sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
f0ed56dd835e824a12a7d6b8666d8443642c6b8f589a0939c9f5a4653b86f1f9 | Python | 46,279 | 1,045 | from dataset import GaborDatasetOrientation, Digit
from torch.utils.data import DataLoader
import torch
import torch.nn.functional as F
from dataset.utils import NoisyDataset, OcclusionDataset
import numpy as np
from sklearn.linear_model import LogisticRegression
from sklearn import svm
from sklearn.metrics import acc... |
41623163d34f548d7170597adcb15bac14d08596257f9af76fa4e9bae35dad2b | Python | 46,343 | 2,034 |
import sys
import mne
import numpy as np
import scipy as sp
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.pipeline import make_pipeline
from pyriemann.estimation import Shrinkage
from pyriemann.tangentspace import TangentSpace
from preproc.utils.transformer import PFD, HFD, Hurst
from pyriema... |
b02746475d0ca6afb342286a0cf8d42b884e3679d49a176a12c12732bf8b02d0 | Python | 46,574 | 1,285 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2020 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Implements support for high-level dataset ac... |
cb0a5b8beabcc589bfd9ed133c27b3a8d8b8019f5205ba60e7c33dfe7a86b27e | Python | 46,593 | 1,062 | """
Approximate a 3D curve with a B-Spline curve from either a set of data points or a set of control points
If a set of data points is given, it generates a B-spline that either approximates the curve in the least square
sense or interpolates the curve. It also computes the derivative of the 3D curve.
getCourbe3D() r... |
05426c3824b4bc2eea4730c16907ea03c658e889c1448a5c7199b5b7b2df2de6 | Python | 46,693 | 1,293 | # Cell detection methods
# Author: David Young, 2017, 2024
"""Detects features within a 3D image stack.
Prunes duplicates and verifies detections against truth sets.
Attributes:
CONFIRMATION: Dictionary of blob confirmation flags.
OVERLAP_FACTOR: Pixel number multiplier for overlaps between adjacent ROIs.
""... |
924a861c3a4bbc2c04a5c36b02b8fc2b0e60356bc8f66f7a8bd1d2cd16e4312a | Python | 46,949 | 1,153 | import os
import pathlib
import shutil
from unittest import TestCase
import numpy as np
import pandas as pd
from pyalfe.data_structure import (
DefaultALFEDataDir,
PatientDicomDataDir,
Modality,
Orientation,
Tissue,
)
from pyalfe.image_processing import Convert3DProcessor
from pyalfe.image_registr... |
aff3e40f0e44a819ab199619e12a315495bfc6ca0e44f7c62e7d650ad2d5b420 | Python | 46,965 | 1,135 | import contextlib
import glob
import inspect
import logging
import logging.config
import math
import os
import platform
import random
import re
import signal
import sys
import time
import urllib
from copy import deepcopy
from datetime import datetime
from itertools import repeat
from multiprocessing.pool import ThreadP... |
552d7b719cce1950e652dea915b5ba1cba497595a60078bbc13a6815a5a92b30 | Python | 46,983 | 1,381 | import importlib
import os
from os.path import dirname, abspath
from sys import stdout
from multiprocessing import Pool
from typing import List, Tuple, Optional, Dict, Set, Union
import yaml
from kgx.validator import Validator
from kgx.sink import Sink
from kgx.transformer import Transformer, SOURCE_MAP, SINK_MAP
fr... |
69a46b44e8625f509791352bd09beaafe589cd7d872721384e63d37f9fdc6e41 | Python | 46,983 | 909 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.distributed
import torch.nn.functional as F
from torch.nn.init import trunc_normal_
from sam2.... |
e00ac78686e40eabc69180925e5985038ea7dcbb7d9db05f73e8169d59bbc871 | Python | 47,038 | 1,248 | from typing import List
from urllib.parse import urlencode
import requests
import logging
from medperf.enums import Status
import medperf.config as config
from medperf.comms.interface import Comms
from medperf.utils import sanitize_json, log_response_error, format_errors_dict
from medperf.exceptions import (
Commu... |
8badacca0d0870aadce2ee6311eae3f0651081bc253d5039c65967567c070c37 | Python | 47,119 | 1,187 | # -*- coding: utf-8 -*-
import copy
import datetime
import json
import pytz
from itertools import chain
from django.db import connection
from catmaid.models import Connector
from catmaid.tests.apis.common import CatmaidApiTestCase
from catmaid.control import stats
from catmaid.control.common import get_relation_to_i... |
