sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
492eb98ede2b908d1e2dd52d97f80cd55e0b4bded7a083bb4cb59ae0e95833dd | Python | 38,417 | 934 | # Copyright (c) MONAI Consortium
# 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 applicable law or agreed to in writing, so... |
f2fcd0e65ad8805029992ded7f3d79cbd8ca167c9ef2434fad7e4c04f5e5d055 | Python | 38,426 | 974 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
_parent_path_str = "scatterternary"
_pat... |
d39896572e64f90d2f688cbeb37f26f8a141c2056970f422d0121f27e5e35a3c | Python | 38,428 | 910 | """
Volume Class creation Courtesy of Timothé Boutelier.
"""
import nibabel as nib
import pydicom
import numpy as np
import warnings
import logging
from slice import Slice
import os
# create the logger of this module
logger = logging.getLogger(__name__)
# redirect warnings to the logging system
logging.captureWarning... |
87830bd2e527e52af4a9ef5864d7cd456424f5a9471177e095209b429c46ed3e | Python | 38,431 | 737 | import torch
import numpy as np
import pandas as pd
import scipy.stats as stats
import sys
import os
import time
from collections import OrderedDict
sys.path.insert(1, os.path.dirname(__file__))
import genotypeio, eigenmt
from core import *
def calculate_cis_nominal(genotypes_t, phenotype_t, residualizer=None):
... |
50e7be9f1d0f4ddd3dab9b24fba3e049d1eff83ed7a9b8594a7e41a62df68d6e | Python | 38,436 | 748 | import numpy as np
from scipy import stats
import itertools
from utils_mutual_info import shuffle_activity
import matplotlib.pyplot as plt
import os
from matplotlib.backends.backend_pdf import PdfPages
from tqdm import tqdm
import sklearn
import scikit_posthocs as sp
import utils_linclab_plot
from utils_analysis import... |
6e9d3c19ce1c96f9c9dbe679e3e781fc6f0a533e581e7f0290ad98ff57ebb5e0 | Python | 38,461 | 1,144 | """Projection and Prediction Heads for Self-supervised Learning"""
# Copyright (c) 2021. Lightly AG and its affiliates.
# All Rights Reserved
from typing import List, Optional, Sequence, Tuple, Union
import torch
import torch.nn as nn
from torch import Tensor
from lightly.models import utils
class ProjectionHead(... |
2cc2455dc35a1a45b5c6e34ff17f9bfb62ee9d2a97d453f80024577c292f1398 | Python | 38,470 | 862 | import numpy as np
import pandas as pd
import time
"""
This modules defines both Session/MultiSession and Analysis/MultiAnalysis classes, which handle combined fiber photometry
and behavioral data analysis.
"""
import os
import matplotlib.pyplot as plt
from scipy import integrate, stats
import seaborn as sns
from typi... |
30055dbdb18b67fa92f612948f1c07922a1d0c4603d9e69ea2f2e05493db581e | Python | 38,544 | 853 | import os
from mirp.extract_features_and_images import extract_features
from mirp.settings.generic import SettingsClass
from mirp.settings.transformation_parameters import ImageTransformationSettingsClass
from mirp.settings.feature_parameters import FeatureExtractionSettingsClass
from mirp.settings.resegmentation_para... |
9ca7dc49e6bae97b2a79bb82c46fa48404fe00090056426bc802b809cc3395de | Python | 38,576 | 1,016 | """
File format detector
"""
import bz2
import gzip
import io
import logging
import os
import re
import shutil
import struct
import tempfile
import zipfile
from collections.abc import (
Callable,
Iterable,
Iterator,
)
from functools import partial
from typing import (
IO,
NamedTuple,
TYPE_CHECK... |
81cf18053abb20734f35317c7c02f52483a3104bee83fcd7bb4d8f94d46dc948 | Python | 38,605 | 1,101 | # adapted from https://github.com/facebookresearch/detectron2/blob/master/detectron2/data/transforms/transform.py
import inspect
import pprint
import sys
from abc import ABCMeta, abstractmethod
from typing import Any, Callable, List, Optional, TypeVar
import numpy as np
from PIL import Image
import torch
import torch... |
ce993a45912d4b2711b1ec26c572d82ece902138d34026175e4f8b0ac957289d | Python | 38,637 | 945 | """r71 A -- the witness-strip class, closed comprehensively (machine-checked immunizer).
The agreed r71 invariant (deletion-closure):
Every replay-structure item that can affect a faithfulness verdict creates a
typed, independently derived OBLIGATION, anchored to structure the replay itself
consumes. Each... |
e28a4e58c5610359005b761bc0dbdfc9009403766bae2907f399a2e53e3e471d | Python | 38,684 | 904 | # -----------------------------------------------------------------------------------
# SwinIR: Image Restoration Using Swin Transformer, https://arxiv.org/abs/2108.10257
# Originally Written by Ze Liu, Modified by Jingyun Liang.
# -----------------------------------------------------------------------------------
# p... |
6363abeb36e60fe6cb9230251fa4fdaf15014df4a80b5967fc775f7a6ef79247 | Python | 38,687 | 985 | """
logreg_plots.py
This script contains functions to create plots for logistic regression analyses
and results (logreg.py) from dictionaries, dataframes and stored models.
