sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d32d4dfb97a0272d9e04ab3c7038011c40b8aed8148f898464f5e0beef1ca318 | Python | 991 | 31 | import sys
import re
import pdb
def is_failtree(linetree):
#perl -pe 's/.*\([^a-z]+ .*//'
if re.search(r'.*\([^a-z]+ .*', linetree) is not None:
return True
else:
return False
def gen_failtree(words):
#use failnode labels?
assert len(words) > 0
#if ("" not in words):
# ... |
37e48c028698caf1bf80a4a845a6cb19249a0fb4fdb98439107e2095dca680a0 | Python | 993 | 33 | import sys
def main():
print("word totsurp")
all_word, all_llmsurp, all_bori, all_bprob, all_iprob = [], [], [], [], []
lines = sys.stdin.readlines()
for line in lines[1:]:
#print(line)
word, llmsurp, bori, bprob, iprob = line.rstrip().split(" ")
all_word.append(word)
... |
ce4c0a97132ae7df75e7da2a94b8f96855084c5d4c739b6cbf8d92c380b016de | Python | 993 | 31 | from distutils.core import setup
setup(
name = 'NeatMS',
packages = ['NeatMS'],
version = 'v0.6',
license='MIT',
description = 'NeatMS is an open source python package for untargeted LCMS deep learning peak curation',
author = 'Yoann Gloaguen',
author_email = 'yoann.gloaguen@mdc-berlin.de',
url = 'h... |
0d9bf9efc1ec22369d97600a76b9fa0be471d051242746b90184a590fa27816b | Python | 995 | 30 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
b50c4af569a528aee7de138eb09540fc4c3e8cfa1665e6d7f5af4a1fa77bc49e | Python | 996 | 35 | #
# Implementation of the Wigner D-matrices via sympy.
#
import numpy as np
import sympy
from sympy.physics.quantum.spin import WignerD
class Memoize:
# https://stackoverflow.com/a/1988826/1142217
def __init__(self, f):
self.f = f
self.memo = {}
def __call__(self, *args):
if not ar... |
c819d90525560a4eadfe50bc9187f3adfe861a300f97a1993f823cc415788e91 | Python | 996 | 37 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize(
"index_without_na",
[
pd.TimedeltaIndex(["1 days", "2 days"]),
pd.PeriodIndex(["2011-01-01", "2011-01-02"], freq="D"),
pd.DatetimeIndex(["2011-01-01", "2011-01-02"]),
pd... |
f3f6060448b629a1e22b42297f14ee8e8bfb533b49ebd93154009cc894d04a07 | Python | 997 | 39 | import sys
import glob
import pandas as pd
import numpy as np
import h5py
file_list = glob.glob(sys.argv[2])
total_data = pd.DataFrame()
for ff in file_list:
data = pd.read_csv(ff, sep=',', index_col=0, header=0)
data = data.transpose()
c = list(range(data.shape[0]))
total_data = pd.concat([total_data... |
42b10cd1efc5f12f091860aee5cb7220b93d72237881e52b0d9b4b84179eddf2 | Python | 998 | 40 | # ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.16.0
# kernelspec:
# display_name: ol-connectome
# language: python
# name: ol-connectome
# ---
# %%
from pathlib import Path
import sys
... |
bfea2eb3b497aab82b3f0ebeded2a4da5a11805faf1c610be7be4ed35e30ef59 | Python | 998 | 28 | import numpy as np
align_to_nbytes = 512
max_raidfile_entries = 64
# 8B
MrParcRaidFileHeader = [("hdSize_", "<u4"), # ID???
("count_", "<u4")] # # of meas
# 152B
MrParcRaidFileEntry = [("measId_", "<u4"), # MeasID
("fileId_", "<u4"), # FileID
... |
990abcd8c724491a55ff106d00fa64f39a59c7ef4e3382c66fd1653a04238002 | Python | 1,000 | 31 | from setuptools import find_packages, setup
with open("README.md", "r") as fh:
long_description = fh.read()
with open('requirements.txt') as f:
requirements = f.read().splitlines()
requirements = [l for l in requirements if not l.strip().startswith('#')]
setup(
name='neuronbridge-python',
package... |
b91ec19749158f514561718d4d7f1a0ffd3fa02f148dd1a500f8798818fa6c04 | Python | 1,000 | 41 | import numpy as np
import vegas
import math
from outputsplitter import log_stdout, unlog_stdout
import gvar
gvar.ranseed(12345)
DIM = 5
@vegas.rbatchintegrand
def f(xd):
r = xd['r']
phi = xd['phi']
# construct Euclidean coordinates, Jacobian
x = np.zeros((DIM,) + np.shape(r), float)
x[:] = r
... |
c96326f52231009a60ae4fc2f06109e0174dbd2c7e76fd604e2c5ef3970ad29c | Python | 1,001 | 40 | """Plot module for gradec."""
import os
from neuromaps.datasets import fetch_fslr
from surfplot import Plot
from surfplot.utils import threshold
from gradec.utils import get_data_dir
def plot_surf_maps(
lh_grad,
rh_grad,
cmap="viridis",
color_range=None,
threshold_=None,
data_dir=None,
):
... |
6313de065213ffc22c0bc8dc2a1bd036945205ff5c512c43e64d499b207ccf66 | Python | 1,003 | 28 | import sys
import argparse
try:
import importlib.resources as pkg_resources
except ImportError:
import importlib_resources as pkg_resources
from .. import templates
if __name__ == '__main__':
argparser = argparse.ArgumentParser('''
Initialize a CDR(NN) config file template.