b4c19ce6fead25d58351a099f2c27be7e99b875258757f72bf879cae966c2c92 | Python | 47,209 | 35 | import numpy as np
from model.Source import Source
class Pipeline():
def getPipeline(self):
return [None]
class DataManager():
def getCurrentPipeline(self):
return Pipeline()
class Plot():
def clear(self):
pass
def setData(self, *args):
pass
cell_me... |
6962c095256370cde24a4c55f3dd8c5cbec09b2b9acb61ce2787cdd630b77d24 | Python | 47,260 | 1,016 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import math
from utils import map_activation_str_to_layer, batch_convert_len_to_mask, mask_seq_by_len, extend_dimensions, gather_indices_by_lens
_INF = -1e30
def get_multi_head_attn_vec(head_q, head_k, head_v, attn_mask=Non... |
1c8eba60a5ddc11dbbee7fbcc5a5184c2b76362bd277544ca1516170e2428c58 | Python | 47,294 | 1,197 | from PyQt5.QtWidgets import (QDialog, QDialogButtonBox, QVBoxLayout, QLabel, QLineEdit, QHBoxLayout, QWidget,
QCheckBox, QGridLayout, QFrame, QGraphicsView, QGraphicsScene, QPushButton,
QComboBox, QMainWindow, QSpacerItem, QBoxLayout, QSizePolicy, QFileDialog)
fr... |
03ef0ac5b0d17cbcc5b9d60fe27358687cfbcaa9efdc174826b290b7f930a6e2 | Python | 47,306 | 1,248 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Dec 13 15:25:24 2022
@author: george
"""
#%matplotlib qt
#%gui qt
import warnings
warnings.simplefilter(action='ignore', category=Warning)
import numba
import numpy as np
import pandas as pd
from tqdm import tqdm
import os, glob
import json, code... |
be5b01e688e95edd694d139194f598b3df5dadb38111c21badc696aabac353d8 | Python | 47,384 | 1,435 | # src/zndraw_joblib/router.py
import asyncio
import json
import logging
import random
import re
from datetime import UTC, datetime
from typing import Annotated
from uuid import UUID
from fastapi import APIRouter, Depends, Header, Query, Request, Response, status
from sqlalchemy import and_, func, update
from sqlalchem... |
10fbd30b4a64fb627c8bd85cd95a3f58b93f18a2f8c0bfc46b2b542ad351ae5c | Python | 47,468 | 867 | import logging
import pickle
import scipy.io
import freesurfer as fs
import sys
from .utilities import Specification
from .BiasField import BiasField
from .ProbabilisticAtlas import ProbabilisticAtlas
from .GMM import GMM
from .Affine import Affine
from .SamsegUtility import *
from .merge_alphas import kvlMergeAlphas,... |
e3f31f4c90cad4997d5d2a91dcc7e5af1df8908263e3c10f4635e52f73ace020 | Python | 47,496 | 1,334 | from collections import defaultdict
from itertools import chain
import json
from typing import Any, DefaultDict, Dict, List, Optional, Tuple
from django.db import connection
from django.http import HttpRequest, JsonResponse
from django.utils.decorators import method_decorator
from catmaid.control.authentication impor... |
1d861c245079012202f58c523bbb8448bb2ddd487667c934de0ca1dccd80ba87 | Python | 47,512 | 1,290 | """Callbacks: utilities called at certain points during model training.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import csv
import six
import numpy as np
import time
import json
import warnings
import io
from collections import deque
f... |
f0a78fe2877ebd033a7e5a22428950d2793ef715857119b83db7e780bab6eaaf | Python | 47,519 | 973 | #!/usr/bin/env python
"""
1. Unlock scans_tsv and update it based on runtype metadata
2. Harmonize discrepancy between nifti and behavioral data
3. Starting from Line 242, Behavioral data conversion to BIDS valid format
Same format occurs for pain, vicarious, cognitive data
convert behavioral file into event lists and ... |
e915e920fe1cb1d7dd2e0b5dd5fe4e48c20b54465e160915e21042feb935eac3 | Python | 47,533 | 1,052 | #!/usr/bin/env python
#
# Copyright 2016, Daehwan Kim <infphilo@gmail.com>
#
# This file is part of HISAT 2.
#
# HISAT 2 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (... |
a643cd4db70b3794cef74688fcf8404ed12a3f00ef6fb0bca6d18e75987751e4 | Python | 47,555 | 863 | #!/usr/bin/python
"""
This file will hold all the classes for a specific case which is SFS. This should taken as example how to use ABC-DLS
rather than only way to use it
"""
import itertools
import os
import sys
from multiprocessing import Pool as ThreadPool
# type hint for readability
from typing import Optional, Uni... |
9d55b14994da521189197e319f2c1c4a62638238a7c59a24cc992839757fcedc | Python | 47,738 | 1,236 | """
Module to define interface, workflow and CLI for the review of functional MRI data.
