sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b83285d3c59836391041c06851e36277991f47af7b51ba81e8d2e23ca86eb9a2 | Python | 9,056 | 325 | import functools
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.utils import spectral_norm
### single layers
def conv2d(*args, **kwargs):
return spectral_norm(nn.Conv2d(*args, **kwargs))
def convTranspose2d(*args, **kwargs):
return spectral_norm(nn.ConvTranspose2d(*args, ... |
98c5e07cd33e7eef8c6beab2aed443421c57c7c5dacc3ed99c86bdf2717c6f80 | Python | 9,058 | 272 | #!/usr/bin/env python
# Given a fasta file of reads-of-insert, qsub N trimPrimers jobs, each
# of which will process a subset of the file. Combine the outpts when
# all are done.
import os
import sys
import optparse
import re # regular expressions
import datetime
from tt_log import logger
VERSION = '20150403... |
d09a05536e84397cd2546567db428c5e5055bc08784119880ec5f57d14bac543 | Python | 9,060 | 298 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from model.utils.config import cfg
from model.faster_rcnn.faster_rcnn import _fasterRCNN
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
import math
impor... |
6dd7052a2fc93aad6869d838d82fcece3f63e999e1059f70656d5490dbbfe9c1 | Python | 9,069 | 294 | import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import fftconvolve
def intrinsic_reliability(traces, window_width=8, dt=0.1):
"""Compute the intrinsic reliability using Kistler window.
"""
rect_size_i = 2 * int(float(window_width) / dt)
rect = np.ones(rect_size_i)
spk_pairs... |
d52b993141fd3c670725e3220bc0347fc3dbbc1f0e3c5865de6fd23712901e76 | Python | 9,069 | 156 | import os, sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
import h5py
from tqdm import tqdm
from functools import partial
import numpy as np
from scipy.spatial.distance import euclidean
... |
a91d26960d90866fc79f086519ed4f5c2cc133552383d2521708aad74f11ea96 | Python | 9,077 | 209 | """
Forcekits (new in polychrom)
----------------------------
The goal of the forcekits is two-fold. First, sometimes communication between forces is required. Since explicit is
better than implicit, according to The Zen of Python, we are trying to avoid communication between forces using
hidden variables (as done in ... |
03d1923a3967a81fc859162235fff9ef6c0d05ebc9a60efc0f2c072b3ca733b6 | Python | 9,081 | 211 | # 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... |
8b0b1ffa50de25c7afc62dc3431e0dea4e526922c0dccad133604fe4076f31a5 | Python | 9,081 | 370 | # Generic
import numpy as np
# Scipy
from scipy import linalg
def triu(M):
m = M.shape[0]
r = np.arange(m)
mask = r[:, None] < r
return M[mask]
def gmm_intersection_matrix(y_pred, y, include_all=False, **params):
"""Compute the GMM intersection area matrix.
.. note: At the moment all distri... |
388511477388d0fc7fec6f9f94e54f2a3d5732f3dcfc796e9853c78c5b8c9d2c | Python | 9,083 | 203 | import mne
import numpy as np
import matplotlib.pyplot as plt
import os
if protocol == 'WORDS':
import config_WORDS as cfg
if protocol == 'PP':
import config_PP as cfg
## logging info ###
import logging
from datetime import datetime
logname = './logs/' + datetime.now().strftime('log_%Y-%m-%... |
e5c31927818e581de1e2b95906847ad16be0259ebe5d6a8eb34c6ac7a0263207 | Python | 9,089 | 241 | """
File: perform_deconvolution.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, e... |
c93ba160835f0ea0a89bc60f0b8671d57076a36efb1eb4c57dec2d3aef1c9191 | Python | 9,090 | 328 | import os
import numpy as np
import nibabel as nib
from numpy.testing import (
assert_array_equal,
assert_equal,
assert_raises,
assert_almost_equal,
)
from bruker2nifti._utils import (
