sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a2d4b1635a767229e2523d57cadf110703b7b10220607b5f0e1770d2c6f07c53 | Python | 6,715 | 190 | import torch
from einops import rearrange, repeat
from einops.layers.torch import Reduce
from torch import nn
from models.aggregators import BaseAggregator
from models.aggregators.model_utils import (FeedForward, PerceiverAttention,
PreNorm, cache_fn, fourier_encode)
class... |
da93965630bfe2e4b5fee41f9de8fcf1f2cc49eb479e5889446c0d7574374df9 | Python | 6,716 | 205 | import warnings
import math
import numpy as np
import torch
from torch import nn
from torch import einsum
from torch.nn.modules.batchnorm import _BatchNorm
import torch.nn.functional as F
from torch.nn import Parameter
from einops import rearrange
class VotingLayer(nn.Module):
"""
用于SNNs的输出层, 几个神经元投票选出最终的类
... |
e9cfe45a662f360fdcd052ceefa7878693d229569629c6447691f711b57bef57 | Python | 6,720 | 222 | # -*- coding: utf-8 -*-
"""
Modified from https://github.com/pytorch/vision.git
"""
import math
import torch.nn as nn
import torch.nn.functional as F
from .modelBase import ModelBase
class VGG(ModelBase):
"""
VGG model
"""
def __init__(self, parameters: dict, configuration):
"""
Ini... |
d432324a1fbd4b1e87609e22e35a7feedf04c5f52a1ce04d1c23d01b466e4c2c | Python | 6,725 | 135 | import io
import json
import tarfile
import pytest
import torch
from PIL import Image
from timm.data import MultiLabelTarget, create_dataset
pytest.importorskip('webdataset')
LABELS = [[5, 1, 0], [2], [], [4], [1, 5], [3], [0, 3], [2]]
def _add_member(tar, name, data):
info = tarfile.TarInfo(name)
info.si... |
c067d7da0dd67d1f593c1842fc4021a19847d4eb8117c8bd487038083579a996 | Python | 6,727 | 134 | import numpy as np
import torch
import tqdm
from typing import Callable, List
from pytorch_grad_cam.base_cam import BaseCAM
from pytorch_grad_cam.utils.find_layers import replace_layer_recursive
from pytorch_grad_cam.ablation_layer import AblationLayer
""" Implementation of AblationCAM
https://openaccess.thecvf.com/c... |
dd74c49bdd490c4ba816cd457720c22aa7378a8fa02c76de01c31242882e7405 | Python | 6,729 | 179 | import os
import numpy as np
import math
import torch
import logging
import yaml
from sklearn.metrics import balanced_accuracy_score, roc_auc_score, roc_curve, f1_score
from sklearn.metrics import auc,precision_recall_curve, r2_score
from sklearn.linear_model import LinearRegression, TheilSenRegressor
from sklearn.line... |
097a650ee53276d7be33e5d651af511a5eeda5b3df35c4123102212cf082cbc3 | Python | 6,730 | 164 | """ Nvidia NovoGrad Optimizer.
Original impl by Nvidia from Jasper example:
- https://github.com/NVIDIA/DeepLearningExamples/blob/master/PyTorch/SpeechRecognition/Jasper
Paper: `Stochastic Gradient Methods with Layer-wise Adaptive Moments for Training of Deep Networks`
- https://arxiv.org/abs/1905.11286
"""
fr... |
21f622b7e4743b96547e6b167cb0fa06a70b8e3a048a8b71d2551db175a56daa | Python | 6,730 | 203 | from typing import Optional
import SimpleITK as sitk
import PIL.Image
import numpy as np
import torch
from torchmetrics import (
StructuralSimilarityIndexMeasure,
MeanSquaredError,
MeanSquaredLogError,
MeanAbsoluteError,
PeakSignalNoiseRatio,
)
from GANDLF.utils import get_image_from_tensor
def st... |
1a634607787520225f9b758014e0e56df92fb1e7e75e1241867a70d290708129 | Python | 6,733 | 151 | """
Author: "Keitaro Yamashita, Garib N. Murshudov"
MRC Laboratory of Molecular Biology
This software is released under the
Mozilla Public License, version 2.0; see LICENSE.
