sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4ed85a715fcc8bdfa73496270addbf2705d6eb97a03906661b71bbc0f87e21bd | Python | 16,303 | 379 | import pandas as pd
import numpy as np
import os, torch, pickle
from tqdm.auto import tqdm
from torch.utils.data import DataLoader
from sklearn.decomposition import PCA
from sklearn.random_projection import SparseRandomProjection
from .feature_extraction import prep_model_for_extraction
from .feature_extraction impo... |
61dc49e885da3603bb94e594847caf9896904847cf60b34b3b19dd71d2a03a51 | Python | 16,314 | 381 | from __future__ import absolute_import, division, print_function, unicode_literals
import argparse
import logging
import os
import sys
import glob
import re
import tensorflow as tf
tf.keras.backend.clear_session()
from callbacks import CallBacks
from model_factory import GetModel
from preprocess import Preprocess, for... |
c27487a743655471d0226a4186b5a4caf6b3d2aa6f9c22c21900858d0090ecdd | Python | 16,324 | 527 | """Partial autoinformation module for segmented data.
Code from https://github.com/Frederic-vW/AIF-PAIF
F. von Wegner, Partial Autoinformation to Characterize Symbolic Sequences
Front Physiol (2018) https://doi.org/10.3389/fphys.2018.01382
"""
from __future__ import annotations # c.f. PEP 563, PEP 649
import itertoo... |
d8d1f7139ee1cd1867d0157d6e8501be03ecc654ea2c9788d04a5842836f1a2d | Python | 16,326 | 564 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
"""
.. testsetup::
from packaging.version import parse, Version
"""
import collections
import itertools
import re
from typing import A... |
e4e52928f24b66fffd33f9a063973a6b21b9d480d43413d173a7db2e38566d94 | Python | 16,334 | 422 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import matplotlib.pyplot as plt
from matplotlib import patches
import os
import numpy as np
from fig_utils import *
def panel_neuron_pos(fig, grid1, il, yratio, xpos0, ypos0, isort, brain_img):
xpos, ypos =... |
ec111b3a113e9773ec4a3a519ebb23823fa7fcda9c7150afaa2560dcb2413761 | Python | 16,336 | 472 | # 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... |
4fd35f1e93a95f4ead04615047ac807646bfbb57e720c38d3251c4a9b8f9577e | Python | 16,340 | 352 | #!/usr/bin/env python
# coding: utf-8
import dgl
import torch
from torch import nn, optim
import numpy as np
from ..model.scHetG import scHetG
from ..model.MLP_model import MLP_model
from ..data.data_utils import make_graph, mnn_edges_svd, knn_edges, precluster, precluster_negative_paris,mnn_edges_pca
from ..t... |
9764b3c82ad4c038cc6eb4ae54e444fa42f5d8bda3e8a8ab7c658e05519ed941 | Python | 16,343 | 440 | """
Script for PSD segmentation
Input: - Pickle files with MbGraphMCF for post- and pre-synaptic membranes
- Membranes segmentation files
- xml file with mb_slice definitions
Output: - Cloud files
- Segmentations
"""
__author__ = 'Antonio Martinez-Sanchez'
########... |
9c2f82c5ed2129bdc19f8c26f58c52ec9c675fc31287582ef3dedcdf26d27638 | Python | 16,347 | 433 | ##
# \file rsfmri_estimate_motion.py
# \brief Estimate motion in resting-state fMRI volumes
#
# \author Michael Ebner (michael.ebner@kcl.ac.uk)
# \date July 2019
#
import os
import numpy as np
import pysitk.python_helper as ph
import pysitk.simple_itk_helper as sitkh
import niftymic.base.stack as st
i... |
a832c6194e340fb6c888c26c29d169b43466f550387d485e3241f4f1a2fa7c44 | Python | 16,353 | 414 | # 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... |
57d2b69edbeb1d012e5278f30541dd3d261bfa41532210ec7b36132f802510cf | Python | 16,357 | 290 | # 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... |
f02c64072b46a08d4668ccf2cf0b2d75d605381a5700e7a88c638234724c8d97 | Python | 16,367 | 456 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import scipy.signal as ss
import pickle as pickle
from hybridLFPy import CachedNetwork, helpers
import analysis_params
from cellsim16popsParams_modified_spontan import multicompartment_params
from plot_methods import (getMeanInpCurrents, getMeanVoltages, plot_population,
... |
3acd6ebde4890624d760c0f0f0fc7448dc42297d3284e006645b1706949c3c21 | Python | 16,368 | 423 | # lightning related imports
from collections import defaultdict
from copy import deepcopy, copy
import torch, sys
import pytorch_lightning as pl
import torchmetrics
# from pytorch_lightning.metrics.functional import accuracy
from wsilearn.utils.cool_utils import is_dict, is_string, is_iterable, is_list
from wsilearn.... |
b04fb6ac6435f8b61aceae4416b41f365447bf60ff1b300d24d4e80edef7d875 | Python | 16,369 | 380 | import sys
import os
import multiprocessing as mp
import numpy as np
import pandas as pd
from Bio import motifs, SeqIO, Seq
from scipy.stats import ttest_1samp, wilcoxon
def load_motifs(motif_dir, pseudocounts=0.05, key='full'):
'''
read in motifs; motifs have to be in jaspar format as below:
... |
9df59cfe1bb63ff04dd08414415612b50a90441c4035ad40cb926a4e25c4e6d0 | Python | 16,376 | 406 | import torch
import torch.nn as nn
import torch.optim as optim
from torch.autograd import Variable
from torch import autograd
import time as t
import matplotlib.pyplot as plt
import sys
plt.switch_backend('agg')
sys.path.append('/home/jmwang/WorkSpace/GENiPPI/gPPMol/models_3d')
import os
from itertools import chain
fro... |
bc099b0f2d64fb12f0ef779547566dada50140ad232e53cd3be033585a4c16d8 | Python | 16,376 | 491 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 4 12:38:46 2024
@author: felipe
'DMD simplified'
"""
import numpy as np
from pydmd import DMD, BOPDMD
from pydmd.preprocessing import hankel_preprocessing
import sys
import os
sys.path.append(os.path.abspath('../'))
import analysis.control as ctr... |
c0999d24115e853b817ce9112fa326076ec4e1411c099adcbf8e6959ccb2bbc0 | Python | 16,388 | 467 | """Tests for regtools.utils.io.points_io."""
