sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d172bcb087f6f798301626b126bfb1f7d5a878422069ed7b4c713948e62677ce | Python | 26,828 | 688 | """Stores class definition of ResearchObject and WritableBagFile."""
import datetime
import hashlib
import os
import shutil
import tempfile
import urllib
import uuid
from collections.abc import MutableMapping, MutableSequence
from pathlib import Path, PurePosixPath
from socket import getfqdn
from typing import IO, TYP... |
b07ac647d64e6368bcea91c3c1d226c9f8a4f67a99f432c6b523071fde0040fc | Python | 26,840 | 789 | ###########################################################################################
# Elementary Block for Building O(3) Equivariant Higher Order Message Passing Neural Network
# Authors: Ilyes Batatia, Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
################################... |
38390942513613c2ab037daaf7ed3579c873573bdc1936e4863d8b6444cfa474 | Python | 26,851 | 795 | """Performs 2D non-linear alignment of sections to sections from reference volume using ANTs."""
import glob
import json
import logging
import os
import shutil
import brainbuilder.utils.ants_nibabel as nib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from brainbuilder.qc.validate_section_ali... |
8a2203a746716d66a10dfcdbab3a2480e8904e0ea54fb91759a27ddec8665191 | Python | 26,897 | 671 | #!/usr/bin/env python
#
# Perform mathematical operations on images
#
# Copyright (c) 2015 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import sys
import pickle
import gzip
import argparse
from typing import Sequence, Union
import textwrap
import numpy as np
import spinalcordtoolbox.... |
c162a9f4e865ef55ec12fb5f097d10e966e0734db93c52acedad1645edb6b2a1 | Python | 27,024 | 683 |
# Third party inports
import tensorflow as tf
import tensorflow.keras.backend as K
from tensorflow import keras
import numpy as np
import pdb as gdb
import math
import neurite as ne
import voxelmorph as vxm
import scipy.io as sio
# batch_sizexheightxwidthxdepthxchan
from scipy.signal import convolve2d
def diceLoss... |
1ce92a615d6eb6ca3e977858bbc513f8d4b4cf80a4829aef403c2de43cb69a0e | Python | 27,030 | 637 | from PyQt5.QtWidgets import QMessageBox, QDialog, QVBoxLayout, QLabel, QProgressBar, QApplication, QPushButton, QFileDialog, QHBoxLayout
import json
def print_error(s, extra_info="", severity=QMessageBox.Critical):
dlg = QMessageBox()
dlg.setWindowTitle("Error Message")
if isinstance(s, tuple)... |
d12897a3d8874642675b7eac5fd96b010017ac6e7d327f173ca9e0e794becee8 | Python | 27,060 | 569 | import logging
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple, Union
from io import StringIO
from celery import shared_task
from celery.utils.log import get_task_logger
import time
import csv
import traceback
from django import forms
from django.conf import settings
from django.core.exceptions ... |
985b71c10d2285d1a2d703082b813c5ea4fe938efce126f416e11c063f706f18 | Python | 27,074 | 802 | """Built-in loss functions.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import abc
import six
from . import backend as K
from .utils import losses_utils
from .utils.generic_utils import deserialize_keras_object
from .utils.generic_utils import seria... |
17690918684372a1e0792f0d5bee4e34bbe0fd1dd37acbd414ad61ad784c3a48 | Python | 27,088 | 586 | import torch
import os
import numpy as np
import dgl
import logging
import datetime
import math
import sys
import gc
import json
import time
import torch.nn.functional as F
import warnings
from functools import partial
from collections import OrderedDict
from torch.utils.data import DataLoader
try:
from torch.utils... |
c0de83f2844a5a42aef3d082ac18e259082afcff6eea88701dbc9b8e1c8b7ace | Python | 27,112 | 751 | import argparse
import json
import os
import random
import time
import h5py as h5
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.stats
import seaborn as sns
import torch
from torch import nn, optim
from torch.utils.tensorboard import SummaryWriter
import nearl
from nearl.io.datase... |
fcf81f1fc19a321593f4aa4da51a2e10a5cf782e3fdf3274e1c69e0cf6d5ad14 | Python | 27,131 | 902 | """Utility objects and functions"""
from __future__ import annotations
from collections.abc import Callable
from collections.abc import Mapping as MappingABC
import copy
import datetime
from glob import glob
import hashlib
import json
from json.decoder import JSONDecodeError
import logging
import os
import os.path as... |
31bfeb17ebc9a2ae358b89ae974eaba6b011a8e28a4eea264f8fad747fbea5c6 | Python | 27,174 | 795 | from rest_framework import status
from medperf.tests import MedPerfTest
from parameterized import parameterized, parameterized_class
class BenchmarkTest(MedPerfTest):
def generic_setup(self):
# setup users
bmk_owner = "bmk_owner"
prep_mlcube_owner = "prep_mlcube_owner"
ref_model_... |
867adec38451e13b5e549f79dbe8e5f0b0f0b3e090c2d5c95d6c0ef287020b04 | Python | 27,196 | 750 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import (GCNConv,
ChebConv,
SAGEConv,
GraphConv,
TAGConv,
ARMACo... |
33111773c95fa026ec134a3876a42fa46e758198a2e7b1535c23f50fd121aebf | Python | 27,202 | 940 | import os
import sys
import pyabf
import paq2py
import numpy as np
import pandas as pd
import seaborn as sns
import scipy.interpolate
from utilities import *
import matplotlib.pyplot as plt
from scipy.stats import linregress
from scipy.signal import find_peaks
from scipy.optimize import curve_fit
#~~~~~~~~~~~~~~~~~~~~~... |
d09edb8e0aa446ac90296263f5f69f76bc3f424861300ab7bf358ff1c311a8f8 | Python | 27,205 | 649 | # coding=utf-8
# Copyright 2021 The IDEA Authors. All rights reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by a... |
45d3dd005d3605adac7648bcf92cc94cf476fc08eb5c17de4eee2a437ebbcfe3 | Python | 27,214 | 481 | """
Automation logic for batch processing analyses across multiple sessions.
