sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a1f63a59c7e4725954d50a099b276ba3c8aaa09a96a93ce981a6dafdd547c6cf | Python | 10,118 | 352 | '''Tests for functions in io_utils.py.
'''
import os
import io
import pytest
from contextlib import contextmanager
from keras.models import Sequential
from keras.layers import Dense
from keras.utils.io_utils import HDF5Matrix
from keras.utils.io_utils import H5Dict
from keras.utils.io_utils import ask_to_proceed_with... |
c73ba24daf46479d9c781084384076f2e31c8c5300acb905dfd92d0333a1afb7 | Python | 10,118 | 329 | """
Mechanism classes
Theses classes represent mechanisms in the model
"""
"""
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... |
d33b7604de8732be7fc0fcc718ce16aad85863a414681ef7b467ad252730d901 | Python | 10,118 | 287 | import statsmodels.nonparametric.kernel_regression
from KDEpy import FFTKDE
from multiprocessing import Pool, Manager, get_context
from scipy import stats
import numpy as np
import os
import pandas as pd
import statsmodels.discrete.discrete_model
from anndata import AnnData
import scipy as sp
_EPS = np.finfo(float).ep... |
7e4fd27e93546ac5a7e70dd419b852a1167370b8948abfe2c0fb343b53452b36 | Python | 10,119 | 171 | # 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... |
80cb323a79be304c55b1868a1227b5ff8d584cfaef4c23cbbc71a4d3db7df421 | Python | 10,119 | 279 | # tests/test_router_jobs.py
"""Tests for job registration endpoint using shared fixtures from conftest.py."""
from uuid import UUID
from conftest import make_room_address
from zndraw_joblib.exceptions import ProblemDetail
from zndraw_joblib.schemas import JobResponse, JobSummary, PaginatedResponse
def test_registe... |
bb0d8776917ef0ec3d0d2534a6416fc2e903ebfd39c65646bff11b85bf03e5d5 | Python | 10,121 | 398 | import os
from medperf.exceptions import InvalidArgumentError
import pytest
import logging
from pathlib import Path
from unittest.mock import mock_open, call, ANY
from medperf import utils
import medperf.config as config
from medperf.tests.mocks import MockTar
patch_utils = "medperf.utils.{}"
def init_mock_isdir(ex... |
4679a53272af0deb117e764d9d26ee4c4b5d5de80b74982d815cc84e1e83d130 | Python | 10,133 | 232 | # -*- coding: utf-8 -*-
"""Normalization layers.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from ..engine.base_layer import Layer, InputSpec
from .. import initializers
from .. import regularizers
from .. import constraints
from .. import backend as... |
67d8f81284b3f5e4f32662ff47ea0bee96d53502635970f4869758f3e1f0d6a7 | Python | 10,135 | 382 | import h5py
import pathlib as pl
pathsToKeep = {
# Labjack barcode data
"barcodes",
"barcodes/labjack",
"barcodes/labjack/indices",
"barcodes/labjack/trains",
"barcodes/labjack/values",
"barcodes/neuropixels",
"barcodes/neuropixels/indices",
"barcodes/neuropixels/trains",
"barc... |
a5fb3b273acd76a81510eec79ba417a170b2323fd34d2e9fcc2036a09ee3d417 | Python | 10,136 | 214 | print('--------Mendeley-2020 dataset----------')
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
from sklearn.utils import shuffle
from tensorflow.keras.models import Model
from tensorflow.keras.layers import Input, Dens... |
f95799f1b0f03cd13def2507b7e7bd8d768a2fb86989acf4470bc86d9fefe1e0 | Python | 10,136 | 276 | import time
import datetime
import sys
from visdom import Visdom
import numpy as np
import torch
import glob
from fastl2lir import FastL2LiR
from bdpy.dataform import Features, load_array, save_array
import os, hdf5storage
class Logger():
def __init__(self, n_iterations, batches_iteration):
# self.viz = Vi... |
e442f55094c973e733073301c47c57d76dedbe33d961ab9252b7515243891995 | Python | 10,147 | 231 | #!/usr/bin/env python
"""Estimate the peak RAM needed to bulk-load RDF file(s) into an in-memory store.
Several Babel data handlers load a whole RDF/TTL/OWL dump into an in-memory
``pyoxigraph.Store`` before querying it (e.g. ``ChemblRDF`` in
``src/datahandlers/chembl.py``). On a large dump this can need far more memo... |
84bb6d21110d369a4c018ef31951e2ba5cb540e839e209dd93d380ddf16ec48f | Python | 10,154 | 320 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Attribute data transfer testing module
... |
aefb470680a7d37e179eaea446fb2dac955d91945258e96c7bebe8d77dd30f96 | Python | 10,164 | 315 | import argparse
import time
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import pickle
import numpy as np
from scipy.stats import gaussian_kde
from sklearn.metrics import roc_curve, auc
from sklearn.metrics import confusion_matrix
from tqdm import tqdm
import torch
import torch.nn as nn
... |
8413336174f78d23db83307b469b59b3112ffeb7fc789a27dd20bac05d1e0da1 | Python | 10,165 | 253 | """Utilities related to model visualization."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from ..models import Model
from ..layers.wrappers import Wrapper
# `pydot` is an optional dependency,
# see `extras_require` in `setup.py`.
try:
im... |
d1477e867ea6370f9c4317b99fda1133ecefc0b54f9b50db28679ee5063d2895 | Python | 10,166 | 313 | import argparse
import os
import pathlib
import subprocess
import sys
from collections import Counter
from multiprocessing import Pool, cpu_count
from typing import Dict, List, Tuple
from test_utils import PY_PACKAGE, ROOT, cd, print_time, record_time
class LintersPaths:
"""The paths each linter run on."""