indians_file_parser,
normalise_b_vect,
data_corrector,
eliminate_consecutive_duplicates,
compute... |
f78925f102f3990d9c23a8a86f81e46ce2b34b0bb45c05622e39ff0b7a27a5ac | Python | 9,090 | 220 | import cv2
from aicspylibczi import CziFile
from pathlib import Path
from os.path import dirname, realpath, join
import pickle
import numpy as np
import colorsys
from .uuuuuu import hex2rgb
# czi_path = '~/Work/Kavli/Data/HERBS_DATA/abraham/Pecorino_mec_slide_1.czi'
class CZIReader(object):
def __init__(self, cz... |
3349ae076835f3207cc180b18deb028a896a2263b6184fa445f150a00ec1cd9f | Python | 9,093 | 219 | # 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... |
317f0d8f3e20b0caed42a99903b8cb7348e6278469c6aa7275e3db1574bfbcf2 | Python | 9,095 | 193 | # Modified from https://github.com/facebookresearch/detectron2/tree/master/projects/PointRend # noqa
import torch
import torch.nn.functional as F
from mmcv.ops import point_sample, rel_roi_point_to_rel_img_point
from mmdet.core import bbox2roi, bbox_mapping, merge_aug_masks
from .. import builder
from ..builder impo... |
8f9e1de7b2ac788d0ade2be02d114994e853d25fc144bee33f6b48804920ac66 | Python | 9,097 | 328 | # -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import seaborn as sns
from sklearn import metrics
from .utils import two_array_to_edges_set
def plot_ratios_curve(ratios, label=None, diag_line=True, grid=True, tight_layout=True,
xlabel='Normalized... |
c5f4391257f8aeca1c5f7cc3fbad73f341d89c8cef7268ce527a4021839f88d4 | Python | 9,098 | 242 | # 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... |
30f4caadb69e63a5815a22e8f5234690713001eb86942fd53f312686979a02ed | Python | 9,099 | 248 | """Parser for GAF/HPOA and related association formats"""
import logging
import re
from dataclasses import dataclass, field
from typing import Dict, Iterator, List, Optional, TextIO, Union
from oaklib.datamodels.association import (
Association,
NegatedAssociation,
ParserConfiguration,
PropertyValue,
... |
e603d7720ffccb493215ab816e7dd50556f46f00fe2547e97558b10062847a6e | Python | 9,099 | 261 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Dict, List, Union
import warnings
import pandas as pd
from Bio import BiopythonWarning
from tmkit.sequence.PDB import P... |
162875180a55f01f5586cc918513d45f2e8896ccc77a34a42a641790b3d5d19d | Python | 9,102 | 301 | # Code written by: Maksim Imakaev (imakaev@mit.edu)
"""
This file contains a bunch of method to work on contact maps of a Hi-C data.
"""
from __future__ import absolute_import, division, print_function, unicode_literals
import sys
import warnings
import numpy as np
from polychrom.polymer_analyses import calculate... |
a118cf8a804e72e8efa757c5c1aaa97356b6dc40324aafa9bd8776285fa3ce74 | Python | 9,102 | 237 | import torch.nn as nn
from torch.nn import Parameter
import torch.nn.functional as F
import torch
from torch import Tensor
from torch.optim.optimizer import Optimizer, required
from torch.autograd import Variable
from torchvision import models
from collections import namedtuple
from .Inpaint_base_model import *
class... |
d2188d0a5088ba8c48c8d83d5039b8b9dac9d55bf5090807babedddbdb054850 | Python | 9,105 | 257 | import torch
import torch.nn as nn
from mol_tree import Vocab, MolTree, MolTreeNode
from nnutils import create_var, GRU
from chemutils import enum_assemble
import copy
MAX_NB = 8
MAX_DECODE_LEN = 100
class Motif_Generation_bfs(nn.Module):
def __init__(self, vocab, hidden_size, device):
super(Motif_Gener... |
4824844090eba16168d2d6035b0b1321bbb2d50d9ec6cb40f5c3a00f9fd76da8 | Python | 9,106 | 235 | from pathlib import Path
