sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b77272e5cde3e18072ebecc3b35fd5a9bb17502b4ce54d11d1af10e6738ee69f | Python | 3,712 | 91 | import torch.nn as nn
from .shuffle_blocks import ConvBNReLU, ShuffleNetV2BlockSearched, blocks_key, FC
class ShuffleNetV2DetNAS(nn.Module):
def __init__(self, model_size='DETNAS-300M'):
super(ShuffleNetV2DetNAS, self).__init__()
print('Model size is {}.'.format(model_size))
n_class = 100... |
b82ff373e74b2966ba15a5b23902bc9c5f4fe2a676c918894349b9918560d44e | Python | 3,714 | 122 | import os
import types
# internal imports
from slideflow.clam.utils.file_utils import save_pkl
from slideflow.clam.utils import *
from slideflow.clam.datasets.dataset_generic import Generic_MIL_Dataset
from slideflow.clam.utils.core_utils import train
from slideflow.clam.utils.eval_utils import *
# pytorch imports
im... |
e03f4354bd5a65716f09b33cba314613072d204e82a30c3d9db415ceffb4a979 | Python | 3,715 | 85 | # Copyright (c) Open-MMLab. All rights reserved.
from collections.abc import Mapping, Sequence
import torch
import torch.nn.functional as F
from torch.utils.data.dataloader import default_collate
from .data_container import DataContainer
def collate(batch, samples_per_gpu=1):
"""Puts each data field into a tens... |
fcea61cfc6583d39a4fe9265a92403f5e690d73cfbc581a36ee360e21dd23274 | Python | 3,716 | 129 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import torch
from .bounding_box import BoxList
from maskrcnn_benchmark.layers import nms as _box_nms
def boxlist_nms(boxlist, nms_thresh, max_proposals=-1, score_field="scores"):
"""
Performs non-maximum suppression on a boxlist, with s... |
130d6ad049fd26e13c8d9dbe6b555302223598c3d5f6c7d90bfe7a458d01bf1a | Python | 3,717 | 129 | import logging
from typing import List, Optional, Union
from pydantic import BaseModel
from oaklib import BasicOntologyInterface
from oaklib.datamodels.vocabulary import HAS_PART, PART_OF
from oaklib.interfaces import OboGraphInterface
from oaklib.query import Query, ancestor_of, descendant_of, subclass_of
from oakli... |
0d28ef4d2c79dc6f304d7ef458a9b2a82b24ba251329941fce99969ebf09b10a | Python | 3,719 | 116 | from __future__ import division
from builtins import object
# Unit tests for sima/spikes.py
# Tests follow conventions for NumPy/SciPy available at
# https://github.com/numpy/numpy/blob/master/doc/TESTS.rst.txt
# use assert_() and related functions over the built in assert to ensure tests
# run properly, beardless of ... |
1ed988ac64d2dc196ebd6b59b6893d9329dea4d6aa84ff194cfa0367fa986622 | Python | 3,719 | 108 | import os
import numpy as np
from IPython.core.debugger import set_trace
import importlib
import sys
from default_config.masif_opts import masif_opts
from masif_modules.MaSIF_ligand import MaSIF_ligand
from masif_modules.read_ligand_tfrecords import _parse_function
from sklearn.metrics import confusion_matrix
import te... |
e129876ccfe3a54b21f268e72695433529e9d105a6fb14a734b9393275748c4b | Python | 3,719 | 109 | #!/usr/bin/env python
#######################################################################
#######################################################################
## Created on January 23rd 2019 to get autosomes from samtools FAI file
#######################################################################
#########... |
f9f567b818c35f995dc4977059673ccf4b6771e6420d48eaf3c3fd37cc2db33b | Python | 3,719 | 103 | #!/usr/bin/env python3
import glob
import itertools
import os
import pytz
import click
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.signal as sg
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error, mean_absolute_error
SRC_DATA_DIR =... |
81a694fea836419de3312a1f28f8cb8bddb7ad7818ac7becbec1dde1465d957d | Python | 3,720 | 107 | """
Entry script redirecting all command line arguments to a specified script
from the utime.bin folder.
Usage:
ut [--help] script [script args]... [--seed]
"""
import logging
import argparse
import os
import sys
import importlib
import pkgutil
import psg_utils
from utime import bin, Defaults
from utime.version impor... |
c4da75d42e37af5f341a78e8397a5c0c9d700fc35d2dd86b874109d336516389 | Python | 3,720 | 118 | """
An example model that has double the number of convolutional layers
that DeepSEA (Zhou & Troyanskaya, 2015) has. Otherwise, the architecture
is identical to DeepSEA.
