sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
534145d87b268ff15cdd052a14813aa0b74d43e0013a73ebd1e121b89e7e157d | Python | 5,380 | 155 | # 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
from dataclasses import dataclass, field
from typing import Dict, List
import torch
from fairseq import metrics, utils
from f... |
5238093623f72a4459aedb552873382bf7a4dbb96339f32ecca3aeb223655025 | Python | 5,384 | 151 | from typing import Sequence, Union
import torch
import torch.nn as nn
from monai.networks.blocks.convolutions import Convolution, ResidualUnit
from monai.networks.layers.factories import Act, Norm
from monai.networks.layers.simplelayers import SkipConnection
from monai.utils import alias, export
class UNet_double(nn... |
cef8f9a3c6a2d4b0aac357f190c3ec9bc075c17cd238fe1aa07332dc6220a4c2 | Python | 5,385 | 152 | from typing import Optional, List
import torch
from torch import Tensor
import torch.nn.functional as F
from torch.nn import (ModuleList, Linear, BatchNorm1d, Sequential, ReLU,
Identity)
from torch_sparse import SparseTensor
from ..models import ScalableGNN
from ..models.pna import PNAConv
cla... |
d35ec82b78b489443324379fe990513c1bf1d7ca61aff1832b1247a2bd3358a9 | Python | 5,386 | 164 | from pathlib import Path
# Method for starting up child processes. Valid values are "spawn" and "fork".
# See https://docs.python.org/3/library/multiprocessing.html#contexts-and-start-methods
process_start_method = "spawn"
# Logging level of process and main loggers.
log_level = "INFO"
# Max number of recent log lin... |
7559da245f696b21117782abf8ce0175cc1ba900e44899f679a47f55c7c7c341 | Python | 5,387 | 137 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
"""
Functions for loading models from checkpoint files.
"""
import torch
import hydra
import warnings
from nequip.model.utils import (
override_model_compile_mode,
_EAGER_MODEL_KEY,
)
from neq... |
74134ddaa4dd3e36cbea991da1a439088097b8a56e89dc15556207706ce4bdb3 | Python | 5,389 | 161 | """Utility functions."""
# Authors: Mainak Jas <mjas@mgh.harvard.edu>
# Sam Neymotin <samnemo@gmail.com>
# Christopher Bailey <cjb@cfin.au.dk>
import numpy as np
from .externals.mne import _validate_type
def _hammfilt(x, winsz):
"""Convolve with a hamming window.
Parameters
---------... |
8ee0d672fbde50a60aee7dfdde1fe277bdae4156720b91f94e809657705c2b39 | Python | 5,390 | 153 | """Build, validate, and reopen a local-only DANDI Dandiset."""
from __future__ import annotations
import logging
import re
from dataclasses import dataclass
from pathlib import Path
from typing import Sequence
from dandi.dandiset import Dandiset
from dandi.organize import FileOperationMode, OrganizeInvalid, organize... |
02253615d5d0f5d97cd0252c1e2a4087ef1a52595131d7c5b1993221da17485a | Python | 5,391 | 165 | """
Loss functions!
"""
from typing import Optional, Sequence, Tuple
import torch
from torch.nn import functional as F
from foldingdiff import utils
def radian_l1_loss(input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
"""
Computes the loss between input and target
>>> radian_l1_loss(torch.tens... |
837f41e14754b6fe3341b807e0416cff0ebfe263c9d53435935a43a8e0978318 | Python | 5,392 | 138 | import pytest
import pathlib
import subprocess
import numpy as np
import torch
from nequip.data import to_ase
from nequip.integrations.ase import NequIPCalculator
from ase.io import read
from conftest import _check_and_print
from hydra.utils import instantiate
@pytest.mark.parametrize(
"device", ["cpu"] + (["... |
9cbda2e81eaa4372c767c4ddc939b487acc773e7b2fa75ca52b537154601463b | Python | 5,392 | 167 | import random
import geomstats.backend as gs
from geomstats.test.data import TestData
from .base import VectorSpaceOpenSetTestData
from .lie_group import MatrixLieGroupTestData
from .matrices import MatricesMetricTestData
class GeneralLinearTestData(MatrixLieGroupTestData, VectorSpaceOpenSetTestData):
trials = ... |
5e8bb371cf4ad42787484ed1d9cfb6bf4d9c8d8c18c7873f0ba66e0353725364 | Python | 5,399 | 159 | from chromadb.api.types import (
Embeddings,
Documents,
EmbeddingFunction,
Space,
)
from typing import List, Dict, Any, Optional
import os
from chromadb.utils.embedding_functions.schemas import validate_config_schema
from typing import cast
import warnings
BASE_URL = "https://api.cloudflare.com/client/... |
88f3e05208a5393a86ab7611a6c1130874bb83cabc9809ee50aff1c75658827b | Python | 5,401 | 171 | """Generates preprocessed metadata (age and sex) from NSRR datasets.
It creates a csv file with columns subject_id, age and sex, one row per subject,
one file per dataset. This file allows analyzing the distribution of per-subject
sleep spindle features by sex and age.