... |
672829a019e2a1112ebb6aab62262c47a9e34089e4c2fa6e2613235f399701e6 | Python | 10,167 | 176 | import json
import numpy as np
import pandas as pd
from feater import io
# from Nearl import utils, data_io
import nearl
#### Task1:
# 1. Check if the QM and MD data are present in the database
# 2. If NO, update the supercedes list
#### Task2:
# Find the ligand atom index in the MD trajectory
# 1. Initial selectio... |
da3e40016bbf663a0ec40698db4ce63d548f5f540b9a8c29e4338cd5b990ae30 | Python | 10,167 | 219 | import argparse
import logging
from typing import Type
from catmaid.control.importer import AbstractImporter, InternalImporter, FileImporter
from catmaid.models import Project, User
from catmaid.util import str2bool
from django.core.management.base import BaseCommand, CommandError
from django.db import connection
from... |
6ad0f820c3b9f5aad0f586b89b9a6fef71c204d0889f7c52f7039d9a27ac1588 | Python | 10,170 | 271 | import torch
import torch.nn.functional as F
import numpy as np
import logging
from PIL import Image
from losses import *
from options import *
"""
Define task metrics, loss functions and model trainer here.
"""
def randrot(img):
mode = np.random.randint(0, 4) #用于生成随机整数0,1,2，3
return rot(img, mode)... |
a95873a267d3887a2b900065a7f4e36f8c2c2594489dc9d5852e64be6adebb71 | Python | 10,170 | 289 | import numpy as np
import json
import copy
import hashlib
import time
from multiprocessing import Pool
INPUT = 'input'
OUTPUT = 'output'
CONV3X3 = 'conv3x3-bn-relu'
CONV1X1 = 'conv1x1-bn-relu'
MAXPOOL3X3 = 'maxpool3x3'
NUM_VERTICES = 7
OP_SPOTS = NUM_VERTICES - 2
MAX_EDGES = 9
ALLOWED_EDGES = [0, 1]
CANONICAL_OPS = [C... |
52cc2c1204ac379838c56be1c95e328b6e9968a509bd231502521e5f2560ea1d | Python | 10,174 | 233 | from fengshen.data.task_dataloader.task_datasets import LCSTSDataModel
from transformers import T5Tokenizer, MT5ForConditionalGeneration
from transformers.optimization import get_linear_schedule_with_warmup
from pytorch_lightning import Trainer, loggers
from pytorch_lightning.callbacks import ModelCheckpoint
from trans... |
e746d28dfd23bb9423d853e360bc641c245493da8dcc867d52df5e4f094e29d7 | Python | 10,177 | 273 | import os
import numpy as np
import pytest
import shutil
from keras import callbacks
from keras.models import Sequential, Model
from keras import layers
from keras import backend as K
from keras.utils import np_utils
from keras.utils.test_utils import get_test_data
from keras.utils.generic_utils import to_list
from ke... |
a37ad26799d274f46ad3831579191caea500a9fa0229b22848febc57b2340db7 | Python | 10,178 | 208 | # Copyright (C) 2020-2021 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""GaNDLFTaskRunner module."""
from copy import deepcopy
import numpy as np
import torch as pt
from openfl.utilities import split_tensor_dict_for_holdouts
from openfl.utilities import TensorKey
from openfl.federated.task.runner_fets_... |
261d6a22b9bed8de8f67c3aaed995c9177c02c35dc1cd1783327d0477c7f9aa3 | Python | 10,180 | 328 | import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import matplotlib.ticker as ticker
import numpy as np
from mpl_toolkits.axes_grid1.inset_locator import zoomed_inset_axes
from mpl_toolkits.axes_grid1.inset_locator import mark_inset
EV_list = [
25,
100,
500,
1000,
]
plt.figure... |
409fc045894b2b40575209b7a10de4f0c117de379cb3c8669be64d28363805ff | Python | 10,183 | 290 | from collections import Counter
from unittest.mock import MagicMock
import numpy as np
import pytest
from mace.tools import AtomicNumberTable
from scipy.special import softmax # type: ignore
from simgen.element_swapping import (
SwappingAtomicNumberTable,
catch_diverged_energies,
choose_indices_to_change... |
f9da565faa7fe95a6f587f0eeb40c570f21d103d5842aafdeae2d398b2e8b108 | Python | 10,186 | 316 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.parameter import Parameter
from torch.nn.modules.module import Module
###################################ZINB###################################
###################################ZINB###################################
#################... |
fa463d1f3806d0b257e3e8fe20a9d85d20cae27ba3624a6063a4f24f01fa416b | Python | 10,203 | 318 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as cp
from mmcv.cnn import build_conv_layer, build_norm_layer
from mmseg.registry import MODELS
from ..utils import ResLayer
from .resnet import Bottleneck as _B... |
bfdbfc7c9f406aa1915c10d50e6f3d3db9acffb7aa4505b84dae39954a29d40e | Python | 10,209 | 277 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Implements high-level operations for attribu... |
89ceb6517faf2f95f096532c7fca3da734e818691f5578ef5dd4630fa5543500 | Python | 10,213 | 275 | # Copyright (c) OpenMMLab. All rights reserved.