"""
import argparse
import sys
import textwrap
import warnings
from abc import ABC
from os.path import basename, join as pjoin, realpath
from textwrap import wrap
import nibabel as nib
import numpy as np
from matplotlib import py... |
adbdd4f3f4681771a969607a0ba8718a2fe1b18563df436e5957504849512a0a | Python | 47,945 | 1,271 | # #############################
#
# Copyright (C) 2018
# Jennifer Dreiling (dreiling@gfz-potsdam.de)
#
#
# #############################
import os
import glob
import logging
import numpy as np
import os.path as op
import matplotlib.cm as cm
import matplotlib.pyplot as plt
from collections import OrderedDict
from Ba... |
2cec7770fd5b153995bb2fdea79960cf210dcf71e5ed886b448c10cfe6d91e0f | Python | 47,972 | 1,034 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import math
from utils import map_activation_str_to_layer, batch_convert_len_to_mask, mask_seq_by_len, extend_dimensions, gather_indices_by_lens
_INF = -1e30
def get_multi_head_attn_vec(head_q, head_k, head_v, attn_mask=Non... |
fda0c1db08e14b69d33486ed60bac589fc4ea840d37c0d1787c272741d8258a2 | Python | 48,288 | 1,165 | # This document holds the functions used as part of
# the poro-mechanical modelling of living tissues
# according to the theory in ./Theoretical_Developments.pdf
#
# Author: Thomas Lavigne
# Date: 18/09/2024
def readme_CL():
print('This document holds the functions used as part of the poro-mechanical modelling of l... |
eba79c1ab5d81d14d106df25dbfddb9297646ef933d75c218ad75b1518b57407 | Python | 48,522 | 1,147 | import contextlib
import copy
import json
import logging
import threading
import time
import numpy as np
from . import config, constants, features, log, utils
from .pipeline import (
_ERROR,
_SENTINEL,
AsyncWriter,
PipelineCancelled,
PrefetchBuffer,
)
__all__ = [
"Featurizer",
]
logger = log... |
e5c74a5d4e21c3013722c8e58c144623c0c606c64bc4abf999e5325651b44248 | Python | 48,537 | 957 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
675c85686fc5786180757471ca91aaa6341e70ec7e9bf4f67c993d84b874afc2 | Python | 48,582 | 1,330 | # Author: Huaxu Yu
# A module to summarize the premade data processing workflows.
# Import modules
import os
from copy import deepcopy
from importlib.metadata import version
import multiprocessing
import pickle
import time
from joblib import Parallel, delayed
import pandas as pd
import numpy as np
from tqdm import t... |
16273a220d4ddcd45165e4bea20d87dffb6617d8d9bc3444859bbaba620bcdae | Python | 48,741 | 1,239 | # Computer vision library functions for n-dimensions.
# Author: David Young, 2018, 2019
"""Computer vision library functions for n-dimensions.
"""
from typing import List, Optional, Sequence, Tuple, Union
import numpy as np
from scipy import interpolate
from scipy import ndimage
from skimage import filters
from skima... |
6f1d2977ca48ec988a42e204f80459f9c5c678d7d28469fdd8e010565700c7a9 | Python | 48,757 | 1,476 | # -*- coding: utf-8 -*-
# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Group test module.
... |
f4e1313e5ce5ed7f0dae4a0130e91d3404dbee612b09cf7e571ecaeac4023297 | Python | 49,069 | 1,236 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 2 14:59:21 2023
@author: george
"""
import pyqtgraph as pg
from qtpy.QtCore import *
from qtpy.QtGui import *
from qtpy.QtWidgets import *
from distutils.version import StrictVersion
import os, shutil, subprocess
import errno
import flika
from fl... |
14798eebd8404850f8485031e3c52769e9842599e46e4fc40269edb7fcce3388 | Python | 49,156 | 1,207 | """
Freesurfer QC module to rate the anatomical accuracy of pial and white surfaces
"""
import argparse
import subprocess
import sys
import textwrap
import time
import traceback
from abc import ABC
from os import makedirs
from pathlib import Path
from subprocess import check_output
from warnings import catch_warning... |
ffca2efebd97cdb307a390c13a65b243635aceea28bb24cd553720f5bdc31dcd | Python | 49,212 | 1,221 | from seqUtil import *
from bamUtil import *
from nanoUtil import *
from nntUtil import *
import matplotlib.pyplot as plt
import matplotlib.patches as mplpatches
import numpy as np
from sklearn.cluster import KMeans
from sklearn.impute import SimpleImputer
from collections import defaultdict
from sklearn.metrics import ... |
22773066051704c93a759cb72eb7243cc2f6f5f4d24b872adee948f79c8be6d9 | Python | 49,240 | 1,372 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from typing import Dict, Optional, Union
import numpy as np
import torch
from torch_scatter import segment_coo
from ocpmodels... |
d7ad4256d489af23dbddccf2e200da1cb0fce5db8157a886b1eaa01ba5f5549f | Python | 49,340 | 1,097 | # -*- coding: utf-8 -*-
"""Convolutional-recurrent layers.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from .. import backend as K
from .. import activations
from .. import initializers
from .. import regularizers
from .. import constraints
from .rec... |
043d7cea15cf97d76d91972bce8966712a8ffe71025b358ceacfe225a7f7f0ef | Python | 49,428 | 898 | #!/usr/bin/env python
"""convert behavioral file into event lists and singletrial format
This code acknowledges frractional tasks as standalone subtasks.
