sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
fee9b1fb9fabd65ae7edf937477057345198d0eaa8085b8998c73a76dcd9c8c9 | Python | 5,186 | 265 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os.path as osp
import shutil
from functools import partial
from glob import glob
import numpy as np
from mmengine.utils import (mkdir_or_exist, track_parallel_progress,
track_progress)
from PIL import Image
COCO_LEN = 1... |
487440a9ce558b81585fdb684f304fe055e7dd79a3cf9ef656e9eb2110e23212 | Python | 5,188 | 160 | import logging
import os
import ase.io as ase_io
import numpy as np
import torch
from simgen.element_swapping import SwappingAtomicNumberTable
from simgen.generation_utils import calculate_restorative_force_strength
from simgen.integrators import IntegrationParameters
from simgen.manifolds import MultivariateGaussian... |
4c6791fb304a4a6777e2599f114457eac843e17bdc97ea01bd999668ced0c944 | Python | 5,189 | 143 | import numpy as np
from scipy.optimize import NonlinearConstraint
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels import Matern
from typing import Any, Mapping, Callable, Optional, Union, Tuple
import random
from scipy import stats
from sklearn import metrics
from te... |
5b3af206f8d03ff43133a4bc5347c115c358eb49125a6e655bf0e8aafb0cb313 | Python | 5,190 | 194 | import sys
import re
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import deepxde as dde
from pathlib import Path
from parameters import N, beta, sigma, S0, I0, R0
sns.set_theme(style="whitegrid")
def dinn(
data_observed,
parameters,
hyperparameters,
e... |
d3fdca89af1328732ef8e69e523960c90907222cc776a1a04948eaeeb9960b54 | Python | 5,191 | 168 | from __future__ import absolute_import
from ..utils.generic_utils import deserialize_keras_object
from ..engine.base_layer import Layer
from ..engine import Input
from ..engine import InputLayer
from ..engine.base_layer import InputSpec
from .merge import Add
from .merge import Subtract
from .merge import Multiply
fr... |
977c61185de96f8e330d349b77ed796481ebedae0ad3c00d5a7aaabe1c5a4e2b | Python | 5,192 | 128 | import numpy as np
import torch as th
from .gaussian_diffusion import GaussianDiffusion
def space_timesteps(num_timesteps, section_counts):
"""
Create a list of timesteps to use from an original diffusion process,
given the number of timesteps we want to take from equally-sized portions
of the origin... |
6cf1510187b2bb70e9795e6fa5fc2e14b6f7a01c1e334b0ad8a0da90035539dc | Python | 5,193 | 117 | # import pandas as pd
# import matplotlib.pyplot as plt
# import numpy as np
# import seaborn as sns
#
# # # Load your dataset
# # df = pd.read_csv('../CSV/Data/Random_Split.csv', low_memory=False)
# # df['PAMPA_clipped'] = df['PAMPA'].clip(lower=-8, upper=-4)
# #
# # df_89 = pd.read_csv('../CSV/Data/mol_length_89.csv'... |
5ee681cf3e9a55993cebf590941bf68ae5e83047990eed92e5cc4100d549a4dc | Python | 5,195 | 115 | import numpy as np
import pandas as pd
import os
def generate_pseudo_bulk(st_adata, label_df, save_csv=False, output_path="pseudo_bulk.csv"):
"""
Generate a pseudo-bulk expression profile by summing expression across spots in each cluster.
Parameters:
- st_adata: AnnData object containing spa... |
c290aa8ad0a8394e947e13ef3230d4463f0f98b01dc285a221c178f666c4bc6a | Python | 5,195 | 191 | import sys
import re
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import deepxde as dde
from pathlib import Path
from parameters import N, beta, sigma, S0, I0, R0
sns.set_theme(style="whitegrid")
def dinn(
data_observed,
parameters,
hyperparameters,
e... |
147eeb80e60114fedd218b6bf2a83ba7be568dddff6da71b16501a6d8cb9ff19 | Python | 5,201 | 161 | # BigStitcher script via ImageJ/Fiji
# Author: David Young, 2017, 2018
"""Stitches multi-series imaginge files (eg CZI format) through the Fiji
BigStitcher plugin.
Attributes:
in_file: Path to the image input file. The dataset filename will be
based on this input name, using the part of the name before th... |
ca30fd3d5ac24719082edef1187506b562adfd1b2767f4228b8eee67b465321b | Python | 5,201 | 159 | #!/usr/bin/env python
"""
MetaWIBELE: abundance_RPK module
Normalize family abundance to RPK (read counts divided by the length of genes in kilobase to normlized for gene/protein length)
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of... |
decdd40fedcfa7e486002fa8945f3531668984cedcfb350fe896beabcf2cf3ab | Python | 5,204 | 150 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import GATConv
# full connected layer
def full_block(in_features, out_features, p_drop=0.0):
return nn.Sequential(
nn.Linear(in_features, out_features, bias=True),
nn.ReLU(),
nn.Dropout(p=p_drop),
... |
8959e8fdd90ec488687a6761654ce9b58c7d17f81a9be7437bb21480bf70dfec | Python | 5,206 | 89 | import ast
