sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b5fa0cae3eadba393b1b8502da8c0be80ae00ee08a69b801c6e2511994a6a64a | Python | 41,259 | 1,116 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2013-2017 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
from __future__ import absolute_import
import os
import re
import sys
try:
import ssl
except ImportError: # pragma: no cover
s... |
7a0b4ed6acf4c5b25b2eee4365be70e9863d09dd2c9e2a6e3dd827f3a6be4427 | Python | 41,285 | 1,064 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
4fab448356821ddc63bddbaab5b8008b6cd4f3386b50d156c6bceea15a3f6af0 | Python | 41,488 | 1,069 | import sys
import argparse
import cv2
import time
import numpy as np
from control._def import *
import threading
import control.toupcam as toupcam
from control.toupcam_exceptions import hresult_checker
def get_sn_by_model(model_name):
try:
device_list = toupcam.Toupcam.EnumV2()
except:
print... |
1a06259a0d9eef221645e6d72220a162d5dd8d4ff8a4615af029523d7eff897d | Python | 41,610 | 996 | # Builtin/3rd party package imports
from functools import reduce
import numpy as np
from numbers import Number
# syncopy imports
from syncopy.shared.parsers import array_parser, data_parser
from syncopy.shared.errors import SPYTypeError, SPYValueError, SPYError
from syncopy.shared.tools import best_match
# local impo... |
f138979f96219cf02157c293e6bac1cee91d26c9ae04d8e7438bffad3b5c2b28 | Python | 41,620 | 1,002 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
import numpy as np
import time
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
import pyqtgraph as pg
#import pyqtgraph.ptime as ptime
import pyqtgraph.dockarea as dock
from pyqtgraph... |
b6b0617e0b74bed5ddab664bee642a8097d88011fb71d6ac17a3a17ab12984db | Python | 41,625 | 973 | import datetime
import logging
import multiprocessing
import os
from functools import partial
import deap
import numpy as np
import pandas as pd
import pypet as pp
from deap import base, creator, tools
from ...utils import paths as paths
from ...utils import pypetUtils as pu
from ...utils.collections import BACKWARD_... |
64168e893143e4d121b1248543c6ea94c435ee4e5e0ef81460eb66632c9476f7 | Python | 41,661 | 915 | """Find bad channels."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
import logging
import mne
import numpy as np
from mne.utils import check_random_state
from scipy import signal
from pyprep.ransac import find_bad_by_ransac
from pyprep.removeTrend import removeTrend
from pyprep.utils import _fi... |
eeb0bcb3fa82765503edf96f92706326c3881af2ee21d0f94058552c3265cfea | Python | 41,668 | 1,216 | """
This python file includes:
format_global
format_func
visualise_imfs_psd
plot_psd_peaks
scatter_ampl_freq_peaks
dotplot_peaks_allP
dot_plot_count
plot_heatmap_psd
scatter_ampl_freq_shade_avg
barplot_count_subj
plot_cycle_allP
plot_cycle_allP_colP
plot_outcom... |
cb575d6aafe396cb016a3f4685b9bfd642c03f6e172c2e5dd49e8d4045964b16 | Python | 41,745 | 972 | # coding=utf-8
# Copyright 2018 The OpenAI Team Authors and HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License... |
ebfd8018f3adada4c1f592b16e903cbef64c4e91e040c8c8bc91419486c0bc9f | Python | 41,790 | 1,806 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 24 23:31:00 2020
@author: usingh
"""
"""
available translation tables compiled from https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes
"""
translation_tables_dict={
"source":"https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/w... |
7f86c84757a41f24ffda06fedba20196e8014c57a62945bd320499400641df93 | Python | 41,853 | 881 | '''
import sys
sys.path.append('/Users/anaconda/Desktop/Code/EC')
import experiments_code_s2p as ec
'''
f_data_path = '/Volumes/2TB_VIRUS/Data' # Path to data
n_stimulations = 10
STIM_END_CONSTANT = 100
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.stats import ttest_rel, pearsonr
... |
96a858d6051e168d57f5af4e76bbeb5cb89dae2db48f13e9c3d682d12e14324f | Python | 41,856 | 1,157 | from __future__ import annotations
import argparse
from pathlib import Path
import pandas as pd
import json
from dataclasses import dataclass
from typing import Any
from itertools import cycle
import numpy as np
import re
import matplotlib.pyplot as plt
import dendritic_spine_args
ntasks_pattern = re.compile("ntasks... |
9b36909d6bf21e25ce9d0eb05ae2cd80f37446b561aa664c15f4e55a0bd06327 | Python | 41,881 | 1,245 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as np
from scipy.io import loadmat
from scipy.stats import stats
import scipy.linalg as linalg
import scipy.signal as signal
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
from numba import njit
#### Additional funct... |
ca94c5ea07d02936f208436f8c525af953e6bd69300fca135a1087be3066d2ad | Python | 41,954 | 976 | import warnings
from contextlib import contextmanager
from functools import partial
from inspect import isfunction
from typing import Any, Dict, List, Tuple
import numpy as np
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torchmetrics
from torch.utils.data import DataLoader
from torchmetrics... |
ec77b6cbf552913b4358317446e86c9503da58bf8cc0d2e40b2a2569bb38d5d2 | Python | 42,047 | 1,137 | """
Tools for updating and expanding lexicons, dealing with logical forms, etc.
