sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d0771643ed874a78083212fef1fbd54011301e44fe79775e9a687cf17b89e791 | Python | 17,548 | 518 | """Schemas for storing ASE-based data."""
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
from ase.io import read
from ase.vibrations.data import VibrationsData
from emmet.core.symmetry import PointGroupData
from pymatgen.io.ase import AseAtomsAdaptor
from quacc import QuaccDe... |
6301ff433255d8638a931e9fd2c26bc1c6437d427ff2295fa08342abaa263b51 | Python | 17,567 | 360 | import copy
import unittest
import pandas as pd
from hed import HedFileError, load_schema_version
from hed.schema import HedKey
from hed.schema.schema_io import df_constants as constants, df_util, hed_id_util
from hed.schema.schema_io.df_util import get_library_name_and_id
from hed.schema.schema_io.hed_id_util import... |
82f9b121dd432b025565b4ff8d17154a8b923a1338e8ab91690b0b54cf3d9407 | Python | 17,567 | 489 | """Custom Espresso calculator and template."""
from __future__ import annotations
import os
import re
from logging import getLogger
from pathlib import Path
from typing import TYPE_CHECKING, cast
import numpy as np
from ase.atoms import Atoms
from ase.calculators.espresso import EspressoProfile
from ase.calculators.... |
5f9e21e657c209f2b5aafb72e533e8064aaa97b1f9ae5565bfc2c07e5766ca25 | Python | 17,572 | 396 | import os
from typing import Any, Callable, Dict, Tuple, Union
import joblib
from torcheeg.io import EEGSignalIO, MetaInfoIO
from ...constants.emotion_recognition.bci2022 import (
BCI2022_ADJACENCY_MATRIX, BCI2022_CHANNEL_LOCATION_DICT)
from ..base_dataset import BaseDataset
FIRST_BATCH_CHANNEL = [
'FP1', '... |
6bec0acdf1164f6940f532a6f59a647d65b7a1a5b570404c3982a095386f76d0 | Python | 17,573 | 424 | # -*- coding: utf-8 -*-
#
# Test Welch's method from user/frontend perspective.
import pytest
import syncopy as spy
import numpy as np
import inspect
import dask.distributed as dd
import matplotlib as mpl
import matplotlib.pyplot as plt
from syncopy.shared.errors import SPYValueError
from syncopy.shared.const_def imp... |
058b390003abc1ad0f8b4994e67ffcd78e3ef91c680cbfdd9be7dffdbc7cb76a | Python | 17,575 | 442 | from collections import OrderedDict
from typing import Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
class SSTEmotionNet(nn.Module):
r'''
Spatial-Spectral-Temporal based Attention 3D Dense Network (SST-EmotionNet) for EEG emotion recognition. For more details, please refer to the f... |
0f009c995dca7506c018a2fc9458a065ea72ddc8d323ee4b644aa349c02fd42c | Python | 17,583 | 383 | """Classes responsible for basic character validation of a string or tag."""
import datetime
from semantic_version import Version
from hed.errors.error_reporter import ErrorHandler
from hed.errors.error_types import ValidationErrors
from hed.schema.schema_io.schema_util import schema_version_greater_equal
from hed.v... |
1af1de1b864e64c867cb4aa1d1728c8f595ded526b3367a202290beca23f6874 | Python | 17,587 | 468 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Apr 17 18:21:00 2022
@author: haotian teng
"""
import os
import copy
import toml
import torch
import itertools
import torchvision
import numpy as np
import torch.utils.data as data
from xron.utils.seq_op import findall
from typing import List,Dict,Calla... |
9df54dd7d34057e0e4023dc6b907ae718886137de603b250de20b5bd0296978e | Python | 17,588 | 451 | from datetime import datetime
