sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1b8716ebcdadbe4af93c95d2bfd2a3dec9b29d518d91848c68c3ac37c39890a2 | Python | 16,736 | 474 | # Mildred A. Herrera, Wojciech Ambrosiak
# Jan Siemens lab
# University of Heidelberg
import matplotlib.pyplot as plt #library for plotting
import numpy as np #numeric library
import pyabf #library to open *.abf files
from scipy.signal import medfilt
from scipy.signal import convolve
from scipy.signal import savgol_fi... |
1cf52293e385a585d108fe9b09e6c8c6585dc1162750a2db542b77750e02278d | Python | 16,738 | 348 | """
Script for extracting particles from a filament network in a single membrane graph
Input: - A STAR file with a list of graphs (MbGraphMCF) as it is returned by
by mb_fils_network.py script:
+ Density map tomogram
+ Segmentation tomogram
+ MbGraphMCF... |
859676b4adb21f1389cf2ec070ae0cf7255c3711809e1ba5006d3e7d7d7b6030 | Python | 16,740 | 358 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
import control.utils as utils
from control._def import *
import control.tracking as tracking
from control.core import *
from queue imp... |
be1d8b4a10164b108f50be52009e4f10475b804cfb21561fb4efbac4e447944c | Python | 16,743 | 410 | # 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... |
f8f0e58e819532373237926128b3165399203f776cd45db90d93c9222cbcf151 | Python | 16,745 | 491 | #! /usr/bin/env python
# ----------------------------------------------------------------------
# Copyright (C) 2018, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can re... |
64d3063e72dfe1ff5dbcb4996cbacb60ac98eb6998c1a14b607461bb0364df70 | Python | 16,748 | 336 | import os
import unittest
from unittest.mock import patch
import pandas as pd
from hed.errors.exceptions import HedFileError
from hed.tools.analysis.key_map import KeyMap
from hed.tools.util.data_util import get_new_dataframe
from hed.tools.util.io_util import get_file_list
class Test(unittest.TestCase):
@class... |
5e993d9adb407e731f2daa2d12a3e5bcd6f36e6b497cd679834291b873c18805 | Python | 16,752 | 433 | #
# Test module for ACME validation functions
#
# Copyright © 2026 Ernst Strüngmann Institute (ESI) of the Max Planck Society
#
# SPDX-License-Identifier: BSD-3-Clause
#
# Builtin/3rd party package imports
import pytest
import numpy as np
import os
import tempfile
import types
import datetime
import time
# Local impo... |
8a6e0eb7a5006f24b658e681d2273d185d95682584bb8eafd7899a17a215974e | Python | 16,760 | 232 | import numpy as np
import copy
import torch
from torch_geometric.loader import DataLoader
from utils.diffusion_utils import modify_conformer, set_time
from utils.torsion import modify_conformer_torsion_angles
from scipy.spatial.transform import Rotation as R
from utils.affine import T
from utils.geometry import axis_... |
b3aa98be1518a9206c5a7f22c0e21d7c2cfae965f0aa2060414ab044f510b528 | Python | 16,769 | 348 | """
Script for extracting particles from a filament network in a single membrane graph
Input: - A STAR file with a list of graphs (MbGraphMCF) as it is returned by
by mb_fils_network.py script:
+ Density map tomogram
+ Segmentation tomogram
+ MbGraphMCF... |
16f8b7518ffd2ce39a8cd2d92632ca334b28639cba06797c39a82e2409740caa | Python | 16,770 | 484 | # 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... |
d3491449d0874b0c70ec08d543084d232ceedac383f4ca311e56d2f51af0eae2 | Python | 16,776 | 442 | # -*- coding: utf-8 -*-
"""
Created on Fri Jun 7 17:07:42 2024
@author: mpolonen
"""
import numpy as np
import pathlib
import scipy.signal as sig
from expyfun.io import read_hdf5, write_hdf5
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
plt.ion()
src = pathlib.Path(__fi... |
4b379d22caeeca798cabd9e25a418380acef8f54807968a2b59481515bb87285 | Python | 16,781 | 379 | from itertools import product
import numpy as np
from examples.drake.iiwa_utils import open_wsg50_gripper, get_box_grasps, get_top_cylinder_grasps, \
get_close_wsg50_positions, get_open_wsg50_positions
from examples.drake.motion import plan_joint_motion, plan_waypoints_joint_motion, \
get_extend_fn, interpola... |
12948ae262a9f137424b6cbb3ec2b96377fcdae2e9b29b8642c9770b6d3c4863 | Python | 16,783 | 337 | import numpy as np
import tensorflow as tf
import tensorflow.contrib.slim as slim
from RNNs import recurrent_networks
import sys, os, scipy.signal
####################################################################################
#Used to initialize weights for policy and value output layers
def normalized_columns_i... |
b1974f76f40745a7e5c2abccccd2e1ea862aa6d996ce50d1058bedfb98fb587c | Python | 16,783 | 474 | import os
import time
import logging
import math
import argparse
import numpy as np
from PIL import Image, ImageOps
from collections import Counter, OrderedDict, defaultdict
import torch
import torch.nn as nn
from torch.autograd import Variable
import torch.backends.cudnn as cudnn
import torchvision
from t... |
0da6760afc6461defe9bbbf5700d4721da839021971326baf6d7e5b39d8a6048 | Python | 16,794 | 417 | """Smoke + signature tests for untested public registration functions.