"""
from collections import defaultdict, Counter
from copy import copy, deepcopy
from functools import reduce
import itertools
import logging
import queue
import re
import sys
from nltk.ccg import lexicon as ccg_lexicon
from nltk.ccg.api ... |
7164c4902446ccd7011837ac09d0019531053a23ead0aba59db2796a61d033ca | Python | 42,095 | 879 | """
This script is used to draw and overlay predictions on video,
Run this file on the cluster instead of downloading pickle files and run locally
"""
import pickle as pkl
import pandas as pd
import numpy as np
import cv2
from scipy.ndimage import gaussian_filter1d
import os
import matplotlib
import sys
sys.path.appe... |
bf32ff9549b5ad3f8d824f0419d9cf9de18291bd99c3bfee42491c5f339e3c4c | Python | 42,103 | 1,555 | import math
import glob
import logging
import os
import re
import smtplib
import ssl
import subprocess
import time
import copy
import collections
import json
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.backends.backend_agg import FigureCanvasAgg
import numpy as np
import pandas as pd
import requ... |
e2fbc50471ef0c5e711ee13e87da0b4bb81d81e9f2535e120dfaa86380df52ec | Python | 42,144 | 770 | """Validates HED annotations in tabular data in stopping stages."""
from __future__ import annotations
import copy
import math
import re
import warnings
import pandas as pd
from hed.errors.error_reporter import ROW_COUNT_KEY, ErrorHandler, check_for_any_errors, sort_issues
from hed.errors.error_types import ErrorCo... |
24c1c60b2ad5927b43ac5b7e3c2c6382a70422caadd9b4d2b54a2725f522b49b | Python | 42,145 | 1,331 | #!/usr/bin/env python
'''prototype LFP simulation analysis'''
import os
import scipy.signal as ss
from scipy.optimize import curve_fit
from mpl_toolkits.axes_grid1 import make_axes_locatable
from hybridLFPy import helperfun
import numpy as np
import h5py
import LFPy
import matplotlib
from mesocircuit.analysis import st... |
9d6273dd97ff7918a8e91ebc5551d45ad2a4563ce8907dcf57040525a99e8212 | Python | 42,200 | 986 | import logging
import warnings
from contextlib import contextmanager
from functools import partial
from inspect import isfunction
from typing import Any, Dict, List, Tuple
import numpy as np
import pytorch_lightning as pl
import torch
import torch.nn as nn
import torchmetrics
from torch.utils.data import DataLoader
fr... |
beef6c2daa1b56a24709d705d1cad97b099a787bf06896929b346e03054aa6f4 | Python | 42,228 | 1,051 | """
Defines class Connections that holds data from one or more observations
(experiments) divided (classified) in groups.
The observations are expected to be generated by scripts celft.py,
connectors.py, connections.py (depreciated) or classify_connections.py
(depreciated).
# Author: Vladan Lucic (Max Planck Ins... |
9e2aa6586021e74840727121548804513a30e75c8373272a8e83e0b915873378 | Python | 42,245 | 998 | #!/usr/bin/env python3
import argparse
import os
import shutil
from pathlib import Path
DEFAULT_DRIVE_ROOT = "/content/drive/MyDrive/research/projects"
ENV_ROOT = "COLABMDA_ROOT"
ENV_PROJECT = "COLABMDA_PROJECT_DIR"
ROOT_HELP = "Override project root (defaults to current working directory)"
def _normalize_equil_prot... |
8843f1714c1e2902a33b43aa69984393c59099dab4ec26a814a4586910cca607 | Python | 42,299 | 1,070 | """Classes for rereferencing data in an MNE Raw object.
CLASSES
-------
Reref : abstract base class
- Abstract class for rereferencing data in an MNE Raw object.
RerefBipolar : subclass of Reref
- Bipolar rereferences data in an MNE Raw object.
