sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1c7f54def972b624215434e77ce4ded1d945d341f9434487405edabfd2e00504 | Python | 3,190 | 93 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# 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 a... |
2fbc5f13471d146cdfe94680fb0525361607a6329a7c375b8901dca889b1702c | Python | 3,190 | 76 | #!/usr/bin/python3
"""
@author: Eduardo Romero
"""
import cgi
import cgitb
import os
import subprocess
UNZIP_DIR = "/opt/bitnami/apache2/cgi-bin/"
cgitb.enable()
print("Content-Type: text/html")
print()
form = cgi.FieldStorage()
state = str(form.getvalue("state"))
state = state.replace("@","DAB")
unzipDirectory = UN... |
0fc517d89538dd9ec0886523cc7eec78b1d9e7c5890e68c474815e2f3b61c30b | Python | 3,191 | 86 | #%%
import os
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
# %%
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import pymaid as pymaid
seg_index = pd.read_csv('da_investigation/csv/segregationinde... |
03cfdfe269ae148524fe9c5c7592ad492faea2a656786731d51aa0325bdd7d34 | Python | 3,192 | 78 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
2171f2f0c4cf66b499184a6583fb4f2aace6573419acf80d551a4228bfe6c795 | Python | 3,192 | 95 | import sys
import os
import re
from collections import OrderedDict
import confusion_matrix
def main():
path = sys.argv[1]
files = os.listdir(path)
files = [os.path.join(path,f) for f in files if f.endswith('.txt')]
res = []
for file in files:
confusion_matrix.main(file)
file_name =... |
66fcb7b27609f454fe187fb92c286ab06ff2d096dabdd843bdbbaeffbe555fc5 | Python | 3,193 | 83 | from dash import html
from dash_extensions.enrich import Output, Input, State, callback
from dash.exceptions import PreventUpdate
from RV.callbacks.utils.stats_utils import get_annotation_stats, get_bad_channel_info
def register_stats_callbacks():
@callback(
Output({'type': 'modal', 'modal': 'RV-stats'},... |
15eb6dcc40e625e67d7a7da2e75e862043876c88cefe7bcb8bd1d691997e45f9 | Python | 3,195 | 89 | '''
Figure 8.
Polar histogram of PIV angles for forward and backward swimming.
'''
from scipy.stats import circmean
from brian2 import *
from os.path import join
from fitting import *
import os
from fitting import *
from file_management import *
width, height = 2, 2
# Load PIV data
filenames = [f.path for f in os.sca... |
3de39dfa24c79e91343caeeb16036bf45e36e21d6a0096129507f550f9c5936b | Python | 3,195 | 77 | #!/usr/bin/env python3
# encoding: utf-8
# @Time : 2018/9/28 下午12:13
# @Author : yuchangqian
# @Contact : changqian_yu@163.com
# @File : init_func.py.py
import torch
import torch.nn as nn
def __init_weight(feature, conv_init, norm_layer, bn_eps, bn_momentum,
**kwargs):
for name, m in feat... |
4a0bbcd0d8b7d0636ae73190a08a131b83c50af9f26cd6732650a9d65a951a05 | Python | 3,195 | 66 | import numpy as np
import h5py
import PatchData as pd
def load_data(input_filepath):
with h5py.File(input_filepath, mode = 'r' ) as hdf5:
data_nr = np.min([len(hdf5.get(i)) for i in ["u", "v", "w"]])
print(hdf5['w'])
indexes = np.arange(data_nr)
print("Dataset: {} rows".format(len(indexes))... |
fe0602eac7d37ab319a5eef0b4a6302569a8cea887ac2587592f6e32e146f3d5 | Python | 3,196 | 83 | """
Written by Nathan Neeteson
Utilities for quantitatively comparing predicted and reference segmentations.
Loosely adapted from: https://github.com/InsightSoftwareConsortium/SimpleITK-Notebooks/blob/master/Python/34_Segmentation_Evaluation.ipynb
"""
import SimpleITK as sitk
import numpy as np
def binarize_numpy_ar... |
5fa1f8f926884a72315968ebd6a34bb3706c4446f8f11cfb5a13a2ea23f48761 | Python | 3,197 | 77 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
728f6f0ff53bbf34b39065453616985b9c6932cafb7c6a59a66edb8f9c7e53de | Python | 3,201 | 72 | import os, sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
PYCHARM_EXEC = os.getenv('PYCHARM_EXEC') == 'True'
import numpy as np
import tensorflow as tf
from tensorflow.keras.callbacks i... |
8631f3237f0ab32e198294d0e2bffafcd2bf122b15089f9840cf825b32ce543f | Python | 3,201 | 102 | import numpy as np
import torch
import torch.nn.functional as F
from timm.utils import accuracy
import M2TR.utils.checkpoint as cu
import M2TR.utils.distributed as du
import M2TR.utils.logging as logging
from M2TR.utils.build_helper import (
build_dataloader,
build_dataset,
build_loss_fun,
build_model,... |
875437863720482a28563566cfd12f57eb09971819ecba3e92d2eb917569cf9b | Python | 3,201 | 108 | '''
Simulates 100 trajectories on a torus with a central attractive stimulus.