# Referred to: https://github.com/KU-CVLAB/CAT-Seg/blob/main/cat_seg/third_party/clip.py # noqa
import hashlib
import os
import urllib
import warnings
from typing import List, Union
import torch
from PIL import Image
from torchvision.transforms import (CenterCrop, Compos... |
c2b984359fe483640fcc2313570bbbd2128eede99bdbf0fa586ec8e0e1a1ecb7 | Python | 10,213 | 285 | import torch
import torch.nn.functional as F
import math
class KANLinear(torch.nn.Module):
def __init__(
self,
in_features,
out_features,
grid_size=5,
spline_order=3,
scale_noise=0.1,
scale_base=1.0,
scale_spline=1.0,
enable_standalone_scale_... |
f6df62a62dc43e9934ab20a63ed5833811bd095e49ba62c71371697282d69114 | Python | 10,218 | 306 | import math
import pytorch_lightning as pl
import torch
import torchmetrics
from torch.nn import CrossEntropyLoss, MSELoss
from omegaconf import DictConfig
from models.alif import EFAdLIF, SEAdLIF
from models.li import LI
from models.lif import LIF
from models.rnn import LSTMCellWrapper
layer_map = {
"lif": LIF,... |
7bbfccb71ae6b9610e940c40967c717ad7d12ed019f016b936aea6d13905b17c | Python | 10,221 | 280 |
#%% file import pre procesing
import pandas as pd
import numpy as np
import io
import os
import glob
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.stats as stats
from matplotlib.ticker import MaxNLocator
from array import *
# frequency and intensity list for later
freq_ls = [1000., 1500., 20... |
a59be7946c233648ecf36d02ed688f828ed6dbd84d04d2782811c9d99c3e617f | Python | 10,222 | 280 |
#%% file import pre procesing
import pandas as pd
import numpy as np
import io
import os
import glob
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.stats as stats
from matplotlib.ticker import MaxNLocator
from array import *
# frequency and intensity list for later
freq_ls = [1000., 1500., 20... |
a6ec00bf0cdf33b63d0c3e3a40851d68460ea024fc4a69ac33f964fa8846573e | Python | 10,227 | 331 | import numpy as np
import pandas as pd
from numba import njit
from scipy.sparse import csr_matrix
from anndata import AnnData
from typing import Optional
from os import listdir
from pathlib import Path
@njit
def bin_indices(coords: np.ndarray, coord_min: np.ndarray = np.array([0,0]), binsize: int = 50) -> int:
... |
7f31d356b278143fba4511aa679e047546235e9a210b07f016c158e0fa60a76b | Python | 10,228 | 281 | # t-leNet model: t-leNet + WW
import tensorflow.keras as keras
import tensorflow as tf
import numpy as np
import time
from utils.utils import save_logs_t_leNet as save_logs
from utils.utils import calculate_metrics
class Classifier_TLENET:
def __init__(self, output_directory, verbose,build=True):
s... |
3e791e553950094512a6713a9e76ec841e9927f98af2640b9d3a2991f7fa05dc | Python | 10,229 | 304 | """These tests are not meant to be run on CI.
