sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
6b097e4edf9a8c95317f09ac297a973a7fa9227edbb6468092213e3ed7b35a61 | Python | 34,099 | 934 | """Honest distributed detection: compat rows plus a typed capture refusal.
Before this guard, a tensor-parallel model traced "successfully" while reporting
``0 total modules`` and ``0 params total; 0 B`` -- the ``linear`` op replaced by
bare ``viewas`` nodes -- and ``tl.compat.report`` reported all-pass for the same
m... |
327c230252d88f291c5dbdb7bf62e66b07f69061b349a59739dcb4bb17a93499 | Python | 34,101 | 866 | """Parse GFF files into features attached to Biopython SeqRecord objects.
This deals with GFF3 formatted files, a tab delimited format for storing
sequence features and annotations:
http://www.sequenceontology.org/gff3.shtml
It will also deal with older GFF versions (GTF/GFF2):
http://www.sanger.ac.uk/Software/form... |
d3366f32f1f73edc24788dfd6b44eb8daf5b8fec70fd72ed3875b01e82d16c88 | Python | 34,110 | 962 | # ----------------------------------------------------------------------------
# Copyright (c) 2015, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------------------------------------... |
3499914f9ac8c0424735e49a04a5caae89e078deef1764e33e2915e643604bcd | Python | 34,111 | 659 | #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Written by Yuichiro Yada
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
################################################
# A code for Fig. 2g
################################################
import numpy as np
import pandas as pd
import seaborn as sns
import os
... |
a793998b696b8abd4534ddc2ef3ab65949319b48f7d78a89d95a1db30424ae51 | Python | 34,150 | 1,068 | # %%
import os, glob
import numpy as np
import pandas as pd
from tqdm import tqdm
import benepar
from spacy.symbols import ORTH
from nltk.corpus import wordnet as wn
from sklearn.dummy import DummyClassifier
from sklearn.linear_model import RidgeClassifier
from sklearn.model_selection import (
StratifiedGroupKFold... |
0632b05c41c725d627597b352d0d6eba704dcb3ea14c30c83ddd5e55bc422442 | Python | 34,156 | 738 | # Copyright (c) 2025, Jay Shah, Ganesh Bikshandi, Ying Zhang, Vijay Thakkar, Pradeep Ramani, Tri Dao.
# A reimplementation of https://github.com/Dao-AILab/flash-attention/blob/main/hopper/flash_fwd_combine_kernel.h
# from Cutlass C++ to Cute-DSL.
import math
from typing import Callable, Type, Optional
from functools im... |
a33d70e336729fc03a3c2e0dc1dcacea0095e535490c4273e29445649c59968b | Python | 34,162 | 849 | # --- 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 = "scatterpolargl"
_pat... |
1c979a2a2bd0bc2ca5d7f65eb579ced1a6af053df642fb43fcc0b3266111a241 | Python | 34,173 | 927 | import errno
import socket
from queue import Empty
from unittest.mock import Mock
import pytest
from kombu.asynchronous import ERR, READ, WRITE, Hub
from kombu.asynchronous.timer import Timer
from kombu.exceptions import DecodeError
from celery.bootsteps import CLOSE, RUN
from celery.exceptions import InvalidTaskErro... |
5a625cff7a023b93bbc7bf50aa030415f983c5ad2c368e3e6fa48f9b82f28313 | Python | 34,174 | 768 | """Code allowing tools to define extra files associated with an output datset."""
import abc
import logging
import operator
import os
import re
from collections.abc import Callable
from decimal import Decimal
from tempfile import NamedTemporaryFile
from typing import (
Any,
Optional,
TYPE_CHECKING,
)
from... |
05e64775d486050dc620fe07c1b35a4a63c4b5503e84f71e9e2a5f520bfe356b | Python | 34,198 | 1,078 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in complian... |
25aef1aa1deadb0089417756746de5ffcc7f2b16454186226d265a0e18fab810 | Python | 34,218 | 668 | """Train Faster-RCNN end to end."""
import argparse
import os
# disable autotune
os.environ['MXNET_CUDNN_AUTOTUNE_DEFAULT'] = '0'
os.environ['MXNET_GPU_MEM_POOL_TYPE'] = 'Round'
os.environ['MXNET_GPU_MEM_POOL_ROUND_LINEAR_CUTOFF'] = '26'
os.environ['MXNET_EXEC_BULK_EXEC_MAX_NODE_TRAIN_FWD'] = '999'
os.environ['MXNET_E... |
3b42fd5bcc94a999c91ede3a99350c6199cbe9cd9844f36175a367e1c02e6066 | Python | 34,232 | 798 | import torch
import torch.nn as nn
from torch.nn import init
import functools
from torch.optim import lr_scheduler
###############################################################################
# Helper functions
###############################################################################
def init_weights(net, i... |
ec32f87527dd0280cdac622fa37507103b810614821ba313223c1eb6266175d8 | Python | 34,239 | 817 | #!/usr/bin/env python3
"""
File: bryois_pic_replication.py
Created: 2022/10/18
Last Changed:
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 source tree.... |
c9d20b283655836607f367975c1234440a95f611b568835013947c2dd06f01f5 | Python | 34,244 | 667 | """Train Doublehead-RCNN end to end."""
