sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
52c922f1608909f7a40d40b9284a9658846ab36fd23dfebea0744447b5a90ba0 | Python | 16,817 | 359 | #!/usr/bin/env python
"""
Camera control specialized for a Point Grey (Spinnaker) camera.
Tested on :
GS3-U3-51S5M
GS3-U3-41C6NIR
Hazen 01/19
"""
import storm_control.sc_hardware.pointGrey.spinnaker as spinnaker
import storm_control.sc_library.parameters as params
import storm_control.hal4000.camera.cameraCont... |
cdd3339600695260643e8be96108797cc3704d92c3ab63a77aa5f8ed0131ef39 | Python | 16,818 | 477 | import copy
import inspect
import typing
from collections import defaultdict
from dataclasses import dataclass, field, make_dataclass
from typing import Any, Callable, Dict, List, Optional, Tuple, Union
import torch
EXCLUDE = {'self', 'args', 'kwargs'}
MAPPING = {
torch.nn.Module: Any,
torch.Tensor: Any,
}
... |
ce0f90bb43ee14db2f6bf2d2832e34a77622e78bdbe3f2aca236c61757a27c7c | Python | 16,821 | 337 | # /------------------------------------------------------------------------------+
# | 27-NOV-2022 |
# | Copyright (c) Bone Imaging Laboratory |
# | All rights reserved ... |
55df1049d8ee1fcaf3d96e3fbddb7518abceced6e1169a6a02da329fc73325c3 | Python | 16,832 | 428 | """
(C) Copyright 2021 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
... |
122524a9df222638a0bfae37b94b414f15ac8aa439342a6f5def782bde851cda | Python | 16,840 | 471 | import unittest
import abc
from copy import deepcopy
import numpy as np
import pandas as pd
from sklearn.ensemble import GradientBoostingRegressor, GradientBoostingClassifier
from sklearn.linear_model import LinearRegression, LogisticRegression
from sklearn.model_selection import GridSearchCV, RandomizedSearchCV
from... |
4b560c9ebcf9c50e672b2c5b854938dc1957c561a63f5734f46eacd7a859259a | Python | 16,843 | 396 | """Gabor-filter entropy features for arbitrary image sets.
This is a standalone Python port of the descriptor behind the
GaborFilterEntropy4x4Cosine model from the EntropyReanalysis MATLAB scripts.
The default settings match that model: 256x256 grayscale images, six octave
frequency bands [1, 2, 4, 8, 16, 32], six ori... |
bcc91b8546123c547005754a65582bc7ec1d35ef602fe1223c58541d55341b10 | Python | 16,864 | 396 | import sys
from pathlib import Path
p_dir = str(Path(__file__).absolute().parents[1])
if p_dir not in sys.path: sys.path.insert(0, p_dir)
import os
import sys
from pathlib import Path
import json
import warnings
import shutil
import random
import string
import torch
from torch.nn import functional as F
import nibabel... |
ef2c45422525d2ddaaee10c02365aeaedf9028cc91765b471bead9fa819e541e | Python | 16,878 | 365 | #!/usr/bin/env python
"""
Handles all interaction / communication with the parameters widget.
This widget is responsible for keeping track of the various
different parameter files that the user has loaded as well as
editting and saving these parameters.
Unlike in Python2/PyQt4 HAL there is no longer a single current ... |
5bbf54df4444984e0841222cad80ea493823982dee44c9b3b65c0597ac44fde1 | Python | 16,882 | 407 | #!/usr/bin/env python
"""
Spot counter. This performs real time analysis of the frames from
camera. It uses a fairly simple object finder. It's purpose is to
provide the user with a rough idea of the quality of the data
that they are taking.
Hazen 05/17
"""
import sys
import time
from PyQt5 import QtCor... |
b1095286db089394e16265383cfdd078225b6c14b501b1707ed173267789e354 | Python | 16,884 | 388 | import concurrent.futures
import json
from pathlib import Path
import cv2
from typing import Dict, List, Tuple, Union
from magicgui import magicgui
from magicgui.widgets import FunctionGui
from superqt import QCollapsible
from qtpy.QtWidgets import QPushButton, QWidget, QVBoxLayout
from matplotlib.backends.backend_qt5a... |
c4865296cd6248d01dc23921e02490fab204a834b42d1408b9f15098889d1d4e | Python | 16,892 | 410 | import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle, ConnectionPatch
import figure_properties as fp
import numpy as np
seed = 11
# 20 Hz, 20AP
c_reg_fn = '100_regular_20Hz_7_Control.npz'
l_reg_fn = '100_regular_20Hz_7_MCUKD.npz'
# 10 Hz, 10AP
c_reg_10 = '100_regular_10Hz_7_Control.npz'
l_reg_10 ... |
1762acc6bbd8973cb625d61d2eba179c0adabecdef6e262c58ec9414f433ce53 | Python | 16,893 | 610 | # tifffile/_imagecodecs.py
# Copyright (c) 2008-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice... |
3618b995d592bc31477564468c23fad3c39dd93d85c1c9d5062cf06ad169cd0b | Python | 16,894 | 411 | import matplotlib.pyplot as plt
from matplotlib.patches import Rectangle, ConnectionPatch
import figure_properties as fp
import numpy as np
seed = 11
# 20 Hz, 20AP
c_reg_fn = '100_regular_20Hz_7_Control.npz'
l_reg_fn = '100_regular_20Hz_20_Letm1.npz'
# 10 Hz, 10AP
c_reg_10 = '100_regular_10Hz_7_Control.npz'
l_reg_10... |