"""
import os
import sys
from pprint import ppri... |
d1aa028a1abe9be92482fa56fc1ec2362513b93d21fd58137f51051fc6fcab33 | Python | 5,409 | 179 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import os
import json
import hashlib
import pathlib
import shutil
from datetime import datetime
from typing import Optional, Callable, Final
from nequip.utils.logger import RankedLogger
logger = Ranke... |
34db57b132f8aa66538336e54b72ee52c2e15a7434f6f9df0e9761ad5d08d2d8 | Python | 5,414 | 148 | from qtpy.QtCore import QPointF, Qt, Signal # type: ignore[reportPrivateImportUsage]
from qtpy.QtGui import QColor, QColorConstants
from qtpy.QtWidgets import QInputDialog, QVBoxLayout, QWidget
from idtrackerai.GUI_tools import (
AddBtn,
CanvasMouseEvent,
CanvasPainter,
CustomList,
LightPopUp,
... |
94bfd9953e5a672076b45a99458d98d9174547e5179c73066bb545e90b95cc3b | Python | 5,416 | 178 | from __future__ import annotations
import numpy as np
import scipy
import scipy.stats as stats
from neurodesign import msequence
def order(
nstim: int,
ntrials: int,
probabilities: list[float],
ordertype: str,
seed: int | None = 1234,
):
"""Generate an order of stimuli.
:param nstim: Th... |
fa5e1109ca80f40acee5f8c3ad7a140622398972de4cf68671febf076219c7be | Python | 5,416 | 155 | # Copyright (C) 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Docs configuration module."""
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/maste... |
175946a71e457bbec938a182353e05e317dc512279596c5a5a770714dce76cf2 | Python | 5,420 | 151 | from typing import Any, Callable, Dict, List, Optional, Sequence, Set
import numpy as np
import numpy.typing as npt
from chromadb.types import (
LogRecord,
VectorEmbeddingRecord,
VectorQuery,
VectorQueryResult,
)
from chromadb.utils import distance_functions
import logging
logger = logging.getLogger(_... |
45839394436e227fe35cebcb05221143fc69203f1a3bb825c4666143de4ec7de | Python | 5,423 | 141 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
pass
import numpy as np
import logging
from openfl.experimental.workflow.interface import FLSpec, Aggregator, Collaborator
from openfl.experimental.workflow.runtime import LocalRuntime
from openfl.experimental.workflow.placement import aggre... |
aa00b04da908e09a4670e82934709724294d886102f42082bc36bbb4476d907d | Python | 5,424 | 155 | """Tools to generate a Snakemake-based BIDS app.
This legacy module once had the core snakebids bidsapp implementation, but now is a
simple wrapper around :mod:`snakebids.bidsapp` with the
:class:`~snakebids.plugins.SnakemakeBidsApp` plugin. For new apps, this functionality
can be more flexibly implemented with:
.. c... |
89fb69cb3fd4219aa867787dc51fc788f293751638f9139542b6567065b7128a | Python | 5,425 | 143 | # Copyright (c) 2020 PaddlePaddle 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
#
# Un... |
069a39ff75ae718b41bbe003cf3ec10fa2a9472f824f6835f9350786b81d2ea3 | Python | 5,426 | 124 | """
This script takes in the sequence fasta files generated from Step2 and processes each sequence in each fasta file through the iupred tool. Note that the input files have to be of naming convention step2/[prot,peptide]_sequences.fasta, and that the results will be stored in the subfolder step3, in the current workin... |
e9bbd0b11f1cc460e62a469581431b9d092f051b6c06384ee8d2f8af497fc13f | Python | 5,426 | 130 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network models and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cognitive... |
a20ff8e30d30950398bbef42077025c5ae63bb162db33b575d910e0f7835a15a | Python | 5,429 | 154 | """Programmatic NaviDiv demo — no Streamlit required.
Loads sample_molecules.csv (bundled in this directory), runs all diversity
metrics, prints a summary table, and writes outputs to ./demo_output/.
Usage:
conda activate NaviDiv
python run_demo.py
Requirements: navidiv installed (pip install -e /path/to/Nav... |
df7dfdabb1df72cbf5a04e39bd76cc5c40e8410e132df177b3df9acd955fdb08 | Python | 5,429 | 145 | import torch
import torch.nn as nn
from .nnutils import create_var, index_select_ND
#from mpn import atom_features, bond_features, ATOM_FDIM, BOND_FDIM
import rdkit.Chem as Chem
ELEM_LIST = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na',
'Ca', 'Fe', 'Al', 'I', 'B', 'K', 'Se', 'Zn', 'H', 'Cu',... |
1b430c39fcdd413325dda18cd383143dc450053354e1f280a5b9c0eae3b9d10d | Python | 5,430 | 150 | # Method signatures differ between Qt bindings, so overrides can't match them all
# pyright: reportIncompatibleMethodOverride=false
import logging
from collections.abc import Sequence
from qtpy.QtCore import Signal # type: ignore[reportPrivateImportUsage]
from qtpy.QtCore import Qt
from qtpy.QtGui import QWheelEvent
... |
0a2ee598da39aeaae676c4548242608f5cd8a137a83ce52e0d79a94420074d25 | Python | 5,431 | 174 | from uuid import uuid4
import pytest
from chromadb.api import ClientAPI
from chromadb.errors import ConditionalWriteConflictError
from chromadb.test.conftest import reset, skip_if_not_cluster
EMBEDDING = [1.0, 2.0, 3.0]
def _collection(client: ClientAPI, name: str = "conditional_txn"):
reset(client)
retur... |
9b88a7aeab335ec90676ae4538cd9e18a380abfcc890465c4f38101b5def07b6 | Python | 5,433 | 152 | """Tests for nltools.algorithms.neighborhoods module."""
