sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e967dd4b7c9874c3a9d1d14e75fba33d26b2c76c24077e60f7f0da148b3321a8 | Python | 2,181 | 90 | # %% [markdown]
# ##
import pandas as pd
import numpy as np
connector_loc = "maggot_models/data/processed/2020-06-10/connectors.csv"
connectors = pd.read_csv(connector_loc, index_col=0)
sizes = connectors.groupby(
["connector_id", "presynaptic_type", "postsynaptic_type"]
).size()
sizes.name = "count"
sizes = siz... |
b178672759bbbbc7b515173d49ab299eb39d13a0771ebf07b7b19fd169b67e3d | Python | 2,182 | 57 | # 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... |
7d5daff8641ea98a9f43147faaee935a8415c4f44f65f1f068f61e0e0e8d1087 | Python | 2,183 | 71 | ##########################################################################################
## Create gene x cell type matrix containing % of cells in each cell type expressing gene
## using human cortex gene expression matrix from Velmeshev 2019 (scRNA-seq)
##
## Author: Yu-Han Hsu
#####################################... |
aca97044998f19d7637bc22c5b28b45e566f393974e0b6cf16900b9e4a947ac5 | Python | 2,185 | 79 | """
Implements basic graph algorithms such as BFS.
Author: Mengye Ren (mren@cs.toronto.edu)
Usage:
"""
import numpy as np
def bfs(adj, src, dst, cache=None):
"""BFS search from source to destination. Check whether a path exists, does
not return the actual path.
Work on directed acyclic graphs where we assume... |
cb63238f91bac7592c1ca4aefe8a52a2da8519102ddbd6014858fb141269fadc | Python | 2,186 | 57 | # 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... |
786caa3ee358c2e89dd23a0c1d7578d323e6dc0cbc022cf7d8d5104d032cb26b | Python | 2,188 | 81 | # An example config file to be sent to wandb
import sys
sys.path.append("E:\BRATS_Research\BraTS-2021\src\model")
from wandb_creds import get_wandb_credentials
from loss import SoftDiceLossSquared
from ..model.spp_3d import Pyramid_Pooling_3D
import wandb
import torch
wandb.login(key=get_wandb_credentials(person... |
b425e48b21f6f03be6f27d7615cd0b648bfac3420a39230dd584e758d0f53de3 | Python | 2,188 | 70 | # Pablo Gainza Cirauqui 2016
# This pymol function loads dot files into pymol.
from pymol import cmd, stored
from pymol.cgo import *
import os.path
import numpy as np
colorDict = {
"sky": [COLOR, 0.0, 0.76, 1.0],
"sea": [COLOR, 0.0, 0.90, 0.5],
"yellowtint": [COLOR, 0.88, 0.97, 0.02],
"hotpink": [COLOR... |
3e9e661ce1851ff5cf5a3d05af610ab2a7da8a0002e877e7f06fa8638a8ce07c | Python | 2,189 | 39 | # 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... |
47f8cc5e2e7290be28372a44391c043b26a24187c24a0a8cff85a1d098ea534c | Python | 2,189 | 58 | # Merge STAR gene count files (counts per sample) to matrix with rows genes, columns samples
# NOTE: Needs Python version 3.5+
import glob
import argparse
parser = argparse.ArgumentParser(description='Merge multiple STAR count files into a matrix.')
parser.add_argument('star_base_path', help='base path from where to s... |
5782766bd72229ff93eb084b3c15deb5bd5445f5080ce9c4f427510588144021 | Python | 2,190 | 43 | import os
import shutil
from tqdm import tqdm
import pandas as pd
dataset_folder = '/data/interesting_side_projects/SSAML/datasets'
predict_folder = '/data/interesting_side_projects/SSAML/models_predictions'
# find the common file names that exist both in dataset and prediction
dataset_files = [x.replace('.csv','') ... |
5cd1b18d3e575d7a5f9f671d5904f38c0dcfdfbbaae2ed1893c821faff6345ab | Python | 2,192 | 67 | import os
import pickle
import torch
from torch.utils.data import Dataset
from torchvision.transforms import Compose, RandomHorizontalFlip, RandomVerticalFlip
from utils.helpers import Fix_RandomRotation
class vessel_dataset(Dataset):
def __init__(self, path, mode, is_val=False, split=None):
self.mode = ... |
bb371dd2011c3c795089bffc59277f528c096cd50d2c5df072b87628ccc1ea65 | Python | 2,192 | 61 | #!/usr/bin/env python3
"""
File: analyse_interactions.py
Created: 2020/03/13
Last Changed: 2020/03/19
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fre... |
d3f5a03092f8d6422006f9f1fd0f1fcfdb15ca649c2b43c13a210a8110a1abb1 | Python | 2,193 | 56 | from spike2calcium import *
import os, sys
import warnings
warnings.filterwarnings('ignore')
from glob import glob
# get cell list information
flist = sorted(glob('GCaMP8_exported_ROIs_s2f_full/dff/*.npz'))
cell_info=["_".join(os.path.basename(f).split('_')[:6]) for f in flist]
cell_info_uq = np.unique(cell_info)
# s... |
136ab5c012a5d8373133cc577433a08bd80e55efa39bab33537f79b8189cdc41 | Python | 2,194 | 73 | # import sys
import fnmatch
def heur(physinfo, name, task='', acq='', direct='', rec='', run=''):
# ############################## #
# ## Modify here! ## #
# ## ## #
# ## Possible variables are: ## #
# ## -task (required) ## #
# ## -run ... |
13dac2301cfd5086cc83519f617a85f1e71c5da89f45957bd39c28c659168239 | Python | 2,194 | 67 | import argparse
import torch
import torch.nn as nn
from mmcv.runner import save_checkpoint
from mmdet.apis import init_detector