2197e9ad952ed5624fcdedaa3cc2bcdc7c045e2d9ab19e5f39dba4e1019cf9e7 | Python | 16,898 | 448 | """ Classes and functions for fitting ivim model """
import numpy as np
from scipy.optimize import shgo
from dipy.reconst.base import ReconstModel
from dipy.reconst.multi_voxel import multi_voxel_fit
from dipy.utils.optpkg import optional_package
cvxpy, have_cvxpy, _ = optional_package("cvxpy")
class IvimModel... |
d211cedc611f33ccc67a81c7375dc502f07c3b8382eeabefa33a2bb7f51df995 | Python | 16,905 | 495 | """
(C) Copyright 2021 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
dis... |
25806e5a2783f3bd207973f52214e738dcc4680a0891d239aa88ee066835d011 | Python | 16,913 | 393 | import torch
from pathlib import Path
import numpy as np
import pickle
import pandas as pd
from collections import defaultdict
from typing import Tuple, Optional, Union, Dict, List
from collections.abc import Callable
import os
def pre_normalization(x: torch.Tensor) -> torch.Tensor:
"""
Prenormalization used... |
406c14338d084465d77f98dc0f3903633efb21882774644214d8094aaf289d8a | Python | 16,930 | 352 | import torch
import numpy as np
import pandas as pd
import json
import os
from transformers import pipeline
from datetime import datetime as dt
from torch.utils.data import Dataset
from tqdm import tqdm
class Twibot20(Dataset):
def __init__(self,root='./Data/',device='cpu',process=True,save=True):
self.ro... |
a7b2353003394ab433f909c0dbd7e5a06b7ae1289939857245ae3062f1eb5901 | Python | 16,930 | 418 | import typing
from typing import Optional, Tuple, Union
import torch
import torch.nn.functional as F
from torch import Tensor
from torch.nn import Parameter
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.nn.inits import glorot, zeros
from tor... |
937c3a9dfa138172b34a91a491c6a680b33df1080a970f6befce2d79121e4c81 | Python | 16,931 | 379 | """
Modified from ConvNeXt official repo: https://github.com/facebookresearch/ConvNeXt/blob/main/models/convnext.py
"""
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
... |
c2732fac485c2ed9edc816f4277d01575319e0b70d6f0fa3d831b6192a9fe6ff | Python | 16,931 | 427 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
"""
# ------------------------------------------------------------------------------
# Reference: https://github.com/facebookresearch/detectron2/blob/main/detectron2/utils/visualizer.py
# Modified by Jitesh Jain (https://github.com/praeclarumjj3)
# -------------------... |
9a4a2b166e31f1bad64ec6dbe3395be291fdd0bbb497a391e55041ad9eeeb2db | Python | 16,934 | 462 | # https://github.com/takyamamoto/Hopfield-Network
from dataclasses import dataclass
import numpy as np
import warnings
from matplotlib import pyplot as plt
import matplotlib.cm as cm
import random
from tqdm import tqdm
from nilearn import image, plotting
from nibabel.processing import resample_from_to
import nibabel a... |
60a8c3de9b958c1801d3725a95438afef1e8bc926a3c880b3097c3895862e6c6 | Python | 16,936 | 295 | import numpy as np
from matplotlib import colors as mcolors
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
import os
import colorsys
import sys
def get_axis_size(ax=None):
"""
ax: matplotlib axis to measure
Returns width, height in inches
"""
... |
2aa9255449caf179e6b3543b84d66227cc63669fec86190000468b52b37e9797 | Python | 16,937 | 386 | import torch
import torchvision
import torchvision.transforms as T
from torch.utils.data import DataLoader
import os, sys, math
from copy import deepcopy
import numpy as np
import h5py
import gc
import click
import matplotlib.pyplot as plt
from EIANN import Network
from EIANN.utils import (read_from_yaml, write_to_yam... |
04e727f8fc3122fc6436ffef22e644faac1b5be58074d7ad8623c78b4d6e0821 | Python | 16,944 | 470 | """
This module implements Zero-Shot Self-Supervised Learning
"""
import torch
import torch.nn as nn
from deepdwi import lsqr, util
from deepdwi.models import mri, resnet, unet
from typing import Callable, List, Optional, Tuple, Union
# %%
def uniform_samp(mask: torch.Tensor, rho: float = 0.2,
acs_... |
4bdd54f7b0fd68aa4bd483470386e21640f935989449adac2d3cfba279650f14 | Python | 16,947 | 466 | """ Dataset reader for webdataset
Hacked together by / Copyright 2022 Ross Wightman
"""
import io
import json
import logging
import math
import os
import random
import sys
from dataclasses import dataclass
from functools import partial
from itertools import islice
from typing import Any, Callable, Dict, List, Optional... |
1824f6c00915fb934226d8f17b2c249cad87e88bb8dd47a89f8a72d65effad41 | Python | 16,948 | 430 | # Copyright 2024 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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... |
26fde721d5af8fdb76ffd707e94c9e285ee74c3a06991fc098d59802a2962286 | Python | 16,955 | 368 | """
drawLDAGraph
@2022 Knowblesse
2022NOV07
This script is for the testing or drawing one session data.