These functions are part of the registration pipeline but had zero
direct test coverage per audit:
- register_ndim (the unified 2D/3D dispatcher)
- transform_input_data (volume-transform analogue of transform_input_points)
- count_registered_... |
ef27b1b054928e48aff0c3d3daf8002f0058732ca3046a11131e86ef60125722 | Python | 16,794 | 424 | ### Define a few global variables
import os
import numpy as np
# Path for figures, data
figure_path = "../figures/"
data_path = "../data/"
# Random state
rng = np.random.RandomState()
### Plotting
# Fontsize
fs = 12
# Figure labels
flbs = ["(%s)"%s for s in "abcdefghijkl"]
flbs = ["%s"%s for s in "ABCDEFGHIJKL"]
#... |
299c18cf8a6bd382e797ed4375b26aa40abc088904aee7fb42719b8d436675a5 | Python | 16,803 | 458 | # 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... |
cd845ab8578df83393d8c4b18d7efe5cb24c72afa06706e0a68538ea5ee17de0 | Python | 16,803 | 396 | """Compare PyPREP results to MATLAB PREP."""
from urllib.request import urlopen
import mne
import numpy as np
import pytest
import scipy
from pyprep.find_noisy_channels import NoisyChannels
from pyprep.reference import Reference
from pyprep.removeTrend import removeTrend
# Define some fixtures for things that will b... |
331b4a7170121edccd8ff1f65264a6dc74993e7bcd67d36b095e82b8eb3ea584 | Python | 16,815 | 539 | import os
import torch
import yaml
import numpy as np
from PIL import Image
import torch.nn.functional as F
def clear(x):
x = x.detach().cpu().squeeze().numpy()
return normalize_np(x)
def clear_color(x):
x = x.detach().cpu().squeeze().numpy()
return normalize_np(np.transpose(x, (1, 2, 0)))
def no... |
9ade7af61463b05c6c3506091b32e53242b4702e73e9fad8f4a3529c9407dffd | Python | 16,817 | 390 | # -*- coding: utf-8 -*-
# modified from：https://github.com/murufeng/FUIR/blob/main/basicsr/models/archs/SCUNET_arch.py
import math
import torch
import torch.nn as nn
import numpy as np
from einops import rearrange
from einops.layers.torch import Rearrange, Reduce
from timm.models.layers import trunc_normal_, ... |
dba91750908b946a697f9c6d9ee09d80fbbdd8f359cac96c12df5a66cdc9c23c | Python | 16,828 | 488 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 26 13:05:23 2021
@author: joaquin
"""
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import scipy.io
import pandas as pd
import os
import mat73
from scipy import signal
from scipy import stats
from statsmodels.tsa.stattoo... |
3c9e61373267e364591a1cc2e5a5b0b6f509bb9d43a0701e3b0dfd4b0dd2c2ad | Python | 16,836 | 485 | """
Measures distance from STAR files particles to segmentations and splits them according their distance
Input: - STAR files
- Segmentation
- Distance parameters
- Particle template preprocessing settings
Output: - The splited STAR files
"""
__author__ = 'Antonio M... |
2c565ef702bf8cfeb72650a7b3afe8001339861620564415dbd63b2f9075ea83 | Python | 16,841 | 380 | from math import log
import pickle
import os
from random import shuffle, randint, seed
import time
import sys
METHYLATION_CUTOFF = 0.3
class DTNode():
def __init__(self, cancerDataSet, healthyDataSet, locations, remainingQuestions, forbiddenQuestions, healthyRatio, NA_VALUE = -1):
myPrint("Starting analys... |
08ad20c70043ffc59d18c0b16e9aed64f08ad0ef8cbc4aca2adc5897324d2deb | Python | 16,844 | 341 | # -*- coding: utf-8 -*-
from typing import List, Tuple
import torch
import torch.nn as nn
from supar.config import Config
from supar.model import Model
from supar.models.const.aj.transform import AttachJuxtaposeTree
from supar.modules import GraphConvolutionalNetwork
from supar.utils.common import INF
from supar.util... |
4cef59ad687996404acfd3c0c1518a314cc25c287c01c825b9e32a2e235823b6 | Python | 16,859 | 430 | # \file TestRegistration.py
# \brief Class containing unit tests for module Stack
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date September 2016
import unittest
# Import libraries
import SimpleITK as sitk
import itk
import numpy as np
import os
# Import modules
import niftymic.base.stack as st
im... |
11f34e94b01d5e16c376afb8066236607461f790b1b56fb6e902f31d0c6c5ca4 | Python | 16,861 | 407 | # 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... |
3b00c50cecf73a9e47ab8756c08364aa372c223e5f0a619271342a222093a107 | Python | 16,874 | 365 | import argparse
import numpy as np
import os
import pandas as pd
import random
import sys
from tabulate import tabulate
from typing import Tuple
import torch