"""
import json
import os
import pandas as pd
import numpy as np
from .backend import DataInstance
from .shuffling import shuffle_cofiring, shuffle_advanced
from .exploration_statistics import generate_general_statistics, generate_local_stati... |
7e4c1690508fd82a90856558a4c3db1ed04d408a0e988a307f2a22bbccfc2318 | Python | 27,220 | 563 | # Provided by the FeTS Initiative (www.fets.ai) as part of the FeTS Challenge 2022
# Contributing Authors (alphabetical):
# Patrick Foley (Intel), Micah Sheller (Intel)
import os
import warnings
from collections import namedtuple
from copy import copy
import shutil
from logging import getLogger
from pathlib import Pa... |
1b82dbe1be95efeec23c5a39a5109cef3bce80da9c982f377e8b4df487f50188 | Python | 27,288 | 548 | # Copyright (c) OpenMMLab. All rights reserved.
from mmengine.utils import is_str
def cityscapes_classes():
"""Cityscapes class names for external use."""
return [
'road', 'sidewalk', 'building', 'wall', 'fence', 'pole',
'traffic light', 'traffic sign', 'vegetation', 'terrain', 'sky',
... |
0e4b73f911e2e4ba724a9121b618cfbc6418c9da07f845bb49ce141b0b57bde0 | Python | 27,294 | 730 | import torch
import torch.nn as nn
import torch.optim as optim
from torch.optim import Adam,AdamW
from torch.optim.lr_scheduler import ExponentialLR, StepLR, LinearLR
import torch.nn.functional as F
import torch.nn.init as init
import matplotlib.pyplot as plt
import torchvision
from torchvision.transforms import tran... |
6042e7ca54b71876ffd9e488d2030aebf8207cc195b55aec3f4ac4fb6e548699 | Python | 27,308 | 501 |
# This file is part of the Firmware project to interface with small Async or Neuromorphic chips
# Copyright (C) 2023-2024 Ole Richter - University of Groningen
# Copyright (C) 2024 Vincent Jassies - University of Groningen
#
# This program is free software: you can redistribute it and/or modify
# it und... |
31365b03dee32ab331975bee3fd54287c66829a53cb1d6bccb91efeb2cb75694 | Python | 27,316 | 639 | # 3D visualization in MagellanMapper
import math
from time import time
from typing import Any, Callable, List, Optional, Sequence, Tuple, TYPE_CHECKING
import numpy as np
from skimage import filters, restoration, transform
from magmap.cv import colocalizer, segmenter
from magmap.io import libmag
from magmap.plot imp... |
c0a94a662cb77edcfd7c03afc4905ecdfe0b947f5a1f63aa2e42e5e1be431bce | Python | 27,350 | 668 | import numpy as np
from dataset import *
from surrogate_model import *
from collections import namedtuple
from abc import ABC, abstractmethod
from collections import defaultdict
import math
import random
import copy
dataset = NasBench('./nasbench_dataset')
CONV3X3 = 'conv3x3-bn-relu'
CONV1X1 = 'conv1x1-bn-relu'
MAXPO... |
0db7fcc879e9f0fdc98edb130a13363bb694d75c8dbd59fb838c8894749655c9 | Python | 27,379 | 1,022 | import subprocess
import sys
import os
from io import StringIO, BytesIO
import dnaio
import pytest
from cutadapt.cli import main
from utils import assert_files_equal, datapath, cutpath
# pytest.mark.timeout will not fail even if pytest-timeout is not installed
try:
import pytest_timeout as _unused
except ImportE... |
99b1ebd8a20777dd54bab572c2ee546ebc868f1d4e5862fa3c742fb075317b1a | Python | 27,390 | 670 | import numpy as np
def get_uniform_mass_bins(probs, n_bins):
assert(probs.size >= n_bins), "Fewer points than bins"
probs_sorted = np.sort(probs)
# split probabilities into groups of approx equal size
groups = np.array_split(probs_sorted, n_bins)
bin_edges = list()
bin_upper_edges = list(... |
04787acf87c73351585a49e591d2ba516fc607484031fa60e5c7d1c73846b52d | Python | 27,404 | 736 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Conv1d, Linear, Module, ModuleList, Sequential
from torch_geometric.nn import knn_graph, radius_graph
from torch_scatter import scatter_softmax, scatter_sum
from models.common import MLP, NONLINEARITIES, GaussianSmearing
class No... |
6669af750f3f7f3f90d00d8dca911924f09739578bba83c0e2c90d11bc01ed05 | Python | 27,475 | 663 | """CLI for the per-source impact report.