import numpy as np
import nibabel as nib
import pytest
from scipy import sparse
from nltools.algorithms.neighborhoods import (
_SphereNeighborhoods,
compute_searchlight_neighborhoods,
)
# ===============================================================... |
0801504e3c35b6da3cb0f6c79c343643db41cafd665da23296636ef14137d937 | Python | 5,434 | 177 | import logging
import os
import shutil
from collections import OrderedDict
import torch
from torch import distributed as dist
from torch import nn
from torch.nn import functional as F
from sklearn.metrics import confusion_matrix
import numpy as np
logger = logging.getLogger(__name__)
def reduce_tensor(tensor, n):
... |
b5515fb918985457a2469508a8667bb87063675e59b07827566dd6cf63116bad | Python | 5,435 | 100 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network model_templates and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cogn... |
11d82a23151d952e4fc596d634428504aaeb62adf71c46a12d47cf5c23c72b76 | Python | 5,437 | 188 | from __future__ import print_function, division
"""
Brain-Glass Interface
Controls the visual feedback on Google Glass.
When connected with USB cable, connect to the local loopback network (127.0.0.1).
adb executable must be in the system's PATH environment variable.
Kyuhwa Lee, 2018
Swiss Federal Institute of Tech... |
81c34c160dfb2fe3d6a836c43152043dc51276bd16257b0942fe8816c125d04c | Python | 5,444 | 148 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
6d38021672c2e2693cb657020e5e9b184e1885ea0d180d908384b6d682b8871e | Python | 5,445 | 190 | #!/usr/bin/env python3
import argparse
import matplotlib.pyplot as plt
import numpy as np
import odil
from odil import plotutil, printlog
"""
Infers unknown constant parameters of an advection-diffusion equation
from the solution at the initial and final time.
"""
def get_ref_u(t, x, args):
"""
Returns an... |
1e0668379ba0a8a55da50c5ad3dc5ab85354e75e44abff4745c795d4b1a79e14 | Python | 5,446 | 135 | """Contract tier: the ML-IAP energy/force writeback, on both couplings.
LAMMPS ships two ML-IAP Python couplings with *different* writeback APIs, and
the difference is invisible until the model has already run:
* ``src/KOKKOS/mliap_unified_couple_kokkos.pyx`` — ``eatoms`` has a getter
(a view sized by ``nlistatoms`... |
04eba62ef527c85d1c998badb0360269aa0ea9a06a4251a1b19e825f2e6e6dbd | Python | 5,452 | 166 | import pytest
import geomstats.backend as gs
from geomstats.test.random import RandomDataGenerator
from geomstats.test.test_case import TestCase
from geomstats.test.vectorization import generate_vectorization_data
class _ManifoldTestCaseMixins:
# TODO: check default_coords_type correcteness if intrinsic by compa... |
c334a5a50c978410997d14f60061d9efc5aae9296400dbbddc2f6c05dc0f953d | Python | 5,456 | 128 | """The antigen nomenclature patch.
`curate/patch.py` was 45 % covered. Three of its behaviours were each chosen to reproduce a
measured legacy result, and none of them had a test: `NA` is a gene symbol rather than a missing
value, duplicate epitopes resolve to the last entry, and an empty patch cell falls back to the
... |
61055f7224af0adea9400500dc52a0582c91692bffb2d75807d44527bde40d61 | Python | 5,457 | 148 | # -*- coding: utf-8 -*-
# ----------------------------------------------------------------------------------------------------------------------------------
# Функция для вычисления Most Similar Words
#
# Парметры:
# tmlda_filename: файл в формате TMLDA, из словаря которого берутся слова для поиска ближайших
... |
36ef5f3b0dbeb67e1c3c7100980bc5a71df8cf637b6b48b5f42be78910b88120 | Python | 5,461 | 169 | #Translates DNA sequences in all 6 reading frames, ignoring start / stop codons.
from Bio import SeqIO
from Bio.Seq import Seq
from Bio import AlignIO
import sys
import tempfile
import subprocess
from collections import Counter
from scipy.spatial import distance
import numpy as np
import os
def translate_6frames(inpu... |
71765c6fa45926b540d3ebd7957862165c79b78f70c50dba9c62b663ced463aa | Python | 5,461 | 188 | import numpy as np
import scipy.signal as sig
import scipy.stats as stats
from scipy.stats import median_absolute_deviation as mad
import pickle
from pyimzml.ImzMLWriter import ImzMLWriter
from pyImagingMSpec.inMemoryIMS import inMemoryIMS
from scipy.io import loadmat
import random
from tqdm import tqdm
from ... |
679ca1ccfc464fb2914b09d9f7802d06fce553d53d21cc6e36377346f0139e9f | Python | 5,462 | 138 | import gc
import logging
from itertools import pairwise
from pprint import pformat
import numpy as np
from idtrackerai import ListOfBlobs, ListOfFragments, ListOfGlobalFragments, Session
from idtrackerai.base.network import IdentifierBase
from idtrackerai.utils import track
def tracker_API(
session: Session,
... |
4f42f6cc4977ff9e4eeed622253630f739206b5babd7d767757e070b971c18a8 | Python | 5,464 | 163 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Common functions for gRPC transport."""