def fuse_conv_bn(conv, bn):
"""During inference, the functionary of batch norm layers is turned off but
only the mean and var alone channels are used, which exposes the chance to
... |
dd361289f71824fc40a0bfc7d0153c676b20357805e433b4ff5854db5955387b | Python | 2,194 | 76 | import h5py
import torch
from torch.utils.data import Dataset
class H5pyDataset(Dataset):
"""PDE h5py dataset"""
def __init__(
self,
data_path,
resolution=128,
transform_x=None,
transform_y=None,
n_samples=None,
):
resolution_to_step = {128: 8, 256:... |
2679f1dfef559df24e4da2bd0aba721ddf9a19e477003a75a0cb62bb8ae8a157 | Python | 2,195 | 71 | import tkinter as tk
import tkinter.filedialog as tkdialogs
import os
from pathlib import Path
def root_deco(dialog):
"""Decorates a dialog with a toplevel that is destroyed when the dialog
is closed."""
def decorated(*args, **kwargs):
#create root and withdraw from screen
root = tk.Tk()
... |
5863cd335bb21cdcf2e211614ea2d20c5467c7c12bc1e7410c2c2fa0eeab7123 | Python | 2,195 | 60 | import random
import torch
import matplotlib.pyplot as plt
from tqdm import trange
from graphxai.explainers import PGMExplainer
from graphxai.gnn_models.node_classification.testing import GCN_3layer_basic, GIN_3layer_basic, test, train
from graphxai.datasets.shape_graph import ShapeGGen
# Load dataset:
# Smaller gra... |
fdae66f9f44abdb3f5a1b58e5329b2056b58f186964e7edb6bd61aa10d00a4c9 | Python | 2,195 | 56 | import argparse
from bunch import Bunch
from loguru import logger
from ruamel.yaml import safe_load
from torch.utils.data import DataLoader
import models
from dataset import vessel_dataset
from trainer import Trainer
from utils import losses
from utils.helpers import get_instance, seed_torch
def main(CFG, data_path, ... |
597c3c1bc8079084ad6503c82739139a912c318eae94d1792f4320262a2f7aa1 | Python | 2,196 | 66 | ####################################################################################################
# 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... |
f2875ef9ca21169dde163fb1ee6323ed09f194351be882e58ce827d79a6297d0 | Python | 2,196 | 82 | import pickle
import numpy as np
import re
from nltk.corpus import stopwords
from charpragcap.utils.image_and_text_utils import devectorize_caption,split_dataset,get_rep_from_id
import copy
def cap_to_words(cap):
return [word for word in re.sub('[^a-z ]',"",devectorize_caption(cap)).split() if word not in stopwords.w... |
0e49b3081811114356e2e6a075ea7bbf570bb0162e10f5c7c2f41db7a60952e7 | Python | 2,198 | 79 | __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
from tmkit.seqnetrr.Controller import Controller
def extract(
method: str,
fasta_fpn: str,
net_fpn... |
7b06bef6d6b201693acd1b7ba9da2286aadf27e052569ceec0b7ccef8b3ee241 | Python | 2,198 | 42 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from eelbrain._experiment.definitions import find_dependent_epochs, find_epoch_vars, find_epochs_vars
from eelbrain._experiment.test_def import find_test_vars
from eelbrain._experiment.variable_def import Variables
def test_find_epoch_vars():
assert find_ep... |
4bc7bcf7839f2f84e4bb8651706c9c2e725a5af86c2ecb2503b16a14a5ab87b5 | Python | 2,199 | 61 | # 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... |
24880c0e6d126226d5183e05a80c741b669b36aee0de9aa19feaefd6ca8e2a73 | Python | 2,202 | 85 | from os.path import basename
from pathlib import Path
import numpy as np
from sacred import Experiment
from sacred.observers import FileStorageObserver, SlackObserver
from graspy.datasets import load_drosophila_left, load_drosophila_right
from graspy.utils import binarize, symmetrize
from src.models import select_sbm... |
2634d4f52b0c4b72d6e1e7ab91c1e3d6d89b076d8b45e96c2364022663aa39be | Python | 2,202 | 67 | from helper.NumpyEncoder import NumpyEncoder
from datetime import datetime
import matplotlib.pyplot as plt
import json
import math
import pathlib
def get_file_locations(architecture, num_examples, solver):
arch_str = '-'.join([str(z) for z in architecture])
plot_dir = "results/plots/%s/%s/%s" % (arch_str, num_exam... |
575808d7e7196f7f6742067c1bffedbaf7219aebac3b096fdbb1068c58a3f88b | Python | 2,202 | 62 | import numpy as np
import skimage.morphology as skmorph
import scipy.ndimage
def compute_statistics(result, skeletonized_result):
'''Summarize results. Inputs must be labeled arrays with classes 0,1,2'''
N_neg = (result == 0).sum()
N_mask = (result == 2).sum()
result ... |
b66cf206d10f07647f8d2654e232f60396a31c0ebca5d94f7a5b48e3fcfe078a | Python | 2,202 | 76 | from keras.callbacks import TensorBoard, ModelCheckpoint, CSVLogger
from models import ResearchModels
from data import DataSet
import tensorflow as tf
import os
import argparse
import numpy as np
from sklearn.metrics import roc_curve, auc
import matplotlib.pyplot as plt
def validate(data_type, model, seq_length=24, sa... |
706ba3208cfc4b4ff65ee15e300c73628d19bc1f8c1e4f273c7197274e46d74e | Python | 2,203 | 66 | # Copyright (c) Open-MMLab. All rights reserved.
