sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6b6eb6192b4e8a441f1f29939a6eb3a965c13f90be7ce1cc5b51bc38ac4ff0f8 | Python | 4,821 | 146 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.op_run import OpRun
def _fft(x: np.ndarray, fft_length: int, axis: int) -> np.ndarray:
"""Compute the FFT return the real representation of the complex resul... |
d37b5b92a35567460575a62fbfb02f95c35a50cfb144875d0876307dd0d28ca4 | Python | 4,821 | 164 | #!/usr/bin/env python3
import inspect
from pathlib import Path
from collections import MutableMapping
def stack_magic(stack):
if len(stack) > 2 and 'exec_module' in [f.function for f in stack]:
if '__builtins__' not in stack[1][0].f_locals:
index = 2 # we are in function scope in module cont... |
294fb0f5c2c1e1c9ab75312cd907c4b78a4acd3a01462f94e6cdaa7a2d9c4656 | Python | 4,822 | 125 | """Canonical time warping distance, from tslearn."""
__author__ = ["fkiraly"]
from sktime.dists_kernels.base import BasePairwiseTransformerPanel
from sktime.dists_kernels.base.adapters import _TslearnPwTrafoAdapter
class CtwDistTslearn(_TslearnPwTrafoAdapter, BasePairwiseTransformerPanel):
"""Canonical time war... |
63e7a5749aef875aa6c1d413feaa2456cea6a5dab54b833d6140a522ef766d19 | Python | 4,825 | 164 | # SPDX-License-Identifier: LGPL-3.0-or-later
from abc import (
ABC,
abstractmethod,
)
import array_api_compat
from deepmd.dpmodel.array_api import (
Array,
)
from deepmd.dpmodel.common import (
NativeOP,
)
from deepmd.utils.data import (
DataRequirementItem,
)
from deepmd.utils.plugin import (
... |
7ce1d50513cde516c772b5efdfdc8a228b6291bf1c334ff4e9dbe720ea95f47c | Python | 4,827 | 127 | from utils import AverageMeter, str2bool
from tqdm import tqdm
import torch
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torch.optim as optim
import archs
from collections import OrderedDict
import pandas as pd
import numpy as np
def train(train_loader, model, criterion, optimizer):
avg_meter... |
1a10b830a4580351ef40f93e5936674ee43c0179103f39cd7b21a9cd186da521 | Python | 4,828 | 150 | #!/usr/bin/env python
import click
import copy
import json
import numpy as np
import os
import pandas as pd
import re
from sklearn.preprocessing import OneHotEncoder
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
os.pardir))
from utils import ... |
feea15c3c41ee278193c6e9886674c89c5b80cad47071dc4eca405cec22a1534 | Python | 4,832 | 130 | """
@file: quantize_model.py
Created on 02.01.2021
@project: CrazyAra
@author: queensgambit
Script for creating INT8 quanitzation weights for the MXNet-CPU backend.
References:
https://cwiki.apache.org/confluence/display/MXNET/MXNet+Graph+Optimization+and+Quantization+based+on+subgraph+and+MKL-DNN
https://medium.com/... |
c3e9e8a87a4c329a90672c2453fb275e8ad252b53e63452eba879fe5153267dc | Python | 4,838 | 148 | import numpy as np
from scipy.signal import find_peaks
def set_rates_na8st(seg, rates, vshift_inact=0):
"""
Sets the rates for the 8-state model in segment seg.
vshift_inact can be used to locally change the voltage
dependence of inactivation rates.
:param seg: the segment to set rates for
:p... |
3e6809c3e57fa215e8202fc871b3e95a98cd53279c9301e1315a8e7613635cfe | Python | 4,839 | 131 | """Image Encoder."""
import torch.nn as nn
import torch.nn.functional as F
import torch
from onmt.encoders.encoder import EncoderBase
class ImageEncoder(EncoderBase):
"""A simple encoder CNN -> RNN for image src.
Args:
num_layers (int): number of encoder layers.
bidirectional (bool): bidirec... |
3f27b749052352e9fa36aa8bf5757075fd5881f98fa7b77cc4cc7539936ecdea | Python | 4,840 | 158 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Creates Figure 2 from Wang et al. (2023) Temporal stability of intracranial EEG
abnormality maps for localizing epileptogenic tissue.
Change the variable "pnt" at the beginning of the script to plot a different
example patient.
