sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7aca12775d181aa332261a1020950d2aa8adf741fd04890601b887b4faab8233 | Python | 23,122 | 547 | import os
import random
import numpy as np
import torch
from PIL import Image
from torchvision import transforms
from .loader import get_image_loader, get_video_loader
from .masking_generator import (
RunningCellMaskingGenerator,
TubeMaskingGenerator,
)
from .transforms import (
GroupMultiScaleCrop,
G... |
09c09cae76c7dc31a97bf72639e6921d44131ba1de5ca48c4373d2f60e8d0e5d | Python | 23,140 | 645 | # 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... |
e3a9ffb7330dda6c40d584ca42d153f71882f0db00b9efca69ce19adeeba9cc6 | Python | 23,146 | 435 | # -*- coding: utf-8 -*-
"""
Created on Tue May 31 10:09:38 2022
@author: Dalton
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pickle
import dill
import os
import glob
import math
import re
import seaborn as sns
from sklearn.decomposition import PCA
from sklearn.pr... |
124ee23eb7d1f0a7a1901810f93ee7b679fcac9b7c84e83887657377d5d84a24 | Python | 23,157 | 584 | import copy
import math
import torch
from torch import nn
from torch.nn import functional as F
from torch_scatter import scatter_min
from torchdrug import core, tasks, layers
from torchdrug.data import constant
from torchdrug.layers import functional
from torchdrug.core import Registry as R
@R.register("tasks.EdgeP... |
664106ff33dcf9d31a600575ca7c126008630fcbe936994b229ff119afe1f707 | Python | 23,159 | 684 | #!/usr/bin/env python
"""
Makes layers in a given region starting from one or between two specified
boundaries. Then it analyzes ovelap of given segments with the layers and
determines the position of gegment centers in repect to the layers.
Important notes:
- In order to make setting up multiple scripts easier... |
e72d12ffaacaa057039e21162b2043a9f28b9a0ba925464c805075e083c94296 | Python | 23,161 | 491 | import os
import numpy as np
import pandas as pd
import anndata as ad
import scanpy as sc
import simba as si
#from util.utils_B import set_seed
from time import time
from memory_profiler import profile
import shutil
from scipy.sparse import csr_matrix
os.environ['PYTHONHASHSEED'] = '0'
#os.environ["HDF5_... |
1a017bbe02c30a5b636bae47aecdc66af857a23fb6029073446ee20ea19bc981 | Python | 23,166 | 579 | # Adapted from https://github.com/LINCellularNeuroscience/VAME
# Under GPL 3.0 License
import yaml
import numpy as np
import pickle
import os
import shutil
from BEBE.models.model_superclass import BehaviorModel
from BEBE.models.preprocess import whitener_standalone
import torch
import torch.nn as nn
from torch.utils.d... |
3d70c568f1191de1be1ff9b98ea3a3ecbb703eb9b48c3b149dad3d16421a251b | Python | 23,189 | 580 | import logging
import time
import math
import numpy as np
import torch
import torch.nn as nn
from torch_scatter import scatter_mean
from pyexpat.model import XML_CQUANT_OPT
from ocpmodels.common.registry import registry
from ocpmodels.common.utils import conditional_grad
from ocpmodels.models.base import BaseModel
fro... |
5dd583d08b59856b2cfe9e24add706130dec4cc65f5775cdb15e98bdb5e1de86 | Python | 23,189 | 539 | import warnings
from typing import Any, Dict, List, Tuple
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torchmetrics
from torch.utils.data import DataLoader
from torchmetrics.image.inception import InceptionScore
from .utils import FrechetInceptionDistance
_EVALUATE_OUTPUT = List[Dict[str,... |
e4428ada862974f6f9bb715a619a5f1e57bd6508d07bb8e66fd03d6abf8f0495 | Python | 23,194 | 629 | """A single parenthesized HED string."""
from __future__ import annotations
import copy
from collections import deque
from collections.abc import Iterable
from hed.models.hed_tag import HedTag
from hed.models.model_constants import DefTagNames
class HedGroup:
"""A single parenthesized HED string."""
