sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6c4e77b00d6291a825445eea60772534897a5b80d4813f64f0b02f087b707eb2 | Python | 6,456 | 231 | """Functions to process data."""
from typing import Optional
import mne
import numpy as np
from scipy import signal
from osl_dynamics.utils import array_ops
def standardize(x: np.ndarray, axis: int = 0, create_copy: bool = True) -> np.ndarray:
"""Standardizes a time series.
Returns a time series with zero... |
9b59c8239e416c6163b3d8b6948b4b42d473cf25206c3e030d643c89958a4319 | Python | 6,456 | 140 | import os.path
import glob
import argparse
parser = argparse.ArgumentParser(description='Make Molgenis Compute samplesheet for ENA.')
parser.add_argument('samplesheet', help='CMC samplesheet from synapse')
parser.add_argument('cram_dir', help='path to cram file dir for input')
parser.add_argument('fastq_dir', help='pa... |
cd0f99b1fb99b2bbe8f23baac0920e958f499d4f3cfac5b5955f2edc0db5a8ae | Python | 6,457 | 220 | # 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 ... |
fc0a8553034def7002d42a2082e069b642c48d834690199f8d194d895d8dd8ec | Python | 6,457 | 149 | """Dual-valence MB model — Bennett 2021 MV formulation, ported to the
larval Drosophila connectome.
This is the Phase 3i upgrade from the single-valence dual-DAN model. It
implements the canonical Bennett-MV equations with parallel appetitive
and aversive memory traces, modulated by cross-valence DAN feedback:
m+... |
3c4df3a1bb749aacab7c0cc6832a20b86173f3d301e73b020eef563a21f2fbd2 | Python | 6,461 | 172 | """
Copyright (C) 2019 NVIDIA Corporation. All rights reserved.
Licensed under the CC BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode).
"""
import torch
import torch.nn as nn
class InstanceNorm(nn.Module):
def __init__(self, epsilon=1e-8):
"""
@notice: avoid... |
b0234eef31629ba10d98e2bc36d0c0df1449bca1dde559c31c5175c6fe38ee49 | Python | 6,461 | 146 | import torch
from .basic_model import BasicModel
from . import networks
from . import losses
class VaeBasicModel(BasicModel):
"""
This is the basic VAE model class, called by all other VAE son classes.
"""
def __init__(self, param):
"""
Initialize the VAE basic class.
"""
... |
94b18c3b01461c7df3824726ee3511c592d49646b5e50fc65a574c40f121a49f | Python | 6,463 | 166 | import glob
import sys
from timeit import default_timer as timer
from datetime import timedelta
from pathlib import Path
path = str(Path(Path(__file__).parent.absolute()).parent.absolute())
sys.path.insert(0, path)
from random import randrange
import pyslow5
import numpy as np
import click
import tensorflow as tf
from... |
a8439687e8521aa645242921cd40a86beee6874b1177fea02c9bcfa69c2f5e91 | Python | 6,463 | 155 | import urllib
import requests
import logging
from dataclasses import dataclass, field
from typing import Any, List, Dict, Union, Iterator, Iterable, Tuple
from oaklib.datamodels import oxo
from oaklib.datamodels.oxo import ScopeEnum
from oaklib.datamodels.text_annotator import TextAnnotation
from oaklib.datamodels.vo... |
3d5d50c492d02c12db576403e3066b70c42fcf9f8683509f5ff1feba0fc93aec | Python | 6,464 | 186 | import time, warnings
warnings.filterwarnings("ignore")
from tqdm import tqdm
import numpy as np
import torch
import torch.nn.parallel
import torch.optim
import torch.utils.data
from torch.cuda.amp import autocast, GradScaler
from utils.metrics import (
AverageMeter,
dice_coefficient,
dice_per_region,
)
... |
233c5a53ab7f842351fd67ab654122fdc20979d532d703fd63967cd607fb302c | Python | 6,465 | 160 | import kgcl_schema.grammar.parser as kgcl_parser
import pytest
from kgcl_schema.datamodel import kgcl
from linkml_runtime.dumpers import yaml_dumper
from oaklib import BasicOntologyInterface, get_adapter
from oaklib.implementations.tabular.robot_template_implementation import (
template_modify,
template_slice,... |
841b3bc47893c1b9f00fd3c230ce03f83685f090433fc9a9ca9c47afc0ac4fc7 | Python | 6,465 | 159 | # %%
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import re
from pymaid_creds import url, name, password, token
from data_settings import data_date, pairs_path
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
from contools import Celltype, Celltype_... |
dd9c7844587d4febfc71443934bf8691a3e3f055d9b40652126222de11ebbe73 | Python | 6,468 | 188 | """Graph encoders."""