The file names take the format fractionaltomspunt, fractionaltomsaxe, fractionalmemory, and fractionalposner
- regressor of interest per task
- duration of epoch
- r... |
fca4d2df6f05682baa318d46821d8fcff0bb83a44ff2ab7d79b79c15f12e357b | Python | 49,437 | 1,400 | # -*- coding: utf-8 -*-
# encodermap/plotting/dashboard.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade
#
# Encodermap is free softw... |
9ed0b49f798628f17775dac757d0c31f2f0085762ecacb93690bed43c1829ff9 | Python | 49,470 | 1,245 | """Generate tutorial screenshots for the GuPPy documentation.
Run with:
uv run --group test python docs/take_screenshots.py
Screenshots are saved to docs/_static/images/ and should be committed to the repository.
Re-run this script whenever the GUI changes.
Playwright browser binaries must be installed:
uv r... |
dd86bee277e83e51a1cc385c344661f0379d7a5971e9666a847c038431c2d558 | Python | 49,618 | 1,388 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from typing import Dict, Optional, Union
import numpy as np
import torch
from torch_scatter import segment_coo
from ocpmodels... |
079fc0bf5d78fe5b5a7c0c4cf61c7cfab6178a3c2a2eb3aec20ea83e31473fa3 | Python | 49,697 | 1,362 | """Module to sample electrical model parameter space with MCMC."""
# 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 ... |
7dbb3f230cfb431f394dc425a6675ae6714cc1a095816141b5ef42cbc2b129fc | Python | 50,095 | 1,622 | """Utility functions for brainbuilder."""
import ast
import contextlib
import json
import logging
import multiprocessing
import os
import re
from collections.abc import Iterable
from subprocess import PIPE, STDOUT, Popen
from typing import List, Optional, Tuple, Union
import ants
import imageio
import nibabel
import ... |
8d94747301f94663a629903091916b0ad3d2af3f7e0b9dde8b4b54e2a12fa643 | Python | 50,517 | 1,058 | # New matplotlib colormaps by Nathaniel J. Smith, Stefan van der Walt,
# and (in the case of viridis) Eric Firing.
#
# This file and the colormaps in it are released under the CC0 license /
# public domain dedication. We would appreciate credit if you use or
# redistribute these colormaps, but do not impose any legal r... |
b1a092f7def0a09ecae77b0ff6b1cfd36eba6dee9bec7a81718a882164f5bc49 | Python | 50,568 | 1,297 | import os.path
import torch
from torch.utils.data import DataLoader, Dataset
import pytorch_lightning as pl
import numpy as np
import h5py
import logging
import yaml
from typing import NamedTuple
import nibabel as nib
import glob
from medutils.mri import ifft2c, rss, fft2c
from scipy.ndimage import binary_erosion
from ... |
f2be9a5daa222bc5ca6834761766e282d66679a03a33b2dfa5f4344252bf80d5 | Python | 50,680 | 1,316 | """
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... |
0da3c93973ba3b076a65ccacf0886b474e27f6e3e5e01cd518629f8f4ae04997 | Python | 50,715 | 1,182 | # -*- coding: utf-8 -*-
import django.utils.timezone
from django.conf import settings
import django.contrib.postgres.fields.jsonb
from django.db import migrations, models
import django.db.models.deletion
forward = """
-- Create table that represents a 3D grid in project space.
CREATE TABLE node_grid_cache (
... |
170b7fe172ca3d43fe400e652199760d3dc7f5d80e0742b13ff0f5d4896cbe25 | Python | 50,730 | 1,360 | # -*- coding: utf-8 -*-
import copy
import json
import logging
from datetime import datetime, timedelta
from collections import defaultdict
from typing import Any, DefaultDict, Dict, List, Tuple, Union
from django.db import connection
from django.db.models import Count
from django.shortcuts import get_object_or_404... |
ab16c45823aadb25b0027573966e3a71724d88e533112b6b996d6cf5718c5a84 | Python | 50,737 | 1,425 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from typing import Dict, Optional, Union
import numpy as np
import torch
from torch_scatter import segment_coo
from ocpmodels... |
e881d3ed96bc3f36a25328a6ff876a81c6e93fbd679ea00a5f2d8fc11f674dda | Python | 50,741 | 1,425 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
from typing import Dict, Optional, Union
import numpy as np
import torch
from torch_scatter import segment_coo
from ocpmodels... |
26101fc165f393ef51505a2cb7df10db72fcdfb4f02e8e79d4c161380e13e1eb | Python | 50,743 | 1,189 | # -*- coding: utf-8 -*-
from itertools import chain
import json
import logging
from timeit import default_timer as timer
from typing import Any, Dict, List
from celery import shared_task
from celery.utils.log import get_task_logger
from django.contrib.gis.db import models as spatial_models
from django.db import conne... |
96bf0f9b7c06c6c79e1fe242954a386ceb2a2ff90caabc885fb2cae8727ba889 | Python | 50,782 | 1,330 | import os
import re
import copy
import inspect
import functools
import collections.abc
from itertools import chain
from textwrap import indent, dedent
from collections.abc import Iterable, Collection
import numpy as np
import pandas as pd
from ..utils import ensure_list_args, ensure_list_attrs, IsNull, NotNull, cyphe... |
8d3a04b34a8ea157108f74cb9c8b1e7e03642743c990678e0ddf34d6cd430263 | Python | 51,400 | 1,423 | import os
import re
import numpy as np
import pandas as pd
import gzip
import pickle
from auditory_cortex import opt_inputs_dir, results_dir, cache_dir, normalizers_dir, saved_corr_dir
from auditory_cortex import valid_model_names
from memory_profiler import profile
import logging
logger = logging.getLogger(__name__)
... |
2f59c94a5cae9cc4a7a58eba61fe2e18ebcb183445a6ddc5da00fe6384760f77 | Python | 51,409 | 1,123 | # Copyright DST Group. Licensed under the MIT license.