All the code used in this script is replicated in the `LDABatchTesting.py` for whole session statistics.
"""
import numpy as np
import matplotlib.pyplot as plt
from Switching.SwitchingHelper import parseAllData, get... |
625dec998bd404a22bc077328564a4ad1ba479ee2d5febe60a621902921106c3 | Python | 16,956 | 534 | # Copyright 2019 Calico 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, ... |
4209438efe435e024c33edfb3b3820b73d892dc318bc9817bbb419321a07bf04 | Python | 16,972 | 436 | import logging
from typing import List, Optional, Tuple, Union
import numpy as np
import torch
from torch import Tensor
from torch_geometric.explain import ExplainerAlgorithm
from torch_geometric.explain.config import ModelMode, ModelTaskLevel
from torch_geometric.explain.explanation import Explanation
from torch_geo... |
bfc7ee086cb76584d01565986c9bb8452cc7e0e7067088c35526eccdea822a8e | Python | 16,976 | 352 | import torch
import numpy as np
import pandas as pd
import json
import os
from transformers import pipeline
from datetime import datetime as dt
from torch.utils.data import Dataset
from tqdm import tqdm
class Twibot22(Dataset):
def __init__(self,root='./Data/',device='cpu',process=True,save=True):
self.ro... |
39316b577e62f896dbb23b9c708f32e418e4cedf9290a74bbd7d295e015c73c5 | Python | 16,992 | 470 | """
This script computes three dimensions from neural activity:
switch evidence, actor outcome, and observer outcome, using TDR
Based on these dimensions angles between these are computed.
Each calculation is repeated resulting in a distribution of angles.
"""
import sys
import os
sys.path.insert(0, os.path.dirname(o... |
6d393b176fcbcbcfea7ac6606b5db9af4c4e7187cbc08605cd0dd9fa76ea0c25 | Python | 16,997 | 677 | #!/usr/bin/python3
#
import os
import sys
import argparse
import shutil
import numpy as np
from sklearn.neighbors import NearestNeighbors
from uac.element import Element
from uac import utils
# Create the parser
my_parser = argparse.ArgumentParser(description="UAC fibre mapping")
# Add the arguments
my_parser.add_ar... |
55065d453499e85b74ba80f16e253faade62ff1229dcf3ecb4f9d95359528f56 | Python | 17,002 | 268 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'dave.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_MainWindow(object):
def setupUi(self, MainWindow):
MainWindow.set... |
f36d954daa5407e483c16e8e75f85d9990218a12ba5c5d22037e3888f04ad013 | Python | 17,009 | 395 | # flake8: noqa
import os
import time
import traceback
from functools import partial
from multiprocessing.pool import Pool
import numpy as np
from . import _timing, utils
from .metrics import Count
from .utils import TrackEvalException
try:
import tqdm
TQDM_IMPORTED = True
except ImportError as _:
TQDM_... |
6ad5dfb132b5e0d7043c8049ae4f7353116f605092d396dad919fb62c461ed49 | Python | 17,016 | 467 | import numpy as np
from numba import njit
from nems.registry import layer
from nems.layers.base import Layer, Phi, Parameter
from nems.layers.tools import require_shape, pop_shape
from nems.tools.arrays import one_or_more_negative
from nems.distributions import Normal, HalfNormal, Uniform
class ShortTermPlasticity(L... |
c564bb5f1ccd633dc399f281510c92902789b2d2887ef69ead815cc153f322b8 | Python | 17,016 | 380 | import torch
import torchvision
import torchvision.transforms as T
from torch.utils.data import DataLoader
import os, sys, math
from copy import deepcopy
import numpy as np
import h5py
import gc
import click
import matplotlib.pyplot as plt
from EIANN import Network
from EIANN.utils import (read_from_yaml, write_to_yam... |
5e211c7a99bd60cda68fb3dc886e8d59efb25bc6f6fd93f4344f9a76cfaffa7e | Python | 17,024 | 614 | # -*- coding: utf-8 -*-
"""
Created on Sat Jun 4 22:17:13 2022
@author: DELINTE Nicolas
"""
import numpy as np
from dipy.io.streamline import load_tractogram, save_tractogram
def tract_to_ROI(trk_file: str):
'''
Returns a binary mask of each voxel containing a tractography node.The
voxels containing st... |
e9f756945bb3a09365adf7c4619ecfd62f3ab8f8ec90f4ad99a0a89a44e5a1fd | Python | 17,024 | 363 | """Test the encoding model's prediction accuracy ID and OOD on NSD-core, and
OOD on NSD-synthetic.
Parameters
----------
subjects : list
List of the used NSD subjects.
