sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c01e5b946238fa6caedc0519b70dafe9aed4c0892dceb6af8c7e419fdbd2306e | Python | 25,303 | 629 | from collections import OrderedDict
import csv
from logging import Logger
import pickle
from random import Random
from typing import List, Optional, Set, Tuple, Union
import os
from rdkit import Chem
import numpy as np
from tqdm import tqdm
from .data import MoleculeDatapoint, MoleculeDataset
from .scaffold import lo... |
900230127132c6ffc79aef81b10f12590e915926690c94130bd71acb2c04ae40 | Python | 25,311 | 638 | # Built-in
import os
import threading
from pathlib import Path
from typing import Any
# Third-party
from numpy.random import Generator, SeedSequence, default_rng
# Local
from cxsystem2.core.tools import load_from_file, write_to_file
__author__ = "Andalibi, V., Hokkanen H., Vanni, S."
"""
The preliminary version of ... |
3093f0526c6b5cd7c86b125cc5ef1bb76bcf48abc6163b7c92c1173aaa5069ba | Python | 25,325 | 541 | # tumor sim pipeline
# Generate tumor according to different label, augment tumor and mask
# Get healthy brain, augment
# Combine tumor and brain to put in arbitrary position, with in certain threshold of (overlap area)/(tumor area) to avoid tumor outside brain; avoid tumor across midline
import os
os.environ['CUDA_VIS... |
bbec0dc4bf0ba38c6e7bc6cac0200e911570ec47694224c1341889a23a82417c | Python | 25,333 | 973 | # %% [markdown]
# # THE MIND OF A MAGGOT
# %% [markdown]
# ## Imports
import os
import time
import warnings
from itertools import chain
import colorcet as cc
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import networkx as nx
import numpy as np
import pandas as pd... |
ac521c861e88775d5cd7ddf8e743eea429677240887c85c9f171905dafbf3e0c | Python | 25,363 | 455 | # general class containing info about a transcribed region. Can come from UCSC Knowngenes (BED) or Ensembl GTF files currently
# Stephen N. Floor
# Fall 2014
class Transcript:
def __init__(self):
#properties defined in UCSC knowngenes
self.name = ''
self.chrom = ''
self.stran... |
c190968ae5a5ab004f569dfd08cce39f5fb49c536f2589a0cb3c7a50804afbfa | Python | 25,373 | 676 | # 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... |
5e56b531b0de2a0f7541df5364b0504d3d4b8a600a59fbdb6cf4fc4524ddf32d | Python | 25,417 | 545 | from typing import List, Tuple, Union
from itertools import zip_longest
from rdkit import Chem
import torch
import numpy as np
from chemprop.rdkit import make_mol
# Atom feature sizes
MAX_ATOMIC_NUM = 100
ATOM_FEATURES = {
'atomic_num': list(range(MAX_ATOMIC_NUM)),
'degree': [0, 1, 2, 3, 4, 5],
'formal_cha... |
1a1765199b14badea082c5d6a98058ed0cc6eac7c64bfc6b31169d4a82876bd9 | Python | 25,421 | 515 | # module for processing networkx graphs in various ways
import pandas as pd
import numpy as np
import csv
import gzip
from tqdm import tqdm
import matplotlib.pyplot as plt
import seaborn as sns
import pymaid
from tqdm import tqdm
from joblib import Parallel, delayed
import networkx as nx
import networkx.utils as nxu
... |
d739fca210fc4ebf37456de43ec8d336ddb9e967fb85289d457eaecc549c2516 | Python | 25,465 | 532 | import logging
import os
import numpy as np
from pprint import pformat
from collections import namedtuple
from argparse import ArgumentParser, Namespace
from utime import Defaults
from utime.utils.system import find_and_set_gpus
from utime.bin.evaluate import get_and_load_one_shot_model
from psg_utils.dataset.sleep_stu... |
9ea8053f652cb069f82ae6d68473fe2b7030a81a3b517493700b936b433b309b | Python | 25,480 | 690 | import json
import logging
import os.path
import tempfile
import collections
from unittest import TestCase
import numpy as np
import pandas as pd
from drugex.data.corpus.corpus import SequenceCorpus
from drugex.data.corpus.vocabulary import VocGraph, VocSmiles
from drugex.data.datasets import GraphFragDataSet, SmilesD... |
ed11b2f358e979deba62e7d618d523ad0f41c8f99b80b153fcd69782769c845a | Python | 25,521 | 839 | # torch
import torch
import torch.nn.init as init
import torch.nn as nn
from torchvision.transforms import ToTensor
import torch
import torch.nn as nn
import torch.nn.functional as F
import math
# from .util import *
# from ..siren.op import FusedLeakyReLU, fused_leaky_relu, upfirdn2d
# debug
from util import *
impor... |
3719d5e3c4d0e7d4a98605a80a98ebfadd48eb8e3716fcbef2806d120194c172 | Python | 25,526 | 555 | #!/usr/bin/env python3
"""Spawn vehicles that drive themselves via autopilot, and destroy them cleanly.