Invocation:
uv run source-impact-report --source EMAPA
uv run source-impact-report --source GARD --concord GARD --concord GARD_label
The CLI discovers where the source contributes (across one or more pipelines),
runs a synthetic re-glom with and without the source for ... |
8b90189b32bcb75b805a3d0b41e3db90107bf9819b473a7eae5e709fc408101c | Python | 27,501 | 705 | # -*- coding: utf-8 -*-
from datetime import timedelta, datetime
from dateutil import parser as dateparser
import io
import logging
import numpy as np
import pytz
from typing import Any, Dict, List, Tuple
from django.db import connection
from django.http import HttpRequest, HttpResponse, JsonResponse
from django.shor... |
2723a08208ef451e8ea573fe8959a4082dab2cc2b6485aec016bba2c5167c9dc | Python | 27,514 | 640 | # coding=utf-8
# Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... |
d0016c7dc11db849e6c65924a40af38887f021e04a57638755923d4137110ecd | Python | 27,556 | 660 | # coding=utf-8
# Copyright 2021 The IDEA Authors. All rights reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by a... |
130314a3c61bbace90bfbaa26c2ee49369113d2930993a1ca0dad8bc6e0d1cc9 | Python | 27,570 | 646 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
import torch_geometric
import copy
from .activation import (
ScaledSiLU,
ScaledSwiGLU,
SwiGLU,
ScaledSmoothLeakyReLU,
SmoothLeakyReLU,
GateActivation,
SeparableS2Activation,
S2Activation
)
from .layer_n... |
fc48971c2edcf2dd6c7030f29cebb525ad7d84b1c9fcb342dd9d84c86b86f036 | Python | 27,576 | 587 | #!/usr/bin/env python
# Functions for ICA-AROMA v0.3 beta
from __future__ import division
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from builtins import str
from builtins import range
from past.utils import old_div
import numpy as np
def runICA(fslD... |
1d34b0375ba905da339543a11f49bb46c6c1885fff32b14f6e8dc866e3df7190 | Python | 27,586 | 611 | from PyQt5 import QtGui, QtWidgets, QtCore
import pyqtgraph as pg
import numpy as np
from copy import deepcopy
from scipy.signal import savgol_filter
from scipy.optimize import curve_fit
from util.conf import sd_params, bd_params
from util.functions import movingAverage, func_exp
from features.Feature import Feature
... |
5f74e27ef948b37441010cede4e7a6d40aa801a8cd4c4c21dfd3c2116592fa31 | Python | 27,640 | 619 | import numpy as np
from copy import deepcopy
import torch
from torch.backends import cudnn
from torch.cuda.amp import GradScaler, autocast
from torch.nn import Identity
from nnunet_mednext.network_architecture.generic_UNet import Upsample
from nnunet_mednext.network_architecture.generic_modular_UNet import PlainConvUN... |
3dc421573f38bc0b20740aabaed1a493889671ab249f5b968c746c72891e03a8 | Python | 27,678 | 933 | # tests/test_resilience.py
"""Red-phase tests for JobManager resilience features.
These tests verify the planned resilience behaviors:
- Fatal errors (404 / PermissionError) trigger immediate exit
- Transient errors (ConnectError) are tolerated up to max_unreachable_seconds
- disconnect() is idempotent, thread-safe, a... |
ac0f3416ca1038f2a5a46bff59955763cb5c52623266a9e60875369ae269fe58 | Python | 27,682 | 790 | # -*- coding: utf-8 -*-
# encodermap/__init__.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is free s... |
2ae11b5a1206a39c5abf585c34aa7f2e41ca7e185b5a18335bdd9ca14afcb796 | Python | 27,739 | 655 | #%%
import numpy as np
import os
# import nibabel as nib
import pandas as pd
import joblib
import time
from sklearn.preprocessing import StandardScaler
from sklearn.svm import LinearSVR, LinearSVC
from sklearn.model_selection import (train_test_split, cross_val_score,
KFold)
from scipy.optimize import linear_sum_as... |
ea2b5fce3109ff01b7ad9013e00b677e34c56b81d89b6d31aba03a329d6e9538 | Python | 27,760 | 597 | """Shared parsers for Babel SLURM run artifacts.
Three kinds of artifact are produced by a Snakemake-on-SLURM run and copied into a
run-analysis directory such as ``data/babel-1.17/``:
- ``benchmarks/<rule>.tsv`` — Snakemake ``benchmark:`` output (actual usage).
- ``reports/slurm/slurm_efficiency_reports/`` — the... |
81582943b47e7598c851943c676e5fc2d81ec4066e627be3643936dfb7db2b01 | Python | 27,772 | 850 | """
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.