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 featur... |
a5107f58adce8a56f7d6c6d74cae295030754730beda244d9f99b168310b35ec | Python | 17,027 | 411 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import copy
import gc
import logging
import os
from collections import defaultdict
from operator import xor
from pathlib import Path
from typing import List, Optional
import numpy as np
import pycocotools.mask as mask_util
import torch
from pycoc... |
6297ea5ca9615a7dec0743106803159fd2b6ea55d605bcb400818758cec0d451 | Python | 17,029 | 574 | from .util import dict_hash, Dict, tweak_module_, lookup_nn, print_to_file
from ..optim import lr_scheduler
import json
from itertools import product
from collections import OrderedDict
from torch.nn import Module
from torch import optim
import inspect
from typing import Callable, Union
import albumentations as A
from ... |
0b9aa4f5fc6e64af39e57041035b1e0170e453a70ea022a3bfd50f617250b11b | Python | 17,030 | 311 | from PyQt5.QtWidgets import QMainWindow, QMenu, QAction, QFileDialog, QApplication
from napari_dmc_brainmap.probe_visualizer.probe_vis.probe_vis.view.MainWidget import MainWidget
# from napari_dmc_brainmap.preprocessing.preprocessing_tools import adjust_contrast, do_8bit
from napari_dmc_brainmap.utils import get_bre... |
ab85b213c9a0705eec557439f6f19ac6d57b25ac6ef50cf0e83f35c4cbb74004 | Python | 17,031 | 381 | """
Modified from ConvNeXt official repo: https://github.com/facebookresearch/ConvNeXt/blob/main/models/convnext.py
这个版本，要把Conv2Former进行改造，使其输入支路为两路，作为融合特征用
"""
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in... |
e3fd8a6bf9bbde1ca1a7f58cb89f5f5c49ab3c5846687016a171c7a3cb9c2c14 | Python | 17,032 | 311 | from PyQt5.QtWidgets import QMainWindow, QMenu, QAction, QFileDialog, QApplication
from napari_dmc_brainmap.probe_visualizer.probe_vis.probe_vis.view.MainWidget import MainWidget
# from napari_dmc_brainmap.preprocessing.preprocessing_tools import adjust_contrast, do_8bit
from napari_dmc_brainmap.utils import get_bre... |
f8a159dde41a8fff6507312525eb09649881e628ba75688638f1878c6d59b638 | Python | 17,047 | 353 | import torch
import numpy as np
import pandas as pd
import json
import os
from transformers import pipeline
from datetime import datetime as dt
from torch.utils.data import Dataset
from tqdm import tqdm
class Twibot20(Dataset):
def __init__(self,root='./Data/',device='cpu',process=True,save=True):
self.ro... |
804bef19899f2f53f482fef612013d242c4b78636e785af4d4043eb10c565962 | Python | 17,053 | 522 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
# Function to reconstruct the tables with the acquisition information
from dipy.core.gradients import gradient_table
# Functions to sample the diffusion-weighted gradient directions
from dipy.core.sphere import disperse_charges,... |
87553bebd7fc4d0b54b4a9241934b1c719043fa0db8b036d5af227f97b49aa84 | Python | 17,053 | 523 | import argparse
import types
from collections import Counter
from collections.abc import Generator, Iterable, Mapping, Sequence
from copy import copy
from dataclasses import dataclass, field
from pathlib import Path
from typing import (
Any,
Literal,
)
import configargparse
import yaml
from eir.models.fusion.... |
0eee87d1ce4a040f8a3bfd1e3493043460754c0012f5521a8344bf2c96c826db | Python | 17,056 | 527 | from typing import Any, Dict, List, Optional, Tuple, Union
import matplotlib.collections as collections # type: ignore
import matplotlib.pyplot as plt # type: ignore
import numpy as np
import scanpy as sc # type: ignore
from anndata import AnnData # type: ignore
from matplotlib.colors import ( # type: ignore
... |
bb41f09c42479f60a42d49f51a1fe5535336280684b4c38dd48423655ab3a912 | Python | 17,059 | 438 | from Models.Help_func import *
import matplotlib.pylab as plt
np.set_printoptions(precision=2)
# ---------------------------------------------------------------------------------
# The SCILD method
# ---------------------------------------------------------------------------... |
93568106815dcd7add18116622c741034f31354e46c726e7226d4cd3d6ac02fc | Python | 17,060 | 473 | """
This module implements the VAE training for DW-MRI
Authors:
Julius Glaser <julius.glaser@fau.de>
Zhengguo Tan <zhengguo.tan@gmail.com>
"""
from __future__ import division
import argparse
import copy
import h5py
import os
import pathlib
import torch
import yaml
import numpy as np
import torch.utils.data a... |
11f03a69576d56b7ba0cad045ce3ecfada8549ab995ecb83e75274e476896400 | Python | 17,070 | 540 | """Position class for 1D and 2D position AnalogSignalArrays"""
import copy
import numpy as np
from .. import utils
from ..core import _analogsignalarray, _epocharray
from ..utils_.decorators import keyword_deprecation
class PositionArray(_analogsignalarray.AnalogSignalArray):
"""
PositionArray for 1D and 2... |
552773d6fe1ecfa370dc189f3302fec142e210732967b1ab76fffc7ba36f1ec0 | Python | 17,072 | 533 | """Color palettes for use with nelpy.