import time
import subprocess
import os
import json
import sys
ZONE = None
## Azure configuration flags.
# Approximate conversion between similar VMs on Amazon and Azure.
AMAZON_TO_AZURE_SIZING = {
"n1-standard-64" : "Standard_E64_v3",
"n1-highmem-64" : "Standard_E64_v4",
"n1... |
6d1adc6e00dbbf4180b85351931ddf685fbe7b2cab689a94cc359d34554a4e9d | Python | 17,592 | 481 | #!/usr/bin/env python
import gzip
import os
from collections import Counter
from itertools import combinations
import networkx as nx
import numpy as np
from scipy.sparse import lil_matrix
from irescue.em import run_em
from irescue.misc import get_ranges, getlen, run_shell_cmd, writerr
from irescue.network import bui... |
92826556cbe5a4ae9d7172173bdd82d66426cd4d78521232b689f7189e16088f | Python | 17,595 | 272 | import itertools
import math
import os
import pickle
import random
from argparse import Namespace
from functools import partial
import copy
import numpy as np
import pandas as pd
import torch
import yaml
from torch_geometric.data import Dataset, Data
from torch_geometric.loader import DataLoader
from tqdm import tqdm
... |
33ce9e301651f8392a046866082b11a79a26cf8a7646911eb53ea5090824d04e | Python | 17,604 | 505 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
3dd86a8a8bbb4c4c076d82e108ed45d09467c7d920c6b031f7812b4a0cc83af7 | Python | 17,604 | 505 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
7ae54f5f14a7ee758ed0ecc55eb812210ea3a54b7734f53e84efd8ada61094e5 | Python | 17,607 | 505 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
448e69a815ca7ce5d5cd9f32944cd4c6d476e7d3aadfae7972f1c041d0c6ea11 | Python | 17,618 | 558 | """Meta FAIR recipes"""
from __future__ import annotations
from importlib.util import find_spec
from math import ceil
from typing import TYPE_CHECKING, cast
from monty.dev import requires
from quacc import job
from quacc.calculators.vasp.params import MPtoASEConverter
from quacc.recipes.vasp._base import run_and_su... |
d8c95b41919134f785327173fcb46aff52a1d10d3a9493b904a9ec5c3db8b388 | Python | 17,618 | 384 | # -*- coding: utf-8 -*-
"""
Created on Thu Oct 28 21:00:17 2021
@author: CY
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.distributed import get_world_size
import numpy as np
class BaseModel(nn.Module):
"""
Base model with: a encoder
"""
def ... |
a7d9cf42c3462453834597a8d7a5c950530339a1e5a8076c025cbc4f14139e0f | Python | 17,633 | 552 | # -*- coding: utf-8 -*-
#
# Load data from Field Trip .mat files
#
# Builtin/3rd party package imports
import re
import h5py
import numpy as np
from scipy import io as sio
from tqdm import tqdm
# Local imports
from syncopy.shared.errors import SPYValueError, SPYInfo, SPYWarning
from syncopy.shared.parsers import io_p... |
24708a94a93037e0d8f92ee9a710807a44194be8524a0368d9138d5d865cfa18 | Python | 17,637 | 419 | #!/bin/env python3
"""
Phase Defect Lines (PDLs)
-------------------------
For a periodic process in a medium, for which a phase can be defined, we call
(large) discrete jumps from one value to another value *phase defect*. A *phase
defect line* (PDL) is a line at such an interface in 2D. In 3D, we would
observe *phas... |
33a38b343d96f55b17cb11d77319cee593488d0d964bda6ffeba5caf68f2fe50 | Python | 17,641 | 384 | import argparse
import collections
import gzip
import math
import os
import random
import shutil
import subprocess
import sys
import time
import numpy as np
import pandas as pd
import utils
import tabix as tb
import tensorflow as tf
import pybedtools as pybt
import pyximport; pyximport.install()
import cython_fxn
f... |
053d2423daa527ff125ad86e3a1a645bee39a86ed6b2556fc717f4343e622534 | Python | 17,667 | 416 | """
Utilities for processing MCF graphs
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 27.11.14
"""
__author__ = 'martinez'
import operator
import copy as pcopy
# import pyseg.graph as gp
# import pyseg.vtk_ext
from . import visitor
from pyseg.globals import *
# import pyseg.dispe... |
32fb2d3212b000ed1762b198e59c2355e2f8679db0e7c7c4d6ed78851e63e69d | Python | 17,680 | 475 | # A nodal network module
import numpy as np
import scipy as sp
import scipy.special as special
DEFAULT_LD = 0.05
EPSILON_FP = 1e-300
#-----------------------------------------------------------------------------------------------------------------------
def ksd(X, *args, **kwds): # Kolmogorov-Smirnov distances (sor... |
334c5d662ddca161c821cbc7fdf6ed086ca4c8160aadc7f62ffa41b975947347 | Python | 17,682 | 325 | import numpy as np
import pandas as pd
import re
import os
from sklearn.preprocessing import StandardScaler, MinMaxScaler
import networkx as nx
from sklearn.model_selection import train_test_split
from joblib import Parallel, delayed
def standardize_gene_id(gene_id):
# 正则表达式去除版本号和其他后缀
match = re.match(r"(ENSG... |
4d9288553604c1c54f1104bf253bc0447e6f16a2b415285236556985925d2617 | Python | 17,683 | 491 | import site
from typing import Callable, List, Dict, Optional, Literal, Tuple
import torch
from torch import nn
from hotpp.layer.radial import ChebyshevPoly
from .base import AtomicModule
from ..layer import EmbeddingLayer, RadialLayer, ReadoutLayer
from ..layer.utils import ElementLinear
from ..layer.equivalent impor... |
c258df9b215f5d4f93102e344692904ced23d3b56971c0542231ba3b512cd858 | Python | 17,691 | 362 | import os
from typing import Callable, Dict, Tuple, Union
import numpy as np
import scipy.io as scio
from ....utils import get_random_dir_path
from ..base_dataset import BaseDataset
class DREAMERDataset(BaseDataset):
r'''
A multi-modal database consisting of electroencephalogram and electrocardiogram signal... |
28f860b5a37757792be3ce2a043f9a88ea582fb6841dde7fe28cbc3322d881d3 | Python | 17,693 | 456 | import sys
import igraph as _ig
from . import _c_louvain
from ._c_louvain import ALL_COMMS
from ._c_louvain import ALL_NEIGH_COMMS
from ._c_louvain import RAND_COMM
from ._c_louvain import RAND_NEIGH_COMM
from collections import Counter
# Check if working with Python 3
PY3 = (sys.version > '3')
def _get_py_capsule(g... |
0582d1c6bbd6ac487b80ca7509d72731c34ce94f7f509b9b719fbb9bc08e3905 | Python | 17,695 | 477 | from __future__ import division, print_function
import operator
import numpy as np
from scipy.stats import gamma
from scipy.ndimage import convolve1d
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
from matplotlib.patches import Rectangle
def compute_joint_isi(spike_train1, spike_train... |
8768d94bdc95749790d1b8cd94c77d6c90101cf113cc6c98a852b52258c9cb89 | Python | 17,698 | 457 | # Copyright (C) 2019 Computational Science Lab, UPF <http://www.compscience.org/>
