sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5aa10e7d71401f5a3fcc30a48849e76c47e4fd3ecfa9f11655b46081bcb1bf01 | Python | 4,974 | 152 | """
====================================================================
Motor imagery classification
====================================================================
Classify motor imagery data with Riemannian geometry [1]_.
"""
from matplotlib import pyplot as plt
from mne import Epochs, pick_types, events_from... |
7f948b0fa6f384b0cf42748e39bae5361b777271bb09a6baba655ad3327373ba | Python | 4,975 | 150 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Title(_BaseLayoutHierarchyType):
_parent_path_str = "layout.xaxis"
_pat... |
addefc654a3a03c28bb58c98a092e95b0118d81fb57c33bab9aebbee04ecaf8a | Python | 4,975 | 123 | """Adaptive-pool descriptor envelope containment regressions.
The published ``UPPER_BOUND`` descriptor for adaptive pooling must CONTAIN the
true adaptive bin geometry for every input/output ratio. The historical edge
pair ``((r, -1), (r, +1))`` under-covered whenever ``r = in/out > 2`` (true bin
end is ``ceil((o + 1)... |
bea12f2d741007b8e2e281ac003eecbca5a68e4d1b2d94a45c52995409f69338 | Python | 4,975 | 150 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Title(_BaseLayoutHierarchyType):
_parent_path_str = "layout.yaxis"
_pat... |
489a6cff876dfc3663a5fa0778cc16e776395f509d7051c235569016d471788f | Python | 4,976 | 149 | from ethoscope_node.utils.device_scanner import EthoscopeScanner
from ethoscope_node.utils.mysql_backup import MySQLdbToSQlite, DBNotReadyError
import os
import logging
import time
import multiprocessing
import traceback
import urllib.request
import json
def receive_devices(server = "localhost"):
'''
Interro... |
6dc19a47817a53c712a812a7b3635edc49d58e3e2efc3f0d89b3a017eb5dc2fb | Python | 4,976 | 148 | import copy
from typing import Any
import numpy as np
import pandas as pd
from mirp._images.generic_image import GenericImage
from mirp._imagefilters.generic import GenericFilter
from mirp._imagefilters.utilities import SeparableFilterSet
from mirp._images.transformed_image import TransformedImage
from mirp.settings.... |
d2268ba0e555ceca1813d99e46308a5ad7e9cdd34bc7aaf1f7a53fa8c2d42d32 | Python | 4,977 | 160 | import numbers
import numpy as np
import pyqtgraph as pg
from .. import mask
from .base import BaseShape, rotate_around_point
class Rectangle(BaseShape):
def __init__(self, x=40, y=30, a=33, b=22, phi=0, point_um=1):
"""Rectangle
Parameters
----------
x, y: float
ce... |
86c8b50d6e6a91bbcc832eea8ff28e401f5918ce914e56f50db7102f2a3daf0d | Python | 4,981 | 142 | import argparse
import numpy as np
import torch
from torchvision import datasets
from torch import nn, optim, autograd
from PIL import Image
import create_oscn as co
import time
import collections
from collections import Counter
from torchvision.utils import save_image, make_grid
mnist_train = datasets.MNIST('./data... |
6461deb989f8089b5fb17e7eb15b4608d1314540cfe709acc8cb203232617f2b | Python | 4,982 | 130 | #!/usr/bin/python
import os
import sys
import pandas as pd
import numpy as np
import ConfigParser
import re
def main():
##### check arguments #####
if len(sys.argv)<2:
sys.exit('ERROR: not enough arguments\nUSAGE ./magma.py <filedir>')
filedir = sys.argv[1]
if re.match(".+\/$", filedir) is None:
filedir += '/... |
d8ab0fc8ca9bd2736994d1e520ad9c234c60fcf9198aca11afec7b97c98a9a1b | Python | 4,982 | 137 | """
The re-implemented distributed sampler for the distributed training of GROVER.
"""
import math
import time
import torch
from torch.utils.data.sampler import Sampler
import torch.distributed as dist
class DistributedSampler(Sampler):
"""Sampler that restricts data loading to a subset of the dataset.