Produces a movie and saves trajectories to file, with physiology data for 10 cells.
'''
from brian2 import *
from behavior import *
import imageio
from plotting import cell_mask, cell_indices
C = paramecium_constants()['C']
N = 100
duration ... |
f26bd5db1188650a5744b839721bbc803003fef5cb146540aa93cd758d925e2d | Python | 3,201 | 76 | from collections import defaultdict
from itertools import product
import os
import numpy as np
import pandas as pd
from sklearn.datasets import make_classification
# creates the output directory
simulation_data_dir = 'datasets'
if not os.path.exists(simulation_data_dir):
os.mkdir(simulation_data_dir)
random_seeds... |
d70e82864404fb0dedd920f4a886a645c73e8cb3f5244cddb00a63539235c54c | Python | 3,202 | 61 | #!/usr/bin/env python
#################################################
## PTDNN - Python Toolkit for Deep Neural Network
## Author: Yajie Miao
#################################################
import os
import sys
from utils.learn_rates import LearningRateExpDecay
class BnfExpConfig(object):
def __init__(self... |
03132384d6ba42405459089e2b4b60b7794d368f298460921ddcdcd838d0881b | Python | 3,204 | 79 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
4d963dd99aa346f9ca02152da1cd0eb1cfe770109bbc99b54f96f5be120bd7bb | Python | 3,205 | 91 | #!/usr/bin/env python3
#
# Copyright (c) 2018-2019 Institute for Basic Science
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... |
99a5ec928df29d9e7de807e9ec30a624951c1be6d90edabda734005f1462503e | Python | 3,205 | 93 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 19 18:07:49 2018
@author: asanofuyuki
.png
Normalized_by_each_mouse_max/ 1 min bin
出来上がったデータを.xlsで再保存して、doubleplotを描く。
データは9:00(ZT0)スタート、9:00(ZT0)終了でエクスポートすること。 (最終日の8:59までのデータがある。)
"""
import glob
import numpy as np
import pandas as pd
import ma... |
a7146799ba680aeefc08bc36ef000aa08855e8466fc51e3542726de2314d3d99 | Python | 3,205 | 105 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Dict, List, Tuple
import numpy as np
from tmkit.util.Reader import Reader as tmkreader
class Mapping:
def tofas(
... |
0b36021719d9dd3623985f434825ba4849f90a0437b716e7aee97a16d5e2f054 | Python | 3,206 | 111 | from future import standard_library
standard_library.install_aliases()
# Unit tests for sima/motion/_hmm.py
# Tests follow conventions for NumPy/SciPy avialble at
# https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
# use assert_() and related functions over the built in assert to ensure tests
# run properly... |
2b2b41d1834b186839ef2da201da4ba2339f613c98f37bbbd7e5ec489b1acf9f | Python | 3,206 | 87 | import GPUtil
import glob
import os
from utils import prepare_result_dir
import config
from time import sleep
import sys
import run_ZSSR_single_input
"""
Code based on ZSSR provided by Assaf Shocher
https://github.com/assafshocher/ZSSR
"""
def main(conf_name, gpu, config_dir):
# Initialize configs and prepare re... |
6d61ab2e7a857e749f30cf42904dae0280890a1ab5b4cbcae77e8693fba90efd | Python | 3,206 | 106 | import torch
import torch.nn as nn
import torch.nn.functional as F
from slideflow.clam.utils import initialize_weights
import numpy as np
class MIL_fc(nn.Module):
def __init__(self, gate = True, size_arg = "small", dropout = False, n_classes = 2, top_k=1):
super(MIL_fc, self).__init__()
assert n_classes == 2
... |
a62dcfe82555ae4e39b2001b8d9c54a71b84842004d9b58685d975835bba810a | Python | 3,206 | 79 | __author__ = 'jieqing jiao'
__contact__ = 'jieqing.jiao@gmail.com'
import os
import nibabel as nib
import numpy as np
from niftypad import basis
from niftypad.image_process.parametric_image import image_to_parametric
from niftypad.models import get_model_inputs
from niftypad.tac import Ref
# dt
dt = np.array([[
... |
2a4aee66310bfb3d7efdf27b79c215fdb2b10f7c15f532fcd39f6f7789ee9da9 | Python | 3,210 | 104 | import os
import sys
import time
import subprocess
LOG_FILE = "validation.log"
ONLY_ANALYSIS = False
NESTED_CROSS_VALIDATION = False
'''
Instances and seeds used for the article 'Binary Classification On Hypergraphs'
'''
INSTANCES = [
#('adult', 1509029032), # 0.8206451 1506844911), # 0.8217306
#('audiology'... |
3489d97f97181531ae1fbd41b42cc27e588c87e27ebb844e9a94d18a01eb74b7 | Python | 3,210 | 99 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
d70627e7eccd32211c325d96594a9d26f2e5a1e07dadc706de0ae4e6173a1b9e | Python | 3,210 | 96 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 19 18:07:49 2018
@author: asanofuyuki
.tiff
Normalized_by_each_mouse_max/ 1 min bin
出来上がったデータを.xlsで再保存して、doubleplotを描く。
データは9:00(ZT0)スタート、9:00(ZT0)終了でエクスポートすること。 (最終日の8:59までのデータがある。)
"""
import glob
import numpy as np
import pandas as pd
import ... |
9f0e7b7dda8e564f2f3b7a054184bafbb0d4763b2957334406ce08552f9d393e | Python | 3,211 | 87 | import GPUtil
import glob
import os
from src.utils import prepare_result_dir
import config
from time import sleep
import sys
import run_ZSSR_single_input
"""
Code based on ZSSR provided by Assaf Shocher
https://github.com/assafshocher/ZSSR
"""
def main(conf_name, gpu, config_dir):
# Initialize configs and prepa... |
7d0ae5c412d4ebf15f3614d3a069abbb0cce7a802815ffe03c0645e89b3d883a | Python | 3,213 | 100 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 16 08:44:29 2021.
