sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
72e0fd69b1abdfcbababd79d370d95b423932e1ded605a8c3977800db3b4ea7e | Python | 11,166 | 259 | import numpy as np
from scipy.stats import rankdata
import h5py
import os
def mann_whitney_u_shuf(x, y, shuf_labels):
"""
Compute Mann-Whitney U statistic efficiently using shuffled labels.
Parameters:
- x: array-like, spike counts for choice A (# shape: (nx,))
- y: array-like, spike counts for c... |
66d98471b7663ff563a4ecb060a1884583ad07dbdd0ee354a5755df635a3d8c9 | Python | 11,178 | 347 | """
Define multiple methods to compare different FLOP and MAC counting tools.
Tools:
- PyTorch Lightning FLOPs counter: https://lightning.ai/docs/pytorch/stable/api_references.html#lightning.pytorch.utilities.measure_flops
- https://github.com/sovrasov/flops-counter.pytorch
- https://github.com/facebookresearch/fvcore... |
8897e81d719224fac73f9d46167eda6d10832b4264193fcaff7ed1d8e32657e9 | Python | 11,179 | 284 | import json
import logging
import numpy as np
import pandas as pd
import argschema as ags
from skeleton_keys.layer_alignment import (
layer_aligned_y_values_for_morph,
cortex_thickness_aligned_y_values_for_morph,
)
from neuron_morphology.swc_io import morphology_from_swc, morphology_to_swc
from neuron_morpholog... |
ff797c0e117d7d586169d9243ab43436feaa6e01e8ef3c9db34a2552cba7d696 | Python | 11,179 | 271 | #!/usr/bin/env python
"""
'Tile' the blocks of a maf file over each of a set of intervals. The
highest scoring block that covers any part of a region will be used, and
pieces not covered by any block filled with "-" or optionally "*".
This version uses synteny annotation if found on the alignment blocks, and
will att... |
6741503065dc2b2b83534b2568bf9c42ea9cdb69f1305bb9e9d0926008633e7b | Python | 11,181 | 243 | #!/usr/bin/env python
"""
Handles the management of one or more camera / feed displays.
Hazen 3/17
"""
from PyQt5 import QtWidgets
import storm_control.sc_library.parameters as params
import storm_control.hal4000.camera.cameraControl as cameraControl
import storm_control.hal4000.display.cameraViewers as cameraViewe... |
6159aa8dfd98b932662bd810c41a7b931170cad4fb0b2158dd662c6c5ac5066e | Python | 11,183 | 347 | # This code is derived from the gammatone toolkit, licensed under the 3-clause
# BSD license: https://github.com/detly/gammatone/blob/master/COPYING
"""Constructs sets of equivalent rectangular bandwidth gammatone filters."""
from __future__ import division
import numpy as np
from scipy import signal as sgn
def er... |
702566dad2b193aad0d79808ca6edf34f8279ad581ce9a0336ef92d6f6b12aee | Python | 11,185 | 302 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import torch.nn.functional as F
import torch.nn as nn
from mmcv.cnn import build_conv_layer, build_norm_layer
from mmcv.runner.base_module import BaseModule
from torch.nn.modules.utils import _pair as to_2tuple
class AdaptivePadding(nn.Module):
"""Appli... |
fa81d3df9b6cf332391850644cd1583592eebff9434143fdb7f81199c5df5f1c | Python | 11,192 | 275 | # This file has been modified by [Qian Yin/Organization].
from inspect import CO_VARARGS
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule
from torch.nn.functional import embedding
from torch.nn.modules import conv
from depth.models.builder import HEADS
from .decode_head import DepthBaseDecodeHead
imp... |
d69e49d5bbec5e944bc8c08a4e6b009a7a2095ff9c7cd8669b449b7764063477 | Python | 11,194 | 305 | from pathlib import Path
import numpy as np
import pandas as pd
import h5py
from tqdm import tqdm
from typing import Any
from scipy.signal import butter, sosfilt
from seisbench import logger
from .das_base import DASBenchmarkDataset, DASDataWriter
class MLSubDAS(DASBenchmarkDataset):
"""
MLSubDAS dataset by... |
2a06f5a7b8fa48253d1b99cd4987e3a18174205f914e05739c089a4917c2e97e | Python | 11,197 | 336 | #!/usr/bin/env python
"""
Convert Siemens physio DICOM files to BIDS tsv files and populate to correct subject/session folders directly
AUTHOR : Mike Tyszka
PLACE : Caltech
DATES : 2021-08-02 JMT From scratch
License
----
MIT License
Copyright (c) 2021 Mike Tyszka
Permission is hereby granted, free of charge, to a... |
e151192636ce9b153ea35d7336734ebd46c079ca062673f1605b311f4e651370 | Python | 11,200 | 281 | import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
class InfoNCE(nn.Module):
def __init__(self, temperature):
super().__init__()
self.temperature = temperature
def forward(self, query, pos, neg):
query = F.normalize(query, dim=-1)
pos = F.normalize(po... |
4c8994c4c32f457895aa66161035cabf6490f364ec30ac313c2161bda3531a7d | Python | 11,202 | 313 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
import glob
import json
import os
from mock import patch, Mock
from pathlib import Path
import pytest
from bluepysnap import Circuit
from bluepysnap.nodes import NodePopulation, Nodes
f... |
e5e9d5be6beaacab2e526ac907f1edabed957869ac051b40ae47b7824745b1d9 | Python | 11,203 | 329 | import os
import tempfile
import unittest
import numpy
import pandas
import thalamus.dataframe
from thalamus.record_reader2 import RecordReader
from thalamus.dataframe import DataFrameBuilder
from thalamus.thalamus_pb2 import StorageRecord, AnalogResponse, Text, Span
from thalamus.record_writer import write_record
c... |
3f79df3e0a4eb6f8c4eea10b5af83037ec42466a00f9cd7024139e604083197f | Python | 11,204 | 292 | import os
from typing import Any, List, Dict, Callable, Tuple
import math
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from torchvision.utils import make_grid
from torchvision.utils import save_image
import torchvision.transforms.functional as T
from py... |
9455fd2aeaaf33b4d52dc40373de9e101b137beb394b0e9d3b7f9e359e0d2014 | Python | 11,204 | 257 | import sys
sys.path.append('..')
