sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
cf80af931b86b4b503c6fa2894b942fdeb78cfb609adec686a7a596a306ebb96 | Python | 9,888 | 171 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'accuracy_measurement_page.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from qtpy im... |
cc30b66355ccd538311a97dc868d8c77c8a5832adcf84e2d8109722dbdd9c8c7 | Python | 9,889 | 171 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'accuracy_measurement_page.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 i... |
644a65e17f8e0666704a32ecab4cf3785cc9439569bf5e57334d1007cc89ed99 | Python | 9,890 | 248 | # Copyright (c) 2022, Kwanhyung Lee. All rights reserved.
#
# Licensed under the MIT License;
# you may not use this file except in compliance with the License.
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTI... |
be533c025e9bcbbda6958e6588919b0a5f8e8d4efb24e787394d8c0297e66a29 | Python | 9,890 | 229 | import timm
import torch
from torch import nn
from collections import OrderedDict
from .smp import ExternBase
from ..util.util import get_device
import re
from typing import List, Tuple
from warnings import warn
__all__ = ['TimmEncoder']
def get_channels_strides(model, example_input=None, verbose=True) -> Tuple[List... |
7b22ad7bb831645c0c87bb9ab5f17bebaf515e5a416a58864dd6b418419c2dc6 | Python | 9,891 | 234 | import os, sys, csv
import pandas as pd
from math import ceil
novascope_scripts = os.path.dirname(os.path.abspath(__file__))
sys.path.append(novascope_scripts)
from bricks import create_symlink, create_symlinks_by_list
#===============================================================================
# Table of Conten... |
6aa37f5ec62343f14f19cc23f67bcfdc839c923c8a12638a6c029bdf0ab588e7 | Python | 9,892 | 274 | # -*- coding: utf-8 -*-
"""
BBR
The script calls the freesurfer bbr method. Inputs are not checked if they are
valid. Two white surfaces are expected corresponding to left and right
hemisphere. Therefore, the input should contain a list with two entries. The
target volume is used as freesurfer orig file. A freesurfer ... |
04f43cd5ede261fc770d51f6c54618e8720ea6e0503c5bc4a6f9dc7b45d24ba9 | Python | 9,894 | 296 | from types import SimpleNamespace
import pytest
from langchain_core.messages import AIMessage
from chemgraph.agent import llm_agent
from chemgraph.agent.llm_agent import ChemGraph, PromptConfig
from chemgraph.models.endpoints import PreparedModel
def _fake_prepared(**_kwargs):
"""Mock ``load_chat_model_prepared... |
731948074ede0f58319ea86fc8b164111047fbbd8610cf0616dedecf46bf98cb | Python | 9,894 | 313 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 20 11:10:05 2024
@author: brainmappers
"""
def metric_regression(subjects_dir, subject, hemi, surface, mesh, rois, weights):
import multiprocessing
import os
from concurrent.futures import ProcessPoolExecutor
import nibabel as ni... |
2537f04a22a1cb082250daa00ace97b614ed007b5cee866aca1a624722b421c9 | Python | 9,896 | 246 | import numpy as np
import torch
from typing import Optional, Tuple
from torch.nn import functional as F
from copy import deepcopy
from albumentations.pytorch import ToTensorV2
import albumentations as A
import cv2
class SammedPredictor:
def __init__(self, sam_model):
super().__init__()
self.model ... |
401421a3876f4a836f40a65fe21eac5e592ce8e2bff4a1c183e80d82438561f6 | Python | 9,897 | 223 | import os
import pandas as pd
import numpy as np
import ipdb
from scipy.stats import rankdata
import subprocess
import logging
def cal_ndcg(scores, labels, rm_list, n=10):
# ndcg topk
denom = np.log2(np.arange(2, n + 2))
ndcgs = []
mrrs = []
p_topks = []
r_topks = []
hit_... |
e73f87695c4c6fb22c90d4b48d701d2a3c6158ad2b4744e7ee0b86de08d19ddf | Python | 9,898 | 253 | """PSTH computation + response metrics aligned to stimulation.
Port of ``calculate_psth_metrics.m``, ``WithinRanges.m``,
``getSpikeLatencyRelStim.m``, ``getStimArtifactDuration.m`` and
``getFrAlignedToStim.m``.
The **individual-electrode analysis** that produces
``StimActivity_NodeLevel.csv`` uses *gaussian* smoothin... |
5de76f4f6dc8066537c765ecfd7f16e0d0da1d4a65aac4e92840ea12aa137e22 | Python | 9,900 | 241 | from transformers import T5EncoderModel, T5Tokenizer
import torch
import numpy as np
import pandas as pd
from read_data import *
device = torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')
def get_max_len_index(data):
train_length_frame = data.str.len()
max_len_index = train_length_fra... |
28ab850f049b7e8c06e595add1c4e968431e1faceb6e479629788dcb6b39afcf | Python | 9,902 | 244 | #!/usr/bin/env python
# author: Jannes Spangenberg
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib
matplotlib.use('Agg')
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Namespace
... |
e19e56ab0bb6c35635392ecd48e3ec2f976509ac77a66b52f71de62838edd180 | Python | 9,902 | 236 | import logging
import numpy as np
import pandas as pd
import pyranges
from kipoi.data import SampleIterator
from mmsplice.exon_dataloader import ExonDataset
from mmsplice.vcf_dataloader import SplicingVCFMixin
from kipoiseq.dataclasses import Interval, Variant
logger = logging.getLogger('mmsplice')
def junction_df_j... |
8c0f27ac4f7d9c20c554aaa4f6682207484d316e71d47e641ccefe0fba991cfe | Python | 9,904 | 322 | """Functions for reading and writing data."""