Authors: Colleen Gillon
Date: October, 2018
Note: this code uses python 3.7.
"""
import warnings
from pathlib import Path
import numpy as np... |
6849c0624a50f243dbf42bb85a457ae0fe2a2137c323ddd8dfc45ae7e0ebdaad | Python | 38,709 | 786 | # 2022/2023 Josue Page Vizcaino pv.josue@gmail.com
# Third party libraries imports
import matplotlib.pyplot as plt
import numpy as np
import torch
from torch.functional import split
import torch.nn as nn
import torch.nn.functional as F
import pathlib, glob, re
import FrEIA.framework as Ff
import FrEIA.modules as Fm
fro... |
7702586d98f8758f4cbca088f927cae3251ab6a56aefbb95c8f91cc56e0a1bf2 | Python | 38,710 | 1,050 | import datetime
import json
from collections.abc import Callable
from concurrent.futures import TimeoutError
from functools import lru_cache
from pathlib import Path
from typing import (
Any,
)
from urllib.parse import urlparse
from celery import current_task
from sqlalchemy import (
and_,
create_engine,
... |
73a90536c2299c4597a499ea580b61d0df130558304064e85c1f5e7c40ce3bde | Python | 38,718 | 985 | """M4: standalone unit suite for the _trace_core substrate.
Zero production consumers yet — these tests prove the substrate honors the
converged semantic contracts (docs/reference/trace_core_design.md section
3.2/3.5) before the M5 Op seam, including executable prototypes of every
hard seam: pool injectivity, parallel... |
35b121dcecf8e01c5aefc39ade076c34790ecd2f9ab15cf5765cb939153ff9d8 | Python | 38,721 | 1,184 | # coding=utf-8
"""
Contains an abstract base class that supports data transformations.
"""
from __future__ import division
from __future__ import unicode_literals
import os
import numpy as np
import scipy
import scipy.ndimage
import time
import dcCustom as dc
import tensorflow as tf
from dcCustom.data import NumpyDat... |
5348e54ba647c4c4412eb41319a1775f24a90d34ea2edf405298bd167c440015 | Python | 38,724 | 1,015 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Pre-processing operations based on NDVars"""
import warnings
from copy import deepcopy
import fnmatch
from itertools import chain
import logging
from os import makedirs, remove
from os.path import basename, dirname, exists, getmtime, join, splitext
from typing... |
3282f3f1ee9bf673e38a7a00a2b812218864a8b5023238e3b60b63bf3a6b0316 | Python | 38,745 | 821 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
21a86fd0b96a86584b248671fef546bd0e96d764de0cb7ae73b587809a126365 | Python | 38,750 | 986 | # SOURCE: vendored from kevinzakka/recurrent-visual-attention @ master (model.py, modules.py)
# SOURCE: vendored from mperezcarrasco/PyTorch-DAGMM @ master (model.py)
# SOURCE: vendored from RomainSabathe/dagmm @ master
# (model.py, compression_networks.py, estimation_networks.py, gmm.py)
# SOURCE: vendored from Dmitry... |
b4dce888e3e982410c82e06a3e5408efa3732bf7021eefba2d47982d28003a09 | Python | 38,750 | 603 | import os
import subprocess
from subprocess import PIPE
from random import randint
import numpy as np
def run_langevin1D(simulation_steps,
analytical_function = "7*x^4-23*x^2", periodic= "NO",
initial_position=0.0, temperature=1, time_step=0.005,
grid_min=-3.0,... |
45663ab1afec6c4be7bede0567f24fc60f8696b3e945096fd3fa1a7c42b7ed03 | Python | 38,779 | 790 | import copy
import dataclasses
import functools
import json
import os
import re
import shutil
import struct
import sys
import textwrap
import threading
import types
from datetime import datetime, timezone
from pathlib import Path
import geopandas as gpd
import pandas as pd
from geopandas.testing import assert_geodataf... |
9e54fa02ff17effb0d0b7e65a814010abc64dc04e1ae3e2e9a775870f5ee6a65 | Python | 38,787 | 1,245 | # SOURCE: vendored from KalmanNet/KalmanNet_TSP @ main (KNet/KalmanNet_nn.py);
# vendored from nicofarr/brainnetcnnVis_pytorch @ master (BrainNetCnnGoldMSI.py);
# vendored from CBICA/BrainMaGe @ master (BrainMaGe/models/networks.py,
# BrainMaGe/models/seg_modules.py);
# vendored from nabeelre/BTSbot @ main (btsbot/arch... |
4d10b50db18225fd9f77c913a5c5c6b772ce402e73f7e556aa2651bced70d6b6 | Python | 38,817 | 1,079 | import builtins
import contextlib
import functools
import os
import ml_dtypes
import numpy as np
import torch
from torch.distributed.tensor import DTensor
from torch.distributed.tensor import Replicate
from keras.src import tree
from keras.src.backend.common import KerasVariable
from keras.src.backend.common import g... |
8ccf1e0ebc40cb1432e646c185177394f209a2961c3d7dc58954401c817902a7 | Python | 38,821 | 1,043 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
c08525843a8215cfa63793bb2ebf6836eabec38adb2b64a11b593b080fdd4bc1 | Python | 38,865 | 824 | '''
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
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 requir... |
705aeeadb458d8e4f6cc16f3711ae3d4c203ce65262ffccf9e63328184b5f5cd | Python | 38,888 | 871 | """SSD predefined models."""