import torch
import torch.nn.functional as F
from torch import nn
from torch.nn import GRUCell, Linear
import dgl
from dgl import function as fn
from dgl.nn.pytorch.conv import GATConv, EdgeGATConv, GINConv, GINEConv, GATv2Conv, HGTConv, EGNNConv
from dgl.nn.functional import edge_soft... |
c46df2b75dfaf3fe7d71b2091836bd5fe27508c9beb5d9b00c9c97fbd1e0bcaf | Python | 11,205 | 252 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Script to denoise a dataset with the Non-Local Means algorithm (from Dipy's
package).
This method requires an estimate of the noise (sigma). There are three methods
available:
1. Provide your own sigma value, if you already know it.
2. Estimate it through Dipy... |
e9c2bc50dbb8f5f6a0f46fa3f02a65a306c7a164dfce80cbfd5d00169183cc90 | Python | 11,207 | 306 | # Copyright (c) 2019, NVIDIA CORPORATION. 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 ... |
5b894c51a013f97c5d068d3d37a5ada1b1d88c86e5583b1ad001344453a208f6 | Python | 11,208 | 306 | # Copyright (c) 2019, NVIDIA CORPORATION. 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 ... |
122c99056e9e7ae324dee3cf8bbd9d6988a883cf7c9615735c41ecd7f578f953 | Python | 11,211 | 264 | import sys
import pandas as pd
import numpy as np
import anndata
from skimage import io as skio
import getopt
import json
import scipy.ndimage as nd
#Print Usage
def apply_alignment_usage():
print("""
Usage :
SEAM.py apply_alignment -i <input.json or input.csv>
-o <output prefix>
... |
2624d7656ea93fdd0e8fee2c83f0290757762c977698ca15014e3e13cde24edf | Python | 11,212 | 335 | """
TMS Explorer was developed to assist with the data preprocessing of transcranial
magnetic stimulation (TMS) as part of the study "Transcranial direct current
stimulation (tDCS) and mindfulness meditation in fibromyalgia" in the "Non-
invasive brain stimulation lab" (NBS) at the university medicine Göttingen ... |
96ba4a545e9f0ba8d0b0748e05b092db5b237a5bb8c9679cdb7e1c71c5a743a0 | Python | 11,216 | 369 | # -*- coding: utf-8 -*-
# python standard library inputs
from math import prod
# external inputs
import numpy as np
import nibabel as nb
from numpy.fft import fft, ifft
from scipy.ndimage import gaussian_filter
from nilearn.signal import clean
__all__ = ["ScaleTimeseries", "FilterTimeseries"]
class ScaleTimeseries... |
2795a2dd074d90dff84800740bb8a45eb705e4e113d36d902700653b896e7311 | Python | 11,219 | 208 | plots
- nc x h2 (obviously, the effect size drives power; also - PCOR MOSTest behaves as GCOR )
- dist x t (most is always better than minp; minp power is growing when t increases; cauchy distribution => minp has thesame power as mostest)
- dist x T (more traits = better power; and too ma... |
2cacf511e851e645db246a408636c7da38adb8ab1a88517cc16c35434d32b825 | Python | 11,220 | 307 | # Copyright (c) 2019, NVIDIA CORPORATION. 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 ... |
39d646b59608b6e9fcd1c991d1da46ff326f067780b1a89dec34985929b0cb52 | Python | 11,220 | 314 | # Copyright (c) DP Technology.
# 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 ast
import collections
import logging
import os
import re
import shutil
import traceback
from typing imp... |
618fa4f94dac9db4c0c69adf8dd5d818de680d84d64e445324b3d98aa9ef312a | Python | 11,226 | 283 | """
Main manuscript - Figure 1: Overview of 3T and 9.4T subject matched datasets
First column: Axial exemplary slice of 3T qMRI data: R1, R2, AI
Second column: Axial exemplary slice of 9.4T qMRI data: R1, R2, AI
Third column: Axial exemplary slice of DTI data: FA, color-coded FA, fiber-to-field angle theta
Author: fl... |
7e15dbfea842a5cbb8f37887e4c75c0ffff7035a927bd2b00460231fe57a190d | Python | 11,226 | 341 | # -*- coding: utf-8 -*-
"""
Illumination correction toolbox.
