sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3606debc76b21473b0ef5e24658f069bd901a2b8d2591b486760daebe1eac2d9 | Python | 19,567 | 340 | # Copyright (c) 2021, Ko Sugawara
# All rights reserved.
#
# 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 notice,
# this list of conditions and t... |
9bd440828978783958b3a8f2efe8da1d6b582761e3a12b7e5ae0b9a45f8f6af7 | Python | 19,569 | 656 | """
Functions for creating stimuli and noise inputs for models.
"""
import inspect
import logging
import numba
import numpy as np
from chspy import CubicHermiteSpline
from ..models.model import Model
from scipy.signal import square
class Input:
"""
Generates input to model.
Base class for other input t... |
d29d2960dd3de4eb060ee182f651e28158726a185ab84203c0854af0cca9b4a8 | Python | 19,571 | 521 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Demonstrate usage of LFPy.Network with network of ball-and-stick type
morphologies with active HH channels inserted in the somas and passive-leak
channels distributed throughout the apical dendrite. The corresponding
morphology and template specifications are in the file... |
4088c0a7de34400b1b80304183cc4827914f79d99787f9c6852d09339b7d9c4e | Python | 19,574 | 513 | # 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... |
ea3c628cf7b8c01afb7d1ba72997b193c68b3b71bab7b66536d733bcae680913 | Python | 19,582 | 451 | #===========================================================================
# Import, Set up MPI Variables, Load Necessary Files
#===========================================================================
from mpi4py import MPI
import time
tic_0 = time.perf_counter() #script runtime calculation value
import os
from o... |
b56d97ab29b2e0b529653d78b1e4de575147811ffb41c00373e21c5260785f78 | Python | 19,587 | 614 | """
This code was taken from: https://github.com/aaren/wavelets
"""
from __future__ import division
import numpy as np
import scipy
import scipy.signal
import scipy.optimize
import scipy.special
from .wavelets import Morlet
__all__ = ['cwt', 'WaveletAnalysis', 'WaveletTransform']
def cwt(data, wavelet=None, widt... |
3330fc268aab7297db7926096e9efec844c24faabbeda6564433450e119345be | Python | 19,605 | 516 | """
m6a_cnn.py
Author: Anupama Jha <anupamaj@uw.edu>
This module predicts whether an
adenine is methylated or not. The
model is trained with Fiber-seq
HiFi read sequence, inter-pulse
distance and pulse width signal
from pacbio. The model is a
convolution neural network.
"""
import torch
import numpy as np
import _pick... |
5724ffa1e1bb07709854f0747ffec40918734e40a59867b740d58dc02184162d | Python | 19,607 | 515 | """
m6a_cnn_ont.py
Author: Anupama Jha <anupamaj@uw.edu>
This module predicts whether an
adenine is methylated or not. The
model is trained with ONT read sequence,
read quality score and methylation score
from oxford nanopore. The model is a
convolutional neural network.
"""
import torch
import numpy as np
import _pi... |
89a67e40c1b58e1779b24da0c98b303e4944da61fa59cd6ecef8e33aa68b9912 | Python | 19,616 | 517 | """Helper classes for trajectory data management and Blender integration.
Provides utility classes for position caching, frame management, Blender property
synchronization, and attribute metadata collection.
"""
import logging
from typing import Optional
import databpy as db
import numpy as np
import numpy.typing as ... |
b16342fe05215b3434164092e9b0f74e3d85be59e4d80c0b9cff0ebdc57f82f4 | Python | 19,616 | 568 | """distutils._msvccompiler
Contains MSVCCompiler, an implementation of the abstract CCompiler class
for Microsoft Visual Studio 2015.
The module is compatible with VS 2015 and later. You can find legacy support
for older versions in distutils.msvc9compiler and distutils.msvccompiler.
"""
# Written by Perry Stoll
# h... |
f1dc23cbc93ecac8bc35e6ac7f22759e09072e86f4164e13e9e9de685e2e9603 | Python | 19,631 | 577 | # 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... |
255c9339a9c2196378153763ebe176fe68e29dbacef54275c8cd4b6d8794b940 | Python | 19,636 | 414 | #####################################
######## Paper Draft Cartoon ########
#####################################
#%%# Catalyzer
import os
import sys
path = os.path.dirname(os.path.realpath(__file__)) + '/../Resources'
sys.path.append(path)
import numpy as np
import torch
import pickle
from Utilities import make_para... |
54dded0a3a542d8782b7fafab97998ec6e5e08ce377ae8672084d238bb29ff3c | Python | 19,636 | 462 | """
Mapping of a base input file columns into HED tags.
