sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
09c3ae48fecaa460bdd569c14056afab3453dc8c716009f49e1f072a22d45c35 | Python | 21,565 | 343 | import os
import random
from agents.model_1d import *
from envs.int_discrim import IntervalDiscrimination
import numpy as np
import torch
from lesion_expt_utils import generate_random_index
import sys
sys.path.insert(1,'/home/mila/l/lindongy/deeprl-timecells')
from analysis import utils_linclab_plot
import argparse
imp... |
09b48c88c2e76afcb825dda91af49d7eb8f523dcf2999443aa9561da90f9f0a5 | Python | 21,570 | 620 | """Stale pre-wrap torch references: every holder shape is disclosed and rescued.
A model built before the process's first capture holds pristine torch
functions (``self.act = F.gelu`` resolved before ``wrap_torch()``). Capture
never rewrites the user's objects; instead an escape signal triggers the
rescue re-run, whos... |
f155b76043f2535b75cfe7944252de093d412aea12892959af40bae2b1d828ac | Python | 21,590 | 634 | #!/usr/bin/env python
"""
Description of the sticky end concept and what does the marking mean. what is the reaction matrix and so on ....
Copyright 2013 B. Gruening and Hitesh Patel
version: 0.3
"""
import argparse
import logging
import multiprocessing
import os
import re
import shutil
import subprocess
import sy... |
30968627874113e99712e2b68555aa71ef8af824edff43004eb121b155c03a9d | Python | 21,629 | 508 | """
Characterizing cell-to-cell variability within spatial domains
"""
from collections import OrderedDict
from typing import Dict, List, Literal, Optional, Tuple, Union
import anndata
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy
from anndata import AnnData
from matplotlib import... |
7adbb3f15d0d3df59b5f68cc3baa033339497950bc190be51d7abcdd44c147a8 | Python | 21,645 | 235 | # pylint: disable=line-too-long,too-many-lines,missing-docstring
"""Kinetics700 video action recognition dataset.
Code adapted from https://github.com/open-mmlab/mmaction and
https://github.com/bryanyzhu/two-stream-pytorch"""
import os
from ..video_custom import VideoClsCustom
__all__ = ['Kinetics700']
class Kinetics... |
a8b95aec8e86132b4fd9dbdffceb14c1e979569e03d6995ebb5413aa6883a453 | Python | 21,667 | 638 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Tools for loading data form eyelink edf files."""
from glob import glob
import os
import re
import shutil
import subprocess
import tempfile
import numpy as np
from .._data_obj import Dataset, Datalist, Var
from .._utils import ui
from .._utils.subp import ge... |
93de152f0746328002ae8f3d55d6ee00b334ee6ec2d7150e176360912d1cc325 | Python | 21,671 | 574 | import pkg_resources
import logging
from PyQt6 import QtWidgets, QtCore, uic
# from PyQt6.QtWidgets import QMessageBox
from matplotlib.widgets import SpanSelector
import numpy as np
import multiprocessing as mp
import time
from bmlab.session import Session
from bmlab.controllers import CalibrationController
from bm... |
eacdfdd981bd48d804e45a7a258e8d09a3d4389e937958894ff8577d87e587e3 | Python | 21,673 | 627 | # Copyright 2022 Deepfold Team
#
# 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 writin... |
32db25ea881f71cac83ce098eeb2dbd29b8c8acda0ce699c53efea970a2890a0 | Python | 21,674 | 259 | import numpy as np
from gym import utils
from gym.envs.mujoco import MujocoEnv
from gym.spaces import Box
class HumanoidStandupEnv(MujocoEnv, utils.EzPickle):
"""
### Description
This environment is based on the environment introduced by Tassa, Erez and Todorov
in ["Synthesis and stabilization of co... |
fd6b662b4dcb0e9822e681f673c3122c0477b5fbcd14a0ddff8942967260dc3a | Python | 21,677 | 576 | """
Code here relates to the creation of stimulus waveforms from epoch tables.
In the waveform editor of ClampEx, you can edit the stimulus waveform table
for each channel (DAC). Each waveform table is made of epochs, which appear
as a single column of values in the waveform editor.