Calculates time-varying D_RS from abno... |
65fdcc6dd8c71d87efd1927f13211e494a5bc94597f2d519246bc5b7b17fff0d | Python | 4,842 | 128 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
3e847ea19992b92d1b3b40b5cad87f39ddd1937351e0dfa87f82ed7f52c7d373 | Python | 4,844 | 149 | import json
import numpy as np
import pandas as pd
from time import time
import seaborn as sns
import matplotlib.pyplot as plt
from genetic_selection import GeneticSelectionCV
from sklearn.feature_selection import SelectFromModel, RFECV
sns.set()
def feature_importance(model, X, Y, threshold=None, save=False):
'... |
987217215e7ef6db4855e1d8bdbf15e81fff86aa4de5d99d4aee64398cfa2294 | Python | 4,844 | 132 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.ops.aionnxml._common_classifier import (
logistic,
probit,
softmax,
softmax_zero,
)
from onnx.reference.ops.aionnxml._op_run_aionnxml import OpRunA... |
abd0a20771eb56a0a9e13f32008146c59b6b29510ca38d82f34feb434e7c1f2e | Python | 4,846 | 151 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Implements adapter for tslearn distances and kernels."""
import numpy as np
__all__ = ["_TslearnPwTrafoAdapter"]
__author__ = ["fkiraly"]
def _subset_dict(d, keys):
"""Subsets dictionary to keys in iterable keys.
Parameters
----... |
d285fabe034b88a91b2a8d8984e4b5b1d986d0ba65ef804a9022d9b519e8fd90 | Python | 4,847 | 149 | import multiprocessing
import os
from dataclasses import dataclass, field
from .helper import run_shell_command
@dataclass
class ANTSTransformationStages:
transformation: str
inverse: bool
@dataclass
class ANTSTransformationParams:
interpolation: str = "Linear"
class ANTSImageTransformation:
def __i... |
2aa8c70ee2e4c19e008e4275792b82f10434095b0b8002553f07661ab3971bb4 | Python | 4,848 | 178 | """
This code is for "breaking the dendrites" from cells. Mostly it just allows us
to remove the dendrites from a hoc file. This is run as a script from the
command line. Run with python break_dendrites.py --help to see the command
arguments.
Note: *** DEPRECATED ***: replaced by compare_hoc.py (use that instead!)
Th... |
0aaf2358314d1bd4af3e99ad8bca320528745616ecebd1bfe6fd8d8e1c83b435 | Python | 4,849 | 158 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
a91b7b4eecde5aa9ea90ca06c2e6b50ed93045e33d51acbdf769d7572d3ce21e | Python | 4,852 | 151 | import torch
import math
import logging
from typing import List, Union, Tuple
def rot(
theta: float,
dir: Union[str, torch.Tensor, Tuple[float, float, float], List[float]] = "z",
) -> torch.Tensor:
"""
Get the rotation matrix for a given angle and axis of spatial rotation.
:param theta: angle of ... |
f4782fce70005925bb8b2b3447840b4f898796c38bca71e7226f87ddd3a711a0 | Python | 4,852 | 134 | from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from pathlib import Path
import pandas as pd
import numpy as np
import os
import argparse
import subprocess
import re
#Get file name and directory
parser = argparse.ArgumentParser()
parser.add_argument('-f', '--file', help='path to csv f... |
5917c3216cafd26790b24aa8177f389c4f4055be94917206f57dd153d34d7de3 | Python | 4,853 | 128 | import numpy as np
import pandas as pd
def _npedges2dfedges(edges, edge_threshold=0, edge_thresholddirection='absabove'):
"""
A function which transforms numpy array edges into dataframe.
This function is required for compatiblity with other functions.
Parameters
---------------------
edges ... |
f38d645325efd41f81f1364050230490a702ba7fed7cf43ae76b9a3a0ea7e8bb | Python | 4,854 | 94 | import plotly.express as px
import pandas as pd
import numpy as np
########## donor #############
df = pd.read_csv('./umap_3d_metadata_donor.txt', sep = '\t', header = 0, index_col = 0)
df.loc[df['cellclass_draft_v2'] == 'OPC', 'cellclass_draft_v2'] = 'IPC4'
# order cell type and extract important cells
cellclass_ord... |
b93866873d392e517201b97e69f49628bb978af049eff17956e3d7330f0626c3 | Python | 4,859 | 141 | r"""
This module contains encoder/decoder/autoencoder model blocks.