@author: spiros
"""
import numpy as np
from scipy import signal
from scipy.ndimage import gaussian_filter1d
def synaptic_metrics(voltage, time, onset=700):
"""
.
Parameters
----------
voltage : np.ndarray
... |
62f0ebd92db96d67d42be9f32555b030ccb8e7713a0eeed18d2410e4485f092f | Python | 3,214 | 98 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import unittest
import copy
import torch
# import modules to to register predictors
from maskrcnn_benchmark.modeling.backbone import build_backbone # NoQA
from maskrcnn_benchmark.modeling.roi_heads.roi_heads import build_roi_heads # NoQA
from mask... |
6e1f1d07479ce42ea0b1867880c9cff426f5181f59b9bbe05629a3cff6fe7a7f | Python | 3,214 | 96 | """
Parse PubMed efetch XML into plain records.
Replaces the PubmedArticle facade previously provided by the unmaintained ``eutils`` package.
"""
import logging
import re
from dataclasses import dataclass, field
from typing import List, Optional
from xml.etree.ElementTree import Element # noqa S405
__all__ = [
... |
36b88429ffece9992acd546921b13c9b9fa0ec4fa0bac8b29f86549188a9ef44 | Python | 3,216 | 89 | # import threading
import torch
import torch.multiprocessing as mp
from torch.cuda._utils import _get_device_index
def get_a_var(obj):
if isinstance(obj, torch.Tensor):
return obj
if isinstance(obj, list) or isinstance(obj, tuple):
for result in map(get_a_var, obj):
if isinstance(... |
514a774e0633c5b09fe4bb8711ec81dca7943712df8693a04a443e8a6cbc1f3c | Python | 3,216 | 50 | import pandas as pd
import numpy as np
import argparse
import sys
from cmseq import __version__
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from .cmseq import CMSEQ_DEFAULTS
from .cmseq import BamFile
def consensus_from_file():
parser = argparse.ArgumentParser(description="outp... |
a25191de94f666036d61517b532bad710b229f286b0ebb72cd5b6aa033c6d1a6 | Python | 3,219 | 79 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
cafc4b1e9538f3670301d8e8853cb4e59cbf2a20d78714236da73582a60c4979 | Python | 3,219 | 100 | #import jax
#jax.config.update('jax_platform_name', 'cpu')
import corticostriatal as cs
import time
import sys
from jax import vmap
from jax import numpy as jnp
from jax.ops import index,index_update
from jax.random import split,PRNGKey,uniform
from functools import partial
import numpy as np
arg_dict = {
'learn':... |
5a847e68bef8e2f99751fe47896ac124121d523c0d852e2e164431dd71f89b1f | Python | 3,220 | 87 | #!/usr/bin/env python3
# Copyright 2020 Prisyach Tatyana (STC-innovations Ltd)
# Apache 2.0.
import json
import argparse
import sys
import re
def get_args():
parser = argparse.ArgumentParser(
"""This script creates chime6.json from ts-vad segments for dev and eval in the format required by pb_chime5
... |
98cb6052da9c944c36dae59e3161f4829ff14ada900b73c5a4e719e1b40a896f | Python | 3,220 | 72 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
247b97ade013b8d4ffea90ddfd243780bf075ed350dcefd5c6cc43e5b72a5699 | Python | 3,222 | 95 | '''
Search for fixed points in vicinity of a plane wave.
args: k1, k2 - wave numbers
===Optimization method discussion===
Use now - `lm` with non-zero starting phase; If it fails - switch to other methods
`hybr` - NOT OK: strange jump and breaks my solve_cycle
'lm' - OK if start with non-zero mean phase
'broyden1' ... |
3a66ccef02138eb81862fc8a2bd13a6dc33562eb981cc9f9f9eef7204171dee5 | Python | 3,222 | 83 | from mmcv.cnn.bricks import build_plugin_layer
from mmdet.core import force_fp32
from mmdet.models.builder import ROI_EXTRACTORS
from .base_roi_extractor import BaseRoIExtractor
@ROI_EXTRACTORS.register_module()
class GenericRoIExtractor(BaseRoIExtractor):
"""Extract RoI features from all level feature maps leve... |
8206be2e51f3b103dde6eb6925dd5a5dc3ed8d100f0c4e0cf1794850d9aa0492 | Python | 3,222 | 101 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 16 08:44:29 2021.