def _... |
bb88ded8a9548bc038fc459959d05098d4c451de845b0ec57ddfeafeb1f00cb2 | Python | 23,196 | 677 | # This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains th... |
78bef540cddefb40e16422d9231ff5b5cb7a592fe0879c2cf26e50b69e116381 | Python | 23,198 | 618 | from __future__ import annotations
import re
import sys
import numpy as np
import pytest
from scipy.optimize import NonlinearConstraint
from scipy.spatial.distance import pdist
from sklearn.gaussian_process import GaussianProcessRegressor
from bayes_opt import BayesianOptimization, acquisition, exception
from bayes_... |
566226b5f34322d3ee521d417be26d656226c5ea8913d069738a6df9a2fd272a | Python | 23,201 | 663 | # 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... |
3ffa0d837ebde837e4c2b5c627187f7dc32a481cc76f5f135e714ceb4b16332c | Python | 23,209 | 566 | import numpy as np
import os
import os.path as op
import mne
import pandas as pd
import matplotlib.pyplot as plt
from pickle import dump
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.linear_model import LogisticRegression, LinearRegression
from sklearn.feature_... |
ac0282d0ab41e8ef983562779614f093e1749fe857389c7c9c1398ad14d0aae9 | Python | 23,213 | 573 | from datetime import datetime as dt
import json
import os
import time
import nibabel as nib
import numpy as np
import pandas as pd
import argparse
import csv
'''ROI Labels from FreeSurferColorLUT.txt'''
'''
10 Left-Thalamus 0 118 14 0
49 Right-Thalamus 0 118 14... |
6699ff134b8698315c0009310a9f615973781569c9e4a116029a8038f06bdc3c | Python | 23,227 | 591 | #!/bin/env python3
"""
Filaments
---------
Filaments are the (instantaneous) rotation centres of rotors in 3D. They are
also called "tip lines". In 2D, we call them "tip" or "filament point".
The class :py:class:`Filament` describes a filament as a collection of points.
.. note::
A :py:class:`Filament` might not... |
2824a8c115e1956ed9b1307eb80bfd5b8dd7173195537a6be4afa7c070f863d7 | Python | 23,239 | 780 | """"""
import cv2
import numpy as np
import pandas as pd
import xarray as xr
from pupil_recording_interface import BaseReader
def _iter_wrapper(it, **kwargs):
""" Dummy iter wrapper. """
return it
class VideoReader(BaseReader):
""" Reader for video data. """
def __init__(
self,
fol... |
ca8e2d05b9d53770e0a5294de8142e47d7f6ef3120948ba0ea9e8eef68463d0c | Python | 23,241 | 600 | import json
import os
import pickle
import subprocess
from misc_utils import hg19_chromsize, overlap_length
import pybedtools
import pandas as pd
from collections import defaultdict
import numpy as np
from pybedtools import BedTool
import matplotlib.pyplot as plt
from scipy.signal import savgol_filter
from multiprocess... |
5450f1d3a6db660b13197e211c04de05c0de601b2f3e464c22543eee94ee0084 | Python | 23,248 | 630 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at you... |
8905e72fc6ad4726f9c5c1a89fd108a062962454c2ce0b10d0bb981201eae60a | Python | 23,255 | 354 | #####################################
######## Paper Draft Cartoon ########
#####################################
#%%# Catalyzer
import os
import sys
path = os.path.dirname(os.path.realpath(__file__)) + '/../Resources'
sys.path.append(path)
path = os.path.dirname(os.path.realpath(__file__))
sys.path.append(path)
impo... |
fbcef7633265eace770dd821418125bea18b5b06c5a3b6941c092e65941d2445 | Python | 23,274 | 458 | """ Authored by: Neel Kanwal (neel.kanwal0@gmail.com)"""
# This file provides training code for binary vision transformer models mentioned in the paper.
# Update paths to processed datasets
if __name__ == "__main__":
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
... |
cc44f7ad67268b44b7e77661557dc1525eccd8180f9f11285395ec522504de34 | Python | 23,276 | 718 | import copy
import os
import numpy as np
import pandas as pd
import tensorflow as tf
import tensorflow_addons as tfa
import tensorflow_probability as tfp
import tensorflow.keras.backend as K
from scipy.stats import spearmanr
from sklearn.utils import class_weight
def seq_to_one_hot(
seq,
model_unknown=False... |
ae0dd0d788acc635a468c245c5f8dc08f770e53788a0a9ea39ed23e643641813 | Python | 23,290 | 599 | """
This module, 'phonons.py', contains recipes for performing phonon calculations using the
ph.x binary from Quantum ESPRESSO via the quacc library.
The recipes provided in this module are jobs and flows that can be used to perform
phonon calculations in different fashion.
"""
from __future__ import annotations
fro... |
438ddc181aeebb5d755a11cdca60870408f774579f9498bf195c52d7e76c015f | Python | 23,295 | 672 | # -*- coding: utf-8 -*-
import os
import yaml
import numpy as np
import pandas as pd
from copy import deepcopy
from dicthash import dicthash
class Network():
"""
Gathers and prepares all data that is needed for setting up the NEST
simulation.
