sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
89f4010495fa30e074f74fd109be55c4dffca0754b2863b849b2382ec20345bb | Python | 1,843 | 59 | from omegaconf import OmegaConf
import detectron2.data.transforms as T
from detectron2.config import LazyCall as L
from detectron2.data import (
DatasetMapper,
build_detection_test_loader,
build_detection_train_loader,
get_detection_dataset_dicts,
)
from detectron2.evaluation import COCOEvaluator
data... |
6717dd54b83564ee91dfc78052ec4bf1fb7fa63b719efa398582d9e40c67b2a5 | Python | 1,845 | 54 | #!/usr/bin/env python3
#
# Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#
#
"""Infer Gem well throughput from the barcode rankplot."""
from __future__ import annotations
import cellranger.cell_calling_helpers as cch
from cellranger.feature.throughputs import HT_THROUGHPUT, MT_THROUGHPUT
ANCHOR_BARCODE_... |
f0fc3dd608afbb242fc61cc9eb4a6752e7a98189e0e8a42740ba53c631dc7efe | Python | 1,848 | 42 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2019-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
09b69cc8f436e93771c2206a0ecbae5b60f8dab71a2e4f0e97d3aec515ea1be2 | Python | 1,851 | 59 | # Copyright (c) Facebook, Inc. and its affiliates.
"""Utilities for developers only.
These are not visible to users (not automatically imported). And should not
appeared in docs."""
# adapted from https://github.com/tensorpack/tensorpack/blob/master/tensorpack/utils/develop.py
def create_dummy_class(klass, dependency... |
9ad627170c5982e8644b5797f6da6612b8f838acde1c9a73a332124327d76794 | Python | 1,851 | 46 | #####DO NOT REVIEW, CHANGES IN PATHS#####
from nilearn.glm.second_level import SecondLevelModel
from nilearn.glm import threshold_stats_img
from nilearn.image import load_img, concat_imgs
import pandas as pd
import nibabel as nib
import os
from nilearn.plotting import plot_stat_map
subjects = [1, 3, 5]
contrast_name =... |
b4ad53fa9b2ed47b615dd1408e6446ff6e7b0e4f2e83a80de1c4de7e2832e66d | Python | 1,856 | 68 | """ 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... |
52f38477bcaf4fd74ce7edb488b616133d9e9e9f52ce37f7801489cd0ff7266a | Python | 1,858 | 61 | '''
Created on 25.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
Description:
Helper tool to compare the number of voxels included in the peri-infarct region for each subject.
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange =... |
f05d738b4b7e067d5c5076b07d27c6c21daf795017f53b708e02eba308566f8e | Python | 1,862 | 57 | from hsnn.simulation._base import _get_uid
from hsnn.core.interfaces import INetwork
__all__ = ["MonitorContext", "StateContext", "ClampContext"]
class MonitorContext:
def __init__(self, network: INetwork, monitor_spikes: bool = True,
monitor_states: bool = False) -> None:
self.network =... |
0ead5f02ab8e6781e65e0fa211b6d7d9a8275a34fa491298ff2dea3b076cda37 | Python | 1,865 | 58 | """MolGpKa GCN network (inference only).
Vendored from MolGpKa (https://github.com/Xundrug/MolGpKa), MIT License.
Patched for SMILES2Docking: only ``GCNNet`` (the released pKa model) is kept;
the unused GAT/MPNN variants and the deprecated ``DataLoader`` import were
dropped so the frozen build pulls no extra PyG conv ... |
9bb6938911c5e7f4d93a27b48de3b98285dbbe62058d8403d60b8b8a7babbe80 | Python | 1,865 | 49 | import pytest
from openfe.setup.atom_mapping.ligandatommapper import LigandAtomMapper
from openfe.utils import ligand_utils
class TestAtomMapper:
def test_abstract_error(self, simple_mapping):
# suggest_mappings should fail with NotImplementedError if the user
# tries to directly user the abstrac... |
b65bbe80c9ba5627b05b473c8902e744d879bfc8ea2760df09bd031e7c0f613c | Python | 1,868 | 55 | #
# Copyright (c) 2024 10X Genomics, Inc. All rights reserved.
#
"""Stage checking if cell annotation is viable but not requested in a multi run."""
import json
import martian
import cellranger.cell_typing.broad_tenx.cloud_cas_utils as cloud_utils
import cellranger.cell_typing.broad_tenx.common as ct_common
import c... |
24d23a32db8d143bd8cea2c38240c86e80400e60228f9f51e96bb817c0f89a37 | Python | 1,870 | 62 | import os
import sys
sys.path.insert(0, os.path.abspath("../.."))
# Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -------------------------... |
b2bb1c224ef5e3546f58b9aa07c5b42a96801ab982804d1ebd905a91bff54cba | Python | 1,870 | 49 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
94d5a9fd409565eaec91bf725f4a00ff6231d8df4f217daaa0a835b17719a99e | Python | 1,872 | 75 | """
Sijbers's method
sijbers2007automatic,
title={Automatic estimation of the noise variance from the histogram of a magnetic resonance image},
author={Sijbers, Jan and Poot, Dirk and den Dekker, Arnold J and Pintjens, Wouter},
journal={Physics in medicine and biology},
volume={52},
number={5},
pages={1335},
year={2007... |
3d9057ff7be90093d6ca31955188c8b04a48a748c2b1882a45f78e07b382a599 | Python | 1,873 | 65 | import solara
from matplotlib.figure import Figure
from mesa.examples.experimental.tram_model.model import TramScenario, TransitSystem
from mesa.examples.experimental.tram_model.utils import (
POSITION_COLOR,
SCALE,
SPEED_COLOR,
TITLE_SIZE,
draw_track_view,
tram_portrayal,
)
from mesa.visualiza... |
736ddb9bd47da835ce29aaba4cba6a4c982a06f860aef7209e2d6ead5e62e468 | Python | 1,873 | 59 | from abc import ABC, abstractmethod
from copy import deepcopy
from pathlib import Path
from typing import Any, Mapping
from omegaconf import ListConfig
from ray.tune.search import BasicVariantGenerator
from ray.tune.search.bayesopt import BayesOptSearch
from hsnn.utils import io
from .tuning import traverse_dict
cl... |
21c436c6be307dca8744e5129164ec3f40d47a0410109025918277acc59719be | Python | 1,874 | 68 | from pathlib import Path
import numpy as np
from steinbock import io
from steinbock.measurement import neighbors
from steinbock.measurement.neighbors import NeighborhoodType
class TestNeighborsMeasurement:
def test_measure_neighbors_centroid(self):
mask = np.array(
[
[1, 1, 0... |
6051769dbeae64d64a6041c1f87c7582e1c40e924a582b208d79ffe313ad3d4a | Python | 1,874 | 57 | import nest
import numpy as np
import pylab as pl
import nest.topology as tp
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True})
print 'iaf_cond_alpha recordables: ', nest.GetDefaults('iaf_cond_alpha')['recordables']
mm = nest.Create('multimeter',
params = {'withtime': True,
... |
bf850549c0f98340fe8b77eda48edf4901bce79efcb7f1d52394dabb3e84d82a | Python | 1,874 | 60 | # Copyright (c) Facebook, Inc. and its affiliates.
from typing import Any
import pydoc
from fvcore.common.registry import Registry # for backward compatibility.
"""
``Registry`` and `locate` provide ways to map a string (typically found
in config files) to callable objects.
"""
__all__ = ["Registry", "locate"]
de... |
df78866185c7d876153a8a1d4c185f9c17744ea855cc6a9530797fef2ce6184c | Python | 1,874 | 69 | #!/usr/bin/env python
#
# Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#
"""Determine if the cloupe was not generated because this is a single sample run of MULTI.
In this case we hard-link the single sample cloupe as the library-level cloupe.
"""
from __future__ import annotations
from shutil import c... |
e319d65d54d7588985bd7ac7b90cb3d3badb913988ec9e47b2d7deeefadf178f | Python | 1,874 | 82 | """
Divide the dataset such that each subject has several droped sessions for certain classes that are available for other subjects
Subject DropCount
0 6
1 7
2 7
3 7
4 7
5 6
"""
import random
import argparse
import torch
import numpy as np
drop_count = [6] * 6 # [... |
7b12adb047fcc69e3b2b856dac5665cb466d7298cd0025f27a2bfa4626dc2887 | Python | 1,880 | 54 |
import mne
import numpy as np
from mne.channels.layout import _find_topomap_coords
def get_ch_locs_2d(info, ch_type):
'''
Getting the 2D locations of the MEG channels with the given type.
Parameters
----------
info : mne.Info
The mesurement info associated with the M/EEG data.
ch... |
a176580bb85de3aa4dbee9fda6eb7f2843802d2495d284ed756dc3dc0652cb53 | Python | 1,882 | 35 | import sys
from pathlib import Path
if len(sys.argv)!=2: sys.exit("USAGE: python pepCount.py <path to peptides containing proteome-discoverer exported file>, \n e.g.,\npython pepCount.py \"L:/promec/HF/Lars/2021/march/Ingrid/KO/210317_Ingrid2-(1)_PeptideGroups.txt\"\n")
#python pepCount.py $HOME/Animesh/Maria/MGF/20... |
d9adb8343954b2e596c9ca5edf6a01bfbb59e53dbd5b246b40f30cc62e960b76 | Python | 1,882 | 56 | #!/usr/bin/env python
#
# Copyright (c) 2024 10X Genomics, Inc. All rights reserved.
#
"""Write out cell_types.h5 to use in diff expression."""
__MRO__ = """
stage WRITE_CELL_TYPES_H5(
in csv cell_types,
in string cell_types_key,
out h5 cell_types,
out json cell_types_map,
src py "s... |
c6bb45924bfe476c0083ecb4ed3a5573d2f178a8774169b78635d4c234cc49ad | Python | 1,887 | 36 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
c6c9d512e346c86d0751b30f5ca048d6e8eefffde2611143ce94ade6a6788467 | Python | 1,895 | 56 | """ Utilities needed for network specification and generation """
import numpy as np
import scipy.special as spc
def generate_piecewise_constant_signal(num_steps, step_duration, max_rate, min_rate, start_time):
"""
Generates a piecewise constant input signal with amplitudes drawn from a uniform distribution
... |
b2d1586c13008738bc5914fb3b6b0d6530cbd857196045de1f8d32c2483adfd5 | Python | 1,901 | 38 | import argparse
import json
import re
def main():
parser = argparse.ArgumentParser(description='Create a JSON from an transformix output points file')
parser.add_argument('--in', metavar='IN', dest='input', type=str, required=True, help='The output points to parse')
args = parser.parse_args()
output ... |
135f2c7a87528f04a0d6d0f7a1d1662aaaf01130feaff3d7a496be2c5e202112 | Python | 1,902 | 60 | import torch
import torch.nn as nn
from .meta.electrode_names import channels
from .VisualTransforms import EEGScalpMap
# EEG_CNN_LSTM
class EEG_CNN_LSTM(nn.Module):
def __init__(self, num_classes=10, hidden_size=128):
super(EEG_CNN_LSTM, self).__init__()
# CNN for spatial feature extraction
... |
b07e55e9dcf747770f802ce6d9d759e760ce9cee9dc6c40703a3e620e029ec58 | Python | 1,902 | 66 | # Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
"""Pick T or B output."""
