sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a2adab5a20d528fd7c420a7da70c171133e2ee81cd09aab1e3fd259e7a009c75 | Python | 8,789 | 251 | # -*- coding: utf-8 -*
import os
import re
from argparse import ArgumentParser
import sys
import gc
from torch.utils.data import DataLoader
from prefetch_generator import BackgroundGenerator
import numpy as np
import torch
import torch.nn.functional as F
from matplotlib import pyplot as plt
from tumor_detector.Dataload... |
da72f698a0d57298404c3c5dce3ea949166a69c0bc1c90d8966988d383d1e497 | Python | 8,790 | 237 | """Defaults and UI constants for Quadrant Folding background subtraction."""
from __future__ import annotations
from typing import List, Dict, Any
# Spinbox Ranges
RMIN_RMAX_RANGE = (-1, 5000)
EQUATOR_HEIGHT_RANGE = (1, 1000)
EQUATOR_CENTER_RANGE = (1, 1000)
LAYER_LINE_RANGE = (1, 1000)
N_PEAKS_RANGE = (0, 20)
PEAK_... |
64669fb25d15f34880226d3f471b3961478250ab75ccf5aa16153bf2fe161951 | Python | 8,791 | 340 | from typing import Dict
import pytest
import yaml
from deepreg.config.v011 import (
parse_data,
parse_image_loss,
parse_label_loss,
parse_loss,
parse_model,
parse_optimizer,
parse_reg_loss,
parse_v011,
)
@pytest.mark.parametrize(
("old_config_path", "latest_config_path"),
[
... |
f625dd518d0a94f30c75e8bac6a8e90d9493905bfdbced22a22b8d04e6e065f3 | Python | 8,792 | 206 | import subprocess, glob, os
from loguru import logger
import re
from typing import Tuple, Union, Type
from rdkit import Chem
from rdkit.Chem.rdchem import Mol
from rdkit.Chem import AllChem, rdDistGeom
logger.add("../logs/optimization.log", format="{time} {level} {message}",
filter="my_module", level="INFO"... |
c7655a8105deb2501c73e2044e3575a1bec65dc709e651f96070fd4ec6ffcf3f | Python | 8,793 | 209 | """Test per-pipeline version numbers: where they come from, and where they go.
Run from the repo root::
uv run python python/test_versions.py
Three pipelines ship from this repository and move at different speeds, so a
single number cannot describe them — and a result is only reproducible if it
records the versi... |
1cfe4a91725bfe19ed99256c677f2eb54b33ec2c7e927dfdfe19e700ea444dc9 | Python | 8,796 | 251 | # -*- coding: utf-8 -*-
"""
Created on Sat Apr 6 02:59:52 2024
@author: aka2333
"""
# In[]
import numpy as np
from scipy import stats
import pandas as pd
# In[]
def scale(x, upper=1, lower=0, method = '01'):
if method == 'std':
x = (x - x.mean()) / x.std() if x.std()>0 else (x - x.mean()) /... |
674a0b1f750994f66f1db16afc1f388133a3ad800eb41206419d000d409b5aa8 | Python | 8,796 | 224 | import numpy as np
from scipy.sparse import coo_matrix
import skimage as ski
import scipy.ndimage as ndi
import warnings
from . import util
def compute_voxel_offseted_linear_indices(pos_ind, mask_size, offset=1):
pos_ind = np.array(pos_ind) if isinstance(pos_ind, (list, tuple)) else pos_ind
mask_size = np.ar... |
bc7848b4d032e04f1139cba83ef265f9dd01731eb84bcb13736e2e48518258e0 | Python | 8,798 | 208 | """Test the functions in the yasa/spectral.py file."""
import unittest
from itertools import product
import matplotlib.pyplot as plt
import mne
import numpy as np
import pytest
from scipy.signal import welch
from yasa.fetchers import fetch_sample
from yasa.hypno import Hypnogram
from yasa.plotting import plot_spectr... |
17847fcf3decc5b48f600d822723ae63ad349ba52d9c6efc83a103fadcc9be37 | Python | 8,801 | 250 | # Copyright (c) DP Technology.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import numpy as np
import torch
from unicore.data import BaseWrapperDataset
from . import data_utils
from numba import njit
from functools import lru_cache
from sci... |
7789e23704e2ee87a542ad43e460d963705a534e00a144ba5fa1e2502cd0772d | Python | 8,803 | 232 | # functions_MoCo2DProject.py
# Functions file used in conjuction with dense_process_MoCo2DProject.py for the post-processing of the DENSE single-slice motion study data
# Not all the functions in this file are used in the dense_process code, some are just superfluous.
import numpy as np
import random
import math
impor... |
5ccdda0b78a973c8005cb8cc52dcfc5ce0296be288da0418cfa94bf519f96b55 | Python | 8,806 | 210 | """Reusable Deep Agent workflow for workspace and coding tasks."""
from __future__ import annotations
from collections.abc import Sequence
from copy import deepcopy
from typing import Any
from deepagents import create_deep_agent
from deepagents.backends import CompositeBackend, LocalShellBackend, StateBackend
from d... |
edc42179d6695ebc24e8c319828a505cda0af2383e9a7cd898c8f9743c3a3ff0 | Python | 8,807 | 193 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Script to resample a tractogram to a set number of streamlines.