Parameters
----------
NN : NeuronNumbers
C... |
b1ce39d10a2a2578b284880233e33a82aaa120e2f0d52af01658e11c7c86e5b6 | Python | 23,299 | 577 | """
Performs Bivariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a ListTomoParticles pickle (SetListTomograms object input) used as reference
- A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input) to analyze
Output: ... |
437ab56d09d64a291c77ea6132c2279f09022cd69d3bade07dd6de27406ebbbb | Python | 23,309 | 843 | # 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... |
840f08753a7f973525bc9c6768a934ec3d8e8b32c7aa894bcfd0ba2868d33e26 | Python | 23,310 | 504 | import torch
import numba
import numpy as np
from scipy.linalg import expm
from torch_geometric.utils import add_self_loops, is_undirected, to_dense_adj
from torch_sparse import coalesce
from torch_scatter import scatter_add
def jit():
def decorator(func):
try:
return numba.jit(cache=True)(fun... |
c4c90b06562ea6091ca37ca5617d4a772b0bf7b6779126075d7020db4e0683cd | Python | 23,310 | 671 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (3): 785-806.
doi: ... |
a534a450b1d28b3943770d1f28cb663e882d6444b8ee60683ae02f1954643371 | Python | 23,320 | 594 | from typing import Union
import numpy as np
from numpy.typing import NDArray
from scipy.linalg import svd, eigh, LinAlgError
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils.validation import check_is_fitted
from pyntbci.utilities import covariance, pinv
def _ill_conditioned_message(name:... |
4dfa62de0faba07795b7286299062778126ae49463f65dbe9ce03a9a43e5b2ef | Python | 23,324 | 672 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (3): 785-806.
doi: ... |
bfdcfd845065996727f2a20d53e77492a94a62a23f3aa60a4b9a932f80130cfe | Python | 23,326 | 549 | """
Set of specific utilities for retrieving a filaments from a tomogram
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 15.09.15
"""
__author__ = 'Antonio Martinez-Sanchez'
import pyseg as ps
import csv
import vtk
import graph_tool.all as gt
from pyseg.globals.variables import *
f... |
71a14083d40137dccaa9b7ef2daad14e0447d89fdb06fb0c9244b6f033c328c7 | Python | 23,352 | 644 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. 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 cop... |
38903feda7d71dc6cc9039818e08ed40f90676f2f65d1d4844e09df85fdf0101 | Python | 23,353 | 625 | import warnings
import numpy as np
from tqdm import tqdm
import matplotlib.pyplot as plt
from scipy.optimize import linear_sum_assignment
import sys
class DummySorter:
# Barebones sorter just for Comparison
def __init__(self, spike_times, name="Sorter"):
self.spike_times = spike_times
self.na... |
47e64462cdc6ccb9185ba2c152f715240b0f8c9f2b05ee6150382dd70fe75709 | Python | 23,363 | 563 | import os
import math
import random
import logging
import warnings
from tqdm import tqdm
import numpy as np
import pandas as pd
import scipy
import torch
from torch.utils import data as torch_data
from torch.utils.data import IterableDataset
from torchdrug import data, utils, core, datasets
from torchdrug.layers imp... |
d97fd649cd090219a6438eac67c5c80d18f168e6d05832a83b3d0e9d1c37f6dd | Python | 23,375 | 685 | # 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... |
53e423bcd5c03b2653afc4c09009aba2306dd388101467fd53bdae72a11b3232 | Python | 23,383 | 599 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles densities by list
... |
246faa1b98e949a5f1b5d5ddc7033a5ca9742809658d914e9883486b97a8a178 | Python | 23,391 | 599 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms (Translocon version)
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles d... |
b1ba7ccd0eaf75484b1bab3ad259b1e2fe4ac251b99d0dccc1fd9cbcc3445fa2 | Python | 23,401 | 610 | # 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... |
e449f76382bdbcd87fb2bc73f70e948bf2776beef8efb6c48126c342707322f0 | Python | 23,405 | 548 | import logging
import warnings
from typing import Any, Dict, List, Tuple
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torchmetrics
from torch.utils.data import DataLoader
from torchmetrics.image.inception import InceptionScore
from .utils import FrechetInceptionDistance
_EVALUATE_OUTPUT =... |
69e7dc24de40cd32f8d3970452609ec1f4c1de5097f0c530651c6f8a93c2b24b | Python | 23,410 | 547 | import os
import time
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import openturns as ot
import seaborn as sns
ot.Log.Show(ot.Log.NONE)
import pandas as pd
from sklearn import datasets
from sklearn.datasets import make_regression
from sklearn.metrics import r2_score
from ... |
578fc43c6a99334c5ef290c226fee9e521c1558198a28751ea200f1ebfe0d205 | Python | 23,422 | 413 | # Class definitions for the cardiac cellular models
from warnings import warn
import numpy as np
from matplotlib import pyplot as plt
from scipy.integrate import odeint
from io_functions import read_pandas
from utils import get_pandas_from_value, get_row_id_name, get_nan_value, change_resolution
class CellularModelE... |
353799f910dab70e135ecaca493c44d96c908e5e6e1f7aa03d31cc3a0d5c6079 | Python | 23,426 | 748 | """Module to control DCAM on the console.