"""
import copy
import warnings
from collections import Counter
from functools import partial
from hed.errors.error_reporter import ErrorHandler
from hed.errors.error_types import ValidationErrors
from hed.models.column_metadata import ColumnMetadata, ColumnType... |
b3dc79085f3c0e84d2d11d2d02706ba12253fbe80b61e3f5f0bb4e374c8532d2 | Python | 19,638 | 431 | """
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... |
f2d551b7b0e8e8cd5cb436b3c0e591e622423134249ae6c4373add5fa38a697e | Python | 19,650 | 360 | import os
import pickle as pkl
from typing import Any, Callable, Dict, Tuple, Union
from ..base_dataset import BaseDataset
class DEAPDataset(BaseDataset):
r'''
A multimodal dataset for the analysis of human affective states.
This class generates training samples and test samples according to the given p... |
b0e317097adbd46907b34d3022f3ed4aaeaf4cf086ea6591a3d78f49dda5b0ab | Python | 19,651 | 353 | import os
import shutil
import tempfile
import unittest
from hed.models.sidecar import Sidecar
from hed.schema import hed_cache
from hed.schema.hed_schema import HedSchema
from hed.schema.hed_schema_group import HedSchemaGroup
from hed.schema.hed_schema_io import _load_schema_version, load_schema_version
from hed.tool... |
002e69327a2d5d6d913269d9f760888fbb15b4236f52897af8c2b7079d9cc1e1 | Python | 19,653 | 498 | # -*- coding: utf-8 -*-
from __future__ import annotations
import os
from typing import (TYPE_CHECKING, Any, Dict, Iterable, List, Optional, Set,
Tuple, Union)
import nltk
from supar.utils.logging import get_logger
from supar.utils.tokenizer import Tokenizer
from supar.utils.transform import Sen... |
2e636cdb90f0e0894b368c4855171e42a03ac8a93596cc3c29b8e4234d3bac1c | Python | 19,656 | 389 | # 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... |
49547a84e89d4a04e1118e66a8650140866562fc071d3c24eb79aa47c78e979a | Python | 19,670 | 410 | # coding=utf-8
# Copyright 2018 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 by applicable... |
e9670d53e88c1a8d01ac3f3e91147244f2d6def51c440c6b0b87061381b0c68c | Python | 19,678 | 493 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Oct 23 13:19:47 2020
@author: hugwei
"""
import os
from typing import List, Union, Tuple
try:
import h5py
h5py_available = True
except ImportError:
print("h5py not installed, some functions will not work.")
h5py_available = False
import ... |
d2d712d5a58032f921c20bd54dc32ae86bbc9dc15a2b43081918a33a52fc04cb | Python | 19,686 | 492 | # Computational model used for studying fragmented network bursts in Doorn et al. 2024.
# Model of neuronal network derived from hiPSCs on MEA (Doorn et al. 2023)
# Using a HH-type model including a slow after-hyperpolarization current and membrane noise (Masquelier, Deco 2013).
# Connected into a network with N neuron... |
89d8fa7197087772f9c4d35e27b89e38bb70ddac0993903ae3151f7ad1f0ab73 | Python | 19,697 | 538 | """
requests.adapters
~~~~~~~~~~~~~~~~~
This module contains the transport adapters that Requests uses to define
and maintain connections.
"""
import os.path
import socket # noqa: F401
from pip._vendor.urllib3.exceptions import ClosedPoolError, ConnectTimeoutError
from pip._vendor.urllib3.exceptions import HTTPErro... |
b25379362c8befbe859b9e9e9c3262d3e3085e0d2a0f4621a59acbf483c16f5c | Python | 19,703 | 472 | import numpy as np
import os
import pandas as pd
import glob
import matplotlib.backends.backend_pdf
import nibabel as nib
from nilearn.plotting import plot_img
from nilearn.image import index_img
import pv_conv2Nifti as pr
import alive_progress as ap
import pv_parser as par
from QC import *
#%% Feature calculation of t... |
b4404fc7caf2c2c9cca2df204f2c708bf778bfb91a669a3196151e420914444b | Python | 19,703 | 499 | """kNN evaluation modules and script.
Copyright (c) 2024 University of Michigan. All rights reserved.
Licensed under the MIT License. See LICENSE for license information.