---
This code borrows heavily from the DimeNet implementation as part of
pytorch-geometric: https://github.com/rusty1s/pytorch_geometric. Licens... |
3d230e728974334ab622ef2534f19401e77e41a6d4a570639c09630fa1c1e6de | Python | 27,784 | 729 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
import wandb
from Utils.dataloader_RSNA_BONE import *
from Utils.config import loaderConfig
from torch_lr_fi... |
240c1f223d28afddabffbfdd6b101576de2264588b8f753336ff44be0911cefa | Python | 27,832 | 744 | import copy
import psutil
from itertools import combinations
from numpy import linalg as LA
from IPython import embed
from abc import ABCMeta, abstractmethod
from pathlib import Path
from collections import deque
from typing import Dict, List, Callable
import math
import time
import mcmc
from ray_model import MuscleNN,... |
2d33c66b5dc5770998708f0ce7009fbd6168dbe9e4cd2cd2acc67dc01de3a253 | Python | 27,919 | 661 | from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
#from builtins import str
from quantities.quantity import Quantity
import sciunit
from sciunit import Test,Score
try:
from sciunit import ObservationError
except:
from sciunit.errors import ObservationEr... |
d587137e0cae96ab6977c989155975cdfaf061b630b5ebe1505e1c38f60727e0 | Python | 27,919 | 928 | import re
import yaml
import h5py
import numpy as np
import pathlib as pl
from datetime import date
from types import SimpleNamespace
from scipy.interpolate import interp1d as interp
from myphdlib.interface.ephys import Population
class SessionBase():
"""
"""
def __init__(self, home, eye='left', loadEphys... |
b2a526b9f98a051b6bbc84dd1a40510c187c7dd28243492a8ba7ab6c601eb6db | Python | 27,927 | 943 | # Config file for shared settings
# Author: David Young, 2017, 2020
"""Configuration storage module.
This module allows customization of settings for various imaging systems,
such as grouped settings for particular microscopes. Additional parameters
such as command-line flag settings and databases can also be stored... |
88f74748615d58f43ac6177ebd8f7d3f78b3fd3200ca411d3543fcdab12fddba | Python | 27,959 | 795 | """Validate interpolation error by comparing original autoradiographs to 2D and 3D interpolated autoradiographs."""
import os
import brainbuilder.utils.ants_nibabel as nib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from brainbuilder.utils.utils import shell
from joblib... |
3d40e2eabb9cdb7b164e89678b7e7be455819b7a5816a6cb721859060fd111e0 | Python | 27,972 | 656 | # -*- coding: utf-8 -*-
# encodermap/callbacks/callbacks.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encoderma... |
b02e5d1ab8b6ee1126050e8102e37b8c8bdc4e54f5d7f101b7efd15478e25476 | Python | 28,011 | 684 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
from Utils.dataloader_BrainTumorMRI import *
from Utils.config import LoaderConfig, ModelConfig
from torch_l... |
28660f96ce6206b4a01f4dd41c19c9a83760c119c4eee7393a27cc028b881ddd | Python | 28,030 | 634 | #!/usr/bin/env python
#
# Perform operations on images
#
# Copyright (c) 2015 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.scripts import sct_apply_transfo, sct_resample
from sp... |
ccb6acb60e1067139978f1345f275096577aae982b26784e7e6ab25faf933ff7 | Python | 28,064 | 693 | import numpy as np
from torch_geometric.data import Data
import math
def PublicPST_GNN(env, *args):
'''
The state function for the GNN model.
It returns the state of the environment in a format that can be used by the GNN model.
'''
PublicPST_GNN.node_sizes = {'ev': 6, 'cs': 4, 'tr': 2, 'env... |
bb1ac2e9c89bbf8ee197ed7bafb9c00368e797d3fddd1c1b7068ac95cbbb7ca8 | Python | 28,102 | 1,240 | import pandas as pd
import matplotlib.pyplot as plt
df = pd.read_csv('Datasets/url dataset/phishing_site_urls.csv')
print("Unique values in 'Label' column:", df['Label'].unique())
df['new_label'] = df['Label'].apply(lambda x: 'Non-Phishing' if x == 'good' else 'Phishing')
original_counts = df['new_label'].value_c... |
3bc227d33ef79e51ce8c840abb63a010a8d9403474b78eb84196286c516da66d | Python | 28,125 | 663 | #%%
import scipy.io as sio
import numpy as np
from custom_functions import dat_prep_4d_section,dist_theta_kfold,circ_dist,circ_mean
from scipy.ndimage import gaussian_filter1d
import matplotlib.pyplot as plt
import pickle
import seaborn as sns
import pandas as pd
import os
import mat73
import matplotlib as mpl
dat... |
d082cdebde4e0472cca053550e85698842cd7a84bafda72c6f97ad5b9c17fde5 | Python | 28,137 | 820 | import os, shutil, subprocess, importlib, re, pickle, math, array, fcntl, time, random, math, time
import numpy as np
import matplotlib.pyplot as plt
import urllib.request
from glob import iglob
from glob import glob
from pathlib import Path
def objtoarr(path, symbol="v"):
dicts={"v": "Vertices",
"s": ... |
5718c5c177d6f1a7d5f44e319bf7cbdd449bfbde5ea1d8e8cdb4ac68e937207a | Python | 28,244 | 836 |
# This file is part of the Firmware project to interface with small Async or Neuromorphic chips
# Copyright (C) 2022-2023 Ole Richter - University of Groningen
# Copyright (C) 2024 Vincent Jassies - University of Groningen
#
# This program is free software: you can redistribute it and/or modify
# it und... |
1167f5a27a30c1b7b9ed417e4309ea4093e72733b29cb7e72ef82feed8ab978c | Python | 28,254 | 645 | '''
Trains CFRNet model.