''')
argparser.add_a... |
7bfa9b63fb8b73c532bf6ec71b915ea00aa8d055bc3df0982d75f1e2c2079537 | Python | 1,003 | 24 | import dgl
import torch
import torch.nn as nn
import torch.nn.functional as F
class GVAE(nn.Module):
def __init__(self, in_dim, hid_dim, z_dim):
super(GVAE, self).__init__()
self.encoder1 = dgl.nn.pytorch.GraphConv(in_dim, hid_dim)
self.encoder2 = dgl.nn.pytorch.conv.GraphConv(hid_dim, z_di... |
98a469233248022e867fd2e380fd8ee036b962b86c063de24a028f4c53b4e9f1 | Python | 1,005 | 33 | from io import StringIO
import pytest
import pandas as pd
import pandas._testing as tm
class TestSas:
def test_sas_buffer_format(self):
# see gh-14947
b = StringIO("")
msg = (
"If this is a buffer object rather than a string "
"name, you must specify a format str... |
9855a307fe05bc7218f912a7d2f36b1151fc0ad5f7bdf1f27e525429e805bfe5 | Python | 1,007 | 24 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
5b695d07c2b6476fee83bd51688e19c0ed5b620b9ccb7aa7b8aac8d0ba74cbd8 | Python | 1,008 | 39 | import sys
import cuegraphcontexts
import pdb
## for each article until eof...
article_number = 0
eof = False
while ( not eof ):
## for each sentence in article...
G = cuegraphcontexts.CueGraph()
for linenum,sent in enumerate(sys.stdin):
if '!article' in sent: break
## for each dep...
for dep in sen... |
ba088cbb0350c86d283d9d835fbd678b555e9444eca18c389432460388600475 | Python | 1,008 | 41 | """
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 torch
from .math_fn import complex_abs_sq
def rss(data: torch.Tensor, dim: int = 0) -> torch.Tensor:
"""
Compute the Root Su... |
c483dc6391f48af50140b41a7ea040ddf273eb9e1ff87a191935295ef6e69793 | Python | 1,008 | 36 | import pytest
import pandas as pd
import pandas._testing as tm
class TestPipe:
def test_pipe(self, frame_or_series):
obj = pd.DataFrame({"A": [1, 2, 3]})
expected = pd.DataFrame({"A": [1, 4, 9]})
if frame_or_series is pd.Series:
obj = obj["A"]
expected = expected["... |
a69ce6c1e558168b33117700aca3dcf10d143e15cc9817b5b163418fb0e5c694 | Python | 1,009 | 29 | import pytest
from pandas._libs.tslibs import Timestamp
from pandas._libs.tslibs.dtypes import NpyDatetimeUnit
class TestTimestampNormalize:
@pytest.mark.parametrize("arg", ["2013-11-30", "2013-11-30 12:00:00"])
def test_normalize(self, tz_naive_fixture, arg, unit):
tz = tz_naive_fixture
ts =... |
fd0dbc02c0bf37bb72b363387c827ce142ef6460b8a414c2131693c9d9985784 | Python | 1,009 | 30 | import os
from unittest import TestCase
import dynast.estimation.alpha as alpha
import dynast.estimation.pi as pi
import dynast.preprocessing.conversion as conversion
import dynast.utils as utils
from .. import mixins
class TestAlpha(mixins.TestMixin, TestCase):
def test_read_alpha(self):
alpha.read_al... |
f3bc41a54dc01ae0058b8e68252078004c9c9e8a467a6524d01cf965254af4f2 | Python | 1,010 | 39 | from src.paths import Paths
import os
import pytest
import json
TEST_FILE = 'test_json.json'
def setup_module():
test_paths = {'PATHS':{'Test1':1, 'Test2':2}}
with open(TEST_FILE, 'w') as f:
json.dump(test_paths, f, indent=4)
def teardown_module():
os.remove(TEST_FILE)
def test_paths_call():
... |
253c9c278f579c65dbe825439a02354b5d6fcfb750096c4df7ea39708aeb162a | Python | 1,011 | 17 | """Give the T1 MRI a FLAIR-like contrast: dark CSF, grey matter brighter than white
matter, bright caps around the ventricles and a few white matter lesions."""
import sys
import numpy as np
import nibabel as nib
t1, sdt, out = sys.argv[1], sys.argv[2], sys.argv[3]
im = nib.load(t1)
v = im.get_fdata().squeeze()
d = nib... |
45a63df9f4961f9d386f0ae2d157e6e882fa06ad7dfb245194f9688076989e1c | Python | 1,011 | 23 | # Copyright (c) 2023, NVIDIA CORPORATION. All rights reserved.