import os
import logging
from pathlib import Path
from typing import Dict, List, Optional, Union
import h5py
import mat73
import mne
import numpy as np
import scipy.io
_logger = logging.getLogger("osl-dynamics")
_allowed_ext = [".npy", ".mat", ".txt", ".fif"]
def valid... |
61c2c447841f6db04cce2af5d39f9846a857b2b9012222e9d11bfc731865d6dc | Python | 9,905 | 283 | """Data rescaling utilities."""
import logging
import torch
from mcmlnet.utils.logging import setup_logging
from mcmlnet.utils.tensor import TensorType, tensor_conversion_decorator
setup_logging(level="info")
logger = logging.getLogger(__name__)
class DataRescaler:
"""
Rescales data using different method... |
da4f10ea2fd40bf8673543b220e192af65e185fbb00be9f0bc4cff0aa44d52d3 | Python | 9,905 | 313 | #!/usr/bin/env python
"""
This script generates simulated RNA-Seq reads (in .bed format) from known gene annotations.
USAGE
gensimreads.py {OPTIONS} <BED-File|->
PARAMETER
BED-File\tThe gene annotation file (in BED format). Use '-' for STDIN input
OPTIONS
-e/--expression [expression level file] \tSpecify ... |
5b620409f0d67f1cb53c11754a5dab4874c57cb2202af00197237b2d04b4f312 | Python | 9,908 | 332 | # Copyright 2025 BrainX Ecosystem Limited. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... |
a2b2666ad267ecab71caa3e386b3f70a4646a557717740360bb7bd26e8fa7a61 | Python | 9,910 | 315 | # %%
import os
import glob
import random
from os import listdir, makedirs
from os.path import join, exists, isfile, isdir, basename
from tqdm import tqdm, trange
from copy import deepcopy
from time import time
import numpy as np
import torch
from torch._dynamo import OptimizedModule
from torch import multiprocessing as... |
96a69f34f73eabb8325737691fa331f0e08746eb2bd079c78fb3c48b543a96c8 | Python | 9,911 | 286 | import unittest
import logging
import numpy as np
import pandas as pd
import diffxpy.api as de
class _TestFit:
def _test_model_fit(
self,
n_cells: int,
n_genes: int,
noise_model: str
):
"""
Test if de.wald() generates a uniform p-value distribu... |
2208d2b9257395079d328949ad85e97fc419aaf199f2348abd3501ba9b053c52 | Python | 9,918 | 224 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import tempfile
import numpy as np
from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
# If they already exist, this only takes 5 seconds (check md5sum)
fetch_data(get_testing_files_dict(), keys=['tracking.zip'])
tmp... |
9541b196b9f8987afc5c85d916df9434b12a457604ca128d7995139536d7275c | Python | 9,919 | 257 | # -*- coding: utf-8 -*-
"""TODO"""
import numpy as np
import core.core_global as core
from core.core_definitions import simulation_timestep
from core.mc_neuron_group import McNeuronGroup
class McLifGroup(McNeuronGroup):
"""TODO"""
def __init__(self, size, num_branches, params={}):
"""TODO"""
... |
d361d0bf147b7d5207f98ac293dfb4abfe11d7f7a04100711c14044444bb662c | Python | 9,925 | 199 | import os
import time
import mlflow
import torch
import torch.nn as nn
import torch.optim as optim
from model_optim.validate import eval_model
from utils.metrics import standard_metrics, prediction_refactoring, label_refactoring, compute_confusion_matrix
from utils.env_config import path_check_and_join, path_dissect_an... |
67a04f42c17be6a2666c9d9797e5015223baae5a23d50a29d34b794360a1dc60 | Python | 9,931 | 314 | # -*- coding: utf-8 -*-
# This file is part of Eigen, a lightweight C++ template library
# for linear algebra.
#
# Copyright (C) 2009 Benjamin Schindler <bschindler@inf.ethz.ch>
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed wit... |
da5c502259ba78e31663c6bbbc0f8df05df32557bf85e217a1831d60a7a3d847 | Python | 9,936 | 298 | from argparse import Namespace
from collections.abc import Sequence
from pathlib import Path
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import torch
from aislib.misc_utils import ensure_path_exists
from sklearn.preprocessing import LabelEncoder, StandardScaler
from eir.data_load.data_util... |
9dc6e23b84edb5494dab1c15f7ca546ec271b7cc9b42369729112c547294b0a7 | Python | 9,938 | 236 | """What this computer is, and what a run will do with it.
