sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
89a47f18718c92d9b864dcdde9bc9a346119b83e51286aaebe81894da18c378b | Python | 1,014 | 39 |
from PIL import Image, ImageFilter, ImageOps
import math
import random
import torchvision.transforms.functional as tf
class TwoCropsTransform:
"""Take two random crops of one image"""
def __init__(self, base_transform1,base_transform2):
self.base_transform1 = base_transform1
self.base_trans... |
0213e6cb0b7c1a5d99d950de92fd1dc1043630dfa550be7541ee0285d26c6e23 | Python | 1,015 | 18 | ####################################################################################################
# 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 ... |
1cdf27b0807af08204cd34be6173da0d5955cb1094844f5b2a065187c652fa80 | Python | 1,015 | 19 | ####################################################################################################
# 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 ... |
64fb340ed7fc5eedec27166b62c5232dba6963fd63f53490834db6a452a469f1 | Python | 1,015 | 18 | ####################################################################################################
# Copyright (c) 2019 - 2021, 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 ... |
65ffabbc1216b7cee8ae84ab953cfb1f311b00908b45c311d4b6e07876f0e71c | Python | 1,015 | 35 | #!/usr/bin/python
import Bio
from Bio.PDB import *
import sys
import importlib
import os
from default_config.masif_opts import masif_opts
# Local includes
from input_output.protonate import protonate
if len(sys.argv) <= 1:
print("Usage: "+sys.argv[0]+" PDBID_A_B")
print("A or B are the chains to include in ... |
ebc43360822562a9e6997268da534f7cd511c2cfe37f09292b2064730e95afae | Python | 1,015 | 39 | from typing import Any, Dict
from pydantic import BaseModel
from oaklib.types import CURIE
class KeyValCache(BaseModel):
"""
Key-value cache for storing arbitrary data.
"""
cache: Dict[str, Dict[str, Any]] = {}
def add(self, curie: CURIE, property: CURIE, value: Any):
"""
Add a... |
03e333d0c0fe9ddd463dba4c3ed7ac2bed35938e6a20b5e8ca7751bf08733226 | Python | 1,016 | 31 | """MNI152 standard brain surfaces.
Pre-extracted surfaces from the MNI152 T1 1mm brain using FSL BET. These files
are downloaded on first use, see :py:mod:`osl_dynamics.files._fetch`.
Files
-----
- smri.nii.gz: MNI152 T1 structural MRI.
- inskull_mesh.nii.gz, inskull_mesh.vtk, inskull.png
- outskull_mesh.nii.gz, outs... |
405376e77786f8a3a8683e57ca1150b80ebf7400036177da372b417a6843bf5c | Python | 1,016 | 19 | ####################################################################################################
# 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 ... |
a3ed1d16c55cf7a2eff205f49f53ae2b66d27ae2f42ba4b7981a602bfa0f6552 | Python | 1,016 | 18 | ####################################################################################################
# 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 ... |
fe1db241dc592602388d4dc210b3cae6120623379a6b7548b28906e74e27bffd | Python | 1,016 | 18 | ####################################################################################################
# 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 ... |
2582c4f5dbbf233bf777974756a0e808ba32fbde66b96294dcd8d02b813c5cdb | Python | 1,017 | 34 | import os.path as op
import numpy as np
import numpy.testing as npt
import nibabel as nib
import nibabel.tmpdirs as nbtmp
import dipy.data as dpd
from dipy.reconst.shm import calculate_max_order
from AFQ.models import csd
def test_fit_csd():
fdata, fbval, fbvec = dpd.get_fnames('small_64D')
with nbtmp.InT... |
3b4266b7cbe8e9bc1a20eb579be1765b9a300a2cf949d906ae1d587ae57fd89b | Python | 1,017 | 19 | ####################################################################################################
# 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 ... |
893ec2d68ad54eec07fcbef4e3136183cfcf0d00f65eddfdd6452f9880c6cb45 | Python | 1,017 | 34 | #! /usr/bin/env python
"""
Convert empty IPython notebook to a sphinx doc page.