"""
import torch
from torch import nn as nn
from torch.nn import functional as F
from torchvision import transforms as TF
from torchvision.transforms import Resize
from vp_suite.model_blocks.conv import DCGANConv, DCGANConvTranspose
from vp_suite.base... |
9b807a74f75abb70533ceb59c3e01288636f9f44b8638af1a5ac9c3063cf6239 | Python | 4,861 | 124 | #-------------------------------------------------------------------------------
# elftools tests
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
import unittest
from io import BytesIO
from elftools.dwarf.constant... |
db72052b9ba4e369970ee04abcf34fa563b19d03a6a46d40c405b71e6f7d4248 | Python | 4,862 | 148 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from collections import namedtuple
from typing import TYPE_CHECKING, Any, NewType
import onnx.checker
import onnx.onnx_cpp2py_export.checker as c_checker
from onnx import IR_VERSION, ModelProto, NodePr... |
d568419429552b9e5752eb5e0177afa441aa47133c4d9a12c777c7a3108dfec9 | Python | 4,865 | 161 | import click
import gzip
from functools import partial
import numpy as np
import pandas as pd
import random
from sklearn.model_selection import train_test_split
from torch import cuda, Tensor
from torch.utils.data import DataLoader, TensorDataset
from explainn.utils.tools import dna_one_hot
##########################... |
069c3c545dd40aafc4e80a5b9deeffafe69e3d7345cf158d7e3676ec5a4129db | Python | 4,867 | 149 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu May 12 17:13:23 2022
Big simulation: short version of shj-multiunitnbank.py - to run SHJ with many
units (hippocampus scale) and save results
@author: robert.mok
"""
import os
import sys
import torch
import pickle
location = 'cluster' # 'mbp' or 'cl... |
b44c89dac89bed99e476fdf85cd4727b90372ec5df04d49fbf17661a6955d883 | Python | 4,868 | 173 | """NIfTI structural manipulation: ROI extraction, merging, splitting, geometry copying."""
import os
from pathlib import Path
from typing import List, Optional, Tuple, Union
import numpy as np
import nibabel as nib
from bcblib.imaging._types import NiftiLike
from bcblib.imaging.io import load_nifti
# -------------... |
1166e76e785f9c09d4554e0980fb2ded03a1348be1124658abb11222820d15f5 | Python | 4,874 | 157 | """Low-level NIfTI I/O helpers: loading, saving, format detection."""
import os
from pathlib import Path
from typing import List, Optional, Tuple, Union
import nibabel as nib
from bcblib.imaging._types import NiftiLike
# ---------------------------------------------------------------------------
# Format detection... |
d8cd2c85248180e87da2ed369f52dfc883ce7ce8c8864f13008fb5d169439259 | Python | 4,875 | 153 | import pandas as pd
import seaborn as sns
from matplotlib import pyplot as plt, patches as patches
from sklearn.metrics import classification_report, roc_curve, roc_auc_score
# Coordinates are best display for the label (not the exact values)
FP_orig = {'Bt133': (61.5, 0.78),
'LYRa3': (84, 0.82)}
FP_mers_... |
c81b5a89aa1b05019443b26bf28a883897ee204601d22700962eecf02b0b67dc | Python | 4,880 | 127 | import cv2 as cv
import numpy as np
from math import sqrt
from multiprocessing import Pool
from skimage.feature import blob_log
import Switches_Static as st_switches
from Switches_Static import rx,cx
import time
# Class to hold outputs; now using list as a class attribute rather than an instance attribute
class OUTPU... |
683d62cb3e3b76f16171a17650626c032cca6f69283bc8f809bbffd0814f435d | Python | 4,881 | 143 |
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Sequential, Linear, ReLU
from torch_geometric.nn import GATConv
from torch_geometric.nn import global_max_pool as gmp
from torch_geometric.nn import GINConv, global_add_pool
from torch_geometric.nn import global_mean_pool... |
aefafb418e6e004b46b6c4630e16f36cd4c0fb30c6fcea1d2d4a98ab07f7e1be | Python | 4,882 | 131 | import collections as col
import logging
import os
import re
import sys
import click
import numpy as np
import scipy as sp
import scipy.spatial
import pandas as pd
import atom3d.datasets.datasets as da
import atom3d.splits.splits as spl
import atom3d.util.file as fi
import atom3d.util.formats as fo
logger = loggin... |
cd13b8a7002649abe078feba3ac6ffd0b070cce9c06cad535734f1dae04e408e | Python | 4,883 | 124 | """
Take in a network, and render its structure using the package 'graphviz'.