import numpy as np
import torch.nn as nn
def constant_init(module, val, bias=0):
if hasattr(module, 'weight') and module.weight is not None:
nn.init.constant_(module.weight, val)
if hasattr(module, 'bias') and module.bias is not None:
nn.init.co... |
8c8eb1b986d003b51348f38ec32039f87550ddb23a1d85245a3d99fc574e3a29 | Python | 2,205 | 64 | import sys
import numpy as np
import torch
from torch_geometric.datasets import TUDataset
from graphxai.explainers import GuidedBP
from graphxai.explainers.utils.visualizations import visualize_mol_explanation
from graphxai.gnn_models.graph_classification import GIN, load_data, train, test
import matplotlib.pyplot as... |
aee4fce42e59145771dd092d391c98f76a48c5885bca2c3c8224d1d7c243ac65 | Python | 2,205 | 85 | from os.path import basename
from pathlib import Path
import numpy as np
from sacred import Experiment
from sacred.observers import FileStorageObserver, SlackObserver
from graspy.datasets import load_drosophila_left, load_drosophila_right
from graspy.utils import binarize, symmetrize
from src.models import select_sbm... |
7512eefc3f989725633a83efc25ac05327f54ccf6a0e7944046736db64852901 | Python | 2,206 | 76 | import torch
import torch.nn as nn
import numpy as np
class fBMGenerator(nn.Module):
def __init__(self, dim, **kwargs):
self.dim = dim
super(fBMGenerator, self).__init__(**kwargs)
def f_(self, DT, alpha):
return 0.5 * (
torch.pow(torch.abs(DT + 1), alpha)
+ tor... |
d6134e5707eeed014f97749c7037a2dc7e78b0d2f8c7f2f0f521d7a383a5a857 | Python | 2,206 | 83 | """Graph decoders."""
import manifolds
import torch.nn as nn
import torch.nn.functional as F
from layers.att_layers import GraphAttentionLayer
from layers.layers import GraphConvolution, Linear
class Decoder(nn.Module):
"""
Decoder abstract class for node classification tasks.
"""
def __init__(self,... |
65ede7aa706eec7d85ce4242c29b7b10ab397dc767b1afea38e5271913058513 | Python | 2,207 | 63 |
# loop through all subdirs to find all fastq files
import os.path
import re
import argparse
parser = argparse.ArgumentParser(description='Make Molgenis Compute samplesheet for MayoCBE.')
