sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
8040cbc58f833059b5e20e922edaa492a9899b4512450894c1eb6db1412f4118 | Python | 4,440 | 151 | import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import matplotlib.ticker as ticker
from matplotlib.ticker import MaxNLocator
import matplotlib.transforms as transforms
import numpy as np
from pathlib import Path
from statistics import mean, stdev
from fpdf import FPDF
import math
import sys
sys... |
4384ca4c99297904f5b9fddd7b9ccc2200bba0bf927c7353e0e503463017a94d | Python | 4,446 | 144 | import torch
import torch.nn as nn
from torch.nn import functional as F
class BasicBlock(nn.Module):
expansion = 1
def __init__(self, in_channel, out_channel, stride=1, downsample=None):
super(BasicBlock, self).__init__()
self.conv1 = nn.Conv3d(in_channels=in_channel, out_channels=out_channel... |
df6bc8242f32aca420459273030d036dc6b81f4889a3cfa18836ebfe4494ac56 | Python | 4,446 | 111 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
"""
Convert a SAM file into GFF3 format (https://uswest.ensembl.org/info/website/upload/gff3.html)
that also includes additional information that GMAP GFF3 for the 'mRNA' type:
--- coverage
--- identity
--- matches
--- mismatches
--- indels
ex: fro... |
574cb02b9406aa4a3e0e7411fbc8561114fe9d0adcc5e7bf4ae5274bd1ce9d94 | Python | 4,447 | 133 | import argparse
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import tensorflow as tf
import seaborn as sns
from tensorflow import keras
import os
#os.environ["CUDA_VISIBLE_DEVICES"] = "-1" # disables GPU
#from tqdm import tqdm
from ast import literal_eval
from tensorflow.keras import layers
i... |
59a48e780355ff97753f67a05165e982b7a2651d5df6f0655763bb9dad249546 | Python | 4,449 | 141 | """ Statistics calculation utility """
import time
import math
import sys
from onmt.utils.logging import logger
class Statistics(object):
"""
Accumulator for loss statistics.
Currently calculates:
* accuracy
* perplexity
* elapsed time
"""
def __init__(self, loss=0, n_words=0, n_cor... |
3bc84126699dfc90a1bac2925503419f54995c5aada600c5ab80c30ca5fce927 | Python | 4,450 | 131 |
from xml.etree import ElementTree
import glob
from tensorflow import keras
import tensorflow as tf
import sklearn
from skimage import draw
from skimage.io import imshow, imread
from skimage import morphology
from skimage import transform
from skimage import util
import numpy as np
from matplotlib import pyplot
# from ... |
8aa3a520319cf6bb20d19787153045d6e79cf0f1fc50a15a0c006e77adca3f25 | Python | 4,451 | 127 |
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib import gridspec
from kcsd import csd_profile as CSD
from kcsd import ValidateKCSD2D
from figure_properties import *
from kCSD_with_reliability_map_2D import make_reconstruction, matrix_symmetrization
def set_axis(ax, letter... |
3d7f11f1716e76f3c2b29392cc801ae917674aa869f9b526fd72c2164c54c34b | Python | 4,452 | 138 | import tensorflow as tf
from const import *
def decode(serialized_example):
features = tf.parse_single_example(serialized_example,
features={
'dims': tf.FixedLenFeature([3], tf.int64),
'img'... |
9b10259c9b31ea6112e3b7b01e153126f988e8cbd840f3ce913f42486020e461 | Python | 4,455 | 127 | from PointSets import pointSets
from Common import pointEvolution
from Surfaces.surfaces import *
from Common.kernelFunctions import *
from Surfaces.secondOrderFiberMatching import *
def compute(createsurfaces=True):
if createsurfaces:
[x,y,z] = np.mgrid[0:200, 0:200, 0:200]/100.
ay = np.fabs(y-1)... |
198615a0cfd367323c0e7541a48d2ebbb3268a1b260123496d03a560bac0531e | Python | 4,456 | 128 | # Time-stamp: <2024-10-11 11:11:00 Tao Liu>
"""Description: refine peak summits
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
# python modules
# ----------------... |
93fc23923600f491def406b9aa0fb050153245185994dfe74e927a0e26564706 | Python | 4,456 | 107 | #!/usr/bin/env python
import os
import sys
import click
import pandas as pd
from DXGB.convert_file import RF20_main as RF20_main
from DXGB.run_features import run_features as run_features
from DXGB.run_models import *
@click.command()
@click.option("--model", default="DXGB", show_default=True, help="model name")
@clic... |
d108830472ef3d9f6139c408553b3f6499084f7d930d7cf1362a1287201c3724 | Python | 4,457 | 109 | # https://github.com/ildoonet/pytorch-gradual-warmup-lr/blob/master/warmup_scheduler/scheduler.py
# Modifications:
# - Update self.last_epoch when self.finished
__all__ = ["GradualWarmupScheduler"]
from typing import Optional, Union
from torch.optim import Optimizer
from torch.optim.lr_scheduler import ReduceLROnPla... |
1f65a9961b64a0727ea405108f9197946953c6565f262fb44af3d58f88c36048 | Python | 4,458 | 123 | """
Utility functions and classes (including default parameters).