We make no claims about the performance of this model. It is being stored
in `utils` so it can be easily loaded in the Jupyter notebook tutorials
for... |
5e4f6e980936dc604e8d11dad006debc6257409dad5d64b1dc3af061844e2010 | Python | 3,722 | 124 | # SCSCSCSCSCSCSCSCSCSC
# CSB Lab | Indian Institute of Science, Bengaluru
# Chinmay K Haritas
# Toggle Triad in 2D with Diffusion
# %%
print("\nSpatial GRNs - Toggle Triad in 2D\n")
# Import Block
import helpers
from tt_vars import *
from helpers import hill, p_i
np, pd, plt, tqdm, time, njit, prange, animator, ma... |
ee1f3bbf65928b46844b44419deae7a30f579df2c80faf0e0956a6cbbeacd813 | Python | 3,722 | 83 | import tempfile
masif_opts = {}
# Default directories
masif_opts["raw_pdb_dir"] = "data_preparation/00-raw_pdbs/"
masif_opts["pdb_chain_dir"] = "data_preparation/01-benchmark_pdbs/"
masif_opts["ply_chain_dir"] = "data_preparation/01-benchmark_surfaces/"
masif_opts["tmp_dir"] = tempfile.gettempdir()
masif_opts["ply_fil... |
f8b69bab4522338e368a8b5f1f09a4b20eaaa061bf70c8513fe04dcf4b21d434 | Python | 3,722 | 124 | # SCSCSCSCSCSCSCSCSCSC
# CSB Lab | Indian Institute of Science, Bengaluru
# Chinmay K Haritas
# Toggle Triad in 2D with Diffusion
# %%
print("\nSpatial GRNs - Toggle Triad in 2D\n")
# Import Block
import helpers
from tt_vars import *
from helpers import hill, p_i
np, pd, plt, tqdm, time, njit, prange, animator, ma... |
507639b431a0e6e038d18c42f3721c8a434d33e92f01ff5584e1f65282ec216e | Python | 3,723 | 247 | ##behavior
behaviors=[
'forward_walking',
'backward_walking',
'pushing',
'rest',
'eye_grooming',
'antennal_grooming',
'foreleg_grooming',
'hindleg_grooming',
'abdominal_grooming',
'proboscis_extension',
'CO2_puff'
]
## Joint_pos = Leg + joint + joint_angle, for example, LF_leg coxa x
list_legs=[
'LF_leg',
'LM_leg... |
6082f4dd11a9bcfc1e61cd4050fc0657dd6d3902021e581813858b31d7563522 | Python | 3,723 | 96 | #!/usr/bin/python
from __future__ import print_function
import sys
import os
import codecs
import argparse
import unicodedata
def process_transcripts(transcripts_dir, transcripts_list):
'''
This looks through each transcript file, and collects the words.
Arguments: transcripts -- file with list o... |
c38a14e447f74ddf5d1d75c43aff46389b3cbb764676d500c7c1f0672fd3a31e | Python | 3,723 | 98 | '''
Author: Naiyuan liu
Github: https://github.com/NNNNAI
Date: 2021-11-23 17:03:58
LastEditors: Naiyuan liu
LastEditTime: 2021-11-24 19:00:42
Description:
'''
import cv2
import torch
import fractions
import numpy as np
from PIL import Image
import torch.nn.functional as F
from torchvision import transforms
from mode... |
5d213fd4e42ef7bc5faa2e351d657d62f13a0b49684af7fa56329cfe64475760 | Python | 3,725 | 80 | from dash_extensions.enrich import Input, Output, callback, clientside_callback, ctx
from dash.exceptions import PreventUpdate
def register_shortcut_callbacks():
# Switch modebar buttons with keyboard
clientside_callback(
"""
function(id) {
document.addEventListener('keydow... |
d1fc872cd4415002e23088ad8017ad39fa1003624b9702ff780dd9848e4d6c6e | Python | 3,725 | 146 | # -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
import time
import nibabel as nib
import numpy as np
import warnings
import scipy
import nibabel as nb
from nipype.interfaces.base import (
TraitedSpec,
File,
... |
c1d79fe786d11975d16f9427d1f1cf0f3fc2bf65f1f8d99e065072a205c72f62 | Python | 3,726 | 128 | import argparse
import sys
import tempfile
from pathlib import Path
import cog
sys.path.insert(0, "base")
from utils.inverter import StyleGANInverter
from utils.visualizer import load_image, resize_image, save_image
class Predictor(cog.Predictor):
def setup(self):
# get default args first
self.... |
549c20708f95cc0f463d79799cbbce103ee2d0b4582aeeb28eb439f420bba2f0 | Python | 3,728 | 113 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
2c204f66e9127d0220b81b5f0e7aa6c6f9a7d68f1ec478a722fcfc746b18019b | Python | 3,730 | 96 | #%%
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from tqdm import tqdm
import pymaid
from pymaid_creds import url, name, password, token
rm = pymaid.CatmaidInstance(url, token, name, password)
from data_settings import data_date, pairs_path
from contools import Promat
... |
7fff41f8eb2410af5993c191cdd89271092b5fec4a17cc925c27471c2a215dd7 | Python | 3,730 | 86 | # 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... |
f7793a16d754405695966861c0e76192c73eb0faa49064fc006533545cbfab03 | Python | 3,730 | 112 | """Controller file for the behavioral classifier
"""
from distutils.command.install_egg_info import to_filename
from dark_ships.behavioral_classifier.transformation_pipeline import process_data, parse_sample, parse_sample_auto, parse_tfrecord, parse_sample_RF, parse_tfrecord_rf
from dark_ships.behavioral_classi... |
033b74f6945faea2c0b35f71ea2f1ebb38f4e7d2687a989b865c79f937028bad | Python | 3,732 | 112 | """