from __future__ import absolute_import
import warnings
from .ssd import get_ssd
from .anchor import LiteAnchorGenerator
from .vgg_atrous import vgg16_atrous_300, vgg16_atrous_512
from ...data import VOCDetection
__all__ = ['ssd_300_vgg16_atrous_voc',
'ssd_300_vgg16_atrous_coco'... |
60aac31e4c3a10e4f41fbb1884acd10fa9e57a5da0eb0a67616f9e959be6b16f | Python | 38,904 | 872 | """SSD predefined models."""
from __future__ import absolute_import
import warnings
from gluoncv.data import VOCDetection
from .ssd import get_ssd
from ..ssd.anchor import LiteAnchorGenerator
from ..ssd.vgg_atrous import vgg16_atrous_300, vgg16_atrous_512
__all__ = ['ssd_300_vgg16_atrous_voc',
'ssd_300_vg... |
480f157191f7f5977afcc76e9b801fa3fc6c6c1158748ca0905a74ec647169fa | Python | 38,936 | 1,028 | import os
import warnings
import numpy as np
import pytest
from absl.testing import parameterized
from keras.src import applications
from keras.src import backend
from keras.src import layers
from keras.src import ops
from keras.src import saving
from keras.src import testing
from keras.src.backend.common import stan... |
17eff24b60c8ff428801d1dab205f13d414161087dd29dadcedec2573be38148 | Python | 38,943 | 833 | __version__ = '0.7.2'
from typing import List, Optional, Tuple
import torch
import torch.nn as nn
# FROM https://github.com/JeppeHallgren/pytorch-crf/blob/master/torchcrf/__init__.py
class CRF(nn.Module):
"""Conditional random field.
This module implements a conditional random field [LMP01]_. The forward co... |
04b6498688db99046b5d2a150251f43e6c52421e0d1bb1d67886252e60baaed1 | Python | 38,972 | 900 | from plot_utils_AUD import *
np.random.seed(0)
random.seed(0)
### Directories ###
date = datetime.datetime.now().strftime("%m%d%Y")
DATADIR = (Path(os.getcwd()) / '..' / '..' / 'data').resolve()
RESULTDIR_LOCAL = (Path(os.getcwd()) / '..' / '..' / 'results').resolve()
PLOTSURFDIR = Path(f'{ROOT}/results/PLOTS_SURF_acr... |
c71c6ff06167c9a2d6e0ac7c65f9d03c0335baff681b9d5c0e6f1bfad8a34642 | Python | 38,998 | 866 | # Copyright (c) 2023, Tri Dao.
import sys
import functools
import importlib.util
import warnings
import os
import re
import ast
import glob
import shutil
import tempfile
from pathlib import Path
from typing import Literal, Optional
from packaging.version import parse, Version
import platform
from setuptools import se... |
8e6e872f9a79a1b9428b5673d83201d370fcf82b31d5b9aef0e780be6ef6bc3e | Python | 39,020 | 994 | """Unit tests for internal algorithms and invariants.
Tests here cover internal implementation details that aren't exercised
through the public API integration tests: field ordering, data structure
invariants, algorithm correctness, etc.
"""
from collections import defaultdict
import pytest
import torch
import torch... |
86bc93b0bbd64a625a9e511a74ddfbb6c752cc4761db078121cbaf171c9701e9 | Python | 39,035 | 886 | from typing import Optional, Union
import numpy as np
import pandas as pd
from anndata import AnnData
from pyvista import MultiBlock, PolyData, UnstructuredGrid
from ....tdr import add_model_labels, collect_models
from .three_dims_plots import three_d_multi_plot, three_d_plot
try:
from typing import Literal
exce... |
e447b8966fdbf4a42b382a9f6b3f92f38a7971be0f9e2b8a201ad95db9d01005 | Python | 39,068 | 826 | import math
from matplotlib import cm
from matplotlib.colorbar import ColorbarBase
from matplotlib.colors import Normalize
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mpl_toolkits.mplot3d import Axes3D
import argparse
import glob
import os
from collections import defaultdict
from platform import machi... |
e3d9e67d1ec2bc61e4dec5591b46072f1b86ca7a185bd5dac7ec5e3cdce0933a | Python | 39,103 | 842 | # Copyright (c) 2024, Jay Shah, Ganesh Bikshandi, Ying Zhang, Vijay Thakkar, Pradeep Ramani, Tri Dao.