"""
from __future__ import absolute_import, division, print_function, generators
import gemmi
import numpy
import json
import scipy.sparse
fr... |
31b8ee1f27efd2d0c6ba991d3d874ea46dedf47e9b6e50efe8eb0895e69c312b | Python | 6,736 | 209 | import networkx as nx
import os
# Column indices of the interesting fields in SNOMED's
# Description and Relationship files
_SNOMED_TERM_FIELD_ID = 0 # term activity (deprecated terms will have active = 0)
_SNOMED_TERM_FIELD_ACTIVE = 2 # term activity (deprecated terms will have active = 0)
_SNOMED_DESC_FIELD_ACTIVE... |
28258cefd737879453d13e7a4673966280904f12d1a1bd16a3c878bbfb004aa6 | Python | 6,744 | 175 | import cv2 as cv
import numpy as np
import tensorflow as tf
import seaborn as sns
import matplotlib.pyplot as plt
from tqdm import tqdm
from copy import deepcopy
from utils.image_preprocessing import PreProcess, normalize, coarse_fine_representation, light_dark_representations, \
lab_representation
from skimage.me... |
9dcb1ac68de8c38fffb9d2982077e2070ad359cef5ecd6b8e513a5e4e7d2de69 | Python | 6,751 | 166 | import time
import numpy
import wx
class ProgressWatcher:
""" Tracks pipeline progress and estimates time to completion """
def __init__(self, parent, update_callback, multiprocessing=False):
self.update_callback = update_callback
# start tracking progress
self.start_time = time.time... |
e0a0b1c9fd11bf0e3a5d9e80ad308ae8a7d3d0f63801d961472d652281f792ec | Python | 6,751 | 227 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
ab4b3be7bbf27f52fa375a3ec0ba62b20b92e7a84ad4d147addd340ed25b06b6 | Python | 6,756 | 235 | from itertools import product
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
##############################################################################
# Constants
results_dir = f"../../results"
n_bins = 20
cm = 1 / 2.54
figsize = (18 * cm, 9 * cm)
grid_rows, grid_... |
721db52dd0fe68125fb127683e03ba8e4179066263b5b3dc3596fa868dcb597a | Python | 6,762 | 178 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Thunderstorm Detection and Tracking - T-DaTing
============================================
This example shows how to use the thunderstorm DaTing module. The example is based on
MeteoSwiss radar data and uses the Cartesian composite of maximum reflectivity on a
1 km g... |
a956e1e05f5d14e1ddbec06f9df15845fa7ba27a5f76b2aa0dcfb9bccac3fce7 | Python | 6,762 | 244 | # -*- coding: utf-8 -*-
"""
pysteps.motion.darts
====================
Implementation of the DARTS algorithm.
.. autosummary::
:toctree: ../generated/
DARTS
"""
import numpy as np
import time
from numpy.linalg import lstsq, svd
from pysteps import utils
from pysteps.decorators import check_input_frames
@c... |
57278271f5743ed5a30a2585e723ae07c68f96b72a59887250638d1a37c4b88f | Python | 6,765 | 130 | # -*- coding: utf-8 -*-
"""
Created on Sat Aug 7 18:23:18 2021
@author: Jing Li, Small steps make changes. dnt_seq@163.com
"""
from sklearn.manifold import TSNE
# from sklearn.datasets import load_iris
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
import pandas as pd
import numpy ... |
d78f9566fec2d96f4245538afafb5412df24e6a2a66f6621906104d95b5fe256 | Python | 6,765 | 217 | # This file is part of pyunicorn.
# Copyright (C) 2008--2026 Jonathan F. Donges and pyunicorn authors
# URL: <https://www.pik-potsdam.de/members/donges/software-2/software>
# License: BSD (3-clause)
#
# Please acknowledge and cite the use of this software and its authors
# when results are used in publications or publi... |
ff55bf3c6e5c5a5afe2de498f49002686135e5ffe3dd8cb452744fd006f2dc7d | Python | 6,766 | 130 | # -*- coding: utf-8 -*-
"""
Created on Sat Aug 7 18:23:18 2021
@author: Jing Li, Small steps make changes. dnt_seq@163.com
"""
from sklearn.manifold import TSNE
# from sklearn.datasets import load_iris
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
import pandas as pd
import numpy ... |
8a2ddc914cb2fe01d30b66dccdaf0cee1c2f7e1691d193630aadbb8f384d0a4f | Python | 6,767 | 147 | #### Master Script 05e: Calculate feature robustness check values in parallel ####
#
# Shubhayu Bhattacharyay
# University of Cambridge
# email address: sb2406@cam.ac.uk
#
### Contents:
# I. Initialisation
# II. Perform robustness checks for ordered and unordered variables based on provided resample row index
# III. Ca... |
4d4adf4136518c6cc7391d527653a3057e8b3c877d6f8bb1a86b9e243c8b433a | Python | 6,782 | 212 | """ Quick n Simple Image Folder, Tarfile based DataSet
Hacked together by / Copyright 2019, Ross Wightman
"""
import io
import logging
import os
from typing import Optional
import torch
import torch.utils.data as data
from PIL import Image
from .readers import create_reader
_logger = logging.getLogger(__name__)
#... |
9b92c8f337576837a4f459f034304da23106883e304aa652aa0326448cf3ac8c | Python | 6,783 | 191 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
df1f9650abcee62a394cd5855f0bbc841d597cc9f44bf4a045869cc9c37b031e | Python | 6,784 | 166 | from e2vid.base import BaseModel
import torch.nn as nn
import torch
from e2vid.model.unet import UNet, UNetRecurrent, UNetDecoder, UNetTask
from os.path import join
from e2vid.model.submodules import ConvLSTM, ResidualBlock, ConvLayer, UpsampleConvLayer, TransposedConvLayer
class BaseE2VID(BaseModel):
def __init_... |
40df548f0fbb8ff8d3dfc21b8c98367bf92fc824d54e5ce6f9b37ef9fb457dc1 | Python | 6,785 | 115 | """General-purpose training script for image-to-image translation.
This script works for various models (with option '--model': e.g., pix2pix, cyclegan, colorization) and
different datasets (with option '--dataset_mode': e.g., aligned, unaligned, single, colorization).
You need to specify the dataset ('--dataroot'), e... |
a056a59cfb3f8058cfadc653743871a5e4b7c39c13c30d5ff5446f27ad1136da | Python | 6,785 | 238 | """
pysteps.utils.spectral
======================
Utility methods for processing and analyzing precipitation fields in the
Fourier domain.