import gym
from gym.utils.seeding import RandomNumberGenerator
from typing import Dict, List, Tuple
from CybORG.Shared import Scenario
from CybORG.Shared import Enums
from CybORG.Shared.AgentInterface import AgentInterface
from CybORG.Shared.Enums import DecoyType... |
bfa808ad7d58bb90671dcce9c235c3e17179f90a3b976e2d912ab8d780e61e25 | Python | 51,482 | 1,546 | import json
import os
import pickle
import re
import tempfile
import warnings
from typing import Optional
import numpy as np
import pytest
from sklearn.utils.estimator_checks import parametrize_with_checks
import xgboost as xgb
from xgboost import testing as tm
from xgboost.testing.ranking import run_ranking_categori... |
a5482df63fda4d9b1ed0fb84a864d4ba1497eb143b149c14dbf1541e75e381eb | Python | 51,651 | 1,766 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# reference: https://bids-specification.readthedocs.io/en/stable/06-longitudinal-and-multi-site-studies.html#sessions-file
import os
import pandas as pd
project_name = 'zoo-bids'
path_root = os.getcwd().split(project_name)[0] + project_name
class Session:
def __ini... |
f1cf8c723522c35fda88895f3056e7888a2701539263f3d233f4eb011b7ee020 | Python | 51,858 | 1,146 | import torch
import numpy as np
from tqdm import tqdm
import sys
import matplotlib.pyplot as plt
from ..models.constants import ConsensusInitializationMode, RegularizationMode
from ..models.losses import GeometricLoss, denoisloss
from ..utils.utils_new import frc, fourier_loss, power_spec2, count_interior_points
def... |
93459e50116d9e209c95ec393a5ea09311fb2b208f33230139fba3696bd23ca1 | Python | 51,907 | 1,092 | import time
from PyQt5 import QtWidgets, QtCore
import numpy as np
from copy import deepcopy
from features.AdjustFrequency import AdjustFrequency
from features.EventDetection import SpikeDetection, BurstDetection
from model.Object import Object
from util.conf import af_params, cs_roi_params
class DataManage... |
28d0eec436fc6645be39d7e7cc6b819502336cab564384fc5135b02d940237cd | Python | 52,065 | 1,521 | # -*- coding: utf-8 -*-
from itertools import chain
import io
import logging
import json
import os
import re
import struct
import sys
import trimesh
import numpy as np
from typing import Any, Callable, Dict, List, Sequence, Tuple, Union
from xml.etree import ElementTree as ET
from django.conf import settings
from dja... |
87115481a063356fa49372cb44e3a1e7d06f17d57d45987435439584e68d3512 | Python | 52,326 | 1,358 | """
Beware, this file is long and horrid.
Bespoke plotting functions to derive each mRS distribution.
To do, pep-8 this
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from outcome_utilities.dist_plot import draw_horizontal_bar, \
draw_connections, draw_horizontal... |
f608dae38378d64e0f38cbb0682394574a76c0e7586676be0d21f636c611509a | Python | 52,350 | 1,597 | """
Adapter finding and trimming classes
The ...Adapter classes are responsible for finding adapters.
The ...Match classes trim the reads.
"""
import logging
from enum import IntFlag
from collections import defaultdict
from typing import Optional, Any, Union
from collections.abc import Sequence
from abc import ABC, a... |
c573f8b9aac0bd29f2b954a299b9198600802023a9126d6fb53a6fb0a1bac9e4 | Python | 52,468 | 1,289 | import freesurfer as fs
import numpy as np
import sys,os
import voxelmorph_sandbox as vxms
import voxelmorph as vxm
import nibabel as nib
from tensorflow import keras
import tensorflow as tf
from tensorflow.keras import layers as KL
from tqdm import tqdm
import copy
def build_atlas(model, wt_fname, sphere_gen, target... |
54671ff0c78297a11799e489fe60788de4c75ac9c339b80455002c493a5eee5f | Python | 52,741 | 1,193 | import logging
import math
import re
from collections.abc import Callable
from io import BytesIO
from pathlib import Path
from typing import ClassVar
import datashader as ds
import holoviews as hv
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import panel as pn
import param
import selenium
fro... |
361b2a2999caa9bcf9e49f5bb022c6f7a99fb07863beaea6c17d8c2cb25c1781 | Python | 52,812 | 1,524 | #!/usr/bin/env python3
import numpy as np
from collections import defaultdict
import scipy.sparse as sp
import sys
g_verbose = False
g_reuse_multigridop = True
def get_shift_csr(dw, nw, zeropad=True, mod=None, dtype=None):
'''
Returns a shift matrix on a grid of size `nw`.