Two questions keep coming back, and neither has been answerable from inside
MEA-NAP: *which of our computers should run the big batch*, and *why is it slow
on mine*. Both need the same three things — what the hardware is, what the
pipeline decided to do with it... |
d1e34f6b8a2478a2a6266c2917b92efd51288f7b23f5de25e8aedccf4780eeb7 | Python | 9,939 | 278 | """
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... |
080befdd8f9006e8995d59173b8f507a1291244ccda48f650348d27804f6a61a | Python | 9,940 | 225 | from .libs import *
def scale_data(to_transform, pd_cols, pd_index):
scaler = MinMaxScaler((0,1))
data_scaled = scaler.fit_transform(to_transform)
data_scaled_df = pd.DataFrame(data_scaled, columns = pd_cols, index = pd_index)
return data_scaled_df, scaler
def inverse_scale(scaler, myyield_tanh, verbo... |
4fc99d7150c797d8ced9afd145bcf5e69461a7add4080d88fc22dcb12120c21f | Python | 9,943 | 245 | #!/usr/bin/env python
# author: Jannes Spangenberg
# e-mail: jannes.spangenberg@uni-jena.de
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib
matplotlib.use('Agg')
from argparse import ArgumentDefaults... |
89b916736107f4e919e2ce37f2527c02b706e6469fd8c5f8e4d1d40ac008f80e | Python | 9,945 | 298 | from argparse import Namespace
from collections.abc import Sequence
from pathlib import Path
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import torch
from aislib.misc_utils import ensure_path_exists
from sklearn.preprocessing import LabelEncoder, StandardScaler
from eir.data_load.data_util... |
8bc34671cc5ea7e43f0a349f3cfdfa1539fbb14bf6cd82e2b770ddfb87da2ad6 | Python | 9,945 | 255 | from typing import Tuple, Union
from sklearn.ensemble import VotingRegressor
from sklearn.utils.validation import check_is_fitted
from sklearn.base import BaseEstimator, RegressorMixin
from sklearn import metrics
import numpy as np
import tensorflow as tf
from tensorflow.keras.models import Sequential
from tensorflow... |
c6674bd19ce9ff6ed8b27f89beaf90fd1ffdc24e2c03a022125721b0028b8972 | Python | 9,945 | 250 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, build_upsample_layer, UPSAMPLE_LAYERS
from depth.ops import Upsample
import torch.utils.checkpoint as cp
class BasicConvBlock(nn.Module):
"""Basic convolutional block for UNet.
This module consi... |
c659e4cfba0c7c118d2c0a63ab94c2bfa349fe5d6a3ee0aa3aab2a8b1205afc6 | Python | 9,948 | 211 | '''
N2O
'''
import numpy as np
import sys
def intro():
print("""
SHORT List of potential energy surfaces for N2O:
P: potential energy, G: Gradient, D: Nonadiabatic coupling vector
This is listed at the end of description to show the availability.
For example: P/G means both potential energy and g... |
4e485d803f4f8c3ff381be3f3486ebb4ac5cc599255af890fd36dcd99aba5620 | Python | 9,949 | 245 | """Prepare the NSD-synthetic betas in fsaverage space.
Parameters
----------
subject : int
Number of the used NSD subject.
zscore : int
Whether to z-score [1] or not [0] the fMRI responses of each vertex across
the trials of each session.
project_dir : str
Directory of the project folder.
nsd_dir : str
Directory ... |
6c5be7c66d3a4df8a6ae4e0ad0d5ba23a867706b227da74de5f3a39036b4f78b | Python | 9,949 | 135 | class BH76():
"""
A class to store molecular data and corresponding calculations for BH76 dataset.
Attributes
----------
molecules : list[str]
List of molecule identifiers used in test calculations.
exp_values : dict[str, float]
Dictionary mapping test identifiers to their expe... |
b4923027687bf30b443e328f70b50f77d15e2255304cb92b3b4c90a6201dab01 | Python | 9,955 | 225 | #This script will create an index (.ndx) file that contains the atoms needed to calculate improper angles for chirality.
#Then the index file is input for the GROMACS command "gmx angle", which will calulate the improper angles
#and output a .xvg file containing the angles for each residue for each frame in the trajec... |
4c33bed19805dbff4815057dc611d490c2ac9073acf0de779a1ee48f5dbb60e7 | Python | 9,958 | 311 | """
This class defines the basic imagestack and instructs lasagna as to how to handle image stacks.
"""
import numpy as np
import pyqtgraph as pg
from PyQt5 import QtGui, QtCore
from lasagna.ingredients.lasagna_ingredient import lasagna_ingredient
from lasagna.io_libs.image_stack_loader import save_stack
class ima... |
2630695a0515f7cc9d82fa02954362974e68cadcc1125ad362a95fd1e6f2692d | Python | 9,959 | 204 | # This code extract document level features of transformer models
import os
import h5py
import pdb
from typing import List
import flair
from flair.data import Dictionary, Sentence, Token, Label
#from flair.datasets import CONLL_03, CONLL_03_DUTCH, CONLL_03_SPANISH, CONLL_03_GERMAN
import flair.datasets as datasets
fr... |
712cb407c401befd268037e16cc5669aa8ea5991c21d9020aa243efe947e0c2a | Python | 9,964 | 303 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import argparse
import logging
import pytest
from cvat_sdk.core.auth import (
CVAT_ACCESS_TOKEN_ENV_VAR,
DEFAULT_SERVER,
AuthStore,
AuthStoreError,
ClientAuthParameters,
ProfileEntry,
configure_client_auth_arguments,
... |
45650fe3577fdc60e235b154274fb0836fd90374eebec9963147c4b933bfd826 | Python | 9,967 | 243 | ######################################################################################
### Recursively moves through directories to extract parameters, firing rates, and ###
### the recall quality measures Q and MI from spike raster data ###
###########################################################... |
c51a5948fcb130bceea8975fe8438826a7769bd903569c9c8ad01f57e2f91ac0 | Python | 9,968 | 317 | # 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.