import json
# Starting with a conflation file, and a set of compendia, create a new compendium merging conflated cliques.
def get_conflation_ids(conffilename):
"""Given the name of a conflation file, where each line looks like:
['RXCUI:1092396', 'RXCUI:849078', 'PUBCHEM.COMPOUND:446284', 'RXCUI:18... |
a2b11159d92fac63f43b72559d940d8d495e56a1da8c415a0583f4547412a8a8 | Python | 5,208 | 173 | """StochKv cell example"""
# pylint: disable=R0914
import os
import bluepyopt.ephys as ephys
script_dir = os.path.dirname(__file__)
morph_dir = os.path.join(script_dir, 'morphology')
def stochkv_hoc_filename(deterministic=False):
"""Return stochkv hoc model filename"""
return os.path.join(
script_... |
94239a8c1ffe2228b263930d8bed8ec9d3e6e2641d284396bc0b78e59deb0c95 | Python | 5,210 | 128 | from PyQt5 import QtGui, QtWidgets, QtCore
import pyqtgraph as pg
import numpy as np
from scipy import signal
from util.conf import sg_savitzky_golay_params, sg_moving_average_params, sg_butterworth_params, sg_scaled_window_convolution_params
from util.functions import movingAverage, butter_lowpass_filter
from feature... |
f0f26c003d26ba2e52057214211c04509ae020579817821a65c23a3258959e90 | Python | 5,210 | 160 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 13 12:47:07 2023
@author: george
"""
import numpy as np
import pandas as pd
import os
from scipy.optimize import curve_fit
from matplotlib import pyplot as plt
# exponential decay functions for curve fitting
def exp_dec(x, A1, tau):
return 1 + ... |
dfc27ed1b32429bf8ba20629abf225049b01ad5ec98b0140f82b04f945803e43 | Python | 5,213 | 129 | # Helper for vertically centered, styled message in the mutagenesis logo container
def mutagenesis_message(msg):
return html.Div(
html.P(msg, style={"color": "gray", "fontSize": "14px", "margin": "0", "fontFamily": "inherit"}),
style={"display": "flex", "flexDirection": "column", "justifyContent": "... |
ae449d274c92176b5916bf422d22e8bc921718753c941b7839f0c576637b46bb | Python | 5,214 | 151 | # Copyright (c) OpenMMLab. All rights reserved.
import pytest
import torch
from mmseg.models.backbones import CGNet
from mmseg.models.backbones.cgnet import (ContextGuidedBlock,
GlobalContextExtractor)
def test_cgnet_GlobalContextExtractor():
block = GlobalContextExtract... |
3d87fa9cf242d7788974eb490a25fcbd4e59466aee9f31adbcfbc59d2859838b | Python | 5,215 | 143 | import os
import sys
import csv
import torch
import numpy as np
from const import *
from itertools import islice
from torch_geometric import data as DATA
from torch_geometric.data import InMemoryDataset
class MyTestDataset(InMemoryDataset):
def __init__(self, root='/tmp', dataset='_drug1',
xd=Non... |
97937e9176de6632a3806ce2fbf86b5707ea7c2ba7c9b71eaf5bab218b74ae6c | Python | 5,218 | 118 | import numpy as np
import matplotlib.pyplot as plt
import hickle as hkl
from grid_cell.higham import nearestPD, isPD
import itertools
from grid_cell.manifold_fitter import label_mesh
from grid_cell.sphere_manifold import Circle_Manifold
from grid_cell.ori_tuning_manifold import Ori_Tuning_Manifold, Place_Cell_Manifold
... |
9bee91e88a5c0d739f62dcd7a40f3672d646801edafd408642219f32165cde84 | Python | 5,218 | 120 | from __future__ import division
from builtins import str
from builtins import range
from sciunit import Score
import numpy
from sciunit.utils import assert_dimensionless
import collections
class ZScore_backpropagatingAP(Score):
"""
Average of Z scores. A float indicating the average of standardized difference... |
3e94088e9615f463a5eaa002b081d0084ae5cd20ab032eed63b3443cd3d61986 | Python | 5,220 | 140 | """
purpose of this file
remove filenames with __dup from the IntendedFor and the scans.tsv
"""