Acting on a field, the matrix ... |
57e5d3c273fa0298971bdab22fba285efc7229d503f718b2014dd6c19171bbdb | Python | 52,859 | 1,386 | """
Tuning module for Ewald summation parameters.
This tuning module is refactored from:
https://github.com/lab-cosmo/torch-pme/tree/main/src/torchpme/tuning
"""
from jax.ops import segment_sum
from mlff.masking.mask import safe_scale, safe_mask
from mlff.nn.observable.observable_sparse import mixing_rules, gamma_cubi... |
3ff9009d8bfce06630e434eb8d87b1238bccdb2708edd93edf115c5ef55c0e75 | Python | 53,317 | 1,325 | # -*- coding: utf-8 -*-
from collections import defaultdict
import itertools
import math
import networkx as nx
import re
from typing import Any, DefaultDict, Dict, List, Union
from django.db import connection
from django.http import HttpRequest, JsonResponse
from django.shortcuts import get_object_or_404
from rest_f... |
a6067d72d57f3d2cf0a24490261a102afdb98aaf872d4899bf0c7301e45214bc | Python | 53,389 | 1,383 | from __future__ import print_function
from __future__ import division
# from builtins import str
from builtins import range
import os
import numpy
import sciunit
import hippounit.capabilities as cap
from quantities import ms,mV,Hz
from neuron import h
import multiprocessing
import zipfile
import collections
import co... |
a223522e454daec082be064a5c2d785805f9d6796651e4645001aee0b3d9aa01 | Python | 53,449 | 1,356 | #!/usr/bin/env python
# Command line parsing and setup
# Author: David Young, 2017, 2020
"""Command line parser and and environment setup for MagellanMapper.
This module can be run either as a script to work in headless mode or
loaded and initialized by calling main().
Note on dimensions order: User-defined dimensi... |
25d00a4c0469e2e960c7d7d184e388c8752e4f58e3c7f68fcac33dcc5fa3d5b5 | Python | 53,686 | 1,182 | from typing import Tuple, Optional, List
import torch
import torch.nn
import torch.nn.functional as F
from torch import nn as nn
from tqdm import tqdm
import sys
import mrcfile
from dynamight.models.blocks import LinearBlock
from dynamight.models.utils import positional_encoding, initialize_points_from_volume
from dyn... |
d8b67e2c6115ecfd8a8896d8d5e95821bdc22ebefd4dcdff85a77e197054cd3b | Python | 53,854 | 795 | # This document holds the functions used as part of
# the poro-mechanical modelling of living tissues
# according to the theory in ./Theoretical_Developments.pdf
#
# Author: Thomas Lavigne
# Date: 18/09/2024
def readme_VF():
print('This document holds the functions used as part of the poro-mechanical modelling of l... |
665ef0506201f61bf62f9d406af8cc7831c06e41935ef03c5dc8f8efa7e53b92 | Python | 54,111 | 795 | # This document holds the functions used as part of
# the poro-mechanical modelling of living tissues
# according to the theory in ./Theoretical_Developments.pdf
#
# Author: Thomas Lavigne
# Date: 18/09/2024
def readme_VFNH():
print('This document holds the functions used as part of the poro-mechanical modelling of... |
7904b45533f513d73527072e170de0de08ab9160a472160806f26112939c8222 | Python | 54,259 | 1,501 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 5 12:24:45 2021
@author: schwab
"""
from pathlib import Path
from typing import Sequence, Optional
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
import torch.fft
from sklearn.decomposition ... |
025016c07f4f76e6bb69b8c461d10d82fa6928bd4af7b1a5892e16c79e1eac66 | Python | 54,304 | 1,154 | import numpy as np
from skimage.transform import resize
import os
import tkinter as tk
from tkinter import filedialog
from tifffile import imread,imwrite
from tkinter import ttk
import tkinter as tk
from tkinter import ttk, PhotoImage
from read_imagej_rois import imagej_rois
import matplotlib.pyplot as plt
f... |
d0b147eadd4e2094c0116199d6ddd4214c553341ae742f402a8c7dc8177be32e | Python | 54,487 | 1,335 | """Model saving utilities.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
import json
import yaml
import inspect
import warnings
import tempfile
from six.moves import zip
from six import string_types
from functools import wraps
import numpy a... |
7b0f6f517ddaa894efb5e00a6145bb8d7decd4a7dc8b7931676e9cc1c8413205 | Python | 54,495 | 1,233 | import ast
import contextlib
import json
import math
import platform
import warnings
import zipfile
from collections import OrderedDict, namedtuple
from copy import copy
from pathlib import Path
from urllib.parse import urlparse
from typing import Optional
import cv2
import numpy as np
import pandas as pd
import requ... |
74e72f6ee5df2faa513868000b33d9415c9ea0edc61d3830baedd1244ab80867 | Python | 54,948 | 1,085 | # coding: utf-8
