sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d2015c6084c37c4f25840b0bf13fe9401599478322cec228c045ec47c6e5360a | Python | 11,849 | 333 | """
Similarity matrix computation for metabolites, proteins, and GO terms.
This module implements three types of similarity computations as described in the paper:
1. Metabolite similarity: Tanimoto coefficient based on Morgan fingerprints
2. Protein similarity: BLAST sequence alignment with BLOSUM62 matrix
3. GO sema... |
9be8a368e564b713410200694dfdb4ff18c8407963883e1e786c44230ae7483c | Python | 11,853 | 273 | import os
import numpy as np
import h5py
import git
import yaml
import sys
import matplotlib.pyplot as plt
from scipy.stats import wilcoxon
pathpath = 'PATHS/filepaths_IBLTuning.yml'#
myrun = 'runIBLTuning_utypeP'
dset = 'IBL'
plot_examples = True
n_ex = 10
tdict_type = 'equaldur'#IBL styler
pthr = 0.001
#layers_a... |
8d8af0f964e154c7d3dcd74e0488b63443f816a4edfb3ff3a54e310c249b3c1d | Python | 11,854 | 343 | import argparse
import logging
import lightning as pl
import torch
from rich.progress import track
from mcmlnet.experiments.utils import (
load_model_configs,
preprocess_datasets_for_model,
save_results_to_csv,
validate_model_metadata_file,
)
from mcmlnet.training.data_loading.preprocessing import (
... |
7c8397d46aae553a6dd88f15e73ad2cdc93bdb0429371f69b5edf202454b9808 | Python | 11,858 | 328 | import os
import os.path as op
import time
import random
import numpy as np
import torch
import matplotlib.pyplot as plt
from torch import nn
from torch.utils.data import Dataset, DataLoader, Sampler
from sklearn.model_selection import StratifiedKFold
from sklearn.metrics import (
accuracy_score, precision_score, r... |
040f307c511b07895245b4a1aa4be1f1bd5aff370b261422c65932cd93616941 | Python | 11,859 | 278 | import torch.nn as nn
import torch
from torch import Tensor
from typing import List, Tuple, Optional, Union
from functools import partial
from bism.modules.unet_block import Block2D, Block3D
from bism.modules.concat import ConcatConv2D, ConcatConv3D
from bism.modules.upsample_layer import UpSampleLayer3D, UpSampleLaye... |
d8fbb856069dea1be5a7325cf2f7e193381580fcb66d02ae0547db7260c3da94 | Python | 11,861 | 389 | import textwrap
from collections.abc import Sequence
from pathlib import Path
import pandas as pd
from docs.doc_modules.experiments import AutoDocExperimentInfo, run_capture_and_save
from docs.doc_modules.serve_experiments_utils import load_data_for_serve
from docs.doc_modules.serving_experiments import (
AutoDoc... |
a634bafca4641b5e78e6c8ae2577947c30089343b2faa6bdc29f2b624465b43d | Python | 11,864 | 337 | """Route-matrix tests for the endpoint × protocol layer.
Each case exercises an endpoint's ``prepare`` directly and asserts the resolved
endpoint name, protocol, base URL, wire model name, credential source, and
final client kwargs, including protocol-specific Argo routing.
"""
from __future__ import annotations
imp... |
f550f621510f30b80173aefdfef8500af147475775dc09b532ab8fd5c6342ae6 | Python | 11,865 | 316 | import os
import os.path as osp
import torch
import numpy as np
import scipy
import pandas as pd
import argparse
import os
import torch_geometric.transforms as T
parser = argparse.ArgumentParser(description='display graph features and summary.')
#parser.add_argument('-d','--devices', help='Specify CUDA_VISIBLE_DEVICES... |
2ab8cb484ba04c41ab7f7b659aa7097a9424892f716f39dbb67f866b9cbfa107 | Python | 11,868 | 308 | # Kai Sandbrink
# 2023-04-27
# Evaluate survey responses
# %% LIBRARY IMPORT
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from human_utils_project import sort_train_test
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from ... |
e8250f32f228a27cdc1c88e80e9bc189389717e1f87ca1ce7e3f615f01a7fabe | Python | 11,871 | 258 | """
One of the design principles of AllenNLP is the use of a modular,
declarative language (JSON) for defining experiments and models.
This is implemented by giving each AllenNLP class a method
.. code-block
@classmethod
def from_params(cls, params: Params, **extras) -> 'ClassName':
...
that contains... |
48d61eba43907307d9d90aed8c9e2f8acc5486a1948e0cfb762c4fe56e82e1ad | Python | 11,878 | 291 | # Copyright 2024 BDP 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 applicab... |
9bb7c4a94323f71de52de24202d3128f3d25264827e0985d94cd2350dd17876d | Python | 11,878 | 265 | import re
import os
import sys
import numpy as np
import pandas as pd
import subprocess
def update_autofp_script(new_pcr_file_path, autofp_script_path):
if not os.path.exists(autofp_script_path):
raise IOError("The file '{}' does not exist.".format(autofp_script_path))
with open(autofp_script_path... |
6ac2b431bcc59929a859c76e541ba026035ae5bd50520890a3c660e7b25b58a5 | Python | 11,883 | 365 | import os
import logging
import unittest
import pandas as pd
import numpy as np
from pandas.testing import assert_frame_equal
from numpy.testing import assert_array_equal
from heig.ldmatrix import (
partition_genome,
find_loc,
get_sub_blocks,
LDmatrix,
LDmatrixBED,
check_input,
)
MAIN_DIR = os... |
94528de8614d0d59d47bc14270d5d38583fcb1d3418443844acda34cfc45ccd2 | Python | 11,883 | 258 | """
One of the design principles of AllenNLP is the use of a modular,
declarative language (JSON) for defining experiments and models.