It is... |
09e6842ff12edc81995ac63fa97119f16d4b8fd38c773232d9f84242f74e8ad6 | Python | 4,983 | 118 | import sys
import numpy as np
sys.path.extend(["../TDNODE", "src"])
import torch
from typing import Tuple
import warnings
import constants
warnings.filterwarnings("ignore")
def make_batch(batch: Tuple[Tuple[any]], device: str):
"""Collate function to process multiple patients at a time during training and eva... |
3d20e2f1ff30cc348b45ca870143b8755c36f264469ab18588d4fdaf308b816e | Python | 4,984 | 169 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Domain(_BaseTraceHierarchyType):
_parent_path_str = "icicle"
_path_str = ... |
502c63ed21f351ce68c2f59e595a21b656c74c5382f9fd4324828414418c924e | Python | 4,984 | 169 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Domain(_BaseTraceHierarchyType):
_parent_path_str = "sankey"
_path_str = ... |
1b499dc91fc9ebf21bab9d856f653ae880edbb510913dfe1a9fc0c12e6fbecc7 | Python | 4,985 | 167 | import os
import copy
from collections import defaultdict
from main import main, run_all
from src.datasets import (
test_datasets,
test_convert_label_to_int,
)
from src.config_test import (
config_test_trainer_vae_cmnist,
config_test_trainer_vae_oscn,
config_test_trainer_mmvae_cmnist_oscn,
conf... |
05f287a9a56f6c8eee14375e8ddb5af11459ec5eeb9fa4e1334bbddcc11aa9d9 | Python | 4,986 | 115 | """
This script shows the training pipeline for k-fold training, without logging it via wandb.
"""
import tensorflow as tf
import tensorflow.keras as keras
import tensorflow_addons as tfa
from sklearn.model_selection import StratifiedKFold
from tf_spiking.helper import TrainingHistory
from tf_spiking import DenseLIF, ... |
1efc2a64b57b2de762da78048d5012cfb57605aff7fba32b8ba656907fafc55a | Python | 4,986 | 143 | from tdt import read_block
import numpy as np
import matplotlib.pyplot as plt
import os
import statistics
def extract_name_streams(blocknames, tankdir, filenames, trimstart, trimend):
for block in blocknames:
full_path = os.path.join(tankdir, block)
data = read_block(full_path)
fields = list(data.streams.keys(... |
4b38d970ec45ef3745513e3b66fda7ec03371fc9280f2b3fd0ea52fa7f6021f7 | Python | 4,986 | 136 | import os
from glob import glob
from distutils.util import convert_path
from distutils.command import sdist
from setuptools.extern.six.moves import filter
class sdist_add_defaults:
"""
Mix-in providing forward-compatibility for functionality as found in
distutils on Python 3.7.
Do not edit the code ... |
e9b21f22d8dc2276cf290b2aa307ac6f7c7dc5cc932b85b9ced7f7c77381c8d2 | Python | 4,986 | 140 | import torch.nn as nn
from . import imdnblock as B
import torch
def make_model(args, parent=False):
return IMDN(args)
# For any upscale factors
class IMDN_AS(nn.Module):
def __init__(self, in_nc=3, nf=64, num_modules=6, out_nc=3, upscale=4):
super(IMDN_AS, self).__init__()
self.fea_conv = nn.... |
3780d3d1e0dab5806fe532b14414c7b65a7817f5fded70b0059b3e7498a642bd | Python | 4,987 | 135 | import os, json, datetime
import logging
users_keys = ['name', 'fullname', 'PIN', 'email', 'telephone', 'group', 'active', 'isAdmin', 'created']
incubators_keys = ['id', 'name', 'location', 'owner', 'description']
class EthoscopeConfiguration(object):
'''
Handles the ethoscope configuration parameters
D... |
106220d6aa36a4c8c8d5cd001558bcc29e75243a5a5c2fac45771f1a24b83d9c | Python | 4,988 | 157 | import logging
import re
from collections.abc import Callable
from typing import (
cast,
)
from alembic import context
from alembic.script import ScriptDirectory
from alembic.script.base import Script
from sqlalchemy import create_engine
from sqlalchemy.exc import OperationalError
from galaxy.model import Base
fr... |
47024b4a39356110b49429f335d3350ec5e4e09be296f6895f2255958d796287 | Python | 4,988 | 144 | import os.path
import numpy as np
from mirp._data_import.generic_file import ImageFile, MaskFile
class ImageNumpyFile(ImageFile):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def is_stackable(self, stack_images: str):
"""
Is the image potentially stackable?
:para... |
dce7f7d8cd96ffb6f96e3b266e6e7d5355a7f7ec35e92dca4a369ac78010a6d8 | Python | 4,988 | 134 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft
# Licensed under the MIT License.
# Written by Bin Xiao (leoxiaobin@gmail.com)
# Modified by Bowen Cheng (bcheng9@illinois.edu)
# ------------------------------------------------------------------------------
fro... |
b4420203862eea05a351587052365b751d1f37ddee7fdedbed24bf2b741dcf5f | Python | 4,989 | 125 | """Lane W051-HONESTY: the honesty fact block carries interventions and honest witness wording.