import logging
from functools import partial
from typing import List, Tuple, Union
import torch
import torch.nn as nn
imp... |
9e2677d09d09198a047fba5d2c217ffb44de1db1ad40b90ca85f607b88feec9b | Python | 9,976 | 168 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'camera-display.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_Frame(object):
def setupUi(self, Frame):
Frame.setObjec... |
a970bbe3b93cc31c28983488f27156a22dc8b507a1148e4bd0a60d3b7c0d5927 | Python | 9,977 | 302 | import re
from types import SimpleNamespace
from dataclasses import dataclass
import numpy as np
import pandas as pd
MAX_ENTRIES_STR = 10
class ClassifyOutput(SimpleNamespace):
"""
A general container to hold the outputs of the classify function of SeisBench models.
This allows each model to provide a d... |
ad4b3a2f9657b41f66980e57a7981e4fe8347b3f467d2e2eabea2c7b17338db0 | Python | 9,977 | 272 | from __future__ import annotations
import pandas as pd
import os
import warnings
import numpy as np
import pingouin as pg
import os.path as op
from glob import glob
from pathlib import Path
from tqdm.notebook import tqdm
# Visualization settings
import seaborn as sns
import matplotlib.pyplot as plt
sns.set_theme(styl... |
4866fbddabe9ac942dabe3e1c07417c79615d59ce86a19c2361a589060075457 | Python | 9,981 | 270 | import json
import os
import Levenshtein
import numpy as np
import torch
from sklearn.model_selection import train_test_split
from torch.utils.data import Dataset
import my_setup
from data_processing import tokenization
from data_processing.sequence_utils import mask_tokens, prepare_sequence
class Sequences:
d... |
f8ed81771e2259ccb385b7a828c060e89905d45a9bab91f6bd06e79ebc4bb502 | Python | 9,981 | 337 | # -*- coding: utf-8 -*-
"""Illustrate nifti images."""
import datetime
import os
import shutil as sh
import imageio as io
import matplotlib.pyplot as plt
import nibabel as nb
import numpy as np
from ..segmentation.flat import orthographic_projection
from ..surface.filter import mris_fwhm
__all__ = ["get_gif", "get_... |
186a1e14281e0147818a435e231433454d077e3986a8c4578df400d43a200bac | Python | 9,982 | 278 | import json
from collections.abc import Sequence
from copy import copy
from pathlib import Path
from typing import TYPE_CHECKING
from aislib.misc_utils import ensure_path_exists
from eir.experiment_io.io_utils import (
check_version,
dump_config_to_yaml,
save_dataclass,
)
from eir.experiment_io.output_obj... |
958930de47fb32b1c1eab3d769d738bbec4e8d4db0babd49db2ec469e5862210 | Python | 9,984 | 271 | from collections import defaultdict
import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator
from sklearn.inspection import permutation_importance
from sklearn.model_selection import StratifiedGroupKFold, GridSearchCV
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import Standar... |
18d4eefa68a59cf3c2bcc17180316dfefc05f0d70260789ada2ff10b4abd0f3a | Python | 9,986 | 230 | #Aidan Fike
#July 21, 2019
#File with function to parse command line arguments and extract relevant information. Also
#informs the user if they make a mistake
import sys
import os
import dihedDir
usage = "\nUSAGE: To use this program run:\n\n\
\n\
python main.py [-flag argument] [-flag argument] [-flags]\n\
\n\
... |
ec9443ee7b5f2597c6dc727b600a849481b6087ec5dd55cda739aeda328260a4 | Python | 9,988 | 228 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This script matches the TIFF image files (donor, acceptor, and FRET channels) in each folder,
performs background correction, fluorescence leakage correction, FRET efficiency calculation,
and outputs the results to CSV files.