This is implemented by giving each AllenNLP class a method
.. code-block
@classmethod
def from_params(cls, params: Params, **extras) -> 'ClassName':
...
that contains... |
bfb3700fb14dcf9e771964259f029797074c305a2dcba5aa46aa5ca8c2d46e6b | Python | 11,883 | 271 | # 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 numpy as np
import torch
from .modeling import Sam
from typing import Optional, Tuple
from .utils.transforms imp... |
18b5f657e6563ad589ad351b32bdef14d2abef0493648d27cae615fab7118e18 | Python | 11,887 | 310 | import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import jax.numpy as jnp
import jax
import os
import json
import sys
import glob
import matplotlib.colors as mcolors
from matplotlib.colors import to_rgba
plt.rcParams["font.sans-serif"] = ["DejaVu Sans"] # Best available
plt.rcParams["font.family"]... |
f4125a596a7871043c3f29217b9ff69dfc779490beec2f743d71d8ffe8c51a40 | Python | 11,891 | 286 | # -*- coding: utf-8 -*-
# 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 numpy as np
import torch
from segment_anything.modeling import Sam
from typing import Opt... |
7c4476719939617fcd0ef01e48edc37f54ad8e22a736d7586317a22667d17c5b | Python | 11,892 | 198 | #!/usr/bin/env python3
"""
04-tpm-transcript-representation.py
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Calculate rna-seq expression (tpm) gene isoform (transcript) representation for patients who have samples in both rna-seq and methylation datasets
"""
__author__ = ('Eric Wafula (wafulae@chop.edu)')
__version__ = '1.0'
__dat... |
72ef0e8bb35cb1dc5e22ede6aadaf975f6233d214f0e32e2e6ad0e7f17582ff4 | Python | 11,895 | 340 | """Globus Transfer file-staging manager.
Transfers files between a local Globus collection and a remote HPC
collection using the `Globus Transfer API
<https://docs.globus.org/api/transfer/>`_. This avoids encoding large
input files (e.g. atomic structures) inside Globus Compute function
payloads.
**Prerequisites**
... |
d693cb3231f6d390f210840e371f73105133444c3e6a041ac31e3d7dab8a2e5a | Python | 11,895 | 361 | import os
import json
from itertools import product
from typing import Optional, Union, List, Tuple, Dict, Any, Generator
import numpy as np
import torch
import pandas as pd
from loguru import logger
from sklearn.preprocessing import StandardScaler, RobustScaler
from sklearn.model_selection import StratifiedKFold, Stra... |
bd40968e7fe7fffb0fb6b7c827c86615fd5cc7e69d931e9e12799fe16dfba49e | Python | 11,896 | 282 | #Lucas Sancéré -
import glob
import os
import shutil
import numpy as np
from PIL import Image as im
from tqdm import tqdm
### Utils Functions
# Check this function as it can just REMOVE files if not used properly
# Maybe add GUI with users to understand fully want is happening
def anaylser2featselect(folderpath: ... |
f2d1466cf49264b1251b08ff1e16db5c15cfa04b151c71c6d226f19c325e1ba0 | Python | 11,896 | 314 | # -*- coding: utf-8 -*-
# cifar10_resnet18_td_vs_baseline.py
import copy, random, os
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader, random_split
from torchvision import datasets, transforms
import matplotlib.pyplot as plt
# ==... |
57d870a9e6f4df8ac5d5b120fed0fb1602055c3692b50029cbe4bacc7b4f6ef2 | Python | 11,898 | 492 | #!/usr/bin/env python3
#
# read_config.py formats Cytosim's configuration files
#
# FJN 13-15.11.2013 - 31.07.2014, 3.09.2015, 12.08.2018, 11.12.2019, 27.05.2021
"""
Read cytosim configuration files
Syntax:
read_config.py FILE
read_config.py - FILE
Description:
Reads a config file and prints... |
698819016cbefafacff907ba2802231ad2a2915a895e6e2f52d665227a0ef1a1 | Python | 11,899 | 383 | import argparse
import os
import tempfile
from argparse import Namespace
from collections.abc import Mapping
from copy import copy
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import pytest
import yaml
from hypothesis import given, settings, strategies
from eir.setup import config... |
fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e | Python | 11,900 | 373 | import pandas as pd
from textwrap import dedent
# brian 2
from brian2 import NeuronGroup, Synapses, PoissonInput, SpikeMonitor, Network
from brian2 import mV, ms, Hz
# file handling
from pathlib import Path
# parallelization
from joblib import Parallel, delayed, parallel_backend
from time import time
default_params... |
eb6aa915edfca2cd3e06180c57c6f515077165878d5f99bdfedb48bbe7f03e85 | Python | 11,902 | 276 | import numpy as np
from scipy import signal
from scipy.ndimage import interpolation
from pipeline.utils import galvo_corrections
class Position:
NONCONTIGUOUS = 0
LEFT = 1
RIGHT = 2
class StitchedSlice():
""" A single slice from a stitched ROI. """
def __init__(self, slice_, x, y, dtype):
... |
0354bedf7abbc8aca835f2c8f34b3727848e73453f3b211262326d0552b52b0b | Python | 11,906 | 242 | """Contains functions, which generate example dataset, attribution, and analysis HDF5 files. These functions are mainly for documentation purposes to
show the structure of the different HDF5 files that can be generated using CoRelAy for the usage in ViRelAy projects.