Title
-----
Membrane time constant
Description
-----------
In this example, we show how to calculate a neuron's membrane time constant
``τm``, a metric that describes how quickly the membrane potential ``V`` decays
to its steady-state value after some perturbation. In simple RC circuits, ``τm``
is calculated as th... |
3e3b09806a8709d3459ea1939524e2783d0d3a15e51ecc54cb6b0f625a9eefef | Python | 3,732 | 112 | import logging
from anndata import AnnData
from scvi._compat import Literal
from scvi.core.data_loaders import ScviDataLoader
from scvi.core.models import ArchesMixin, BaseModelClass, RNASeqMixin, VAEMixin
from scvi.core.modules import VAE
from scvi.core.trainers import UnsupervisedTrainer
logger = logging.getLogger... |
4e656c1dfa08cefa7f9758a466546c3e95b814d52ebb7fcba69b5578eac31a65 | Python | 3,734 | 129 | import numpy as np
import joblib
from scipy.special import logsumexp, gammaln
from tqdm.auto import tqdm
def get_obs_parameters(arhmm):
from pybasicbayes.util.general import inv_psd
sigs = [inv_psd(o.sigma, return_chol=True) for o in arhmm.obs_distns]
obs_parameters = {}
obs_parameters["As"] = np.stack([o.A[:, :-... |
e5ba27b934ab8d32fae6d2c61d42e50c617e0873f0a4e71d9fc013a55523c985 | Python | 3,734 | 101 | import time
from typing import Dict, Tuple
import loguru
from nilmtk import MeterGroup
from numba import njit
import numpy as np
from pandas import DataFrame
from datasources.datasource import SITE_METER
from utils.logger import TIMING, debug, timing
def create_multilabels_from_meters(meters: DataFrame, meter_group... |
073fa9dbc186ca7a2c1e27a6d641782b0b326acea1e86fb87a10134d883e4e9c | Python | 3,736 | 96 | # Builtins
from pathlib import Path
import pdb
from typing import Type
from context.context_module_base import ContextBase
class Context(ContextBase):
'''
Set context (paths, filenames, etc) for the project.
Each module orders self.context.property name from context by calling set_context()
Paths and... |
af5f6558bf83590808e0c8bfb5c5f52d3415a4708ecb85d134e2b1e2eecb4f25 | Python | 3,738 | 101 | import pytest
from jax import vjp
import jax.numpy as jnp
from jax.config import config
import jax.test_util as jtu
import numpy as np
import scipy.sparse as sp
from scipy.sparse.linalg import spsolve as spsolve_scipy
from simphox.primitives import spsolve, TMOperator
np.random.seed(0)
config.update("jax_enable_x64",... |
e146a9e11db2929684f4bf0d4aec46da184903ad87b38b7c9cd955d21b260508 | Python | 3,739 | 112 | # Copyright (c) Open-MMLab. All rights reserved.
from pathlib import Path
from ..utils import is_list_of, is_str
from .handlers import BaseFileHandler, JsonHandler, PickleHandler, YamlHandler
file_handlers = {
'json': JsonHandler(),
'yaml': YamlHandler(),
'yml': YamlHandler(),
'pickle': PickleHandler(... |
e28edb84f3910ea3021fc72eab92e8c14c86c1c57cc55e1539ef6aa163bd8e0a | Python | 3,739 | 93 | # 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... |
8ad8139ba63e4be6cda14b2c2fd83e49e747df0acc09c438b645981900aba080 | Python | 3,740 | 106 | #!/usr/bin/env python
# Apache 2.0
#
# This script truncates the rttm file using UEM file and writes it to a new rttm file.
# We use some utility functions from the dscore toolkit.
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import sys
from dscore.scorelib.turn import... |
9ad93779b78558736de4f34b65ac8f78a4505bb089ffacb40ce4387c4bfcdbca | Python | 3,743 | 137 | # %% [markdown]
# ##
import datetime
import os
import time
from pathlib import Path
from tqdm import tqdm
from src.data import join_node_meta
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pymaid
import seaborn as sns
from giskard.plot import dissimilarity_cluste... |
fef79a4528081c8f8d02973c6326fa0e7099ca422ba7ba13667076a95dd1b42d | Python | 3,744 | 114 | from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
import os
import models
import traceback
import numpy as np
import imlib as im
import tflib as tl
import tensorflow as tf
import argparse
from glob import glob
img_size = 128
parser = argparse.ArgumentParser... |
2e3b8434f3a8fc0149d6e47c1d96d9051a6cf2b50e78a384c9d44e2d626d1555 | Python | 3,745 | 132 | #!/usr/bin/env python
import numpy as np
import pandas as pd
import copy
from collections import defaultdict
from sklearn.cluster import DBSCAN
from scipy.spatial.distance import pdist, squareform
from scipy.optimize import curve_fit
from sklearn.metrics.pairwise import nan_euclidean_distances
def calc_med_dist_mat(... |
5d1772603b249c743984d35dd2d90794528827ea582c0828e6e552918179b5ff | Python | 3,745 | 78 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'graderTemplate.ui'
#
# Created by: PyQt5 UI code generator 5.12.3
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
... |
15631f01359e1cfe466dcd9ef52aa5ba2d2ce605df2329e765d0d81db85ca02e | Python | 3,746 | 113 | """Train models using pytorch lightning."""
