sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
82f5daf1a40335bdda420b6f2cb0ceeec57f2136eafd9ff343717163018f2f78 | Python | 37,988 | 957 | import torch
import torch.nn as nn
import torch.optim as optim
from torch.optim import Adam,AdamW
from torch.optim.lr_scheduler import ExponentialLR, StepLR, LinearLR
from torchvision.datasets import STL10
import torch.nn.functional as F
import torch.nn.init as init
import matplotlib.pyplot as plt
import torchvision
... |
f56ae4ae85093ea9241a1d72ba47c562e4c4f39fd000fc3e1f57b54d28f9b37f | Python | 37,988 | 1,083 | #!/usr/bin/env python3
import scipy.sparse
import numpy as np
import os
import math
from util import TIME, TIMECLEAR, Timer
import pickle
from argparse import Namespace
import util_min
from multigrid import Multigrid, MultigridDecomp
from tfwrap import tf
class Domain:
def __init__(
self,
ndim=... |
174f5e0e906d295ab2d8b533acbf126da9de8c14e83acd538329ba7a87107ea5 | Python | 38,115 | 1,028 | """Tests for Keras metrics classes."""
import pytest
import numpy as np
import math
from keras import metrics
from keras import backend as K
if K.backend() != 'tensorflow':
# Need TensorFlow to use metric.__call__
pytestmark = pytest.mark.skip
class TestSum(object):
def test_sum(self):
m = met... |
6854821cb6bd06c220dc0333da65a6c7fe2f9c718982abf932db300289595659 | Python | 38,293 | 872 | from cmath import nan
import simLogger
import surrogateTraining
import weightAnalysis
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from matplotlib.lines import Line2D
import scipy
from scipy.optimize import curve_fit
import matplotlib.font_manager as font_manager
def typeOuptut(output):
n... |
05ee71c0ff9313ef07259cc551f137fe456fda440c1c3dc8961b9e55ef267551 | Python | 38,299 | 793 | '''
Created on 17 Nov 2022
@author: Francois STÜDER
'''
import regex
from os import path
from threading import Thread,RLock
from time import time
guibsonSeq = {'+':'XXX','-':'XXX'}
polyT = {"+": "XXX", "-": "XXX", "s+": "XXX", "s-": "XXX"}
polyTPair = {'+':'XXX','-':'XXX'}
barcodesX = {}
barcodesY = {}
lengthBC = 0... |
f58bfc3622a74823d4d0e2e96e0e1ed3a66db36c38d2ff3d95606b89eaeaba13 | Python | 38,318 | 942 | # Numpy archive import/export.
# Author: David Young, 2019, 2020
"""Import/export for Numpy-based archives such as ``.npy`` and ``.npz`` formats.
"""
import ast
import operator
import os
import pathlib
import pprint
import re
from time import time
from typing import Any, Dict, Optional, Sequence, Tuple, TYPE_CHECKING, ... |
be8de216e4967152e09b5df15578e67f239c85efe5cff643504fe2df2ec65645 | Python | 38,504 | 870 | from enum import Enum
from ipaddress import IPv4Network
from typing import Dict, List, Type, Tuple
import inspect
from gym.utils.seeding import RandomNumberGenerator
import numpy as np
from CybORG.Agents import SleepAgent
from CybORG.Agents.SimpleAgents.BaseAgent import BaseAgent
from CybORG.Agents.SimpleAgents.Enter... |
ccebd67ec1c34ac8076257bfd20100e3fb7361fe7bceec83e7abacce4044cde2 | Python | 38,692 | 1,060 | import pytest
import numpy as np
from numpy.testing import assert_allclose
import keras
from keras.utils.test_utils import layer_test
from keras.layers import recurrent
from keras.layers import embeddings
from keras.models import Sequential
from keras.models import Model
from keras.engine import Input
from keras.layer... |
d5858950a8851cec1dc9492340a1deb46e10245aca434752e9bdd27d56ef95b2 | Python | 38,721 | 995 | # -*- coding: utf-8 -*-
# tests/test_losses.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is free sof... |
58cc264183de012b2d207f8130c9706d6c38a476de98bf260e6864f72a537ea3 | Python | 38,755 | 839 | """Renderers for the source-impact report.
``render_markdown`` produces the human-readable report committed to
``docs/sources/<SOURCE>/impact-report.md``. ``render_json`` produces the same data as a
structured payload for downstream consumers.
Both inputs are the output of:
- ``src.model.source.discover_source(name, ... |
a65725ed29c792ec0ce0fa463ad78a2c95c4030dbf570cb18842e7bec4c57e42 | Python | 38,819 | 861 | # Detect blobs within a chunked stack through multiprocessing
# Author: David Young, 2019, 2020
"""Stack blob detector.
Detect blobs within a stack that has been chunked to allow parallel
processing.
"""
from enum import Enum
import os
from time import time
from typing import NamedTuple, Sequence, TYPE_CHECKING, Opti... |
453f322d1b7e1bc6ddb2ddb81157ebe576bf80ceb58fd045d932b00c05fdce91 | Python | 38,942 | 911 | '''
Ingredient for data loading and creating data loaders.