# 1. git annex unlock scans.tsv
# 1-1. delete row of __dup file from scans.tsv
# 1-2. git lock scans.tsv
# 2. git annex unlock .json
# 2-1. delete item of __dup from .json
# 2-2. need to handle list of items (commas?)
impo... |
8406b35d4cc2b944282c51066701f8ca11dffbd8304218512266040f0d99c593 | Python | 5,222 | 146 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 3 10:34:51 2023
@author: schwab
"""
from pathlib import Path
from typing import Optional
import torch
from torch.utils.data import DataLoader
from typer import Option
import os
import sys
from ..data.handlers.particle_image_preprocessor import \... |
9087d02d1d294b86eca4b0a78f8b10e9dc3a911cf40d8166cc8608c6e470c551 | Python | 5,222 | 112 | import catmaid.fields
from django.conf import settings
import django.contrib.postgres.fields
import django.contrib.postgres.functions
from django.db import migrations, models
import django.db.models.deletion
import uuid
forward = """
CREATE TABLE catmaid_project_token (
id int GENERATED BY DEFAULT AS IDEN... |
9bea0797d39d39a2f48a5ad95d46ce7ed8d1174919efd364239198e0bbc9b837 | Python | 5,222 | 121 | """Context-Aware Implicit Neural Representations to Compress Earth Systems Model Data
DEVELOPED AT:
Department of Chemical Engineering
University of Utah, Salt Lake City,
Utah 84112, USA
DIRECTOR: Prof. Salah A Faroughi
DEVELOPED BY:
... |
92989ab3a0eb5d8fad36baccbc16379f8dc473e06036ec5bd4e10e1f6bd5ae23 | Python | 5,227 | 150 | # 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:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
17094668f09362926cdd184f11ee8abda5301a6b6d2613949cea5103f53c87d7 | Python | 5,229 | 162 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
# pyre-strict
# pyre-ignore-all-errors[2]
import typing
import unittest
from collections import Counter, defaultdict
from typing import Any, Dict, List, Tuple
import torch
import torch.nn as nn
from fvcore.nn.activation_count import activation_c... |
7d6e1026facdbb81f0f8dac7eae2d506c5d818b7e27f1ac10d825b99346ad8c6 | Python | 5,229 | 151 | """
Add `extra_repr` into DropPath implemented by timm
for displaying more info.
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from e3nn import o3
def drop_path(
x: torch.Tensor, drop_prob: float = 0.0, training: bool = False
) -> torch.Tensor:
"""Drop paths (Stochastic Dept... |
947ec5a5eec8e2852f7ff12b8cc4c885fb7be86aeb2f94e4641106a92d0b8213 | Python | 5,230 | 186 | import os
import shutil
from glob import glob
from pathlib import Path
import datetime
from collections import defaultdict
import urllib
import numpy as np
from datasets import DatasetDict, Dataset
from transformers import AutoTokenizer
from transformers import AdapterType
from transformers import AutoConfig, AutoMode... |
81b92abb85145693db499e6ba036853a980e9e96412a443c692fcddc0dd27aa7 | Python | 5,232 | 116 | import h5py
import numpy as np
import pandas as pd
import pytest
from guppy.analysis.control_channel import (
add_control_channel,
create_control_channel,
curveFitFn,
helper_create_control_channel,
)
def test_curve_fit_fn_known_params_at_x_zero():
# a + b * exp(-(1/c) * 0) = a + b
result = cu... |
402f9f14b5e461df79b0ae26db8c6ad9804c8fb2d5e2e4ba10452e3baf4845f2 | Python | 5,233 | 167 | import logging
from pathlib import Path
import anyio
from fastapi import HTTPException, Security
from fastapi.security import APIKeyCookie, APIKeyHeader
from fastapi.templating import Jinja2Templates
from importlib import resources
from urllib.parse import urlparse
from fastapi.requests import Request
from... |
6279855adbf0cce0042873ae816565b6e6d376beed90a2d88bd2d5920521a212 | Python | 5,236 | 114 | try:
import cPickle as pickle
except:
import pickle
import gzip
import numpy
import os
import matplotlib
import matplotlib.pyplot as plt
#base_dir = '/mnt/csoport31-2/Modellezo_csapat/CA1_pyramidal/Spine_project_validation_results6/Basic_set_newopt/Active_all_spine_na_dend_soma_start/temp_data/oblique_integra... |
0f2bf563d3b0e22474111566b9bcdf3cf7d4e0e98bbe31a3c05970d70699dd1e | Python | 5,240 | 89 | # 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... |
f0e73a175b6648923b36d0a89cf3c46ab8b2b99f3e96704506c66ed536f17b76 | Python | 5,241 | 173 | """StochKv3 cell example"""
# pylint: disable=R0914
import os
import bluepyopt.ephys as ephys
script_dir = os.path.dirname(__file__)
morph_dir = os.path.join(script_dir, 'morphology')
def stochkv3_hoc_filename(deterministic=False):
"""Return stochkv3 hoc model filename"""
return os.path.join(
scri... |
13b93d351e837103362cf276f2f5df6c352174d69a8e7f402d3effda5a9370b6 | Python | 5,243 | 134 | import logging
from pathlib import Path
import socketio
from fastapi import FastAPI, Request
from fastapi.exceptions import RequestValidationError
from fastapi.responses import FileResponse, JSONResponse
from starlette.staticfiles import StaticFiles
from zndraw.database import lifespan
from zndraw.dependencies import... |
17390adba85dce99744f8d91794674988c2f5d85353574db206491206321321e | Python | 5,243 | 203 | #!/usr/bin/env python
# coding: utf-8
# # Fichier Exemple : utilisation des modèles développés
# ### 1. Modèle IA pour TC
# ### 2. Modèle IA pour PC
# ### 3. Modèle IA pour ACEN
# ### 4. Modèle IA pour NBP - normal boiling point
# ### 5. Modèle IA pour TTR - point triple
# ### 6. Modèle IA pour VC
# ### Copyright - LR... |
7a22ae00ad121cee64bcd1aff7260b9b40b08b621bfbaa6c9784ddd5a6ff9767 | Python | 5,243 | 141 | import numpy as np
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
def get_sphere_mesh():
u = np.linspace(0, 2 *np.pi, 100)
v = np.linspace(0, np.pi, 100)
x_sphere = np.outer(np.cos(u), np.sin(v))
y_sphere = np.outer(np.sin(u), np.sin(v))
z_sphere = np.outer(np.ones(np.size(u)... |
74adcf6952ae9c55782968f126a752b0c7200b9c8a6e7e09e8b05cc5f4b641c7 | Python | 5,245 | 122 | DOCS = """
train the model on the a dataset (gabor or mnist) and show the robustness of the model to noise.
currently figure 4.