"""
import os
import logging
from shutil import copy2
from functools import partial
from typing import List, Union, Dict, Any
import yaml
import n... |
2c6e3bbc9d012b160904af3c62e75478cd2a10a2851a421172a9fd55ab3aad80 | Python | 19,705 | 564 | #!/usr/bin/env python3
import pysam
import numpy as np
import argparse
import logging
import pomegranate as pom
import array
import git
D_TYPE = np.int64
def get_commit_hash(short=7):
repo = git.Repo(search_parent_directories=True)
sha = repo.head.commit.hexsha
return repo.git.rev_parse(sha, short=short)... |
8391d27ee562737b2a2c10539a83dcde6b9a59c0970ded150529c315c84d2376 | Python | 19,731 | 547 | # basic
import os, glob, gc, random, math, tsaug
import numpy as np, pandas as pd
import matplotlib.pyplot as plt, seaborn as sns
from collections import OrderedDict
from Bio.Seq import IUPACData
from tqdm.auto import tqdm
from joblib import Parallel, delayed
from itertools import product
# pytorch
import torch
from t... |
eb90d16fa7934aaa99fcb8853d388a2129eebe7fcbed1d19a54ff086c3dd3d78 | Python | 19,732 | 533 | from __future__ import division, unicode_literals, absolute_import
from builtins import int, range, dict, map, zip
import io
import os
import re
import sys
import queue
# Future warning from cython in h5py
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import h5py
from tqdm import tq... |
37fe7dc1043fe34d3d7c7d8aa8042b4b368cf76deb13e181264c8cf51c9531ff | Python | 19,735 | 431 | """
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... |
cf0682baa1d601d62a99439562ff063967599dcd137a490a2b5511afda9d5adc | Python | 19,743 | 525 | import os
import pygame
import random
from dataclasses import dataclass
pygame.init()
pygame.font.init()
pygame.mixer.init()
@dataclass
class G:
'''
Keeps track of globals, game constants and variables not related to the players or the cards.
Fields:
FPS: The number of times the game loop runs p... |
1cd8ae8632648d5f6854313b51959d43046bc0f5552ac1dff225c128519d0120 | Python | 19,749 | 629 | import numpy as np
import numba
from ...utils import model_utils as mu
def timeIntegration(params):
"""Sets up the parameters for time integration
:param params: Parameter dictionary of the model
:type params: dict
:return: Integrated activity variables of the model
:rtype: (numpy.ndarray,)
... |
d22f1c260aeaba9cdaebb2013d9feef635ef9d2c6be54065544894a9d90fb582 | Python | 19,752 | 537 | from __future__ import absolute_import
import collections
import functools
import logging
from ._collections import RecentlyUsedContainer
from .connectionpool import HTTPConnectionPool, HTTPSConnectionPool, port_by_scheme
from .exceptions import (
LocationValueError,
MaxRetryError,
ProxySchemeUnknown,
... |
b9a925b846c97a2e579e6bde889b66d584082f9f5f5b21d97c93e198b4d241d0 | Python | 19,753 | 474 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 7 15:39:18 2024
@author: deeperthought
"""
import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import nibabel as nib
from skimage.transform import resize
from tensorflow.keras import Input, Model
from tensorflo... |
d2b0b9e4a788e9cea2a078d6bef50be969482b359c5ec4b614cdccf3d3e4b62e | Python | 19,754 | 450 | """
DeepLabCut2.0 Toolbox (deeplabcut.org)
copyright A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
"""
from __future__ import print_function
import wx
import... |
8fa1bc546a3ad34e053eca1a19f578da01703da969a0f6573f7ab287b0ebe962 | Python | 19,759 | 513 | """Linear mixed models with one random intercept, shared by Milo, Dialogue and the differential expression interface.
Random intercepts are written as ``(1 | variable)`` in formulas, the syntax of lme4 and R Milo.