The module provides a function to correct illumination/vignetting systematic
variations in intensity.
The intensity image :math:`I(x)` given a flat field :math:`F(x)` and
a background :math:`B(x)` the image is corrected to :math:`C(x)` as:
.. math:
... |
e5a4342bbecd94d162bc5d2856ffc09b02c050af67d25649f18a94f1baf2dc84 | Python | 11,227 | 241 | import os
import os.path as osp
import torch
import random
import numpy as np
import pandas as pd
from torch_geometric.data import (Data, InMemoryDataset, download_url,
extract_gz, extract_tar, extract_zip)
from torch_geometric.data.makedirs import makedirs
from torch_geometric.utils ... |
2ed2f72d50651e1024cae724a44db08b22914732fa36c9f339140dc98f61963a | Python | 11,228 | 316 | import logging
import os
import os.path as op
import dipy.tracking.streamlinespeed as dps
import numpy as np
from dipy.io.stateful_tractogram import Space, StatefulTractogram
from dipy.tracking.streamline import select_random_set_of_streamlines
import AFQ.recognition.sparse_decisions as ars
import AFQ.recognition.uti... |
abaefa62351dd7317b71deaf7f22fdd6376699359d00cb0d46c59ed1bd67d240 | Python | 11,236 | 302 | # -*- coding: utf-8 -*-
import logging
import os
import numpy as np
from scilpy.tractanalysis.streamlines_metrics import compute_tract_counts_map
from scilpy.utils.filenames import split_name_with_nii
def compute_lesion_stats(map_data, lesion_atlas, single_label=True,
voxel_sizes=[1.0, 1.0... |
f6318aa57e3509e86cb15f5619b2a8dd3a6f5a782ce4799eb840d0f21851e707 | Python | 11,237 | 394 | from __future__ import annotations
import functools
from collections.abc import Callable
from pathlib import Path
from typing import TYPE_CHECKING
from typing import Final
from unittest.mock import MagicMock
import numpy as np
import osam.types
import pytest
from pytestqt.qtbot import QtBot
from labelme._automation ... |
f8ef8701928bc68d3af53fdf37709c78d11ac468c9bdb0b12055a3c561c9d123 | Python | 11,244 | 260 | """ Exponential Moving Average (EMA) of model updates
Hacked together by / Copyright 2020 Ross Wightman
"""
import logging
from collections import OrderedDict
from copy import deepcopy
from typing import Optional
import torch
import torch.nn as nn
_logger = logging.getLogger(__name__)
class ModelEma:
""" Model... |
b2c3e4cb4a2bb285e261dbf2ca647815bb3b4ad759ad715b6d3efdd920d4d3f7 | Python | 11,246 | 277 | import json
import numpy as np
import pandas as pd
from typing import Dict, List, Tuple, Union
from pathlib import Path
from napari.utils.notifications import show_info
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.model.calculation import fitGeoTrans, mapPointTransform
from napari_dmc_brainmap.utils... |
6da6dc49c0e00b950e3706c50c30e3ea4e23077fe48b92dd7df9e494b6dd1939 | Python | 11,247 | 291 | """
Predict using trained EfficientNet3D models on validation set and full dataset
"""
import os
import argparse
import torch
import torch.nn as nn
import numpy as np
import pandas as pd
from torch.utils.data import DataLoader, Subset
from data.dataset import MRIDataset
from models.efficientnet3d_pretrained import make... |
39f2acc64810c2cd12bd8bdd6b9f0882e4648b72c1f334bc30ffdc9e3be6a6b4 | Python | 11,256 | 300 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""Monkey patches to update/extend functionality of existing functions."""