"""
from dataset import GaborDatasetOrientation
from model import ShallowMLP, DenoisingAE
from experiment.utils import set_seed, init_model, Logger, Trainer, AETrainer, Checkpointer
from data... |
338eb69fe62f239e96a7a11dc246b74954e7ddb689ce40f7f657e6ec961142c3 | Python | 5,249 | 128 | import torch
import numpy as np
import usb.core
import time
class FPGAInterface:
"""Hardware interface for 32x32 memristor crossbar array"""
def __init__(self):
self.connected = self._initialize_hardware()
self.analog_mode_enabled = False
self.layer_mapping = {
'data_process... |
736d27a33874d2e55a69d65389ba78bb1b0eb9d48ac29bbdd74e96f70160db3c | Python | 5,250 | 101 | """
Functions to get distance from PMJ for processing segmentation data
Copyright (c) 2021 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import logging
import numpy as np
from spinalcordtoolbox.image import Image
from spinalcordtoolbox.centerline.core import get_centerline
from spin... |
0453db4f9d94ae5942a51adb0cb92660e2b830715fbc282ea159636a5bcf4ebb | Python | 5,252 | 133 | '''
Date: 2022-08-06 13:47:37
LastEditors: yuhhong
LastEditTime: 2022-11-21 16:05:50
'''
import os
import argparse
from tqdm import tqdm
import pandas as pd
from rdkit import Chem
# suppress rdkit warning
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
from rdkit.Chem import AllChem
from rdk... |
70be151facded2212662d843820eddd2d8e4141325421dd3c2bbf4f701d87b37 | Python | 5,252 | 163 | from medperf.asset_management.gcp_utils import (
CCWorkloadID,
GCPAssetConfig,
GCPOperatorConfig,
)
from medperf.entities.dataset import Dataset
from medperf.entities.model import Model
from medperf.entities.user import User
from medperf.asset_management.asset_storage_manager import AssetStorageManager
from... |
e32f5dcda80c8530e05b25d2ee8e0bb903e295f0716098ffdeb636fe4fb66f11 | Python | 5,252 | 174 | import os
import re
import yaml
if os.name == 'nt':
import win32api
import pathlib as pl
from datetime import date
from string import ascii_uppercase as letters
from myphdlib.interface.muscimol import MuscimolSession
from myphdlib.interface.dreadds import DreaddsSession
from myphdlib.interface.mlati import MlatiSes... |
ac28b8f1cb0e6c9ec73e004549cabe5d2f8a8e4f6d3707bcd194003af7cdf73a | Python | 5,254 | 158 | import os
import sys
import csv
import torch
import numpy as np
from const import *
from itertools import islice
from torch_geometric import data as DATA
from torch_geometric.data import InMemoryDataset
class MyTestDataset(InMemoryDataset):
def __init__(
self,
root="/tmp",
dataset="_drug1"... |
69e5c744a4a5fcce0e4b118a3ea4d54efb1c389bef9da4f91d05bf3fac01439d | Python | 5,259 | 158 | import threading
import random
import torch
import torch.multiprocessing as multiprocessing
from torch.utils.data import DataLoader
from torch.utils.data import SequentialSampler
from torch.utils.data import RandomSampler
from torch.utils.data import BatchSampler
from torch.utils.data import _utils
from torch.utils.da... |
45c05656b1c2316dd48b913257b5d51c4999e2b482d129f025134db361ced63e | Python | 5,261 | 114 | from experiment import *
import numpy as np
import pandas as pd
from datetime import datetime, timedelta
from zigzeg import find_runs
def get_datetime(date, timestamp):
Y, M, D = date.split("_")
h, m, s = timestamp.split("-")
return datetime(int(Y), int(M), int(D), int(h), int(m), int(s))
if __name__ ==... |
7fd5ba199d21e627a80c0a8a703ad412b9a5d8f20188390e158450f04bcb9eb1 | Python | 5,261 | 138 | from django.db import migrations
forward = """
CREATE OR REPLACE FUNCTION refresh_skeleton_summary_table_selectively(skeleton_ids bigint[]) RETURNS void
LANGUAGE plpgsql AS
$$
BEGIN
-- Cable length, nodes, creation info, edition info
WITH filtered_treenode AS (
SELECT *
... |
16dad0e2e75bd87fc29a6176627db69d6b3d4278e7f3c3df1a35bff74757dcb3 | Python | 5,265 | 155 | import datetime
import os
import sys
import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from unittest import TestCase
import ffmpeg
TEST_DIR = os.path.dirname(os.path.abspath(__file__))
PROJECT_DIR = os.path.abspath(os.path.join(TEST_DIR, os.pardir))
sys.path.insert(0, PROJECT_DIR)
from... |
548c10d8e0831d40e4d4c899c03742e6e8db3eb78fe3e906944916d7a16c6723 | Python | 5,267 | 106 | """``babel-clique-diff`` — compare the cliques in two Babel compendium builds.
Argument parsing and output formatting only; the diff itself lives in
:mod:`src.model.compendium_diff`, so a second tool or a pipeline rule can reuse it.