Commands:
spawn --count 40 [--filter vehicle.*] [--safe] [--seed 42]
[--tm-port 8000] [--no-autopilot] spawn at map spawn points
line --at X,Y,Z --count 5 --gap 15 [--backward] [...]... |
8e08df7435c2a093bc77470ec6379e5dd62065737e5cf7036394c8f2bcb535c0 | Python | 25,527 | 609 | """
File: main.py
Created: 2020/04/23
Last Changed: 2020/06/09
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 ... |
7d010fe007ceaab66642eef7fa473041f4869949d14be122351b0385d5f36fc8 | Python | 25,553 | 574 | import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import Scale, normal_init
from mmcv.runner import force_fp32
from mmdet.core import distance2bbox, multi_apply, multiclass_nms
from ..builder import HEADS, build_loss
from .anchor_free_head import AnchorFreeHead
INF = 1e8
@HEADS.regist... |
26ad0676d50717aa7780f1baa200ddec410d17555dc7f391c875785bf8fce01f | Python | 25,563 | 588 | import mmcv
import numpy as np
import torch
from torch.nn.modules.utils import _pair
from .builder import ANCHOR_GENERATORS
@ANCHOR_GENERATORS.register_module()
class AnchorGenerator(object):
"""Standard anchor generator for 2D anchor-based detectors.
Args:
strides (list[int] | list[tuple[int, int]]... |
0121f01de1c91ae21da624d58a4a473039592f51d5213d3afc5c9dfbf54a7ac5 | Python | 25,572 | 809 | import tempfile
import enum
import logging
import numpy as np
import pandas as pd
import AFQ.viz.utils as vut
from dipy.tracking.streamline import set_number_of_points
try:
import plotly
import plotly.graph_objs as go
import plotly.io as pio
from plotly.subplots import make_subplots
import plotl... |
ce88f31d44551d249168619eaf229533d71fe6c925bf01319d28e62e74a6d136 | Python | 25,574 | 786 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Plot sensor maps."""
from collections.abc import Sequence
from math import sin, cos, asin
import os
import numpy as np
import matplotlib as mpl
from matplotlib.lines import Line2D
from .._data_obj import Datalist, as_sensor
from ._base import EelFigure, ImLa... |
2647ddeb04ffa9bd9b983b9b2d13312629903a715d899c5b242603468fdb5c69 | Python | 25,576 | 929 | #%% Imports and file loading
import pprint
import sys
from pathlib import Path
import networkx as nx
import numpy as np
import pandas as pd
import pymaid
from src.data import load_networkx
from src.io import savecsv
from src.pymaid import start_instance
output_name = "2020-09-23"
output_path = Path(f"maggot_models/d... |
bd5e9867bb392dec283a4b447aa60c8db158dd1d671c216390b1c29d96af9acb | Python | 25,577 | 930 | #%% Imports and file loading
import pprint
import sys
from pathlib import Path
import networkx as nx
import numpy as np
import pandas as pd
import pymaid
from src.data import load_networkx
from src.io import savecsv
from src.pymaid import start_instance
output_name = "2021-01-29"
output_path = Path(f"maggot_models/d... |
abb82cab33180379c0272cac37b3a4c2a6800ab809fabc4862956e08e229f5c0 | Python | 25,588 | 615 | # SPDX-FileCopyrightText: © 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# SPDX-License-Identifier: MIT
"""
This file contains scripts to start the grpc server to render images. Example command line to start server:
docker run --env "CUDA_VISIBLE_DEVICES=0" --name="nre_1" \
--gpus all --rm --net=host ... |
d2b91f7865981bb3bea1c5afe847ca381e49e216c5fe70c3a6fa1dff03239be2 | Python | 25,588 | 619 | #!/usr/bin/env python
# compare_tripseq_clusters.py
# Compare input lists of clusters against each other searching for genes that have transcripts in the different clusters.