parser.add_argument('samplesheet', help='MayoCBE samplesheet from synapse')
parser.add_argument('fastq_dir', help='path to fastq f... |
040432d81f203efab206bc0a963076a630c3e3cefbb631c9a494f41cb8b1f845 | Python | 2,208 | 88 | import pickle
from copy import deepcopy
import numpy as np
import grr.GIF_network as gfn
from lib import generate_models_argparser, load_generate_models_opts
# Parse commandline arguments
args = generate_models_argparser.parse_args()
opts = load_generate_models_opts(
args.opts,
{
'dt': None,
... |
65b51c25d1e6cff8b80034846562651f307d8de8232eb0d4992aa94ba1e66769 | Python | 2,208 | 55 | from ..builder import DETECTORS
from .two_stage import TwoStageDetector
@DETECTORS.register_module()
class FastRCNN(TwoStageDetector):
"""Implementation of `Fast R-CNN <https://arxiv.org/abs/1504.08083>`_"""
def __init__(self,
backbone,
roi_head,
train_cfg,
... |
8c761d3a9c591dcebc5799bb803ed3239e754a8d7c2d421131dcb86fa3fd6c7a | Python | 2,210 | 74 | from dataclasses import dataclass
from pathlib import Path
from typing import TYPE_CHECKING, Optional, Type, Union
from class_resolver import HintOrType
if TYPE_CHECKING:
from .interfaces import OntologyInterface
__all__ = [
"OntologyResource",
]
@dataclass
class OntologyResource:
"""
A representat... |
00d91a58df67ee425be02da84c030824a5c575ea44a10f469b315901253c09aa | Python | 2,211 | 78 | # 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... |
5927dd4831506c26851252640402831cc45b761bfb6d20437fe52686c678a2a8 | Python | 2,211 | 57 | import tqdm
import argparse, sys, os
import random as rand
import torch
from graphxai.explainers import *
from graphxai.datasets import load_ShapeGGen
from graphxai.datasets.shape_graph import ShapeGGen
from graphxai.utils.performance.load_exp import exp_exists
from graphxai.gnn_models.node_classification.testing impo... |
d92ac59a2453d293cb9fbbfe9527956850820ec1fabf0de9eb2afeaeb520a91b | Python | 2,212 | 87 | """
From https://github.com/wanghao14/Stain_Normalization
Normalize a patch stain to the target image using the method of:
E. Reinhard, M. Adhikhmin, B. Gooch, and P. Shirley, ‘Color transfer between images’, IEEE Computer Graphics and Applications, vol. 21, no. 5, pp. 34–41, Sep. 2001.
"""
from __future__ import div... |
19ad82121804f0b97114904ed7af58abea342c59b1557aa7c1d278e13e653b90 | Python | 2,213 | 63 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from pathlib import Path
import numpy as np
from numpy.testing import assert_array_equal
from eelbrain import Dataset, datasets, load
from eelbrain.testing import TempDir, assert_dataobj_equal, assert_dataset_equal, file_path
def test_r_tsv_io():
"Test re... |
057ba316e18d694c26d77ff0ae68d38199c596c0024c54271647bae818aa7de3 | Python | 2,214 | 71 | import tensorflow as tf
def adam(loss, lr, train_vars, beta1=0.9, beta2=0.999, epsilon=1e-8):
opt = tf.compat.v1.train.AdamOptimizer(
learning_rate=lr,
beta1=beta1,
beta2=beta2,
epsilon=epsilon,
name="Adam"
)
grads_and_vars = opt.compute_gradients(loss, train_vars)
... |
184007f780b707e0cdb7e355317a01a60114221a6cc6b4dd1889359f035bbfac | Python | 2,214 | 71 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import multiprocessing
import tensorflow as tf
from tflib.data.memory_data import MemoryData
_N_CPU = multiprocessing.cpu_count()
class Mnist(MemoryData):
def __init__(self,
batch_si... |
a6719a366a12947f53e03e7e4bf9ed3ac18a4fe2985d6b1d37f87926e7f719c8 | Python | 2,214 | 73 | """Step 1: Preprocessing."""
from pathlib import Path
import mne
import matplotlib
matplotlib.use("Agg")
from osl_dynamics.meeg import parallel, preproc
# ----------------------------------------------------------------------------
input_dir = Path("BIDS")
output_dir = Path("derivatives")
qc_dir = Path("qc")
log_dir ... |
e23e15e93faafabb6356d3c1bc5907185950b30a240e1edbb115c3d0831818ee | Python | 2,214 | 61 | import ipdb
import random as rand
import torch
import argparse
import numpy as np
from graphxai.gnn_models.node_classification.testing import GCN_3layer_basic, GIN_3layer_basic, test, train, val
from graphxai.datasets.shape_graph import ShapeGGen
from graphxai.datasets import load_ShapeGGen
parser = argparse.Argumen... |
74ed2361d6fd45cc59181e4984d3240332e2e47dd796e60d595d90620e5f1c55 | Python | 2,215 | 61 | # Merge STAR gene count files (counts per sample) to matrix with rows genes, columns samples
# NOTE: Needs Python version 3.5+
import glob
import argparse
parser = argparse.ArgumentParser(description='Merge multiple STAR count files into a matrix.')
