sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d403610ded9c2e4d3007992ad38dceed8bec64886ca3755a09e1c0b090ed324a | Python | 1,937 | 62 | # Node group "Hydrogen Bonding Partner" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are... |
8f968b33d6bdc12c7a787d68cb8ef7a12909d3684658da6d065568e2cd60ff7d | Python | 1,938 | 71 | """
pygments.filter
~~~~~~~~~~~~~~~
Module that implements the default filter.
:copyright: Copyright 2006-2023 by the Pygments team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
def apply_filters(stream, filters, lexer=None):
"""
Use this method to apply an iterable of filter... |
c3930e5c436c42ab0f72ce2daa3ddf1a7fd22a64ff11849c0bef81a081e2b271 | Python | 1,938 | 62 | from setuptools import setup,find_packages,Extension
from setuptools.command.install import install
import numpy as np
import os
# read the contents of your README file
with open('README.md') as f:
long_description = f.read()
print(long_description)
class CustomInstallCommand(install):
def run(self):
pr... |
5fb47a19e0187248d6513d618b080b9019aef04ef611af60a178a0eb93a5128f | Python | 1,939 | 73 | import numpy as np
import sklearn.utils.linear_assignment_ as la
from sklearn.metrics import accuracy_score
from sklearn.metrics.cluster import normalized_mutual_info_score
from sklearn.cluster import KMeans
def best_map(l1, l2):
"""
Permute labels of l2 to match l1 as much as possible
"""
if len(l1) ... |
90d5901864fd97211702cfba1e5356564be9ec41d69207130ae025b248d0b970 | Python | 1,939 | 72 | from .basic_euclidean import eucl_dist
import math
import numpy as np
PI = math.pi
HPI = math.pi / 2
def ordered_mixed_distance(si, ei, sj, ej, siei, sjej, siei_norm_2, sjej_norm_2):
siei_norm = math.sqrt(siei_norm_2)
sjej_norm = math.sqrt(sjej_norm_2)
sisj = sj - si
siej = ej - si
u1 = (sisj[0]... |
e7c7519db1f5a33c52c8c46082999be1b7f92dc1b39cc154ab28d5d506ad3017 | Python | 1,940 | 64 | import unittest
from torcheeg.datasets import DTUDataset, DTUProcessedDataset, KULDataset, KULProcessedDataset, AVEDDataset, AVEDProcessedDataset
class TestAuditoryAttention(unittest.TestCase):
def test_dtu_dataset(self):
kwargs = {
'record': 'fake_record',
}
kwargs.update(DT... |
fb73a89e504b8fd61e6d9c293962f770b965ed28a68a651b387d2566a21e2005 | Python | 1,941 | 70 | import pytest
import elasticai.creator.ir2torch as ir
from elasticai.creator.experimental.ir.shape_inference import (
IrShapeInference,
Shape,
get_default_shape_inference,
)
factory = ir.IrFactory()
@pytest.fixture
def infer_shape():
infer = get_default_shape_inference()
@infer.register_node()
... |
a6008ef65eefda745caa668d8c500bd746aa3acb4e478c1d0480553be05079d8 | Python | 1,942 | 57 | import torch
import torch.nn.functional as F
from torch import nn
from ..operators import ACSConv
class _EncoderBlock(nn.Module):
def __init__(self, in_channels, out_channels, dropout=False):
super(_EncoderBlock, self).__init__()
layers = [
ACSConv(in_channels, out_channels, kernel_size... |
04f0948743e8de7f819eb2d015f043ffef4ff221cf02da60194f53f86992cfcd | Python | 1,943 | 66 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import itertools
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterP... |
6c7ad618bd4d1030abdde34ff75a567ca1f1ee7af716e8e226269be0a41746ce | Python | 1,944 | 66 | from __future__ import print_function,division
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
"""
self.layers = nn.Sequential(
# input is Z, going into a convolution
nn.ConvTranspose2d( nin, ngf * 8, 4, 1, 0, bias=False),
nn.BatchNorm2d(ngf * 8),
activation()... |
9a7102b735e88e2901a93f903a60b43a56a88b522d63e8a22b04583270a0d815 | Python | 1,944 | 66 | #!/usr/bin/python
# -*- coding:utf-8 -*-
from torch import nn
import warnings
# ----------------------------inputsize >=28-------------------------------------------------------------------------
class CNN(nn.Module):
def __init__(self, pretrained=False, in_channel=3, out_channel=10):
super(CNN, self).__i... |
3dee174d8635dd1160ee40d85538939f1e8a38a320d155d74f479cdde5f77148 | Python | 1,945 | 70 | # Node-group asset "MN Color" (ShaderNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKING
from b... |