from timeit import default_timer
from typing import List, Union
import numpy as np
# import open3d for io if built. Otherwise,
# the class will build, but no files will be loaded.
try:
import open3d as o3d
o3d_warn = False
except ModuleNotFoundError:
o3d_warn = True
try:
imp... |
408db4952ac003d9cc9a7a98c572773cbefcfa0df8e219628b06ed4ef15490f5 | Python | 9,107 | 208 | import numpy as np
import pandas as pd
import scanpy.api as sc
import anndata
import bbknn
import os
from scipy import sparse
import pickle
from multiprocessing import Pool
from sklearn.metrics import auc, roc_curve
import sys
from read_pickle_data import *
sc.settings.verbosity = 3 # verbosity: errors (0), warnings ... |
636e76b8f433e6a2056554e680b246ef8563b1db96a49908d7f60b52cfcd2560 | Python | 9,109 | 265 | # --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick and Xinlei Chen
# --------------------------------------------------------
from __future__ import absolute_import
from __future__ i... |
85c406eda0200f73babc90c828cd9652c54692ede24e1db18ce74cfb06e9e9ba | Python | 9,110 | 239 | #!/usr/bin/env python
# Copyright 2016 Johns Hopkins University (Author: Matthew Wiesner)
# Apache 2.0
# ======= Prepare dictionary directory (e.g. data/local) from lexicon.txt =====
# This script takes a valid kaldi format lexicon (lexicon.txt) as input and
# from it creates the rest of the files in the dictionary d... |
1a4c80f43a3a50fd1fbeca22268558172949e6c99273ccc35246e64f204bbb5f | Python | 9,113 | 229 | #!/usr/bin/env python3
"""
File: create_cf_correlation_heatmap.py
Created: 2022/01/25
Last Changed: 2022/02/10
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... |
d20ac8175c53e57c73537350f85ca76192ed2876284583b1982a4f1d490ffc49 | Python | 9,113 | 253 | # 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... |
ebc2d0f19880f3d4cdab767dd41138f7c1c1dabf37f88a7ac75254bd86079d54 | Python | 9,113 | 280 | #%% [markdown]
# # Larval *Drosophila melanogaster* brain connectome
#
# Recently, authors mapped a connectome of a *Drosophila melanogaster* larva. This
# synaptic wiring diagram is comprised of 3,013 neurons and over 544,000
# synapses. Importantly, this work yielded a complete reconstruction of both the left
# and r... |
97aa174d6c98a47862c244982ffef48728be1492e6dce50a117fcf1e670a1bec | Python | 9,115 | 303 | """
<Script to read Nifty data and corresponding labels in CSV file, and save data as binary file>
Copyright (C) <2019> <Cecilia Ostertag>
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 Foundat... |
c982a1a0af98247ff2d12077761b4cdf451a777c259e330d1f15cd11718b6e4a | Python | 9,117 | 261 | import logging
from abc import ABC
from dataclasses import dataclass, field
from enum import Enum
from typing import Dict, List, Tuple, Iterable, Union, Iterator, Optional, Any
from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface, RELATIONSHIP_MAP, RELATIONSHIP
from oaklib.types import CURIE, ... |
1534cb2c2d7ef6d52cd68cd2125f3287618385547bb5901d97b7da3b8ada53e5 | Python | 9,120 | 196 | #!/usr/bin/env python3
"""Read and change a running CARLA server's WorldSettings, then verify.
Commands:
show print the current WorldSettings (+ derived fps)
sync --fps 20 enable synchronous mode at a fixed step
sync --delta 0.05 same, giving the step d... |
4c378125ee9b20be3dde9c8bdab9cd677140b834edbd25b0b1620ef46f66213b | Python | 9,120 | 228 | #!/usr/bin/env python3
"""
File: simple_cell_fraction_gene_correlations.py
Created: 2021/02/02
Last Changed:
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
... |
0703cf168fe08110bfde32807503d3ea4b93edfb48ef88b7ecf291ac55ad6116 | Python | 9,123 | 258 | # Copyright 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 agreed to... |
0b44142eef35bac51f0f45914129a31d0932716a74c4b730c078f5cb6c83555b | Python | 9,128 | 254 | # Built-in
from typing import Any
# Third-party
import brian2 as b2
from brian2.units import *
# Local
import cxsystem2.neurodynlib.neuron_models as nd
"""
This module is a stub. It contains placeholders for multicompartment neuron models.
"""
class LeakyCompartment(nd.PointNeuron):
"""
Not implemented!
... |
7223f50129a96e501e0635642577996dca6e2c5006fa2933c9a37f02ad213512 | Python | 9,131 | 346 | #!/usr/bin/env python3
"""
I/O and related utils.
Attributes
----------
EXT_1D : list
List of supported TXT/1D file extensions, in lower case.
EXT_MAT : list
List of supported matlab file extensions, in lower case.
EXT_ARRAY : list
List of supported 1D and 2D array-like file extensions, in lower case.
