
"""
# Numeric
import numpy as np
# Dataframes
import pandas as pd
# Image processing
from scipy import ndimage as ndi
# Low-level subpixel localization utilities
from .helper import (
assign_methods,
ring_mean,
rs,
I0_is_c... |
389ddf47467305a6a9c75eb8253b79505ca196528a95e931887779b9cb68375f | Python | 14,559 | 384 | # --------------------------------------------------------
# Pytorch multi-GPU Faster R-CNN
# Licensed under The MIT License [see LICENSE for details]
# Written by Jiasen Lu, Jianwei Yang, based on code from Ross Girshick
# --------------------------------------------------------
from __future__ import absolute_import
... |
aa6ba6f0733780c3266bd60e08361e73a9ff981f2c693e257c4435949365b405 | Python | 14,566 | 461 | # Auto generated from input_specification.yaml by pythongen.py version: 0.9.0
# Generation date: 2023-04-13T08:19:53
# Schema: inputspec
#
# id: https://w3id.org/oaklib/input-specification
# description: A data model for representing a set of inputs to OAK
# license: https://creativecommons.org/publicdomain/zero/1.0/
... |
f3392309fc61ac443c0c52ccbdb8fe13eef615660b89eb302dda7d3ca924779f | Python | 14,574 | 335 | import torch
class Regressor(object):
def __init__(self, model, criterion, optimizer=None,
lr=0.001, betas=(0.9, 0.999), ws=30, itrtn=50, pred=1):
"""
Notice max_pred_step include now step prediction. So, for example,
if you set two on max_time_step, only now and one step ... |
c64be6e1cb64645100056b7f8302a3d17e0b66c0a99a74710e6349930e5fb5f9 | Python | 14,579 | 415 | """
code to track produced figures or results and classify them
"""
import contextlib
import numpy as np
import logging
import os
import socket
import sys
import inspect
import datetime
import yaml
import argparse
from tctx.util.defaults import DEFAULTS
from pathlib import Path
import filelock
logging.getLogger('py-f... |
1115ed937e02921add3cd88c375eed5ad938f23b08a57c38be21d7463bca0418 | Python | 14,580 | 376 |
from tokenizer.mof_tokenizer import MOFTokenizer
from model.transformer import TransformerRegressor, Transformer, regressoionHead
from model.utils import *
from datetime import datetime, timedelta
from time import time
from torch.utils.data import dataset, DataLoader
import os
import csv
import yaml
import shutil
imp... |
79f915e51f477366c46893c6cbc5f3288bf4f591ac5a7369e4f79ee745599e3b | Python | 14,582 | 487 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# navis documentation build configuration file, created by
# sphinx-quickstart on Sun Jul 9 22:17:00 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# auto... |
788ed2efec18966c2cb50cfc7ba27ec517106a7719d09663e33510fc28a277a1 | Python | 14,585 | 349 | import json
from logging import Logger
import os
from typing import Dict, List
import numpy as np
import pandas as pd
from tensorboardX import SummaryWriter
import torch
from tqdm import trange
from torch.optim.lr_scheduler import ExponentialLR
from .evaluate import evaluate, evaluate_predictions
from .predict import... |
baf6591b4cab8ac5d7c3e52b4fa879b50cb38dcceb03e650a35db814898fa5c0 | Python | 14,603 | 305 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 2 13:37:38 2021
@author: paulmueller
"""
import glob
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
from scipy.stats import wilcoxon
from iEEG_STC import utils
import os
sns.set_palette("tab10")
sns.set... |
caa29eece0b68a46fd0b9729a9678c47a5598b31c0d161584c1b302721ad9f31 | Python | 14,607 | 401 | """
Refer to https://github.com/rosinality/stylegan2-pytorch/blob/master/lpips/dist_model.py
Refer to https://github.com/richzhang/PerceptualSimilarity/blob/master/lpips/trainer.py
"""
from __future__ import absolute_import
import sys
import numpy as np
import torch
from torch import nn
import os
from collect... |
3ffd2fea66a4385966cd01629c7361707c3633029174b3009e7b4855c71f3590 | Python | 14,622 | 357 | """
Tests for C++ polymer topology functions in _polymer_math module.