"""
import h5py
import numpy
def make_group_examp... |
510f36ea8c8c7b70a72f8198bb979389b3d7ee0c1725048fe9e7230ed8db7d07 | Python | 11,908 | 332 | #!/usr/bin/env python3
"""
Split-half robustness analysis for laminar gradients.
- Uses the same connectivity construction as your main pipeline.
- Keeps the original number of gradients (n_components).
- On each iteration:
* randomly splits subjects into two halves
* builds group FC for each half
* runs g... |
c72489e65f761009137303ae8a51157e3979eddc7fc5b74ef9c458ec8ab675be | Python | 11,910 | 348 | """
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... |
90a47fc770537b16ea382cfd32e301c1d772dc8357e5db067f9209b75587ff3b | Python | 11,916 | 242 | """Contains functions, which generate example dataset, attribution, and analysis HDF5 files. These functions are mainly for documentation purposes to
show the structure of the different HDF5 files that can be generated using CoRelAy for the usage in ViRelAy projects.
"""
import h5py
import numpy
def make_group_examp... |
981842450500de27eebcb18f240de48457da7df1956a7d30a975eb5ce04d75e2 | Python | 11,916 | 300 | import os
import time
import tqdm
import itertools
import numpy as np
import scipy.sparse as sparse
import scipy.sparse.linalg
def read_eigenvectors(file):
"""
Takes a dataset and returns the J1J2 values that
are associated for the eigenvector for each line
:param file: str - file location
:return... |
3ee216f330da319c87ff3122b28f0a7571e4c178d64422fc187aa7477b67cbe9 | Python | 11,917 | 321 | """
Center Settings Widget for Quadrant Folding
This widget provides UI controls for setting the center point of images,
including calibration, manual setting, chords, and perpendiculars methods.
"""
from PySide6.QtWidgets import (
QLabel,
QPushButton,
QGridLayout,
QDialog,
QVBoxLayout,
QRadio... |
840a37fc8c4d5c07d31c3366db7255515a275f1bab0ef947ba840fa326455926 | Python | 11,917 | 309 | import os
import time
import copy
import argparse
import torch
import torchvision
from torchvision import datasets, transforms, models
from torch.utils.data import DataLoader, random_split, Dataset
import matplotlib.pyplot as plt
import seaborn as sns
from tensorboardX import SummaryWriter
import numpy as np
from torch... |
92688dae6edd2c98114b0408ea45515231ebe039771173140efd86181badc0bc | Python | 11,917 | 335 | # The ImpedanceFitter is a package to fit impedance spectra to equivalent-circuit models using open-source software.
#
# Copyright (C) 2018, 2019 Leonard Thiele, leonard.thiele[AT]uni-rostock.de
# Copyright (C) 2018, 2019, 2020 Julius Zimmermann, julius.zimmermann[AT]uni-rostock.de
#
# This program is free ... |
b7ca44098889ba21d78c3046971efd0e4e7e41d3a6854233e44527c024877b44 | Python | 11,917 | 288 | # Import Packages, Libraries and Files
from psychopy import visual, core, event, __version__, data, gui, logging, monitors,constants
from psychopy.hardware import keyboard
from psychopy.hardware.emulator import launchScan
import os
import random
import exp_utils
"""
The active condition consisted of two complex figure... |
e775840189b51254e5d4c08663d23e103067d74a1a9c2c3913188de1d12429a0 | Python | 11,917 | 289 | import pandas as pd
import random
import tensorflow as tf
def create_fake_index_list(max_events, max_nodes):
"""Create indices for fake patients e.g. [[56,23,99], [34,3,98]]
such that each sublist would be [start_node, end_node, timestep].
Returns:
list of lists: indices for 3D matrices.
"""
... |
26dc94ba6aaa2c9510b5b5c932ac189313267c7460f3f76923df636d3e410202 | Python | 11,918 | 254 | import logging
import os
import pickle
import pandas as pd
from dgl.data import DGLDataset, download, check_sha1
from project.utils.deepinteract_utils \
import construct_filenames_frame_txt_filenames, build_filenames_frame_error_message, process_complex_into_dict, \
zero_out_complex_features
class CASPCAPRI... |
50300dc6719cc0ca14c598abfeae1750682105c56779a99c3fbf87c3ffd6ddc4 | Python | 11,926 | 290 | #Lucas Sancéré -
import json
import os
import numpy as np
import yaml
from attrdictionary import AttrDict as attributedict
from histo_miner.utils.misc import (
convert_flatten,
convert_flatten_redundant,
noheadercsv_to_dict,
rename_with_ancestors,
)
script_dir = os.path.dirname(os.path.abspath(__fil... |
c2ebdf0f8141e4958681bd3dd06552b2f7e9fb0d5cd6de5b9ff05e12d65d559c | Python | 11,928 | 267 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from typing import Any
import numpy as np
from .byte_tracker import STrack
from .oc_sort import OCSORT, OCSortTrack
from .utils import matching
from .utils.gmc import GMC
from .utils.reid import build_encoder, smo... |
2d27ace7a1d2efbd87b835f32b7015b02ddf9170d9bfc014e7c3f43f10873f66 | Python | 11,929 | 320 | """Classes and utilities for mutliple alignments from the EPO pipeline"""
import logging
import os
import pickle as cPickle
import re
from collections import namedtuple
from ._epo import ( # noqa: F401
bed_union,
cummulative_intervals,
fastLoadChain,
rem_dash,
)
log = logging.getLogger(__name__)
c... |
ad49cb897740e24369e1b500074a0212093ecc2120fabd4412985a1222329b13 | Python | 11,929 | 361 | # -*- coding: utf-8 -*-
"""
Most of this code was modified from code by Emmanuel Caruyer
<caruyer@gmail.com>.