Default behavior:
- If the number of requested streamlines is lower than the streamline count:
DOWNSAMPLE
- If the number of requested streamlines is higher than the streamline count:
UPSAMPLE (to preven... |
13e4dbf4b72b0a29addcbde139ac472e0dc83eef6ff76a17fd0d433ac5245e0a | Python | 8,808 | 270 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import csv
import json
import os
import random
import sys
from itertools import product
NAME = "comments"
def read_rules(name):
rules = []
with open(os.path.join(sys.argv[1], f"{name}.csv")) as f:
reader = csv.DictReader(f)
... |
1787918ab06b7a9154c2e2c097367af2168d8a2b0b6b9b3241e78159f9f81017 | Python | 8,808 | 243 | """
Calculate model trainable parameters and memory usage
"""
import torch
import torch.nn as nn
import torch.optim as optim
from models.resnet3d import ResNet3D18
from models.efficientnet3d import EfficientNet3DB0
from models.eTSCnet_dual import sTSCnetDual
from models.resnet3d_dual import DualResNet3D
def count_par... |
36ea5671c6a788b74e94cee0658a2c6ec62f18e68d1d1200376d5c4c348d9a89 | Python | 8,810 | 258 | from typing import Literal
import numpy as np
from PIL import Image
from matplotlib import pyplot as plt, animation
from matplotlib.patches import Ellipse
from tqdm import tqdm
from neuralib.typing import PathLike
from neuralib.util.verbose import fprint
from stimpyp import AbstractStimlog
__all__ = [
'compute_w... |
9ca545d3939e307686b772051f7c7171f6d349d970218da9528087528a0c3e14 | Python | 8,810 | 211 | import json
import os
import os.path as osp
from collections import defaultdict
from typing import Callable, Dict, List, Optional
import torch
from torch_geometric.data import (
HeteroData,
InMemoryDataset,
download_google_url,
extract_zip,
)
class HGBDataset(InMemoryDataset):
r"""A variety of h... |
fee79e97ffbfd3795f3733da57e75293d3dd3b4c0ea5aa0bba75355603ed8b1b | Python | 8,810 | 218 | #!/usr/bin/env python
from __future__ import print_function
from logging import info
import random
import numpy as np
import datetime
from ltlib.evaluation import conll_summary, per_type_summary, is_iob_tagging
from keras.models import Model
from keras.layers import Input, Embedding, merge, Flatten, Dense
from kera... |
615a96f94d7b17130cd2472ffe1d02eeb2b03051a4b2b9db9cf05d4c5eb6b4e3 | Python | 8,811 | 223 | from subprocess import run
from tempfile import gettempdir, mkdtemp
from uuid import uuid4
import nibabel as nib
import numpy as np
from harmonization.model_architectures import Generator
from tensorflow import convert_to_tensor
from tensorflow.config import list_physical_devices
from HD_BET.run import run_hd_bet
from ... |
b74925ebc3ee420737f88fff0fdd0c960d1d01e4fb5783dcb807b70dd03d50ca | Python | 8,813 | 158 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'lockdisplay.ui'
#
# Created by: PyQt5 UI code generator 5.7
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_GroupBox(object):
def setupUi(self, GroupBox):
GroupBox.se... |
03294433599b6e3ca489970200f5b3dbb86d2f8f22c4f66f78b61ab831c7e7d5 | Python | 8,815 | 273 | import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
import matplotlib.cm as cm
import json
with open('results/tables/mechanistic_benchmark.json', 'r') as f:
mech_results = json.load(f)
R = 8.314
F = 96485
T = 25 + 273.15
i_target = 150e-3
electrode_thicknesses = ... |
f8adfe897d64f4b7f9a37c572dd46e09287d755399582abeea1c36a7bd560376 | Python | 8,819 | 259 | """Execution backend configuration and factory.
Reads the ``[execution]`` section from ``config.toml`` (or env-var
overrides) and returns an initialised :class:`ExecutionBackend` instance.
Environment variables
---------------------
``CHEMGRAPH_EXECUTION_BACKEND``
Override the backend name (``"parsl"``, ``"ensemb... |
7156e495feaa7ec87eeef43414d71ce600a30fd3317014dc7603f2209f6ff88c | Python | 8,822 | 196 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import tempfile
from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(), keys=['others.zip'])
tmp_dir = tempfile.Tempo... |
e594baff327a5122f93682c504f84d9792a1a0f68aa17a52c9e16fecc7d0e0a3 | Python | 8,822 | 240 | #!/bin/env python
import os, sys
import numpy as np
import cPickle as cp
import matplotlib
matplotlib.use('AGG')
import matplotlib.pyplot as plt
import matplotlib.font_manager as ftman
import matplotlib.colors as colors
import matplotlib.cm as cmx
import matplotlib.colorbar as cb
INP = sys.argv[1]
OUT=sys.argv[2]
X =... |
8cb27b2aa8fa02428377d6d83342575a70d24a6ec761f9a831b890d03f207a88 | Python | 8,824 | 243 | # -*- coding: utf-8 -*-
"""
DWI_functions.py
====================================
This module can be used to calculate ADC/IVIM maps.