RerefCommonAverage : subclass of Reref
- Common-average rereferenc... |
56fd7ba92510ebc8bdc0162a703733d7a4d108bb4689190d96f812cb82d3c7bd | Python | 42,465 | 862 | # Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
import csv
import os
import matplotlib.pyplot as plt
import numpy as np
from sklearn import metrics
from scipy.ndimage import gaussian_filter
import pickle
from DiscRisk_utilities import *
from DiscRisk_models im... |
741a4e606df81915fa48bf24fcb6d2f6bc593cc8cb8e8325819d373f3e479aa7 | Python | 42,498 | 2,382 | ######################## BEGIN LICENSE BLOCK ########################
# The Original Code is Mozilla Communicator client code.
#
# The Initial Developer of the Original Code is
# Netscape Communications Corporation.
# Portions created by the Initial Developer are Copyright (C) 1998
# the Initial Developer. All Rights R... |
291b8ef96aab66f58cea7043ff33eb68c267f712f9a425781bb1047264a0c137 | Python | 42,517 | 668 | import os
from warnings import warn
import multiprocessing
import numpy as np
from matplotlib import pyplot as plt
import pymp
import pandas as pd
from vtkmodules.vtkIOLegacy import vtkUnstructuredGridReader
from vtkmodules.util import numpy_support as VN
from io_functions import export_ensight_initialise_case, export... |
13c1cc21e6758f04a139f7c7277468cf2fe422e118ad920a77ed435d4b74bd66 | Python | 42,553 | 1,207 | """
Contains class Labels for general manipulations of an image that contains
integer values (label field).
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import zip
from builtins import range
__ve... |
27482f306ec3260acd6c9f352a7aea3574d1391e615a8231b102ddc18464b1c4 | Python | 42,587 | 1,001 | """ Module to extract low-dimensional properties from npx dataset;
plot population activity in pc space, both average and selected trials;
plot cross-correlogram between avg whisking activity and each PC's;
plot distribution cc peaks fo each PC's;
plot loadings to compare distribution of information across neurons for
... |
5b29d8083bf89cc00f0ec0172fd67d30ac37ff682ac729139ac849f019366ccc | Python | 42,589 | 925 | """
Script to compute and collect properties of different clusters.
"""
import os
import sys
if not ('data_analysis' in os.getcwd()):
sys.path.append(os.path.join(os.getcwd(), 'data_analysis'))
import itertools
import pdb
import align_fun
from meta_data import load_meta
from align_fun import align_spktrain, load_d... |
9a8e8eca8bff2e4734b82cd9698146a41a890007e3f260db7dc89fa04c39142d | Python | 42,639 | 1,036 | """ chemical rules"""
import copy
import traceback
import numpy as np
import multiprocessing
import rdkit
import rdkit.Chem as Chem
rdkit.RDLogger.DisableLog('rdApp.*')
from SmilesPE.pretokenizer import atomwise_tokenizer
from MolNexTR.abbrs import RGROUP_SYMBOLS, ABBREVIATIONS, VALENCES, FORMULA_REGEX,SUBSTITUTIONS
im... |
9ffbc0b179d5df4912b5ea7b8e6672e343c36dc061a8acf663773da079ebbd65 | Python | 42,647 | 1,376 | # script to train and evaluate all the networks on AP10K and AP36K datasets
## For individual animals
import ap36_train as a36
import glob
import re
from reuse import *
import cv2
ap36 = False
if ap36:
im_dir = '/groups/branson/bransonlab/datasets/APT-36K/data'
json_files = glob.glob('/groups/branson/branso... |
314bf646822970b26d7a617d7df4fcb8110b76a2074553fa1e9b75f232e30930 | Python | 42,699 | 1,790 | # This file is autogenerated by the command `make fix-copies`, do not edit.
from ..file_utils import requires_backends
class TensorFlowBenchmarkArguments:
def __init__(self, *args, **kwargs):
requires_backends(self, ["tf"])
class TensorFlowBenchmark:
def __init__(self, *args, **kwargs):
requ... |
621d9e57727c45b88eab269711459222cd6e5c5d3cc3800a2e6a8f10afeb18a2 | Python | 42,799 | 1,045 | """
Feature creation based on burst rate modulation for bursts
with distinct shapes.
"""
import numpy as np
from help_funcs import dict_bycondition
from time_res_features import significant_components
from plot_burst_features import features_modulation, features_modulation_nd
from plot_tf_features import chars_modula... |
ce79c25eb2f19e5a7fcbb735ef92161b1f085a4f66c284ee047a11e56a88f74a | Python | 42,821 | 962 | """Training-free entropy-guided GrabCut tissue masking.
The most accurate masker in this project: **0.9817 mean Dice / 0.9373 worst over 33
ground-truth cases across 11 intensity sources** - three Nissl builds, serial two-photon,
light-sheet fluorescence, three MRI contrasts, MERFISH, CCF average template and Waxh... |
073f96579d85e0b114cde0f2357e97ae2f26aa33ef0085736f058fcadaedd7e3 | Python | 42,979 | 1,058 | import abc
import numba
import numpy as np
from neurolib.control.optimal_control import cost_functions
from neurolib.utils.model_utils import computeDelayMatrix, adjustArrayShape
import logging
import copy
from numba.core import types
from numba.typed import Dict
def getdefaultweights():
weights = Dict.empty(
... |
3e77cf20dd5e6c9f6f2bae1c40fe51e0405fef1f745fe4da28ff82dc9fcffe9b | Python | 43,056 | 1,173 | """Tests for StringQueryHandler, parse_hed_string, and string_search.