See his original code on GitHub:
https://github.com/ecaruyer/qspace/tree/master
The code was reorganized, but general process is kept the same.
"""
import numpy as np
from scipy import optimize
from scilpy... |
9ea85442e22416f2825ca04357d0f9d4a3380e91d8b549ec4d43a4f26c9ea56e | Python | 11,931 | 384 | # -*- coding: utf-8 -*-
"""Apply transformations."""
import datetime
import os
import shutil as sh
from shutil import copyfile
import nibabel as nb
import numpy as np
import numpy.linalg as npl
from sh import gunzip
from .. import execute_command
from ..io.affine import apply_affine_chunked
from ..io.filename import... |
fb489969f23f293a90955863b755a1ee63f45936f12b77e6f42cf8f936104940 | Python | 11,931 | 296 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
"""Module for building position mapping models based on a flatmap"""
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import progressbar
from scipy.inter... |
4268b482bca2b6c4e525012c31fd512fa1a8adef7bdaeacfa610d5e3149310b2 | Python | 11,932 | 387 | # -*- coding: utf-8 -*-
import logging
from enum import Enum
from dipy.core.gradients import get_bval_indices
import numpy as np
DEFAULT_B0_THRESHOLD = 20
class B0ExtractionStrategy(Enum):
FIRST = "first"
MEAN = "mean"
ALL = "all"
def is_normalized_bvecs(bvecs):
"""
Check if b-vectors are nor... |
8d78f491e55286754c0faad9f70fac8e329f7073c930d7aa68962cb2aae69938 | Python | 11,932 | 292 | '''
Modified from https://raw.githubusercontent.com/pytorch/vision/v0.9.1/torchvision/models/mobilenetv2.py
BSD 3-Clause License
Copyright (c) Soumith Chintala 2016,
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditi... |
225e6a3634ee63e6356df13a0ad795559b7588f889693e835df6522cc9d9e332 | Python | 11,935 | 210 | import multiprocessing
import os
from time import sleep
from typing import List, Type, Union
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import load_json, join, save_json, isfile, maybe_mkdir_p
from tqdm import tqdm
from nnunetv2.imageio.base_reader_writer import BaseReaderWriter
from... |
e4e3daadf485f9203ce7e2afb765b4364c10f764e96a7417a9a4663790b01c24 | Python | 11,935 | 382 | import os
import random
import warnings
# audio
from ctypes import POINTER, cast
from datetime import datetime
import pandas as pd
from comtypes import CLSCTX_ALL
# psychopy
from psychopy import core, event, gui, sound, visual
from psychopy.constants import FINISHED
from pycaw.pycaw import AudioUtilities, IAudioEndp... |
a6b785c4644ff6249e16bf4608f0841f28d867c290df4091d302d1a16a484147 | Python | 11,936 | 345 | #%% Imports
from IPython.display import display
import pickle
from pathlib import Path
import numpy as np
import pandas as pd
from sklearn.metrics import confusion_matrix
from config.config import settings
from data.preprocessing import run_full_preprocessing
from evaluation.performance import compute_operating_metric... |
6194fd087714fbaa620e89430713781268b63366683b88b4bd499d26e1af1fb6 | Python | 11,943 | 330 | from nipype.interfaces.base import BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File, Directory, Str, traits
import os
import glob
import re
import subprocess
import numpy as np
import nibabel as nib
from cvdproc.config.paths import get_package_path
HCP842_QA = get_package_path("data", "standard", "MNI152", "... |
a449344b4d2e9d8072cfd09a0e3504172f2475b8ddce2cb92abbeb6548db5800 | Python | 11,943 | 307 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Agatha Schmidt, Henrik Zunker
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complian... |
62a6a7f5bd210479d165bb4287567993a01ba862ec41aa1e5404412c3880311d | Python | 11,950 | 380 | """
HUMOTO dataset loader: Mixamo GLB/GLTF + YAML → normalized COCO-17 clips.