.. autosummary::
:toctree: ../generated/
corrcoef
mean
rapsd
remove_rain_norain_discontinuity
std
"""
import numpy as np
from . import arrays
def corrc... |
18a75bafa4300a4085fbbd4e8eef1dccdd84fd48b413f47b3eea404d5af3ebef | Python | 6,786 | 135 | ## This script performs the regularisation sweep of the dynamic decoders. Results are saved.
import popoff
from Session import SessionLite, build_flu_array_single
from linear_model import PoolAcrossSessions, LinearModel, pca_session, LabelEncoder, largest_PC_trace, largest_PC_loading, do_pca
import numpy as np
import ... |
aec4d081ecfc8254e5e4914145d129ffedf2e56f752de87d45ab457d556555ab | Python | 6,796 | 154 | """Module for pixel-based classification on Sentinel-2 L1C imagery."""
from __future__ import annotations
import os
from typing import Any
import cv2
import numpy as np
from lightgbm import Booster
from .pixel_classifier import PixelClassifier
from .utils import MODEL_BAND_IDS, cv2_disk
MODEL_FILENAME = "pixel_s2_... |
bd76aefccee5922df1ca94d3476639d41150f24d26b2cd09bc8d6ebb0cfd9122 | Python | 6,797 | 200 | # Inheritaed from open-mmlab/mmclassification
# Modified by Hangyu LIN
import random
import warnings
import numpy as np
import torch
import torch.distributed as dist
from models import build_models, build_losses
from datasets import build_dataloader, build_datasets
from runner import build_optimizers, build_runner
... |
8b1baed854884620ef950fcffe664e738f31496bf7ccc11d8f85ad9ce4df2bdd | Python | 6,799 | 185 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
c8f6d855fc158efe8b8a95bb1d394a5f1141010f474beed25b69b39b626d8f1d | Python | 6,805 | 238 | import pickle
import numpy as np
import torch
import yaml
from yaml.loader import SafeLoader
import pdb
import os
import matplotlib.pyplot as plt
from tqdm import tqdm
import networkx as nx
from DT_for_WDN_leak_localization.network import WDN
torch.set_default_dtype(torch.float32)
NET = 3
CONFIG_PATH = f"conf/net_{s... |
83409449f4625448edc6b29fc6824e016677e9729577ce243e779d9876b43415 | Python | 6,813 | 187 | # coding=utf-8
# Copyright 2020 The SimCLR Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... |
ae37cb4fa3d7a66dc38e9ea2eb7cf6fc86513faa385f82b5d7a002352c7eb0f6 | Python | 6,814 | 256 | import logging
import threading
import time
import wx
from cellprofiler_core.setting import ValidationError
import cellprofiler.gui.constants.module_view as mv_constants
from cellprofiler.gui.module_view._validation_request_controller import (
ValidationRequestController,
)
LOGGER = logging.getLogger(__name__)
... |
224b699dfddd54b2831e4871f2387f0bdfb8d0ec4bcf6af02833d0da8d3a1d5e | Python | 6,818 | 193 | import time
import sys
import argparse
import random
import copy
import torch
import gc
import torch.autograd as autograd
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
import numpy as np
import re
import sklearn.metrics
from nn.framework import MGLattice_model
from utils.data import ... |
c9dc4efed885969a41f3b45159f3ec224bddf2f179d78cef3cfa58bcceddd29e | Python | 6,818 | 159 | # Pytorch Tabular
# Author: Manu Joseph <manujoseph@gmail.com>
# For license information, see LICENSE.TXT
# Inspired by implementations
# 1. lucidrains - https://github.com/lucidrains/tab-transformer-pytorch/
# If you are interested in Transformers, you should definitely check out his repositories.
# 2. PyTorch Wide an... |
e2f1b6c319ec4e8afcec1fd5ca1eb4a3eea908ed014e270694b31d2b57255707 | Python | 6,820 | 192 | import numpy as np
from allensdk.core.brain_observatory_cache import BrainObservatoryCache
from visual_coding_2p_analysis.core import get_L0_events
# MANIFEST_FILE = '/allen/aibs/technologyEVENTS_DIR/allensdk_data/2018-01-30T10_59_26.662324/boc/manifest.json'
MANIFEST_FILE = '/allen/programs/braintv/workgroups/nc-oph... |
5fe5c3d7bdae4cf1e3d57df29bbc6f3631dd24ee27a249181284c557bc00b7f3 | Python | 6,835 | 207 | """ adapted from https://github.com/TissueImageAnalytics/tiatoolbox/blob/master/tiatoolbox/tools/stainextract.py """
import sys
import numpy as np
from sklearn.decomposition import DictionaryLearning
from .utils import (
get_luminosity_tissue_mask,
dl_output_for_h_and_e,
rgb2od,
h_and_e_in_right_order,... |
cae22226ba373473021ab8cb00ac81538ead9e44681032282e264babf53f70cb | Python | 6,838 | 154 | import scipy.sparse
from matplotlib import colors
import numpy as np
from . HiCMatrixLikeTrack import HiCMatrixLikeTrack
import logging
import itertools
DEFAULT_MATRIX_COLORMAP = 'RdYlBu_r'
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger(__name__)
class HiCMatrixTrack(HiCMatrixLikeTrack):
SUPPOR... |
9cae122aa0624872bd4c9221a8cd686e7d6276bb5ef9cb011a72e8b8c31464e5 | Python | 6,840 | 203 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 13 16:14:06 2018
@author: saskiad
Core functions used across stimulus specific analysis scripts
"""
import os
import numpy as np
import sys
def get_save_path():
'''provides the appropriate paths for a given platform
Returns
-------
save_pat... |
5d7b9822764d36d962ef7f4ab048fb9668c9772a37ee2d1b82f2d65b466714b9 | Python | 6,842 | 214 | """Low-level HDF5 helpers.