# Intended to be applied to fractionated polysome sequencing data (a la tripseq) but theoretically can work for any data involving transcript-s... |
43e1cf8eeba1d5f6670e26d529d5cae868a36d5dfbf91acfb100dc9aa85317c9 | Python | 25,610 | 635 | """Datasets"""
import os
from cv2 import transform
import torch
from torch._C import dtype
from torch.utils.data import DataLoader, Dataset
from torchvision import datasets
import torchvision.transforms as transforms
import torchvision
import glob
import PIL
import random
import math
import pickle
import numpy as np
... |
ad781a1e5cb21b207c1807b33bb3962e7085460eadc9d2f20cde4851cbf51545 | Python | 25,610 | 641 | # Classification analysis of social perceptual features based on fMRI responses to audiovisual perception of these features
#
# Sections:
# 1. Make dataset for full brain classification analysis
# 2. Make dataset for ROI analysis
# 3. Tune hyperparameters for neural network (full brain dataset)
# 4. Run between... |
d67932714af7a8a614a1e927f13eeb48d424b14fed8227fb274ff1395cccaaf6 | Python | 25,706 | 600 | import jax.numpy as jnp
import numpy as np
import scipy.sparse as sp
from scipy.sparse.linalg import eigs
from .grid import YeeGrid
from .typing import Size, Spacing, Optional, Tuple, Union, Callable, Size2
from .utils import poynting_fn, Box
from .viz import plot_power_2d, plot_field_2d, plot_field_1d, hv_field_1d, h... |
2f0b664121bf21ea185cfda67bf04d164406d610e08dd0bc303ade097cd1069f | Python | 25,728 | 725 | """Multi-Dynamic Network Modes (M-DyNeMo).
See the :doc:`model description </models/mdynemo>` for more details.
See Also
--------
`Example script <https://github.com/OHBA-analysis/osl-dynamics/blob/main\
/examples/simulation/mdynemo_hmm-mvn.py>`_ for training M-DyNeMo on simulated
data (with multiple dynamics).
"""
... |
5e3cb9cd2532af3a192ce48027beed19d8202a68639531c707396c2c3fd33fa6 | Python | 25,737 | 526 | # Copyright 2020-21 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... |
bb7701528c1c8a01a120035fef1e9f53415ec6b5ea03aa26bf38d0709b148bea | Python | 25,740 | 571 | import math
from dash import Patch, ALL
from dash_extensions.enrich import Serverside, Output, Input, State, callback, clientside_callback, ctx, no_update
from dash.exceptions import PreventUpdate
import mne
import pandas as pd
import numpy as np
import RV.constants as c
from RV.callbacks.utils.annotation_utils impo... |
6db641a1fde221b19313cec0abebbe1c2610d5bf35362363f79cefe1491f2f4b | Python | 25,742 | 393 | import os, sys
import shutil
import time
import tkinter
import h5py
import matplotlib.pyplot as plt
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
import tensorflow as tf
# tf.enable_eage... |
73fe1df13f6ac9c088dbee2c4c8172abaa81fc6d56b04f0ec777726aa125c1a2 | Python | 25,749 | 661 | ####################################################################################################
# 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... |
21cad4b74fce328dee378a294f72c00622689332aa3233a8209c8e34236f53bf | Python | 25,782 | 771 | import os
import time
import numpy as np
import random
import glob
import matplotlib
import matplotlib.pyplot as plt
import torch
import torch.nn as nn
from torch.utils.data import Dataset, DataLoader
import torch.nn.functional as F
import torch.optim as optim
from sklearn.metrics import f1_score
import scipy.ndimag... |
715e418cc9603453538d15d1b8dc36a4cc5916ae841605b46279da128c991d32 | Python | 25,795 | 970 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy
import seaborn as sns
from sklearn.metrics import pairwise_distances
from graspy.embed import ClassicalMDS
from graspy.match import GraphMatch
from graspy.plot import... |
0aa9c384f64de7be05202b774cee7ec771b29b7f1c95f081a50074f73394a017 | Python | 25,835 | 613 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module containing useful functions for fine tuning with PyTorch.
Created on Mon Apr 8 14:13:08 2019
@author: nicolas
"""
import copy
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.widgets as widgets
from skimage import measure, draw
import cv2
... |
d7d4cb6d70421da8908c92748ef5e099112a29e5a84c6e21a58a5f962e841369 | Python | 25,838 | 734 | """Dynamic Network Modes (DyNeMo).
See the :doc:`documentation </models/dynemo>` for a description of this model.
"""
import os
import logging
from dataclasses import dataclass
from typing import List, Optional, Tuple
import numpy as np
import tensorflow as tf
import osl_dynamics.data.tf as dtf
from osl_dynamics.in... |
6e892b90b550a434b496763af5e210525564289e276cbef01c976ef19a48ff9b | Python | 25,849 | 488 | """Cosmos 3 worker: drives a ``vllm serve <Cosmos3> --omni`` process over its videos API.