The numba kernels fit ``y ~ X + (1 | group)`` by REML and compute Satterthwaite degrees of freedom like `... |
77c6d00c7b8f1779bd531ba48c1dbdddd3bcb6101c6594d1283462467a3824e9 | Python | 19,761 | 508 | from os import SEEK_SET, SEEK_END, SEEK_CUR
from datetime import datetime, date, timedelta
from logging import getLogger
from struct import unpack
from numpy import array, dtype, empty, fromfile, iinfo, memmap, nan, pad, where
from numpy.lib.recfunctions import append_fields
N_ZONES = 15
MAX_SAMPLE = 128
MAX_CAN_VIEW... |
018e9677996bbd9bad6d47ec62764442ad693ea6d266951be2a839a0dfdfe8dd | Python | 19,764 | 430 | from dreamcoder.fragmentUtilities import *
from dreamcoder.grammar import *
from dreamcoder.program import *
from itertools import chain
import time
class FragmentGrammar(object):
def __init__(self, logVariable, productions):
self.logVariable = logVariable
self.productions = productions
s... |
db86c74a602a5b1eb03ad5b672d39aa67cd7b19cf45ef85aa216406b9c1c3a44 | Python | 19,787 | 403 | import numpy as np
import json
import torch
import torch.nn as nn
from torch.utils.data.sampler import SubsetRandomSampler
import os
from dataset import *
from setting import *
### Functions for TCGA data
def get_number_features(data):
for X, y in data:
n_feat = X.shape[0]
break
return n_feat
... |
02ca388a4ac5aebebc177c56016e7a7c35e39140223af5607d052370e0174b1b | Python | 19,788 | 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... |
4ee30c55c8351fdd13b7491c04bbc5f8fdd29f202a918d66a7fca1ec30e72e06 | Python | 19,792 | 520 | # coding=utf-8
# Copyright 2019 The Open AI Team Authors 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
#
# ... |
dd9b08d5ecd8e7895dc628d9413bd21a2384aae39cd8f33c83b5aa48914ff371 | Python | 19,794 | 392 | from nipype.pipeline.engine import Workflow, Node
from nipype import DataGrabber, DataSink, IdentityInterface
import nipype.interfaces.fsl as fsl
import nipype.interfaces.freesurfer as fs
import nipype.interfaces.spm as spm
import nipype.interfaces.matlab as mlab
import os
import json
from nipype.interfaces.utility imp... |
4db061edcbb04ca6a548801761892727a4b2c24fc7e3d64a09f2df6aacba66f2 | Python | 19,800 | 755 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 13 20:01:56 2020
@author: usingh
"""
import os
import sys
import time
import multiprocessing
from contextlib import closing
import gc
#import pyximport; pyximport.install()
import orfipy_core as oc
import subprocess
import orfipy.utils as ut
import ... |
8d56c2ca938384298db4936528e8990d53d2bc7920fc8303d1673b430c9e8df4 | Python | 19,804 | 600 | """Utilities for train_and_predict.py script."""
import os
import warnings
from collections import Counter, defaultdict
from pathlib import Path
from typing import Any
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib_scalebar.scalebar import ScaleBar
# from... |
68a4b9861e5450a3b2af0810942a370c913eb6830da4f1d08799473837d7a774 | Python | 19,805 | 506 | from __future__ import print_function
import sys
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import torch.backends.cudnn as cudnn
import torchvision
import random
import os
import argparse
import numpy as np
from PreResNet_cifar import *
import dataloader_... |
2856490b09f0ac7690481a5a0acb0769fb24a62fcdeecadc05d587106ab253a7 | Python | 19,809 | 436 | """
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... |
865b54f14a683467e23d2de4bd0d4a5600357d8d4116c3979fc0a2c17773fec8 | Python | 19,810 | 639 | import warnings
from typing import Optional, Tuple, Union
import jax
import jax.numpy as jnp
import numpyro.distributions as dist
import torch
import torch.nn.functional as F
from numpyro.distributions import constraints as numpyro_constraints
from numpyro.distributions.util import promote_shapes, validate_sample
from... |
83874655351699ff60453aa34d1c2b0c07c87c1a342b55f44f9a7b7442586d7f | Python | 19,828 | 441 | from __future__ import print_function
import time
from collections import namedtuple, Sized
from heapq import heappush, heappop, heapreplace
from operator import itemgetter
from pddlstream.algorithms.common import is_instance_ready, EvaluationNode
from pddlstream.algorithms.disabled import process_instance, update_bi... |
c5864a7d873e074c0b909c09b3fcc93002a984d578869960ed5a979d8d0c1523 | Python | 19,830 | 570 | import logging, time, yaml, os, shutil
import numpy as np
import torch
from torch import nn
import pytorch_lightning as pl
from pytorch_lightning.utilities import rank_zero_only
from pytorch_lightning.callbacks import ModelCheckpoint, LearningRateMonitor
import torch.nn.functional as F
from torch.optim.swa_utils import... |
4b7dd3f9c0b02829b3243011212172e8be0a2b08b43a262038b331e5ab5d616f | Python | 19,832 | 426 | ###########################################################################################
# #
# Evaluator class: Implements the most popular metrics for object detection #
# ... |
84560830b5fc162b7c145d8d4aad66ec551966e78c5daa58b2668f02779cff01 | Python | 19,835 | 388 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team, The Hugging Face 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... |