Used to back ``TimeSeries.to_hdf``/``from_hdf``; current
``TimeSeries.to_hdf`` writes via ``xarray.DataArray.to_netcdf`` (engine
``netcdf4``), so this module is largely unused but kept for any legacy
callers that still touch records on disk in this format.
"""
from __future__ import annotati... |
906fa8968792a20555f3df8342711553d9289e2742b2ef2fd5a553d23a28f130 | Python | 6,847 | 174 | """ AdaHessian Optimizer
Lifted from https://github.com/davda54/ada-hessian/blob/master/ada_hessian.py
Originally licensed MIT, Copyright 2020, David Samuel
"""
import torch
class Adahessian(torch.optim.Optimizer):
"""
Implements the AdaHessian algorithm from "ADAHESSIAN: An Adaptive Second OrderOptimizer fo... |
16bd1de9ee85da3fa3050b5b7175102060f55db99a2cf272db58d5e14f7b4ba5 | Python | 6,850 | 188 | """This module implements an abstract base class (ABC) 'BaseDataset' for datasets.
It also includes common transformation functions (e.g., get_transform, __scale_width), which can be later used in subclasses.
"""
import random
import numpy as np
import torch
import torch.utils.data as data
from PIL import Image
import... |
52d09a1d4bef273a1b64d89eba71b0d2a81672e026de4c5495a67f0b8de22b69 | Python | 6,850 | 237 | import pdb
import torch
import torch.nn as nn
from DT_for_WDN_leak_localization.model_architectures.transformers import DecoderLayer, EncoderLayer, PositionalEmbedding
from DT_for_WDN_leak_localization.models.parameter_encoder import (
CategoricalEmbeddingLayer,
ParameterEncoder,
TransformerEmbedding
)
cl... |
b6d95333ab5250cd74c7cc8ff8ffe99811cf627677b1d6b6bc683f8224b34139 | Python | 6,851 | 135 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import sys, os
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
import tensorflow_probability as tfp
from tensorflow.python.framework import constant_op
from tensorflow.python.fram... |
061c1dcb31b1d55b088cb548fa6e28ae0ff69830c097da1396b0463c0d7c2c67 | Python | 6,866 | 153 | import os
import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
import matplotlib.pyplot as plt
from matplotlib import gridspec
import matplotlib.transforms as transforms
import seaborn as sns
import statsmodels.api as sm
from statsmodels.formula.api import ols
import scipy.stats as s... |
41c66f722e6fa43a1b8c786e07e51b4552a2523c8f010d0f615fe06ff9262e6d | Python | 6,866 | 202 | import os
import json
import argparse
import datetime
import pickle
import numpy as np
import torch
from torch.optim import Adam, SGD, RAdam
from torch.utils.data import DataLoader, RandomSampler, SequentialSampler
from tensorboardX import SummaryWriter
from torchvision import transforms
from sklearn.model_selection i... |
ba4c1c4191c22aec8e02eb90e86c431fc9f88b4e659de9e73a02f6935b83e894 | Python | 6,877 | 230 | #!/usr/bin/python3
import logging
import numpy as np
import pandas as pd
import gzip
import itertools
from scipy.io import mmread,mmwrite
from scipy.sparse import coo_matrix
from os.path import join as pjoin
from os import linesep
np.random.seed(12345)
#Number of NTC gRNAs to keep
ng_negselect=15
#Number of TSS targe... |
585b9682807d1c88807c58832eb929295752ca7dd3f5d8353689ac624c59bd60 | Python | 6,883 | 180 | import os
import torch.distributed as dist
import pickle
import numpy as np
from torchvision.datasets import CIFAR10 as CIFAR10_pytorch
from PIL import Image
from .base_dataset import BaseDataset
from utils.parallel import get_dist_info
from .utils import download_and_extract_archive, check_integrity
class CIFAR10(Ba... |
e567bb69647b7f3ea1259933caa02f5b6b58742d114e3292f7547406c87404f7 | Python | 6,884 | 219 | from netCDF4 import Dataset
import numpy as np
import os, pathlib
#==========================================================
# Set main directory
#==========================================================
hdir = '/home/jhkim/model/deep_detection'
#====================================================================... |
be293ce826bb5be733385cb09bbd34d61e67f1096a95aac0cfe18dd193e825c9 | Python | 6,885 | 293 | # -*- coding: utf-8 -*-
import datetime as dt
import numpy as np
import pytest
from numpy.testing import assert_array_equal
from pytest import raises
from pysteps.utils import dimension
test_data_not_trim = (
# "data, window_size, axis, method, expected"
(np.arange(6), 2, 0, "mean", np.array([0.5, 2.5, 4.5]... |
81aae29fcba411a7e821e0a4bc3c0785563b2e721086f121ad306324a607d713 | Python | 6,889 | 202 | import torch
import torch.nn as nn
import torch.optim as optim
import os
import utils
from model import UNet, PatchGAN, UNet_Pruning
from dataset import *
from config import args
from initial import init_weights, set_requires_grad
from loss import VGG19
from torchvision import transforms
from statistics impo... |
1f76829ae126a91aecef0edf88e2783aa669892ece5424757885e2252da80cd7 | Python | 6,896 | 168 | import sys, os, argparse, time
import numpy as np
import torch
import utils
import time
sys.path.append('..')