License: BSD 3-Clause
Author: Hanna M. Tolle
'''
import sys
sys.path.append('../../')
from sacred import Ingredient
from torch_geometric.loader import DataLoader
from sklearn.model_selection import KFold, train_test_split, StratifiedKFold
from torch_geometri... |
a14b774ad17e11e378f0f91c938da845a7d188db6d5d26950ea7d394ef009bd5 | Python | 38,964 | 1,108 | #!/usr/bin/env python
# SQLite database connection
# Author: David Young, 2017, 2020
"""Connects with a SQLite database for experiment and image
analysis storage.
"""
import os
import glob
import datetime
import sqlite3
from time import time
from typing import List, Optional, Sequence, Tuple
import numpy as np
from ... |
a255c9c779f67b25676e6bb8744afcb1e399224423a1317bf5685931d5cf76a3 | Python | 39,125 | 807 | import os
import json
import math
import torch
import torch.nn.functional as F
import argparse
from PIL import Image
from safetensors.torch import load_file
from tqdm.auto import tqdm
from torchvision import transforms
from datasets import load_from_disk
from diffusers import UNet2DModel, DDPMScheduler, DDIMScheduler, ... |
28b79ce5930fb29d960973ca94f058c8e875c12a8220e18b7c2711859ba5bd87 | Python | 39,227 | 1,184 | #from nipype.interfaces.freesurfer import MRIMarchingCubes
from lapy import TriaMesh, Solver
from lapy.diffgeo import tria_compute_gradient, tria_compute_divergence
import warnings
from collections import OrderedDict
import scipy.optimize as optimize
import subprocess
import os
import nibabel as nib
#from nilearn impor... |
fee45ee676f977d405a4fb082a8cc4799fbfefa09251cf46d310b56819162185 | Python | 39,299 | 597 | #参数少点，维度32
import numbers
import torch
import torch.nn as nn
import torchvision.models as models
import torch.nn.functional as F
from transformernet import *
from utils import *
up_kwargs = {'mode': 'bilinear', 'align_corners': True}
def conv1(in_chsnnels, out_channels): # "1x1 convolution with padding"... |
914b16a48260226d0552d7f145a907f115c304be02f7d4c585d40c5a764f151e | Python | 39,309 | 1,096 | import os
import numpy as np
import scipy
import matplotlib.pyplot as plt
import auditory_cortex.utils as utils
from auditory_cortex import results_dir
from auditory_cortex.analyses import Correlations, STRFCorrelations
from auditory_cortex.encoding import TRF
from auditory_cortex.dataloader import DataLoader
from au... |
afcdf573f98a0841629a2a93de6ce4f45ff05f1eed458c98b34d142cdc605c1c | Python | 39,378 | 1,102 | from typing import Dict, List, Optional, Tuple
import numpy as np
import torch
from torch import nn, Tensor
import torch.nn.functional as F
from torch_scatter import scatter_mean
from oa_reactdiff.dynamics import EGNNDynamics
from oa_reactdiff.utils import (
get_n_frag_switch,
get_mask_for_frag,
get_edges... |
7e0fb6ad40e773432e23f9287d4c1fe43cd195fcafd133c5fbf392c930131167 | Python | 39,413 | 944 | import glob
import ast
import inspect
import re
import numpy as np
import scipy.stats as st
import matplotlib.pyplot as plt
import torch
from scipy.optimize import curve_fit
import matplotlib.colors as mcolors
from scipy.interpolate import griddata
def sigmoid(x, a, b):
return 1 / (1 + np.exp(-a * (x ... |
5c78005fd6263bd59e99b7c63e2ea237835003aa97645f12c88a80f4d4859af3 | Python | 39,547 | 1,277 | import numpy as np
import multiprocessing
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib.collections import LineCollection
from matplotlib.colors import Normalize
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from scripts import oed
from scripts import load
def tra... |
01f2dd9bac21997db376692b2d78f8be158e77cd1830ec178b8b5ae536c0ae86 | Python | 39,576 | 1,038 | import re
import yaml
import pickle
import numpy as np
from decimal import Decimal
from scipy.stats import pearsonr
from myphdlib.interface.session import SessionBase
from myphdlib.pipeline.stimuli import StimuliProcessingMixin
from myphdlib.pipeline.events import EventsProcessingMixin
from myphdlib.pipeline.saccades i... |
7df8fb961652a83b45f001089260465b2b672128e0356ed032e1f3c91b6cf2c6 | Python | 39,603 | 1,067 | # -*- coding: utf-8 -*-
# encodermap/loss_functions/loss_functions.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
#... |
504fae3f7e4e6a0ddb294a0921ba62656dbbdf5ac427ae7fd3c4132b6fbbfeae | Python | 39,613 | 947 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Import ontology and classification from Pavel's database. The resulting
# CATMAID onrology will be similar to what is expressed as a database scheme
# there:
#
# Experiments
#
# flake8: noqa
import copy
import json
import pprint
import pymysql.cursors
import pymysql
im... |
e35f532a5805030a53fe69c99105a704ad3c70a3c7f77d19b6431cb23a3645eb | Python | 39,668 | 1,249 | from lapy import TetMesh, TriaMesh, Solver
from lapy.diffgeo import tria_compute_gradient, tria_compute_divergence
import warnings
import subprocess
import tempfile
import os
import nibabel as nib
import numpy as np
from scipy.spatial import Delaunay, KDTree
from scipy.spatial.distance import squareform, pdist
from b... |
e06a43d212205a113c2f57295e9e0dd94f357a4850bb5faac1bc265d5d06af37 | Python | 39,703 | 968 | """Tests for Keras confusion matrix metrics classes."""