Directory layout expected:
humoto_/
├── humoto_0805/
│ ├── carry_frying_pan_both_hands_walk_around-505/
│ │ ├── carry_frying_pan_both_hands_walk_around-505.glb ← used
│ │ ├── carry_frying_pan_both_hands_walk_a... |
879e0bde09224f63a2255ec8e59117e882b6a43b71221f4be7cdfd860f1b35aa | Python | 11,950 | 274 | # Kai Sandbrink
# 26.06.2022
# Implements a bandit task with k regular arms but stochastic transitions
import numpy as np
import random
from PeekTakeTorchTask import PeekTakeTorchTask
class ObserveBetEfficacyTask(PeekTakeTorchTask):
def __init__(self, **kwargs):
#print("Setting bias to 0")
self... |
662e6ad2e780b4b82ed2139df87b85964259eaa6f4b13aaf71626315506d18f4 | Python | 11,953 | 269 | import hashlib
import os
import warnings
import tempfile
from subprocess import call
from pathlib import Path
import numpy as np
import imageio
from imageio_ffmpeg import get_ffmpeg_exe
from . import _perlin
from .util import generate_frames, filter_frames, filter_frames_index_function, XYSCALEBASE, discretize
class... |
258daf8640f89401233e20c15cf869a7684228eb597d26998ccedd3a94e9dac1 | Python | 11,959 | 257 | import logging
import os
import pickle
import pandas as pd
from dgl.data import DGLDataset, download, check_sha1
from project.utils.deepinteract_utils \
import construct_filenames_frame_txt_filenames, build_filenames_frame_error_message, process_complex_into_dict, \
zero_out_complex_features
class DB5DGLDat... |
20427d08eb48f402d7cc65de61a9f701be36f5227d0915807f753934e5c828e0 | Python | 11,966 | 292 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: GM
@edit: CD
#-----------------------------------------
Brain AGE v2 - hold-out
#-----------------------------------------
Age prediction of brain images with convolutional neural networks.
---
Before using this script, please be s... |
e4009f0d249ff0cd3926c3168979eb15805ad8c83ec235bbc6312b4a05c9a2db | Python | 11,967 | 252 | """
Script to save fitted PLS models.
"""
import numpy as np
import pandas as pd
import scanpy as sc
from joblib import Parallel, delayed, dump
from numpy.random import default_rng
from sklearn.utils import shuffle
from itertools import chain
import gc
from sklearn.cross_decomposition import PLSRegression
from skle... |
1000f704a64efcc2c4bae9198b395093fbe1b4fff8223dafb8b631425aa95e71 | Python | 11,968 | 243 | from brainvoice.data.estimates_loader_utils import load_estimate_labels, load_latent_variables_estimates
from sklearn.decomposition import PCA
from sklearn.metrics import adjusted_rand_score, adjusted_mutual_info_score
from sklearn.cluster import KMeans
import pingouin as pg
import matplotlib.pyplot as plt
from matplo... |
262aab63d6b8066b7decff5a16458cad3afceaa4bee3933525feb65ae3b352f5 | Python | 11,973 | 365 | from __future__ import annotations
import math
import typing
import numpy as np
import pytest
from numpy.typing import NDArray
from labelme._automation import MASK_REQUIRED_SHAPE_TYPES
from labelme._automation import AiOutputFormat
from labelme._automation import Detection
from labelme._automation import assign_avai... |
9b6f724e6d4c5f35edc0fcb8ccc085a1b58266feee25a6931c7ca8d4b783b761 | Python | 11,973 | 263 | import argparse
import torch
import torch.utils.data
from simulation.dataset import SimulationDataset
from model.eghn import EGHN
from utils import collector_simulation as collector, MaskMSELoss, EarlyStopping
import os
from torch import nn, optim
import json
import random
import numpy as np
parser = argparse.Argumen... |
eadbdf0c2ffd06f07333dfddb0149615e2b9c1b9fe7233a94f4702f9981ce29a | Python | 11,974 | 354 | # tifffile/examples/write_dng.py
# Copyright (c) Christoph Gohlke
# SPDX-License-Identifier: BSD-3-Clause
"""Write Digital Negative (DNG) compatible file using tifffile.
Writes a synthetic, 12-bit CFA (Bayer mosaic) array as a DNG 1.7 file.
DNG-specific TIFF/EP tags are passed via TiffWriter's extratags parameter.
F... |
40fde3d4734e6235a137c8f6490c723900423a4a4421f0c083c4632420d1261c | Python | 11,976 | 361 | import os
import logging
import hail as hl
import heig.input.dataset as ds
from heig.wgs.relatedness import LOCOpreds
from heig.wgs.utils import read_genotype_data, init_hail, get_temp_path, clean
"""
TODO:
1. consider providing more preprocessing options? such as --chr
"""
def parse_ldr_col(ldr_col):
"""
... |
245fca17900cdc7edbfa2c979ef5b957e9917b679e84f07c12797abe9d5256d0 | Python | 11,981 | 312 | # Copyright (c) 2026 Rohit Jena. All rights reserved.
#
# This file is part of FireANTs, distributed under the terms of
# the FireANTs License version 1.0. A copy of the license can be found
# in the LICENSE file at the root of this repository.
#
# IMPORTANT: This code is part of FireANTs and its use, reproduction, or... |
2c77f18c44dcedd9efeb54454163903006b307e23ee4d14bdbf31536424a7135 | Python | 11,981 | 276 | import os
from itertools import groupby
import subprocess
import numpy as np
import pandas as pd
from tqdm import tqdm
import mne
import lunapi as lp
proj = lp.proj()
def add_symmetric_detection(df1, df2, ch1, ch2, col_ch, col_start, col_stop, col_other):
df3 = []
for i in range(len(df1)):
... |
454731940f60866ae870ac7681d15b6d40dce5a289993cc8d15beed6ee0da256 | Python | 11,981 | 241 | #!/usr/bin/env python3
# -*- coding: utf-8
"""
Script that evaluates model based on single-cell spatial data.