Most test cases are directly ported from test_query_handler.py, replacing
HedString-based assertions with raw-string assertions. Because StringNode
leaf nodes set ``tag_terms = (text,)`` for single-component tags (e.g. ``"a"``
→ ``("a",)``), the li... |
dd0583cbc148fad6f821e1b05da22953223c29adc42c0bd83c86730446fea617 | Python | 43,077 | 969 | from typing import Dict, Union
import torch
import numpy as np
from sklearn.decomposition import PCA
from torch.fft import fft, ifft
from torch.nn.functional import pad
from ..base_transform import EEGTransform
class RandomEEGTransform(EEGTransform):
def __init__(self, p: float = 0.5, apply_to_baseline: bool = ... |
20041aeb8b8699db58b228024e9752c689b0f7489c5a42019a9132f68e6c2475 | Python | 43,131 | 1,214 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
28986d913dd08db363b03633b694b19ab66a0cc4b4ff2340e6c6881ff620e3fb | Python | 43,181 | 1,052 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
1e4db5d677282379fe11e6e5b0ac2710375275ec7c32546a648561e94d09a2fc | Python | 43,285 | 1,083 | # coding=utf-8
# Copyright 2020 The SqueezeBert authors 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... |
4d2b290a9f1d731139334b908ca7637e9fc6365ba9e41aeec4b253e6771b5f57 | Python | 43,305 | 1,039 | from abc import abstractmethod
import numpy as np
import uuid
import cv2
from skimage import measure
from typing import List
from typing import Tuple
from typing import Dict
from shapely import geometry
import h5py
import merlin
import pandas
import networkx as nx
import rtree
from scipy.spatial import cKDTree
import g... |
d402e8eae929e0079ee031499d35a7063dcf1b29e65a1be223f36c3a6c8df8aa | Python | 43,392 | 1,018 | # coding=utf-8
# Copyright 2021 The Eleuther AI and HuggingFace Inc. team. 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-... |
642c1537213a5743bc4d4161fda6b752e0ff72f4d09cbb74ca69cc6683808853 | Python | 43,414 | 1,494 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
db36fd2ad729e348935c84140c68153f6188fb63c8cbfb6237ec191332a7b8a5 | Python | 43,424 | 1,042 | #!/usr/bin/python3
import os
import numpy as np
import tensorflow as tf
from osgeo import gdal
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from tensorflow.keras import layers as k_layers
from tensorflow.keras.layers import Layer, Conv2D, BatchNormalization, \
Activation, Dropout, Add, Ave... |
625790c305cb71635f27c48019c6e988474155e1822e15043485afb4c8e14275 | Python | 43,444 | 1,067 | from __future__ import annotations
import warnings
from typing import Any
import numpy as np
from matplotlib import pyplot as plt
from scipy.integrate import simpson, trapezoid
from SurvivalEVAL.evaluations.calibration import (
coverage_ic,
d_cal_ic,
ksd_cal_ic,
one_cal_ic,
)
from SurvivalEVAL.evalua... |
8c3f7f7f8338f78f31324f3626767f8d6b89bb1f9328b51cf45272b56a994f4c | Python | 43,444 | 1,240 | """
A collection of routines for use in topology optimization comprising
convolution filters (kernels), projection operators, and morphological
transforms.
"""
import sys
from typing import List, Tuple, Union
import numpy as np
from autograd import numpy as npa
from scipy import signal, special
ArrayLikeType = Union... |
7d79a464269ff4e03498e0f8a7f91b982a0d10772f71eee12064e8c508ed3b57 | Python | 43,510 | 1,233 | #!/usr/bin/env python
# Copyright (c) 2018-2020 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides all atomic scenario behaviors that reflect
trigger conditions to either activate another behavior, or to sto... |
6bd1c41d32824726c0bf95295ab88998eb8b70678b34abdfb75daf7a6a77f1fd | Python | 43,604 | 848 | # Copyright 2020 The HuggingFace Team. 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 applicabl... |
c9256db8eabd35a233df6e73cd05b72ab372c71c362a3183eaaaa0cdeca16e71 | Python | 43,605 | 927 | """
Figure galleries and per-section thumbnails for the registration report.
Collects figure images (JPG/PNG) under a run's output directory, renders
them as an embedded-image gallery, and picks a single representative
thumbnail for a batch-2D section. Stdlib only; never raises.