from constants import BIN_LOCATIONS1, BIN_LOCATIONS2, N_ITEMS
from src.models import get_reyclassifier, get_reyregressor
from old_code.dataloaders.dataloader_ite... |
a4ecbbcc1ee885720973fd5e9fe5b0850e1507c1b5b396e1f1995e17405901c5 | Python | 16,891 | 426 | # Adopted from optical_nls.py from all-optical-neural-networks https://github.com/tomdbar/all-optical-neural-networks
import torch
from utils.complex_utils import complex_utils as Z
from utils.optics_utils import super_gaussian, gaussian, gaussian_beamlets
class PhaseReset(torch.nn.Module):
def __init__(... |
6c387661a3304d92ea6636120bfd09361ab9a80f4e20d90435b4fefff01580bb | Python | 16,892 | 508 | import argparse
import cv2
import time
import numpy as np
import threading
from control._def import *
from ids_peak import ids_peak
from ids_peak_ipl import ids_peak_ipl
from ids_peak import ids_peak_ipl_extension
def get_sn_by_model(model_name):
ids_peak.Library.Initialize()
device_manager = ids_peak.Device... |
1d9bbbaa55aa46c6743f20d5cf7df7f5cd430d7131ff823f5619b19297ede36f | Python | 16,893 | 540 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
a877a57e2867b5a5db26f525974d8e35a470c6c7203496ccd4ebe1d626a0c547 | Python | 16,893 | 406 | """
PyQt5 dialog widgets for the stitching GUI.
Owns:
- ``StitchingPreviewWorker`` - QObject/QThread worker that stitches a single
section preview in the background and emits results via signals.
- ``PreviewWindow`` - QDialog that lets the user scrub through
sections and open per-section napari pre... |
14efbb5b7781be63c8d205dcf64bc62abd344d5bbd637d12cc96c2a0b4912aa7 | Python | 16,895 | 543 | import jax
import jax.numpy as jnp
import numpy as np
from functools import partial
import functools
from typing import (Optional, Sequence)
# from jax.scipy.special import logsumexp
import matplotlib.pyplot as plt
from jax.scipy.special import gammaln
from netket.utils import mpi
import tqdm
import flax
import jax
im... |
d4d6a3f73e6e4a4287fc0073f55008661a2697a53c9ba83e697975704e2a6beb | Python | 16,895 | 476 | """Schemas for molecular DFT codes parsed by cclib."""
from __future__ import annotations
import logging
import os
from inspect import getmembers, isclass
from pathlib import Path
from typing import TYPE_CHECKING
import cclib
from ase.atoms import Atoms
from cclib.io import ccread
from quacc import QuaccDefault, ge... |
3603479a5c742c57063b07ccb98b1301c69d31fc68fe953bea82a3107cf706dc | Python | 16,897 | 428 | from collections import OrderedDict
from typing import Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
class SSTEmotionNet(nn.Module):
r'''
Spatial-Spectral-Temporal based Attention 3D Dense Network (SST-EmotionNet) for EEG emotion recognition. For more details, please refer to the f... |
8aee6f913e21d9b5769d7bba825f48b8a578c25677dc91a18f1ddc957c623856 | Python | 16,898 | 427 | # 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... |
e110f4fa34721551106df8f3cf096472da4e959f8264765816b54ca7e548d164 | Python | 16,910 | 398 | import argparse
import cv2
import glob
import mimetypes
import numpy as np
import os
import shutil
import subprocess
import torch
from basicsr.archs.rrdbnet_arch import RRDBNet
from basicsr.utils.download_util import load_file_from_url
from os import path as osp
from tqdm import tqdm
from realesrgan import RealESRGANe... |
30e889e09f7cbbdd82042fcd09acb51407c23f6444d7ab6bd32740ebd1733ed5 | Python | 16,911 | 476 | # 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... |
f859f9f44edf490e41d68a99213e57ccec457a56737cd8b5f5008e18cdc31bfc | Python | 16,918 | 429 | import os, argparse, math
import numpy as np
from glob import glob
from tqdm import tqdm
import sys
import time
import logging
import shutil
from medpy import metric
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.data
import torch.optim as optim
from medpy.metric.binary import hd, dc, assd, ... |
53ea8f60a7554bf5dd04bf674af827db38c2fe7266b3993c080dc8686467f2a3 | Python | 16,920 | 360 | # -*- coding: utf-8 -*-
# @title Emulate configuration file similarly to fpga
# @file emulate_fpga.py
# @author Romain Beaubois
# @date 06 Oct 2023
# @copyright
# SPDX-FileCopyrightText: © 2022 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief
... |
7513a0e0076568d6db1c017c07afdc1f9611a4d71d4e08c6de0e6fb47ef08f49 | Python | 16,926 | 292 | import os
import time
import numpy as np
from geometry_functions import EikonalGeometry
from propagation_models import EikonalDjikstraTet, PrescribedLAT