9c9da1e27fc5bf841d93421e5e46f64bf813d9d503a395f68f414f7c1bd6d8b5 | Python | 1,945 | 77 | # Node-group asset "Angstrom to World" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHEC... |
b47baefcfd4e9f02aacf48c38269786dcf63eaae90d49aef6ece4e0783e7298d | Python | 1,945 | 55 | from unittest import TestCase
from unittest.mock import patch
from codex.service.network import compile_network_html
from tests import get_testing_neuron_db
class ConnectivityTest(TestCase):
@classmethod
def setUpClass(cls):
cls.neuron_db = get_testing_neuron_db()
def test_full_network_generatio... |
05623a1f42f2495841e06b320d610828509674973c7793da566c868bea439d08 | Python | 1,946 | 62 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
3e7b5a97d25c7e8633c9da9d2cd2c4776afbc62178de7f7abc79c5eafee9584a | Python | 1,946 | 66 | import pytest
@pytest.fixture(scope="module")
def _qapp():
try:
from PySide6.QtWidgets import QApplication
except Exception as exc: # pragma: no cover
pytest.skip(f"PySide6 unavailable: {exc}")
return QApplication.instance() or QApplication([])
def _patch_git(monkeypatch):
... |
98075ed17e978bc6ff32642d236a7d845c4a0420d7a1d3f634ff25ff46c640f3 | Python | 1,946 | 57 | from typing import Any, cast
from elasticai.creator.arithmetic import FxpArithmetic, FxpParams
from elasticai.creator.base_modules.prelu import PReLU as PReLUBase
from elasticai.creator.nn.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.fixed_point.math_operations import MathOperations
from... |
b71b3eb803fcc82e7d6e3ccaab9eeac6e2004b8ceec3670b53e5aa099ba4f005 | Python | 1,947 | 40 | # Copyright (c) 2021, Ko Sugawara
# 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 conditions and t... |
eeb565bd1c781d64fcada3fc6237359b2f2e1edcae6136ce803fe792e1522ac7 | Python | 1,947 | 74 | import sys, os
import numpy as np
from collections import Counter
import pandas as pd
import pysam
### Initialize ###
try:
inputBamFile = sys.argv[1]
except:
sys.exit('Please, give input bamfile')
if not os.path.isfile(inputBamFile):
sys.exit('bamfile not found')
bamfile = pysam.AlignmentFile(inputBamFi... |
5bc5d9a3d0cfeaa64c961940c5a1f4a20804a3c29cda341de322ab311dc396cf | Python | 1,948 | 62 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
708c1f5bdf43ac1da94ee921e93cbe4354ab2c9f22820829ae6c3b2d5ba19860 | Python | 1,948 | 62 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
bda86acd0a40b9ea338d082ca84942cdb96140ce162ae35265e665bf91024143 | Python | 1,948 | 61 | # coding=utf-8
# Copyright 2026 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... |
cb378254c50760b7b864e235f289089754ab57550227aa0222ab22ddad735163 | Python | 1,948 | 70 | '''
Description:
Prepare data for PRESCIENT model.
Codes are adopted from PRESCIENT source codes.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
Reference:
https://github.com/gifford-lab/prescient/blob/master/prescient/commands/process_data.py
'''
import numpy as np
import sklearn
import umap
import tor... |
eba7eb22452a01675bd1921d26dc4b7ac3acc620c3877b87285de8a39efb7da2 | Python | 1,948 | 62 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
87fc557a76ec721fad89d601d5ee536ff471defa5935a71a83cf69860bd68c79 | Python | 1,949 | 62 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
f9d3315e5f091d5d6c54e300669f416d99888823ff74d29274a4762ceee0790c | Python | 1,949 | 69 | """Shared I/O utilities for workflow scripts."""
import glob
import pathlib
import pandas as pd
from tqdm import tqdm
def load_files(dirname):
"""Load CSV result files from a directory or list of paths.
Parses parameter key=value pairs encoded in filenames (separated by '~').
Parameters
----------
... |
34c315b686d220712cf9b5ab2bb6da1fbc30fc7b665a503a72303f32898cb048 | Python | 1,950 | 59 | #%%
import numpy as np
import ants
import matplotlib.pyplot as plt
import os
import glob
from PIL import Image,ImageFilter
#%% preprocessing
tmp_ind = 3
savename = 'target.png'
# input file
img_files = glob.glob('input*.png')
# split channel red for input.
img_list = [ants.from_numpy(np.asarray(Image.... |
1e2b2566caff35e60913509cff27395cb7734638ab511b3ca5cbff817293a0a8 | Python | 1,951 | 40 | """Pure metric helpers of the attractor diagnostic (no model)."""
