sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5fc26c080738c383006b643c998cb9684ce0a5e3b03d399683ddfecab964e58e | Python | 7,400 | 132 | """Equivalent volume processing, minimal DTI output and selective resumption."""
import argparse
from pathlib import Path
import sys
import tempfile
from threading import Lock
import time
import unittest
from unittest.mock import patch
import nibabel as nib
import numpy as np
import SimpleITK as sitk
from preprocessi... |
b56486765451768bd8d50ea45c0e37e528335a70147229769c8432606b71cda8 | Python | 7,401 | 206 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import time
import torch.optim as optim
from torch.autograd import Variable
import re
import os
import matplotlib.image as mpimg
from torch.utils.data import DataLoader, Dataset
import sys
import scipy.io as io
import cv2
'''
class Bl... |
897b708ad01a37d817977d364c26837937f1920abbf3dfc87f27ebb079a0d9d6 | Python | 7,402 | 188 | # Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
774f39b54eb28d61c413feb22568a3a76d17fde07d5e6b8a61247ead80fcc376 | Python | 7,405 | 191 | import numpy as numx
import pydeep.base.numpyextension as npExt
from pydeep.base.activationfunction import Sigmoid
import pydeep.rbm.model as RBM_MODEL
import pydeep.rbm.sampler as RBM_SAMPLER
import pydeep.rbm.estimator as RBM_ESTIMATOR
class BinaryBinaryDBM(object):
def __init__(self, input_dim, hidden1_dim... |
c265a91e8ada9450d81eca8cb91bdd2973730d5d2f743cc6635c4d0f4809a1ce | Python | 7,405 | 214 | """Chain for summarization with self-verification."""
from __future__ import annotations
import logging
import warnings
from pathlib import Path
from typing import Any
from langchain_core._api import deprecated
from langchain_core.callbacks import CallbackManagerForChainRun
from langchain_core.language_models import... |
f20c27139074ee861011b758330789875776f5097786d35b66911620bd353ad4 | Python | 7,409 | 153 | """Optionally extract a native DWI brain mask with FreeSurfer SynthStrip."""
from __future__ import annotations
import argparse
import json
import os
from pathlib import Path
import shutil
import subprocess
import sys
import tempfile
if __package__ in (None, ''):
sys.path.insert(0, str(Path(__file__).resolve().pa... |
45fd107899644953f958281b36a6c1305232fea804d81471a9197db5626b3953 | Python | 7,417 | 212 | """Unit tests for verifying event dispatching.
Much of this code is indirectly tested already through many end-to-end tests
that generate traces based on the callbacks. The traces are all verified
via snapshot testing (e.g., see unit tests for runnables).
"""
import contextvars
from contextlib import asynccontextmana... |
ea04b41dd938e9ccadf919cfda5c53b3c8ad544f913c2a16b1257552548d236b | Python | 7,423 | 132 | # Copyright 2020 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... |
7b8305a83545a719eda1710bfebdc0e4281a701cc396f817245b7efe9c1e2ff1 | Python | 7,425 | 163 | import numpy as np
import uncertainpy as un
from scipy.integrate import solve_ivp
from edNEGmodel.edNEGmodel_params import *
from functions.initial_values import *
import time
def model_setup(t,k, g_Na, g_DR, g_Ca, g_AHP, g_C):
Na_sn, Na_se, Na_sg, Na_dn, Na_de, Na_dg, K_sn, K_se, K_sg, K_dn, K_de, K_dg, Cl_sn... |
b60d9ddc4221a3af8d649388d4854aa5c07bffe73122045cc875217f7e876dc9 | Python | 7,425 | 152 | # Copyright (c) 2008-2026 the MRtrix3 contributors.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Covered Software is provided under this License on an "as is"
#... |
4effbe66d7e3b526454d6f7451043a48f6caf1ccf0e4acdd5f61573b5b04d07d | Python | 7,426 | 184 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 6 21:39:56 2021
@author: athanasiadis
"""
from sklearn.cluster import DBSCAN
import numpy as np
def computer_local(eigenvectors,min_samples,epsilon,nvalues):
"""
computer_local
______________________
This is a function that ... |
53cb66372a0e508fc65000e508986070f93d465c76469960f09bd089b4e289ab | Python | 7,427 | 203 | ########################################################################
# 2D diffusion on an infinite strip from line "point source".
# AIMS: to verify STEPS spatial-stochastic solver 'Tetexact' supports
# local initial conditions and calculates surface diffusion rates correctly.
# STEPS equivalent model: Stochas... |
4489313d8cfd31885c4982eeff2f4ca74c43395b8645c2881cb7eed1daa3fbc2 | Python | 7,428 | 184 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2023/9/28 10:40
# @Author : zhangchao
# @File : trainer.py
# @Software: PyCharm
# @Email : zhangchao5@genomics.cn
import os
import time
import torch
import numpy as np
from torch.utils.data import DataLoader
from spatialid import SpatialModel, KDLoss, DN... |
00d3778f4504c6816f9644a55e72bfa2211a26747efc99a9a56c0c4088b24d6d | Python | 7,429 | 241 | #!/usr/bin/env python
# coding:utf-8
"""
This is the old version of vectorization, maybe used in research work instead of engineering one.