from cellular_models import CellularModelBiomarkerDictionary
from ecg_functions import PseudoEcgTetFromVM
from electrophysiology_functions import ElectrophysiologyAPD... |
00bf980b38a5fb2f3ea803f8da58e06a80191aadb08f7927b27ac432601053ac | Python | 16,931 | 367 | import concurrent.futures
import multiprocessing as mp
import os
import tempfile
import threading
from pathlib import Path
from unittest.mock import patch
import numpy as np
import pandas as pd
import unittest
from torcheeg import model_selection
from torcheeg.datasets import BaseDataset
from torcheeg.io import EEGS... |
3a1b0d884255d5ddd5f16e9ecc396efc5d7bf2ea68ca915a390fd38840008855 | Python | 16,939 | 331 | import argparse
import os
import os.path as osp
import torch
import torch.nn as nn
import torch.optim as optim
import network
import loss
import pre_process as prep
from torch.utils.data import DataLoader
import lr_schedule
from data_list import ImageList
import multiprocessing
def image_classification_test(loader, m... |
04cffd127a693271b3ab10887299427b5ec429c3db5aa1fd7197a8174c288702 | Python | 16,946 | 537 | # 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... |
470a2eeb90469ce8a9a1617a9aa73fbfe6804f0a1213c9ad33e8312c0fb90197 | Python | 16,947 | 390 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import matplotlib.pyplot as plt
import dill
import os
import time
import glob
from sklearn.metrics import auc
import statsmodels.api as sm
from scipy.fft import rfft, r... |
ad0ae5c789ece83f0581d4faeefcba5b0cbd41c45781e2837b3b24de5183f019 | Python | 16,950 | 351 | """Shared test fixtures for the regtools test suite.
Provides a suite-wide autouse guard (``_no_real_window_spawn``) that keeps a
test run from putting a real window on the developer's screen: no terminal
launches through ``_TerminalJobMixin``, no tkinter modals, headless matplotlib.
See that fixture's docstring ... |
54a3b9c24e48dac6b09a0b9461e272c56db95d5988ea5b2a2e86a8aacac19559 | Python | 16,959 | 428 | # MIT License
#
# Copyright (c) 2020 Mehran Maghoumi
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, mer... |
cc2d92dbaec250226351fe60645d118860e6e3311c1959b4a9c7f2b5accf3715 | Python | 16,967 | 428 | """Tests for cog._adt module (FieldType, PrimitiveType)."""
from typing import Annotated, Any, Dict, List, Optional, TypedDict
import pytest
from typing_extensions import TypedDict as ExtensionsTypedDict
from cog import Opaque
from cog._adt import FieldType, PrimitiveType, Repetition
class ExampleTypedDict(TypedDi... |
2d4a613ccf75dd28c3b3107221f54f1abd6d109d5eff7cf8149c3aee6d676e4e | Python | 16,973 | 485 | """Morphology reconstruction data structure."""
import math
from collections import deque
import numpy as np
from treem.io import SWC, load_swc, save_swc
from treem.tree import Tree
from treem.utils.geom import norm, rotation_matrix
class Node(Tree):
"""Morphology data storage."""
def __init__(self, value... |
3078c150a86e567c1449bcc2d066b7e2d1459ca7a9a7dcdeaa83bced2e4bddda | Python | 16,974 | 370 | import argparse
import collections
import gzip
import math
import os
import random
import shutil
import subprocess
import sys
import time
import numpy as np
import pandas as pd
import utils
import tabix as tb
import tensorflow as tf
import pybedtools as pybt
import pyximport; pyximport.install()
import cython_fxn
f... |
8ff0c2793f0d911d2e052eb09f602e1cf47d8c13279ad3967f7d50179429a8ad | Python | 16,975 | 368 | import argparse
import collections
import gzip
import math
import os
import random
import shutil
import subprocess
import sys
import time
import numpy as np
import pandas as pd
import utils
import tabix as tb
import tensorflow as tf
import pybedtools as pybt
import pyximport; pyximport.install()
import cython_fxn
f... |
10b4b0bfa699fc536e2a386a4189d15fd0d9a8567ab351dede26334a5d7d1818 | Python | 16,986 | 481 | # 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... |
569b867857699fc054ebd1919ee5920ad4fba0d070d393646ca157418b454782 | Python | 16,995 | 478 | # 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... |
637dca0c18364755633364b3c2706c2456c5715a95f9869599a8ba467653826f | Python | 17,002 | 461 | # 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... |
8af2a54c668d220616b93f5f7808aaa0c7951cc3dc763338976e6335014879b4 | Python | 17,006 | 499 | """
@Mariellapanag
Created on March 2023
@author: mariella
Functions for computing abnormalities from continuous iEEG data.