IVIM fitting is done in a segmented fashion: https://doi.org/10.3389/fonc.2021.705964
@authors: s.zijlema, p.vhoudt, k.baas, e.kooreman
Group: Uulke van der Heide - NKI
"""
import nump... |
3c8bba5162c3dddb487fea1c776a75ff71937f33b37adfa572661aebdc83f3e6 | Python | 8,825 | 249 | import json
import argparse
from chemgraph.tools.ase_tools import run_ase
from chemgraph.tools.cheminformatics_tools import molecule_name_to_smiles, smiles_to_atomsdata
from chemgraph.models.ase_input import ASEInputSchema
import datetime
import subprocess
def get_smiles_from_molecule_name(name: str) -> dict:
"""... |
519793fbd8dceee905abfc606e85ffedcc68ec90a0fe0a4ca6b33136fc21defe | Python | 8,825 | 270 | #!/usr/bin/env python3
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import argparse
import os
import os.path as osp
import re
import shutil
import sys
import textwrap
from collections.abc import Callable
from glob import iglob
from inflection import underscore
class Processor:
_referenc... |
a3e7ff2f3dd3f30c754a57ffe53fef8811aced46c5920043aba3f966ead11afc | Python | 8,828 | 202 | import pathlib
import time
import numpy as np
import h5py
from postprocessing_modules.axonal_delay_kernel import get_axonal_delay_kernel
from neuron_interface.neurosim.simulation.dendritic_delay_simulation import DendriticDelaySimulation
from helper_functions import __file__
from helper_functions.cell_type_lib import... |
831769d0fb7981f5922fe3d31c3c91110d392cbde81bb84194cbe62b53e4488d | Python | 8,829 | 235 | import logging
import dipy.tracking.streamline as dts
import dipy.tracking.utils as dtu
import nibabel as nib
import numpy as np
from scipy.spatial.distance import cdist
import AFQ.recognition.utils as abu
logger = logging.getLogger("AFQ")
def clean_by_overlap(
this_bundle_sls,
other_bundle_sls,
overla... |
ca5aa97c29b4d12baf0f57533b1afd65315301b107a3deb13af122d2a4ef4cf7 | Python | 8,831 | 253 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
"""
Text Tokenizer.
Copied and lightly adapted from VE repo, which in turn copied
from open_clip and openAI CLIP.
"""
import gzip
import html
import io
import os
import string
from functools import lru_cache
from typing import List, Optional, U... |
b56355ff22f5ee353b11499731239fc55f5f066c6611cb1c0cba52fe9f989cc2 | Python | 8,833 | 229 | # -*- coding: utf-8 -*-
"""
ClearMap default parameter module.
This module defines default parameter used by various sub-packages.
See Also:
:mod:`~ClearMap.Settings`
"""
#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New York City
#:license: GNU, see LICENSE.txt for details.
import ... |
4b11f1dc67584897963d47abefb5501ba20a98d9390b5b9e6a4ee9b87e3caaf4 | Python | 8,834 | 164 | from pathlib import Path
import numpy as np
import pandas as pd
from brainscore_core.supported_data_standards.brainio.assemblies import BehavioralAssembly
from brainscore_core.supported_data_standards.brainio.packaging import package_data_assembly
'''
Experiment Information:
- 25 or 50 subjects depending on condi... |
8db68a75bafa3e2f87b2317b222b82bd9e32da6f6702395939878fe215bf309f | Python | 8,834 | 212 | """The machine report: what it says about this computer, and what it warns about.
The page exists for two questions — *which of our computers should run the
batch* and *why is MEA-NAP slow on mine* — and both are answered by numbers
that must be the ones the pipeline will really use. So the checks here are
mostly abou... |
98bdd8f9bc275aed74d99a1cc37acc7e6d04af556b48e29dc19a3d2ab4598c16 | Python | 8,834 | 193 | ##############################################################################################
### Script to average data from the same columns in data files stored in different folders ###
##############################################################################################
### Copyright 2017-2022 Jannik Lub... |
b1f67ef93e642d0c652c73e6cb664381cfd400199aaab7e811d92ad389ee91ef | Python | 8,840 | 178 | ## ------------------------------------------------------------
## IMPORTS
## ------------------------------------------------------------
import torch
import torch.nn as nn
## ------------------------------------------------------------
## Explain the block
## --------------------------------------------------------... |
b9ed7acb54ac012d2b9226e982d74dd2011f8822468f904a735993995701645e | Python | 8,841 | 249 | # 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 math
import numpy as np
import torch
import torch.nn as nn
class RowSelfAttention(nn.Module):
"""Compute self-attention over rows... |
298a7f4ed6d1894c69052f6743e737a0c3cbce93587bae6ef93fd363616a74c5 | Python | 8,842 | 231 | """
Tests for `bx.phylo.newick`.
"""
import pytest
from bx.phylo.newick import (
Edge,
newick_parser,
Tree,
)
trees = [
r"(B:6.0,(A:5.0,C:3.0,'Foo ''bar':4.0)Q_X:5.0,D:11.0)label;",
"((raccoon:19.19959,bear:6.80041):0.84600,((sea_lion:11.99700, seal:12.00300):7.52973,(( monkey:100.85930,cat:47.14... |
f50caeeb44ae262d7f6dfa7ed38cfd0ddda50e6abf6fbefd1196f07be2c1ea68 | Python | 8,845 | 294 | # myelinfccoupling/model.py
from typing import Dict, Optional
import numpy as np
import pandas as pd
import statsmodels.formula.api as smf
from .config import Config
def _ols_r2(X: np.ndarray, y: np.ndarray) -> float:
"""
Compute R^2 for OLS y ~ X (with intercept) using linear algebra.