# Copying and distribution is allowed under AGPLv3 license
#
# This script implements a Wasserstein GAN (WGAN) with weight clipping (WGAN-CP)
# for generating 3D voxel data using a Generator and Discriminator model.
# It includes functi... |
44d6e559c37ca1e53393abd0033181840ddbe1d6038fff7632395a4a941c734f | Python | 17,713 | 422 | """Lightweight HED search operating directly on raw HED strings.
Provides a string-based search system that sits between the fast but limited
:mod:`basic_search` (flat regex on pandas Series) and the full
:class:`~hed.models.QueryHandler` (requires :class:`~hed.models.HedString` objects
with a loaded schema).
Key cla... |
3b98738df4073a1dc4a7adfda6c16af8e061417b0f1a0b04cd1660b8288794d4 | Python | 17,714 | 523 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
b56b9460026a03c8c99717c3db035fe6b0fd751e548a28b6326dd09ee3aa169b | Python | 17,717 | 368 | """
Created on Tue Apr 19 16:19:13 2022
@author: Haotian Teng
"""
import os
import sys
import time
import toml
import torch
import argparse
import numpy as np
from tqdm import tqdm
from typing import List, Dict
from functools import partial
from xron.utils.seq_op import length_mask
from xron.nrhmm.hmm import RHMM,Gaus... |
6d7552b4417da00dd4e9f9a1779057f52b4a0ec78cca76a83b90e6c4fe0e1669 | Python | 17,721 | 515 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
6e84b498d0be0f370861428d46ae880ad8e5b603d5b7008e284d85515e765a5a | Python | 17,722 | 434 | from __future__ import division
from __future__ import print_function
import datetime
import json
import logging
import os
import pickle
import time
import numpy as np
import optimizers
import torch
import torch as th
from config import parser
from models.base_models import LPModel
from utils.data_utils import load_d... |
499b3567355f51e3ee77c316fcaa4b74c12170b575251a64bcb10029c717cfa0 | Python | 17,726 | 482 | import logging
from pathlib import Path
import torch
import torch.nn as nn
from elasticai.creator.nn.integer.addition import Addition
from elasticai.creator.nn.integer.concatenate import Concatenate
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.gr... |
a184699e8192a8d0af3d039c57ee1f2c0ef9beede43bc8dc67e4ddc13f1c2941 | Python | 17,729 | 270 | """IDENTITY.py 2026-10-08. Pre-registration: 04-NOTES/PREREG-2026-10-08c-IDENTITY.md
Is v2LN30 what I say it is? Checks against published real data, not against the model:
D2 Liu & Wilson 2013 (Fig. 2): 29 dye-filled OK371 glutamatergic local neurons — 11 many-glomerulus, 8 one ventral glomerulus,
10 posterior t... |
7349ef6f6847d753e71dffe89e564d128fda38e6efa2ecf8ed82b09d0489e33f | Python | 17,731 | 492 | import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib import cm
import os
import colorcet as cc
import math
import random
import networkx as nx
def describe_dataset(data):
# Number of classes
print(f'The dataset contains {len(data.label_key)} classes. Here are the classes an... |
e73ec915db94063dfb2352f04d7740e193ad342f2e7f86c37c53844e362c97a2 | Python | 17,735 | 496 | from pkg_resources import resource_filename
import pandas as pd
import numpy as np
from pyfaidx import Fasta
import torch
from torch.nn import functional as F
import gffutils
import argparse
import logging
import vcf as pyvcf
from model.model import SpTransformer
from pyensembl import Genome
from model.SpliceAI import ... |
0e78942f2bd0d5b6cbb96c337eef8afa380c0f728cfec8d7db695cdd7e322b15 | Python | 17,743 | 405 | from __future__ import annotations
from typing import TYPE_CHECKING, Literal
import numpy as np
import pandas as pd
import scanpy as sc
from anndata import AnnData
from fast_array_utils.conv import to_dense
from sklearn.cluster import HDBSCAN, KMeans
from pertpy._logger import logger
from pertpy._types import cast_f... |
aebc47e0bc94a90b5462d43fb542b592b5f817ae7190ae69d4baac857613d786 | Python | 17,750 | 485 | # -*- coding: utf-8 -*-
#
# computeFunctions and -Routines to post-process
# the parallel single trial computations to be found in ST_compRoutines.py
# The standard use case involves computations on the
# trial average, meaning that the SyNCoPy input to these routines
# consists of only '1 trial' and parallelising over... |
3a0134a65d5e59c5d8e7187266a14ebc7c1fb6e3dc633d06485263977e30fe08 | Python | 17,753 | 367 | import time