import logging
import threading
from concurrent.futures import ThreadPoolExecutor
import grpc
from openfl.protocols import aggregator_pb2
logger = logging.getLogger(__name__)
MAX_METADATA_SIZE_... |
563cd382c63746016c37926f1cfdbcb52ee7c6b97f7f891deb87b235e774f65e | Python | 5,465 | 147 | import pydicom as dicomio
import SimpleITK as sitk
import glob
import xml.etree.ElementTree as ET
import platform
import numpy as np
import nibabel
directory_split = "\\" if platform.system() == "Windows" else "/"
def get_length(number_of_slices, thickness):
return (number_of_slices * thickness) / 10
def convert... |
6dc5e18728d430616feb494fd4f59b6cb728557a3c35cf9dfcac2e2700cfa26f | Python | 5,468 | 151 | '''
Utilities to perform the creation of JSON files starting from the xml files.
'''
import json
import xml.etree.ElementTree as ET
import argparse
import os
parser = argparse.ArgumentParser()
parser.add_argument("voc07_path", help="Path to VOC2007 folder", type=str)
parser.add_argument("voc12_path", help="Path to VOC... |
1041700ea68593789e3e276ed01d888e18936be9f78839783c4e89964af92f3c | Python | 5,469 | 101 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 6/12/23 11:29 AM
# @Author : zhangchao
# @File : demo.py
# @Email : zhangchao5@genomics.cn
import os
import sys
import warnings
import argparse
from typing import Union
from spatialign import Spatialign
sys.path.append(os.getcwd())
warnings.filterwarnin... |
534775572864c65830e6c7086fdc5657247e70864c0e0b0cdbdc0de97e6bd48f | Python | 5,472 | 143 | """Exercise the real checkpoint downloader with offline HTTP responses."""
import io
from email.message import Message
from pathlib import Path
from unittest.mock import Mock
import pytest
from mace.calculators import foundations_models as fm
class Response(io.BytesIO):
"""Minimal context-managed HTTP response... |
e4890fb93ce399e79c14c30e7c27f43e30c101222cf9ce6b098dd01f046b2986 | Python | 5,472 | 181 | #! /usr/bin/env python
import platform
from pathlib import Path
import os
import subprocess
import shutil
from setuptools import setup, find_packages, Command
from setuptools.command.build_py import build_py
descr = """Code for biophysical simulation of a cortical column using Neuron"""
DISTNAME = "hnn-core"
DESCRIP... |
63c5376a484396576b6ea53b992bd014db20e483dc5fc03c8185c08ac1f32ae2 | Python | 5,473 | 108 | # Copyright 2020 Forschungszentrum Jülich GmbH and Aix-Marseille Université
# "Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements; and to You under the Apache License, Version 2.0. "
from mpi4py import MPI
import os
import json
from nest_elephant_tvb.utils import create_... |
3521e57c08e5777dfb6579aa201c36c3637d7c32b00d26e1e146f1b67bb38184 | Python | 5,474 | 169 | #!/usr/bin/env python
from hnn_core import (
MPIBackend,
duecker_ET_model,
simulate_dipole,
)
from hnn_core.hnn_io import (
write_network_configuration,
)
def create_duecker_model_with_drives():
"""Create a Duecker ET model network model including 3 evoked drives.
Builds the Duecker ET netwo... |
8055f060a2ea4f2a2d6e1cdbfa0adfaefea242e817925861611a9a9670e330e6 | Python | 5,474 | 147 | import paddle
import paddle.nn.functional as F
from ppdet.modeling.losses.clrnet_line_iou_loss import line_iou
def distance_cost(predictions, targets, img_w):
"""
repeat predictions and targets to generate all combinations
use the abs distance as the new distance cost
"""
num_priors = predictions.... |
28e2f95f8c0b0e1b37c4dfc42dd7018a7835d6d0e1e570bb408998718e9435f2 | Python | 5,476 | 169 | from PyQt5.QtWidgets import QMainWindow, QAction, QShortcut
from PyQt5.QtGui import QKeySequence
from PyQt5.QtWidgets import QStackedWidget
from PyQt5.QtGui import QIcon
from sleepy.gui.tagging.view import NullView, TaggingView
from sleepy.gui.tagging.control import TaggingControl
from sleepy.gui.processing.core ... |
c40f7305d04cb09b6a27990f99c0bc14548afd43e64113081879cd7609ed0693 | Python | 5,476 | 172 | """
Shared pytest fixtures for nltools test suite.
This module provides common fixtures used across test modules.
# Brain Data Fixtures Guide
# =========================
#
# Choose the right fixture for your test:
#
# | Fixture | Voxels | Samples | Use Case |
# |----------------... |
6d46e0ecb1d6db148fa5037ffda06104f84090543dd5d875bbaa731f65c186de | Python | 5,477 | 101 | import numpy as np
from scipy import sparse
import time
from suns.PostProcessing.evaluate import GetPerformance_Jaccard_2
def refine_seperate(masks_final_2, times_final, cons=1, thresh_mask=0.5, ThreshJ=0.5):
'''Refine segmented neurons by requiring them to be active for "cons" consecutive frames.
The ou... |
357919d2a7c093bd56df0f9102d6310206920226224ad706e0a493def5fa609b | Python | 5,478 | 165 | """
Auditory Steady State Response Stimuli
@author: Mathieu Scheltienne
"""
import numpy as np
from ._sound import _Sound
from ... import logger
class ASSR(_Sound):
"""
Auditory Steady State Response Stimuli.
