sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3cd5d02c7635e8ac48e0232194530d0829022852a0caaab79008590c29533bfd | Python | 4,797 | 125 | # basic imports
import os
import gc
import pickle
import numpy as np
import pyqtgraph as qg
# framework imports
from cobel.agents.sfma import SFMAAgent
from cobel.interfaces.gridworld import InterfaceGridworld
from cobel.misc.gridworld_tools import make_empty_field
# store experiment directory
cwd = os.getcwd()
# shal... |
d8d63e48733ee5f1cf2387483d14b8a1b97767df43b2755c5effbf8e7a4ebca7 | Python | 4,798 | 123 | # merge psi (percent spliced-in) tables together
import glob
import argparse
import os
parser = argparse.ArgumentParser(description='Merge rMATs files.')
parser.add_argument('psi_base_dir', help='Base dir which contains all subdirectories from which files need to be merged')
parser.add_argument('output_directory', he... |
7c68886a93e46fe493cf5586e7830a9f7a70adddf437c93604023d4bb5f1f84f | Python | 4,800 | 152 | # Scaling module is adapted from here
# https://github.com/ahendriksen/msd_pytorch/blob/master/msd_pytorch/msd_model.py
import numpy as np
import torch
import torch.nn as nn
from torchvision import models
def scaling_module(num_channels):
c = nn.Conv2d(num_channels, num_channels, 1)
c.bias.requires_grad = Fal... |
202f6d0933eaa23291e4cc3f802694ec541cd2fb3b7d1c2b96172452a1bdfee7 | Python | 4,801 | 125 | """
Handles computing and outputting the difference scores
"""
from .handler import PredictionsHandler
class DiffScoreHandler(PredictionsHandler):
"""
The "diff score" is the difference between `alt` and `ref`
predictions (`alt - ref`).
Parameters
----------
features : list(str)
List ... |
62e0e766ccbdbf44c4b4735ec6c90dcd4d15c79be22e8b93d7c8df430037370a | Python | 4,801 | 181 | #%%
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from scipy.ndimage import gaussian_filter1d
from src.data import load_maggot_graph, load_palette
from src.io import savefig
from src.visualization import adjplot, set_theme
from src.visualization import HUE_KEY, ORDER_KEY
set_theme(font_scale... |
fbcf4ffacf0e16ee6566bd1c93a17562175f0048105de6ae6635eb2bdf2856d4 | Python | 4,802 | 136 | from __future__ import print_function
# --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick
# --------------------------------------------------------
import os
from os.path import joi... |
d9b9b9cf36d24da81572e6b68d91e5df2f92ce3ddede696f0dc6d9e8d1eb3997 | Python | 4,804 | 139 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import logging
import os
import torch
from maskrcnn_benchmark.utils.model_serialization import load_state_dict
from maskrcnn_benchmark.utils.c2_model_loading import load_c2_format
from maskrcnn_benchmark.utils.imports import import_file
from mask... |
988bae02cdc38db6f36211314097605d01929b94ed996d05cc30066bbe7a42f1 | Python | 4,805 | 151 | """
DyNeMo: Plotting Networks
=========================
In this tutorial we will plot networks from a DyNeMo model trained on source reconstructed MEG data. This tutorial covers:
1. Load regression spectra
2. PSDs
3. Power maps
4. Coherence networks
5. Coherence maps
"""
#%%
# Download post-hoc spectra
# ^^^^^^^^^^^... |
4957ccc96912681d9a9df863d0ef893f5fe1e688dc73017a257ff2944b020bca | Python | 4,807 | 129 | # -*- coding: utf-8 -*-
'''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
import torch.nn as nn
import torch
from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence
import numpy as np
class RNN_LSTM(nn... |
42de36f4de9e30b11054c414e87077a0e1e29957ab63e50f4d65f5631630ca59 | Python | 4,808 | 185 | #%%
from src.data import load_maggot_graph
from pathlib import Path
import pandas as pd
import time
from graspologic.cluster import DivisiveCluster, AutoGMMCluster
from src.visualization import CLASS_COLOR_DICT
import numpy as np
import matplotlib.pyplot as plt
from giskard.plot import crosstabplot
import datetime
from... |
fe9a756281e351459bc98b096d2abdfaa48849eaf2f264f41c8eb531b03edd13 | Python | 4,809 | 138 | #!/usr/bin/env python3
"""
File: get_gene_expression.py
Created: 2021/05/19
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 F... |
650c2e42d7d4b2365dfb2fb78a9ea00e4a9575ccb5af0c7c506cab96ceb51d01 | Python | 4,810 | 199 | #%%
import datetime
import time
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from pkg.data import load_network_palette, load_unmatched
from pkg.io import FIG_PATH, get_environment_variables
from pkg.io import glue as default_glue
from pkg.io import savefig
from pkg.plot ... |
5bf0e857dcd6485046f86005b2b7cb14ab46139bbf83ef2268ff3714da6b573b | Python | 4,811 | 109 | #!/usr/bin/env python3
"""Inventory the .scenic scenarios reachable from this environment.