The overall strategy here is that ... |
76ccf3ace751aece8c226ef298fd457fc07fc6e6f251a6820d9af4d83e03d010 | Python | 21,682 | 354 |
#functions from "Figure 1 and 2 - Foraging decisions emanate from high arousal states.ipynb" originally worked on this in December 2020
import os
import pandas as pd
import numpy as np
import ssm
from ssm.util import one_hot
import re
import copy
from numpy.linalg import norm
from scipy.stats import multivariate_norma... |
126179dc367e1929c1dd82faa1de8f712d0efb4cb5afafd81d8ed53416f387ae | Python | 21,685 | 571 | # --- 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 Line(_BaseTraceHierarchyType):
_parent_path_str = "scatter3d"
_path_str =... |
32d6ef57ca586b23af9294fe87d1d2dca56530b45364694f0ab90044029b0e9b | Python | 21,685 | 675 | import argparse
import json
import os
import warnings
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import plotly
import plotly.graph_objs as go
from galaxy_ml.model_persist import load_model_from_h5
from galaxy_ml.utils import read_columns, SafeEval
from sklearn.feature_sele... |
b88c923ce00d21034cb5e883131e8e32fe7b1b99fe9d82e0c16983d1d55fd3e3 | Python | 21,691 | 481 | from core import *
import genotypeio
import torch
from torch.utils import data
import numpy as np
import pandas as pd
import scipy.stats as stats
from collections import OrderedDict
import sys
import os
import time
sys.path.insert(1, os.path.dirname(__file__))
def _in_cis(chrom, pos, gene_id, tss_dict, window=100000... |
162860ba61099260d113073a8f168ad20b132194dd526a5ed5fd4fac1bc60da1 | Python | 21,704 | 543 | # pylint: disable=missing-function-docstring, line-too-long
"""
SlowFast Networks for Video Recognition
ICCV 2019, https://arxiv.org/abs/1812.03982
Code adapted from https://github.com/open-mmlab/mmaction and
https://github.com/decisionforce/TPN
"""
import torch
import torch.nn as nn
import torch.utils.checkpoint as cp... |
fcbaaa5ee0670f86d9ab5882a8215fc30e741f252b508b564d4f30f9a7437866 | Python | 21,714 | 527 | from __future__ import annotations
import argparse
import logging
import os
import subprocess # nosec - needed
import sys
from itertools import product
from typing import Optional, Union
from bream4.device_interfaces import device_wrapper
from bream4.device_interfaces.devices.base_device import BaseDeviceInterface
f... |
d4324ade5d90a93e9478907adc7294ebede0f1de3c3d85f616cc5257f24ec993 | Python | 21,721 | 530 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
from tqdm.auto import tqdm
import torch
import torch.nn.functional as F
from trainingUtils import MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Encoder,Decoder,VAE,CellStateEncoder,CellStateDecoder, CellStateVAE, SimpleEncoder,Loca... |
d3effd0f41adb54ec55d40a83279d963ea466fefdd6de106939140cf47ded87b | Python | 21,739 | 575 | from importlib import resources
import logging
from PyQt6 import QtWidgets, QtCore, uic
# from PyQt6.QtWidgets import QMessageBox
from matplotlib.widgets import SpanSelector
import numpy as np
import multiprocessing as mp
import time
from bmlab.session import Session
from bmlab.controllers import CalibrationControll... |
6ef1708ee231b92b056e3d9adffe74d1153e8ae9de888678b8babf8c5223615e | Python | 21,740 | 625 | """Phase 14 error catalog and cross-cutting intervention API audit tests."""
from __future__ import annotations
import gc
import threading
import weakref
from collections.abc import Callable, Iterable
from pathlib import Path
from typing import Any
import pytest
import torch
from example_models import TinyReluAdd as... |
947a9da4e541fde66cff7c39159c3ac983f01f7f3e1449394d85515fbfd49707 | Python | 21,743 | 511 | #!/usr/bin/env python3
"""
File: visualise_interaction_eqtl.py
Created: 2022/04/07
Last Changed: 2022/07/20
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 th... |
3bd1865b8601cddbbaafa6db0d24db5353d1984b66a0b785b61502a828e1b7b8 | Python | 21,758 | 620 | '''learning module'''
import sys
from abc import ABCMeta, abstractmethod
from typing import cast, Any, Optional, Dict
if sys.version_info >= (3, 8):
from typing import TypedDict, Protocol
else:
from typing_extensions import TypedDict, Protocol
import os
import warnings
import uuid
import pickle
import copy
im... |
56ccc844590675738b2348662b7750ab52d7fa584dc60e0086b9aaa27d7281f8 | Python | 21,771 | 416 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
e8f75e568e22561338b9f4c45c8d8edc6a6c63f5791cb46bc3f77bef0cbda66c | Python | 21,771 | 484 | """
Tests for transformer objects.
"""
from __future__ import division
from __future__ import unicode_literals
from deepchem.molnet import load_delaney
from deepchem.trans.transformers import FeaturizationTransformer
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = ... |
8e8bca7fca6daf4a78281dd8f3f5890c20145b5001bfde0448b656508f885e86 | Python | 21,798 | 663 | """Worker remote control command implementations."""
import io
import tempfile
from collections import UserDict, defaultdict, namedtuple
from billiard.common import TERM_SIGNAME
from kombu.utils.encoding import safe_repr
from celery import states
from celery.exceptions import WorkerShutdown
from celery.platforms impo... |
1343f1e1a4ece3098e3b6875e6169ab3949ce836ccdcd7f32e6cbf244e144439 | Python | 21,803 | 485 | """
Job control via the DRMAA API.