from __future__ import annotations
from typing import TYPE_CHECKING
import martian
if TYPE_CHECKING:
import cellranger.mro_types.filetypes as mro_filetypes
import cellranger.mro_types.structs as mro_structs
__MRO__ = """... |
8764eea3b9e70a66d44bee32d4bc8b614ce2e0ecc30cf9b229ad1829ccfe223a | Python | 1,907 | 72 | '''
Created on 20.08.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
try:
zrange = xrange
except NameError:
zrange = range
import os
import sys
import numpy as np
from scipy import ndimage
import proc_tools as pt
def circle... |
a41c0507b47d38a4d6d944cfc29f30bcbcc78030e632bae132b4f79203afd900 | Python | 1,909 | 70 | import numpy as np
import pytest
from chemprop.data import LazyMoleculeDatapoint, MoleculeDatapoint
SMI = "c1ccccc1"
@pytest.fixture(params=["@", "@@"])
def stereo_smi(request):
return f"C[C{request.param}H](O)NC\C=C/C"
@pytest.fixture(params=range(1, 3))
def targets(request):
return np.random.rand(reques... |
2fab9ea38e54b4312c9fce26f7b551f6055a5aaf20ebb0cf662962d59c706101 | Python | 1,916 | 66 | """Tests for shared input validation across embedding entry points (#147)."""
import numpy as np
import pytest
from brainspace.gradient.embedding import (
diffusion_mapping, laplacian_eigenmaps, DiffusionMaps, LaplacianEigenmaps,
)
def _psd(n, seed):
rs = np.random.RandomState(seed)
a = rs.randn(n, n + ... |
fd361fae633bc2b311c074048ad726e0a93f7203db8b68637c5dd51328ab7887 | Python | 1,919 | 50 | import logging
from collections import Counter
from os import PathLike
from pathlib import Path
from typing import Generator, Sequence, Tuple, Union
import networkx as nx
import pandas as pd
from .. import io
logger = logging.getLogger(__name__)
def convert_to_networkx(neighbors: pd.DataFrame, *data_list) -> nx.Gr... |
4a2f485bd435cc3705810ab428a7531261349836fd85e1dc174f077280c7163d | Python | 1,922 | 54 | """Paths associated with Azimuth."""
from pathlib import Path
AZIMUTH_CALIBRATION_MODELS_BASE_DIR = (
Path(__file__).parent / "azimuth_models" / "latest" / "calibration"
)
AZIMUTH_CALIBRATION_MODELS_PREFIX = "temp_scaler_L_"
AZIMUTH_CALIBRATION_MODELS_SUFFIX = ".onnx"
AZIMUTH_CALIBRATION_MODELS_PATHS_SORTED_LIST ... |
4a745d95940d5b2743b5f745e57afe160e4ba8f5850c501fa78b49c48e3ffdb4 | Python | 1,928 | 60 | """Tests for the allianceformation meta-agent example."""
from __future__ import annotations
from mesa.examples.advanced.alliance_formation.model import (
AllianceScenario,
MultiLevelAllianceModel,
)
from mesa.meta_agents import MetaAgents
def test_alliance_model_records_overlapping_memberships(monkeypatch)... |
7af21ab1a59c0a2f1dc044a1f9b609a57bdddb06714a00640b1dd0c527e748a5 | Python | 1,929 | 53 | import argparse
def main(args):
import glob
import random
import numpy as np
import json
mpnn_alphabet = 'ACDEFGHIKLMNPQRSTVWYX'
mpnn_alphabet_dict = {'A': 0,'C': 1,'D': 2,'E': 3,'F': 4,'G': 5,'H': 6,'I': 7,'K': 8,'L': 9,'M': 10,'N': 11,'P': 12,'Q': 13,'R': 14,'S': 15,'T': 16,'V': 17,... |
223cb0cdf5fbae03532572dbb000ddb65abdaf9f09bcd9854c6601d86705a9b0 | Python | 1,930 | 53 | from __future__ import annotations
from dataclasses import dataclass, field
from typing import Any
from src.protonation.base import ProtonationError, Protonator
from src.protonation.dimorphite_adapter import DimorphiteProtonator
from src.protonation.openbabel_adapter import OpenBabelError, OpenBabelProtonator
@data... |
3f7193818b47490f6262e78d87be354b058f8865c9bd24bce56e514dfc264438 | Python | 1,931 | 65 | #
# Copyright (c) 2025 10X Genomics, Inc. All rights reserved.
#
"""Remove meta cells from cell types."""