parser.add_argument('star_base_path', help='base path from where to s... |
d4e26cffe1198b5f2577b119de4cb34985b2c017125d02ce7f7d8e6457c55a8b | Python | 2,215 | 61 | import numpy as np
import torch
import torch.nn as nn
from mmcv.cnn import constant_init, normal_init
from mmdet.models.anchor_heads.ssd_head import SSDHead
from mmdet.models.registry import HEADS
from .operations import conv_dw_head
@HEADS.register_module
class SSDLightHead(SSDHead):
def __init__(self,
... |
4025c606cd9d8d1a3fd5122a4232d335e30f3ce679f218d6db9428671d16953b | Python | 2,216 | 60 | ####################################################################################################
# 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... |
105ff5e23f2eb0949ea3bb40f6e6ec700bd3464ff8b76393707cd64afbb5af4d | Python | 2,218 | 59 | # 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... |
2d1a0618605cc87b41b376f543ecb5beb25491861d0f00f28d6de05fb7c6c815 | Python | 2,218 | 71 | """ A utility for testing config options for the zebra test. Change settings until
the program identifies exactly 1 blob over the fish"""
"""IMPORTS"""
import numpy as np
import cv2
from skimage import feature
import time
import matplotlib.animation as am
from matplotlib import pyplot
import csv
import configpars... |
542225a61d0fe467b4ce70607c0227ccb415a1698d7e5e12c2f46031e031f98b | Python | 2,219 | 61 | # 0. Choose a blueprint for the walkers
world = client.get_world()
blueprintsWalkers = world.get_blueprint_library().filter("walker.pedestrian.*")
walker_bp = random.choice(blueprintsWalkers)
walkers_list = []
all_id = []
# 1. Take all the random locations to spawn
spawn_points = []
for i in range(50):
spawn_poin... |
6bff488385a96425d99522462dc8fc1494f8f8d49cc27f1287895d217207d91d | Python | 2,221 | 53 | # 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... |
1b0716e4caa9e8a18cebebf3f6f767858ce135bc73faa4bf46001cdea0485830 | Python | 2,222 | 50 | # 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... |
2a825e37d92ecfbb03348a1f10e26c50ea0844d230256f714e85726dbbe9546b | Python | 2,223 | 73 | """Computing the path length covered by each mitochondrion"""
import sys
import argparse
from collections import defaultdict
from tqdm import tqdm
import numpy as np
import pandas as pd
sys.path.append(".")
from lib import compartment, skel, u
def main(mitodffilename, idfilename, mitotoskelfilename, outputfilename)... |
9f6cb815f1c31bcdda54721b21aa4c94f8b7a588c76d3ab23de694613889ab0a | Python | 2,223 | 91 | """
Process an image that we can pass to our networks.
"""
from keras.preprocessing.image import img_to_array, load_img
import numpy as np
import cv2
import random
import tensorflow as tf
from keras_preprocessing import image
def process_image(image, target_shape,):
"""Given an image, process it and return the arr... |
1791c8d7487e5b05b4d99e45904fed16eab217b51242288c7928a3fb06ce8601 | Python | 2,224 | 58 | import numpy as np
from utils.postprocessing import PostProcessing
from utils import embedding_matrix_2_kNN
from utils.Config import Config
from utils.ArticlesProvider import ArticlesProvider
class SelectLabelsPostprocessor(PostProcessing):
"""
Select smartly the articles to label to optimize the result
"... |
72d88d13307e9b8cd01b83fedc10840fde150c5853f0350ee111ae1c0afc7a73 | Python | 2,224 | 85 | import random
import numpy as np
from deap import base
from deap import creator
from deap import tools
from deap import algorithms
import argparse
import pandas
import os
import numpy as np
import matplotlib.pyplot as plt
import functools
from collections import Counter
import math
import random
def main(args):
... |
9f931e7da37f6a3ae3e72a4a99cad9cd88f332008e9a7c55007bf8bf191a39ce | Python | 2,225 | 63 | """
THESE FUNCTIONS WERE ADDED BY HELLE FROM:
https://github.com/BenevolentAI/guacamol/blob/8247bbd5e927fbc3d328865d12cf83cb7019e2d6/guacamol/utils/data.py#L11
to solve AttributeError: module 'utils' has no attribute 'canonicalize_list'
"""
from typing import Optional, Iterable, List
from rdkit import Chem
def canon... |
8e02ed9de9a1ec95365f1cb2c8acc03ffa159aed1a1f4ad16f03df4823130c3f | Python | 2,226 | 64 | # -*- coding: utf-8 -*-
import sys
from pathlib import Path
class DirectionTree(object):
"""generate file tree like `tree E:/xxx/xxx` command in windows
pathname: target directory
filename: save directory, default = 'tree.txt'
"""
def __init__(self, pathname='.', filename='tree.txt'):
sup... |
2b58eb1dec37e965680ac7003f4ece9b346c1a9e27bf6422978c23c00a22f530 | Python | 2,227 | 92 | """
Test the `InputSignal` class in input_architect.py and all its methods.