EXT_... |
b40ba40da8bd41f3dcf07d7b396d836bee0fd5bac498831d8db349cc7f6e048d | Python | 9,139 | 215 | """
File: gene_network_decomposition.py
Created: 2020-04-30
Last Changed: 2021-01-08
Author(s): H.H.Wiersma
Code to create distribution plot and a mask image used in the research plan
Copyright (C) 2019 H.H.Wiersma
This program is free software: you can redistribute it and/or modify
it under the terms... |
d7ee578eb4f759381946c6e71c2e3f1548cda7c562426d4219cd1afb7342ab2b | Python | 9,144 | 239 | import sys
import time
import random
import numpy as np
import scipy.spatial as sp
import matplotlib.pyplot as plt
from voronoiUtilities import *
class Voronoi:
def __init__(self, Nx, Ny, shape, notchWidth, lamda, seed=1):
"""
Nx,Ny: number of points along each dim
notchWidth: number of mi... |
630c611027447f1817b6da30d78f571e6a0a7710524c259cd9a297c9ed3bf461 | Python | 9,148 | 325 | import sys
import pandas as pd
import numpy as np
import os
from itertools import groupby
import utils.general_utils as general_utils
import utils.plot_utils as plot_utils
import utils.plot_setting as plot_setting
import utils.math_utils as math_utils
import utils.sync_utils as sync_utils
import utils.list_twoP_exp a... |
1722e5331b6286857e15537a9abb3dbd2ef3b90bb602eb27fb19428c1b89e6e3 | Python | 9,149 | 257 | #!/usr/bin/env python3
"""
File: visualise_cell_fractions.py
Created: 2020/11/24
Last Changed:
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 Softwa... |
2e2c06275af93aed846c2072c37d9ad246f57489176db289cdd02da56d11c715 | Python | 9,152 | 280 | import torch
# Original implementation:
# https://github.com/warmspringwinds/pytorch-segmentation-detection/blob/master/pytorch_segmentation_detection/utils/flops_benchmark.py
# ---- Public functions
def comp_multadds(model, input_size=(3,224,224), magnitude='M', half=False):
assert magnitude in ['K', 'M', 'B']
... |
e0b62998b5f72443e14f175d624d92e2d49be1693369bd99fc0d696ae8f98432 | Python | 9,161 | 226 | import os
from os.path import join
import numpy as np
import pandas as pd
from collections import OrderedDict
from itertools import chain
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import ShuffleSplit
from sklearn.model_selectio... |
d1d1062854cc049627cea6ee710e4505bae8aa89810755595bd88ab3e00d4db4 | Python | 9,162 | 249 | from __future__ import annotations
from qtpy.QtWidgets import (
QDialog,
QLabel,
QVBoxLayout,
QHBoxLayout,
QPushButton,
QStyle,
QTreeWidget,
QTreeWidgetItem,
)
from qtpy import QtCore
import logging
from magicgui.widgets import LineEdit
from .image_pipeline import ImagePipeline
class ... |
24aa173d690e1cc4b5eba2b12e63751eac451777cf3a932640cc12bca3649d2f | Python | 9,166 | 204 | #!/usr/bin/env python3
"""
File: create_psychencode_idlinks.py
Created: 2021/10/08
Last Changed:
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 Sof... |
8c53bcef678a0b8bc74af61bd8b0d0646451591625c869d81dc151257efe2172 | Python | 9,167 | 232 | # 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... |
9b36128cbd5299e9eda8c500266c445be0c49746fde9b7ea66b3e65ac8607237 | Python | 9,168 | 259 | import logging
import os
import os.path as osp
import time
from collections import OrderedDict
import numpy as np
import torch
from torch.utils import model_zoo
import torch.distributed as dist
import mmcv
from mmcv.runner.utils import get_dist_info
from tools.multadds_count import comp_multadds_fw
def set_data_pat... |
6e0bca113af77f78f2d93911c3896312c057def49493248ff95192897ab138be | Python | 9,171 | 206 | # Copyright (c) 2016, Konstantinos Kamnitsas
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the BSD license. See the accompanying LICENSE file
# or read the terms at https://opensource.org/licenses/BSD-3-Clause.
from __future__ import absolute_im... |
94958add42aae048c20cdeab683b99231c1bf4150c063c25573913d97121df30 | Python | 9,173 | 237 | #!/usr/bin/env python3
# encoding: utf-8
# @Time : 2018/10/3 下午1:45
# @Author : yuchangqian
# @Contact : changqian_yu@163.com
# @File : syncbn.py.py
"""Synchronized Cross-GPU Batch Normalization Module"""
import collections
import threading
import torch
from torch.nn.modules.batchnorm import _BatchNorm
from to... |
1d5c875407d634d26f2318ff189d5574d9e7868fcd0bb33e88e6e30f47fa7384 | Python | 9,176 | 291 | from __future__ import absolute_import, division, print_function, unicode_literals
import copy
import json