Assumes X, y ar... |
07040d6a401b511f64ffab5f281ea60abcbe972d35f99d82cef9f01697884185 | Python | 8,846 | 198 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from copy import copy
from typing import Any
import torch
from ultralytics.data import ClassificationDataset, build_dataloader
from ultralytics.engine.trainer import BaseTrainer
from ultralytics.models import yolo... |
a1542c56c467522cd3bcdd82500f28e4f6576db2d59f9796a3e992a7bfc0fbdd | Python | 8,846 | 211 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Agatha Schmidt, Henrik Zunker, Khoa Nguyen
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file excep... |
60838f1086f6caf2f93acde7394ecbacc12af666e93fa9aa83d5a5fa9b7eb35c | Python | 8,849 | 206 | import os.path
import unittest
import tests.bam
import tests.base_test
import tests.gtf
import tests.output_parser as output_parser
import tests.test_config
import tests.util
class Test(tests.base_test.BaseTest):
def setUp(self):
super().setUp()
self._test_base_dir = tests.test_config.TEST_BASE_... |
19a45bde3115896a787ec77d6dcac7983018c17bb394761b7fec1f4361814e3f | Python | 8,850 | 203 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import torch
from sam3.model.model_misc import SAM3Output
from sam3.train.utils.distributed import get_world_size
from .loss_fns import CORE_LOSS_KEY, Det2TrkAssoc, Masks
class DummyLoss(torch.nn.Module):
"""A dummy loss that always retu... |
bcb0c2560adef5c7cf5f4712272815e761c886499586f9e400aefe03c879af5e | Python | 8,853 | 216 | """
This class overrides the behavior of the parent ViewBox to handle operations for
for scaling and translating of one or more linked axes
"""
import pyqtgraph as pg
from PyQt5.QtWidgets import *
import numpy as np
import pyqtgraph.functions as fn
from PyQt5 import QtCore, QtWidgets
import platform
class lasagna_... |
28e984fe233f9d9b7aed0ef1e4f7dbb2386542d042df58eb511bdc526820a4e3 | Python | 8,854 | 253 | from __future__ import annotations
import re
import urllib.parse
from types import NoneType
from typing import Any, ClassVar, Protocol
from uuid import UUID
import attrs
from django.utils.html import escape
from rq.job import Job as RQJob
from cvat.apps.redis_handler.apps import (
QUEUE_TO_PARSED_JOB_ID_CLS,
... |
009f7b9a8ee5cc45b4127e1f602a5b7d22fb6717e9b18de87f035b25f27e87e9 | Python | 8,855 | 241 | import torch
import torch.utils.data as Data
from model.network_947331 import Network
from torch import nn
import time
import random
import numpy as np
from torch.optim.lr_scheduler import ReduceLROnPlateau
from torch.utils.data import Dataset
import pandas as pd
import os
# Configuration parameters
CONFIG = {
"cu... |
8cc3342c601c6e41d969bc956d3bdea652ac18d21cb31973c2bbca1ce9a724da | Python | 8,857 | 247 | '''
Quick script to traverse all participant data in the
experiment folder and estimate the free energy model
at any point in time for each participant. Note that
this script handles _all_ spaces, but not necessarily
at once. E.g., a 'normal' run of this will run spaces
for speaker-specific and -invariant priors with... |
84f96e741a8242a5c9bf767591ebf201c9a6d1b68b18d30679fb81cb34df67e7 | Python | 8,860 | 164 | from __future__ import division
import nipype.pipeline.engine as pe
from nipype import SelectFiles
import nipype.interfaces.utility as util
from nipype import IdentityInterface, DataSink
#from .utils import *
from utils import *
import os
def create_bullseye_pipeline(scans_dir, work_dir, outputdir, subject_ids, na... |
37d627dfee69f676d3fca78f352ec28f09c00baf3cb77fd470f6abdfd4887681 | Python | 8,862 | 293 |
###############################################################################
#################### Boilerplate ########################
###############################################################################
import pandas as pd
import matplotlib.pyplot as plt
import os
import matplotl... |
95bd752547200641109b128db53f43a1eaf8d3280bf89e71866b3113b353404f | Python | 8,863 | 275 | #!/usr/bin/env python3
import os
import argparse
from typing import Tuple, List, Optional
import numpy as np
import nibabel as nib
from PIL import Image
from fury import window, actor
def robust_norm_nonzero(vol: np.ndarray, p_low: float, p_high: float, eps: float = 1e-6) -> Tuple[float, float]:
v = vol[np.isfi... |
f555508fd1eebd3c6582d4cea1a5d27168b8988059392c833bba677e8699b6a6 | Python | 8,863 | 242 | from subprocess import PIPE
import unittest
import numpy as np
class TestFileIO(unittest.TestCase):
def test_feed_pipe(self):
from python.segmentation.FileIO import feedPipe
from unittest.mock import Mock
mockPipe = Mock()
mockPipe.communicate.return_value = ("result", "")
... |
faf5450e90e356fceaa760a1e761943d382d9c48370c3af00ee0f32ad25af12b | Python | 8,863 | 202 | #!/usr/bin/env python
"""
HAL module for controlling a Pi controller.
Adapted from Hal module for a tiger controller by Hazen 05/18.