This imports dcamapi4 and implements functions and classes
Dcamapi and Dcam to make DCAM easier to use.
Dcamapi initializes DCAM only.
The declarations of classes and functions in this file
are subject to change without notice.
"""
__date__ = '2021-06-30'
__copyright__ = 'Co... |
6d01a3409b5f5e5a5003efe218c984819008e728481f409674c1a8657fd8d88b | Python | 23,428 | 468 | """Control window for continuous sliding-window generation ("Infinite Nekrasov").
Besides run parameters it offers live operator injection, an optional external neural cue,
and a runtime leak-rate control. Every control acts on the running system through the
engine worker; the text colors only display recorded token p... |
ca7cd0cb4ebd2c4bf7b8154a276cf9c45d8c8a9d750fb19539863d0afe4251f7 | Python | 23,432 | 523 | from __future__ import print_function
import torch
import torch.nn as nn
from torch.nn.parameter import Parameter
from torch.autograd import Variable
import torch.nn.functional as F
import copy
def choose(matrix, idxs):
if type(idxs) is Variable: idxs = idxs.data
assert(matrix.ndimension()==2)
unrolled_i... |
ab95d2526a9af10767556d70809dc2c38d88fdca51f08423989ddd4198148b80 | Python | 23,435 | 596 | ##
# \file reconstruct_volume.py
# \brief Script to reconstruct an isotropic, high-resolution volume from
# multiple stacks of low-resolution 2D slices including
# motion-correction.
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date March 2017
#
import os
import nump... |
b8914c6ada37d3731e46c072d9a8fd91801172b4326c3bc52afefbecbce42346 | Python | 23,462 | 491 | import time
from collections import Counter, Sequence
from pddlstream.algorithms.common import INTERNAL_EVALUATION, add_fact
from pddlstream.algorithms.downward import make_axiom
from pddlstream.language.constants import AND, get_prefix, get_args, is_parameter, Fact, concatenate, StreamAction
from pddlstream.language.... |
ecfd4e27b5543e4363ea58b46510eefba90ea55122b2b92d8894e2773403655d | Python | 23,466 | 629 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 26 13:05:23 2021
@author: joaquin
"""
import matplotlib.pyplot as plt
import numpy as np
import scipy.io
import pandas as pd
import os
from scipy import signal
from scipy import stats
#%% load experiment data for thy recordings
names = ['150610'... |
21afa926f56a94bfb20085d1422dd6e698c0b197f0f9d2ccefd67f3afcc66e49 | Python | 23,468 | 522 | #!/usr/bin/env python
# -*- encoding: utf-8 -*-
"""
This is a helper module for scripts that auto-generate bindings for different languages.