Includes
load_atlas
load_patient_channel_json
get_info_from_parc_scale
match_most_common_channel_set
keep_consensus_chan
subset_channel_df
map_chan2rois
map_c... |
4710188776d4711920fd50f763bd2196b24e38cac681295f4a17a4558c9bebd3 | Python | 17,007 | 504 | """ Logic for template building
Execute using the 'bifrost' executable installed by setuptools
"""
import logging
import os
import shutil
import sys
from glob import glob
import ants
import numpy as np
import scipy
from skimage.exposure import equalize_adapthist
from skimage.filters import threshold_triangle as tria... |
77c8481f0c0d37495518937b443eb322e74daa19724daae7f23a4c9f479983ee | Python | 17,015 | 316 | ##### MODEL AND DATA LOADING
import time
start = time.time()
import torch
# torch.cuda.empty_cache()
import torch.utils.data
import torchvision.transforms as transforms
import torchvision.datasets as datasets
from torch.autograd import Variable
import numpy as np
import matplotlib.pyplot as plt
import cv2
from PIL imp... |
e65181a96b283f6f9c78bf8d4908c592fc6657bb7652350254c444a68d2009e0 | Python | 17,017 | 460 | import numpy as np
import csv
from cv2 import imread
from preprocess import preprocess, preprocess_basic
import os
from helpers import File, create_directory
from sklearn.utils import shuffle
import time
import math
from collections import defaultdict
from restore_predict import restore
from config import DATA_DIR, DE... |
d8d9efb75e6b963c00274d64006d5d915d1b482ef76c0fd2a89d7fefa5fe4cf1 | Python | 17,018 | 380 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""flyb_to_bin.py —— 把 MaleCNS v1.0 的 FLYB v1 二进制转换为本项目 sim-core 的格式三件套。
输入（只读）：vendor/fly-brain-minecraft/src/main/resources/connectome/malecns-v1.0.flyb.gz
FLYB v1 格式规范见 vendor/fly-brain-minecraft/PROVENANCE.md 第 4 节（本解析器按其实现）。
输出（写 game/data/）：
1. connectome-malecn... |
7e7b9ed7d8a21459e1a4593ae3ed47023f9a163a11021dd0014a80232501a005 | Python | 17,026 | 410 | # -*- coding: utf-8 -*-
#
# Load data from NWB file
#
# Builtin/3rd party package imports
import os
import sys
import h5py
import subprocess
import numpy as np
from tqdm import tqdm
# Local imports
from syncopy.datatype.continuous_data import AnalogData
from syncopy.datatype.discrete_data import EventData, SpikeData
... |
8e82ac99a875d3df2585b9586dd7ad174852a95d2e2b850d69e516a07bc26601 | Python | 17,027 | 454 | from __future__ import annotations
import os
from copy import deepcopy
from pathlib import Path
from types import SimpleNamespace
import numpy as np
import pytest
from ase.build import bulk, molecule
from ase.calculators.emt import EMT
from ase.io import Trajectory, read
from ase.mep import NEB
from ase.optimize impo... |
f7671810e801feccc27d62da1706a6ca2645a7ab0e86f8eafb351c770852ae42 | Python | 17,030 | 318 | """Context construction and Clean/Fly isolation regressions.
Random tiny weights: these are software tests of what reaches the model, not evidence
about language behavior. Tests using `qwen_engine` exercise the genuine Qwen3 tokenizer,
chat template and special tokens.
"""
from threading import Event
import numpy as ... |
9066b0b6c3afd68a2e1fc98085e3be6684ab994d5e3ce144c3a5c4cfa7b45d7f | Python | 17,036 | 398 | """
Generates a ListTomoParticle object for the statistical spatial analysis of particles
Input: - A STAR file with particles
- A STAR file for paring picked particles and (sub-)volumes segmentations (Volume Of Interes, VOI)
Output: - A STAR file with the pickled ListTomoPaticles objects
""... |
517815b15eb4153e1ad553a13bb91bb8b9b8946b283e5529738237e102c0c90c | Python | 17,047 | 398 | """
Generates a ListTomoParticle object for the statistical spatial analysis of particles
Input: - A STAR file with particles
- A STAR file for paring picked particles and (sub-)volumes segmentations (Volume Of Interes, VOI)
Output: - A STAR file with the pickled ListTomoPaticles objects
""... |
9837087d79d13264e04958e329504c14c6044bec589d314fedd93f66d338ee28 | Python | 17,047 | 390 | """Re-quantification of cell counts and region volumes against a (possibly
modified) CCF annotation volume.