1119aeb3851a525cc3723bad547beba072f50a84afaf67b268674b4bb9643a5c | Python | 19,840 | 446 | import os
from typing import Callable, Dict, Tuple, Union
import numpy as np
from scipy.io import loadmat
from scipy.signal import filtfilt, firwin
from ....utils import get_random_dir_path
from ..base_dataset import BaseDataset
def _apply_fir_filter(eeg_data: np.ndarray, lowpass: float, highpass: float, sampling_r... |
c9c8532cec1ad0d72fb71e40268a006318ecc032ac9592c8b29efebae3538f31 | Python | 19,840 | 521 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
2704f75e8bd0ec6d6377b2d52324d9b693d3020a0d0142857012b13f4775277a | Python | 19,841 | 437 | """
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... |
aebd753f915d1a8e532576a61341a02a90e4d7b60af660348f82351dd29b4941 | Python | 19,857 | 618 | # 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... |
5220b498f7d38842effdc0192ea3cba0d01be2a1c9235e411f07816b739284a8 | Python | 19,858 | 453 | #!/bin/env python
from libraries import *
class OpEquilibrium(nn.Module):
def __init__(self, kf, kb, fact, gmin, qe, Hill=1):
super().__init__()
self.kf = nn.Parameter(torch.tensor(kf))
self.kb = nn.Parameter(torch.tensor(kb))
self.fact = fact
self.gmin = nn.Parameter(gmin)... |
9878444e2e74eebe6fbc75e9653a1f8009d911cdccb39a7c028541f19a2014ee | Python | 19,859 | 437 | """
Assembly detection related utility functions (mostly loading simulation related stuff)
author: András Ecker, last update: 06.2023
"""
import os
import json
import h5py
import warnings
from collections import namedtuple
import numpy as np
import pandas as pd
from libsonata import EdgeStorage
from bluepysnap import ... |
b66362ac38412e87958d1f524be6fbc16c89b27754ca3543348e3789adddddf3 | Python | 19,861 | 481 | """
Contains (abstract) class MultiData for input of data stored in multiple files.
Each file contains results (data) of one observation (experiment).
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from builtins import object
__version__ = "$Revision... |
1d12cb5977f21d88dc7689e66a430abb01e250c763ab97885d18894d78fd31e3 | Python | 19,871 | 401 | import time
import os
import subprocess
import sys
sys.path.insert(0, '/home/jupyter/repos/genformer')
import re
import argparse
import collections
import gzip
import math
import shutil
import numpy as np
import time
from datetime import datetime
import random
import seaborn as sns
import logging
os.environ['TPU_LOA... |
b3f91db54bf8de647aacd5855cd89d760e7a1aee3e7c1518dc3d2c352ecca71a | Python | 19,871 | 433 | """
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... |
4824e9e50d17ba322d42dbad6b13df7bc23c1599f6464413116e51dfbd69bb65 | Python | 19,883 | 666 | # map.py
import sys
from collections import Counter, defaultdict
from multiprocessing import cpu_count
from pathlib import Path
from tempfile import _get_candidate_names
import dnaio
import numpy as np
import pandas as pd
import pysam
from packaging import version
from umi_tools import UMIClusterer
from umi_tools imp... |
e7f7cbb75c349ebc206d4470318e2376c703308676781913619a1d5719726c26 | Python | 19,884 | 468 | # -*- coding: utf-8 -*-
#
# Test functionality of SyNCoPy-container I/O routines for NWB format files.
#
# Builtin/3rd party package imports
import os
import tempfile
import pytest
import numpy as np
from glob import glob
import matplotlib.pyplot as ppl
# Local imports
import syncopy as spy
from syncopy.datatype impo... |
4c8cf44b716dd4535ac7094d5a7fa18552d6582f9c553f4c652f24ba63ccec98 | Python | 19,887 | 673 |
import time
from xml.etree.ElementTree import Element as e, SubElement as se
from xml.etree import ElementTree
from xml.dom import minidom
import pickle as pickle
import collections
class OrderedSet(collections.MutableSet):
def __init__(self, iterable=None):
self.end = end = []
end += [None, en... |
b3d437b8f89bc6048cbaf702a8543e7a7e2b46b511de9edf4be0886990888b49 | Python | 19,889 | 475 | import argparse
import copy
import random
import sys
import shutil
import time
import numpy as np
import os
import pandas as pd
from typing import Tuple
import torch
from torch import optim
from torch.utils.tensorboard import SummaryWriter
from src.preprocessing.augmentation import AugmentParameters
from old_code.dat... |
4427248645bfa9d822134468d08e39fa921e113a3f48c5b0285e9bd6b9551ddc | Python | 19,897 | 586 | from pycocotools.coco import COCO
import os
import matplotlib.pyplot as plt
import cv2
import numpy as np
import json
import re
from deeplabcut.utils import auxiliaryfunctions as dlc_aux
import deeplabcut as dlc
import pandas as pd
import pickle
plt.ion()
def describe_dataset(coco):
for catid,cat in coco.cats.item... |
4928042a56fdc1d33ac8c4db04613930d64d0e06ed934794a49e27b61c8e3d95 | Python | 19,910 | 516 | #!/bin/env python3
"""
Simulation result data
----------------------
The SimData class is used to store the results of a simulation of ithildin.