import argparse
import os
# disable autotune
os.environ['MXNET_CUDNN_AUTOTUNE_DEFAULT'] = '0'
os.environ['MXNET_GPU_MEM_POOL_TYPE'] = 'Round'
os.environ['MXNET_GPU_MEM_POOL_ROUND_LINEAR_CUTOFF'] = '26'
os.environ['MXNET_EXEC_BULK_EXEC_MAX_NODE_TRAIN_FWD'] = '999'
os.environ['MXN... |
43d15e39fda7d7b990572e134902e0878a2e8d3b746e202dd150483117239410 | Python | 34,257 | 896 | from __future__ import absolute_import, division
from tqdm.auto import tqdm
import torch
from torch.autograd import Variable, grad
from torch.nn import Parameter
import torch.nn.functional as F
import numpy as np
import pandas as pd
import sys
import random
import os
import math
def reset(nn):
def _reset(item):
... |
52ffb08b0a49603dd70b43dfeb3fec05ac094b3372f9d40a44642a3f225175a2 | Python | 34,260 | 1,080 | """
seq_figs.py
This script contains functions defining sequence figure panel analyses.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
from util import logger_util
from analysis import seq_analys, misc_analys
from paper_fig_util import helper_fcts
logger = logger_util.get_module... |
b248e7db77bd41dfdaeebae470438773c5ff22955649ea89f97bd826cf2d2afc | Python | 34,292 | 1,131 | try:
import llspy
except ImportError:
import os
import sys
thisDirectory = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(thisDirectory, os.pardir, os.pardir))
import llspy
import logging
import os
import shutil
import sys
import click
import voluptuous
from llspy im... |
be3faf7d0e2e9b8719e2e0472c501fbd90118b15be422b92632a1a1b5765b55c | Python | 34,336 | 1,068 | """Clustering."""
from math import floor
import warnings
from joblib import Parallel, delayed
import numpy as np
from sklearn.base import BaseEstimator
from sklearn.cluster import KMeans as sklearnKMeans
from sklearn.utils.validation import check_random_state
from .classification import MDM
from .datasets import samp... |
60afed5a0f53b9a65d3d5a3c697c348cac1a490f8dd22874734105ae3e5b67f2 | Python | 34,364 | 807 | import math
import os
import csv
import random
import torch
from torch.utils import data
import numpy as np
from dateutil import parser
import contigs
from util import *
from kinematics import *
import pandas as pd
import sys
import torch.nn as nn
from icecream import ic
def write_pdb(filename, seq, atoms, Bfacts=None,... |
7fe2cdb12a3524d85284234b2227379a6d9d11a149498cfc69fe5eae54dc29b6 | Python | 34,364 | 807 | import math
import os
import csv
import random
import torch
from torch.utils import data
import numpy as np
from dateutil import parser
import contigs
from util import *
from kinematics import *
import pandas as pd
import sys
import torch.nn as nn
from icecream import ic
def write_pdb(filename, seq, atoms, Bfacts=None,... |
769a15fa8c35a77eae18e4b46e7aad95acf74273366496e03869da343350a0d1 | Python | 34,365 | 709 | # dependencies
import itertools as it
import copy
import numpy as np
from scipy.stats.mstats import sem
import matplotlib as mpl
import matplotlib.pyplot as plt
from ssm.plots import white_to_color_cmap
from matplotlib import cm
import pandas as pd
import seaborn as sns
from mpl_toolkits.axes_grid1 import make_axes_loc... |
8966a541176a5eab65e4c7e2e20c5458fc7d3e68c7e6a7e4ffccbb907ee70a32 | Python | 34,440 | 634 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
50_figures.py — 生成投稿用图（研究设计 + 校准 + 重测信度 + 综合判读）
================================================================================
输入：out/aifi_calibration_metrics.csv
out/aifi_retest_reliability.csv
out/aifi_imm_predicted_ages.csv
out/aifi_sound_predicte... |
b568c33a3f162e00f171117e5635479e0d70c9396a47ea0697be80e145f2156b | Python | 34,441 | 705 | #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Written by Yuichiro Yada
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
################################################
# A code for Fig. 4
################################################
import numpy as np
import pandas as pd
import seaborn as sns
import os
i... |
303384e4f3e95b4a70f74bb11d13fb93ef8ef3ed9207323ce141b6780144782d | Python | 34,457 | 929 | #!/usr/bin/env python
"""REST Translation server."""
import codecs
import sys
import os
import time
import json
import threading
import re
import traceback
import importlib
import torch
import bioseq2seq.opts
from itertools import islice, zip_longest
from copy import deepcopy
from collections import defaultdict
from a... |
4e0bf360aaa59a1ebd88fec8866ca1cbbdd0a47dcd9936d3288d75798766e3e4 | Python | 34,458 | 950 | """
decoding_analys.py
This script contains functions for decoding analysis.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import itertools
import numpy as np
import pandas as pd
import scipy.stats as scist
from util import gen_util, logger_util, logreg_util, math_util, rand_ut... |
164d402de0631f02f9f5ec452bcc9657909054cfb44b9e14ef8309c26118fae6 | Python | 34,574 | 1,147 | """Phase-0 render identity oracle for the visualization refactor.