Composed of a carrier frequency 'fc' which is amplitude modulated at 'fm'.
By default, a ... |
54d0494ecc56c3f1726e0dfd4686aaa177979ca0c633ccd3ef20c2d294ac4583 | Python | 5,479 | 177 | from collections import Counter
from pathlib import Path
import click
import pydicom
def print_stats(counter: Counter) -> None:
for key, value in counter.items():
print(f"\t\t{key} - {value}")
@click.command()
@click.option(
"-d",
"--dicom-dir",
type=click.Path(exists=True, readable=True, p... |
a1982d1c26f36e217589ab44bc02c06b3ea1e4bd6f625294ef77b1d50ce2e7d9 | Python | 5,483 | 131 | # -*- coding: utf-8 -*-
#
#
# PyRates software framework for flexible implementation of neural
# network models and simulations. See also:
# https://github.com/pyrates-neuroscience/PyRates
#
# Copyright (C) 2017-2018 the original authors (Richard Gast and
# Daniel Rose), the Max-Planck-Institute for Human Cognitive... |
0e4121960a1c60603505122886b7f81b83b497d69880d0a4d026c8fc5091dd45 | Python | 5,485 | 160 | import types
import pytest
import torch
from e3nn import o3
from mace.calculators.lammps_mliap_mace import LAMMPS_MLIAP_MACE
from mace.modules import blocks
from mace.modules.blocks import (
RealAgnosticDensityResidualInteractionBlock,
RealAgnosticResidualNonLinearInteractionBlock,
)
from tests.integrations.l... |
8f47c818cc803397f27221abf52b3fe173ee92cb5dcae745499951059ca800e4 | Python | 5,487 | 162 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: malfatti
@date: 2019-07-27
Loads data recorded by Open Ephys in Binary format as numpy memmap.
DatLoad(Folder, Processor=None, Experiment=None, Recording=None, Unit='uV', ChannelMap=[])
Parameters
Folder: str
Folder containing at least the s... |
dacf03e1c2d7afa429fa074e59b12bf44445e99bd211f11256225af813360220 | Python | 5,488 | 191 | """Exponential barycenter.
Lead author: Nicolas Guigui.
"""
import logging
import geomstats.backend as gs
from geomstats.geometry.euclidean import Euclidean
from geomstats.geometry.lie_group import LieGroup, MatrixLieGroup
from geomstats.learning.frechet_mean import (
BaseGradientDescent,
LinearMean,
_Ba... |
05d23960667994bde0cbcb3f4bf8a4a413887147ad536ea24eab88ffaf182ab8 | Python | 5,492 | 156 |
# This document contains functions used to analyze time series of vasomotion
# Input data is time series data from 2p imaging. Images are first processed in FIJI to create csv files of diameter changes over time
# Output is values from the provided functions that can be used to examine metrics of vasomotion time s... |
c1fd59909dda59b43cfdc1a353f3b6417eeeb21609692828e4cc8885db40ad8c | Python | 5,493 | 142 | """
Analysis of Delayed Differential Equations
==========================================
In this tutorial, you will learn how to implement and solve delayed differential equation (DDE) systems via PyRates.
DDEs take the general form
.. math::
\\dot{\\mathbf{y}} = \\mathbf{f}(\\mathbf{y}, t, \\mathbf{y_{\tau}})
... |
72b537736302b1a2549c3fb6407f2d5103e9ed17e07c4b3fc9f7c7f0ae329f73 | Python | 5,494 | 211 | import numpy as np
from numba import njit
import pandas as pd
@njit
def _computeDistance(p1, p2, dxy=0.1, dz=0.5):
"""compute euclidean distance of two points in space. Points are in (Z, Y, X) format"""
di_z = (p1[0] * dz - p2[0] * dz) ** 2
di_y = (p1[1] * dxy - p2[1] * dxy) ** 2
di_x = (p1[2] * dxy - ... |
a3836c956d46530349c8f866505e49588fd88a529da17281923f584911c87f00 | Python | 5,494 | 154 | """mass_ss.py: Defines the MASS class that manipulates the MASS database."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
from sleeprnn.data.dataset import Dataset
from sleeprnn.data.dataset import KEY_EEG, KEY_MARKS, KEY_N2_PAGES, KE... |
5a1f895eb75f84038acf0128d49c528284f2317c7d4c8784662e41a65471cd96 | Python | 5,497 | 160 | """
Create BANKSY Matrix from annadata
Yifei May 2023
"""
import os
import numpy as np
import matplotlib.pyplot as plt
import scipy.sparse as sparse
from scipy.sparse import csr_matrix, issparse
import anndata
import gc
from datetime import datetime
from banksy.main import concatenate_all
def create_banksy(adata: a... |
0f51f59e940352355c07e3407c5adea698039e0ecf0d74678aa0e85f2b3b283d | Python | 5,498 | 193 | # ==============================================================================