"""
import sys
from subprocess import check_call as sh
def convert_nb(nbname, execute=False):
if execute:
# Execute the notebook
sh(["jupyter", "nbconvert", "--to", "notebook",
"--execute", "--inplace", nbname... |
ceeccbc618bef454a920b3f8898d9f76c6568f6579aebdaa134cbb7239121de9 | Python | 1,017 | 37 | import torch
from cgtasknet.instruments.correct_answer import (
_is_correct_output,
_is_correct_output_batches,
)
def test_correct_output_good_answer():
real_outputs = torch.zeros(10, 1, 2)
target_outputs = torch.zeros(10, 1, 2)
real_outputs[:, 0, 0] = 1
target_outputs[:, 0, 0] = 1
asser... |
97a9bec62f3dbc1abbf4b2d63967cf63d07f39e4cb574f6ec641b8e8970485a5 | Python | 1,018 | 26 | # Copyright (c) 2026 Computer Vision Center (CVC) at the Universitat Autonoma de
# Barcelona (UAB).
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
import re
from . import SmokeTest
class TestBlueprintLibrary(SmokeTest):
def test_blueprint_i... |
c26ee44312f60f6c8ca785feeee105d68f8aea5df6cc3cfaef395e31ecaacaef | Python | 1,018 | 19 | ####################################################################################################
# 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 ... |
c43b85ceae8fdc9c82142346a5deb86c153f62b28542feb2feb76c1266532c16 | Python | 1,018 | 34 | import sys
import os
import config
from src import train_hrnet
"""
Code based on ZSSR provided by Assaf Shocher
https://github.com/assafshocher/ZSSR
"""
def main(input_img, ground_truth, kernels, gpu, conf_str, config_str,results_path):
# Choose the wanted GPU
if gpu is not None:
os.environ["CUDA_VIS... |
e53352ced433545c5dd07143b52f44aebfc0e70827017d6036ce29427b317afd | Python | 1,018 | 18 | ####################################################################################################
# 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 ... |
4905a3cad13337627e8ee20452321925f5f9f39ff2f41bc7cfc7d6ee79310e27 | Python | 1,019 | 18 | ####################################################################################################
# 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 ... |
0d085b971ae347e23a9ba88c61724da7b65256302e0aeab536ea250da745d209 | Python | 1,020 | 37 | '''
Selection of deciliated cells (for Fig. 3).
Discards cell with abnormal passive properties.
'''
import pandas as pd
from file_management.configuration import *
from os.path import join
from numpy import exp
table_folder = join(config['root'],'Deciliated', 'tables')
# Make the panda table
df = pd.read_csv(join(tab... |
147b818c064f841b8474a336047c142bf3ae289953cb27406fae03bce93853a2 | Python | 1,020 | 37 | """MEG scanner layouts and channel names.
These files are downloaded on first use, see
:py:mod:`osl_dynamics.files._fetch`.
"""
import numpy as np
from osl_dynamics.files import _fetch
_SUBDIRECTORY = "scanner"
_CHANNEL_NAMES = {
"ctf275_channel_names": "ctf275_channel_names.npy",
"neuromag306_channel_name... |
ae49ae0913dfe6b4fb22ed7b6d89de9d2e9666330b240766e8d171f0101e8e78 | Python | 1,020 | 34 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module for the manual annotation window widget.
This page lets the user create manually annotations for some selected frames
to then fine tune the network on. The process can be repeated as will.
Finally, the rest of the AxoID pipeline will be applied to the data.
Cre... |
fa4e1d324a6bfc9743ea52e8410660d08d3e800d8813bdc5e211ee3ee660307e | Python | 1,020 | 37 | '''
Selection of ciliated cells with PIV (for Fig. 4).
Discards cell with abnormal passive properties.