"""
import json
import logging
import os
import shlex
import string
import time
from typing import (
TYPE_CHECKING,
TypeAlias,
Union,
)
from galaxy import model
from galaxy.jobs.handler import DEFAULT_JOB_RUNNER_FAILURE_MESSAGE
from galaxy.jobs.job_destination import Job... |
f0ff761ca7c0f6168870c18d1593498b209efe55ec788fa4a5fb3188c88d6df3 | Python | 21,805 | 483 | from core import *
import genotypeio
import torch
from torch.utils import data
import numpy as np
import pandas as pd
import scipy.stats as stats
from collections import OrderedDict
import sys
import os
import time
sys.path.insert(1, os.path.dirname(__file__))
def _in_cis(chrom, pos, gene_id, tss_dict, window=100000... |
648076c066dd71bd3afb5beb1ae606d7e801d77f5c50bee5d324a84df628b60e | Python | 21,808 | 549 | import os
import numpy as np
import pandas as pd
from mirp.settings.generic import SettingsClass
from mirp.settings.transformation_parameters import ImageTransformationSettingsClass
from mirp.settings.feature_parameters import FeatureExtractionSettingsClass
from mirp.settings.resegmentation_parameters import Resegmen... |
4f5e13357162d7db235eea4e5eb69cffd936c6c8ac8658c62550cf3707c998bd | Python | 21,825 | 505 | # 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... |
b4d5a346b30b96ac8b17b78ea62732d6c58fb5da9e0e8fbc204613664708e76b | Python | 21,835 | 622 | __author__ = "quentin"
# flake8: noqa: E402
from collections import deque
import cv2
from .adaptive_bg_tracker import BackgroundModel
CV_VERSION = int(cv2.__version__.split(".")[0])
import logging
import os
import matplotlib.pyplot as plt
import numpy as np
from scipy.spatial import distance
from ethoscope.core.d... |
e7488c43f585cb9e1540960eede23fbb0d54814872f8f2506d0d717d72c2eb82 | Python | 21,837 | 579 | """Corruption-path regression tests for portable TorchLens bundles."""
from __future__ import annotations
import io
import json
import pickle
import re
from pathlib import Path
from typing import Any
import pytest
import safetensors # noqa: F401
import torch
from torch import nn
import torchlens as tl
from torchle... |
88a668f6a418f4bae08c810426d0fd6a43834f7c7cf8653599a62f5c46a4e92c | Python | 21,839 | 551 | from functools import partial
from typing import Callable, Optional, Tuple
import cutlass
import cutlass.cute as cute
import torch
from cutlass import Boolean, Int8, Int32, const_expr
from flash_attn.cute.block_sparsity import (
BlockSparseTensors,
BlockSparseTensorsTorch,
to_cute_block_sparse_tensors,
)
... |
515ba8e62961e5eef97334683d8109add3de8fa0babf9321b6f0a0993c34aab9 | Python | 21,847 | 666 | """Hardening tests for ``tl.debug.infer_input_shape`` (round 22).
Three mandated properties:
1. NO SIDE EFFECTS: the caller's model (state_dict, training flags, lazy-init
status) is identical after any call, across lazy, train-mode BatchNorm, and
meta-device models.
2. NO ESCAPE: ``on_failure="return"`` never r... |
82920d410a690b148154e33900aec56c8ef8e2ed3ccafdc89e64cada628c92e0 | Python | 21,860 | 445 | import json
import os
from math import ceil
import pandas
from matplotlib.widgets import Slider, RadioButtons
# will not work without this imported
from mpl_toolkits.mplot3d import Axes3D
import mne
from mne.datasets import fetch_fsaverage
from scipy.stats import scoreatpercentile
from mp_dip.utils.multivariate_atom... |
8fcac78f0c00ee819f6e87a1456601ed1a992d729ffb243d62f0e9d19ba30784 | Python | 21,860 | 470 | from os.path import join, exists
from ovseg.utils import io, path_utils
from ovseg.utils.dict_equal import dict_equal, print_dict_diff
from ovseg.data.Dataset import raw_Dataset
from ovseg import OV_PREPROCESSED
import os
import torch
from time import sleep, asctime
try:
from tqdm import tqdm
except ModuleNotFoundE... |
ed4a478965360430043f2a593e5dd147f15fbd9c0c810c0eda4c501ce8850adb | Python | 21,864 | 690 | from flask import Flask, request, jsonify, render_template, send_file
import os
import json
import numpy as np
from math import isnan
from natsort import natsorted
#from pprint import pprint
# Our modules
import power
import data
import image
import cohort
import correlation
import session
import image_math
app = Fla... |
b3e0897e1eb1c3b80ea47c2f7f5abcd3fa1a7b86d81ab807e1472665f967c7a9 | Python | 21,869 | 500 | # pylint: disable=arguments-differ, missing-docstring
"""Encoder and Decoder functions.
Encoders are used during training, which assign training targets.
Decoders are used during testing/validation, which convert predictions back to
normal boxes, etc.
"""
from __future__ import absolute_import
import numpy as np
from ... |
23fcd98649886c39bf1ea2c8d96582f6f8d712777990d01d436935c6d537f338 | Python | 21,874 | 555 | from __future__ import absolute_import
import errno
import logging
import operator
import os
import shutil
from optparse import SUPPRESS_HELP
from pip._vendor import pkg_resources
from pip._internal.cache import WheelCache
from pip._internal.cli import cmdoptions
from pip._internal.cli.base_command import Requiremen... |
279f188b64070ba8a700890ab8da5414189e2d5986eeb17fd772be8fae634f1d | Python | 21,874 | 493 | import copy
import logging
from collections import defaultdict
from dataclasses import dataclass
from pathlib import Path
from typing import Sequence, Union
import numpy as np
import pandas as pd
import torch
from ase import data as ase_data
from monty.serialization import loadfn
from pymatgen.analysis.graphs import M... |
7d19c9731337d0d11252c36b3b79e68aed6ddc4b38d2a07f1d12dd3e52a6ab08 | Python | 21,907 | 610 | """
Evaluation of simulated models against reference data.