The cell points are never moved - counts change only because region
boundaries moved in the annotation.
"""
from __future__ import annotations
import logging
import numpy as np
import pandas as pd... |
e51b4ef9d0836494ecaa3ca59364700caf17e52def159b3392d3851297d5e108 | Python | 17,047 | 452 | """Data utils functions for pre-processing and data loading."""
import os
import pickle as pkl
import sys
# from config_debug import parser
import networkx as nx
import numpy as np
import scipy.sparse as sp
import torch
import pandas as pd
from scipy.linalg import block_diag
from torch.utils.data import Dataset, DataLo... |
545707b21e5a366c5d8498d185a9222e60a0dd9df83f674e0b53f3b14d3ef74b | Python | 17,051 | 438 | import numpy as np
from skimage.filters import threshold_otsu
from functools import cached_property
import tempfile
import torch
import tifffile
import logging
from typing import Dict, List, Optional, Tuple
from .utils import get_cosine_similarity_with_sequence_np
from .features import OptopatchGlobalFeatureContainer
... |
d8afc33ee47b40438b202145dbf83284a53876297b61f99cf8acc073b94bb626 | Python | 17,051 | 382 | # Node-group asset "Orient to Best View" (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_CH... |
0a85f6646d3b493a8639e8b46459b885d67d959f9e313c00ccc377f18e800ecf | Python | 17,054 | 446 | import warnings
warnings.filterwarnings("ignore")
import torch
import torch.nn as nn
from torch_geometric.nn import HypergraphConv
from torch_geometric.data import Data
import anndata as ann
import numpy as np
import scanpy as sc
import pytorch_lightning as pl
import torchvision.transforms as tf
from sklearn.cluster im... |
3d4c9af87fba16c48bd48d78b2176b50dd68489902214be2d1c49f15deb906cf | Python | 17,066 | 453 | # 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... |
0a204f88128301319f28d208aa588c97fb9dec215142ee77e1203262aafb7ac4 | Python | 17,070 | 463 | # 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... |
fd1d5a76d4469ca647b064f13744b0b28fbe12219cc2f32097f65c48a0c82ec3 | Python | 17,075 | 364 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 6 09:17:37 2022
This script calls every script necessary to analyse the differences between contexts.
PATHS['ScriptsPathRoot'] should correspond to the GitHub folder of the Bayesian Battery.
If not, it can be changed in the first lines of this scrip... |
7349819c7b949d01543ed40fe8a5ba805782f706c90eef14b4efa213384ea8ce | Python | 17,080 | 384 | from torch.utils.data import Dataset
import torch
import pandas as pd
import numpy as np
from typing import Tuple, Optional, Union
from mnp.molecular_featurizer import MolecularFeaturizer
from tqdm import tqdm
tqdm.pandas()
class MolecularGraphMetaDataset(Dataset):
"""
Pytorch dataset to represent molecula... |
992593d486a53fbefad92a130d796c8ca5bb23726c1e08e7e2d90bccb8069654 | Python | 17,081 | 407 | """
Unit tests for regtools/stitching/core/tile.py and stitcher.py
Covers:
- Tile: trim, apply_average_tile, get_image_region, initialize_image
- Stitcher: initialize_images
"""
import numpy as np
import pytest
# ===========================================================================
# Tile
# ... |
b9187d430227dbab36376d6ef7711b35b226c55abfe450db3c5860d281d44766 | Python | 17,087 | 624 | # 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... |
96a4bc1c072bb1c901ca926701f236f88fee9d15986874ca275ed4c12a290100 | Python | 17,088 | 387 | import copy
import gc
from collections import OrderedDict
from multiprocessing import pool, cpu_count
from operator import itemgetter
import model
from torch.utils.data import DataLoader
from tqdm.auto import tqdm
from .models import *
from .client import Client
from .utils import *
logger = logging.getLogger(__name... |
b3bb51d0d1968011df8f182749242cbb0176a71a37e37c51e24f0fab840932b9 | Python | 17,090 | 462 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''plotting script for figure 4 in manuscript preprint on output of
example_parallel_network.py
Copyright (C) 2018 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Lic... |
518988fba91c4feb1385f787a2c4e6633c04ba8d6b680f2f6d02bc7d86078b4b | Python | 17,095 | 455 | import gzip
import os
from pathlib import Path
import bpy
import databpy
import numpy as np
from gridData import Grid
from ...blender import coll
from ...nodes.geometry import (
DensityStyleISOSurface,
DensityStyleSurface,
DensityStyleWire,
)
from .base import Density
def cell_vectors(lengths, angles) -> ... |
417f5f06e5daac73e9a94d24c3b6c8313a409320763ab806beb9b48210a5b733 | Python | 17,099 | 439 | # Copyright (C) 2019 Computational Science Lab, UPF <http://www.compscience.org/>
# Copying and distribution is allowed under AGPLv3 license
#
# This script implements conditional Generative Adversarial Networks (cGANs) for 3D molecular structure generation,
# as well as graph-based neural networks (GNNs) for learning ... |
d6c5c414f61a2171c9ac3beddc241b99f7952b8ab2501b3a7f7fd1be238728c2 | Python | 17,102 | 471 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Demonstrate extracellular electric stimulation of a LFPy.Network instance,
using the LFPy.Network.enable_extracellular_stimulation() method.