# Copyright 2019 Sinovation Ventures AI Institute
#
# 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... |
057558b6baf859cb651629cd78de33db3dec6146e2c4a43716dd881404c89ae2 | Python | 55,073 | 1,604 | from lapy import TetMesh, TriaMesh, Solver
from lapy.diffgeo import compute_geodesic_f
import warnings
import subprocess
import tempfile
import os
import nibabel as nib
import numpy as np
from scipy.spatial import Delaunay, KDTree
from scipy.spatial.distance import squareform, pdist
from brainspace import mesh as me
... |
27e134832d21b29964da1a2396ed75dbb682409043d2008917bf4fc294b4bbf2 | Python | 55,156 | 1,198 | import os
import copy
import threading
import warnings
from concurrent.futures import ThreadPoolExecutor
from textwrap import indent, dedent
import ujson
import pandas as pd
from ..client import inject_client, NeuprintTimeoutError, _deepcopy_no_register
from ..utils import ensure_list_args, tqdm
from .neuroncriteria ... |
c5d61dfd91816103649490b57f280d10bbce148191d09ec7e5103b9964199454 | Python | 55,355 | 1,408 | #
# Copyright (c) 2010 Marcel Martin <marcel.martin@scilifelab.se> and contributors
#
# 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 rig... |
106d73ce7f21c4d9402a1cce685a59e446ff14c032f6ac57275c69064033638c | Python | 55,417 | 1,801 | # pylint: disable=too-many-arguments, too-many-branches, too-many-lines
# pylint: disable=too-many-return-statements
"""Data dispatching for DMatrix."""
import ctypes
import functools
import json
import os
import warnings
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
List,
Optional,
... |
ce56950d310964473c5e7f3947a3e3e6c7027aedcea19b42edfd2838ae25b3d8 | Python | 55,466 | 1,434 | """Classes and methods relevant for all CWL Process types."""
import abc
import copy
import functools
import hashlib
import json
import logging
import math
import os
import shutil
import stat
import textwrap
import urllib.parse
import uuid
from collections.abc import (
Callable,
Iterable,
Iterator,
Map... |
bb71287879b2de71cf6df2b5e80f4bec08ff213a4e8389b417c10eeabcacc3da | Python | 55,489 | 1,065 | import io
from collections import defaultdict
from os import path
import src.datahandlers.doid as doid
import src.datahandlers.efo as efo
import src.datahandlers.mesh as mesh
import src.datahandlers.obo as obo
import src.datahandlers.umls as umls
from src.babel_utils import (
get_prefixes,
glom,
read_badxr... |
cd5e7a89028deeaf294fa61c1a5bbe03ebd0574f376c9187958fe98f80d1b859 | Python | 55,688 | 1,498 | #!/usr/bin/env python3
# PYTHON_ARGCOMPLETE_OK
"""Entry point for cwltool."""
import argparse
import copy
import functools
import io
import logging
import os
import signal
import subprocess # nosec
import sys
import time
import urllib
import warnings
from codecs import getwriter
from collections.abc import Callable, ... |
11a98ed6feab46874b20edd763ec6b1feff80db17784de397afc72f4b13aa8a5 | Python | 55,769 | 1,248 | import os
import json
import math
import torch
import random
import numpy as np
from prompts import *
from itertools import permutations, product
from torch.utils.data import Dataset, DataLoader
from torch.nn.utils.rnn import pad_sequence
from transformers import LlamaTokenizer
class GridTask:
def __init__(self,... |
e60ba1ab3918d188f8e667eea81bf202189851449de433458ba799b26c2d0666 | Python | 55,822 | 1,356 | # -*- coding: utf-8 -*-
import time
from django.db import connection, transaction, InternalError
from django.test import TestCase, TransactionTestCase
from guardian.shortcuts import assign_perm
from catmaid import history
from catmaid.models import Class, Project, User
class HistoryTableTests(TransactionTestCase):
... |
98a98efaf83b2c7b3d1496e46a469de9f36a0195c57c509cc3db1230f0c5b272 | Python | 56,164 | 1,359 | import os
import matplotlib.pyplot as plt
import matplotlib.patches as mplpatches
import matplotlib.colors as colors
import matplotlib as mpl
mpl.rcParams['pdf.fonttype'] = 42
mpl.rcParams['font.size'] = 12
import numpy as np
import pysam
from bisect import bisect_left
from tqdm import tqdm
from sklearn.cluster import ... |
54187c784af11cfbe832901eff1f61ddac0a6d8431b7b19fd54af130bcca123e | Python | 56,724 | 1,625 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch.nn as nn
# from typing import Dict, Optional, Union
from typing import Callable, Dict, Optional, Tuple, Union
fro... |
d81d04d79f2e130481cd5ee9529a2246dae0f577553859e0cce639454d874b4e | Python | 56,887 | 1,363 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and the HuggingFace Inc. 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
#
# U... |
3ecd2d34aa53b6d2309361407cb68b309518e0afefe1429e85ce251cdcff9baa | Python | 57,071 | 1,636 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch.nn as nn