Created on 2021/07/16
@author romain_lopez
"""
import os
import click
import numpy as np
from utils import metrics_vector, discrete_histogram
import scanpy as sc
import matplotlib.pyplot as plt
import seabo... |
2fd749f128be72bfc53626e020c6d4c20f286144e270ce26a1143a97fb68b7e1 | Python | 11,983 | 343 | # This file is part of Zennit
# Copyright (C) 2019-2021 Christopher J. Anders
#
# zennit/canonizers.py
#
# Zennit is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation; either version 3 of the License, or (at ... |
060575fd3ab116f595bed3d5623de2f685ee7304a57cb2ed71700b91a6b0c149 | Python | 11,984 | 281 | # 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 numpy as np
import torch
from .modeling import Sam
from typing import Optional, Tuple
from .utils.transforms imp... |
b786ee24166dccad1530e46aa8e1825e2c15a7e309db40aa3b03ef5d5e606ffc | Python | 11,988 | 273 | # -*- coding: utf-8 -*-
"""
Example script to set up the parameters for the image processing pipeline
"""
######################### Import modules
import os, numpy, math
import ClearMap.Settings as settings
import ClearMap.IO as io
from ClearMap.Alignment.Resampling import resampleData;
from ClearMap.Alignment.Elas... |
7e326faa06dbe9a7e22c3e00723dba47b99a9107f34cf4bbc4d58e1f1aad2ed2 | Python | 11,989 | 382 | # -*- coding: utf-8 -*-
"""BOLD correction for VASO."""
import os
import nibabel as nb
import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline as Interp
from sh import gunzip
from .. import execute_command
from ..io.filename import get_filename
__all__ = [
"split_vaso",
"boco_vaso_regr... |
a2cca83fb56063e1305ae3e43bbfa1e89ce99dbc66be51d0ce959a240d72b148 | Python | 11,993 | 357 | import attrs
import numpy as np
from attr import field
from typing import Literal, get_args
from typing_extensions import Self
from neuralib.suite2p import Suite2PResult, get_neuron_signal, sync_s2p_rigevent
from rscvp.util.cli.cli_suite2p import NeuronID, get_neuron_list
from stimpyp import Session, SessionInfo, Rigl... |
45d962db8f1aa4ae9b7d81dfa898de28282ea865ff6018d037f348f969bbe7b5 | Python | 11,994 | 369 | """
Support for scoring alignments using arbitrary scoring matrices, arbitrary
alphabets, and affine gap penalties.
"""
from numpy import (
float32,
int32,
ones,
zeros,
)
class ScoringScheme:
# note that gap_open and gap_extend are penalties, which means you should make them positive
def __in... |
75473cb9427f2c6d6223377780da94aec08f8d5da4f92ca4da73e360fef28e47 | Python | 12,005 | 255 | """A module that contains unit tests for the :py:mod:`corelay.utils` module."""
import re
import sys
from types import LambdaType
from typing import Any, Callable
import numpy
import numpy.testing
import pytest
from corelay.utils import get_fully_qualified_name, get_lambda_expression_source_code, get_object_represen... |
da827206212796d035c12049dcd644e7e808f203d0f2cab87161e23ddccdcec6 | Python | 12,005 | 278 | """Test CAT-NAP against raw data it may not own: read-only, shared, or remote.
Run from the repo root::
uv run python python/test_catnap_derived.py
Three changes, all aimed at making a suite2p folder something the pipeline only
ever *reads*, and reads once:
A. **Derived files leave the raw folder.** Denoising... |
ac23849884bad12053815e826043f083c06f1807bc183c4eaaad2c02ed726e6a | Python | 12,006 | 406 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import colorsys
from dataclasses import dataclass
from typing import List, Tuple
import cv2
import matplotlib as mpl
import matplotlib.colors as mplc
import numpy as np
import pycocotools.mask as mask_utils
def rgb_to_hex(rgb_color):
"""
... |
aaa0d830ffab130bbadb9d946cd8c26e07ae800dadba0f73a3d6d5b1273e9e79 | Python | 12,023 | 283 | # -*- coding: utf-8 -*-
"""
EPI <-> EPI <-> ORIG registration
The purpose of the following script is to compute the deformation field for the
registration between anatomy in conformed freesurfer space and native EPI space
via a registration between two EPIs and application of an already existing
EPI <-> deformation. T... |
9cd5f79102d88f6ba06e2dae6e6d358b2c0eb5bdbbfdfea2132ddc6c0764f440 | Python | 12,024 | 384 | from __future__ import annotations
import dataclasses
import datetime
import logging
import time
import uuid
from typing import Any, Collection
from chemgraph.agent.events import (
EventCallback,
_TurnEventCallback,
_call_name,
_message_tool_calls,
)
from chemgraph.graphs.single_agent import construct... |
c0c1d0ef6a3991e3fa869aa45eef84224bafa258539ac7010785c8b48f1d6f06 | Python | 12,027 | 334 | """Data loading utilities for Monte Carlo simulations."""
import os
import numpy as np
import pandas as pd
import torch
from mcmlnet.utils.env import require_env
from mcmlnet.utils.logging import setup_logging
logger = setup_logging(level="info", logger_name=__name__)
class SimulationDataLoader:
"""
Unifi... |
075b8770d9541439536a75afb178b3387b11a70c1326e6f66e7851fe29276ad5 | Python | 12,028 | 289 | """LangChain ``@tool`` wrappers for OCSR: read a structure image, return a SMILES.