This module connects to a PI controller (model E873) which controls 3
translation stages (model Q545.140) that are assembled in a 3D stage configuration
Alistair 10/19
"""
imp... |
3d454b2e5a46c4591f5ee781ea021f7de2443c57660d75b489ac2dc2c9573e75 | Python | 8,866 | 313 | # user feature generation: Alhosseini
import re
import json
import datetime
from operator import itemgetter
from math import log
import pandas as pd
import numpy as np
import csv
import collections
def read_json_1dict(path):
"""
读取json，用于一个dict
:param path: 路径
:return: 一个dict
"""
with open(path... |
37f81fcabd252938bfbc2cae49ea818a923af023bebdb96d2f541214fb9392ef | Python | 8,868 | 225 | from collections import OrderedDict
import logging
import os
import numpy as np
from PIL import Image
from brainscore_vision.model_helpers.activations.core import ActivationsExtractorHelper
from brainscore_vision.model_helpers.utils import fullname
SUBMODULE_SEPARATOR = '.'
class PytorchWrapper:
def __init__(s... |
db5c5f06387df0762888bdbaeb13c2a227e79967c75e27a5bf3c370c2d1112d6 | Python | 8,868 | 300 | """dataclasses.py."""
import logging
from dataclasses import dataclass
from typing import Any
import jax.numpy as jnp
import numpy as np
import numpy.typing as npt
import pandas as pd
from jax import Array
from jax.tree_util import tree_map
logger = logging.getLogger(__name__)
NUM_DIMENSIONS = 2
@dataclass
class ... |
e915684a024e987924890f8c0e654806d4636bcd2d0be3d9d299d0e10c8e4c69 | Python | 8,868 | 178 | """
Generate validation set comparison report
"""
import pandas as pd
import numpy as np
import os
def generate_comparison_report():
"""Generate complete comparison report"""
val_flair_csv = './results/val_predictions/val_predictions_flair.csv'
val_t2_csv = './results/val_predictions/val_predictions_t... |
857ecdbbe5e367e999b2c1cec9ed48540d3dd53ad5292f58665791fb0a4346d7 | Python | 8,870 | 276 | # -*- coding: utf-8 -*-
"""TODO"""
import os
import time
import numpy as np
from mpi4py import MPI
from core.logger import LogMessageType
from core.core_definitions import (simulation_mindelay, simulation_timestep)
from core.sync_buffer import SyncBuffer
def _progress_bar(fraction):
"""TODO"""
bar = ""
... |
0a1b2d547cdcb8babaa6f3bb8dd733be4fde85ee01bd6530fd4126f038b661a8 | Python | 8,873 | 314 | #!/usr/bin/env python3
# coding: utf-8
import sys
import os
import re
import numpy as np
from neuron import h
# This is super annoying: without neuron.gui, need
# to explicit load 'standard' hoc routines like 'run',
# but this is chatty on stdout, which means we get
# junk in our data if capturing output.
def hoc_e... |
65e8a548db3442bcd998e20718ebe514d8543a67b756a77f55fb1167697f16ab | Python | 8,878 | 288 | #Pure training, the analysis of the network can be done with the app
#The images and their names are in the images_compressed.npz and names.py
import numpy as np
import os, torch, h5py, time, sys
import torch.nn as nn
from torch.utils.data import DataLoader, Dataset
from torch import optim
import torch.nn.functional a... |
eec9fa0965c8c57ae5c76df36b9d46afbaec1df280c29360799934f698a5d6f1 | Python | 8,878 | 248 | import os
import random
import shutil
import zipfile
import nibabel as nib
import numpy as np
from tensorflow.keras.utils import get_file
from tqdm import tqdm
# if wget is installed remove the following line from comment
# import wget
# if already in the abc/DeepReg directory then do nothing, otherwise
# use os.chd... |
f650225f6212ed4747be0e9f944f2b7b24281df9821c0c5d43a4b2e686a675eb | Python | 8,881 | 240 | # Copyright (c) 2020, Soohwan Kim. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... |
f04597240fe6459722dd9ae6bb46fc62dfeffe15fe6f3982a378de3e4795e5a7 | Python | 8,885 | 251 | import json
import argparse
from chemgraph.tools.ase_tools import run_ase
from chemgraph.tools.cheminformatics_tools import molecule_name_to_smiles, smiles_to_atomsdata
from chemgraph.models.ase_input import ASEInputSchema
import datetime
import subprocess
def get_smiles_from_molecule_name(name: str) -> dict:
"""... |
6bf649c3bf2031260988bbf83a4296d928a256de7a36fa00090724adbff61b97 | Python | 8,887 | 237 | # -*- coding: utf-8 -*-
# @Author : LG
from PyQt5 import QtCore, QtGui, QtWidgets
from ISAT.ui.category_edit import Ui_Dialog
from ISAT.widgets.undo_commands import (
ShapeStateCommand,
_snapshots_match,
snapshot_shape,
)
class CategoryEditDialog(QtWidgets.QDialog, Ui_Dialog):
def __init__(self, pa... |
73ec4f331716e3d7b56f8ac188546d4c4995e1ba4016354ac95d29bae45065e9 | Python | 8,887 | 211 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
class BasicBlock(nn.Module):
def __init__(self, in_channels, out_channels, stride=[1, 1], padding=1) -> None:
super(BasicBlock, self).__init__()
# 残差部分
self.layer = nn.Sequential(
nn.Conv2d(in_channe... |
9e6b2c87bfef3065e698c9ca39a6f1de6deff3042f129d166fdb04482dd46bdb | Python | 8,888 | 302 | # Copyright 2025 BDP Ecosystem Limited. All Rights Reserved.