Author: Sara Mathieson, Rebecca Riley
Date: 9/27/22
"""
# python imports
import numpy as np
from scipy.stats import norm
class Parameter:
"""
Holds information about evolutionary parameters to infer.
Note: the value arg is NOT the starting ... |
7117aa9b82a76873533b2296943871abf33e3ed282e82db959105b8d4df7a288 | Python | 4,459 | 119 | import numpy as np, matplotlib.pyplot as plt, sys
import pumpprobe as pp
plt.rc("xtick",labelsize=18)
plt.rc("ytick",labelsize=18)
plt.rc("axes",labelsize=18)
shuffle_connectome = False
shuffle_connectome_n = 1
for s in sys.argv:
sa = s.split(":")
if sa[0] == "--shuffle-connectome":
shuffle_connectom... |
cc6f499f266f8a2c31726418a099bf673ad78932a40052caf68daf285902649c | Python | 4,460 | 158 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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... |
70a9d7feee8e02989b3943ce84ff6e2b7e0dce1c9708ff412b474072ff7d2074 | Python | 4,463 | 122 | # Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
aa8aa42073a67a2beb35056c6407d1fa9cd929372fa2e32fc2a25559259ba882 | Python | 4,464 | 125 | import inspect
import dask.dataframe as dd
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
from matplotlib.axes import Axes
from ..utils import skit
from functools import wraps
##
# todo: this is overcomplicated and should be removed
#
##
class ForceReturnException(Exception... |
cc1fb9b64f1e2a5e6e8bfa8f77fc06d6e725abb0b6846808694b12e1e26d4574 | Python | 4,466 | 121 | from rdkit.Chem import Draw
import numpy as np
import io
from PIL import Image
def show_png(data):
bio = io.BytesIO(data)
img = Image.open(bio)
return img
def draw_mol_with_highlight_varying_colour(mol,attribution_dict,absolute_scale=True,absolute_limit=1,label_values=False):
"""
funct... |
53ef18fcf3ffe080ca2bb9cf1fec8484779345cc2570c234d7f261be1a314e3f | Python | 4,467 | 126 | import torch
import numpy
import matplotlib.pyplot as plt
import bionetwork
import pandas
import seaborn as sns
import copy
#Load network
networkList, nodeNames, modeOfAction = bionetwork.loadNetwork('data/macrophage-Model.tsv')
annotation = pandas.read_csv('data/macrophage-Annotation.tsv', sep='\t')
uniprot2gene = di... |
fd88f846044696935876ad50e7c0eb647e0f260abc721bc1089977b184ca5796 | Python | 4,469 | 149 | #!/usr/bin/env python3
from . import conf
from .utils import PheWebError
import sys, json
import os
import importlib
import functools
import math
from typing import List,Dict,Callable
if sys.platform.startswith('win'):
raise Exception("PheWeb doesn't support Windows, because pysam doesn't support windows.")
if ... |
7f1c7f65fed5911d1e3dd993ca0d9cc093a534fa73c5a3483c02105d3e30d660 | Python | 4,470 | 121 | from __future__ import absolute_import
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
import torch
import torch.nn as nn
from torch.autograd import Variable
import math
from layers import ShuffleLayer, Conv, CondenseConv, CondenseLinear
__all__ = ['Conden... |
85969bc3edb72b86013dd703a5f981bb7e6785e97fd2df6f3b116223a8c7126f | Python | 4,470 | 161 | import pandas as pd
fd2label = {0.5: "scrubbing.5", 0.2: "scrubbing.2"}
group_name_rename = {
"CONTROL": "control",
"BIPOLAR": "bipolar",
"SCHZ": "schizophrenia",
}
group_order = {
"ds000228": ["adult", "child"],
"ds000030": ["control", "ADHD", "bipolar", "schizophrenia"],
}
def lazy_demographic... |
b35225d0a904cd7c8cfaa0cec0ee4067da5b89b5d8a7c11c4569701633449fb5 | Python | 4,470 | 121 | import os
import numpy as np
from fastmri_prostate.data.mri_data import zero_pad_kspace_hdr
from fastmri_prostate.reconstruction.utils import center_crop_im, ifftnd
from fastmri_prostate.reconstruction.grappa import Grappa
def t2_reconstruction(kspace_data: np.ndarray, calib_data: np.ndarray, hdr: str) -> np.ndarray... |
0dc7a86a723990e1a42ca2dc75df1f362055c3eb4a6a30a228f39241477097c5 | Python | 4,471 | 106 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
79c8fed3df967d0d92ce1bb0bcd90c7d21dd7bc3f45ad59ae1b3646c3b0aa182 | Python | 4,471 | 112 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue May 9 2023
Script to test nonlinear registration of OpenPain after updating the DB
and uploading the images to COS.