Usage:
import bindings as b
b.init(language="C#", output_dir="CSharp")
for schema in b.schemas():
name = schema["name"]
b.write_to_file("schemas/%s.cs... |
d58528802a103c3fe1bab8adbe94f13bdbc6ba3b5707ee7e6afd1bb1ff8fd95f | Python | 23,470 | 587 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
- Analysis settings
Output: - Plots by tomograms:
+ Number of particles by list
+ ... |
0022cf5d2b90ff6ae11a2e9d56aadb188e973a4a5855cbb084f8338d5552b869 | Python | 23,474 | 569 | # Modified version of resnet from from https://github.com/tensorflow/models.git
# Copyright 2017 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... |
c333457ff8a4f2dbcf1e09d953806521b7195500bdc777845cfd89ab46dec87f | Python | 23,474 | 645 | # --------------------------------------------------------
# BAE-ViT Model Architecture
# --------------------------------------------------------
import itertools
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as checkpoint
from timm.models.layers import DropPath as T... |
5938c7da24276c22eba89ff1b6b6ffa75628b4e46061ed8d64ff91b4a042537f | Python | 23,475 | 592 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Copyright (C) 2020 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at you... |
dd9374bf8fdb20fa0363b4bd21411c0d22a0f6bb453c81b520ffe4d8daf3e71e | Python | 23,488 | 441 | # MEGIT batch process (video based) functions
import copy
import json
import h5py as h5
import numpy as np
from shapely.geometry import Point, Polygon
from .fio import hml_read, cjsh_read
from .data import (get_lbl_det, conv_hm2js_blob, conv_hm2js_max, arr_raw_jsl, get_proc_rng, pad_nan, sel_mtp,
... |
6d714b386f060fa08fd629737c1a9319aa4606dbf9e3b7c69867b90d4923d222 | Python | 23,495 | 380 | from hed import load_schema_version
from hed.models.hed_tag import HedTag
from hed.schema import HedKey, from_string
from tests.schema import util_create_schemas
from tests.validator.test_tag_validator_base import TestHedBase
# Load the schema once, globally
hed_schema_global = load_schema_version("8.4.0")
class Tes... |
fe616e98a4586c93d704e4f20636484d8396afd1a843d29448d609b97dc373bb | Python | 23,497 | 746 | from __future__ import print_function
from builtins import range
import numpy as np
import numba as nb
from tqdm import trange
import sys
def validate_seq(x, a, n_clones=None):
"""Validate an input sequence of observations x and actions a"""
assert len(x) == len(a) > 0
assert len(x.shape) == len(a.shape) ... |
586fff2f201ad86c2603aa92a0426dbc913c4440352d9a5b4a2cf2f16be124b9 | Python | 23,513 | 739 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2012-2017 The Python Software Foundation.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
"""
Implementation of a flexible versioning scheme providing support for PEP-440,
setuptools-compatible and semantic versioning.
"""
import logging
import re
from .compat import string_types
f... |
248bad36e77a755c45fc48f51177579fdb40487ea89ebf99c9f5c4273de8efac | Python | 23,538 | 472 | ######## Name
######## BiochemSimulSwift
######## Requires
######## {Modules}
import numpy as np
import numba
class BiochemSimulSwift:
"""Class 'BiochemSimul' Illustration!
It is an essential part of the 'BiochemAnalysis' class!
########
Attributes
########
Methods
... |
d8eaa17ac5f4b902b894a4b864aa100df96104b5de4ec424d725d8109aefb4db | Python | 23,540 | 404 | """
ERROR_OR_STRUCTURE.py written 2026-09-22. "One voice or a choir?"
Pre-registration: 04-NOTES/PREREG-2026-09-22c-ONE-VOICE-OR-A-CHOIR.md (written before this ran).
Within a neuron, two synapses' transmitter votes agree more the closer they are, over tens of
microns (RHOBAR_CI.py, arm D). Is that ERROR (noisy co... |
d5b1c5c6b07f9e3b65efa95483b98826554148ba5af8a0815f8f8153676eac39 | Python | 23,543 | 705 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 26 13:05:23 2021
@author: joaquin
"""
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import scipy.io
import pandas as pd
import os
import h5py
import mat73
from scipy import signal
from scipy import stats
from sklearn.dec... |
56eb3d5320ee3424ff3df663c2edb9df02f4bf93e243d9a288c666748ae8e703 | Python | 23,577 | 692 | """distutils.msvccompiler
Contains MSVCCompiler, an implementation of the abstract CCompiler class
for the Microsoft Visual Studio.