Reads each file's header statically — no Scenic import, no server — so it works
before anything is installed and cannot be broken by a bad model import.
python3 list_scenic.py every scenario, its model and map... |
c50d0769a77e8f261cd0f4a26244f9ba10d3a646c19350bc62d9559f82524e60 | Python | 4,811 | 136 | #!/usr/bin/env python3
"""
File: combine_rosmap_ihc_files.py
Created: 2020/06/30
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 Softw... |
e5176835ee2801fa7b8bdab0522f62406a0d76fb2f3f4e123722d995951077a6 | Python | 4,811 | 174 | # -*- coding: utf-8 -*-
import queue
class CSummaryTree(object):
def __init__(self, root_node):
assert isinstance(root_node, CSummaryNode)
self.root_node = root_node
def get_same_level_max_node_depth(self, query_node):
if query_node.name == self.root_node.name:
return 0
... |
5f3441e6d0f61ae38fdfe491c2c9f53cf5b6dc8ada312e3993a564689dd2798c | Python | 4,813 | 141 | #!/usr/bin/env python3
#
# Copyright (c) 2018 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
# to u... |
33dc0389260e879507ab76abfe479b2d8678557854907c53cb07487d392174de | Python | 4,814 | 130 | #%%
import os
import sys
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
# %%
import sys
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/maggot_models/')
sys.path.append('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
fr... |
5be0738e478586a90738a5f9a7398dd7f1fe1afc0dc0f661f1ab08e59247a31c | Python | 4,816 | 135 | # 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... |
8bb436100328dd4ffb48e7519c62d2c6f20eee34d5f355cdeae5fe1e21739ab3 | Python | 4,816 | 141 | '''
Mean-field Dyn
@YX 1210 Edit
'''
import numpy as np
import matplotlib.pylab as plt
import matplotlib
from numpy import linalg as la
from scipy import linalg as scpla
import scipy
# import seaborn as sb
from cmath import *
from scipy.optimize import fsolve,leastsq,minimize
import scipy.integrate
from math import tan... |
202037d5c27184d3193f4f5994b7bd2e7ac348d8415b75f36290a8d8f60eb8bb | Python | 4,819 | 156 | """
The example with nx=3, ny=4 should run ~1.5secs
"""
import numpy as np
import carpet.visualize as vis
import matplotlib.pyplot as plt
# =====Ring=====
import carpet.lattice.ring1d as lattice
# Geometry
N = 6 # number of cilia
a = 18 # [um] lattice spacing
e1 = (1, 0) # direction of the chain
## Initialize
# G... |
cdc03f3e50e691d70198a3e2de5c9c15256b66058842a91de638b6298d3fd6e5 | Python | 4,819 | 128 | import numpy as np
import math
class SamplePadder(object):
# this transformation object will pad the image and the masks so that:
# - they are the same size
# - they are properly aligned
# - they are square
# - the side length is a multiple of <img_size_mult>
# optionally, the transformation c... |
9a73c9ae5931541feca6089927581695df9b4d2e19091e14ceb85030da6d3449 | Python | 4,820 | 118 | """In-editor half of import-carla-ue58-prop. Runs inside UnrealEditor via
`-run=pythonscript`; never invoke directly.
Reads a job JSON, imports each FBX as a StaticMesh, measures it, and writes a
result JSON. Three UE 5.8 facts shape this file:
* print() and unreal.log() from the pythonscript commandlet do NOT reac... |
14727f4a9e462d7a2e70956dc866a61bdb5bb1c8a82fca152a52b8be171cf7dd | Python | 4,822 | 140 | import numpy as np
import matplotlib.pyplot as plt
import time
from helper import *
from ALsim import ALsim
import sim
import sys
import os
from ALsimParameters import std_paras
import random
"""
Run and experiment to investigate the effect of decreasing response with higher concentration.