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import manifolds
from layers.att_layers import GraphAttentionLayer
import layers.hyp_layers as hyp_layers
from layers.layers import GraphConvolution, Linear, get_dim_act
import utils.math_utils as pmath
device ... |
5ddc54cac5735def6e77354c98b9dc88493ad0ce67a02d8403364aa7b21dc9bc | Python | 6,469 | 145 | # basic imports
import os
import numpy as np
import pickle
import pyqtgraph as qg
# framework imports
from cobel.agents.sfma import SFMAAgent
from cobel.interfaces.gridworld import InterfaceGridworld
from cobel.misc.gridworld_tools import make_gridworld
# store experiment directory
cwd = os.getcwd()
# shall the system... |
c5f97ab1b78f15092fbd733f868bf42aec03b47fd3b193a237258aaa4273389f | Python | 6,469 | 154 | import mne
import numpy as np
import matplotlib.pyplot as plt
import os
#import config_protoPPmusic_ConvolutionEGI as cfg
## logging info ###
import logging
from datetime import datetime
logname = './logs/' + datetime.now().strftime('log_%Y-%m-%d.log')
logging.basicConfig(filename=logname,level=logging.I... |
f042867dd9c7829930f83e6331145f903821616e1706485168d79642e14ed98f | Python | 6,469 | 143 | # config.py
import os.path
from .config_util import get_min_max_size, get_kmeans_wh_size, get_kmeans_area_size, size_index, conv4_3_size
# gets home dir cross platform
HOME = os.path.expanduser("~")
# for making bounding boxes pretty
COLORS = ((255, 0, 0, 128), (0, 255, 0, 128), (0, 0, 255, 128),
(0, 255, 2... |
3afcda77d36e28b63db691425f9d714e2261b78c1850c2fe3d594958c7979678 | Python | 6,471 | 164 | import functools
from inspect import getfullargspec
import torch
from .utils import cast_tensor_type
def auto_fp16(apply_to=None, out_fp32=False):
"""Decorator to enable fp16 training automatically.
This decorator is useful when you write custom modules and want to support
mixed precision training. If ... |
af5fced183b1501c558e572f76dd66588740b5211a95949dd4f64c2f86e6bc16 | Python | 6,473 | 177 | """The shipped models and the inference pipeline, against what 0.1.12 gave with the same weights.
reference_0_1_12.json was recorded by running pyoxynet 0.1.12's own test_pyoxynet on the bundled
example tests (see "recorded_with" in the file).
"""
import json
import pkgutil
import random
from io import StringIO
from p... |
200bc11de973fc78dec4f34b691e1a5621367ad85de8bf436408b65354141a99 | Python | 6,477 | 147 | # 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... |
2199663e844b93c01988906ecd757cb0444419450e363e7a069e5f42f7caa1f9 | Python | 6,481 | 177 | import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import RepeatedKFold,\
RepeatedStratifiedKFold,LeaveOneGroupOut, GridSearchCV, LeaveOneGroupOut
from sklearn.svm import SVC
from sklearn import metrics
from tqdm.auto import tqdm
def prepare_features(
... |
e698510805c4bf2dd7966f4d1a56da63d2192fbd39bed8049cdf8ce40f21b794 | Python | 6,485 | 224 | import argparse
import json
import os.path as op
from glob import glob
import matplotlib.pyplot as plt
import pandas as pd
import ptitprince as pt
import seaborn as sns
from kneed import KneeLocator
from numpy import mean
def _get_parser():
parser = argparse.ArgumentParser(description="Perform QCFC analyses")
... |
8a892231823ea0ce2b49b19b15a5943ce09ccf14e8c3a7b1af23715068705c00 | Python | 6,487 | 186 | """
DeepCT architecture (TODO: Add our names).
"""
import numpy as np
import torch
import torch.nn as nn
from torch.utils.tensorboard import SummaryWriter
class DeepCT(nn.Module):
def __init__(
self,
sequence_length,
n_cell_types,
sequence_embedding_length,
cell_type_embedd... |
d153101b830920c3f951186ddd87853aeb0a2d02ad561f9a3438bf1ca38355a7 | Python | 6,487 | 176 | #%%
import os
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/maggot_models/')
print(os.getcwd())
except:
pass
# %%
import matplotlib.pyplot as plt
import seaborn as sns
from graspy.plot import gridplot, heatmap
from graspy.utils import binarize, pass_to_ranks
from src.data import load_metagraph
... |
f03d651041aa6a4650b33be23da1d64e1bb81930f68138d4f278ea0bd512be8b | Python | 6,490 | 178 | # Copyright 2021-2022 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... |
d0f3cae3f3be77d65bdecab48049fe48e3119c45ebde7626c2ba6a47ea029da5 | Python | 6,494 | 155 | # 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>.