import pytest
import numpy as np
from keras import metrics
from keras import backend as K
from keras.utils import metrics_utils
if K.backend() != 'tensorflow':
# Need TensorFlow to use metric.__call__
pytestmark = pytest.mark.skip
import tensorflow as t... |
c6e89b578f0897082af2df7deaad4a50ff0bc5ba6b267a6b1d3b2793d5fd9974 | Python | 39,742 | 833 | from django.db import migrations, models
import django.contrib.gis.db.models.fields
forward_summary_update = """
-- The summary table does not have a history table associated.
-- Add num_imported_nodes column
ALTER TABLE catmaid_skeleton_summary
ADD COLUMN num_imported_nodes bigint;
UPDATE catmai... |
04ae0c2a0d7ff81531e0fd3521723125e76ebc4bdc6f578c59272555cfe133c9 | Python | 39,821 | 757 | #!/usr/bin/env python
#
# Compute maximum spinal cord compression (MSCC) or maximum canal compromise (MCC) using AP diameter or other
# morphometrics.
#
# Copyright (c) 2023 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
# TODO: maybe create an API or move some functions
import sys
impor... |
d69941a0d4b26f50be6239dcac5e166c6c36ef5692406f6bc86cf1375f4a7d36 | Python | 39,822 | 1,215 | import h5py
import numpy as np
import pathlib as pl
from scipy.signal import find_peaks as findPeaks
from scipy.stats import pearsonr, chi2_contingency
from matplotlib import pylab as plt
from myphdlib.general.toolkit import psth2
from myphdlib.figures.analysis import GaussianMixturesModel, g, convertGratingMotionToSac... |
3d5f1e697e9a29c08bd5fe9c9b4a615a9ee36966dfaa9e78231dc9e819ad68cf | Python | 39,936 | 1,020 | # Anatomical ontology management
# Author: David Young, 2019
"""Handle ontology lookup.
"""
import os
from collections import OrderedDict
from enum import Enum
import json
from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple, Union
import numpy as np
import pandas as pd
from pandas.errors import Pa... |
25a2607a8e700b784873eddfe6e8f3b8575b1fb05bb207d9393dc72010c35454 | Python | 40,063 | 736 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
35229e7ef6eca48735171b1a21b3a97c918b6a8f9578a16341c67b6bb09e380a | Python | 40,091 | 984 | """
(AKA dbic-bids) Flexible heuristic to establish BIDS DataLad datasets hierarchy
Initially developed and deployed at Dartmouth Brain Imaging Center
(http://dbic.dartmouth.edu) using Siemens Prisma 3T under the umbrellas of the
Center of Reproducible Neuroimaging Computation (ReproNim, http://repronim.org)
and Cente... |
2a24e0463d1471ae60a66c31036db68f7019f3a9e0e885c418cbbdecf1ca216e | Python | 40,093 | 930 | # -*- coding: utf-8 -*-
# Generated by Django 1.9.10 on 2016-11-29 19:08
from django.db import migrations
# This fixes two function calls in history view and table construction:
#
# - create_history_view_for_table() has one parameter instead of two
# - initialize_new_history_table() expects three parameters instead... |
470cce8faf7ba3d88abd40182eea71bb54d21859907bf42a6b52f22a40ea8902 | Python | 40,670 | 1,088 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
import wandb
from Utils.dataloader import *
from Utils.config import loaderConfig
from torch_lr_finder impor... |
c6739abcd303b3a87c9076ec380e7fac7eefb17a6a8f247b4ee47d7e8fbd76b2 | Python | 40,836 | 1,213 | # tests/test_providers.py
"""Tests for provider system endpoints."""
import asyncio
import json
import uuid
from conftest import make_room_address
from zndraw_auth import User
from zndraw_joblib.dependencies import request_hash
from zndraw_joblib.models import ProviderRecord
from zndraw_joblib.schemas import (
P... |
9d09fc34b1429c46b9853ce2fc3b85fcfb1fc3d312bc8b3bbfa4705ae05954d5 | Python | 40,858 | 818 | import argparse
import os
import platform
import sys
from copy import deepcopy
from pathlib import Path
FILE = Path(__file__).resolve()
ROOT = FILE.parents[1] # YOLO root directory
if str(ROOT) not in sys.path:
sys.path.append(str(ROOT)) # add ROOT to PATH
if platform.system() != 'Windows':
ROOT = Path(os.pa... |
48ad99416f8bafce6cec1dfabbf3315e0a46d8df7aaad26d5cd19fcd563aee9d | Python | 40,902 | 1,167 | # -*- coding: utf-8 -*-
"""
Functions for calculating and manipulating spatial autocorrelation
Some functions: Ross Markello, netneurolab
the rest: Nikitas Koussis, SNGNewy
"""
import os
import tempfile
from pathlib import Path
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
from scipy import... |
07b3bdeebde55dd498c6baf8205bbad94ccdaeb780958d4c37bd887476d65b67 | Python | 40,907 | 1,109 | ###########################################################################################
# Implementation of MACE models and other models based E(3)-Equivariant MPNNs
# Authors: Ilyes Batatia, Gregor Simm
# This program is distributed under the MIT License (see MIT.md)
###############################################... |
efe5d05181cf9d8e6f34c276b838ad26e9cc16a66e9b4bcbfc527455293f0f87 | Python | 41,052 | 1,106 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import itertools
import unittest
from typing import Any, Tuple
import numpy as np
import torch
from fvcore.transforms import transform as T
from fvcore.transforms.transform_util import to_float_tensor, to_numpy
# pyre-ignore-all-errors
class Te... |
672e6c5dd28ecb28340cbb8535698b02e541ccb309a1759f6609a1d343ad65c5 | Python | 41,234 | 1,133 | # Author: Huaxu Yu