"""
from __future__ import print_function
import keras
from keras import backend as K
from keras.utils import multi_gpu_model
import numpy as np
import pytest
import time
import tempfile
import tensorflow as tf
from keras.preprocessing.image import ImageDataGenerator
py... |
e39747837389550743534636528742d1a182e956d255823f0706c5c5eb7bdb8c | Python | 10,229 | 252 | import logging
from pathlib import Path
from medperf.commands.execution.execution_flow import ExecutionFlow
from medperf.entities.dataset import Dataset
from medperf.entities.benchmark import Benchmark
from medperf.entities.report import TestReport
from medperf.exceptions import InvalidArgumentError
from medperf.utils... |
00d6b5e14b594aa6521b41110ce930ba95ee93633204078842406e25bba99060 | Python | 10,239 | 270 | import argparse
import random
import time
import numpy as np
from tqdm import tqdm
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.utils.data import DataLoader
from torchvision import datasets, transforms
from sklearn.metrics import roc_auc_score, average_prec... |
122b509dc8b8f6802f9f3c2300358c6e536e2bceca030c594d22a9bc8ff7c511 | Python | 10,247 | 270 | import argparse
import random
import time
import numpy as np
from tqdm import tqdm
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.utils.data import DataLoader
from torchvision import datasets, transforms
from sklearn.metrics import roc_auc_score, average_prec... |
327d26d8cd404b6411259006a55d56388389d363d2dcd90f6f32a5f47cfaecb8 | Python | 10,247 | 282 | # -*- coding: utf-8 -*-
# tests/test_dihedral_to_cartesian.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encoder... |
40c4c0f49fa299a0d2032d72f3d90665819250f1c841476c40feacf2e5c0155f | Python | 10,250 | 228 | import numpy as np
import torch
from torch.nn.functional import relu
def eval_gabors(img, gabor_filters, resp, batch_size=100, device=torch.device('cuda'), rectify=True):
# response to images
for k in np.arange(0, img.shape[-1], batch_size):
kend = min(img.shape[-1]*1.0, 1.0*(k+batch_size))
ke... |
ca7f70bb0ef60f8d24e2f8ed76c3b563ef123cc0fdb5174b2ff2d6c28022be42 | Python | 10,251 | 273 | ## BRIE model
import time
import numpy as np
from scipy.sparse import issparse
import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow_probability import distributions as tfd
class Model_init():
"""Random initialize parameters for BRIE2 model
"""
def __init__(self, Nc, Ng, Kc, Kg, i... |
fdd96b013173561bf0fd1761f77903a1c299c82a7214aae13efd3bf932ad02c2 | Python | 10,256 | 292 | # TODO: break this up by modules
from heudiconv.cli.run import main as runner
from heudiconv.main import workflow
from heudiconv import __version__
from heudiconv.utils import (create_file_if_missing,
set_readonly,
is_readonly)
from heudiconv.bids import (popul... |
fa718f92a1c031f56f4cc929504bf3e55b751f7c9bc06dfde9184d30f9aac59b | Python | 10,268 | 254 | #!/usr/bin/env python
# ----------------------------------------
# scikit-ribo
# ----------------------------------------
# main wrapper
# ----------------------------------------
# author: Han Fang
# contact: hanfang.cshl@gmail.com
# website: hanfang.github.io
# date: 3/28/2017
# -------------------------------------... |
78f202c98f8b86005c3879728925d3cb6d601af575a0e8f245e8ce7ce43a4e69 | Python | 10,269 | 202 | """Measure the GARD_label concord: what it links, and how often the same rule would be wrong.
The concord itself only ever runs on the GARD ids no other concord places, so its own rows cannot be
checked against anything. This script gets a precision number by running the *same rule* over the
GARD ids MONDO and DOID **... |
1d8674b908e82bb3dd632a70d91d0df0977e2f299843007257b7a6895e902da5 | Python | 10,281 | 311 |
from typing import Dict, Set, Any, List
from ordered_set import OrderedSet
import sqlite3
from kgx.sink.sink import Sink
from kgx.utils.kgx_utils import (
extension_types,
build_export_row,
create_connection,
get_toolkit,
sentencecase_to_snakecase,
)
from kgx.config import get_logger
log = get_log... |
64c2c0c5ea879839f668408264d902b05074429486c8d0ed03d4d7fc9e1b3e01 | Python | 10,290 | 235 | import os
import torch
import torch.nn as nn
import torch.nn.functional as F
from transformers import BertConfig,TransfoXLConfig
from transformers.configuration_utils import PretrainedConfig
from transformers.modeling_utils import PreTrainedModel
from transformers.utils import cached_path,hf_bucket_url
from fengshen.mo... |
e66ccc1d2da46929e0864b7bd2a916cc2a4015ec0fcf5ca89feaa53c17763968 | Python | 10,291 | 283 | """
Absolute checks on the geometry of the voxelization kernel.
``frame_interp_global`` no longer strides the whole grid per atom; it visits the
integer bounding box of the atom's cutoff ball. Two details make that delicate:
* the two passes cover **different** extents. The normalizer runs over the
buffered grid, w... |
cbda2c5d7a15d60041e2043342939d870254564a2b8ae06e5257a45faafa5685 | Python | 10,292 | 179 | # 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... |
52621c1173206207817fd51fcf6c11b3577579ce6444f90fa6bdb5a45837fb8a | Python | 10,297 | 305 | """
This script computes and saves regression
results for layers of DNN models and neural areas.
It uses the TRF class to compute the regression
and saves the results in a CSV file.
It also allows for the option to save the
parameters of the regression model.