Some of these functions are Copyright (c) 2012-2016, Michael L. Waskom
"""
import colorsys
from itertools import cycle
import matplotlib as mpl
import numpy as np
from matplotlib.colors import to_rgb
from . import (
colors,
utils, # import get_color_cycle, desaturate
)... |
8f2d17b341b86f120f3f7b60cc553d20773216a3bf78193189be4dae26760d7b | Python | 17,072 | 438 | # -*- coding: utf-8 -*-
"""
GO terms associated with pleio and non pleio genes
We need to download in the same directory and run great_library_phenotypes.py
"""
import obonet
import numpy as np
import os
import networkx as nx
import matplotlib.pyplot as plt
import pandas as pd
import matplotlib as mpl... |
ed08a19cd02588c97eeb7fb9d1de4049758161ab12d3e8aeb46edf0317e1ce9e | Python | 17,072 | 462 | # index_annotations.py
# Helper class to list annotated images and load saved labels/masks / find video files.
# This duplicates the logic used in your inspector verbatim (so behaviour stays identical).
import os
import cv2
import numpy as np
import box_geometry as bg
class AnnotationIndex:
def __init__(
self,
s... |
6bcced1b27f13d496db2b679980a4d8bab0c189c3ec26b62970d9e69056a328f | Python | 17,073 | 513 | from typing import List, Optional, Union
import torch
from torch import nn
from torch_harmonics import RealSHT, InverseRealSHT
import tensorly as tl
from tensorly.plugins import use_opt_einsum
from tltorch.factorized_tensors.core import FactorizedTensor
from deepcardio.neuralop_core.utils import validate_scaling_fac... |
ada985291ecc18f53dd10c33b732cadc1a80c54c40a63974b06e8ca810ed015e | Python | 17,073 | 371 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""Scale-only calibration for monocular depth models.
The log-depth head predicts relative scene structure (shape); absolute scale is a separate
two-parameter log-affine ``d' = exp(a·log d + b)`` stored in the head's ``cal_a``/``cal_b``
buffers. This ... |
d361fe3d2aae15985aca82d7affb45c48ce6ab31fc6ec764ae9ea107d6948c27 | Python | 17,085 | 322 | #!/usr/bin/python
#-----------------------------------------------------------------------
# File : fim+psf+psr.py
# Contents: Pattern Spectrum Filtering and Pattern Set Reduction
# (for transactional data/frequent item set mining)
# Author : Christian Borgelt
# History : 2014.05.06 file created from file... |
2a40f5c50f249e937e2cf6fd3e0a872f2b546292a5955e9e443a97c5bada8c5f | Python | 17,086 | 480 | """Tests for mcmlnet.training.data_loading.data_augmentation_classes module."""
import pytest
import torch
from mcmlnet.training.data_loading.data_augmentation_classes import (
BezierContrast,
BrightDarkVariation,
DataAugmentation,
NoiseAddition,
NoiseAdditionWithExponentialDecay,
RandomOrder,... |
e4def5fbb8f19e0c05db22ae4fe690cb53b3a68bdc31bf328328dd95c70a67a3 | Python | 17,086 | 450 | """
Functions for preprocessing
"""
import numpy as np
import mne
#======================================================================================
# PROCESSING TRIGGERS
#======================================================================================
"""
Filters the trigger signals s... |
2d36ef31439f00598c388c86a8132b23e59f1d6e344d4b73645b2956038cf74f | Python | 17,089 | 409 | """
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... |
9e06073ca3a44d73421fcdae78d304f865674297bea080d0c4243e61481deebc | Python | 17,101 | 433 | #!/usr/bin/env python
"""Map features from the target species to the query species of a chain alignment file.
This is intended for mapping relatively short features such as Chip-Seq
peaks on TF binding events. Features that when mapped
span multiple chains or multiple chromosomes are silently filtered out. TODO:
(1)fo... |
c9c914ec461cf3983d15f62be924137d304018888d289cd8d7f3c8595dff779d | Python | 17,102 | 425 | """Doublet detection in single-cell RNA-seq data."""
import collections
import warnings
import anndata
import numpy as np
import phenograph
import scipy.sparse as sp_sparse
import tables
import scanpy as sc
from scipy.io import mmread
from scipy.sparse import csr_matrix
from scipy.stats import hypergeom
from sklearn.... |
f28de0eb53477321fd3440cd93a4649f8d941308f4703516fa194b4d6bde2782 | Python | 17,109 | 459 | import os
import tempfile
from collections import namedtuple
from collections.abc import Callable
from unittest import TestCase, mock
from unittest.mock import Mock
import numpy as np
from datumaro import AnnotationType, Bbox, LabelCategories
from datumaro.components import media
from datumaro.components.dataset impor... |
4ee64ea492eab888ab7297a5b88ae91cb96b69fa247c2d1771615ba75813c060 | Python | 17,111 | 480 | # Scaling Up Your Kernels to 31x31: Revisiting Large Kernel Design in CNNs (https://arxiv.org/abs/2203.06717)
# Github source: https://github.com/DingXiaoH/RepLKNet-pytorch
# Licensed under The MIT License [see LICENSE for details]
# Based on ConvNeXt, timm, DINO and DeiT code bases
# https://github.com/facebookresearc... |
70efd2d3afc4a3fb747bbe6b8935d39909cb6c9d3a0f6bb6ca754f0e1cc2fb54 | Python | 17,124 | 384 | """A module that contains unit tests for the :py:mod:`corelay.io.storage` module."""