import sys
import warnings
import os
import stat
import re
import shutil
import ast
from pathlib import Path
from packaging.version import parse, Version
import platform
import sysconfig
import tarfile
import itertool... |
84c5dd0b7010e9d2f64e925369ac3cb8e55ac65cee4f1079fabfb3f67663518b | Python | 39,108 | 858 | #!/usr/bin/env python3
"""
File: fast_interaction_mapper.py
Created: 2021/11/16
Last Changed: 2022/03/22
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this ... |
90e50ed5346b927d7265e5a991e2d58b8c42935eef0f76484c70dfffab941198 | Python | 39,125 | 998 | import io
from unittest import mock
import os
from carbontracker import exceptions
from pyfakefs import fake_filesystem_unittest
from carbontracker import parser
from carbontracker.parser import (
extract_measurements,
parse_logs,
print_aggregate,
get_stats,
parse_equivalents,
)
class TestParser(... |
b02794c65d2375b96cdfe9c0fc90979ea8b94c19059698f47742f4be7c4f21a6 | Python | 39,139 | 1,057 | """Tests for representation-geometry numeric helpers."""
from __future__ import annotations
import importlib
import re
import subprocess
import sys
import warnings
from pathlib import Path
from typing import Any
import numpy as np
import pytest
import torch
from PIL import Image, ImageDraw
from torch import nn
impo... |
78a230a7c0c4414c3a64ca4b88fe0ff42fe9c5b1a4ac5230f272484959792d64 | Python | 39,150 | 1,038 | """Streaming bundle writer used during forward-pass out capture.
This module implements the strict streaming writer behind
``trace(storage=tl.to_disk(...))``. It writes one safetensors blob
per saved out into a temporary bundle during the forward pass, then
finalizes ``manifest.json`` and ``metadata.pkl`` at postproce... |
f3e95e2dcb9af2932b73ef23a0501f938051b858eaf9f5af2a484dbe931b416a | Python | 39,156 | 1,209 | import errno
import os
import re
import signal
import subprocess
import sys
import tempfile
import time
from unittest.mock import Mock, call, patch
import pytest
import t.skip
from celery import _find_option_with_arg, platforms
from celery.exceptions import SecurityError, SecurityWarning
from celery.platforms import ... |
82fa87d6e5b398abfac163ee1efb745305da251ce70d4ae9c5450a0d123d58d6 | Python | 39,164 | 1,149 | """
corr_analys.py
This script contains functions for USI correlation analysis.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import copy
import numpy as np
import pandas as pd
from sklearn.linear_model import LinearRegression
import scipy.ndimage as scind
from util import gen_... |
a45d500eba88507a54483bf6b43e91fddfed273f7ad01469f3210b68264fd490 | Python | 39,197 | 948 | # Copyright (c) 2024 PaddleHelix Authors. All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommo... |
dd8fe797228cdb1ff2f29e7e017bdf427de894ca8f2d371e8b246cf39452ba34 | Python | 39,200 | 824 | #!/usr/bin/env python3
"""plot_aggregation.py
Top level command-line interface for generating plots related to the
aggregation, i.e., applying the LSS to rough / fine alignments.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you can redistribute it and/or ... |
b84b4e5f5fd926456cd00710ddcd7100e35054825dd9ae2e30b2e8e6b5053726 | Python | 39,265 | 1,148 | #############################################
# This file contains scripts to perform the #
# Convolutional Oligo Kernel Network #
# experiments. #
# #
# Author: Jonas Ditz #
############################################... |
c2ce835eb719dd12a900a58e1823e1fd8c54358803bc9c32b6f8bfc861ef9217 | Python | 39,277 | 836 | __version__ = '0.7.2'
from typing import List, Optional, Tuple
import torch
import torch.nn as nn
# FROM https://github.com/JeppeHallgren/pytorch-crf/blob/master/torchcrf/__init__.py
class CRF(nn.Module):
"""Conditional random field.
This module implements a conditional random field [LMP01]_. The forward co... |
49e4194936f2f3bbf22251a5e5c529702eb35f2cd69092fe99b7480f6cc1843b | Python | 39,293 | 998 | import os
import time
import math
import numpy as np
import pandas as pd
import pickle as pkl
import nibabel as nib
from os.path import join as pjoin
from scipy.stats import pearsonr, permutation_test
from scipy.optimize import curve_fit
from sklearn.linear_model import LinearRegression
from sklearn.metrics import r2_s... |
4dee42308724e3a87e67daf58382cc988876cff4d443eba4b08e7563419094d7 | Python | 39,302 | 1,001 | import copy
import inspect
import typing
import warnings
from keras.src import backend
from keras.src import ops
from keras.src import tree
from keras.src.backend.common import get_keras_mask
from keras.src.backend.common import global_state
from keras.src.backend.common import set_keras_mask
from keras.src.layers.cor... |
b32bb9247ab029bad1f9798a06d65d8a4b55b0cba1a8b5e18462bbb169af6cd4 | Python | 39,306 | 912 | """
quant_analys.py
This module contains functions to run quantile analyses on data
generated by the Allen Institute OpenScope experiments for the Credit
Assignment Project.
Authors: Colleen Gillon
Date: October, 2018
Note: this code uses python 3.7.