@author: Eduardo Castro
"""
import ibm_boto3
from botocore.client import Config
from os.path import join as opj
import sqlalchemy as db... |
a547d2fbeb57bdc88df73de6ca7071acb33914538ebe93555177b8fdd5337311 | Python | 4,471 | 113 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
ed12a6c35e63786988a1b21a05204f362b4073e85fe6d61c47d135a906ba0ee2 | Python | 4,471 | 118 | # Copyright 2018-2020 Xanadu Quantum Technologies Inc.
# 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... |
cd9bb4e08f19e1f6ffc5d698a09542285330f21f5e9c6a361c04f649ae4c2ff2 | Python | 4,473 | 106 | # Filename: process_plate_image.py
# Author: Alessandro Gerada
# Date: 2023-01-27
# Copyright: Alessandro Gerada 2023
# Email: alessandro.gerada@liverpool.ac.uk
"""Pre-processing of agar plate images to extract individual colonies"""
import cv2 # pylint: disable=import-error
from imutils import contours
from ty... |
257901c8e647877e3263d8f7a4fd77cc8b2ca847d2dd4e792a27662994c1094e | Python | 4,475 | 121 | #!/usr/bin/env python
import argparse
import csv
import os
import pandas as pd
from common import *
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import seaborn as sb
import numpy as np
sb.set(style="whitegrid")
def main():
parser = argparse.ArgumentParser()
parser.add_argume... |
263a889f092f4b6ff3fc808ebdd21495512715673eb6534ce455e771101c19c5 | Python | 4,475 | 165 | """Pytest fixtures for samalg tests."""
from __future__ import annotations
import numpy as np
import pytest
import scipy.sparse as sp
from anndata import AnnData
@pytest.fixture
def random_seed() -> int:
"""Provide a consistent random seed for reproducibility."""
return 42
@pytest.fixture
def small_expres... |
4d18bb273a68952d2ffdd3a0b1094b049a5f253805ddba82db61fd12a3aa92eb | Python | 4,478 | 126 | '''
Created on Apr 21, 2012
@author: robert
'''
import neuron
from . import reader
from . import cell_parser
from . import synapse_mapper as smap
from . import sim_control
import numpy as np
'''anatomical parameters'''
# ? look @ vpm -> L5tt mapping results
# vpm -> L4 about 0.4; therefore 0.2 good guess
convergence... |
55ad2a56cc696a97af9680ce201240d56217dfbdcd0860a0fa2bb0a74af15d03 | Python | 4,478 | 111 | import csv
import argparse
from Common import loggingUtils
from Surfaces.surfaces import *
from Common.kernelFunctions import *
from Surfaces import surfaceMatching, surfaces, surfaceTimeSeries as match
import threading
import Queue
def threadfun(q):
while True:
print str(q.qsize())+' jobs left'
os... |
d1ed272f7562642acc0ed8563f81c9778bae2ef1acf89312b656dc29555d3a87 | Python | 4,480 | 142 | # cython: language_level=3
# Time-stamp: <2025-02-05 12:38:24 Tao Liu>
"""Utilities for reading and writing MACS3 bedGraph files.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ----------------------... |
35fc2cf15f9f8b83f6a8591201e5a906717f91497cb5ce11429cb8cb945e5d31 | Python | 4,483 | 153 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
ClassVar,
Self,
)
from uuid import (
UUID,
uuid4,
)
import numpy as np
import pytest
from pandas.core.dtypes.common import is_list_like
from pandas.core.dtypes.dtypes import (
ExtensionDtype,
register_extension_dtype,
... |
c06704e878dc19aecdac756efce4749a3f970e66b39cff92f46cdf07ca0b6b1e | Python | 4,486 | 125 | from __future__ import absolute_import
#__version__ = '0.0.0'
#import from data_utils
from data_utils import load_csv_data
from data_utils import load_Xy_one_hot_data2
from data_utils import load_Xy_data_noheader
from data_utils import drop_impute_and_scale_dataframe
from data_utils import discretize_dataframe
from d... |
443984a87bf255d6062b39bc4217076b0616e9eb857612920d9d6c5122fe47a5 | Python | 4,489 | 91 | import sys
import os
import argparse
from cdr.config import Config
base = """#!/bin/bash
#
#SBATCH --job-name=%s
#SBATCH --output="%s-%%N-%%j.out"
#SBATCH --time=%d:00:00
#SBATCH --mem=%dgb
#SBATCH --ntasks=%d
"""
if __name__ == '__main__':
argparser = argparse.ArgumentParser('''
Generate SLURM batch jobs t... |
8ffb2ec74175cc608589a7cb28d54fc330148fd11843876b45c59ed9fb7a4eb1 | Python | 4,490 | 130 | """Scatter view."""
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
import inspect
import logging
import numpy as np
from phy.plot.visuals import ScatterVisual
from phy.utils.color import selec... |
2451980f34b5e50738fe5534f2758146ec015fa31b4ecc8de82c000293dd16c8 | Python | 4,491 | 113 | # Copyright 2022 Xanadu Quantum Technologies Inc.