Causal modelling approach. Similar to VGAE + MLP join training in train_jointly.py,
but uses two MLP heads, for predicting each treatment condition separately.
Authors: Hanna M. Tolle
Date: 2025-04-16
License: BSD 3-Clause
'''
import sys
sys.path.append('graphTRIP/')
from sacred import Exper... |
993e205ce43319a5c8ae53bfdd5897ca8f586c19e730469d8372c0b1b00bddb1 | Python | 28,301 | 793 | from enum import Enum
import os
import pandas as pd
import numpy as np
import collections.abc
from typing import Dict, Union, List, Tuple, Optional, cast
import math
import re
import torch
from torch.utils.data import Dataset
from torch_geometric.utils.smiles import from_smiles
from torch_geometric.data import Data
fr... |
939dfa8a97878f17a3bf16d250c15799831f4c52a6238ea40706f54390dc4723 | Python | 28,315 | 744 | """
KGX Validator class
"""
import re
from typing import List, Optional, Dict, Set, Callable
import click
import validators
from bmt import Toolkit
from kgx.error_detection import ErrorType, MessageLevel, ErrorDetecting
from kgx.config import get_jsonld_context, get_logger
from kgx.graph.base_graph import BaseGraph
f... |
14a3d2882db357ad3271e6eababf5c0671cf8797af30c3bb96ea3deac0f2a534 | Python | 28,317 | 955 | """Integration tests for the ZnDraw Python client.
These tests verify client functionality against a running server.
The ZnDraw client works with ase.Atoms objects as frames.
"""
import uuid
import ase
import httpx
import pytest
from zndraw import ZnDraw
def make_atoms(positions: list[list[float]], symbols: str =... |
d82151b649300e8df5bf331666a2aad7b3ad47c6820676827f228a2ad3eaec6d | Python | 28,346 | 763 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import build_norm_layer
from mmcv.cnn.bricks.transformer import FFN, build_dropout
from mmengine.model import BaseModule
from mmengine.utils import to_2tuple
from mmseg.registry import MODEL... |
c815e7c8a01e2f10c72a29862074cc4173f07d7f37b6b880dcdf283abed64859 | Python | 28,404 | 696 | '''
BrainGraphDataset class for loading and processing brain graph data.
License: BSD 3-Clause
Date: 2024-10-30
Author: Hanna M. Tolle
'''
import sys
import os
import numpy as np
import pandas as pd
from tqdm import tqdm
import torch
from torch_geometric.data import InMemoryDataset, Data
from torch_geometric.utils i... |
148e9f8101462e683a242098b578e1b680e1fb337bb2c45edcd5339a55705892 | Python | 28,417 | 830 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
# pyre-strict
# pyre-ignore-all-errors[2,56]
import logging
import typing
import unittest
import warnings
from collections import Counter
from typing import Any, Dict, List
import torch
import torch.nn as nn
from fvcore.nn.flop_count import FlopC... |
41cc9e15f4c296f4d17412e3c2167b827fa4f34b92cca1d75692c315c5de0a6c | Python | 28,453 | 841 | import h5py
import numpy as np
from matplotlib import pyplot as plt
from scipy.signal import find_peaks as findPeaks
from matplotlib.colors import LinearSegmentedColormap
from myphdlib.general.toolkit import psth2
from myphdlib.figures.modulation import BasicSaccadicModulationAnalysis
from myphdlib.figures.analysis imp... |
682abf2fbb46891e7df23b034aa8f9d00ad493fb1cfa7b441c24b5a0fd961ac9 | Python | 28,459 | 860 | # dicom operations
from __future__ import annotations
from collections.abc import Callable
import datetime
import logging
import os
import os.path as op
from pathlib import Path
import sys
import tarfile
from typing import (
TYPE_CHECKING,
Any,
Dict,
Hashable,
List,
NamedTuple,
Optional,
... |
e2edf59c5276517bcb7f76a47c8942bd18b47d98590087794d2a0b2eeb6fa614 | Python | 28,462 | 670 | import json
import logging
import shutil
from collections.abc import Callable
from pathlib import Path
import holoviews as hv # noqa: F401
import numpy as np
import panel as pn
from guppy.extractors import (
CsvRecordingExtractor,
DandiNwbRecordingExtractor,
DoricRecordingExtractor,
NpmRecordingExtra... |
d7517cf3d34be1e85da9eb8e8ab3e402522d11c42056fb55ca809ba84c0b8627 | Python | 28,515 | 750 | # Main script for MEA analysis
# Takes pre-processed HDF5 files and exports Matlab files for further processing.
# Last modified : 2022.02.22 (Run selection shortcut = Ctrl + Shift + E)
## ------------------------
# Import packages
# -------------------------
import numpy as np
import scipy.io
import scipy.signal as... |
e74b0b261ac00fdb9f84f2806690dc7707da862e90c0020a7d6ea1fe7f33f886 | Python | 28,565 | 693 | from typing import Any, Dict, List
import hydra
import numpy as np
import omegaconf
import pandas as pd
import torch
import pytorch_lightning as pl
import torch.nn as nn
from pymatgen.core import Structure
from torch.nn import functional as F
from torch_scatter import scatter
from tqdm import tqdm
... |
732572d07420084737a68f6d5907f630714d6940243f5bb4916875a7eadf32e6 | Python | 28,587 | 725 | """
Author : Alexis Lebrun (PhD student)
School : Université Laval (Qc, Canada)
This module provides funtions to generate new spectra by adding different variations to
existing spectra.