import typing
from io import BytesIO
from pathlib import Path
import h5py
import numpy
import pytest
from corelay import io
from corelay.io.storage import DataStorageBase, HashedHDF5
@pytest.fixture(name='data', scope='module')
de... |
02068fab99479d22e2446dc55b24478b41cee10c2783f0b04206e48a6b3f2847 | Python | 17,126 | 565 | """
Read MHD stacks (using the vtk library) or TIFF stacks
@author: Rob Campbell - Basel - git<a>raacampbell.com
https://github.com/sainsburywellcomecentre/lasagna
"""
import imp # to look for the presence of a module. Python 3 will require importlib
import os
import re
import struct
import warnings
import numpy as ... |
c1349ef199aebe6c5173d53021fae4106e71adf2b5b6a05980d3e5e84820f489 | Python | 17,127 | 398 | import numpy as np
import torch
import torch.nn as nn
import my_setup
from torch import Tensor
from custom_layers.attention import Attention
from custom_layers.dense import Dense
from custom_layers.multihead_attention import MultiHeadAttention
from custom_layers.transformer import TransformerEncoder
class Transform... |
7b451271cd10fdda93d83608355317c58659a46abc53bdf31da7108abacc08a1 | Python | 17,128 | 392 | import numpy as np
import pandas as pd
import distinctipy
import matplotlib.pyplot as plt
from skspatial.objects import Line, Points # scikit-spatial package: https://scikit-spatial.readthedocs.io/en/stable/
from napari_dmc_brainmap.utils import get_animal_id, get_info, get_bregma, coord_mm_transform
from napari_dmc_br... |
208e005839a317d2ff4f78d847ff08eaf75273abc4dc34d50a81d7417d327b78 | Python | 17,134 | 312 | from PyQt5.QtWidgets import QMainWindow, QMenu, QAction, QFileDialog, QApplication
from napari_dmc_brainmap.results.probe_vis.probe_vis.view.MainWidget import MainWidget
# from napari_dmc_brainmap.preprocessing.preprocessing_tools import adjust_contrast, do_8bit
from napari_dmc_brainmap.utils.atlas_utils import get_... |
95c01cd43367563df35edcae21cf4a48c6d3957846654b7c4003afc5d8ccbfcf | Python | 17,134 | 451 | """
patchlib (python version)
Library for working with N-D patches.
Modelled after the MATLAB patchlib (https://github.com/adalca/patchlib)
"""
# built-in
import sys
from pprint import pformat
from random import shuffle
import random
# third party
import numpy as np
# local
import pynd.ndutils as nd
from imp impor... |
8081984511b7f504f07a6ebe550c33714eb540bf9336fa0d505f34a91fbb1c7c | Python | 17,138 | 396 | """What each computer does in a shared run, from joining to done.
Two roles. A **helper** waits until the main computer has started the run,
analyses the recordings it was given into its own corner of the shared
folder, and reports progress there as it goes. The **main computer** does
the same for its own share, then ... |
7af20e7ed0bf38b6594c94e70d42d972d3186d8621fdf174167ede11bb0e37fa | Python | 17,140 | 547 | import ast
import datetime
import os.path as op
import platform
from AFQ.api.bundle_dict import * # interprets bundle_dicts loaded from command line # noqa F403
from AFQ.api.bundle_dict import BundleDict
from AFQ.api.utils import kwargs_descriptors
from AFQ.definitions.image import * # interprets masks loaded from c... |
9f0fce8ae9abc0d606c0fd4ef76bb7b09de0df11fdcf1ad36db90a74478aeab2 | Python | 17,143 | 387 | # -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import
import argparse
import os.path as osp
import random
import numpy as np
import sys
import collections
import time
from datetime import timedelta
import torch
from torch import nn
from torch.backends import cudnn
from torch.utils.data import ... |
fc0a57100623c8560121bc61e69d9e0308c8acceb753424efb98f0eeea7fea1c | Python | 17,164 | 416 | import torch
import math
import numpy as np
import os
import json
import h5py
import time
from glob import glob
from matplotlib import pyplot as plt
import scipy.constants as sc
from scipy.ndimage import zoom
from data_prepare import Dataset_exp
from DS_network import Network
from func import frankotchellappa, prCo... |
159437927c0baf2de414be2dc7c19673c55f4dc793310fb58536729723c6b9e8 | Python | 17,169 | 498 | import pandas as pd
import numpy as np
from collections import defaultdict
from scipy import sparse
from copy import copy
complements = {
'A': 'T',
'C': 'G',
'G': 'C',
'T': 'A',
'N': 'N'
}
def reverse_complement(input_seq):
"""
Get the reverse complement of a sequence
"""
rev_input... |
3e07dcd170ae75841b8549b3424575fab0732786446b78e23f61966ca16efaf4 | Python | 17,174 | 391 | '''
Because we have morphs in the learning task but would still
like to estimate semantic effects that must technically be
in reference to word_a or word_b within the morph (e.g., for
morph /_i:/ between /si:/ and /ti:/, we must compute surprisal
either for /si:/ or /ti:/), we would like to use an LLM as a
surrogate mo... |
454cc3bab446f08dcc57a269794d6f5716f0b94e67070c2f5869d8dab7033835 | Python | 17,174 | 573 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from itertools import repeat
import os