import logging
from collections import OrderedDict
from . import (
fbnet_builder as mbuilder,
fbnet_modeldef as modeldef,
)
import torch.nn as nn
from . import fpn as fpn_module
from maskrcnn_benchmark.m... |
bece587edd6225c4d1b8a23653db1fec02de2e30754627cf69938e9f1bc82258 | Python | 9,181 | 252 | import numpy as np
import tensorflow as tf
import pathlib
import json
from datetime import datetime
from mip.get_nn import get_nn
import time
from multiprocessing import Pool
import os
from helper.misc import infer_and_accuracy, clear_print, printProgressBar
from helper.misc import extract_params, get_weighted_mean_bou... |
fe5110644dc0b1435d14755b42790d660b9de9126b6649fec39722e9c3eec4c7 | Python | 9,183 | 219 | """
File: create_deconvolution_matrices.py
Created: 2020/04/07
Last Changed: 2020/07/15
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 Found... |
6dffaa67d1b9bdb10e1081bf03720b4a4f0f39ee875e34ce53a0b2dab7edd8c6 | Python | 9,186 | 319 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib.patches import Circle
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mpl_toolkits.mplot3d.art3d import Poly3DCollection
from sci... |
077ff0ef08474d8a2a8fed8b32c3a993d147788c11bdc5a558d3cad5c5df4cfc | Python | 9,187 | 205 | from modules.parameters import ParameterSet, ParameterSpace, extract_nestvalid_dict
from modules.input_architect import EncodingLayer
from modules.net_architect import Network
from modules.io import set_storage_locations
from modules.signals import iterate_obj_list
from modules.analysis import single_neuron_dcresponse
... |
67b1d558e52db7c1b7b37534ea160b526eb3fad7e2e924488a0525e5a68a586c | Python | 9,187 | 256 | from __future__ import division
from future import standard_library
standard_library.install_aliases()
from builtins import zip
from builtins import range
from builtins import object
from past.utils import old_div
# Unit tests for sima/motion/_hmm.py
# Tests follow conventions for NumPy/SciPy avialble at
# https://gith... |
50d3f826acd0667ed9d1ab51a04a8e5eead9163506d6613f0d4bd76f77164563 | Python | 9,190 | 358 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Any, Dict, Tuple
import pandas as pd
from tmkit.property.HelixSurface import HelixSurface as hs
def generate_helix_su... |
24fb9b76d1f029e6c1297d989bed2c032d9d2afe5ffffb36fe1781d8520f8bea | Python | 9,191 | 275 | from collections import namedtuple
import numpy as np
import pandas as pd
from graspologic.utils import remove_loops
from scipy.stats import combine_pvalues
from statsmodels.stats.multitest import multipletests
from .binomial import binom_2samp, binom_2samp_paired
from .utils import compute_density
# from .combine i... |
8388435ef436ad9658cf7c1a2815c8af90b5b2a8cd106f64828549d59e75d4ec | Python | 9,191 | 247 | # Copyright 2020 Google Research. All Rights Reserved.
#
# 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... |
db395b303fabbc38c40309a11fdfa105316993410c6bbd1accef3e20986ba0e3 | Python | 9,192 | 188 | #
# 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... |
eb1254857a22201d9b7e363bf71280ab452e3f815f5b9db115c8031e6a8ad5ff | Python | 9,192 | 286 | import argparse
import yaml
from model.dataloader import TripletData
from model.model import PairModel, TripletModel, TripletGraphModel
import os
import torch.utils.data as Data
import torch
import random
import numpy as np
import pandas as pd
from tqdm import tqdm
import sys, os
def build_dataset(cfg, train=1):
... |
b542cf04fc7677e9fd2ccfb9abd6337d8584b7cb1ac0d8ff20295075b5042bdb | Python | 9,194 | 218 | # 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... |
f3f428107adabbe9dbfeda39972cde458b43a1d233f74cd53a2cc7e599f35503 | Python | 9,194 | 217 | """Command line client logic for postprocessing Finnish parliament data."""
import json
import re
from datetime import date
from logging import Logger
from pathlib import Path
from typing import Any
from typing import Dict
from typing import List
from typing import Optional
from typing import Tuple
import pandas as pd... |
dd9db9484cfab8f1091ed6da15c27be2986138f60da9d254623cab28742320fd | Python | 9,195 | 223 | # basic imports
import numpy as np
import pickle
import matplotlib.pyplot as plt
def count_points(replays: list, width: int, height: int, bin_size=1) -> np.ndarray:
'''
This function counts how often replays start in a given area of the environment.