"""
import numpy as np
from sklearn.utils import shuffle
def _range_converter(param_range, multiplier_cond=False):
"""
Ret... |
520d4833281115edc57dd36b1dc7e0a9c840b210e23131f8e3ca582efd9e8e81 | Python | 28,609 | 742 | import json
import logging
import os
from collections import namedtuple
from io import StringIO
from uuid import uuid4
from prov.constants import PROV_ATTRIBUTES, PROV_MENTION, PROV_BUNDLE, PROV_LABEL, PROV_TYPE
from prov.model import ProvDocument, ProvEntity, ProvBundle, ProvRecord, ProvElement, ProvRelation, Qualifi... |
1157e3a46cb602124f34c2ade67d16b6f77b12a9a8bcc6e88f431878f3b62298 | Python | 28,648 | 873 | import os
from typing import List
from pprint import pprint
import pytest
from kgx.utils.kgx_utils import GraphEntityType
from kgx.transformer import Transformer
from tests import RESOURCE_DIR, TARGET_DIR
from tests.integration import (
DEFAULT_NEO4J_URL,
DEFAULT_NEO4J_USERNAME,
DEFAULT_NEO4J_PASSWORD,
)
... |
0e69bbcc3f98a43bebe7a43aff690cbde80aa7641d89d94ae8d366f39aaa4ed3 | Python | 28,649 | 748 | import os
import pdb as gdb
import nibabel as nib
import numpy as np
import freesurfer as fs
import tensorflow as tf
from tensorflow.python.eager.context import context, EAGER_MODE, GRAPH_MODE
from tensorflow.keras.callbacks import Callback
from shutil import copyfile
def switch_to_eager():
switch_execution_mode(... |
6ffdcdd818cdaa0780aa804d10ef8613fd5436573e1575321599fdc56a3c6671 | Python | 28,693 | 678 | # coding=utf-8
# Copyright 2021 The IDEA Authors. All rights reserved.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by a... |
cff9b4faf9ac8ce92c351731f73f546312bbcf9aeb80ab6652e02f4155646849 | Python | 28,723 | 717 | import multiprocessing
import pickle
import csv
import os
import sys
import numpy as np
import sklearn.model_selection as ms
import torch
import time
from torch.utils.data import TensorDataset
from tqdm import tqdm
from transformers import AutoTokenizer, AutoModel
from layers.embedder import PackedBert
from argparse i... |
51ce92c7593bcf68099e4b865b22e210883046208a827e86a4d77e6395a5d278 | Python | 28,745 | 758 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
import wandb
from torch_lr_finder import LRFinder
METRICS_LOSS_NDX = 0
METRICS_TP_NDX = 1
METRICS_FN_NDX =... |
6caaa5ecf33e40db7ad237c3bd7db416d2e0243dd4cf3871da788c592257801d | Python | 28,770 | 878 | """Tests for Trajectory REST API endpoints (download/upload + download tokens)."""
import io
from typing import Any
import ase
import ase.io
import numpy as np
import pytest
from asebytes import decode, encode
from helpers import auth_header, create_test_room, create_test_user_in_db
from httpx import AsyncClient
from... |
6cfcd32eedb83e268cb6104abea795020d58cf41a02674619f8e0b828fe10add | Python | 28,780 | 728 | import copy
import math
from typing import List
import torch
import torch.nn as nn
import torch_geometric
from .activation import (
GateActivation,
S2Activation,
SeparableS2Activation,
SmoothLeakyReLU,
)
from .drop import EquivariantDropoutArraySphericalHarmonics, GraphDropPath
from .layer_norm import... |
c128f8a1e015acdffe7a29e21ee015b032d6ded56b4287a652ed9eba61b8c4b8 | Python | 28,783 | 768 | import pandas as pd
import numpy as np
import os
from tqdm import tqdm
from scipy.stats import pearsonr
import matplotlib.pyplot as plt
import seaborn as sns
import sys
import warnings
import textwrap
def load_phenom(y_group="_miller_mh_v1",
BASE_FOLDER='/Users/karinsaltoun/Documents/UKBB_files'):
... |
9302d7c7b5f972b833dbe96f29e596bc91ce5a5941430aef9f283133ba2b3005 | Python | 28,861 | 734 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
import wandb
from Utils.dataloader_COVID import *
from Utils.config import loaderConfig
from torch_lr_finder... |
ddc266ef5f998d7d3b4f957ddf9f853184c1ffb4fbad29e6c0036c0a0fcc63e1 | Python | 28,863 | 783 | import copy
from typing import Tuple, Optional, Dict, List, Any, Set, Union
import networkx as nx
from ordered_set import OrderedSet
from kgx.config import get_logger
from kgx.graph.base_graph import BaseGraph
from kgx.utils.kgx_utils import (
get_prefix_prioritization_map,
get_biolink_element,
get_biolin... |
e6acd2ea78e07706f6e2c0a0576fa8494bebac9bb10e5f96269fa56a18a7d567 | Python | 28,916 | 687 | import json
from pathlib import Path
import holoviews as hv
import numpy as np
import panel as pn
import pytest
from guppy.analysis.io_utils import fetchCoords
from guppy.frontend.artifact_removal import load_pair_traces
from guppy.frontend.artifact_windows_page import (
CONTROL_TRACE,
FIT_TRACE,
MARK_MOD... |
a006bd595cfc78e9e9dc4d8a89c7888a11f5e5455f0591d2d628d0a4c5b215e0 | Python | 28,947 | 682 | #!/usr/bin/env python