"""
import numpy as np
import pytest
try:
from polychrom import _polymer_math # noqa: F401
HAS_POLYMER_MATH = True
except ImportError:
HAS_POLYMER_MATH = False
pytestmark = pytest.mark.skipif(not HAS_POLYMER_MATH, reason="_polymer_ma... |
2090915bd6d0df6f322dc1423e8b5e4cc5a54a9a7c18b25640231b49f65e2241 | Python | 14,636 | 387 | #!/usr/bin/env python
# Script to build windows installer packages for LAMMPS
# (c) 2017,2018,2019,2020,2021,2022,2023,2024,2025,2026 Axel Kohlmeyer <akohlmey@gmail.com>
from __future__ import print_function
import sys,os,shutil,glob,re,subprocess,tarfile,gzip,time,inspect,hashlib
try: from urllib.request import urlr... |
3d79e5176aecb3820a3eb6cbea4e37f03298448feb05ddb3f842b04776cd52a6 | Python | 14,639 | 443 | import math
import numpy as np
import networkx as nx
import scipy.spatial as sp
def addNode(p,nodes,tol=1e-1):
"""
Auxilliary function for adding node to a preexisting list
"""
for idx,n in enumerate(nodes):
if abs(p[0]-n[0]) > tol: continue
if abs(p[1]-n[1]) > tol: continue
ret... |
6bc13cc8eaca25bd207abdc7a4b643fa6fd5a0bb96ac83e5b31635bcd82dc25d | Python | 14,639 | 304 | # Part of the convolution layers and l-DDT computation are modified from DeepAccNet
# Improved protein structure refinement guided by deep learning based accuracy estimation
# Naozumi Hiranuma, Hahnbeom Park, Minkyung Baek, View ORCID ProfileIvan Anishchanka, Justas Dauparas, David Baker
# Nature Communications doi: 1... |
35ddb64b6c8cd4618d0f8e5013fa9eb6c77e204bce1c7ed5868b3cf1ff2c73ac | Python | 14,653 | 576 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import scipy
import seaborn as sns
from graspy.match import GraphMatch
from graspy.plot import heatmap
from graspy.simulations import sbm
from src.data import load_metagraph
from src.graph import pre... |
7a67aeb63e01eed7e6fdb5748dadb866853238638958da92fbb72848eb2488ec | Python | 14,674 | 462 | # -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
import time
import numpy as np
import warnings
import scipy
import SimpleITK as sitk
from ..utils.utils import get_unet
import os
from nipype.interfaces.base import (
... |
0fca18df30631351791243dab058eaba90c010648c2334c38e9109ce926fc15c | Python | 14,681 | 356 | import pysam
import debarcer.umi_network_collapse as network
from debarcer.utilities import get_umi_from_name
def umi_count(contig, region_start, region_end, bam_file, truncate, separator):
'''
(str, int, int, file, bool, str) -> (dict, dict)
:param contig: Chromosome, eg chrN
:param region_start... |
6e4e6758690a89d874e7916f6dadec4d6a498323142e09e6a8e8f200eb1f13ef | Python | 14,681 | 412 | from fnmatch import fnmatchcase
from itertools import combinations
import numpy as np
from ._data_obj import (
NDVar, Case, Dataset,
ascategorial, asdataobject, assub,
cellname, dataobj_repr,
)
from ._stats.stats import variability
from ._utils.numpy_utils import FULL_SLICE
class Celltable:
"""Divid... |
7f4f83124dc3d53d7d6f94ad12f4a6d0d02bee04bd646a728b5c7d0127e951c7 | Python | 14,681 | 432 | import numpy as np
import sys
import datetime
import warnings
from csbdeep.utils import normalize
from scipy.ndimage.filters import gaussian_filter
from scipy.ndimage import map_coordinates, zoom
from scipy.optimize import minimize_scalar
from skimage.measure import regionprops, label
from skimage.feature import corner... |
180dc9a64c329fab3abf9a67315dc7c425578e39314f9ee4b4416fd36de6d70e | Python | 14,691 | 480 | #%% Imports and file loading
from pathlib import Path
import glob
import json
from os import listdir
from operator import itemgetter
import pandas as pd
import networkx as nx
import numpy as np
from graspy.plot import gridplot
from src.data import load_networkx
# File locations
base_path = Path("./maggot_models/data/... |
76fc0267145f7596626cfb129d9fee7aefee4b8ff069cfb320d3586378017c4c | Python | 14,696 | 328 | #!/usr/bin/env python3
"""Query the live CARLA world: actors, level bounding boxes, raycast, snapshot.