# 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... |
30eb87359a96a356ca94273a308af3fc3f44f013aabcab848e7e49d5ac57f54a | Python | 4,491 | 104 | import torch
from tnn.layers import View, LinearLayer
from tnn.networks import FullyConnected, HamiltonianResNet
from tnn.regularization import SmoothTimeRegularization, TikhonovRegularization, BlockRegularization
from tnn.training.batch_train import train
from tnn.utils import seed_everything, number_network_weights, ... |
4d16880849d2c4edb989ab4a1ab98f1043013be742aa2ac970b2a7cdcb42661e | Python | 4,492 | 152 | #%%
#Imports
import numpy as np
import os
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.gridspec import GridSpec
import matplotlib.backends.backend_pdf
plt.style.use('seaborn-talk')
import pandas as pd
from sklearn.preprocessing import StandardScaler
from sklearn.decompositio... |
5255621f3f95fcceb1d309cb53550082c1e52e096f99f5381be14f3d0a46d6cf | Python | 4,494 | 157 | import os
import numpy as np
import torch
from sklearn.metrics import accuracy_score, roc_auc_score
from sklearn.model_selection import train_test_split as split
from roost.roost.data import CompositionData, collate_batch
from roost.roost.model import Roost
from roost.utils import results_multitask, train_ensemble
t... |
5b22008013138f8acb3a1239ddaf173fa251fa7f2f655152c2372aef644e7f9a | Python | 4,494 | 114 | import argparse
import json
import time
import os
import socket
from pathlib import Path
from uuid import uuid4
import numpy as np
from distributed_computing.api import start_head_node, start_node
from distributed_computing.api import Pool as WorkersPool
from evolutionary_experiment.config import config
from evolutio... |
db12d9253ebabf612a30ba366a256d94c62fadbea18592265a65b6baf6713baa | Python | 4,494 | 114 | import numpy as np
import pandas as pd
import pickle
from sklearn.model_selection import KFold
import torch.utils.data as tdata
import cvxpy as cp
from raman_dataset import RamanSpectraSeqDataset, NMFRamanSpectraSeqDataset
from imblearn.over_sampling import SMOTE
from imblearn.under_sampling import RandomUnderSampler
... |
c56559d7716e96e0a8ee932903bcaa4732ad00259d9206131b3406937a891510 | Python | 4,495 | 107 | # download from https://github.com/benfulcher/AllenSDK/blob/master/MakeCCFMasks.py
# modified by JKB on 2/6/23
import numpy as np
import csv
import os
import nrrd
import scipy.io as sio
import pandas as pd
import sys
# import matplotlib.pyplot as plt
# %matplotlib inline
#---------------------------------------------... |
3dc2033933e2f0aeee35468a5dc91fdfe611f6afd984bfab53cd3fa253d7249b | Python | 4,497 | 144 | import os
import torch
import torch.nn as nn
import numpy as np
import torch.nn.functional as F
import matplotlib.pyplot as plt
import matplotlib as mpl
plt.style.use('ggplot')
from src.models import NeuralKalmanFilter, KalmanFilter
from src.utils import *
device = "cuda" if torch.cuda.is_available() else "cpu"
print(... |
94e18aacf71dea402acff1aa5f7120acfd36e865e5a84effa70b367ec20e5852 | Python | 4,497 | 121 | """Base classes for the decode module."""
import logging
from abc import abstractmethod
from nimare.base import NiMAREBase
LGR = logging.getLogger(__name__)
class Decoder(NiMAREBase):
"""Base class for decoders in :mod:`~nimare.decode`.
.. versionchanged:: 0.0.12
Moved from ``nimare.base`` to ``ni... |
d5e599752587e9ffa11f044ae1c1f8ade94858356d2bee22b47d197b11ab175d | Python | 4,498 | 126 | """Code for making expt_config files to describe experimental info."""
import pathlib
from pathlib import Path
from typing import Any
import yaml
from ruamel.yaml.main import round_trip_dump as yaml_dump
from ruamel.yaml.main import round_trip_load as yaml_load
def create_expt_config(
expt_name: str | None = No... |
aec81abb92fc55e7efd8d6a32df07383eea274e42d0ffad1d638d1a86abeca84 | Python | 4,499 | 105 | import torch
from torch import nn
from torch_geometric.utils import scatter
from e3nn import o3
from e3nn.nn import FullyConnectedNet
# Typing
from torch import Tensor
from typing import List, Optional, Tuple
class Interaction(nn.Module):
"""NequIP equivariant interaction/convolution layer.
Refe... |
027bf134091597de257cfcae73f048edc603fec878bfc9ae627da8b40d47c30f | Python | 4,500 | 157 | """
.. _metas_ibma:
====================================
Image-based meta-analysis algorithms
====================================
A tour of IBMA algorithms in NiMARE.
This tutorial is intended to provide a brief description and example of each of
the IBMA algorithms implemented in NiMARE.
For a more detailed intro... |
f22e27e018df5781e8e2aff959d88bc44a51c8af11dfbe7e4617dde2bee11169 | Python | 4,502 | 114 | import sys
import pandas as pd
from .util import stderr
def read_tabular_data(X_paths, Y_paths, series_ids, categorical_columns=None, sep=' ', verbose=True):
"""
Read impulse and response data into pandas dataframes and perform basic pre-processing.