import numpy as np
from liquidaion_fly.attractor import (answered, default_conditions, detect_period, js_divergence,
kl_divergence, repeated_ngram_fraction, text_similarity, transient)
def test_period_detection_di... |
2fec023cfeaee2bfd277ea5090a63400455be42711cb8ab9c53af5a84a033f01 | Python | 1,951 | 59 | '''
Description:
Compute testing data distribution shift based on l2 distance.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import numpy as np
from benchmark.BenchmarkUtils import loadSCData, tpSplitInd, splitBySpec
# ======================================================
from scipy.spatial.distance impor... |
14f324b08e192f42bf98f5a0db1d1456e23da79b2e6c70251d71ec14042e65d8 | Python | 1,952 | 60 | from cloudvolume import CloudVolume
image_in = 'gs://neuroglancer/pinky100_v0/image_single_slices'
image_out = 'gs://neuroglancer/pinky100_v0/aligned_test_v12'
image_mip = 0
roi_in = 'gs://neuroglancer/pinky100_v0/image_single_slices/roicc'
roi_out = 'gs://neuroglancer/pinky100_v0/aligned_test_v11/roicc'
roi_mip = 6
c... |
c3e580afa1c701f862a929a06bcdaefae20ca4d39f1e7875b28abaeac3cf61b4 | Python | 1,952 | 53 | #------------------------------------
#----- CLEAN/GENERATE DATASETS -----#
#------------------------------------
import pandas as pd
import numpy as np
import scipy as sp
from utils import *
# read in matlab data files from: https://github.com/hhcho/hyplinear
def load_mat_file(path):
# load .mat files with gaussi... |
4c9778ca5c59d34d420a6cecadd20c311d9252dbc8aac133c0bbe2ca84bb7721 | Python | 1,953 | 49 | import unittest
from types import SimpleNamespace
from unittest.mock import patch
from torcheeg.utils import LazyLoader
class TestLazyLoader(unittest.TestCase):
def test_import_is_deferred_and_cached(self):
module = SimpleNamespace(value=42)
with patch('torcheeg.utils._import_module', return_valu... |
0b7dffb5336a379cc9a646d7c9006b26eabc251c265e71ceadda7c05e87e668e | Python | 1,954 | 53 | # coding=utf-8
# Copyright 2026 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... |
737d6e4fc431c8df4a11cd9e7b8bb3e6e0f1dabcd86a80883a19dad532867feb | Python | 1,954 | 58 | import glob
import numpy as np
import os
import pickle
import matplotlib.pyplot as plt
from src.SIRE.SIRE_filter import ProcessSIRE3DImage
from src.dijkstra.shortest_path import ExtractPaths
def main(data, **params):
SIREFilter = ProcessSIRE3DImage(**params["SIRE_filter"])
PathExtractor = ExtractPaths(**param... |
9e91b797d93711db279fc33dd42cf90d36a248141f24e5d9a207e882e25f7e49 | Python | 1,954 | 63 | import numpy as np
import h5py
import modisco
import h5py
import click
@click.command()
@click.option('--input',
'input_file',
required=True,
type=click.Path(exists=True, readable=True),
help='h5 score file of ism')
@click.option('--output',
'outpu... |
8d36f695c6511c286acf3e10b757f877b3ad10b1f48785c14319e47b35ce15d5 | Python | 1,955 | 53 | from ETL.Extract.extract import extract_sidecar_data
from ETL.Transform.transform import transform_sidecar_data
from ETL.Load.load import load_sidecar_data, database_setup
from ETL.PostTransform.post_transformation import update_subject_ids, update_transformation_id, backpropation
import logging
# Main Workflow funct... |
c521809dd05e5041c885e73eff38a47a0f1530b4f1612a55d429593cd4ce2919 | Python | 1,955 | 58 | # flake8: noqa