This is the RESOLVER skill — use it to turn an ambiguous description ("a prius",
"the nearest walker", "the 3rd one") into a concrete actor id that the action
skills (telemetry, bounding-boxes, control-vehicle, contr... |
958f567cfa6e4d7bde302301bf9f336c54971cf59d9bd26e1495e018087c4e41 | Python | 14,703 | 382 | import math
from math import inf
from typing import List, Optional, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
from transformers import AutoModel
PAD_ID = 0
class SentenceLevelEncoder(nn.Module):
"""BiLSTM att... |
66de3bbdba4447fd356fdcbd4a8e964a42978af3d407939e3e2541bcdee97073 | Python | 14,708 | 405 | from logging import handlers
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
import matplotlib.ticker as mtick
import math
color_list = ['royalblue', 'orange', 'limegreen', 'crimson', 'mediumorchid', 'dimgray', 'mediumpurple', 'chocolate', 'lime', 'lightpink', 'maroon', 'nav... |
88ca634b580aa3d764b9fecf59c9caf99120c562be1927fb0bea5093840e1f91 | Python | 14,715 | 511 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy
import seaborn as sns
from joblib import Parallel, delayed
from scipy.optimize import curve_fit
from graspy.match import GraphMatch
from graspy.plot import heatmap
fr... |
96dd7a19c7de4f13520ccfc1075ded3350ff4946493be3561b9918a46218f415 | Python | 14,719 | 525 | import torch
import torch.nn as nn
import torch.nn.functional as F
class REBNCONV(nn.Module):
def __init__(self,in_ch=3,out_ch=3,dirate=1):
super(REBNCONV,self).__init__()
self.conv_s1 = nn.Conv2d(in_ch,out_ch,3,padding=1*dirate,dilation=1*dirate)
self.bn_s1 = nn.BatchNorm2d(out_ch)
... |
9eb49da3b1b93bbb7c09b0e82fc5e5df3b0d64f5548340aebae4b32a3755f1aa | Python | 14,741 | 322 | """
File: create_matrices.py
Created: 2020/10/08
Last Changed: 2021/12/07
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either ... |
d94e4da91af96a919061bc190edf22140d33946187bb2a481f7dc211db182eb9 | Python | 14,741 | 395 | ####################################################################################################
# Copyright (c) 2019, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free softwar... |
e7dbee99bc346560484b20a0883dfa731a86812269900316a9a76033bf3853d7 | Python | 14,742 | 483 | #%% Imports and file loading
from pathlib import Path
import glob
import json
from os import listdir
from operator import itemgetter
import pandas as pd
import networkx as nx
import numpy as np
from graspy.plot import gridplot
from src.data import load_networkx
# File locations
base_path = Path("./maggot_models/data/... |
57a11bc8d5a1149c2288bea4a7e70f8316ce53f71e9d4bf517aa69cb62a05e98 | Python | 14,743 | 383 | """
Adapter for UniProt endpoint (experimental).
.. warning ::
this is currently highly incomplete
This is an adapter for the uniprot triplestore, which includes:
- entries for individual proteins
- triples connecting these proteins to other IRIs, including vocabulary terms
The adapter treats all entries as on... |
d0cdc2ad1bf83c2df0239620a58fad5e77021a73c9b0d7125adba5353d8b8af5 | Python | 14,750 | 541 | # %% [markdown]