tstart = time.time()
# Arguments
parser = argparse.ArgumentParser(description='')
# Common parameters for all methods
parser.add_argument('--seed', type=int, default=1)
parser.add_argument('--mini'... |
f92025d7c4b486bf5436aa89ca9876f713bff3f32ae327b1fdd3aba6a6810df9 | Python | 6,896 | 273 | #!/usr/bin/env python3
import os
import sys
from itertools import combinations, product
import identification as ide
import numpy as np
import pandas as pd
import pkg_resources
from etspredict.pipelines.ioutils import IOManager
from etspredict.prepare_data import prepare_connectomes as pc
def load_subject_list(dat... |
6094e1304eabd8606515d44d9f3cb14442a18649fd5e00123df7f4ed562aeae8 | Python | 6,914 | 226 | import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from neuron import h
from Functions.globalFunctions.ExtracellularField.stimulation_EcF import \
singleSquarePulse
font = {'family': 'helvetica',
'size': 10}
save_figs = True
mpl.rc('font', **font)
h.nrn_loa... |
629f65b609251d192e532525d999f01909f141a1a5fea78340a3167bd877ad6e | Python | 6,921 | 141 | from __future__ import print_function
import os
from datetime import datetime
import pandas as pd
class Data_logger():
'''Class for logging data from a pyControl setup to disk'''
def __init__(self, sm_info=None, print_func=None):
self.data_file = None
self.print_func = print_func
... |
1efb55598f1bb046b0b06dc5fa1fc0179a621f60ee8307a8f6ce2120caca7e3f | Python | 6,924 | 203 | import sys
import os
import argparse
from pathlib import Path
from pcrp.walker import Walker
from pcrp.utils import generate_seed_list, annot2gene, filter_ids, read_col
from pcrp.gdv import sgdv
from pcrp.stattests import ptest_rwr, ptest_gdv, linkage_test
def cli(argv, Inpath):
parser = argparse.ArgumentParser... |
b33e33465d5a8214ef546ff2ca822cbe2454120c16279472045e6db227119b4d | Python | 6,928 | 132 | import glob
import json
import os
import sys
import time
import warnings
from typing import Literal
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from matplotlib import cm
from scipy import integrate
import Functions.globalFunctions.ExtracellularField as EcF
from Analyses.SDC.tools import VTA... |
02c580be908565ab8a26813e4369a3b85325d8a8dfda62e590ac21b0ed281f65 | Python | 6,930 | 198 | """
Performs GLM solver.
@author: JingyiGF
"""
from .toolkits import *
from .family import *
from .metrics import *
def null_solver(family, link, y, beta0, eta, kappa=2, theta=None, learning_rate=2e-1,
max_iter=1e5, xtol=1e-6, verbose=False):
if beta0 is None:
beta0 = np.random.uniform(0,... |
18ad45fb9c7669a56bf33405354214c39ae51b27578685ca5a2b6211c49cb406 | Python | 6,936 | 193 | import sys
import torch
from .loss_interface import AbstractSegmentationLoss, AbstractLossFunction
class MulticlassDiceLoss(AbstractSegmentationLoss):
"""
This class computes the Dice loss between two tensors.
"""
def _single_class_loss_calculator(
self, prediction: torch.Tensor, target: torc... |
718e3f5a9fa0958e0502283f180dd4c89e9d298e6054ba5d9223456121ccda46 | Python | 6,936 | 195 | import numpy
import six.moves
import cellprofiler_core.image
import cellprofiler_core.measurement
import cellprofiler.modules.unmixcolors
import cellprofiler_core.object
import cellprofiler_core.pipeline
import cellprofiler_core.workspace
import tests.frontend.modules
INPUT_IMAGE = "inputimage"
def output_image_nam... |
24f508da2ad15c99fd3002cb04b5f96cca1df44a312a8c2dad2c1d20e0c649e5 | Python | 6,939 | 152 | import os
import time
import torch
import torch.optim as opt
from torch.utils.data import DataLoader, TensorDataset
from einops import rearrange
from itertools import combinations
from model.egnn import EGNN_Network
from model.molformer import Molformer
from utils.utils import parse_args, set_seed, Logger
def main(m... |
a2ccf1189cea36dfe455496408621e9c7ee863c94ebee94a6b24bdee44a4fb3e | Python | 6,939 | 179 | # File used to create the final test sets of 100 complexes (DIPS) and 25 complexes (DB5.5). These test sets created