Tips:
- Embeddings are extracted to numpy matrix
- Use pickle instead of json file to avoid string variations ???
- Vectorization and padding can be done togethe... |
68b8c244f0df1eb409c171d08ea851818d13e4ee5827d28923ff693e4ade3206 | Python | 7,430 | 149 | import argparse
import os
import random
import logging
import numpy as np
import mxnet as mx
import mxnet.ndarray as nd
from mnist_rnn_factory import MovingMNISTFactory
from nowcasting.config import cfg, cfg_from_file, save_cfg
from nowcasting.helpers.gifmaker import save_gif
from nowcasting.my_module import MyModule
f... |
ea458beb68a783f436d573102cbb34d233747386ce73e46c334dca9663d0b8d0 | Python | 7,431 | 196 | import numpy as np
import os
import json
import random
from mimic3models.feature_extractor import extract_features
def convert_to_dict(data, header, channel_info):
""" convert data from readers output in to array of arrays format """
ret = [[] for i in range(data.shape[1] - 1)]
for i in range(1, data.sha... |
9649e62aa3d1bfeed6798eef26acab4b3b0c8acdf183c77e68557c58447fa4de | Python | 7,432 | 123 | # Copyright 2020 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... |
46dcfc1fb3c56dccc98f2348d575f25a73df0628676a939ace16ddcffcfa03bc | Python | 7,433 | 216 | # This script is used to convert the green view index results saved in txt to Shapefile
# considering the facts many people are more comfortable with shapefile and GIS
# Copyright(C) Xiaojiang Li, Ian Seiferling, Marwa Abdulhai, Senseable City Lab, MIT
def Read_GSVinfo_Text(GVI_Res_txt):
'''
This function is... |
1bf2c504ecf23acd1ef76d9ce0f0dc8f767a103eef29eaf41adc55374d337b5d | Python | 7,434 | 168 | import unittest
import os
from EPI_MRI.EPIMRIDistortionCorrection import DataObject
from EPI_MRI.InitializationMethods import *
class TestInitializationMethods(unittest.TestCase):
def setUp(self):
""" Initialize any common data or setup needed for the tests. """
torch.manual_seed(81) # reproducib... |
ab9da6485e431e39a281128d5dae6151f0fc23b642b11d3d4fb2ad3dbb0e91bb | Python | 7,434 | 180 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
from timm.models.layers... |
ae11c2b11c3040bbab21cd3104dd0d3a0149c60f0bc16972470b0cc7b9b389db | Python | 7,434 | 145 | from OCC.Extend.TopologyUtils import TopologyExplorer
from OCC.Core.BRepGProp import brepgprop
from OCC.Core.GProp import GProp_GProps
from feature_test import Compound
def ask_face_centroid(face):
"""Get centroid of B-Rep face."""
mass_props = GProp_GProps()
brepgprop.SurfaceProperties(face, mass_props)
... |
44ab503a3694a4ba5f6bbe3a99228e1df16a07f2a176f2fe016905dabcf791b9 | Python | 7,438 | 217 | import os
import sys
import re
import types
import itertools
from cgatReport.Tracker import *
from cgatReport.odict import OrderedDict as odict
from RnaseqReport import *
class TrackerGenemodels(RnaseqTracker):
mPattern = "_gene_expression"
def getTracks(self, subset=None):
print("getTracks")
... |
9ded5f160966997c17b5122ca7df5945ca76a59d2469e8fa6cf445eb2e31ac5c | Python | 7,443 | 167 | """Agent toolkits contain integrations with various resources and services.
LangChain has a large ecosystem of integrations with various external resources
like local and remote file systems, APIs and databases.
These integrations allow developers to create versatile applications that combine the
power of LLMs with t... |
f0ece05dcdf1f75596537b674f09c82e897b4ac47fe101c51c16551756d738b8 | Python | 7,445 | 189 | import diffrax
import equinox as eqx
import jax
# import jax.numpy as jnp
from jax import random as jr, numpy as jnp
import pysindy as ps
import sympy as sp
import sympy2jax as sp2j
import numpy as np
from CEL.networks.models.PhyCDE import CDEModel, RNN
@jax.custom_vjp
def ste_func(input):
return (input > 0).ast... |
5e4d266f775ba751b5416b9e50e8970fb41b47d5d472657b57c3058bd990ade3 | Python | 7,446 | 154 | """
Module to plot effect of different stimulation powers on behaviour.