# There's no way to ignore "F401 '...' imported but unused" warnings in this
# module, but to preserve other warnings. So, don't check this module at all.
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
3b10b8ac73dffa818b67bd06bc3fb894dd28011b67f906375212442b96057c9a | Python | 1,956 | 54 | hitScoreM = [0, 0, 0.014, 0, 0, 0.395, 0.317, 0, 0.389, 0.079, 0.445, 0.508, 0.613, 0.851, 0.732, 0.828, 0.615, 0.804,
0.685, 0.583]
def calcMitScore(string1, string2, startPos=0):
"""
The MIT off-target score
see 'Scores of single hits' on http://crispr.mit.edu/about
startPos can be used ... |
77181fd114339c201c0504b44ef5fd3db1afe24cd07fbaff00f527898e86f37c | Python | 1,956 | 48 | ############################################################
# This file plots the results from ISC as computed by the #
# ISCToolbox (Kauppi et al., 2014) for the pilot_iii data. #
# #
# author: ana.trianahoyos@aalto.fi #
#################################... |
c3890002fa9beca53112fa057e812c111f80c290988f142180fc2f2f8f855a87 | Python | 1,956 | 66 | # coding=utf-8
# Copyright 2026 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... |
940c197f9b4c038da2d75cb58f4874db9615108e0d88047cb7eefddc5ce00732 | Python | 1,957 | 71 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Demonstrate usage of LFPy.NetworkCell with a ball-and-stick type
morphology with active HH channels inserted in the soma and passive-leak
channels distributed throughout the apical stick. The corresponding morphology
and template-specification is in the files BallAndStic... |
c7514b15d8707c0cfd36cb363c7cdd12511c26ebf57af7cf61b02a8962048b1e | Python | 1,958 | 95 | from __future__ import annotations
from pathlib import Path
from typing import Any
_SEPARATOR = "=" * 72
def _technical_record_dir(output_dir: str | Path) -> Path:
output_dir = Path(output_dir)
technical_record_dir = output_dir / "Technical_Record"
technical_record_dir.mkdir(parents=True, exist_ok=Tru... |
f3bf9b3002e9b6600e329f1cedaaeb9134c7ba2616a8689f8730a5712a200e5f | Python | 1,958 | 27 | """posthoc_cutout_per_side_2026-10-02.py (post hoc, after seeing the whole-brain per-side split). On the antennal-lobe cut-out
(spiking, 50 channels, 3 trials, seed 11 as DAMPING_SOURCE), read the left v2LN30's flip side by side: how much of the
cut-out's larger effect is the other side? Output: 06-OUTPUT/posthoc_cut... |
32f904753f1841ba693b8b63343b3b2947b1c8f90959725474ed4bd2071e5e46 | Python | 1,959 | 66 | # coding=utf-8
# Copyright 2026 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... |
545e000faa25edb358d1ea488277077ca9dae610cd849e1c48d17ba4e84f2cad | Python | 1,959 | 61 | from typing import Dict, List, Union
from ..base_transform import LabelTransform
class Select(LabelTransform):
r'''
Select part of the value from the information dictionary.
.. code-block:: python
from torcheeg import transforms
t = transforms.Select(key='valence')
t(y={'valenc... |
8a885e06cbb62f2129748080c36fbb575e7c595d10d3a75d9bb6f08b07868c6c | Python | 1,959 | 68 | import torch
import torch.nn as nn
import torch.nn.functional as F
from segm.model.utils import padding, unpadding
from timm.models.layers import trunc_normal_
from torch.distributions import Categorical
class Segmenter(nn.Module):
def __init__(
self,
encoder,
decoder,
n_cls,
... |
a524dded8c58479410726810c549fd2aaeb09baf1a16274784998178142655a5 | Python | 1,959 | 48 | import os
from typing import Dict, Union
import pandas as pd
from ..utils import get_random_dir_path
from .utils import ensure_cache, validate_metadata
class BaseModelSelection:
r'''Common initialization, checks and cache access for dataset splitters.'''
def __init__(self, split_path: Union[None, str] = No... |
e862bddf230d65b6d2012f016c42b7612350e4674b707fb3210128bd60671555 | Python | 1,959 | 55 | """
Test functions for snapping coordinates
calling:
python test_snap_coordinates.py <subject>
will plot the original and snapped coordinates for that subject
"""
from snap_coordinates import *
import mayavi.mlab
def plot_coordinates(coordinates, color=(0,1,0)):
"""
Plots a set of coordinates in 3d space
... |
3637c8e9b6cb83b6efd0a6cb68dc06dbe99f070c34fcc9697bf2365a83a3c976 | Python | 1,960 | 46 | # SPDX-FileCopyrightText: 2024 Blue Brain Project / EPFL
#
# SPDX-License-Identifier: AGPL-3.0-or-later
'''
Compute average complexity across (maximal simplices) for all connectomes and their controls.
Runs quickly, can be run interactively.
Author(s): Daniela Egas S.