Here a simple model of neuron ball-and-stick is used to populate two
morphologies with active HH channels inserted in the somas a... |
cc73e18d4970ae6ff477c20d99e630ce8378d0243297fcccb22e84aba871c553 | Python | 17,103 | 434 | # 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... |
3a628fb2071b9d6900346faf1f6528dfb06dcda97c7291b08fd2f8929a7999a7 | Python | 17,104 | 453 | """Data utils functions for pre-processing and data loading."""
import os
import pickle as pkl
import sys
# from config_debug import parser
import networkx as nx
import numpy as np
import scipy.sparse as sp
import torch
import pandas as pd
from scipy.linalg import block_diag
from torch.utils.data import Dataset, DataLo... |
38f89082f28b9527ca673f7f9dbabf3423e32d2e8e51461c1535d631163a8e9d | Python | 17,107 | 331 | import mne
import scipy
import glob
import numpy as np
import pandas as pd
from scipy.stats import zscore
from scipy.io import loadmat, savemat
def castToList(x):
# Casts x to a list
if isinstance(x, list):
return x
elif isinstance(x, str):
return [x]
try:
return list(x)
ex... |
3ead347c71bee8372688c34154c8030d8b361497677c6d94ee54c42540594f49 | Python | 17,110 | 449 | #!/usr/bin/env python
import argparse
import pathlib
import time
try:
import apex
except ImportError:
pass
import numpy as np
import torch
import torch.nn as nn
import torch.distributed as dist
import torchvision
from fvcore.common.checkpoint import Checkpointer
from pytorch_image_classification import (
... |
ec5d3e6b18c94a22d135666e3fa1a7587ea2c0406956dbd23c393029356f2696 | Python | 17,110 | 452 | import argparse
import logging
import os
import anndata
import h5py
import numpy as np
import pandas as pd
import scipy.sparse
from pandas import CategoricalDtype
from cirrocumulus.anndata_dataset import read_adata
from cirrocumulus.anndata_util import dataset_schema, get_scanpy_marker_keys
from cirrocumulus.io_util ... |
3aa7c1ba0ccb58a9eb8d30238f31c24bf3c342d5d19513540f6979960b649c1f | Python | 17,118 | 406 | """Compare PyPREP results to MATLAB PREP."""
# Authors: The PyPREP developers
# SPDX-License-Identifier: MIT
from urllib.request import urlopen
import mne
import numpy as np
import pytest
import scipy
from pyprep.find_noisy_channels import NoisyChannels
from pyprep.reference import Reference
from pyprep.removeTrend... |
0a650240dcd415d600043de5d7393a63b6d102877e855eedd6c3a1ad2c0a4a9a | Python | 17,121 | 513 | # -*- coding: utf-8 -*-
"""
Created on Fri Sep 15 10:31:15 2023
@author: Dustin Garner
"""
import math
import itertools
from enum import Enum
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.ndimage import gaussian_filter
from fafbseg import flywire
import flycode.reduction as reduct... |
eea38afd0950438a8a991ba3260e02067c00857246d65302cda15db6deca8b20 | Python | 17,129 | 518 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 17 11:55:01 2025
@author: deeperthought
"""
GPU = 1
import tensorflow as tf
if tf.__version__[0] == '1':
config = tf.ConfigProto()
config.gpu_options.allow_growth = True
config.gpu_options.visible_device_list="0"
tf.keras.backend.s... |
8a1b524e0eb355293b46875266361dbb787333bda207249505b071ac204446c9 | Python | 17,133 | 354 | """
Script for extracting particles from a filament network of a unoriented single membrane graph
Input: - A STAR file with a list of graphs (MbGraphMCF) as it is returned by
by mb_fils_network.py script:
+ Density map tomogram
+ Segmentation tomogram
+... |
efb3a8dcd74dc6695ccc3470e6a5ecc4643b453514a05a3f5da73cc0b335272d | Python | 17,134 | 405 | """Fill-based label rewrite for the CCF boundary editor.