@author: spiros
"""
import numpy as np
from scipy import signal
from scipy.ndimage import gaussian_filter1d
def synaptic_metrics(voltage, time, onset=700):
"""
.
Parameters
----------
voltage : np.ndarray
... |
de1313afa093cdedf159ab8b97bad573d96b7ba15ac2a30b2481f543e4510f8e | Python | 3,222 | 84 | import logging
from abc import ABC
from typing import Any, Dict
from linkml_runtime.dumpers import json_dumper
from oaklib.converters.obo_graph_to_cx_converter import OboGraphToCXConverter
from oaklib.converters.obo_graph_to_fhir_converter import OboGraphToFHIRConverter
from oaklib.converters.obo_graph_to_obo_format_... |
f64d9538edca06044c1650e36274f54a33fef4fcb4fa6fe9b550f5b1acf95b22 | Python | 3,226 | 102 | """
Kuramoto-type model.
v1 supports
- Sinusoidal coupling
- Cosine + sine coupling
- Define an arbitrary coupling function
- NOT accelerated with numba
"""
import numpy as np
import math
def define_sine_coupling(sin_str):
'''
:sin_str: coefficient in front of sine, units of [rad/s]
In case of t... |
1e7efb427ca541509af00a664d088cbc8ecef573c9d74e84bd4c248dc55cdda7 | Python | 3,227 | 88 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
6a9af5a1e7575f164b0134449d3a1745ceee45b0c89f83ba4f6bfed8e7dcc879 | Python | 3,227 | 92 | from rdkit import Chem
from drugex.logs import logger
from drugex.molecules.converters.interfaces import MolConverter
class dummyMolsFromFragments(MolConverter):
"""
A converter to create dummy molecules from fragments.
"""
@staticmethod
def addCCToFragments(frag):
"""
Add CC to ... |
9260c83f6b440fcdaabe30e4eacc07e2bd832e950e214d9e9f3c6d6c95f74144 | Python | 3,228 | 86 | from app_scripts import *
from scipy.optimize import curve_fit
import streamlit as st
import numpy as np
import pandas as pd
## Page setup
st.set_option('deprecation.showfileUploaderEncoding', False)
st.sidebar.subheader('Data:')
st.sidebar.markdown("Drag and drop HEKA .asc export files. Keep table display at 'None' w... |
2bd798abc6df0aae4a13757c30406e018805bc6b194bfc583585197d4ae627c3 | Python | 3,229 | 107 | '''
Figure 7.
Zoom on action potential.
Ionic current in the example, based on passive subtraction.
Estimation of calcium accumulation.
'''
from brian2 import *
from brian2.units.constants import faraday_constant as F
import yaml
from file_management import *
from pylab import *
import matplotlib.font_manager as fm
imp... |
c67b73b98fbb3ac8f3b13cfb24cb0e9730c36c54bf5fc9567440836bf2c3a7a4 | Python | 3,230 | 91 | import torch.nn as nn
from mmcv.cnn import ConvModule, constant_init, xavier_init
from mmdet.core import auto_fp16
from mmdet.models.builder import HEADS
from .fcn_mask_head import FCNMaskHead
@HEADS.register_module()
class CoarseMaskHead(FCNMaskHead):
"""Coarse mask head used in PointRend.
Compared with st... |
6b45ac429aa3001cdade2d55425abbc86820f3fe04af69bb081c8ebbee254952 | Python | 3,232 | 110 | #!/usr/bin/env python