"""
from glob import glob
from itertools import chain
from typing import List, Union, Tuple, Dict
import datetime
import numpy as np
import os
import pandas
import re
import... |
b40c18aa685b254e8042c80219ba2a52622ba6df1c676aa5d28aa40070d0c119 | Python | 19,912 | 427 | import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(__file__)))
import warnings
warnings.simplefilter("ignore")
import json
import time
import tqdm
import util
import pprint
import random
import torch
import scipy.stats
import numpy as np
import pandas as pd
from datetime import dateti... |
2b3938016e883325ff878eb859c941bfa54383ded9d206f00b3f88b333804063 | Python | 19,914 | 409 | import numpy as np
from scipy.stats import gamma, norm, truncnorm, multivariate_normal
import matplotlib.pyplot as plt
from numpy.random import multivariate_normal as multi_norm
from scipy.misc import logsumexp
import sys
sys.path.append("../useful_functions/")
import useful_functions as uf
def ibis(actions, rewards,... |
067128d31407ec09f89d2eadaef0eb8fbc0643367fc6c874d2d9b6a9a39bb379 | Python | 19,924 | 608 | """
Tests for CALIB module
FIXME need satrecov tests
FIXME need sensitivity correction tests
FIXME need test with edge correction
"""
import math
from six import StringIO
import pytest
import numpy as np
from fsl.data.image import Image
from oxasl import Workspace, calibration, m0
pytest.skip("skipping calibration... |
fba8ca71c51e91602a47ab6be8201045895211d86fcc9f6d9f04ab2b5b3967dc | Python | 19,928 | 437 | """
Generates a ListTomoParticle object for the statistical spatial analysis of particles
Input: - A STAR file with particles
- A STAR file for paring picked particles and (sub-)volumes segmentations (Volume Of Interes, VOI)
Output: - A STAR file with the pickled ListTomoPaticles objects
"... |
8def0fd405a1cc2454f948f9a28cba74c42c3464902b13d93afaebcdff708d61 | Python | 19,933 | 546 | """
Performs Univariate 2nd order analysis from a STAR file with a set of ListTomoParticles entries
Input: - A STAR file with a set of ListTomoParticles pickles
Output: - Plots with the analysis
- Matrix with the analysis for further post-processing
"""
################# Package import
im... |
a6ec3e7ed70e0915e643cc28189adfda5cb5a8b4b61554a9616c547eb1b23ed4 | Python | 19,939 | 546 | """
Performs Univariate 2nd order analysis from a STAR file with a set of ListTomoParticles entries
Input: - A STAR file with a set of ListTomoParticles pickles
Output: - Plots with the analysis
- Matrix with the analysis for further post-processing
"""
################# Package import
im... |
e9101cfecaf4c549a8a38d05116c0030433dd2a490bcc98fccb0726e5693e8b4 | Python | 19,945 | 622 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
:AUTHOR: Jens Petersen
:ORGANIZATION: Heidelberg University Hospital; German Cancer Research Center
:CONTACT: jens.petersen@dkfz.de
:SINCE: Wed May 17 14:29:20 2017
:VERSION: 0.1
DESCRIPTION
-----------
Create longitudinal analysis for XNAT subject
REQUIRES
--------... |
f05a28d58cc6a2f7df402a8bfaae3eca87c5850f2ca4868e2b9bb5ed786d0259 | Python | 19,954 | 408 | import logging
import os
import pickle
from collections import OrderedDict
from contextlib import redirect_stdout
from multiprocessing import Process, Queue, cpu_count
import numpy as np
import psutil
from .hs2 import HSClustering
from skopt import gp_minimize
from skopt.space import Integer, Real
from tqdm import tqd... |
41107e24552de0356bc0f591af930acd4c51dfb785f5a1d44ae403eccda71f98 | Python | 19,957 | 444 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader
import pytorch_lightning as pl
from pytorch_lightning import Trainer
from pytorch_lightning.logging import TensorBoardLogger
from pytorch_lightning.callbacks import EarlyStopping
from Loader import SignedPairsData... |
890125b9ef5b37a11d11ad1888209c78f88a93d292a7a5f444ff7c5dc73a2e2b | Python | 19,965 | 528 | """Main module.
Holds the `BayesianOptimization` class, which handles the maximization of a
function over a specific target space.