import csv
import json
import os
import martian
import cellranger.cr_io as cr_io
from cellranger.cell_typing.common_cell_typing import BARCODE_KEY
__MRO__ = """
stage REMOVE_META_CELLS_FROM_CELL_TYPES(
in ... |
24992f2d94ecc250c7e96afdcb37e611bf9698b12b1baa9c27a0c0c22e134748 | Python | 1,932 | 54 | #!/usr/bin/env python
#
# Copyright (c) 2014 10X Genomics, Inc. All rights reserved.
#
# General utilities for manipulating nucleotide sequences
#
from __future__ import annotations
NUCS: list[bytes] = [b"A", b"C", b"G", b"T"]
NUCS_INVERSE: dict[bytes, int] = {b"A": 0, b"C": 1, b"G": 2, b"T": 3}
DNA_CONVERT_TABLE: ... |
af820d608e76aa3c700c84f9a5752ec29a65c2ec425064e44953b903dbf388bf | Python | 1,933 | 53 | import torch
import torch.nn as nn
from torch.distributed.fsdp import (
FullyShardedDataParallel,
MixedPrecision,
BackwardPrefetch,
ShardingStrategy,
FullStateDictConfig,
StateDictType,
)
from torch.distributed.fsdp.wrap import size_based_auto_wrap_policy
import pytorch_lightning as pl
def get_... |
5cbe18904790f9c5c1b4cd10d498d58a312eb361f4f7beb4f8cd0744dae0b25d | Python | 1,936 | 60 | from __future__ import annotations
from typing import Any
import pytest
from hypothesis import given
from hypothesis import strategies as st
from pytest_mock import MockerFixture
from snakebids.plugins.version import Version, impm
from tests.helpers import allow_function_scoped
@given(version=st.text())
def test_e... |
b710d000bfae50d5a21a00f9938e669bc154db995db7c7717e73eb61d04ca6db | Python | 1,936 | 98 | from numpy import *
import nest
import time
import sys
###### Parameters #####
## simulation
lnts =4 #local num threads
dt = 1. # the resolution in ms
simtime = 30.*1000. # Simulation time in ms
delay = 2. # synaptic delay in ms
startRec= 10000. #start for recording devices (cut transients)
stopR... |
637212ec18ea115c9f5c3292deb85c1fd073aadae6265b521f9c9f7df56fbb8a | Python | 1,939 | 57 | #!/usr/bin/env python
#
# Copyright (c) 2017 10x Genomics, Inc. All rights reserved.
#
import os
import martian
import cellranger.hdf5 as cr_h5
import cellranger.matrix as cr_matrix
__MRO__ = """
stage REANALYZER_PREFLIGHT(
in h5 filtered_matrices_h5,
src py "stages/analyzer/reanalyzer_preflight",
) using ... |
a6ce3d3863e9a9231b609fa053a4bf8c5d6642b38706b845f011d488531eb04d | Python | 1,942 | 63 | ## eelbrain_utils
import eelbrain as eb
import numpy as np
import mne
def ds_from_evoked_depsampt(data_1, data_2, key_data_1, key_data_2):
for d_1, d_2 in zip(data_1, data_2):
if type(d_1) != mne.evoked.EvokedArray or type(d_2) != mne.evoked.EvokedArray:
raise TypeError('Data needs to be of ... |
9fd1b002df21269549d2a97f68041908e61f2215a1cbcdda7c4b75663553f514 | Python | 1,943 | 51 | """Reproduce the OpenMM reference energy for the solvated ethanol test system."""
from pathlib import Path
from xml.etree import ElementTree
import openmm
from openmm import Context, Platform, VerletIntegrator, app, unit
data_dir = Path(__file__).resolve().parent.parent / "data"
pdb = app.PDBFile(str(data_dir / "et... |
2c9b722ee90c4ee0c2a0adc31b8ebaa499931b11710e9d614f44769439d4d026 | Python | 1,944 | 52 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from detectron2.data.catalog import Metadata
from detectron2.evaluation import COCOEvaluator
from densepose.data.datasets.coco import (
get_contiguous_id_to_category_id_map,
maybe_filter_categories_cocoapi,
)
def _maybe_add_iscrowd_annotation... |
a697afc39da5fb1083b7a255282896d7d09c17240eb8b9cfc99a208cb618f338 | Python | 1,944 | 66 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
# pyre-unsafe
import pickle
import torch
from torch import nn
from detectron2.utils.file_io import PathManager
from .utils import normalize_embeddings
class VertexDirectEmbedder(nn.Module):
"""
Class responsible for embedding vertices.... |
e102484f5bd27ab828de8db66a726fa7bac27c3e78b966f5fbbd8d1f6ec9919c | Python | 1,944 | 47 | # Copyright (c) Facebook, Inc. and its affiliates.
import numpy as np
from torch.utils.data.sampler import BatchSampler, Sampler
class GroupedBatchSampler(BatchSampler):
"""
Wraps another sampler to yield a mini-batch of indices.
It enforces that the batch only contain elements from the same group.
It... |
103736ef473d42bf8e915c57e56ca44bde6afed5d3f86f61f6aa8801791833b8 | Python | 1,945 | 55 | #!/usr/bin/env python
# Copyright 2017-2018 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
883f41ed22335038c34ee12d49c41bb4b09e2ce22390dd39ffd32e4d7127c77c | Python | 1,947 | 74 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
"""
TensorMask Training Script.