# Read a MatchAnnot output file, output entries for selected gene9s)
# only. Optionally reverse the order of exon match lines.
import os
import sys
import optparse
import re
from tt_log import logger
VERSION = '20150331.01'
REGEX_EXONS = re.compile ('(\s*\S+)')
def main ():
logger.debug... |
87087f71a4f629bb113f15298090e131233adbbad21b677b834d4d407283f2f0 | Python | 3,234 | 160 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
1d33987190788c4bf94be5ec09dc25833d83a0909f9f258c5f9a9298f78a5b2a | Python | 3,235 | 102 | import argparse
import pandas
import os
import numpy as np
import matplotlib.pyplot as plt
import functools
from collections import Counter
import math
import random
def accuracy(decision_vector):
ok = len([s[2] for s in decision_vector if confusion_matrix_label(s) in ['TP', 'TN']])
return float(ok) / len(dec... |
f5d97bafca2457aa1717cc29348ea0164488efb0c0017dab7e52b4216d4311aa | Python | 3,236 | 106 |
import time
import cv2
import numpy as np
from PIL import Image
from yolo import YOLO
if __name__ == "__main__":
yolo = YOLO()
mode = "predict"
video_path = 0
video_save_path = "video_out/"
video_fps = 25.0
test_interval = 100
dir_origin_path = "img/"
dir_save_path ... |
4eef10ed614286f72eb06a84c17d9e4c2d6143cfc89bd441b34fec82784732f5 | Python | 3,237 | 113 | import numpy as np
from scipy.stats import chi2_contingency, fisher_exact, boschloo_exact
from statsmodels.stats.contingency_tables import mcnemar
from statsmodels.stats.proportion import test_proportions_2indep
from .fisher_exact_nonunity import fisher_exact_nonunity
def binom_2samp(x1, n1, x2, n2, null_ratio=1.0, ... |
672e3567b6f19ba06983d48e8008676a2d798753377be7d35a5774980f694f97 | Python | 3,238 | 91 | #!/usr/bin/env python3
"""Unit tests for pcd_io: write a binary PCD, read it back with the tiny
parser, and check voxel downsampling. Runs with plain python (numpy only):
python3 PythonAPI/examples/av_stacks/autoware/map_tools/tests/test_pcd_io.py
"""
import os
import sys
import tempfile
import numpy as np
sys.... |
4cdae2bcc23043c527c0351e94e38701651683d74af7d5de781aa43951775e53 | Python | 3,239 | 93 | import sys
sys.path.insert(0, '.')
import argparse
import torch
import os
from utils.simplesum import simplesum
from utils.complexsum import complexsum
from utils.valsum import valsum
from utils.runtime import runtime
###### add your model ######
from models import MiniSeg_K2 as net
#from models import UNet as net
#fr... |
6d202a560c30ea85f8e100e93ac71bbced2084bff4dcbc33326a74bd4a4ba716 | Python | 3,239 | 70 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
bdcdf00ed10bb085b6ad8268fa71d3bc06be488d80eb5b9c2d0aa50d4fd4bc89 | Python | 3,239 | 83 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
4693c83f4948a912eaf25b766123e825f5b40bb367f4f686a7b37914ca1a5495 | Python | 3,240 | 83 | import os
import sys
from datetime import datetime
from scipy import spatial
import math
import textwrap
def tprint(str):
print('[{0}] {1}'.format(datetime.now().strftime('%d.%m|%H:%M:%S'), str))
sys.stdout.flush()
return
def cosine_similarity(u, v):
cosine_distance = spatial.distance.cosine(u, v)
... |
6b97856be009f5ecf1a0b344e7930c93b6d0d4f19cc457507749ea3aea7eaf7b | Python | 3,240 | 99 | '''
Check mesh constraints
'''
import unittest
import numpy.testing as nptest
import numpy as np
import scipy.linalg as lin
import mesh
from angle_area import is_angle_satisfied, is_area_satisfied
rtol = 10 ** - 8
atol = 10 ** - 8
class TestCircleRefinement(unittest.TestCase):
def test_mesh(self):
cen... |
08eb1da3af86445808385038603628a0e1c2466acd7237f7b6871d345553789b | Python | 3,241 | 101 | import logging
from abc import ABC
from dataclasses import dataclass
from typing import Iterator, List
from oaklib.datamodels.obograph import Graph
from oaklib.interfaces import OboGraphInterface
from oaklib.interfaces.basic_ontology_interface import (
RELATIONSHIP,
BasicOntologyInterface,
)
from oaklib.types ... |
ad21e4964d514d828deea7ff8868dc812f9daba2a3d65c3697f7db016545c237 | Python | 3,241 | 102 | import matplotlib as mpl; mpl.use('Agg')
from matplotlib import pyplot as plt
import numpy as np
import pandas as pd
import sys
#gp0_devalue_sim11_.npy
def evidence(h,q,ylast):
n = ( (1-h) * np.exp(ylast) + h )
d = ( h * np.exp(ylast) + (1-h) )
y = np.log( q ) + np.log( n / d )
return y
def get_ctx( ... |
83fe3b24d885d7c0bc12e2e2af56b52d281ccfb91654e6294ccf307e32486738 | Python | 3,242 | 108 | #!/usr/bin/env python3
class BoxerDataSource:
"""
This will use the normal indexed data source with a backing volume
"""
def __init__(self, image, labels, input_shape):
"""
Args:
image: an image with channels (n, c, z, y, x) n & z can be
swapp... |
b359e8f9fb281f94130080b8a47a308c589f2ea995639e8c467738fff8d562b0 | Python | 3,242 | 82 | from typing import Dict
import argparse
import logging
import os
from allennlp import __version__
from allennlp.commands.configure import Configure
from allennlp.commands.elmo import Elmo
from allennlp.commands.evaluate import Evaluate
from allennlp.commands.fine_tune import FineTune
from allennlp.commands.make_vocab ... |
405c524740bccdb12730a1019e49bd81e21e5dbf0132991dd1708e64e37ca7d5 | Python | 3,244 | 107 | # Copyright 2021 Google Research. 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 applicable law... |
58ba211b1dc8a5fd42e727ad12e6f23f15fb2f909937eec4fb0961ea6589d407 | Python | 3,245 | 99 | import logging
import unittest
from linkml_runtime.dumpers import yaml_dumper
from oaklib.datamodels.search import SearchConfiguration
from oaklib.datamodels.vocabulary import IS_A, PART_OF
from oaklib.implementations.wikidata.wikidata_implementation import (
WikidataImplementation,
)
WD_PECTORAL_FIN_MORPHOGENES... |
0d157e17501bb02ca7ce76b01f9800736a0d4ba7fdc2d803c54fffc32e65cbff | Python | 3,248 | 93 | ####################################################################################################
# Copyright (c) 2019 - 2023, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
7d64f2b4eee1365a5b08f004003d0741b4be2089261c66c3db7003a73841698f | Python | 3,248 | 130 | """Example script for running DyNeMo on simulated HMM-MVN data.
