sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e9c55bda4afc1e31839e572148f09b2a525c328ce085d043539f88ccc647e95d | Python | 4,350 | 160 | # 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... |
e98828b4ab2bb044afc2ae6929df8e77f44a16a1ef458bf02e21caf0cc34f784 | Python | 4,351 | 138 | from __future__ import division
from __future__ import print_function
from builtins import str
from builtins import range
from scipy import signal
from scipy.stats import uniform, norm
import numpy as np
import seaborn as sns
import matplotlib.mlab as ml
import matplotlib.pyplot as plt
from sima import spikes
######... |
010950641a1faf2882214c461e8db2714c118a2f9d0a631ec60ba7bfb58dba74 | Python | 4,352 | 130 | # taken from https://github.com/tonylins/pytorch-mobilenet-v2/
# Published by Ji Lin, tonylins
# licensed under the Apache License, Version 2.0, January 2004
from torch import nn
from torch.nn import BatchNorm2d
#from maskrcnn_benchmark.layers import FrozenBatchNorm2d as BatchNorm2d
from maskrcnn_benchmark.layers imp... |
a06c072a55779795c881f80b0becf468fa77f53d19582e914f5a8f3b971c93c0 | Python | 4,354 | 137 | import gc
import os
import tempfile
import numpy as np
from src.transforms import *
gc.enable()
import random
import numpy as np
random.seed(666)
from selene_sdk.utils import load_path
from selene_sdk.utils.config_utils import get_full_dataset, interval_from_line
CHROM_SIZES = {
"chr1": 249250621,
"chr2... |
2b33e8b4889fb917e080f1447e8bd5141b7668ec282200bb95339c0319984f4c | Python | 4,355 | 130 | import torch
from torch import nn
class GeneratorLoss(nn.Module):
def __init__(self, model_path, device):
super(GeneratorLoss, self).__init__()
ctf_model = regression_model.ResidualLowpass()
ctf_model.to(device)
checkpoint = torch.load(model_path)
ctf_model.load_state_dict(checkpoint['model_state_dict'])
... |
274b0ba62946507c21b3518f0d5a72b5dcf377e0d99bc077304e40816aff4494 | Python | 4,356 | 111 | """
Plotting tools in nilearn
==========================
Nilearn comes with a set of plotting functions for easy visualization of
Nifti-like images such as statistical maps mapped onto anatomical images
or onto glass brain representation, anatomical images, functional/EPI images,
region specific mask images.
See :ref... |
5c11d551052d50ecd83c6d8387fdc141afc0aca8fde71c9a3f5d74d8d40984b0 | Python | 4,356 | 197 | # Generic
import torch
import skorch
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
# Basic Functions in Torch
from torch import nn
from torch import optim
from torch.utils.data import DataLoader
# Basic Functions in Skorch
from skorch import NeuralNet
from skorch.callbacks import EpochTimer
f... |
85563fadc9a24ec8689630a5c932eeff35ac1083dcabb30b46de68a82efbc287 | Python | 4,356 | 136 | # 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... |
40b7f231319ac091e62a8c8cd8d92efd89bc4490369964a5e30d1916dd4a774a | Python | 4,357 | 147 | from datetime import datetime
import itk
import numpy as np
import torch
TIMESTAMP = datetime.now().strftime("%Y%m%d_%H%M%S")
PANDAS_FCSV_KWARGS = {
"comment": "#",
"names": [
"id",
"x",
"y",
"z",
"ow",
"ox",
"oy",
"oz",
"vis",
"s... |
33846375caa24ecbb90a87f3f6959f8bd467399273f29569c02a1a333972574e | Python | 4,358 | 101 | import numpy as np
def linear_(x, params):
a, b = params
return a*x+b
def spike2calcium(spike_times, ca_times, param):
tau_r = param[0] # rise
tau_d1 = param[1] # decay1
tau_d2 = param[2] # decay2
k = param[3]
ca_trace = np.zeros(len(ca_times))
for n, spk in enumerate(spike_times):
... |
617fc24f37566918e24c50b351cee135a9665f5ea3966017a541e1cfb85e9d34 | Python | 4,358 | 120 | import torch.nn as nn
from mmdet.core import bbox2result
from ..builder import DETECTORS, build_backbone, build_head, build_neck
from .base import BaseDetector
@DETECTORS.register_module()
class SingleStageDetector(BaseDetector):
"""Base class for single-stage detectors.