"""
Regression test for https://github.com/carla-simulator/carla/issues/9898:
sensor.camera.rt_lens'... |
221b5b325c067290bbaf42cfc3c221c7a659194cbe615ba585ef93a2f03369a2 | Python | 6,496 | 206 | import numpy as np
from skimage.feature import blob_log
import faulthandler
import dask
import dask.array as da
from dask.diagnostics import ProgressBar
from params import nC, sigma
faulthandler.enable()
from functools import reduce
import operator
from scipy.spatial.distance import cdist
import gc
import math
from i... |
f54904bc8655789f14a43b9d8cd3dbdb06eeda029889f3a762704ac1c1569005 | Python | 6,497 | 159 | # 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... |
a6ba0f503806222c089a09b1624db11bd27952ed60c468b2f9b496e343f2f76c | Python | 6,498 | 200 | #!/usr/bin/env python
# Read a fasta file of reads, and a fasta file of primers. Find
# multiple occurrences of primers at the end of reads, and chop them
# off. Write a new fasta file.
# Some reads are so scrambled that it isn't obvious what to trim, or
# that they contain any useful sequence at all. A conservative
... |
68d1aff3e6e1992626cb440182dde7f780939939ad6aeb06645637b3a3440443 | Python | 6,499 | 185 | #!/usr/bin/env python3
import glob
import itertools
import os
import pytz
import click
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.signal as sg
from sklearn.linear_model import LinearRegression
# Input/Output Directories
SRC_DATA_DIR = "./AlanaDISData"
DEST_DATA_DIR = "./Alan... |
2abd2118c5173b9c84ab0d6fceed360ab79a1719526bb577429a1c3b698ad69e | Python | 6,502 | 185 | # 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... |
fb6e0699e9ab1d0a726c8ec5f9f8c0220e296e2722a7d60325ff75862afcf468 | Python | 6,506 | 211 | import torch
import torch.nn as nn
from torch.autograd import Function
from torch.autograd.function import once_differentiable
from ..utils import ext_loader
ext_module = ext_loader.load_ext('_ext', [
'sigmoid_focal_loss_forward', 'sigmoid_focal_loss_backward',
'softmax_focal_loss_forward', 'softmax_focal_los... |
5116e357a396ed5cbde6cfc6c87ed1644ed4bce832ccf22ae3ca8426217d983e | Python | 6,510 | 194 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module containing functions used for registration with cross-correlation.
For more details, see: Manuel Guizar-Sicairos, Samuel T. Thurman, and
James R. Fienup, "Efficient subpixel image registration algorithms,"
Opt. Lett. 33, 156-158 (2008).
Created on Mon Oct 29 ... |
fa9a39d8789edf0511272d15699d0066d4a5c66cd3d1b925b5a2d3ae00b21665 | Python | 6,510 | 127 | #!/usr/bin/env python3.9
# -*- coding: utf-8 -*-
"""
Run a model simulation from the arguments given in the command.
"""
import numpy as np
from iEEG_STC import utils
import models
import os
import sys
import time
import ast
import pandas as pd
t0 = time.perf_counter()
# Default parameters
params = {'N': 400, # Netwo... |
4199c06ebd79e60f4d553ac1e51f6cfac7da465294ec8c6d180df40485198b24 | Python | 6,524 | 167 | # 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
import array
import carla
import time
class TestV2X(SyncSmokeTest):
... |
2da859c3988d076393e4b2a6b8a44f3fabe908a9464e24829d9caef754adc752 | Python | 6,527 | 181 | import torch.nn as nn
from torch.autograd import Function
from torch.autograd.function import once_differentiable
from torch.nn.modules.utils import _pair
from ..utils import deprecated_api_warning, ext_loader
ext_module = ext_loader.load_ext('_ext',
['roi_align_forward', 'roi_align_b... |
62c7725643166bf0f690309766ca4fd25dc09935b82978887d8d5c284923ae65 | Python | 6,527 | 188 | # 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... |
b4822f582fc1c31a098a0df8c860dd656aff529b7d9870524695b9fd94707da6 | Python | 6,527 | 150 | import numpy as np
import torch
from mmdet.core import bbox2roi
from mmdet.models.losses import SmoothL1Loss
from ..builder import HEADS
from .standard_roi_head import StandardRoIHead
@HEADS.register_module()
class DynamicRoIHead(StandardRoIHead):
"""RoI head for `Dynamic R-CNN <https://arxiv.org/abs/2004.06002>... |
08454bd6436c8ac8229875df9247e53a34a21b0fd0fa7871ed847baa308371e3 | Python | 6,533 | 181 | from collections import namedtuple
import torch
from torchvision import models as tv
from IPython import embed
class squeezenet(torch.nn.Module):
def __init__(self, requires_grad=False, pretrained=True):
super(squeezenet, self).__init__()
pretrained_features = tv.squeezenet1_1(pretrained=pretrained... |
95bbc2ec10695d8e0eb5ae98bd448eb607f9cae286a8655e94d12206e739342d | Python | 6,539 | 204 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
from maskrcnn_benchmark.structures.bounding_box import BoxList
# TODO check if want to return a single BoxList or a composite
# object
class MaskPostProcessor(n... |
619e79563db4b0643ef651303fc57dbbdb8024b8bbaa3217457f236d49868d74 | Python | 6,540 | 161 | import argparse
import math
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
from pytransform3d.urdf import UrdfTransformManager
from pytransform3d import rotations as pr
from pytransform3d import transformations as pt
from dataloading.model import Camera
SKIP = -1
def parse_a... |
8df0cc8c10db0445309ba6fd86ebb2698179f8fc507fb52bd02a91e86db02d9f | Python | 6,540 | 156 | import pdb
import torch
import torch.nn as nn
from torchvision import models
class MRNet(nn.Module):
def __init__(self):
super().__init__()
self.model = models.alexnet(pretrained=True)
self.gap = nn.AdaptiveAvgPool2d(1)
self.classifier = nn.Linear(256, 1)
def forward(self, x):... |
ca48e54c0db09cc7eb948087d6b4f7d127fedb56878d2c36b7616f0698e90e15 | Python | 6,544 | 197 | # Copyright (c) 2015-present, Facebook, Inc.