import numpy as np
import pandas as pd
import pytest
class TestLoadPoints:
def test_legacy_txt(self, tmp_path):
from regtools.utils.io.points_io import load_points
p = tmp_path / "pts.txt"
p.write_text("index\n3\n10 200 300\n11 201... |
3b65e552f1bcca1e922bb285fa1b04c7be75f9dfab6b110b707a407f0ba87c77 | Python | 16,390 | 457 | 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... |
ea60417ccf7be613248db2bb376f6cb03826a4d53ece8ca9811d35e333525835 | Python | 16,392 | 565 | # 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... |
3e310b30bc4a1bf8aedc75a328039d2a1b8dac77d68297531764389ce6ec65e3 | Python | 16,397 | 408 | import email.feedparser
import email.header
import email.message
import email.parser
import email.policy
import sys
import typing
from typing import Dict, List, Optional, Tuple, Union, cast
if sys.version_info >= (3, 8): # pragma: no cover
from typing import TypedDict
else: # pragma: no cover
if typing.TYPE_... |
235880f4abd219242c8b3d4e96e28f76f4b79c9beea3ba28503537a1a4c92f70 | Python | 16,399 | 461 | """
This script contains supplementary functions for dFIC project data analysis, written by J.Stasinski unless stated otherwise.
documented with help if Chat GPT 3.5
"""
import numpy as np
import scipy.io as sio
import scipy.signal as sig
import csv
from scipy.stats import ks_2samp, ks_1samp
from scipy.stats import sk... |
424aa230df337dd85540a7324e5c9356e2a9bcb03e095829c8628d107e77b29f | Python | 16,399 | 352 | import matplotlib.pyplot as plt
import matplotlib.pylab as pl
from Functions.f_SignalProcFuncLibs import *
from Functions.f_ECGAnalysis import *
import matplotlib.colors as colors
import numpy as np
def PlotBandEvolutionAllPaths(m_Data, m_DataStd, s_windStep, v_FreqBands_Names, v_FreqBands, v_ChanNames,
... |
8a49542ec53c28a31a552378f30ff13e05479730653f4772df721aa5fca49b83 | Python | 16,399 | 459 |
import copy
import sys
import numpy as num
# from wx import AboutDialogInfo
# from version import DEBUG, __version__
DEBUG = False
__version__ = '0'
# KB 20190424: long is int in python 3
if sys.version_info >= (3,):
long = int
class ShapeParams:
def __init__(self,major=0,minor=0,area=0,ecc=0):
sel... |
9683a77b2f59e77d81bf6942ad9a4ba24591d2f60c66b5c3a2d56cefa74b6391 | Python | 16,401 | 463 | """Utility functions to expand configuration directives or special values
(such glob patterns).
We can split the process of interpreting configuration files into 2 steps:
1. The parsing the file contents from strings to value objects
that can be understand by Python (for example a string with a comma
separated ... |
3124281777431cda64bcf99aa173fdff314e20b18f0a604740c49012a42763a3 | Python | 16,416 | 395 | # -*- coding: utf-8 -*-
# Este archivo se encarga de analizar los resultados obtenidos por cnn2_load_and_test.py
from math import e
from re import T
from unittest import result
import pandas as pd
from scipy.stats import spearmanr, ttest_ind
import matplotlib.pyplot as plt
import sys
import os
import numpy as np
solo... |
6c062bb7bc7f547e2da0da48d3ae8b4316c7a581a9635331c6664086ca6996fc | Python | 16,416 | 439 | # SPDX-FileCopyrightText: 2015 Eric Larson
#
# SPDX-License-Identifier: Apache-2.0
"""
The httplib2 algorithms ported for use with requests.