#
# 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... |
45a293bdcb4914b6044dc1b335b44409fa3d1f95a268f8bd54c0203ecea096fb | Python | 8,890 | 276 | import os
from langgraph.graph import StateGraph, START, END
from langchain_openai import ChatOpenAI
from langgraph.checkpoint.memory import MemorySaver
from langgraph.prebuilt import ToolNode
from chemgraph.tools.cheminformatics_tools import (
molecule_name_to_smiles,
smiles_to_coordinate_file,
)
from chemgra... |
b001e2a2d403ab19962a73551d499a37f64a35cf51f34a1ef9c798eb9ce01cd8 | Python | 8,891 | 281 | #!/usr/bin/env python3
"""
=============================================================================
Austin Dibble
University of Glasgow
2026
scripts/run_inference.py
Command-line interface for NeuroFM inference.
Accepts a single NIfTI file, a directory, or a CSV with an 'input' column.
Examples
--------
Single ... |
27f4c4833d5672e2c3edb174278b1dbd8e8e941ce9337844b6e98c9928c70ece | Python | 8,892 | 182 | # BIDS discovery of diffusion weighted images for batch processing
#
# Finds sub-<label>/[ses-<label>/]dwi/*_dwi.nii[.gz] with their .bval/.bvec (and .json sidecar), parses the BIDS
# entities, and groups the runs into datasets: every run on its own, or pairs of runs with opposite phase encoding
# (e.g. dir-AP ... |
71c17c343a96aee5b0c8cf248599608de735c33d53d0cc426c6e85d4ed27d44b | Python | 8,894 | 282 | import pytest
from langchain_core.messages import AIMessage
from langgraph.checkpoint.memory import MemorySaver
from chemgraph.cli.commands import ALL_WORKFLOW_TYPES
from chemgraph.registry import (
AgentRegistry,
AgentSpec,
DuplicateRegistryEntryError,
RegistryUnavailableError,
UnknownRegistryEntr... |
79bfd3b807c2c03640064c446406243cc846bd7617b2252b7fa663926c5f7c94 | Python | 8,894 | 299 | # -*- coding: utf-8 -*-
"""EPI <-> ANA registration
The purpose of the following script is to compute the deformation field for the
registration between antomy and EPI in native space. The mask should be in ana
space. Optionally, a second mask can be applied which must be in orig space. The
script consists of the foll... |
b39677b1ee2b0030775b2f9c311f916b502826fa62f09be19c3eb4a517892984 | Python | 8,894 | 253 | """Downsample the image features with PCA.
Parameters
----------
subject : int
Number of the used NSD subject.
data_ood_selection : str
If 'fmri', the ID/OD splits are defined based on fMRI responses.
If 'dnn', the ID/OD splits are defined based on DNN features.
model : str
Name of deep neural network model used t... |
159491306ce205f803681b1f6a30c6ba4edd2a4cd6ecfff6ed5916a056b977d5 | Python | 8,898 | 221 | #!/usr/bin/env python
"""
These wrap a CameraFrameDisplay and possibly a ParamsDisplay in
a single object that Display interacts with.
Hazen 4/17.
"""
from PyQt5 import QtCore, QtWidgets
import storm_control.hal4000.display.cameraFrameViewer as cameraFrameViewer
import storm_control.hal4000.display.paramsViewer as p... |
1ed5ba25386362f54ed40f41fb373c6d4704423ab04e2b8f194282d544d2c7cc | Python | 8,898 | 222 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
from typing import Dict, List
import numpy as np
import PIL
import torch
from . import box_ops
from .data_misc import FindStage, interpolate
from torchvision.transforms import v2
class Sam3Processor:
""" """
def __init__(self, model,... |
7115ce9d390facf20547544b658cb5fea47611e18698d9e47fb95f9665631bbc | Python | 8,900 | 214 | # -*- coding: utf-8 -*-
"""TODO"""
import numpy as np
from scipy.special import expit
from scipy.stats import logistic
import core.core_global as core
from core.core_definitions import simulation_timestep
from core.connection import Connection
from core.euler_trace_2d import EulerTrace2D
class RewiringConnection(Co... |
a1521e168d825378764dc9c1deb154ccf1e80f31982b87c599bde6b0830191e0 | Python | 8,900 | 192 | import src.data_generator as adg
import src.utils
import glob
import cmat
import pandas as pd
import pickle
import argparse
import os
import src.config
def loso_cv(config, dataset_path=None):
##### Load config #####
# Load dataset path
if dataset_path is None:
dataset_path = config.TRAIN_DATA
... |
041cc4dd84f2aba414abbfc0e1cc59db998b6199e02b9916886880257b4fc867 | Python | 8,901 | 253 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 13 21:23:50 2023
@author: jstout
"""
import pandas as pd
import MEGnet
from os import path as op
import os
import glob
from scipy.io import loadmat
import numpy as np
import copy
import pickle
from MEGnet.megnet_utilities import fGetStartTimesOver... |
6cbca8969bca249a6e41ebcbb6cf8b34a1e00368c57f03dda1c2b544c8e96967 | Python | 8,903 | 288 | #!/usr/bin/env python
"""
Test autofocus lock.