This intentionally characterizes the current Graphviz implementation. The
records are a tripwire: do not update them except for an explicitly approved
rendering change.
"""
from __future__ import annotations
import hashlib
import json
import re
impor... |
5242ec5474ab4e5c80582354efed12586b6adb3ec0e5a88acd44e31c87952156 | Python | 34,596 | 903 | from __future__ import absolute_import, division
from tqdm.auto import tqdm
import torch
from torch.autograd import Variable, grad
from torch.nn import Parameter
import torch.nn.functional as F
import numpy as np
import pandas as pd
import sys
import random
import os
import math
class Encoder(torch.nn.Module):
def... |
4958d1b5c18061040735432ddc1ac8bb2e826cb31e7fdb94ea8131eb512c5454 | Python | 34,604 | 794 | """Transactional execution providers for the unified :meth:`Trace.run` surface."""
# ruff: noqa: F401
from __future__ import annotations
import dataclasses
import math
import struct
import sys
from collections.abc import Callable, Iterable, Mapping, Sequence, Set as AbstractSet
from contextlib import contextmanager,... |
9df0914b759953bce753fe5303a2434c72a4f481933410d5611b64113110abe6 | Python | 34,637 | 656 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
8649cf5c06ecb359dbc8f26f715bd05bf3825036e05d030eb2e872e8fcf78b97 | Python | 34,661 | 1,066 | import sys
import itertools
import csv
import pprint
from pathlib import Path
import numpy as np
import torch
from torch import optim
from sklearn.manifold import TSNE
from sklearn.metrics import (
confusion_matrix,
ConfusionMatrixDisplay,
silhouette_samples,
)
from mpl_toolkits.mplot3d import Axes3D
from ... |
38457ae3c72d70b9ebb6a7225e05c513a18cac07e2880a2f7dbfb5cbfc357138 | Python | 34,667 | 816 | """Module that contains functions used to interpret a trained CMKN model.
Authors:
Jonas C. Ditz: jonas.ditz@uni-tuebingen.de
"""
import math
import os
import numpy as np
import torch
from .data_utils import ALPHABETS
def seq2ppm(seq, alphabet="DNA_FULL"):
"""Converts sequences into a position probability... |
4711eccaa3dc8b1b45982f2db3a56dc7c34ffe381c25ed924990821eb65df41a | Python | 34,704 | 712 | import pandas as pd
import scipy.io as sio
import scipy.interpolate
import numpy as np
import scipy.sparse
import scipy
import gzip
import subprocess
import collections
from collections import defaultdict, Counter
import scipy.sparse as sp_sparse
import warnings
import pickle
import os
#warnings.filterwarnings('ignore'... |
1d9eec631585a793ab814cb5e3d4b13d4062654c116542881f2b689a1ec47acc | Python | 34,715 | 914 | F"""
This code started out as a PyTorch port of Ho et al's diffusion models:
https://github.com/hojonathanho/diffusion/blob/1e0dceb3b3495bbe19116a5e1b3596cd0706c543/diffusion_tf/diffusion_utils_2.py
Docstrings have been added, as well as DDIM sampling and a new collection of beta schedules.
"""
import enum
import mat... |
44f131f6fa0396a25084bfb9e31ff49c7d0555f19c0b44cf59990bc73df43a44 | Python | 34,717 | 873 | """Parse GFF files into features attached to Biopython SeqRecord objects.
This deals with GFF3 formatted files, a tab delimited format for storing
sequence features and annotations:
http://www.sequenceontology.org/gff3.shtml
It will also deal with older GFF versions (GTF/GFF2):
http://www.sanger.ac.uk/Software/form... |
978cebdd04eabd07528df82856e3ac7f04afc540b36b74b569a08dfeea8c1343 | Python | 34,723 | 839 | """
Neural Network implementation for image segmentation
For more information about autotune:
https://www.tensorflow.org/guide/data_performance#prefetching
Copyright (c) 2022 Giansalvo Gusinu <profgusinu@gmail.com>
Copyright (c) 2021 Emil Zakirov and others
Copyright (c) 2020 Yann LE GUILLY
... |
5290e9a8d5209b63c4db049332419fb8906d6bddb01d73fa6a0b398323a21fd6 | Python | 34,734 | 865 | import contextlib
import email.utils
import enum
import glob
import hashlib
import http.client
import json
import logging
import math
import os
import re
import secrets
import shutil
import ssl
import tempfile
import time
import urllib.parse
import urllib.request
from datetime import datetime, timezone
from pathlib imp... |
10b4804fa0d7d423abf61e90992ed56ddecba1fdc8d42217a43a2c17194b2eff | Python | 34,753 | 482 | #!/usr/bin/env python
# Created on: July 10, 2013
__author__ = "Sven Kreiss, Kyle Cranmer"
__version__ = "0.1"
import optparse
parser = optparse.OptionParser(version=__version__)
parser.add_option("-q", "--quiet", dest="verbose", action="store_false", default=True, help="Quiet output.")
