sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
42954777c50c25ee4dc764d761f56f8a68de6e3c5039abbf6a159293b0f48415 | Python | 29,754 | 668 | """Interface converters for Keras 1 support in Keras 2.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
import warnings
import functools
import numpy as np
def generate_legacy_interface(allowed_positional_args=None,
... |
d2ea5a41553871159b23a49ed0a3c84abfcc40e7273cef1cf562b8141f5798e4 | Python | 29,777 | 891 | """Cell template class"""
"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by the F... |
81eb98e13aeb6f43aa23614ec5eda402d050299c0f46acab275fd9f9e9a2331e | Python | 29,788 | 801 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# tests/long_training.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
... |
49181ee1d43492a00c8d75253f434d3e5e1fa8ec9b1a71032435d68462c2d790 | Python | 29,803 | 890 | import math
from math import pi
from typing import Optional, Tuple, Callable
import torch
import numpy as np
from torch import nn, Tensor
from torch_geometric.nn.conv import MessagePassing
from torch_scatter import scatter, scatter_mean
from oa_reactdiff.model.util_funcs import unsorted_segment_sum
from oa_reactdiff... |
cd1811fcd13419919a5ad24a7b2553d886032141414d7b747a4390f78d070766 | Python | 29,843 | 757 | # Copyright (c) OpenMMLab. All rights reserved.
import warnings
from collections import OrderedDict
from copy import deepcopy
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as cp
from mmcv.cnn import build_norm_layer
from mmcv.cnn.bricks.transformer import FFN, build_d... |
82bc78cd12f596282e792c0a587fd35c32cc9fac113d2fd128a61ac7e4c94838 | Python | 29,865 | 709 | """Decide whether a DANDI asset, or a whole dandiset, holds photometry GuPPy can read.
The question is answered off the remote bytes rather than off the archive's metadata, because the
metadata does not carry it (see :mod:`guppy.utils.dandi_search`). Reading is arranged so that the
answer costs a few kilobytes per fil... |
0d9d2048c0f18e909229cf98f124773a15558db7d307048160441ae8f93e511b | Python | 29,870 | 976 | import hashlib
import os
import re
import sys
import time
from itertools import groupby
import h5py
import numpy as np
import pytraj as pt
from . import config, constants, log
# torch and scipy are imported where they are used. Both are heavy -- torch
# alone is ~580 ms -- and nothing on the featurization path needs... |
90bf0f8bd427f8685d9ad34e3270c34c18498a52841300747b9d2de47681e58f | Python | 29,870 | 742 | import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import numpy as np
import pandas as pd
from rdkit import Chem
import torch
from torch.utils.data import IterableDataset
import dgl
import random
from dgl.dataloading import GraphDataLoader
from rdkit.Chem.BRICS import Fin... |
de932e1a854828c9c5ea6e9f7f53add62a1fc4fb5c5753893ebb008e8f239ee3 | Python | 29,894 | 863 | import pytest
import json
import numpy as np
from keras.layers import Dense, Dropout, Conv2D, InputLayer
from keras import layers
from keras.engine import Input, Layer, saving, get_source_inputs
from keras.models import Model, Sequential
from keras import backend as K
from keras.models import model_from_json, model_fr... |
38db5cec966c3997cf5b0927975c16569199fbb9875c0831abf0c49f1ae8b179 | Python | 29,925 | 671 | """Pure core for the GuPPy NWB-export metadata form (channel-centric, schema-driven).
GuPPy owns the fiber-photometry channel structure (it wrote ``storesList.csv``),
so the form auto-derives everything structural and the user only supplies what
GuPPy cannot know: the hardware/biology device library, per-channel wavel... |
f2d52dea5f4682666643323a97bd9fa59d576a24fec43eb50839cf993cd4b265 | Python | 29,946 | 635 | """Recommend right-sized SLURM ``mem`` / ``cpus`` from run data.
Joins *actual* usage (Snakemake ``benchmark:`` TSVs) against *requested* resources
(the SLURM efficiency report, falling back to the per-rule logs) and, for each rule,
classifies the fit and recommends a size. The recommendation is the observed peak
time... |
9b77139c2dd388929f47e83a62f1689d7a94dd25b90fbe716a41d619ddb627f5 | Python | 30,004 | 838 | # -*- coding: utf-8 -*-
import json
from typing import Any, Dict, List, Optional, Tuple
import yaml
from typing import Set
from guardian.shortcuts import (assign_perm, get_objects_for_user, get_perms_for_model)
from django.db import connection
from django.db.models import Exists, OuterRef
from django.http import Htt... |
edeac83a49a4a2c2e2d65bba74516efe3a9af45f7e39e8dde2148094b50cb551 | Python | 30,040 | 797 | import numpy as np
import pandas as pd
import sklearn as skl
def run_sz_alarm(curr_df, sz_mask, sz_onsets, wins_per_min, lookback, sph_, sop_, df_pred_mva, y_pred_tile_std, corr_, thresh=0.5, chunk_size=None, verbose=False):
sph = sph_ * wins_per_min
sop = sop_ * wins_per_min
# Debugging variables
... |
bfbcf006c438ebe84872945b0f7b972364077cc3049cc1625b281759a2b6fc70 | Python | 30,123 | 671 |
import numpy as np
import os
# import nibabel as nib
import pandas as pd
import joblib
import time
from sklearn.preprocessing import StandardScaler
from sklearn.svm import LinearSVR, LinearSVC
from sklearn.model_selection import (train_test_split, cross_val_score,
KFold)
import matplotlib.pyplot as plt
from tqdm i... |
ef584f0a4755671d5f84101ed85e145e0b6eb61c28ab1b5c31e7137a4d0ca3e6 | Python | 30,173 | 582 | # SPDX-License-Identifier: Apache-2.0
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Versi... |
119ad3dabaa719748167b62ed4a820ede3e9f7be6dd9bf640fcd51f7431807d5 | Python | 30,183 | 847 | """Tests for Socket.IO room functionality."""