"""
import logging
import re
import calendar
import time
from email.utils import parsedate_tz
from pip._vendor.requests.structures import CaseInsensitiveDict
from .cache import... |
efc7b78adf8c254a43ec3bc73dd80950af731338e33c9810f981d2f07bba646b | Python | 16,422 | 528 | # 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... |
becbf23df3e6f758388543bac0940965dee38f8b08bf18f11571a42441b18f9f | Python | 16,426 | 413 | from . import _c_louvain
from .VertexPartition import LinearResolutionParameterVertexPartition
from collections import namedtuple
from math import log, sqrt
import sys
# Check if working with Python 3
PY3 = (sys.version > '3')
class Optimiser(object):
""" Class for doing community detection using the Louvain algori... |
cf8145653d8d486b81c3e777b18265dacce08e4d20c2d3ff8c20d6436eec2e27 | Python | 16,427 | 397 | # -*- coding: utf-8 -*-
"""
Created on Mon Jun 15 11:28:26 2020
@author: David Quiroga
"""
#################### Load libraries and set directories #######################
from random import shuffle
from psychopy import prefs
prefs.hardware['audioLib'] = ['PTB']
#prefs.hardware['audioLib'] = ['pyo']
from psychopy impor... |
758e938ff2598fed59e65607315337a93a98910d8c94039de67b2f2bcc143246 | Python | 16,429 | 372 | """CCF-to-brain alignment behaviours for the viewer, packaged as a
mixin so the alignment surface (param changes, drag-align, lock,
corner markers) lives in its own file instead of the 4000-line
viewer.py.
The mixin assumes the consuming class declares these instance
attributes in its ``__init__`` BEFORE any mix... |
9f550b690fd7d72a2a8fccafd1ec58e6bee340a2134578c11ad96fb0f5c1711c | Python | 16,431 | 669 | from __future__ import annotations
"""Fast image-shape preflight and 2D binary storage canonicalization."""
from dataclasses import dataclass
from pathlib import Path
from typing import Iterable
import numpy as np
import tifffile
from PIL import Image
PREFLIGHT_VERSION = "MG_2D3D_PREFLIGHT_V1"
@dataclass(frozen=T... |
769d8f636d1099290b5a81a78cc2cf14c022390152ed0f45247932b9ef3b42bb | Python | 16,439 | 330 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Jan 21 12:34:05 2023
@author: daltonm
"""
# import toolboxes
import numpy as np
import re
import pynwb
from pynwb import NWBHDF5IO, TimeSeries
from pynwb.epoch import TimeIntervals
import glob
import datetime
import pytz
import matplotlib.pyplot as plt... |
dfd0c6818c484407548fd5e78933f2a1c759168fe2752c71e7c7d35cf2a91c31 | Python | 16,439 | 368 | import torch
import torch.nn.functional as F
from prettytable import PrettyTable
import numpy as np
import random
from sklearn import metrics
import wandb
from tqdm import tqdm
from utils import *
import os
def normalized_laplacian(A):
"""
Input A: np.ndarray
:return: np.ndarray D^-1/2 * ( D - A ) * D^-1... |
e75831333b755a46232bfe979fde2e4a48c5723604818da40221256b95431cb3 | Python | 16,439 | 451 | # 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... |
9642bd4b1af57f8ef0daf26fa8c32192cca2f59dd1048c60ef232913392930be | Python | 16,441 | 401 | r"""Test Ketcher KET (JSON) format using the OpenBabel Python bindings.