options,args = parser.parse... |
2b860591389d12581d1ef3d05f7f25933217beef64135d6262cec1e866a81c61 | Python | 34,763 | 1,045 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Carpet(_BaseTraceType):
_parent_path_str = ""
_path_str = "carpet"
_valid_props = {
... |
7b8d217d70a1ced3852e97c4524fc475ddfcb412a2be0730bc1ed74080e6dfe4 | Python | 34,783 | 720 | # -*- coding: utf-8 -*-
"""
Tier 2: instantiate each pyoperant/behavior/*.py Behavior class from its
real example_configs/*.json and step it through some real usage, with
hardware replaced by tests/fixtures.py's FakePanel. Catches logic-level
bugs Tier 0 (syntax) and Tier 1 (import) can't -- e.g. file modes,
signature ... |
15403b20884d730db098dd534258be0cd433649446a8ac1cc0a11c5bc2b52929 | Python | 34,791 | 899 | """Routines related to PyPI, indexes"""
from __future__ import absolute_import
import cgi
import itertools
import logging
import mimetypes
import os
import posixpath
import re
import sys
from collections import namedtuple
from pip._vendor import html5lib, requests, six
from pip._vendor.distlib.compat import unescape
... |
68af92e5847d66e5adab0a9872b282610a2720d32f5f4bc166ca329395070011 | Python | 34,796 | 840 | import numpy as np
import keras as keras
from keras import backend as kb
from keras.utils.conv_utils import normalize_tuple
import warnings
import collections
from csbdeep.utils import axes_dict
import pywt
import random
# Contains code for data loading and generation before
# being passed into the network.
class Dat... |
8f45c0b45220da352fa033f5c21aeafc6f81d5d37ba7a6ec560fbeb792b0f1d2 | Python | 34,802 | 900 | import os
import pandas as pd
import requests
from collections import Counter
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
from rdkit.Chem import Mol
from tqdm import tqdm
from Bio.PDB import PDBParser
from typing import Union, List, Tuple, Dict, Set
from rdkit.Chem.AllChem import Assi... |
3eb47c23dd56f33a0b06ff69478834c35f9f2ceda913c572a32ab69f030a2554 | Python | 34,808 | 1,065 | """Explore - the zero-configuration entry point to Larvaworld.
Three states in one page: a gallery of curated scenarios, a live run, and a
result view. The promise is one click and no decisions between arriving and
watching virtual larvae behave.
Everything here is display-only: runs are capped, nothing is written to... |
43ed3da46139717c8887a0cab36a162b813245cfe30b8ed5bd927af41a11db9d | Python | 34,832 | 978 | import time
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 zscore
from scipy.spatial.distance import cdist
from scipy.signal import detrend
from scipy.fft import fft, fftfreq
from sklearn.decomposition import PCA, FactorAnalysi... |
6742fe59e0162a028a7e111497c2f3114b51b859daa092851f5cbcee394eebae | Python | 34,845 | 759 | # pylint: disable=line-too-long,too-many-lines,missing-docstring,arguments-differ,unused-argument
import mxnet as mx
from mxnet import init
from mxnet.gluon import nn
from mxnet.gluon.nn import HybridBlock
from ..resnetv1b import resnet18_v1b, resnet34_v1b, resnet50_v1b, resnet101_v1b, resnet152_v1b
__all__ = ['resnet... |
57765a766db60a2fa0546a6d5e420b0ed0fa5cd1d0154082b1fe4c28dc5e9942 | Python | 34,848 | 896 | import functools
import inspect
import itertools
import string
import numpy as np
from keras.src import backend
from keras.src import tree
from keras.src.api_export import keras_export
from keras.src.backend.common import is_float_dtype
from keras.src.backend.common.variables import standardize_dtype
from keras.src.l... |
0116c8a160d24480d44841f825c3981bb1332e756abfe56e91caad8447c3bc90 | Python | 34,861 | 794 | """
This module creates the craniosynostosis distance maps.
"""
import warnings
import numpy
import vtk
import vtk.util.numpy_support
def define_shape_model_landmarks():
"""
Defines the 10 landmarks on the shape model data,
as defined on our publicly available statistical shape model.
Indices start at... |
0cdb4987ff645b9596376603bebd8b21bc9953ef7f2fcc54afe175ad69c86f8f | Python | 34,864 | 953 | """
The general utility functions.