import asyncio
import uuid
import pytest
import socketio
from httpx import AsyncClient
from zndraw_socketio import wrap
from zndraw.exceptions import NotInRoom, RoomNotFound
from zndraw.schemas import PresenceResponse, RoomCreateResponse
from zndraw.socket_events import ... |
bc4e2719054453c92307e140b192f42c21dd55cd465f5320ec0ee420b3baaadf | Python | 30,198 | 834 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import sys
import time
import numpy as np
import torch
import torch.nn as nn
from ocpmodels.common.registry import registry
... |
732eee48370fc27d6db67007e00f8cc8170b3d1e0746715ac8080b307467ee82 | Python | 30,209 | 825 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from mmcv.cnn import ConvModule
from mmengine.registry import init_default_scope
from mmseg.models.backbones.unet import (BasicConvBlock, DeconvModule,
InterpConv, UNet, UpConvBlock)
from mmseg.models.ut... |
02553f95c46d0b622228fdbdebaa30294fc8df1027c47e61529f737a495a8f24 | Python | 30,281 | 1,043 | from ocpmodels.common.utils import setup_imports
import torch
import itertools
import json
import hashlib
import os
import torch.nn as nn
import torch.optim as optim
import torch_geometric
import torch_scatter
import torch.multiprocessing as mp
from torch.utils.data.distributed import DistributedSampler
from torch.util... |
7bc557083ec3305206e10bb6753da7b5ee09718a71ea269ca431b6a229e48a80 | Python | 30,318 | 767 | """Independent Bruker TDF2 reader for macOS/Linux/Windows.
The module reads ``analysis.tdf`` with Python's standard-library SQLite
driver and decodes ``analysis.tdf_bin`` itself. It does not import OpenTIMS,
AlphaTims, NumPy, pandas, or Bruker's TDF-SDK.
Python 3.11 does not include a ZSTD decoder, so compressed fra... |
0975763cbb6515fc5369cdcdf5f770b04f70e27de9681434352b7c3c6734a6d2 | Python | 30,343 | 889 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# tests/run_docbuild_tests_and_cover.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade
#... |
f280919beb3ed916d272ebac4934dfd3f13e179fdb7c2d3e3b4e0dc83b4f113b | Python | 30,371 | 819 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import datetime
import errno
import logging
import os
import random
import subprocess
from abc import ABC, abstractmethod
from collections imp... |
3bb7f8fb4111a2bbd7e30b14a55744ed940922a59f7423247aa1e978e8c916b5 | Python | 30,385 | 620 | import os
import numpy as np
from tqdm import tqdm
from collections import OrderedDict
import pandas as pd
from sklearn.metrics import adjusted_rand_score
import scanpy as sc
import torch
from torch import nn
from torch.utils.tensorboard import SummaryWriter
from torchvision.models import resnet50, densenet121, swin_s,... |
a2ac071e61c5242dd08c15045ed2e6a5e446a92050e6f138e98aae56a416f35c | Python | 30,403 | 808 | import filelock
import os
import os.path as op
import logging
from math import nan
import shutil
import sys
import random
import re
from .due import due, Doi
from .utils import (
read_config,
load_json,
save_json,
write_config,
TempDirs,
safe_copyfile,
safe_movefile,
treat_infofile,
... |
0c9d0bfff06a931fb69d5fc7e43b05432384e0eae39c34e5eb304118b8b5d470 | Python | 30,526 | 563 | # pytest unit tests for sct_analyze_lesion
import os.path
import shutil
import pytest
import logging
import math
import pickle
import numpy as np
from scipy.ndimage import center_of_mass
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.utils.fs import extract_fname
from spinalcordtoolbox.utils.sys i... |
d852c3ff1187594dae163357d29c38b0c6579b728f92eb1b69172d362ee3cfe5 | Python | 30,544 | 610 | # The DuckDB exporter can be used to export particular intermediate files into the
# in-process database engine DuckDB (https://duckdb.org) for future querying.
import os.path
import stat
import tempfile
from contextlib import contextmanager
from pathlib import Path
import duckdb
from src.memory import _bytes_to_gib,... |
2ed2d1e81059c7ebe221f1ce8641fa9fbf4b0f4e481bee62366ef6ca35051d65 | Python | 30,574 | 762 | import random
import scipy.sparse as sp
import torch
import torch.nn as nn
import sys
import pickle as pkl
import torch.nn.functional as F
import pickle
import os
import yaml
from sklearn.svm import SVC
import numpy as np
from sklearn.utils import shuffle
import networkx as nx
from scipy.linalg import fractional_matrix... |
b8124de26a554b3576fc7d80104c21b047812ebdd5e6d4c8123b6583e0504e9c | Python | 30,601 | 899 | """
Classical KGX graph summary module.