"""
from sns_toolbox.networks import Network
from sns_toolbox.color_utilities import set_text_color
import warnings
graphviz_available = True
try: # see if graphviz is available
from graphviz import Digraph
except ImportError:
wa... |
ead27519fe12f58562e16aff071d354602bcfc1b3b60a3156adbf2cc67a5c617 | Python | 4,883 | 159 | import logging
import os
import os.path as osp
from pathlib import Path
import torch
import glob
import matplotlib.pyplot as plt
import numpy as np
def get_model_folder(args):
make_dir(args.save_dir)
path = Path(args.save_dir) / get_model_fname(args)
path.mkdir(parents=True, exist_ok=True)
return path... |
cf337abedf02d88f75e1bc7bbf6f471530caf283d1083cfa3e2dbd0ee166247b | Python | 4,885 | 120 | import os
import pandas as pd
from rdflib import Graph
BDSO_ONT = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../../bdso-full.owl")
PCL_ONT = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../resources/pCL_4.1.0.owl")
PCL_MAPPING_OUTPUT = os.path.join(os.path.dirname(os.path.realpath(__file_... |
24c297aa32e57d7a1b6e21d9bca3a6c9933905f762625b0a78b8346dd1e8cfb9 | Python | 4,888 | 185 |
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pickle
import os
import sys
import pandas as pd
import Levenshtein as lev
MAX_DISTANCE = 4
TL_BASE_PATH = '../data/tl_train/U6T7/'
def get_folders(path):
folders = []
names = []
for folder in os.listdir(p... |
3a4a262a24a9ed7f796f80b6ddb54c31eba93e78293cb490b577dc8dcbca86b8 | Python | 4,888 | 176 | #-------------------------------------------------------------------------------
# elftools: elf/constants.py
#
# Constants and flags, placed into classes for namespacing
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#---------------------------------------------------------------------------... |
730332c03eb21b27e4151f1746da0895116c73a84c2cc89dbdf9293043b88002 | Python | 4,888 | 137 | import numpy as np
from scipy.stats import entropy
import matplotlib.pyplot as plt
import seaborn as sns
import sciunit
class kl_divergence(sciunit.Score):
r"""
Kullback-Leibner Divergence :math:`D_{KL}(P||Q)`
Calculates the difference of two sampled distributions P and Q in form of
an entropy measur... |
902457db73fdb5b8fba52e56dc554bef74c140a3f2bdf3cfa6d566f3beba3b49 | Python | 4,888 | 120 | """
@file: train_cli.py
Created on 10.11.23
@project: CrazyAra
@author: queensgambit
Provides a command-line interface to run training experiments.
For the main configuration files please modify
* CrazyAra/DeepCrazyhouse/configs/main_config.py
* CrazyAra/DeepCrazyhouse/configs/train_config.py
A decision was made to o... |
6173886b1b6e12c62133d046f761d068ac32669e0f22db21723b878f05aeab3d | Python | 4,889 | 113 | import sys
import os
import pickle
import numpy as np
import rdkit
import random
import torch
import torch.nn as nn
import pandas as pd
from rdchiral.main import rdchiralReaction, rdchiralReactants, rdchiralRun
from datetime import datetime
from pathlib import Path
from typing import Dict, List, Optional, Tuple, Union... |
c87b5ec39f8c5a8bca1599d816768a98e1978e60aef932bf8aa700582b100f25 | Python | 4,889 | 159 | """BCBToolKit run_disco.sh wrapper."""
import os
import re
import subprocess
import sys
import warnings
from pathlib import Path
from typing import Dict, Optional
from bcblib.tools.lesion_features._constants import DEFAULT_BCBTOOLKIT
def find_bcbtoolkit(path_hint: Optional[str] = None) -> Path:
"""Locate the BC... |
3021f41cf07bb193210ef3b5f2298ab80f7d39b7d313b62d4fd4703962f8b306 | Python | 4,892 | 128 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 9 10:42:51 2018
@author: tpisano
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from matplotlib.mlab import bivariate_normal
from matplotlib.colors import ListedColormap
from matplotlib.colors import Norm... |
9305baf1e05a7f8c91cdd302ffa5dca494d23248e37c8f66bc0849c32df39001 | Python | 4,892 | 158 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
00a5f635ac00982ab8aa150ee8c2f6b249e50d5fca8696c66267250a8c9a0963 | Python | 4,893 | 136 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import os
import tempfile
import numpy as np
import numpy.testing as npt
import pytest
import onnx
import onnx.helper
import onnx.model_container
import onnx.numpy_helper
import onnx.reference
def _... |
977ce42e5136f040049a0ef9b6ff72a7561889a1d591fe198bcaca9fd4d4595b | Python | 4,893 | 113 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
85d8ba35a4ad2e1eb76a888f42d92c1fbb385751e6f16add4a7ac0494850fac0 | Python | 4,894 | 154 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Jan 17 12:20:45 2018
@author: tpisano
"""
import cv2
import skvideo.io
from skimage.external import tifffile
import skimage
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
from mpl_toolkits.mplot3... |
fe7dd1b610636b0ad63766c9c49d7ce655fd6dcedf6e156a03040a187a581081 | Python | 4,898 | 155 | import torch
from torch import nn, rand
from collections import OrderedDict
def save_model(path, epoch_id, model, optimizer=None):
if isinstance(model, torch.nn.DataParallel):
state_dict = model.module.state_dict()
else:
state_dict = model.state_dict()
data = {'epoch': epoch_id,
... |
bd579e4b727cb9b711802544840e876eccc3a775a05647ecb5a02f4dcf87d006 | Python | 4,899 | 139 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
f8fb8e81dde67b2a79fc2e0f1be93d75ca70b758e9d75b8d1a7b369a1f603391 | Python | 4,901 | 156 | from __future__ import division
import re
import sys
import numpy as np
import pandas as pd
from SPHARM.lib import spharm
import SPHARM.lib.parallel as prl
from helper_lib import filelib
def extract_metadata_Tcells(inputfile, spectrum_file):
stat = pd.read_csv(inputfile, sep='\t')
# extract group info
... |
a4e06dadbaf1eb9caa786518fc46aab85f0f7a944e8b8949594e3ddb1d5b5178 | Python | 4,902 | 138 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
628d979c5500903fe6a966e2d5186df16d4c13d4a0e8583d2533cadaae91e1ec | Python | 4,903 | 115 | import os, sys
import numpy as np
import torch
import pytorch_lightning as pl
from six.moves import cPickle
from evoaug import evoaug, augment
sys.path.append('../../evoaug_analysis')
import utils
from model_zoo import CNN
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
output_dir = '../resul... |
8aeed364b2f5091dc54e4f048a10508885cd9f843c375ad7325c7c2aa8791659 | Python | 4,903 | 148 | from __future__ import division
import numpy as np
from SPHARM.classes.surface import Surface
from SPHARM.classes.profile import Profile
import SPHARM.lib.transformation as tr
class Ellipsoid(Surface):
"""
Class for a surface of a ellipsoidal object.