import logging
from datetime import datetime
from pathlib import Path
import hydra
import mlflow
from dotenv import find_dotenv, load_dotenv
from hydra.utils import instantiate
from omegaconf import DictConfig, OmegaConf
from pytorch_lightning import Trainer
from pytorch_lig... |
525208f6d2ac388cfb6b702412d95fd4d33f3bec04e85fabfda6f3bed248b8a2 | Python | 3,746 | 121 | # coding=utf-8
# Copyright 2020 The Google Research Authors.
#
# 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 applicab... |
3461f563ca83f9fb158108365bb394f10376b057abebe5c1f0ddcdb9f5782cd9 | Python | 3,747 | 152 | # chemistry.py: Chemical parameters for MaSIF.
# Pablo Gainza - LPDI STI EPFL 2018-2019
# Released under an Apache License 2.0
import numpy as np
# radii for atoms in explicit case.
radii = {}
radii["N"] = "1.540000"
radii["N"] = "1.540000"
radii["O"] = "1.400000"
radii["C"] = "1.740000"
radii["H"] = "1.200000"
radii... |
13816a9eaf7088d7e26dbe7fe0aed6cfa779013760aa1fbfbbeb91f3583be2d5 | Python | 3,748 | 103 | #!/usr/bin/env python
"Pre-emptive caching of commonly used TemplateFlow templates"
import templateflow.api as tf
def fetch_MNI2009():
"""
Expected templates:
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_T1w.nii.gz
tpl-M... |
5670153f4145c0db8dc51a485df4b4ca2cd48c783c3483b7f5394029573d38a9 | Python | 3,749 | 95 | """
This file runs ridge regression encoding model on all labels and all non-food labels and outputs the improvement in R2 by including food labels.
Example run:
python food_label_R2_improvement.py -s 1 -v voxel_path.npy -t stim_id_path.npy -c coco_prop_path.npy -o output.npy
-s : subject
-v : path to preprocessed v... |
fda788989ee4c23100596e8a92a39e75bd00a78af3e260636df1885ae9add030 | Python | 3,750 | 94 | import argparse
def main():
parser = argparse.ArgumentParser()
# dataset
parser.add_argument('--dataname', type=str, default='TripletData')
parser.add_argument('--trainroot', type=str, default='data_IO/triplet.csv')
parser.add_argument('--testroot', type=str, default='data_IO/test_pairs.csv')
p... |
ef034ebbceb566e271dca994a99624a8ec2be0b4f0eb8860365b01e743ab3f9d | Python | 3,751 | 108 | ### reference code from https://github.com/quark0/darts/tree/master/cnn --- Differentiable Architecture Search
import torch
import torch.nn as nn
from .conv_ws import ConvAWS2d
from .registry import CONV_LAYERS
import torch.nn.functional as F
OPS = {
'skip_connect': lambda C, stride,affine,groups: Identity() if... |
1d571bde97973c0fb9b010106fb6ec512aa202bd445d7326930ffbb94edae29a | Python | 3,752 | 108 | import pandas as pd
#read pdb by cols
"""
COLUMNS* DATA TYPE FIELD DEFINITION
-------------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer serial Atom serial number.
13 - 16 Atom name ... |
231d5f48e3c252ef968c433f8f920c2d26e5fd7f4d55acbe5eef8b940d318f11 | Python | 3,754 | 114 | import os
import re
import argparse
import copy
def statistics_module(path, fc=False):
files = os.listdir(path)
layers = []
for f in files:
if fc:
if "power" in f:
with open(path + "/" + f, 'r') as rpt:
lines = rpt.readlines()
... |
75d57dcf13fa0484484bd196fd310b172a31ab64d6f4cf5a976e1abcaee1367c | Python | 3,755 | 103 | import numpy as np
import os
from os import listdir
from os.path import join, isfile, isdir
# GET DATA
def getData(tmp, cutoff=0, bertpath=""):
data = np.load(tmp)
# 3D coordinate information
idx = data["idx"]
val = data["val"]
# 1D information
# angles = np.stack([np.sin(data["phi"]),
# ... |
f5ab4e88436726981f191a45a5b862ea05ec8788efa3050cf3680189f338059d | Python | 3,756 | 129 | #!/usr/bin/env python
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import contextlib
import sys
from collections import Counter
from multiprocessing im... |
1ab87ca865b91b06804224204f014fb1b9399979230765fa07677ce4464df329 | Python | 3,757 | 107 | '''
Helper functions for loading and preparing data.