Mirrors the structure of testcdjsonformat.py. Covers:
- reading a single-molecule KET file
- reading multi-molecule KET files
- reading a reaction KET (arrow + plus -> OBReaction)
- writing valid JSON output
- minified -xm output option
- SMILES <... |
1ab876e2ac2ff398630ee0d467d2cb80279a2ccdc027461b6fc76b1ad457073a | Python | 16,445 | 357 | import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(__file__)))
import warnings
warnings.simplefilter("ignore")
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 datetime
from torc... |
4bb6995cbb62932ce779edefc998deb7d69e822ce7f7c9bcb78a00234133efe6 | Python | 16,448 | 439 | import numpy as np
import torch
from torch.nn import init
from torch_geometric.nn import MessagePassing
from torch_geometric.utils import degree
import torch.nn.functional as F
from torch_geometric.nn.inits import uniform
from torch_geometric.nn import global_mean_pool, global_add_pool
#import dgl
### GIN convolution ... |
6b942d5f63965bf46a2c229172a981b708758a37b21a0ac961ce41489f88c9f2 | Python | 16,448 | 331 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Jan 21 12:34:05 2023
@author: daltonm
"""
# import toolboxes
import numpy as np
import re
import pynwb
from pynwb import NWBHDF5IO, TimeSeries
from pynwb.epoch import TimeIntervals
import glob
import datetime
import pytz
import matplotlib.pyplot as plt... |
b91501db1631ce5061533a25098b57d8fd31e464b5ffdae40671a3948891bc90 | Python | 16,465 | 515 | import os
os.environ["OMP_NUM_THREADS"] = "4" # export OMP_NUM_THREADS=1
os.environ["OPENBLAS_NUM_THREADS"] = "4" # export OPENBLAS_NUM_THREADS=1
os.environ["MKL_NUM_THREADS"] = "4" # export MKL_NUM_THREADS=1
os.environ["VECLIB_MAXIMUM_THREADS"] = "4" # export VECLIB_MAXIMUM_THREADS=1
os.environ["NUMEXPR_NUM_THREA... |
d366dfbb2716ca815661d314ca38d994d2301d534e87cf8be8db52e881ad45b9 | Python | 16,465 | 367 | """
Pre-processing for mb_graph_batch.py of un-oriented and oriented membranes from TomoSegMemTV output
Input: - STAR file with 3 columns:
+ _rlnMicrographName: tomogram original
+ _rlnImageName: TomoSegMemTV density map output
+ _psSegLabel: (optional) label f... |
b0ca9a7c6a923746ba06d36008ea9166ad8350462f1e5206b048a1d48807049f | Python | 16,468 | 479 | import torch
import numpy as np
import torch.nn.functional as F
from PIL import Image
# Global Flags
PIXELS_PER_METER = 5
class Renderer():
def __init__(self, map_offset, map_dims, data_generation=True):
self.args = {'device': 'cuda'}
if data_generation:
self.PIXELS_AHEAD_VEHICLE =... |
b2cc59330f34c53a68a6eba2f743fa82fd79dd9944d56cbb13801e28950306ce | Python | 16,469 | 378 | # -*- coding: utf-8 -*-
################################################################################
## Form generated from reading UI file 'dgn_preprocz_ctrl.ui'
##
## Created by: Qt User Interface Compiler version 6.8.0
##
## WARNING! All changes made in this file will be lost when recompiling UI file!
#... |
14204181cabe05db2d735284e69ebf5531b28e41170c59dc28c24933ddce5243 | Python | 16,470 | 318 | """
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
"""
import pandas as pd
import numpy as np
from pathlib im... |
23e95a83a5e1cc78505e4cbf18c6c58448397b70075009662c122c64f45c75ad | Python | 16,470 | 507 | from rdkit.Chem.rdmolfiles import MolToPDBBlock, MolToPDBFile
import rdkit.Chem
from rdkit import Geometry
from collections import defaultdict
import copy
import numpy as np
import pandas as pd
import torch
from utils.affine import T
from scipy.spatial.transform import Rotation as R
from Bio.PDB import PDBIO, MMCIFIO, ... |
857c17c4383c41d4ad2a0d69da0f8f8af70ee5450654c94c66fc1e36dc920ad0 | Python | 16,473 | 426 | #
# 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,... |
378c83c9e013c3ff1e753aae320e3ff6cc05beba5ca71a5331e0a3dac4996b81 | Python | 16,474 | 302 | """
OPTIC_LOBE_TISSUE.py written 2026-09-22. "Is the choir the cell or the tissue?"
Pre-registration: 04-NOTES/PREREG-2026-09-22d-OPTIC-LOBE-TISSUE.md (written before this ran).
ERROR_OR_STRUCTURE.py arm N cleared classifier tissue-context only in the hemibrain, which has no
lamina. This redoes it in FlyWire, wher... |
fa2555733c13a270fa22632ca922389016b383db7eb8ac6acb10f0163f80d9c1 | Python | 16,475 | 374 | """
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... |
2327719df6ab3729cb4ab450a7d1ce059da4919f0c1bf76dd70a8b296f10a436 | Python | 16,476 | 529 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
try:
import analysis.Wavelets as Wavelets
except ModuleNotFoundError:
import KuramotoNetworksPackage.analysis.Wavelets as Wavelets
import numpy as np
import numpy.linalg as linalg
import scipy.signal as signal
import scipy.ndimage as ndimage
def effectiveFrequen... |
352574c97a014bffa92b0d6254192874a34508743c86ce6bb25110730451bb77 | Python | 16,493 | 520 | import sys
import os
import time
import numpy as np
import numpy.ma as ma
from scipy.fftpack import rfft, irfft, rfftfreq
from scipy.signal import hilbert
from scipy.stats import zscore
from scipy.io import loadmat, savemat
import matplotlib.pyplot as plt
try:
import pyfftw
pyfftw.interfaces.cache.enable()
e... |
7435de98962717b6202f65278788c8ee81331225bd5177b9d754a50992831208 | Python | 16,500 | 379 | # MEGIT zoomview preprocess GUI
import os
import cv2 as cv
from ..data import get_frm, brt_con, draw_text
from PySide6 import QtCore, QtGui, QtWidgets
from .dgn_preprocz_ctrl import Ui_ControlViewer
from .dgn_preproc_frmv import Ui_FrameViewer
from .dgn_preproc_load import Ui_MainLoader
# Global definitio... |
4b917c18847ef246b8dce5fa48bd0108eedd127d97dff0d643077cc0344f64ac | Python | 16,504 | 407 | import logging, time, yaml, os, shutil
import numpy as np
import torch
from torch import nn
import pytorch_lightning as pl
from pytorch_lightning.callbacks import ModelCheckpoint, LearningRateMonitor
import torch.nn.functional as F
from torch.optim.swa_utils import AveragedModel
from ase.data import atomic_numbers
from... |
dce998677b42a113c63ab10b4a04161bed3733e6d01dadbe54203747f9c901a5 | Python | 16,504 | 505 | """
The main purpose of this module is to expose LinkCollector.collect_sources().