Author: jonas.braun@epfl.ch
"""
import os
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.backends.backend_pdf import PdfPages
import seaborn as sns
from scipy.stats import... |
82d713087b503d7504fc66b1810b2f3cb42741dce0cc4e1a46afda07d234dd2d | Python | 7,447 | 182 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
from timm.models.layer... |
d37e721aa86e13a50a28017e9a16b88dbb9f222d77502e91a7984ef655fde4ab | Python | 7,450 | 172 | from typing import List
import numpy as np
import copy
import pickle
import lmdb # install lmdb by "pip install lmdb"
class ImageFeaturesH5Reader(object):
"""
A reader for H5 files containing pre-extracted image features. A typical
H5 file is expected to have a column named "image_id", and another column... |
b2de3f622899c3d41cadf69760303847e2e4e06a8ac2e5686f6d7cdbbc10b142 | Python | 7,454 | 250 | # -*- coding: utf-8 -*-
import os
import re
# Add any Sphinx extension module names, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
import sys
import importlib_metadata
# -- General configuration ----------------------------------------------------
# If your do... |
77bac6796342f767b5fd8c380f8ae5f40a9be8f7c83d09048fc6d1497dd4c4f6 | Python | 7,455 | 198 | # Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
ee183971a61ae935b684e3ccfa7913e97bfcaacf433cd30be5912a286297f380 | Python | 7,455 | 217 | """
Wrapper classes for providing a minimal consistent interface to cheminformatics toolkits
Currently supported toolkits:
* The `OpenEye Toolkit <https://docs.eyesopen.com/toolkits/python/quickstart-python/index.html>`_
* The `RDKit <http://www.rdkit.org/>`_
* `AmberTools <http://ambermd.org/AmberTools.php>`_
.. to... |
fa6909e68723a09ee5390b970834a84be4685f1ab2bc0c83393329920cdd73ee | Python | 7,456 | 194 | import numpy as np
import os
from scipy import interpolate
from scipy.ndimage import binary_fill_holes
from skimage.morphology import binary_dilation, disk, medial_axis
from skimage import transform
from skimage.measure import find_contours
import matplotlib.pyplot as plt
from matplotlib import rc
rc('font', size=17)
r... |
25d3bc17ebb3d02e6684f901830a6a6f30e8863b8998a6635e0d3692ed77be85 | Python | 7,463 | 305 | # -*- coding: utf-8 -*-
from typing import Callable, Optional
import torch
from torch import nn
from torch.nn.parameter import Parameter
from torch.distributions import Normal
from torch.distributions import kl_divergence as kl
class GraphConvolution(nn.Module):
"""
Simple GCN layer, similar to https://arxi... |
9f13eac317a327df6180d9bb53ce4060bf8c7470d8d5b4a65d98d2a8abcdeaaf | Python | 7,469 | 202 | #!/usr/bin/env python3
import traceback
from torch.autograd import grad
import torch.nn as nn
from .utils import clone_module, update_module
def maml_update(model, lr, grads=None):
"""
[[Source]](https://github.com/learnables/learn2learn/blob/master/learn2learn/algorithms/maml.py)
**Description**
... |
10f5e55d9bff53b50d968c53a2ff69ae060b3f78abfead20bf73a6d1149a793e | Python | 7,470 | 235 | # coding=utf-8
import random
import numpy as np
import torch
import sys
import os
import torchvision
import PIL
def set_random_seed(seed=0):
# seed setting
random.seed(seed)
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
torch.backends.cudnn.deterministic = True
... |
97b7f9b8def1efeb5ae4b88a7d4fe1b2ac02e26aef2877add55353a630de4ca9 | Python | 7,470 | 187 | # Take 1 cell-type, say inkt
# Take its metadata for everything: training, testing, dev
# Make a pandas df with gene and category
# Then for each of the other samples, join gene and category.
# merge by gene
# Sconda conda activate TensorFlow_CPU_01
# cd /mnt/BioAdHoc/Groups/RaoLab/Edahi/Projects/09.TimeCourse5hmC/Fo... |
a2e7f3e4c55ec5fd6d6545ffb8b13a5114ed69c73bfd637919c037717eddc492 | Python | 7,471 | 251 | """Unittests for langchain.agents.chat package."""
from textwrap import dedent
from typing import Any
from langchain_core.agents import AgentAction, AgentFinish
from langchain_core.prompts.chat import (
ChatPromptTemplate,
HumanMessagePromptTemplate,
SystemMessagePromptTemplate,
)
from langchain_core.tool... |
af53c056047429bd561e92c6449858cb7791e8a9b85093381a7e1b28f163a489 | Python | 7,474 | 238 | import os, cv2
import _pickle as cPickle
import logging
import numpy as np
import pandas as pd
import torch
from torch.utils.data import Dataset
import lmdb, pickle
import clip
logger = logging.getLogger(__name__)
os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
LABEL_MAP = {"amusement": 0, "awe": 1, "contentment": 2, "... |
2fd69c79a059da0c4c9df60d41446ab2e114eaaa221396cd35954588379c4220 | Python | 7,475 | 162 | # Copyright (c) MONAI Consortium
# 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 writing, so... |
cec1663de319718d8eed8c6a22f340cf7e18f0af3b5e4efd48a51be09d8699de | Python | 7,475 | 234 | """
This file collects key functions for preprocessing data and annotations.