# All rights reserved.
import torch
import torch.nn as nn
from functools import partial
from timm.models.vision_transformer import Mlp, PatchEmbed , _cfg
from timm.models.registry import register_model
from timm.models.layers import trunc_normal_, DropPath
__all__ = [
... |
ccd1456226d642af6857a24a8144d5bc339829c82626691660f67a479b908e9d | Python | 6,547 | 216 | """CTF Rest Dataset: TDE-HMM for Dynamic Network Analysis.
In this script we train a Time-Delay Embedded Hidden Markov Model (TDE-HMM)
on source reconstructed resting-state MEG data.
The examples/toolbox_paper/ctf_rest/get_data.py script can be used
to download the training data.
Functions listed in the config are d... |
8928c2f37811d472e791e0c39b38e6a53724877cd942a123844f982df73d3929 | Python | 6,555 | 188 | import torch
# transpose
FLIP_LEFT_RIGHT = 0
FLIP_TOP_BOTTOM = 1
class Keypoints(object):
def __init__(self, keypoints, size, mode=None):
# FIXME remove check once we have better integration with device
# in my version this would consistently return a CPU tensor
device = keypoints.device ... |
badf643a96b1cff858f5a9df6db1e7da215ce67bd96f4509a49c3ef3dc2e8f2a | Python | 6,555 | 168 | import numpy as np
import pyshtools as pysh
import torch
import plotly.graph_objects as go
from cv2 import getGaussianKernel
from plotly.subplots import make_subplots
def plot_pc(pc, second_pc=None, s=4, o=0.6):
fig = make_subplots(rows=1, cols=2, specs=[[{"type": "scene"}, {"type": "scene"}]],)
fig.a... |
d9a90c9eea8f9aa47707f0ca00b535fe0cbafe466f4ac1c9e92ec1081fbcc03a | Python | 6,556 | 173 | import numpy as np
from pathlib import Path
from configparser import ConfigParser
import imageio
import shutil
from flexdata import display
from flexdata import data
from flextomo import projector
from flexcalc import process
from flexcalc import analyze
import cupy
import cupyx.scipy.ndimage
import skimage
import scip... |
ae80b172e9eedad3c7d0b99b1e40906e58ce5dc46522b3785d28f2007a6c04ca | Python | 6,561 | 212 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Tuple
import pandas as pd
from tmkit.contact.Evaluator import evaluator
from tmkit.contact.Reader import Reader as rrcre... |
90b18844086196fab4d233cad81ad3e1901137093ce9ed08c2a5a91151b4e043 | Python | 6,567 | 137 | __author__ = 'duarte'
import sys
from preset import *
import numpy as np
"""
spike_noise_input
- standard network setup, driven with noisy, Poissonian input
- quantify and set population state
- run with noise_driven_dynamics in computations
- debug with noise_driven_dynamics script
"""
run = 'local'
data_label = 'ex... |
269b201f944626c3944ebd43a871a941d53adefe4c66bdb1d084083ef0bf6c0b | Python | 6,568 | 131 | import os
import shutil
from dash_extensions.enrich import Serverside, Output, Input, State, callback, clientside_callback
from dash.exceptions import PreventUpdate
from RV.callbacks.utils.annotation_utils import get_annotation_label_radioitem
from RV.callbacks.utils.channel_selection_utils import get_channel_topogra... |
3d993c748ee7a7d76b4cb60fe9740630e22c7f64950185ac7eea25a3a261edf2 | Python | 6,570 | 179 | import pytest
import torch
from tltorch import FactorizedTensor
from ..spectral_convolution import SpectralConv, ConditionalSpectralConv
@pytest.mark.parametrize("factorization", ["Dense", "CP", "Tucker", "TT"])
@pytest.mark.parametrize("implementation", ["factorized", "reconstructed"])
@pytest.mark.parametrize("sepa... |
99929da5bd54f5659dd0ff2e44dd0f12de68a4aeb17b87398fe11a4f981a2729 | Python | 6,570 | 201 | import pytest
import torch
from torch.nn.modules.batchnorm import _BatchNorm
from mmdet.models.necks import FPN
def test_fpn():
"""Tests fpn."""