"""
import collections
import email.message
import functools
import itertools
import json
import logging
import os
import urllib.parse
import urllib.request
from html.parser import HTMLParser
from optparse import Values
from typing impor... |
5fd32655f332c13b598f39b5bd8afe473737fad0283f71aaa0f8b6044e05e3e6 | Python | 16,517 | 498 | from typing import Callable, Dict, Optional, Sequence, Union
import schnetpack as spk
import schnetpack.nn as snn
import torch
import torch.nn as nn
import torch.nn.functional as F
from schnetpack import properties
import spainn
from spainn.properties import SPAINN
__all__ = ["Atomwise", "Nacs", "Forces", "Dipoles",... |
582024ec0f948c5bb637700cfa6aee67ffe5707aeb390982430a0ed852d53d3a | Python | 16,529 | 336 | def update_param(name, param):
if name in ('alpha', 'lambda'):
param['ptype'] = 'numeric, [numeric]'
param['dtype'] = 'Union[float, List[float]]'
return param
return None # param untouched
def class_extensions():
def get_regression_influence_diagnostics(self, predictor_size=None):... |
5d5b6e1628ba73805f70bc6faea3f97de09ea31974ea6fb6ff7cdfe2ed726674 | Python | 16,533 | 333 | """
Script to run pan-cancer/cross-cancer classification experiments (i.e. train
on one gene across all but one cancer types, test on another gene in another
cancer type).
"""
import sys
import argparse
import itertools as it
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
import... |
f8738a9dc2a0814067eb5159ac92df6fb7bcc09c327c7abde486265e89560f11 | Python | 16,533 | 443 | """Functions to transform the input data and the estimates."""
import multiprocessing as mp
from typing import Callable
import numpy as np
import xarray as xr
from numpy.random import RandomState
from pandas import MultiIndex
def _check_sf_consistency(epoch_data, estimates):
if epoch_data.sfreq != estimates.sfr... |
2cafe5ff982716fe83d3662dc89441a79904dd25a61d5102ec26c129edad8e4f | Python | 16,537 | 406 | """distutils.command.build_py
Implements the Distutils 'build_py' command."""
import os
import importlib.util
import sys
import glob
from ..core import Command
from ..errors import DistutilsOptionError, DistutilsFileError
from ..util import convert_path
from distutils._log import log
class build_py(Command):
d... |
9f7ffa12dcfa5766cc74609ac9ead20cb5a8c4d1bda7e4de2dbdbc2959389a16 | Python | 16,539 | 480 | """Classes for AGFusion database objects
"""
import logging
import sqlite3
import sys
from os.path import abspath, exists, join
from agfusion import utils
logger = logging.getLogger("AGFusion")
try:
import mysql.connector
except ImportError:
logger.debug("Could not import mysql.connector.")
class AGFusion... |
57bfe16667d2dc8d92ac9d98a73843dca303facbe64d63056c088b4a9df25c44 | Python | 16,547 | 540 | """
goodness_of_fit: Function set for goodness of fit measure between two signals.
================================================
Documentation is available in the docstrings
Contents
--------
goodness_of_fit require numpy.
The package provides the following measure :
- Mean Error : m... |
231025f5be41ece88995dec3222bca375ee7df4bef30b38551e77c47a7777407 | Python | 16,549 | 415 | import pandas as pd
import numpy as np
import os
import sys
import warnings
warnings.filterwarnings("ignore")
# os.environ['PATH'] = '/gxr/jixian/anaconda3/envs/refine/bin:/rhome/jixian.zhang/.local/UCSF-Chimera64-1.16/bin:/rhome/jixian.zhang/.local/bin:/gxr/jixian/anaconda3/bin:/gxr/jixian/anaconda3/condabin:/gxr/jixi... |
0b47933ca566ffb1b4d58712ffa358cda415fe0f84150d5ff367fb6d7b6db31b | Python | 16,554 | 420 | from functools import reduce
try:
import binutil # required to import from dreamcoder modules
except ModuleNotFoundError:
import bin.binutil # alt import if called as module
from bin.rational import RandomParameterization
from dreamcoder.domains.arithmetic.arithmeticPrimitives import (
f0, f1, fpi, real... |
7274afb19e316e993826526208aefc6cd168e929c774e20a135ec8ae61996ae4 | Python | 16,555 | 315 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 21 09:30:55 2022
This script create the figure 5.