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software and relat... |
9f0b36a66211ea2fcbc24fe7fde48494eedf6bf6f2ad2676014f29d16a840a1c | Python | 1,011 | 33 | #
# Equivariant batch normalization layer
#
# Uses L_batch_norm.py to take batch norm across all Ls of inputs
#
from keras import backend as K
from keras.engine import InputSpec
from keras.layers import BatchNormalization
import tensorflow as tf
import protein_holography.network.L_batch_norm_gpu as lbn
class Spherica... |
a1177c84272be4f56c563f447bc598248d7e602c74945efb0de0ffba644c51a1 | Python | 1,011 | 38 | import json
import os
from datetime import datetime
def start(params, sys_desc):
"""Capture exp start """
exp_start = datetime.now()
experiment_id = params['experiment_id']
search_space = []
for key, val in params.items():
search_space.append("{}: {}".format(key, val))
msg = [{
... |
123b82079876acbc4d4e1ab90d664275a0abc6693da81b12ff798a08aab47e58 | Python | 1,012 | 38 | #! /usr/bin/python3
# -*- coding: utf-8 -*-
# @FileName: setup.py
# @Author: Li Chengxin
# @Time: 2023/7/4 13:43
import setuptools
with open('readme.md', 'r', encoding='utf-8') as f:
long_description = f.read()
with open('requirements.txt', 'r') as fr:
pkg_requirements = fr.read().split('\n')
pkg_requir... |
ade2ceb0945b1d1e3fe76c7b3e537806740f99bdaeb4c9ea0f8cc41c59eacc53 | Python | 1,012 | 26 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
f0eb4f735160caa9cd403ac7435a4024bd2deeb0dddc20136e63fb0d6a3919fd | Python | 1,012 | 35 | import numpy as np
nonlin_c = [4.9048901e-33, -1.0354900e-27, 8.3495897e-23, -3.2744900e-18, 6.5422602e-14, -7.0451200e-10, 7.7333998e-6, 9.0207702e-1]
nonlin_corr = np.poly1d(nonlin_c)
wavelen_c = [3.8541e-1, -1.8392e-5, -1.5460e-9, 1.7836e2]
wavelen_corr = np.poly1d(wavelen_c)
probe_A_cm2 = 1
#Load calib_file
calib... |
e5bcbbc6a276a8fda6cdc188e30f679dce518eab45065da383d346f60bcb3019 | Python | 1,014 | 34 | import cv2
import math
import numpy
from utils.logging import init_log
def psnr1(img1,img2):
mse = numpy.mean((img1/1.0 - img2 / 1.0)**2)
if mse < 1e-10:
return 100
psnr1 = 20 * math.log10(255/math.sqrt(mse))
return psnr1
def psnr2(img1,img2):
mse = numpy.mean((img1 / 255.0 ... |
fe7c0c7a9ac6a9b9493fad895b2c4a73e3e009b1dd4338ddc621bb6eb43ab6ed | Python | 1,015 | 28 | import numpy as np
def Normalize(images, type, show=0):
show = 0
if show == 1:
print("min", np.min(images))
print(" max", np.max(images))
if type == 1: # values from 0 to 1 (2)
im_n = (images - images.min()) / (images.max() - images.min())
if type == 2: # random
... |
d4c33c058c13c96830d6066ab19e48398bee4e2e611ec9497b96ce6879131231 | Python | 1,016 | 40 | from ._cohens_d import cohens_d, gene_selection
from ._data_loader import SuematsuData
from ._go import go, gprofiler, get_go
from ._preference import (
kwarg_savefig, eda_longitudinal_args, sgoa_longitudinal_args,
venn3_palette1, venn3_palette2, venn3_palette_alias,
artist_pipeline_adgile, eda_pipeline_ad... |
f8367d1bb81238fcf27cba3004a8a36d906e394da4384ad113b65a33e72dd65a | Python | 1,016 | 33 | """torch_compile is off unless a config asks for it."""
import torch
from tests.test_critical_fixes import make_cartpole_runner
def _count_compiles(monkeypatch):
# the runner compiles modules; example networks may decorate a function at import
calls = []
def fake_compile(model, *args, **kwargs):
... |
0b5658ffbceca86153cebcbeffdad41eeaf1c60f6ff34283d35a11f2a7606855 | Python | 1,017 | 30 | from typing import List
import torch
from ...image import Stack, Volume
def stack_intersect(stacks: List[Stack], box: bool) -> Volume:
return volume_intersect([stack.get_mask_volume() for stack in stacks], box)
def volume_intersect(volumes: List[Volume], box: bool) -> Volume:
volume = volumes[0].clone()
... |
774e9cd733dddf83134a4979384ec8e1fe18396df8a1eb1dfd2cffb440661660 | Python | 1,017 | 31 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
aaa9387445637ae43028f2384f4628600bffa0bfd3279f4745ec3ead4b7ae54e | Python | 1,017 | 28 | import sys, argparse
argparser = argparse.ArgumentParser('''
Reads a space-delimited data table and renames user-specified columns. Column source and target names must alternate: col_1_source col_1_target [col_2_source col_2_target [etc...