"""
from typing import Dict, List, Optional, Any, Callable
import re
import yaml
from json import dump
from json.encoder import JSONEncoder
from deprecation import deprecated
from kgx.error_detection import ErrorType, MessageLevel, ErrorDetecting
from kgx.utils.kgx_utils impo... |
d657e4679d6c11678c6616fd99b4fbc516484144423de501d029a4bad1034134 | Python | 30,646 | 736 | # Copyright (c) OpenMMLab. All rights reserved.
from functools import partial
from typing import Dict, List, Tuple
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, build_norm_layer
from mmcv.cnn.bricks.transformer import BaseTransformerLayer
from mmcv.ops import point_sample
from mmengine.dist impor... |
7905719a4ddbd31a1f0ac4650be8690720aafc621bb7dd34ed3e3c160d0cdd66 | Python | 30,655 | 847 | """
Functions for computing metrics from neuroimaging data.
License: BSD-3-Clause
Author: Hanna M. Tolle
Date: 2024-10-31
"""
import sys
sys.path.append('../')
import os
import numpy as np
import pandas as pd
from typing import List
import glob
from nilearn import datasets
from nilearn.maskers import NiftiLabelsMa... |
0ed5383a98b4ed4e4d0f1d89d166e7839bc31e49228d1b2d754127228bf82ef3 | Python | 30,841 | 761 | # -*- coding: utf-8 -*-
import json
from django.contrib.auth.models import Permission
from django.db import connection, transaction
from django.http import JsonResponse
from django.test import TestCase, TransactionTestCase
from django.test.client import Client
from guardian.shortcuts import assign_perm
from guardian.... |
6854821402c59468de5e3c1e036403a97050db7ff3ec4e654c03b64e938a4208 | Python | 30,847 | 737 | # Stack manipulations
# Author: David Young, 2017, 2019
"""Import and export image stacks in various formats.
"""
from collections import OrderedDict
import os
import glob
from typing import List, Optional, Sequence
import numpy as np
from skimage import transform
from skimage import io
from matplotlib import animati... |
4771d84a7a96ba6b5b7aa0a20699567ed97570424d61e653fca58484438cd6e8 | Python | 30,876 | 862 | import gzip
import typing
from typing import Set, Dict, Union, Optional, Any, Tuple, List, Generator
import rdflib
from linkml_runtime.linkml_model.meta import SlotDefinition, ClassDefinition, Element
from rdflib import URIRef, RDF, Namespace
from kgx.error_detection import ErrorType, MessageLevel
from kgx.prefix_man... |
36dbe9c5a9c49d09be0f235c600941f904bd6952e56773afd1e95926b4083055 | Python | 30,963 | 915 | from functional import compose, partial
from functools import reduce
from scipy.ndimage import rotate as scipy_rotate
import copy
import glob
from . import constants as const
import nibabel as nib
import numpy as np
import os
import pickle
import pydicom
import scipy.interpolate as interp
import scipy.stats as stats
im... |
9415b3530eddf35c30543fc4a470b53445133d6911bba20d770d7879e63545c2 | Python | 31,037 | 790 | """
Functions for performing SPICE-based electrical simulation of a neuron given
its synapses and skeleton using a simple linear passive model.
Try the `interactive simulation tutorial`_ for a tour of basic simulation options.
.. _interactive simulation tutorial: notebooks/SimulationTutorial.ipynb
.. note::
Th... |
47ac61a00aeb3648f6f2cd62c6ce48f0f0ef16bf7a79f3e5983847f42491dc81 | Python | 31,074 | 821 | import logging
import time
import math
import hydra
import numpy as np
import torch
import torch.nn as nn
from omegaconf import omegaconf
from pyexpat.model import XML_CQUANT_OPT
from fairchem.core.common.registry import registry
from fairchem.core.common.utils import conditional_grad
from fairchem.core.models.base i... |
62c1fa4f9493d9178838131e427969f285826fa5506429cc11990e30edbe167c | Python | 31,081 | 711 | # Blob verifications against ground truth
import os
from typing import Optional, Sequence, Tuple
import numpy as np
from scipy import optimize
from scipy.spatial import distance
from magmap.cv import colocalizer, detector
from magmap.io import df_io, libmag, sqlite
from magmap.settings import config
from magmap.stats... |
f8801e26df065e780ba6a41e8eb9519c6c10489bd6f1b916cf2b7551baa5b9f4 | Python | 31,093 | 958 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import warnings
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule, build_activation_layer
from mmcv.cnn.bricks.transformer import build_dropout
from mmengine.logging import print_log
from mmengine.model import ... |
34bc2f489ef5077e068bd5dd73c043718b424349bd516a6e70c3f6e9a11de03b | Python | 31,128 | 768 | ##
## CPCantalapiedra 2019
from os.path import isfile as pisfile
import sys
import time
from collections import defaultdict, Counter
from ..emapperException import EmapperException
from ..common import get_call_info, get_data_path, ITYPE_PROTS, ITYPE_CDS
from ..utils import colorify
from ..search.hmmer.hmmer_seqio im... |
126e03d478f9d4c78026b6470b541a78776a70ff0ad6101a9fa7fc974156458b | Python | 31,220 | 1,045 | import numpy as np
from matplotlib import pyplot as plt
from matplotlib.gridspec import GridSpec
from myphdlib.general.toolkit import smooth, psth2
from sklearn.decomposition import PCA
from scipy.ndimage import gaussian_filter as gaussianFilter
from scipy.ndimage import zoom
from scipy.interpolate import interp2d
impo... |
808e507607299979208ddf45b5ca7ed566d790a8f4348d35369c5fe15df02e52 | Python | 31,267 | 788 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors, and NVIDIA.