It first loads subjects results (with fitted priors and reports),
the weights of generative priors in T1 (on all trials)
and the weights of fitted priors and of explicited priors in T2
on trials af... |
63fb7f7203fe762712e05cba641651b1afe7accd2edbb1727cefff07b334a128 | Python | 16,559 | 464 | """setuptools.command.bdist_egg
Build .egg distributions"""
from distutils.dir_util import remove_tree, mkpath
from distutils import log
from types import CodeType
import sys
import os
import re
import textwrap
import marshal
from setuptools.extension import Library
from setuptools import Command
from .._path import... |
b2a7d2a7797e9dffeecc2339d576c94a1420f590b2584bfa101acac86147e81e | Python | 16,562 | 356 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 9 07:09:45 2022
@author: heavens
"""
from faulthandler import dump_traceback_later
import os
import sys
import toml
import random
import argparse
import itertools
from typing import List
from xron.utils.seq_op import Methylation_DP_Aligner
from xro... |
60562a413742fcf78148c9a535376bef019f199941dcf2f3be3d27653e14c82d | Python | 16,566 | 396 | """
Multiclass test for 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 e... |
98cc0fe1689a10c75a517dc0501c121520603ff0a2be870b56f8ebfd63790b1b | Python | 16,570 | 453 | import re
import anndata
import fsspec
import h5py
import numpy as np
import pandas as pd
from cirrocumulus.ot.population import Population
from cirrocumulus.ot.util import chain_transport_maps, find_path, unique_timepoint
from cirrocumulus.util import get_scheme
class TransportMapModel:
def __init__(self, tmap... |
bb48bea0d4f50cc5a560b8b6516c24ff2572e8d0d1aae4cb1906431b5abd3b02 | Python | 16,572 | 260 | import os
import argparse
import numpy as np
import pickle
import rtPupil_config
from EventCollector import EventCollector
from EventCollector import get_data, find_string_time, pull_pupil_sample, plot_mean_timecourses
from StimulusDecider import StimulusDecider
def main(subject_list, plot_timecourses, baseline_du... |
12627c09adca8e7f9ca4b629ef604218e3d26416aadbe32c5487f6c5bb46a249 | Python | 16,577 | 488 | """
Accuracy metrics for comparing detected cell centroids against ground truth.
Provides functions to compute precision, recall, F1 score, and visualize
match quality between two sets of 2D or 3D point coordinates using
distance-threshold matching with the Hungarian algorithm.
Typical usage
-------------
>>... |
79d252a802879db54b3332059301ba7b59049299ed5c646903acdb7e48891954 | Python | 16,586 | 423 | import logging, re
# from logging import info
import functools
from copy import deepcopy
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision
from torch.nn.modules.padding import ReflectionPad2d, ZeroPad2d
from torch.optim.lr_scheduler import ReduceLROnPlateau, CyclicLR
from wsilearn... |
64954d27142d7f0de42d9e30c52fe6a2ad6e6c52fa733aed47d713b15821d5b9 | Python | 16,589 | 513 | """Module contains the different types of data formats.
The main class is Data, all the other classes should depend on it. The other
classes are given only as convenience, but they should not overwride
Data.__call__, which needs to be very general.
"""
from collections import OrderedDict
from collections.abc import It... |
e6e5c227a9bbc7bae3bc741de2b43d6dcd6f7ca947468b77687bd51eaa2670e5 | Python | 16,589 | 474 | # -*- coding: utf-8 -*-
#
# Test connectivity measures
#
# 3rd party imports
import pytest
import itertools
import numpy as np
import matplotlib.pyplot as ppl
# Local imports
import syncopy as spy
from syncopy import synthdata
import syncopy.tests.helpers as helpers
from syncopy.shared.errors import SPYValueError, SP... |
7bb0778352713bee8fd2407e5d13b1e961984eb484966c1a8a63732ead89bce4 | Python | 16,591 | 268 | import os
from warnings import warn
import math
import numpy as np
from matplotlib import pyplot as plt
import pandas as pd
from io_functions import read_dictionary, read_pandas
from postprocess_functions import visualise_tornado_sa, visualise_scatter_sa, visualise_heatmap_sa
from path_config import get_path_mapping
... |
45a9416f6ad14475ecdb518e26570fb0dc145740909c5e61e55b36abbf7df7a0 | Python | 16,599 | 402 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from scipy.sparse import load_npz
import os
import json
from torch_geometric.nn import SGConv, GCNConv, global_mean_pool, Sequential, graclus, max_pool_x
from torch_geometric.nn.pool.pool import pool_batch, pool_edge
from torch_geomet... |
0f0fbdbd42c5a0d23d08e5da8e19a0272f41c0e1c2e9ca11c27db4a97f9f36b1 | Python | 16,602 | 352 | """
Script for extracting particles from a filament network of a unoriented 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
+... |
e181c90a0439bdca2fc1228c0ee3b51b90fecd7a763d7e9dbafc54c9b09c4fac | Python | 16,602 | 485 | # TODO