import pathlib
import shutil
import ants
import json
import pandas as pd
import numpy as np
import mbflim.shared as sha
import mbflim.utils as ut
import mbflim.image.image_processing as pro
import mbflim.flim.flim_processing as fl
... |
88b7db4c57983822503ee1528555709c3f9924a6109478aed92fc95a3496d8cf | Python | 17,178 | 469 | import torch
from torch.nn import functional as F
import numpy as np
import math
from dgd.utils import PlaceHolder
def sum_except_batch(x):
return x.reshape(x.size(0), -1).sum(dim=-1)
def assert_correctly_masked(variable, node_mask):
assert (variable * (1 - node_mask.long())).abs().max().item() < 1e-4, \
... |
ef8ac7312d1e1d45201ad9a05d61717f6f8b33f3b5c9b63bb4ce48f244596b67 | Python | 17,188 | 413 | import h5py
import numpy as np
import os
import matplotlib as mpl
from pfcmap.python import settings as S
from pfcmap.python.utils import unitloader as uloader
from pfcmap.python.utils import som_helpers as somh
nmin_per_block = 3
def get_units(detailfile,metricsfile,somfeats,split_dict={},chop_to_blocks=False,nperblo... |
205d6f4159c4da25086dc4f9390eef4502d61aa1bc2e6be62dbf6128c605b102 | Python | 17,192 | 473 | from PySide6 import QtGui, QtWidgets, QtCore
from PySide6.QtWidgets import QWidget, QMenuBar, QMainWindow, QVBoxLayout, QLabel, QHBoxLayout, QGridLayout, QPushButton, QCheckBox, QSlider, QTableWidget, QTableWidgetItem, QTabWidget, QGroupBox, QSpinBox, QFileDialog, QMessageBox
from PySide6.QtGui import QAction, QIcon, Q... |
2bf41f94c453be5e4c6261c51ee3b35c004dc4aa324a46fa47f8e43f5d119b76 | Python | 17,197 | 581 | import functools
import inspect
import logging
import os
import os.path as osp
import warnings
from collections.abc import Iterable
from dataclasses import asdict
from typing import Any
import torch_geometric.graphgym.register as register
from torch_geometric.io import fs
try: # Define global config object
from ... |
3a8878ca549e404956bb89a456869f0612c421de3892549899c76f7f54b91645 | Python | 17,200 | 456 | """
Schema validation for EBM model inference data.
This module provides comprehensive validation of inference data against
the model's expected schema, ensuring correct feature names, types, and order.
"""
from dataclasses import dataclass, field
from enum import Enum
from typing import Any, Dict, List, Optional, Se... |
542c4bb46dc5c45c6fbd7aa79735597e55521544cb7a552913bf331fb0be1db4 | Python | 17,201 | 459 | """
MEG: Preprocessing, Source Reconstruction, Parcellation
=======================================================
This tutorial walks through the full MEG processing pipeline step by step:
1. Preprocessing — Filter, downsample, detect bad segments/channels, ICA artefact rejection.
2. Surface Extraction — Extract sk... |
9384aeb84760dac134511c48d919fc0e3792b7fbcccb8f64a2b711f51dbb2f1f | Python | 17,204 | 372 | """Binned correlation on the ``F`` / ``spks`` / ``denoised F`` paths.
These paths never involved a lag: they correlate whole traces at zero lag, and
the number in the output folder was only ever the frame period, filed under a
name (``30mslag``) that read like a 30 ms STTC window. So the number is now a
real, user-cho... |
978997427b0f3d33aa8667116c791de6cd33697e413b515c556c4a3356618aa1 | Python | 17,204 | 467 | import os
import os.path
from functools import partial
from statistics import mean
from typing import Callable, Union, Dict
import torch
import torch.nn as nn
import torch.optim.lr_scheduler
import torch.optim.swa_utils
from torch import Tensor
from torch.cuda.amp import GradScaler, autocast
from torch.utils.data impo... |
4e24cf530480543481ff077f6836ad50b3d8d12bf99e187800a9c357acfe639c | Python | 17,208 | 467 | """Helper functions for iterative 2D background fitting.
Headless (no file I/O, no matplotlib) support code for
:mod:`musclex.utils.background_fitting`:
* image geometry -- center crop to a fit size and reconstruct model
backgrounds at the original full resolution;
* wedge-based initialization of the general-backgr... |
24357429a81ff6ae905a161bcd635f3474b21a096312a110411c9b48ab6e9845 | Python | 17,211 | 390 | import torch
import torchvision
import torchvision.transforms as T
from torch.utils.data import DataLoader
import os, sys, math
from copy import deepcopy
import numpy as np
import h5py
import gc
import click
import matplotlib.pyplot as plt
from time import time
from EIANN import Network
from EIANN.utils import (read_f... |
5d4d874cf6e0249ffa853fbe5f4276c645e58826edefffa1b9bf67b8851096e8 | Python | 17,213 | 320 | import os
import os.path as osp
import sys
from typing import Callable, List, Optional
import torch
from torch import Tensor
from tqdm import tqdm
from torch_geometric.data import (
Data,
InMemoryDataset,
download_url,
extract_zip,
)
from torch_geometric.io import fs
from torch_geometric.utils import ... |
73979c440d1296ddd81664278d6f8b046e48a8194091712350743684abe52163 | Python | 17,220 | 492 | #!/usr/bin/env python
"""
Communicates with the National Instrument card(s).