Last updated: 01.2024
'''
import pandas as pd
im... |
cf4850a075214c7a770cc508f4f78a2fa3123bd2afc5c34afd0daf412ca0a332 | Python | 1,960 | 80 | import os
import sys
import matplotlib.pyplot as plt
import numpy as np
import meep as mp
from meep import mpb
examples_dir = os.path.realpath(os.path.dirname(__file__))
sys.path.insert(0, examples_dir)
def tri_rods():
# Import the ModeSolver defined in the mpb_tri_rods.py example
from mpb_tri_rods import ... |
d4a4eb0332b877bc0acfcf1ef76a5aca96766518a7f1c7f3182d1040eece2151 | Python | 1,960 | 58 | import json
import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
from src.analyze.utils import init_mpl
from src.analyze.performance_measures import PerformanceMeasures
from constants import ABSOLUTE_ERROR, ERROR_TO_LABEL
_FIG_SIZE = (8, 4)
colors = init_mpl()
def make_plot(results_dir,... |
eb7446d74c3ef9e4e9176a81c42b4e0121b46229c9364818aa1e4c10b3e8b744 | Python | 1,961 | 59 | import pytest
import numpy as np
@pytest.fixture(scope="session", autouse=True)
def set_seed():
np.random.seed(42) # noqa: NPY002
import logging
from ase.io import read
from quacc import get_settings
from pathlib import Path
from ts_workflow_examples.geodesic_ts_without_hessian.using_mace import geodesic_ts_no... |
12f812f89cf7b361942fad5294bec0500710892499a2e147e39af3140129ae74 | Python | 1,962 | 54 | from collections.abc import Iterator
from typing import cast
import torch
from elasticai.creator.nn.design_creator_module import DesignCreatorModule
from elasticai.creator.vhdl.design.design import Design
from .design import Sequential as _SequentialDesign
class Sequential(DesignCreatorModule, torch.nn.Sequential)... |
ed6e715229ed4bd69e4d91826a294dc0f7df57aa8e19f2b8251fb2d20bb163ec | Python | 1,962 | 69 | """ Changs's method
{chang2005automatic,
title={An automatic method for estimating noise-induced signal variance in magnitude-reconstructed magnetic resonance images},
author={Chang, Lin-Ching and Rohde, Gustavo K and Pierpaoli, Carlo},
booktitle={Medical Imaging},
pages={1136--1142},
year={2005},
organization={Interna... |
0aee615a3f6d8c50ba673765558987047b21ccd070feb950d788354374d5a6e9 | Python | 1,963 | 68 | ##
# \file data_reader_test.py
# \brief Unit tests for data reader
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date January 2018
import os
import unittest
import numpy as np
import re
import SimpleITK as sitk
import pysitk.python_helper as ph
import niftymic.base.data_reader as dr
from niftymic.de... |
0c9d544ec3073f30565e1b39d5328d462c6734d5df45bb8e519e628573319da0 | Python | 1,963 | 68 | """Pure unit tests for --reg_effort emission from build_registration_cli_args.
Qt-free; mirrors test_registration_cli_args.py.
"""
from regtools.registration.gui.cli_args import build_registration_cli_args, RegistrationOpts
def _args(**kwargs):
return build_registration_cli_args(RegistrationOpts(**kwar... |
78186e67d95d4494b7223341bb80f5e75a64941b0ba9a64d7ab74bd099d35c4d | Python | 1,964 | 72 | ##
# \file installation_test.py
# \brief Class to test installation
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date October 2017
# Import libraries
import unittest
from nipype.testing import example_data
import niftymic.base.stack as st
import niftymic.registration.flirt as flirt
import niftymic.... |
23376573309c96a0da401dbb7794ff6fb44d3293bb0af08884a2e617ef757a82 | Python | 1,965 | 72 | import imp
import numpy as np
import pandas as pd
import axelrod
process_data = imp.load_source("processe_data", "src/process_data.py")
def test_strategies_properties():
df = process_data.get_strategies_properties()
assert isinstance(df, pd.DataFrame)
assert len(df) == len(axelrod.strategies)
for... |
36ff577699cb71875edd578ca6dc0f8740916040c75ada4e871dbf0a09b58cab | Python | 1,965 | 52 | import unittest
import numpy as np
import torch
from torch_geometric.data import Data
from torcheeg.datasets.constants import DEAP_ADJACENCY_MATRIX
from torcheeg.transforms import ToDynamicG, ToG
class TestPyGTransforms(unittest.TestCase):
def test_to_g(self):
eeg = np.random.randn(32, 128)
tran... |
6aa427ae421738a4776a630dabf343065a2f3621c59a83d3a5ac54169a36a19e | Python | 1,965 | 43 | """Keyboard shortcut overlay text for the CCF boundary editor.
Kept as plain HTML in a separate module so the (long, drift-prone)
help block doesn't bloat viewer.py and so it can be edited / proof-
read independently. Imported by the viewer; not used elsewhere.