"""
import copy
import warnings
import numpy as np
import pan... |
0b5aba529ab933cd18b748ddcd0cfbec84577f7f442b6afff1eeacf583a61bf3 | Python | 39,382 | 869 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import math
from collections import Counter, defaultdict
from functools import lru_cache
from typing import Any
import cv2
import numpy as np
import torch
from ultralytics import YOLO
from ultralytics.solutions.co... |
eb24161c3db36f345e888110f5ee16db520b8399497a17853e8241722d940265 | Python | 39,398 | 1,001 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 7 22:07:39 2021
@author: emilia
"""
import random
import numpy as np
import torch
from torch import nn, optim
import pickle
import os
from scipy.ndimage import gaussian_filter1d
from scipy.io import savemat
from src.generate_data_von_mises import c... |
7344b808aa4eb6ebc5c48ab821485e32feea1397a14a540433191e08895d9c33 | Python | 39,401 | 1,090 | # Copyright (c) 2025, Tri Dao.
import math
import hashlib
import inspect
import os
from functools import partial
from typing import Type, Callable, Optional, Tuple, overload, NamedTuple
import cutlass
import cutlass.cute as cute
from cutlass import Float32, Int32, const_expr
from cutlass.cute import FastDivmodDiviso... |
62586a5f09971186280cb9b65abe04508dec46714387193bc4fb61f7a4e155eb | Python | 39,402 | 936 | """
Galaxy FilesSource implementation for eLabFTW.
This module implements a FilesSource that interacts with an eLabFTW [1] instance. eLabFTW revolves around the concepts
of *experiment* [2] and *resource* [3]. Experiments and resources can have files attached to them. To get a quick
overview, try out the live demo [4]... |
610436c692e9dac58e7fca36657c1821715acdab8d01992c1a38b23fcd6ae408 | Python | 39,428 | 754 | from typing import Any
from dataclasses import dataclass
from mirp.settings.utilities import setting_def
@dataclass
class FeatureExtractionSettingsClass:
"""
Parameters related to feature computation. Many are conditional on the type of features that will be computed (
``base_feature_families``). Features... |
5a633e1e14af0efb666cd802a14d4be418413723dccc74d7b696f25e23316421 | Python | 39,432 | 1,029 | import gc
import logging
import platform
import time
from datetime import datetime, timedelta, timezone
from uuid import uuid4
import billiard as multiprocessing
import pytest
import celery
from celery import chain, chord, group
from celery.canvas import StampingVisitor
from celery.signals import before_task_publish,... |
6c0d43430827b6ec0516bc98a14d64f71feb0ffa5535fb46298d9befe3bc31c6 | Python | 39,471 | 1,026 | #!/usr/bin/env python
import os
import sys
import pandas as pd
import argparse
import configparser
import multiprocessing
import time
import datetime
from sqlalchemy import create_engine
from sqlalchemy.pool import NullPool
import tqdm
import statsmodels.stats.multitest as multitest
import snps
import genes
import int... |
d76370138c855e8587ad6ae7d84dbeee08c30950322b346a573f212ed2966f9d | Python | 39,476 | 1,135 | #!/usr/bin/env python3
import argparse
import matplotlib
import matplotlib.pyplot as plt
import scipy
import scipy.stats
import numpy as np
import pandas as pd
import math
import os
import pints
import pints.plot
import regex as re
import uuid
from numba import njit
import subprocess
import sys
import datetime
import ... |
0e85798f381ee7ab3f3aa7a6acdfe8326a048ff6c342eb0e03191d2127d119b7 | Python | 39,484 | 1,168 | """
roi_plots.py
This script contains functions for plotting ROI masks and projections.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import itertools
import numpy as np
import matplotlib as mpl
import matplotlib.patches as mpatches
from util import gen_util, logger_util, plot_u... |
cd2993572f715157422d2cb40e3139fd57d0bf07b1ddbabd51ec152f2f6c796c | Python | 39,533 | 827 | '''
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
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 requir... |
cf5df9f2972be7cad9878df7ea321804617d769f47823984abbe0a9b1cbc460b | Python | 39,534 | 1,014 | from __future__ import annotations
import collections.abc as cabc
import logging
import os
import sys
import typing as t
from datetime import timedelta
from itertools import chain
from werkzeug.exceptions import Aborter
from werkzeug.exceptions import BadRequest
from werkzeug.exceptions import BadRequestKeyError
from... |
dab89f724fb9d53e9bed776426e1cf48bb7661a9f2c9a6a8548d9cc11757c476 | Python | 39,556 | 876 | """
The AI page is just a different view of the calculator. It relies on the same modules.
The page itself is defined as a `DashBlueprint` that encompasses both layout and callbacks.
Contrary to the Home page, the AI page requires more intermediate processing to obtain the metrics.
These are due to the continuous inf... |
2281f90fdacd47968aa92ef37416f5638294cceb0e1e7741ac68448ce3a766eb | Python | 39,557 | 1,056 | """Rescue-rerun mechanism tests (stage-2 safety net).