Single-stage detectors directly and ... |
2d4189588667ac41952dcd2f1b5353fabc13cd654f0bc2e551572179bb23c9ef | Python | 4,360 | 98 | #%%
import pymaid
import navis
#import pyoctree
from pymaid_creds import url, name, password, token
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
import connectome_tools.process_skeletons as skel
# allows text to be editable in Illustrator
plt.rcParams['pdf.fonttype'] =... |
c5a8445cef54f9796a3994cb0458faec570d8d6c3e58b62a0d2c1791d8a93d32 | Python | 4,360 | 127 | import argparse
import os
from bruker2nifti.converter import Bruker2Nifti
import bruker2nifti._utils as utils
def main_scan():
"""
Parser from terminal with
$ python2 bruker2nifti_scan -h
$ python2 bruker2nifti_scan -i input_file_path -o output_file_path
"""
parser = argparse.ArgumentParser(... |
0aaab76224b1a7ca7e16b24ab4be5d63e0212794fbc21d12a0bf56c6de60d763 | Python | 4,361 | 102 | # 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... |
a648d2a44277569e8dc26d29b2ac3545563198a82341610cb7790825aa18830d | Python | 4,361 | 106 | import numpy as np
import torch
import random
import os
import argparse
from pathlib import Path
from tqdm import tqdm
from torch.utils.data import DataLoader
import aug_accuracy as util
from aug_accuracy import InputError
def train(config, dataset_name, data_type, nn_type, run_num):
data_root = config['General']... |
79fe493bd2db224db9591d88f3bff8190ca989cd2926fc1220284c5e80dd817e | Python | 4,363 | 104 | import re
import torch
import logging
from collections import OrderedDict
def remap_for_paramadapt(load_path, model_dict, seed_num_layers=[]):
seed_dict = load_checkpoint(load_path, map_location='cpu')
logging.info('Remapping for parameter adaptation starts!')
# remapping on the depth level
depth_map... |
b4022c0d9800ccad99369615d6694ed841affb182ed5418a85c55d4e439478f2 | Python | 4,363 | 126 | # 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... |
05d9807f67b535f52b5592f525154a0a2d5c827398084e5993f9e2ae1e825f51 | Python | 4,364 | 119 | import logging
import numpy as np
logger = logging.getLogger(__name__)
def expand_to_dim(values, dim):
expanded = []
for v in values:
if not isinstance(v, (tuple, list, np.ndarray)):
v = [v]
if isinstance(v, np.ndarray):
v = list(v)
if len(v) != dim:
... |
5180a33a4d77e897d6f75ec5fd3c94d77eb6771f674ef14fa25816e80ce8319c | Python | 4,367 | 130 | import torch
from torch import nn
def skip_connection(
in_features, out_features, n_dim=2, bias=False, skip_type="soft-gating"
):
"""A wrapper for several types of skip connections.
Returns an nn.Module skip connections, one of {'identity', 'linear', soft-gating'}
Parameters
----------
in_fe... |
843fc4ad0cc428d8b7174ffe700d9bb0f2f064f60831b02392e80dcc9c16900e | Python | 4,367 | 120 | # -*- coding: utf-8 -*-
"""
Created on Sun May 22 21:44:18 2022
@author: earg8
"""
from PIL import Image
from numpy import asarray
import numpy as np
from skimage import filters
from skimage.color import rgb2gray
from attention import Attention
class InputReader:
def __init__(self, numPixels = 108, state = ... |
32f87d45d6450865f12479d91ee06490388bfed1568902280b4736fc7f8c7c7a | Python | 4,368 | 111 | """
A randomly sampling batch sequence object
Samples randomly across uniformly randomly selected SleepStudy objects
Does not sample uniformly across classes (see BalancedRandomBatchSequence).
"""
import logging
import numpy as np
from utime.sequences import BatchSequence
logger = logging.getLogger(__name__)
class ... |
9b7ac4f1e603f1589a26d921889e5c30f3302fe03b40b64b9b9a002b429e0d2a | Python | 4,368 | 143 | import torch.nn as nn
import torch.nn.functional as F
import torch
class AttU_Net(nn.Module):
def __init__(self, classes=2, aux=True):
super(AttU_Net, self).__init__()
n1 = 64
filters = [n1, n1 * 2, n1 * 4, n1 * 8, n1 * 16]
self.Maxpool1 = nn.MaxPool2d(kernel_size=2, stride=2)
... |
c08f6b3cefb33dcf48d318b9ab3a65e01bb80755d78957752d8d99b7c456be34 | Python | 4,368 | 136 | from cgtasknet.tasks.reduce import (
CtxDMTask,
CtxDM1,
CtxDM2,
CtxDMTaskParameters,
)
def test_dm_task_size():
assert CtxDMTask().feature_and_act_size == (3, 3)
assert CtxDM1().feature_and_act_size == (3, 3)
assert CtxDM2().feature_and_act_size == (3, 3)
def test_ctx_task_run_one_data_s... |
739e9e6e367aa46ac553dbf30a09d1caf55b1b8179a9a1704c56910f35317776 | Python | 4,370 | 119 | import numpy as np
from . import kt, models
__author__ = "jieqing jiao <jieqing.jiao@gmail.com>"
class TAC:
def __init__(self, tac, dt):
self.tac = tac
self.dt = dt
self.mft = kt.dt2mft(dt)
self.km_results = []
def run_model(self, model_name, model_inputs):
km_resul... |
1419bc353dd5cb83646b0743ae09383a8d276237d7b0bfb80a1aad662b9c5f11 | Python | 4,371 | 106 | # -*- coding: utf-8 -*-