This script is a simplified version of the training script in detectron2/tools.
"""
import os
import detectron2.utils.comm as comm
from detectron2.checkpoint import DetectionCheckpointer
from detectron2.config ... |
25d29d0c664b8d8b6e2e43ab3f044770eee8c1d0b9996f4dd5e69d9a1693493b | Python | 1,948 | 55 | '''
Created on Oct 9, 2025
@author: voodoocode
'''
import pyexcel
import os
import numpy as np
META_PATH = "/mnt/data/Professional/LMU/data/Beta-prevalence/"
DATA_PATH = "/mnt/data/Professional/LMU/data/Beta-prevalence/database4/original/"
def main():
sub_rec = {}
for subj_name in os.listdir(DATA_PATH):
... |
14c55695ec3c102e0f1e87688d97583cbc90067b5a5bf1ce2704d08f3d0648e1 | Python | 1,949 | 45 | import os
import unittest
from unittest.mock import patch
from nnunetv2.paths import nnUNet_preprocessed, nnUNet_raw
from nnunetv2.utilities.dataset_name_id_conversion import find_candidate_datasets
class TestPaths(unittest.TestCase):
def test_missing_env_var_only_raises_when_converted_to_path(self):
wit... |
80e1f2b02881f9655caaa2000927795d720e70a363063800a033d4ddcefa9cba | Python | 1,950 | 39 | """resources.py - memory and runtime for AccuSNV jobs.
Every job starts in the first (smallest) tier. If it OOMs or times out, Snakemake resubmits it
with a higher `attempt`, which moves it to the next tier up.
"""
TIERS = {
'create_mapping_index': [(2000, 60), (8000, 60), (320000, 240)],
'mapping': ... |
4be94716b0a203d3fe0679e1a345515a7f8ca7ff2a9658353b9b0f77e9d9102f | Python | 1,951 | 60 | # Copyright (c) Facebook, Inc. and its affiliates.
import random
import unittest
from densepose.data.video import FirstKFramesSelector, LastKFramesSelector, RandomKFramesSelector
class TestFrameSelector(unittest.TestCase):
def test_frame_selector_random_k_1(self):
_SEED = 43
_K = 4
rando... |
d95579bbdbbf01cfd5baab6284590d0887b53dc377d3e8ee0453ccb154b142a8 | Python | 1,952 | 62 | # Copyright (c) 2020 10x Genomics, Inc. All rights reserved.
"""A wrapper to avoid importing tables directly.
We need to monkey patch it on the fly to avoid issues with it changing thread
usage under the hood. See CELLRANGER-2936
"""
from __future__ import annotations
import sys
import numexpr
import tables
# Ho... |
43bc94348c98a09b17429df34c0324e37a8751b745ab53a4feae5053309c8ff0 | Python | 1,953 | 82 | #!/usr/bin/env python
# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
3887fdfaac02fce0d73fdb1b3c8a4b0fa4854c80092ac9162160efc184545372 | Python | 1,954 | 46 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from dataclasses import fields
from typing import Any, List
import torch
from detectron2.structures import Instances
def densepose_inference(densepose_predictor_output: Any, detections: List[Instances]) -> None:
"""
Splits DensePose predictor ... |
89148c81a0edbcdb8cbf69f3ea6a8e1b032e2fa4c3b6d789ec6c4c4ded1d5036 | Python | 1,956 | 63 |
""" Put module information here """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import re
import os
import sys
from enum import IntEnum
from pandas import read_csv
# Discover whether application is running in docker
_run_docker = os.path.isdir("/mnt/code")
class SupportedDatasets(IntEnum)... |
ba958573aba350b16a3802df60e85dbf7000c7bb88b70ffdacd983cc56a57ec1 | Python | 1,956 | 65 | import shutil
from pathlib import Path
from typing import Mapping, Optional
import pandas as pd
import ray
from ..core.backends import create_network
from ..utils import io
from .. import simulation as sim
__all__ = ["SimulatorActor", "setup_ray"]
@ray.remote
class SimulatorActor(sim.Simulator):
def __init__(s... |
cd05bb4fa151dad622d23f617340774320d4705b8d0eea881647d80a8a21369e | Python | 1,957 | 51 | # Copyright (c) Facebook, Inc. and its affiliates.
# -*- coding: utf-8 -*-
import copy
import os
import tempfile
import unittest
from torch.hub import _check_module_exists
from detectron2 import model_zoo
from detectron2.utils.logger import setup_logger
from detectron2.utils.testing import get_sample_coco_image
try:... |
34ad9562b09571a59f1d22e2f5b5446da3e0109158ceb027dbb3d286d1bfa62d | Python | 1,958 | 52 | #!/usr/bin/env python
# Copyright 2016-2022 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
752a641d75a6b368fd3e5f18271dd69ce48a5c76b7050889a02bfd8f2a18307d | Python | 1,959 | 51 | #!/usr/bin/python3
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "So... |
32c7d22c964211ba4ee481eb7a62bc915dbd9c63e8acd1ee075bd05224bcd6a8 | Python | 1,961 | 74 |
'''This file contains functions that can be applied to discrete signals into bins with different strategies.'''
import numpy as np
def adaptive_binning(source, n_bins):
'''
Binning the signal into bins with equal number of data points (adaptive binning).