Args:
dataset_name: str ['ucsf', 'ucdavis'], -d
mod... |
c3145491af6ec92326aa1e9abc30c1d9e454cf0f2e871d823445e48add5ee1a1 | Python | 10,301 | 271 | import argparse
import random
import time
import numpy as np
from tqdm import tqdm
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.utils.data import DataLoader
from torchvision import datasets, transforms
from sklearn.metrics import roc_auc_score, average_prec... |
c11c69300624049f7c1a3f22cb7e6fc99ff060d8aa61b4dcca3d6c5096c47483 | Python | 10,309 | 271 | import argparse
import random
import time
import numpy as np
from tqdm import tqdm
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.utils.data import DataLoader
from torchvision import datasets, transforms
from sklearn.metrics import roc_auc_score, average_prec... |
2cc6f2c977e685fb48946b7dcbe87488f9c92178dc78c9d026dcd4673c330cb8 | Python | 10,320 | 294 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, Linear, build_activation_layer
from mmengine.model import BaseModule
from mmseg.registry import MODELS
from ..utils import resize
from .decode_head import BaseDecodeHead
class ReassembleBl... |
005c8ed61a9034c217e9851f97c0072072eb98f68241aaccd3ba4a22f1233e20 | Python | 10,327 | 334 | import os
import pytest
from deprecation import deprecated
from kgx.graph.nx_graph import NxGraph
from kgx.graph_operations.summarize_graph import (
summarize_graph,
generate_graph_stats,
GraphSummary,
TOTAL_NODES,
NODE_CATEGORIES,
NODE_ID_PREFIXES,
NODE_ID_PREFIXES_BY_CATEGORY,
COUNT_B... |
cadc2e5ece8c8ac1a8ef45fa4d29ed952364c89d7afa7da4706fe610e97ad141 | Python | 10,329 | 268 | """Unit tests for the panel that renders what one DANDI asset holds.
The streaming preview is a constructor injection point, so every test here runs against an
in-memory stand-in with no archive access.
"""
import holoviews as hv
import numpy as np
import pytest
from guppy.frontend.dandi_preview_panel import (
C... |
5a04cd45853f91cfb581c26443bdd43f65622a28a5d43d8c8d873ed83d38d32c | Python | 10,336 | 213 | import json
import os
import shutil
import time
import apybiomart.classes as _apy_classes
from apybiomart import find_attributes, find_datasets, query
from src.util import ensure_parent_dir, get_config, get_logger
logger = get_logger(__name__)
# apybiomart's pre-flight connectivity check uses HTTPS and fails with S... |
b9d21e182aca9a16245316f0ba4e7fe25a14008685885b6a6ce4fd8912ea80b1 | Python | 10,336 | 353 | from __future__ import annotations
import sys
from typing import Any, Optional
import numpy as np
import pandas as pd
def _getArea(box: list[int]) -> int:
"""Return area of box.
Args:
box (list[int]): box of object
Returns:
area (int): area of box
"""
area = (box[2] - box[0]) ... |
8aaab55965afa7290061f600c2f385d20edea2f367365322c560b7a048b63d04 | Python | 10,337 | 244 | from ml_training.dataset import CustomDataset, train_val_test_split, extract_data, train_val_test_split_custom
from ml_training.model import LocalTransformer, GRU, BasicTransformer, LSTM
from ml_training import config
from ml_training.config import update_config
from torch.nn import BCEWithLogitsLoss
from torch.optim i... |
5020e320c185ae5354123ad133196a8b7a0264d9f102a28c90cb2cab0a4ef6ba | Python | 10,342 | 297 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from dash_bootstrap_templates import load_figure_template
import dash_bootstrap_components as dbc
from dash import Dash, dcc, html, dash_table
# =============================================================================
# import callbacks and components
# I tranfered ... |
9ddd7a6c633cb6615f400beb3aa1a9ba44bd61380c2dbbd12ab483cf20a8645c | Python | 10,342 | 221 | import numpy as np
from collections import Counter, defaultdict
import sys
from glob import glob
from sklearn.base import clone as CLONE
import sklearn.metrics as metrics
from sklearn.preprocessing import StandardScaler
# Imputation
from pickle import dump, load
# Models
from sklearn.tree import DecisionTreeClassifie... |
3a4cd07140987127a16f9fc5cf6de097a5357d4af06af55510fe9f0422d09399 | Python | 10,344 | 199 | # Jason Keller
# Feb 2020
# =============================================================================
# Program to set BlackFly S camera settings and acquire frames and write them
# to a compressed video file. Based on FLIR Spinnaker API example code. I have
# also tested with a Flea3 camera, which works b... |
f1411cb45f03ab04af8bed4e4e5c6797fe3901d093fcb738f86cb299c0da4674 | Python | 10,355 | 208 | import os, argparse, time, json
import numpy as np
import pytraj as pt
from scipy.stats import entropy
from collections import OrderedDict
import nearl
import nearl.data
from nearl.io import Trajectory
def parser():
parser = argparse.ArgumentParser(description="Featurize the trajectories")
parser.add_argument... |
f1df683b36132a445b7fdcb6945276a94941dbaf9378bbab42ea1f54ea940e0c | Python | 10,355 | 279 | # Copyright (c) OpenMMLab. All rights reserved.
import threading
from queue import Queue
from typing import List, Optional, Tuple
import numpy as np
import torch
from mmengine import Config
from mmengine.model import BaseModel
from mmengine.registry import init_default_scope
from mmengine.runner import load_checkpoint... |
dcdb7757c8c94d0de7bdf0621f4c6a8a354bec2f34b02ad83695126a5e7263be | Python | 10,357 | 309 | import torch
import itertools
import json
import hashlib
import os
from matplotlib.ticker import FormatStrFormatter, StrMethodFormatter
import umap
from matplotlib import pyplot as plt
import torch.nn as nn
import torch.optim as optim
import torch_geometric
import torch_scatter
import torch.multiprocessing as mp
from ... |
e317cdd5ea87f678928816cabbfd107dba7f511b78ff986b9ff917bcf60d6f53 | Python | 10,357 | 289 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
import os
import sys
import time
import numpy as np
import tensorflow as tf
from datetime import datetime
from tensorflow.contrib.slim.python.slim.nets import inception
from tensorflow.contri... |
b43c63ba46b22114829b27b9dda236876aabdf9d155719f42c53970a439a3b51 | Python | 10,360 | 251 | """
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.