Runs one or more models under a reference dataset's conditions and scores the
resulting behaviour against the recorded distributions and cycle curves.
"""
from __future__ import annotations
from typing import Any
import copy
import os
import warnings
from .... |
c62d81eb1941451ffc56d626be76416559b1125e05a11fd0cd638b9a267c5b0d | Python | 21,914 | 685 | import argparse
from networkx.generators import community
from scipy.spatial import distance_matrix, minkowski_distance, distance
import scipy.sparse
import sys
import pickle
import csv
import networkx as nx
import numpy as np
import pandas as pd
import time
from sklearn.manifold import TSNE
from sklearn.metrics impo... |
efabd5ff527584cfee855b42c34ee6d33abd850a7a75ea41b5c2370f689ec93e | Python | 21,916 | 585 | import os
import csv
import copy
import datetime as dt
from pyoperant.behavior import base, shape
from pyoperant.errors import EndSession, EndBlock
from pyoperant import components, utils, reinf, queues
class TwoAltChoiceExp(base.BaseExp):
"""A two alternative choice experiment
Parameters
----------
... |
15347f0a70216990a8f2cd0b534421a77587021acde9e4c1bc894d5afb2bb5e4 | Python | 21,921 | 591 | import numpy as np
from keras.src import backend
from keras.src import initializers
from keras.src import layers
from keras.src import testing
class SimpleRNNTest(testing.TestCase):
def test_basics(self):
self.run_layer_test(
layers.Bidirectional,
init_kwargs={"layer": layers.Simp... |
23dab7629c32108d903f6c4931dba21311cd9bf2316cf61c7682d74d5c9cfcef | Python | 21,925 | 599 | """
Superclass Manager and Serializers for Sharable objects.
A sharable Galaxy object:
has an owner/creator User
is sharable with other, specific Users
is importable (copyable) by users that have access
has a slug which can be used as a link to view the resource
can be published effectively making ... |
a9b418230459f876ff969a76bfc0a9d67b54cffe94237eae76bd1e2771953aec | Python | 21,935 | 439 | import unittest
from spitfire import Library, Dimension
from spitfire.chemistry.library import LibraryIndexError
import numpy as np
from copy import copy, deepcopy
machine_epsilon = np.finfo(float).eps
class Slice1D(unittest.TestCase):
def test_full(self):
l1 = Library(Dimension('x', np.linspace(0, 1, 16... |
657b10f7cb575389d56cb89b1ca80eecd7ab5c3778cadc7f1aeed58c2e279646 | Python | 21,944 | 410 | from __future__ import generators
import logging
import glob, os, functools
import sys
import gc
os.environ['CUDA_VISIBLE_DEVICES'] = "3"
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
import SimpleITK as sitk
from scipy.signal import medfilt
import numpy as np
from numpy import median
import scipy
import nibabel a... |
a7af01499945967c02c8cae01044acfa7c1ea65c44491406d74cd30c728253ca | Python | 21,945 | 605 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Plots for color/style legends"""
from collections.abc import Iterator
from itertools import chain
from typing import Any, Dict, Literal, Sequence, Union
import numpy as np
import matplotlib
import matplotlib.axes
import matplotlib.cm
from matplotlib.colors im... |
ed47430dbf498fd267760aa244010b92e5047c3b560c56b58db1b1663da4c297 | Python | 21,950 | 514 | """P3D, implemented in Gluon. https://arxiv.org/abs/1711.10305.
Code adapted from https://github.com/qijiezhao/pseudo-3d-pytorch."""
# pylint: disable=arguments-differ,unused-argument,line-too-long
__all__ = ['P3D', 'p3d_resnet50_kinetics400', 'p3d_resnet101_kinetics400']
from mxnet import init
from mxnet.context imp... |
87223418472ffc3e214b7b902c6c7751462a69c62e65bb4daef75cc093525ba4 | Python | 21,952 | 474 | # miscellaneous tools
import os
import subprocess
import sys
import pandas as pd
from collections import defaultdict
import gzip
from numpy import unique
import numpy as np
import pickle
#import HTSeq
#import pysam
#PATH = './'
PATH = os.path.dirname(__file__)
HOME = os.path.expanduser('~')
STAR_PATH = os.path.joi... |
e62a86806af8564263b7a3904174df85b3a76d40ebbf0aa7e2b7e83a9ce90555 | Python | 21,963 | 627 | import os
import grain
import numpy as np
import pytest
import tensorflow as tf
from absl.testing import parameterized
from tensorflow import data as tf_data
from keras.src import Sequential
from keras.src import backend
from keras.src import layers
from keras.src import models
from keras.src import saving
from keras... |
0cf64bd5cc30fa04ee162e8958eed9996adab03e8372f8253f5992d27a056f5e | Python | 21,964 | 558 | import os
import csv
import copy
import datetime as dt
from pyoperant.behavior import base, shape
from pyoperant.errors import EndSession, EndBlock
from pyoperant import components, utils, reinf, queues
import serial
import random
class Visit(utils.Event):
"""docstring for Visit, a variant of trial for place pref... |
11c398de667b7320f9000a6f537b0b13de245e3f8008494113818510c2c161bf | Python | 21,976 | 656 | from rdkit import Chem
import re
from torch.autograd import Variable
import torch
import numpy as np
from multiprocessing import Pool
import pandas as pd
from rdkit.Chem.Scaffolds import MurckoScaffold
from Metrics.SA_Score import sascorer
from Metrics.NP_Score import npscorer
from rdkit.Chem.QED import qed
from rdkit.... |
e82529657842627db856117dc668e6e78588549a2a1904dcae99b7dfcfeb4024 | Python | 21,981 | 281 | """Все параметры мира в одном месте. Ничего не хардкодим в движке."""