"""
import json
import os
fr... |
76cc9a10586853303779798def0416e9dd7bd85cc314a08cc61e4d5707bbaf60 | Python | 43,668 | 1,327 | from math import ceil
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import pytorch_lightning as pl
from seq2exp.layers import (
ConvBlock,
GELU,
Residual,
AttentionPool,
RELU0_17,
Attention,
SoftmaxPool,
mixup_augmentati... |
2e6ad344c5c1f8a9e90b0d0812ea4e50a2f3f92febe92da346dc1e49076e94eb | Python | 43,731 | 652 | import multiprocessing
import os
import sys
from warnings import warn
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from datetime import datetime
if __name__ == '__main__':
anatomy_subject_name_list = ['UKB_1097970']# ['UKB_1000268', 'UKB_1002772', 'UKB_1010096', 'UKB_1005678', 'UKB_10081... |
dc08cd6fee3a0344f8086ea59547d962b57034e7b578ae5c8d13a171d3077635 | Python | 43,739 | 1,084 | import torch
from utils.complex_utils import complex_utils as Z
from utils.loaders import load_h5_dataset
import torch.nn as nn
import torch.nn.functional as F
import math
class led_input_device(torch.nn.Module):
def __init__(self,config,isfloat=True):
super().__init__()
self.num_ch... |
cd83f7bb6b6f750801704fbbdf9c3d3b77451ca8e8378567b36389662c7e8811 | Python | 43,863 | 726 | import os
import time
from warnings import warn
import numpy as np
from matplotlib import pyplot as plt
import multiprocessing
from adapter_theta_params import AdapterThetaParams, RoundTheta
from cellular_models import CellularModelBiomarkerDictionary, MitchellSchaefferAPDdictionary
from conduction_system import Empty... |
460aaceb9f15b09dd1dbce39ab09d90fc5d0af25760b35b0da6821c0bbf1c6c2 | Python | 43,898 | 1,082 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2013-2020 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
from __future__ import unicode_literals
import base64
import codecs
import datetime
from email import message_from_file
import hashlib
i... |
299d2a964b355b4ab56c7350d7b859adf59768ce1135eb3f7cf140d0beef8f0e | Python | 43,942 | 1,204 | """
Unified Data I/O Module
=======================
Auto-detects input format (NIfTI, NRRD, DICOM, TIFF), loads data into a
common ``VolumeData`` container with metadata (spacing, affine, orientation),
and validates format compatibility per-module.
Supported formats
-----------------
- NIfTI (.nii, .nii.gz... |
1793e2a6cc2e2400480ccc49f1f100ace968685fba2d5de3a9f9b754e360b97f | Python | 43,969 | 1,051 | import argparse
import collections
import gzip
import math
import os
import random
import shutil
import subprocess
import sys
import time
import numpy as np
import pandas as pd
import tensorflow as tf
import pybedtools as pybt
import tabix as tb
from datetime import datetime
from tensorflow import strings as tfs
from... |
33c60e84e9bc5dede02d9a30744f9d0130ab612e3855ca895e0129d1331b9374 | Python | 44,026 | 1,003 | """
PyQt5 GUI for Cellpose-SAM cell detection and segmentation.
Launches detection in a separate terminal window with ANSI color output,
matching the pattern used by the stitching GUI.
Structure
---------
- ``launch_helpers.py`` - pure-Python model discovery / CLI-arg helpers (no Qt)
- ``dialogs.py`` ... |
94f4c2b22cf96a9dc38190bd979427708f2caebebe315d0e5a87735ccba2c2b8 | Python | 44,102 | 675 | # this lib, together with the preprocess_mice_trials script
# is used to process the raw excel files that have the tracking
# of the mouse in the arena looking for the hidden food
#
# the experiments were originally performed by Kelly Xu from Len Maler lab
#
# the original excel files are not going to be included in th... |
0077869718349835d834e801f666133271cb8ef7423cd8bfb92c492a073692e0 | Python | 44,150 | 1,085 | """
Defines class Vesicles that holds data from one or more observations
(experiments) divided (classified) in groups.
The observations are expected to be generated by scripts/vesicles.py.