from __future__ import annotations
import time
from contextlib import contextmanager
from copy import copy
from pathlib import Path
from typing import Any
import cv2
import n... |
a65de313ec9b8ee5fc3b77c44f31ac59a6ee6eed3ea8560a074b73f697eef897 | Python | 11,257 | 281 | import tqdm
from natsort import natsorted
import numpy as np
from scipy.stats import qmc
from skimage.morphology import closing, cube, label
from napari_simpleitk_image_processing import label_statistics
from tqdm import tqdm
import numpy as np
from natsort import natsorted
import pandas as pd
import os
from glob impor... |
8b72a73ca67e877fe7cd870c608f7863c51f2015b28c98518cc502233e05966a | Python | 11,259 | 328 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
from collections import OrderedDict
from typing import Callable, List, Optional, Tuple, Union
import torch
import torch.nn as nn
from torch.utils.checkpoint import checkpoint
from .model_misc import LayerScale
class ResidualAttentionBlock(nn.... |
ed443443cb94711a50f998b54dff88c33750803f45f7e663a94bf312c9d13f7c | Python | 11,259 | 338 | import sys
sys.path.append("./src")
from napari_dmc_brainmap.utils.atlas_utils import xyz_atlas_transform
from napari_dmc_brainmap.utils.atlas_utils import get_decimal
from napari_dmc_brainmap.utils.atlas_utils import coord_mm_transform
from napari_dmc_brainmap.utils.atlas_utils import sort_ap_dv_ml
from napari... |
84574866e077231fd846ba4d83bc0bfc6f14d32be436628157a2dd100feb0bde | Python | 11,260 | 230 | import os
import subprocess
import shutil
import nibabel as nib
import numpy as np
import pandas as pd
from nipype.interfaces.base import BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File, Directory, traits, CommandLineInputSpec, CommandLine, isdefined
from nipype.interfaces.utility import IdentityInterface
from... |
1b4a5194105a89177ce0848911e673a23a430ada5c38aeae59e13b9e1b602acd | Python | 11,261 | 385 | # -*- coding: utf-8 -*-
"""
Label and annotation info from Allen Brain Atlas (v2)
Notes:
- The annotation file is assumed to be in './Data/Annotation/annotation_25_right.tif'
but can be set in the constant :const:`DefaultLabeledImageFile`
- The mapping between labels and brain area information is ... |
c2c6f543ef764a28b07608c9ad49716eec322927a115b25136b19c6ab32ec052 | Python | 11,266 | 361 | from __future__ import annotations
import hashlib
import socketserver
import threading
import time
from collections.abc import Iterator
from pathlib import Path
import osam
import pytest
from pytestqt.qtbot import QtBot
from labelme._model_manager import ModelManager
@pytest.fixture
def manager(
*,
qtbot: ... |
3c407b571a097dcdaa236084fe5f388ed9c261dfa1fdf26e11537b8d7144a5d5 | Python | 11,268 | 251 | """
this file describes a class that handles the axis behavior for the lasagna viewer
"""
import pyqtgraph as pg
from lasagna.ingredients.imagestack import imagestack as lasagna_imagestack
from lasagna.utils.lasagna_qt_helper_functions import find_pyqt_graph_object_name_in_plot_widget
from lasagna.utils import prefe... |
245f739d5e04dc0600d1b6e9b11b0a1c8897b9ef290f84ba5fc111112a74016d | Python | 11,272 | 270 | import torch
from torch_geometric.data import DataLoader
import torch.optim as optim
import torch.nn.functional as F
from torchvision import transforms
from gnn import GNN
from tqdm import tqdm
import argparse
import time
import numpy as np
import pandas as pd
import os
### importing OGB
from ogb.graphproppred import... |
72020d8583b2102abfbc998044948ec142a6e1dc7dc08f3d0bb2ff987adc1c39 | Python | 11,273 | 311 | '''Compute total motion energy from greyscale videos.
'''
import numpy as np
from .utils import (iterator_func,
pointwise_square,
)
# Make tqdm optional
with_tqdm = True
try:
from tqdm import tqdm
except ImportError:
with_tqdm = False
def process_motion_energy_from_fil... |
a42a259adba1b07d3afbfd8ac308f536b9cd276e8d6ccb32794282c535f53598 | Python | 11,277 | 383 | from contextlib import contextmanager
import warnings
from types import SimpleNamespace
import pandas as pd
from napari_dmc_brainmap.utils.data_loader import DataLoader
from napari_dmc_brainmap.utils.dataframe_utils import clip_negative_first_row
from napari_dmc_brainmap.visualization.vis_plots.brainsection_visualiza... |
418738d450e116a65e4ba8440b1a5a1555378b0ec4e512b1b02205b6f3aeb959 | Python | 11,278 | 364 | import logging
import math
import os
import sys
import time
from typing import Any, Dict, Optional
import torch
from torch_geometric.graphgym import register
from torch_geometric.graphgym.config import cfg
from torch_geometric.graphgym.imports import Callback, pl
from torch_geometric.graphgym.utils.device import get_... |
28907d327316486d559b6e0051a00e780c0c78b61adbdf5802bd2784d9b5633a | Python | 11,280 | 279 | import os.path as op
from typing import List, Self, Tuple, Union
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
from scipy.interpolate import make_interp_spline
from ..system.utils import vectorize
minZero = 1e-8
np.seterr(all="ignore")
class makesnr:
"""Class object that computes and... |
350c5511b8a616aaf0c4844d101a4e61d6a90e674bae972ac605b3c52982ad06 | Python | 11,281 | 365 | from collections import OrderedDict
from collections.abc import Callable, Iterable, Sequence
from copy import deepcopy
from pathlib import Path
from typing import (
TYPE_CHECKING,
Any,
Literal,
)
import torch
from torch import nn
from torchview import draw_graph
from transformers import PreTrainedModel
fr... |
0e579f8a6241e08844d8838d665be6f3d709eb5f005c63c87d7d995cee34efb9 | Python | 11,285 | 287 | """Functions that calculate curve data for cross validation plots."""