"""
from typing import Optional
import ase.db.sqlite
import ase.io.trajectory
import numpy as np
import torch
from torch_geometric.data import D... |
7c1c8e6397cc73d1c2065b83d95b141b52f7c1664526d812a49c27c4cd65d9b7 | Python | 10,364 | 236 | """
This scripts trains four ablation models:
- Ablate neuroimaging features: train an MLP on clinical data only
- Ablate VGAE: train a MLP on PCA-reduced neuroimaging features
- Ablate VGAE: train a MLP on t-SNE-reduced neuroimaging features
- Ablate MLP: train a VGAE with a linear regression head
Dependencies:
- exp... |
8ca7ac0277c28f4095bb8765eeacc1cd588b7b90f5904054df68ce93efad4478 | Python | 10,372 | 328 | #!/usr/bin/env python
"""
MetaWIBELE: ddi_DOMINE_protein module
Summary the domain-domian interaction based on DOMINE database
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Sof... |
08b718c908adb4e4bfeb2dd4d00765ae1e026398558c867d27e8ded32a07d6df | Python | 10,377 | 303 | import cv2
import numpy as np
from basicsr.metrics.metric_util import reorder_image, to_y_channel
import skimage.metrics
import torch
def calculate_psnr(img1,
img2,
crop_border,
input_order='HWC',
test_y_channel=False):
"""Calculate PSNR... |
1bd751120e14c3c121d98582037bfe55a591a99d51cf0b6051fe6fe42ca0db1a | Python | 10,377 | 300 | # Copyright (c) 2021, EleutherAI
# This file is based on code by the authors denoted below and has been modified from its original version.
#
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complian... |
b7748b7c11ce3adea841dd8046544bd627df52d714d8a79fede56ddc3e8bad08 | Python | 10,387 | 282 | import numpy as np
import pandas as pd
from stns import find_nearest
from scipy.stats import zscore
__all__ = ['get_ISI_per_time', 'calculate_percentile', 'split_spike_data_into_list_of_segments',
'pad_spike_data_to_compensate_for_terminal_silence', 'check_all_neurons_included_add_filler_if_not',
... |
7d9cacff2d10f75da5d6da4bc3ed8412268a5fca63ea7744b02d4deb3e48cbd4 | Python | 10,402 | 254 | """Regression tests for the cross-compendium DuckDB report queries.
These exercise the two-pass duplicate-detection rewrite in
``src/reports/duckdb_reports.py``: a spillable ``COUNT(*)`` pass that finds the
duplicate keys, followed by a ``LIST()`` pass restricted to those keys. The
fixtures are deliberately tiny; the ... |
3c61251f0088d6a6c41f0d8e6a4b8922701d1c2d499e8173e6f60732bb35a3ac | Python | 10,403 | 274 | from dataclasses import dataclass
from torch.utils.data._utils.collate import default_collate
import copy
import torch
import numpy as np
@dataclass
class CollatorForLinear:
args = None
tokenizer = None
label2id = None
def __call__(self, samples):
cls_token = "[CLS]"
sep_token = "[SEP... |
597b2b435ea05a411e06e3ba67751b4c52060865b20fafc4b3c174fb03e2efb3 | Python | 10,404 | 309 | """################################################################################
> # **Introduction**
> The notebook is divided into 4 major parts :
* **Part I** : define the functions
* **Part II** : define the CNN model
* **Part III** : optimization using the search algorithm
##############################... |
206d3f3d92fcb241d9706db97f3b31b47461ad782eac2e614c7670a31f6689eb | Python | 10,408 | 291 | """Count reads in transcript for well-based scRNA-seq or bulk RNA-Seq"""
import sys
import time
import numpy as np
import multiprocessing
from .sam_utils import load_samfile, fetch_reads, check_pysam_chrom
def _check_SE_event(gene):
"""Check SE event"""
if (len(gene.trans) != 2 or
gene.trans[0].exons... |
103db3e501176161457a72b1ee6171fcf2ee73f65a06fcaf4214f443caf7b964 | Python | 10,416 | 295 | """
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 math
import numpy as np
import sympy as sym
from scipy import special as sp
from scipy.optimize import brentq
def Jn(r: float, n: i... |
1d35584b30fc07f1763848e0edaa476c8324f35dd9e85d42e7158240b4d1c513 | Python | 10,416 | 306 | from scripts import load
from scripts import oed
import os
import json
import numpy as np
def gene_aser_aiy_synapse_change(
gene_number, start, stop, num, gene_path="../result/Result_aiy_aiz_negative.json"
):
"""
ASER-AIYのシナプス特性を変化させる。
gene_number: 改変する遺伝子の番号
start: 10,11の結合(ASER-AIY)に対して加える範囲の最小
... |
10924e56999dfe00095787f31465a4decfd267088c3b297c1b48c8ff6051aa1f | Python | 10,420 | 278 | #!/usr/bin/env python
"""
MetaWIBELE: mspminer_protein module
Extract annotation of MSPs
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software withou... |
5dd5de40f6a583f0350acc747510120dba0a05f51e3470291f18c64ecf13cf3c | Python | 10,420 | 295 | """
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 math
import numpy as np
import sympy as sym
from scipy import special as sp
from scipy.optimize import brentq
def Jn(r: float, n: i... |
aac28fe8a13f59779fd07255cdf9769352a373f7179c77665597f32fb14e66d9 | Python | 10,423 | 369 | """Connection management for zndraw-cli.