AUD-HONESTY M5: ``tl.trace(m, x, intervene=...)`` zero-ablates a site while the
capture settles ``complete``; ``to_agent_json()``, ``to_pandas().attrs``, the export
preamble, and ``explain`` carried NO intervention fact, so ... |
535474d138a44f02898d174bee0165aeae87e3328957f2c97671b11d7ec58dd2 | Python | 4,990 | 163 | # -*- coding: utf-8 -*-
# ---
# jupyter:
# jupytext:
# formats: ipynb,py:light
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.4.2
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
#... |
be269a44962f547076c272ab0c98b3e2fde3a6ae993c4f182339a3b4e5ece106 | Python | 4,990 | 110 | from model import *
from utils import *
import numpy as np
from sklearn.model_selection import KFold
import torch
import os,sys
import warnings
warnings.filterwarnings("ignore")
# trained_model protein length capacity should >= new protein length capacity
# trained_model should have same embedding method with new dat... |
9eba869448b8419e926a0e599049cace9b2e5c9689b29ea358c671cda68e441d | Python | 4,991 | 119 | import numpy as np
from keras.src import backend
from keras.src import ops
from keras.src.api_export import keras_export
from keras.src.backend.common import is_int_dtype
from keras.src.backend.common import standardize_dtype
@keras_export("keras.visualization.draw_segmentation_masks")
def draw_segmentation_masks(
... |
466ae0473fafb76da0c473e01370fac8491389646aa93ba9845e9106e0d0c237 | Python | 4,992 | 98 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
79b5eb7745e2c7f97c29fc1128c48240e22fbab9523dca2c45f53044d60226ad | Python | 4,992 | 108 | import glob
import h5py
import numpy as np
import os
import pandas as pd
from sklearn.linear_model import RidgeCV
from sklearn.model_selection import GroupKFold
from sklearn.linear_model import LinearRegression
from sklearn import preprocessing
import sys
from scipy.stats import pearsonr
"""
This script will run ridge... |
9522579bdc819048878aab5593407a5e7607aa845c56cdf5b46149b0caf30c5e | Python | 4,993 | 132 | #!/usr/bin/env python
# Retrieves data from external data source applications and stores in a dataset file.
# Data source application parameters are temporarily stored in the dataset file.
import os
import sys
from json import (
dumps,
loads,
)
from urllib.parse import (
urlencode,
urlparse,
)
from urll... |
a6f2f35c422fee8d5c7bf88822164835e6281ed62c92dcd474b40f6becd7e0c9 | Python | 4,993 | 171 | """
A set of methods to extract tissue networks from segmented ROIs
"""
import numpy as np
import sknw
from skimage.morphology import skeletonize, thin
from tqdm import tqdm
class TissueNetwork:
"""
Convert cell segmentation masks to tissue network
"""
def __init__(self, cell_interior_mask):
... |
41c900f9c5fe165ccf7b082206a1bf6f4180d9a897690de355c79dab6d1e9123 | Python | 4,994 | 125 | # Copyright (c) ByteDance, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
# This file is basically a copy of: https://github.com/facebookresearch/ConvNeXt/blob/06f7b05f922e21914916406141f50f82b4a... |
4629e1fd4dcd8cff760be46507452be078dd586762e39eec7ab0fb77aa09ab90 | Python | 4,994 | 141 | # This example requires the following dependencies to be installed:
# pip install "lightly[timm]"
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import pytorch_lightni... |
d1e9e853c99d4e13083d923ed3c7d708e7c565589b26fe7544edb17499b84d96 | Python | 4,996 | 101 | import os
from Bio.PDB import PDBParser
import shutil
from tqdm import tqdm
import pandas as pd
import numpy as np
def drop_duplicate_entries(tmp):
"""Drop cases where mutation and ddG/dTm value is the same, but other info is different"""
arr = np.empty(tmp.shape[0], dtype=object)
# get unique entries by... |
2c2fc2468b71f150fa3cff6e2d24ef3605ef613b9c7dc630fcee260a32f3d2ff | Python | 4,997 | 118 | """
Regression tests for ``face_rhythm.point_tracking.PointTracker``.
Locks the fix for GitHub issue #80: when ``rois_masks=None`` and the
``BufferedVideoReader`` is in ``method_getitem='by_video'`` mode (the mode the
standard demo/pipeline uses), ``PointTracker`` must build a full ``(H, W)`` ROI
mask. Previously it i... |
6c1347bf67e8c394d748901dbd145c02208528e23437484acdaecbe5b466ed33 | Python | 4,997 | 137 | # %% [markdown]
# # Sharding
# (advanced:sharding)=
#
# [Sharding](https://zarr.dev/zeps/accepted/ZEP0002.html) is a technique in [Zarr](https://zarr.dev/) for bundling multiple chunks into a single storage unit.
# In terms of storage, this can drastically reduce the number of files written,
# and thus reduce the overh... |
e08e22a96d5530dace3a190b318c12ee83bb609972e8648f045d8187437a64b0 | Python | 4,997 | 128 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 21 15:30:53 2020
@author: ml
"""
import os
import numpy as np
import pandas as pd
from collections import defaultdict
def feature_dataframe_inparcel(subjects, fname, tbi_dir, camcan_dir, bands, parc='aparc'):
rows = []
for i, subject in... |
8a0a5cc12f1b6bf51e3cfba64f33ac5839f8bd91c0ce793e1de65731b9df5f01 | Python | 4,998 | 191 | """
Widgets for editing the larva groups placed in an experiment.