''')
argparser.add_argument('cols', nargs='+', type=str, help='column names to ... |
485229d012cbf8bfc23c73e9b5b050f7a01fb5a0d32a6d9d725698833b9e66b0 | Python | 1,018 | 34 | from enum import Enum
# This assumes a list with dicts, loop over all dicts, and get the unique
# keys
def get_fieldnames(data):
fieldnames = set()
for item in data:
[fieldnames.add(key) for key in item.keys()]
return list(fieldnames)
class SnifferType(Enum):
list_with_dicts = 1
list_wit... |
7b83fb021e95da2bcb670a62fb98119a6d98361f026b9f2608828899b2e3ab6f | Python | 1,018 | 27 | # License: see [LICENSE, LICENSES/legged_gym/LICENSE]
import inspect
class BaseConfig:
def __init__(self) -> None:
""" Initializes all member classes recursively. Ignores all namse starting with '__' (buit-in methods)."""
self.init_member_classes(self)
@staticmethod
def init_member_cl... |
0438ecc10f45adb514cbc5854c80ab6528241702e47b69607c63412c066a3a97 | Python | 1,019 | 36 | import numpy as np
from abc import ABC
class AcquisitionParameters(ABC):
"""Acquisition parameters."""
def __init__(self, b, td, small_delta=None):
"""Initialize the acquisition parameters."""
# b-values or shells
self.b = np.array(b)
# diffusion time Δ
self.td = np.ar... |
b2252a2c40ead461e383f18377ed4e2ab477293ca28716d87547aed3d4e02071 | Python | 1,019 | 26 | import pandas as pd
import numpy as np
### Enable logging
snake_log_obj = snakemake.log # class(snakemake.log) = 'snakemake.io.Log
sys.stdout = open(str(snake_log_obj), "w") # could not find better ways than calling str(snake_log_obj) to get the log filepath
### Get parameters from snakemake
GENELOC_FILE = snakemak... |
f76c888a2f2592bdbd860e5d870331bc1ce84f2a17efef3e8e0cc70532a8ef42 | Python | 1,019 | 27 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
fab01421e2ca13b1e8e86ca35b52780fcd66d67b8586714aaeb77b9ac02ec0d9 | Python | 1,019 | 23 | from .spike_detection import spike_detection
import barrel_cortex
#from . import spaciotemporal_binning
excitatory = barrel_cortex.excitatory
inhibitory = barrel_cortex.inhibitory
def split_synapse_activation(sa, selfcheck = True, excitatory = excitatory, inhibiotry = inhibitory):
'''Splits synapse activation in ... |
952f42501c21972585b68b270375e823c20a72482e86f401f2d7ddef7f2a9743 | Python | 1,020 | 41 | """common utilities"""
from __future__ import annotations
from typing import (
Any,
Literal,
)
def _mklbl(prefix: str, n: int):
return [f"{prefix}{i}" for i in range(n)]
def check_indexing_smoketest_or_raises(
obj,
method: Literal["iloc", "loc"],
key: Any,
axes: Literal[0, 1] | None = ... |
b00053f1ce80e495251bb3e3177aad405c19552f978909d7495394844ba53431 | Python | 1,021 | 31 | # code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
# with some minor adjustment
import re
from sphinx.application import Sphinx
from sphinx.ext.napoleon import NumpyDocstring
def process_return(lines):
"""Process the return section of a docstring."""
for line in lines... |
ffb32e829635683e15e0c70b96ab5b0324a81c0d347b929369d87925641d2cd7 | Python | 1,021 | 29 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.run_utils import version, seeds, default_num_frames
kuka_env = 'allegro_kuka_throw'
_frames = default_num_frames
_name = f'{kuka_env}_{version}'
_params = ParamGrid([
('seed', seeds(8)),... |
2a7fb9bb2794ad0f8c0b9d61973aff980850df13a5848721d0028b13951e0cf4 | Python | 1,022 | 42 | import re
import dependency
#read dependencies from file
#[[deps of s1], [deps of s2],...]
def readDepsFromFile(f):
fdeps = []
sDeps = []
for line in f:
# print(line)
if line != "\n":
d = dependency.Dependency()
d.read(line.strip())
#print(d.label)
... |
7a849b9986e54cc3135ec60787e8439e69ce0c24c6c87ad5a0a4f101a928fa30 | Python | 1,023 | 42 | # JN 2016-08-26
"""
Converts refscheme.mat to refscheme.csv
The format of refscheme.csv is
file_name;ref_file_name
"""
from __future__ import division, print_function, absolute_import
import csv
import os
from scipy.io import loadmat
from argparse import ArgumentParser
OUTFNAME = 'refscheme.csv'
def convert(fname_i... |
2e8081cfb4f2f26769a13acc72cf22cc4e776e1e4f9ef0c869c60bdfa1ca6b54 | Python | 1,025 | 28 | #!/usr/bin/env python
"""This script is used to merge the coverage and PIR if introns
Usage: %prog <PIR_bed> <cov_bed> <merged_bed>
"""
import pandas as pd
from sys import argv, exit
try:
PIR_bed = argv[1]
cov_bed = argv[2]
merged_bed = argv[3]
except:
exit(__doc__)
PIR = pd.re... |
4b723d03f1009c4ebf4fe1122960c6b2e212b945bf944fbe95127159ed6b4aa1 | Python | 1,025 | 38 | """
stats.py : stats module for ScanOMetrics software
"""
import numpy as np
def fdr(p, q=0.05):
"""Compute False Discovery Rate (FDR)'s parametric and non-parametric thresholds. Returns 0.0 if no sample is found
below the FDR.