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)
# $Id$
"""
from __future__ import unicode_literals
from __futur... |
dd30e5a47272abd11bbfb280dc37af27a50086b03290c9c156492480671f9823 | Python | 44,166 | 1,160 | import numpy as np
from enum import Enum
from client_tcp import ClientTCP
import reram_register
import globals.global_func as gf
MAX_PACKET_LEN = 0xFFFF
CMD_HEAD = 0x3A
RESPONSE_HEAD = 0x3B
PACKET_HEAD_LEN = 0x07
CMD_NULL = 0xFF
CMD_COMMON_START = 0x80
CMD_DEBUG = 0x01 + CMD_COMMON_START
CMD_WRITE_R... |
7b23b89f491eff9285f6ab8239320023b24120620b7953da89fe9dcab8b99527 | Python | 44,177 | 1,105 | import numpy as np
import matplotlib.pyplot as plt
# Plot boundaries for different updating
e_hat = np.argmax(sem_model.results.post, axis=1)
frame_boundaries = np.concatenate([[0], e_hat[1:] != e_hat[:-1]])
e_hat = np.argmax(sem_model.results.post_pe, axis=1)
frame_boundaries_pe = np.concatenate([[0], e_hat[1:] != e_... |
dd915f632eebeb7e9a1ba413ab72f9ba0405f0738ef2731867914c2bdad6050c | Python | 44,211 | 934 | # Copyright 2022 HYBRID Team INCIA, UMR5287, CNRS, Université de Bordeaux
# 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 b... |
477752dbdf8698a3a9076dbc765c660fe57c86d10536b8be81f3c109303577d4 | Python | 44,257 | 915 |
# coding: utf-8
# In[ ]:
import tensorflow as tf
from tensorflow.python.ops import control_flow_ops
from tensorflow.contrib.framework.python.ops import variables
from tensorflow.contrib.layers.python.layers import utils
from tensorflow.python.framework import ops
from tensorflow.python.layers import normalization a... |
43c04cefe143c42eb5bc28351a13acf725619b20410b8edf13e6058cd74bf488 | Python | 44,309 | 918 | options = dict(
verbose=True,
model_extensions=[
'h2o.model.extensions.ScoringHistoryTrees',
'h2o.model.extensions.VariableImportance',
'h2o.model.extensions.FeatureInteraction',
'h2o.model.extensions.Trees',
'h2o.model.extensions.SupervisedTrees',
'h2o.model.exte... |
e5be3ce6d13a590e690a4a96b833eae9c38a1feb00a7a354f8bb53d31c03b789 | Python | 44,360 | 1,083 | import math
import warnings
from copy import copy
from collections.abc import Sequence
from matplotlib import pyplot as plt
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
import torch
from torch_scatter import scatter_add, scatter_min
from torchdrug import utils
from torchdrug.data import cons... |
5363d482064ef959be85c34a14636ef3e7fabe6d2aa9e9319536d036ea01f55a | Python | 44,362 | 847 | import os
import math
import numpy as np
import json
import scipy.io
import pandas as pd
import pymp, multiprocessing
from vtkmodules.vtkIOLegacy import vtkUnstructuredGridReader
from vtkmodules.util import numpy_support as VN
from warnings import warn
from ecg_functions import resample_ecg
from utils import initiali... |
c548ea2aa88957c1e8fd7cc1a40b6fe4916854f4aea4af92517bed8f28141eac | Python | 44,375 | 2,151 | # This file is automatically generated by tools/idna-data
__version__ = '15.0.0'
scripts = {
'Greek': (
0x37000000374,
0x37500000378,
0x37a0000037e,
0x37f00000380,
0x38400000385,
0x38600000387,
0x3880000038b,
0x38c0000038d,
0x38e000003a2,
... |
6a96a18e6ba4288bd5ca995b654a9b08f9151e0258224cff5e282df28e02fcaf | Python | 44,379 | 1,267 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import math
import numbers
import random
import numpy as np
import PIL
import torch
import torchvision
import torchvision.transforms.functional as F
from PIL import Image
from torchvision import transforms
from . import fu... |
1bc6703e5418fc5dcbad8e089e56852c7c404f9998c278f8f318cd0944c9f122 | Python | 44,427 | 837 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pickle
import dill
import os
import time
import glob
import math
import seaborn as sns
from sklearn.decomposi... |
2a5c9a178dbd810cb69d38096cbbbc86c2359ef1c2f791025fe630194e86da9b | Python | 44,427 | 1,133 | # -*- coding: utf-8 -*-
#
# Definition of the respective ComputationalRoutines
# for the `freqanalysis` frontend. The *method*_cF function
# definitions serve as middleware connecting the pure
# backend methods to the ComputationalRoutines. The
# 1st argument always is the data, and the last argument
# `method_kwargs` ... |
8bb2da17eed0a5f2d33b56fe48d6d3453e7525d35766c24daf6357d04ce62b3a | Python | 44,491 | 1,577 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
# Copyright (c) 2023 University of Minnesota
# Copyright (c) 2024 University of Chicago
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistrib... |
d69d73192ef0d551d910a4a1f1450c274fa5eca93ec222a3bc2111af1666ab7d | Python | 44,539 | 1,163 | from __future__ import division
from __future__ import print_function
from builtins import str
from builtins import range
from builtins import object
import tensorflow as tf
import os
import PoseTools
import multiResData
from enum import Enum
import numpy as np
import re
import pickle
import sys
import math
from past.... |
31ef6c2d69fe3aa4c01c320971a4d13d37e22a79b72e0eb164efb5051338c25f | Python | 44,542 | 987 | """
Find columns on synapse tomograms (ListTomograms) and measure their statistics.
Files for columns visualization in VTK format.