"""
from __future__ import annotations
from typing import Any
import param
from larvaworld.lib import reg, util
from larvaworld.lib.param.custom import ClassDict
from .distribution_widget import build_distribution_widget
from .widget_base import cla... |
8d3c323e4c64277b79046cfc1464ba9cb5d0fe7b33d205d0160eb1acf6dfdd6e | Python | 4,998 | 187 | # Copyright (C) 2003, 2004, 2006 by Thomas Mailund <mailund@birc.au.dk>
#
# 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 2 of the License, or (at
# your option) any later versio... |
a3a9407a1cdbe6708898c061411ebde48384c487189d5fa8ae71bf0aefaa773c | Python | 4,999 | 129 | from __future__ import division
import unittest
import numpy as np
np.random.seed(42)
from wyrm.types import Data
from wyrm.processing import calculate_csp
class TestCalculateCSP(unittest.TestCase):
EPOCHS = 50
SAMPLES = 100
SOURCES = 2
CHANNELS = 10
def setUp(self):
# create a random... |
a88c880f27df7ab977db2c722dcc5146a9b2ef4d2aa1de9b6c1b0aeff6a3f645 | Python | 4,999 | 141 | # -*- coding: utf-8 -*
import torch
import pickle
import time
import numpy as np
import random
import copy
from CGraph import to_direct, soe_from_triedges
ROOT_DATA = '../data'
def cal_cb(n, ca, c):
b = ca - n
c = c - ca
a = np.cross(b, c)
cb = -0.58273431*a + 0.56802827*b - 0.5406746... |
7362ae3ceaf0fe398a98cd92f97c5c59c809ff3089762ced2d2b6ed0c4daf287 | Python | 5,000 | 123 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Continuous neural data (CND) format used for mTRF-Toolbox"""
from pathlib import Path
from typing import Optional, Sequence, Union
import mne
from mne.externals.pymatreader import read_mat
import numpy
from .._data_obj import Dataset, Factor, NDVar, Scalar, ... |
8fb31747a6c99674f09b3f24f8479442e71142850ac7a9c993d39f3c8300977c | Python | 5,000 | 133 | from . import InvertibleModule
from typing import Union
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
class PermuteRandom(InvertibleModule):
'''Constructs a random permutation, that stays fixed during training.
Permutes along the first (channel-) dimension for multi-d... |
0ba1d835ae67baf5d8acb46b035e0ac5e196cf75b16e578106551195e5a0a7f9 | Python | 5,001 | 143 | """
Convenience class that lets singletask models fit on multitask data.
"""
from __future__ import division
from __future__ import unicode_literals
import os
import sklearn
import tempfile
import numpy as np
import shutil
from deepchem.utils.save import log
from deepchem.models import Model
from deepchem.data import ... |
23b1d4e2ac2eea80579da75ae0275eb89ab7442471bc71e679a7192cc3bc52b6 | Python | 5,001 | 163 | import numpy as np
import pandas as pd
from nnunet.evaluation import metrics
import SimpleITK as sitk
import os
import matplotlib.pyplot as plt
from pylab import *
import glob
import scipy.stats
def stars(p):
if p < 0.0001:
return "****"
elif (p < 0.001):
return "***"
elif (p < 0.01):
... |
57c46da12002dc386227a49d725e47eea200190b99d1f08d7f865529d6fb4138 | Python | 5,001 | 150 | """
Mask R-CNN Visualization Functions
Original Code:
- Copyright (c) 2017 Matterport, Inc.
- Written by Waleed Abdulla
- Licensed under the MIT License (see LICENSE for details)
- Source: https://github.com/matterport/Mask_RCNN
Modifications:
- Jason Landen, 2024
- I adjusted the display_instances function to suppor... |
7dfaf8ee8bc6a0850eda030c4ab27058f3fa312ca4dff4b55ee4b4d8ac5132ee | Python | 5,003 | 165 | """Abortable Tasks.
Abortable tasks overview
=========================
For long-running :class:`Task`'s, it can be desirable to support
aborting during execution. Of course, these tasks should be built to
support abortion specifically.
The :class:`AbortableTask` serves as a base class for all :class:`Task`
objects ... |
8770400f84eacca214530e90416da82223ea71e99af44038edbd43dd331f039b | Python | 5,003 | 120 | """
Network Simulations
===================
`RectiPy` provides basic support for numerical simulations of network dynamics.