Hazen 4/17
"""
import ctypes
import numpy
import time
import traceback
import threading
import PyDAQmx
import storm_control.sc_library.halExceptions as halExceptions
timeout = 1.0
def getLock():
return threading... |
2d0aad0c09aa452d74e0eb958423090bdcf4494be3f33e988abc6426968fde4b | Python | 17,230 | 493 | # 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 itertools
import os
from typing import Sequence, Tuple, List, Union
import pickle
import re
import shutil
import torch
from pathlib imp... |
3f3a636a2e4a2d5ff492090090af32013d31b9f37f29eea81f8b1d0865d03dd7 | Python | 17,236 | 628 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import json
import operator
from collections import defaultdict
from collections.abc import Generator, Iterable
from copy import deepcopy
from pathlib import Path
import pytest
from shared.utils.config import ASSETS_DIR, SHARE_DIR
class Container... |
13ebabe243e33c3502b9de54220b100efc211cff0b7ce05b9c44c25104688c91 | Python | 17,237 | 430 | import os
import time
import cv2
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from skimage.morphology import remove_small_holes, remove_small_objects
from EvaluationCNN.detect import predict_image_quality
from keypoint.detect import key_detect
from mol_segment.detect import segmente... |
63b54e16063936289bbfed56b069ef95ca6dfa8c9efdd2da8efef3f55d7246d0 | Python | 17,244 | 437 | from euler_gpu.grid_search import grid_search
from euler_gpu.preprocess import (initialize,
max_intensity_projection_and_downsample)
from euler_gpu.transform import (transform_image_3d, translate_along_z)
from evaluate import calculate_gncc
from tqdm import tqdm
from typing import Dict, List, Tuple, Callable
from d... |
6eb285ce8eab42060c9b9249279afb20ce803058fc5ccd8b6bd009b24b08b6a0 | Python | 17,248 | 490 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: avelinojaver
"""
# %%
import os
import glob
import datetime
import tables
import pandas as pd
import numpy as np
from functools import partial
from multiprocessing import Pool, Lock, cpu_count
from tierpsy.helper.misc import TimeCounter, print_flush
from tie... |
95f22e42479ec04984543de04638629f2cc4b9504c5a3839d62b10d9c73412dc | Python | 17,254 | 367 | """CAT-NAP adjacency-matrix construction.
Port of ``Functions/twoPhoton/suite2pToAdjm.m`` (everything after the denoising
call — the loading/denoising itself lives in ``loader.py`` / ``denoising.py``).
Takes a loaded :class:`~meanap.catnap.loader.Suite2pData` and produces the
functional-connectivity adjacency matrice... |
ced32d9998dd5f980ac6851e8b0c473d5cd02aa848be71bb0484ee8272962b64 | Python | 17,259 | 413 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
"""Main module for model building:
- main(...): Main function for running model building, given a model building config dict
* Loads a SONATA connectome
* Extracts connectivity speci... |
313b43efd1a03f3fc7d188f68d55d5d44e5bf21aaae5fa1e66e3ca3d82de3fe3 | Python | 17,265 | 515 | from dataclasses import replace
from pathlib import Path
from typing import List
from unittest.mock import Mock, patch
import numpy as np
import pandas as pd
import pytest
from brainways.pipeline.brainways_params import AtlasRegistrationParams
from brainways.project.brainways_project import BrainwaysProject
from brai... |
f5c33b9b3f5b79ff340600fc1d1a28ba4ff937e29b47b3ffafdfb3bd336965af | Python | 17,265 | 423 | import argparse, math, sys, scipy.sparse, gzip, random, numpy as np, joblib, linecache, pandas as pd, itertools, copy
from collections import OrderedDict
from sklearn.tree import DecisionTreeClassifier
from sklearn.metrics import roc_curve, auc, average_precision_score, mean_squared_error
import torch
import torch.nn... |
ce9ff86a0c3a1890e35ae7c0f1e8a2253e6d8604dd4b32347b9edff8e06a60d8 | Python | 17,273 | 445 | """
Pose-JEPA pretraining script.
Two usage modes:
1. Named datasets via $KINESCOPE_DATA_DIR:
kinescope pretrain --datasets humoto amass --output ./checkpoints/ --epochs 100
Datasets are loaded from $KINESCOPE_DATA_DIR (default: ~/kinescope_data/):
~/kinescope_data/amass/ → AMASS .npz files
~... |
7da996ba01f0cdfca0e56899a5130703783e3be35a30c74637f5040b84b40b01 | Python | 17,274 | 461 | """ Normalization + Activation Layers
Provides Norm+Act fns for standard PyTorch norm layers such as
* BatchNorm
* GroupNorm
* LayerNorm
This allows swapping with alternative layers that are natively both norm + act such as
* EvoNorm (evo_norm.py)
* FilterResponseNorm (filter_response_norm.py)
* InplaceABN (inplace_a... |
489d71ede446b8c7e7c51ec406d4074dd60c3b791af0870b5c10322932b0c949 | Python | 17,276 | 506 | '''Some helper functions for PyTorch, including:
- get_mean_and_std: calculate the mean and std value of dataset.
- msr_init: net parameter initialization.
- progress_bar: progress bar mimic xlua.progress.
'''
import os
import time
import torch
import torch.nn as nn
from functools import reduce
import opera... |
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