:param p: vector of input p-values
:type p: numpy (N,) array
:param... |
d31f440a181b8ed78bd044bad3720463188fb68c857c9341b249f026d714db87 | Python | 1,025 | 47 | #
# File for testing the Batch Normalization layer
#
import numpy as np
import tensorflow as tf
import protein_holography.network.L_batch_norm as lbn
import protein_holography.network.spherical_batch_norm as sbn
s = [2,3,1]
L_MAX = 5
sbnl = sbn.SphericalBatchNorm(0,L_MAX)
#make spherical input
input = {}
for l i... |
5652df842575309805d5c796e207a116489deed69187d98a7cb6c07e4c181d9b | Python | 1,027 | 40 | __all__ = [
"normalize_by_max",
"normalize_by_sum",
"dot_product",
"spectral_angle",
]
import numpy as np
import torch
import torch.nn.functional as F
def normalize_by_max(x: torch.Tensor) -> torch.Tensor:
x_max = x.max()
if x_max > 0:
x = x / x_max
return x
def normalize_by_sum... |
0c361b6d9c45d7fa0e84e39e5f8772383a86da67371bb8f8e5c3c53222b2c310 | Python | 1,028 | 29 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.run_utils import version, seeds, default_num_frames
kuka_env = 'allegro_kuka_regrasp'
_frames = default_num_frames
_name = f'{kuka_env}_{version}'
_params = ParamGrid([
('seed', seeds(8)... |
04538654ff367daab0ad0892e91bdd9bf8e6f38ccd8ab4960835cd3b7094286c | Python | 1,029 | 35 | import numpy as np, sys, matplotlib.pyplot as plt
import pumpprobe as pp
head_only = "--head-only" in sys.argv
funa = pp.Funatlas(merge_bilateral=True,merge_dorsoventral=False,merge_AWC=True)
funa.load_extrasynaptic_connectome_from_file()
esconn_ma = funa.esconn_ma # Monoamines
esconn_np = funa.esconn_np # Neuropept... |
160452a7b2f75730944f13e40a69e8e0ad5ad0a85f87574c2742ad3607323d32 | Python | 1,029 | 18 | """Convert labeled datasets from other pose estimation tools into Lightning Pose projects.
Two converters, one per source format:
- :func:`lightning_pose.converters.dlc.convert` -- reads a DeepLabCut project directory
(``labeled-data/<video>/CollectedData*.{csv,h5}``) and writes a Lightning Pose project
directory... |
5a5647d096fbad3f3c77fe0afaf11a5b70b27f31a7e6912ec3b4393a80acd458 | Python | 1,029 | 34 | """empty message
Revision ID: 8450b363cf25
Revises: 35fca522d209
Create Date: 2021-10-06 09:46:34.517521
"""
from alembic import op
import sqlalchemy as sa
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision = '8450b363cf25'
down_revision = '35fca522d209'
branch_labels = No... |
ff6f48e0d3de044fa9edae14897706ef775c8cd4da21825c32cc1a14b7313482 | Python | 1,029 | 26 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.allegro_kuka_pbt_base import kuka_env, kuka_base_cli
from isaacgymenvs.pbt.experiments.run_utils import version
_pbt_num_policies = 8
_name = f'{kuka_env}_manip_{version}_pbt_{_pbt_num_policie... |
6e39976183fe4cdc8823eeb6b524e47c5366669b131b027630edf87ad83a8d2f | Python | 1,031 | 30 | from sys import path as sys_path
sys_path.append('..')
from base import loggingUtils
from base.imageMatchingLDDMM import ImageMatching, ImageMatchingParam
import matplotlib
matplotlib.use("qt5agg")
import matplotlib.pyplot as plt
import pyfftw
pyfftw.config.NUM_THREADS = -1
loggingUtils.setup_default_logging('', stdO... |
c53576708802ee6495ffcd97af8f58b128cc7e4bc63494042b87d5e35468d246 | Python | 1,031 | 24 | from datetime import datetime
import sys
sys.path.append("..")
from app import db
from sqlalchemy.dialects.postgresql import JSON
class Visit(db.Model):
__tablename__ = 'visit'
id = db.Column(db.Integer, primary_key=True)
external_id = db.Column(db.String(255))
subject_id = db.Column(db.Integer, db.F... |
c7bbb1f0177676c90a7ba689e852bdb56fbd68312a4150e7bb44f7c0d439a7f2 | Python | 1,033 | 27 | from Surfaces.surfaces import *
from Common.kernelFunctions import *
from Surfaces.surfaceMatching import *
from affineRegistration import *
def compute():
fv0 = Surface(filename='/Users/younes/Dropbox/ADNI_toyExample/test/amgy_length7_sub101.byu')
fv1 = Surface(filename='/Users/younes/Dropbox/ADNI_toyExampl... |
dff4e22fe82e84f733df957f3ad9dc2c9b815bcc35385a080cc2003da34eaf55 | Python | 1,034 | 25 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
934df0b026b9d1481f509ba90248515e17989fc600c5910fdf9fc62c862c6bcb | Python | 1,036 | 38 | """Data containers, loading and saving data."""