Neuron models of the RNN layer are governed by differential equation systems of the form
.. math::
\\dot y = F(y, \\theta, t)
With state-vector :math:`y`, parameter vector :math`\\theta`, ... |
c20b627e41b29b359b67abcd9f18af168f2976377f51fe130bbe444ee939cae5 | Python | 5,003 | 146 | import argparse
import os
import torch
import wandb
import schnetpack as spk
from pathlib import Path
from torch.optim import Adam
from schnetpack import AtomsData
from schnet_trainer import Trainer
from schnetpack.train import CSVHook, ReduceLROnPlateauHook, EarlyStoppingHook
from schnetpack.train.metrics import MeanA... |
d314608524da2a40c20cc166b7a02c385dfa04045edf82bf119584572be55e9a | Python | 5,003 | 127 | """Unit tests for larvaworld.lib.plot.ga (GA optimization-progress plotting)."""
from __future__ import annotations
import matplotlib.figure
import pandas as pd
import pytest
from larvaworld.lib import reg
from larvaworld.lib.plot.ga import ga_progress_plot
@pytest.mark.fast
class TestTurnerNoiseParamRegistration:... |
57d7506d2fdb944796bbacdef22b7b52c43accb92982f4a8e7167e37f46eb422 | Python | 5,004 | 137 | """grind-r8 cluster 4.0.8: subprocess grandchildren, arm 2 (R40).
``PR_SET_PDEATHSIG`` protects only the DIRECT child: on a hard parent
SIGKILL the session-leading child dies, but a plain non-detached grandchild
(``sh -c 'sleep &'``, a forking dot plugin) survived with nothing left to
kill its group (sol probe; the gr... |
64303894061f3a9ae178294f0f7500deb0863502f53abb49a7882df79653c7c6 | Python | 5,004 | 160 | """No import runs while the RNG monitor window is armed on a process's first capture.
An import inside the host-nondeterminism monitor window runs the
``sys.meta_path`` finders' ``find_spec`` frames, and the monitor's frame-reachable
inventory walks those frames as roots. A large object graph behind a finder
(pytest's... |
04aa2b69f7b72a43a3fadb7e6c42f7f51ef8bb69e3bfeffbad11df45a8ebdd2b | Python | 5,005 | 187 | """Remote Debugger.
Introduction
============
This is a remote debugger for Celery tasks running in multiprocessing
pool workers. Inspired by a lost post on dzone.com.
Usage
-----
.. code-block:: python
from celery.contrib import rdb
from celery import task
@task()
def add(x, y):
result =... |
2f7aa8f9389e08a48a2d3475f895c88cde095379f9d5e7272ce594b028dedae1 | Python | 5,005 | 120 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Caffe2 to PyTorch checkpoint name converting utility."""
import re
def get_name_convert_func():
"""
Get the function to convert Caffe2 layer names to PyTorch layer names.
Returns:
(func): function t... |
8d6c2e47717602058989199cd57425993e8f5f9bee665b50e9a43a7ad703414b | Python | 5,005 | 173 | """Tests for the internal fastlog predicate orchestrator."""
from __future__ import annotations
import pytest
import torch
from torch import nn
import torchlens as tl
import torchlens._state as torchlens_state
import torchlens.capture.projections as fastlog_state
from torchlens.fastlog.exceptions import PredicateErr... |
6fd02fffdf732df6187313f87f7d50402941608e8acca247b3be15b4d3e083db | Python | 5,006 | 285 | #!/usr/bin/env python
'''Generate models for affinity predictions'''
# variables:
# non-linearity: ReLU, leaky, ELU, Sigmoid, TanH (PReLU not current ndim compat)
# normalization: none, LRN, Batch
# learning rate: 0.01, 0.001, 0.1
modelstart = '''layer {
name: "data"
type: "MolGridData"
top: "data"
top: "l... |
acf52e5a68df96179f2e3bab927ea5ed129a1f3eba7d598614649015b6334d23 | Python | 5,006 | 143 | import numpy as np
from neurogym.core import TrialEnv
from neurogym.utils import spaces
from neurogym.utils.ngym_random import TruncExp
class PostDecisionWager(TrialEnv):
"""Post-decision wagering task assessing confidence.