"""
import datetime
from functools import lru_cache, partial
import h5py
import importlib.util
import json
import numpy as np
import pathlib
from pathlib import Path
import platform
import torch
from tqdm import tqdm
from typing import Option... |
98934429245cb59ba444a1fff552d510e291b9c4d42c3d63880ca0f738318661 | Python | 7,477 | 208 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import time
import torch.optim as optim
from torch.autograd import Variable
import re
import os
import matplotlib.image as mpimg
from torch.utils.data import DataLoader, Dataset
import sys
import scipy.io as io
import cv2
'''
class Bl... |
a2b4c343f964ec7de4c876d37e8ba86a8eaf16c156adf230d3279f013f022379 | Python | 7,481 | 184 | import torch
import numpy as np
import logging
import os
from torch.utils.data import DataLoader
from qm9.data.dataset_class import ProcessedDataset
from qm9.data.prepare import prepare_dataset
def initialize_datasets(args, datadir, dataset, subset=None, splits=None,
force_download=False, su... |
4714e8c2a77f5452e2c1df58d2bc867e26345f66505db0c9e33d693ba26f00f0 | Python | 7,483 | 220 | """VectorStore agent."""
from typing import Any
from langchain_core._api import deprecated
from langchain_core.callbacks.base import BaseCallbackManager
from langchain_core.language_models import BaseLanguageModel
from langchain_classic.agents.agent import AgentExecutor
from langchain_classic.agents.agent_toolkits.v... |
007c123fc72a4b402b9ff2bf964068367c63baa8224cbea95e4eec8f29c560c6 | Python | 7,487 | 199 | import numpy as np
import os
from scipy import interpolate
from scipy.ndimage import binary_fill_holes
from skimage.morphology import binary_dilation, disk, medial_axis
from skimage import transform
from skimage.measure import find_contours
import matplotlib.pyplot as plt
from matplotlib import rc
rc('font', size=17)
r... |
d74b2b5ba790eeff54ae786e576829f148b074c806c0c836756d19ee31b7afca | Python | 7,489 | 192 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
POCIF-BAT R2 — Extraction des trajectoires par cycle du corpus Kim et al. (2025).
Source : Kim, I. et Choi, J. W. (2024) 'Battery raw data', Mendeley Data, V2.
doi:10.17632/h2y7mj4kt7.2 — licence CC BY 4.0.
Article : Kim, I., Kim, H., An, S., Oh, J., Kim, M. ... |
b7b462d82c602221eccdcce8920df55d0bbdde1e3525c53317e02094e4f311f8 | Python | 7,490 | 153 | #!/usr/bin/env python3
#$ -cwd
#$ -V
#$ -N m5_his_c
#$ -e /cluster/uz_lab/cmives/TRP_channels/MDS/permeation_analysis/z_histogram/m5_his_ce.err
#$ -o /cluster/uz_lab/cmives/TRP_channels/MDS/permeation_analysis/z_histogram/m5_his_ce.out
#$ -pe smp 2
#$ -jc long
import os
import sys
import time
import numpy as np
import... |
17c87e11602faab313130ff54580d0b938af5529d653ef041866eef6b9fda00b | Python | 7,494 | 176 | import torch
import torch.nn as nn
from rde.modules.common.layers import AngularEncoding
class AAEmbedding(nn.Module):
def __init__(self, feat_dim, infeat_dim):
super(AAEmbedding, self).__init__()
self.hydropathy = {'-': 0, '#': 0, "I": 4.5, "V": 4.2, "L": 3.8, "F": 2.8, "C": 2.5, "M": 1.9, "A": 1.... |
3d11337f2df2e602e56f121f744435d07e04aafec968477511fd007cb81fa588 | Python | 7,496 | 162 | #!/usr/bin/env python3
# coding: utf-8
"""
Create list of Bash commands to run ABCD task prep jobs simultaneously with SBATCH
Greg Conan: gconan@umn.edu
Created: 2021-02-26
Updated: 2021-09-20
"""
# Import standard libraries
import argparse
from glob import glob
import os
import sys
def find_myself... |
0ba6950996f27bb95be08c39ae0f0cc93eabd1c2388fc2a5234f7e3629839269 | Python | 7,500 | 177 | """
Script to build an aggregated dataset for a study, where all subjects
are described within the same file, from the original data, which is made of one
data file per subject. The dataset is structured such that data that are
uniquely defined at the level of a trial, a session, or a subject are contained
in their res... |
59c8b08648b3e9c0d3bc83e0a83a31cda89f8899a41eba82511d0dd1fe3e441d | Python | 7,501 | 179 | # import shutil
# import subprocess
# import time
# import unittest
# import zipfile
# from pathlib import Path
# from random import randint
#
# import pytest
# from MRdataset import import_dataset, load_mr_dataset, MRDS_EXT
# from MRdataset.utils import is_same_dataset
# from numpy.random import default_rng
#
# from m... |
73f6ba23b825ac39834b74f7e838559a5bce203be883d1ca9ef261e2aeb8b832 | Python | 7,506 | 202 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import pickle
import os
import json
import datetime
import argparse
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn.impute import SimpleImputer
import torch
import torch.nn.functional as F... |
2ef7d1f005c9c919bfbc33d89e35627455c34218b5cb63ae42ea80d1df141c7b | Python | 7,508 | 212 | import sys
sys.path.append(".")