"""
# Written by Perry Stoll
# hacked by Robin Becker and Thomas Heller to do a better job of
# finding DevStudio (through the registry)
import sys
import os
import warnings
from .err... |
98f1173dbe9d0f20d3c389b56b4773afc433d3ec2d9d763687e4dcba8c950c0f | Python | 23,580 | 658 | ##
# \file DataReader.py
# \brief Reads data and returns Stack objects
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date July 2017
#
import os
import re
import six
import natsort
import numpy as np
import nibabel as nib
import SimpleITK as sitk
from abc import ABCMeta, abstractmethod
impo... |
3d9c174464c3e2037e69e22bec8b51da8e417d5b0b6a0ef1cc92a3c48f8980a9 | Python | 23,581 | 525 | # Nucleus 2022.04
# Tiago Rito, The Francis Crick Institute
#
#
# general functions to predict images: predictor, stitching, overlay with COCO
import numpy as np
import matplotlib.pylab as plt
import cv2
import torch
from pycocotools.coco import COCO
from matplotlib.patches import Polygon
from matplotlib.collections im... |
52e40c3bfbcdbe5c24a996569d98fd3cbf8371975648834b5a6fadf34feb248c | Python | 23,597 | 480 | import math
import torch
from torch import nn
import torch.nn.functional as F
import timm
class latentTFBackbone(nn.Module):
"""
Multi-scale Fusion Transformer for image + pos_embedding feature fusion
image_architecture: Architecture used in the image branch. ResNet, RegNet and ConvNext are supported
... |
c187d9d17d5822625a32568d53bd8fbf8553e3732edfe5d0af327e8acc31a662 | Python | 23,608 | 498 | """
This code is ported from following implementation:
https://github.com/Luolc/AdaBound
Following is the original license of the code:
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS... |
a8b2c27dbcf60184845cc5aa4cac905412d61e71405fd64f739bb7cf19ae8bf8 | Python | 23,613 | 708 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 26 13:05:23 2021
@author: joaquin
"""
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import scipy.io
import pandas as pd
import os
import h5py
import mat73
from scipy import signal
# define functions
def eegfilt(data,sr... |
b70dd61c66432a5bf92dd8f416c83605e610e793b495a243f302d81eb3a30e0e | Python | 23,614 | 596 | #!/bin/env python3
"""
Filaments
---------
Filaments are the (instantaneous) rotation centres of rotors in 3D. They are
also called "tip lines". In 2D, we call them "tip" or "filament point".
The class :py:class:`Filament` describes a filament as a collection of points.
.. note::
A :py:class:`Filament` might not... |
d409629d8d22f4802342997933ded3f5f160249a380370cbb76340530325c106 | Python | 23,625 | 658 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
6f6398996ed1d4186a780577e0b905edc570d1c36760abb5713054bf2d4dff85 | Python | 23,627 | 561 | # coding=utf-8
# Copyright 2020-present 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 ap... |
dbd8dfcb9eccecaae9762a942cf64ed66363a5b03b159891fbd3e386da84c6ce | Python | 23,629 | 544 | """
Classes for building proper SkelGraphs objects for structures attached to biological
membranes
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 08.09.14
"""
__author__ = 'martinez'
__version__ = "$Revision: 002 $"
try:
import disperse_io
except:
import pyseg.disperse_io
... |
3c31b2f12a8ea9a75a72d7644332b3ee0b51db6fca5da8941fd09a80f5fab90d | Python | 23,640 | 579 | """
Classes with additional functionality for applying the spatial analysis on stacks of images
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 12.04.16
"""
__author__ = 'martinez'
import os
# import cv2
import math
import numpy as np
from pyorg import pexceptions
from .sparse impo... |
5fe045658e55ba287a9f2d22f05206ea1aa069d26660dd7b988b54e8ced3fa15 | Python | 23,643 | 517 | # 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... |
18c3b9aea980da6d226d20822baf16b16f0ea30ed593cbd37c31e47bc03f5def | Python | 23,649 | 521 | """Consumer-level coverage for the CRITICAL frame-conversion fix, plus the
2-D path's grid guard (Important 3) and run-side plane-threading capture
(Important 1).
``regtools/tests/test_hemisphere_frames.py`` (Task 11) already pins
``MidsagittalPlane.reoriented_to`` itself, hard: 2304 round-trip frame pairs,
per-... |
123a6093327ae8af4b1d9b569ae95f921e79d332a82810c057d2256aa09fda77 | Python | 23,661 | 570 | #!/usr/bin/env python3
import os,sys
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
os.environ['CUDA_VISIBLE_DEVICES']=""
import tensorflow as tf
import tensorflow.keras.mixed_precision as mixed_precision
import tensorflow_probability as tfp
import copy
import numpy as np
import matplotlib.pyplot as plt
import time
i... |
0cce8ce7e50da9c36df085658d04a8e3080a35ab7134c51649ce54b58391244c | Python | 23,678 | 621 | """
A collection of objects and helper methods for defining objective functions
used in topology optimization.
"""
import abc
from collections import namedtuple
from typing import Callable, List, Optional
import numpy as np
from meep.simulation import py_v3_to_vec, FluxData, NearToFarData
import meep as mp
from .fil... |
e2f95f4c49472f415a7532f17eb3972393845721703417c93c236192f5d38297 | Python | 23,684 | 935 | """Various functions used for the GUI.