Parameters
----------
replays : ... |
59be13e047518d8632105d1dbee2fa940eb0580262b2048c601078c270c6eb60 | Python | 9,198 | 203 | #%%
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... |
3e976fbc9d39468d71b1e64b70a1702b16fd797b43b1caa879c6a80dd55fb778 | Python | 9,206 | 204 | ####################################################################################################
# Copyright (c) 2019 - 2021, 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 ... |
741846e94aad3a342c4f4144552037e46a9b77fcfb226979983c2af7a28b30b5 | Python | 9,207 | 321 | from matplotlib import pyplot as plt
from matplotlib import patches as mpatches
from matplotlib import lines as mlines
from matplotlib.legend_handler import HandlerLine2D, HandlerTuple
import numpy as np
def panels( w,pf,pm,r,
my_xlims = [0,200],
my_xticks = [0,50,100,150,200],
dm... |
0f92057bc1809e6b46036e311b2af1c20cf7aa8e18c9d3148126e70e69c9c5ca | Python | 9,210 | 335 | #import packages
import networkx as nx
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from pytorchtools import EarlyStopping
from scipy import spatial
from scipy.spatial import cKDTree
import scipy.sparse as sp
import time
import json
from networkx.readwrite... |
e8583b33d9ca80e92c8cc577db00343d7445fab154a2487b3e848c32bb421535 | Python | 9,216 | 234 | import json
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
import seaborn as sns
import matplotlib.pyplot as plt
import sklearn.metrics
import os
from IPython.core.debugger import set_trace
"""
parse_json_tmscore_rocauc.py: Compute the ROC AUC values for MaSIF-ligand and ProBiS
Pablo Gainza - LPDI STI EP... |
2e661f20964e037fecba97e48c52002c3f42da9ba7abe99c16b747c28e336e03 | Python | 9,220 | 294 | import os
import pika
from multiprocessing.pool import ThreadPool
import threading
import pickle
from functools import partial
from typing import Tuple
from queue import Queue
import time
from abc import ABCMeta,abstractmethod
import sys
sys.setrecursionlimit(100000)
import functools
import termcolor
import datetim... |
d75d60248e1409391443a1d7b36e23c0f3efb345dbd74a19932ce200cd066a4f | Python | 9,221 | 361 | # %% [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... |
6fa7632ba2097008862bea7272e2af81a953750f1a5d9862ef398e27686a2eb9 | Python | 9,222 | 302 | import os
import cv2
import json
import logging
import numpy as np
from heapq import heappushpop, heappop
from shutil import rmtree
import torch
from ..rl.genotypes import OP_NAMES, AGG_NAMES
def load_ckpt(ckpt_path, ckpt_dict):
logger = logging.getLogger("maskrcnn_benchmark.nas.helpers")
best_val = epoch_... |
29249cd3e3d180bf0b04274ba869c4d48d861ce9b970c04d22593d974a5adfce | Python | 9,224 | 203 | # Copyright 2020-21 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... |
f0f9dccea4b6f071d7dc03e87c3bd49016e7400551995188e3224327033b29b6 | Python | 9,230 | 240 | # -*- coding: utf-8 -*-
"""
Created on Mon Dec 6 23:35:24 2021
@author: Fuyuki Asano
"""
import glob
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import sys
import os
from scipy import signal
import csv
import math
import statistics
import scipy
#mac
#p... |
3b4eba5a03d6c7571a930704abfbe24ebe88d29fad8f80b98ce967a1105cdbf6 | Python | 9,233 | 318 | import os
import operator
from collections import Counter
import numpy as np
from scipy import sparse as sp
from scipy.sparse import csgraph
from scipy.spatial import cKDTree
from meshparty import trimesh_io
import networkx as nx
import h5py
from . import ngl
MESHMETA = trimesh_io.MeshMeta()
MITOMESHDIR = "data/mit... |
5c86313a5077feb59bab2a10248c834ee4ff15b523bb4ec7793bf069b630775f | Python | 9,234 | 201 | import tensorflow as tf
from tensorflow import keras
from tensorflow.keras.layers import LSTM, Dense, Dropout, Activation, SimpleRNN, Bidirectional, Flatten, BatchNormalization, AvgPool1D
from tensorflow.keras.layers import Conv2D, MaxPool2D,Reshape
import numpy as np
def Model_acp():
# left model: Conv + cha... |
13b730a3f0af6c165e308f7ff79ee14aeac872aa8682506d1369086850aa8c6f | Python | 9,235 | 312 | from napari import Viewer
from napari.qt import thread_worker
import os
from .processing import ImagePipeline
from .processing.steps import *
from qtpy.QtWidgets import (
QDialog,
QErrorMessage,
QLineEdit,
QPushButton,
QWidget,
QVBoxLayout,
QHBoxLayout,
QLabel,
)
from qtpy.QtCore import... |
ed78c78639472360eb54bacb33a2ef3f7ba8f7f2c087d69233c907a1fafe0485 | Python | 9,236 | 252 | """``Capture`` honours the ``aovs`` tuple literally.
``semantic`` writes ``semantic_<camera>.mp4`` (CityScapes palette, the source
``--mask-classes`` needs) and ``instance`` writes the instance-coloured
``seg_<camera>.mp4``; asking for both gives both, from two sensors, frame for
frame.
The CARLA sensors are faked — ... |
11a9acaea22a3f341f0a0309871fc3e81bd8a7d629d7ba7853b3ee90de61b77c | Python | 9,246 | 228 | # Copyright 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 agreed to... |
17e455a34351a886ac0b9f86181424f34a0c6fc4a38789d33ac07df88d7830de | Python | 9,248 | 277 | import numpy as np
from scipy.stats import gamma
import nibabel
from scipy.stats import zscore
from scipy import signal # for detrending
from scipy.ndimage import gaussian_filter # for smoothing
from numpy.linalg import pinv
from scipy import stats
from scipy.stats import t as tdistribution
def hrf_convolve(X, hrf)... |
cd81a9344f7e5c8a7afe671b1c8b8eb4cade96980f6c510567854dd1d3fa6eca | Python | 9,249 | 291 | import torch
import torch.utils.data
from torch import nn
from torch.nn import functional as F
import numpy as np
import argparse
class ModelFactory:
@staticmethod
def create(args):
if args.n_layers == 1:
if args.gating == "manual":
return Gatednet(args)
elif ar... |
c7370d5f8f9413560ae74c20e543c4d9fe85087bf82f7b292569ee6f032723b5 | Python | 9,254 | 192 | """Shared torchrun rank supervisor (``cosmos_workers.common.ranks``) with the fake engines on CPU.