#
# 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 ... |
6497a3b46e0be31b20da2f932bff5aa926c4235756825684041205a6b144ed80 | Python | 31,285 | 834 | import warnings
import numpy as np
import pandas as pd
import networkx as nx
import torch
import copy
import itertools
from pymatgen.core import Element
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
from pymatgen.analysis.graphs import StructureGraph
from pymatge... |
2c83783133049e416ce01490f3cf9812778bd8e546edc7c7094bb5c5774680fd | Python | 31,301 | 691 | import os
import numpy as np
import datetime
from typing import Sequence, Dict, Optional, List, Any, Tuple, Callable, Union
from argparse import ArgumentParser
import pandas as pd
import math
import sklearn.metrics
import matplotlib.pyplot as plt
import torch
from torch_geometric.loader import DataLoader
import torch.n... |
ade022b8fe2bd68576389aa98ee123a7709f52d40bbad132f9dfdfef405eeeeb | Python | 31,310 | 853 | # -*- coding: utf-8 -*-
"""
Created on Sat May 23 10:38:20 2020
@author: george.dickinson@gmail.com
This program is a Python script developed to analyze the motion of intracellular Piezo1 proteins labeled with a fluorescent tag.
It allows the user to load raw data from a series of image files and track the movement o... |
181cf825b43b3278ba168865aa380cb86f2cfb8ca92c334fc21db26c9b95d2e2 | Python | 31,380 | 794 | import itertools
import json
import logging
import os
from pathlib import Path
import neurokit2 as nk
import numpy as np
import pandas as pd
# from . import get_logger, set_logger_level
# def get_logger(name=None):
# """Return a logger to use"""
# return logging.getLogger("physio" + (".%s" % name if name els... |
eb7db0a4d0d7efec411d3b5b7039719111c18ec15702ec9ce6f7061654e1c9e3 | Python | 31,426 | 704 | '''
Computes GRAIL patterns for all patients with all fold models.
Does not cluster results and only saves mean alignment values.
Additionally, computes fold-wise performance of each model and saves it.
Dependencies:
- data/raw/receptor_maps/f{atlas}/f{atlas}_receptor_maps.csv
Authors: Hanna M. Tolle
Date: 2025-05-03... |
9e4f3f86fc3f20258a677ebbec3fc120e2a8f74c5d388d79b396e6a9e80837f6 | Python | 31,473 | 512 | # This document holds the functions used as part of
# the poro-mechanical modelling of living tissues
# according to the theory in ./Theoretical_Developments.pdf
# Theta Wilson method
# Author: Thomas Lavigne
# Date: 18/09/2024
#
def readme_VFTW():
print('This document holds the functions used as part of the poro-m... |
d2a800583f5a545397b18386c3e5734bae20c8a4bb88137a4a18284b3601fae4 | Python | 31,486 | 883 | import json
import os
import pickle
import sys
import urllib
from collections.abc import Generator
from pathlib import Path
from typing import IO, Any, cast
import arcp
import bagit
import pytest
from rdflib import Graph, Namespace, URIRef
from rdflib.namespace import DC, DCTERMS, RDF
from rdflib.term import Literal
... |
c72d94b29813da98b8dc759368fa434afa3e62e1d2331fcbc0c390e77e6da2b0 | Python | 31,579 | 759 | # coding=utf-8
# Copyright 2021 The IDEA Authors. All rights reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by a... |
64f299df0d5673a67bad77aa4a57842194baf3b2c4bf55c1231a470337e81fa6 | Python | 31,598 | 703 |
try:
import cPickle as pickle
except:
import pickle
import gzip
from hippounit import plottools
import matplotlib.pyplot as plt
import os
import numpy
import seaborn as sns
big_errors_spiking = []
all_features = []
spiking_features = []
base_dir= '/mnt/csoport31-2/Modellezo_csapat/CA1_pyramidal/Spine_project... |
e33f720b58f34ca09f3b2f4f7caa77b03b03c738d31b4a911a253f5658bba1d0 | Python | 31,671 | 904 | import json
import logging
import os
from collections.abc import Sequence
from pathlib import Path
import numpy as np
import pandas as pd
logger = logging.getLogger(__name__)
RAISE_ISSUE_URL = "https://github.com/LernerLab/GuPPy/issues/new"
_RUN_FOLDER_PREFIX = "output_"
_RUN_NAME_MARKER = "_" + _RUN_FOLDER_PREFIX
... |
59a2ed95b82157685c12e90d81994d93a5843425dc8f88bb305614e00f4e3812 | Python | 31,688 | 628 | # Copyright (c) ByteDance, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import os
import sys
import datetime
import time
import math
import json
import numpy as np
import utils
i... |
81293d739248f3e18cf08e9edd35d03bb2b868a2d063d79ad31b38cf6cae04d8 | Python | 31,710 | 741 | # 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... |
d7c354d5161167621f4c271b71d3dea44f72bc2a9e78c87d23e7ff326de87f5c | Python | 31,832 | 792 | # -*- coding: utf-8 -*-
"""Pooling layers.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from .. import backend as K
from ..engine.base_layer import Layer
from ..engine.base_layer import InputSpec
from ..utils import conv_utils
from ..legacy import int... |
ec7f73402ee88013a29a7f37bb3f795e5f1e93062ab1309667ae6e9078b344de | Python | 31,835 | 709 | # This script reads the replay files and evaluates the performance.