"""
from __future__ import annotations
SHORTCU... |
8dc18d3e2ddda44242a3ec8d2134c625d39a13ab088765bbcf7f6ecc62f39f63 | Python | 1,965 | 68 | # Node-group asset "Cumulative Length" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHEC... |
948d82a19931e16bcc873332660b76ef7a339c2d577174ac59a2cee5507b714d | Python | 1,965 | 73 | import os
import hostlist
from pathlib import Path
import torch
import torch.distributed as dist
import segm.utils.torch as ptu
def init_process(backend="nccl"):
print(f"Starting process with rank {ptu.dist_rank}...", flush=True)
if "SLURM_STEPS_GPUS" in os.environ:
gpu_ids = os.environ["SLURM_STEP_... |
0f73b5a41c6b299f950e36086d125fc820638d0b6165ad8df03a1038704869c0 | Python | 1,966 | 53 | import unittest
import numpy as np
import torch
from torcheeg.transforms import (after_hook_normalize, after_hook_running_norm,
after_hook_linear_dynamical_system,
before_hook_normalize)
class TestHooks(unittest.TestCase):
def test_before_hook(s... |
10ee9cab0bd393e8003c7d17026831d18f76861c2c7ad7c016864034467bd16a | Python | 1,966 | 62 | import torch
import numpy as np
class Coord:
idx2glb_scale = None # (w,h,d)->(x,y,z)
idx2glb_trans = None # (w,h,d)->(x,y,z)
@ staticmethod
def idx2glb(idx):
# (d,h,w)->(w,h,d)
if type(idx) is torch.Tensor:
is_tensor, device = True, idx.device
... |
25a065490bec31573663e1690db8c71bec00c7af07f3a4fb2fb76fc2b05e4c8c | Python | 1,966 | 49 | from elasticai.creator.arithmetic import (
FxpArithmetic,
FxpParams,
)
from elasticai.creator.base_modules.hard_sigmoid import HardSigmoid as HardSigmoidBase
from elasticai.creator.nn.design_creator_module import DesignCreatorModule
from .design import HardSigmoid as HardSigmoidDesign
class HardSigmoid(Desig... |
2e7426e37c76063eff919ec0adf17edd25c0ce178782c1d5fddc88d63229de16 | Python | 1,966 | 62 | import torch
import torch.nn as nn
import torch.nn.functional as F # noqa
__all__ = ['shallow_cnn']
class ShallowCNN(nn.Module):
def __init__(self, dropout, n_outputs):
super(ShallowCNN, self).__init__()
# setup layers
self._conv1 = nn.Conv2d(1, 32, kernel_size=(5, 5))
self._co... |
3270feaa8b7beeaef1938d071c8696b7994be1d5f1744e9f26aa9981b00fd1a5 | Python | 1,966 | 87 | # coding=utf-8
# Copyright 2026 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... |
34bd965d0d64a08467793232b88b7d2dbe7cc86947ddc89ae829e0a2ed1a5405 | Python | 1,967 | 60 | import time
import threading
import numpy as np
class ADC:
def __init__(self, queue, is_values):
self.queue = queue
self.is_values = is_values
self.t0 = time.time()
for i in range(5):
self.queue.put(['measure','adc'])
time.sleep(1)
... |
63f61a10284704ed0c88bd4cc005d123949df1170005dedd2e1ec3569388c5f8 | Python | 1,967 | 57 | from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.vhdl.auto_wire_protocols.port_definitions import create_port
from elasticai.creator.vhdl.design.design import Design
from elasticai.c... |
b836d9df13c4df3d3bff17dbf7b3458cf4168a8e46c643d71e049e9b2565bc46 | Python | 1,967 | 75 | import socket
import _thread
import sys
import os
from protonet_score import PretrainedProtonetDistScore, \
load_image_path, load_image
cache = {}
model = PretrainedProtonetDistScore(os.path.dirname(os.path.realpath(__file__))
+ "/results-OM/best_model.pt")
def eprint(*args, **kwa... |
d107d6f6aaf0db5110f80ba87b1fcd20bcf3e0391c83971154f56b0c0bebbbbf | Python | 1,967 | 56 | from typing import Any, cast
from elasticai.creator.arithmetic import (
FxpArithmetic,
FxpParams,
)
from elasticai.creator.base_modules.linear import Linear as LinearBase
from elasticai.creator.nn.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.fixed_point.linear.design import Linear... |
ef68d66485ebc681a7ec7e794035cda48a8f597e0ee7d9576c043f05fe6c7876 | Python | 1,967 | 51 | """Opt-in per-generation inference log capturing the exact model inputs.
Levels:
summary - counts, stop reasons, cache/hook/trim events and SHA-256 digests only;
no conversation text or token ids leave the process.