"""
def __init__(self, grid_shape, size, rotation... |
011b601ca3c2c04c14578975d1074d1457c1894c4ef537cc7349c9ebe6558cd7 | Python | 4,904 | 125 | """
Evaluate models on synthetic data: classification and interpretability performance.
"""
import os
import numpy as np
from six.moves import cPickle
from tensorflow import keras
from gradient_correction import helper, explain, model_zoo, geomath
import tfomics
#------------------------------------------------------... |
aff482b3480d4b8c2642cd1cd978d74e0989cb766b429376fe723ed3c0be37d2 | Python | 4,904 | 169 | # Copyright 2019 DeepMind Technologies Ltd. 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 appl... |
54092ee1b74fd021ee858f8151417d2fa8bcf7e4f7dc7cce127fa9ee8c0b7746 | Python | 4,910 | 128 | """
Find the neighbors of each vertex of the surface mesh and outputs to a text file.
Parameters:
---------
a,b,c,x,y,z: Outputs from the coord_nodes.py file
subjects_dir, subject, hemi: These are defined in the curveball.py file
Returns:
-------
ndl: vertex neighbor information stored in a circul... |
3b3cb10a98880730ec0d9ad251d7d8498f60eff41bc0d914607e5ec21e160eb3 | Python | 4,915 | 147 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""The readout gate of a bridging window on the pt fitting networks.
A bridged descriptor hands the fitting a per-atom source gate. The gate fades
the learned part of the output, the deviation of the output from the per-type
bias the fitting stores, so an atom whose gate is... |
045f5ca9a7c85027c066c4746c276be599c95215cce47099ce6cf6f64431c14c | Python | 4,919 | 122 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Tests for BaseAligner API points."""
__author__ = ["fkiraly"]
import numpy as np
import pandas as pd
from sktime.datatypes._check import check_raise
from sktime.tests.test_all_estimators import BaseFixtureGenerator, QuickTester
from sktime.ut... |
0b6a87a63222ce7a392aebcb4ec75358da07264b698d5fbe6c82b095115af7ae | Python | 4,919 | 156 | from collections import OrderedDict
import copy
import numpy as np
from .geometry import Box, Vec3d
from .tensor import TensorData
from . import utils
class Dataset(object):
"""Dataset for volumetric data.
Attributes:
spec (dict): mapping key to tensor's shape.
data (dict): mapping key to Te... |
94ef4d1b60614225ee81c52b122fc1bd9afc7a01aab5454fb179e2e91fd8c951 | Python | 4,920 | 146 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
b36b8a747840abe19c8d7cc3271ea6441f9313363bf49e600913ebabd249d73d | Python | 4,923 | 102 | # The test_gnudebugaltlink* and test_debugsup* files have been generated as
# follows:
# $ cat test_sup.c
# int main(int argc, char** argv)
# {
# return argc;
# }
#
# $ gcc test_sup.c -o test_debugsup1
# $ gcc test_sup.c -o test_debugsup2
# $ dwz test_debugsup1 test_debugsup2 -m test_debugsup.common --dwarf-5
#
... |
cc9518244a42a2111d0c420e4efd75901796e8ceb078c881c4c681035cc74438 | Python | 4,923 | 147 | #!/usr/bin/env python
import sys, os
import string
from ftplib import FTP
use_message = '''
'''
ftp_address = 'ftp.illumina.com'
user_id = 'igenome'
password = 'G3nom3s4u'
visible_organisms = \
['Homo_sapiens',
'Mus_musculus',
'Rattus_norvegicus',
'Bos_taurus',
'Canis_familiaris',
'Gall... |
f2866171a84171e85a614062e9da3f5d36c8b14727d4c951ac4f7fdb264041e2 | Python | 4,925 | 163 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... |
eae31a6ddf5c689cca4e13196102a8dec6e2f46989442f86939dac17e5c185cb | Python | 4,926 | 110 | #-------------------------------------------------------------------------------