from typing import List
import warnings
import numpy as np
import pandas as pd
from sklearn import metrics
def calculate_roc_curve(curve_data):
"""Calculates ROC curve on the folds
Args:
curve_data (dict) : dict of curves produced... |
ae757acb1a173760c965830c143ab0004bdbae161e2441eb9a9a0923f692f4e5 | Python | 11,289 | 367 | from itertools import chain
from pathlib import Path
from typing import TYPE_CHECKING
import matplotlib
import numpy as np
import pandas as pd
from matplotlib.axes import Axes
from matplotlib.figure import Figure
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from aislib.misc_utils import ensure_path_exists
fr... |
052fdf1a09a0626a9573958349b0d5acc2c807fa722eafcd3ea9a8436673c503 | Python | 11,291 | 340 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
import numpy as np
import os
import pandas as pd
import pytest
from bluepysnap import Circuit
from utils import TEST_DATA_DIR
from connectome_manipulator.connectome_manipulation.manipul... |
578707a758335a31f6e1825b08c2f7f01aec0707baa3c876874efcf4f7476a6a | Python | 11,292 | 315 | from __future__ import annotations
import hashlib
import threading
import weakref
from pathlib import Path
import osam
import pytest
from PySide6 import QtCore
from PySide6 import QtGui
from PySide6 import QtWidgets
from pytestqt.qtbot import QtBot
from labelme import _automation
from labelme._shape import Shape
fro... |
7dd1ac025983b44bc0863c0dcde171d63348486f619e3a3fdd0006eef802f26d | Python | 11,295 | 394 | import gzip
import os, sys
import pickle
from tqdm import tqdm
from multiprocessing import Pool
import lmdb
# '2022.09.3'
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.rdMolAlign import GetBestAlignmentTransform
import numpy as np
import torch
split_key = sys.argv[1]
split = torch.load("split... |
799607c26f184e72f52c2edade576ac76157bc06a101d19ac781842363440a1f | Python | 11,298 | 355 | import json
import random
import torch
torch.manual_seed(123)
import numpy as np
import pandas as pd
from jarvis.core.graphs import Graph
from jarvis.core.atoms import Atoms
from pymatgen.io.jarvis import JarvisAtomsAdaptor
from pymatgen.core import Structure
#from alignn.models.alignn import ALIGNN
from alignn_mult... |
9feafa27242828f80f845a98da6c2001fd7b19cef9d3a4ae8ecfa65c1afceb95 | Python | 11,298 | 355 | import json
import random
import torch
torch.manual_seed(123)
import numpy as np
import pandas as pd
from jarvis.core.graphs import Graph
from jarvis.core.atoms import Atoms
from pymatgen.io.jarvis import JarvisAtomsAdaptor
from pymatgen.core import Structure
#from alignn.models.alignn import ALIGNN
from alignn_mult... |
cce78e441cb0f208702180ec0dd7abd44027a1231eedac1d4afdd8a574203a8b | Python | 11,299 | 282 | import os
import functools
import logging
from collections import OrderedDict
from multiprocessing.pool import ThreadPool
from typing import List, Any, Callable
import numpy as np
from brainscore_core.supported_data_standards.brainio.stimuli import StimulusSet
from brainscore_core.supported_data_standards.brainio.as... |
6bf19d87619b2bc6b6560dcfa3a91e2917962fec73f87f5d9746a68b7c437a78 | Python | 11,303 | 253 | ## ------------------------------------------------------------
## IMPORTS
## ------------------------------------------------------------
import torch
import torch.nn as nn
from LSTMConvCell import *
## ------------------------------------------------------------
## Explain the block
## -----------------------------... |
bbc037ecfd93befdfb2de5931e1f939401438ccd04dd60a9d15e065477baaa01 | Python | 11,303 | 359 | from __future__ import annotations
import os
import re
import pandas as pd
from nipype.interfaces.base import CommandLineInputSpec, File, TraitedSpec, CommandLine, BaseInterfaceInputSpec, BaseInterface
from traits.api import Str, Int, Directory
from pathlib import Path
from typing import Dict, List, Optional, Tuple, Un... |
a9952221e71d668b0d2039e3b29873ab7857d3774640789e5e284fd28ba6700d | Python | 11,306 | 288 | import torch.nn as nn
import torch
from torch import Tensor
from typing import List, Tuple, Optional
from bism.modules.runet_block import RBlock2D, RBlock3D
from bism.modules.layer_norm import LayerNorm
from bism.modules.concat import ConcatConv2D, ConcatConv3D
from bism.modules.upsample_layer import UpSampleLayer3D, ... |
afcba40a8ddfb430ac2ba5e7b6f1509741452faa7843a65321dbc3e6e9bc9470 | Python | 11,307 | 326 | """
Copyright 1999 Illinois Institute of Technology
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, publis... |
077438866b23182831220619d7200061e7c42c792728562783d9351f09540236 | Python | 11,309 | 337 | import argparse
import logging
import os
import random
import sys
from datetime import datetime
import torch
import torchmetrics as tm
from torch.utils.data import RandomSampler, WeightedRandomSampler, DataLoader
from model import ProTact
from utils.data import get_dataset
from utils.utils import setCpu, Seed_everyt... |
8d8f6336bdeb726d4858e68c7b68090c9bf200540e54c3e4b29595493d36d88a | Python | 11,309 | 325 | """
Negative sample generation with indirect association filtering.
This module implements the negative sampling strategy described in Methods 2.2,
which excludes metabolite-disease pairs that share proteins to avoid false negatives.