"""
import json
import os
import sys
impor... |
0a2860be9e9f20db8a15513c505b599e4a4004e7e0b574d6c78fa9437f64d34f | Python | 9,992 | 286 | from __future__ import annotations
from typing import Final
from typing import NamedTuple
import numpy as np
import scipy.ndimage
import scipy.spatial
import skimage
from loguru import logger
from numpy.typing import NDArray
from .._shape import CIRCLE_POINT_COUNT
from .._shape import MIN_POLYGON_POINT_COUNT
from ..... |
f0edc2200f3fb18b5b7dd278234ada5158c734468f11194f08d74bd4f501d4de | Python | 9,995 | 278 | from __future__ import annotations
import os
import tempfile
from pathlib import Path
from typing import List
import numpy as np
from auxiliary.runscript import ScriptRunner
from auxiliary.turbopath import turbopath
from auxiliary.io import read_image
from brainles_preprocessing.registration.registrator import Regis... |
1ac09ac6b0d3ab82dfdb80a573e1043cdca00cff9381b89b848af35ad6df7091 | Python | 9,996 | 250 | import torch
import os
import argparse
import datetime
import numpy as np
import random
from torch.utils.data import DataLoader
from tqdm import tqdm
import pandas as pd
from brainCT.networks.gen_model import GUNet
from monai.transforms import (
Compose,
ToTensord,
RandAffined,
ScaleIntensityd,
Ran... |
4e1956b716b97f3711795cd36a543e51b2f8b7ad5592eac0286dc8a7253a0c05 | Python | 9,996 | 314 | from collections.abc import Callable
from typing import Any
import torch
from torch import nn
from torch.nn import functional as F
from eir.models.layers.attention_layers import SwiGLU, Transformer
from eir.models.layers.norm_layers import LayerScale
from eir.models.tensor_broker.projection_modules.sequence import (
... |
927b3a6ec4dee0ad57fb753fdc236cd0ed24118d6a760cf57090d2126b30f455 | Python | 9,998 | 266 | import os
import pandas as pd
import numpy as np
from sklearn.metrics import cohen_kappa_score
from util.config_vars import config
def rater_comparison_workflow():
"""
Coordinates the multi-step comparison and reconciliation of manual ratings between two raters.
Step 1: Identifies discrepancies in init... |
5e612e2921272a74e5e8c037fbc2fe185b017017266ccab009cfdd986858ecbe | Python | 10,002 | 279 | # -*- coding: utf-8 -*-
"""
Created on Tue Mar 15 15:37:12 2016
@author: ajaver
"""
import glob
import os
import numpy as np
import pandas as pd
import tables
import warnings
from scipy.signal import savgol_filter
from tierpsy.analysis.ske_orient.checkHeadOrientation import isWormHTSwitched
from tierpsy.helper.misc... |
ab338ab470b45ecaef7d90632a8e9d8628a2fc40c3186cca0b9d09c21fbbdc12 | Python | 10,002 | 317 | import numpy as np
from paraview.util.vtkAlgorithm import (
VTKPythonAlgorithmBase,
smdomain,
smhint,
smproperty,
smproxy,
)
from vtkmodules.numpy_interface import dataset_adapter as dsa
from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid
import os
paraview_plugin_version = '0.1'
alg_inpu... |
f2113ab3c6e01675d44abc395e10a66f9755d19b169cb1b9ade1a661e3295f15 | Python | 10,003 | 186 | import re
from pathlib import Path
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
from Switching.SwitchingHelper import parseAllData, getZoneLDA
from sklearn.decomposition import PCA
FolderPath = Path(r'D:/Data/Lobster/FineDistanceDataset')
outputData = []
pbar = tqdm([p for p in FolderPath.gl... |
61bb05fc8c7eba0ea37a54c89345d6ad0577852bd30527c16b5e067023b8a8d5 | Python | 10,004 | 196 | from sklearn.metrics import accuracy_score, f1_score, precision_score, recall_score, roc_auc_score
from layer import SimpleHGN
import pytorch_lightning as pl
from torch import nn
import torch
from Dataset import BotDataset
from torch.utils.data import DataLoader
import argparse
from torch.optim.lr_scheduler import Cosi... |
64c4264ac40f03a2e75eb8a0bfdacee61d6620c7fea5dcd34361ec2186279231 | Python | 10,004 | 215 | import os
import random
import numpy as np
from scipy.sparse import coo_matrix
import torch
from pytorch3d import transforms
from torch.utils.data import Dataset
from MDAnalysisData import datasets
import MDAnalysis as mda
from MDAnalysis import transformations
from MDAnalysis.analysis import distances
class MDAnaly... |
e2745d5c3e5483e35c9db3689e40f6acbf9a8f2cc231355b0ed33256f3eee7b0 | Python | 10,005 | 169 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file '/media/lg/disk2/PycharmProjects/ISAT_with_segment_anything/ISAT/ui/category_edit.ui'
#
# Created by: PyQt5 UI code generator 5.15.10
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this... |
0ecf43096c37321469af594100571c8c21eb08ae629ad9763a8e49f718e9efbf | Python | 10,007 | 268 | import sys
import yaml
import os
import numpy as np
import h5py
import git
import pandas as pd
precut = 3.
ttags = ['prestim']
postcut = 0
block_licking = True
savepattern = '%s__TSEL%s{}__STATE%s%s.h5'.format(int(precut)) #% (aRec.id, ttag, statetag,reftag)
active_buff = np.array([-1,1])
quiet_buff = np.array([0,0])... |
85f159b9639235bfb0eb2dfbd91d9a342d09855d9f72940eb347ce87b4f3aa3c | Python | 10,007 | 231 | import argparse
from os.path import join
import pickle
import keras
from keras.optimizers import Adam
from keras.callbacks import EarlyStopping, ReduceLROnPlateau
import utils
from model_zoo import ResidualBind_heteroscedastic
import plotting
import pandas as pd
import wandb
from wandb.integration.keras import WandbMet... |
1821cb6720d9295a9f008bcf7dfc8894133e55372a30f18610e6f56e93ea538b | Python | 10,009 | 350 | """
Module for performance profiling
"""
import os
import json
import time
import queue
import typing
import datetime
import threading
import contextlib
import multiprocessing
import grpc
#from . import trace_event_grpc_pb2 ... |
92102cc6762cd395cefbccaa6f38eae4cc12aff23f37a18ef1e07fc02219a5f1 | Python | 10,009 | 240 | """Model of gene-expression matrix.