# Copyright 2025 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
import jax.numpy... |
9f374fed7d187743294fc355893ab677dd38d8a5b6db6cb569727e5cd740bc97 | Python | 5,499 | 162 | from sleepy.processing.processor import Algorithm
from sleepy.processing.parameter import Parameter
from .Classifier import classifierTSI
from .Tree import Tree
import numpy as np
import csv
from .utils import sfd, flatten
import dill
import multiprocessing
from multiprocessing import Semaphore
from .Simulation import ... |
a099fae7f2fbe61693726ef96b89a1cd897ad0c5baa5f801030523d5fe8877ce | Python | 5,501 | 170 | import os
import click
from corgie.log import logger as corgie_logger
from corgie.boundingcube import get_bcube_from_coords
from corgie.cli.compute_stats import ComputeStatsJob
from corgie.argparsers import (
LAYER_HELP_STR,
corgie_optgroup,
corgie_option,
create_stack_from_spec,
)
from corgie.cli.norm... |
3f1aad85853a304e099d8e6cdeddaf0f8c9582d1042c3020ad0004a0d8cc54f1 | Python | 5,503 | 171 | import gc
import torch
import torch.nn as nn
import torch.nn.functional as F
crossentropyloss = nn.CrossEntropyLoss()
# the reconstruction function: mse, mse, bce
def reconstruction_loss_BCE(X, A_norm, X_hat, Z_hat, A_hat):
"""
reconstruction loss L_{rec}
Args:
X: the origin featur... |
8a854d321e67dccbabc25e92de0dfb6af8194a4fb3a04b1f1894ec1270e224b6 | Python | 5,505 | 162 | import matplotlib.pyplot as plt
import numpy as np
import csv
ekw = dict(ecolor=(0, 0, 0, 1.0), lw=1, capsize=3, capthick=1)
color1 = (0, 176/255, 80/255, 1)
color2 = (1/255, 127/255, 157/255, 1)
color3 = (120/255,110/255,120/255,1)#(117/255,117/255,117/255,1)#(253/255, 97/255, 0, 1)
#color11 = (0, 176/255, 80/255, ... |
6ff8daf1ef03393ab189d4d2197dded64eab78fc5d55e44fb40fc821999f795a | Python | 5,508 | 113 | """The proteome authority for `antigen.gene` (#632): the table's shape, and what it must not claim."""
from __future__ import annotations
from pathlib import Path
import polars as pl
import pytest
from vdjdb.curate import antigens as A
TABLE = Path("proofreading/epitope_proteome.tsv")
@pytest.fixture(scope="modul... |
ccfaf6d97fea7bf59b054f6225ebabbfe13ccb2d0eb2ccd5bdedb3168f3fefab | Python | 5,512 | 151 | """Copying that leaves the clone owning its own buffers.
A data class holds polars frames whose storage may be a view onto a NumPy
array the user still holds, and frames whose `pl.Object` cells are Python
objects shared with the original. Copying either naively hands the clone a
buffer or a cell somebody else can muta... |
7bae53ce8d71fedc9d500895d2758ae96a5ed2619c205eac32465cd6a624cf43 | Python | 5,514 | 182 | import pickle
import os
import random
import torch
import numpy as np
from torch.utils.data import Dataset, DataLoader
from .mol_tree import MolTree
from .jtnn_enc import JTNNEncoder
from .mpn import MPN
from .jtmpn import JTMPN
from .vocab import Vocab
class PairTreeFolder(object):
def __init__(self, data_fold... |
84e4a3fc65ce74bae401763b8e7a83aa57bf0bb4db3e87209a90cd5bcfe07694 | Python | 5,515 | 93 | """Distinct-junction overlap screens for tracing experimental provenance."""
from __future__ import annotations
import polars as pl
STRATUM = ["species", "antigen.epitope", "mhc.a", "mhc.b", "mhc.class"]
GROUP = ["chunk.file", "reference.id"]
MIN_SHARED = 5
MIN_CONTAINMENT = 0.20
def overlaps(records: pl.DataFrame,... |
80f30e028b812ce15c4644ca48d1d7f605e5ab564f288409a636d0160b36bbbb | Python | 5,517 | 141 | import numpy as np
from scipy.stats import pearsonr
from numpy.testing import assert_warns, assert_raises, assert_array_almost_equal, assert_allclose
try:
from gemmr.estimators import SparsePLS
from gemmr.estimators.r_estimators import _check_penalty, _check_penalty_cv, _fit_and_score_spls, \
_select_... |
61fef6104617ba5d26fe5c90b356baeb2bbce83de11904514812e6b0b9d72869 | Python | 5,522 | 219 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from brian2 import *
from scipy import optimize
import re # regular expressions
# Initialization
areas = ['EC', 'DG', 'CA1', 'CA3']
types1 = ['exc', 'inh']
types2 = ['E', 'I']
scale_aussel = 150*umetre
# ==============
# Optimization
# ==============
def parse_coords(fn... |
0a3d00c09e062be66c61f6d7d3b9d07dfef3562404b5edbd8aa4c39e329f808d | Python | 5,524 | 183 | """
Implementation of dFC methods.