s = 64
in_channels = [8, 16, 32, 64]
feat_sizes = [s // 2**i for i in range(4)] # [64, 32, 16, 8]
out_channels = 8
# `num_outs` is not equal to len... |
7edfaf68fb6bde1c72e396c5c229f2ef74c5a6ac189a8c1b006c7fec2cc12a3d | Python | 6,571 | 152 | from torch import nn
import torch
import numpy as np
from torch_geometric.data import DataLoader
from .train_utils import EarlyStopping, evaluate_score, data2iter, multitask_mse, multitask_print, save_results
def seed_all():
np.random.seed(123)
torch.manual_seed(123)
torch.cuda.manual_seed_all... |
a50489bd949b046bf6a1683ce539b4a621911fcf61613f6f3cc618f19950e677 | Python | 6,575 | 167 | import logging
import tarfile
import tempfile
import time
from dataclasses import dataclass, field
from typing import ClassVar, Dict, List, Optional
from urllib.parse import urlparse
from urllib.request import urlretrieve
import requests
from defusedxml.ElementTree import fromstring
from oaklib.utilities.publication_... |
3e9ec125a09a0e506be81a24cd3e9b6b76902ed3b7ab89cfbe15fba7cdaf3713 | Python | 6,577 | 213 | """
Training script for Darcy flow equation using neural operators.
This script trains a neural operator on the 2D Darcy flow equation,
which models fluid flow through porous media. The script supports
distributed training and multi-grid patching for high-resolution data.
"""
from pathlib import Path
import sys
impo... |
68b1640819b3fd0b87135a917af03a2012b59d85f8b2844580b0d3b5a6ff8e7e | Python | 6,577 | 184 | __author__ = 'duarte'
import sys
from preset import *
import numpy as np
"""
spike_pattern_input
- main spike_input stimulus processing
"""
run = 'local'
data_label = 'example4'
# ######################################################################################################################
# PARAMETER RANGE ... |
9acd3cb72a39dd2904c2e8c582c1dd86bec0af92b9b2a889a897baa9dcecabdf | Python | 6,577 | 239 | #%%
import os
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from tqdm import tqdm
from graspy import __version__ as graspologic_version
from graspy.match import GraphMatch
from src.data import load_metagraph
from src.graph import MetaGraph
from src.io import ... |
eeb3bb9e48cf87d57685d4c88183003a07487ba243bc079d06b7221748091be5 | Python | 6,577 | 184 | """VOC Dataset Classes
Original author: Francisco Massa
https://github.com/fmassa/vision/blob/voc_dataset/torchvision/datasets/voc.py
Updated by: Ellis Brown, Max deGroot
"""
from .config import HOME
import os.path as osp
import sys
import torch
import torch.utils.data as data
import cv2
import numpy as np
if sys.ver... |
4ec717391723d62be5b2e422d63521a4d8cfcd9b210abef89d677a88494b0116 | Python | 6,579 | 136 | '''
collection of chemisorption models.
newns_anderson:
'''
import torch
import numpy as np
class Chemisorption:
def __init__(self, model_name, **kwargs):
# Initialize the class
if model_name == 'gnn':
self.model_num_input = 2
if model_name == 'newns_anderson_semi':
... |
f60428683ffdbdf56012a0592d36d312f0c3c4782c9f493d85b66c98b7c9c922 | Python | 6,579 | 136 | '''
collection of chemisorption models.
newns_anderson:
'''
import torch
import numpy as np
class Chemisorption:
def __init__(self, model_name, **kwargs):
# Initialize the class
if model_name == 'gnn':
self.model_num_input = 1
if model_name == 'newns_anderson_semi':
... |
4f7f43018eb84a310ce42e54ba6c3c087b383505ac13d9012a32692f5a57c568 | Python | 6,580 | 136 | import os, torch,json
from collections import defaultdict
def qual_analysis_gossipcop():
doc_embeds_file_text = os.path.join(os.getcwd(), '..', 'data', 'complete_data', 'gossipcop', 'cached_embeds', 'doc_embeds_roberta_lr_test.pt')
node2id_file = os.path.join(os.getcwd(), '..', 'data', 'complete_data'... |
ec174ca748324d706bb89edc8b07c2b3cc21dc9e085241f29a2ff9b8345e9595 | Python | 6,580 | 230 | # %%
import os
from pathlib import Path
import colorcet as cc
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pymaid
import seaborn as sns
from matplotlib.collections import LineCollection
from matplotlib.lines import Line2D
from sklearn.decomposition import PCA
from umap import UMAP
fro... |
971a0af5ef76ce265759e6ce99f82563ea381f773be88026a5b7c463e2462e47 | Python | 6,581 | 165 | import torch
from ..builder import BBOX_CODERS
from .base_bbox_coder import BaseBBoxCoder
@BBOX_CODERS.register_module()
class TBLRBBoxCoder(BaseBBoxCoder):
"""TBLR BBox coder.