This script should take less than a couple minutes to run and
achieve a dice coefficient of ~0.99.
"""
import os
import pickle
import numpy as np
from osl_dynamics.simulation import HMM_MVN
from osl_dynamics.data import Data
from osl_dynamics.models.dyn... |
ab4e7e51a6313e54bb3f218e19dd4e313b95c263eca11a6c90a0d549de51882e | Python | 3,248 | 113 | from __future__ import print_function
# --------------------------------------------------------
# Faster R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick and Sean Bell
# --------------------------------------------------------
import numpy as n... |
c0deb0dedd166c7d73cbd67f1e599d9b1b4bc9c66ad37d56a8973923068197d6 | Python | 3,252 | 113 | """
Assembling data associating mitochondria to skeleton nodes
"""
import sys
sys.path.append('.')
import numpy as np
import pandas as pd
from scipy.sparse import csgraph
import h5py
from lib import skel, compartment, u
def main(mito_filename, id_filename, output_filename,
refine=False, no_diam=False):
... |
46eaef05a2c608d87bbbf0e3ab491639f4149d63f0a80aeb9010e616f447ab62 | Python | 3,253 | 97 | import torch
from ..codano import CODANO
import pytest
@pytest.mark.parametrize("hidden_variable_codimension", [1, 2])
@pytest.mark.parametrize("lifting_channels", [2, None])
@pytest.mark.parametrize("use_positional_encoding", [True, False])
@pytest.mark.parametrize("n_variables", [3, 4])
@pytest.mark.parametrize("po... |
4d4c1b34ef70f1fa8faf7a30abfb4b0f97c3613d4249b605fc0f3b04e24a11aa | Python | 3,253 | 77 | """
Localization - Analysis By Ferret
Flattens data across vowel identity
Input
-----
Data comes from the analysis directory; i.e. some preprocessing has already been done to remove correction trials and equate sound durations (F1311)
We also define the variables that we want to:
- Maintain (and thus plot) - e.g... |
effcae519d54ab658d76aaaeb7750bdd27b8500b72963cb9c230ec024ec9587b | Python | 3,253 | 103 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""
Reuires https://github.com/maenu/scholar.py
"""
from argparse import ArgumentParser
from pathlib import Path
from string import ascii_lowercase
import re
from pybtex.database import BibliographyData, parse_bytes, parse_file
from scholar.scholar import Schola... |
4febc99e7d829be05c4f1135cf9f4d6ee93955282b5419d6e25e7c216e60cb3d | Python | 3,256 | 78 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Script to generate the synthetic dataset for the training.
See synthetic_generation.ipynb for more details.
Created on Thu Nov 22 10:01:56 2018
@author: nicolas
"""
import os, sys, time
import warnings
import numpy as np
from skimage import io
# Add parent folder ... |
5668c3e24f642b9224b3c6c0b97f2c06b4f5820497c634c3f084f660eca56298 | Python | 3,256 | 84 | import os, sys
currentdir = os.path.dirname(os.path.realpath(__file__))
parentdir = os.path.dirname(currentdir)
sys.path.append(parentdir) # PYTHON > 3.3 does not allow relative referencing
import argparse
from configparser import ConfigParser
from datetime import datetime
import ddmr.utils.constants as C
TRAIN_DAT... |
1fbd50cb03da1bac1ca6788090fc9acf595dcb01544ed1758f4940678e9a9cf8 | Python | 3,260 | 100 | import os
import shutil
import zipfile
import numpy as np
import pytest
from backend.pipeline import PipelineManager
from backend import root_tracking
from backend import tracking_matcher
from backend.settings import Settings
from base.backend.app import get_cache_path, setup_cache
import torch
@pytest.fixture(scop... |
25ab9562bffbd50ba881fec27150743971f02954dfe1e693d4b7d4d93b07c0b5 | Python | 3,260 | 113 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from os.path import join
import mne
from numpy.testing import assert_array_equal
from eelbrain import gui, load, set_log_level
from eelbrain.testing import TempDir, gui_test
from eelbrain._wxgui.select_epochs import Document, Model
@gui_test
def test_select_e... |
ad7d4ce5a74edb101ffded8e1028f697fef5270f2f37f3ce909b20321afd7e9c | Python | 3,260 | 89 | #
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under t... |
65fcdd519fdff47f493d660fbc8458cb882032afd959eed67ee53bc0fd19f75f | Python | 3,261 | 136 | # %% [markdown]
# ##
from src.hierarchy import signal_flow
from src.data import load_metagraph
from src.visualization import matrixplot
from src.visualization import CLASS_COLOR_DICT
from src.io import savefig
import os
from src.graph import preprocess
import numpy as np
import pandas as pd
import matplotlib.pyplot as... |
252236cfd51db8ed71de48f953c8c41b4bc1ebecdb56e3f4f60198e5199afc2b | Python | 3,262 | 102 | """
This module provides the DNaseFileSampler class.