We generate N_odour-1 odour... |
772e7db79873a9829aa127693930528b25158404b3ecf207fe83766b5cb1beb8 | Python | 4,822 | 121 | # Copyright 2020 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... |
14e8bc266aca502cfc2ea314c96b3ce933305dcf0e7b3e41551f202724005488 | Python | 4,823 | 151 | '''
MRNet Challenge Submission script
Output predictions file should be a 3-column CSV file (with no header),
where each column contains a prediction for abnormality, ACL tear, and
meniscal tear, in that order
Yash Bhalgat, yashbhalgat95@gmail.com
'''
import numpy as np
import os
import pickle
import sys
import torc... |
3f2b5a213fd84075a994843fecfb4b6c0640f1c6831c12a85f0621e62db43ea6 | Python | 4,825 | 163 | #!/usr/bin/env python3
"""Tests for io."""
import os
from pathlib import PosixPath
from unittest.mock import patch
import numpy as np
import pytest
from phys2cvr import signal
# ## Unit tests
def test_spc():
# Test case 1: test with a single time series
ts = np.array([1, 2, 3, 4, 5])
expected_result =... |
58babcc19df9527da6ff90b829ff374864fa290ad5d4e08eb4ad6158d1b713e6 | Python | 4,826 | 134 | # Copyright 2020 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... |
f2689122479eaf5b5f691afde8dffa8aaf58d4c75a88d9d89c0c06f76445e473 | Python | 4,828 | 127 | # 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... |
10d629a8b3333da1acd3413c0aa352df27e2820ee3f9ae36f2fea3971b232d14 | Python | 4,830 | 174 | import numpy as np
import pytest
import tensorflow as tf
from typing import List, Tuple
TypeFixture = Tuple[tf.Tensor, tf.Tensor, tf.Tensor, List[int]]
#-------------------------------------------------------------------------
@pytest.fixture
def setup_flip_img(img_dims: List[int]) -> TypeFixture:
""" Create fix... |
6cc337a9d7f0dbac6193a822516c6cdc101b6440fa54b8c6826dd84799b1c61c | Python | 4,830 | 138 | import torch.nn as nn
import torch.nn.functional as F
from torchvision import models
class InceptionV3(nn.Module):
"""Pretrained InceptionV3 network returning feature maps"""
# Index of default block of inception to return,
# corresponds to output of final average pooling
DEFAULT_BLOCK_INDEX = 3
... |
36d992eb8860f4897a3105af82388e83feece7874e2754388e41afc4b1b5beeb | Python | 4,831 | 103 | 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 ... |
946fefad5a80c8de8118a0c0aa57c1c209a82d2868d08b43dde919a444141c66 | Python | 4,834 | 125 | from PIL import Image
import numpy as np
import pandas as pd
import torch
from torchvision.transforms import transforms
import mne
from RV.model.utils import tf
from RV.callbacks.utils.channel_selection_utils import get_10_20_channels
def segment_metadata(raw: mne.io.Raw, events: np.array, window_size: float):
... |
e135056401c1810a80c785c0c43d95a3476d9bb5996dbee578829a883cda215d | Python | 4,834 | 135 | #!/usr/bin/env python3
"""
File: get_trait_info.py
Created: 2020/11/17
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 Foundat... |
b17c04762b78c7e556db8c86e1b7dc75f93661f4595f38931d43f9067bed0535 | Python | 4,835 | 140 | # Copyright 2020 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... |
0ab4c08ccee7b477f5e0a514cefb46eb23a826b3e28166083c58ef095de104c6 | Python | 4,836 | 139 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import logging
import os
import torch
from maskrcnn_benchmark.utils.model_serialization import load_state_dict
from maskrcnn_benchmark.utils.c2_model_loading import load_c2_format
from maskrcnn_benchmark.utils.imports import import_file
from mask... |
1c5069e41b11705e2f6b526a91eaf59dd30cfb808dbe6ddb10a99fe19f07e441 | Python | 4,836 | 123 | # -*- coding: utf-8 -*-
import os
import json
import shutil
import argparse
from drugex.logs import logger
from drugex.logs.utils import enable_file_logger
from drugex.utils.download import download_file
from qsprpred.data.sources.papyrus import Papyrus
def DownloadArgParser():
parser = argparse.ArgumentParser... |
afb9fa181231c9e88c586155c16eaeeab77f828b73c928c7d53a274e286c6ce0 | Python | 4,836 | 134 | # Copyright 2020 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... |
e23139ff702f5bc96d879e1604a8c567c02ab8d288890e6d300c16a545db4e43 | Python | 4,841 | 128 | ####################################################################################################
# Copyright (c) 2019 - 2023, EPFL / Blue Brain Project
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free software: you can redistribute it and/or modify it unde... |
e5b382aca4746633345da57fcfc9c617edb67571514fb175ba681d71a1722297 | Python | 4,842 | 121 | # Copyright 2020-2021 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 agre... |
8f6b480518285733f7db1cb81981f571e4a7ce9fad472b3dc875c95c17e046cf | Python | 4,843 | 129 | # basic imports
import os
import numpy as np
import pickle
def recoverStates(replay):
'''
This function extracts the states of replayed experiences.
| **Args**
| replay: A sequence of replayed experiences.