import os
import subprocess
import sys
import re
import argparse
import collections
import gzip
import math
import shutil
import matplotlib.pyplot as plt
import wandb
import numpy as np
import time
import pandas as pd
from datetime import datetime
import random
#import logging
#from silence_tensorflow impo... |
40654bfeaf66c13e4bdb12782539575590a499bd4f88147f7f2ef0d064b67e1c | Python | 17,757 | 375 | """
Script for extracting particles from a filament network of a oriented single membrane graph
Input: - A STAR file with a list of graphs (MbGraphMCF) as it is returned by
by mb_fils_network.py script:
+ Density map tomogram
+ Segmentation tomogram
+ M... |
93ef2996ede783c6b1530c82fb671dc011ceafe8f023464c872c12003488ac32 | Python | 17,769 | 391 | import os
import csv
import glob
import pickle
from tqdm import tqdm
import numpy as np
import pandas as pd
from copy import deepcopy
from Bio.PDB import PDBParser
import torch
from torch.nn import functional as F
from torch.utils import data as torch_data
from torchdrug import core, data, datasets, utils
from tor... |
7cfa1b0b5fa8b4c6731b43a6d2cb8a96d0037e16d980e7b02c6b5265dd81422e | Python | 17,777 | 411 | from __future__ import annotations
from typing import Any
import flax.linen as nn
import jax
import jax.numpy as jnp
import numpy as np
import optax
import pandas as pd
from anndata import AnnData
from fast_array_utils.conv import to_dense
from flax.training import train_state
from jax import random
from sklearn.mode... |
afd2bad77f602dd7b4cc78d11df4b306f1cecc2890c9191427648df14995ebdc | Python | 17,777 | 444 | '''
Description:
Use scNODE predictions to help recover smooth and continuous cell trajectories.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import scanpy
import torch
import numpy as np
from benchmark.BenchmarkUtils import loadSCData, tunedOurPars
from plotting.__init__ import *
from plotting.PlottingUt... |
f3cd09c96671ab8941de8cb1196d63d5ff2095fd6aa678bfa9187372a64f925b | Python | 17,780 | 445 | """ Code to process output of DeepLabCut
Attention: now possible to select whisker data based on time
of CNO dropping; can select either before or after drop time"""
# Import modules & packages
from pathlib import Path
import numpy as np
import pandas as pd
# for phase extraction
from scipy.signal import buttord, bu... |
6d7c9d7e5e0f75ebebc1944b5a09ed1cc80227e6e3aac7fac7244ee3b69e9614 | Python | 17,786 | 485 | import os, sys, yaml, importlib, datetime, argparse
from utils.train_utils import *
for _path in path_to_pad:
sys.path.append(_path)
import numpy as np
import pandas as pd
from utils.utils import *
import tensorflow as tf
from sklearn.model_selection import train_test_split
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2... |
22bc93b023f9de6a25451830857c0109805ba69a33742e045be32184325df03e | Python | 17,790 | 560 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
eaab9a9ed63edecc9c096cfe3b0ca6c9507ab163a5d369a9415b93b7d7344770 | Python | 17,792 | 455 | #!/bin/env python3
"""
Visualisation with ParaView using XDMF
======================================
Functions for creating files in the eXtensible Data Model and Format (XDMF).
For information about this format, visit:
https://www.xdmf.org/index.php/XDMF_Model_and_Format
XDMF files generated with this submodule sho... |
15da276de79bbd83829702db6f364aeedd94c87a67b8cc37bc1251329b6d6dd6 | Python | 17,806 | 426 | import argparse
import os
import time
from collections import defaultdict
from collections import namedtuple
import numpy as np
from learn_tools.active_gp import ActiveGP, POUR_MLP_HYPERPARAM_3000, SCOOP_MLP_HYPERPARAM_3000
from learn_tools.collect_simulation import start_task, complete_task, sample_task, get_paramet... |
88e0d3bcc5cfb13cdae3c3a65260c6a42c580336f341f9217af687f1c7806d27 | Python | 17,807 | 427 | """Warp + writer tests - kept apart from the pure-function tests because these
touch ANTs and the filesystem."""