# ## The goal of this notebook:
# investigate regularization approaches, for now, just on the full graph
# these include
# - truncate high degree
# - truncate low degree
# - plus c
# - levina paper on row normalization
# - others?
# %% [markdown]
# ##
import os
import time
import wa... |
97d36e79fd7fca03681a608267947da180aec314c076b922fe1c3ae9f9aace78 | Python | 14,763 | 113 | #!/usr/bin/env python3
"""
File: partial_deconvolution.py
Created: 2020/06/29
Last Changed: 2020/11/22
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fr... |
32d5efcebfad6c36771cf247f7adb6f4313651ac5e186a49666e855e226c4d36 | Python | 14,765 | 467 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 applicable law or agreed to... |
edb437bd546765c5cc7c76a972e8a58b2d4c9ea62efca8509acc42386f1ab556 | Python | 14,775 | 347 | from typing import Sequence, Union, Tuple, Callable
import numpy as np
import torch
from matplotlib import pyplot as plt
from tensorflow.examples.tutorials.mnist import input_data
from sklearn import utils
import os
from artemis.experiments import ExperimentFunction
from artemis.experiments.experiment_record import... |
294640b83853b884f48ce875a2f88b5b4e14de91ca401977cb3defd568e4bb84 | Python | 14,786 | 378 | """
This work heavily relies on the implementation by Icarte:
https://bitbucket.org/RToroIcarte/bnn/src/master/
"""
import gurobipy as gp
from gurobipy import GRB
import numpy as np
from helper.misc import infer_and_accuracy
from globals import INT, BIN, CONT, EPSILON, GUROBI_ENV, LOG, DO_CUTOFF
vtypes = {
INT: GRB.... |
d50f82bc6993fd9480705a4462276f7e5ec47d68a96ba7697b5f198bfd891f2e | Python | 14,801 | 286 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 24 10:18:25 2020
@author: jacks
"""
# %% Imports
import time
from numpy import pi
import pandas as pd
pd.options.mode.chained_assignment = None #suppresses a warning that shows up in the genodock preprocessing
# defs contains all of the circuit definitions as well as au... |
8f1bc94af144e9dd8d91acc737371e889798bb818d664a257cf63b1f866416a6 | Python | 14,824 | 378 | import argparse
import random
import time
import warnings
import torch
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.distributed as dist
import torch.optim
import torch.multiprocessing as mp
import torch.utils.data
import torch.utils.data.distributed
import torchvision.transforms as transf... |
607951badf9c7363ffec07c0f8ef29e351ff0ba91745ed1364f20c08b10aab4a | Python | 14,832 | 484 | #%% Imports and file loading
from pathlib import Path
import glob
import json
from os import listdir
from operator import itemgetter
import pandas as pd
import networkx as nx
import numpy as np
from graspy.plot import gridplot
from src.data import load_networkx
# File locations
base_path = Path("./maggot_models/data/... |
bdad6685ceff17a48319534ad1a5c0ea61f4d1bb12a04026017dac4372c24f6f | Python | 14,835 | 445 | import torch
from torch.autograd import Variable
from torch.nn import functional as F
from torch.nn import init
from contextlib import contextmanager
from functools import partial
class UnidirectionalInterface(torch.nn.Module):
"""Basic `Interface` for unidirectional communication.
Can be used to manually p... |
49570a0f5f188ec683784bd897e5540b1050c67cd22595415f0d0434ed4d0be2 | Python | 14,841 | 366 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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 applicable law... |
e9295f2551db756d3fe853d560a75215da5338e8d9d988b6ba46bf8b02a486f0 | Python | 14,844 | 356 | import os
import sys
import datetime
import stat
from collections import defaultdict
import numpy as np
from pycocotools.coco import COCO
from pycocotools.cocoeval import COCOeval
from mindspore.train.callback import Callback
from mindspore import log as logger
from mindspore import save_checkpoint
from model_utils.con... |
12fe595c19091f09102873f51c7933cfcf8bdb0dfbdfb5ef2e0d77ccb2e22d9a | Python | 14,851 | 420 | import hashlib
import json
import os
import tempfile
import typing as tp
import numpy as np
import PIL.Image
from backend import postprocessing
from backend import jobs
import backend
from base.backend.pubsub import PubSub
from base.backend.app import get_cache_path, get_models_path
import torch
SEGMENTATION_CACHE_... |
0a963e63ae81b23eb225f720988b59b78cc3959f04be88b03e23a06187135f6b | Python | 14,864 | 331 | """Live check of the path-traced tag AOV (sensor.camera.rt_lens_instance).