# Versión 3.0 clase posición reducida
# Autor: José Miguel Ramírez Sanz
#imports
import numpy as np
import math
#Posiciones versión 3.0 reducida
class Posicion():
# param x: lista con los valores del eje x de los puntos obtenidos con detectron
#param y: lista con los valores del ... |
012de6d9a00cd34951669ce651ee1bdd4ecf10686c289389ef93a5baa70384a3 | Python | 4,372 | 103 | # 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... |
9f209fac57109a5a62d5abaf8f5d2e6d952d137727314a3f6aa5e35bf05a2ee0 | Python | 4,373 | 135 | from Classes.RelationshipMap import RelationshipMap
from Classes.RelationshipCollection import RelationshipCollection
from Classes.SearchComponent import SearchComponent
class RelationshipIdentifier(SearchComponent):
def GetDirectRelationships(self, keywords):
# Search between keyword matches and subreg... |
bf777c5fdb1eb38a633aa72486eecc494c81b2d7c945c755bd4c9870650011a6 | Python | 4,374 | 147 | """
interfaces
Created by: Martin Sicho
On: 06.04.22, 16:54
"""
from abc import ABC, abstractmethod
from drugex.logs import logger
from drugex.molecules.converters.interfaces import ConversionException
class Molecule(ABC):
@abstractmethod
def annotate(self, key, value):
pass
@abstractmethod
... |
01142d159fc79f95c146286646609bb756f14dec535f2b66a951e8ab1330b56f | Python | 4,375 | 143 | from abc import ABC, abstractmethod
from drugex.logs import logger
from drugex.molecules.converters.interfaces import ConversionException
class Molecule(ABC):
@abstractmethod
def annotate(self, key, value):
pass
@abstractmethod
def getAnnotation(self, key):
pass
@abstractmethod
... |
cdde1046140d3bff29c7908516765c2d0e1bfdc9c9a9749d8e21b6798b06427a | Python | 4,375 | 97 | # 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... |
e440f23f9e88f14391ff7a086283522d9d3e787ea14d9a48bb797231722d26ef | Python | 4,377 | 125 | # A simple torch style logger
# (C) Wei YANG 2017
from __future__ import absolute_import
import matplotlib.pyplot as plt
import numpy as np
__all__ = ['Logger', 'LoggerMonitor', 'savefig']
def savefig(fname, dpi=None):
dpi = 150 if dpi == None else dpi
plt.savefig(fname, dpi=dpi)
def plot_overlap(logger,... |
2ed6102fcd53ac35d62205d3a391e6c0798317af66dceda0a77341bd0f507186 | Python | 4,378 | 136 | """Configuration file for pytest.
Initialize different fixtures for automatically loading test transcripts and creating objects for
testing. Keeping the test data for full transcript (subsections) in csv files helps keep the test
files clean and readable. Other long strings, that do not need the hook for automatic gen... |
35e2501969cd56bf2f87e663f75e71006717d776371b693cbba30a1b9e6582b9 | Python | 4,378 | 130 | import torch
from torch import nn
import regression_model
class GeneratorLoss(nn.Module):
def __init__(self, model_path, device):
super(GeneratorLoss, self).__init__()
ctf_model = regression_model.ResidualLowpass()
ctf_model.to(device)
checkpoint = torch.load(model_path)
ctf_model.load_state_dict(checkpoin... |
f350c6f0c3ac609779f92790aa53ef18dfa60f7f673adaf36b52867250c49f68 | Python | 4,378 | 96 | from .vehicle_wheel_smoke_test import VehicleWheelSmokeTest
import carla
import math
# A steered front wheel passes well beyond this while the vehicle is turning,
# and settles well inside it once the steering command returns to centre. The
# exact angle depends on the asset's steering curve, so nothing here asserts ... |
feb5253299c1abac509980e8243a119ffc33ddf16a09b2f086996a79739c980e | Python | 4,378 | 167 | #%%
from pathlib import Path
import colorcet as cc
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import seaborn as sns
from umap import UMAP
from graspologic.embed import LaplacianSpectralEmbed
from graspologic.plot import heatmap, pairplot
from graspologic.utils import ... |
e041c1be57d933f00dd27dfbb0b6f8a5bac2db1d4578b81c6fc7d7a1576ab710 | Python | 4,379 | 109 | import logging
from typing import Callable
from tensorboardX import SummaryWriter
import torch
import torch.nn as nn
from torch.optim import Optimizer
from torch.optim.lr_scheduler import _LRScheduler
from tqdm import tqdm
from chemprop.args import TrainArgs
from chemprop.data import MoleculeDataLoader, MoleculeDatas... |
ec78488a729e42060aa5165005396d98dc22e599622f8fd1de723702eee7a94e | Python | 4,379 | 149 | import gzip
import logging
import sys
from typing import List, Optional
import click
from semsql.sqla.semsql import ObjectPropertyNode, Statements
from oaklib import get_adapter
from oaklib.datamodels.vocabulary import (
DESCRIPTION,
EQUIVALENT_CLASS,
HAS_DEFINITION_CURIE,
OWL_SOME_VALUES_FROM,
RD... |
fbe96d7d060dfaf47a0788fcd6fc53b2a657b499a9194a92affe599e65bea6a3 | Python | 4,380 | 150 | #%% IMPORT MODULES