# from typing import Dict, Optional, Union
from typing import Callable, Dict, Optional, Tuple, Union
fro... |
bc92f119398c30901b84b730984e4e86487461e60c298f26134260f2c12ca7ab | Python | 57,108 | 1,168 | import os, copy, torch, random, time, datetime
import numpy as np
import pandas as pd
from torch import nn
import torch.nn.functional as F
from torch.utils.data import Dataset
from torch.utils.data import DataLoader
from sklearn import metrics
from sklearn.feature_selection import mutual_info_classif
from sklearn.model... |
856ee0f0b9590ac0cf5ee2907910eb9f67852163d4faf6133fbe2e4f4a6d023e | Python | 57,205 | 1,637 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch.nn as nn
# from typing import Dict, Optional, Union
from typing import Callable, Dict, Optional, Tuple, Union
fro... |
a829e1654622ff4a3fb4cc94b8b9c9c006073e721830ab87618d73b1cf6d7ca5 | Python | 57,372 | 1,647 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch.nn as nn
# from typing import Dict, Optional, Union
from typing import Callable, Dict, Optional, Tuple, Union
fro... |
c6f2bd7a57a22921c043832da90c53ff833cbb0e645f1927cd4d3dfc1768a372 | Python | 57,462 | 1,121 |
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 25 14:41:11 2024
@author: guill
"""
import numpy as np
import scipy.sparse as sparse
import scipy.stats as stats
from numba import jit
class SpikingNetwork():
def __init__(self, N_pyr=500, N_mit=1000, N_fbi=0, v_reset=-0.065, v_rest=-0.065, v_t... |
c6bed2593f8982ceeee38e898de585d34d4875f4d892444fc2bdfafc59222e5d | Python | 57,565 | 1,257 | # Spatial distribution analysis
from PyQt5.QtCore import pyqtSignal
from PyQt5.QtWidgets import QMessageBox
import numpy as np
import xarray as xr
from .pop_up_messages import print_error
from matplotlib import cm
from typing import List, Optional
from pyvistaqt import QtInteractor
import pyvista as pv
import colorcet ... |
8e04507c5e910dcf326b72b44dc246198126015124b10797b08a08a5832b83ba | Python | 57,728 | 1,373 | # Regional volume and density management
# Author: David Young, 2018, 2019
"""Measure volumes and densities by regions.
Intended to be higher-level, relatively atlas-agnostic measurements.
"""
from enum import Enum
from time import time
from typing import Callable, Dict, List, Optional, Sequence, Tuple, Union
import... |
f793fb712620118cffdd7011c6879bffbb11664b79de9176b35ea5d6cb4810eb | Python | 58,150 | 1,036 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jul 22 05:56:04 2020
@author: takeiyuuichi
"""
#setting##############################################
n_jobs=16 #並列処理の数
t_n_jobs=16
PARAMETER_DIR='/Volumes/Siena/CP/parameter/'
#n_jobs=40 #並列処理の数
#t_n_jobs='cuda'
#PARAMETER_DIR='/home/takeiyuuichi/Dr... |
09a60687b73d0e759c1ade8a0e8203c3644ead0d67c8d2f8d5bc7dc620cd4a8b | Python | 58,202 | 1,124 | from __future__ import print_function, division
import os
from functools import partial
import time
from glob import glob
from collections import OrderedDict
import json
import math
import numpy as np
import tensorflow as tf
from keras import backend
from keras.models import Input, Model, load_model
from keras.optim... |
05ab0cd72e17233ace804eeba2204dc240dbae243db1af2d6b46e654427be3f4 | Python | 58,258 | 1,530 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Eigenmode resampling on the cortex
"""
from .utils import (
_get_eigengroups,
eigen_decomposition,
transform_to_spheroid,
transform_to_ellipsoid,
normalize_data,
)
import os
from .geometry import (calc_surface_eigenmodes,
... |
54041cb1f4be265b3f061b8c64ca04e19c89576f9e59668cfd5290f35a9806c8 | Python | 58,408 | 1,161 | # find isoforms in longread data
from math import inf
import pysam
# from BCBio import GFF # never stop running. is there a bug?
# from: https://techoverflow.net/2013/11/30/a-simple-gff3-parser-in-python/
from collections import namedtuple, Counter
import gzip
from urllib.parse import urlparse
import os
import numpy a... |
1f3b157f71f2f616aa8873121852bf75514f81b70990d1d1159b11e7afe8e576 | Python | 58,526 | 1,543 | """
Module to define interface, workflow and CLI for the review of diffusion MRI data.
"""
import argparse
import asyncio
import sys
import textwrap
import time
import warnings
from abc import ABC
from os.path import basename, join as pjoin, exists as pexists
from textwrap import wrap
import nibabel as nib
import nu... |
e0c054112f21bfa63620f2026c8bb2e0f4e284b138d09426a08d39f2e882c3f2 | Python | 58,777 | 1,172 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import warnings
from collections import OrderedDict
import torch
from tqdm import tqdm
from sam2.modeling.sam2_base imp... |
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