# Core data models and processing operations for raw MS data.
# imports
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
import matplotlib.font_manager as fm
from dataclasses import dataclass, field
from time import time
from ..params import Params
from ..feature_d... |
b82020e1f17f704ca05ce0226717791b55e63f69011e771312d320a53a301d0d | Python | 41,275 | 1,149 | """ZnDraw main client class implementing MutableSequence[ase.Atoms]."""
from __future__ import annotations
import logging
import re
import uuid
import warnings
from collections.abc import Iterable, MutableSequence
from dataclasses import dataclass, field
from typing import TYPE_CHECKING, Annotated, Any, Literal, cast... |
9fe99159a3ef29488c0540f987ae65be94d6cc7b3bdfcb8eba0b39f0c5edddaa | Python | 41,449 | 1,062 | import copy
import datetime
import functools
import logging
import threading
from collections.abc import MutableMapping, MutableSequence, Sized
from typing import TYPE_CHECKING, Optional, Union, cast
from cwl_utils import expression
from cwl_utils.types import CWLObjectType, CWLOutputType, SinkType
from schema_salad.s... |
66bfdc6514c39105fa9a116efd6e081f681f6aa8eb67e20b2038776f2b14539f | Python | 41,465 | 1,245 | """Module with overloaded things from bluepyopt."""
# Copyright (c) 2022 EPFL-BBP, All rights reserved.
#
# THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PU... |
c00ec14ee6765af259767e3998a92635d98db9c0c2591e3985df1c129ef0b5a0 | Python | 41,518 | 1,035 | import os
import keras
from keras import ops
from tsgm.types import Tensor as TensorLike
# a keras_dataset can be tf.data.Dataset or Torch DataLoader
from tsgm.backend import tf_function_decorator, Keras_Dataset, get_backend
import numpy as np
import numpy.typing as npt
from tqdm import tqdm, trange
from collections im... |
7e8ff4d918e97c171741a708aafa2c38c49850a15ad6fbf2db7553c5e5350ce4 | Python | 41,612 | 1,071 | #
# CalciPy (calci.py) - A python script for processing ratiometric calcium fluorescence data
#
# By George McMullen
#
# One of the primary challenges in processing ratiometric data is that the two
# signals which make up the ratiometric data are actually captured separately,
# and it is not known which is which. Calci... |
bf8916a814e6d4281c8d32ea271d609f8d0aebd1895445480cfac8094e2c1f4a | Python | 41,622 | 1,052 | # Copyright (c) MONAI Consortium
# 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, so... |
ac43162d32caec93194408c1cf8f168682b8bae369c1c12aed6287bd34f48b1f | Python | 41,755 | 806 | import time
import os
import argparse
import sys
import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
import resource
import datetime
import torch
from torch.utils.data import Dataset, DataLoader
from torch import nn, optim
from torch.nn import functional as F
from sklearn.decompositi... |
80b9008372f7828212edd846d3e378103c1fe0822f2288e9f63946f9e6783bf0 | Python | 41,796 | 1,023 | """
(AKA dbic-bids) Flexible heuristic to establish BIDS DataLad datasets hierarchy
Initially developed and deployed at Dartmouth Brain Imaging Center
(http://dbic.dartmouth.edu) using Siemens Prisma 3T under the umbrellas of the
Center of Reproducible Neuroimaging Computation (ReproNim, http://repronim.org)
and Cente... |
68808af30d05fd05d395607f964afe64a35bbce0c126647433c5e78844fa7cac | Python | 41,856 | 1,288 | from __future__ import annotations
from math import sqrt
from functools import partial
from itertools import product
from collections import namedtuple
from beartype import beartype
import torch
from torch.nn import Module, ModuleList, ModuleDict
from torch import nn, is_tensor, Tensor
import torch.nn.functional as ... |
1f465d2994377304ddf9f6304125a2f0e482990d41cd102eecb0ba4082cf0d4f | Python | 41,892 | 1,073 | # -*- coding: utf-8 -*-
# encodermap/misc/saving_loading_models.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# En... |
19b3335a248edbe0c20e84ac86e3b79e859852edf604dc2b7aefd6da478de889 | Python | 41,917 | 808 | import time
import os
import argparse
import sys
import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
import resource
import datetime
import torch
from torch.utils.data import Dataset, DataLoader
from torch import nn, optim
from torch.nn import functional as F
from sklearn.decompositi... |
3fc3be93ac4257d132922e4784dc20c6588c710d8dca40a8aacee294b5313a1e | Python | 41,996 | 1,143 | import pytest