Parameters
----------
source : np.nd... |
c6cdf1690284a1d878da293893ef5b5558f62e0bde007d4067a8f2603d721a6b | Python | 1,961 | 83 | """ 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... |
9dbc47c4c6ee3afe2f3146c6b5d94bb2425ffb1ad7580b691ba07d1a5e6f7786 | Python | 1,962 | 59 | import pygame, time, random, Numeric, pygame, pygame.sndarray
sample_rate = 44100
def sine_array_onecycle(hz, peak):
#Compute one cycle of an N-Hz sine wave with given peak amplitude
length = sample_rate / float(hz)
omega = Numeric.pi * 2 / length
xvalues = Numeric.arange(int(length)) * omega
return ... |
88b17c0fc612240caf84f100e7c2dbcaa16131e74f17ae996bf0449d123d7651 | Python | 1,963 | 66 | import math
class BasePIController():
def __init__(self,
expected_kl: float,
init_beta: float = 0.,
beta_min: float = 0.,
Kp: float = 0.01,
Ki: float = 0.0001):
assert init_beta >= beta_min, \
f"beta(0) ({init... |
5b344313ef5548e64403fc4178838ed8ef24cc38c1cf03cf30388a6753136cd6 | Python | 1,974 | 86 | """
Wrapper functions to more user-friendly calling of certain math functions
whose output data-type is different than the input data-type in certain
domains of the input.
"""
__all__ = ['sqrt', 'log', 'log2', 'logn','log10', 'power', 'arccos',
'arcsin', 'arctanh']
import numpy.core.numeric as nx
... |
4880c7d9926a13416fdd9256baf83ef85385170f60bc952e0a89742305f56b36 | Python | 1,976 | 48 | from detectron2.config import LazyCall as L
from detectron2.layers import ShapeSpec
from detectron2.modeling.box_regression import Box2BoxTransform
from detectron2.modeling.matcher import Matcher
from detectron2.modeling.roi_heads import FastRCNNOutputLayers, FastRCNNConvFCHead, CascadeROIHeads
from detectron2.layers.b... |
62754ca4b73d92648a9deda14e0cc7164fae9be05a8cd1e0d40f55b6b4b7a24b | Python | 1,976 | 39 | #python peptideGroupsMQDIANNcombine.py L:\promec\TIMSTOF\LARS\2025\250319_Alessandro\combined\txt\peptides.txt L:\promec\TIMSTOF\LARS\2025\250319_Alessandro\DIANNv2\report.pr_matrix.tsv
#!pip3 install pandas matplotlib --user
import sys
if len(sys.argv)!=3: sys.exit("\n\nREQUIRED: pandas; tested with Python 3.12 \n\nUS... |
6fef288222527d31354d25bc28f7e7b0e0ed8aaeabeb573dd9d079775db7c875 | Python | 1,976 | 71 | #
# Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#
"""Define the pipeline mode for spatial imaging subpipeline."""
from __future__ import annotations
from enum import Enum
from typing import NamedTuple
class Product(str, Enum):
"""Product being analyzed."""
VISIUM = "Visium"
CYT = "CytAs... |
b35ea48a8a7c9ac24f2e428f52ad7f3c0fbb6302a4224d66b3d600e6727856d7 | Python | 1,976 | 60 | from __future__ import annotations
import os
import sys
from pathlib import Path
APP_NAME = "smiles2docking"
def is_frozen() -> bool:
return bool(getattr(sys, "frozen", False))
def is_appimage() -> bool:
return bool(os.environ.get("APPIMAGE")) or "/.mount_" in str(Path(__file__).resolve())
def user_data... |
9068d792d0caa9efc55d14c37ad6495dd11f75c90daa5d99a4d14dcdb2a59f37 | Python | 1,979 | 59 | from configargparse import ArgumentError, ArgumentParser
import numpy as np
import pandas as pd
import pytest
from chemprop.cli.common import process_common_args, validate_common_args
from chemprop.cli.train import TrainSubcommand, process_train_args, validate_train_args
@pytest.mark.parametrize(
("external_data... |
bf8127d7505393714620af8eec0c51b16615543816e1ecff58b7c298b2426406 | Python | 1,980 | 66 | import os
import shutil
import pandas as pd
import numpy as np
import smma.src.utilities as utilities
import napari
import functools
from skimage import io
from loguru import logger
logger.info('Import OK')
input_folder = utilities.locate_raw_drive_files(
input_path='raw_data/raw_data.txt')
output_folder = 'resu... |
b9778f8749e6c351c4638f89ee1b437f6bc20b50f32e1b5c42f329cad77a7e4a | Python | 1,981 | 59 | import pytest
from openff.utilities.testing import skip_if_missing
from openfe.setup import LigandAtomMapping
from openfe.utils.visualization_3D import view_components_3d, view_mapping_3d
@pytest.fixture(scope="module")
def maps():
MAPS = {
"phenol": {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8,... |
99b51795bbb5193440fb0314ba5c2f6700625150241cc96b647cf75efd35f33c | Python | 1,983 | 62 | from dataloader import DataLoader
from pathlib import Path
import os
def load_data(
data_folder,
server_mount_drive="S:",
get_recording=True,
make_folder=True,
load_sorting=False,
save_folder_name=None,
first_N_files=4,
):
dataloader = DataLoader(
data_folder, ma... |
ea1132bf5d71d222ce46fb9dbec9d5f39157a6d1c9cbd16e9be8ca02c0126488 | Python | 1,984 | 51 |
import numpy as np
from brainspace.gradient.alignment import procrustes_alignment, ProcrustesAlignment
def test_alignment_options():
rs = np.random.RandomState(0)
# Create two datasets that are just shifted and scaled versions of each other
d1 = rs.randn(10, 5)
# Shift and scale d2
shift = 5.... |
4b3eccc62b630dbc541978aa75bfb602119a135125897842181c322c2c911470 | Python | 1,985 | 79 | ############################################################################
# Copyright (c) 2024-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
import sys
from enum import IntEnum
class IsoQuantExitCode... |
ef9298623ad94b45660a495e44af9b95355af1f25150b4857b953001c9cee22f | Python | 1,987 | 59 | """Tests for multi-level and overlapping meta-agents."""