from dataclasses import dataclass, asdict, field
import json
@dataclass
class Config:
# --- воспроизводимость ---
seed: int = 1
# --- мир ---
grid_h: int = 128
grid_w: int = 128
patch_freq: float = 0.05 # ниже = круп... |
56f4a0c36f6d2fae02f6c496cd60fc2b439fc8f5de0e266b9cb5a3bf4f1afb0c | Python | 21,982 | 454 | """b5 R45-2 / SF-41: string private-attribute reach-ins are ledgered, not free.
``getattr(trace, "_raw_to_final_op_labels", {})`` is a private reach-in that
the linter cannot see: SLF001 flags ``trace._raw_to_final_op_labels`` but NOT
its string spelling, so the measured 1771-1777 SLF001 hits UNDERCOUNT the real
encap... |
e97809afd8fbff0738d746191801a7f64c07263288c2706871d9205320824b05 | Python | 21,989 | 497 | import functools
import gc
from multiprocessing import Pool, cpu_count
from typing import Optional, Tuple, Union
import numpy as np
import psutil
import scipy
from ..logging import logger_manager as lm
# ---------------------------------------------------------------------------------------------------
# Spatial sm... |
a40b49cb47045bcbd59bc45b7c3ca9dc04a4ae7e86698f7b725072941e584c2f | Python | 21,992 | 676 | """Tests for the CodeCarbon CLI main function."""
import io
import os
import sys
from types import SimpleNamespace
import pytest
import requests
import typer
from typer.testing import CliRunner
from codecarbon.cli import main as cli_main
class FakeApiClient:
def __init__(self, endpoint_url=None):
self.... |
d7719765f2476192f04e220b3795446379202abf9cfc60bdb9176200332f22b7 | Python | 21,995 | 612 | """Tests for streaming out save during ``trace``."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import pytest
import safetensors # noqa: F401
import torch
from torch import nn
import torchlens as tl
import torchlens.postprocess as postprocess_module
from torchlens import tra... |
ad28f728959fe1eed91fff8694071791e7e9bfcd85d7ecb9b786c29676a06c91 | Python | 21,999 | 527 | import math
from collections import OrderedDict
from datetime import datetime
try:
from zoneinfo import ZoneInfo
except ImportError:
from backports.zoneinfo import ZoneInfo
import math
import packaging.version
import pytest
from rpy2 import rinterface
from rpy2 import robjects
from rpy2.robjects import vector... |
af484c4e477b2de78859ddebe97acba87d67599fe27deca57b2400f9f0b6dc87 | Python | 22,002 | 454 | """
evaluation_07.py — figures, statistics and CSV export
Two changes matter relative to the earlier version.