'''
import pandas as pd
from file_management.configuration import *
from os.path import join
from numpy import exp
table_folder = join(config['root'],'Ciliated with PIV', 'tables')
# Make the panda table
df = pd.rea... |
5025288757ed36ffe806266c3bbb9be09a2ef05e4222dedf163d8baa13ea2b67 | Python | 1,021 | 27 | # 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... |
7c7f2484c2d86864915d3204465d1bce56913c1c86759b675bc04753a755fe15 | Python | 1,021 | 26 | # 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... |
95dda201c6087d948441680f61f3e15fd822045334e44f95b10a1bd782b6fd4c | Python | 1,021 | 27 | # 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... |
4a9e4b85d06388f6dc480850f8c6647e338fc5af647b90751747290f4d994be3 | Python | 1,022 | 35 | _base_ = ['../faster_rcnn/faster_rcnn_r50_fpn_1x_coco.py', '../_base_/datasets/voc0712.py']
model = dict(
pretrained='torchvision://resnet101',
backbone=dict(
type='ResNet_MD',
depth=101,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=1,
norm_cfg=dict(type=... |
ed1b1629f2fba900f4f9e19b0f37c6b4699e1ff09c5b109637b978dcb4b72642 | Python | 1,022 | 40 | import subprocess
def get_commit_hash():
message = subprocess.check_output(["git", "rev-parse", "--short", "HEAD"])
return message.strip().decode('utf-8')
class WavBinaryWrapper(object):
def __init__(self, data):
super(WavBinaryWrapper, self).__init__()
self.data = data
self.posi... |
ef22f3613817e64a22e60a5616fe56aa7ffc706ea064cd60d83af508f6c6b0d0 | Python | 1,022 | 37 | _base_ = '../faster_rcnn/faster_rcnn_r50_fpn_1x_coco.py'
model = dict(
pretrained='torchvision://resnet101',
backbone=dict(
type='ResNet_MD',
depth=101,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=1,
norm_cfg=dict(type='BN', requires_grad=True),
mdconv=... |
fdb394400e910626737b69d13e9ecb73d6d0e7af2eaeb0637cda22f2701623e5 | Python | 1,022 | 28 | # 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... |
6ce8d2361acffb50e9c4525e9c938cd678f6d31945acc538bf589067098de44e | Python | 1,023 | 36 | import argparse
import gc
import numpy as np
import pandas as pd
import tqdm
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('tsv_path',
help='The path to the tsv to turn into a dataframe and pickle',
)
parser.add_argument('... |
62a421015024d50fc5ec6d1a23830749eb6d7e2e10dc0072ac2470e61c97866b | Python | 1,024 | 37 | _base_ = '../retinanet/retinanet_r50_fpn_1x_coco.py'
model = dict(
pretrained='torchvision://resnet101',
backbone=dict(
type='ResNet_MD',
depth=101,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=1,
norm_cfg=dict(type='BN', requires_grad=True),
mdconv=dict... |
c785a005890469b7fa50e90d080b7fa54ac7bed0eaca8273d1fe69e0e7b775ee | Python | 1,024 | 35 | _base_ = ['../faster_rcnn/faster_rcnn_r50_fpn_1x_coco.py', '../_base_/datasets/voc0712.py']
model = dict(
pretrained='torchvision://resnet101',
backbone=dict(
type='ResNet_MD',
depth=101,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=1,
norm_cfg=dict(type=... |
e41aa37df23988bd34e3f24302251add4aef6892284eeeaa481af627984883be | Python | 1,026 | 18 | ####################################################################################################
# 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 ... |
20d2f9cdfab9fd689a2f403fb9e734b2e55fdfe0e209ea0de7626dc7db8d7ef0 | Python | 1,027 | 26 | # 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 ... |
30169ad73abc27de03fc124d81bc2f4e2783bf3fa6318bf8c8a808a090482372 | Python | 1,027 | 26 | import h5py
import tensorflow as tf
num_feature = 5
def parse_proto(example_proto):
features = {
# 'X': tf.FixedLenFeature((num_feature,), tf.float32, allow_missing = True)
# 'X': tf.FixedLenFeature((num_feature,), tf.float32)
'X': tf.compat.v1.FixedLenFeature([num_feature], tf.fl... |
4bd4a12b65588dff3dd0c570a266b906f55591a3773f722461539d23cb364279 | Python | 1,027 | 38 | """Base simulation class."""
import numpy as np
class Simulation:
"""Simulation base class.
Parameters
----------
n_samples : int
Number of time points to generate.