import os
import numpy as np
import pytest
nib = pytest.importorskip("nibabel")
def _mod():
from regtools.registration import segmentation_quantification as sq
return sq
def ... |
6469d93fbdf83918e2ba91cb5a6e9d079669cf4bbd3242a016bebf2e011ee43f | Python | 17,815 | 526 | """Generate E3FP fingerprints.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
from __future__ import division, print_function
import os
import logging
import argparse
import sys
from python_utilities.scripting import setup_logging
from python_utilities.parallel import (
make_data_iterator,
Parallelizer,
... |
46708fea8fc0acbd505c6f31891735e16368812d72015627296ac81380bb425a | Python | 17,832 | 460 | # -*- coding: utf-8 -*-
"""
Created on Mon Jun 15 11:28:26 2020
@author: David Quiroga-Martinez
"""
#################### Load libraries and set directories #######################
from random import shuffle
from psychopy import prefs
prefs.hardware['audioLib'] = ['sounddevice']
from psychopy import visual, core, sound... |
407c61704e8a242c03072a6950e61fcf5310e961b566ce9168a1a3a5e9088c57 | Python | 17,839 | 397 | # OWNER : SUBINOY ADHIKARI
# EMAIL : subinoyadhikari@tifrh.res.in
import sys
import os
import pickle
import numpy as np
import tensorflow as tf
tf.compat.v1.disable_eager_execution()
from tensorflow.keras import Model
from tensorflow.keras import backend as K
from tensorflow.keras.optimizers import Adam
fro... |
650ce29bc57c28032aa0f79d60f25d537af9866f5ba8b38cddbf2425887d638b | Python | 17,841 | 469 | """Pure data model for manual contour correspondence editing.
``ContourCorrespondenceStore`` holds all mutable state for a contour
registration session - control points, curve->target links, sampled
correspondence points, the undo stack, and dirty/save tracking - with
no matplotlib, Qt, or Tk dependencies.
The... |
4aa853199220948fa44bfa02cdc0eb3641c0761793ff67a6b950e4a1dd31487d | Python | 17,847 | 329 | import tensorflow as tf
from tensorflow.keras.layers import Input, Dense, GlobalAveragePooling2D, Flatten, GlobalMaxPooling2D, AveragePooling2D
from tensorflow.keras.layers import *
from tensorflow.keras import Model
from tensorflow.keras import regularizers
import logging
import sys
from tensorflow.keras.regularizers ... |
3dc8dc66ccee9e5070d05448088afadcb00073c954428aa26bd1912de3f3a9cd | Python | 17,861 | 435 | """distutils.cmd
Provides the Command class, the base class for the command classes
in the distutils.command package.
"""
import sys
import os
import re
import logging
from .errors import DistutilsOptionError
from . import util, dir_util, file_util, archive_util, dep_util
from ._log import log
class Command:
"... |
e561cc12275bd674704c3d9389fab2436c4dc65428121ebad92c638d2bf4676b | Python | 17,861 | 402 | """A group of BIDS files with specified suffix name."""
import csv
import json
import logging
import os
import re
import pandas as pd
from hed.errors.error_reporter import ErrorHandler, check_for_any_errors
from hed.errors.exceptions import HedFileError
from hed.models.model_constants import NAME_WHITESPACE
from hed... |
607510d6e9d27b68ceeba5195d2aaf88ceb31b0df33a5c2a796aa553acbced76 | Python | 17,862 | 456 | # ----------------------------------------------------------------------
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/... |
64efe8e10e152dd3c7da27bd93b2c4c2daa0ab3e912530aa8ff9055cf392afbc | Python | 17,863 | 460 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
7ed2f11cb9e2f68227e208d508be640bb84f1ffe6cf48a236e98239b8b8ade44 | Python | 17,866 | 473 | # Copyright 2018 The TensorFlow 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 applica... |
e4f08ee069c3127504362163e2f0ffd509803231cdb6f37a1d76c44d9f541a89 | Python | 17,872 | 552 | """
Requirements file parsing
"""
import logging
import optparse
import os
import re
import shlex
import urllib.parse
from optparse import Values
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Generator,
Iterable,
List,
Optional,
Tuple,
)
from pip._internal.cli import cmd... |
8e0d2fccf685fcb357268c42ee49b56a091d5eb94b03fa5f89032fc2b9119f02 | Python | 17,875 | 573 | """
Loss functions
scvi-tools distributions:
https://github.com/scverse/scvi-tools
log likelihood loss:
https://github.com/YosefLab/scVI/blob/6c9f43e3332e728831b174c1c1f0c9127b77cba0/scvi/models/log_likelihood.py#L206
"""
import os
import sys
import functools
from typing import *
import torch
import torch.nn as nn
... |
b9d25799e56358db2558d5b1ff8eb9fb002c3133ef703d8b6ee34d6c9764dbf0 | Python | 17,875 | 589 | from scipy.signal import savgol_filter
from scipy import sparse
from scipy.linalg import norm
import pandas as pd
import numpy as np
from scipy.stats import binned_statistic
from maldi_nn.utils import topf
import matplotlib.pyplot as plt
import h5torch
import torch
class SpectrumObject:
"""Base Spectrum Object cl... |
2982d55b839573636df40cc9c7b6e9db1c7924e44f6011b9ca350b5396fc97fb | Python | 17,885 | 450 |
from dolfin import *
import numpy as np
import matplotlib.pyplot as plt
import sys
import time
import os
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--order", type=int, default=1)
parser.add_argument("--variation", type=str, default="base")
parser.add_argument("-res", "--resolution", type... |
172ad7adf2452a740f7c39fbf0094fae5023c6e4805d87ed9cc9c870dec18aa6 | Python | 17,891 | 403 | import numpy as np
import nibabel as nib
from pandas import DataFrame
from joblib import Parallel, delayed
from sklearn.preprocessing import minmax_scale
from pyrelimri.icc import sumsq_icc
from nilearn import image
from nilearn.maskers import (NiftiMasker, NiftiMapsMasker, NiftiLabelsMasker)
from nilearn.datasets impo... |
9cfcd18d85d232135cab5a86bce3e4963263a9cd41b30e3bae6809d6c345f70c | Python | 17,895 | 455 | """
Generate a synthetic set of microsomes with different membrane bound proteins
Input: - Data set parameters:
+ Number of tomograms (one microsome each)
+ Tomogram size
+ Resolution (pixel size)
+ SNR range
+ Missing wedge (sem... |
a709a6ac7f8a6cfba5c2c0b09b79bee671e243ac21a6fe0530a523a314f0edc9 | Python | 17,897 | 455 | """Integrated calibration indices and calibration curves at a specified time."""