The outcome corpus (``test_detached_reference_capture_outcomes.py``) pins
per-escape-class outcomes; THIS module pins the driver mechanics: the net is
never armed on a clean primary capture, ineligible captures skip the rescue,
RNG is restored to capture entry so s... |
ffa9e4955cf91dbf795c4379d30b10c2f95959f216669f0adabb83551b6a57c8 | Python | 39,562 | 971 | import torch
from torch import Tensor
import torch.nn.functional as F
from torch.nn import Sequential, Linear, ReLU, BatchNorm1d
import torch_geometric
from torch_geometric.nn import (
Set2Set,
global_mean_pool,
global_add_pool,
global_max_pool,
MetaLayer,
GCNConv,
CGConv,
)
from torch_scatt... |
05c27d7c227ec47a4a3395ff5afa80120dd4aaca64861ef5f4b578b0e42e49c2 | Python | 39,640 | 946 | """Job control via the HTCondor DRM using the htcondor2 Python API.
See the Galaxy cluster documentation (doc/source/admin/cluster.md) for
configuration, architecture details, and testing instructions.
"""
import json
import logging
import os
import select
import shlex
import subprocess
import sys
import threading
fr... |
5ee0930dccaceeab5671eb9f34533b8ebb49129586d0d23fe1cf9b54574169a3 | Python | 39,644 | 1,313 | # -*- coding: utf-8 -*-
"""
Created on Thu Oct 26 11:22:48 2023
@author: LABadmin
"""
import numpy as np
from matplotlib import pyplot as plt
import matplotlib as mpl
import random
import sklearn
import scipy as sp
import matplotlib.ticker as mtick
import matplotlib as mpl
from matplotlib.colors import L... |
2aecb339b88eae0c17d78ea6ecf7c13ba0b10c5ab52727a12af98d6490784a15 | Python | 39,660 | 927 | """CenterNet object detector: Objects as Points, https://arxiv.org/abs/1904.07850"""
from __future__ import absolute_import
import os
import warnings
from collections import OrderedDict
import mxnet as mx
from mxnet.gluon import nn
from mxnet import autograd
from ...nn.coder import CenterNetDecoder
__all__ = ['Cente... |
43eb5f33c7a7836904beac50dec06adc19d2c503b43f43f639483ce92eac06b1 | Python | 39,713 | 1,165 | """
The dataset manager app.
Lists the datasets in the workspace and drives their processing, annotation
and deletion.
"""
from __future__ import annotations
from html import escape
from pathlib import Path
import pandas as pd
import panel as pn
from larvaworld.lib.process.dataset import LarvaDataset
from larvawor... |
108dd9632a00f5e7bfac11a04944102dee7cdd85c148f80a18d18596a9bb7fb7 | Python | 39,743 | 947 | """Worker Consumer Blueprint.
This module contains the components responsible for consuming messages
from the broker, processing the messages and keeping the broker connections
up and running.
"""
import errno
import logging
import os
import warnings
from collections import defaultdict, deque
from time import sleep
f... |
a95eb3eb1c59b6d4e48e093c22a5cedccdff1521854be6159f176eb1bf8679bd | Python | 39,782 | 1,108 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Legend(_BaseLayoutHierarchyType):
_parent_path_str = "layout"
_path_str... |
a6412791d0fda01e2315eda74fd721667c72784fc7ab1b7dde65380aaf1f617f | Python | 39,808 | 997 | import math
import string
import numpy as np
from keras.src import backend
from keras.src import constraints
from keras.src import initializers
from keras.src import regularizers
from keras.src.api_export import keras_export
from keras.src.backend.common import get_keras_mask
from keras.src.backend.common import set_... |
f0d3c9d2a77e66d4e43a47684ae309be8a0aeec6bea3bfbe9fb47558cd3bf84f | Python | 39,843 | 1,170 | """Tests for Phase 11 unified ``.tlspec`` writer and reader behavior."""
from __future__ import annotations
import json
import re
import warnings
from collections.abc import Callable
from pathlib import Path
from types import SimpleNamespace
from typing import Any
import pytest
import torch
from torch import nn
imp... |
74daadf8bbf23c70e28371b0f73d821e8ef8213d1474263dd6a53216ba2e8acc | Python | 39,849 | 854 | #!/usr/bin/env python3
import os
os.system('date')
"""run_tear_convert.py
Convert a downloaded webknossos tear annotation file into stored dills.
and preprocess tear annotations into format required for the tear fixing.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free... |
33b969040d63002d11d059006c0e0be4979fb4e344ffaccbb53f578f7b8b1255 | Python | 39,884 | 1,110 | """
seq_plots.py
This script contains functions for plotting sequence analyses.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import numpy as np
from util import gen_util, logger_util, plot_util, math_util
from sess_util import sess_plot_util
from analysis import misc_analys
fro... |
d528a586dd39e1dd0e18dcda62c94bf87b56f0410447e9c75046268015f040ab | Python | 39,897 | 696 | import numpy as np
from typing import Any
from dataclasses import dataclass
from mirp.settings.utilities import setting_def
@dataclass
class ImagePostProcessingClass:
"""
Parameters related to image processing. Note that parameters concerning image perturbation / augmentation and
resampling are set separ... |
1e69308a8d1491858dd9cbc23498615465c913faad358e04d037e2c9ec7348de | Python | 39,957 | 1,172 | """Base definitions for R objects."""