"""
import csv
import logging
import os
import pickle
import random
from argparse import Namespace
from collections import defaultdict
from logging import Logger
from typing import List, Set, Tuple, Union, Dict
import numpy as np
import torch
from rdkit import Chem
from rdkit.Chem.Sc... |
dc45070323d0799fe479a796bbb736011627bb24d2102970e9dc7975635cbcb6 | Python | 34,882 | 842 | # 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... |
3d7ce0e89ca2f1862e0882a40478340fd3b2517e342951cb7ee83372ae59d7c5 | Python | 34,889 | 663 | """
Functions processing segmentation data
Copyright (c) 2019 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import math
import platform
import numpy as np
from skimage import measure, transform
import skimage
from scipy.ndimage import map_coordinates, gaussian_filter1d, zoom
import l... |
052eee3e73e9903ec5fdcfc7ee683fcfb869a85ea1cc33e775c78e78d72c59da | Python | 34,897 | 594 |
# create a script from a matrix and a vector of labels - plot connectome
import pandas as pd
import matplotlib.pyplot as plt
import scipy.io
import mne
import numpy as np
#%%
## functions
def isSquare (m): return all (len (row) == len (m) for row in m)
def regions_bst_to_lobes( argument ):
'''
gather bra... |
0fb9f9f9bd749c08463d794b1775c91ed99bc123fb8cabc73985102e5ae179e4 | Python | 34,950 | 1,105 | """
any new class added here need to be added to web_utils/control_thread.py too
"""
__author__ = "quentin"
import logging
import random
from ethoscope.hardware.interfaces.interfaces import DefaultInterface
from ethoscope.hardware.interfaces.optomotor import OptoMotor
from ethoscope.hardware.interfaces.sleep_depriv... |
5504fdb70d07050e0ed3cb0fe06e291bc4f45203b854ee0385f53a199a3e6153 | Python | 35,000 | 897 | # 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... |
63564182872ad0f250ef6ee06f552f4592569b3636568b52a5c78c49479a3e73 | Python | 35,013 | 822 | """Tensor-variant detection and pre-flight guards for ``trace``.
TorchLens was designed around standard dense ``torch.Tensor`` /
``torch.nn.Parameter`` objects on real (CPU/CUDA/MPS) devices. A number of
tensor variants break the logging pipeline in different ways:
================ =================================... |
db32ddb86e99c1a10901b5b04870933dba8528a2cce5afa723e021e09d863eec | Python | 35,020 | 883 | """
Auxiliary functions to aid in the interpretation functions for the spatial and spatially-lagged regression models.
"""
from typing import Callable, List, Optional, Union
from joblib import Parallel, delayed
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import n... |
598849db25c44f9c2d0a8c0ae64296855dee54cceda5155120710cf53e4e15d8 | Python | 35,038 | 925 | """Object config serialization and deserialization logic."""
import importlib
import inspect
import types
import warnings
import numpy as np
from keras.src import api_export
from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.backend.common import global_state
from keras.src.ba... |
c7f1a888cdc6f8ce022d6d861b11288688755cb3d481d249b23946485b9912fa | Python | 35,055 | 874 | # coding=utf-8
#########################################################################################
# This code provides SCT integration into FSLeyes for the following tools:
#
# - sct_propseg
# - sct_deepseg_gm
# - sct_deepseg_sc
# - sct_label_vertebrae
# - sct_register_to_template
# - sct_proce... |
f9cf837f4fe8f59ae674202c23eb6ca4dd0fcaca309c354bcc4417b046b350c3 | Python | 35,063 | 934 | """
sess_load_util.py
This module contains functions for loading data from files generated by the
Allen Institute OpenScope experiments for the Credit Assignment Project.
Authors: Colleen Gillon
Date: August, 2018
Note: this code uses python 3.7.
"""
import copy
from pathlib import Path
import warnings
import c... |
b2a5d3f729442ed643481deb41dabf71179a07e5e4446cc887f4bf36988fba25 | Python | 35,073 | 866 | '''Utilities for fmriprep.'''
import csv
import glob
import itertools
import os
import re
import json
import warnings
from collections import OrderedDict
import numpy as np
import nipy
import nibabel
import pandas as pd
import bdpy
class FmriprepData(object):
'''FMRIPREP data class.'''
def __init__(self,... |
d22ddb458a162ea678a97f29afaf3aeda9242c22bd4f98f4bb22650e9aab43a4 | Python | 35,073 | 727 | import numpy as np
import pandas as pd
from src.subspace import Geometry
import pickle
import importlib
import matplotlib.pyplot as plt
import src.plotting_funcs as plotter
import src.plane_angles_analysis as angles
import src.vec_operations as vops
import src.preprocess_rep_geom_data as ppc
import src.stats as stats
... |
3cea8dbdf9c8e2a4b81716295aea521a7188f3a06b78822502c0067f449ebd1f | Python | 35,091 | 1,022 | """Run simple cell optimization"""
"""
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN... |
c01685a57f1add12139be5a5d81d7bbdaf1b49089e21652cbe2db6b40fadc019 | Python | 35,100 | 665 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import torch
from torch import nn
from . import LOGGER
from .metrics import bbox_iou, probiou
from .ops import crop_mask, xywh2xyxy, xywhr2xyxyxyxy, xyxy2xywh
from .torch_utils import TORCH_1_11, autocast
class T... |
7e9a40828d14ae37568854071e1c7131ab7440b4dbb495c8961a3a9d5c5a75a7 | Python | 35,251 | 911 | """r-b4 R27-1: capture-entry input walkers are depth-bounded and cycle-guarded.