Mapping of a carla-cosmos job to vLLM-Omni's transfer request
(``vllm_omni/diffusion/models/cosmos3/transfer.py``, verified 2026-08-26):
* controls ``depth``/``seg``/``wsm`` -> ``extra_params[<hint>] = {"control_path": <worker-l... |
86dfdcb73b58279ce161067588acb932f5fd408dfeb4a15f234d3d5c0024d000 | Python | 25,885 | 574 | # 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 in... |
9b420d00047774222636e1636438762d6f7aafe12551e5a4484119c591d20a11 | Python | 25,888 | 552 | #!/usr/bin/env python3
"""
File: visualise_ct_mediated_eqtl.py
Created: 2020/09/23
Last Changed: 2022/02/10
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
th... |
98d841d03526459a99edce821956930a67db3d6eb9ed3f9708193cd1f1c4da36 | Python | 25,896 | 590 | ####################################################################################################
# Copyright (c) 2019 - 2021, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of VessMorphoVis <https://github.com/BlueBrain/VessMorphoVis>
#
# This program is free ... |
39a05600ebacd3b0f3d7f3bf6721291580886aa2eca3b5fbeb8f21d8d575b98a | Python | 25,919 | 589 | import torch
import torch.nn.functional as F
from mmdet.core import (bbox2result, bbox2roi, bbox_mapping, merge_aug_bboxes,
merge_aug_masks, multiclass_nms)
from ..builder import HEADS, build_head, build_roi_extractor
from .cascade_roi_head import CascadeRoIHead
@HEADS.register_module()
class... |
89b5c22677fc866a2f268c9ea666a23c7e2279333262150a4ee808805429ea1d | Python | 25,933 | 723 | # Copyright 2021 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... |
babb1149af9d9658f969f3e861b1018e8a31032ba5ace8531ff627084b438f3a | Python | 25,947 | 708 | """
This module provides the `TrainModel` class and supporting methods.
"""
import logging
import math
import os
import shutil
from time import strftime, time
import numpy as np
import torch
import torch.nn as nn
from sklearn.metrics import (
ConfusionMatrixDisplay,
average_precision_score,
confusion_matri... |
30973011e5df878010482b1856a596a92aa7fcc05bd145cd25e1e26770b3db0e | Python | 25,968 | 511 | # 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... |
fbf4f98e766de9ad0bf7b7e692bef74b014b88218d27396aa9dc9d4bddf02a03 | Python | 25,971 | 677 | from src.utils.sanifix import AdjustAromaticNs
from src.utils.tokenizer import smi_tokenizer
from rdkit import RDLogger
from rdkit import Chem
import math
import re
import random
import pandas as pd
RDLogger.DisableLog("rdApp.*")
def num_in_list(tokens):
"""
Create sequences with bond already exists error.
... |
9c1287316c0f8bac6da6af4b4d45218c4d22c3ddc3855e94fccc496aca86bbb1 | Python | 25,975 | 715 | """
This module provides the `TrainModel` class and supporting methods.
"""
import logging
import math
import os
import shutil
from time import strftime, time
import numpy as np
import torch
import torch.nn as nn
from selene_sdk.utils import (
PerformanceMetrics,
initialize_logger,
load_model_from_state_di... |
8d6241d6d798cdf4eeb24c510a5dbb39270b8a8634654a068d973493f840f950 | Python | 25,998 | 743 | from collections import defaultdict
from numpy.core.defchararray import array
import pytorch_lightning as pl
from pytorch_lightning.metrics.regression import MeanAbsoluteError as MAE
from pytorch_lightning.metrics.regression import MeanSquaredError as MSE
from pytorch_lightning.metrics import F1
from pytorch_lightning.... |
23eda39f84dca77198d033ce35a68d0101c1f38c6ae933369fdd515363cc5929 | Python | 26,045 | 692 | # SPDX-FileCopyrightText: © 2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# SPDX-License-Identifier: MIT
"""
Track and Pose Interpolation Module
This module provides classes for managing and interpolating object trajectories (tracks)
in NUREC scenarios. It handles different pose representation formats ... |
6ac7d482e2c7cf32e12df8513dcf706b839d4534f09d4a5fbd1b755e43abcc82 | Python | 26,047 | 458 | import argparse
import math
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
from pytransform3d.urdf import UrdfTransformManager
from pytransform3d import rotations as pr
from pytransform3d import transformations as pt
from dataloading.model import Camera, TurnSignal
SKIP = -1
... |
2fe029b83b82caa8c2b75d018425fb0cccce2e64d13957e634094ffb6516adf8 | Python | 26,109 | 727 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Plot uniform time-series of one variable."""