'''
states = []
for experience in replay:
states ... |
3424f7a4396f06f737105b5152554aa3629c536c666f60afd0ad658265a1ca34 | Python | 4,844 | 135 | # 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... |
7b8373f8bf4bf408cf6f88e0ed91e2bd2fd730c646212611cf436992c273311e | Python | 4,845 | 122 | # Copyright 2020 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... |
84d57cb45f744646ced56fa0990ddf6c2474d5a3e7bc1fec0b44f1da0823c7ba | Python | 4,845 | 115 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import itertools
import torch
from torch.utils.data.sampler import BatchSampler
from torch.utils.data.sampler import Sampler
class GroupedBatchSampler(BatchSampler):
"""
Wraps another sampler to yield a mini-batch of indices.
It enfo... |
444414bf96b6dacc0c7863c6b78984b8ab32e0836e8d9c7fab24c4d0efc23099 | Python | 4,846 | 113 | # -*- coding: utf-8 -*-
import mne
import pandas as pd
import numpy as np
from scipy.spatial.distance import cdist
import glob
import seaborn as sns
Brain = mne.viz.get_brain_class()
subjects_dir = str(mne.datasets.sample.data_path()) + '/subjects'
mne.datasets.fetch_hcp_mmp_parcellation(subjects_dir=subjects_dir,... |
1cae412ac18ee2fbc734421065dad25402bf11a08bc7feff94dd65e7f464541d | Python | 4,847 | 124 | """
In this script, we use KFold Cross Validation to train the model.
We save all of the K best models.
"""
from __future__ import print_function
import numpy as np
import random
import pandas as pd
from scipy import stats
import sys, os
import logging
import tensorflow as tf
from keras import layers
from keras import... |
426c1bd0b987e60089d83a3d25e81115ec375674fd772c63fa0a0feede30f76b | Python | 4,848 | 113 | """Phase 3i regression tests: dual-valence Bennett-MV / Felsenberg-POM model.
Headline behaviour: parallel appetitive (w+) and aversive (w-) traces, with
cross-valence DAN feedback (M+ excites D-, M- excites D+). This is the
mathematical instantiation of Felsenberg 2018's parallel-opposing-memories.
The diagnostic fo... |
16cf4da5f8cd989911c7327fa7a97ce8aa836825e665f7b2e3795ce10ed2188b | Python | 4,849 | 119 | import warnings
warnings.filterwarnings("ignore")
import numpy as np
import sys
import os
from Bio.PDB import *
from sklearn.neighbors import KDTree
from IPython.core.debugger import set_trace
# Pablo Gainza 2019 - eval zdock results for comparison with MaSIF.
def test_alignment(target_pdb_fn, source_pdb_fn, aligned... |
660be04dd9cf03dfba8817fc946bb8127502778694f2d936f1b7ef2dbc73bdc5 | Python | 4,855 | 156 | # -*- coding: utf-8 -*-
#
# PIDGINv4 documentation build configuration file, created by
# sphinx-quickstart on Thu Aug 2 09:36:15 2018.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# ... |
9bc8e8c8c7d6133c3e7cd8cd0ea256eb3c31eb208421bd98b2a87d0a44423467 | Python | 4,857 | 159 | # -*- coding: utf-8 -*-
#
# bruker2nifti documentation build configuration file, created by
# sphinx-quickstart on Fri Jul 28 10:16:25 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
... |
8ae316364e5c51e8d02319cb9a7f26d17650badcebe90f575b61f5047607ba3a | Python | 4,858 | 104 | # -*- coding: utf-8 -*-
import numpy as np
from scipy import stats
from . import utils
from ._base import _EmbeddingCausality, _DirectCausality
class ConvergeCrossMapping(_EmbeddingCausality):
def fit(self, data):
self._preprocess(data)
self._fit_data()
def _fit_data(self):
n_row = s... |
99eb6741d35d63cb380c637f53a3b0dfbc0ceda3a178768fc61afad4cf3e1c9a | Python | 4,858 | 118 | import os
import numpy as np
import torch
from cgtasknet.instruments.instrument_accuracy_network import CorrectAnswerNetwork
from norse.torch import LIFAdExState
from tqdm import tqdm
from create_dataset import create_dataset_default_values
from load_network import load_network
criterion = torch.nn.MSELoss()
def r... |
d00cfc412ce011273bf18c2b44965cc9f74df05a28f454fe35c547889d7593ea | Python | 4,858 | 121 | """Tensorflow model utility functions."""