full - additionally the rendered chat template, input token ids, decoded
... |
03403dc05b9dbffe3f6c05002a2765c17841c635386df61c73f665ac7682e0ea | Python | 1,968 | 65 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
154161319cc6931f4c6e8468eddfd9b3da00f14ee5108b7234a52bf56f38892c | Python | 1,968 | 112 | pres_dose = {
'zzzCFPatient00': 50.4,
'zzzCFPatient01': 54
}
dic_gamma = {
'name': [],
'noise': [],
'valid_gammas': [],
'pass_rate': [],
'mean_gamma': [],
'T2_gamma': [],
}
dic_roi = {
'name': [],
'noise': [],
'valid_gammas': [],
'pass_rate': [],
'mean_gamma': [],... |
4a8e263e84a35e45e2487893cf3aae1f7555c950ff9e35e51c9484c583d7028c | Python | 1,968 | 68 | import functools
from typing import Callable, Generator, Iterable, Iterator, Optional, Tuple
from pip._vendor.rich.progress import (
BarColumn,
DownloadColumn,
FileSizeColumn,
Progress,
ProgressColumn,
SpinnerColumn,
TextColumn,
TimeElapsedColumn,
TimeRemainingColumn,
TransferSp... |
876730dd1258bd84b891bb9bc4445dbc888446e2668b29a04d4206f3cd18a8ac | Python | 1,968 | 61 | # coding=utf-8
# Copyright 2026 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... |
ce77336e42882fa60f07ce36da5cbad8ba048974e68482bf050f7b1be97dc19c | Python | 1,968 | 67 | import re
from collections.abc import Iterable
from typing import Any
import pytest
import elasticai.creator.plugin as p
import elasticai.creator.plugin.plugin_spec as ps
def test_importing_plugin_with_missing_fields_raises_meaningful_error() -> None:
config_from_file = {
"api_version": "0.1",
"... |
cfce2110522322c9b25792b1094b4882de52d0c5fdd424891b9c79c38a04b3f5 | Python | 1,968 | 57 | import numpy as np
import matplotlib.pyplot as plt
import nibabel as nib
from matplotlib.colors import ListedColormap
import argparse
def overlay_slices(image_path, mask_path):
# Load the NIfTI image and mask
image = nib.load(image_path)
image_data = image.get_fdata()
image_data[image_data >200] = 200... |
10ffa74e350856f893b9d6245bc143d219affae765286491c855250295e56cd3 | Python | 1,969 | 52 | """ Compute modulation spectrum of the stimuli according to Ding et al. (2017). """
import brian2hears as b2h
import brian2 as b2
import numpy as np
import pandas as pd
from pathlib import Path
from helpers import load_config
from speech_utils import compute_modulation_spectrum
if __name__ == '__main__':
config ... |
44bba9ece1a436f7e1c3ba7cb34840064481f1b0ea022516e828b03a4496f81f | Python | 1,969 | 58 | #!/bin/env python3
'''
Define a Feynman diagram
'''
import pdlfeynman as fy
import yaml
diagram = fy.diagram.Diagram()
x = 1
time = 470
n00 = fy.diagram.Node.Reaction(time=time, reaction=fy.particle.growth.pair_production)
diagram.add_node(n00, x=x, y=0)
x += 1
time = 478
n10 = fy.diagram.Node.Reaction(time=time, re... |
58eb37193ea026655214eea9eba43531c9cd384091763dc3e20f43d84ae30c71 | Python | 1,969 | 67 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import itertools
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterP... |
c05713ad3d73a642447d6b38ed9723ebbefe08cfc072f54778455f051e4aca67 | Python | 1,969 | 66 | #!/usr/bin/env python3
import os
import pandas as pd
from nilearn import masking as nmask
# ------------------------------------------------------------------
# Create group mask across subjects for HCP 7T movie data
# ------------------------------------------------------------------
# base directory of HCP 7T data
... |
2a689c1d14d2b5bedeceb4963d0157d40d379a5ded241a93a48ecd19939cff8d | Python | 1,970 | 59 | import numpy as np
import networkx as nx
import sys
sys.path.append('../Model/ES/')
sys.path.append('./MouseBrainLib/')
import networkx as nx
from ES_Adaptive import ES_Adaptive
from DataUtils import DataUtils
class MBN_No_RC(ES_Adaptive, DataUtils):
def __init__(self,
nepochs=10000,
... |
061572d5975e8715cceeb1a9843bfdcc933a160832bb236e7961d0b49d6cf674 | Python | 1,971 | 35 | # 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
#
# ht... |
19a62188a431754b10f610a5f3a5cede51cf70f135147abbbc4ef633d1e72a9d | Python | 1,971 | 86 | import dataclasses as dc
import dataclasses
from jax import tree_util as jt
import yaml
# import torch
def register_jax_dataclass(cls):
"""Registers a dataclass as a JAX pytree."""