Converts a slice's edited contour polygons into a new label slice by
rasterising each polygon and reassigning orphan pixels to the nearest
pristine non-region label. No deformation field, no smooth warp, no
RBF backend - the polygon *is* the new boundary.
... |
9ff823c4bf5c61d8b1cc492db4599800b29b2d63ca6cf2310a94744cfcf8faeb | Python | 17,136 | 412 | import pandas as pd
import itk
import SimpleITK as sitk
import os
import sys
import json
import argparse
import logging
class AllenDatasetBuilder:
downsample = 8 # downsample = 2^3
#path="/Users/jtduda/projects/Allen/Downsampled/example_batch_with_alignment"
#atlasPath="/Users/jtduda/projects/Allen/Downsa... |
a51ac4cb36954c184db2cea817b66f264fd9f48f2a3459699fe6f550a1b709ce | Python | 17,137 | 533 | #!/usr/bin/env python
# coding: utf-8
# ### LASSO parameter range experiments, summary across all genes
# In[1]:
import os
import itertools as it
from math import ceil
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
from scipy.stats import pearsonr, sp... |
a744a3092b72794acc4af992b3a32ad120cca358efd0ef254020b9b823b2e3ce | Python | 17,137 | 383 | """Format templates for HED schema error messages."""
from hed.errors.error_reporter import hed_error
from hed.errors.error_types import ErrorSeverity, SchemaAttributeErrors, SchemaErrors, SchemaWarnings
@hed_error(SchemaErrors.SCHEMA_DUPLICATE_NODE)
def schema_error_hed_duplicate_node(tag, duplicate_tag_list, secti... |
f5bfc537b7ca3fb55ff20e0a52ff0de2646513e00c097e683999f77fa7b4e2bd | Python | 17,140 | 418 | # 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... |
fa2b25c37e0d219078ae712c9eed7778e63a955ed1e6bcf55335ac86deb29a12 | Python | 17,141 | 535 | # qc.py
import dnaio
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from pathlib import Path
from itertools import cycle
from itertools import islice
from fba.levenshtein import (
create_index,
query_index,
select_query
)
from fba.utils import open_by_suffix, get_logger
logger = g... |
219d49e86cd05d2fda27ffa054b3ac08aee07209e12c8bf3eb290ac132383d38 | Python | 17,142 | 492 | import torch
import h5torch
import numpy as np
from maldi_nn.utils.drug import (
SmilesToIndex,
SmilesToECFP,
SmilesToAlphabet,
SmilesToDEEPSmilesAlphabet,
SmilesToSelfiesAlphabet,
SmilesToImage,
SmilesToLINGOKernel,
)
import re
from maldi_nn.spectrum import SpectrumObject
from lightning imp... |
1113e24c80f2c27743b59432446d640eb2cc3d0aff77ebc54a5417ba941ba7e4 | Python | 17,145 | 292 | """
TRANSCRIPTOME_TEST.py written 2026-09-23.
Pre-registration: 04-NOTES/PREREG-2026-09-23b-TRANSCRIPTOME.md (sha256 71be79d5...), Addenda 1 and 2.
Inputs frozen before this ran: 06-OUTPUT/FROZEN-2026-09-23-DELTA-ALL-TYPES.csv, 06-OUTPUT/transcriptome_type_map.csv.
Output: 06-OUTPUT/transcriptome_test.txt, 06-OUT... |
e8ff8f952ac3d11ec5fd94ad88dd91c17e658b7f91d01dcdeacc7e534032a762 | Python | 17,155 | 540 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
fff5dc2be20d9467645ed0dc9e0c399de6c262533a56d0d4a07b9beaeff254c9 | Python | 17,156 | 479 | """Custom Espresso calculator and template."""
from __future__ import annotations
import logging
import os
import re
from pathlib import Path
from typing import TYPE_CHECKING
import numpy as np
from ase.atoms import Atoms
from ase.calculators.espresso import EspressoProfile
from ase.calculators.espresso import Espre... |
5f8f80a96f756983e13f1ebec5b7faeb21c540a6eaa9f0bfe59b785a42d7d477 | Python | 17,177 | 495 | from __future__ import absolute_import
import hmac
import os
import sys
import warnings
from binascii import hexlify, unhexlify
from hashlib import md5, sha1, sha256
from ..exceptions import (
InsecurePlatformWarning,
ProxySchemeUnsupported,
SNIMissingWarning,
SSLError,
)
from ..packages import six
fr... |
648760d59f00dd1c86eec796e67b9016cc5650f62a94ea7d657533a193e1c326 | Python | 17,178 | 400 | """
Generates a ListTomoParticle object for the statistical spatial analysis of particles
Input: - A STAR file with particles
- A STAR file for paring picked particles and (sub-)volumes segmentations (Volume Of Interes, VOI)
Output: - A STAR file with the pickled ListTomoPaticles objects
""... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.