from mrpro.data import enums, traj_calculators, acq_filters
from mrpro.data.AcqInfo import AcqIdx, AcqInfo
from mrpro.data.CsmData import CsmData
from mrpro.data.Dataclass import Dataclass, InconsistentDeviceError
from mrpro.data.DcfData import DcfData
from mrpro.data.En... |
91a2e4a39963cefbe6c4198d6d044aa529778165421fab480c54f300637ec36d | Python | 1,037 | 31 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
bf23d70c9eb6cb0541ec87d9b46772acf1cf652a5401e913909686df0d39ee7d | Python | 1,037 | 29 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.run_utils import version, seeds, default_num_frames
kuka_env = 'allegro_kuka_reorientation'
_frames = default_num_frames
_name = f'{kuka_env}_{version}'
_wandb_activate = True
_wandb_group =... |
55b506b9a567c77581a8916d53e026909bfb85c7b2d3acf2af3d949015915d8d | Python | 1,038 | 40 | import time
import numpy as np
from StimulationProcess.BasicStimulationProcess import BasicStimulationProcess
from psychopy import visual, core, event
import math
class IdleProcess(BasicStimulationProcess):
def __init__(self) -> None:
super().__init__()
def change(self):
self.co... |
eb346d58b2fa3b2817817a7c7985be9e97fe44844eaa6ed6ab68cf8dbcfd4fca | Python | 1,039 | 39 | from setuptools import setup, find_packages
from Cython.Build import cythonize
setup(
name='dissect-deconv',
version='0.1.1',
packages=find_packages(),
install_requires=[
# 'numpy>=1.19.5',
# 'scikit-learn>=1.1.2',
# 'pandas>=1.4.3',
# 'anndata>=0.8.0',
# 'h5py>=... |
0b528b5770dd06f12d9800b18b6bc5321fb63eafdcd9c37a79fb7521d7a789cc | Python | 1,042 | 29 | #!/usr/bin/env python-real
# -*- coding: utf-8 -*-
from __future__ import print_function
import sys
from radiomics.scripts import parse_args
if __name__ == '__main__':
if sys.argv[1] == '--xml' or sys.argv[1] == '-x':
with open(__file__[:-6] + '.xml', 'r') as xmlFP: # Cut off "Script" from filename
prin... |
3d98199c406e66998c06f77de86973466e77f1c6136afbd5f02c48b3230d13d1 | Python | 1,042 | 24 | from functools import partial
import pandas as pd
import dask
import numpy as np
from single_cell_analyzer.membrane_potential_analysis import simple_spike_detection
def spike_in_interval(st, tmin, tmax):
return ((st>=tmin) & (st<tmax)).any(axis = 1)
def _helper(x, threshold = 0):
'''reads out a voltage trac... |
858d583633a6422e50f772b765444364e0fc39f391c2d1e27f7de6df9ba4fc5a | Python | 1,042 | 38 | """
Tests involving custom Index subclasses
"""
import numpy as np
import pandas as pd
import pandas._testing as tm
class CustomIndex(pd.Index):
def __new__(cls, data, name=None):
# assert that this index class cannot hold strings
if any(isinstance(val, str) for val in data):
raise T... |
d8bf55746f90383827e3d2ed8a25e19bde0dac74c4886d12ecf3902b7cf1f565 | Python | 1,043 | 27 | import os
import cv2
image = cv2.imread("figure/2-1.jpg",cv2.IMREAD_GRAYSCALE) # imput origin image data
zoomScale = 0.8
res_image = None
res_image = cv2.resize(image, dsize=None, fx=zoomScale, fy=zoomScale, interpolation=cv2.INTER_LINEAR) # resize image
blur_image = cv2.GaussianBlur(res_image,(13,13),cv2.B... |
06df4b2dcec5404932eb6389a0b2a9e3559c9d05b02d01dc01039f04279e5821 | Python | 1,045 | 29 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.run_utils import version, seeds, default_num_frames
kuka_env = 'allegro_kuka_two_arms_reorientation'
_frames = default_num_frames
_name = f'{kuka_env}_{version}'
_params = ParamGrid([
('... |
029d7c49e0f14b58cce25e4880d1faace7dd3197cece0eb28db9f51ae2809b27 | Python | 1,046 | 34 | ############################ Speed and Acceleration ############################
PIPE_VEL_X = -4
PLAYER_MAX_VEL_Y = 10 # max vel along Y, max descend speed
PLAYER_MIN_VEL_Y = -8 # min vel along Y, max ascend speed
PLAYER_ACC_Y = 1 # players downward acceleration
PLAYER_VEL_ROT = 3 # angular speed
PLAYER_FLAP_ACC... |
b3332e8b2b3f0ec9e1bdec0d20d3a7442618375a1176aa177fab0b8abe78e8c7 | Python | 1,047 | 37 | import os
from flask import Flask, jsonify, g, request
from flask_sqlalchemy import SQLAlchemy
from flask_cors import CORS, cross_origin
from flask_migrate import Migrate
from psycopg2.extensions import register_adapter, AsIs
import numpy
db = SQLAlchemy()
migrate = Migrate()
def create_app(config_name):
"""Creat... |
85bc4b43122798a57553646425630e8e8ba7d874d9b03646170cc21d9d544b88 | Python | 1,049 | 29 | from glob import glob
from os.path import basename, splitext
from setuptools import setup, find_packages
# from distutils.core import setup, find_packages
setup(
name="pgen",
version="0.2.3",
description="Generating new protein sequence by gibbs sampling masked protein language models",
author="Sean Jo... |
c16d677a964c0975351ec0d594158ba927c4f2695a5cb2fd9a39f2b305d8f025 | Python | 1,049 | 39 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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 agre... |
75df8de001a4e53139f1568b57d36d52835d7e28ddf2fb53cfcc2c045425ee19 | Python | 1,051 | 26 | import pandas as pd
import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from app import create_app, db
from app.models import FileType
from config.globals import ENVIRONMENT
import pdb
... |
03aefd242434300ce8e5a4e2c65c5f6e9dc9fc6340393aaf755c930b492571d6 | Python | 1,052 | 28 | """LLM advisory layer for the PyCaret Control Plane.