import argparse
import tarfile
import queue
import multiprocessing as mp
from tqdm import tqdm
import numpy as np
import pandas as pd
from crystallm import (
CIFTokenizer,
bond_length_reasonableness_score,
extract_data_formula,
extract_numeric_property,
extract_spac... |
7659b9b792e1f740759f260abf9cfe8264cf5c1f721ee3f1d6002d2faa66b9dc | Python | 7,509 | 221 | import logging
try:
from collections import Mapping
except:
from collections.abc import Mapping
from pathlib import Path
from zipfile import ZIP_DEFLATED, ZipFile
import h5py
import numpy as np
from tqdm import tqdm
logger = logging.getLogger(__name__)
def zip_dir(zip_name: str, source_dir):
"""
Zi... |
9d143167511314a86444df47d47902ab04cdf8d243340de1652ed32663b24418 | Python | 7,513 | 217 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torchvision.transforms import Normalize
import pickle
from training.diffaug import DiffAugment
from training.networks_stylegan2 import FullyConnectedLayer
from pg_modules.blocks import conv2d, DownBlock, DownBlockPatch
from pg_m... |
9571462f292be95f71f5ae7fdf1f7001c1bf2e30c598c00a640376ae16138b89 | Python | 7,514 | 171 | #pylint: disable=E1101, E0401, E1102, W0621, W0221
import argparse
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
import random
import time
from random import SystemRandom
import models
import utils
parser = argparse.ArgumentParser()
parser.add_argument('--niters', type=int, default... |
1471307ecdab5c7185013660b79e56b6c10c59ff621df32409658f2b4037aa02 | Python | 7,515 | 159 | #!/usr/bin/env python3
#$ -cwd
#$ -V
#$ -N m5_his_a2
#$ -e /cluster/uz_lab/cmives/TRP_channels/MDS/permeation_analysis/z_histogram/m5_his_ce.err
#$ -o /cluster/uz_lab/cmives/TRP_channels/MDS/permeation_analysis/z_histogram/m5_his_ce.out
#$ -pe smp 2
#$ -jc long
import os
import sys
import time
import numpy as np
impor... |
574b6964262e300294fdce450ce78d325cf6f556e34b6237eade73d5df3d2b5a | Python | 7,517 | 157 | import gym
import random
from gym import spaces
import numpy as np
import logging
from random import sample, uniform
from math import ceil
from DSS_Initialize import *
from state_action_reward import *
from gym.utils import seeding
logging.basicConfig(format='%(asctime)s %(levelname)s: %(message)s', level=l... |
a264ca75bbe7d62b2c3eef2f3c8a1a1f12e2087d33edd837deb79f623a8837c0 | Python | 7,518 | 158 | """
In this file the DSS engine is set up.
The objects for circuit, bus, and branch are also set up for further use in the RL environment.
This file also includes function to modify the base DSS circuit with sectionalizing, tie switch, and generator information.
The translation of DSS Circuit into a graph structure... |
c7bafb65f2777d53b86ba2bd3ec75828ff458d70df264b844649dee7b85c2a7f | Python | 7,518 | 179 | import os
# this stops jax from stealing all the memory
os.environ["XLA_PYTHON_CLIENT_PREALLOCATE"]="false"
import jax
import jax.numpy as jnp
import jax.random as jrng
import tensorflow as tf
import seaborn as sns
import hydra
from omegaconf import DictConfig
from math import sqrt
# from clu.metrics import Collectin... |
606a23adb058cd507671f0b1b149c92ec792f5035317ed66077f0a0da6e40089 | Python | 7,520 | 164 | file_name = 'CellJ.json'
Step = 0.1 #ms
Edel = 100 #ms
stopTime = [20000] #ms
rangesL = [10000] #phase calculation crop limit low
rangesH = [-10000] #phase calculation crop limit high
signalInd = 0
import pycircstat
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import efel
from sc... |
20d2b8c6d99dc9dc905c22dc61bd10a2f3f95e8bc5fee763aa9683c03255649c | Python | 7,524 | 229 | """Utilities for working with iterators."""
from collections import deque
from collections.abc import Generator, Iterable, Iterator
from contextlib import AbstractContextManager
from itertools import islice
from types import TracebackType
from typing import (
Any,
Generic,
Literal,
TypeVar,
overloa... |
ee34c7b91b188e7fae64428f48efc305b123747e3075aa3374d392d40c95858b | Python | 7,528 | 164 | file_name = 'CellJ.json'
Step = 0.1 #ms
Edel = 100 #ms
stopTime = [20000] #ms
rangesL = [10000] #phase calculation crop limit low
rangesH = [-10000] #phase calculation crop limit high
signalInd = 0
import pycircstat
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import efel
from sc... |
dfc362b8f74847d05a945e977fecc0d37f0eea5b5516cc86ea419200681b5119 | Python | 7,531 | 238 | # Copyright (c) MONAI Consortium
# 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 writing, so... |
05e07d894e497830fdd095025722eb62886969c44a6521bf96af362a1829742f | Python | 7,533 | 198 | import torch
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
from pymatgen.analysis.graphs import StructureGraph
from pymatgen.analysis import local_env
from .mat_utils import lattice_params_to_matrix
CrystalNN = local_env.CrystalNN(
distance_cutoffs=None... |
a3b512edfdee21014dd2d5227a5bb30d82541f85c0ca15c936cbce2e40a8efa2 | Python | 7,534 | 222 | from pathlib import Path
from unittest.mock import AsyncMock, Mock
import pytest
from langchain_tests.integration_tests.vectorstores import VectorStoreIntegrationTests
from langchain_core.documents import Document
from langchain_core.embeddings.fake import DeterministicFakeEmbedding
from langchain_core.vectorstores i... |
746a0f017d45f6a0f55d449f67a1dbabc80ffcb39c41b3f68f639ae28964fa43 | Python | 7,535 | 208 | """Chain pipeline where the outputs of one step feed directly into next."""