# elftools example: dwarf_range_lists.py
#
# Decode DW_AT_ranges from .debug_ranges (DWARF <= 4) or .debug_rnglists
# (DWARF 5), showing the resulting code address intervals [begin, end).
# The beginning address is included; the ending add... |
36d6ed2c6c13f7342931093435aeb1eeb5e84b23550c758f650370d8c9ee413d | Python | 4,928 | 162 | # SPDX-License-Identifier: LGPL-3.0-or-later
import copy
import unittest
import numpy as np
import paddle
from deepmd.pd.model.model import (
get_model,
)
from deepmd.pd.utils import (
decomp,
env,
)
from deepmd.pd.utils.nlist import (
extend_input_and_build_neighbor_list,
)
from ...seed import (
... |
94365682c4dcef38b980e625919d13082d10e830208ed815fecbd9d7160630de | Python | 4,932 | 99 | # load the annotations from Brat
# brat files were generated using generate_brat_annotations.py
# then domain experts annotate the brat files by ticking or unticking the true_phenotype/false_phenotype, and may add notes if necessary
# this program then post-process the brat annotations and fill the results to the ... |
a111c59fa35bc4ebc6555b648275ae34a2b886bfc374f9ce3d9db0a37e078b04 | Python | 4,935 | 185 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 28 17:05:56 2016
@author: tpisano
NOTE WITH CROPPING THIS DOES NOT YET HAVE AN EFFECT ON THE ANNOTATION FILE....THIS NEEDS TO BE INCOROPORATED
"""
import os, numpy as np
from tools.utils.io import listdirfull, makedir, removedir, chunkit, writer, ... |
e9daf7fb9867240fa742c6b4027e92cd7629d1cd7c5b447959deda1d7d12cecb | Python | 4,937 | 130 | """
@file: input_representation.py
Created on 17.08.23
@project: CrazyAra
@author: queensgambit
Input representation v3 which is compatible to all available lichess variants and passed to the neural network.
"""
import numpy as np
import chess
from DeepCrazyhouse.src.domain.variants.default_input_representation import... |
c432d1b4945b8162aa93031195d4815e4e8ece76cf4ca2554b666a8b41f532df | Python | 4,938 | 144 | """
Data Summary Module for pciSeq
This module provides functionality to summarize and format the results of the
pciSeq analysis for visualization and reporting. It processes both cell and spot
data into structured DataFrames.
Key Functions:
------------
cells_summary:
Summarizes cell-level information including:... |
f9e2da8c66e3073854f6a73af8118855fb1610e1e941ad1df21510b6dc743671 | Python | 4,941 | 149 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import locale as pylocale
import unicodedata
import warnings
import numpy as np
from onnx.reference.op_run import OpRun, RuntimeTypeError
class StringNormalizer(OpRun):
"""The operator is not rea... |
b40a0de84cd75c594598ffb8f8af8b34f6b9e46272cbbbaea496a09819b8c049 | Python | 4,942 | 133 | import logging
import os
from typing import Any
from flair.trainers.plugins.base import TrainerPlugin, TrainingInterrupt
from flair.trainers.plugins.metric_records import MetricRecord
from flair.training_utils import AnnealOnPlateau
log = logging.getLogger("flair")
class AnnealingPlugin(TrainerPlugin):
"""Plugi... |
b41af7d068521c53a61106a0a8d7ab60a61e0e5fda27c7bc3108335db2ca2026 | Python | 4,942 | 148 | """Hampel filter for univariate anomaly detection."""
import numpy as np
import pandas as pd
from sktime.detection.base import BaseDetector
__author__ = ["SpitFire19"]
class HampelDetector(BaseDetector):
"""
Anomaly detector based on Hampel filter described in [1].
Parameters
----------
window... |
49650e15264136789369a98371656c80b9cc57a554c037cdb4f2bd92f66a39cc | Python | 4,943 | 131 | # Copyright 2022 DeepMind Technologies Limited
#
# 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 agr... |
91d8dcab5d721d1fe79a753eaa2f28a24e39b5fd473e559d65eeebce56735eb3 | Python | 4,945 | 145 | from typing import List
import pandas as pd
from sklearn.utils import check_random_state
class ValidationClassifierChain:
"""Classifier chain that takes training and validation set. Code modeled
after sklearn.multioutput.ClassifierChain
Args:
model (DepthwiseXGBPipeline or LogisticRegressionMode... |
f3e3c0e9709e3eacc946d3bc8701b371687cb875759f5fa2df4c09b8fdef8099 | Python | 4,945 | 140 | import pytest
# Assuming these tokenizers are in flair.tokenization
from flair.tokenization import (
SegtokTokenizer,
SpaceTokenizer,
SpacyTokenizer,
JapaneseTokenizer,
SciSpacyTokenizer,
StaccatoTokenizer,
TokenizerWrapper,
)
# Helper function for basic serialization/deserialization test... |
50177ac54e1e9942b7161e404eacfee8f9e25f78a426b34e80056dcc085ba179 | Python | 4,947 | 126 | #!/usr/bin/env python3
#This tool was developed for the purposes of the Vertebrate
#Genomes Project. Redistribution and use in source and binary forms,
#with or without modification, are permitted provided that the
#following conditions are met:
#
#1. Redistributions of source code must retain the above copyright
#not... |
dff8b5bdc5589f6e28dac5ac046072482350f612fa48e71c3e04b6a37a487396 | Python | 4,947 | 158 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
d9e7dd435a38f4b6a51fad9df686230ab4933918a7a9b70821913de5233a3bd1 | Python | 4,948 | 127 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""forbidden_dims_from_model accessor handling (CodeRabbit #5779)."""