from mesa import Agent, Model
from mesa.meta_agents import MetaAgents
def test_overlapping_meta_agents():
"""An agent can belong to multiple meta-agents simultaneously."""
model = Model()
meta_agents = MetaAgents(model)
agent1 = Agent(model)
... |
f08d93e854abf6363d442dd6ffa7a6b0a2a8f8d190e0d3a2c7508fe29971481d | Python | 1,991 | 67 | """ Created on Wed Jun 25 14:49:00 2025
@author: dcupolillo """
from PyQt5.QtCore import Qt
from PyQt5.QtWidgets import (
QMainWindow, QAction, QMenu, QDialog, QVBoxLayout, QHBoxLayout,
QLabel, QSpinBox, QPushButton, QApplication, QWidget)
from PyQt5.QtCore import pyqtSignal
from pyqtspinner import Waiting... |
8abff14b2b7e27abe5ce0d92f3186110a909a77c101de9c28db4e231200a5598 | Python | 1,993 | 70 | """
This script crawls the package space and generates .md files in
the references directory of the mkdocs site. For example:
```
# side/reference/connectivity/adjacency.md
::: connectivity.adjacency
```
It also generates a SUMMARY.MD file that contains the
navigation structure of the generated .md files. We
then use... |
14bbb15b4bd6b29de691b32d89942b7f57135d75450061d43172a822263e96d8 | Python | 1,995 | 64 | import pytest
from src.structure_generation.builder import StructureBuilder, StructureGenerationError
def test_prefers_mmff_when_available() -> None:
builder = StructureBuilder(
{
"embed_seed": 61453,
"max_attempts": 2,
"optimize_geometry": True,
"force_fie... |
8ce40e5cf6a7c8fd8e98544b58f312850f7716c1ca8c0f37d64dc856f462bb8c | Python | 1,995 | 51 | import numpy as np
import pandas as pd
from hsnn.analysis.measures import _summarise_information
def _frame(values: dict[int, list[float]], sides: list[str]) -> pd.DataFrame:
return pd.DataFrame.from_dict(
values, orient="index", columns=sides
).rename_axis("nrn")
def test_summarise_information_pre... |
253a327543f8a7cba7dc6a56d46eba88123f29e6b184a15b1ee362cc42b6a038 | Python | 1,999 | 53 | import os
import argparse
import glob
import pandas as pd
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='This script processes NIfTI files in a directory. It extracts relevant parts of the file name and creates a DataFrame.')
parser.add_argument('-i', '--input', required=True, help='P... |
01abb8dc385d60182507c2743b4baaa6e970beec7fe831c53c3521eab53970a0 | Python | 2,003 | 53 | # Copyright (c) Facebook, Inc. and its affiliates.
import unittest
import torch
from detectron2.structures.masks import BitMasks, PolygonMasks, polygons_to_bitmask
class TestBitMask(unittest.TestCase):
def test_get_bounding_box(self):
masks = torch.tensor(
[
[
... |
548468625f134354ea1b9c4829ab0af369591769ef43994e3bc2c4ec9e2c4ed1 | Python | 2,004 | 56 | from __future__ import annotations
import pytest
from src.protonation.dimorphite_adapter import DimorphiteProtonator
from src.protonation.factory import (
NullProtonator,
ProtonationError,
build_protonator,
)
from src.protonation.openbabel_adapter import OpenBabelProtonator
def test_build_returns_null_w... |
b6d3458d6b589b18eb72e6ef71f1717a86532c9a4ffcb8ba5f035db6df3a48c2 | Python | 2,004 | 50 | #!/usr/bin/env python
# Copyright 2017-2018 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
b7f57297e75d11743904125bf5e0509e1d8d54cc50385f8cbd347ecb18bb4042 | Python | 2,012 | 66 | from itertools import chain
from typing import Iterator, Optional
import numpy as np
from torch.utils.data import Sampler
class SeededSampler(Sampler):
"""A :class`SeededSampler` is a class for iterating through a dataset in a randomly seeded
fashion"""
def __init__(self, N: int, seed: int):
if ... |
551cbc938e8c1e64089a73c52145e438e531724bb5ad241b43a056cece72b43e | Python | 2,013 | 47 | #!/usr/bin/python3
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "So... |
b8951b750d243b37cd67a597a459dafc92747e2f6823d8a4ecb80bc210d9fd8d | Python | 2,014 | 63 | #!/usr/bin/env python