Implements the router pattern from `docs/revamp/DECISIONS.md § session 13 · 3`:
provider-agnostic from day one, with Anthropic (Claude) and OpenAI as two
first-class backends. The ``FakeLLMProvider`` backs tests so CI never hits a
real API.
Every consultation retur... |
0be2e50812a7cc712b839bd13138e60a1646d33d61f3adade0eab2fd605a8fc9 | Python | 1,052 | 29 | """qMRI signal models."""
from mrpro.operators.models.SaturationRecovery import SaturationRecovery
from mrpro.operators.models.InversionRecovery import InversionRecovery
from mrpro.operators.models.SpoiledGRE import SpoiledGRE
from mrpro.operators.models.MOLLI import MOLLI
from mrpro.operators.models.WASABI import WAS... |
2dbb3167c3826e608e13681a03de2766688d5056563cac0ba7f9765d5966006c | Python | 1,052 | 35 | """Install package."""
import re
import os
import sys
import subprocess
import traceback
from setuptools import setup, find_packages, Command
from setuptools.command.bdist_egg import bdist_egg as _bdist_egg
from setuptools.command.develop import develop as _develop
from distutils.command.build import build as _build
... |
0045dc2d3e8b005873572537872f5b910494c9df17e3d2ce43cc321b5a789f76 | Python | 1,055 | 45 |
import os
seqs = ['hifi', 'ont']
coverages = ['5x', '10x','20x', '40x']
input_path = "/mnt/d/workspace/svision-pro/paper_revision/run_time/pc_8_s5"
# input_path = "/mnt/d/workspace/svision-pro/paper_revision/run_time/cluster_24_s5"
for seq in seqs:
for coverage in coverages:
file_path = os.path.join(... |
e13b4aba3f66355dcf724b1ae88ca0a1c96f6ce0b16541bba52089c8e5d80872 | Python | 1,055 | 32 | # Copyright 2018-2024 Xanadu Quantum Technologies Inc.
# 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... |
285606b198989c44d7ac6e1bb23feca0a91401313a18cd92454e47e8acf6bbbd | Python | 1,056 | 33 | """Transforms for gradec."""
import numpy as np
from neuromaps import transforms
from nilearn import image
from gradec.utils import _rm_fslr_medial_wall, _zero_fslr_medial_wall
N_VERTICES = {
"fsLR": {
"32k": 59412,
"164k": 298261,
}
}
def _mni152_to_fslr(metamaps, fslr_density="32k", neurom... |
3a0646fe902c3a8261bccd9d7492aef0ebcec7ba2db16315685bea32e7e7de9b | Python | 1,056 | 41 | import torch
import torch.nn as nn
import torch.nn.functional as F
class CNN(nn.Module):
def __init__(self):
super(CNN, self).__init__()
self.conv1 = nn.Conv2d(3, 64, kernel_size=3, padding=1)
self.conv2 = nn.Conv2d(64, 128, kernel_size=3, padding=1)
self.conv3 = nn.Con... |
930dd2831cd7775c9c3c0e6c6eedc2e1f8cad5a4339afff9a72e4294ae6186fb | Python | 1,056 | 24 | # Copyright 2018-2021 Xanadu Quantum Technologies Inc.
# 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... |
cd41dddf228ea94fd999831b02721309ca233aa8dab9dd6cb1c391e0c8e78c30 | Python | 1,057 | 34 | from sys import path as sys_path
sys_path.append('/cis/home/kstouff4/Documents/MeshRegistration/MeshLDDMMQP/master-KMS/py-lddmm/')
sys_path.append('/cis/home/kstouff4/Documents/MeshRegistration/MeshLDDMMQP/master-KMS/py-lddmm/base')
from base.meshes import Mesh
########################################################... |
805de1600e58e5c9a1489d304ecaf0b89a8b642337f7ecd607663c25c170be1e | Python | 1,058 | 35 | # Copyright (c) 2018-present, Facebook, Inc.
# 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
def repackage_hidden(h):
"""Detaches hidden states from their history."""
if isinstance(h, torch.Tensor):... |
036ea3fb15e67cdb9ddb4a69588c86ab611a746ff41a1abcd5fb48b2aa48a3da | Python | 1,059 | 40 | import pickle
from scipy.io import savemat
import glob
import os
import time
import sys
try:
# for Python2
import Tkinter as tk
import tkFileDialog as filedialog
except ImportError:
# for Python3
import tkinter as tk
from tkinter import filedialog
def pickle2mat(filename, overwrite=False):
matname = filename.re... |
20b8bdc9860bcb75e5238b459e55a2e1a4616fc6ec8978f2d113ef02a29bb002 | Python | 1,059 | 34 | """Tests the Knoise class."""
import pytest
import torch
from mrpro.data import KNoise
def test_knoise_to_complex128(random_test_data) -> None:
"""Change dtype to complex128."""