"""
from __future__ import annotations
import json
from collections import deque
from collections.abc import Iterable
from os import PathLike
from pathlib import Path
from typing import ... |
ca4aacca9aa41ca9a6826e6ffd91760db7a95d51860fc945fc5c81937d31de7f | Python | 19,966 | 374 | # https://github.com/Perik-Zavodskii/TCRscape
import numpy as np
import pandas as pd
import seaborn as sns
import scipy.stats as stats
from scipy.io import mmread
import matplotlib.pyplot as plt
import matplotlib as mpl
from sklearn.decomposition import PCA
import umap.umap_ as umap
import hdbscan
pd.options.mode.cha... |
97f644a4bb66f9648507d5754b8a9eb01f10796952f1af1ac7f5c6e759711faa | Python | 19,970 | 353 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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
#
# ht... |
6468792a669d195a6bb3fa1688c46dce3cf14990772c245ed72b7da79dabcec1 | Python | 19,973 | 630 | # 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... |
818d95b9511c59c7bca0c91f6c2b09f1f6b57d302fad9c0da35b563e26fa7b1f | Python | 19,974 | 556 | from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
!pip install dotmap
import math
import tensorflow as tf
import time
import matplotlib
import math
import time
import random
import numpy as np
import pandas as pd
from dotmap import DotMap
from __f... |
dd9ab5af7a0855497874d131e9dd57fa41818a88bb3bf2e8766840f8c83e3cd0 | Python | 19,976 | 402 | """
DeepLabCut2.0 Toolbox (deeplabcut.org)
copyright A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
Hao Wu, hwu01@g.harvard.edu contributed the original OpenC... |
f9899ffbd4583e2cf25e95147c8250e7e3bc2159b7195c890fd112bde5bac1cf | Python | 19,977 | 617 | # 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... |
47cec51d61bfd6878ddd50e13ff32debe396a9d5bf309c2bb84976ad967ad30f | Python | 19,980 | 382 | """Tests for combining partnered library schemas with their standard partner (schema_io.schema_merge)."""
import os
import shutil
import tempfile
import unittest
from hed import schema
from hed.errors import HedExceptions, HedFileError
from hed.schema import HedKey, from_string, hed_cache, load_schema, load_schema_ve... |
5050e847d63eacdef4d716729d88ac6e6c01bbe5cf62ed9625b80b12e0bb1f08 | Python | 19,985 | 431 | """
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... |
3a0de04fb6fee22d2972491f0986577d6c677a52b2372d1409c0ff2c7aeb7b9c | Python | 19,993 | 515 | import argparse
import pickle
import time
# Libraries
from functools import lru_cache
from math import exp, pi, sqrt, tan
import matplotlib.pyplot as plt
import numpy as np
import scipy.integrate
import scipy.signal
import uptake.figures.utils as fiu
import uptake.model.system_definition as sysdef
... |
2fe96f2d1d61e86777730f3f1ac826a442f0eb6e3595d9786bf5dfb225121140 | Python | 19,994 | 561 | from __future__ import absolute_import, division, print_function
import os
import sys
from typing import List, Union
import numpy as np
import torch
import torch.nn.functional as F
import torch.utils.data
from topaz import mrc
from topaz.denoising.datasets import DenoiseDataset, PatchDataset
from topaz.denoising.mod... |
8319122d4f0403c3a573edbc113c24a3bb3b7b0bb6c004c2a8ff4f4033d100ab | Python | 19,995 | 437 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import dill
import os
import time
import glob
import itertools
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import auc
import statsmodels.api a... |
52006c6bc977999c672a301b9d01f0e765cd14303bb571556f743fb3e2eda22d | Python | 20,007 | 431 | """
Unsupervised and deterministic classification of membrane-bound particles
Input: - The STAR file with the particles to classify
- Classification parameters
Output: - A set of STAR files with the new classes
- 2D rotational averaged around membrane normal exemplars and inter-p... |
75ab24fc317c4239efb1318767a03a18bd73073649b1ab1c0252ec2cf09f7ab1 | Python | 20,016 | 479 | from classifiers.CustomClassifiers import AggregateClassifier,AggregateClassifierGrid
from sklearn.svm import SVC
from sklearn.metrics import accuracy_score, classification_report, f1_score,roc_auc_score
from sklearn.model_selection import cross_val_predict,GridSearchCV,StratifiedKFold,LeaveOneOut,train_test_split
from... |
30bd48ca207380fecbbeb419c52c3397915c7c7f335a1c02c37f8e17d4ed7547 | Python | 20,019 | 554 | """Functions for statistical tests and validations
"""
import warnings
import numpy as np
import glmtools as glm
from scipy import stats
from sklearn.decomposition import PCA