from __future__ import annotations
import matplotlib.pyplot as plt
import numpy as np
from scipy.optimize import minimize
from scipy.special import logsumexp
from SurvivalEVAL.evaluations.calibration.single_time.util import (
_clogl... |
38dc1b60a8509133c399f790404dad528f9c69a0c27d581eb603074c56892096 | Python | 17,898 | 468 | # -*- coding: utf-8 -*-
import numpy as np
from scipy import stats, integrate
import pandas as pd
from itertools import product
from data_loader.microcircuit import p as p_PD
from data_loader.microcircuit import K_ext as K_ext_PD
from data_loader.hcp_dti import HcpDesikanKilliany, VolumesDK
from data_loader.synapse_cel... |
9e3bf6d1b3d528abac2116ecf0c77560d5a5199415d665b97d63cd91d631f902 | Python | 17,899 | 470 | """distutils.fancy_getopt
Wrapper around the standard getopt module that provides the following
additional features:
* short and long options are tied together
* options have help strings, so fancy_getopt could potentially
create a complete usage summary
* options set attributes of a passed-in object
"""
im... |
07a7cdd028e28042609377282f3c80ad0b3e913bb252255b4886835b16e46297 | Python | 17,906 | 393 | """
Prosper_nn provides implementations for specialized time series forecasting
neural networks and related utility functions.
Copyright (C) 2022 Nico Beck, Julia Schemm, Henning Frechen, Jacob Fidorra,
Denni Schmidt, Sai Kiran Srivatsav Gollapalli
This file is part of Propser_nn.
Propser_nn is free software: yo... |
718756404ce1aa8e5d89e4e61ac02d560b7a01696ad9f8089222a7ab0ddc8f19 | Python | 17,914 | 624 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
340723ee5a2e68ba1369b3df5679b9e2fb309d4913a3d75c611a2bd2e3916b6c | Python | 17,915 | 411 | import torch, numpy as np
import os, sys, yaml
from torchvision.datasets.utils import download_url
MODEL_CODE_DIR = os.path.dirname(os.path.abspath(__file__))
_download_dir = MODEL_CODE_DIR
sys.path.append(MODEL_CODE_DIR)
# ImageNet Transforms -------------------------------------------------------------------------... |
71aecd1fa64351abcd7a3e02ea1fbe43118dc55b801cbd24f990df594a53beae | Python | 17,922 | 539 | """"""
from itertools import combinations
from queue import Queue, Full
from threading import Lock
import logging
import cv2
import numpy as np
from pupil_recording_interface.decorators import process
from pupil_recording_interface.process import BaseProcess
from pupil_recording_interface.externals.methods import gen... |
7792b5994a83f91610e59777ac28943caf20e086730c3b89b99658c4fff8e994 | Python | 17,923 | 596 | #!/usr/bin/env python
# coding: utf-8
# # LIT-PCBA
# this dataset is a proposed "more difficult" test than DUD-E. I used a 75/25 (sklearn default) stratified split. The dataset is heavily imbalanced, like DUD-E.