import operator
import matplotlib as mpl
import numpy as np
from .._celltable import Celltable
from .._data_obj import ascategorial, asndvar, assub, cellname, longname
from .._stats import stats
from . import _bas... |
b9679be3bc47806d446978bc8165bed853178e600268f14d99c19d2115f635e0 | Python | 26,149 | 498 | # %%
from pymaid_creds import url, name, password, token
from data_settings import pairs_path, data_date_A1_brain, data_date
import pymaid
rm = pymaid.CatmaidInstance(url, token, name, password)
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib as mpl
impor... |
d822ef13c61859d333d259a1266fec18e19e862f43c29f68768f1c57a3455666 | Python | 26,168 | 721 | # 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... |
57aca7e1af5b14649ac5c83acd27117cfa49e2a9d8506d12a7f741aa0b430082 | Python | 26,205 | 596 | #!/usr/bin/env python
# coding: utf-8
import json
import csv
import PredysUtil8ans as pu
import numpy as np
import os
from sklearn.svm import SVC
from sklearn.svm import LinearSVC
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import accuracy_score
impo... |
51a123e8d97ebebb02eb183476620075e7c4300db3833046f892fc9ac2b415b1 | Python | 26,217 | 505 | import collections
import datetime
import pandas as pd
import inspect
import os
import numpy as np
import itertools
import tqdm
import AIS_interp
import functions_basic_sak as funsak
from sklearn.cluster import DBSCAN
from scipy.interpolate import interp1d
import AIS_parameters
import re
import PIL
imp... |
d661902c0cc5f9316a8b80e62b571e91167a80f7d569de9437792bf34d3f6965 | Python | 26,250 | 764 | import numpy as np
import logging
import nibabel as nib
from dipy.segment.mask import median_otsu
from dipy.align import resample
from AFQ.definitions.utils import Definition, find_file, name_from_path
from skimage.morphology import convex_hull_image, binary_opening
__all__ = [
"ImageFile", "FullImage", "RoiIm... |
9042463774e25c48bad3bca34c8fa936a8530abc246be1ac099bbb2c646a15f1 | Python | 26,270 | 773 | """
Training script for UQNO (Uncertainty Quantification Neural Operator) on Darcy flow.
This script implements a two-stage training process:
1. Train a base solution model on Darcy flow data
2. Train a residual model to predict uncertainty bounds
3. Calibrate the uncertainty predictions for reliable coverage
The UQN... |
1c2a9844add6ce890e110d011a1c6b4dd56b625a01d701f9e420e222ed07d913 | Python | 26,278 | 604 | # 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... |
2c3cbbe379339f4ff40b282a94ce981e5e66d8ad7249cc504c87d1da81059439 | Python | 26,289 | 400 | #!/usr/bin/env python3
"""
File: visualise_replication_opposite_effects.py
Created: 2021/08/03
Last Changed: 2021/09/02
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as pub... |
cff64a03468f192ed3e04fc7ec10592bb63503add1ce0dd415ccbc00a4fa712b | Python | 26,301 | 837 | # %% [markdown]
# ##
import os
import time
from pathlib import Path
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from graspologic.embed import OmnibusEmbed, selectSVD
from graspologic.models import DCSBMEstimator, SBMEstimator
from graspologic.ut... |
37ee02a72aa6cce6689faa729699fad20efc5ab254aea7000943d2356ed8396c | Python | 26,310 | 663 | import time
import os
import sys
from os.path import dirname, realpath, join
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5.QtCore import *
import pyqtgraph.opengl as gl
import nrrd
import pickle
import shutil
import requests
import numpy as np
import pandas as pd
from .atlas_loader import process... |
fb257b12ed4c886d936f0901914000b456c34110888e22fb12492511596c4e4c | Python | 26,328 | 637 | # Analysis
# from numpy import NaN
import numpy as np
import pandas as pd
# This computer git repos
from cxsystem2.core.tools import (
change_anat_file_header_value,
read_config_file,
parameter_finder,
)
# Builtins
# from argparse import ArgumentError
from pathlib import Path
import shlex
import subproces... |
37e0dc130f2afc9b2382bbf0994b3eb47edf13514f60cce2c7765eb941897c76 | Python | 26,339 | 533 | import argparse, sys
import collections
import torch
import numpy as np
import logging
from pathlib import Path
import data_loader.data_loaders as module_data
import model.loss as module_loss
import model.metric as module_metric
import model.model as module_arch
from utils.parse_config import ConfigParser
from utils.t... |
841424793e937a5f366d9688feca641fe50a0368191666b88d80466493ccb7be | Python | 26,387 | 603 | # -*- coding: utf-8 -*-
import torch
import numpy as np
import pickle
import time
from utils.get_detected_info import get_anchor_nums, get_anchor_box_size
prior_info = 0
min_area = None
saved_matching = {}
saved_conf_loc = {}
prior_to_ratio = None
matching_timer = 0.