"""
def __init__(self, n_samples: int) -> None:
self.n_samples = n_samples
self.time_series = None
... |
8cbdc0935bb1a0a4c4c03ca4a6f51efcd0bc4bfdbec76c118fffe236b0ac4e2a | Python | 1,027 | 28 | import csv
import pandas as pd
skeletons = pd.read_csv('axon_dendrite_data/splittable_skeletons_all.csv', header=0, skipinitialspace=True, keep_default_na = False)
connectors = pd.read_csv('axon_dendrite_data/splittable_connectors_all.csv', header=0, skipinitialspace=True, keep_default_na = False)
print(len(skeleto... |
377eb0997caaf7c023698a4a5362487667f5fb5b66176e62b98264a8df8d1980 | Python | 1,028 | 30 | from functools import partial
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from pycpd import rigid_registration
import numpy as np
import time
def visualize(iteration, error, X, Y, ax):
plt.cla()
ax.scatter(X[:,0], X[:,1], X[:,2], color='red', label='Target')
ax.scatter(Y[:,0], ... |
ff98d87c3fc0f90a78b3471b93733010305b533c6e7e511faa06c8059b3a5393 | Python | 1,028 | 31 | import unittest
from linkml_runtime.dumpers import yaml_dumper
from linkml_runtime.loaders import yaml_loader
from linkml_runtime.utils.introspection import package_schemaview
from oaklib.datamodels import ontology_metadata
from tests import output_path
class TestOntologyMetadataDatamodel(unittest.TestCase):
de... |
64e247dd8d84284f1fd4902106508044489c9007aaead52bcdf0885d30d47ceb | Python | 1,029 | 36 | # 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... |
6860ee38322876eba8fe446688a6a8973ff4df35ec711b01d14030b957ffd681 | Python | 1,029 | 36 | # 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... |
88595ae4f6bd54bf3ebc78fb22d3a23455b2d594b31438aad22e6fa066b552b7 | Python | 1,029 | 27 | # 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... |
e986cbc8a179975af2c062c0a72fd12093f38fc2bd614c4fce8e764c690506a0 | Python | 1,029 | 32 | # This updates usage/methods.rst to the latest API methods
# Developers can run this after modifying any arguments the user can see
from AFQ.api.utils import methods_descriptors
from textwrap import dedent
prologue = """
.. _methods_docs:
The pyAFQ API methods
---------------------
After defining your pyAFQ API obje... |
1213ed12156098e5aa58d7ca072ea75dce3dd52ec49be660080badd421cc69b1 | Python | 1,030 | 37 | # 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... |
1846546bb16c268a26b389a92b4fcaa33ee835a4a964fa0188eee38e112e9181 | Python | 1,030 | 26 | #!/usr/bin/python
# This code was designed to build a fake dataset to test out SSAML
import numpy as np
import os
import pandas as pd
# MAIN CODE
# CONSTANTS
COVAfile = 'COVA-FAKE.csv'
# First make fake COVA data
how_many = 2000
COVA = pd.DataFrame(columns=('actual','CoVAScore','Prob-none','Prob-Hosp','Prob-ICU-MV',... |
9653daeae7f3672498a01424bfb4b1a36d7aaeb74a5375ecb47197c3a42b2cb7 | Python | 1,030 | 24 | # 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... |
9caded59b2d7033ef9d6fa63dd5a3c74c34aeccdf5e0e0e08db9152e37677acb | Python | 1,030 | 32 | import pytest
import torch
from ..attention_kernel_integral import AttentionKernelIntegral
from ..embeddings import RotaryEmbedding2D
def test_AttentionWithRoPE():
"""Test for Attention kernel integral with rotary position embeddings
Checks the output size
"""
head_n_channels = 32
channels = 32
... |
bde3546a827780a59b9f3cffc6384ff3ceb21260656ad0afc202aafcc6bff5d5 | Python | 1,030 | 33 | import numpy as np
from classifiers import *
from pipeline import *
from tensorflow.keras.preprocessing.image import ImageDataGenerator
# 1 - Load the model and its pretrained weights
classifier = Meso4()
classifier.load('weights/Meso4_DF.h5')
# 2 - Minimial image generator
# We did use it to read and compute the pr... |
d1393eb047e6eb47c29685fe94a843ea7ca3a0d9f88a41f0cc842a566e03ad51 | Python | 1,030 | 43 | import torch
from cgtasknet.instruments.instrument_pca import PCA
def test_pca_number_of_components_shape():
data = torch.zeros((10, 10))
pca1 = PCA(1)
pca2 = PCA(2)
pca3 = PCA(3)
pca4 = PCA(4)
pc1 = pca1.decompose(data)
pc2 = pca2.decompose(data)
pc3 = pca3.decompose(data)
pc4 =... |
fe5e857adfb92b686cbbf717442ca3c3ed713a9e2c2c4c20def866110992ce17 | Python | 1,030 | 19 | ####################################################################################################
# Copyright (c) 2019, 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 softwar... |
12780756d1c9dbec692eab2ec90f7413d520e5e8a5e232bc4d34ea65c8a4d5be | Python | 1,031 | 19 | ####################################################################################################
# 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 ... |
866a0f374eca3b03a68e11c2f01079279b27cc5f361bdd71e3f74d8a709da811 | Python | 1,031 | 19 | ####################################################################################################
# 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 ... |
c109f7c55cb865095d6ed2b6e4e5ebc29db6934f93e9470a379ba9dcf0bbe8cc | Python | 1,031 | 22 | # 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... |
f751ec7395586de5bc40ecbec0d6830b0589489d0adb0a6668ea0bae84b91f99 | Python | 1,031 | 26 | # 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... |
b5b1b98529c01a538dc2a6d79316607254d3dfa4bb6bb0ba5931a2c678ad375e | Python | 1,032 | 31 | import torch
class PCA:
def __init__(self, num_components: int = 1, calculate_derivation=False):
self._num_components = num_components
self._calculate_derivation = calculate_derivation
def decompose(self, data: torch.Tensor, center: bool = True):
X = torch.clone(data)
if cente... |
5a97ace69522e6f4074867e60e1163545541d48c6f8d58e806ce3f2d05b26db8 | Python | 1,033 | 19 | ####################################################################################################
# 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 ... |
8a906b96d3a5cb13522454f65100168c942a9abb601f969189efd48b9ca36678 | Python | 1,033 | 32 | """
get_split.py: Once a pocket has been align, print the pockets that do not align at 0.5 or more
to at least one pocket in the training set.