import yaml
import os
import pickle
from copy import deepcopy
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import torch
import datetime
import time
from ev2gym.models.ev2gym_env import EV2Gym
from ev2gym.baselines.heuristic... |
17afef16b3f1ef18696a3c9d0e067cf42e2e27e301cb44ad56deac01a7bdc60f | Python | 31,902 | 965 | """Tests for Frame REST API endpoints."""
from typing import Any
import ase
import msgpack
import pytest
from helpers import (
auth_header,
create_test_room,
create_test_user_in_db,
decode_msgpack_response,
make_raw_frame,
)
from httpx import AsyncClient
from sqlalchemy.ext.asyncio import AsyncSes... |
0d910a72b9f74f50602b1a68a020992a761e730d86df3a9722d598d0886f6b0d | Python | 31,994 | 845 | # Input/Output for SimpleITK/SimpleElastix objects
# Author: David Young, 2019
"""Input/Output for SimpleITK/SimpleElastix objects.
Manage import and export of :class:`simpleitk.Image` objects.
"""
import os
import shutil
from typing import Callable, Dict, List, Optional, Sequence, Tuple, Union
try:
import itk
ex... |
c39426bcb6d254b9c38fb70c0fbf0710b022b45746f5b062978863ed227a9bad | Python | 32,012 | 830 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import os
from collections import defaultdict
from typing import Dict, Optional
import numpy as np
import numpy.typing as npt... |
202daf7d1b034cd9f9dc82672a9a0be5c2ea73bbb671c5577ca342fad7b2f4a6 | Python | 32,026 | 625 | from nilearn.plotting import view_img
from pathlib import Path
import pandas as pd
import nibabel as nib
import base64
from modules.plot_mosaics import get_axial_slices, get_coronal_slices, get_sagittal_slices, save_axial_mosaic, save_coronal_mosaic, save_sagittal_mosaic
def save_report(output_file, svr_param... |
30bff0a16e1672fd46b55ac82558398f2d1958752d2b6d342b9b6bde3b233e97 | Python | 32,034 | 684 | import logging
import re
import shutil
import warnings
from pathlib import Path
from typing import Any
import h5py
import numpy as np
import pandas as pd
from guppy.analysis.io_utils import is_channel_label
from guppy.extractors import BaseRecordingExtractor
from guppy.extractors.detect_acquisition_formats import _is... |
0c40e04792c2bbe3f0e92c9dd9b6545ccf2801bcd5ce9fafa19d374191aa4e50 | Python | 32,137 | 902 | # Author: Huaxu Yu
# A module to annotate metabolites based on their m/z, retention time and MS2 spectra
# imports
import os
import pickle
import numpy as np
import pandas as pd
import json
from tqdm import tqdm
from ms_entropy import read_one_spectrum, FlashEntropySearch
from .utils_functions import extract_signals... |
d0091f63e95fe3661f99e76e75438ee5caf94997c672136592705ddf7577f46c | Python | 32,138 | 783 | ###########################################################################################
# Training script for MACE
# Authors: Ilyes Batatia, Gregor Simm, David Kovacs
# This program is distributed under the MIT License (see MIT.md)
####################################################################################... |
f0c069f10e73be2433eaf6cc373c3e59ab7a47dabe9bdec32ff17373b49e07a8 | Python | 32,176 | 1,136 | import importlib
import re
import time
import uuid
import sqlite3
from enum import Enum
from functools import lru_cache
from typing import List, Dict, Set, Optional, Any, Union
import stringcase
from inflection import camelize
from linkml_runtime.linkml_model.meta import (
TypeDefinitionName,
EnumDefinition,
... |
57e93ea4a5fcb92f0d4479de6555160aa1e38f454a8807f8ebb5dcef5954a45e | Python | 32,267 | 744 | import copy
import datetime
import logging
import urllib
import uuid
from collections.abc import MutableMapping, MutableSequence, Sequence
from io import BytesIO
from pathlib import PurePath, PurePosixPath
from typing import TYPE_CHECKING, Any, TypedDict, cast
from cwl_utils.types import (
CWLDirectoryType,
CW... |
845d447551e7244cb4e1dfbcba74e17ffda323022ee3df037d07c339dfe14b87 | Python | 32,270 | 831 | import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import numpy as np
import pandas as pd
from rdkit import Chem
import torch
from torch.utils.data import IterableDataset
import dgl
import random
from dgl.dataloading import GraphDataLoader
from rdkit.Chem.BRICS import Fin... |