:param X_paths: ``str`` or ``list`` of ``str``; path(s)... |
3eb0900d3b0f4cace3f931b683b034e4cb7a8bdcd9d571f543048f6c2e2790d8 | Python | 4,503 | 138 | import numpy as np
import pandas as pd
import time
import datetime
from .esw_star import esw_star
from ..utils.compute_pvalues import compute_pvalues
from ..summarydata import SummaryData
def _det(mean: pd.DataFrame, var: pd.DataFrame, n_cells: pd.DataFrame, verbose: bool=False):
"""Computes Differential Expressio... |
7d9499a6e88aac0e40b58ee71f350c94bf6437372048daae98da291dcf024d6b | Python | 4,504 | 126 | # Copyright 2025 Xanadu Quantum Technologies Inc.
# 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... |
2a356a81a444ef38ade4637a6e0284c9aa1f51af0d6778d62843b9008db0acb3 | Python | 4,505 | 116 | import argparse
import logging
def get_args():
"""
Get arguments from command line with argparse.
"""
parser = argparse.ArgumentParser(
prog='sam-merger.py',
description="""Merge a series of SAM format files from a chunked alignment pipeline.""")
parser.add_argument("-i", "--infile... |
b5b61b168b807b0e0c5996abd05d9d3f0ff99a22d64e061e1590f75d14a6abc1 | Python | 4,506 | 131 | import unittest
from unittest import TestCase
from evcouplings.utils import *
class TestUtilsApp(TestCase):
def setUp(self):
self.config_file = ""
def test_run_ExternalToolError(self):
"""
tests whether the ExternalToolError is properly raised
assuming we are running on a un... |
f77c342005ee5055b24d2f19c15f2c9c8c89bda4c82f029e2030fd7f68c06587 | Python | 4,506 | 124 | """
.. _annotations_gclda:
====================
GCLDA topic modeling
====================
Train a generalized correspondence latent Dirichlet allocation model using abstracts.
.. warning::
The model in this example is trained using (1) a very small,
nonrepresentative dataset and (2) very few iterations. As ... |
0943416ba70fa31804b60f116ab038a1105f020b9d7ea96c6addfe4d7a4402b0 | Python | 4,508 | 143 | import argparse
import hashlib
import os
from pathlib import Path
from global_config import config
# SeRANN are generated using multiple process, so the GPU cannot be used.
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = ""
from tensorflow import keras
import numpy as np
import pa... |
f317604f33a5f8a2da2c93bc4cd91963654e272fd2f447cb786627beabbd5ba4 | Python | 4,508 | 115 | import scipy.io as scio
import numpy as np
from scipy import sparse
# 需要补充生成元图的函数
def get_Matrix(dataFileb, resMatrix):
# d = sparse.load_npz(dataFileb)['permission']
d = sparse.load_npz(dataFileb)
res=np.dot(d,d.T)
print(res) # 依旧是稀疏矩阵
#res_new =res.todense()
#scio.savemat(resMatrix, ... |
aa0e669936306e7c55eed1d5e11d722af91173c7aa81931f38dbaee89816383c | Python | 4,514 | 140 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def test_compare_axis(axis):
# GH#30429
s1 = pd.Series(["a", "b", "c"])
s2 = pd.Series(["x", "b", "z"])
result = s1.compare(s2, align_axis=axis)
if axis in (1, "columns"):
indices = pd.Index([0, 2])
... |
fc6dcca2fabf304c2d022e75272cebc3cbcdc41cb1c0018f91a26765cbd7b89b | Python | 4,516 | 159 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch.nn as nn
from torch import Tensor
from typing import Callable, Union, Optional,Tuple
import torch
import torch.nn.fu... |
06d1a878469dbfa632878ffb8f4e62ceeb6cf6ce20cce303720dace7b17b9651 | Python | 4,518 | 135 | """Soft-dependency introspection helpers.
Originally adapted from sktime; rewritten for PyCaret 4.0 to drop:
- `distutils.version.LooseVersion` (removed in Python 3.12)
- the `importlib_metadata` backport (stdlib `importlib.metadata` is enough on >=3.11)
Versions are now returned as `packaging.version.Version` object... |
5788ccb6107d298c0f6b80fca537dbf31559223c82a30014c4234c15eabccc1f | Python | 4,518 | 116 | """Deterministic synthetic NIfTI + manifest generator.