def point_form(boxes):
""" Convert prior_boxes... |
44288ae50bb601ee933a472f5020c9e95c616cd4464444331ffac94f1120d421 | Python | 26,445 | 714 | import numpy as np
import sys
from modules.parameters import ParameterSet, copy_dict
from defaults.paths import paths
def set_kernel_defaults(run_type='local', data_label='', **system_pars):
"""
Return pre-defined kernel parameters dictionary
:param default_set:
:return:
"""
keys = ['nodes', 'ppn', 'mem', 'wall... |
bce3d6a630b6755f074de178acd91d7886c3fd64ec28f8a9fc5dd1d66334715c | Python | 26,474 | 725 | # Auto generated from mapping_cluster_datamodel.yaml by pythongen.py version: 0.9.0
# Generation date: 2023-02-27T10:04:41
# Schema: mapping-cluster-datamodel
#
# id: https://w3id.org/oak/mapping-cluster-datamodel
# description: A datamodel for specifying mapping clusters, such as those retrieved from boomer. A mapping... |
4b12eff7050cf4895e67f1cc46f8d6e6a83640ebefecc3a01d365bc6f13f0c30 | Python | 26,504 | 449 | import itertools
import logging
import os.path as osp
import tempfile
import numpy as np
from mmcv.utils import print_log
from terminaltables import AsciiTable
from .builder import DATASETS
from .coco import CocoDataset
@DATASETS.register_module()
class LVISDataset(CocoDataset):
CLASSES = (
'acorn', 'a... |
2da2e7e5d3349aa3d79a0d10c245ab6613bd0a13a237ae62c5eb05a1f12135e7 | Python | 26,510 | 628 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 19 2022
@author: yuxiushao
"""
import numpy as np
import matplotlib.pylab as plt
import matplotlib
from numpy import linalg as la
from scipy import linalg as scpla
import scipy
# import seaborn as sb
from mpl_toolkits.axes_grid1 import make_axes_l... |
0cbd14d8ca996666878dcb0e7d0a49a84441f0d1aa10767e3d1b754655f18c2e | Python | 26,538 | 639 | #!/usr/bin/env python3
"""
File: afr_replication.py
Created: 2022/02/11
Last Changed: 2022/05/26
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Soft... |
cc17eae4c64e2518b93c05dcd255aae68d6cbd358ed3b7d7e5f20d53b880c7ab | Python | 26,540 | 565 | import torch
from torch import Tensor
import torch.nn as nn
import copy
from typing import Callable, Tuple
from torch_geometric.nn import GCNConv
from torch_geometric.utils.loop import add_self_loops
from torch_geometric.utils import k_hop_subgraph
from torch_geometric.data import Data
from ._decomp_base import _BaseD... |
657aeb84951ce0a2db29b0e094e4a53a97c307cef79d7efc5cc3ce8bb7e8235d | Python | 26,570 | 742 | import itertools
from typing import List, Optional, Tuple, Union
from ..utils import validate_scaling_factor
# Set warning filter to show each warning only once
import warnings
warnings.filterwarnings("once", category=UserWarning)
try:
from typing import Literal
except ImportError:
from typing_extensions i... |
ea65c19736c474a543edc1f9f96393e456571e3057b59a0b555b93b84d3da8d2 | Python | 26,584 | 599 | import os
from functools import reduce
from typing import Iterable, List, Union
import numpy as np
import pandas as pd
from scipy.interpolate import interp1d
from src.util.camera import ImagingSystem, transform_reflectance
class CameraCalibration(object):
def __init__(self, filename, sort=False, model="9.2.4.1")... |
2f9c9b31c5704fdb2cf15e6c472efa7832723c39120c02edf9f054159b6419fc | Python | 26,611 | 715 | from PyQt5.QtWidgets import *
from PyQt5.QtCore import *
from PyQt5.QtGui import *
import numpy as np
from .uuuuuu import read_qss_file
dialog_style = '''
QDialog {
background-color: rgb(50, 50, 50);
color: white;
font-size: 12px;
width: 50px;
}
QLabel {
color: white;
width: 50px;
}
'''
clas... |
ccd49b5d0dc0fecbcde98b353b4a97c863db82c1ea3b79dc09fca3ef74774e70 | Python | 26,670 | 1,017 | # %% [markdown]
# # THE MIND OF A MAGGOT
# %% [markdown]
# ## Imports
import os
import time
import warnings
from itertools import chain
import colorcet as cc
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import networkx as nx
import numpy as np
import pandas as pd... |
8b90da59a2d575b7a75826d6de2c014fb81b9cc12347e08b499f6990585222aa | Python | 26,688 | 768 | # Copyright 2021 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... |
c09320b3c062d18f527438f4c7cfcfb8ef52c1fd557fd1b1a122dce26e547e18 | Python | 26,706 | 636 | #!/usr/bin/env python3
"""Listen to a CARLA sensor and save its data, show it in a window, or summarise it.
Select an existing sensor (spawn one with the create-sensor skill first):
--id N | --type sensor.camera.rgb | --attached-to hero
Commands:
info [--seconds 5] grab one reading and pr... |
2629f7bf917f871b0be6e58bbbf029dfb888912c4019c2a9cf4b28ffed8193c5 | Python | 26,708 | 636 | #!/usr/bin/env python3
"""
File: visualise_sn_eqtl.py
Created: 2021/01/28
Last Changed: 2021/02/22
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free So... |
d9abe841c976ec5cd11f285ecedc705e1215d78fc22ad5f1d0942774577ae9e4 | Python | 26,737 | 814 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""I/O objects for phys2bids."""