import abc
import collections.abc
from collections import OrderedDict
import enum
import itertools
import typing
from rpy2.rinterface_lib import embedded
from rpy2.rinterface_lib import memorymanagement
from rpy2.rinterface_lib import openrlib
import rpy2.rinterface_lib._rinterfac... |
15ca908580815879011c05f6b9bb0d00967a2e5caecbde79bbbf830a5d4a5ad3 | Python | 39,962 | 1,135 | ''' Tools for aligning spatial transcriptomics data
The LDDMM fits (LDDMM, LDDMM_3D_to_slice, and align_cells for two sets of cells),
rasterization and the transforms of fitted mappings are implemented in private modules next
to this file (_lddmm*.py, _cells.py, _raster.py, _transforms.py) and exposed here. The LDDMM... |
6da425130652e7b59b8ac0f520f1e070ce0ac1cccbd59f210c605816a6b512cd | Python | 39,986 | 1,181 | """Task results/state and results for groups of tasks."""
import datetime
import time
import types
from collections import deque
from contextlib import contextmanager
from weakref import proxy
from dateutil.parser import isoparse
from kombu.utils.objects import cached_property
from vine import Thenable, barrier, prom... |
a7c9e9b2f7a80f0c6145bc7fefdcecd04d2167f31bd29e353c52868f57201e25 | Python | 40,036 | 801 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 23 17:58:34 2021
@author: emilia
This file contains all decoding analysis functions, including:
1) decoding of uncued stimulus colour in the post-cue delay
2) cross-temporal decoding
3) comparison of maintenance mechanisms between mode... |
da5e22a12094c87bca8ddeed82d955443cbd3d6a5de068be7c185824cb9eb957 | Python | 40,041 | 1,170 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import logging
import math
# import cv2
import random
import numpy as np
import torch
import torchvision as tv
import torchvision.transforms.functional as F
from PIL import Image, ImageFilter
from scipy.ndimage import gaus... |
ad82dbeb1f7bed76b037391778eb1a040004e2e9ddb4341c4b29c05e03b6df47 | Python | 40,198 | 1,077 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Axis(_BaseTraceHierarchyType):
_parent_path_str = "indicator.gauge"
_path... |
d035446dcc10afe7b3b88a1278653f888c3866d56ff229bf32aaebf3d08a965e | Python | 40,206 | 928 | """Module implementing representational similarity analysis (RSA) at the sensor level.
Kriegeskorte, N., Mur, M., & Bandettini, P. A. (2008). Representational similarity
analysis - connecting the branches of systems neuroscience. Frontiers in Systems
Neuroscience, 2(November), 4. https://doi.org/10.3389/neuro.06.004.2... |
cf4b869a12f22a52118f6d758bba340689574882dba33ea3d2c563ea04c4926d | Python | 40,216 | 933 | import glob
import matplotlib.pyplot as plt
import numpy as np
import pickle
import random
from numba import jit, njit
def load_HILLS(hills_name="HILLS"):
"""Load 1-dimensional hills data (includes time, position_x, position_y, hills_parameters
Args:
hills_name (str, optional): Name of hills file. D... |
b93b3fd9af16a4ceb81382862af78b6217be6aa4bbfad22cfb6e7be0522bd2d8 | Python | 40,244 | 932 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
7013aa658d8b826f4719fb5ef28c10d4f27a2714f85fa00120126241280e17e5 | Python | 40,384 | 1,123 | """Unified ``.tlspec`` manifest writer helpers."""
from __future__ import annotations
import contextlib
import json
import os
import shutil
import sys
import uuid
from collections.abc import Iterable
from datetime import datetime, timezone
from hashlib import sha256
from pathlib import Path
from typing import Any, Li... |
5df7960fdb4ef060c64f49e4b61b855752e790dcae55a69d54f11ac9e3ce7074 | Python | 40,482 | 993 | #!/usr/bin/env python
"""
Unit tests for the unified notification manager.
"""
import datetime
from unittest.mock import MagicMock, Mock, patch
import pytest
from ethoscope_node.notifications.manager import NotificationManager
class TestNotificationManager:
"""Test cases for NotificationManager class."""
... |
4096b3ecd7a226669108082efc0e9e3ce0264d94354b33a56b833c19478a44f5 | Python | 40,542 | 1,076 | from __future__ import annotations
import logging
import warnings
from typing import Dict, List, Literal, Optional, Sequence, Union
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.distributions import Distribution, Normal, kl_divergence
# Import GATv2Conv with fallbac... |
4fa077fb4e6e7289ecddf22cf86749183a2ebc32e550cf25e15e8bd9c6fb23bb | Python | 40,575 | 940 | """
This script implements miscellaneous functions and global variables
used at page loading or when a csv is uploaded.
"""
import os
import copy
import base64
import io
import yaml
import pandas as pd
from types import SimpleNamespace
from utils.utils import check_CIcountries_df, unlist, put_value_first
from bluep... |
df7cdaa2dc3595906ee21727e42cf5ec1d7595a6ec8c20c0bfe8336b25946944 | Python | 40,583 | 925 | # Copyright 2025 Google.