The four input-boundary walkers (``walk_input_boundary``, ``snapshot_input_boundary``,
``backends.default_specs._simple_leaves``, ``utils.arg_handling.copy_arg_tree``) share
ONE nesting ceiling (``INPUT_TREE_MAX_DEPTH``) and refuse deep or... |
190ebae8a36ab25a3a296c4979d4957c5e7d104b8a8b9a4baa57311f27dde31c | Python | 35,330 | 703 | #!/usr/bin/env python
#
# This command-line tool is the interface for the deepseg API that performs
# segmentation using deep learning from the ivadomed package.
#
# Copyright (c) 2020 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
# TODO: Add link to example image so users can decide wet... |
9a677f4aa4ee81d23a11de0cc72890d9f039e6139727738bd7994287f4b8c587 | Python | 35,345 | 758 | import matplotlib.pyplot as plt
import seaborn as sns
import random
from scipy.special import softmax
from sklearn.linear_model import LinearRegression, Ridge
from sklearn.decomposition import PCA
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import KFold
from sklearn.linear_model import... |
e763f01b6c01cbc3a1a64072c3d9196abfd909575e53d3bb3da72ed3c1bd8935 | Python | 35,356 | 744 | """Frame and video visualization: overlay points/text on images and write videos.
``FrameVisualizer`` wraps OpenCV's video writer and draw primitives; helper
functions play back buffered readers with overlaid trajectories and produce
interactive image stacks for Jupyter contexts.
"""
from typing import Union, Tuple, ... |
3a16d454e500228f7e2306fd7c0d7e046462f4955a908c56930a92e3f40b46c4 | Python | 35,358 | 947 | """
Script that uses the movingpandas and geopandas libraries to facilitate spatial data processing.
Analysis starts from scratch meaning it only uses the primary tracked xy coordinates of the midline and contour.
The data used for this illustration is loaded from a stored reference dataset under the RefID.
Only the re... |
f86fadcf08a075273bcd721d57faa48a38f64747ea81d9f92a9159e4b93dc290 | Python | 35,359 | 634 | """
Functions dealing with spinal cord straightening
Copyright (c) 2019 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
# TODO: only input Image instead of file names
import os
import time
import logging
import bisect
import numpy as np
from spinalcordtoolbox.types import Centerline... |
71e012867281b111f37c8e4c7e507a7e72ef8536987b17d86cf4b40e4edbce6a | Python | 35,381 | 942 | import email.utils
import urllib.request
import io
import warnings
from datetime import datetime, timedelta, timezone
from pathlib import Path
from urllib.error import HTTPError
import pytest
from pyrosm import get_data
# The folders of the download logs and host locks, before each test gets its own (see
# conftest.p... |
ef6eb4e22069ee5b0d58fcd34fa9fc89f1d5c3eaeeeb8c1a1272d89eeba08ec5 | Python | 35,403 | 1,125 | """
sess_str_util.py
This module contains basic functions for getting strings to print or save
files for Allen Institute OpenScope experiments for the Credit Assignment
Project.
Authors: Colleen Gillon
Date: October, 2018
Note: this code uses python 3.7.
"""
from sess_util import sess_gen_util
from util import g... |
2b90a53aedd722c91a05bc6c4e6012a8fed34434199021fb176df4d21697c91a | Python | 35,409 | 855 | """
Neural Network implementation for image segmentation
For more information about autotune:
https://www.tensorflow.org/guide/data_performance#prefetching
Copyright (c) 2022 Giansalvo Gusinu <profgusinu@gmail.com>
Copyright (c) 2021 Emil Zakirov and others
Copyright (c) 2020 Yann LE GUILLY
... |
05c91e7bd8717608ca5abe4fe4a50afccf6918a2e185df54c03045632e8fb040 | Python | 35,436 | 1,115 | """
This module includes the main class that handles the data generation from the Metal PDB files.
PDB/CSD Record Format
COLUMNS DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------------------
... |
7543b11dedf0d823476578c777a9c844fb86a1a83dff71665eb280e93dec7f6f | Python | 35,448 | 1,156 | # Copyright 2023 DeepMind Technologies Limited
#
# 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 agree... |
7f462bda6954c7f7bd79c80b7a953948d2acab52186452847a6cec89d7b6a46a | Python | 35,449 | 791 | import copy
import logging
import sys
import warnings
from typing import Generator, Any
import numpy as np
import pandas as pd
from mirp.settings.generic import SettingsClass
from mirp._workflows.baseWorkflow import BaseWorkflow
from mirp._data_import.read_data import read_image_and_masks_generator
from mirp._images... |
52211dfbc6009933c7946e6c44396e3252267ed6d1a7a24707b55bf413e7fbfc | Python | 35,451 | 936 | """Schedules define the intervals at which periodic tasks run."""
from __future__ import annotations
import re
from bisect import bisect, bisect_left
from collections import namedtuple
from datetime import datetime, timedelta, tzinfo
from typing import Any, Callable, Iterable, Mapping, Sequence, Union
from kombu.util... |
b8edce129428930dc47cead2330057af15c0a89923cf2dc675f33bffdb97149f | Python | 35,530 | 714 | import numpy as np
import random
from gym import spaces
'''
Trial-Unique, Delayed Nonmatch-to-Location (TUNL) task in a triangular arena.