Handles server URL resolution and token resolution via ClientSettings
(pydantic-settings source chain). Provides a Connection dataclass
that wraps httpx.Client with base_url and auth header.
"""
from __future__ import annotations
import contextlib
import json
import sys
from ... |
5774dc9bcc6142b3bc76e3c1ddb82129d9b85a4bd9c085b998b2e438f43646ef | Python | 10,425 | 232 | import numpy as np
import pandas as pd
import pytest
from guppy.analysis.standard_io import write_tonic_to_hdf5
from guppy.frontend.tonic_epochs import (
TonicEpochConfig,
TonicResultsView,
build_tonic_results_view,
)
from guppy.utils._hdf5_io import write_hdf5
@pytest.fixture
def run_folder(tmp_path):
... |
a3813281481bb7039b0dba65ebdf2a7a6c5e0d6f8ea670547135bf6cccba1d1e | Python | 10,426 | 201 | ##### Data preparation file for training Restormer on the DPDD Dataset ########
import cv2
import numpy as np
from glob import glob
from natsort import natsorted
import os
from tqdm import tqdm
from copy import deepcopy
from joblib import Parallel, delayed
import multiprocessing
from pdb import set_trace as stx
def ... |
a67c8d562d040ee98ea4815272adaa6d3f531fb7288b9d5a4efcc2f08574b4bf | Python | 10,443 | 333 | import errno
import io
import os
import sys
from abc import ABC, abstractmethod
from enum import Enum
from pathlib import Path
from typing import BinaryIO, Optional, TextIO, Any
import dnaio
from xopen import xopen
from cutadapt.utils import logger
try:
import resource
except ImportError:
# Windows
resou... |
b8bb6e49bb3d14dbd0c28dbfd20cf3fba7e46aa425a80b7b030b51794d6fff48 | Python | 10,447 | 326 | """
Django settings for medperf project.
Generated by 'django-admin startproject' using Django 3.2.5.
For more information on this file, see
https://docs.djangoproject.com/en/3.2/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/3.2/ref/settings/
"""
from pathlib... |
1e471186594f4c941f78eb843c575d679efbf970762c758e37bde09912b24c4f | Python | 10,450 | 364 | from ._version import __version__
from pathlib import Path
from os import getenv
BASE_DIR = Path(__file__).resolve().parent.parent.parent
major_version, minor_version, patch_version = __version__.split(".")
# MedPerf server
server = "https://api.medperf.org"
certificate = None
local_server = "https://localhost:8000... |
fa6561f41aafb2e84418627f8c8a29e7ec5a0455b400759fc51c00abdf8b1218 | Python | 10,452 | 236 | # Script to load, perform basic postprocessing, and plot data analysis for the
# GCaMP mice data.
import sys
import os
sys.path.append("./utilities")
from pylab import *
from scipy.stats import pearsonr
from matplotlib.animation import FuncAnimation
from mpl_toolkits.axes_grid1.axes_divider import make_axes_locatable... |
05cb79933ec1d8e67d2ee128732caddddecd2ec262d024a69bc7f2a482d29643 | Python | 10,461 | 286 | import numpy as np
import pyqtgraph as pg
from PyQt5 import QtCore, QtGui
from PyQt5.QtWidgets import QApplication, QTreeWidget, QTreeWidgetItem, QHBoxLayout, QWidget
app = QApplication([])
windows = {}
def view_arrays(arrays, *args, **kwargs):
layers = [{'data': array, 'name': str(i), 'visible': True} for i, a... |
1a60e7f61bef1fc2010d10f032f2c4f9afc7d09e1c0a15a5e3a329b3a98bc11e | Python | 10,462 | 282 | from collections import defaultdict
import json
import logging
import select
import signal
import time
from typing import Dict, List, Set
from django.conf import settings
from django.core.management.base import BaseCommand
from django.db import connection
from catmaid.control.edge import get_intersected_grid_cells
f... |
f8870752bc2d878c356ad8d82ca7373cfc8f05b56d4393976febf64ed98e4dad | Python | 10,462 | 295 | # Copyright DST Group. Licensed under the MIT license.