The tool delegates to a plain function, so a human or a test can call the same logic
without an agent: :func:`image_to_smiles` is a ``StructuredTool`` and is not callable
directly, :func:`image_to_smiles_core` is. Same split as
:mod:`ch... |
a824d44d98b9076fc650ad73e6e5ae6a5c9db2c3707978969596f21c593cc374 | Python | 12,028 | 330 | """
Functions used to perform MIRACLE (Motion Insensitive RApid Configuration reLaxomEtry)
Author: florian.birk@tuebingen.mpg.de
"""
import numpy as np
from numba import jit
@jit(nopython=False, error_model='numpy')
def fgss_T1(fid: np.ndarray, fid2: np.ndarray, tr: float, te1: float, te2: float, flip: float, t2: ... |
64527c29d4bd913242e8d9f29d10705fab95c656c13d81be2dad007f445d1bcd | Python | 12,030 | 346 | import pandas as pd
import torch
import numpy as np
import pandas as pd
from glob import glob
from tqdm import tqdm
import os
import random
from torch_geometric.utils import to_undirected, remove_isolated_nodes, remove_self_loops, train_test_split_edges, negative_sampling
import multiprocessing
from itertools import pr... |
85224bcb07b29b00ac905a06a8be8d8661f0cdab166971a7b919030c91f4eb30 | Python | 12,033 | 391 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
96829565659251cf57efaed4925a2248a4f001654a40e6d3881ce625c3c724bc | Python | 12,042 | 337 | from typing import List, Optional, Union
import torch
from torch import nn as nn
from torch.nn import functional as F
from .config import use_fused_attn
from .create_conv2d import create_conv2d
from .helpers import to_2tuple
from .pool2d_same import create_pool2d
class MultiQueryAttentionV2(nn.Module):
"""Multi... |
e02a061bc5572c99ac1312031a58c3edb9bae865c23b2f526a24fb6bfd860096 | Python | 12,044 | 340 | ##
#Load Modules
import numpy as np
from numba import njit
import pdb
@njit()
def EPGMotion(opt, MotionScale = None, Sequence = 'DW-SSFP'):
#Account for DW-SE Sequence
if Sequence == 'DW-SE':
opt['nTR'] = np.asarray([2], dtype='f8')
#Initialise some values to prevent repeat calculations
n... |
50c7047182fcd616076b30b3e18d8cd1a73f7335d0d2fdf487bbc8f2f58c1c44 | Python | 12,046 | 400 | import base64
import json
import os
from collections.abc import Sequence
from functools import partial
from pathlib import Path
from shutil import copytree
import matplotlib.pyplot as plt
import numpy as np
from PIL import Image
from docs.doc_modules.experiments import AutoDocExperimentInfo, run_capture_and_save
from... |
48a1579bb2d0db82009809b2d09c02762eec234faa908eca204412e843232563 | Python | 12,048 | 345 | """
Tests for deepreg/model/layer_util.py in
pytest style
"""
from test.unit.util import is_equal_tf
from typing import Tuple, Union
import numpy as np
import pytest
import tensorflow as tf
import deepreg.model.layer_util as layer_util
def test_get_reference_grid():
"""
Test get_reference_grid by confirming... |
811f6fd954d46a8da1e7410aece5a184ce5a6550285851835c4a1322c93cf6a5 | Python | 12,050 | 367 | """inference.py."""
from functools import partial
from typing import Any, Literal, TypeAlias
import jax.numpy as jnp
import numpy as np
import numpy.typing as npt
import numpyro.distributions as dist
import pandas as pd
from jax import Array, jit, pmap, random, vmap
from jax.lax import scan
from jax.tree_util import ... |
095b409305e4e53890d245e833f0075c2ebfa007a7dd82c21b4d3be5fc8658ae | Python | 12,058 | 389 | #!/usr/bin/env python3
import os
import re
import numpy as np
import pandas as pd
from nctpy.utils import matrix_normalization
from nctpy.energies import get_control_inputs, integrate_u
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
# =========================================================... |
cce66a1607e9b2a391b97ace783321fd4cbf8587f6a3bfcafac9db95c8c8ebc0 | Python | 12,063 | 348 | """
Ported to pytorch thanks to [tstandley](https://github.com/tstandley/Xception-PyTorch)
@author: tstandley
Adapted by cadene
Creates an Xception Model as defined in:
Francois Chollet
Xception: Deep Learning with Depthwise Separable Convolutions
https://arxiv.org/pdf/1610.02357.pdf
This weights ported from the Ke... |
351e9fe5b14c9d1a6c3494981940c50ba356ad577f1fc95a8c9cc68a588e954b | Python | 12,064 | 379 | """Metrics for evaluating model performance."""
import numpy as np
from scipy.linalg import eigvalsh
from sklearn.metrics import confusion_matrix as sklearn_confusion_matrix
from tqdm.auto import trange
def alpha_correlation(alpha_1: np.ndarray, alpha_2: np.ndarray) -> np.ndarray:
"""Calculates the correlation b... |
be308ad897d7ead625d36a28142c27ec4376b050a882b256ca99711bc09872f0 | Python | 12,065 | 366 | """
LightGBM classifier for metabolite-disease association prediction.