'''
from typing import List
from pathlib import Path
from dataclasses import dataclass, field
import pandas as pd
import numpy as np
def name_wrapper(
filename: str, savepath: str = '', fileextension: str = '') -> Path:
'''
Prepends the filename wi... |
7213329042c86ea51f666d15373fb9927ea3587689563ed863da03cb138e7c8f | Python | 3,757 | 105 | # 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... |
54158738a854f2f5adec999eff811c593840945fd23187af6c9d9a830bdeec56 | Python | 3,759 | 118 | from abc import ABC
from typing import Iterable, List, Optional
from oaklib.datamodels.search import SearchConfiguration
from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface
from oaklib.types import CURIE
__all__ = ["SearchConfiguration", "SearchInterface"]
class SearchInterface(BasicOntolo... |
694bfe8196c511a839a8f50d9dbdaed6aa4a5934a5504d4549a6ba44b0954e36 | Python | 3,759 | 125 | #
# calculation of synthetic accessibility score as described in:
#
# Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity and Fragment Contributions
# Peter Ertl and Ansgar Schuffenhauer
# Journal of Cheminformatics 1:8 (2009)
# http://www.jcheminf.com/content/1/1/8
#
# seve... |
1633fdcca71e47f242899524354cadb16f477f5dda59349773940abfe0556d43 | Python | 3,760 | 99 | # 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... |
524ff21b3d4f6694e27de8a5c2b2931c429de4aca393f69df13b66a596c0b2a3 | Python | 3,760 | 125 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""
Miscellaneous utility functions
"""
import torch
from torch import nn
from torch.nn import functional as F
from maskrcnn_benchmark.config import cfg
from maskrcnn_benchmark.layers import Conv2d
from maskrcnn_benchmark.modeling.poolers import P... |
3219623a637ff2db6b79da289674e0e511a582b77d2035cbc393e38efef6c74a | Python | 3,761 | 131 | import torch
class Sampler(object):
"""Base class for all Samplers.
Every Sampler subclass has to provide an __iter__ method, providing a way
to iterate over indices of dataset elements, and a __len__ method that
returns the length of the returned iterators.
"""
def __init__(self, data_sourc... |
782c15d416e9fdabb89d083de0e84610e75b391bb0c14afe2211093cc71b5246 | Python | 3,762 | 103 | """
==========================
Callosal bundles using AFQ API
==========================
An example using the AFQ API to find callosal bundles using the templates from:
http://hdl.handle.net/1773/34926
"""
import os.path as op
import matplotlib.pyplot as plt
import nibabel as nib
import plotly
from AFQ.api.group impo... |
dccf260b9e0aa7fa100b54b80fdb5c9d0b6fb55aee5ab2c0caaaf0d323f1ec09 | Python | 3,763 | 108 | from __future__ import print_function, division
import csv
import functools
import json
#import you
import random
import warnings
import math
import numpy as np
import torch
import os
from torch.utils.data import Dataset, DataLoader
from torch.utils.data.dataloader import default_collate
from torch.utils.data.sa... |
f3b1bf5362397d5ccc0352e446ac727927665e727c096d20ab51f4bb902a766e | Python | 3,763 | 116 | # 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... |
083d8b7dbfed758fc44f2ce6e56e920eda35529fb15d8ff05ef65b8a123e6cbf | Python | 3,767 | 66 | # Form implementation generated from reading ui file 'graderTemplate.ui'
#
# Created by: PyQt6 UI code generator 6.6.0
#
# WARNING: Any manual changes made to this file will be lost when pyuic6 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt6 import QtCore, QtGui, QtWidgets
clas... |
80a31cb92c062b624f91caace8103697df4479d17a317cb6851916bd082d0706 | Python | 3,768 | 86 | 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 tensorflow as tf
from tensorflow.keras.callbacks import ModelCheckpo... |
7e159de84bb38614e91d59406b824414c17c2f8fcac9eb0ddb61f0b6c49e8351 | Python | 3,769 | 128 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Take in 32x32 size squares
"""
from keras.models import Sequential
import keras.layers as layers
import keras.optimizers as optimizers
from keras.utils import Sequence
import keras
import unetsl.data
import unetsl.model
import unetsl.cli_interface
import os,sys
impo... |
4cc684f677b2f9fcf43498382ec8d16fb21222bcd240e5fc72fb10449c2fdd83 | Python | 3,771 | 95 | '''
Fitting ciliated cells, simultaneously to electrophysiology and particle flow angle.
With multifitting to enforce resting calcium concentration.
Note:
- for nans: debug with numpy.seterr(all='raise') (and numpy code generation)
'''
from file_management import *
from brian2 import *
from brian2modelfitting import M... |
132f164bc7cde9a046e976d232f40f49c1f1447d637f27a66aecc8a1ad1c6bdc | Python | 3,772 | 88 | """MobileNetV1 for Semantic Segmentation"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from models.baselines.base import BaseModel
class EfficientNet(BaseModel):
def __init__(self, classes=2, aux=False, backbone='efficientnet', pretrained_base=False, **kwargs):
super(EfficientNet,... |
163ece6d42849ec7d18aa0186ea6e4630a394e44b0287434f0166675f87b1834 | Python | 3,773 | 98 | import concurrent
from tqdm.auto import tqdm
from drugex.parallel.interfaces import ParallelException, ParallelProcessor
class ParallelSupplierEvaluator(ParallelProcessor):
"""
Class implementing parallel evaluation of `MolSupplier` instances on input data (see `ParallelSupplierEvaluator.apply`).