Following the practice in `FSAF <https://arxiv.org/abs/1903.00621>`_,
this coder encodes gt bboxes (x1, y1, x2, y2) into (top, ... |
4d763396b8473467077ae5cbf73acd0dfdae106e5075aefcd0dba21d5b50b5a4 | Python | 6,582 | 164 | import torch
from mmdet.core import bbox2result, bbox2roi
from ..builder import HEADS, build_head, build_roi_extractor
from .standard_roi_head import StandardRoIHead
@HEADS.register_module()
class GridRoIHead(StandardRoIHead):
"""Grid roi head for Grid R-CNN.
https://arxiv.org/abs/1811.12030
"""
de... |
5332eef735d55589b901c246c4c929ec43159715b1ea390563d3cef6bb45fb64 | Python | 6,590 | 161 | import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.lines import Line2D
import numpy as np
from ddmr.utils.visualization import add_axes_arrows_3d, remove_tick_labels, set_axes_size
import os
def _plot_graph(graph, ax, nodes_colour='C3', edges_colour='C1', plot_nodes=True, plot_edg... |
48b0d4ed2cedcf29c5b352130dd0cfd1f042d82448fe13bad47b697585a63023 | Python | 6,591 | 148 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""
Cluster-based permutation t-test
================================
.. currentmodule:: eelbrain
A cluster-based permutation test for a simple design (two conditions).
The example uses simulated data meant to vaguely resemble data from an N400
experiment, but ... |
9c7e0747290819b6b4493e3deab79c388bfd6d742ad857ce4120ce6e470f67dd | Python | 6,594 | 176 | import numpy as np
from PIL import Image
class Signal :
Text_array = {
'a':0,'b':1,'c':2,'d':3,'e':4,'f':5,'g':6,
'h':7,'i':8,'j':9,'k':10,'l':11,'m':12,'n':13,
'o':14,'p':15,'q':16,'r':17,'s':18,'t':19,'u':20,
'v':21,'w':22,'x':23,'y':24,'z':25
}
def __init__ ( self, Name, Path, P... |
535db7fbcf8d9625f2a5b71ab4bfc7e4677ffa2757b0115527e39c7631083c8a | Python | 6,595 | 230 | # %% [markdown]
# ##
import os
from pprint import pprint
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from mpl_toolkits.axes_grid1 import make_axes_locatable
from giskard.utils import powerset
from src.data import load_metagraph
from src.io import savefig
FNAME = os.pa... |
8196bc04b57ffd904a60d6e984e4ddc8538d177cbecf8ba0b7279366b8192934 | Python | 6,598 | 156 | ### reference code from https://github.com/quark0/darts/tree/master/cnn --- Differentiable Architecture Search
import torch
import torch.nn as nn
from .conv_ws import ConvAWS2d
from .registry import CONV_LAYERS
import torch.nn.functional as F
#from torch.autograd import Variable
class Identity(nn.Module):
d... |
fc35f175087777d2a4b3e7a0ce0949cea3ce93aebb222bf6cb03b7148cdd5574 | Python | 6,598 | 181 | """Test the matching of Kaldi CTMs and segments to the transcript statements."""
from unittest.mock import MagicMock
import numpy as np
import pandas as pd
import pytest
from _pytest.fixtures import SubRequest
from pytest_mock.plugin import MockerFixture # type: ignore
from fi_parliament_tools.segmentFiltering impor... |
0edd1282207f49d963a922e6e77f4b92416c784db553cfd1d9b5a1c7461b6cf6 | Python | 6,599 | 148 | """Paper Figure 1: substrate, compartment recovery, and the four-architecture lineup.
Layout (2 x 2):
A — Substrate composition (MB subgraph cell counts)
B — DAN x MBON shared-KC Jaccard heatmap (hierarchical reorder)
C — Top canonical pairs with subtype labels (DAN-i1 <-> MBON-i1, etc.)
D — Architecture schem... |
4b11cf2cc981a9a0c3849f50fc653d8d2241fe5752e0d8a763466a34ab0cb4b5 | Python | 6,600 | 215 | from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
import numpy as np
import argparse
import pandas as pd
from keras.models import Sequential
from keras import layers
import os
from keras.optimizers import SGD
from keras.callbacks import (
CSVLo... |
835ea4fcab18e4a9e50c6294c3bb89ddfc7038a7a0e4e74ac2ebed8e6ca1ccd3 | Python | 6,603 | 158 | # 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... |
94937f45e7302609c663554be08ac0086871111c2440cd41526bca5832d59150 | Python | 6,604 | 167 | #%%
import numpy as np
import pandas as pd
from contools import Promat
from pymaid_creds import url, name, password, token
from data_settings import data_date, pairs_path
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
# datasets generated from https://github.com/clbarnes/brain_completion/blob/m... |
73b34f232722c35ca5458694b387ce40793d01bd76bc0fe9c8b603604e30bff4 | Python | 6,605 | 235 | from typing import List, Literal, Optional, Any
from zencfg import ConfigBase
class ModelConfig(ConfigBase):
model_arch: str
data_channels: int
out_channels: int
class FNOConfig(ModelConfig):
model_arch: str = "fno"
data_channels: int
out_channels: int
n_modes: List[int]
hidden_chann... |
c6d730ba339b207c9024199ec8015486a377895ad5e13fca4d9e7a7745dff0d7 | Python | 6,605 | 138 | # 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... |
2c9ed5cff4b7c420da30e404cf81386fd31e27c4d9f0f6c549ccb05b482f60e0 | Python | 6,608 | 170 | """
This package serves as the master index for all implementations.