The multi-rank cases launch two real ``torchrun`` ranks that rendezvous over gloo; they need torch in the
test interpreter (the model venvs have it; a bare API venv does not -> skipped with the reason).
"""
from __futur... |
bddfa9909e5527ffa908c10a90e959247b98b360fe2b47669268366a361c7f4b | Python | 9,255 | 288 | '''
Created by: Zhiqing Guo
Institutions: Hunan University
Email: guozhiqing@hnu.edu.cn
Copyright (c) 2020
'''
import torch
import torch.nn as nn
import math
import torch.utils.model_zoo as model_zoo
import torch.nn.functional as F
__all__ = ['ResNet', 'resnet18_mta', 'resnet34_mta', 'resnet50_mta', 'resnet101_mta',
... |
ccd927355abade3177753f4252fb6a972ebef592a7ab54148df0eb2b068f4671 | Python | 9,257 | 192 | import math
from pathlib import Path
import cv2
import numpy as np
from .saveFilesC import saveFilesC
class positiveStrideC:
def __init__(self):
super().__init__()
def positiveStride(self):
acceptance_boolean, overlapping_percentage = (
self.check_if_lesions_and_gland_mask_over... |
ddb7c34d3244c0257da1da39f265b21e77e722e0bbe38291a35f2568cc738cee | Python | 9,257 | 200 | # basic imports
import os
import pickle
import numpy as np
import matplotlib.pyplot as plt
def count_pairs(replays: list) -> (list, list, list):
'''
This function counts the number of forward, reverse and unordered replay pairs.
Parameters
----------
replays : A list... |
5b76d57457bf5ad7d7c04ea2b939cf50d762381ac4e2578ffc6848cc1f5e8964 | Python | 9,266 | 196 | import numpy as np
from nipype import Workflow, Node, MapNode, IdentityInterface
from nipype.interfaces.fsl import maths, BET, MCFLIRT, FLIRT, ApplyXFM, ImageMaths, Smooth
from qipype.fitting import LtzWaterMT, LtzWaterMTSim, LtzAmNOE
from qipype.commands import ZSpec
from qipype.utils import PCA, Select
def prep(zfr... |
0941fa791d1fa0e24fc4da62982cb4f661f8ecb1649c091f96428af8093bcb57 | Python | 9,268 | 218 | import os
from bruker2nifti._utils import bruker_read_files
from bruker2nifti._getters import get_list_scans, get_subject_name
from bruker2nifti._cores import scan2struct, write_struct
class Bruker2Nifti(object):
"""
Facade to collect users preferences on the conversion and accessing the core methods for the... |
e5c1b4e69e6cbfbbea9ef2a85ffe5e953193208bebc3c7ba96dac41a7cb79bf5 | Python | 9,274 | 275 | # Built-in
import json
import pickle
import re
import zlib
from pathlib import Path
from typing import Any
import brian2.units as b2u
# Third-party
import numpy as np
class SpikeData:
def __init__(self, filename: str | Path) -> None:
self.data_filename = filename
self.filename_stem = Path(file... |
a7b69db47b6df51d62dcc85d8b68da938236cf16e222a16f14c3d09abf3b605d | Python | 9,277 | 234 | from torch_geometric.loader import DataLoader
from typing import Tuple
import torch
import torch.nn as nn
import random
import numpy as np
import matplotlib.pyplot as plt
from sklearn import metrics
import pandas as pd
import os
class TargetSelectTransform(object):
def __init__(self, target_id=0):
... |
f8b281e16cdfd723e7f57144a51b735132d501aaa65cf83708239f52dfc2038f | Python | 9,278 | 287 | '''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import numpy as np
import pickle
from torch.utils.data import WeightedRandomSampler, DataLoader, TensorDataset
import pandas as pd
import torch
def load_train_... |
c4974fe611cec4436c082c6b4aaae5dd1919f9ab5daeceac960109a60e6832a1 | Python | 9,281 | 216 | import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule, xavier_init
from mmdet.core import auto_fp16
from ..builder import NECKS
@NECKS.register_module()
class FPN(nn.Module):
r"""Feature Pyramid Network.
This is an implementation of paper `Feature Pyramid Networks for Object
... |
06e30f01551fc3d0d1d31bcb7934a5fbb01a47ac0db88626260096c398dd09cd | Python | 9,282 | 277 | '''
Information about cell folders
This is only useful for data with old formats, except cell_orientation.