aa6e6e81080ed85e362327ec97d5d5215832306d6ece55e843b9a1e77c5ce6c1 | Python | 32,287 | 831 | import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import numpy as np
import pandas as pd
from rdkit import Chem
import torch
from torch.utils.data import IterableDataset
import dgl
import random
from dgl.dataloading import GraphDataLoader
from rdkit.Chem.BRICS import Fin... |
7322fbb584e27ffa832040057ce7ba2c52c765d2ced14aa50579af84394c3c63 | Python | 32,296 | 881 | import merlinth
import numpy as np
import torch
import wandb
import os
import glob
import ants
import matplotlib.pyplot as plt
import h5py
import nibabel as nib
import warnings
from medutils.mri import ifft2c, rss
from scipy.stats import linregress
from scipy.ndimage import binary_erosion
from skimage.metrics import pe... |
56d0392879ceb3734d17620fb855e0b7282c7892ced1260217286b758201937e | Python | 32,297 | 679 | from django.db import migrations, models
import django.contrib.gis.db.models.fields
forward = """
-- We rewrite the table from scratch, because all indices have to be
-- rewritten anyway. This also allows us to regenerate all indices in one go
-- and check all constraints also only once at the end. The ne... |
26402e748eef78bc7f3206b8bec3b6a72c70be72f5ae30a16b789db3c4b5bb11 | Python | 32,307 | 1,193 | import numpy as np
from matplotlib import pylab as plt
from matplotlib import widgets as wid
from matplotlib import lines
from matplotlib.backend_bases import MouseButton
from matplotlib.colors import LinearSegmentedColormap
import matplotlib as mpl
def removeArrowKeyBindings():
"""
"""
pairs = (
... |
fc21590096649933d84c5a4a9fb0706e0c28346fc7f571f6709ec2143987beac | Python | 32,341 | 686 | import argparse
import contextlib
import json
import os
import platform
import re
import subprocess
import sys
import time
import warnings
from pathlib import Path
import pandas as pd
import torch
from torch.utils.mobile_optimizer import optimize_for_mobile
FILE = Path(__file__).resolve()
ROOT = FILE.parents[0] # YO... |
7fadcc4bb27caa5ca2e2d95b73c763d94dd7dc88c136ceba54315bd91b79fde5 | Python | 32,367 | 743 | from typing import Any, Dict, List
import hydra
import numpy as np
import omegaconf
import pandas as pd
import torch
import pytorch_lightning as pl
import torch.nn as nn
from pymatgen.core import Structure
from torch.nn import functional as F
from torch_scatter import scatter
from tqdm import tqdm
fro... |
d64b5a231cbedea72b16b9844c341490ab729dd3afe24c5ea614cd28ba84344a | Python | 32,468 | 792 | # Microscope profile settings
# Author: David Young, 2020
"""Profile settings for processing regions of interests.
These setting typically involve high-resolution such as microscopy images.
"""
from magmap.settings import config
from magmap.settings import profiles
from magmap.settings.profiles import RegKeys
class... |
e47f1d06112fb2bcdbcceadd2a455eab4d40ecc37fcb92bb34732680751f2d86 | Python | 32,480 | 602 | #!/usr/bin/env python
'''convert behavioral file into event lists and singletrial format
- regressor of interest per task
- duration of epoch
- rating onset
- potential covariates?
'''
# %%
import numpy as np
import pandas as pd
import os, glob, re, json
from os.path import join
from pathlib import Path
import argpar... |
0d8ffe92b4f434544124ff63f3e97d7e21271f2fdb77d1547324346e1ea8d9db | Python | 32,541 | 797 | import os, datetime, mne
import numpy as np
import scipy as sp
import pandas as pd
import nibabel as ni
from fooof import FOOOFGroup, sim
import matplotlib.pyplot as plt
from surfer import Brain
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from seaborn import despine
from scipy.stats import pearsonr, sp... |
3e256bdd2ce779f0651b9bdc85d837f5d579b12158737890fa75d528c23f711f | Python | 32,575 | 906 | """REST API manager for the ZnDraw client."""
from __future__ import annotations
import json
import logging
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Any
import httpx
import msgpack
from zndraw.exceptions import PROBLEM_TYPES, ProblemDetail, RoomLockedError, ZnDrawError
if TYPE_CHE... |
fb26019b46f794d70308faff5f77c9d991ae4cba2683995d9c3fa57bc00a5257 | Python | 32,752 | 919 | """
This module implements all the read modifications that cutadapt supports.