"""
... |
d61c185d76de5eda39274aa5498c1687d727d9629c1a529b2414f433e30f254c | Python | 3,773 | 117 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""I/O for wave files"""
import os
import numpy as np
from .._data_obj import NDVar, Scalar, UTS
from .._utils import ui
FILETYPES = [("WAV files", "*.wav")]
def load_wav(filename=None, name=None, backend='wave'):
"""Load a wav file as NDVar
Parame... |
5da2cd29dedce6bf47d72b3c6572893103c50305e4fd719cb8b39a88b1b3edac | Python | 3,774 | 58 | """Reproducible surface revision; preserves the straight wheel-detail master.
Run in Blender. Artist material estimates; not measured manufacturer BRDFs.
"""
import bpy, bmesh, os, json
from pathlib import Path
from mathutils import Vector
P=Path(os.environ.get('CARLA_MODEL3_WORKDIR',Path(__file__).resolve().parents[4]... |
16b14f6b85b99c5aedb9fc79bf58f6686bae6c76e280a447cb1c02ae1c0d6ede | Python | 3,775 | 100 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..builder import LOSSES
def ae_loss_per_image(tl_preds, br_preds, match):
"""Associative Embedding Loss in one image.
Associative Embedding Loss including two parts: pull loss and push loss.
Pull loss makes embedding vectors from sa... |
b6b293bf02d0fc6e3f7eb1f420608a87148fe5e7a5fb60c3ae3c89624835319f | Python | 3,775 | 80 | import torch.nn as nn
from maskrcnn_benchmark.modeling.backbone.shuffle_blocks import ConvBNReLU, ShuffleNetV2BlockSearched, blocks_key
class ShuffleNetV2DetNAS(nn.Module):
def __init__(self, cfg):
super(ShuffleNetV2DetNAS, self).__init__()
model_size = cfg.MODEL.BACKBONE.CONV_BODY.lstrip('DETNAS-... |
f5fb756e1164349643d85b6115f63993d326cfb0780a57fa0d05a98831f421c0 | Python | 3,775 | 88 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
8cb636460fb9c893bec5a9b5bf38c05c6b034d2d7438356de078457b385994d1 | Python | 3,779 | 109 | """
Extract, for each sequence, metrics about its:
- How far it goes (distance to furthest follower)
- How long does it go for (delay to latest average follower)
"""
from tctx.analysis import simbatch as sb
from tctx.util import spike_trains as spt
import pandas as pd
import numpy as np
DESC = 'extent'
def get_f... |
984547022ffcebb25ee438e7b333a3c9c64d0e11f864ef032eae321c9bc6ce68 | Python | 3,779 | 99 | # Copyright 2021 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... |
d0519d9ff005985885f1ee0764bf3446e1fedbdaefc1d763bf189ccef5fb0806 | Python | 3,779 | 105 | """Regression tests for the ``is_mask`` argument of ``load_resample_itk``.
ADC/HBV (and T2W) are intensity images and must be resampled with B-spline
interpolation, i.e. ``is_mask=False``. A prior bug passed ``slice_number``
positionally into ``is_mask`` (a truthy int -> ``True``), so intensity images
were resampled a... |
8d2c3b3c9fd1d0b7f83154da802bc4ccdebe3778fa691192bebe12ec7b7feb8c | Python | 3,781 | 90 | import mne
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
## logging info ###
import logging
from datetime import datetime
logname = './logs/' + datetime.now().strftime('log_%Y-%m-%d.log')
logging.basicConfig(filename=logname,level=logging.INFO, format='%(asctime)s - %(l... |
5a50aded6a3a402e68ce1bae4e76da0c9d169a3ca84c69acf7087badfd6f4d5a | Python | 3,783 | 89 | """Bennett et al. 2021 MV reinforcement-prediction-error mushroom-body model.
Single-valence reduction:
KC sparse code from PN->KC connectome
MBON rate output m = ReLU(w @ kc)
DAN d = r - m_hat (prediction error from valence-opposing MBON feedback;
single-valence... |
1011f1576416f04bbd797a6907de614a75fbb8982542ca25e3155ea7afe0111d | Python | 3,784 | 135 | import time
import itertools
import scipy
import scipy.stats
import numpy as np
import math
from PIL import Image as PIL_Image
from keras.preprocessing import image
from keras.models import load_model
from utils.image_and_text_utils import index_to_char,char_to_index
from utils.config import *
from bayesian_agents.rsaW... |
21fb2cdb86943466f62662630fecd2f64bf514c32449d669d177c2c9651f9671 | Python | 3,787 | 125 | """
Makes summary data tables for supplementary ferrets not tested with cooling
Created on 2021-10-10 by Stephen Town
"""
from dataclasses import dataclass
import os, sys
from pathlib import Path
import pandas as pd
sys.path.insert(0, os.path.abspath( os.path.join(os.path.dirname(__file__), '../../..')))