noise = KNoise(data=random_test_data).to(dtype=torch.complex128)
assert noise.data.dtype == torch.complex128
@pytest.mark.cud... |
800eae64d2d57ed9fb1a723c0a9e598b8a9343a3762ae4dc1897d83154122951 | Python | 1,059 | 38 | # Configuration file for the Sphinx documentation builder.
from scanometrics import _version_major, _version_minor, __version__
# -- Project information
project = 'scanometrics'
copyright = '2024-2025, SCAN-Lab'
author = 'SCAN-Lab'
release = '%d.%d' % (_version_major,_version_minor)
version = __version__
# -- Gene... |
84de909246355f343669587d52a91d4862028ee4bf56359e4eafae64167138e2 | Python | 1,059 | 34 | import torch.nn as nn
#diff
class EMA(object):
def __init__(self, mu=0.999):
self.mu = mu
self.shadow = {}
def register(self, module):
for name, param in module.named_parameters():
if param.requires_grad:
self.shadow[name] = param.data.clone()
def updat... |
26fc48e0e3b75603b0ccfeca49e5607fd1b079f99c1c2a761aee73e6457cf0fa | Python | 1,061 | 29 | import sys
with open(sys.argv[2],'r') as fin:
line = fin.readline()
line = fin.readline()
if sys.argv[1] == '-b':
while line != "":
line = line.strip().split()
if int(float(line[-1])) == 1:
sa = line[-3]
sb = line[-2]
namea,alr ... |
69de5d2bd5c2470cae6d1ecf22f47c3ae6a14308cee320af648fbf1e58a0d0cf | Python | 1,061 | 32 | # Copyright 2023 Xanadu Quantum Technologies Inc.
# 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 agre... |
5f27876dbe53832e5df6fbce70b61038dbcf8b4cc1c8abe25859fd314308c99a | Python | 1,062 | 29 | from sys import path as sys_path
sys_path.append('..')
sys_path.append('../base')
from base.loggingUtils import setup_default_logging
from base.kernelFunctions import Kernel
from base import surfaceMatching
from base import surfaces as surfaces, surfaceTimeSeries as match
setup_default_logging('../Output/Temp', fileN... |
15d18e57b88c67b31176d79c014427a3546ffad0372f09bc9706d42883436812 | Python | 1,065 | 33 | #-----------------------------------------------------------------------------
# SASA Feature
#-----------------------------------------------------------------------------
import os
import sys
import fileinput
from DXGB.featureSASA import sasa
def cal_SASA(out,fn,lig,pro,datadir):
"""
Calculate SASA features
... |
801c180f470ab03f09c6192fb549accc7b7492df4d879d67ee7b658dec4c544d | Python | 1,065 | 25 | # -*- coding: utf-8 -*-
import numpy as np
from pydrake.all import MathematicalProgram, Solve
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon as matplotlib_polygon
import matplotlib
import math
from pydrake.math import sin, cos, sqrt
import pickle as pkl
from scipy.interpolate import interp2d
imp... |
24eb288bc983c58afd926ec7ed481a13857b3b6aaae957e4fe485b7f603b4f2f | Python | 1,066 | 39 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import windseer.utils as utils
import windseer.nn as nn_custom
parser = argparse.ArgumentParser(
description='Training a neural network for predicting wind data from terrain'
)
parser.add_argument('-y', '--yaml-config', required=Tru... |
dbdc5579448072b534e11dcb543490fae2875860352d33aa8c1696769cab493d | Python | 1,066 | 37 | # -*- coding: utf-8 -*-
import numpy as np
from .red_blue import RedBlueMove
__all__ = ["WalkMove"]
class WalkMove(RedBlueMove):
"""
A `Goodman & Weare (2010)
<https://msp.org/camcos/2010/5-1/p04.xhtml>`_ "walk move" with
parallelization as described in `Foreman-Mackey et al. (2013)
<https://ar... |
0562a21ffba8b53ed27fae7b767c89ab86a053ec66e1a87dc6af383443e36f26 | Python | 1,067 | 29 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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 agre... |
c6498115649bdc6b21e0c5e6bb9dc0a4789b8801f9dd9f41a1466dc4d4c324ca | Python | 1,068 | 44 | """
pandas._config is considered explicitly upstream of everything else in pandas,
should have no intra-pandas dependencies.
importing `dates` and `display` ensures that keys needed by _libs
are initialized.
"""
__all__ = [
"describe_option",
"detect_console_encoding",
"get_option",
"option_context",
... |
6a1c27a879a02941de02008cecf427d52a2487e7b60aacae7a0d099eee76ca4b | Python | 1,069 | 30 | from isaacgymenvs.pbt.launcher.run_description import ParamGrid, RunDescription, Experiment
from isaacgymenvs.pbt.experiments.run_utils import version, seeds, default_num_frames
kuka_env = 'allegro_kuka_reorientation'
_num_gpus = 8
_frames = default_num_frames * _num_gpus
_name = f'{kuka_env}_{version}_{_num_gpus}gp... |
79d483f8be7492efb07c37ec88068446fba1abe1f8f9ff879cb4ed2a6846b9f0 | Python | 1,069 | 24 | import sys, re, argparse, pandas as pd
argparser = argparse.ArgumentParser('''
Reads a space-delimited data table and outputs only user-specified columns.
''')
argparser.add_argument('-c', '--cols', dest='c', nargs='+', action='store', help='column names to output')
argparser.add_argument('-x', '--exclude', dest='x', ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.