'''
import os
import re
import datetime
from clampy import *
import yaml
import numpy as np
__all__ = ['read_lab_notes', 'is_PIV', 'protocol', 'protocols', 'stimulus_time', 'protocol_description',
're... |
9aa7c1195094df5ba10a6b3552fec0ccc52c72f5e92e75410f7aa4eb07c3a9a2 | Python | 9,282 | 216 | import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule, xavier_init
from mmcv.runner import auto_fp16
from ..builder import NECKS
@NECKS.register_module()
class FPN(nn.Module):
r"""Feature Pyramid Network.
This is an implementation of paper `Feature Pyramid Networks for Object... |
b7abdcae287546455917ffa83c3f2daea90397da8d32e5c66afba3eb123c011e | Python | 9,288 | 256 | #!/usr/bin/env python3
"""
File: compare_inter_matrices.py
Created: 2020/04/06
Last Changed:
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 Softwar... |
8614815d130da8b545b3dcd2be236ba736f1d61ebb84f62556523e5b56262822 | Python | 9,293 | 302 | # To add a new cell, type '# %%'
# To add a new markdown cell, type '# %% [markdown]'
# %%
from IPython import get_ipython
# %%
# General imports
import os
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import statsmodels.api as sm
from IPython.display import display
#... |
bc2a53146cebb98c15b9143373fccc519ed994374f223582f449dc5a62b310fc | Python | 9,294 | 244 | #!/usr/bin/env python3
"""
File: gene_expresion_cohort_correction.py
Created: 2020/08/31
Last Changed: 2020/09/02
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 publishe... |
231ecba5ea4b311b9d53ebbaa3a8acacede0beba566a41096db0cce4addff717 | Python | 9,296 | 289 | # -*- coding: utf-8 -*-
import numpy as np
from sklearn.neighbors import NearestNeighbors, KDTree
from scipy.spatial.distance import cdist
from scipy.special import psi
from . import utils
def cal_mi_from_knn(x, y, n_neighbors=3, norm=True, norm_mode='min'):
"""Compute mutual information between two continuous v... |
e6ee66d12c08b612a2ee7d9e60b7ff992f31f0d0bdb1c431ae5ed60145f63c16 | Python | 9,297 | 234 | #!/usr/bin/env python3
"""
File: create_extra_CIA_jobs.py
Created: 2020/10/25
Last Changed: 2020/10/27
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... |
dc85d971f96f78c8e94856d679531ea77260d158b2d61a9946e67e7237891b58 | Python | 9,299 | 215 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Variational Animal Motion Embedding 0.1 Toolbox
© K. Luxem & P. Bauer, Department of Cellular Neuroscience
Leibniz Institute for Neurobiology, Magdeburg, Germany
https://github.com/LINCellularNeuroscience/VAME
Licensed under GNU General Public License v3.0
"""
import... |
f34e6caf238b7307c374c8b62d525bc6fe2ea932bee459607d889cc400fc355c | Python | 9,300 | 320 | import torch
import torch.nn as nn
from torchtext.legacy.data import TabularDataset, Field, BucketIterator, Iterator
import random
import os
from src.utils.tokenizer import smi_tokenizer
from src.transformer import Encoder, Decoder, Seq2Seq
def init_weights(m: nn.Module):
if hasattr(m, "weight") and m.weight.di... |
00499948919223de119d44c6c8068ce98912fa1b42aac0b96c7baebfe70faa61 | Python | 9,306 | 214 | import numpy as np
import imageio
from pathlib import Path
from scipy import ndimage
import skimage
from tqdm import tqdm
import shutil
import flexsim
def write_playdoh_volume_stats(obj, out_folder):
mat_counts = obj.get_stats()
labels, nfeatures = ndimage.label(obj.volume == 2)
sample_class = nfe... |
04efcb72fd6fa0be90e3d4461c129a2e1042064e676d381ab88e95740fae6e5a | Python | 9,309 | 183 | import ship_pairing_analysis
import collections
import pandas as pd
import inspect
import re
import os
import numpy as np
import itertools
import tqdm
import AIS_interp
import functions_basic_sak as funsak
from sklearn.cluster import DBSCAN
from scipy.interpolate import interp1d
import AIS_infer_mmsi
... |
dc83445361bde380fe2451eb5ca00961bc4552080f61a1529a485c2a4a52d503 | Python | 9,309 | 249 | import sys
import time
import torch
import random
import argparse
import numpy as np
from voronoi import Voronoi
from joblib import Parallel, delayed
sys.path.append('../generation')
from voronoiUtilities import *
sys.path.append('../learning')
from model import *
from utilities_gru import getNotchEdges
from utilities... |
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