The agent first performs a perceptual discrimination task (see for more
details ... |
25ac844b254d5627d26143814d031ed6e33dc820dacb213e375b7df0318cfe14 | Python | 5,007 | 170 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Domain(_BaseLayoutHierarchyType):
_parent_path_str = "layout.map"
_path... |
1dbc6d99e08db42f8ca61a9eaf4de80b2497fd176eb818a40ba36b1512cfa7cd | Python | 5,008 | 157 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# For a full list of documentation options, see:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
#
# ----------------------------------------------------------------------------
import os
from os.path import dirnam... |
f5bea83e46faa77a7377e1d72251d802b56f58a18c5a1a2cd15df500faa2518a | Python | 5,011 | 155 | # -*- coding: utf-8 -*-
from __future__ import print_function, division
import mxnet as mx
import numpy as np
from mxnet import gluon, nd
from mxnet.gluon import nn
from mxnet.gluon.data.vision import transforms
from networks import resnet18, resnet34, resnet50
import gluoncv as gcv
gcv.utils.check_version('0.6.0')
f... |
9f688b47c7f532561e187b55da81710e95222fec322da420c120055fe60812fe | Python | 5,012 | 148 | import os
import sys
import imp
from itertools import product, starmap
import distutils.command.install_lib as orig
class install_lib(orig.install_lib):
"""Don't add compiled flags to filenames of non-Python files"""
def initialize_options(self):
orig.install_lib.initialize_options(self)
self... |
4f651d33b849649bc26051a8e264b281dd84ba59a13b46ae8527bda49229ec14 | Python | 5,013 | 123 | from __future__ import annotations
from collections import defaultdict
from typing import Optional
import pandas as pd
from bream4.toolkit.procedure_components.feature_manager import ChannelNotifierState
class SaturationWatcher:
"""Used to watch and record when channels become saturated. Example:
* Instan... |
76c8f41049b73e024fdac74caa894af939fe5fb22ce35fe69a6d09080926cdc9 | Python | 5,013 | 170 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Domain(_BaseTraceHierarchyType):
_parent_path_str = "parcats"
_path_str =... |
992675f6626488a4eae7a2429256432d54a66759e73b7d4e97229db10f8584d9 | Python | 5,013 | 170 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Domain(_BaseTraceHierarchyType):
_parent_path_str = "treemap"
_path_str =... |
f4bcd73395909c5ec38cd1b5c4715f65baa19ad630474540b8f021b9964bc1ed | Python | 5,013 | 120 | """Tests for collect_run_data."""
import os
import pytest
from bids.layout import BIDSLayout, parse_file_entities
from niworkflows.utils.testing import generate_bids_skeleton
import xcp_d.utils.bids as xbids
from xcp_d.data import load as load_data
# Pairs of runs in the sibling_runs skeleton whose names differ onl... |
c8f7ecbcc1d2aac0ea4be1959d8c1811db16877a07935a77725dd78d61dbbd37 | Python | 5,014 | 126 | import torch
from torch import nn
from einops import repeat, rearrange
from survival_plus_x.models.vit import Transformer
def patch_to_img_3d(batch_of_patches, patch_shape, n_patches_per_dim):
"""
Reconstruct a batch of 3D images from the patch representation.
Params
------
batch_of... |
5b6752ce85b9d0aaf1b7f4d89940566928b6c991ef61be36387cf861993e90b8 | Python | 5,015 | 138 | from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.optimizers import optimizer
@keras_export(["keras.optimizers.Lion"])
class Lion(optimizer.Optimizer):
"""Optimizer that implements the Lion algorithm.
The Lion optimizer is a stochastic-gradient-descent method that use... |
c162c0bf5bcbbd9086843b6d67f7add09a4dee869f872ea89064ee8eed281076 | Python | 5,015 | 156 | import sys
sys.path.insert(1, '/u/home/r/ryo10244/Xiao_lab/dsRNA_pred/script/utils')
import re
import pysam
import argparse as ap
import pandas as pd
import numpy as np
from utils import *
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import train_test_split, cross_val_scor... |
33b8603eca87e83eb161204e2f713d96b4f477f736d8bf6c0d3af674239e3ecb | Python | 5,016 | 134 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Configure Eelbrain"""
import multiprocessing
import os
import sys
from matplotlib.colors import to_rgb
from ._utils import IS_OSX
SUPPRESS_WARNINGS = True
CONFIG = {
'n_workers': multiprocessing.cpu_count(),
'eelbrain': True,
'autorun': None,
... |
2a28b768cf825d1478c7313d8b1fde72166c2f8415a612224643ec6f2c1e8b9b | Python | 5,017 | 181 | """S2 capture-spine per-op overhead benchmark."""
from __future__ import annotations
import argparse
import json
import statistics
import time
from pathlib import Path
from typing import Any
import torch
from torch import nn
import torchlens as tl
from torchlens.fastlog import RecordContext
class ThousandOpModel(... |
88b03741d321e2be74e017ddf3a9d63aa6810cb22b9c4983750aedcaf8084ea7 | Python | 5,017 | 132 | import copy
from rdkit import Chem
from rdkit.Chem import Mol
from rdkit.Geometry.rdGeometry import Point3D
from typing import List, Tuple
try:
from ccdc.molecule import Molecule
except:
print('CSD Python API not installed')
class ConversionError(Exception) :
pass
# Mol is a RDKit molecule
# Molecule is... |
4618169be30bc6960f81cf5c677f80dd3a0df7d67380cf3e89ae050c1e7c9283 | Python | 5,018 | 134 | from contextlib import contextmanager
import os
from os.path import dirname, abspath, join as pjoin
import shutil
from subprocess import check_call
import sys
from tempfile import mkdtemp
from . import compat
_in_proc_script = pjoin(dirname(abspath(__file__)), '_in_process.py')
@contextmanager
def tempdir():
td ... |
27da1d543d5ec0d6c3b27f514d01f9442e86b064710737c91e52e37bf8e92aba | Python | 5,019 | 115 | #!/usr/bin/python3
import os
import sys
import argparse
import pandas as pd
version = "0.1.5"