One slice_dataframe object corresponding to one gem file
"""
import time
import numpy as np
import pandas as pd
from sklearn import preprocessing
"""Model for manipulate the coordinate of spots in one slice
One slice_xyz object corresponding to one gem file
"""
class slice_xyz:
... |
6bd906bbe0b75580e51ab2b35828f5fb550eaa528eceadc18c1cf11cc53816e7 | Python | 10,012 | 210 | # (C) Copyright 2019 IBM Corp.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
bdfaa4eb92eadeec2107d88b34be603591f02c4703b1b9feb2fb5b3a66327387 | Python | 10,012 | 270 | """
UDysRS dataset loader: JSON pose exports → COCO-17 (T, 17, 2) clips + scores.
Three tasks, each with its own JSON file and joint schema:
Drinking / Communication — 15 joints:
head, neck*, face*, Lsho, Rsho, Lelb, Relb, Lwri, Rwri,
Lhip, Rhip, Lkne, Rkne, Lank, Rank
(* neck and face dropped; not in C... |
1284fd53322304aa90ca19d3655aa9771e888ef5e01f77b20dd56b0245efd7de | Python | 10,015 | 200 | """
PyVISAScope provides an interface to different scopes.
Copyright (C) 2016 Ye-Sheng Kuo <yesheng.kuo@gmail.com>
Copyright (C) 2019 Julius Zimmermann <julius.zimmermann@uni-rostock.de>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Publi... |
6461b18c50537394f1acfef6ff29f7c9f7f28aa218790fe179d81ab4ecc60167 | Python | 10,016 | 347 | from __future__ import annotations
import base64
import json
from pathlib import Path
import numpy as np
import pytest
from PySide6.QtCore import QMimeData
from PySide6.QtCore import QPointF
from PySide6.QtCore import Qt
from PySide6.QtGui import QDropEvent
from pytestqt.qtbot import QtBot
from labelme import _utils... |
379d71804bc7ea13a6c2f923be15bc83abe10968bb28db9d69a64e2a7ec9ba97 | Python | 10,017 | 224 | import os
import sys, time, json, traceback
import numpy as np
import nibabel as nib
from nipype.interfaces.base import BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File, Directory, traits
from dipy.io.image import load_nifti
from dipy.io.gradients import read_bvals_bvecs
from dipy.core.gradients import gradient... |
c51f8ec5e430f0b2b5183b45c968f0549c8678df06463e5123bfd24688e9b942 | Python | 10,024 | 231 | """ This file contains several functions that help in the first analysis of the FMCW radargram dataset.
The functions find_h5_files(), extract_data_from_h5_file() and collect_extracted_data() are jointly used to find and
extract all relevant information from the raw dataset which was initially stored in a folder of HDF... |
d06c194f64cc08477786aeceb1b3c43e989fd5c9c83bef509cca33f212200ac2 | Python | 10,025 | 271 | # torch imports
import torch
import torch.nn as nn
def get_bond_length_ABA(pos, nintdist):
"""
function that calculates the interatomic distances
of a molecule with ABA symmetry (such as HeH2+ or H2O)
This function does not take permutational invariance
into account.
the numbering is (fo... |
2c27ce13fa35b263525ebdcc94170ad23d7c79331ff635296602d032a0aa28cb | Python | 10,031 | 275 | import pandas as pd
import numpy as np
from typing import List, Optional, Union
import uuid
from collections import Counter
def get_person_time_df(t: pd.Series, y: pd.Series, a: Optional[pd.Series] = None, w: Optional[pd.Series] = None,
X: Optional[pd.DataFrame] = None, return_individual_series... |
cad006b94164437bcce0a3c39cf7e60d83f740ccdeb8fc615b20482dda223622 | Python | 10,032 | 297 | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A basic class for the control of the PSD4 syringe pump from Hamilton
# ----------------------------------------------------------------------------------------
# Jeff Moffitt
# 11/20/21
# jeffrey.moffitt@child... |
9364763aab761511af941f0ad8de106cb986dd24016f28e5ec7fa573166c8464 | Python | 10,033 | 257 | from __future__ import division
import numpy.ma as ma
import numpy as np
import scipy as s
import math
from mofapy2.core.utils import *
from mofapy2.core import gpu_utils
from time import time
# Import manually defined functions
from .variational_nodes import BernoulliGaussian_Unobserved_Variational_Node
from .varia... |
f11e83d7ff065e120102d931188eb46670ab5392de9bdaf5f85b546d93b0949b | Python | 10,034 | 295 | import ftplib
import os
import time
from pathlib import Path
import requests
from lxml import etree
from tqdm import tqdm
import seisbench
def download_http(