"""
from ast import literal_eval
from logging import getLogger
from math import ceil, floor
from numpy import arange, nan
from os.path import dirname, join, realpath
from PyQt5.QtCore import QRectF, QSettings, Qt
from PyQt5.QtGui import (QBrush,
QPen,
... |
6f2c58269f609e355eca1465677513320a3f2e191787569fbcdf30241b4071cf | Python | 23,685 | 668 | """
pygments.cmdline
~~~~~~~~~~~~~~~~
Command line interface.
:copyright: Copyright 2006-2023 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import os
import sys
import shutil
import argparse
from textwrap import dedent
from pip._vendor.pygments import __version__... |
ab6575524e2b10830b62349ed0200b5a5bd25a2f33e612ea18d6f33d1b5ab3ee | Python | 23,689 | 656 | # 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... |
50c49a4f3bd6f6d47ad343b25a0e9ca5085e08a766c87c74278d6f341f2cd9b7 | Python | 23,690 | 579 | """
Classes with additional functionality for applying the spatial analysis on stacks of images
# Author: Antonio Martinez-Sanchez (Max Planck Institute for Biochemistry)
# Date: 12.04.16
"""
__author__ = 'martinez'
import os
# import cv2
import math
import numpy as np
import pyseg as ps
from pyseg.spatial.sparse im... |
d408bfa3da3dd023611acfd036a68f6c099d17c434db0a8129eb339bf3c64f89 | Python | 23,696 | 493 | 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... |
7b6a4029c19d8c8d507f9d5cfa7e0e7797e5f2aaa8dd154f9eb077466dd8afa2 | Python | 23,697 | 502 | #!/usr/bin/env python3
"""
Copyright (C) 2018-2020 Intel Corporation
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 applic... |
c578c0b03b808152b20892b4753069a8722f33491e2bfea4fe4b6f8e49e9b251 | Python | 23,697 | 487 | import csv
import io
import os
import shutil
import socket
import unittest
import numpy as np
import pandas as pd
from hed import schema
from hed.errors.error_types import ErrorContext, ValidationErrors
from hed.errors.exceptions import HedFileError
from hed.models.base_input import BaseInput
from hed.models.column_m... |
3313f47cdf01b00c760631c52223f618afa2921a2791f36417ca57a4a9aaee39 | Python | 23,705 | 540 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Sep 3 07:39:59 2023
@author: daltonm
"""
# -*- coding: utf-8 -*-
"""
Created on Tue May 31 10:09:38 2022
@author: Dalton
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.colors import ListedColormap
import p... |
e0fe551822a1bf3fa7b313fcd04342960228d4e2b4551f461519f298b8bae19d | Python | 23,714 | 618 | """Python function to run SLM with user-defined template data directory
(as fetch_template_surface set to default in the original function)
Modified from BrainStat toolbox https://brainstat.readthedocs.io/en/master/_modules/brainstat/stats/SLM.html#SLM
© Copyright 2021, MICA Lab, CNG Lab Revision 1f3068fb
V... |
26884d2fb7b2d6d16351fb586bf5abe2f66eaee8329eb809dd712fd30b5686a5 | Python | 23,718 | 689 | # 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... |
6698526b194d1cb556c9cd15ad7f9bfed7622005a682ef067c9351fe9a9b521d | Python | 23,721 | 659 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
3c69f36524c7edf9616b0683d794ece03641b2fff2cf233c0c6a4cc6344bb7c6 | Python | 23,731 | 561 | from dreamcoder.domains.tower.towerPrimitives import ttower, executeTower, _empty_tower, TowerState
from dreamcoder.domains.tower.tower_common import renderPlan
from dreamcoder.task import *
class SupervisedTower(Task):
def __init__(self, name, program, mustTrain=False):
if isinstance(program,str):
... |
2f24d5636740371fa2fd3124e58afd61cc14b62cb41ce10508042ad45ff8e9ca | Python | 23,737 | 733 | """Exceptions used throughout package.
This module MUST NOT try to import from anything within `pip._internal` to
operate. This is expected to be importable from any/all files within the
subpackage and, thus, should not depend on them.