# using this script can be found in test_sets_pbd/, so you don't have to run this script again.
import os
import random
from biopandas.pdb import PandasPdb
import numpy as np
import pandas as pd
from s... |
39fc1daccbbbddc25ecf25887038c01b4192e91d2048f939b98578a1c297414e | Python | 6,943 | 230 | import numpy
import pytest
from cellprofiler_core.image import Image
from cellprofiler_core.object import Objects
from cellprofiler_core.object import ObjectSet
import cellprofiler_core
class TestObjects:
def test_dimensions(self):
x = numpy.zeros((100, 224, 224, 3), numpy.float32)
parent_image =... |
13925c662f055c28868b354025bd5ac72039cce990df61b8c3060ee96c2f5541 | Python | 6,949 | 258 | # -*- coding: utf-8 -*-
import matplotlib as mpl
mpl.use('agg')
from matplotlib.testing.compare import compare_images
from tempfile import NamedTemporaryFile
import os.path
import pygenometracks.plotTracks
ROOT = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"test_data")
tracks = """
[t... |
be5e83e586604651f9feddb5669b09bddb50a6b1510c972bb327cd5281f310cd | Python | 6,949 | 181 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
8b3a6245d0fef6c473ad51842f01471f018c5ecc5fa209ca8f8cd90a39ba3106 | Python | 6,963 | 176 | import io
import centriole.filter
import centriole.smooth
import numpy
import scipy.ndimage
import skimage.restoration
import cellprofiler_core.image
import cellprofiler_core.measurement
import cellprofiler.modules.smooth
import cellprofiler_core.object
import cellprofiler_core.pipeline
import cellprofiler_core.works... |
4dce0328fbc080bc1b14f6d90e36e5cce97e2c6e16bcbdcf0767a0bdf3c5b34d | Python | 6,972 | 207 | # -*- coding: utf-8 -*-
import os
import tempfile
from datetime import datetime
import numpy as np
import pytest
from numpy.testing import assert_array_almost_equal
from pysteps.io import import_netcdf_pysteps
from pysteps.io.exporters import _get_geotiff_filename
from pysteps.io.exporters import close_forecast_file... |
ac9301766d3596fb93f4f30b88e109f5924954024db53db095709ddb4eb4e4b2 | Python | 6,983 | 225 | import json
import os
from urllib.parse import urlparse
import requests
from pyld import jsonld
from .context_url import CONTEXTFILE_URL
from .models import identify_model_class
from .utils import fixing_old_schema, lgr, start_server, stop_server
def _is_url(path):
"""
Determine whether the given path is a ... |
2dae37e529aa98cb8d572f3fa39b2680b27cad8bba9e8eecef18aa8b06d24f38 | Python | 6,986 | 161 |
from pathlib import Path
from datetime import datetime
import torch
from pytorch_lightning.trainer import Trainer
from pytorch_lightning.callbacks import EarlyStopping, ModelCheckpoint
import numpy as np
import torchio as tio
from breaststudies.data import BreastDataModule, BreastDataModuleLR, BreastDataModule2D,... |
7f5c19571e11225a8ecbbeeb721ef226b25326c53da0ae4ac5eb8a0a6382ffdc | Python | 6,992 | 195 | import os
import os.path as op
import nibabel as nib
import numpy as np
import shutil
from scipy import ndimage
from src.utils import utils
from src.utils import freesurfer_utils as fu
def remove_large_negative_values_from_ct(ct_fname, new_ct_fname='', threshold=-200, overwrite=False):
'''
Opens the CT, chec... |
b412fba63a5ffe8c591506b4999d9093dcc6f8260a02df9d5e7046ca4d8fe06a | Python | 6,995 | 248 | """
Testing helper functions
=======================
Collection of helper functions for the testing suite.
"""
from datetime import datetime
import numpy as np
import pytest
import pysteps as stp
from pysteps import io, rcparams
from pysteps.utils import aggregate_fields_space
_reference_dates = dict()
_reference_... |
07a1989cb0dcf8f29b299701b0a7156ea7e6f76d824d3bf9958c1fc5ebe333d9 | Python | 6,996 | 175 | from abc import ABC, abstractmethod
from numbers import Integral
from typing import Dict, List, NamedTuple, Optional, Tuple, Union
LabelNames = Union[List[str], Tuple[str, ...], Dict[Union[int, str], str]]
class DatasetInfo(ABC):
def __init__(self):
pass
@abstractmethod
def num_classes(self):
... |
629387669c312ea0152e88c7d317c1c87b337e04960c09d0f1ab3ef963763978 | Python | 6,997 | 179 | import numpy as np
import pandas as pd
from time import time, strftime
from sklearn.utils import class_weight
import torch
import torch.nn as nn
import monai
from monai.data import DataLoader, Dataset
from monai.transforms import Compose, MapTransform, EnsureChannelFirstd, RandRotate90d, \
... |
527d0244d098e6dabee61cd02b67b7b2d99e70bf882bc7344c682022ac742ba8 | Python | 6,998 | 189 | """ PyTorch MADGRAD optimizer
MADGRAD: https://arxiv.org/abs/2101.11075
Code from: https://github.com/facebookresearch/madgrad
"""
# 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 ma... |
c32a9a8617e01735cbe94951db93ef10abd6cef43af22556fda82292d55d1b0a | Python | 6,998 | 161 | """Regression tests for specific bowtie2 issues.
Each test names the GitHub issue (or behaviour) it guards and uses the
lambda phage example shipped in example/. New regression tests belong here
when they do not fit naturally in one of the topic modules.