# converts count data to fpkm and tpm values
# needs some mofifications before running ....
# prepare data
# print data frame
def _print_df(mydf, outfile, index_label):
mydf.to_csv(outfile, sep='\t', mode='w', header=Tr... |
c8396cde5c7506caad6ff5551b6d29849b1c2f7aa865a3eb4ebab7b4967addcb | Python | 5,020 | 152 | # 05/24/2023 Fengyao Yan
# This folder file create a deep learning model, train the model and validate the model
# all the data res stored in the data folder in the root
import os
import pickle
import random
import pandas as pd
import numpy as np
import tensorflow as tf
from scipy.stats import pearsonr
from sklearn.p... |
ae01f51460e6151ef747438fe138212bb3dd02a53ae77f2e2f7e90edc87db89a | Python | 5,021 | 108 | import glob
import h5py
import numpy as np
import os
import pandas as pd
from sklearn.linear_model import RidgeCV
from sklearn.model_selection import GroupKFold
from sklearn.linear_model import LinearRegression
from sklearn import preprocessing
import sys
from scipy.stats import pearsonr
"""
This script will run ridge... |
af25fedad2993778097649d8881e8e5584ae9f8e134127eabee55f86d3d4b02c | Python | 5,021 | 158 | import pytest
import inspect
import rpy2.robjects as robjects
rinterface = robjects.rinterface
import array
identical = rinterface.baseenv['identical']
Function = robjects.functions.Function
def test_init_invalid():
with pytest.raises(ValueError):
Function('a')
def test_init_from_existing():
ri_f =... |
b8386ec946450c05f2ad040dab13c8dcf1921225ac5f3a2e7bd94bdd98dc5043 | Python | 5,021 | 116 | """
This script shows the training pipeline for k-fold training, without logging it via wandb.
"""
import tensorflow as tf
import tensorflow.keras as keras
import tensorflow_addons as tfa
from sklearn.model_selection import StratifiedKFold
from tf_spiking.helper import TrainingHistory
from tf_spiking import DenseLIF, ... |
fff162fae7b29b58afe5d34c33547a078aba0b03329a391401bd2cff47989bac | Python | 5,021 | 116 | """
This script shows the training pipeline for k-fold training, without logging it via wandb.
"""
import tensorflow as tf
import tensorflow.keras as keras
import tensorflow_addons as tfa
from sklearn.model_selection import StratifiedKFold
from tf_spiking.helper import TrainingHistory
from tf_spiking import DenseLIF, ... |
8e3379448dfaf7cdb8564dc2577a3e398e37916ee0ec7574db2f34879e0bf1a9 | Python | 5,022 | 166 | from abc import ABC, abstractmethod
import numpy as np
import torch
class SplicingMechanism(ABC):
"""
Represents a splicing mechanism.
"""
@abstractmethod
def predict_motifs(self, rna):
"""
Predict the motifs on the given RNA sequence.
Input: RNA sequence (N,), elements ... |
ca15550cd46407024c2ee551c4d0f188b2ed647b34a3f21b72aabc8eb1bd3c54 | Python | 5,022 | 126 | import numpy as np
from absl.testing import parameterized
from tensorflow import data as tf_data
from keras.src import backend
from keras.src import layers
from keras.src import ops
from keras.src import testing
class RandomGrayscaleTest(testing.TestCase):
def test_layer(self):
self.run_layer_test(
... |
41ddc478a128f9bc61532117e6d6493988022c533f2aaf837763e696bcaf65ba | Python | 5,024 | 207 | # coding=utf-8
# Copyright 2023 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... |
8a6199843fa38a562acca822eecd1a0f1a814753bcbc9d8e84c9050fddbccf4e | Python | 5,025 | 130 | """
Functions for all atom design.
"""
import numpy as np
from copy import deepcopy
from utils.utils import multimer_collate_fn, tree_map, tree_flatten
from helixfold.data import pipeline_aa_utils
MSA_NAMES_0_DIM = [
'aatype', 'between_segment_residues'
]
MSA_NAMES_1_DIM = [
'deletion_matrix_int', 'msa', 'te... |
dd16b26182d3744f511635d925635461012f8f87b5fd431b3d6d382d101a30b6 | Python | 5,025 | 125 | import unittest
import pickle
from os.path import join, abspath
from cantera import Solution
from spitfire import ChemicalMechanismSpec, CanteraLoadError
class MechanismSpec(unittest.TestCase):
def test_create_valid_mechanism_spec_from_xml(self):
try:
xml = abspath(join('tests', 'test_mechanis... |
e5ca6ff38dc9ed983964c1022f6522e6cd2c6fd4625e3acae435e43d876a040b | Python | 5,025 | 142 | from collections import OrderedDict
import numpy as np
import pytest
from gym.spaces import Dict, Tuple
from gym.vector.utils.numpy_utils import concatenate, create_empty_array
from gym.vector.utils.spaces import BaseGymSpaces
from tests.vector.utils import spaces
@pytest.mark.parametrize(
"space", spaces, ids=... |
e69a75a116a05c089c0574dd82cce319fc65fd931da284e7bf457d33914f87ea | Python | 5,025 | 163 | import numpy as np
def encode_domains(X, y, domain):
r"""Encode the domains of the matrices in the labels.