A modifier must be callable and typically implemented as a class with a
__call__ method.
"""
import re
import logging
from collections import defaultdict
from types import SimpleNamespace
from typing import Optional
from collections.abc impo... |
76f06d85cf30d4d940f702c863a2252c3a4b2fdca3f4772f97e51ec69208a774 | Python | 32,893 | 1,109 | # pylint: disable=invalid-name, too-many-lines
"""Utilities for data generation."""
import gc
import multiprocessing
import os
import string
import zipfile
from concurrent.futures import ThreadPoolExecutor
from dataclasses import dataclass
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Gen... |
7b26ca1dd0fa7a2b279bef0e127414fa75a9f3fbd4c913b110ce2fe467b01307 | Python | 32,910 | 950 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import inspect
import pprint
from abc import ABCMeta, abstractmethod
from typing import Any, Callable, List, Optional, TypeVar
import numpy as np
import torch
from .transform_util import to_float_tensor, to_numpy
__all__ = [
"BlendTransfor... |
8782cda9e6a4f2268e63ca7d3a2eb8441f88133aa48ab5e669a1abb1d7a1a825 | Python | 32,936 | 847 | '''create JSON/ACC files for Arbor from a set of BluePyOpt.ephys parameters'''
# pylint: disable=R0914
import io
import logging
import pathlib
from collections import ChainMap, namedtuple, OrderedDict
import re
import jinja2
import json
import shutil
from bluepyopt.ephys.acc import arbor
from bluepyopt.ephys.morpho... |
6ada4924bc587d65d7128d5309b3a471b881c797e492993abb15c0ae488cbb21 | Python | 32,968 | 884 | ## The following code contains work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105.
## Additionally, we waive copyright and related rights in the utilized code worldwide through the CC0 1.0 Universal public domain dedication.
import pprint
from copy import deepco... |
5c3c991f4de67fd34db5144d1a72ada196cb2b73cb0de2a0678304120a1dde27 | Python | 32,984 | 589 | import numpy as np
from grid_cell.util import select_arr_by_t, get_data_filename_by_keywords, reduce_true_elements, digitize_arr
from sklearn import random_projection
import grid_cell.tuning as gct
import matplotlib.pyplot as plt
from scipy.ndimage import gaussian_filter
from sklearn.decomposition import PCA
from scipy... |
02e14ef8181d5d15258a3f0359ed785b10050254f1314f35fc663405cf374a4a | Python | 33,026 | 952 | """create JSON/ACC files for Arbor from a set of BluePyOpt.ephys parameters"""
# pylint: disable=R0914
import io
import logging
import pathlib
from collections import ChainMap, namedtuple, OrderedDict
import re
import jinja2
import json
import shutil
from bluepyopt.ephys.acc import arbor
from bluepyopt.ephys.morpho... |
8d3c1b1191512774a749fe1f5fdbd97a71b4015a79203853d3e4181c2bb7207a | Python | 33,107 | 872 | import pandas as pd
import numpy as np
import os
from tqdm import tqdm
from scipy.stats import pearsonr
import matplotlib.pyplot as plt
import seaborn as sns
import sys
import warnings
import textwrap
from adjustText import adjust_text
GREY50 = "#7F7F7F"
GREY30 = "#4d4d4d"
# Loading data should have para for differen... |
a81f85678e5a362043b80c88c6870c00fb50191628a11f741861a835ad082ddd | Python | 33,159 | 719 | """
Author : Alexis Lebrun (PhD student)
School : Université Laval (Qc, Canada)
This module provides neural network model specifically designed for the
classification of vibrational spectra.
"""
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
import warnings
import tensorflow as tf
from tensorflow import keras
fro... |
5b95b8b1daca5f6f0bb947dafb76f2e3802e952e73b4cefde2e7c7e18bfa9254 | Python | 33,181 | 777 | """
Functions for UV melting analysis
"""
import numpy as np
import pandas as pd
from scipy import stats
import os, json
import matplotlib.pyplot as plt
from matplotlib.ticker import (MultipleLocator, FormatStrFormatter,
AutoMinorLocator)
from matplotlib.backends.backend_pdf imp... |
3581131292e694d188114716271134199ee6a75c87f56d4ce74e2df2b9c7278e | Python | 33,182 | 769 | # coding=utf-8
# Copyright 2022 IDEA-CCNL The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... |
eced0096259cd8cc3c4c538abf52bc2ceb6c161b46c2d162084135a522267a2a | Python | 33,190 | 896 | """
Routines for printing a report.