from Resu... |
778eef945f6708bf03781be82afed5c667aacb8e79645a434a9dfe70ca3e2642 | Python | 3,788 | 109 | """Build a table with basic info on members of parliament."""
from logging import Logger
from pathlib import Path
from typing import List
import pandas as pd
from lxml import etree
from fi_parliament_tools import MPID_FILTER
from fi_parliament_tools.parsing.documents import MPInfo
from fi_parliament_tools.parsing.que... |
f4da99e61e0c98a8f456e2a6bfea91001a28e5c2517672f2ae84743af5bc14e2 | Python | 3,788 | 138 | import ast
import json
import pathlib
import subprocess
import time
from glob import glob
from pathlib import Path
import os
from bokeh.client import pull_session
from bokeh.embed import server_document
from flask import Flask, request, session
from flask_cors import CORS, cross_origin
from lib import segmentation, u... |
8aa1655fe3502124d8cd296d7a444f42f099a651ab7dbc4eeb713c86f965ddd8 | Python | 3,789 | 142 | '''
Fig. 11.
Collective behavior.
Simulation of trajectories with breathing paramecia.
'''
from brian2 import *
from behavior import *
import imageio
from plotting import cell_mask, cell_indices
from brian2 import *
from behavior import *
import imageio
from plotting import cell_mask, cell_indices
movie = True
C = p... |
1b1c320ea1a307db175e894894419a384b9795599657231d08ab645c49524315 | Python | 3,790 | 111 | import pandas as pd
import torch
from dataset import ViscosityDataset
from torch.utils.data.dataloader import DataLoader
import argparse
import glob
import os
import numpy as np
from model import ViscosityNet
from utils import seed_everything
from utils import generate_esp_grids, get_esp_grids
from utils import DEFA... |
55923fd42c0795ce2ab9c9d7ea9ae251ee1b521a6ca34b7524ca790effa85fdb | Python | 3,791 | 105 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
a719242f05c7f9d89737ad66d0abcff149f2cc4546c468c4f29fec2462f19a89 | Python | 3,792 | 124 | # %% [markdown]
# ##
import numpy as np
import pandas as pd
import pymaid
from src.data import load_metagraph
from src.pymaid import start_instance
from tqdm import tqdm
mg = load_metagraph("G")
meta = mg.meta
start_instance()
splits = pymaid.find_treenodes(tags="mw axon split")
splits = splits.set_index("skeleton... |
d4bc9da7ebb45a30a2e1dc29dffd6fda62da1de630d1fa452ee5a2b940375cea | Python | 3,793 | 98 | import torch
from sklearn import metrics
from .vae_basic_model import VaeBasicModel
from . import networks
from . import losses
class VaeRegressionModel(VaeBasicModel):
"""
This class implements the VAE regression model, using the VAE framework with the regression downstream task.
"""
@staticmethod
... |
c7891bf845ecec91d8ea695376c92c632179fecf19a476bf167334b951d3d9c7 | Python | 3,796 | 109 | import tensorflow as tf
from tensorflow.keras.layers import *
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.models import Model
def Dense_layer(prev_layer,num_filter):
eps = 1.1e-5
#dense layer 1
batch = BatchNormalization(axis=1, epsilon=eps)(prev_layer)
conv = Conv2D(num_filter... |
07c4ede9ada4cd3fb7106dbe027faa3e7d864e0ce8a96ec88a949e103e8c370b | Python | 3,798 | 104 | # 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... |
390ad14b1cf60fcaf00c22e415d64bdd7e3fc3475b8a5fb69a7510543e1a7248 | Python | 3,799 | 125 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init
def conv_block(in_ch=1, out_ch=1, threeD=True):
if threeD:
layer = nn.Sequential(nn.Conv3d(in_ch, out_ch, kernel_size=3, padding=1),
nn.BatchNorm3d(out_ch),
nn.ReLU()
)
else:
layer = nn.Sequential(nn.... |
a96b4f953a722e3d917e086ad732a31d6813eb6f81b20b99687154cfd43cfe0c | Python | 3,799 | 121 | import sys
import h5py
import logging
import warnings
from pathlib import Path
import torch
import numpy as np
from scipy.ndimage import zoom
from unet3d import Basic3DUNet
warnings.filterwarnings(action='ignore', category=UserWarning)
log = logging.getLogger(__name__)
PAD = 64
def segment_mitochondria(input_path,... |
5d4c286a13791ca3f51eba2b2fc09e4db5e03a60d28283081f1a0ba519c88152 | Python | 3,804 | 94 | from numpy import random
from train import train
from tqdm import tqdm
from model import Unquantified_2layer_CNN
from utils.dataTrans import get_dataloader
from sklearn.model_selection import train_test_split
from experiment import setup_seed, mfcc_general_data, stft_general_data
BATCH_SIZE = 64
LR = 0.003
E... |
633ad175d4fcfd606e078db68a5e9e0583d5cee756619c091a12f598ad39bef7 | Python | 3,806 | 105 | import itk
from subprocess import call
import sys
def combine_transforms(transforms_arr: list):
composite = itk.CompositeTransform[itk.D, 3].New()
for i in transforms_arr:
t = itk.transformread(i)[0]
composite.AddTransform(t)
return composite
def resample_from_comp(image, transform, out... |
aa44a5662f06333eb2ba590fbdcdb4c2490337c87ef7a08f93d30a7430112356 | Python | 3,806 | 97 | from .vehicle_wheel_smoke_test import VehicleWheelSmokeTest
import carla
import math
import os
import tempfile
RECORD_DELTA_S = 0.05
REPLAY_DELTA_S = 1.0 / 60.0
ROLE_NAME = "wheel_replay"