This module implements the LightGBM-based binary classifier that operates on
concatenated node-disease embeddings learned from HGNN.
"""
import numpy as np
import lightgbm as lgb
from sklearn.model_selection import KFold
from typing import Dict, L... |
3bed00505c06566fd20552bef1075dea2a19856d7a665dc3a0d732c1af9ec8cf | Python | 12,067 | 258 | import argparse
import torch
import torch.utils.data
from motion.dataset import MotionDataset
from simulation.dataset import SimulationDataset
from model.eghn import EGHN
from utils import collector_simulation as collector, MaskMSELoss
from tqdm import tqdm
import os
from torch import nn, optim
import json
import rand... |
1ecf71b230e8088888256cd9836106b264f2950c30588865c1acc35118bb8d7b | Python | 12,072 | 293 | """Turn a bundle back into an ordinary output folder.
An express run keeps only the ``.meanap``, because every figure in it is a pure
function of the data it carries and re-drawing one takes about a tenth of a
second. That is the right trade for the person who ran the analysis. It is the
wrong trade for the person the... |
30cb3d6eff54c9fde722f4bf80e53745b631955803416539dac11a7350ebd939 | Python | 12,072 | 330 | """Hermetic gRASPA tests exercise the public tool, real preparation and parser."""
from concurrent.futures import ThreadPoolExecutor
from importlib.resources import files
import json
from pathlib import Path
import subprocess
import sys
from unittest.mock import Mock
from ase import Atoms
from ase.io import write
imp... |
d9c4e721eeda9cd5fdedebf13d5ffaca0dddb1ff5662fba369c637d23cea8765 | Python | 12,072 | 249 | """Generates a random dataset and random attributions for this dataset, which can then be used to generate a meta-analysis and ultimately a test
project for ViRelAy.
"""
# pylint: disable=duplicate-code
import argparse
import json
import os
import h5py
import numpy
from numpy.typing import NDArray
def append_sampl... |
500418b08e8b5f7126f39a689b2507b3363389dcceabf8a8d7a8f47cbff1f3bb | Python | 12,073 | 285 | # -*- coding: utf-8 -*-
"""
Created on Tue Mar 7 14:34:59 2023
@author: gu47yiy
"""
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Feb 6 13:51:12 2023
@author: mgruenig
"""
# import libraries
import tensorflow as tf
from tensorflow.keras.models import Model
from tensorflow.... |
c2f500b2b2cf7775fa9003113920afbcaf46da87c2295cb4682d5a9f04c7fb5b | Python | 12,073 | 353 | import numpy as np
eps = 1e-6
def projection(va, vb):
return np.dot(va, vb.T) / np.dot(vb, vb.T) * vb
def get_rotation_matrix(theta, d):
x, y, z = d[0], d[1], d[2]
M = np.zeros((3, 3))
cos, sin = np.cos(theta), np.sin(theta)
M[0][0] = cos + (1 - cos) * x * x
M[0][1] = (1 - cos) * x * y - si... |
7376a762904bb8c3911d0a43844109c2061680d1fad1f38e23f92121c9066624 | Python | 12,076 | 317 | import sys
sys.path.insert(0, '../')
sys.path.insert(0, '../../')
sys.path.insert(0, '../../../')
sys.path.insert(0, '../../../ogb')
import os
import argparse
import time
from shutil import copy
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
from ogb.linkproppred import PygLinkPr... |
d1db421805f18ec829440de493464bdb599b754fe7836f04ea2b4905442e977b | Python | 12,080 | 269 | '''
Sampling
-------------------
Functions for sampling a synthetic retina.
'''
import numpy
from numba import jit
#######################
# SCANNING FUNCTIONS #
######################
@jit(nopython=True)
def performScanning(retina_params_pixels, pixel_value_array, x, y, nstdev=6.0):
'''Performs the scanning... |
3e804c4509f7e54b2f87448ed55541482b618d55316874e2eacb2cc50ba58aea | Python | 12,086 | 256 | import os
import os.path as osp
import torch
import random
import numpy as np
import pandas as pd
from torch_geometric.data import (Data, InMemoryDataset, download_url,
extract_gz, extract_tar, extract_zip)
from torch_geometric.data.makedirs import makedirs
from torch_geometric.utils ... |
ea7125497a4f09fdb58db45edea3ee9c49b7025da6f5886feda46744435ee378 | Python | 12,086 | 283 | import re
from scipy.io import savemat
from sklearn.model_selection import StratifiedKFold
from tqdm import tqdm
from LocationRegressionHelper import *
import time
from numpy.random import default_rng
import argparse
import platform
import numpy as np
from pathlib import Path
import requests
print("Code is running o... |
f165d976e8b3568a874d018be2171a87303da01dfbfe82f51aa42b4d5582f6da | Python | 12,092 | 332 | #!/usr/bin/env python3 -u
import os
import sys
import json
import pickle
import logging
from typing import Dict, Any, List, Tuple
import numpy as np
import torch
from unicore import checkpoint_utils, distributed_utils, options
from unicore import tasks
from unicore.logging import progress_bar
logging.basicConfig(
... |
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