Produces a small, fake-but-structurally-realistic dataset (NIfTI volumes
with a synthetic "brain" blob, plus a matching manifest CSV) so the full
data path (`oasis`/`manifest` -> `labeling` -> `volumes` -> `augmentation`
-> `splits`) is exercisable end to end with... |
9f320f567ef62d70cd99baaf88b4848219d7d6d993f4da04680ab1e1ef31e10b | Python | 4,519 | 170 | import itertools
import logging
import math
from contextlib import contextmanager
from typing import Callable, Optional, TypedDict, Union
import torch
import torch.nn as nn
class _Stats(TypedDict):
variance_in: float
variance_out: float
n_samples: int
IndexFn = Callable[[], None]
def _check_consisten... |
3dcc041bee98778e4e2f8580ae67ddb2981e802ea0f19cfa4535258e41c0ceb3 | Python | 4,520 | 111 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
ac7d48aaa964e022cfebd2c510d8286cc196c7ff72ca9f25d718b98d51a1d8be | Python | 4,522 | 143 | import numpy as np
import tensorflow as tf
import wandb
from rl_toolkit.networks.models import DuelingDQN
from ...core.process import Process
class Tester(Process):
"""
Tester
=================
Attributes:
env_name (str): the name of environment
render (bool): enable the rendering
... |
21a3ec2972b572e3fc3b0e9341e2f8ee39dc7f8610071372e7f59b7ef061f74f | Python | 4,523 | 136 | import numpy as np
# from scipy.io import loadmat
# from scipy.io import savemat
from hdf5storage import loadmat
from hdf5storage import savemat
import pandas as pd
from sklearn.preprocessing import StandardScaler
import os
import pickle
def process(domain, save=False, dat_perm_seeds=1234):
data = {}
... |
4e28506755f9e224d45d35b672b0bdfdba0974d4c6a1949cef7be73471d782c9 | Python | 4,525 | 151 | import argparse
import os
import time
from os.path import join
from string import Template
from subprocess import PIPE, Popen
SBATCH_TEMPLATE_DEFAULT = (
"#!/bin/bash\n"
"conda activate conda_env_name\n"
"cd ~/project\n"
)
def str2bool(v):
if isinstance(v, bool):
return v
if isinstance(v... |
00bd671bc753f61c6e7beeb1959247abb4f53d01e06cc1de20c86d78e9289b50 | Python | 4,526 | 136 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2026 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use... |
81d793d512ad0c941dba5c4aba99e87d64992bc1b4d089051a931d34bbd6d133 | Python | 4,526 | 104 | import torch
from tnn.layers import View, LinearLayer
from tnn.networks import FullyConnected, HamiltonianResNet
from tnn.regularization import SmoothTimeRegularization, TikhonovRegularization, BlockRegularization
from tnn.training.batch_train import train
from tnn.utils import seed_everything, number_network_weights, ... |
fd368557a0561d4fdb7a6aab006fcbf5adc7cc57b1060cc0fe87c3d540ce3e69 | Python | 4,526 | 103 | import numpy as np
import pandas as pd
from copy import copy
from msmfcode.core.logging import log
from msmfcode.core.config import *
from msmfcode.models.cann import Grid, FMSMF, DMSMF, DiffSolverError, EmptyFields
from msmfcode.execution.parallel import ParallelExecutor
from msmfcode.evaluation.data import load_expe... |
54656c03925dde40a49ef6c3a4bdcd017ea51fa5e552d6ed52ee0092414ab6c7 | Python | 4,527 | 116 | # License: see [LICENSE, LICENSES/legged_gym/LICENSE]
import sys
from isaacgym import gymapi
from isaacgym import gymutil
import numpy as np
import torch
# Base class for RL tasks
class BaseTask():
def __init__(self, cfg, sim_params, physics_engine, sim_device, headless):
self.gym = gymapi.acquire_gym()
... |
3d0f1fb955f504c336e3d131dce3dbbe2cc174706287fa243fa5b3d509b78d14 | Python | 4,528 | 136 | """Generate fixtures for tests."""
import os
from shutil import copyfile
import nibabel as nib
import numpy as np
import pytest
from nilearn.image import resample_img
import nimare
from nimare.tests.utils import get_test_data_path
from ..utils import get_resource_path
# Only enable the following once in a while for... |
94b69152814fb6ea80af9e74b2aff8bd54bbb86c3aabffcea06437b76073c399 | Python | 4,532 | 135 | """Generate fixtures for tests."""
import os
from shutil import copyfile
import nibabel as nib
import numpy as np
import pytest
from nilearn.image import resample_img
import nimare
from nimare.tests.utils import get_test_data_path
from nimare.utils import get_resource_path
# Only enable the following once in a while... |
ae5b039a86b589a6f97d69773e0a5ae424174ee3989412d030ec3c4ec433d436 | Python | 4,532 | 119 | from datetime import datetime
import pytest
from pandas._libs import tslib
import pandas as pd
@pytest.mark.parametrize(
"date_str, exp",
[
("2011-01-02", datetime(2011, 1, 2)),
("2011-1-2", datetime(2011, 1, 2)),
("2011-01", datetime(2011, 1, 1)),
("2011-1", datetime(2011, ... |
fb2273ebd04db573f12c79d941fec9ee2d297303b01fc4138df4b09b0562347f | Python | 4,532 | 104 | from typing import List, Literal, Union
import pandas as pd
from med_associates_utils.session import FieldList, SessionCollection
def calculate_cumulative_events(
df: pd.DataFrame, event: Union[str, list[str]], groupby: Union[str, list[str]], time_key: str = "time"
) -> pd.DataFrame:
df = df.copy() # make a... |
194a09f17a575c421803b271d6a56ed090fcb4b70f9093b28d2245b36eec485b | Python | 4,533 | 135 | import random
from typing import Union
import numpy as np
import pytorch_lightning as pl
import torch
from scipy.ndimage import gaussian_filter
from .datasets import SyntheticDataset
class TAVRDataModule(pl.LightningDataModule):
def __init__(self,
dataset_name: str,
dataset_kw... |
262c3547b35212f23427c1f4edbd5ba61b8a0ca27d68c0222bc096a4aa7c9174 | Python | 4,534 | 137 | """Workspace CRUD.