if not dc.is_dataclass(cls):
raise TypeError('%s is not a dataclass.' % cls)
keys: float = [field.name for field in dc.fields(cls)]... |
2b2d05b1a8c90946e676911fc1e6a368602f7b15c0902e98b8256a6ff151471d | Python | 1,971 | 64 | # 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 os
import subprocess
import pytest
from pathlib import Path
notebook_dir = Path(__file__).parents[1] / "examples"
notebook_fns = noteb... |
35507ae8628647249df9aebc11f171f4d245f6a754aba23817ee208ba5098ca5 | Python | 1,972 | 40 | # 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
#
# ht... |
8b703c2d5a821f101bd71f8d56262454886fcdebc223a65ebc83595f6147797a | Python | 1,972 | 66 | #!/usr/bin/env python
import os
import glob
import torch
from torch.utils.cpp_extension import CUDA_HOME
from torch.utils.cpp_extension import CppExtension
from torch.utils.cpp_extension import CUDAExtension
from setuptools import find_packages
from setuptools import setup
requirements = ["torch", "torchvision"]
... |
8f89fd7492e2b4fef1f22fb55d895f9d21f47659d7c8efe23d76df6849d27795 | Python | 1,972 | 63 | #####################################################################################################################
'''
TESTS
'''
#####################################################################################################################
import os
import control.core as core
import control.core_tracking as... |
c7edbfa63288f0f6512997ed860e339ae4d2626b24f35a70886389b1077bef23 | Python | 1,972 | 63 | import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import numpy as np
def plot_prop(prop):
if "per_" in prop:
x = np.load("target_{}.npy".format(prop[4:]))
y = np.load("output_{}.npy".format(prop[4:]))
n = np.load("n_atoms.npy")
while len(n.shape) < len(x.shape):
... |
0c3547f49fd4944030e53a197af5060e462298fdcf5aad0c79ef4f2d813fc679 | Python | 1,974 | 61 | # coding=utf-8
# Copyright 2026 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... |
80a2385f163b543c69bc92a51fcb2ce41732640b3d30a3a382742fac54bdcc90 | Python | 1,974 | 76 | """Shared pytest fixtures and synthetic-trace builders."""
from __future__ import annotations
from dataclasses import dataclass
import numpy as np
import pytest
from msfeature.config import DatasetConfig
@dataclass
class InjectedSaccade:
onset_s: float
duration_s: float
amp_x_deg: float
amp_y_deg:... |
ae8f81415e4231400f18f931d05b900b6635159b7bb60d1e593cea4f59ba5cb7 | Python | 1,974 | 70 | # Node-group asset "Is Backbone Edge" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECK... |
bcf020074bd938ed36afd27095260e32f0be57905d781da8f683ba15f414fdec | Python | 1,974 | 59 | r"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into bu... |
43ef5c636d5c1d7002109d572fb9866f30d4174a74abfff17b6d705a35486a1d | Python | 1,975 | 83 | # -*- coding: utf-8 -*-
"""
Created on Wed Dec 4 11:54:21 2019
@author: rhann
"""
# Goal 1:
# Write a script in Python/Java (other other programming language of interest)
# that a) tries to find the issue we showed in that notebook above
# Add a bit to your script that runs this expression a few (~100) times,
# and... |
62d9cc135948be3222ba14a6a4cf665da85024cebf91bdc9a6d92d0f43438a2d | Python | 1,975 | 67 | import argparse
from pathlib import Path
import json
import typing
from functools import partial
import cv2
import numpy as np
from tqdm import tqdm
def main(args: argparse.Namespace):
image_dir = Path(args.images)
tracking_file = Path(args.tracking)
output_dir = Path(args.output)
output_dir.mkdir(ex... |
87efab05b8f77c154b611cc8b0fb93e0bc552f257143a4d0f7d677a8eda2c0ca | Python | 1,975 | 73 | import numpy as np
from vanhateren import VanHateren
import vanhateren.preprocess as pp
def load_patches(n, shape=(32, 32)):
vh = VanHateren(calibrated=True)
rng = np.random.RandomState(9)
return vh.patches(n, shape, rng=rng)
def show_patch(ax, patch):
ax.imshow(patch, cmap='gray')
ax.set_xtick... |
d55982c519ad60135857a3cde559e6d7b41e63dd6d23521c8155cae216e97b57 | Python | 1,976 | 63 | """Base jobs for Gaussian."""
from __future__ import annotations
from typing import TYPE_CHECKING
from ase.calculators.gaussian import Gaussian
from quacc import get_settings
from quacc.runners.ase import Runner
from quacc.schemas.cclib import CclibSummarize
from quacc.utils.dicts import recursive_dict_merge
if TY... |
0e9bebf361d4fe31573525be8b55d31cd33b858ccb0f1ef8a2bf33b53be4f513 | Python | 1,977 | 42 | import json
import time
from unittest.mock import MagicMock
import pytest
from NDATools.upload.validation.v1 import Validation
@pytest.fixture
def validation(monkeypatch, validation_config_factory, load_from_file, tmp_path, shared_datadir):
file_path = (shared_datadir / 'validation/file.csv')
args, config =... |
c5b9146eb83f106aa436bfe2ddf7aa057cf421736a4bf8abc054b5318ead8b25 | Python | 1,977 | 50 | import os
import random
import shutil
import unittest
from torcheeg import transforms
from torcheeg.datasets import DEAPDataset
from torcheeg.datasets.functional.operators import from_existing
class TestOperators(unittest.TestCase):
def setUp(self):
# if os.path.exists('./tmp_out/'):
# shutil... |
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