from typing import Any
from langchain_core.callbacks import (
AsyncCallbackManagerForChainRun,
CallbackManagerForChainRun,
)
from langchain_core.utils.input import get_color_mapping
from pydantic import ConfigDict, model_validator
fro... |
9dcdd188b448daae494cd27975b116fd959f2b1da3ffc0c2c7206b57612e5d44 | Python | 7,535 | 209 | # this script quality check the segmentation for tiles
# Mask-RCNN on detectron2:
# the folder structure should be:
# data/train, val (images)
# pretrained: the pretrained model model_best.pth
# qc: quality check
# ini_infer: inference with no training on the data
# training: training on the new dataset
# Run... |
46257bd88303dc580899149248eeddba7dab7a4831573b9e82bcbb9139066190 | Python | 7,536 | 217 | import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
import pandas as pd
import sys, os
import pickle
from mantis_ml.config_class import Config
clf_alias = {'ExtraTreesClassifier': 'ET', 'SVC': 'SVC', 'DNN': 'DNN', 'RandomForestClassifier': 'RF', 'XGBoost': 'XGB', 'GradientBoostingClassifier': 'GB'... |
d01f5f21553003d9042beb2c256e0ed27d9f01902702c945706afa212de64162 | Python | 7,538 | 222 | from sklearn.svm import SVC
from sklearn.metrics import accuracy_score
from sklearn.model_selection import StratifiedKFold
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader, TensorDataset
import os
from sklearn.metrics import confusion_mat... |
10c1941cdeae88ca7f029feec86da9c8ec1ef27a6a01f7d42fb0f2dc14bbc799 | Python | 7,541 | 200 | """
%Copyright (C) 2020, Manel Vila-Vidal, for the translation from Matlab to Python
Contact details: m@vila-vidal.com
%Copyright (C) 2019, Adria Tauste Campo, for the adapted Matlab code (https://github.com/AdTau/DI-Inference)
%Contact details: adria.tauste@gmail.com
%Copyright (C) 2019, Jiantao Jiao, for the original... |
3a8263330573551200a266ed9eefd7a6be3d745af10c288ade7f999b22b27c74 | Python | 7,541 | 208 | import torch
from rfdiffusion.potentials import potentials as potentials
import numpy as np
def make_contact_matrix(nchain, intra_all=False, inter_all=False, contact_string=None):
"""
Calculate a matrix of inter/intra chain contact indicators
Parameters:
nchain (int, required): How many chai... |
be7ed7728f035b503544e0c838c99840a05b82d873d2fc79ff51114f2e1ca258 | Python | 7,543 | 274 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 27 11:12:51 2023
@author: weihan
"""
import pandas as pd
def read_fasta_to_dict(fasta_file: str = 'demo.fa') -> dict:
"""
Read fasta to py dict.
The seq name is dict keys and seq is values.
Parameters
----------
fasta_... |
0751554a8b504577e17f1faf47653bde1a284806b36194a020978dcfaf418c3f | Python | 7,544 | 199 | import numpy as np
import torch
import torch.nn.functional as F
from torch import nn
from utils import RBFExpansion
from torch_scatter import scatter
from torch.nn import Embedding
from typing import Union
from torch import Tensor
from torch_sparse import SparseTensor
from torch_geometric.nn.conv import MessagePassin... |
efeb775fd42eaae647bdd51c395a88d031b4e8ecff781f59c83794c0e05f081b | Python | 7,544 | 182 | from tensorboardX import SummaryWriter
import torch
import json
import sys
import os
import argparse
import numpy
import pickle
import pandas
def parse_arg():
''' This Function Parse the Argument '''
p=argparse.ArgumentParser( description = 'Example: %(prog)s -h', epilog='Library dependency :')
p.add_argum... |
beeae7aa0cfb62d67d2e50398759ddb999d8bb0e626ca862a6bf0873329a94fc | Python | 7,548 | 195 | import linecache
import os
import subprocess
from typing import Dict, List, NamedTuple
import numpy as np
import torch
from torch.nn.utils.rnn import pad_sequence
from torch.utils.data import Dataset
from transformers import BatchEncoding, PreTrainedTokenizer
from transformers.trainer_utils import PredictionOutput
de... |
f4561f649c88a8739be16bf5d7b1d1fb2485de85fc1f6f395bc1e7bca1b96148 | Python | 7,548 | 233 | import math
from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
def get_inplanes():
return [64, 128, 256, 512]
def conv3x3x3(in_planes, out_planes, stride=1):
return nn.Conv3d(in_planes,
out_planes,
kernel_size=3,
... |
eebad623e634accc327cacfafeef3cea02df5b8465b4ae06f13ea63accdd351b | Python | 7,550 | 172 | import anndata as ad
from typing import Optional, Literal, Union
import numpy as np
import pandas as pd
class AnnotatedData(ad.AnnData):
"""Creates annotated cellsdata (see anndata library for more information on AnnotatedData) object based around the Ca2+ matrix of the imaging trial."""