Created on Jun 29 2023
@author: Mohammad Torabi
"""
import time
import numpy as np
from ksvd import ApproximateKSVD
from sklearn.linear_model import orthogonal_mp_gram
from ..dfc import DFC
from ..time_series import TIME_SERIES
from .base_dfc_method import BaseDFCMethod
#########... |
9e9c476f349d74d1f021e0014dbcb1977284c48e7dad57692dcdc28feceb1fc2 | Python | 5,524 | 139 | """experiment for the ADT Network."""
import glob
import json
import logging
import os
# set gpu private
os.environ['TF_GPU_THREAD_MODE'] = 'gpu_private'
import tensorflow as tf
import numpy as np
import sys
# add base path to sys
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..'))
from task2_regres... |
95823a44e6656e885d97b8d8e7743db2cff47df117fa0d53440bfdeb5e0547f9 | Python | 5,527 | 187 | # -*- coding: utf-8 -*-
import random
import os
#import sys
#import collections
#import gc
import numpy as np
import tensorflow as tf
from sklearn.model_selection import KFold
#from sklearn.utils import shuffle
#from JSLog import JSLog
#from JSData import JSData
#from JSModels import JSModel_MH_DSCNet
#from JSExpe... |
904c7331364164d80ca90f207491fdfa9f95e614af4e3ddf8789d6bb21ce436b | Python | 5,530 | 139 | from typing import Optional
import config
import pandas as pd
explicit_folder_coding = {
'184_styleGAN2_Gamma2_013000kimg': 'StyleGAN 2 & $\\gamma$: 2',
'184_styleGAN2_Gamma5_020000kimg': 'StyleGAN 2 & $\\gamma$: 5',
'184_styleGAN2_Gamma8_025000kimg': 'StyleGAN 2 & $\\gamma$: 8',
'184_styleGAN3_Gamma2... |
f76d5d6bb6bfa6d4baab9eab252364b26d97801137637f9075ce504987cddf36 | Python | 5,530 | 147 | import logging
from idtrackerai import IdtrackeraiError, ListOfBlobs, Session
from idtrackerai.utils import create_dir, remove_dir
from .segmentation import compute_background, load_custom_background, segment
def animals_detection_API(session: Session) -> ListOfBlobs:
"""Segments the video and returns the detec... |
cb6f5022c1896063b269b3847d308bc1668c3c5b8cc2aacdbf59c6aa51e812b6 | Python | 5,533 | 167 | # Copyright (C) 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""You may copy this file as the starting point of your own model."""
from logging import getLogger
import numpy as np
from torchvision import datasets, transforms
from openfl.federated import PyTorchDataLoader
logger = getLogger(__n... |
5f2598f28ffb532a540dfc96362f7dfbf7a2be52afddf92d2196179c16d3b5b1 | Python | 5,534 | 218 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from brian2 import *
from scipy import optimize
import re # regular expressions
# Initialization
areas = ['EC', 'DG', 'CA1', 'CA3']
types1 = ['exc', 'inh']
types2 = ['E', 'I']
scale_aussel = 150*umetre
# ==============
# Optimization
# ==============
def parse_coords(fn... |
e124d8bb416be75b322429e64882990f3e8138a57b2b93139ff8bf1fd499e15e | Python | 5,535 | 155 | import numpy as np
import torch
from torch_geometric.nn import to_hetero, SAGEConv, GraphConv, TransformerConv, GATConv
from torch.nn import Linear, Dropout, ReLU, Tanh
import random
class GrigSearchGNNEncoder(torch.nn.Module):
def __init__(self, hidden_channels, out_channels, nb_hidden_layer=2, layer_type='s... |
5e24fc41109a3b1c08648e1f5ad613dd5d181d5730e0a985a1d0f3ed99580e88 | Python | 5,536 | 207 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 27.08.2021
# Author: Moritz Smolka
# Maintainer: Hermann Romanek
# Contact: sniffles@romanek.at
#
import bisect
import re
import statistics
import sys
import time
from typing import TYPE_CHEC... |
6ad845dfdd829583db5ef90d1baef00bca6f9ae5e0a2bc345eba9e6f0a93e18a | Python | 5,536 | 139 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from nequip.model.utils import _EAGER_MODEL_KEY
from nequip.train.lightning import _SOLE_MODEL_KEY
from nequip.nn import graph_model
from nequip.data._nl import DEFAULT_NEIGHBORLIST_BACKEN... |
0fdc817e35038306d0a6a25a0036c123bac88743d94823b655bacacefb0e009e | Python | 5,539 | 149 | # Copyright (c) 2022 PaddlePaddle 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 ... |
70c1b9fd8f827374b97ca55bdacd883fa46fd06af0b3a93ac87fd519a7508cdf | Python | 5,540 | 150 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from torch import nn
from typing import Optional
from utils import logger
from ..layers import LinearLayer, GroupLinear, norm_layers_tuple
supported_conv_inits = [
"kaiming_normal",
"kaiming_uniform",
... |
6391d92e574e58b995eab5f0a61d148cb1bce0ad9109c015d75c0ba5dc8d9811 | Python | 5,541 | 163 | """Transformer for manifold-valued data.
Lead author: Nicolas Guigui.