# Copyright (c) Facebook, Inc. and its affiliates.
# -*- coding: utf-8 -*-
import argparse
template = """<details><summary> install </summary><pre><code>\
python -m pip install detectron2{d2_version} -f \\
https://dl.fbaipublicfiles.com/detectron2/wheels/{cuda}/torch{torch}/index.html
</code><... |
4ac4db1b3d54fc62d25241d5fa1827d81d7311e252bf4b9312e175d4c0dd007a | Python | 2,017 | 49 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
from detectron2.modeling import ROI_HEADS_REGISTRY, StandardROIHeads
@ROI_HEADS_REGISTRY.register()
class PointRendROIHeads(StandardROIHeads):
"""
Identical to StandardROIHeads, except for some weights conversion code to
handle old models.... |
50e223d8e5c292fe84716e0c2256694c2581fc27ad9943223fe389ddfe1ee02c | Python | 2,017 | 68 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from plugcli.params import NOT_PARSED, MultiStrategyGetter, Option
def _load_molecule_from_smiles(user_input, context):
from rdkit import Chem
from openfe import SmallMoleculeComp... |
5a6716e04d2fefa36ea32130c0568c6632c69db751f6885b81f58e0813592a48 | Python | 2,018 | 62 | """
Batch recompute session_responses.pkl for all control sessions
that have analyzer_final.zarr after stage 3 merge.
"""
import sys
import os
import time
import traceback
from pathlib import Path
PROJECT_ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
if PROJECT_ROOT not in sys.path:
sys.path.i... |
b2bb7d6794c5cb311852084df35f1885128399ea0323d0ef7cd700ef7dc55992 | Python | 2,023 | 66 | import dominate
from dominate.tags import *
import os
class HTML:
def __init__(self, web_dir, title, image_subdir='', reflesh=0):
self.title = title
self.web_dir = web_dir
# self.img_dir = os.path.join(self.web_dir, )
self.img_subdir = image_subdir
self.img_dir = os.path.jo... |
7d13111a41d3dcf5a1cf0619f83bb75a914bac7367f296584b1a913216c73549 | Python | 2,024 | 77 | # emacs: at the end of the file
# ex: set sts=4 ts=4 sw=4 et:
# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
"""
Stub file for a guaranteed safe import of duecredit constructs: if duecredit
is not available.
To use it, place it into your project codebase to be imported, e.g. copy as
... |
6407f26064231f8dee6bb7be728926cdf57bbdf4bfd267b2c933cbd9a96bad04 | Python | 2,028 | 57 | from typing import List, Sequence
import numpy as np
import xarray as xr
from .managers import MonitorContext, StateContext, ClampContext
from ..core.interfaces import INetwork
from .. import ops
def flush(network: INetwork, duration: float):
network.clear_input()
if duration > 0:
with ClampContext(... |
9dfd463ccf03440b73cf8990347766b6854533b041442988c8beab166fe722ef | Python | 2,029 | 66 | import tensorflow as tf
import numpy as np
import math
import json
def uniform(shape, scale=0.05, name=None):
initial = tf.random_uniform(shape, minval=-scale, maxval=scale, dtype=tf.float32)
return tf.Variable(initial, name=name)
def glorot(shape, name=None):
init_range = np.sqrt(6.0/(shape[0]+shape[1]... |
430e4bec6492dd1f051dd7da691c451941ce8e46c8d01b32b2576085a8cf807d | Python | 2,031 | 88 | from matplotlib.markers import MarkerStyle
from mesa.examples.basic.boid_flockers.model import BoidFlockers, BoidsScenario
from mesa.visualization import Slider, SolaraViz, SpaceRenderer
from mesa.visualization.components import AgentPortrayalStyle
# Pre-compute markers for different angles (e.g., every 10 degrees)
M... |
0d8acc665a931f9590f922acee38f04434bdcd13621522e0a44e12d25287ec27 | Python | 2,034 | 93 | import numpy as np
import pytest
from rdkit import Chem
from chemprop.featurizers import MultiHotBondFeaturizer
SMI = "Cn1nc(CC(=O)Nc2ccc3oc4ccccc4c3c2)c2ccccc2c1=O"
@pytest.fixture(params=list(Chem.MolFromSmiles(SMI).GetBonds()))
def bond(request):
return request.param
@pytest.fixture
def bond_types():
r... |
7dbd2a77620e467d643dad27ff8d8df55d0b3d058bbe9a226c9d5f0793d8329d | Python | 2,039 | 52 | import requests # for making requests to the API
import json # for parsing text responses to json
import pandas as pd # for parsing a JSON response object into a Pandas DataFrame
def get_token(email_address, secret):
url = ("https://analytic.tbportals.niaid.nih.gov/api/Token?" +
f"emailAddress={email_addre... |
6c0209a5d72c2a6636b5f63477ba00cabbd0fd1e8dd737726237d39040988d9f | Python | 2,040 | 69 | #!/usr/bin/env python
# Copyright (c) Facebook, Inc. and its affiliates.
import glob
import os
from setuptools import find_packages, setup
import torch
from torch.utils.cpp_extension import CUDA_HOME, CppExtension, CUDAExtension
def get_extensions():
this_dir = os.path.dirname(os.path.abspath(__file__))
exte... |
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