Pablo Gainza - LPDI STI EPFL 2019
Released under an Apache License 2.0
"""
import os
from IPython.core.debugger import set_trace
import numpy as np
for fn in... |
a4ade25e6896c05ffcb08e5568a2cd76440272b8de5111415ea212f8c8602592 | Python | 1,033 | 20 | # Copyright 2018 SciNet (https://github.com/eth-nn-physics/nn_physical_concepts)
#
# 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... |
5de3a18aed5876a790931ab7459bc14685ef2c3f4ad74d11423bb910e75281b0 | Python | 1,034 | 20 | ####################################################################################################
# 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 ... |
89ec75812fa7d92fa0e07e033983941cfc2a66fe5a05e9e60158ef394964954b | Python | 1,034 | 27 | import os
# Heuristics created by Vincent for Abbas dataset sample6.
# 27th Nov. 2019
# updated 23th Jan. 2020
def create_key(template, outtype=('nii.gz',), annotation_classes=None):
if template is None or not template:
raise ValueError('Template must be a valid format string')
return template, outtype,... |
110da2caf1d2ae7831b044332be5d6409f5de1e0db785a0cf94b42a4c7ce0bac | Python | 1,035 | 31 | import numpy as np
import nibabel as nib
import sys
import os
from utils import largestAfterOpen
from scipy import ndimage
out_path = sys.argv[1]
prefix = sys.argv[2]
if out_path[-1]!='/':
out_path = out_path+'/'
brain_mask = nib.load(out_path+prefix+'brain_mask.nii.gz').get_fdata().astype(bool)
affine = nib.load... |
7094fde8b85e8af597f83b3f4205adb680b9f54cb6ff676543f633ee9a143de1 | Python | 1,035 | 29 | import logging
from PyQt5 import uic
from PyQt5.QtGui import QTextCursor
from PyQt5.QtWidgets import QWidget, QTextEdit
LoggingDialogUI, LoggingDialogBase = uic.loadUiType("LoggingDialog.ui")
class LoggingDialog(LoggingDialogBase, LoggingDialogUI):
def __init__(self, parent: QWidget = None):
# uic boile... |
4467e4d065e6d1d6026188386aeb1ee37452015be8a6776e693f29d580fb9b60 | Python | 1,036 | 36 | # 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 ... |
4560750c843b7ad248eff80957110b58362a41cbb9c4a4846d8e172cca8ef15b | Python | 1,036 | 37 | import numpy as np
import math
import PIL
def postprocess(x):
"""[0,1] to uint8."""
x = np.clip(255 * x, 0, 255)
x = np.cast[np.uint8](x)
return x
def tile(X, rows, cols):
"""Tile images for display."""