For v1, workspace visibility is determined by membership — users only see
workspaces where they have a ``WorkspaceMember`` row. Admins (superuser) see
all workspaces.
"""
from __future__ import annotations
from typing import Annotated
from fastapi import APIRouter, Depends, HTTPException, status
... |
01164e88a5b21c5fa957d412622af86b68684dde6a381f23953c61215fdb5adf | Python | 4,535 | 115 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
2b1898e68cbd03a5b2151ec397198f1290b32e1b9cf1109d3a0ab242b9f343bd | Python | 4,537 | 149 | import ctypes
import zoneinfo
import pytest
import pandas as pd
import pandas._testing as tm
pa = pytest.importorskip("pyarrow", minversion="16.0")
def test_series_arrow_interface():
s = pd.Series([1, 4, 2])
capsule = s.__arrow_c_stream__()
assert (
ctypes.pythonapi.PyCapsule_IsValid(
... |
d252f9dda91d8f23fe7003304d4c56405041f365355130b4b035c120bb833e76 | Python | 4,537 | 141 | from viewContainer import viewContainer
from StimulationSystem.StimulationProcess.StimulateProcess import StimulateProcess
from StimulationSystem.StimulationProcess.FinishProcess import FinishProcess
from StimulationSystem.StimulationProcess.IdleProcess import IdleProcess
from psychopy import visual
import copy
i... |
f9a76ad19a14b1f2ee0ba99bfb7a332a40a63e94291828c236dc4305ef9f1723 | Python | 4,539 | 100 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# 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... |
b732a5d561065acff4c8705f81c25b4499268f46857dec913791db9852768c4b | Python | 4,540 | 114 | """WASABI signal model for mapping of B0 and B1."""
from collections.abc import Sequence
import torch
from torch import nn
from mrpro.operators.SignalModel import SignalModel
from mrpro.utils.reshape import unsqueeze_right
from mrpro.utils.unit_conversion import GYROMAGNETIC_RATIO_PROTON
class WASABI(SignalModel[t... |
90ce7d686f2c58635f007774343df5e4ebf9f565c2196053d1e8ccda3fcb0ecd | Python | 4,545 | 131 | # Time-stamp: <2024-10-02 16:55:48 Tao Liu>
"""Description: Random sample certain number/percentage of tags.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
# ------------------------------------
# pyth... |
e578647fe0dc6faf2dc56fdf2b0adc91f9a791e849053ef2cfd7ba7c64306568 | Python | 4,545 | 115 | import torch
from torch import nn
from torch_geometric.nn import MessagePassing
from torch_geometric.utils import scatter
# Typing
from torch import Tensor
from typing import List, Optional, Tuple
class GatedGCN(MessagePassing):
"""Gated GCN, also known as edge-gated convolution.
Reference: https://arxi... |
e8d60d67b1a1c4cd2341028c0449ea5ea7c7307349e6d8c9b94c9707b5f8c689 | Python | 4,545 | 141 | # Copyright 2024 Xanadu Quantum Technologies Inc.
# 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... |
7a7041bde5ec84fee78c8b77a68903dc3d36c5964201e785178c9ff141f5afa3 | Python | 4,553 | 143 | """Convenience methods to retrieve meta data from .rtdc files"""
import functools
import pathlib
import dclab
import numpy as np
class dataset_monitoring_lru_cache:
"""Decorator for caching RT-DC data extracted from DCOR or files
This is a modification of dclab.util.file_monitoring_lru_cache
with an ex... |
4a775876a4f014d34815daf7cee6c340689865eb099861c6c9641d00df2a96b4 | Python | 4,554 | 164 | import contextlib
import importlib.machinery
import importlib.util
import os
import pathlib
import sys
import tempfile
from unittest import mock
import matplotlib
import numpy as np
from pandas import (
DataFrame,
DatetimeIndex,
Series,
date_range,
)
try:
from pandas.plotting import andrews_curve... |
71462c99b014845123b5063ee9420ddefb5f069187bed2512085b856dd8894dd | Python | 4,554 | 85 | # Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
59da528aa90f77d1bfda671f27c74944be190b5ba0f5ffdc873cc82f1e18146b | Python | 4,555 | 140 | import numpy as np
import pandas as pd
import time
import datetime
from .esw_star import esw_star
from ..utils.compute_pvalues import compute_pvalues
from ..summarydata import SummaryData
def _ges(data: pd.DataFrame, mean: pd.DataFrame, nnz: pd.DataFrame, n_cells_per_anno: pd.DataFrame, verbose: bool=False) -> pd.Data... |
3fc32652be134c1985be206667fd3102dcb2b81db6c7dc9abefc03977a4f72a8 | Python | 4,557 | 128 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# 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... |
d2251e433088d075fa59ddfdbd8e3133474db85c0e5d9eabf3d4edee31b895c4 | Python | 4,557 | 113 | import typer
import torch
import pkg_resources
from dotenv import load_dotenv, find_dotenv
load_dotenv(find_dotenv())
import pandas as pd
from typing import List, Tuple
from rxn_yields.core import SmilesClassificationModel
import sklearn
try:
import wandb
wandb_available = True
except ImportError:
wandb_a... |
110352a48ccbc78b1ae3344c0ca452511c3ac08e127adf98fa87e86df6dc0ceb | Python | 4,559 | 114 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
import os, sys
from bx.intervals import IntervalTree, Interval
from Bio import SeqIO
from csv import DictWriter
try:
import BED
except ImportError:
print("Cannot find BED.py! Please make sure you have cDNA_Cupcake/sequence in $PYTHONPATH.", file=sys.stderr)... |
abbd61c943f808cb81313fbe432b77826208f34da9d1c97c16a62362a9ba5cfd | Python | 4,560 | 122 | from sys import path as sys_path
sys_path.append('..')