import pytest
import torch
from deepmd.pt.utils import (
compile_compat,
)
from deepmd.pt.utils.compile_compat import (
build_inductor_compile_options,
forbidden_dims_from_model,
)
class _W... |
0b3cf2c7d111176fa5e0cad6ab7026a2a35a926e3a0fa9e62204eee886db9317 | Python | 4,949 | 174 | """This module implements a Mel Filter Bank.
In other words it is a filter bank with triangular shaped bands
arnged on the mel frequency scale.
An example ist shown in the following figure:
.. plot::
from pylab import plt
import melbank
f1, f2 = 1000, 8000
melmat, (melfreq, fftfreq) = melbank.comput... |
b86344ed98ef67deaa9c2cc8bc76a6df6f3bb3d178f0c07ce977d836f8aa0cab | Python | 4,950 | 163 | import pytest
import torch
import torchvision # type: ignore[import-untyped]
from packaging import version
from tests.fixtures.genotype import GenotypeNetwork # type: ignore[attr-defined]
from tests.fixtures.tmva_net import TMVANet # type: ignore[attr-defined]
from torchinfo import summary
from torchinfo.enums impo... |
17a000712b388f0e09c4b7679b76574e07229edeeed7ba7995b691d3f6aeb2ee | Python | 4,952 | 140 | """CLI: bcb-lesion-features — extract lesion and disconnectome features."""
import argparse
import sys
from pathlib import Path
def _build_parser():
p = argparse.ArgumentParser(
prog="bcb-lesion-features",
description=(
"Stage 2 of the lesion-features pipeline: compute atlas overlap "... |
b3ef9dce9428d1b8753c711e3f9c89a7d12e8e05e3f28875d9a4de311349a893 | Python | 4,953 | 174 | #!/usr/bin/env python
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqUtils import gc_fraction
import click
import copy
import importlib
import json
import random
import re
import sys
lib = importlib.import_module("subsample-seqs-by-gc")
CONTEXT_SETTINGS = {
"help_option_names": ["-h", "--help"],
}
@c... |
07f393b51b2256f19f615a954223632d6c7432b26d5ae44d2c0e0b226fffa1ba | Python | 4,955 | 173 | # Copyright 2019-2020 The ASReview Authors. 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 appl... |
2efc2c9413ce723dc68b86bd4f6c0b86c38b7b168131f4af727dfbee2f5423b9 | Python | 4,955 | 122 | # Copyright 2019 DeepMind Technologies Ltd. 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 appl... |
3ba5334210bc49143d84b6b3276077745f33d9a9b7e1d766f010be4ccdbe682a | Python | 4,956 | 139 | # BASILISK: A generative, probabilistic model of side chains in proteins
#
# Copyright (C) 2010 Tim Harder and Jes Frellsen
#
# BASILISK 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 version 3 ... |
15e8ec2b795c5802710258593994ffc68f01a06b04c811e3231267da194dccfd | Python | 4,957 | 138 | import os
import biom
import numpy as np
import pandas as pd
import birdman
from scipy.stats.mstats import gmean
from birdman.model_base import TableModel, SingleFeatureModel
import warnings
def _normalization_func(table, norm='depth'):
if norm == 'median_ratios':
K = table.matrix_data.todense().T + 0.5
... |
eba91ce8310006580c563a0efd867b6ec18928425f26af5efdf492afc46d4d63 | Python | 4,957 | 133 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
from ampligraph.datasets.partitioning_reporter import PartitioningReporter
from... |
0ba62e1bdbf1fc3c2b87461aa3c5635c984f80480936b0b9e4b951d8f6acb8da | Python | 4,958 | 146 | #-------------------------------------------------------------------------------
# elftools: common/construct_utils.py
#
# Some complementary construct utilities
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
from... |
393a06f4622415d06310e5d31a25df6971a5971e3eb2c14344ecd42429594d5d | Python | 4,958 | 142 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 agr... |
0081715b47de491cc87657bef3c60bc0bf8407292a8ea23530426cba58b0a5e1 | Python | 4,960 | 155 | from gensim.test.utils import common_texts
from gensim.models import Word2Vec
from gensim.models import FastText
import pandas as pd
import numpy as np
from gensim.models.callbacks import CallbackAny2Vec
class EpochLogger(CallbackAny2Vec):
'''Callback to log information about training'''
def __init__(self):
... |
7c08741c77ea21c495fd61b04db430c2e2067b1973d5c671d78e1c0213f46359 | Python | 4,961 | 144 | # Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import contextlib
import tqdm
from tensorflow.python.framework import errors
... |
1f47815e2b5b460677a88a6a19ad401fa07d60dae3b6515f6390e1dda62d65b4 | Python | 4,964 | 144 | #!/usr/bin/env python
"""Defacing utility for MRI images."""