Input: - 3 STAR files (layers) with the ListTomoParticles pickles
Output: - Plots by tomograms and globally:
+ Number of columns
+ Column... |
87b5691e55774b75259f0ba73eac3e25402fa1f1706629d9dbd9b422e8448516 | Python | 44,562 | 1,354 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
4ff0f10f42e4e6f7dbc9994b030ee0bc2ca05b60c4b0ec4eefe43f739354aa33 | Python | 44,713 | 729 | """ Authored by: Neel Kanwal (neel.kanwal0@gmail.com)"""
# This file provides training code for SOTA DCNNs models mentioned in the paper.
# Update paths to processed datasets
if __name__ == "__main__":
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
warnings.simp... |
10ab90db000311eaa88def71d347ba978604cfcfd9debf7df978ba68e4d243ea | Python | 44,741 | 743 | """Single frozen transformer, two independent chats, and measured reservoir activity.
The engine is owned by one worker. Its lock also serializes direct API calls; only
Telemetry.snapshot and a cancellation Event need to be accessed from the UI.
"""
from __future__ import annotations
import json
import time
import uu... |
c8fcd934cc681e1b4fdecd1c3fba97e38ba01f57040a2a54cb81aca8f0e5e5c2 | Python | 44,778 | 1,134 | """
Class Morphology for calculation of morphological quantities of a segmented
image(label field).
# Author: Vladan Lucic
# $Id$
"""
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import division
from builtins import str
from builtins import zip
from builtins import ran... |
2aeaad5077af1eec1e8690282a869c5cdd278f8e1d3a802714dac0fb2b309017 | Python | 44,859 | 1,308 | #!/usr/bin/env python3
# ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... |
eb0efec1bc619a0164539b24938c9c4855c1d80ebb8c7e3f3d9333ffe770c2e1 | Python | 44,890 | 845 | # 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
#
# ht... |
f30d03372efd73dbb42d222773d1f6e007b3c6c68a9de39653b16b938ecb1a1f | Python | 44,898 | 1,092 | from math import fsum, sqrt
from copy import copy
from traceHandler import sizeError
import efel
import numpy as np
import modelHandler
import time
import random
import threading
import matplotlib.pyplot as plt
import threading
try:
import copyreg
except:
import copyreg
from types import MethodType
import os
... |
adebfba02c8c08ea78cc93933b2d1b3b2d6be2e6ab5fe731c5571211f8cc5a69 | Python | 44,916 | 1,003 | """
This file provides more general implementations of Python methods used to
create surrogate models for various loads of an office cell with attached overhang
with respect to overhang depth and height. Besides originally intended purpose,
these methods allow interested researchers to use them independently in order t... |
f2324c0687e1dec37e98ad8a677a97ba8d56ad874f6976baa9e4e662852ab997 | Python | 45,054 | 1,137 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
3dfc3aec79b55ecb93fd09d548859586caeb5aa97288513a2f34e22fdbaa719c | Python | 45,141 | 1,214 | # This file is meant primarily for people who want to see an example
# of how to use part of the OpenBabel API, with a secondary use as a
# set of quick unit tests to make sure there's no strange but obvious
# problem with your OpenBabel setup.
# Regression tests, coverage tests, stress tests, performance tests,
# etc... |
9318bad6f05bd9b6b09235e50eabd5d24a8fc2be7bad1e8b3ae6215fc2b4a956 | Python | 45,186 | 938 | """Per-region plaque segmentation statistics for warped label volumes.
Called from the Apply Transforms pipeline when ``--is_segmentation`` is set
and the direction is data->template. The warped segmentation lands in atlas
(Allen CCF 25 µm) space, so the annotation volume aligns natively - no atlas
warping is ne... |
39ef87f9b1cebf613cf9c7284242d897994402ce6af772390a9ad59dccb6d46a | Python | 45,213 | 747 | # the implementation for CG MAML-based regression framework
import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(__file__)))
import warnings
warnings.simplefilter("ignore")
import json
import util
import time
import tqdm
import torch
import pprint
import random
import numpy as np
import ... |
a026cd5cf869e55260b4eb1073860483612055613c1394566d6526135a71f83c | Python | 45,258 | 893 | ################################################################################
# Import, Set up MPI Variables, Load Necessary Files
################################################################################
import os
from os.path import join
import sys
import matplotlib
import matplotlib.pyplot as plt
from matp... |
cb9c672a77ef2478fa4cbb5bdbc14f66e625aec4e899c3c0ad4b08de671345c3 | Python | 45,338 | 1,044 | """
GUI tab for creating NIfTI volumes from TIFF image data.