import numpy as np
from numpy.testing import assert_allclose
from keras.utils.test_utils import layer_test
from keras import backend as K
from keras.layers import convolutional
from keras.models import Sequential
from keras.backend import load_backend
# TensorFlow does not support full convolution.
if ... |
551b952ce055f625cd4d80a527c80f5db0ee2e35e224d197a168cc9913bd5a6a | Python | 42,089 | 874 | import sys
from tkinter import Tk, Label, Button, GROOVE, CENTER, StringVar, END, LEFT, ttk, filedialog
from PIL import ImageTk, Image
import os
import pyedflib
import matplotlib.pyplot as plt
import math
import numpy as np
from scipy.signal.windows import dpss
from scipy.signal import detrend
from scipy.fft import rff... |
a536af33b1885720be8ab50ca5addb7f7d8d9812a901e945b4e856e134d0006c | Python | 42,128 | 770 | import os
import numpy as np
import pickle
from .SamsegUtility import *
from .utilities import requireNumpyArray
from .figures import initVisualizer
from .Affine import Affine
from .ProbabilisticAtlas import ProbabilisticAtlas
from .Samseg import Samseg
from . import gems
"""
Longitudinal version of samsegment
The i... |
1407d8ec2ba3796850146caf2285f9c7c7cdf293901d81010583f21e52f2a8d9 | Python | 42,191 | 1,096 | import datetime
import errno
import functools
import itertools
import logging
import math
import os
import re
import shlex
import shutil
import signal
import stat
import subprocess # nosec
import sys
import threading
import time
import uuid
from abc import ABCMeta, abstractmethod
from collections.abc import Callable, ... |
9de660c556634250c323df2f200c83fb5fb263d0c3685c06b70065e91dfca425 | Python | 42,231 | 917 | from __future__ import print_function
from __future__ import division
from future import standard_library
standard_library.install_aliases()
#from builtins import str
from builtins import range
from quantities.quantity import Quantity
from quantities import mV, nA
import sciunit
from sciunit import Test,Score
try:
... |
475aab454223a960ccf28ad5f86e1266b56b8adde9ccdf74af58c02ef1b828ee | Python | 42,445 | 739 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jul 22 05:56:04 2020
@author: takeiyuuichi
"""
#setting##############################################
n_jobs=16 #並列処理の数
t_n_jobs=16
PARAMETER_DIR='/Volumes/Siena/CP/parameter/'
#n_jobs=40 #並列処理の数
#t_n_jobs='cuda'
#PARAMETER_DIR='/home/takeiyuuichi/Dro... |
63c4a2f6bd4bc6a1bf532d40008f2a85580bc1c5defec030139ee30d4e588eeb | Python | 42,501 | 993 | from pathlib import Path
from typing import Dict
import napari
import numpy as np
import pandas as pd
import starfile
import torch
from PyQt5.QtCore import Qt
from magicgui import widgets
from matplotlib import pyplot as plt
from matplotlib.figure import Figure
from matplotlib.widgets import LassoSelector, PolygonSele... |
c86030378cb3233d0cd0da9ad9ee5169d8db4bf39cfddd44378f259c0d8cc744 | Python | 42,686 | 1,040 | """Training-related utilities.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import inspect
import collections
import copy
import numpy as np
import six
import warnings
from collections import OrderedDict
from .. import backend as K
from .. import los... |
c0e5b3e8b7eefdac9a6a1db782573909e0c1b87037a602b84657f45a8541662b | Python | 42,714 | 1,272 |
import os
import sys
import warnings
from collections import Counter
from genericpath import exists as pexists
from os import makedirs
from os.path import basename, join as pjoin, realpath, splitext
from pathlib import Path
from shutil import copyfile, which
import nibabel as nib
import numpy as np
import visualqc.c... |
c6db1a665294874b6e058f542abb585eeae96ff4cf151c739995c4112fc3bd6a | Python | 42,849 | 813 | import time
import resource
import datetime
import argparse
import sys
import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
import torch
from torch.utils.data import Dataset, DataLoader
from torch import nn, optim
from torch.nn import functional as F
from sklearn.decomposition import ... |
dee6f2100d0afff2ef0c731038b01a24309edfebf52e4e16fcd603883a671ef5 | Python | 42,869 | 1,111 | """Access point module."""