We handle the possibility of having different domains for the datasets by
extending the labels of the matrices and including this information to
them. For instance, if we have a matrix X with cl... |
3c5ec708c4317119481ee576ec982d79fbdd9b2271f6ae74ffb76337abab69b8 | Python | 5,027 | 155 | # copyright (c) 2021 PaddlePaddle Authors. All Rights Reserve.
#
# 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 applica... |
f77818d482e443b02ca07a758baf95d123bee96e1dbc998dacf974f43de2e1da | Python | 5,027 | 150 | #!/usr/bin/env python3
import numpy as np
from scipy.spatial.distance import squareform
"""
Dec-16-2021 by Guo Jiahui and Ma Feilong
This script contains functions to read RDMs and masks.
All RDMs are in the vectorized upper triangle format, i.e., the output of `squareform`.
For example, the vectorized upper triang... |
5812e088c8fe6c9f80297849b9a6d17622b9959588cc68184e8f8b7686664a5c | Python | 5,029 | 159 | """
Top-level Galaxy job manager, moves jobs to handler(s)
"""
import logging
from functools import partial
from typing import (
TYPE_CHECKING,
Union,
)
from galaxy.exceptions import (
HandlerAssignmentError,
ToolExecutionError,
)
from galaxy.jobs import (
handler,
NoopQueue,
)
from galaxy.str... |
93b4fd0b37984793d94abd0c8d256f16ceb3a5f9196a5f41ae5f31bbebcfa579 | Python | 5,029 | 197 | """Internal state.
This is an internal module containing thread state
like the ``current_app``, and ``current_task``.
This module shouldn't be used directly.
"""
import os
import sys
import threading
import weakref
from celery.local import Proxy
from celery.utils.threads import LocalStack
__all__ = (
'set_defa... |
523c99ec8c5019fd6bdea0a82a8c2508dedb98e61e792641861c2b47e7bbb7c4 | Python | 5,030 | 170 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Domain(_BaseTraceHierarchyType):
_parent_path_str = "sunburst"
_path_str ... |
18494e47502edf88dc7b6625bf1c560e4a0451cada22c10d538a02f3d3a1f1df | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
327eb3fe5413379d411974633fbd8f68813abbbc59885d0fc412add8e873430f | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
41802cd7099ccd75e9c82060c4e89a3b08e7fec05b7b3a4690842cc961eab8f4 | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
446b3036a69e6a8327a3e1cdb3fe72d10d0aa1f2c4f4fb3ad350e23a65882c8a | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
4da28cab9e8edf0363a62212f8afb34ee3809101aecff41c9b1aeee0695a5771 | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
515cd5dd812914c0e5084069f2538f4d06fa9d4d2edcbb547fc3f02af1a2d926 | Python | 5,031 | 124 | # General imports
import os
import glob
import sys
import torch
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import pytorch_lightning
from tqdm.auto import tqdm
# EUGENe imports and settings
import eugene as eu
from eugene import models, evaluate, settings
from eugene.mo... |
9792ff186e7fee37107b786d8047260e6eef07b5c4e229940f4fecc7510c6ccc | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
c22e70a16af4b22c5ea7e1320a3b0932f63910f20300d56efaee3db6f8a99281 | Python | 5,031 | 119 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
14d248f00d6f9e3e301ef76ce5b1a8b5e9de54f6cdf6bb19aa369b26269c8008 | Python | 5,032 | 132 | """A09 agent stage-0 item 1: the composed lazy-payload honesty gate.
Record-shaped AND memory-shaped acceptance (the agent memo P0's exact
demand -- record-shaped tests alone are how the silent-None bug shipped):
- ``.out`` on a lazily loaded trace materializes one sha-verified blob or
raises typed ``PayloadUnavail... |
566e024145a0863ca10f947ced7f213ab68f686bd34402990892cd2c4db5055f | Python | 5,032 | 133 | import os
import sys
from argparse import ArgumentParser
import torch
import torchvision.transforms as transforms
from monai.networks.nets import UNet
from torch.utils.data import DataLoader
import utils.data_transforms as data_transforms
from utils.datasets import DiffusionDataset
from utils.epoch_cycle import run_c... |
b5b3afd2b75252699b255faedbb471b0946f402add5150366c1cc9f292d6aba9 | Python | 5,032 | 120 | #!/usr/bin/env python
# -*- coding: ascii -*-
__doc__ = """
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on perceptual decisions. J Vis, 14(7): 9.
See Copyright notice below
Copyright (C) 2014 Ingo Fründ
This code reproduces the analyses in the paper
... |
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