"""
import sys
sys.path.append('../../../')
sys.path.append('../')
import numpy as np
# nest.init(sys.argv + ['--verbosity=QUIET', '--quiet']) # turn off all NEST messages
from modules import parameters
from modules import input_architect ... |
ff75d8d9ec2a0adc2e707a666cafdd2213f8092d62b90ff258ce496b18af9a55 | Python | 2,228 | 55 | import argparse
import mne
import numpy as np
from os import path
from ..infer import EEGInfer
from ..utils import inst_load, output_stages, pick_chan_names, graph_summary
def main():
parser = argparse.ArgumentParser()
parser.add_argument("file", type=str)
parser.add_argument("--out_form", type=str, defau... |
74b1a9a02603a9adcaf38266428147b6b6c79654e403495b69ceed3d80fa9332 | Python | 2,229 | 57 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
from torch import nn
from torch.nn import functional as F
from maskrcnn_benchmark.layers import Conv2d
from maskrcnn_benchmark.layers import ConvTranspose2d
from maskrcnn_benchmark.modeling import registry
@registry.ROI_MASK_PREDICTOR.register("... |
ee36dac0984c7d83018e741b2a461b1e317473854c3cfc7c69a8e075386b480d | Python | 2,229 | 68 | # 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
import os
import sys
from datetime import datetime, timezone
# -- Path setup ---------... |
7ac143adf6fa54012d3a0bbe984f3ca36104aab99028af0b6d34f6ab48cf184f | Python | 2,231 | 60 | ####################################################################################################
# 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 ... |
7cf93e02ccb3a39b984d43e69d0838c2e487198b7c3fe7a6d8b43763615e4ff5 | Python | 2,231 | 65 | import sys
import numpy as np
import torch
from torch_geometric.datasets import TUDataset
from graphxai.explainers import GuidedBP
from graphxai.explainers.utils.visualizations import visualize_mol_explanation
from graphxai.gnn_models.graph_classification import GCN, load_data, train, test
import matplotlib.pyplot as... |
e5c3527c67c0784238dbcb38c6fd5d7f6cc94605e874fa1712dbb9b4342da854 | Python | 2,231 | 62 | # 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... |
3d5871e1e98b9b5cdbca2b208e208c639835bb6ab37854d6b33acdf5417676d5 | Python | 2,232 | 59 | import torch
import pickle
import os
import numpy as np
import pandas as pd
from rulenn.rule_nn import RuleNNModel
VERBOSE = False
def print_rules(df: pd.DataFrame):
for row in df.iterrows():
print(" & ".join(df.columns[:-1][row[1][:-1]>0.3]) + " => " + str(row[1][-1]))
def apply_rules(container:RuleNN... |
0ff0736a8351f6ea890972555b52802213ecba1d0f0bc7144feee930c94e960f | Python | 2,233 | 46 | # functions/add.py
import torch
from torch.autograd import Function
import numpy as np
class AffineGridGenFunction(Function):
def __init__(self, height, width,lr=1):
super(AffineGridGenFunction, self).__init__()
self.lr = lr
self.height, self.width = height, width
self.grid = np.ze... |
04cc4d95a107af527d8fe0230f49bedef668c5fb7fd1322860710830e64bddc9 | Python | 2,234 | 64 | from functools import reduce
from mne import SourceSpaces
import numpy as np
from .._data_obj import _point_graph
def merge_volume_source_space(sss, name='Volume'):
"""Merge multiple volume source spaces into one
Notes
-----
Only intended to work properly if ``sss`` is the output of a single
:f... |
2973d9383eabaec859b83dc8da3d9c9ca7e560b82eeb531c350f53d1948eac98 | Python | 2,236 | 63 | '''
Ohmic IK model with bell-type time constant, for fitting depolarized responses in deciliated cells.
p = 2 and baseline time constant nearly 0.
Time constant peaks at V_IK, with slope twice the activation slope.
Maximum time constant 3 ms.
'''
from file_management import *
from brian2 import *
from brian2modelfittin... |
7ae515bdddde9d43de42ac7094bd7c4a3936af951031ade1f91d3fe4acfc0ee6 | Python | 2,238 | 86 | from os.path import basename
from pathlib import Path
import numpy as np
import pandas as pd
from sacred import Experiment
from sacred.observers import FileStorageObserver, SlackObserver
from sklearn.model_selection import ParameterGrid
from graspy.datasets import load_drosophila_left
from graspy.utils import binariz... |
68ba499324745ea02e843a7b7d8bc68b1648df0974765ed51d47dbbe07a40201 | Python | 2,242 | 54 | # 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... |
d47539217e4d9b0cba82c87fea99ca7544b9d1540d0365e183c7e20ac2c6dbc1 | Python | 2,242 | 67 | import argparse
import os
import sys
import torch
from PIL import Image
import torchvision.transforms as transforms
from networks.drn_seg import DRNSub
from utils.tools import *
from utils.visualize import *
def load_classifier(model_path, gpu_id):
if torch.cuda.is_available() and gpu_id != -1:
device = ... |
9cd5d974a4508a5cfa72917e9d29d026b47c14b5f954310e2fbd356044ef84f1 | Python | 2,243 | 59 | import torch
from torch.utils.data import Dataset
import os
import numpy as np
class LoadDataset_from_numpy(Dataset):