"""
from dataclasses import dataclass
from io import StringIO
import textwrap
from collections import defaultdict, Counter
from typing import Any, Optional
from collections.abc import Iterator, Mapping
from .adapters import (
EndStatistics,
AdapterStatistics,
FrontAdapte... |
7613acb9581d509b05ec9436af707181e5575da3345cbd02d064593690ce91e6 | Python | 33,254 | 751 | # -*- coding: utf-8 -*-
# Generated by Django 1.9.9 on 2016-08-17 19:09
from django.db import migrations
# Create view generating functions and a new version of the history table
# creation function, which implements history table initialization in a
# separate functions (which makes future changes easier). As part o... |
631415030187ae8572724e62850da51be6eba2ca41e9abad643d825e2acd9ef1 | Python | 33,266 | 599 | #!/usr/bin/env python2.7
import os, sys
os.environ["OMP_NUM_THREADS"] = "1"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["VECLIB_MAXIMUM_THREADS"] = "1"
os.environ["NUMEXPR_NUM_THREADS"] = "1"
import argparse
import shlex
import shutil
import glob
import re
import traceba... |
1ac7e5a26dc10995651f1c0078f8eaae6708aeecc05bce097670e459f61e4293 | Python | 33,315 | 636 | """
Custom object and error types.
Copyright (c) 2013 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
from operator import itemgetter
from numpy import dot, cross, array, einsum, stack, zeros
from numpy.linalg import norm, inv
import numpy as np
import scipy
class Coordinate:
""... |
7e631e5d319466f3b5001b4668c51f14f51c65c0786613d8c746be42b4401d86 | Python | 33,471 | 761 |
import os
import sys
import time
from pathlib import Path
from typing import Optional
import numpy as np
import torch
import mrcfile
import typer
from tqdm import tqdm
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter
# from torch_geometric.nn import knn_graph, radius_graph
fr... |
7de43dca4ef79b3817a453984dd9b471aee1235f445ce0ff9881cf24852c54af | Python | 33,478 | 751 | # 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... |
637d1ed2f5de1ff5b63c2753a2b892960030479064e0da678b39695fe1bbc973 | Python | 33,484 | 852 | import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import numpy as np
import pandas as pd
from rdkit import Chem
import torch
from torch.utils.data import IterableDataset
import dgl
import random
from dgl.dataloading import GraphDataLoader
from rdkit.Chem.BRICS import Fin... |
cfc0041f0c910fb67ff2902ac8a9795ba618d49651762e28b64c055943d7bb58 | Python | 33,501 | 764 | from PyQt5.QtWidgets import (QVBoxLayout, QHBoxLayout, QWidget, QAction, QStyle, QLabel, QComboBox,
QApplication, QTableWidgetItem, QTableWidget, QMenuBar, QLineEdit, QPushButton)
from PyQt5.QtGui import (QIntValidator, QDoubleValidator, QColor)
from PyQt5.QtWidgets import QFileDialog
impo... |
4d1fccf213e2323a2c7df5f51f90f8da6ea4adf840241fd9dae8495897d29177 | Python | 33,525 | 897 |
"""
Define the training pipeline
Do not import from `nnn` as those use a different environment
"""
import os
import torch
os.environ['TORCH'] = torch.__version__
import numpy as np
import pandas as pd
from scipy import stats
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
import seaborn a... |
1de6a7cd586a34b9e1fd2596c4dace4abadb3ea01fa51e72bcaeffc0c59ae432 | Python | 33,551 | 787 | # Code is adapted from the PyTorch pretrained BERT repo - See copyright & license below.
# Copyright 2018 The Google AI Language Team Authors and The HugginFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not ... |
880216880bea7a2d918a12f182d3da8be596b7111a68f942ed475c72a4adb760 | Python | 33,552 | 1,006 | # -*- coding: utf-8 -*-
from __future__ import division, print_function, absolute_import
import os
import random
import numpy as np
from PIL import Image
import pickle
import csv
import warnings
import tensorflow as tf
try: #py3
from urllib.parse import urlparse
from urllib import request
except: #py2
from... |
85db71eae5007ec812bb8778f71c5196f58204e4db688e60286fb34fdd9db58b | Python | 33,561 | 1,006 | # -*- coding: utf-8 -*-
from __future__ import division, print_function, absolute_import
import os
import random
import numpy as np
from PIL import Image
import pickle
import csv
import warnings
import tensorflow as tf
try: #py3
from urllib.parse import urlparse
from urllib import request
except: #py2
from... |
5d199d183f837331fe9d6627c3c36d492d8e4d063c689cdefe4c1730656dca7f | Python | 33,575 | 718 | """Contract tests for DoricRecordingExtractor."""
from pathlib import Path
import h5py
import numpy as np
import pytest
from guppy.extractors.doric_recording_extractor import DoricRecordingExtractor
from .recording_extractor_test_mixin import RecordingExtractorTestMixin
# ------------------------------------------... |
7e9bef7aca0ba4e0da1c65c62da8063dc799bfe5f6900ebaeb75f9307ec5f30c | Python | 33,649 | 984 | #!/usr/bin/env python
"""
Module for calculations related to grid manipulations.
This is temporary, functions should be organized in separate files.
"""
import numpy as np
import mrcfile as mrc
import torch
from typing import Tuple, Union, TypeVar, List
from scipy import interpolate
import matplotlib.pylab as plt
T... |
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