Key Principle:
--------------
If a metabolite M associates with protein P, and prote... |
e63b59c5ad430c46feda2526da5562f0b868074706c1ea128198290742633034 | Python | 11,309 | 210 | import numpy as np
from brainscore_core import Metric
from brainscore_core.supported_data_standards.brainio.stimuli import StimulusSet
from tqdm import tqdm
from typing import Dict
import xarray as xr
from brainscore_vision import load_dataset, load_stimulus_set, load_metric
from brainscore_core.supported_data_standard... |
54c8d02e0f02e9e03a8deb0ff2373786c0b1436ff28e4d7c2b0294e41deb41b8 | Python | 11,311 | 242 | import logging
from typing import Union
import numpy as np
from tqdm import tqdm
from brainscore_vision.metric_helpers.xarray_utils import XarrayRegression
from brainscore_vision.utils import fullname
# do not import tensorflow at top level to avoid forcing users to install it if they don't use this metric
def mask... |
510efe765fb904b4c622c76aceb14e181d82d8c9cff11d985e7286c39814286f | Python | 11,314 | 462 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Project on template and average
"""
import os
import mbflim.utils as ut
import mbflim.visualization as vis
import mbflim.image.image_processing as pro
import mbflim.image.image_set_processing as setpro
import mbflim.flim.flim_visualization as fl_vis
import mbflim.pa... |
4f61ab21d7d3debe770b50dd5aca84274188775a85f5ddf563df426d7104c83f | Python | 11,315 | 333 | # Copyright 2024 Google LLC
# 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, sof... |
788acb587f12b38479ed9eebd794a83a8b7978d929bdf7d4af9925f93bc62a22 | Python | 11,316 | 255 | #!/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=['MT.zip'])
tmp_dir = tempfile.Temporary... |
e04430ffa34b3c0ad786924bedf89a0799debf907cb4ef44e4eb06b42206c17e | Python | 11,316 | 371 | '''
Auxiliary functions to help with signal
processing.
'''
from typing import Any, Union, Callable, Dict
import numpy as np
import sklearn, scipy
from .math import *
def align_y_with_x(x: np.ndarray, y: np.ndarray, f: Callable = cosine, epsilon: float = 1e-27) -> int:
'''
'''
# get parameters
... |
1d00c9dfdeec1a72aa71a3f929c09e3b2307582381d0e2732dc1dbbf056df65f | Python | 11,319 | 462 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Project on template and average
"""
import os
import mbflim.utils as ut
import mbflim.visualization as vis
import mbflim.image.image_processing as pro
import mbflim.image.image_set_processing as setpro
import mbflim.flim.flim_visualization as fl_vis
import mbflim.pa... |
960b4c137aca58d6a88519cbb7a507bcfba1b3cee2b95c29c6c3c7d2e3791589 | Python | 11,321 | 230 | #!/usr/bin/python3
# -*- coding: utf-8 -*-
# from qtpy.QtPrintSupport import QPrintDialog
from qtpy.QtGui import QAction
from qtpy.QtWidgets import QMessageBox, QMainWindow, QMenu, QFileDialog, QApplication
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view.ModeToggle import ModeToggle
from napari_dm... |
b6921faec60eb0ea5ffce4eb6505d70c245a0dfb642ba2b94198b9b6dbe53b07 | Python | 11,321 | 242 | import pathlib
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import seaborn as sns
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import layers
from tensorflow.keras import backend
from functions import *
from the_model import *
#fu... |
10c7961e4109bfc7c54e6e35b4826d06a5f4dede5bfcce84503d1e34eec2349e | Python | 11,325 | 335 | import random
from datetime import datetime
import pandas as pd
# camera recording
import win32gui
from psychopy import core, event, visual
from psychopy.constants import FINISHED, NOT_STARTED, PAUSED, PLAYING
from psychopy.hardware.emulator import launchScan
from pywinauto.application import Application
def run_vi... |
d5a4a0c082e90a6d5b91e68bb08b8fb8ab8afd9e0fee4ee1982127f28b88a123 | Python | 11,326 | 265 | """Test the functions in the yasa/others.py file."""
import unittest
from itertools import product
import mne
import numpy as np
import pytest
from mne.filter import filter_data
from yasa.fetchers import fetch_sample
from yasa.others import (
_index_to_events,
_merge_close,
_zerocrossings,
get_center... |
ff8fbbc709aac8e6a5e7e8b516e6680cb30f9f3647acf1f78f73e899d090350e | Python | 11,328 | 249 | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A wrapper class for the Hamilton MVP valve chain and the Widgets that display
# their status. All interactions with the valve chain should go through this
# class.
# ------------------------------------------... |
1dbafcdd5751f689b6443649e0a21628fb6782f9b1822b7d58d820aeb618d7a3 | Python | 11,343 | 332 | from unittest.mock import Mock
import numpy as np
import pytest
import torch
from mcmlnet.training.data_loading.datasets import (
DatasetMCPred,
DatasetMCPredDirect,
mix_spectra_randomly,
)
class TestDatasetMCPredDirect:
"""Test cases for DatasetMCPredDirect class."""