# resnet
# Now segment_coo have some bug in getting second-order derivative
# https://github.com/rusty1s/pytorch_scatter/issues/299
# from torch_scatter import segment_coo
# Different channel for different order?
# parameterdict cannot be scripted
# https://github.com/pytorch/pytorch/issues/128496
# parameters o... |
c9a23d821f2b0cf39a26ddf1e0291073ec30e60fb797218cd4788d9da386e0d3 | Python | 16,603 | 387 | """
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
""... |
575bec79da42ceb9a3577947dc2ffd4e1f916d9a85b6638f6f1ebddc6362f8f7 | Python | 16,604 | 281 | class ElementLookUpTable():
'''Class for looking up atomic numbers and element identifiers.'''
element_identifiers = ['H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K',
'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn'... |
f1813e78d5cc499d6582c25983e1e7228f0475a19f88e336b7711a2e52c3e4e8 | Python | 16,610 | 506 | """Backing implementation for InstallRequirement's various constructors
The idea here is that these formed a major chunk of InstallRequirement's size
so, moving them and support code dedicated to them outside of that class
helps creates for better understandability for the rest of the code.
These are meant to be used... |
566feb4964fdbdf2a529ae74777d8b09d6211a733d84096112d8d00c3e293466 | Python | 16,612 | 388 | import itertools
from math import pi
import numpy as np
from scipy.stats import qmc
import uptake.multiprocessing.utils as mputils
from uptake.model.system_definition import Fixed_Mechanical_Properties, MembraneGeometry, ParticleGeometry, Wrapping
def params_tester_qMC_cstsigma(expected_sample_size, CPUs,... |
5ebff95311dfdf1e800ab04c53b51d44285611d33f4397a097c991d3c7a4e671 | Python | 16,613 | 511 | # 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... |
3b0d21225f7622d179b8ffc64475b5d63ceeea598c39cb26d637020da6e6fb4b | Python | 16,634 | 426 | import os
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
import numpy as np
import pytest
from unittest.mock import MagicMock
pytest.importorskip("PySide6")
from PySide6.QtWidgets import QApplication
from regtools.registration.gui.batch_2d_tab import Batch2DTab
from regtools.registration.gui.batch_2d... |
764bc176974b50a537276a0aa68d1c80947581cea2a4a484822f1e1a0a636159 | Python | 16,650 | 394 | import numpy as np
import utils
import scipy as sp
from scipy.stats import truncnorm
class SubspaceModel:
def __init__(self, translation_vector, basis, eigenvalues, base_mesh=None):
self.translation_vector=translation_vector
self.basis=basis
self.eigenvalues=eigenvalues
self.base_m... |
37a4b39c8ca89dbb00b69b8b1cd34a18fc566b86af50d00d4569d1ec3f8af322 | Python | 16,654 | 529 | # demulitplex.py
import re
import sys
import hdbscan
import numpy as np
import pandas as pd
import scipy.sparse
import statsmodels.api as sm
import matplotlib.pyplot as plt
import seaborn as sns
from pyclustering.cluster.kmedoids import kmedoids
from sklearn.preprocessing import StandardScaler
from pathlib import Path... |
3b2cf13a993d639a26c3bd345e8ad54ee912d89de4cb2acebf95f9302a4ac44c | Python | 16,656 | 467 | # 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... |
a438fa3beb5f43bf97c0497c50e949aa7fb126dfc001d238150a419ebdcdbb2c | Python | 16,657 | 473 | #!/usr/bin/env python3
from __future__ import annotations
import argparse
import csv
import re
from dataclasses import dataclass
from datetime import datetime, timedelta
from pathlib import Path
@dataclass
class PhaseResult:
run_label: str
run_path: Path
phase_name: str
output_dir: str
exit_code:... |
8338451156934e579bf8630318922f017eee98e73778bae28994410fd7e3746c | Python | 16,664 | 395 | import numpy as np
import pca_utils as utils
import scipy as sp
from scipy.stats import truncnorm
class SubspaceModel:
def __init__(self, translation_vector, basis, eigenvalues, base_mesh=None):
self.translation_vector=translation_vector
self.basis=basis
self.eigenvalues=eigenvalues
... |
cd21af6506a3698d5d2733d72351f7291e72bf59d7466777999be5bd8e0a73c8 | Python | 16,667 | 545 | """
Bonito Input/Output
"""
import os
import sys
import csv
import pandas as pd
from threading import Thread
from logging import getLogger
from collections import namedtuple
from contextlib import contextmanager
from os.path import realpath, splitext, dirname
import mappy
import numpy as np
from pysam import Alignmen... |
6dbe28374a7e06e24894fc2b4f44a5643a69f2060f9311c63c39edeeae3d8158 | Python | 16,676 | 356 | # %%
import numpy as np
import pandas as pd
import pickle
from pathlib import Path
from plotnine import *
import copy
import math
# https://github.com/neudorf/PLS_wrapper
from PLS_wrapper import pls
ATLAS = '220'
BEHAVIOURAL_DATA_DIR = Path('../../../data/Cam-CAN/data_processing/behavioural_data')
BEHAVIOURAL_DATA_FI... |
c62ec565e5b3d63068b8cb0cf849caf572218d98c1568c10bab591d053209019 | Python | 16,676 | 405 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import cProfile
import pstats
import numpy as np
from examples.continuous_tamp.primitives import get_value_at_time
from pddlstream.language.temporal import get_end, compute_duration
from examples.pybullet.namo.stream import BASE_RESOLUTIONS,... |
df9ff0e35a6eeea0053a10549a6ff1ac68c0ed245307bf961ddea2f3baea8e8f | Python | 16,677 | 372 | list()#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri May 14 01:23:05 2021
Generate text transcript from the time-aligned TextGrid data annotations.