Invocation::
uv run babel-clique-diff --before <dir> --after <dir> --files Disea... |
8094fb8239271a209a6cb969ee1d466cbaf18807cb6ffa6e4ba121d9a1f0f298 | Python | 5,267 | 106 | import os
import xml.etree.ElementTree as ET
import pandas as pd
# Define the exact directories for suspicious and source documents
suspicious_folder = r"C:\Users\medhat6969\Downloads\ExAraCorpusPAN2015\ExAraCorpusPAN2015\ExAraCorpusPAN2015\ExAraPlagDet-10-08-2015-Training\suspicious-documents"
source_folder = r... |
b44c53daa1e450fe1cdf20c7262459164a7da8d1b9b3c89ff14d16036272f2e3 | Python | 5,267 | 151 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Defines the CNN that performs the classification
@author: Andrei Istudor andrei.istudor@gmail.com
"""
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
from torch.nn import Linear, ReLU, Cross... |
db4ffd34263440d365eba698e6d4c8942a11afb8bb00323ff4e6f9cdec4b65d2 | Python | 5,267 | 159 | from typing import Tuple
import numpy as np
import pytest
import xgboost as xgb
from xgboost import testing as tm
from xgboost.testing.updater import get_basescore
rng = np.random.RandomState(1994)
class TestEarlyStopping:
@pytest.mark.skipif(**tm.no_sklearn())
def test_early_stopping_nonparallel(self):
... |
69e9d392dc06f93fd9461e94f593be4f0ac7a4ce27d5549b81b7440662e0c810 | Python | 5,269 | 148 | from bs4 import BeautifulSoup
import matplotlib.pyplot as plt
import numpy as np
from analysisUtil import *
from surrogateParams import surrParams
import pandas as pd
from guppy import hpy
from multiprocessing.pool import Pool
import os
h = hpy()
print(h.heap())
# get list of valid simtags
reportFolder = './reportHTM... |
9afc3679bf9304749d59f29573e2a930ddda1137d7dd453dbdafa2bada60087f | Python | 5,269 | 160 | import typing as T
import logging
import numpy as np
import tsgm.types
logger = logging.getLogger('dataset')
logger.setLevel(logging.DEBUG)
class DatasetProperties:
"""
Stores the properties of a dataset. Along with dimensions it can store properties of the covariates.
"""
def __init__(self, N: int... |
cc80211e8dba30aeeed2304cd146c1fce493059764083afae3eb4b8dfe5cb1ef | Python | 5,278 | 111 | from PyQt5 import QtWidgets, QtCore, QtGui
from view.Plot import Plot
class ActivateMultipleDialog(QtWidgets.QDialog):
"""
Dialog that lets the user check for every object if the feature should be
activated or deactivated.
"""
def __init__(self, data_manager, index):
""... |
d8512601ec1bbbfa43a0bc9bd8bf8ef35d963f5519e304a795a6f6cb7018636b | Python | 5,279 | 178 | from heudiconv.cli.run import main as runner
import os
import os.path as op
from mock import patch
from six.moves import StringIO
from glob import glob
from os.path import join as pjoin, dirname
import csv
import re
import pytest
from .utils import TESTS_DATA_PATH
import logging
lgr = logging.getLogger(__name__)
t... |
77bf3cd6b27416938bfec20b8594cd099f6bb24ac3026b7acdb90c9a130b069a | Python | 5,280 | 130 | ## 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.
from ipaddress import IPv4Address
from... |
3211c0761bf0a15ee3050afe5dd7e15d58b61b158e92c654db3a403630c40367 | Python | 5,283 | 164 | """Tests for current_user_scoped_session dependency."""
import pytest
from httpx import AsyncClient
from zndraw_auth import TokenResponse, UserCreate
async def _register_and_get_token(
client: AsyncClient, email: str, password: str, login_form_class: type
) -> str:
"""Register a user, login, and return the ... |
c6dc351191ecb3072baa9c7b365f115996e965e4ae994e804d59bb5da18ae801 | Python | 5,285 | 159 | """Create evaluator with LFP related efeatures"""
"""
Copyright (c) 2016-2022, 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.... |
87179ccea013b17af87156be35e646bebf99f41d20ed27a232fd62b670dd3766 | Python | 5,290 | 149 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import os
import shutil
import itertools
from multiprocessing import Pool
import numpy as np
from dmriqcpy.io.report import Report
from dmriqcpy.io.utils import (add_online_arg, add_overwrite_arg,
assert_inputs_exist, asser... |
317ac667ce4fce5840053bb168f384a34a9bca34c1999d4c1ed19054a4289ca6 | Python | 5,291 | 150 | # Copyright (c) OpenMMLab. All rights reserved.