# How far the replayed spin may stray from the body's travel in a tick.
SPIN_TOLERANCE = 0.3
class TestVehicleWheelReplay(Vehic... |
c1e6e2013cd0d139fcce586071423370c8a9f7de5306e59737ce82c2fac740d0 | Python | 3,807 | 104 | # Copyright 2022 Huawei Technologies Co., Ltd
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
9dde4005f11d4738550c9e83a17a20bf97f23b8e05cca5375c38dd6963a96d12 | Python | 3,808 | 110 | import sys
import argparse
from pathlib import Path
import logging
import numpy as np
import pandas as pd
import tifffile as tf
from cenfind.core.data import Dataset, Field
from cenfind.core.loading import load_foci
from cenfind.core.visualisation import visualisation, create_vignette
from cenfind.core.statistics impo... |
d67c2bede075806e59fbef959a5890839e579e68fe79ef977dc34cc0948bc6b6 | Python | 3,810 | 102 | # coding=utf-8
# Copyright 2020 The Google Research Authors.
#
# 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 applicab... |
ea8395e43871fc13e5ca3a2ae53b6b30dd069649b8dadebc6b3c33ddf5e28273 | Python | 3,812 | 103 | import torch
import torch.nn as nn
from .resnet_updated import resnetbank50all as resnetbank50
from .globalNet import globalNet
class Model(nn.Module):
def __init__(self, n_kpts=10, pretrained=True, output_shape=(64, 64)):
super(Model, self).__init__()
self.K = n_kpts
channel... |
bfa0f294be6ac0e717a5afaa1a05cd98b40bfe5b3f95c4543153133eda15ec7b | Python | 3,813 | 146 | # -*- coding: utf-8 -*-
import json
import os
import sys
from pathlib import Path
SUPPORTED_FTYPES = ('acq', 'txt') # 'mat', ...
def check_input_dir(indir):
"""
Checks that the given indir doesn't have a trailing '/'
"""
if indir.endswith('/'):
indir = indir[:-1]
return indir
def ch... |
c83f0e77a074b047e7f3e3d60c9182256fce03da233b595948de16baae0b5c88 | Python | 3,813 | 90 | import ctypes
import numpy as np
import os
import sys
import torch
import pdb
class _gnn_lib(object):
def __init__(self, args):
dir_path = os.path.dirname(os.path.realpath(__file__))
self.lib = ctypes.CDLL('%s/build/dll/libgnn.so' % dir_path)
self.lib.GetGraphStruct.restype = ctypes.c_voi... |
e29d35a338f402529bfd08ac1912f4852bb2c6e0025d0ad2b84def29366499aa | Python | 3,814 | 110 | import random
import torch
from torch_geometric.data import Data
from torch_geometric.utils import degree
from torch_geometric.utils.subgraph import subgraph
from torch_geometric.utils.random import erdos_renyi_graph
from torch_geometric.utils.convert import to_scipy_sparse_matrix
from IPython.display import SVG
from... |
094aa4b77f9f16ae8a51b60a818b666e799c679c991a60e5c63b068e8caf8745 | Python | 3,815 | 127 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
import os
from keras.applications.inception_v3 import InceptionV3
from keras.preprocessing.image import ImageDataGenerator
from keras.models import Model
from keras import layers
fro... |
62afc1a6a2354e6b83ee0cd1d4a9d591eaa6ed00e517ed9d0de0922f80721af8 | Python | 3,815 | 78 | import os
import torch
import argparse
import numpy as np
from feature import create_feature
from network.resEGNN import resEGNN, resEGNN_with_mask, resEGNN_with_ne
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Predict.')
parser.add_argument('--input', type=str, required=True)
p... |
a7396c5db60cde74a19e37ff2f98e8cf1f8cb0df8bf6a3b766f03d4b77ed1d0e | Python | 3,815 | 92 | # basic imports
import os
import pickle
import numpy as np
# framework imports
from cobel.agents.sfma import SFMAAgent
from cobel.interfaces.gridworld import InterfaceGridworld
from cobel.analysis.rl_monitoring.rl_performance_monitors import EscapeLatencyMonitor
def single_run(world: dict, trials: int = 20, trial_ste... |
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