#
# 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 applicable law or agreed to in writing, soft... |
6cccd4ca7f534980927d77ad4f49cecd6e5082074fb3e38c1f408ff07cec927b | Python | 40,594 | 949 | ''' tbd. '''
import sys
import pickle
sys.path.append('..')
import gzip
import os, io
import numpy as np
from functools import reduce
import re
from typing import Any, Dict, Mapping, Optional, Sequence, Tuple, List
from Bio.PDB import PDBParser
import helixfold.data.mmcif_parsing_paddle as mmcif_parsing
from helixfold... |
cee2f69ce7c462cb12a7dcef9f6ce395ad0c016e4e9bfd1a6db079cca1fbda1e | Python | 40,594 | 1,136 | """PyPI and direct package downloading"""
import sys
import os
import re
import shutil
import socket
import base64
import hashlib
import itertools
import warnings
from functools import wraps
from setuptools.extern import six
from setuptools.extern.six.moves import urllib, http_client, configparser, map
import setupto... |
7a859b14a993a78bb9049e419fadc76b21bdc29c8b542683f64e10d6ca9f0cad | Python | 40,609 | 1,023 | """
MySQL Backup Module - Low-level Database Operations
This module handles the core database operations for backing up MySQL data to SQLite files.
It provides the fundamental database connectivity, schema management, and data transfer
functionality that powers the ethoscope backup system.
Key Responsibilities:
=====... |
6e6eeb5e90917bd7522c46da2ab7d9327f0d3e26da47705f37fdafadcbd4d5a7 | Python | 40,622 | 894 | from logging import info
import os
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import train_test_split
from sklearn.metrics import confusion_matrix
from sklearn.model_selection import KFold
import matplotl... |
1bf8bbf204618a60458b45a857189051b97d8b4e6527a97e0dc62d48793b7ee9 | Python | 40,744 | 1,026 | """
Tests for independence_tests.py.
"""
from __future__ import print_function
import numpy as np
import pytest
from scipy import stats
from tigramite.independence_tests.parcorr import ParCorr
from tigramite.independence_tests.robust_parcorr import RobustParCorr
from tigramite.independence_tests.parcorr_wls import Par... |
1605333d14f5cb1b16bec9e299aaf2f07bf10ec0f076c89ff814ca7219bb86fa | Python | 40,768 | 897 | # for one people
import math
import ipdb
import torch.nn as nn
import torch
import torch.optim as optim
from tqdm import tqdm
import matplotlib.pyplot as plt
import os
import argparse
import datetime
import numpy as np
from torch.optim.lr_scheduler import StepLR
from torch.utils.tensorboard import SummaryWriter
from o... |
93d41497e53f01a10926a1b54f4708479e8920a01eb03d9d2420915ef450d729 | Python | 40,776 | 909 | from pybedtools import BedTool, Interval
from pybedtools.featurefuncs import midpoint
from sklearn.model_selection import train_test_split
from sklearn.cluster import KMeans
import torch
from torch.utils.data import Dataset, TensorDataset
import os
import glob
import subprocess
import sys
import pandas as pd
import num... |
4c3b51dbd1c3baf25eb8dda8eb3506b4a6f31da3c2038ff2fd02ea50d7ee5797 | Python | 40,820 | 1,026 | # Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
bae445699ce326de45bf7666c8a514b8bb63c75dbff06f5120b8a019e7388ab2 | Python | 40,838 | 1,301 | """
Improved support for Microsoft Visual C++ compilers.
Known supported compilers:
--------------------------
Microsoft Visual C++ 9.0:
Microsoft Visual C++ Compiler for Python 2.7 (x86, amd64)
Microsoft Windows SDK 6.1 (x86, x64, ia64)
Microsoft Windows SDK 7.0 (x86, x64, ia64)
Microsoft Visual C++ 10.0... |
3651153ea84a9e35cad29a48f41531d341d4a980a2c7e73985562704c305c461 | Python | 40,851 | 1,148 | """Honest detection of distributed (DTensor / device-mesh / TP / PP) model state.
TorchLens captures a *rank-local eager* forward pass. Several distributed
execution modes leave the model looking like an ordinary ``nn.Module`` while
replacing its parameters with tensor subclasses whose real work happens under
``__torc... |
75097fd54e489723275d765737b9a8872a79ac99653345c84eed5656a13b9bf6 | Python | 40,851 | 730 | #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Written by Yuichiro Yada
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
################################################
# The notation is different from that in the paper.
# paper, this code
# alpha, beta
# beta, gamma
# gamma, q
# z, mu_Z... |
f584b6a3d01802802989bbd1174039d8eb709308ca00183e527380c8a8e30ba7 | Python | 40,870 | 1,106 | """Test functions in xcp_d.utils.utils."""
import numpy as np
import pandas as pd
import pytest
from scipy import signal, stats
from xcp_d.utils import utils
def test_estimate_brain_radius(ds001419_data):
"""Ensure that the brain radius estimation function returns the right value."""
bold_mask = ds001419_da... |
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