import tensorflow as tf
import os
import tempfile
def get_layer_index_by_name(model, name):
for i, layer in enumerate(model.layers):
if layer.name == name:
return i
def negative_log_likelihood(y_true, y_pred):
'''Implemented by Fred Howard, adapte... |
c26a304fa5068327d8aaabeca0636d729771906b8bf18fd21e00d971da6b7ef8 | Python | 4,859 | 125 | # 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... |
e3e9d4c8bddda110829090fbd755433bd373721d3c68169e04ddeaab18bd4ba3 | Python | 4,860 | 118 | # 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... |
f1c4ad1d87eee73c01fba5a49de70b12fff5391cdad9e8f164ea1a19fa66fe26 | Python | 4,861 | 129 | # 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... |
303acd927f435a6ec90198ef9d046ac0460776c3bca38e83b038363cdc011b94 | Python | 4,866 | 143 | #!/usr/bin/env python3
"""
File: gradient_plot.py
Created: 2020/04/15
Last Changed: 2020/06/02
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 Softw... |
48bd11c1c8c54a9ef34a7e9712d827a76c1cfa4d753a46b1df10ec3e9fc194e6 | Python | 4,866 | 142 | import numpy as np
import pandas as pd
'''
Descirption
study: EEG music convolution study
Protocol: Coma PP music
Resp.: F Perrin
Lead.: L Heine
Code: L Heine - A Corneyllie
this file gives general settings for the study 'Early Evocked'
'''
################################### ... |
1738f93457db3fff5a84a07d7b3b3a1e4a6e01f729c40f3f47b5d2b63c004289 | Python | 4,868 | 125 | # Copyright 2021-2022 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... |
33705856f9d13e60118507b0822260e018a68f7c02df331e0828df3671589aca | Python | 4,869 | 175 | from neuron import h
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import find_peaks
from cell_models import OLMCell
from opt import myinit, mystyle
# Make plots nicer!
plt.style.use("seaborn-colorblind")
plt.rcParams.update(mystyle())
cellname = 'olm'
# If we had not included gui in the list... |
a435376cfc9c9428a38e75ed71f996aa8f6b2ebc9afeddd2c8a99a51947c5126 | Python | 4,869 | 139 | #!/usr/bin/env python3
import sys, pathlib, os
import unetsl.cli_interface
import unetsl.model
import unetsl.data
import unetsl.config
import math
import time
import tensorflow as tf
import click
def trainModel(config, n_gpus, base_name):
input_file = base_name
model_output_file = base_name
if pathli... |
63f098d8eef81cdc78568c48df0b28b2554b968e47c7cc755140c97adb5ec610 | Python | 4,870 | 151 | #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 in wr... |
cb1f7173af6ef5c84dd79c924806d0dd96e49ea876e5442e377519550521b71b | Python | 4,870 | 122 | # Google utils: https://cloud.google.com/storage/docs/reference/libraries
import os
import platform
import subprocess
import time
from pathlib import Path
import requests
import torch
def gsutil_getsize(url=''):
# gs://bucket/file size https://cloud.google.com/storage/docs/gsutil/commands/du
s = subprocess.... |
5f8550fa7b8a177b0807bf5dc539edb75973d0edc275307f84d087076db6ecae | Python | 4,871 | 175 | from neuron import h