Including the no-memory verion.
'''
class Tunl(object):
def __init__(self, len_delay, len_edge, rwd, inc_rwd, step_rwd, poke_rwd, rng_seed=1234):
"""
:param l... |
9e04b7f5be277cf7747c2c53b3f3a1d51f8970931c182f14c0dbb06c3beedc2a | Python | 35,543 | 876 | """Dataset implementation for specific task(s)"""
# pylint: disable=consider-using-generator
import logging
import os
from pathlib import Path
import warnings
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from PIL import Image
import cv2
from ..data import is_url, url_data
from ...utils.filesys... |
6d448b646f77d65c2661f45038c7f0abb21d1ebcf027ba25a2ea4bce6ec65327 | Python | 35,568 | 994 | from __future__ import annotations
from html import unescape
from pathlib import Path
from types import SimpleNamespace
from bokeh.document import Document
import panel as pn
import pytest
from larvaworld import DATA_DIR
from larvaworld.portal.datasets import import_datasets_app
from larvaworld.portal.datasets.disco... |
cba69aeb19abb06b9d716a1f1aca7557a3f8d717ef4bbd806b2e98554097241f | Python | 35,568 | 1,038 | """Regression tests for loop-rolling and module-rolling reconciliation."""
from __future__ import annotations
import os
import re
from pathlib import Path
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.options import CaptureOptions
from torchlens.visualization._render_nodes im... |
4feba3c58f1134e0a804b68c5ddbf521677d4492057dfcb989c9baf7bd97d99d | Python | 35,569 | 484 | import os
import pandas as pd
import numpy as np
from joblib import Memory
import pdb
import random
from scipy import stats
from os.path import join
meta_path = '/home/abraun/meg_data'
fig_folder = '/home/abraun/meg_data/sr_labeled/figures'
memory = Memory(cachedir=os.environ['PYMEG_CACHE_DIR'], verbose=0)
path = '/hom... |
6abab6a19140c11b975d00f63671f6e1543115d6c442bee65a3dd4ac56a115e3 | Python | 35,587 | 1,008 | from copy import deepcopy
import pathlib
from traitlets import List, Dict, observe, Integer
from plotly.io._renderers import display_jupyter_version_warnings
from .basedatatypes import BaseFigure, BasePlotlyType
from .callbacks import BoxSelector, LassoSelector, InputDeviceState, Points
from .serializers import custom... |
d1234198bafcb71bbb94a0b0e33b034e01ef76c8c8250fad68f65abb9eb3558f | Python | 35,595 | 828 | import logging
from typing import (
Any,
cast,
Literal,
)
from urllib.parse import urlsplit
from uuid import uuid4
from pydantic import (
BaseModel,
Field,
UUID4,
ValidationError,
)
from galaxy.exceptions import (
Conflict,
InternalServerError,
ItemOwnershipException,
Messa... |
de9b6cbf9d436951c007b380119214061ded9baa354a6d8589604af896d41e05 | Python | 35,658 | 889 | """Completeness lint for portable scrub policy coverage."""
from __future__ import annotations
import functools
import inspect
import pickle
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens import trace as trace_fn
from torchlens._... |
32c408ee558f6732069a2edda8d33c35ed2567a843c9942c9a7a3a8312f70023 | Python | 35,673 | 988 | # -*- coding: utf-8 -*-
"""
Created on Mon Nov 29 23:59:48 2021
@author: yihaoy
"""
import matplotlib.pyplot as plt
from scipy.spatial import distance
from scipy import signal
import numpy as np
import jsonpickle
import json
from Neuro2Nets import Neuro2Nets
#%% test random map 4 sites
net = Neuro2Nets... |
78e60715c6a9c20ad391822482f258d233013cb2b046c2298d862a00d1f14616 | Python | 35,692 | 990 | """
usi_plots.py
This script contains functions for plotting USI analyses.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
import copy
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_an... |
96aaa1280b80efd59994e42ea5aca6503e1d1e8f6efdcc56ba24ddd7fb9bd726 | Python | 35,764 | 1,201 | """Estimation of SPD matrices."""
import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.covariance import shrunk_covariance
from sklearn.metrics.pairwise import pairwise_kernels
from .geometry.covariance import (
covariances,
covariances_EP,
cross_spectrum,
coherence,... |
87af0ab81dbf9e5657a1834abac8ba2b5230fb716fbe174ac51c11d5e38db6b8 | Python | 35,811 | 904 | from absl.testing import parameterized
from keras.src import dtype_policies
from keras.src.dtype_policies import deserialize
from keras.src.dtype_policies import get
from keras.src.dtype_policies import serialize
from keras.src.dtype_policies.dtype_policy import AWQDTypePolicy
from keras.src.dtype_policies.dtype_polic... |
929978c75f1f7a2abceea57a2e669ddb93ebfb14dd4b7c288366469d1f5f40a7 | Python | 35,833 | 857 | """The validation tripwire's own exemption ledger (grind r2 row 19 / matrix R08).