tiling = np.zeros((rows * X.shape[1], cols * X.shape[2], X.shape[3]), dtype = X.dtype)... |
c81f1a7e54d3c8b46edad20061ccfaeec1bec9c1dc63bb91c61242a4c1668b4b | Python | 1,037 | 19 | ####################################################################################################
# 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 ... |
ca3a34189528b6a9bb42a3ff6b52bb05105ee0f001ecccfd966f307d8ea9ae35 | Python | 1,037 | 20 | ####################################################################################################
# Copyright (c) 2016 - 2021, 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 ... |
7bfc97e51f5930bac6889097b1f6ff72c53fe8b4762e187ba9fb5d20c72fe27d | Python | 1,038 | 30 | # 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... |
301bde5082887ee4835c8501cef12798450dec802a7215f5ca4c690575d704d2 | Python | 1,039 | 20 | from .auto_augment import AutoAugment
from .compose import Compose
from .formating import (Collect, ImageToTensor, ToDataContainer, ToTensor,
Transpose, to_tensor)
from .instaboost import InstaBoost
from .loading import (LoadAnnotations, LoadImageFromFile,
LoadMultiChannelI... |
60bdb55f4f6014de3f83219747a3b34cef95baac95ddfe85a25afc86f34eb0e8 | Python | 1,039 | 20 | ####################################################################################################
# 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 ... |
e74a3c6d7334d120872923c8c995bc2f398eb5d6cc2a29e66a734ae8548fb3d7 | Python | 1,041 | 35 | """
Splitting the data into train and test subsets.
"""
# import needed libraries.
import os
import random
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
random.seed(123)
np.random.seed(123)
# Define output directories for saving split data.
out_dir = 'sv'
os.makedirs(o... |
3f1d50e346e709da623eed90fd695cd6efeef0b81075b9156c3e79ad0eff1d60 | Python | 1,042 | 40 | import os
import torch
from torch import nn
from torch.nn import functional as F
module_path = os.path.dirname(__file__)
class FusedLeakyReLU(nn.Module):
def __init__(self, channel, negative_slope=0.2, scale=2 ** 0.5):
super().__init__()
self.bias = nn.Parameter(torch.zeros(channel))
s... |
05c508dd1847a34d4c5b83246ce1872ae3da11773ddd4a906698c5824b1fea9e | Python | 1,043 | 38 | import numpy as np
import matplotlib
from matplotlib import pyplot as plt
# ----------------------------------------------------------------------
def plot_eeg(data, channels, sample_rate, cmap='tab20', nxlabel=10, sca=1, offset=0, fig=None, ax=None, size=(15, 5), dpi=90):
""""""
if fig is None:
plt.... |
60c10407a1b8e67043b64890fb732bf004100c494579888f7225cc0fbbe8ba4b | Python | 1,044 | 22 | from .builder import DATASETS, PIPELINES, build_dataloader, build_dataset
from .cityscapes import CityscapesDataset
from .coco import CocoDataset
from .custom import CustomDataset
from .dataset_wrappers import (ClassBalancedDataset, ConcatDataset,
RepeatDataset)
from .deepfashion import D... |
be5c808a3f1187f2e7b0af7fcad4a5f8ba9f147b708dc0c5572f818598dd611f | Python | 1,044 | 27 | """Phase 3g regression tests: robustness analysis tools."""
import numpy as np
from mb_dual_dan.robustness import run_seeds, sweep_param
def test_run_seeds_returns_means_and_bands():
def expt(seed: int) -> np.ndarray:
rng = np.random.default_rng(seed)
return rng.normal(loc=1.0, scale=0.2, size=1... |
5f06f81c7277c2cf9b12e55ec927a21dc3cc376435506cff59404f9714fe508b | Python | 1,046 | 22 | # Copyright 2018 SciNet (https://github.com/eth-nn-physics/nn_physical_concepts)
#
# 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
#... |
b0b33c0689289ac366bff42551af7bf35a790a6568e9ff4d91eeacdd55d79bef | Python | 1,047 | 25 | from typing import Union, Tuple, List, Optional, Dict, Callable, Iterable
import jax.numpy as jnp
import numpy as np
import scipy.sparse as sp
Shape2 = Tuple[int, int]
Shape3 = Tuple[int, int, int]
Size2 = Tuple[float, float]
Size3 = Tuple[float, float, float]
Size4 = Tuple[float, float, float, float]
Shape = Union[S... |
2b572907315f0eb9bdab26304e2fb29600e8818d8ff11a359455433a7bf450b8 | Python | 1,048 | 30 | import os
import numpy as np
all_ranks = []
user_time = 0.0
for results_dir in os.listdir('results/'):
full_dir = os.path.join('results/', results_dir)
results_file = os.path.join(full_dir, 'results.txt')
if os.path.exists(results_file):
results_line = open(results_file).readlines()
fields ... |
6fbd405dfa5dd23e758ff63ef83ddde46285b9149d22bf6fb33ad02c8137b1e5 | Python | 1,049 | 40 | from io import BytesIO
import lmdb
from PIL import Image
from torch.utils.data import Dataset
class MultiResolutionDataset(Dataset):
def __init__(self, path, transform, resolution=256):
self.env = lmdb.open(
path,
max_readers=32,
readonly=True,
lock=False,