# Initialize your data, download, etc.
def __init__(self, np_dataset):
super(LoadDataset_from_numpy, self).__init__()
# load files
X_train = np.load(np_dataset[0])["x"]... |
b50bebd0dd439e8638d58a6cbf72ac0919ddc91441fa6129d2436d4ec6ffd8e7 | Python | 2,244 | 68 | import logging
from dataclasses import dataclass, field
from typing import Type
import rdflib
from linkml_runtime.dumpers import rdflib_dumper
from linkml_runtime.utils.yamlutils import YAMLRoot
from rdflib import SH
from rdflib.term import Node
from oaklib.datamodels.obograph import RDF, PrefixDeclaration
from oakli... |
e39b1a700209554be392385934f6c2126210bd76532247a6907d24de0d98d87c | Python | 2,244 | 77 | '''
IV curves for Fig. 6
(Ciliated cells with 0 and 4 mM KCl)
'''
import pandas as pd
from brian2 import second, volt, amp, ms
from pylab import *
import matplotlib.pyplot as plt
import numpy as np
from file_management import *
from os.path import join, split
import os
width, height = 2,2
overwrite = True
table = pd... |
42da9269456ebd87dff89e61925a262d4913eed83c2df2a4f7d199e0873938ba | Python | 2,246 | 63 |
import unittest
import torch
import numpy as np
from torch_geometric.data import Data, Batch
from deeprank_gnn.community_pooling import community_detection, community_pooling, community_detection_per_batch
class TestCommunity(unittest.TestCase):
def setUp(self):
self.edge_index = torch.tensor([[0, 1, 1,... |
f77c891e4a8e558ec143b6ae81a626666959e2daa7961ae09d6d812e24f372d8 | Python | 2,247 | 63 | import subprocess
BaseCase = __import__('base_case').BaseCase
class LoadResultsTest(BaseCase):
def test_basic_load_results(self):
self.open_main(static=False) #currently nonstatic required
filenames = [
"PD_T088_L004_13.11.18_091057_015_SS_crop.tiff",
"PD_T088_L0... |
0b9b091d4a84054d2e1cde2938c0458b5c65c65d354d5da5d6216ed1c47f6387 | Python | 2,248 | 72 | # Activation functions
import torch
import torch.nn as nn
import torch.nn.functional as F
# SiLU https://arxiv.org/pdf/1606.08415.pdf ----------------------------------------------------------------------------
class SiLU(nn.Module): # export-friendly version of nn.SiLU()
@staticmethod
def forward(x):
... |
22cb5f8b56ee943954b94fc082492029e09f009994421123899f717b790f419b | Python | 2,248 | 59 | import torch
def build_optimizer(optim_params, cfg):
"""
Construct a stochastic gradient descent or ADAM optimizer with momentum.
Details can be found in:
Herbert Robbins, and Sutton Monro. "A stochastic approximation method."
and
Diederik P.Kingma, and Jimmy Ba.
"Adam: A Method for Stochas... |
8dabbee1accaa0e11929a6a1267e25fd3650f6c53efc5850d2ac57bc3ba8b098 | Python | 2,248 | 68 | import os, glob
import torch
import argparse
import numpy as np
def aggregate_results(exp_method, metric, level, path):
'''
Metrics should match:
{exp_method}_{metric}_{level}
Also performs filtering for None's
Assumes they are each dictionaries (standard usage in Owen's parallelization)
... |
e25041537c7337abdd744bb40732c32b65e574f48413892b761d9f7f6e2930d7 | Python | 2,248 | 49 | import numpy as np
import pandas as pd
import pcwa as pcwa
import matplotlib.pyplot as plt
# read the raw mass scpectroscopy data and truth values
# df_raw = pd.read_csv('n100sig66_dataset_1_25/Dataset_7/RawSpectra/noisy7.txt',sep=' ')
# df_true = pd.read_csv('n100sig66_dataset_1_25/Dataset_7/truePeaks/truth7.txt',sep=... |
44a85c92e83aa72badda2787dca290c4d9aac84b4012f7614a17f0826c0a264a | Python | 2,249 | 48 | from pycpd import DeformableRegistration, RigidRegistration
import numpy as np
import time
from scipy.interpolate import Rbf
import warnings
def cpd_non_rigid_transform_pt(pt, Y, G, W):
from scipy.interpolate import LinearNDInterpolator
interp = LinearNDInterpolator(points=Y, values=np.dot(G, W), fill_value=0.... |
8c323e69e1c203609bd78db8565cb9d33e45fa643d37d266f311e8e5dc648e3e | Python | 2,251 | 94 | import re
import numpy as np
from scipy.spatial import KDTree # aliasing this
import matplotlib.pyplot as plt
POS_REGEXP = re.compile(r"\[([0-9]*) +([0-9]*) +([0-9]*)\]")
def extract_centroids(df):
# old df format
# return np.array(list(zip(df.centroid_x, df.centroid_y, df.centroid_z)))
return np.arra... |
4d9dbbc4da129b8a1bc2e8e36ed0747cdd9e02e24521246a2b3e3402d85bedcb | Python | 2,252 | 53 | # 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... |
7e3b10914a1a30a761154676d13638d34e57e4772e9a86b39a1ed1b1062b6c69 | Python | 2,253 | 36 | """Detail-preserving, temporally smoothed Harmonizer merge.