#
# Parser for PropSeg binary.
#
# Copyright (c) 2015 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
# TODO: remove temp files in case rescaled is not "1"
import os
import pathlib
import sys
import logging
from typing import Sequence
import textwrap
import numpy a... |
8cf070fd0cf71fb283cec5dc3f3a5dc10452f378a397b50f7ae13f4565afd40c | Python | 28,984 | 899 | import os
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
import pandas as pd
import seaborn as sns
from joblib import Parallel, delayed
from scipy.ndimage import gaussian_filter
from skimage.transform import resize
from brainbuilder.utils.utils import get_logger
logger = get_logger(__name__... |
1a2d9485ec263163da69a3214400eb53eaa056bb433735def69c98d9022c536c | Python | 28,990 | 688 | # Copyright (c) OpenMMLab. All rights reserved.
from typing import Any, Dict, List, Optional, Tuple
import numpy as np
import torch
from mmengine.runner.checkpoint import load_checkpoint
# yapf: disable
from sam.utils import (MaskData, area_from_rle, batch_iterator,
batched_mask_to_box, box_xyxy... |
b403ce4c51987af8f2e7bdbcf8bf3b9bdda3b6d362eb12b719c92c3282b29664 | Python | 29,026 | 740 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
import wandb
from Utils.dataloader_GRAZPEDWRI import *
from Utils.config import loaderConfig
from torch_lr_f... |
682ec1cf3915ae8491d8fcfa5dfe879f5ee5b9c6c456419d5a54160bee681fcc | Python | 29,031 | 937 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
# pyre-strict
# pyre-ignore-all-errors[2,3,14,53]
import typing
import unittest
from collections import Counter, defaultdict
from typing import Any, Dict, Tuple
import torch
import torch.nn as nn
from fvcore.nn.flop_count import _DEFAULT_SUPPORTE... |
c9a1b95fa60a6938aa28fc6892673dc20fd31941036e430a8c1af63398e13e6d | Python | 29,076 | 675 | import logging
import math
import os
import shutil
from pathlib import Path
from typing import Any
import numpy as np
import pandas as pd
from numpy import float32, float64, int32, int64, uint16
from guppy.extractors import BaseRecordingExtractor
from guppy.utils._hdf5_io import write_hdf5
logger = logging.getLogger... |
708334ed2ba44b2f116274382d3d865321a9dff9201fa80be39b95a396cd259a | Python | 29,079 | 672 | from ray.tune.utils import validate_save_restore
from itertools import combinations
import importlib
from IPython import embed
import mcmc
import argparse
import numpy as np
import json
import pickle
import os
from pathlib import Path
from typing import List, Tuple, Dict
from ray_model import SimulationNN_Ray, load_fro... |
d7bdf29558fb7c3e6503607b3279a0dc4c811ac130e99417831537e0e5e63e33 | Python | 29,089 | 618 | """Tests for the release-note drafting script (``releases/scripts/draft_release_notes.py``).
Covers the two parts that are easy to get quietly wrong: which PRs are folded away as routine, and
the number formatting in the `Summary of changes` table (a dropped `\\-` escape or a mis-shaped
from-zero row is invisible unti... |
9be479cc97d00a7d6b3c5a67aef180b81e698e96f4df2a12f40d18e4d860b50a | Python | 29,096 | 799 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 2 16:32:14 2023
@author: george
"""
from .io import FileSelector_overlay
from .helperFunctions import *
from pyqtgraph import HistogramLUTWidget
from qtpy.QtCore import *
from qtpy.QtGui import *
from qtpy.QtWidgets import *
import numpy as np
imp... |
e0edcfda7cc394a91303e60a48a12acc093042643ddf12dc8a9a831ec8ceac6d | Python | 29,154 | 688 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 4 12:18:02 2023
@author: schwab
"""
from Bio.PDB import PDBParser, MMCIFParser
import numpy as np
import torch
from .utils_new import*
import mrcfile
#from emda import emda_methods
def pdb2graphs(name):
O_e = 8
N_e = 7
C_e = 6
... |
f79dba1aa7032893a14b5e18113a863fa631c9bb569d3599070c6de6d11e8630 | Python | 29,186 | 762 | """
Esophageal Peristalsis Model
============================
Python translation of EsophagusModel.nb (Mathematica 13.3)
Model description
-----------------
Simulates esophageal peristalsis using three coupled variables per spatial
lattice point:
u : ENS (Enteric Nervous System) neural activity
v : ENS recovery v... |
b20ef0b6d058f9c1f50ff60fa7f2cfd33e33496aa79b3391809f040ee848d8f1 | Python | 29,264 | 637 | """
Functions dealing with metrics aggregation (mean, std, etc.) across slices and/or vertebral levels