import datetime
from ipaddress import IPv4Address, IPv4Network
import CybORG.Shared.Enums as CyEnums
class NetworkInterface:
"""A class for storing network interface information """
def __init__(self,
hostid: str = None,
... |
75ac444c50954d00e18f535f204ca43e7b20934a6737c177b32482c754efde25 | Python | 10,475 | 297 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
import imageio
import os
import sys
import tqdm
import numpy as np
import SimpleITK as sitk
import tensorflow as tf
from tensorflow.contrib.slim.python.slim.nets import inception
from geomstat... |
7a6dee7066c75ba7d47ec60ce280c9a817403878f21fe1467890564f79152089 | Python | 10,477 | 338 | import numpy as np
import scipy.optimize
from argparse import Namespace
from tfwrap import tf
import math
class Optimizer:
def __init__(self, name=None, displayname=None, dtype=None):
self.name = name
self.displayname = displayname if displayname is not None else name
self.dtype = dtype
... |
f637ae4a38be525d287c3f0c85075a6a5159f769d91ae3c085b28094e56d788c | Python | 10,480 | 202 | # Sapbert (https://github.com/RENCI-NER/sapbert) requires input files
# in a particular pipe-delimited format:
# biolink:Gene||NCBIGene:10554||AGPAT1||1-acylglycerol-3-phosphate o-acyltransferase 1||lysophosphatidic acid acyltransferase, alpha
# i.e. the format we need is:
# biolink-type||preferred ID||preferred la... |
028ece4b77e96907bc852dc781ea5f92f3f10f9a53322ce36d886250ed308307 | Python | 10,486 | 302 | ##
## CPCantalapiedra 2020
import os
import subprocess
from argparse import Namespace
from collections import defaultdict
from ...common import get_pfam_db, get_call_info, ESL_REFORMAT, TIMEOUT_LOAD_SERVER
from ...emapperException import EmapperException
from ...search.hmmer.hmmer import HmmerSearcher
from ...search... |
f299b44126dedb2d2d7b8398b0801f79beac7acb7f8bb873ff8ff983b5a9e911 | Python | 10,491 | 297 | import logging
from collections import Counter
from collections.abc import Sequence
from pathlib import Path
import numpy as np
import pandas as pd
import torch
from torch.utils.data import DataLoader, TensorDataset
from DiastereomericResolutions.main import ModelTask
from DiastereomericResolutions.main.molecule_db i... |
583d8fb3e93b0c95cc87bdf96500b8d9644c560ca1c5d06dcedeacd9c9999ae2 | Python | 10,495 | 305 | import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import data_utils as du
from pathlib import Path
import time
from datetime import datetime
import gc
import os
from tensorflow.keras import layers, models, optimizers, callbacks
from tensorflow.keras.callbacks import Callback
from dfa_lib_pyt... |
4352bdcbff430f8f0e6f56b8e929d5ebd58a0e44a6acb7a677c451a1b1fcf4d1 | Python | 10,505 | 174 | '''
Created on 24 Apr 2020
@author: Francois STÜDER
'''
import argparse
import sys
from Bio.Seq import Seq
from datetime import datetime
from multiprocessing import Pool
from os import path
from time import time
from SysISTD import __version__
from SysISTD import tools
from SysISTD import misc
from SysISTD import ... |
103bc5943bb2c1544bdcc6da7309277181b29ecf0f52bdd1a49c4d6d137a39ed | Python | 10,507 | 310 | """
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 torch
from torch_scatter import segment_coo
from torch_sparse import SparseTensor
from .utils import get_inner_idx, masked_select_spar... |
5451e88841a20ee0c357a7659b9b2593b1e12e83fadbe019b38c21cffb64ebd0 | Python | 10,510 | 301 | import numpy as np
from scipy.special import expit
import scipy
from cogmodels.base import CogModel2ABT_BWQ, CogParam
class RL_4p(CogModel2ABT_BWQ):
def __init__(self):
super().__init__()
self.fixed_params.update({"b0": 1.0, "q_init": 0.0, "gam": 1.0, "CF": False})
# used fixed for hyperp... |
374fb974866c623a68f277ad1a5d98ff5b2afffa069244015b93a4f0f05bae19 | Python | 10,512 | 275 | import logging
import math
import re
from pathlib import Path
import numpy as np
import pandas as pd
from .io_utils import (
make_dir_for_cross_correlation,
recording_site_from_preprocessed_label,
)
from .psth_utils import create_Df_for_psth, getCorrCombinations
from ..utils.utils import output_label_under, r... |
688d024ecdad8ff069b03df7bdad2f4baea99cb715b00851a25b35e573528503 | Python | 10,513 | 208 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.cluster import DBSCAN
from sklearn.metrics import silhouette_score, silhouette_samples
from scipy.spatial.distance import cdist
from sklearn.neighbors import NearestNeighbors
# Constants definition
CSV_READ_PATH = r'detect_spi... |
ca2fe4d0b45b0f4de2a873d57e791a9dd7da277075ce9c9dd84e56b7959b8477 | Python | 10,515 | 382 | import os
import tempfile
import weakref
from typing import Any, Callable, Dict, List
import numpy as np
import pytest
from hypothesis import given, settings, strategies
from scipy.sparse import csr_matrix
import xgboost as xgb
from xgboost import testing as tm
from xgboost.data import SingleBatchInternalIter as Sing... |
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