sys_path.append('../base')
from base.surfaceExamples import Sphere, Heart
import os
from base.surfaces import Surface
from base.surfaceSection import Hyperplane, SurfaceSection
from base.surfaceMatching import SurfaceMatchingParam
from base.surfaceToSectionsMatchin... |
d4f9435b71a2e30cb865b88d066c2263022aae187f2c0552735a671cda6df52b | Python | 4,561 | 127 | # -*- coding: utf-8 -*-
# @File name: plot_utils.py
# @Author: Alicia Garrido-Peña
# @Date: 2023-08-18 14:09:53
# @Contact: alicia.garrido@uam.es
# "Copyright (c) 2023 Alicia Garrido-Peña. All Rights Reserved."
# Use of this source code is govern by GPL-3.0 license that
# can be found in the LICENSE file
# Code us... |
6b46dcb876cb24f87231f11bc3bf2836db4085af00629f1332f5990697130fde | Python | 4,562 | 132 | """Test the main CLI entry point."""
import logging
import sys
from importlib.metadata import version
from pathlib import Path
import pytest
from lightning_pose.cli.commands import COMMANDS
from lightning_pose.cli.main import _build_parser, _setup_logging, main
_CLI_REFERENCE_DIR = (
Path(__file__).resolve().pa... |
4092cd9c9449e67b91cd7e2f374841d04924f2941f7c4236228faf590e9742fa | Python | 4,563 | 95 | import numpy as np, matplotlib.pyplot as plt, sys
import pumpprobe as pp
plt.rc("xtick",labelsize=18)
plt.rc("ytick",labelsize=18)
plt.rc("axes",labelsize=18)
ds_list = "/projects/LEIFER/francesco/funatlas_list.txt"
matchless_nan_th = None
matchless_nan_th_from_file = "--matchless-nan-th-from-file" in sys.argv
match... |
37e8af25733334d9505ba620dd2538c5aaf4ea9cac7dac8a733f086f74012f47 | Python | 4,564 | 124 | """Benchmark: Triton GAE vs PyTorch GAE.
Compares the custom Triton kernel against the original Python loop
implementation from a2c_common.py for correctness and performance.
"""
import torch
import time
import argparse
def pytorch_gae(mb_rewards, mb_values, mb_dones, last_values, last_dones, gamma, tau):
"""Or... |
f6c58fc1d392eb38ada949d875d4064b6b7aacc765db0206496eb9986a37eba5 | Python | 4,565 | 133 | # Copyright 2026 Xanadu Quantum Technologies Inc.
# 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... |
5710f790e7b302e73aac7d4a0509cb9f41a24ca2a2b976f8d735bbcbfae007c2 | Python | 4,567 | 105 |
import numpy as np
import dgl
from dgl import DGLGraph
import torch
from rdkit import Chem
def one_hot_encoding(x, allowable_set, encode_unknown=False):
if encode_unknown and (allowable_set[-1] is not None):
allowable_set.append(None)
if encode_unknown and (x not in allowable_set):
x = None
... |
d42e277d44739daa4f34315dd59a3346d7ba72c9e8edf957fb85e57f89c7d546 | Python | 4,567 | 99 | # ----------------------------------------------------------------------------
# Copyright (c) 2016-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
20ce888f3e8ee7905a0469894fb62f7db5b4a2b81e3f9667892cf8818cf2a2cc | Python | 4,570 | 125 | """Tests for Einsum Operator."""
from collections.abc import Sequence
import pytest
import torch
from mrpro.operators.EinsumOp import EinsumOp
from mrpro.utils import RandomGenerator
from tests import (
dotproduct_adjointness_test,
forward_mode_autodiff_of_linear_operator_test,
gradient_of_linear_operato... |
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