The Harmonizer's useful work on an inserted car is low-frequency (tone, shading, edge softening); its high-frequency
output jitters from frame to frame. Keep the composite's detail and apply only the low-frequency delta, smoothed
over time: out_k = comp_k + u... |
1b8e6b1f78c4991cc240081000de6418e639c151402b104a7f2d29bccd285fb8 | Python | 2,256 | 59 | # 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... |
a4f3bb0f5c6f3e0f8c27a47374dd73abd7ce95c3b629714bde37415409d71676 | Python | 2,258 | 58 | # 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... |
794b4825061cf2b39961afbcaeb392a9eeebd07f2e3c119a5ee744126205bee2 | Python | 2,259 | 71 | # 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... |
6de15e71d03eacccd25d07ade342f4ccff4e5186141dbaaec8a4f650eb87c163 | Python | 2,260 | 86 | import csv
import os
import sys
def feature_to_index(cases, column_nb, offset=0):
feature_set = set()
for case in cases:
feature_set.add(case[column_nb])
l = list(feature_set)
index = {}
i = 0
for f in l:
if f != '':
index[f] = i + offset
i += 1
retur... |
a06acc7be864667a2b7a8322496b17216fd0c7e15e14f558edfe25600908ebd2 | Python | 2,260 | 67 | import cv2
import torch
import numpy as np
from torch.utils import data
from config import config
from utils.img_utils import random_scale, random_mirror, normalize, \
generate_random_crop_pos, random_crop_pad_to_shape
class TrainPre(object):
def __init__(self, img_mean, img_std):
self.img_mean = img... |
ce6ad1f49782eba04b3527c98c7f7d1a2757247eeda317d82522e30bbe5b7894 | Python | 2,261 | 36 | """Stills on a World Partition map (Town15 by default, MAP=... to change) with a hero vehicle parked under each
camera, so the map streams the area. Without the hero a -game server renders only the cells around the
spectator start and the shot comes out empty.
wp_shots.py OUTDIR "name=x,y,z,yaw,pitch;hx,hy,hz" ...... |
d89feb62673d51f812180f6f79bf494a0eb26665a30c3aaeb4a59144bb923b52 | Python | 2,262 | 65 | from tqdm.auto import tqdm
from copy import deepcopy
import numpy as np
# prepare data for kernel regression
def prepare_data(
df,
standardize_features=False,
dlight_key="signal_reref_dff_z",
sz_cutoff=23 * 30 * 60,
feature_variables=[],
powers=None,
):
szs = df.groupby("uuid").size()
... |
b0adb65c8564c4a23075419cf7f2e1d0d9b042d21fb73405c37c0297591af093 | Python | 2,263 | 67 | # 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 --------------------------------------------------------------
# Built... |
f2a6b3782b2aff1170b6d4bbf5641dce3f6b42136e747bc9749640eb0ada63db | Python | 2,264 | 79 | import sys
import numpy as np
import circularFiltering as flt
from time import time
kappa_z_array = np.array([0.01,0.03,0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1,2,3,4,5,6,7,8,9,10,30,100])
len_kz = len(kappa_z_array)
# translate input varibles
kappa_star = float(sys.argv[1])
beta = float(sys.argv[2])
sigmaN = float(sys.... |
07269acfab7d9334fba2443808745f428d3630b7af07046268a898548e237e27 | Python | 2,265 | 66 | from abc import ABC
from typing import Dict, List, Tuple, Iterable, Union
from oaklib.interfaces.basic_ontology_interface import BasicOntologyInterface, RELATIONSHIP_MAP, RELATIONSHIP
from oaklib.types import CURIE, LABEL, URI, PRED_CURIE
from oaklib.utilities.graph.relationship_walker import walk_up
class RelationG... |
756e3350bb49ad4edfc1ed34af3194cf07d4ce50e7241630da1a1cec7f5376e9 | Python | 2,265 | 54 | # 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... |
adbfafe04e772478f9994bdc65383f6ccf7e906671e2d59e9ae0ec98ff4630f2 | Python | 2,265 | 65 | """
© 2022, ETH Zurich
"""
from rdkit import Chem
from rdkit.Chem import DataStructs
import argparse
import os
from rescoss_logp_ml.utils import FOLDER_NAMES, PROC_DATA_PATH, DATA_PATH
import pandas as pd
import numpy as np
from tqdm import tqdm
import pickle
def get_2d_features(smiles_list):
from rdkit.Chem im... |
ec47b96b1b6f89239f98ac712bfd468141497c41fda30489fb1990b30c89b991 | Python | 2,266 | 58 | from linkml_runtime import CurieNamespace
from oaklib.datamodels.ontology_metadata import slots as omd_slots
import oaklib.datamodels.ontology_metadata as omd
WIKIDATA = CurieNamespace('wikidata', 'http://www.wikidata.org/entity/')
WDP = CurieNamespace('wdp', 'http://www.wikidata.org/prop/direct/')
NAMESPACES = [omd.O... |
0ffc34134c26b9318a1e3cdf57448ef14d124f025a93c99db0b17caf8869307f | Python | 2,267 | 75 | '''
Figure 8.
Example of reversal asynchrony between anterior and posterior side.
2020-10-12 16.08.21
'''
from brian2 import *
import yaml
from file_management import *
from pylab import *
import matplotlib.font_manager as fm
import os
from os.path import join
from fitting import *
from plotting import *
from mpl_toolk... |
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