# In[1]:
import pickle
from sklearn.metrics import roc_auc_score
import numpy as np
import seaborn as s... |
6458e0cc1602a9e4cae10065827ad5ef2f42e8c3832e7e997a7d56cee1e72a1b | Python | 17,925 | 453 | # Copyright (c) MONAI Consortium
# 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 in writing, so... |
8eb7aa4ab117df0e9406a43a2318a22e5902ef6042dd6861d9c0b92af8f812c2 | Python | 17,943 | 408 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
9cad7d1e50c981f6c051d0b7fff59bad02cdb3231f1d38655b307fc4f292c3e2 | Python | 17,961 | 499 | #!/usr/bin/env python
import sys
import os
from pyclamp.dsp.strfunc import isnumeric
from pyclamp.dsp.lsfunc import *
DEFLBWUSE = 'qt'
def use(_LBWUSE = None):
if _LBWUSE is None:
_LBWUSE = DEFLBWUSE
global LBWUSE
try:
lbwuse = LBWUSE # force error for when setting default
LBWUSE = _LBWUSE.lower()
... |
6ce7833ed76781e4f1d578176e0345531633007988248ec69bcc0cdd9237af8e | Python | 17,964 | 538 | """
All combinations except those that do not produce some sort of
chimeric protein are commented out
"""
import itertools
import os
agfusion_db = os.path.join(os.path.split(__file__)[0], "data", "agfusion.db")
AGFUSION_DB_URL = "https://s3.amazonaws.com/agfusion/agfusion."
# this is mostly contigent on the maximum... |
a6ef97b131750ff77c300b1ad044b968cf81cd9f7244ec89123b1cfc40d268b2 | Python | 17,965 | 521 | import ctypes
from ctypes import *
from control.TUCam import *
import numpy as np
import threading
import time
from control._def import *
def get_sn_by_model(model_name):
TUCAMINIT = TUCAM_INIT(0, './control'.encode('utf-8'))
TUCAM_Api_Init(pointer(TUCAMINIT))
for i in range(TUCAMINIT.uiCamCount):
... |
e96f977893be0941ee29f6ee2822433f55c0848f18fc2659a6cc31c7011ed52d | Python | 17,971 | 387 | import os.path
from collections import defaultdict
import pandas as pd
import re
from ckg.graphdb_builder import mapping as mp, builder_utils
#########################
# UniProt #
#########################
def parser(databases_directory, import_directory, download=True, updated_on=None):
config = bui... |
d86a97f0fef7159898e02040212adbe6235960a95d5c7dece8adce10b0e44d05 | Python | 17,981 | 483 | # coding=utf-8
# Copyright 2020 Microsoft and the HuggingFace Inc. team.
#
# 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... |
07832377dd215bca9b8ce51caf01d1b41e55ca333f01a35c1b6a17f770ff3063 | Python | 17,983 | 503 | import os
import sys
import string
import re
import json
import collections
voltage_scales={"V":0.001,"mV":1,"uV":10**3}
current_scales={"uA":10**(-3),"nA":1,"pA":10**3}
features_scales={"V":0.001,"mV":1,"uV":10**3, "uA":10**(-3),"nA":1,"pA":10**3}
scales={"voltage" : voltage_scales, "current" : current_scales, "featu... |
d7f12172545694cc97179ccfd956134c24dcfe274c29cadc7f35cd71b5e7fa8f | Python | 17,990 | 569 | import numpy as np
import pandas as pd
from pandas.api.extensions import ExtensionScalarOpsMixin
from pandas.core.arrays import ExtensionArray
from pandas.core.dtypes.base import ExtensionDtype
class Trace:
def __init__(self, val, meta=None, orig=None):
# print(orig)
if meta is None:
m... |
9cd65d1651af723cea11eb69848d86f1e173f57da892c0954d1e575c9784f75a | Python | 17,993 | 538 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
53b798f89bdfabbb5a1fb44d85515f547f6f2fb14400e007618d201aea2af564 | Python | 18,011 | 619 | """ cli.py
Command line interface
"""
import argparse
import gzip
import shutil
import sys
from os import mkdir, remove
from os.path import exists, join, split
from pathlib import Path
from urllib.error import HTTPError
from urllib.request import urlopen
import pyensembl
from agfusion import __version__, database, ... |
24f3e2d2f07770c76967bc14635de0c6b9c67996402d2ae67f42b89a22a4f925 | Python | 18,015 | 341 | # dataset/data_handling/protein_dataset.py
# Import custom modules
import os
import functools
import torch
import collections
import numpy as np
import pandas as pd
from pathlib import Path
class ProteinDataset(object):
def __init__(self, gnn_model_id, data_dir='./data'):
# Assign inputs to class attribut... |
cc1ecd8c9badb5911097750e54b597c0679d8639d844c062d8920f4ee603e71d | Python | 18,018 | 490 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
94e4560d6174797ee491ac702e3c8f608a6392e1db0d24a9cbac2166e7a0012d | Python | 18,023 | 404 | #!/usr/bin/env python
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
Object crash without prior vehicle action scenario:
The scenario realizes the user controlled ego vehicle
moving along the road and encountering a cyclist ahead.
"""
from __fu... |
99bcae6c9d528a8967d0ade668ecf8ccfc7eb29050e9d082d1b4b60e302de774 | Python | 18,028 | 416 | """Rectangle-drag multi-label selection + deletion mixin for the
CCF Boundary Editor.