Hazen 09/19
"""
import numpy
import random
import storm_analysis.simulator.draw_gaussians_c as dg
import storm_control.sc_hardware.utility.af_lock_c as afLC
# 2D Python version.
def test_afLCPy():
afc = afLC.AFLockPy(offset = 0.0)
cx = 16.0
cy = 32.0
... |
b4254c1514f516a96e924add70dfaa4b68d85af558a1ccb7fbf65e0a95b02049 | Python | 8,905 | 246 | # Code adapted from the G-Retriever paper: https://arxiv.org/abs/2402.07630
from typing import Any, Dict, List, Tuple, no_type_check
import numpy as np
import torch
from torch import Tensor
from tqdm import tqdm
from torch_geometric.data import Data, InMemoryDataset
from torch_geometric.nn.nlp import SentenceTransfor... |
c25304f145f4cde25f72e02d21a7bc6bed47360abf8508b43f5391d376185529 | Python | 8,905 | 216 | import os
import logging
from collections import OrderedDict
import numpy as np
import torch
from PIL import Image
from brainscore_vision.model_helpers.activations.core import ActivationsExtractorHelper
from brainscore_vision.model_helpers.utils import fullname
SUBMODULE_SEPARATOR = '.'
class PytorchWrapper:
d... |
b4a60542cb2beb2578af865652236a1b72d02237d5a15de3e83a6fa4b592f342 | Python | 8,907 | 260 | import concurrent.futures
import numpy as np
import pandas as pd
import heig.input.dataset as ds
from heig.image import ImageManager
from heig.utils import inv
def projection_ldr(ldr, covar):
"""
Computing S'(I - M)S/n = S'S - S'X(X'X)^{-1}X'S/n,
where I is the identity matrix,
M = X(X'X)^{-1}X' is th... |
db844144c89ee58fb7b69d096bc25ee9dd55d0c485c3aaee2a8100558a63977c | Python | 8,907 | 213 | # -*- coding: utf-8 -*-
"""TODO"""
import numpy as np
from scipy.special import expit
from scipy.stats import logistic
import core.core_global as core
from core.core_definitions import simulation_timestep
from core.connection import Connection
from core.euler_trace_2d import EulerTrace2D
class RewiringConnection(Co... |
849f6771c898ea3063177b0e745ca6e1a158e6aebb61b73d092b26b723b7c50c | Python | 8,909 | 268 | import hashlib
import random
import torch
import numpy as np
from collections import OrderedDict, namedtuple
import git
import inspect
import datajoint as dj
import os
import datetime
import warnings
def gitlog(cls):
"""
Decorator that equips a DataJoint class with an additional dj.Part table that stores the... |
1cfe79140f61af429babacdeced74f714fb2bb9b12a135b575dbf363a388d131 | Python | 8,911 | 177 | #!/bin/python3
# Plot functions for neuronal and synaptic variables as well as spike raster plots
# Copyright 2021-2024 Jannik Luboeinski
# License: Apache-2.0 (http://www.apache.org/licenses/LICENSE-2.0)
# Contact: mail[at]jlubo.net
import numpy as np
import matplotlib.pyplot as plt
import json
import os
from pathl... |
f1a3a0a8c92900bdddb25d836999b6b51dd00424a81b9b440e44209961153ad3 | Python | 8,914 | 237 | """Window construction and forecast-target assignment.
One sample = an observation window of `obs_min` minutes ending at time t, paired
with the KSS self-report covering time t + `horizon_min`. Features are split into
`step_s`-second sub-windows so recurrent/convolutional models see a sequence
rather than a single poo... |
bc2dcacdcf6c43f1c4a1fe3ea20c2e4e8726d65192bda1c7266f9fc896257e05 | Python | 8,917 | 217 | from __future__ import annotations
from collections.abc import Callable
from typing import cast
from PySide6 import QtCore
from PySide6 import QtGui
from PySide6 import QtWidgets
from .. import _ai_models
from .. import _automation
from .._utils._qt import new_icon
from ._info_button import InfoButton
from ._integer... |
013692871ada886a6ab8eec29f6ba08f034c6441de8a9fba4fac06e8b89f7ae7 | Python | 8,920 | 185 | #! /usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Detect when data strides are different from [1, 2, 3] and correct them.
The script takes as input a nifti file and outputs a nifti file with the
corrected strides if needed.
Input file can be 3D or 4D. Only the first 3 dimensions are considered
for the stride correct... |
3958199064dd89aa46557b47a5d94802eb4baad0552454bca71b571530ad7880 | Python | 8,921 | 222 | # -*- coding: utf-8 -*-
import os
from parser.utils import Embedding
from parser.utils.alg import eisner
from parser.utils.common import bos, pad, unk
from parser.utils.corpus import CoNLL, Corpus
from parser.utils.field import BertField, CharField, Field
from parser.utils.fn import ispunct
from parser.utils.metric im... |
b5da596a225451a4d0ad37a53d4733bbe8d8de9332edef6281b1bb30b190d517 | Python | 8,923 | 230 | import logging
import unittest
import numpy as np
import pandas as pd
import scipy.stats as stats
from batchglm.api.models.numpy.glm_nb import Simulator
import diffxpy.api as de
class TestConstrained(unittest.TestCase):
def test_forfatal_from_string(self):
"""
Test if _from_string interface is ... |
39b34ceacc5a38f09bf461fd256270d534fa6f7329861946be2cff1e0d0b26e0 | Python | 8,924 | 225 | import os
from rdkit import Chem
from rdkit.Chem import Draw, AllChem
from rdkit.Geometry import Point3D
from rdkit import RDLogger
import imageio
import networkx as nx
import numpy as np
import rdkit.Chem
import wandb
import matplotlib