The sensor renders through the same lens as sensor.camera.rt_lens but outputs, per pixel, the
CARLA tag of the primary hit in the byte layout sensor.camera.instance_segmentation already uses
(R = semantic label, G = actor id low byte, B = actor... |
916235c6d6f7a2957a068e08cdd1292f8da8f94bc27e1c0fb124d9cbef28b608 | Python | 14,870 | 430 | from copy import deepcopy
import os
import re
import mne
from .._mne import combination_label, labels_from_mni_coords, rename_label, dissolve_label
from .definitions import DefinitionError, Definition, tuple_arg
SEEDED_PARC_RE = re.compile(r'^(.+)-(\d+)$')
class Parcellation(Definition):
DICT_ATTRS = ('kind',... |
99dc131c321fedfd08fcf723a34edb5172fcd90626380d310420336259011b98 | Python | 14,871 | 428 | import torch
import torch.nn as nn
from torchnlp.nn import Attention
from neural_networks.base_models import BaseModel
from blitz.modules import BayesianLinear, BayesianConv1d
from neural_networks.custom_modules import ConvDropRelu, LinearDropRelu, BayesianConvDropRelu, BayesianLinearDropRelu
from blitz.utils import v... |
14197ab131342b88875e9a43a893139e1decdd3cba3c761cae8e6b797fe4b979 | Python | 14,890 | 408 | import pandas as pd
from drugex.data.corpus.vocabulary import VocSmiles, VocGraph
from drugex.logs import logger
from drugex.data.interfaces import DataSplitter, FragmentPairEncoder
from drugex.molecules.converters.interfaces import ConversionException
from drugex.molecules.interfaces import MolSupplier
from drugex.pa... |
a348adfdb9db138f925e6e87096256a75ba0181ef70e93473ddd352cfa6ac285 | Python | 14,903 | 265 | from __future__ import division
import os
import numpy as np
import pymworks
import matplotlib.pyplot as plt
from collections import Counter
from mw_parse_initial_170623 import get_animals_and_their_session_filenames
def analyze_sessions(filepath):
animals_and_their_session_filenames = get_animals_and_their_sessi... |
42de769e25179d313468b6674c023bea420073d96553890f2906ea8b8e01c7e0 | Python | 14,906 | 539 |
# coding: utf-8
# In[51]:
from __future__ import print_function
feature_count = 42
predict_column = -2
target_cluster = 0
pop_size = 25
max_fitness = 3.0
max_gens = 80
pool_size = 15
seed_with = None #[0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,... |
6e1551c8cf16d8e8f98ca2ddf11852d481234fbc29d5552015699aedc5b069d8 | Python | 14,908 | 266 | # Copyright 2020-2021 Huawei Technologies Co., Ltd
#
# 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 applicable law or agre... |
4f27a6944ea88360f5ea0905e55d0e0cebf1efbfe11963cc37fcf0f7d8e0be5d | Python | 14,912 | 280 | #%%
import os
import sys
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/maggot_models/')
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
except:
pass
from pymaid_creds import url, nam... |
16c48e397c387cf7375c64cc0194c8ed8ae43004ee409681dbaad59e9e60e4af | Python | 14,920 | 391 | """Test cases for the command line client in __main__ module."""
import glob
import json
import os
import shutil
from pathlib import Path
from typing import List
from typing import Optional
from typing import Tuple
from unittest import mock
from unittest.mock import MagicMock
import pytest
from _pytest.fixtures import... |
a88d0986e5898f9e7993cf8a2d6f2167307fdf32ca810f8cf1027c50b5c3cef4 | Python | 14,924 | 467 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Apr 5 21:42:12 2020
This script will train PACIFIC and save the model, training and validation
plos in specified folders.
@author: Pablo Acera
"""
import argparse
parser = argparse.ArgumentParser(description=
"""
... |
a76083073991527de81b2eb23bb7c3e6b0518a67e3757c2677924995e8638e61 | Python | 14,928 | 447 | # -*- coding: utf-8 -*-
from unetsl.cerberus.cerberus_config import getDefaultCerberusPredictionConfig, getTrainingConfig, HeadConstants
import click
import unetsl
import unetsl.model
import re
import numpy
import time
import scipy.ndimage
import tensorflow.keras.models
import tensorflow.keras.layers
from tensorflow ... |
f45833766d5a04f7dbfddea8911a63f2921e9705cda3ffce80caa44a3a8e7b01 | Python | 14,937 | 416 | """code to interface with nest simulator"""
import numpy as np
import pandas as pd
import logging
from tctx.util import sim
from tctx.util.profiling import log_time
from tctx.util.defaults import DEFAULTS
from tqdm.auto import tqdm as pbar
############################################################################... |
3d57c31a702750551cb889f396163d7f1426a28b18287b85f1638559f56b5451 | Python | 14,942 | 376 | from __future__ import print_function
from __future__ import absolute_import
# --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick
# ----------------------------------------------------... |
4f81486609a6f8359d25f9f982f937864f3f246d845851bea64f679660f313e4 | Python | 14,950 | 352 | import torch
import random
import numpy as np
from itertools import compress
from rdkit.Chem.Scaffolds import MurckoScaffold
from collections import defaultdict