``CLAUDE.md`` -> "Validation Integrity (LOCKED PRINCIPLE)": the ``validation/``
pipeline is a TRIPWIRE, and the ONLY legitimate exemption is behavior that is
*correct by design and provably outside the check's contract*, scoped narrowly
... |
a13b5b9bf2acf073ef1e5485d9f6ad8ecbaa03205cf798f6391a08b25e1e8c0c | Python | 35,859 | 1,051 | from functools import wraps
import warnings
from array_api_compat import array_namespace as get_namespace, device as xpd
from scipy.stats import chi2
from ._backend import (
apply_xp_cov,
diag_indices,
hann_window,
fast_mcd,
ledoit_wolf,
oas,
)
from ._check import check_function, check_init, c... |
890d8edf180a225626fbe59a5bdbbc40b1491b5be01c15d0814e76c5ec2c5f9c | Python | 35,861 | 923 | """
This code started out as a PyTorch port of Ho et al's diffusion models:
https://github.com/hojonathanho/diffusion/blob/1e0dceb3b3495bbe19116a5e1b3596cd0706c543/diffusion_tf/diffusion_utils_2.py
Docstrings have been added, as well as DDIM sampling and a new collection of beta schedules.
"""
import enum
import math... |
a0e954a7a800f210689825b98896ec77537c6b15da2f587f96eca031ee1a64d9 | Python | 35,885 | 1,043 | """Run simple cell optimization"""
"""
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN... |
e478a2de2b07dd26e75cbdcf6f0922e84590952a753861e75469bc35476bfb24 | Python | 35,898 | 903 | """Trace task execution.
This module defines how the task execution is traced:
errors are recorded, handlers are applied and so on.
"""
import logging
import os
import sys
import time
from collections import namedtuple
from warnings import warn
from billiard.einfo import ExceptionInfo, ExceptionWithTraceback
from kom... |
afca0603c456457010f8dfd93235a67968c570002506f66b34f5269d145f2a3e | Python | 35,909 | 918 | # 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... |
24688a2b2e92c5b0bd92fe053f7777b26a9fab62222891331367452efa24c807 | Python | 35,919 | 734 | import warnings
warnings.simplefilter("ignore")
import torch
import numpy as np
from os import environ, makedirs, listdir
from os.path import join, basename, exists
import matplotlib.pyplot as plt
try:
from tqdm import tqdm
except ModuleNotFoundError:
tqdm = lambda x: x
from time import sleep
from skimage.measu... |
11587012277790f637d60fc10750e70ff013650fa423a38588c1f123a7bb80ba | Python | 35,929 | 980 | """Miscellaneous utility functions for xcp_d."""
import itertools
import multiprocessing
import nibabel as nb
import numpy as np
from nipype import logging
from xcp_d.utils.doc import fill_doc
LOGGER = logging.getLogger('nipype.utils')
def _get_template_transform(template, from_space, cohort=None):
"""Get a T... |
8f72aa007090a7957984ef127175e358fdd999afe144056f207d7a904a9ea016 | Python | 35,935 | 839 | """
Code here provides direct access to the header and signal data of ABF files.
Efforts are invested to ensure ABF1 and ABF2 files are supported identically.
This file is LIMITED TO THE MANAGEMENT OF HEADER AND DATA information.
Analysis routines are not written in the ABF class itself. If useful, they
are to be writ... |
91a0005d9b0b179681f64d0cc48d0f38eded16e7df4f204e0036b1ef18f133c7 | Python | 35,964 | 989 | """
Evolutionary optimization of model parameters.
Runs a genetic algorithm over the model search space, scoring each generation
against a reference dataset and breeding the best genomes into the next.
"""
from __future__ import annotations
from typing import TYPE_CHECKING, Any, List, Optional
if TYPE_CHECKING:
... |
3c5f6972a72d10b44f2928aa2b4e91b27b962ca7a8650891c8e901b7bb97210c | Python | 35,969 | 795 | """
Functions for finding nearest neighbors, the distances between them and the spatial weighting between points in
spatial transcriptomics data.
"""
import os
import sys
from functools import partial
from typing import Optional, Tuple, Union
import anndata
import numpy as np
import pandas as pd
import scipy
from annd... |
406bb58eb4f8e3ea1c7d37c9ca0bfa2c01631291f40b73751eb52cce174339de | Python | 35,984 | 777 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
BAM file will be input use pysam and each line in BAM file will be looped to find the possible missed small exons, with
the threshold: small_exon_size <= 100 (default) and abs(delta_ratio) <= 0.5 (default).
The realign region will only be aligned to the exon seque... |
98af0938e1945367f73fafff2928fb97ef7e43a9dccce50ed1affa4caf82dbeb | Python | 36,025 | 861 | """Functions for building the input features (reference ccd features) for the HelixFold model."""
import collections
import os
import time
from functools import partial
from typing import Any, KeysView, Mapping, MutableMapping, Optional, Tuple, Sequence, Union, List
from absl import logging
import numpy as np
from rd... |
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