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import find_peaks
from cell_models import OLMCell
from opt import myinit, mystyle
# Make plots nicer!
plt.style.use("tableau-colorblind10")
plt.rcParams.update(mystyle())
cellname = 'olm'
# If we had not included gui in the li... |
38ea19710b813d9578abaa05ab12f0a8c2b8a051abd0f0f0001e9e8cf8d84df3 | Python | 4,874 | 124 | import os
import time
import numpy as np
import cortex
import warnings
warnings.warn('''
`glabtools.save_3d_views.save_3d_views()` has moved to
`glabtools.viz.pycortex_extras.save_3d_views`''',
UserWarning)
file_pattern = "{base}_{view}_{surface}.png"
_combine = lambda a,b: ( lambda c: [c, c.update(b)][0] )(dict(a))... |
b094938444edcb114f704193ce83a4d304765dab772ae216835614c872b359ae | Python | 4,874 | 127 | # 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... |
54d793b3931711256a9027df3be0f229c23dd06321a3dc7c5fce2d31287f1d6b | Python | 4,875 | 123 | from typing import Optional, Callable
#from collections.abc import Callable
import torch
from torch_geometric.utils import k_hop_subgraph
from torch_geometric.data import Data
from torch_geometric.utils.num_nodes import maybe_num_nodes
from graphxai.explainers._base import _BaseExplainer
from graphxai.utils import Ex... |
bfe435f606b4920f468b2ab59dfeb99d7d4b09a478f179ff25a01845537edeb3 | Python | 4,875 | 135 | import copy
import platform
import random
from functools import partial
import numpy as np
from mmcv.parallel import collate
from mmcv.runner import get_dist_info
from mmcv.utils import Registry, build_from_cfg
from torch.utils.data import DataLoader
from .samplers import DistributedGroupSampler, DistributedSampler, ... |
f7491b0d3631e0fe7264582441489a0e97b6815ef792423d6da903da121db562 | Python | 4,875 | 119 | # Copyright 2020 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... |
265cd1b2a4c9a21d02dacd2fa4625d97875066b05f0f0f349c242326053ca27b | Python | 4,876 | 124 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
7b9be4e210f14911659afc602faa2b34cd8850530be34906c45acc2573259f5f | Python | 4,878 | 150 | """High-level loaders for MedMNIST-NAS-Bench data.
The benchmark ships two parallel formats per (dataset, search_space):
* ``<search_space>_<dataset>_bench.parquet`` — flat tidy table of all
scalar metrics. Best for SQL-style queries, ranking architectures, and
pandas/polars/duckdb workflows.
* ``<search_sp... |
33e4c671fe21810447a60755d957980eed050b56a9e5a16f7eed66c574902823 | Python | 4,879 | 137 | import argparse
import torch
import sys
import os.path as osp
sys.path.append(osp.join(sys.path[0], '..'))
import mmcv
import models
from mmcv.parallel import MMDataParallel, collate, scatter
from mmcv.runner import load_checkpoint, obj_from_dict, parallel_test
from mmdet import datasets
from mmdet.core import coco_e... |
f765d0e5bffc3c18deffa3e4b92288aa7bc332a42b1055c2bb212aa10685f648 | Python | 4,879 | 119 | # 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... |
373b1c4e0c2c9991c211807b7c99fd9cce779232bf8168ec95a9dcb95dc39a8d | Python | 4,881 | 140 | # 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... |
7fcff5ffa8a4b86ab40f407c3261ff0b8bdbbbd435f1e69cad593999afcdd49d | Python | 4,882 | 127 | """MobileNetV2"""
import torch.nn as nn
from models.baselines.base_model.basic import _ConvBNReLU, InvertedResidual
__all__ = ['MobileNetV2', 'get_mobilenet_v2', 'mobilenet_v2_1_0',
'mobilenet_v2_0_75', 'mobilenet_v2_0_5', 'mobilenet_v2_0_25']
class MobileNetV2(nn.Module):
def __init__(self, num_clas... |
9ca06c05241097723dceeb6d3c442aa9bf7965b20404575d9507b795af88d16f | Python | 4,888 | 157 | import numpy as np
from matplotlib import pyplot as plt
from matplotlib.patches import Rectangle
from matplotlib import rcParams
from matplotlib.backends.backend_pdf import PdfPages
rcParams.update({
'font.family':'sans-serif',
'font.sans-serif':['Liberation Sans'],
})
fnames = [
'learn.np... |
3869d56fd9e0c8075fb361e2301968e15a873f1ed55f8d6f170992bef459928a | Python | 4,889 | 171 | # %% [markdown]
# ##
import datetime
import os
import time
from pathlib import Path
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pymaid
import seaborn as sns
from src.data import load_palette
from src.graph import MetaGraph
from src.io import savecsv, savefig
f... |
d4b720ac3190d67b5f9e60e2d230338803449e31b05b33bb5df8f8b93a4f472d | Python | 4,889 | 120 | from base.backend.settings import Settings as BaseSettings
import typing as tp
import torch
class Settings(BaseSettings):
exmask_enabled: bool
use_gpu: bool
too_many_roots: int
@classmethod
def get_defaults(cls):
defaults = tp.cast(tp.Dict[str, tp.Any], super().get_defaults())
defa... |
5679b4c96b8e82a944ee71b9286e2fd4e210391b87a6cbc1a30c0ed282cbd670 | Python | 4,890 | 126 | """
Handles computing and outputting the absolute difference scores
"""
import numpy as np
from .handler import PredictionsHandler
class AbsDiffScoreHandler(PredictionsHandler):
"""
The "abs diff score" is the absolute difference between `alt` and `ref`
predictions.