Run from the repository root after `make`:
python3 -m pytest ... |
33739b4f07d63fc0f9be7f39fb2b46bb0ebac458e88e752edd2db948fc1c4bfc | Python | 7,000 | 214 | import os
import json
import argparse
import datetime
import numpy as np
import torch
from torch.optim import Adam
from torch.utils.data import DataLoader, RandomSampler, SequentialSampler
from tensorboardX import SummaryWriter
from torchvision import transforms
from sklearn.model_selection import train_test_split
fr... |
822ea92eba3567886986fd9258e49ddf52aa42c8e2608313f73fc21a8dc870d7 | Python | 7,006 | 159 | import numpy as np
import os.path as op
import glob
import time
import traceback
from src.utils import utils
from src.utils import labels_utils as lu
from src.utils import geometry_utils as gu
links_dir = utils.get_links_dir()
SUBJECTS_DIR = utils.get_link_dir(links_dir, 'subjects', 'SUBJECTS_DIR')
MMVT_DIR = utils.g... |
87e4fa139770e470f9a4510e575ec9b2b918ca7be15edd5d86384a2c834113f0 | Python | 7,021 | 153 | #!/usr/bin/env python3
import os
import unittest
import logging
import shutil
import tempfile
import pandas as pd
import ciftify.config
from ciftify.utils import run, TempDir
import pytest
from unittest.mock import patch
def get_test_data_path():
return os.path.join(os.path.dirname(os.path.dirname(__file__)), 'da... |
362e0f93bb29ff1b404f3daeed10fbfc5b93847778553d941f35cce554b47efa | Python | 7,022 | 169 | import glob
import os
import tensorflow as tf
def enforce_4D(image, dtype=tf.float32):
"""Enforce an image shape [batch, x, y, channels]"""
if not isinstance(image, tf.Tensor):
image = tf.convert_to_tensor(image)
ndims = image.get_shape().ndims
if ndims == 2:
image = image[None, :, :,... |
89699f4bf3a1b7762c72673ca5c6c668096dd975fa088ce547a4feba399e2944 | Python | 7,023 | 229 | from io import StringIO
import json
from pathlib import Path
import prov
import rdflib
from nidm.core import Constants
from nidm.experiment import Project, Session
def test_1(tmp_path: Path) -> None:
project = Project()
# save a turtle file
with open(tmp_path / "test.ttl", "w", encoding="utf-8") as f:
... |
c58be332e66cb376a9b37aba7defb3f56aa0f52fea5512d7298b870e15af4024 | Python | 7,032 | 197 | import os
import numpy as np
import torch
import scipy.io as sio
import logging
import shutil
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
class SalEval(object):
def __init__(self, nthresh=49):
self.nthresh = nthresh
self.thresh = torch.from_numpy(np.linspace(1./(nthres... |
48aa0bd28488617a51049faf95b27878cb56b8c08d744cc95f17175aeafb89c6 | Python | 7,036 | 239 | """"
Adjusted based on https://github.com/fcakyon/confplot
"""
from typing import List
from typing import Optional
from typing import Tuple
import matplotlib.font_manager as fm
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sn
from matplotlib.collections import QuadMesh
from ... |
42cb125a84dafd39d8fea44a5e52709b564d37b6e7c6d70f1f1a3a93267316cb | Python | 7,046 | 197 | import pdb
from matplotlib import pyplot as plt
import torch
import networkx as nx
from DT_for_WDN_leak_localization.inference.true_data import TrueData
class InverseProblemMetrics():
def __init__(
self,
true_data: TrueData,
posterior: list
) -> None:
self.true_data = true... |
71c91828e9647300d674ca89c48198867964c2ce22384e07c2fbff30aa0b0bad | Python | 7,054 | 208 | """Tests for running inplace prediction."""
from concurrent.futures import ThreadPoolExecutor
from typing import List, Type, Union
import numpy as np
import pandas as pd
import pytest
from scipy import sparse
import xgboost as xgb
from xgboost import testing as tm
from xgboost.testing.data import np_dtypes, pd_dtype... |
d61195608b953c513bd22eeff8e9da0b4af1028a918df24ec2edd51322afe48e | Python | 7,059 | 192 | """Run simple cell optimisation"""
"""
Copyright (c) 2016, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by t... |
5984c85d216746fd83bab0833421755fa31b871921e4719cf4ef1f923ef4d137 | Python | 7,060 | 192 | """Run simple cell optimisation"""
"""
Copyright (c) 2016, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by t... |
827c6d4f6cb1722fc7254c85e1e9405f96cde224b9e1e09aed28671555ad30c7 | Python | 7,065 | 192 | """Run simple cell optimisation"""
"""
Copyright (c) 2016, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by t... |
c98058c0876fb71d3bec59c8ce5602685a03809d4f804afea3ea2b96017bcfa4 | Python | 7,065 | 170 | """
ECA module from ECAnet
paper: ECA-Net: Efficient Channel Attention for Deep Convolutional Neural Networks
https://arxiv.org/abs/1910.03151
Original ECA model borrowed from https://github.com/BangguWu/ECANet
Modified circular ECA implementation and adaption for use in timm package
by Chris Ha https://github.com/V... |
de55b9f6433304c7b9cf7ef692fc6e0ed48373483357a0bf888b363e460985ef | Python | 7,065 | 209 | from cellprofiler_core.module import Identify
from cellprofiler_core.setting.subscriber import ImageSubscriber