import logging
import re
from copy import deepcopy
from itertools import groupby
import numpy as np
TRIGGER_NAMES = ["trig", "trigger"]
LGR = logging.getLogger(__name__)
LGR.setLevel(logging.INFO)
def is_valid(var, var_type, list_typ... |
ec615ff405fda162636545fcb23862539d0c40f4caff50cf98c03654199d0618 | Python | 26,745 | 642 | #!/usr/bin/env python3
"""
File: visualise_sn_eqtl.py
Created: 2021/01/28
Last Changed: 2022/02/10
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free So... |
9530f77e7b2a9b837ad62be7b3ef203127eaad51c9e35475ece75410b2d24744 | Python | 26,750 | 861 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.stats import poisson
from graspy.embed import OmnibusEmbed, selectSVD
from graspy.match import GraphMatch
from graspy.models import DCSBMEstimator... |
251b92426a6d9335076bd6beb706bd014c6fcb97529f40e641f77bae85563d8e | Python | 26,773 | 651 | # 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... |
b287dcb040118b16e64667908a4a9636d8598c053f0bc51a0d4c1329821e9208 | Python | 26,814 | 626 | # 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... |
f51409624c3d88c1f44e5e3a01219b88f7fc19d7a5e48d6d1a6df6fe612e5188 | Python | 26,880 | 709 | import math
import torch
import torch.nn as nn
from blitz.utils import variational_estimator
from torchnlp.nn.attention import Attention
from neural_networks.base_models import BaseModel
from neural_networks.bayesian import ShallowBayesianRegressor, BayesianConvEncoder
from neural_networks.custom_modules import ConvDr... |
c425118e639051ce2e3ada125f7e20a6a038678ba998e97724a33d45a8812c30 | Python | 26,908 | 870 | # %% [markdown]
# ##
import os
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.stats import poisson
from graspy.embed import OmnibusEmbed, selectSVD
from graspy.match import GraphMatch
from graspy.models import DCSBMEstimator... |
661593bf24cc5a68e86e1f268c83972611d585bbd720797943bf757c08775206 | Python | 26,915 | 618 | import numpy as np
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, bias_init_with_prob, normal_init
from mmcv.runner import force_fp32
from mmdet.core import (build_anchor_generator, build_assigner,
build_bbox_coder, build_sampler, images_to_levels,
m... |
a4da831d7afa1efe958d16bd6d99c3a9b40297c04faddd3b9ede28badacafb21 | Python | 26,937 | 635 | from fileinput import filename
import sys, argparse
from cv2 import normalize
sys.path.append('..')
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
from ui.ui import Ui_Form
from ui.mouse_event import GraphicsScene
import cv2
import torch
from ui.util import number_color, number_ob... |
7e214c92bc522c999bafa368e2304793e4c92d78c93afb184ea2871ae400d913 | Python | 26,939 | 749 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Color tools for plotting."""
from collections.abc import Iterator
from itertools import product, chain
from math import ceil
import operator
import numpy as np
import matplotlib as mpl
from matplotlib.colors import LinearSegmentedColormap, Colormap, Normalize... |
cd616cadc648bc8a971d614cf9156892b544839a143fe09f9641b8b99a5cfeac | Python | 27,008 | 540 | """Frame-exact multi-camera capture from a live or replayed CARLA world.
The world runs in synchronous mode at ``fixed_delta_seconds = 1/fps`` (previous
settings are restored on exit). Every sensor image is matched to the frame id
returned by ``world.tick()``; a missing or skipped frame raises
:class:`FrameDesyncErro... |
188302645b1b498d52fe2d934603ad09a48e064ec5ece37156b48e499c926fa4 | Python | 27,022 | 519 | #!/usr/bin/env python3
"""
File: pre_process_TPM_expression_matrix.py
Created: 2021/11/23
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fr... |
e2a2b60e424038bb6166d83d4a5d543d09e2a852f05d3675d6fbf00a544d190b | Python | 27,070 | 639 | #!/usr/bin/env python
# coding: utf-8
import json
import csv
import PredysUtil5ans as pu
import numpy as np
import os
from sklearn.svm import SVC
from sklearn.svm import LinearSVC
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import accuracy_score
imp... |
f02a55e54a058e21f2fc34202d30f0729cfbc9228d7568cab0db42d709811032 | Python | 27,097 | 640 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2016 Johns Hopkins University (Author: Matthew Wiesner)
# Apache 2.0
# ============ Make unicode-based graphemic lexicon =============
#
# This script takes a list of either words or words and corresponding
# morphemes and returns a graphemic lexicon in the ... |
1d073ec511474539191b068f8c14748cf314055a6b58713a541e45831d31944a | Python | 27,146 | 468 | import numpy as np
import itertools
import os
import pandas as pd
from sklearn import preprocessing
import torch
from torch.utils.data import WeightedRandomSampler