from __future__ import division
import os
from textwrap import dedent
import pandas as pd
import h5py
from ezephys.rectools import ABFLoader
from grr.CurveFit import extract_gating_data, fit_gating_curve
#%% LOAD DATA
OUTPUT_PATH = os.path.join(os.getenv('DATA_PATH'), 'processed', '5HT')
if no... |
735979d80c49f686573db40f36190c5ba9fbea8317c3f3f1375129aa453534cd | Python | 4,382 | 125 | import pandas as pd
import random
import pickle
from src.preprocess import standardization_pipeline, remove_smiles_duplicates
if __name__ == "__main__":
# set random seed, used for error generation & initiation transformer
SEED = 42
random.seed(SEED)
name = 'selective_ki'
errors_per_molecule... |
65195700fb30ad1ad4bf7565347fa6fa8c65146f8b6a03ea41a53b45cef36d56 | Python | 4,386 | 136 | # model settings
model = dict(
type='MaskRCNN',
pretrained='torchvision://resnet50',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=1,
norm_cfg=dict(type='BN', requires_grad=True),
norm_eval=True,
... |
ab94c570768bfb8c8c41b58fd647356b002378cba2030207d63ee76718b936a1 | Python | 4,386 | 138 | # Code adopted from https://github.com/tomasjakab/keypointgan
import os
import torch
import re
import numpy as np
from collections import defaultdict
def swap_points(points, correspondences):
"""
points: B x N x D
"""
permutation = list(range((points.shape[1])))
for a, b in correspondences:
... |
11325c926ad6cb0b3ce6606705e2e4344d148165ebcf34ad76ef083b98c7dcf9 | Python | 4,387 | 185 | """
Create pipeline
===============
Sample file to create a pipeline.
"""
# %%
# First of all, lets import the main libraries and load the iris data.
# Generic
import os
import yaml
import time
import torch
import pickle
import pprint
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
# Librari... |
365df63d8d4bc3d078b89a9c219982798c2964305721d07ae7482babcfa6a117 | Python | 4,387 | 86 | #! /usr/bin/env python3
"""Python API, single-view Cosmos 3 with the world-scenario (``wsm``) control.
python api_cosmos3_wsm.py --clip ./clips/carla_town10_1700000000 \\
--prompt "heavy rain, headlights on" [--backend cosmos3-super] [--results ./cosmos-results]
The clip's ClipGT scene package (``<clip>/s... |
693c69f1edd2465a8d8035ceed36438268ddfa00f94f7e47cfadf7c2aac7cd1e | Python | 4,388 | 131 | ###################################################################
####
#### Version: 1.1.7
#### Date: 6/24/2023
#### Description: This contains all the functions used to create GUI elements.
#### Author: Evan Cobb
####
###################################################################
import sys
from PyQt5.QtWidge... |
75755a8720b24a7820792ed37de89443c7a0de5a3bdb170fbdef43f09a164a50 | Python | 4,389 | 125 | __author__ = 'jieqing jiao'
__email__ = "jieqing.jiao@gmail.com"
from . import models
from . import kt
import numpy as np
class TAC:
def __init__(self, tac, dt):
self.tac = tac
self.dt = dt
self.mft = kt.dt2mft(dt)
self.km_results = []
def run_model(self, model_name, model_... |
b0616c1a61b04549cd14f46b8919798fd6e62edc4f6a521c0e1919b87a01c63d | Python | 4,390 | 112 | # 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... |
18fffa06d9dd17f9c0ab52a08f9b79315e29545d6182a372c35508e2495d81a7 | Python | 4,392 | 118 | import pytest
from kgcl_schema.grammar.render_operations import render
from oaklib import get_adapter
from oaklib.datamodels.synonymizer_datamodel import RuleSet, Synonymizer
from oaklib.utilities.lexical.synonymizer import apply_synonymizer, apply_synonymizer_to_terms
from tests import CYTOPLASM, INPUT_DIR, NUCLEAR_M... |
3e65b6f3b333b750b399e89d45498541c72ecdbc735ee929b50f01534b28ac74 | Python | 4,392 | 101 | import sys
sys.path.append("/Volumes/GoogleDrive/My Drive/python_code/connectome_tools/")
import networkx as nx
from networkx.utils import pairwise
import pandas as pd
import numpy as np
import connectome_tools.process_skeletons as proskel
import math
from tqdm import tqdm
import csv
# import and split skeletons int... |
0a458b7d655bc9c53501bf18e326e15a163ba7b333f1907c114418b23579db92 | Python | 4,393 | 125 | # 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... |
1b9ff458b99e1f7927f26c7ee3e53b3e52b7f43fd0d84b5e5c9570d6ada9e641 | Python | 4,393 | 135 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 27 17:45:40 2022
@author: spiros
"""
import os
import pickle
import pandas as pd
def zero_entries(df):
return df[(df.values == 0).any(axis=1)].index.values.tolist()
dirname = "data_synapses_new2/"
with open(dirname + 'circuitry_analyzed.pkl... |
44cfd68c4151933186ba6298d7663f148c0aefc80a4df4e601ceb027082aa3d4 | Python | 4,393 | 114 | '''
Inspired by https://stackoverflow.com/a/24092195
Use `run_parallel` function to parallelize a job.