"""
from sklearn.base import BaseEstimator, TransformerMixin
import geomstats.backend as gs
from geomstats.geometry.matrices import Matrices
from geomstats.geometry.skew_symmetric_matrices import SkewSymmetricMatrices
from geomstats.geometry.symme... |
ba159f58931f06ee1bf4e70ca3f00e5e92e9a536453a9c89e2d723924b5136e9 | Python | 5,544 | 124 | import os.path as osp
import numpy as np
from tqdm import tqdm
import torch
from sklearn.utils import shuffle
from torch_geometric.data import InMemoryDataset, download_url
from torch_geometric.data import Data, DataLoader
class MD17(InMemoryDataset):
r"""
A `Pytorch Geometric <https://pytorch-geometric.... |
bc4fad5a0af81befa87d076a240cea2458e30c294730eccba5d2eb0aba63aa4b | Python | 5,544 | 159 | import vimba
from video_stream import ImageSource
import time
import numpy as np
FRAME_QUEUE_SIZE = 10
class AlliedVisionImageSource(ImageSource):
default_params = {
**ImageSource.default_params,
"exposure": 8000,
"trigger": True,
"frame_rate": None,
"cam_id": None,
... |
ada4d4f6ce98a5a0cf63610d1ea0ef1723b0f908af21a936b2eb6c2b4bb7da68 | Python | 5,547 | 138 | #!/usr/bin/env python3
"""Enforce the v0.6.0 keyword-only ``*`` marker convention (CLAUDE.md).
The convention: a keyword-only ``*`` marker is required after the primary data
argument in ``__init__`` and in any public method/function with 3+ kwargs.
This is a *structural-absence* check (the ``*`` is missing) which semg... |
5d7c91422e3aa22d0bbd120a78e97b614e2ecda1a7a7e562f3f7b46daea5aae1 | Python | 5,550 | 160 | from typing import Sequence, Union
import torch
import torch.nn as nn
from monai.networks.blocks.convolutions import Convolution, ResidualUnit
from monai.networks.layers.factories import Act, Norm
from monai.networks.layers.simplelayers import SkipConnection
from monai.utils import alias, export
class UNet_single(nn... |
b5d6e58175c203aa1a50ff9d115b894f1f7de268ad52d8bd27dcaacef0afc04b | Python | 5,551 | 137 | import pickle
import numpy as np
from aux_fun import remove_SPH ,construct_target_A, performance
from regularization import get_firing_power, alarm_generation, alarm_processing
from evaluation import alarm_evaluation, sensitivity, FPR_h, statistical_validation
import os
def main_testA(patient, approach, data_li... |
2e44bd2c95005ec5d52a9ce44203099c7e8e8496a9d61ce48482126eff01689e | Python | 5,555 | 119 | import sys
import os
import re
import numpy as np
import subprocess
import math
import scipy
import silhouetteRank.spatial_genes as spatial_genes
from shutil import copyfile
from operator import itemgetter
from scipy.spatial.distance import squareform, pdist
from scipy.stats import percentileofscore
from sklearn.metric... |
e67aeac4d125f8759c352a673d658c4464f20418c4598f401558ffcf30654e91 | Python | 5,556 | 178 | from __future__ import annotations
from collections import Counter
from typing import Any, Dict, Iterable, List, Optional, TypedDict
from chromadb.api.types import Documents, SparseEmbeddingFunction, SparseVectors
from chromadb.base_types import SparseVector
from chromadb.utils.embedding_functions.schemas import vali... |
3a950d926b909c7404639e8b0b237434c2deb33eb527199b028e9fe3017430df | Python | 5,557 | 174 | """Create a model adapter from a Torch pickle file"""
__all__ = ["create_adapter"]
import os
import time
import uuid
import pathlib
import pprint
import logging
import torch
from reinvent import models
from reinvent.utils import prior_registry
from reinvent.models import meta_data
logger = logging.getLogger(__name... |
243793ed5e86beab02170eafe29d7e5fc83d42b279a060c635261209a5d06ff9 | Python | 5,558 | 150 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
78e5ad257a8832bd0161ca572320681f688d96e2b7a30a485e091badcadb02d3 | Python | 5,558 | 181 | # ==============================================================================
# Copyright 2023 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
import jax.numpy... |
87b03f2401184e738271a03956ec42c70307c421929cab46b648cc1662ef2073 | Python | 5,560 | 168 | import numpy as np
from sklearn.metrics import matthews_corrcoef, confusion_matrix, roc_curve, auc, precision_recall_curve
import prettytable as pt
import torch
def eval_metrics(probs, targets,cal_AUC=True):
threshold_list = []
for i in range(1, 50):
threshold_list.append(i / 50.0)
if cal_AUC:
... |
b34eda7b7961886e8852f9edd1438d7f93620ab597aca4957a519515364bdd25 | Python | 5,560 | 149 | import torch
import torch.nn as nn
import torch.nn.functional as F
import rdkit.Chem as Chem
from .nnutils import create_var, index_select_ND
ELEM_LIST = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na',
'Ca', 'Fe', 'Al', 'I', 'B', 'K', 'Se', 'Zn', 'H', 'Cu', 'Mn', 'unknown']
ATOM_FDIM = len(... |
605104f11437b2ff95a93f1b52288c2f396734566d1726948e25b05dd67a38fa | Python | 5,562 | 135 | """
The GOOD-CMNIST dataset following `IRM
<https://arxiv.org/abs/1907.02893>`_ paper.
"""
import os
import os.path as osp
import gdown
import torch
from munch import Munch
from torch_geometric.data import InMemoryDataset, extract_zip
class GOODCMNIST(InMemoryDataset):
r"""
The GOOD-CMNIST dataset following ... |
ea70a47c387b23b3dc4845dcec47713091300e48fe6c2b32063c29fe39c5029a | Python | 5,563 | 185 | import os
import sys
import copy
import random
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import matplotlib.pyplot as plt
import seaborn as sns
import utils as u
import analysis_utils as au
from ray.tune import Trainable
l... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.