... |
87c544877046309b74a7fb019fbb9b37e1d2b6df5015ef33a40de2d35251a2d0 | Python | 1,050 | 34 | from pathlib import Path
import pandas as pd
import pytest
from cenfind.core.data import Dataset
from cenfind.core.detectors import extract_cilia
ROOT_DIR = Path(__file__).parent.parent
if not (ROOT_DIR / "data/cilia").exists():
pytest.skip(
"data/cilia fixture is not present (it is gitignored and not "... |
bf1347027c8f35293a9b4efcceafa54e2899e91acc00487c657cc23fb1265171 | Python | 1,050 | 19 | ####################################################################################################
# Copyright (c) 2019, 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 softwar... |
8374b10399d8a507c68fe6c577c52ca3c0882a6657a889c88b5ad50a593c37e6 | Python | 1,051 | 24 | import pandas as pd
import os
import scanpy as sc
import pickle
import seaborn as sns
import numpy as np
for type in ['order_distal', 'proximal']:
with open("vis_id_"+type+"__all_scanpy_obj.pyn", "rb") as f:
adata = pickle.load(f)
print(adata.obs['louvain'])
a=adata.obs.loc[:,["cluster", "louv... |
d814747d3309e2d83744ccee64e32e25416c432982d1b9e32cf07bfdac6d0994 | Python | 1,051 | 38 | from setuptools import setup
with open("README.md", "r") as fh:
long_description = fh.read()
setup(
name="axoid",
version="0.1",
author="Nicolas Talabot",
author_email="nicolas.talabot@gmail.com",
description="Regions of interest detection and tracking over 2-photon neuroimaging data",
lon... |
f7325c928c0f0a2c0667df2bad8b1708bbfc55d1bc227bb12380c67f41f2f183 | Python | 1,051 | 30 | import os
import numpy as np
all_ranks = []
user_time = 0.0
for results_dir in os.listdir('results/'):
full_dir = os.path.join('results/', results_dir)
results_file = os.path.join(full_dir, 'results.txt')
if os.path.exists(results_file):
results_line = open(results_file).readlines()
fields ... |
1233e11747f5457b5e2be30d7a2007df0f07c29433c4e9fe45530e86b831cecc | Python | 1,053 | 13 | from .base_options import BaseOptions
class ReadOptions(BaseOptions):
def initialize(self, parser):
parser = BaseOptions.initialize(self, parser)
parser.add_argument('--shuffle', action='store_false', required=False, help='Shall the data be shuffled?')
parser.add_argument('--no_data_info',... |
b7aba6766bd403c14c5ecd19258d32b810ce86a8bb55be2343ce68fcba12a260 | Python | 1,053 | 36 | from typing import Any, List, Optional
from zencfg import ConfigBase
from .distributed import DistributedConfig
from .models import ModelConfig, OTNO_Small2d
from .opt import OptimizationConfig, PatchingConfig
from .wandb import WandbConfig
class CarCFDDatasetConfig(ConfigBase):
root: str = "~/processed-car-pres... |
4c34734fee9f092c0bd18cb5870a71cd5eb40f9fe40d6c5b7cec748e97c21c75 | Python | 1,055 | 36 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from tmkit.seqnetrr.combo.Param import Param
class Segment(Param):
def __init__(
self, seq_sep_inferior: int = None, seq_sep_su... |
a5dc212ddb0236919b7f7c13794eda064a661049261dca173c760055c9cce240 | Python | 1,055 | 20 | ####################################################################################################
# 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 ... |
1754d58af831f0d4660db2d64b161b9c7c5e2659ee48777791b68af5435e669e | Python | 1,056 | 13 | """Weather and camera-profile grids from a looks.py --mode matrix capture. grids_matrix.py MATRIX_DIR FINAL_DIR TOWNTAG"""
import os, subprocess, sys
R, F, TAG = sys.argv[1:4]
W = ["ClearNoon", "CloudyNoon", "WetNoon", "MidRainyNoon", "HardRainNoon", "ClearSunset", "SoftRainSunset", "ClearNight", "HardRainNight"]
P = [... |
8fc36fd8c7ab5cf6290ac5b8bf06d136c822b343923f84b9bf4f2daa94a047db | Python | 1,056 | 29 | import logging
import unittest
from oaklib.parsers import MEDGEN_MIM_G2D
from oaklib.parsers.association_parser_factory import get_association_parser
from tests import INPUT_DIR
G2D_INPUT = INPUT_DIR / "example-g2d.mim2gene.tsv"
class MIM2GeneAssociationParserTest(unittest.TestCase):
"""Tests parsing of medgen ... |
cc9a4c33087752dae1a7db03f796d1cb9fc906a0f31b93e563f679017131d31e | Python | 1,057 | 33 |
class ScheduledOptim:
'''A simple wrapper class for learning rate scheduling'''
def __init__(self, optimizer, init_lr, d_model, n_warmup_steps=4000):
self._optimizer = optimizer
self.init_lr = init_lr
self.d_model = d_model
self.n_warmup_steps = n_warmup_steps
self.n_st... |
dede8d022f79f92bad37d90fa2906f280a47902e059acc1bcd82db154036b343 | Python | 1,057 | 30 | from eAE.eAE import eAE
def main():
# Setting up the connection to interface
ip = "interfaceeae.doc.ic.ac.uk"
port = 443
eae = eAE(ip, port)
# Testing if the interface is Alive
is_alive = eae.is_eae_alive()
if is_alive != 200:
raise Exception("!!!")