Navigation results are keyed by phase as well as by group:
navigation = {phase: {group: [TrialResult, ...]}}
Previously a single group-keyed dictionary was passed in, so whichever phase
was written last o... |
4377388725a1436f9c76983e406fa8f94ff07838a898d45d0d8ce154f2398a42 | Python | 22,026 | 615 | """
behav_analys.py
This script contains functions for running and pupil analysis.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import numpy as np
import pandas as pd
from util import gen_util, math_util, rand_util
from sess_util import sess_load_util
from analysis import basic... |
3dd12ab4063cfb4bfdcebbc430efea91a4e33ff64ea6c4f07f8163bda74b1c12 | Python | 22,028 | 501 | import os
import pandas as pd
import numpy as np
from collections import namedtuple
from .swcch import soma_check, general_check, parentindex_check, datatype_check, typeid_check, index_check, spiderleg_check
from .swcco import (
contour_convert,
swc_sort,
set_unspecified_typeID,
set_standard_somaID,
... |
dada14f4d1c145309152ff49b7fa0970527cce37b9528c1c5bde72bfddc58a7b | Python | 22,028 | 573 | """
roi_analys.py
This script contains functions for ROI mask and projection analysis.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import numpy as np
import pandas as pd
from util import gen_util
from sess_util import sess_load_util
from analysis import misc_analys
# PRESET ... |
2d6c9b8a842cd7e1225c3dca151447d2512b34efff76020f12ca883079fbca4d | Python | 22,071 | 661 | from functools import lru_cache
from typing import Generator
import numpy as np
from mirp._features.cm_matrix import MatrixCM
from mirp._images.generic_image import GenericImage
from mirp._masks.base_mask import BaseMask
from mirp._features.histogram import get_discretisation_parameters
from mirp._features.texture_fe... |
16f13c60db87c051aec086eae82263dc7227207a8c2326c0365f013471c2609f | Python | 22,073 | 526 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import contextlib
import math
import os
import random
from collections.abc import Iterator
from pathlib import Path
from typing import Any
from urllib.parse import urlsplit
import numpy as np
import torch
import to... |
cd3ecd50ebfc205eb2ee53065b4e6e48a05be46520f40e7955aa127539d4652b | Python | 22,074 | 724 | from numpy import linalg as la
def lambda_dist(A1, A2, k=None, p=2, kind="laplacian"):
"""The function is migrated from NetComp package. The lambda distance between graphs, which is defined as
d(G1,G2) = norm(L_1 - L_2)
where L_1 is a vector of the top k eigenvalues of the appropriate matrix
assoc... |
54f624233c2300b545a6b61d90c317fae7c0b06b40599f91fcb467ba4b9b7f6b | Python | 22,077 | 582 | import os.path
import pytest
CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
def _type_converter(type_str: str):
if type_str == "int":
return int
elif type_str == "float":
return float
elif type_str == "bool":
return bool
elif type_str == "str":
return str
... |
21d14097566563ac82edbe914ce64d9676c6835bc84bf29c569f7ddf2cb975a3 | Python | 22,078 | 502 | """r57 C3 immunizer -- op-agnostic FakeTensorMode allocation preflight, allowlist DELETED.
r55 closed the allocation-bomb class with a ``FakeTensorMode(allow_non_fake_inputs=True)``
per-call projection, but GATED it behind a hand-maintained ``_SIZE_DRIVING_QUALNAME_TAILS``
op allowlist. r56 found the allowlist re-open... |
4a259e61207bfcfea8e194a1f4f1c3de47f41e058bede013348a19af61393edc | Python | 22,079 | 619 | """
Unit tests for Session Management.
Tests secure session creation, validation, and cleanup for authentication.
"""
import datetime
import time
import unittest
from unittest.mock import Mock, patch
from ethoscope_node.auth.session import SessionManager
class TestSessionManager(unittest.TestCase):
"""Test sui... |
d563bcb8131fca7e8941f180d66d9fc7aa95b470503e8145467651908ca61852 | Python | 22,082 | 525 | # Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
9e87eee70630220cb25c2ff740f7d3c2f9ce07fe8b3037ddff646223b076e77a | Python | 22,119 | 515 | # 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... |
bed3f5388ca1a58c4f2b20708e3d1714d5a7cd4899bc3eb491800bff882cc612 | Python | 22,133 | 573 | # --- 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 = "funnel"
_path_str = ... |
4927f23256b185fbdb5644c3db36536c2dc648f2e0298e72420c2cb0decc32df | Python | 22,135 | 529 | import os.path
import pytest
import numpy as np
from mirp.data_import.import_image_and_mask import import_image_and_mask
from mirp._data_import.read_data import read_image_and_masks
from mirp._images.generic_image import GenericImage
from mirp._masks.base_mask import BaseMask
from mirp._images.ct_image import CTImage
... |
91cfa2502f61a348573d11451e0d583d94f853723de60978b43636bcf0538af6 | Python | 22,144 | 535 | from typing import Dict, List, Optional, Tuple, Union
import networkx
import numpy as np
import plotly.figure_factory as ff
import plotly.graph_objects as go
from plotly import callbacks
from ...logging import logger_manager as lm
class PlotNetwork:
def __init__(self, G: Union[networkx.Graph, networkx.DiGraph],... |
62a02ac162e8d97191e8a864d540d5a0bca700977dca3c187b2f85aca5c57372 | Python | 22,145 | 452 | #!/usr/bin/env python3
"""Экспериментальный раннер: калибровка, уровень шума, сравнение условий.
python experiments.py calibrate # кривая чувствительности метрики
python experiments.py noise --seeds 10 # разброс одного условия
python experiments.py compare --seeds 20 # se... |
ee4f3bc9ae3876a26caf5c11350c53b954f434dc63234deec5be72cf590c8219 | Python | 22,149 | 578 | import os
import numpy as np
import pytest
import keras
from keras.src import layers
from keras.src import models
from keras.src import ops
from keras.src import random
from keras.src import testing
from keras.src.legacy.saving import legacy_h5_format
from keras.src.saving import object_registration
from keras.src.sa... |
affafadec0475882464cfa235ad7c0627cda3bf543e2a75dbf0be2f2fdb9ed1c | Python | 22,167 | 571 | """
simulation_06.py
================
SimPy wheelchair navigation driven by REAL classifier accuracy.