"""
import numpy as np
from selene_sdk.samplers.file_samplers import FileSampler
from selene_sdk.samplers.samples_batch import SamplesBatch
from tqdm import trange
class DNaseFileSampler(FileSampler):
"""
A sampler for which the dataset is loaded directly f... |
30b835fd1e12fe99c4686be99b214e0d279cbb359783a62b62abaeefff626a79 | Python | 3,262 | 92 | #!/usr/bin/env python3
# Copyright 2017 Johns Hopkins University (Shinji Watanabe)
# Apache 2.0 (http://www.apache.org/licenses/LICENSE-2.0)
import json
import argparse
import logging
import sys
def hms_to_seconds(hms):
hour = hms.split(':')[0]
minute = hms.split(':')[1]
second = hms.split(':')[2].spl... |
e081af285d5a3e1455a60aa83e3fe251f352cfd97cd212dd8069208cbcdd7005 | Python | 3,262 | 92 | import logging
from abc import ABC
from dataclasses import dataclass, field
from typing import List, Optional
from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface
from oaklib.utilities.basic_utils import pairs_as_dict, triples_as_dict
from oaklib.utilities.iterator_utils import chunk
from oakl... |
0ad9b1bbeb441bbf806721e6e052a1947489357f09ae96a18eeb5cd28abaad71 | Python | 3,263 | 89 | """Mock worker: returns the input RGB (or a control) after a delay, with progress.
Serves any backend id it is told to. Useful for API development, the test
suite and ``scripts/smoke_test.sh`` on machines without GPUs. Behaviour knobs:
``--delay`` seconds per job (default 3), ``--steps`` progress events, ``--fail``
... |
8b9c013c347abce9a069d83d243d76459d213f3cbb71f963330e702826903920 | Python | 3,263 | 79 | # basic imports
import os
import pickle
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection
def generate_polygons_replay(replay: list, dims: tuple) -> np.ndarray:
P = []
for e, exp in enumerate(replay):
a = exp['a... |
f7e61212873d6b040dc59c31131a4da50417e7d1392ea7783d9f36e12e101556 | Python | 3,266 | 90 | '''
Fig. 8
Anterior vs. posterior reversal time.
'''
from brian2 import *
import yaml
from file_management import *
from pylab import *
import matplotlib.font_manager as fm
import os
from os.path import join
from fitting import *
from plotting import *
from scipy.stats import circmean, linregress
from scipy.stats impor... |
0278c1437f2272b49c5b3522dfafbf9d0d737dd17d5a904614707021b750f3bd | Python | 3,267 | 64 | import torch
import torch.nn as nn
class ViscosityNet(nn.Module):
def __init__(self, num_channels=2):
super(ViscosityNet, self).__init__()
nfilt = num_channels
ks = 3
dilation = 1
if num_channels == 2:
self.convnet = nn.Sequential(nn.Conv3d(num_channels, nfilt,... |
9668f0371ceabb869baa4d8ff8de947a87bf605263160213203ae38eea2e8dda | Python | 3,267 | 111 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Simulate EEG data"""
import numpy as np
import scipy.signal
import scipy.spatial
from .._data_obj import Dataset, Factor, Var, NDVar, Sensor, UTS
from .._ndvar import gaussian, powerlaw_noise
from .. import _info
def _topo(sensor, center, falloff=1):
i ... |
05867ffca9c82d04cb73632b66a8f87e61c66278a50f48d1466d1324f401e451 | Python | 3,268 | 111 | # This script is part of navis (http://www.github.com/schlegelp/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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... |
140c4b2d2a0d7f9ba65ca7f0daf666aaef589c5d617d264074bf4d1e84322976 | Python | 3,268 | 96 | """Decoders Matter for Semantic Segmentation"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from models.baselines.segbase import SegBaseModel
__all__ = ['DUNet']
# The model may be wrong because lots of details missing in paper.
class DUNet(SegBaseModel):
def __init__(self, classes=2, aux... |
2338c80dfbdea91cb27f0919dadf81db0b755c8fb6f3b90b7850ab34427f00cc | Python | 3,269 | 76 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
from .box_head.box_head import build_roi_box_head
from .mask_head.mask_head import build_roi_mask_head
from .keypoint_head.keypoint_head import build_roi_keypoint_head
class CombinedROIHeads(torch.nn.ModuleDict):
"""
Combine... |
4da52f49d49d9c0d7e1bf2524102a1ecf2b51c3ba7d58066c00ebcf7dfa44f58 | Python | 3,269 | 87 | """
Copyright Dejan Kostyszyn 2019
This method computes the standard deviation and mean of the
complete dataset. This is then used for normalizing the data
for preprocessing.