Parameters
----------
fea... |
8bbc37d946eda193928828e468bdaa0d5cdcda6ffc21dac57d25d72396cacb9a | Python | 4,891 | 111 | import torch
from torch.nn import functional as F
def plasticity_rule(activation, e, params, feedback, Theta, vec, fbk):
"""
Pool of plasticity rules.
This function receives the network weights as input and updates them based
on a meta-learned plasticity rule. It's worth noting that the weights ... |
76c30f41177ad9910c9a390fdbfb66174d943511f635e849e6db61818b27c59e | Python | 4,893 | 144 | # Time-stamp: <2024-10-02 16:55:48 Tao Liu>
"""Description: Random sample certain number/percentage of tags.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
# pyth... |
58e4e56b404fa286b2f9c08412e6fd469ed02d256aa904e87ff6dc4f957a8241 | Python | 4,895 | 156 | #!/usr/bin/env python
# Copyright 2015 David Snyder
# Apache 2.0.
#
# This script creates four files for each HUB4 Broadcast News
# transcript file. The four files are for the music, speech, ad,
# and other transcripts. Each line of the output files define the
# start and end times of the individual events.
#
# This ... |
11b805da27d737457601cf23fc3b7cf8fa15446ebe0e5d982e75b17a113bb246 | Python | 4,896 | 131 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
from collections import OrderedDict
from torch import nn
from maskrcnn_benchmark.modeling import registry
from maskrcnn_benchmark.modeling.make_layers import conv_with_kaiming_uniform
from . import fpn as fpn_module
from . import resnet
from . im... |
6baec7d898cc59f05e0bd38a4c63f4f55250032b04f24bb53cb0b9d28b4cd06d | Python | 4,896 | 130 | """
File: data_filter.py
Created: 2020/09/04
Last Changed: 2021/08/04
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
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 ver... |
39d9a65f1754a5891921766407610e8d5cebf8235a3c2d0a82fa996694e64e47 | Python | 4,898 | 140 | from __future__ import division
import math
import numpy as np
import torch
from mmcv.runner import get_dist_info
from torch.utils.data import Sampler
class GroupSampler(Sampler):
def __init__(self, dataset, samples_per_gpu=1):
assert hasattr(dataset, 'flag')
self.dataset = dataset
self.... |
9c80a038877a8fe02b4f3d2ff3aa59b2924c412b0e2475f97e4f1054275a8f08 | Python | 4,898 | 132 | import os.path as osp
import warnings
from mmcv.runner import Hook
from torch.utils.data import DataLoader
class EvalHook(Hook):
"""Evaluation hook.
Notes:
If new arguments are added for EvalHook, tools/test.py may be
effected.
Attributes:
dataloader (DataLoader): A PyTorch dataload... |
e3c9d2aca8a77aec4b9477e1ec44ecdd58935359729b5cd5b837986b867702f5 | Python | 4,898 | 158 | import os
import warnings
import subprocess
import platform
import shutil
import sys
import pytest
from bruker2nifti.converter import Bruker2Nifti
here = os.path.abspath(os.path.dirname(__file__))
root_dir = os.path.dirname(here)
def test_convert_the_banana(open_converted=False):
pfo_study_in = os.path.join(r... |
8000c1b60fecbfb2f84b87c270015ddc242fbd0efa2034fc5dc141266b6b4685 | Python | 4,901 | 144 | # Copyright Copyright 2021 Huawei Technologies Co., Ltd (authors: zhangqi)
# 2023.02 - Modified code to support Mindspore
# 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 ... |
1e691fb922f368ad9fd6f543625a11095c2ab02f69df87d417a2ef9db67160b5 | Python | 4,902 | 136 | """Modified version of UNet model for brain parcellation with encoding and decoding blocks."""
from torch import nn
class BaseUnetModel(nn.Module):
"""Implementation of BPARC-UNet model for brain parcellation.