import argparse
from nibabel import load, Nifti1Image
from pkg_resources import require
import pydeface.utils as pdu
import sys
import shutil
import numpy as np
import os
def is_interactive():
"""Return True if all in/outs are tty"""
# TODO: check ... |
b328dab2d5c9e31e11509be94f4ba1b4bfc4d088ad3f60cdbe5e618e90f4bfe1 | Python | 4,964 | 128 | import os
import glob
from lxml import etree
import rdflib
from pyontutils.core import LabelsBase, Collector, Source, ParcOnt
from pyontutils.core import makePrefixes
from pyontutils.namespaces import nsExact
from pyontutils.namespaces import FSLATS
from pyontutils.namespaces import NCBITaxon, UBERON
from nifstd_tools.... |
bc45432ed42181c0f3c84849e878f41d55db485ee163ba2869b461debca51edc | Python | 4,968 | 136 | #!/usr/bin/env python
import logging
import os
import importlib
import sys
import numpy as np
import pandas as pd
import torch
from torch.utils import data
from torch import save, load
import my_data
from torch import cuda, device
from sklearn.metrics import mean_squared_error
from scipy.stats import pearsonr, spearman... |
c8e0837fae5c2bf6e097b3235ab3df88230482cc6cdc61680831aeff0f18785f | Python | 4,973 | 158 | from dataclasses import dataclass
import numpy as np
import pandas as pd
import matplotlib as mpl
import pytest
from numpy.testing import assert_array_equal
from seaborn._marks.base import Mark, Mappable, resolve_color
class TestMappable:
def mark(self, **features):
@dataclass
class MockMark(... |
0ab92cf19b21607a00332666de293311d177a361403815fc0334451be5138a5e | Python | 4,977 | 146 | #!/usr/bin/env python
"""Training on a single process."""
import os
import torch
from onmt.inputters.inputter import build_dataset_iter, \
load_old_vocab, old_style_vocab, build_dataset_iter_multiple
from onmt.model_builder import build_model
from onmt.utils.optimizers import Optimizer
from onmt.utils.misc import... |
7769d84dfebb1bd57d00dc745f27bc4df2ba0f339ccb91d64edafb484506f32a | Python | 4,979 | 154 | #!/usr/bin/env python
import os, imp
import collections
import torch
from torch.nn import functional as F
import dataprovider3 as dp
import forward
import utils
import models
def main(noeval, **args):
#args should be the info you need to specify the params
# for a given experiment, but only params should ... |
8544f8c85c6e0271d15b870cd19c686047969725d77a89a764d6fbde26557534 | Python | 4,982 | 156 |
import cv2
import matplotlib.pyplot as plt
import numpy as np
import torch
from scipy.stats import mode as major_value
from sklearn.metrics import confusion_matrix
####
class BaseCallbacks(object):
def __init__(self):
self.engine_trigger = False
def reset(self):
pass
def run(self, state... |
03d2d8546fe56a1c350da841b2deca74289bbb39443a27e76671ab8302d6ebb3 | Python | 4,984 | 142 | # Copyright 2019-2021 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
import abc
class AmpligraphDatasetAdapter(abc.ABC):
"""Abstract class for... |
bfc041da34997e5c28a41e606be56b81942a0b89acf3d0b40becef41790e6c0c | Python | 4,988 | 155 | import os
import unittest
import pathlib as pl
import pytest
import ontquery as oq
import augpathlib as aug
from pyontutils import sneechenator as snch
from pyontutils.core import OntGraph
from pyontutils.config import auth
from pyontutils.namespaces import rdf
from pyontutils.integration_test_helper import Repo
from .... |
948048ca57d9466db019394aa0bd6a1e3ee2218576234307d1141d3a196ea913 | Python | 4,991 | 143 | import numpy as np
import pytest
from mock_data_stream import MockStreamData
from pyxdf.pyxdf import _detect_breaks
# Segment at absolute time-intervals exceeding a given threshold. Sequences of
# identical absolute intervals should be segmented the same regardless of
# whether they are positive or negative.
# Monot... |
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