# Copyright (c) 2022 EPFL-BBP, All rights reserved.
#
# THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN ... |
9698b0d7abcdb94d4557505fdc3929eb9a53604933d2ef296f03592e699688f1 | Python | 42,982 | 815 | import time
import resource
import datetime
import argparse
import sys
import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
import torch
from torch.utils.data import Dataset, DataLoader
from torch import nn, optim
from torch.nn import functional as F
from sklearn.decomposition import ... |
2772419a0623558550f94d52b4caa18ca78ae4512cd7033871218f280b739913 | Python | 43,074 | 1,040 | # -*- coding: utf-8 -*-
# encodermap/misc/xarray.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is fre... |
be7f3b45e9d86ecbe78bb28ac72e5a90772daee84a8e455b8d0884ea74da20fe | Python | 43,148 | 1,208 | import os
import pandas as pd
import numpy as np
import random
import matplotlib
import matplotlib.pyplot as plt
import hdbscan
import umap.umap_ as umap
from sklearn import metrics
from pathlib import Path
from natsort import index_natsorted
from mpl_toolkits.axes_grid1 import make_axes_locatable
def evaluate_model... |
97aac12362f8bcd0968c9ad580655bcb6aad053efa6c3da0e3cae5eb6776fc95 | Python | 43,303 | 1,131 | import abc
import math
import tsgm
import typing as T
# import keras3.0 here, the LocallyConnected1D is not supported in keras3.0, I replace it with Conv1D
import keras
from keras import layers
# replace tf with ops in keras3.0
from keras import ops
from prettytable import PrettyTable
class Sampling(keras.layers.L... |
39737803f78f594f09b50dcea1dab10a79add46c879759e095257ea2ef75250f | Python | 43,378 | 997 | from io import BytesIO
from types import SimpleNamespace
import holoviews as hv
import numpy as np
import pandas as pd
import panel as pn
import pytest
from guppy.frontend.parameterized_plotter import (
ParameterizedPlotter,
available_psth_metrics,
build_plotter,
make_dir,
overview_y_options,
... |
df9124f750c9ae261cc6f5f0a91933196d26a7320942bd8d79ba0076f43ead90 | Python | 43,601 | 995 | import numpy as np
from ..gui.sda_widgets import check_cofiring, _precalculate, calculate_fpr, calculate_single_value_windowed_data, add_distance_to_fpr
from ..gui.pop_up_messages import ProgressWindow
import matplotlib.pyplot as plt
import random
from matplotlib.backends.backend_qt5agg import (
FigureCanvasQTAgg a... |
509dc5c90dea86dbfc6f3d79e8e6e12e3bbcbfd6e0b537d0e284ea15dbc9e06e | Python | 43,625 | 1,144 | import torch
import transformers
import json
import sys
sys.path.append('/root/autodl-tmp/lako/LaKo-main/data_process')
import pickle
import nltk.stem.porter as pt
from re import template
from tqdm import tqdm
import numpy as np
import os.path as osp
import numpy as np
from rank_bm25 import BM25Okapi
import pdb
import ... |
0c6efdcd949a4797b5009ee8c28e0b092f98b5227f33d424d4453a5a0d21a3bf | Python | 43,657 | 1,074 | # Long ago, before the days of freesurfer 7, python files in the scripts
# directory imported some utilities from a fsutils.py file. Now that we
# have a legitimate python library, all the tools from fsutils have been
# copied here. Those particular python scripts, like aparcstats2table, will
# now import 'fsuilts' via... |
66ac13565569f26465d7e6a9be8abd1bcbb86d7fbcefc87af53445f2eb62ad1a | Python | 43,734 | 657 | # -*- coding: utf-8 -*-
from django.conf import settings
from django.conf.urls import include
from django.urls import re_path
from django.contrib.auth.decorators import login_required
from django.views.decorators.csrf import ensure_csrf_cookie
from django.views.generic import TemplateView
from django.urls import rever... |
76b5340ab23cdcd7a8da0f13916c447ebd3d1ca55339e6f2f2020b4840a597b2 | Python | 43,749 | 1,202 | import logging
from pathlib import Path
import numpy as np
import pandas as pd
from .io_utils import (
COVARIATE_PREFIX,
PSTH_SIGNIFICANCE_PREFIX,
decide_naming_convention,
fetchCoords,
get_control_and_signal_channel_names,
is_covariate_label,
read_hdf5,
recording_site_from_channel_lab... |
750e35a67eee8071bf39778b11e62277689148cb190373079941835a625648bf | Python | 43,821 | 1,269 | """
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 logging
import math
import time
from math import pi as PI
import torch
import torch.nn as nn
import torch.nn.functional as F
from torc... |
ecdc7d1d102d99b859f26415588ffca4db86dc969ebb309973d318f1653460aa | Python | 43,954 | 1,094 |
import numpy as np
import pandas as pd
import sklearn as skl
import sys
from datetime import datetime
from joblib import Parallel, delayed
from tqdm import tqdm
from sklearn.metrics import roc_curve, auc, f1_score, precision_recall_curve
import logging
logger = logging.getLogger(__name__)
# handler to discard con... |
e6f16b6a4b35901043a29519925c1a11c3739491da05f3d72ff46565a3a5ee6b | Python | 43,995 | 1,092 | from __future__ import print_function
import multiprocessing as mp
import os
import sys
import threading
import pytest
import numpy as np
import six
from keras.models import Sequential
from keras.layers.core import Dense
from keras.utils import Sequence
from keras import backend as K
pytestmark = pytest.mark.skipif(... |
3bf5bb62d11ffda2a3df737f648b9fcd2e8766756a6bcd32e03966fbf2f9664d | Python | 44,025 | 1,084 | from collections import namedtuple
import torch
from Utils.models import *
import numpy as np
import datetime
import pandas as pd
import xlsxwriter
from sklearn import metrics
import time
import shutil
import os
import wandb
from Utils.dataloader import *
from Utils.config import loaderConfig, modelConfig
from torch_lr... |
a262bb776032dcae225a0036ab539d00cb1437a9c7b31aa4e1f18c18b36020f5 | Python | 44,028 | 845 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
33904c7dc4b16465c15ea7f2ae43d9e3e5be0dc59caf3817ffe09cc847cbe2e9 | Python | 44,073 | 1,278 | """Acquisition functions for Bayesian Optimization.