Important:
- Threads have access to the same memory.
- Must be careful that they don't overwrite some shared object.
- Can cause a slowdown when reading shared memory.
- The most natural way to avoid these prob... |
8258e8c3782bc70c92703a14be9683c42e3b707c57e10efd12d774f2bfef4a66 | Python | 4,393 | 154 |
if __name__ == '__main__':
# ------------------
# Libraries
# ------------------
# Generic libraries
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
# Basic functions in sklearn
from sklearn import datasets
from sklearn import metrics
from sklear... |
93917896c2c2c6abf1e7e1a55236f2d9cd53b7971a9f9cbe442783700b363074 | Python | 4,394 | 164 | """Example script for training HIVE on HMM simulated data.
- Should achieve a dice score close to 1.
"""
import os
import numpy as np
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from osl_dynamics import data, simulation
from osl_dynamics.inference import metrics, modes, tf_ops
from osl_dynam... |
96c4ec5d19273e9b0d13878218d1aed1f2bacc2d252aa7a1f2180d887b993aa9 | Python | 4,397 | 115 | from dash_extensions.enrich import Serverside, Output, Input, State, callback, clientside_callback, ctx
from dash.exceptions import PreventUpdate
import numpy as np
import RV.constants as c
def register_scale_callbacks():
# Update scale using +/- keys on keyboard
clientside_callback(
"""
... |
9e787f65834961037058e29407594d49f9effba1cecbc1c032db446058a4205f | Python | 4,397 | 135 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 27 17:45:40 2022
@author: spiros
"""
import os
import pickle
import pandas as pd
def zero_entries(df):
return df[(df.values == 0).any(axis=1)].index.values.tolist()
dirname = "data_synapses_new2/"
with open(dirname + 'circuitry_analyzed.pkl... |
aa5a363940f18d1348e7a964e1ca7495ea3c5cfcf9858051fb1efe9a0bef486a | Python | 4,397 | 150 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import pathlib
import sys
import unetsl.data
import skimage.draw
import random
SPECKLE_TAG="%start speckle%"
WIDTH=64
import numpy
class Box:
def __init__(self, x, y, w, h):
self.x = x
self.y = y
self.w = w
self.h = h
def conta... |
322e83ceb10444ecacf616dcbfa9885d33b4ab82ef16f0bd36cffe26529e7013 | Python | 4,398 | 98 | # basic imports
import numpy as np
import pickle
import matplotlib.pyplot as plt
def load_data() -> dict:
'''
This function loads simulation data and prepares it.
Parameters
----------
None
Returns
----------
data : The prepared data.
'''
... |
7c8a4d19e30b39b8ddcf6e10ed0638fe562ea0f02be7fca0c83420617fe3ea69 | Python | 4,399 | 126 | dataset_type = 'CocoDataset'
#data_root = './data_wenhekoulou/coco/'
data_root = './data/coco/'
img_norm_cfg = dict(
mean=[123.675, 116.28, 103.53], std=[58.395, 57.12, 57.375], to_rgb=True)
albu_train_transforms = [
dict(
type='ShiftScaleRotate',
shift_limit=0.0625,
scale_limit=0.0,
... |
743e332ab8485e8b4a690edff1027dcd4dba9d8f775925b45560d61026fd9bac | Python | 4,401 | 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... |
db970a089141f8a27f867848e0c939a8ed299bb98c284a06bf8358e182e3efcf | Python | 4,401 | 121 | """Version-neutral TCP transport between CARLA Python 3.10 and Alpamayo Python 3.12."""
from __future__ import annotations
import json
import socket
import struct
from dataclasses import dataclass
from typing import Any, Mapping
import numpy as np
MAGIC = b"CA2S"
VERSION = 1
MAX_HEADER_BYTES = 1 << 20
MAX_ARRAY_BY... |
e3189e8455b34091cdb721b3200d1abf409d7e0c33d435e9f7441b68a9fa72da | Python | 4,401 | 119 | import warnings
import mmcv
from ..builder import PIPELINES
from .compose import Compose
@PIPELINES.register_module()
class MultiScaleFlipAug(object):
"""Test-time augmentation with multiple scales and flipping.
An example configuration is as followed:
.. code-block::
img_scale=[(1333, 400), ... |
79e1b2564837f263dfc881a9dbf7427698afd5001394e634d9052715d135389e | Python | 4,402 | 134 | #!/usr/bin/env python
# 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>.
"""Visualize the radar data"""
import argparse
import math
from numpy import... |
b62a48ecf9e81c18ba733bffad39d3ab2ef86c9f1dfdc68c2eb44b7fd64a1ba1 | Python | 4,402 | 93 | """
This file contains code that will read Google Earth annotation files from an s3 bucket and saves the contained
information in pandas dataframes as feather files.