Control paradigm
----------------
The decoders are binary (left hand vs right hand), so the simulation uses
shared control (Millan et al. 2010; Rebsamen et al. 2010): at each control
cycle an autonomous planner propos... |
68043aec0ce14452932bdc0093c6537fa90881f8b138f061102b7296a2c8d487 | Python | 22,174 | 494 | """
Author: Bruno De Santi, PhD
Affiliation: Multi-modality Medical Imaging Lab (M3I Lab), University of Twente, Enschede, The Netherlands
Date: 20/09/2023
Description: Learning model of MUVINN-reg
Acknowledge: The code was adapted from
1) J. M. Wolterink, J. C. Zwienenberg, and C. Brune, “Implicit Neural Representat... |
7ddef9e03cdafda81a3f1ee715cf9bbdb936f8ac7b65f079c090fd422db2091a | Python | 22,177 | 504 | import math
import os
import time
import torch
import torch.nn as nn
import numpy as np;
from torch.autograd import Variable
import scipy
import matplotlib.pyplot as plt
import scipy.io as sio
from sklearn.preprocessing import normalize
from sklearn.cluster import KMeans
from sklearn.metrics import normalized_mutual_in... |
0151f6b27d39a9bb1d73a7063defd4c1ac4d6ac12fecc28d7f1d404a62247f2d | Python | 22,179 | 662 | import warnings
from pathlib import Path
from textwrap import dedent
from typing import Generic, List, Optional, Set, Tuple, Type, Union, cast
print('Not using')
import cyvcf2
import joblib
import numpy as np
import pandas as pd
import pyBigWig
import pysam
import zarr
from natsort import natsorted
from numcodecs impor... |
908322f6d30adf016e72818a392a3a5f5c9af7ec9548ef163495bb5a55c68c47 | Python | 22,191 | 595 | """Regression coverage for batch-4 Lane P cache, I/O, and perf fixes."""
from __future__ import annotations
import gc
import warnings
import weakref
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens import user_funcs
from torchlens.... |
dd588219fa31eb8d714274d8d48ff35916d384c0be7b60a20e045e2c0e430fce | Python | 22,193 | 499 | """Input alias topology and non-tensor tree contracts."""
from __future__ import annotations
from collections.abc import Callable, Iterable, Mapping, Sequence
from typing import TYPE_CHECKING, Any, cast
import torch
from . import _state
from ._runnable_state import (
RunResourceCeiling,
_guarded_defensive_m... |
18873010c94ea4eb3fd4649ab27556d82ae12eab07ff081a74f1f37239a2dda6 | Python | 22,195 | 607 | import time
import unittest
from unittest.mock import MagicMock, Mock, patch
from ethoscope.stimulators.multi_stimulator import MultiStimulator
from ethoscope.stimulators.stimulators import DefaultStimulator, HasInteractedVariable
# Optional imports for specific stimulator tests
try:
from ethoscope.stimulators.sl... |
1799d977591c32e88594443779aa0986eca7d2ccd10f81356a162b974be8c3a0 | Python | 22,206 | 612 | from __future__ import division
from os.path import abspath, dirname, join as joinpath
import subprocess
import pytest
import numpy as np
from pandas import read_hdf
from scipy.special import binom
from scipy.sparse import dok_matrix
from scipy.sparse.linalg import spsolve
from pyrho.utility import (get_table_idx,
... |
f28cc7e0a055e00077acb79e3483bf3180175435bb43da41b3e14ebb4227224d | Python | 22,206 | 346 | #### Master Script 1b: Calculate summary statistics and missingness of different study sub-samples ####
#
# Shubhayu Bhattacharyay
# University of Cambridge
# email address: sb2406@cam.ac.uk
#
### Contents:
# I. Initialisation
# II. Load and prepare summary characteristics of full TIL dataset
# III. Calculate summary s... |
19a2625722349350f4c53e97abb674354a5b855195668053babeb0498e1004ed | Python | 22,209 | 592 | """Spatial position and occupancy related functions."""
import warnings
import numpy as np
import pandas as pd
from spiketools.utils.data import assign_data_to_bins
from spiketools.utils.checks import check_array_orientation
from spiketools.utils.extract import create_mask, get_values_by_time_range
from spiketools.u... |
f60891623a9bfb108c9a0c018f13a8ccedd0b5f49c1235fac5d16b7075caa0b3 | Python | 22,216 | 469 | #!/usr/bin/env python3
"""plot_wafer_region_order.py
Top level command-line interface for generating plots showing the ordering
of the sections on top of their original locations on a wafer.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you can redistribut... |
054029f2c3daa633948827e84d5eb945b3b41e398df49f31fc5e0764d7b49245 | Python | 22,218 | 751 | import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
import phantominator as ph
from skimage.transform import radon, iradon
# import cupy as cp
from time import time
from skimage.metrics import structural_similarity as ssim
import sys
# cambiar para drive
# import DataLoading as dl
def TwIST(y, A, AT... |
4d4f2f9d630996c254f8b30015abd8d84e620674b717e3c552f6d0cd25883aef | Python | 22,218 | 564 | """P3 proofs: persisted attestation, N1-N5 gates on real surfaces, F6 latch.