# Initialize i... |
e8019a3b4afcf38f900ef327a67f9558ad677f9e2114d87588e3d9ce411a279e | Python | 1,058 | 12 | import os
from tqdm import tqdm
from scripts.nn_predict import main
lats = [-8.685, -8.7362, -8.7808, -8.8033, -8.7759, -8.8261, -8.8432, -8.8287, -8.8155, -8.8224, -8.7923, -8.6471, -8.626, -8.6186, -8.5573, -8.3447, -8.2721, -8.2424, -8.1594, -8.1584, -8.1537, -8.1542, -8.155, -8.1714, -8.1993, -8.1883, -8.2292, -... |
1e15c91002e33e4be4cb3f3e0fcb3c6bd560735ea58da77dd8e6b8ad844cc9a4 | Python | 1,059 | 33 | import torch
from torch_geometric.data import Data
from torch_geometric.utils import convert
from networkx.algorithms.swap import double_edge_swap as swap
from networkx.linalg.graphmatrix import adjacency_matrix as adj_mat
from IPython.display import SVG
from sknetwork.visualization import svg_graph
from old import ... |
286c52d4f4528d61758ec75529bed1d8424d09704ea61d0ca2638f96ae1edaed | Python | 1,059 | 41 | __author__ = "Christopher Schröder"
__copyright__ = "Copyright 2020, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"
from os import path
from snakemake.shell import shell
# Extract arguments.
extra = snakemake.params.get("extra", "")
sort_extra = snakemake.params.get("s... |
464f110823f105add542c91a813a2024f7d06802da5f767c57c20a099fba51ee | Python | 1,059 | 33 | import unittest
from oaklib.datamodels.vocabulary import SKOS_CLOSE_MATCH, SKOS_EXACT_MATCH
from oaklib.implementations.translator.translator_implementation import (
TranslatorImplementation,
)
# TODO: use mock tests
class TestTranslatorImplementation(unittest.TestCase):
"""
Tests :ref:`TranslatorImpleme... |
109bc7b8e31f48eaeb045a2b8b1e1ca0802dd05739074cbee36d13c0cc4ce8b7 | Python | 1,061 | 29 | import unittest
from deeprank_gnn.DataSet import HDF5DataSet, DivideDataSet, PreCluster
class TestDataSet(unittest.TestCase):
def setUp(self):
self.database = 'tests/hdf5/1ATN_residue.hdf5'
def test_dataset(self):
dataset = HDF5DataSet(database=self.database,
no... |
3b218fa89d43760ece4da65496b13b39096490d211379a823ac7562f033d6a55 | Python | 1,061 | 21 | ####################################################################################################
# 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 ... |
8d5eafcf6be24e6a20945b8f31f31b857a66fc96d0d8c8d02d983d71d1793338 | Python | 1,061 | 49 | __author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@gmail.com.com"
__license__ = "MIT"
import os
from snakemake.shell import shell
input_known = snakemake.input.known
extra = snakemake.params.get("extra", "")
bed = snakemake.input.get("bed", None)
if bed is not None... |
0cf1e7774df5a7904933405bc4cec576d73ed3964e821566f10d590e68341cce | Python | 1,062 | 24 | # 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... |
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