@author rdalrymple
"""
import boto3
import pandas as pd
import numpy as np
from datetime import datetime
from bs4 import BeautifulSoup
from tq... |
22acd16b0d6aeb5f4dad442dedc48cf4016c1f68c1a17a535440a4f9ad9773e0 | Python | 4,403 | 120 | '''
@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... |
6821e74f4af898e62778b3c5e23b14479dad7cc39820b7bdfe62a88142ad7997 | Python | 4,403 | 131 | """
PyTorch dataset classes (torch.utils.data.Dataset) for flat data (non-graphs).
Refer to the pytorch dataset tutorial page for the concept of Dataset and DataLoader.
"""
import os, json
import torch
import numpy as np
import h5py
from torch.utils.data import Dataset, DataLoader
import sys
DEFAULT_DTYPE = torch.floa... |
8cd717de250b1b5bf10b34afbe02550183ad0c5a65d5bbcb0b832deadaf9acb4 | Python | 4,404 | 113 | #!/usr/bin/env python3
# encoding: utf-8
import argparse
import os
import os.path as osp
import cv2
import numpy as np
import torch
import torch.multiprocessing as mp
from config import config
from datasets.cityscapes.cityscapes import Cityscapes
from engine.evaluator import Evaluator
from engine.logger import get_lo... |
67926ba2f77ef6551523a525df7e36c3fbd15d0493c97223daaa45da5d1ab814 | Python | 4,405 | 123 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
import torchvision
import os
from PIL import Image
from maskrcnn_benchmark.structures.bounding_box import BoxList
from maskrcnn_benchmark.structures.segmentation_mask import SegmentationMask
from maskrcnn_benchmark.structures.keypoint... |
9ae61cbb98629190cb4f87c155984383ac335c9b94730708e5bb65ffc34ff56d | Python | 4,405 | 120 | from pymol import stored
def interfaceResidues(cmpx, cA="c. A", cB="c. B", cutoff=1.0, selName="interface"):
"""
http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/interface.php
interfaceResidues -- finds 'interface' residues between two chains in a complex.
PARAMS
... |
dffa2c132d61a7dbbec9096b210a68d3aa0292d4aaa47f7df70acd1420fe37cd | Python | 4,405 | 108 | # 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... |
a4ba97cad7890bf0ec8ab614e2d9dd2502cf99089bedb272b44414e12a3df553 | Python | 4,410 | 115 | # Built-in
from pathlib import Path
# Third-party
import brian2 as b2
import matplotlib
from matplotlib import pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
# Local
from cxsystem2.core.tools import load_from_file
class rasterplot_pdf_generator:
def __init__(
self, workspace_path: st... |
a6f030971401c2b0806d5f2775709c20195db965c00f9bfb9eacce33e77f35c4 | Python | 4,414 | 126 | import os
import csv
import sys
import time
import subprocess
LOG_FILE = "validation.log"
ONLY_ANALYSIS = False
'''
Instances and seeds used for the article 'Binary Classification On Hypergraphs'
'''
INSTANCES = [
('adult', None), # 1509029032), # 0.8217306
#('audiology', 1506863181), # 0.9886078
#('breas... |
097cf1285306c03d90effaba9514c90ebb0b9f579b8d921eb1bb38863778f6a8 | Python | 4,415 | 117 | from __future__ import print_function, division, absolute_import
import torch.nn as nn
from seg_opr.seg_oprs import ConvBnRelu
from utils.pyt_utils import load_model
__all__ = ['Xception', 'xception39']
class SeparableConvBnRelu(nn.Module):
def __init__(self, in_channels, out_channels, kernel_size=1, stride=1,
... |
43864a3cef80e71c11e781a218ea4af86a07cc90a2948d4ce8ab9da4c629c13d | Python | 4,415 | 123 | """
utils
Created by: Martin Sicho
On: 17.05.22, 9:55
"""
import os
import re
import json
import shutil
import logging
import datetime
import git
from drugex.logs import config, setLogger, logger
from drugex.logs.config import LogFileConfig
BACKUP_DIR_FOLDER_PREFIX = 'backup'
def commit_hash(GIT_PATH):
try:
... |
7bab7c23da6afb30dff1c3c10b405ce791e9609935bbdaa0fbfff3e33b8a623f | Python | 4,415 | 134 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import pytest
from eelbrain import Factor, datasets, plot
from eelbrain._wxgui.testing import hide_plots
@hide_plots
@pytest.mark.parametrize('Barplot', [plot.Barplot, plot.BarplotHorizontal])
def test_barplots(Barplot):
"Test plot.Barplot"
ds = dataset... |
fd43735fc9157d2923b51be85caa6b07e93a8df2764d814931f3390ca718ccce | Python | 4,417 | 144 | import torch
import torch.nn as nn
import numpy as np
def conv3x3(in_planes, out_planes, stride=1):
"""3x3 convolution with padding"""
return nn.Conv2d(in_planes, out_planes, kernel_size=3, stride=stride,
padding=1, bias=False)
class BasicBlock(nn.Module):
expansion = 1
def __i... |
6c51f37a96d353f80c0521c594c6363741372ae61c53d321ddde4b8e7f8fbbb7 | Python | 4,418 | 158 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from math import floor
import numpy as np
from numpy import newaxis
FULL_SLICE = slice(None)
FULL_AXIS_SLICE = (FULL_SLICE,)
INT_TYPES = (int, np.integer)
def digitize_index(index: float, values: np.ndarray, tol: float=None):
"""Locate a scalar ``index``... |
c0aad1cb4e243e555c85f74bede0b5c66544fd53f32bf42532e7a3d0bd22a8aa | Python | 4,422 | 104 | """Exports a YOLOv5 *.pt model to ONNX and TorchScript formats
Usage:
$ export PYTHONPATH="$PWD" && python models/export.py --weights ./weights/yolov5s.pt --img 640 --batch 1
"""
import argparse
import sys
import time
sys.path.append('./') # to run '$ python *.py' files in subdirectories
import torch
import to... |
0410600452023ea5275679c4e2da86be25ea76c760876160cb753b5c07e6d993 | Python | 4,423 | 112 | # 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... |
68bdb98df363464ce56f4778e387b9b5f5cc91dfc9346abf132bf33633d0e131 | Python | 4,424 | 100 | #!/usr/bin/env python