Persistence round-trips (adopt / derive / no-upgrade / tamper-degrade), the
capability gates armed on real products at their real entries, the F6
stop-request latch for every swallowed-signal spelling, Recording and
PartialTrace outcome surfa... |
9eba0af333268a5e193924706d44371caeda7d95315406ce133a721293527334 | Python | 22,220 | 538 | """
Deals with key and mouse events
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published ... |
41a58f8874daf2baec5df170be2065eb23b7e2dd587ac3611fecaf923eaf3bdb | Python | 22,223 | 547 | import torch as th
import torch.nn.functional as F
import dgl
import numpy as np
import random
import dgl.function as fn
from torch import nn
import pandas as pd
##
#the model architecture of graph transformer is modified from https://github.com/BioinfoMachineLearning/DeepInteract
def glorot_orthogonal(tensor, scale)... |
7cfaaf9b65a7d4e3d787ca6ebb21fec9a79a3f5d10dff4093a45f0fe4f6502bf | Python | 22,230 | 434 | """Mask RCNN Estimator."""
# pylint: disable=consider-using-enumerate,abstract-method,arguments-differ
import os
import math
import time
import logging
from multiprocessing import Process
import numpy as np
import mxnet as mx
from mxnet import gluon
from mxnet.contrib import amp
from .... import data as gdata
from ..... |
58d5535ef3fc64bff7b6c1f38ad3aa0431b4a028dfb2e5dd37c17a90ba2101c2 | Python | 22,243 | 433 | #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Written by Yuichiro Yada
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
################################################
# A code for Fig. 5b-d
################################################
import numpy as np
import pandas as pd
import seaborn as sns
import os... |
66de3b670c4f904e549abc371766676152ad499dd3133f6f3806278554a1cda3 | Python | 22,251 | 657 | """Portal Module Inspector: kind-aware standalone module stepping and signal plots."""
from __future__ import annotations
import logging
from html import escape
from typing import Any
import panel as pn
from bokeh.models import ColumnDataSource
from bokeh.plotting import figure
# Suppress Bokeh patch ... |
a214b7b947409629c46f4487ed6d8b6d629c6762c05bf2bf035bb9b30caec1fd | Python | 22,279 | 600 | """Image-translation / generative-GAN family: CycleGAN, CUT, DCGAN, DF-GAN, DiGAN, DeepFillv2.
A compact, faithful atlas pack of the distinctive generator/discriminator cores from a
cluster of well-known GANs. Each entry reproduces the *distinctive primitive* of its paper
at small random-init scale (atlas bar = archit... |
2892300bd5ac704e1151cc3e7ca4720341d8b6e921d8187ebbec85dcea2a1ee6 | Python | 22,285 | 551 | # Copyright (c) 2021 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... |
ee2b16b62634ada014e8cd9cb8ae8bdbee634ebbfe661712005d46248600867c | Python | 22,287 | 670 | # -*- coding: utf-8 -*-
### Functions for à trous wavelet transforms
### Synonyms: stationary wavelet transform, non-decimated wavelet transform,
### starlet transform
import numpy as np
from scipy import signal
from scipy import ndimage
from scipy.ndimage import convolve1d
import itertools as itt
from .constants... |
085d69be8bac36ea3c1fa3a1bf5f0e3134a393aea0a1aefd22ea13f545f0a65d | Python | 22,302 | 507 | """r59 whole-class immunizer -- aggregate replay resource ceiling (allocation-DoS close).
r57 bounded per-op allocation BYTES via a ``FakeTensorMode`` projection. r58 found two
seams the byte budget is structurally blind to:
* free_1 -- ``tensor_split(x, N)`` drives N *empty* output tensors (~0 bytes) off ONE int
l... |
b84dd2dc5f8867b55396f631a5ac1799450a6f14e17b0aee988bf2a581817ea7 | Python | 22,310 | 470 | #! /usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Local streamline HARDI tractography using scilpy-only methods -- no dipy (i.e
no cython). The goal of this is to have a python-only version that can be
modified more easily by our team when testing new algorithms and parameters,
and that can be used as parent classes ... |
fac4c7f1cccd1b280c33ced24fc737eee8be9151fe2fe67709aea08074747cb5 | Python | 22,315 | 458 | import abc
import json
import six
import warnings
import h5py
import tensorflow
import tensorflow.keras.backend as K
import tensorflow.keras as keras
from tensorflow.keras import layers
from tensorflow.python.ops.gen_nn_ops import Softmax
from data import DataGenerator
from utils import img_to_kspace, kspace_to_img, ... |
314f9df18f09c258f7bc60190e3d5f90117f65995d9468280cba93cc68362f5f | Python | 22,359 | 611 | """Reading logic for ome-zarr."""
import logging
import math
from abc import ABC
from collections.abc import Iterator
from typing import Any, Optional, TypeVar, Union, cast, overload
import dask.array as da
import numpy as np
from .axes import Axes
from .format import format_from_version
from .io import ZarrLocation... |
7135b4a0a05002f20d71a7416002a0f4dd158e34572da5112117e1dbec5cc391 | Python | 22,362 | 556 | import logging
import os
from autouri import AbsPath, AutoURI
from .caper_backend_conf import CaperBackendConf
from .caper_base import CaperBase
from .caper_labels import CaperLabels
from .caper_workflow_opts import CaperWorkflowOpts
from .cromwell import Cromwell
from .cromwell_backend import (
CromwellBackendAw... |
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