url, target, progress_bar=True, desc="Downloading", precheck_timeout=3
):
"""
Downloads file from http/https source. Raises a ValueError for non-2... |
1e972eeabfde7dd6ab352ac3daa7a94a13e3e295cc84fff91bb494c99adb7b9c | Python | 10,037 | 196 | from sklearn.metrics import accuracy_score, f1_score, precision_score, recall_score, roc_auc_score
from layer import SimpleHGN
import pytorch_lightning as pl
from torch import nn
import torch
from Dataset import BotDataset
from torch.utils.data import DataLoader
import argparse
from torch.optim.lr_scheduler import Cosi... |
9a247dd8aee384308855a9be645dcf675c64f6eacf21b3dc8aee12d8d2d29a4f | Python | 10,038 | 277 | from collections.abc import Sequence
from copy import copy
from dataclasses import dataclass
from functools import partial
from pathlib import Path
from random import sample
from typing import TYPE_CHECKING, Literal, Union
import polars as pl
from aislib.misc_utils import ensure_path_exists
from lightning.fabric impor... |
78a9fa541ab859f911ff1378ccfdd764eb5f421907a142135adca677e8f1c650 | Python | 10,040 | 238 | # (C) Copyright 2020 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... |
0deefb80a1fee091af4bdf5b4651ece5c4c9c877297ac86bbe76ade1ab54b9bc | Python | 10,043 | 304 | """
Implementation of Moran spectral randomization.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import numpy as np
import scipy.sparse as ssp
from scipy.spatial.distance import cdist
from sklearn.utils import check_random_state
from sklearn.base import BaseEstimator
from ..mes... |
2f221a4bdd24942cc92cd14303408b9af5401504d7896a972ee322c648b116f1 | Python | 10,045 | 248 | """Command-line interface for privacy analysis and anonymisation."""
from __future__ import annotations
import argparse
import json
from pathlib import Path
from typing import Any, Sequence
import numpy as np
import pandas as pd
from .corelogic import (
add_noise,
bin_numeric_values,
calculate_k_combine... |
994cadc52448a7e8e77680dff9a66897b82f68dcd79f67aa0c0f72b1bb1baf81 | Python | 10,045 | 220 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
"""Triton kernel for euclidean distance transform (EDT)"""
import torch
try:
import triton
import triton.language as tl
HAS_TRITON = True
except (ImportError, ModuleNotFoundError):
HAS_TRITON = False
triton = None
tl = No... |
e1bb49991a2388c92387a92f0d741de361e834f5dc96c3257a9512cc3ac0d32c | Python | 10,045 | 274 | """
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... |
178b470c0ab4897145b054f1b58d10207b7b3ea695000f5c746f1afb9a61574d | Python | 10,047 | 247 | import os
import cv2
import sys
import matplotlib.pyplot as plt
sys.path.append("/LiNet")
import torch
import numpy as np
from torch.autograd import Variable
import argparse
import random
from lib_alban.utils_analyse import def_masks_extract
import os.path as osp
os.environ["OPENCV_IO_ENABLE_OPENEXR"] = "1"
import ... |
ab613154531938d501741a7fd8fbf3758aa6cd12984cac09811381381cbbb995 | Python | 10,048 | 196 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import tempfile
from scilpy import SCILPY_HOME
from scilpy.io.fetcher import fetch_data, get_testing_files_dict
fetch_data(get_testing_files_dict(), keys=['btensor_testdata.zip'])
tmp_dir = tempfile.TemporaryDirectory()
def test_help_option(script_runner):
... |
462412a16a66af992babf2db88fd6866863a201085c058144bd4653078af1d12 | Python | 10,049 | 276 | import pandas as pd
import numpy as np
import scanpy as sc
from sklearn import linear_model
from itertools import combinations
from .stats import *
import random as rand
### from stats import *
def csRenameOrth(adQuery,adTrain,orthTable,speciesQuery='human',speciesTrain='mouse'):
_,_,cgenes=np.int... |
433d24b3d5a6be882f4951c372c57ffa847dcad22aa9bca19875d63f29b821c1 | Python | 10,053 | 237 | # -*- coding: utf-8 -*-
"""
Created on Fri Apr 11 19:03:57 2025
@author: axthi
"""
import os
import shutil
import numpy as np
import pickle
import datetime
from copy import deepcopy
from .preparation import create_cereb_surface, get_central_gm_with_mask, get_center_pos, _relabel_internal_air
from .simulation import _... |
5c9f8ef343f8dfb57a017084311d11b34a0a9e132ee02f3bb0f9eeef5b87a10e | Python | 10,053 | 265 | import sys
import yaml
from glob import glob
import os
import numpy as np
import h5py
import git
import pandas as pd
precut = 2.