from sklearn.model_selection import StratifiedKFold
# splitter function
def generate_scaffold(smiles, include_chirality=False):
"""
Obtain Bemis-Murc... |
a70aecdafeda455077fa06a42201d76bdeda31d056ae7b2ff4ac9a5161883269 | Python | 14,955 | 421 | from __future__ import print_function, division
import random
import sys
from matplotlib import rcParams
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import h5py
# Pytorch packages
import torch
import numpy as np
import torch.optim as optim
from torch import nn
from torch.utils.data import ... |
2511c85ca867d771ece71815ec4f68ce1124656cf6cd3d7b665a7b32de5b3a4e | Python | 14,969 | 334 | from . import config
import torch
import torch.nn as nn
import numpy as np
from collections import namedtuple
ModelParams = namedtuple(
'ModelParams', [
'vocab_size', 'token_embedding_dim', 'hidden_dim', 'encoder_layers_cnt',
'decoder_layers_cnt', 'latent_dim', 'device', 'x_dim'])
ModelParams._... |
d549174a06c16c8f22d5d374906c116a2efc37678974abdcc015a4c8578ec59f | Python | 14,971 | 376 | #
# Copyright (c) 2018 Institute for Basic Science
#
# 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... |
87e8d10652a13a9b0af60149e40ce7410afee1f562270f89b5b903ffadf19d9e | Python | 14,972 | 374 | import mne
import numpy as np
from itertools import combinations, product
import pandas as pd
import re
import torch
from torch.nn import NLLLoss
from torch.nn import functional as F
import csv
from os.path import join
import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle
import matplotlib
from datet... |
82c8bb9a53a3936db202f3a684f161834983cd97e479150d3e17c60dd7c0d486 | Python | 14,975 | 559 | # %% [markdown]
# # THE MIND OF A MAGGOT
# %% [markdown]
# ## Imports
import os
import time
import warnings
from itertools import chain
import colorcet as cc
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd
import seaborn as sns... |
96388cac5695ee0daf41b55ab9bf8d91c2ced4b1f5f87efb9527d56aebb9fe96 | Python | 14,975 | 373 | # Copyright (c) 2026 Computer Vision Center (CVC) at the Universitat Autonoma de
# Barcelona (UAB).
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
from . import SyncSmokeTest
from . import SmokeTest
import carla
import time
import math
import num... |
e50258c049d1102fb6555e0c0fc2b38858e88174eab80a32649385bde8b9a32a | Python | 14,981 | 361 | from data import *
from utils.augmentations import SSDAugmentation
from layers.modules import MultiBoxLoss
from ssd import build_ssd
import os
import sys
import time
import torch
from torch.autograd import Variable
import torch.nn as nn
import torch.optim as optim
import torch.backends.cudnn as cudnn
import torch.nn.in... |
93f6cea947b1ae6fd624d05da107b8b6e93db19128cf44d7c424a431e1893062 | Python | 14,986 | 334 | # Copyright 2016 The TensorFlow Authors. All Rights Reserved.
# Modifications Copyright 2017 Abigail See
#
# 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... |
22a402c175d415b22b9fc4ac2197eeaae613b6828f138554a4e33c13e32edc4e | Python | 15,006 | 295 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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 applicable law or agre... |
6c8885734259b05275839ab2aae4a000356c351ad549477ee437f3cdcb1438b4 | Python | 15,012 | 318 | #!/usr/bin/env python3
"""
File: correlate_align_metrics_with_genes.py
Created: 2021/12/07
Last Changed: 2022/03/31
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... |
9181d5c182384983f69f3e47e21881304b86a661f873c99692b6f87464ec72c1 | Python | 15,020 | 367 | """Implementation of optimization based attack,
CW Attack for object adding.
Based on CVPR'19: Generating 3D Adversarial Point Clouds.
"""
import pdb
import copy
import time
import torch
import torch.optim as optim
import torch.nn.functional as F
import numpy as np
from sklearn.cluster import DBSCAN
from util.po... |
cc9eca44e000d55e127b51b1fc270379d1dd31609e8f3f436d8d261a6834256a | Python | 15,021 | 637 | #!/usr/bin/env python
# -*- coding: latin-1 -*-
#
# Copyright 2016-2019 Blaise Frederick
#
# 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/LICEN... |
73f8ce0850a1e70915980d42397655fbccdbe9ece0f01e3ecf1d5922008e9484 | Python | 15,028 | 387 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
##################### IMPORTS #######################
import os
import sys
from keras.models import model_from_json
from matplotlib import pyplot as plt
import numpy as np
from keras.callbacks import ModelCheckpoint
from rdkit.Chem.Draw import IPythonConsole
import os,... |
c00592f405655c257eb93a560d1d891451822b6e5bf80240fba46271ab264499 | Python | 15,039 | 392 | from __future__ import annotations
from typing import TYPE_CHECKING, Callable, Dict, Iterable, List
import os
import pandas as pd
from palm_tools.utils.read_file import check_file_and_read
import logging
import glob
import numpy as np
if TYPE_CHECKING:
from palmari import Acquisition
from palmari import Expe... |
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