from cellprofiler_core.setting.text import LabelName
from cellprofiler_core.utilities.core.module.identify import (
add_object_location_measurements,
add_object_count_measurements,
get_object_measu... |
ed85e26c0450d24c7fc70a98e7866584cecc2a905bae7b86b3ed5fa5db47f415 | Python | 7,065 | 185 | import wx
import wx.lib.rcsizer
from cellprofiler_core.setting import DataTypes
from ._module_view import ModuleView
from ..utilities.module_view import edit_control_name
class DataTypeController:
"""The DataTypeController manages a DataType setting"""
DTC_NONE = "None"
DTC_TEXT = "Text"
DTC_INTEGER... |
db267d61dd632a2171100efa69e9fc298fb12c7cede6781fc66a0670c66fcf16 | Python | 7,066 | 118 | import numpy as np
import torch
from tests.utils import reset_seed, reset_layers, run_forward_pass
from networks.dfc_network import DFCNetwork
from networks.dfc_network_single_phase import DFCNetworkSinglePhase
eps = 1e-20
torch.set_default_dtype(torch.float64)
def test_dynamical_inversion_single_phase(n_in=10, n_hi... |
41d1dcee82fbe6d4e78096511972156bf6e3145a24fb40f541df7a7af5c49845 | Python | 7,088 | 192 | """Run simple cell optimisation"""
"""
Copyright (c) 2016, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by t... |
a15d623110b44223d52ea6092d4d169fc612ccf9afc01dd95f60423031a3417f | Python | 7,089 | 199 | import fnmatch
import logging
from itertools import islice
from typing import Collection, Optional
from torch import nn as nn
from timm.models import group_parameters
_logger = logging.getLogger(__name__)
def _matches_pattern(name: str, patterns: Collection[str]) -> bool:
"""Check if parameter name matches an... |
b22c01961a094e4083a092685c52798354cd103cbfd49d66ab9d1505d8cb00f0 | Python | 7,101 | 194 | # rvt.vis quick TEST
# test files: https://www.dropbox.com/sh/p7ia8fk6mywa8y3/AABWuw4wFUvULU7SeNXyWhjka?dl=0
import time
import rasterio as rio
import rvt.vis
import numpy as np
def test_slope_aspect(input_dem_path, output_path, ve_factor=1, output_units="degree"):
input_dem_dataset = rio.open(input_dem_path)
... |
9f1995c2efc3cf4b8813a01567c4dd74890a757b157d1d57025aeee82edfc131 | Python | 7,105 | 220 | import logging
import re
from pathlib import Path
from typing import Optional, Sequence, Union
import numpy as np
import tifffile
from xtiff import to_tiff
from imctools import __version__
from imctools.data import Acquisition
from imctools.io.utils import get_ome_xml
logger = logging.getLogger(__name__)
class Acq... |
3bf1c9c1292f3b12d147e966581c7cc723aacd8f1ee9309c476f62b25fe114cf | Python | 7,106 | 187 | # --------------------------SetShift Habituation Protocol Task File----------------------
# This is simplist form of 5CSRT either hole 2 or hole 4 illuminates and response to illumination give reward
# cue presentation [hole-2 or hole-4] ==> Correct response @ Illuminated hole ==> reward(@reward port) ==>... |
5c75640c7a432c0974f0a1c2f05647af84d0ec249acf398f73138cefbc7486a8 | Python | 7,107 | 231 | from abc import ABCMeta
from os.path import join
import nibabel as nib
from numpy import array, isclose, mean, ones, sqrt, zeros
from mrHARDI.traits.metrics.base import get_from_metric_cache
from mrHARDI.traits.metrics.diamond import (DiamondMetric,
MdisoMetric,
... |
12a83987d500fa60ce9c1b1cd40e2129e73ee6330e1dd56664685f20b50384eb | Python | 7,109 | 192 | """Compute a per-landmark rater-reliability prior from the afids-data release.
The AFIDs multi-rater data release (Taha et al., 2023, Sci Data 10:449) ships,
for each subject, the placements of several trained raters plus a consensus
"groundtruth". This script computes, for each of the 32 AFIDs, the distribution
of an... |
fc8cee099d5e8ce8f3fffeacec9db50a172855b26385fa7de5764494403cdcce | Python | 7,111 | 219 | import io
import centriole.cpmorphology
import centriole.filter
import numpy
import pytest
import scipy.ndimage
import cellprofiler_core.image
import cellprofiler_core.measurement
import cellprofiler.modules.morph
import cellprofiler_core.object
import cellprofiler_core.pipeline
import cellprofiler_core.setting
impor... |
cef9f69e59c5dfe8ba835e85d2e9b5c8d4fe634ddeda3e4022e799b4a6df9287 | Python | 7,113 | 194 | """
ConvertObjectsToImage
=====================
**ConvertObjectsToImage** converts objects you have identified into
an image.
This module allows you to take previously identified objects and convert
them into an image according to a colormap you select, which can then be saved
with the **SaveImages** module.
This m... |
37aeee03c66039e68034012cbde29caf1775f3a64a02f6b4042c0315df413e87 | Python | 7,115 | 336 | # -*- coding: utf-8 -*-
import numpy as np
import pytest
from numpy.testing import assert_array_almost_equal
from pysteps.utils import conversion
# to_rainrate
test_data = [
(
np.array([1]),
{
"accutime": 5,
"transform": None,
"unit": "mm/h",
"thres... |
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