postcut = 0.7
ttag = 'psth'
block_licking = True
savepattern = '%s__TSEL%s{}to{}__STATE%s%s.h5'.format(int(precut),int(postcut*10)) #% (aRec.id, ttag, statetag,reftag)
active_buff = np.arr... |
33089f15d8b177cca522be260c65971884ac67664edfebfb082af5e951df1c1f | Python | 10,054 | 203 | # -*- coding: utf-8 -*-
"""
Created on Thu Jun 18 14:35:49 2020
@author: Yoshi
"""
import os
import shutil
import numpy as np
from polar_coordinates_calculator import *
from best_angle_calculator import *
def arrow_coordinate_calculator(path,cell_flags,cell_locations,map_type,mode,width,height,scale):
# ... |
12fe3baf5d0b3641faea3d676e44cbd7f4ed451b27ad4ada45c0ad97f93895a3 | Python | 10,055 | 269 | import warnings
import torch.nn as nn
import torch
from torch import Tensor
from typing import List, Tuple, Optional, Union
from bism.modules.unet_block import Block2D, Block3D
from bism.modules.concat import ConcatConv2D, ConcatConv3D
from bism.modules.upsample_layer import UpSampleLayer3D, UpSampleLayer2D
from fun... |
8c411face8f7026a22ce8252ba09ea0537ca7c8c5c7b78830fa0e1e485f35d60 | Python | 10,058 | 221 | # @String(visibility="MESSAGE",value="<html>This script merges Sholl profiles from multiple files into a single table and plot,<br>obtaining Mean±StdDev profiles for groups of cells. It assumes that files share<br>the same structure and the same (case-sensitive) column headings.<br> ") MSG
# @File(label="In... |
c6fce9f1a8d27fe8a118097a3763f9f00c5505a302f85b8cf1ef5f08bf9e8901 | Python | 10,063 | 417 | import numpy as np
from matplotlib import pyplot as plt
import pandas as pd
from scipy.optimize import curve_fit
import os
from Tissue_compartment_modeling import CM_vB_wrap
if "Users" in os.getcwd():
# Local runtime with data from Example_data folder
print("Local runtime")
WDIR = "./Example_data/"
elif "... |
f5c180c1feed3d15d2ff8d7d1606f74cd276b41198e92f3848dfd19d54252070 | Python | 10,066 | 240 | import os.path
import unittest
import tests.base_test
import tests.output_parser as output_parser
import tests.test_config
import tests.util
class Alternative5SpliceSiteNovelBaseTest(tests.base_test.BaseTest):
def setUp(self):
super().setUp()
self._test_base_dir = tests.test_config.TEST_BASE_DIR... |
225a51062829e0d5a83229a7215138e50862a51a4e30a8dc0af743610ed0454d | Python | 10,070 | 298 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from collections.abc import Callable, Iterator
from functools import wraps
from itertools import islice
from typing import Any, TypeVar, overload
import attrs
from attr import field
T = TypeVar("T", bound=int | float | str)
def _parse_self_and_ot... |
2b5bc3964c02828215fecec7a7e74a3d7a265018998f74002095b4cfa34c25d1 | Python | 10,071 | 251 | import h5py
from glob import glob
import os
import yaml
import numpy as np
import matplotlib.pyplot as plt
import sys
from scipy.stats import sem
import pandas as pd
varnames = ['B_mean','M_mean','rate_mean']
pfc_only = True
sg_on = True
pathpath = 'PATHS/filepaths_carlen.yml'
pathpath2 = 'PATHS/filepaths_IBL.yml'... |
b808ab8b329a0e97109372d067bfb89278218767e4b5a5dff258d794da1f842b | Python | 10,071 | 211 | #!/usr/bin/env python3
"""Stage 5 -- ablation studies.
Six axes, all evaluated under the same nested leave-one-subject-out protocol as
the main comparison:
modality blink-only / EDA-only / both
gating reliability gate on / off
fuzzy layer type-2 warning layer vs raw thresholding (post hoc)
... |
8eb4baad01b562ecf748d7e0b40e8e2262197445bd0a3b29672c1e2be6587313 | Python | 10,072 | 242 | # -*- coding: utf-8 -*-
import logging
import os
import sys
import nibabel as nib
import numpy as np
from scilpy.image.volume_math import concatenate
from scilpy.io.image import load_img
from scilpy.io.utils import get_acq_parameters
from scilpy.reconst.mti import adjust_B1_map_intensities, smooth_B1_map, \
proce... |
f81b022ed1d46477565436b18df078c4cd7015bf7645b1cb49e1b9a8332840fa | Python | 10,074 | 240 | import os.path
import unittest
import tests.base_test
import tests.output_parser as output_parser
import tests.test_config
import tests.util
class Alternative3SpliceSiteNovelBaseTest(tests.base_test.BaseTest):
def setUp(self):
super().setUp()
self._test_base_dir = tests.test_config.TEST_BASE_DIR... |
41df148f49e7611dcba3847546b78f34f7e064292c3fdaf83405522fbe87d429 | Python | 10,075 | 253 | from __future__ import annotations
import pandas as pd
import csv
import gzip
import os.path
import pickle
import datetime
from tqdm import tqdm
from metaphlan.utils.merge_metaphlan_tables import merge
from .utilities import run_cmd, ReadsData, check_conda_qiime2
import json
import shutil
import tarfile
import os
impo... |
66ac4d14415c89f64979427b9cc7f7b6b91fa7fc805d1f592e86be97655d6b9d | Python | 10,076 | 254 | from __future__ import annotations
import pandas as pd
import csv
import gzip
import os.path
import pickle
import datetime
from tqdm import tqdm
from metaphlan.utils.merge_metaphlan_tables import merge
from .utilities import run_cmd, ReadsData, check_conda_qiime2
import json
import shutil
import tarfile
import os
impo... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.