The acquisition functions in this module can be grouped the following way:
- One of the base acquisition functions
(:py:class:`UpperConfidenceBound<bayes_opt_dnn.acquisition.UpperConfidenceBound>`,
:py:class:`ProbabilityOfImprovement<bayes_opt_dnn.acquisition.Pr... |
a635f8a01ece65149d3f626a9330bf4ad8dd648cc1425f4e0d8f4f71ac466f89 | Python | 44,281 | 1,136 | # RMDNet： RNA-aware Attention-based Multi-Branch Integration Network
import os
import sys
BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.insert(0, os.path.dirname(BASE_DIR))
import numpy as np
np.set_printoptions(threshold=np.inf)
import pdb
import torch
import torch.nn as ... |
de486277873631a1ab4202e6e7139c9b16f783a436d897db9dbb45652f155772 | Python | 44,322 | 1,269 | """
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 copy
import importlib
import itertools
import json
import logging
import os
import sys
import time
from ... |
523757de5effaf3d9381ffc82cf4ffdbf46aa01998d6bfc4b39e7d3a616ba2dd | Python | 44,519 | 1,042 | import os
import pickle
import string
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import matplotlib.colors as mcolors
import matplotlib as mpl
from matplotlib import cm
import seaborn as sns
from itertools import product
def load_results(labels, fns, a... |
2cfe66d4f455d1dc5e948a8df7715961ebd76c1c16d61640a974ac53f28c9b63 | Python | 44,523 | 1,038 | # -*- coding: utf-8 -*-
import datetime
import enum
import glob
import json
import logging
from math import cos, sin, radians
import os
import os.path
import math
import msgpack
import numpy as np
from PIL import Image as PILImage, TiffImagePlugin
import requests
from time import time
from typing import Dict, List, Tu... |
e27ea031677c7e97906b1d9f58f95ff5d538c96dea180f32fd7232b9fe1b85d8 | Python | 44,549 | 975 | import torch
import torch.nn as nn
from collections import OrderedDict
from zytlib.utils.classfunc import save_args
from zytlib import vector, table
from zytlib.utils.wrapper import registered_property
import random
from torchfunction.lossfunc import softmax_cross_entropy_with_logits_sparse
from torchfunction.select im... |
d756b5138ed1077b708b4a891d3e25933e41f7b0b633f4861bedea4124758540 | Python | 44,790 | 1,174 | import json
import types
from pathlib import Path
import numpy as np
import panel as pn
import pytest
from guppy.extractors import NpmRecordingExtractor
from guppy.frontend.store_labeling_instructions import StoreLabelingInstructionsNPM
from guppy.orchestration.store_labeling import (
_compute_npm_channel_preview... |
b1afd44f480b8266365bec23c5d7d4bae899dc1832766aca43308b3b5cdd8a77 | Python | 44,793 | 837 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
1c4f4bde9617f6f1a9b210a97b1a5093aab8e2bb13b3267f59123e1edf611fe1 | Python | 44,825 | 951 | """
Tools for motion correction (moco)
Copyright (c) 2014 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
# TODO: Inform user if soft mask is used
# TODO: no need to pass absolute image path-- makes it difficult to read
# TODO: check the status of spline()
# TODO: check the status of c... |
59e3ac7fb8412fba8570bd7169e2b0e7c389d2f4703197615c4a4e70ca096d8e | Python | 44,825 | 955 |
try:
import cPickle as pickle
except:
import pickle
import gzip
from hippounit import plottools
import matplotlib.pyplot as plt
import os
import numpy
import seaborn as sns
big_errors_spiking = []
all_features = []
spiking_features = []
big_errors_spiking2 = []
all_features2 = []
spiking_features2 = []
base... |
96146a8269140beeba14aa167ff7a61d5edc448af2ffa474982815dd9527b317 | Python | 44,941 | 1,088 | # -*- coding: utf-8 -*-
from functools import wraps
from itertools import groupby
import json
import re
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple, Union
from psycopg2 import ProgrammingError
from guardian.core import ObjectPermissionChecker
from guardian.models import UserObjectPermission,... |
292806cd6c8771a2290f72efc9043f1c69d8bbcbe565dcaeb1b554bc749b9d9a | Python | 45,193 | 1,267 | # -*- coding: utf-8 -*-
# encodermap/models/layers.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is f... |
8dfc1327d626dd6b20dabbdd9742d9358b1c932c47b9e6918fa872a3ad239f27 | Python | 45,267 | 1,044 | # -*- coding: utf-8 -*-
from django.db import connection, migrations, models
from django.conf import settings
# Indicate whether history tables are enabled for this migration. If they are
# not, only history tables will be created, but no triggers are installed and no
# initial population of history tables will happ... |
5d6db3fef67cf227366b8a9c795cec61868ce2442d9dd0cd365cc5292d0e65eb | Python | 45,420 | 1,048 | from sklearn.linear_model import Ridge
from sklearn.metrics import r2_score
import pandas as pd
import numpy as np
from tqdm import tqdm
import os
'''
Predict LBACs (or MBACs) from a phenotypic domain
THe idea is such:
Linear Regression predicts pattern X change
Given variables from a certain class (cognitive, me... |
32a8408e87f74b76fc1b37fad57932b330555a2270b9026b1c723177d5f453e1 | Python | 45,423 | 1,273 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import os.path as osp
from unittest import TestCase
import mmcv
import numpy as np
import pytest
from mmengine.registry import init_default_scope
from PIL import Image
from mmseg.datasets.transforms import * # noqa
from mmseg.datasets.transforms import (Loa... |
92fcf4b0cb4e036400e2b27d7a353cbce4e8501e8a3768a670227fcbd8a0eb7d | Python | 45,460 | 1,420 | # Library functions shared within MagellanMapper
# Author: David Young, 2017, 2023
"""Shared functions with the MagellanMapper package.