"""
import os
import subprocess
import sys
import time
import numpy as np
from natsort import natsorted
from PySide6.QtWidgets import (
QWidget,
QVBoxLayout,
QHBoxLayout,
QLabel,
QFileDialog,
QCheckBox,
QPushB... |
2935e8b1e3eaebfce51dfa2ee81001218490d143e94ce804455de56049d6582d | Python | 45,350 | 987 | """
Assembly detection related plots
author: András Ecker, last update: 07.2023
"""
import numpy as np
from scipy.cluster.hierarchy import dendrogram, set_link_color_palette
from assemblyfire.utils import group_clusters_by_patterns, count_clusters_by_patterns_across_seeds
import matplotlib
matplotlib.use("Agg")
import... |
ffc2419526aed1cdb3f0434e64c8b5849eccd59198e34f04e3e8578c7cb28350 | Python | 45,525 | 1,307 | import re
from functools import partial, reduce
from math import gcd
from operator import itemgetter
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Iterable,
List,
NamedTuple,
Optional,
Tuple,
Union,
)
from ._loop import loop_last
from ._pick import pick_bool
from ._wr... |
779cd4cf9b8b5fd92265f3b1fdc805686aae4fb741803921625fa68cf5df6274 | Python | 45,598 | 837 | # 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
#
# ht... |
e3dd506dd12cee551b554b61dd699d68e9df42b3692630c90a0ff057a190e265 | Python | 45,611 | 1,064 | # -*- coding: utf-8 -*-
#
# Syncopy spectral estimation methods
#
# Builtin/3rd party package imports
import numpy as np
# Syncopy imports
from syncopy.shared.parsers import data_parser, scalar_parser, array_parser
from syncopy.shared.tools import get_defaults, get_frontend_cfg
from syncopy.datatype import SpectralDa... |
ee1ae0b42741720ecfe19a6bfaf51eb938625f019e71707534d7e6d18e32a7b4 | Python | 45,621 | 1,225 | # This module is a slow Qt/matplotlib-based implementation of BQA.
# BUT! It is obsolete, untested and might not work: use qmod.py instead.
import sys
import os
import webbrowser
import time
import matplotlib as mpl
import numpy as np
import scipy as sp
import scipy.stats as stats
from matplotlib.backends.backend_qt4a... |
081d2aac28b92a509a6f98ea88ef81a7c3ab87c877320ca16362764efb9e0898 | Python | 45,657 | 923 | ################################################################################
# Import, Set up MPI Variables, Load Necessary Files
################################################################################
import os
from os.path import join
import sys
import matplotlib
import matplotlib.pyplot as plt
from matp... |
2b73cdc41e6266579540b3adf24a2a0df3d271c14a936cedb26c1126fba2038f | Python | 45,668 | 856 | import os
import multiprocessing
import random
import numpy as np
os.environ['TF_ENABLE_EAGER_CLIENT_STREAMING_ENQUEUE']='False'
import tensorflow as tf
from tensorflow import strings as tfs
import src.metrics as metrics
import src.utils
from src.losses import poisson_multinomial
tf.keras.backend.set_floatx('float3... |
501e527ddd92d7193a73db9077e859bedb51b6ad31fe468590ae6ec94e33fe6a | Python | 45,672 | 1,188 | from __future__ import division
import sys
import os
import logging
import cv2
import copy
import numpy as np
import tensorflow
vv = [int(v) for v in tensorflow.__version__.split('.')]
if (vv[0]==1 and vv[1]>12) or vv[0]==2:
tf = tensorflow.compat.v1
else:
tf = tensorflow
from itertools import islice
import t... |
978254a1a9e19b7bf651f136620f9da7f498ed5888195efb4c77128b6cd568d8 | Python | 45,706 | 650 | import copy
import math
import random
import numpy as np
class Train_FewshotBatchSampler:
def __init__(self, subset, dataset, K_shot, K_query, query_min, batch_size, seed, **kwargs):
self.subset = subset # selected subset for meta-training
self.dataset = dataset # complete pytorch Datas... |
be1c8286c7c8bf473abe00538fefa300a307893e9a9912702fc938c0617c0085 | Python | 45,720 | 953 | """Base translation model with different variations"""
import os
import shutil
from abc import ABC, abstractmethod
import numpy as np
import tensorflow as tf
class BaseModel(ABC):
"""
This is the base class for the translation model. Child class defines encode and decode
architecture.
Attr... |
1fdadab063a8b77e1c8e7c0f93e6a169b9f6df9cec7db183905700c77a064a91 | Python | 45,745 | 1,374 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
bff2ba7841bc9c38d9d683b938863be5f851210f3d47d0ddb888d076c26a3002 | Python | 45,859 | 1,082 | # coding=utf-8
# Copyright 2018 The OpenAI Team Authors and HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License... |
c32793fd6fea7e1235c58e63d9a75c5d0a26b9f992da4abe41b4e2f2945acde3 | Python | 45,903 | 1,063 | # If using multiprocessing, this module will be imported dynamically
import logging
# no need to set handler here, since we already set handler in root logger (utils.py), this child logger inherit that.
logger = logging.getLogger(__name__)
logger.info('Import event_models.py')
import numpy as np
import tensorflow as... |
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