import math
from mmcv.cnn import build_conv_layer, build_norm_layer
from mmseg.registry import MODELS
from ..utils import ResLayer
from .resnet import Bottleneck as _Bottleneck
from .resnet import ResNet
class Bottleneck(_Bottleneck):
"""Bottleneck block for ResNe... |
85b42c1a8ce08b10f535bb9602247a3e4be1b8d66791868c63517c9ab7750ba4 | Python | 5,299 | 162 | #!/usr/bin/env python
import sys, os, random
from argparse import ArgumentParser, FileType
from multiprocessing import Process
def shuffle_reads(read_fname, random_list):
reads = []
read_file = open(read_fname)
for line in read_file:
if line[0] == ">":
reads.append([])
reads[-1... |
88775c42c01da6a61f0a08795b6199f9cae36af27065028c82d7e94c9e35a7a6 | Python | 5,299 | 161 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------
# @File : main.py
# @Time : 2024/03/14 15:48:58
# @Author: Zhang, Zehong
# @Email : zhang@fmp-berlin.de
# @Desc : None
# -----------------------------------
import os
import math
import numpy as np
import pandas as pd
import torch
... |
a34c92b06459286bbc4e4b986bb0a89562a857993b5c27cb315f6fe301218dea | Python | 5,305 | 138 | from medperf.exceptions import MedperfException
from medperf.asset_management.gcp_utils import (
GCPAssetConfig,
CCWorkloadID,
upload_string_to_gcs,
encrypt_with_kms_key,
set_kms_iam_policy,
set_gcs_iam_policy,
update_workload_identity_pool_oidc_provider,
)
from medperf import config as medp... |
69fdfd1d61dd48b0114f90b8201ed3d4c2abc35fd45fefae68db49a65a5b35a2 | Python | 5,309 | 119 | import numpy as np
#-------------------------------------------Raw sequences-----------------------------------------
# -----Public Databases-----
VDJ_DATA_PATH = './datasets/filtered_vdj.csv'
MCPAS_DATA_PATH = './datasets/filtered_mcpas.csv'
IEDB_DATA_PATH = './datasets/filtered_iedb.csv'
MIRA_DATA_PATH = './datasets... |
f9eb003eec4924f0144da3a4445ab4d91afd22a782287f99f25d47120c5cb03e | Python | 5,309 | 133 | """Base class for assembling fragments and performing model updates."""
from typing import Dict, List, Optional
import torch
from torch import nn
from oa_reactdiff.model import MLP, EGNN
class BaseDynamics(nn.Module):
def __init__(
self,
model_config: Dict,
fragment_names: List[str],
... |
8013528b4521717753e144012a6793b870409912551c50d32e963b9c4593f4d7 | Python | 5,310 | 106 | """Why the GARD website browses 6,265 diseases while the list Babel ingests holds 16,214.
The question this answers is whether the ~9,949 terms with no page are deprecated entries Babel
should be filtering out. They are not: the CSV's own ``URL`` column marks which terms have a public
page, the partition is exact, and... |
028b7f527339a1a2fed7133f87b831d7bb29056602f59cffa62f3f230c634e5a | Python | 5,311 | 158 | import logging
from pathlib import Path
import ase
import ase.io as ase_io
import numpy as np
import typer
import zntrack
from simgen.element_swapping import SwappingAtomicNumberTable
from simgen.generation_utils import calculate_restorative_force_strength
from simgen.integrators import IntegrationParameters
from sim... |
619dbf2caa34719e4a5dfc48983380ce0fc29c01101d6a21dfa856d27b69af90 | Python | 5,311 | 140 | import torch
import torch.nn as nn
from collections import OrderedDict
# -------------------------
# XBlock for RegNetX
# -------------------------
class XBlock(nn.Module):
def __init__(self, in_channels, out_channels, stride=1, group_width=16):
super(XBlock, self).__init__()
# Calculate t... |
d6d4110ac9600c322d1c5ce401d18e929a968398931b4b0c7b5094853be77cb4 | Python | 5,311 | 154 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 11 09:42:59 2023
@author: schwab
"""
from pathlib import Path
from typing import Optional
import torch
from torch.utils.data import DataLoader
from typer import Option
import os
import sys
from ..data.handlers.particle_image_preprocessor import ... |
55fa94968828c13d6581ef62633b071c626d9f8c35dbe63fa446cfa0ec20c724 | Python | 5,312 | 170 | #!/usr/bin/env python
# coding: utf-8
import os.path as op
import random
import time
import matplotlib.pyplot as plt
import numpy
import sklearn
import torch.nn.functional as nn_func
from sklearn import preprocessing
from sklearn.metrics import adjusted_rand_score
from torch.nn import Linear
from torch_geometric.data... |
1bcee9940907e25ae3980568433057c6dabaa54597d1ab199c618e6f8effa20b | Python | 5,313 | 143 | import torch
def ablate(ab_type, ab_level, src, model, args):
"""
Apply ablation to the model based on the specified type and level.
Args:
ab_type: 'mask', 'bernoulli', 'gaussian')
ab_level: Level of ablation to apply (e.g., 0.1, 0.2, etc.)
src: Input data
model: Model to ab... |
0a1776a736ce6e49e023e58f5efd2790adbab6b96f5b05b8404fd66884bf0540 | Python | 5,314 | 154 | import cv2
import os
import tensorflow as tf
import numpy as np
import tensorflow as tf
from tensorflow.keras import backend as K
from tensorflow.keras.layers import Input, Conv2D, BatchNormalization, Activation, MaxPool2D, Conv2DTranspose, Concatenate
from tensorflow.keras.models import Model
from tensorflow.k... |
117bfa4220432094cafb07526ce2e3dcf358b1f0138e0051d74f921b50ff066b | Python | 5,315 | 166 | """Run simple cell optimisation"""
"""
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
... |
5cbe2e9dca6d726ca76f0436c711666fa2270d2ba90cab8fbfb1e3813ec9ac9a | Python | 5,315 | 160 | #!/usr/bin/env python
#
# This program is a wrapper for the isct_dice_coefficient binary
#
# Copyright (c) 2013 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import sys
import os
from typing import Sequence
from spinalcordtoolbox.utils.shell import SCTArgumentParser, Metavar
from spina... |
6a57dd687851ad3db770cb30bb63ede1f13955ddf54db802f690c2849e02ae27 | Python | 5,315 | 137 | import numpy as np
import pytest
from guppy.visualization.covariate_correlation import (
build_covariate_panel,
build_covariate_scatter,
)
@pytest.fixture
def scatter(panel_extension):
"""A three-bin scatter with one unusable bin, so the drop is observable."""