import torch.optim as optim
from PrePro import sep_eight_channels, standardize
from DataLoaders import DataLoaderLabels, DataLoaderNoLabels, init_data_loade... |
19c450bcf12cb88c92a913e6e1e6040d875e3e884921205bb2c5f26f794ef56e | Python | 27,156 | 631 | import torch
import torch.distributed as dist
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule, Scale, bias_init_with_prob, normal_init
from mmdet.core import (anchor_inside_flags, bbox2distance, bbox_overlaps,
build_assigner, build_sampler, distance2bbox,
... |
8dd65165a1f3752b45a0c1e2ebbfe2bb32b4f6cb2ff33cd9327c7ec2e89e154d | Python | 27,169 | 666 | import math
import torch
import numpy as np
import torch.nn as nn
from pytorch_lightning.loggers import wandb
from torch import Tensor
from typing import Dict, Tuple
import pytorch_lightning as pl
import torch.nn.functional as F
from constants.constants import *
from utils.nilm_metrics import NILMmetrics
from neural_ne... |
de67190a8b00bd280ee32c810b9cb3f4ac61ce8ea87733c8fcab1363ee0eebca | Python | 27,172 | 693 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# conda version : 4.8.3
# conda-build version : 3.18.12
# python version : 3.7.6.final.0
# brian2 version : 2.3 (py37hc9558a2_0)
from __future__ import annotations
import sys
from typing import Optional, Union
import numpy as np
from brian2.units import Quantity, ms, pA
... |
77b60faace8e3cb39d182d16ce97823cdfdad01c75c0d0f5fe0efc4fb60c6275 | Python | 27,206 | 828 | # %% [markdown]
# ##
import os
import time
import colorcet as cc
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.transforms as transforms
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.linalg import orthogonal_procrustes
from scipy.optimize import linear_sum_assignme... |
5c25a0571a5dc5f34cc9168eb1e4534957eda3db5696900d157d9b12e14478c0 | Python | 27,222 | 905 | #%% Imports and file loading
import json
import os
import pprint
import sys
import time
from collections import defaultdict
from datetime import timedelta
from pathlib import Path
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import navis
import pymaid
from src.pymaid im... |
08fdd03418e03a4fe2d1f7bb2e1497522d6a40dcd2c25bb289d266361fa5d04b | Python | 27,274 | 597 | """HTTP client for the carla-cosmos server.
::
client = CosmosClient("http://node:8000", token="cc_...") # or COSMOS_URL / COSMOS_TOKEN
client.wait_ready()
job = client.submit_clip(Clip.load("clips/abc"), "cosmos3-nano",
prompt="golden hour, wet asphalt",
... |
2bbcda57ea8dcaa5ea472f18473726295ea82dd01b87c03bc874f194be551a03 | Python | 27,292 | 635 | #!/usr/bin/env python3
"""
File: compare_decon_cell_profiles.py
Created: 2021/09/17
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Sof... |
107a686c5262453587d7d9c5ae0d373915cb789735d3213bd702c0d5d057c110 | Python | 27,343 | 584 | #!/usr/bin/env python3
"""
File: visualise_main_eqtl_replication.py
Created: 2021/08/03
Last Changed: 2021/09/02
Author: M.Vochteloo
Copyright (C) 2020 M.Vochteloo
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published ... |
d46b428f6f1c2e9ff0663246ae82991c2fb110d25085c966b5f4479318869e8a | Python | 27,381 | 644 | import colorsys
import os
import sys
import cv2
import copy
import pyqtgraph.functions as fn
import numpy as np
import pyqtgraph as pg
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5.QtCore import *
from pyqtgraph.Qt import QtGui, QtCore
import scipy.ndimage as ndi
from .image_stacks import ImageSt... |
556b8f71f0ef2ef6c432efc844cd5621ee7f38fc20c469665cedb3a3ace7dfa9 | Python | 27,389 | 754 | import logging
from abc import ABC
from collections import defaultdict
from copy import copy
from dataclasses import dataclass, field
from enum import Enum
from typing import Any, Dict, Iterable, Iterator, List, Optional, Tuple, Union
from sssom.constants import RDFS_SUBCLASS_OF, RDFS_SUBPROPERTY_OF
from oaklib.datam... |
594a279a55b17720141cbf9e68a1587c63cdffce92db682627af35de34066d08 | Python | 27,422 | 519 | #%%
import sys
sys.path.append('/Users/mwinding/repos/maggot_models')
from pymaid_creds import url, name, password, token
import pymaid
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pandas as pd
import numpy.random as random
import cmasher as cmr
import connectome_tools.process_mat... |
d3f3eb8ff5d2290cd9b828eea9ea165b94b46d37a1af7200a4d80d8773fb28ea | Python | 27,478 | 538 | import os
import time
import numpy as np
import pandas as pd
import sklearn as sk
from sklearn.preprocessing import label_binarize
from util import util
from util import metrics
from torch.utils.tensorboard import SummaryWriter
class Visualizer:
"""
This class print/save logging information
"""
def _... |
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