def __init__(self, ... |
15c3f206f612bcb913f00caa52dc78e5358b9895a14be5501ed5590014c2bb97 | Python | 7,551 | 201 | from SMdRQA.RQA_functions import entropy
from SMdRQA.RQA_functions import average
from SMdRQA.RQA_functions import maxi
from SMdRQA.RQA_functions import mode
from SMdRQA.RQA_functions import percentmorethan
from SMdRQA.RQA_functions import diaghist
from SMdRQA.RQA_functions import onedhist
from SMdRQA.RQA_functions imp... |
38e21e7071f224aff09ca1c1a7088f1eb95bebaecccd84bf92603a3fb054f756 | Python | 7,551 | 262 | """Fixtures used for testing."""
import numpy as np
import psims
import pytest
import yaml
from pyteomics.mass import calculate_mass
@pytest.fixture
def mgf_small(tmp_path):
"""An MGF file with 2 annotated spectra."""
peptides = ["LESLIEK", "PEPTIDEK"]
mgf_file = tmp_path / "small.mgf"
return _create_... |
e523bdc50ec1fbe51865b21e5c265c109406166cd79d5eb1082accf79b0b7de4 | Python | 7,553 | 312 | # -*- coding: utf-8 -*-
"""
Created on Sat Feb 20 12:16:32 2021
@author: Xingyan Liu
Basic functions
"""
import os
import logging
from typing import Sequence, Union, Mapping
import json
import pickle
import time
import datetime
import numpy as np
import pandas as pd
from scipy import sparse
def strline(seq):
... |
326b041214ade509b5ddc4c232fcb9885373ee939f01b16a327f892b9d1c062d | Python | 7,554 | 222 | from datetime import datetime as dt
from datetime import timezone
from typing import Any, TypeVar
import pytest
from langchain_core.exceptions import OutputParserException
from langchain_core.messages import AIMessage
from langchain_core.output_parsers import BaseOutputParser
from langchain_core.prompts.prompt import ... |
e7e684cb72b78906cd95903f11619768ec93698d1f715953be74293eb532ea84 | Python | 7,554 | 186 | # *=========================================================================
# *
# * Copyright Erasmus MC Rotterdam and contributors
# *
# * Licensed under the GNU GENERAL PUBLIC LICENSE Version 3;
# * you may not use this file except in compliance with the License.
# *
# * Unless required by applicable law or agre... |
2517bd191515307798588ae492ec9cc90b786db616769ae1413441a1199b6f0f | Python | 7,561 | 210 | """Mass spectrometry file type input/output operations."""
import collections
import csv
import operator
import os
import re
from pathlib import Path
from typing import List
import natsort
from .. import __version__
from ..config import Config
class MztabWriter:
"""
Export spectrum identifications to an mzT... |
eafac899c37f42ed87def7e19b110adc353b91b22fad56b004b31cc013df6c22 | Python | 7,565 | 164 | """
In this file the DSS engine is set up.
The objects for circuit, bus, and branch are also set up for further use in the RL environment.
This file also includes function to modify the base DSS circuit with sectionalizing, tie switch, and generator information.
The translation of DSS Circuit into a graph structure is ... |
9a94791423a6db3362a1f4b9afeda8e2d2ff114a7f3518d2f464b53a7443d32c | Python | 7,566 | 253 | '''pipeline_quickstart.py - setup a new pipeline
=============================================
Purpose
-------
This script creates a new pipeline according to the cgat
pipeline layout. This is useful when starting a new pipeline
from scratch.
Usage
-----
To start a new project, use :file:`pipeline_quickstart.py`:... |
ad9a64f1e234b352408ff68ec941b4de5e807f7fb40ab1f289620a36501b610f | Python | 7,566 | 195 | from collections.abc import Sequence
from langchain_core.language_models import BaseLanguageModel
from langchain_core.prompts.chat import ChatPromptTemplate
from langchain_core.runnables import Runnable, RunnablePassthrough
from langchain_core.tools import BaseTool
from langchain_core.tools.render import ToolsRenderer... |
ec975c4e6e94b7ad6485d265894462d49d026ccd64ba212e692ae8d309d208d4 | Python | 7,570 | 219 | ########################################################################
# Stochastic degradation-diffusion process.
# AIMS: to verify STEPS spatial stochastic solver 'Tetexact'
# supports spatially-separated initial conditions and computes
# diffusion and reaction rates correctly when applied to a
# degradation-di... |
07491857f9e64e7fa06b0b7222f07b78c264525edc29cca1ee27e6ba8062c93e | Python | 7,574 | 219 | """Loading datasets and evaluators."""