This allow us to compute word-level feature in line with the annotations when
using an LSTM or Transformer model on the text.
@author: hugwei
"""
impo... |
8a8764eb9eecdb684e2149bcc4611c8d35c998a6239287271aaaf9f61400c881 | Python | 16,682 | 367 | #!/usr/bin/env python
from __future__ import division, print_function
import argparse
import multiprocessing
import os
import sys
import time
from typing import List, Union, Iterator, TextIO, Iterable, Tuple
import numpy as np
import pandas as pd
import topaz.cuda
import topaz.predict
import topaz.utils.files as fil... |
23bcefa3c2ccd9d2ccd909236e43b11d7832ca1ae0d04f49a7b181242f7a288e | Python | 16,683 | 324 | 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 parame... |
d91470c9fa31c312ba3c2b29024bdad980988f835d4d50c945f3012ef8672255 | Python | 16,686 | 392 | """Shared utilities for schema validation, sorting, and format conversion used by CLI scripts."""
import os.path
from collections import defaultdict
from hed.errors import HedFileError, get_printable_issue_string, separate_issues
from hed.schema import HedKey, from_dataframes, from_string, load_schema
from hed.schema... |
bac250b38cf5c27c7525d6d2921f1c51caa314613bc9b7dfe15b408efcc1a2ac | Python | 16,687 | 468 | """Morphology reconstruction data structure."""
import math
from collections import deque
import numpy as np
from treem.tree import Tree
from treem.io import SWC, load_swc, save_swc
from treem.utils.geom import rotation_matrix, norm
class Node(Tree):
"""Morphology data storage."""
def __init__(self, valu... |
c8e3004d2826a4f3214c968bb7e827c1b637fc8442f3bc78986ed4d38f05d68f | Python | 16,689 | 494 | import copy
import datetime
import numpy as np
import os
import pandas as pd
import torch
import torch.optim as optim
import torch.nn as nn
import torch.utils.data as udata
from abc import ABC, abstractmethod
from torcheval.metrics import MulticlassAccuracy
from tqdm import trange, tqdm
from typing import Dict, Iterab... |
10fc1c04e388862672ba3389ef264ead56601b29419e7c64441016291e1998ef | Python | 16,697 | 523 | import numpy as np
import pandas as pd
from os.path import join
from moabb.datasets import (
Zhou2016,
BNCI2014004,
BNCI2014001,
MunichMI,
Weibo2014,
Cho2017,
)
from preprocess import (
load_sub,
apply_preprocessing,
Dreyer2023,
)
from help_funcs import load_exp_variables
# -----... |
479d70daae74b01c8f620e139f3c08eca14d99014d439e431a62d4ca72b34eb1 | Python | 16,697 | 351 | import logging
import glob
import os
import numpy as np
import h5py
import scipy.io
from . import functions as func
from .collections import dotdict
class Dataset:
"""
This class is for loading empirical Datasets. Datasets are stored as matrices and can
include functional (e.g. fMRI) and structural (e.... |
547d859f55c8703ad9f47e38c165bbe0a0384d83de930e5fe37b76df56b9e32e | Python | 16,701 | 364 | import numpy as np
import nibabel as nib
from pandas import DataFrame
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 import (
fetch_atlas_aal,
fetch_a... |
cd7f87f20c2b1a3a879c882d557947c1e930ec0bda8a309fc577752c6199e6f7 | Python | 16,703 | 427 | """
Hidden pyrophosphorylation page.
This module adds a self-contained, *unlisted* page to the Sitetack webserver that
runs ONLY the pyrophosphorylation models that are in development (the four models
in the PyroPhos_prediction project folder):
1. Without labels - trained on raw sequence, no known sites ... |
f017c4d9dbf6548635d330c135f35a899b86ea5264f159d3f0f939ecf98bc026 | Python | 16,711 | 411 | '''
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
Loader structure adapted from DeeperCut by Eldar Insafutdin... |
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