# Copyright 2014 Johns Hopkins University (Authors: Vijayaditya Peddinti). Apache 2.0.
# 2015 Tom Ko
# script to generate multicondition training data / dev data / test data
import argparse, glob, math, os, random, scipy.io.wavfile, sys
class list_cyclic_iterator(object):
def __ini... |
fb4704d8dcbfeceb40ce2bead6250e5cf0385767281ce728604b1a9013f797a2 | Python | 4,426 | 128 | #!/usr/bin/env python3
# Copyright 2016 David Snyder
# 2017 Matthew Maciejewski
# Apache 2.0.
"""This script converts a segments and labels file to a NIST RTTM
file. It creates flat segmentation (i.e. no overlapping regions)
from overlapping segments, e.g. the output of a sliding-window
diarization syst... |
5b40829ef71e5958b9c5ee15113a672d795df2e47dbf1e73e2809adb67d90591 | Python | 4,431 | 150 | #%%
from pathlib import Path
import networkx as nx
import numpy as np
import pandas as pd
import pymaid
from src.pymaid import start_instance
from src.visualization import adjplot
#%%
date = "2021-03-10"
def load_meta():
meta = pd.read_csv(
f"maggot_models/data/processed/{date}/meta_data.csv", index_c... |
00c33b3a0b2c95c93405929f2e36998e653c0c8d1f4cb412c29edc71e9a97f89 | Python | 4,434 | 171 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 27 14:53:08 2021
@author: Hiroshi Yokoyama
"""
from IPython import get_ipython
from copy import deepcopy, copy
get_ipython().magic('reset -sf')
#get_ipython().magic('cls')
import os
current_path = os.path.dirname(__file__)
os.chdir(current_path)
f... |
18204e7331699fdb1d273c1fb21d7ed927e215502fdc6b6fbb3fa7edc85c5912 | Python | 4,438 | 122 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Variational Animal Motion Embedding 1.0-alpha Toolbox
© K. Luxem & P. Bauer, Department of Cellular Neuroscience
Leibniz Institute for Neurobiology, Magdeburg, Germany
https://github.com/LINCellularNeuroscience/VAME
Licensed under GNU General Public License v3.0
"""
... |
76eb8ed249b753a9231d1c209e09148fea8e5d5bb98572122e0a67b27f4e48d4 | Python | 4,438 | 151 | from abc import abstractmethod
from typing import List
import torch
class Transform(torch.nn.Module):
"""
Applies transforms or inverse transforms to
model inputs or outputs, respectively
"""
def __init__(self):
super().__init__()
@abstractmethod
def transform(self):
pas... |
c2f31c03b03f5164e81b278dbd30dfb3a1f83986f812d6ddd01c508650995034 | Python | 4,438 | 119 | import torch
import torch.nn as nn
import torch.nn.functional as F
class DilatedParllelConvBlock(nn.Module):
def __init__(self, nIn, nOut, add=True):
super(DilatedParllelConvBlock, self).__init__()
self.conv0 = nn.Conv2d(nIn, nOut, 1, stride=1, padding=0, dilation=1, groups=1, bias=False)
s... |
80331ffa95d20ec5aea10a818c9e9fd4d5f0463cdecb5773adf7fc3e4a9d202b | Python | 4,439 | 109 | from lab.nilm_experiments import *
from constants.constants import *
from constants.enumerates import *
devs_taus = {
ElectricalAppliances.KETTLE: 0.7, #0.5
ElectricalAppliances.MICROWAVE: 0.975,
ElectricalAppliances.FRIDGE: 0.9,
ElectricalAppliances.WASHING_MACHINE: 0.5, #0.025,
ElectricalApplianc... |
7cce72b4e45069bea44526718af6a844bdaac78c0d08d4e4497bebaab5e34fb2 | Python | 4,440 | 118 | import torch
import torchvision.transforms as TT
from maskrcnn_benchmark.config import cfg
from maskrcnn_benchmark.data import transforms as T
from maskrcnn_benchmark.structures.image_list import to_image_list
from maskrcnn_benchmark.structures.bounding_box import BoxList
from maskrcnn_benchmark.modeling.roi_heads.box... |
1e5967d9c375721e69436badbca76cbbb29bf207f1e0d499caa8268d3d1a00d8 | Python | 4,441 | 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 a... |
693d26c5f2d2f4baf4bcf09abe90106a7d0dd74798b85088d68fbfcfbb4e4bb8 | Python | 4,442 | 120 | import os
from os.path import join