"""
import configparser
import contextlib
import locale
import logging
import path... |
7e4fd9755e8a505778cc98730fee109dd6d0ec3cf82c6a6e3c37f6f8f12c0698 | Python | 23,739 | 629 | import torch
import warnings
import numpy as np
import networkx as nx
from torch_geometric.data import Data
from .edge import Edge
from .node import Node
from .element_look_up_table import ElementLookUpTable
class Graph:
"""Class for representing chemical graphs with all necessary information."""
def __ini... |
113b90c456159f5207268e953c0232f0d9a195f6125ad072dce1e1e0b15f9497 | Python | 23,742 | 463 | # 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... |
32725dec53234493bcb1c25725ad9e74ebc90294ed6d9b36d3fbaea1be12059c | Python | 23,749 | 442 | #####################################
######## Paper Draft Cartoon ########
#####################################
#%%# Catalyzer
import os
import sys
path = os.path.dirname(os.path.realpath(__file__)) + '/../Resources'
sys.path.append(path)
path = os.path.dirname(os.path.realpath(__file__))
sys.path.append(path)
impo... |
6381477ea430ca865dcf9561aa21d946121394e4888292cfbdf2b4e7086bdcd3 | Python | 23,758 | 567 | #!/usr/bin/env python
# Copyright (c) 2019 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides Challenge routes as standalone scenarios
"""
from __future__ import print_function
import math
import xml.etree... |
7dc11d040bf45c84bb98c2d0a73136d047ca20fde04b57c86c788037a3f22943 | Python | 23,767 | 628 | import os
import os.path as op
import numpy as np
import matplotlib.pyplot as plt
from functools import reduce
import mne
import mne_bids
import pandas as pd
from autoreject import get_rejection_threshold
from params import BIDS_ROOT as bids_root
from params import PLOT_DIR as plot_dir
from params import FREQUENCIES ... |
e0ca7c8aa3b2aeea4db0f7e7173ac173013492366d050c6cbb33c7ee3049c66d | Python | 23,774 | 556 | import json
import os
import shutil
import tempfile
import unittest
from hed.tools.bids.bids_util import get_schema_from_description, group_by_suffix, parse_bids_filename
class TestGetSchemaFromDescription(unittest.TestCase):
def setUp(self):
"""Set up temporary directory for test files"""
self.t... |
3ff3ca3b96b7818e58cc5012cf0ece7fa45ad8f763358d4524b6e495afe15f7b | Python | 23,780 | 602 | from atom3d.filters import filters
import os
import torch
import numpy as np
import pandas as pd
import random
import torch
import torch_geometric as tg
# import e3nn.point.data_helpers as dh
from transformers import BertTokenizer, BertForMaskedLM
import os
from eudockscore.utils.interface import get_pair_interface_... |
a6a6ddbf91800d1c34497f35a6bf5022b373a2324e3766d1838373521f06fec6 | Python | 23,821 | 475 | # 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
#
# http://w... |
279b8da6b41f1d211c15c608dd9ca7d82625d6ff7def61217fd1bc8478814281 | Python | 23,832 | 522 | # coding=utf-8
# Copyright 2020 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 ... |
55d603877e1755e0153dea1a2557a98eac5780bcbd7afff337284a0a5d72979c | Python | 23,848 | 561 | import numpy as np
import pandas as pd
import os, torch
import importlib
filepath = os.path.dirname(os.path.abspath(__file__))
model_typology = pd.read_csv(filepath + '/model_typology.csv')
model_typology['model_name'] = model_typology['model']
def subset_typology(model_source):
return model_typology[model_typol... |
f33c0bb39e6df9be6c0fcc2f24d06020fbe359ac199e34d0e7377ea3d0e85088 | Python | 23,854 | 610 | from collections import namedtuple
from typing import Callable, List, Union, Optional, Tuple
import numpy as np
from autograd import grad, jacobian
import meep as mp
from . import LDOS, DesignRegion, utils, ObjectiveQuantity
class OptimizationProblem:
"""Top-level class in the Meep adjoint module.
Intende... |
3ea45ae601c89b0fb5905139db49f34c073985a28b9e47be9b21b219cca84c42 | Python | 23,881 | 625 | # pylint: skip-file
import math
import numpy as np
import tensorflow as tf
# from spe_tf import *
from einops import rearrange, repeat
from functools import partial
#from util import *
import src.layers.util as util
BIG_CONSTANT = 1e8
def create_projection_matrix(m, d, seed=0, scaling=0, struct_mode=False):
r""... |
cbd34fc4b5aa3b9fc3cfbf93f4a311584edd599fdd1cf7dcfea9a47e10ecee25 | Python | 23,885 | 466 | """
Created on Wed Apr 27 09:01:02 2022
This script is writen to load a HMM model and used it to summirize the output
of a basecalled dataset.
@author: Haotian Teng
"""
import os
import time
import toml
import torch
import itertools
import numpy as np
from scipy.stats import binom
from tqdm import tqdm
from matplotlib... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.