return build_covariate_scatter(
... |
81c4ffa0b63de8176636310d703f88e8cfe97ba62f19a201c008524392f84e2c | Python | 5,315 | 142 | import os
import yaml
import argparse
from utils import get_file_basename, get_file_extention
class SanityChecks:
def __init__(self, data_path, params_file):
"""A class wrapper for doing sanity checks on prepared dataset.
The checks consist of raising an AssertionError if:
the frames... |
3e1888c5f8eff3969ee7152bd90846cd0112f76c045eb95202a3c8e2638dca72 | Python | 5,319 | 137 | #!/usr/bin/env python
#
# Utility function to denoise diffusion MRI images
#
# Copyright (c) 2022 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import os
import sys
from typing import Sequence
import textwrap
import numpy as np
from spinalcordtoolbox.image import add_suffix, Image
fro... |
180f2082b370760b94306f208f46149a360125b3c30cfd26444a4fc1a114869a | Python | 5,321 | 145 | import torch
import pickle
import numpy as np
from utils import run_forward
from test import evaluate
class TrainingState:
"""
For maintaining results and tracking validation for early stopping
"""
def __init__(self, run_i):
self.run_i = run_i # run
self.step = 0 # step of training (to... |
46449d181b464a0c7569e41a9d4372aa4ac36e03fbeb3be4df89a938be65f71f | Python | 5,321 | 109 | """Shared clique-building scaffolding used by multiple compendium modules.
Factors out the common skeleton of turning a set of identifier files and concord files
into union-find clique state via :func:`src.babel_utils.glom`:
load each ids file -> glom into the clique state
load each concord -> optionally f... |
a3bcf697c7a02d6641dcc240d60aaebae1f796c3b003a89303c1e746e291b417 | Python | 5,321 | 154 | import cv2
import os
import tensorflow as tf
import numpy as np
import tensorflow as tf
from tensorflow.keras import backend as K
from tensorflow.keras.layers import Input, Conv2D, BatchNormalization, Activation, MaxPool2D, Conv2DTranspose, Concatenate
from tensorflow.keras.models import Model
from tensorflow.k... |
d8cefd4c3783c8040be4ae66b0714334a07e7582ef63e67abe80324dec7e3a75 | Python | 5,321 | 140 | import copy
import json
import os
import urllib.request
import zipfile
import generate_models as gm
import pytest
import xgboost
from xgboost import testing as tm
def run_model_param_check(config):
assert config['learner']['learner_model_param']['num_feature'] == str(4)
assert config['learner']['learner_tra... |
bccfbc3810e65d203dcaa951644bef482a2b31a4eaee6068ac00fa1fba15d49e | Python | 5,323 | 160 | # Copyright (c) OpenMMLab. All rights reserved.
import gzip
import html
import os
from functools import lru_cache
import ftfy
import regex as re
@lru_cache()
def default_bpe():
"""Return default BPE vocabulary path."""
return os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'bpe_voca... |
88e5e51b8165be527b67d5bfc9ab5ca81f8a385618eceff4fe4c3a1b64716291 | Python | 5,324 | 147 | from textwrap import indent, dedent
from ..utils import ensure_list_args, cypher_identifier
from ..client import inject_client
class SynapseCriteria:
"""
Synapse selection criteria.
Specifies which fields to filter by when searching for Synapses.
This class does not send queries itself, but you use ... |
dd6dd5ef61867657cdd7ab0732ff4f6be117ceb4152ffc814c4f0a2c1fc7d255 | Python | 5,324 | 144 | import torch
class MLP(torch.nn.Module):
def __init__(self, input_size=1, output_size=92, hidden_sizes=None,
compress_output=False, input_embedding=False,
init_bias_last_layer=1, conv_layer=False, conv_kernel_size=3,
fixed_kernel=False, even_odd=False):
s... |
82a134a57a2808c300cc02128b0100ca5f9e8ff3ce236df8f58c038ec124ea6f | Python | 5,329 | 109 | import os
import argparse
import numpy as np
from utils import *
import datetime
def main():
parser = argparse.ArgumentParser(description="Load training curves and"
"perform PCA.")
parser.add_argument("--input_dir", type=str,
default="/P... |
d72fcdcb6a5d0d5c791477054de3a228475c8a4cbcf005b6957ac18cfecc0a9b | Python | 5,329 | 119 | from typing import cast
import pytest
from ruamel.yaml.comments import CommentedMap
from schema_salad.sourceline import cmap
from cwltool.command_line_tool import CommandLineTool
from cwltool.context import LoadingContext
snippet = cast(
CommentedMap,
cmap(
[
{
"cwlVersion... |
7aab509096c7a53441de550c25586200a27dcfa196b5d401013106a19cce6a04 | Python | 5,330 | 148 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn.functional as F
from mmcv.cnn import ConvModule
from mmengine.model import BaseModule
from mmseg.registry import MODELS
from ..utils import resize
class CascadeFeatureFusion(BaseModule):
"""Cascade Feature Fusion Unit in ICNet.