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import ShuffleSplit, GridSearchCV
from sklearn.metrics import (mean_absolute_error, mean_squared_error,
... |
eaec08d6b36eb9338da2ee9918d3049b40ad8f22c606f6bb335e5ca945f6a2bb | Python | 4,443 | 96 | # 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... |
2536c2a7b7adf5f172c9c44e6933e7dcf902dbd93f99ded1c25e8a703f2dff50 | Python | 4,444 | 104 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Softmax
from models.baselines.segbase import SegBaseModel
__all__ = ['CCNet']
class CCNet(SegBaseModel):
def __init__(self, classes=2, aux=True, backbone='resnet50', pretrained_base=True):
super(CCNet, self).__init__(c... |
8a783d228ce0faaf9d12f545fc3668d5a0f8ae27169b29c307a0d54a401b4f59 | Python | 4,448 | 105 | import pandas as pd
import os
from argparse import ArgumentParser
import re
DICT_MODEL_NAMES = {'BASELINE': 'BL',
'SEGGUIDED': 'SG',
'UW': 'UW'}
DICT_METRICS_NAMES = {'NCC': 'N',
'SSIM': 'S',
'DICE': 'D',
'DICE ... |
0eb762d612cc6c0bba54da544d03e828172c8f41209613df07b8f770ba3d15b5 | Python | 4,449 | 112 | __author__ = "Jianfeng Sun"
__version__ = "v1.0"
__copyright__ = "Copyright 2023"
__license__ = "GPL v3.0"
__email__ = "jianfeng.sunmt@gmail.com"
__maintainer__ = "Jianfeng Sun"
from typing import Optional
import pandas as pd
from tmkit.seqnetrr.combo.Param import Param
class Separation(Param):
"""
Class f... |
25794b531b86ef23699fe3c2ad828e47f0ef51f1581eb018f937df9d375880d7 | Python | 4,450 | 100 | import random
import torch
import torch.nn.functional as F
def if_edge_exists(edge_index: torch.Tensor, node1: int, node2: int):
'''
Quick lookup for if an edge exists b/w `node1` and `node2`
'''
p1 = torch.any((edge_index[0,:] == node1) & (edge_index[1,:] == node2))
p2 = torch.any((edge_index... |
01a0e6b8ef085db3a9ea2c7e9cf1edd2c4e1d0f787085ae907131ffeb40ae319 | Python | 4,452 | 123 | # 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... |
b26220e86f6bccefddcc380e27132911c2fab60877b412d18bad7f23b18a6752 | Python | 4,452 | 131 | from __future__ import division
import argparse
import os
import os.path as osp
import sys
import time
sys.path.append(osp.join(sys.path[0], '..'))
import torch
from torch.utils import data
import models
from mmcv import Config
from mmdet import __version__
from mmdet.apis import (get_root_logger, init_dist, set_ran... |
6669077901cab386363672d9313a6a838ab78aa9f28b9978f165b75e16101b41 | Python | 4,454 | 113 | # 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... |
8c4ae943c2b739e1b85a24699ca394513b29b55181907ef1b72a0b8b11d170e6 | Python | 4,454 | 127 | """Abstract Base Class Adapter for EUtils."""
import logging
import os
import time
from abc import ABC
from dataclasses import dataclass
from typing import ClassVar, Iterable, Iterator, List, Optional, Tuple
from xml.etree.ElementTree import Element # noqa S405
import requests
import requests_cache
from defusedxml.E... |
54fa4440bf9dde53992ccdfe72010c77e10d978430b225cb97c15d82aa2301a9 | Python | 4,456 | 74 | import numpy as np
import pytest
from simphox.grid import Port
from simphox.sim import SimGrid
from simphox.typing import Size, Size2, Size3, Size4, Union, List, MeasureInfo
np.random.seed(0)
EPS_20_20 = 1 + np.random.rand(20, 20) + np.random.rand(20, 20) * 1j
SOURCE_20_20 = np.random.rand(2, 3, 20, 20) + np.random.... |
0a8faf60a48e2bba49612dc1e4f45a56c077ee1b03b1ee42f332e0f1a1ba09dc | Python | 4,457 | 114 | from collections import defaultdict
import logging
from typing import Dict, List
from .predict import predict
from chemprop.data import MoleculeDataLoader, StandardScaler
from chemprop.models import MoleculeModel
from chemprop.utils import get_metric_func
def evaluate_predictions(preds: List[List[float]],
... |
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