from collections.abc import Sequence
from typing import Any
from langchain_core.language_models import BaseLanguageModel
from langchain_classic.chains.base import Chain
from langchain_classic.evaluation.agents.trajectory_eval_chain import (
TrajectoryEvalChain,
)
from langc... |
631f9af0f48a8f9bdacee91f7f94f30f6100eb18e404f7076355d6afbba878c9 | Python | 7,574 | 241 | import torch
import warnings
def _handle_unused_kwargs(solver, unused_kwargs):
if len(unused_kwargs) > 0:
warnings.warn('{}: Unexpected arguments {}'.format(solver.__class__.__name__, unused_kwargs))
def _rms_norm(tensor):
return tensor.pow(2).mean().sqrt()
def _mixed_linf_rms_norm(shapes):
de... |
51dd81be0572192274d08d6a5b61594c0ee853d1de56ef940f1c07715364710d | Python | 7,581 | 211 | import os
import re
import tempfile
import numpy as np
import torch
from pathlib import Path
import argparse
import pandas as pd
from rdkit import Chem
from tqdm import tqdm
try:
import utils
except ModuleNotFoundError as e:
print(e)
def calculate_smina_score(pdb_file, sdf_file):
# add '-o <name>_smina.s... |
57a3e9ae989a9018b986ed2d4d51e0991863ce0902ca41ed440e128b1080b1e2 | Python | 7,584 | 203 | import os
import numpy as np
np.random.seed(0)
from collections import defaultdict, Counter
# import pickle5 as pickle
import pickle
import torch
import torch.nn as nn
import scipy.sparse as sp
import sys
sys.path.append('../../')
from BrainAlign.SR_RSC.utils import process
#import sys
class embedder:
def __init__... |
317de5dac2244243533ef7018a9db9467435f6a55b221e13122fa5864259b705 | Python | 7,586 | 158 | # Copyright (c) 2008-2026 the MRtrix3 contributors.
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Covered Software is provided under this License on an "as is"
#... |
242238988e15d4f0b3b584d39f096b07c45cd09d950b5830929e70686c423255 | Python | 7,587 | 219 | ########################################################################
# Stochastic degradation-diffusion process.
# AIMS: to verify STEPS spatial stochastic solver 'Tetexact'
# supports spatially-separated initial conditions and computes
# diffusion and reaction rates correctly when applied to a
# degradation-di... |
4fa8d8b342be4377806c2a963b371fdbc22edc2a484608e56bdb9b9524cb0d5f | Python | 7,588 | 209 | import os
import pandas as pd
import torch
import numpy as np
from torch_geometric.data import DataLoader
import random
import torch.nn as nn
import torch.optim as optim
from torch_geometric.nn import global_mean_pool
from torch_geometric.nn import GATConv
import torch.nn.functional as F
from sklearn.metrics import roc... |
af59a6f18b3db32a319755adb6b2473f96f4f0507919736ea320130a367631fa | Python | 7,598 | 184 | import os
import numpy as np
import matplotlib.pyplot as plt
import skimage.io
from cellpose import models
import pandas as pd
import argparse
import torch
from Classifier_functions import predict_batch
from calculs_masks_1et2 import calcul_masks_1et2
from mosaique_images_brutes import generate_mosa_raw_images
from m... |
efd2bd73de378c4ed66f656a7ec7ba2b57a467acfddd4ae85ddb7dd9f2bba630 | Python | 7,601 | 220 | """Hybrid density synthesis: soft GTOs via FT+IFFT, sharp GTOs via real-space.
Opt-in only (``density_eval_mode=hybrid_fft``). Default training stays real-space.
"""
from __future__ import annotations
from typing import Optional, Sequence, Tuple, Union
import torch
from scdp.model.gto_fourier import density_from_g... |
a8e79620e1779c69f6730e01e646b679e1435bab7e99ba7a04939c66be92b2fa | Python | 7,606 | 207 | import os
import sys
import re
import types
import itertools
import matplotlib.pyplot as plt
import numpy
import numpy.ma
import Stats
import Histogram
import cpgReport
from cgatReport.Tracker import *
from cgatReport.odict import OrderedDict as odict
##################################################################... |
dcc897b2c643e733feb4da60573dad09ec417001074924ab07865a4cd695a472 | Python | 7,614 | 183 | #!/usr/bin/env python3
# pylint: disable=line-too-long
"""
Various functions that take genome annotations, and determine the metabolic pathways they encode.
"""
# Imports
import os
import logging
from itertools import chain
# Local
from enrichm.databases import Databases
from enrichm.module_description_parser import Mo... |
8522f7c0e2935cfdf058cf8a0a0b05a86532de4f18ec296dc0a86e29141d9573 | Python | 7,615 | 271 |
import numpy as np
from mpl_toolkits.axes_grid1 import make_axes_locatable
import pandas as pd
import DAE_params as prms
from time import time
import datetime
#################################################
#
# This script activates each node at the
# bottleneck layer for the full ensemble
# of networks and comp... |
8220b8955fad1d45563f343e9d38af053f2e47fd9da806ca48374e40276a0d5f | Python | 7,617 | 167 | # -*- coding: utf-8 -*-
"""
%Copyright (C) 2020, Manel Vila-Vidal, for the translation from Matlab to Python
Contact details: m@vila-vidal.com / manel.vila-vidal@upf.edu
%Copyright (C) 2019, Adria Tauste Campo, for the original Matlab code (https://github.com/AdTau/DI-Inference)
%Contact details: adria.tauste@gmail.com... |
f11bded526ae1129b9a2948c32045cc4ff55630900685e2e62e026c33d4356a0 | Python | 7,623 | 194 | """Test pepolar type of fieldmaps."""
from os import cpu_count
import pytest
from niworkflows.interfaces.bids import DerivativesDataSink
from nipype.pipeline import engine as pe
from ..pepolar import (
check_pes, _split_epi_lists, init_prepare_epi_wf, init_pepolar_unwarp_wf
)
def test_split_epi_lists(bids_layout... |
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