def setup_method(self) -> ... |
7cd655d2ad80e25ce1650c9e3d12c74abb6e5a36f1431befdd5ee878dcc12d59 | Python | 11,343 | 327 | import warnings
from typing import NamedTuple, Optional
import torch
from torch import Tensor
from torch_geometric.utils import cumsum, degree, to_dense_batch
class KNNOutput(NamedTuple):
score: Tensor
index: Tensor
class KNNIndex:
r"""A base class to perform fast :math:`k`-nearest neighbor search
... |
3c6cec4587b39f16e01ea92f6104cb3708db911b53f614729f5343bb5123bee3 | Python | 11,344 | 230 | import os
import tqdm
from glob import glob
import json
import numpy as np
import pandas as pd
import skimage.io as skio
from natsort import natsorted
from metrics import generate_dice_scores, instance_dice
from skimage.morphology import closing, cube, label, remove_small_holes
from napari_simpleitk_image_processing im... |
5394e4b7750c36629b95c7ccedd959aa090d3411bf07b7edec7f0ec98f3a308e | Python | 11,346 | 368 | from itertools import chain
from pathlib import Path
from typing import TYPE_CHECKING
import matplotlib
import numpy as np
import pandas as pd
from matplotlib.axes import Axes
from matplotlib.figure import Figure
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from aislib.misc_utils import ensure_path_exists
fr... |
e718055203f2a553214fdc041ab7f2604f7dfed04f57cc147dec3c24bf4ece26 | Python | 11,355 | 207 | """Evaluate fixed OpenPlant splits and export metrics and per-image predictions."""
from __future__ import annotations
import argparse
import csv
import json
import math
from pathlib import Path
from .train_utils import (boolean, choose_device, create_model, file_sha256, load_checkpoint,
loa... |
1aff9045c1e1f16479164a203e576afa83f889e0c12ea30c7dca6600e91537a6 | Python | 11,356 | 312 | """Affine construction, nearest-streamline lookup, and streamline-plane angle.
The angle cases are anchored at values that can be verified by inspection:
a streamline perpendicular to the plane is 90 degrees, one lying in the plane
is 0, and one at 45 degrees is 45.
"""
import numpy as np
import pytest
from ccf_stre... |
eda5539d1ac238cc3b73b9681a762cc52c46266d5e599dc6b47b61ec2990844f | Python | 11,358 | 338 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import base64
import json
import shutil
from abc import ABCMeta, abstractmethod
from collections.abc import Callable, Mapping
from enum import Enum, auto
from pathlib import Path
from typing import Any, TypeVar, cast
from attrs import define
import... |
db57f5761062f5b797386b59c53599b38a1a02e2f381698157d66dc582eb8771 | Python | 11,361 | 436 | """
Utility Functions for H-FNO
This module provides helper functions for:
- Reproducibility (seed setting)
- Device management
- Checkpoint loading/saving
- Model analysis
- Visualization
"""
import torch
import torch.nn as nn
import numpy as np
import random
from pathlib import Path
from typing ... |
3fea5812e69cd4324b7532bd370273c312fff9497f2b7eec1eefed7d4e253552 | Python | 11,366 | 333 | from copy import copy
import argparse
from tqdm import tqdm
import torch
import torch.nn.functional as F
from torch.nn import ModuleList, Linear, ParameterDict, Parameter
from torch_sparse import SparseTensor
from torch_geometric.utils import to_undirected
from torch_geometric.data import NeighborSampler
from torch_ge... |
782e947ac718118278257a0413cb8c275971f97dad546e786893cb15085e59bb | Python | 11,368 | 286 | import argparse
import numpy as np
import fbpca
import warnings
from numpy.linalg import pinv
from scipy.io import savemat
from scipy.signal import hilbert
from scipy.stats import zscore
from utils.cpca_reconstruction import cpca_recon
from utils.load_write import load_data, write_out
from xmca.tools.rotation import v... |
fbc53a81d79e794727aa82d6152030671f109dcbbc1ebaee8d75ee9fc4048885 | Python | 11,368 | 252 | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A wrapper class for the custom valve widget defined in ui_layouts/ui_qt_valve.
# This class provides the basic I/O required to set and read various valve
# properties.
# --------------------------------------... |
ecd571eac9eab8c479e77291cfd977c8c872edae84d3b4ed270112425c0783f7 | Python | 11,373 | 324 | from __future__ import annotations
import builtins
from abc import ABC, abstractmethod
from collections.abc import Callable, Iterable
from math import ceil, log10
from typing import TYPE_CHECKING, TypeVar, Union, cast
from magicgui.types import Undefined, _Undefined
from ._value_widget import BaseValueWidget, ValueW... |
e8cf6e7e799e51f0dc321aecd994fbd92e29cd53e033ef32307c36d479e04098 | Python | 11,374 | 297 | ###1_Shiaelis_et_al
# %%
class SimpleCNN_RGB(nn.Module): #https://doi.org/10.1021/acsnano.2c10159 , input is of size 17*17*3 padded with 0
def __init__(self, attention_output_size, classifier_hidden_dim, dropout_prob=0.2):
# def __init__(self, num_classes, attention_output_size ):
super(SimpleCNN_... |
7592dc32c46fe1116c7e87facc82f94c2f9e36914873cf439acd103764878642 | Python | 11,376 | 286 | import h5py
import sys
import yaml
import os
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from sklearn.metrics.pairwise import cosine_similarity