Drives the ``ToolMode.SELECT_DELETE`` mode. The user drags a
rectangle on the canvas to add region IDs under it to a transient
selection set; Ctrl-drag removes them. A "Delete N selected" button
commits the set into the existin... |
a7a973c03dddce22e1654633b41176bec93f7a4cf8d4afc63e881c3c5e1cdcbe | Python | 18,029 | 410 | """
Generates a ListTomoParticle object from a input STAR file (translocon project version)
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import vtk
impor... |
5ca752f8ce7d04f8212636e0f442f0641b5777a80267c89ebeac65c6fee05e6d | Python | 18,031 | 352 | import glob
import neurokit2 as nk
import pandas as pd
import numpy as np
import scipy
import matplotlib.pyplot as plt
from scipy.interpolate import interp1d
from scipy.stats import zscore
def castToList(x):
# Casts x to a list
if isinstance(x, list):
return x
elif isinstance(x, str):
retu... |
69a4a49b7b9b3062daeaaf3871256453dd8fcef9e8529ba8ec7b8c2d7786e601 | Python | 18,031 | 448 | """Test the find_noisy_channels module."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
import numpy as np
import pytest
from pyprep.find_noisy_channels import NoisyChannels
from pyprep.ransac import find_bad_by_ransac
from pyprep.removeTrend import removeTrend
# Set a fixed random seed for repro... |
c949c227abfa120f5f6db15c92e0b694aee75b57f6dd7f2337322f3a9513c25d | Python | 18,032 | 517 | """Unit tests.
"""
import unittest
from os.path import abspath, curdir, join
import pyensembl
from Bio import Seq, SeqIO
from agfusion import database, model, parsers
data = pyensembl.EnsemblRelease(84, "mouse")
db = database.AGFusionDB(abspath(join(curdir, "agfusion.mus_musculus.84.db")))
db.build = "mus_musculus_8... |
bb72227cbf101e79864aeb82dc79c7379df2f7846438bf476494580b54b75253 | Python | 18,035 | 483 | #!/usr/bin/env python
import os
from collections import OrderedDict
from timm.models.layers import DropPath
import torch
from torch import nn
import torch.nn.functional as F
import torch.utils.checkpoint as checkpoint
from .attention import MultiheadAttention
import logging
logger = logging.getLogger(__... |
e643c7ab1739efb1e59725c6c3c004e482cf3673f43f6bf73adfdd337b901372 | Python | 18,035 | 504 | #!/usr/bin/env python
"""
This tool will extract the docstrings from the meep package and add them to the
hand-written documentation tree.
It is expected that the docstrings will be Markdown compatibile and will not
need to be massaged in any way. One reason for this is to help ensure that the
Look and Feel of the API... |
a1a1144ef49a1786d49ded346b651b355f616a08b71614109f6adc3f66459db8 | Python | 18,040 | 424 | """Evaluation of event-time point predictions."""
from __future__ import annotations
import numpy as np
from lifelines.statistics import logrank_test
from SurvivalEVAL.evaluations.custom_types import Numeric, NumericArrayLike
from SurvivalEVAL.evaluations.discrimination import concordance
from SurvivalEVAL.evaluatio... |
c72e3f49a6e2f3c320eff0ee5cd5d50a95920b217e950e3eeee2769947501dfe | Python | 18,040 | 449 | from __future__ import annotations
import logging
from copy import copy
from typing import TYPE_CHECKING, Any
from wikibaseintegrator import wbi_fastrun
from wikibaseintegrator.datatypes import BaseDataType
from wikibaseintegrator.models.aliases import Aliases
from wikibaseintegrator.models.claims import Claim, Claim... |
9dfd14badf0429704c73bbe13499301537d54cfcef819dcec11f122fb76055b7 | Python | 18,041 | 415 | """
Batch 2D Registration Script
=============================
Register multiple 2D slices from a directory to their corresponding CCF template
slices, driven by a CSV mapping file.
CSV format (no header row required, but one is allowed):
slice_index, ccf_index
0, 264
5, 270
12, 300
- slic... |
00fc7173fbfd4a5bc51b6f5da5f1dea28518e3a9f94f800e83c62654cf8e2b72 | Python | 18,046 | 427 | import pytorch_lightning as pl
from torch.utils import data
import pandas as pd
from utils.logger import get_logger
from utils.util import check_cache_files
import numpy as np
from torch import from_numpy
import dgl
import torch
import shutil
from torch.utils.data import DataLoader, TensorDataset, RandomSampler, Weight... |
69e404c4558456d8d418fbd2c65a6bbe54c3594083ae9234e100f63e47484149 | Python | 18,053 | 394 | # Implementation: https://github.com/alexandrosstergiou/keras-DepthwiseConv3D
import keras.ops as kops
from keras import backend as K
from keras import initializers
from keras import regularizers
from keras import constraints
from keras import layers
from keras import InputSpec
from keras.src.legacy.backend import _pr... |
5d16ad436d3742aaf0091a10ea18a3ff2780acd34ed486878be5ba4105859d65 | Python | 18,055 | 463 | import os
import os.path as op
import numpy as np
import pandas as pd
from tqdm import tqdm
import mne
import nibabel as nib
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib.colors import Normalize
from scipy import stats
from params import PLOT_DIR as plot_dir
from params import... |
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