# matplotlib.use("macOSX")
import matplotlib.pyplot as plt
class MolecularVis... |
91a4898f5d7af33bc756f94971dc259fbeba7f7c62125c944449156fc92941de | Python | 8,925 | 162 | import mlflow
import os
import math
def get_mlflow_experiment(experiment_name):
""" Check if experiment with name experiment_name exist. Otherwise, create an experiment with that name. Get ID. """
try:
EXPERIMENT = mlflow.get_experiment_by_name(experiment_name)
EXPERIMENT_ID = EXPERIMENT.experi... |
79ff1190676dbd67c8f5c3b85b8887dae017b4b72b6da1b9c67be20ffa7b3fdb | Python | 8,927 | 245 | import numpy as np
import pandas as pd
import json
import os
import networkx as nx
import pickle as pkl
from sklearn.manifold import TSNE
import matplotlib.pyplot as plt
from sklearn.cluster import KMeans
import matplotlib.colors as col
from matplotlib import cm
from sklearn import metrics
from sklearn.preprocessing im... |
f905ec655f59491397d1fabf98107fe2fb1412c8e20c4604c723aeef28e259c3 | Python | 8,934 | 245 | # %%
import argparse
import gmsh
from mpi4py import MPI
from dolfinx.io import gmshio
import numpy as np
from dolfinx import fem, default_scalar_type
import ufl
from pathlib import Path
from dolfinx.fem.petsc import assemble_vector, assemble_matrix, \
create_vector, apply_lifting, set_bc
from petsc4py import PETSc... |
97eb005626fc4c0e177fbf2846f24fe7da532f9c31f1fac521def4387d3c367c | Python | 8,935 | 252 | import os.path as op
import numpy as np
from dipy.io.stateful_tractogram import Origin, Space, StatefulTractogram
from dipy.io.streamline import load_tractogram, save_tractogram
from nibabel.affines import voxel_sizes
from nibabel.orientations import aff2axcodes
try:
from trx.io import load as load_trx
has_t... |
9dce189fc20c7419711f0467a71678c815ec423c25e35b031f91e7af93688918 | Python | 8,935 | 254 | from typing import Literal, Final
import numpy as np
import pingouin as pg
import polars as pl
import scipy
import seaborn as sns
from matplotlib import pyplot as plt
from rich.pretty import pprint
from argclz import as_argument
from neuralib.plot import plot_figure
from neuralib.util.verbose import fprint, publish_a... |
a3516cb316bbb3fa97162eb634df7d0a7f162def3508d66b4c6698e0378e1853 | Python | 8,936 | 292 | import os.path as op
import dipy.data as dpd
import dipy.data.fetcher as fetcher
import nibabel as nib
import numpy as np
import numpy.testing as npt
import pytest
from dipy.io.stateful_tractogram import Space, StatefulTractogram
from dipy.stats.analysis import afq_profile
import AFQ.api.bundle_dict as abd
import AFQ... |
fc02245bae0451f123751733ab1b835f147af8cb1f3475c38ab59cf09c4ccd58 | Python | 8,937 | 191 | import os
from labdatatools.analysis import *
import argparse
def recursive_map(f, it):
return (recursive_map(f, x) if isinstance(x, tuple) else f(x) for x in it)
class AnalysisSpksibl(BaseAnalysisPlugin):
def __init__(self,subject,
session = None,
datatypes = [''],
... |
0489095ff2fad7e9395dbb3c79f511d1a199c8f88f76526543e86e6baec00fd2 | Python | 8,939 | 174 | """
If you use this code, please cite the first SynthSeg paper:
https://github.com/BBillot/lab2im/blob/master/bibtex.bib
Copyright 2020 Benjamin Billot
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 ... |
902d88ab1f1107ac54b4f02b3736754b0c77a49ef83985f195f22ed6b47b4977 | Python | 8,939 | 294 | import base64
import json
import os
from collections.abc import Sequence
from functools import partial
from pathlib import Path
from shutil import copytree
import numpy as np
from PIL import Image
from torchvision import transforms
from docs.doc_modules.experiments import AutoDocExperimentInfo, run_capture_and_save
f... |
e6a02ee27ed428009deb0931fcf9875a54c671c9d079749baf395a7a17739f06 | Python | 8,939 | 249 | import json
import argparse
from chemgraph.tools.ase_tools import run_ase
from chemgraph.tools.cheminformatics_tools import molecule_name_to_smiles, smiles_to_atomsdata
from chemgraph.models.ase_input import ASEInputSchema
import datetime
import subprocess
def get_smiles_from_molecule_name(name: str) -> dict:
"""... |
72faf955b06dd20eec4cb6355188c44548d14b0aab9f9913cb56c032e1355a48 | Python | 8,941 | 253 | """
(C) Copyright 2019 IBM Corp.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
... |
f467231c656c8d8ff955c7690aa1d90899e2b282ff1623be12bc6b4183609afa | Python | 8,943 | 239 | import os
import shutil
import zipfile
import nibabel as nib
import numpy as np
from tensorflow.keras.utils import get_file
from tqdm import tqdm
DOWNLOAD_FULL_DATA = False
DATA_PATH = "dataset"
main_path = os.getcwd()
project_dir = os.path.join(main_path, r"demos/paired_mrus_brain")
os.chdir(project_dir)
######## ... |
c90280a3a369f0cd9a5efef4d5afee859b4ef565a355607d0a4cc9ef139a1a9f | Python | 8,945 | 231 | import dtiplayground.dmri.preprocessing as prep
import dtiplayground.dmri.common as common
import yaml,os
from pathlib import Path
import dtiplayground.dmri.common.dwi as dwi
import dtiplayground.dmri.common.tools as tools
import sys
### Functions of Filter ###
### Function with two parameters : exclude gradients... |
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