"""
from functools import lru_cache
import os
import pathlib
import shutil
import sys
from typing import Any, Callable, Generator, List, Optional, Sequence, Tuple, \
Union
import ... |
38581136f9c8af7771f38a0346d72d4ce6eeb93623458565fb5bc4f08a25db4a | Python | 45,521 | 863 | #!/usr/bin/env python
#
# Register anatomical image to the template using the spinal cord centerline/segmentation
#
# Copyright (c) 2013 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
# TODO: for -ref subject, crop data, otherwise registration is too long
# TODO: testing script for all c... |
ac8a1b94fb972ea53c34ba20e0ecf37fd9fcac9ef5354a06b7887c0e6edfb551 | Python | 45,545 | 1,284 | from __future__ import annotations
__docformat__ = "numpy"
from collections.abc import Callable
import logging
import os
import os.path as op
import random
import re
import shutil
import sys
from types import ModuleType
from typing import TYPE_CHECKING, Any, List, Optional, Tuple, cast
import filelock
from nipype im... |
a947e3f295796d0c828a85991241de09d526eef016767b52fd236703e218fc5e | Python | 45,563 | 989 | import copy
from textwrap import dedent
import numpy as np
import pandas as pd
from ..client import inject_client
from ..utils import tqdm, iter_batches
from .neuroncriteria import NeuronCriteria, neuroncriteria_args
from .synapsecriteria import SynapseCriteria
from .connectivity import fetch_adjacencies
# Some data... |
8e9362ec3c64ee04f1984ce560c3b3edbd15caf2b6325a588c38c4999621bfdd | Python | 45,616 | 889 | import pytest
import json
import keras
import keras.backend as K
import numpy as np
import os
def test_dense_legacy_interface():
old_layer = keras.layers.Dense(input_dim=3, output_dim=2, name='d')
new_layer = keras.layers.Dense(2, input_shape=(3,), name='d')
assert json.dumps(old_layer.get_config()) == js... |
5847e2b2de9b24aa68f14da56930ad5d8be06e470d90b3998a2309cc666e1670 | Python | 45,732 | 1,083 | #!/usr/bin/env python3
import os
import sys
script_dir = os.path.dirname(os.path.realpath(__file__))
grandparent_dir = os.path.dirname(os.path.dirname(script_dir))
sys.path.append(grandparent_dir)
from collections import defaultdict
import argparse
import json
import math
import numpy as np
#os.environ['CUDA_VISIBLE... |
eef97a7a51b8549eeff1f307832d0f56b2ed1536ec6a7fb94463302f19a608d5 | Python | 45,898 | 943 | #!/usr/bin/env python
"""
1. Unlock scans_tsv and update it based on runtype metadata
2. Harmonize discrepancy between nifti and behavioral data
3. Starting from Line 242, Behavioral data conversion to BIDS valid format
Same format occurs for pain, vicarious, cognitive data
convert behavioral file into event lists and ... |
38027a441b126195252077b2a2f40c663c234ec0fff168e9e15b688456f77543 | Python | 45,944 | 846 | import csv
import json
from collections import defaultdict
from pathlib import Path
from src.babel_utils import TypedClique, reduce_to_most_specific_tree_codes, write_compendium
from src.categories import (
ACTIVITY,
ANATOMICAL_ENTITY,
BIOLOGICAL_PROCESS,
CHEMICAL_ENTITY,
CLINICAL_FINDING,
CLIN... |
8a98571d69e01ce11a9359cbb8f26cf2f79a0c80297123e605a4bfa505d6922a | Python | 46,181 | 1,265 | """Handle BIDS specific operations"""
from __future__ import annotations
__docformat__ = "numpy"
from collections import OrderedDict
import csv
import errno
from glob import glob
import hashlib
import logging
import os
import os.path as op
from pathlib import Path
import re
from typing import Any, Optional
import wa... |
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