from sklearn.model_selection import KFold, GridSearchCV, cross_val_score
from sklearn.pipeline import Pipeline
from sklearn.preprocessing impor... |
d5358398f51f0275113db117ab34169ace1d34de9ce7f453cd7c97b831307afd | Python | 20,030 | 432 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 22 12:55:12 2021
@author: Eve Shalom
"""
#%% Import all relevent functions
from matplotlib import pyplot as plt
import numpy as np
from matplotlib.gridspec import GridSpec
from ROIselection import ROISelector, ICfromROI,ROILasso,maskto4d
from TKMo... |
762d0f190f88475cfe967573ca89499e7a34894cd3eb95704d7539663b963fd9 | Python | 20,038 | 565 | from __future__ import annotations
from importlib.util import find_spec
from pathlib import Path
from shutil import copy
import pytest
from ase import units
from ase.calculators.lj import LennardJones
from ase.io import read
from ase.optimize import FIRE
from pymatgen.io.qchem.inputs import QCInput
from quacc import... |
9a94e2f80b5316b530a90d984b10b20905c8fb63ac4a99f05cae529f24fab2e9 | Python | 20,038 | 558 | """
Created on Mon Apr 19 13:59:01 2021
@author: Haotian Teng
"""
from numpy import ndarray
import os
import vbz_h5py_plugin
import h5py
import pod5
import itertools
import numpy as np
from pathlib import Path
from tqdm import tqdm
from typing import List
import contextlib
from typing import Dict
from scipy.signal imp... |
d6b94d0147b0b5b16617c5b142a2153abdaf4987fb4039c2725c7b519bc7990a | Python | 20,043 | 534 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Demonstrate usage of LFPy.Network with network of ball-and-stick type
morphologies with active HH channels inserted in the somas and passive-leak
channels distributed throughout the apical dendrite. The corresponding
morphology and template specifications are in the file... |
fac495d3fe00c6a6eae92118c2ea6be0cf80e4a52081df3780193b829f9953f6 | Python | 20,043 | 582 | import math
import os
from glob import glob
import numba
import numpy as np
import pandas as pd
from numba import njit, prange
from scipy.stats import t
from .numerics import (
_calc_mean_shrunken_residuals,
_calc_mean_shrunken_residuals_and_mfracs,
_count_n_cpg,
)
from .scbs import _find_peaks
from .smoo... |
be3c27b86735e0c2214a69936f89d55324850dcdf58bf217144a1f9863a53bc7 | Python | 20,075 | 566 | # adapted from scVI-tools
# A Python library for probabilistic analysis of single-cell omics data
# Adam Gayoso, Romain Lopez, Galen Xing, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Naza... |
26de511196e9787deb3b9769948dc91185185bbb998a6bf6ed355ac283d8eb6b | Python | 20,082 | 461 | # -*- coding: utf-8 -*-
#
# Syncopy data selection methods
#
# Builtin/3rd party package imports
import numpy as np
import h5py
# Local imports
import syncopy as spy
from syncopy.shared.tools import get_frontend_cfg, get_defaults
from syncopy.shared.parsers import data_parser
from syncopy.shared.errors import SPYValu... |
aca5bb663fc91791d63bb8869be586dc633fba0119b6a876575e6a7f118568fc | Python | 20,091 | 534 | """A PEP 517 interface to setuptools
Previously, when a user or a command line tool (let's call it a "frontend")
needed to make a request of setuptools to take a certain action, for
example, generating a list of installation requirements, the frontend would
would call "setup.py egg_info" or "setup.py bdist_wheel" on t... |
4a4924fbe01c60dc3d4150a8d091d11c87cc7c2013b237a853560116f2f53412 | Python | 20,110 | 555 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
78f7668dbf1d61dde08cf46eee81ccfa855ab4de505abdd71afc289f8710b76d | Python | 20,111 | 586 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
b751f8b5d19ae8409fb44157ab2d9412ad81aa0be4075ea344afab648bd0da31 | Python | 20,113 | 629 | import json
import os
import numpy as np
from numpy.random import default_rng
import random
import math
from dreamcoder.task import Task
from dreamcoder.type import arrow, tint, tlist
from dreamcoder.domains.arc.arcPrimitives2 import *
import dreamcoder.domains.arc.arcPrimitives2 as p
def make_rotation_tasks():
... |
e448608820d3b407e54bcef110176d59fb3ca4dbc228b8d01ee62b936323f008 | Python | 20,119 | 604 | from __future__ import division, print_function
import copy
import numpy as np
import networkx as nx
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import operator
from sklearn.cluster import KMeans
from plots import multi_plot
class EigenvectorModularity(object):
def __init__(self, g, heuristic_s... |
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