import git
import scipy.cluster.hierarchy as hac
from scipy.spatial.distance import pdist
import pandas as pd
pathpath, myrun, ncluststr, cmeth... |
7fbe72755170d1de2d48386b4019cf45588d42765dc6a9993b1c1dcf6eb53d6d | Python | 11,376 | 243 |
import sys, os
# os.environ['SDL_VIDEODRIVER'] = 'windows'
import pygame
import random
import tkinter.font
import numpy as np
import pandas as pd
import func_training_mrikey, func_MRI_mrikey, func_MRI_prac_mrikey
config_name = 'myapp.cfg'
if getattr(sys, 'frozen', False):
application_path = os.path.dirname(sys.e... |
6f5b6a1c62171c45f3a5643fbfdb85358b38755779a5be158e1f227178fcca8d | Python | 11,386 | 266 | import importlib
import cv2
import math
import numpy as np
from skimage.exposure import rescale_intensity
import tifffile as tiff
from napari_dmc_brainmap.utils import get_info
# todo warning for overwriting
def create_dirs(params, input_path):
save_dirs = {}
for operation in params['operations']:
i... |
f3ccd2c91658ef16e0d340d6ba60619bf002054f3aee4d33bd1a4aece77003b3 | Python | 11,389 | 326 | import pandas as pd
import numpy as np
import tensorflow as tf
from tensorflow import keras
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import matplotlib.patches as patches
import matplotlib.cm as cm
from tqdm import tqdm
from PIL import Image
from skimage import measure, morphology
# -----... |
bd02df0750fab1b26a32ff3a87002999eba72812e51315f609257b48499094cc | Python | 11,390 | 321 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
"""Triton kernel for faster and memory efficient sigmoid focal loss"""
import torch
import triton
import triton.language as tl
from torch._inductor.runtime.triton_helpers import libdevice
"""
The sigmoid focal loss is defined as:
prob = i... |
ea10cfa41c1c738703b17c26f6eed627ed85989b753e6f2130c8576ec35cd27b | Python | 11,394 | 289 | """
Tests for deepreg/dataset/loader/grouped_loader.py in
pytest style
"""
from os.path import join
from typing import List
import numpy as np
import pytest
from deepreg.dataset.loader.grouped_loader import GroupedDataLoader
from deepreg.dataset.loader.h5_loader import H5FileLoader
from deepreg.dataset.loader.nifti_l... |
e25095e811415af89b1eeb1eae77364e4ee3bb389566199ba70a5e716a8e5321 | Python | 11,397 | 311 | # Copyright (c) 2019, NVIDIA CORPORATION. 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 ... |
45f9948fa05209105f395ebfd532a1641d5d5de1ae9e768cc815855c4ba576cc | Python | 11,398 | 311 | # Copyright (c) 2019, NVIDIA CORPORATION. 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 ... |
fd4120006fdee1a9c7a1b2c5eabcc017c638070bf7b458937778969d7be0a90d | Python | 11,399 | 342 | #!/bin/python3
# adapted from Jannik Luboeinski's example here: https://github.com/jlubo/arbor_ou_lif_example
import random
import subprocess
import arbor as A
from arbor import units as U
import numpy as np
import matplotlib.pyplot as plt
def make_catalogue():
# build a new catalogue
out = subprocess.getou... |
39e32c8c8fde386bd59e82c484f50ab240158bba99507cd57711af187b750f3d | Python | 11,400 | 279 | """ Mask classification functions. """
import numpy as np
def classify_manual(masks, template):
""" Opens a GUI that lets you manually classify masks into any of the valid types.
:param np.array masks: 3-d array of masks (num_masks, image_height, image_width)
:param np.array template: Image used as backg... |
446dce8e57aab34646f08798932aed67413ec612f1e3e4e229a33e418781bd31 | Python | 11,400 | 324 | #!/usr/bin/env python
"""
This module handles communicating with HAL to capture images. The
captured images are directly added to the item store.
Hazen 10/18
"""
import contextlib
import os
import warnings
from PyQt5 import QtCore, QtGui
import storm_control.sc_library.parameters as params
import storm_control.steve... |
6b7ec4f9030ff8916700e2ee494138cec70e7ca3c9e4cbbb4aaa21648ba06f76 | Python | 11,400 | 270 | """Tests for HRTFGainLayerMLP and HRTFGainLayerMLPReg sample_from_priors behavior.
Verifies that sample_from_priors correctly resamples MLP weights/biases
and that JSON save/load does NOT resample (preserving fitted parameters).
"""
import pytest
import numpy as np
from nems import Model
from nems.layers.state impor... |
99fd59cd57abcebb89bf5345aff877f18edb4d47e1ee89b3e900adb5f02dd79b | Python | 11,400 | 373 | from collections.abc import Sequence
from functools import partial
from pathlib import Path
from aislib.misc_utils import ensure_path_exists
from docs.doc_modules.c_sequence_outputs.utils import get_content_root
from docs.doc_modules.experiments import AutoDocExperimentInfo, run_capture_and_save
from docs.doc_modules... |
9c3730b469d14c930597c00275219d0167dddb701ad9ea006c9262be3fad1b7d | Python | 11,402 | 195 | import matplotlib
matplotlib.rcParams['pdf.fonttype'] = 42
matplotlib.rcParams['ps.fonttype'] = 42
from brainvoice.data.brainvoice_loaders import load_data, load_labels
import argparse
import pandas as pd
import rsatoolbox
from rsatoolbox import rdm
from rsatoolbox.vis.colors import rdm_colormap_classic as rdm_colorm... |
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