mean = x.sum() / N, where N = x.size
std = sqrt(mean(|x - x.mean()|**2))
"""
import ReadData as rd
import numpy as np
import torch, nrrd, time... |
e5cd9ffb2346a6291ff99ac60acfe723aa85288468c6ecdfb9932190b2a68b41 | Python | 3,269 | 99 | import torch.nn as nn
import torch
import numpy as np
def compute_flops(module, inp, out):
if isinstance(module, nn.Conv2d):
return compute_Conv2d_flops(module, inp, out), 'Conv2d'
elif isinstance(module, nn.BatchNorm2d):
return compute_BatchNorm2d_flops(module, inp, out), 'BatchNorm2d'
el... |
f0d38699590b4ceaeeca8a860a4f26a4ef106a6a2a7dcb41bdf63da9596647fd | Python | 3,269 | 96 | import preprocess as ppc
import epoch as epo
import cleaning as cln
import evoked as erp
import stats as st
import plotting as pl
import mne
import sys
import datetime
import os
import fnmatch
########### Setup for logging ################
protocol = 'WORDS'
if protocol == 'WORDS':
import config_W... |
02f5399df8fb7eb599140a7af97a115e048c135c1c7d7bd835e1679b8864a158 | Python | 3,270 | 92 | from h5functions import save_to_h5
import re
class DicomData:
def __init__(self):
self.sequenceNames = []
self.spacing = []
self._phaseImages = []
self._magImages = []
# vel and mag Components
self.u = None
self.v = None
self.w = None
self.... |
874928c8181cab0a345162f722e75b17a8709c606dd75f1d152d197fc7ce2f90 | Python | 3,270 | 87 | # Copyright 2020-2022 Huawei Technologies Co., Ltd
#
# 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... |
aaa7af7ad6f1762c7927e2e5181fada4e092b99e19871c18c8c72391c271754e | Python | 3,270 | 98 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
e0ced79e011c18799e99379314873ac68f72667f5cd03d2fbc68482fb4b59e7e | Python | 3,270 | 68 | import json
from typing import Tuple
from overrides import overrides
from allennlp.common.util import JsonDict
from allennlp.data import Instance
from allennlp.service.predictors.predictor import Predictor
from scicite.data import Citation, read_s2_jsonline
from scicite.helper import JsonFloatEncoder
from scicite.co... |
bef96479efd35e1194577d395112f56fb8aee8ca5860c3416460862672a0e95c | Python | 3,271 | 101 | import numpy as np
import torch
class Normalizer(object):
"""Normalize a Tensor and restore it later. """
def __init__(self, tensor):
"""tensor is taken as a sample to calculate the mean and std"""
self.mean = torch.mean(tensor)
self.std = torch.std(tensor)
def norm(self, tensor):... |
5e75ebf95b9b73c6fd6f1d40b95619cf52a75d3fe72a58ab41448ece9458a10b | Python | 3,273 | 91 | import numpy as np
from mip.mip_nn import MIP_NN
from globals import BIN, CONT, TARGET_ERROR, MARGIN, EPSILON
class SAT_MARGIN(MIP_NN):
def __init__(self, data, architecture, bound, reg, fair):
MIP_NN.__init__(self, data, architecture, bound, reg, fair)
# Cutoff set so as not too optimize fully.
self.c... |
1715ffeaf6e05fe4b16f6feef0c69214265b4d868e9d3d9c7a3926e29f2bfad1 | Python | 3,274 | 109 | """
This module provides functionality for streaming data from iniVation
USB DVS cameras into GeNN models using libcaer on Linux and Mac.
To use this functionality, please install libcaer using the instructions
at https://gitlab.com/inivation/dv/libcaer to install libcaer
before installing GeNN.
Instantiation... |
4c4e2b6f2c167ff5073664ed5e8c3d91b669f7dd79678dd597d412dc51cae68f | Python | 3,274 | 80 | import torch.nn as nn
import torch
import torch.nn.functional as F
class ASPP_Sep(nn.Module):
def __init__(self, dim_in, dim_out, BatchNorm=None, rate=1):
super(ASPP_Sep, self).__init__()
self.branch1 = nn.Sequential(
nn.Conv2d(dim_in, dim_out, 1, 1, padding=0, dilat... |
ba31a941a8a94fd31386e75f4f4e3a94b06c6a13c91c867cf1902a279ffefb91 | Python | 3,275 | 122 | """ from https://github.com/keithito/tacotron """
'''
Cleaners are transformations that run over the input text at both training and eval time.
Cleaners can be selected by passing a comma-delimited list of cleaner names as the "cleaners"
hyperparameter. Some cleaners are English-specific. You'll typically want to use... |
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