"""
from functools import cache
from class_resolver import ClassResolver
from oaklib.implementations.aggregator.aggregator_implementation import (
AggregatorImplementation,
)
from oaklib.implementations.agrkb.agrkb_implementation import AGRKBIm... |
8c1d0905cec211132d320e530454dbdcb02cac0533a9a8baaf446012173c6977 | Python | 6,610 | 120 | __author__ = 'duarte'
from modules.parameters import ParameterSet, ParameterSpace, extract_nestvalid_dict
from modules.input_architect import EncodingLayer, InputNoise
from modules.net_architect import Network
from modules.io import set_storage_locations
from modules.signals import iterate_obj_list
from modules.visuali... |
855c782ede832bc5dfe41eff2aa56685ee2faa563352d024456817b4387822d3 | Python | 6,611 | 224 | """
ipyleaflet map for validating candidate TPA sites
"""
import geopandas as gpd
import ipyleaflet as ipyl
import ipywidgets as ipyw
# define XYZ tile layers to add to map
tile_layers = {
"google": "http://www.google.cn/maps/vt?lyrs=s@189&gl=cn&x={x}&y={y}&z={z}",
"esri": "https://server.arcgisonline.com/Ar... |
217cc6861e65cab997a59001cfd5670aa347bf805d161a95d2a028ae29ef9003 | Python | 6,614 | 227 | import contextlib
import warnings
import torch
from torch import autograd
from torch.nn import functional as F
enabled = True
weight_gradients_disabled = False
@contextlib.contextmanager
def no_weight_gradients():
global weight_gradients_disabled
old = weight_gradients_disabled
weight_g... |
6a74fd989896cd820769c5fd3b97642d84eb7dd9fae361e7729e5e48d8328247 | Python | 6,615 | 162 | import torch.nn as nn
from mmcv.cnn import ConvModule, caffe2_xavier_init
from mmcv.ops.merge_cells import GlobalPoolingCell, SumCell
from ..builder import NECKS
@NECKS.register_module()
class NASFPN(nn.Module):
"""NAS-FPN.
Implementation of `NAS-FPN: Learning Scalable Feature Pyramid Architecture
for O... |
dd58715cb7d80bdc82d6a97dcd167c2a7395319813510bc09f74333b2f8b1954 | Python | 6,616 | 140 | from functions import *
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import copy
from datetime import datetime
import pickle
starttime = datetime.now()
pickledump = True #Should results of this run be saved (True), else load previously stored results (False)
#Load dictionaries from pkl files t... |
49166d4dd653f8708d991f7f919b1a395f5332584ad9593ff6ea2d562b4a606a | Python | 6,620 | 205 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 8 16:13:47 2021
@author: user
"""
fdir = __file__
from IPython import get_ipython
from copy import deepcopy, copy
get_ipython().magic('reset -sf')
#get_ipython().magic('cls')
import os
current_path = os.path.dirname(__file__)
os.chdir(current_pa... |
ed2eeee154fb5866c8c96ce957519e7bcd32dc617f534f85f8282663bda01d97 | Python | 6,626 | 190 | import argparse
import ast
from datetime import datetime
import json
import logging
import os
import shutil
import sys
import re
crg2_dir = "/srv/shared/pipelines/crg2"
def replace_str(filename, target, replacement):
# pythonized sed
with open(filename, "r") as file:
lines = file.readlines()
with... |
e4662e65ffa492c1b710820a4fd305570e563860b4f61e7889a4ef9d2bc08468 | Python | 6,627 | 191 | from functools import partial
import numpy as np
import torch
import torch.nn as nn
from pg_modules.blocks import DownBlock, DownBlockPatch, conv2d
from pg_modules.projector import F_RandomProj
from pg_modules.diffaug import DiffAugment
class SingleDisc(nn.Module):
def __init__(self, nc=None, ndf=None, start_sz=... |
8a76b3f2281ea9f3a591488885e3076e45b70614397a6c56daf46ab5cb4067b5 | Python | 6,628 | 202 | from builtins import object
# Unit tests for sima/imaging.py
# Tests follow conventions for NumPy/SciPy avialble at
# https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
# use assert_() and related functions over the built in assert to ensure tests
# run properly, regaurdless of how python is started.
from nu... |
f636f2e3f3dd21ebe849bc9262b7d645fe0b17c6ad1fe4a2a5d5331532231153 | Python | 6,631 | 193 | from __future__ import print_function, division
import torch
import torch.nn as nn
import torch.nn.functional as F
class ConvLayer(nn.Module):
"""
Convolutional operation on graphs
"""
def __init__(self, atom_fea_len, nbr_fea_len):
"""
Initialize ConvLayer.