Copyright (c) 2019 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
# TODO: when mask is empty, raise specific message instead of throwing "Weight sum to zero..."
import os
import num... |
b93cf13a5955df047ad6ac90bfd041ed8d21c3f283c5ee01f7d8d8174bbce69d | Python | 29,308 | 721 | # -*- coding: utf-8 -*-
import torch
import numpy as np
import torch.nn.functional as F
import math
import torch.nn as nn
import torchvision
import kornia.filters as KF
# from loss_ssim import ssim
shape = (256, 256)
import torch
import torch.nn.functional as F
from torch.autograd import Variable
import ... |
37490f8c942f9f8e08b2f700ad8a09f32c2d90c383c2597c9ec2b971ef41fb21 | Python | 29,353 | 861 | # src/zndraw_joblib/client.py
"""Client SDK for ZnDraw JobLib workers."""
import json
import logging
import random
import signal
import threading
import time
import traceback
from abc import ABC, abstractmethod
from collections.abc import Callable, Iterator
from dataclasses import dataclass
from enum import StrEnum
fr... |
bf6a5165c218e8141f572c8b45d80c60cf4d8120d6939db1d4dae0fa66fa9b5a | Python | 29,356 | 868 | import sys
import os
import numpy
import pdb
from keras.models import Sequential
from keras.layers.core import Dense, Dropout, Activation, Flatten
#from keras.layers import Input, merge, LSTM
from keras.layers.normalization import BatchNormalization
from keras.layers.advanced_activations import PReLU
from keras.utils i... |
91863d0a6cce3e476515d896fbdba4825c645ade025737c018c6d4951cb32a25 | Python | 29,401 | 815 | # 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 complianc... |
273265c8c664c877250e3d52f4bdd093d2f3d40ab74682e33ef697a3ae8a0392 | Python | 29,405 | 735 | import os
import sys
# sys.path.insert(0, f'{PROJECT_DIR}/guided-diffusion') # 加在前面，不再读取库文件的东西。
import subprocess
import io
import torch.nn as nn
from torch.nn import functional as F
import torch
import torchvision.transforms.functional as TF
import torchvision.transforms as T
import math
import requests
import cv2
f... |
48490397526374c58c1e0e023036cbee5b7aab165ef2260b85ae0f3b29798778 | Python | 29,487 | 894 | """Create GM volume from segmented images."""
import json
import os
import re
import shutil
from glob import glob
import ants
import imageio.v3 as iio
import numpy as np
import pandas as pd
import SimpleITK as sitk
import torch
from joblib import Parallel, delayed
from skimage.filters import (
threshold_li,
th... |
7b102589748fcb289919e2fec7154e899e9e4e22f83375efdb8f852390ab5c71 | Python | 29,514 | 1,160 | """
MetaWIBELE: utilities module
Utilities relating to third party software, file permissions, and file formats
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
... |
2aabfe798bcfca30425b5fdb97a8ac803db56a00c9a57d47d843fd33c3acab87 | Python | 29,523 | 695 | """Command line builder."""
import copy
import logging
import math
from collections.abc import Callable, MutableMapping, MutableSequence
from decimal import Decimal
from typing import IO, TYPE_CHECKING, Any, Optional, cast
from cwl_utils import expression
from cwl_utils.file_formats import check_format
from cwl_utils... |
6fe8f21d6176c3da270e7f7ae265aa8acb300dafc2dc7d6b04bd2c7536614a53 | Python | 29,561 | 1,774 | # Part of the following data is extracted from https://periodictable.com/
# Frames per slice that the CUDA kernels can aggregate. Mirrors MAX_FRAME_NUMBER
# in src/constants.h. Frames map to blockIdx.y, so this is the CUDA grid limit
# rather than a buffer size; beyond it the kernels raise instead of truncating.
MAX_F... |
9b0da21d343776935e3c689c2a6a5ab6cdca2ba454768e521bb5df51659af141 | Python | 29,584 | 892 |
# Copyright (c) ByteDance, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
"""
Mostly copy-paste from torchvision references or other public repos like DETR:
https://github.com/facebookresearch/de... |
f05acaf9e6b49da6f3e206b9a630e6ef7955ebfe2e4fdc01e96b630c90676397 | Python | 29,677 | 611 | """
This scripts performs all post-hoc interpretability analyses.
Dependencies:
- experiments/outputs/graphtrip/weights/seed_*/
- experiments/outputs/graphtrip/grail/seed_*/
- experiments/outputs/graphtrip/regional_attributions/seed_*/
- same for medusa model
Outputs:
- experiments/outputs/grail/posthoc_analysis/
- e... |
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