Args:
in_dim (int): size of input layer
hidden_dim (int): size of hidden layer
... |
3e30e0524679a5536f5681c03f2549a51b58a6cd4f4c0573f8c0b960fbafaddc | Python | 4,903 | 172 | import base64
import json
import re
import sys
import uuid
from io import TextIOWrapper
from pathlib import Path
from typing import Callable, Iterator, List, Optional, TextIO, Union
import kgcl_schema.datamodel.kgcl as kgcl
import kgcl_schema.grammar.parser as kgcl_parser
from kgcl_schema.grammar.render_operations imp... |
22ff52a431896e36a6008b57426bfa10672f5564a428af5fe16c7d0eb4d94633 | Python | 4,904 | 149 | ########################################################################
# Interplay of membrane curvature and actin assembly #
# Modeling the shape and size of GUV dumbbells #
# Felix Frey, TU Delft, 2022 #
#########################... |
640f852f0bd8195e7cf6be06b123b3b054343b79f775108db551ac6f4aac9f71 | Python | 4,905 | 128 | # 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... |
791ecc851dcb83ff84e70653a8c0abe894df8db7e36e31070185d6388c3867f3 | Python | 4,908 | 104 | import argparse
import numpy as np
from keras.models import load_model
from plotread import *
def evaluateresults(model, opt, trainx, trainy, validx, validy, testx, testy, output_size):
#Evaluate on training, validation and test data
train_l = model.evaluate(np.array(trainx), np.array(trainy), batch_size=opt.... |
4547959eb333e34ffa10b82cfcf6731c6d37f702895227aa143485b933a7770b | Python | 4,910 | 182 | # -*- coding: utf-8 -*-
"""
Spyder Editor.
This is a temporary script file.
"""
from neuron import h
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import find_peaks
from cell_models import CCKCell
from opt import myinit, mystyle
# Make plots nicer!
plt.style.use("tableau-colorblind10")
plt.rc... |
17e3ea1c38ffd1b9531f0e4219e0a7d660957294a24e3d30cd78e37a47ddb117 | Python | 4,911 | 125 | import math
from queue import Queue
from IPython import embed
import torch
import torch.distributed as dist
import torch.cuda.comm as comm
from torch.autograd.function import once_differentiable
from torch.nn.modules.batchnorm import _BatchNorm
import torch.nn.functional as F
import syncbn_gpu
from maskrcnn_benchmark... |
0f001495176787ba1ca83b366602824cc87163efa27cf4a984076bbc2fea13eb | Python | 4,913 | 171 | import numpy as np
from scipy import signal
import weave
from .Trace import getRisingEdges
def getIndicesFarFromSpikes(
T, spikes_i, dt_before, dt_after, initial_cutoff, dt
):
T_i = int(T / dt)
flag = np.zeros(T_i)
flag[: int(initial_cutoff / dt)] = 1
flag[-1] = 1
dt_before_i = int(dt_befor... |
998f1ff63e7b3e0f417a8e308e8532c45aec3c14884c17bbfbdb11bf5bb02d33 | Python | 4,913 | 183 | # -*- coding: utf-8 -*-
"""
Spyder Editor.
This is a temporary script file.
"""
from neuron import h
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import find_peaks
from cell_models import CCKCell
from opt import myinit, mystyle
# Make plots nicer!
plt.style.use("seaborn-colorblind")
plt.rcPa... |
bcce29df61cabf1763fffe6f1154c437c2da4485408db292c0697bde88a4fcae | Python | 4,914 | 150 | # Copyright 2020 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... |
3897cf010f573276a6de7127c2eff8d56a91e9589b8bfdf768079fdfef98534c | Python | 4,915 | 136 | #%%
import os
try:
os.chdir('/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/')
print(os.getcwd())
except:
pass
#%%
import sys
sys.path.append("/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/")
import pandas as pd
import numpy as np
import connectome_tools.process_matrix as promat... |
4029f2931a3939ee5a3f1e3952840a99f8bb6df2f281e19a96f978c40645f55a | Python | 4,916 | 115 | '''
@author: Mahbub Ul Alam (mahbub@dsv.su.se)
@version: 1.0+
@copyright: Copyright (c) Mahbub Ul Alam (mahbub@dsv.su.se)
@license : MIT License
'''
'''@file early_sepsis_detector.py
run this file to go through the complete neural net training, testing and evaluating procedures,
look at the 'early_sepsis_detector_con... |
9ec0edfda7af0a73d39a956df816dd4dd2e7926fcd1494de573b4f9783f1ad9d | Python | 4,916 | 135 | #! /usr/env/python
import warnings
from os.path import exists as pexists
from os.path import join as pjoin
from os.path import pardir
import pandas as pd
from bids import BIDSLayout
class ThingsMRIdataset:
"""
Data loader for the THINGS-fMRI BIDS timeseries dataset.
"""
def __init__(self, root_path... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.