Args:
lo... |
24534e407f3705be30a51238ed55d2427de32bed9eaf83966b3b9b21b8b885a7 | Python | 5,336 | 155 | # pylint: disable=unbalanced-tuple-unpacking, too-many-locals
"""Tests for federated learning."""
import multiprocessing
import os
import subprocess
import tempfile
import time
from typing import List, cast
from sklearn.datasets import dump_svmlight_file, load_svmlight_file
from sklearn.model_selection import train_t... |
9e3237bf98babf32e576d5b1acfcbc4254e171aa2715fe26cb43dfbf3ff2b522 | Python | 5,336 | 148 | import mne
from scipy.signal import detrend
import sys, os
from tqdm import tqdm
from glob import glob
import numpy as np
import itertools
import pandas as pd
try:
from braindecode.preprocessing import exponential_moving_standardize
from braindecode import EEGClassifier
from braindecode.util import set_ran... |
64ef9d074abd75b1880e39faa19567e11f7af7041540d7db007101c8838fa41a | Python | 5,340 | 132 | #!/usr/bin/env python
#
# Copyright 2008, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
c7cbcbaeba6c172284a08324527ce69103f9b3165a4090c72f6912f57718f03b | Python | 5,343 | 157 | import os
import glob
import random
import pickle
from data import common
import numpy as np
import imageio
import torch
import torch.utils.data as data
class SRData(data.Dataset):
def __init__(self, args, name='', train=True, benchmark=False):
self.args = args
self.name = name
self.train... |
0d18acdb4c203a67e15be7c47e8ccfbbdc923625c5363cfd8afa434a504e35a3 | Python | 5,344 | 133 | import time, os, subprocess
import pytraj as pt
import numpy as np
import dask
from dask.distributed import Client, performance_report, LocalCluster
import nearl
from nearl import features, utils, _tempfolder
# Only needs the fingerprint of the
def parallelize_traj(traj_list, focused_res):
traj_list = [i for i in ... |
1332cd94959a5a0dc0bc61c243839c25296dd98aaa9591d1b19b24db3ebc3b1e | Python | 5,344 | 159 | import logging
from pathlib import Path
import ase
import ase.io as ase_io
import numpy as np
import typer
import zntrack
from simgen.element_swapping import SwappingAtomicNumberTable
from simgen.generation_utils import calculate_restorative_force_strength
from simgen.integrators import IntegrationParameters
from sim... |
de146875d90ed81191b3c95fe710f5b2b47b7f4903f1e4fde4a941517fdb9a7a | Python | 5,347 | 155 | import cv2
import os
import tensorflow as tf
import numpy as np
import tensorflow as tf
from tensorflow.keras import backend as K
from tensorflow.keras.layers import Input, Conv2D, BatchNormalization, Activation, MaxPool2D, Conv2DTranspose, Concatenate
from tensorflow.keras.models import Model
from tensorflow.k... |
b5ff01ccb07aab3ff68f5429703a61a56ba92288e5c495e2ad7c3af243db1072 | Python | 5,349 | 111 | from PyQt5 import QtWidgets, QtCore, QtGui
from copy import deepcopy
class SetMultipleDialog(QtWidgets.QDialog):
"""
Dialog that lets the user check for every object if the feature settings
of the currently selected object should be copied.
"""
def __init__(self, data_manager, index):
... |
902c6a613cffe332756fd1f50e359bedbc0e1305f41ced54f73fd43acd6006aa | Python | 5,350 | 181 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... |
f3b294c908491b589279e4fc8a3d0442dfab8f02877290c217a04440f3dbc35f | Python | 5,355 | 167 | #!/usr/bin/env python
import argparse
import torch
from torch.utils.data import DataLoader
from tqdm import tqdm
from MCMG_utils.data_structs_GM import MolData, Vocabulary
from models.model_MCMG import transformer_RL
from torch.optim import Adam
from MCMG_utils.Optim import ScheduledOptim
from MCMG_utils.early_stop.p... |
3d2d9f561085b0b497148b31d2f721ad101f7b148064787961d556a72e72d776 | Python | 5,357 | 196 | from datetime import datetime
from pydantic import BaseModel, Field, validator
from typing import Optional, Union
from medperf.enums import Status, CryptoKeyType
class MedperfSchema(BaseModel):
for_test: Optional[bool] = False
id: Optional[int]
name: str = Field(..., max_length=128)
owner: Optional[i... |
25a94903a4721e0fd48ceaccb27c066f41f545fec4f800f76912d1bd12c0eb16 | Python | 5,359 | 141 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 28 15:20:55 2023
@author: george
"""
import pandas as pd
import json, codecs
import numpy as np
from qtpy.QtCore import QUrl, QRect, QPointF, Qt
from qtpy.QtGui import QDesktopServices, QIcon, QPainterPath, QPen, QColor
from qtpy.QtWidgets import Q... |
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