Parameters
... |
4c9e5da0f16f2a92d81a363e8ec499ba127a6312b3bf34c7551fc6f1e9d6aafd | Python | 6,633 | 154 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
class ConvBlock(nn.Module):
def __init__(self, in_planes, out_planes, stride=1):
super(ConvBlock, self).__init__()
self.conv = nn.Conv2d(in_planes, out_planes, 3, stride=stride, padding=1, bias=False)
self.bn = n... |
9c642d9f54989aafa4d1335c1c1d1222161799c9ffd43a4bc0d8d8399f4f8433 | Python | 6,633 | 175 | import argparse
def check_odd_integer(value):
ivalue = int(value)
if not (ivalue % 2):
raise argparse.ArgumentTypeError(f"{ivalue} is not a valid odd integer")
return ivalue
# PARSER CREATION FUNCTION
def create_parser():
parser = argparse.ArgumentParser(
description='HRpQCT Segmenta... |
7485724fe48f19b9fbadd70774f6c41d5289520a36d0e3416a1356e37bc08c8e | Python | 6,639 | 191 | ####################################################################################################
# Copyright (c) 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 i... |
f69c8b455800d9fef35d14602fb08b9f7e5cbd3a962fb7ea7b207d84ec5b08c2 | Python | 6,640 | 227 | from zarr import load
from argparse import ArgumentParser
from glob import glob
import os
# import random
from params import *
from image_manipulation import image_mip, image_read, image_warp
import pandas as pd
import napari
from matplotlib.cm import get_cmap
from matplotlib.colors import rgb2hex
from scipy.ndi... |
397b88e7af91b4b9e7f35a8cc8402d41c7309639569ba119bd731735d9fa164b | Python | 6,644 | 165 | # 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... |
88519e18dd655a75620828f1e86459a812286cb35048171f953a54f3b464c3bc | Python | 6,646 | 199 | __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, List, Tuple, Union
from functools import wraps
import pandas as pd
class Writer:
"""
A class that p... |
bf1652ac5a51daccf6ac6853fc5617435645a96ec9fee0760f3d8c8fb5a3240b | Python | 6,651 | 175 | import cv2
import numpy as np
# import time
import torch
from torch.nn import functional as F
import torch.nn as nn
def encode_segmentation_rgb(segmentation, no_neck=True):
parse = segmentation
face_part_ids = [1, 2, 3, 4, 5, 6, 10, 12, 13] if no_neck else [1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 13, 14]
mouth_... |
7874e4977211ceadcbff0293df6c59e7f97e888ae431b334ce7f564a0927a726 | Python | 6,653 | 130 | ########################################
# UNCLASSIFIED #
########################################
"""
This lat_lon_xy_utils.py file is used to get a pixel location within an image based on latitude and longitude
coordinates.
"""
import warnings
import numpy as np
from haversine import... |
a6944ee42d7e8fdfc795186b3459a2d9b764b25d697348a95c2e97768e88b950 | Python | 6,653 | 183 | ####################################################################################################
# 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 ... |
e1cfe3d12688d248e96b9fda6d553b52c5f29b89ecf5c876ba2226783466764a | Python | 6,654 | 282 | # %% [markdown]
# # THE MIND OF A MAGGOT
# %% [markdown]
# ## Imports
import os
import time
import warnings
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
from anytree import LevelOr... |
e4fdeb164bb712b5f8ae2a4a22a970367e774905344342794b75b16df822552e | Python | 6,658 | 220 | import copy
import random
from functools import wraps
import torch
from torch import nn
import torch.nn.functional as F
import numpy as np
from torchvision import transforms as T
from torchvision import models
from net.models.modeling import VisionTransformer, CONFIGS
# helper functions
def default(val, def_val):
... |
019059506521c59508e340e892ea435f667de5ef5810bddaa778500ceee51742 | Python | 6,659 | 162 | #!/usr/bin/env python3
"""
File: preprocess_mds_file.py
Created: 2020/10/26
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 Software F... |
a5e3c27426e2687a23b543fbda655b9a645c8f3b331e6ebfd0d3cb2ba4cd4d76 | Python | 6,659 | 141 | #!/usr/bin/env python3
"""
File: export_to_excel.py
Created: 2022/04/06
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 Software Founda... |
f4d23b7a98f0258595ec1197f665d313e5e15f34f6db4436a0649c5d149e36d1 | Python | 6,659 | 210 | # --------------------------------------------------------
# Fast/er R-CNN
# Licensed under The MIT License [see LICENSE for details]
# Written by Bharath Hariharan
# --------------------------------------------------------
from __future__ import absolute_import
from __future__ import division
from __future__ import pr... |
532a7092a7a1a2817b087469743a2ab88467809a7eb5de81975f72937f57a76f | Python | 6,660 | 185 | # Copyright 2021-2022 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... |
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