sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5717edd94574f6f68792432d10905d9548b8f58cbab66ac1a3af82dd027c08df | Python | 3,739 | 101 | import os
import matplotlib.pyplot as plt
import scanpy as sc
import deepstkit as dt
import pandas as pd
from sklearn import metrics
# ========== Configuration ==========
SEED = 9 # Random seed for reproducibility
DATA_DIR = "/DATA1/Roxana/GraphST-main/Data/1.DLPFC" # Directory containing spatial d... |
105f57f47808a67c577d03a3d2a1be5a0fd85f36d6765ed9673568bc49769dcf | Python | 3,742 | 70 | from batchgenerators.utilities.file_and_folder_operations import *
import shutil
from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json
from nnunetv2.paths import nnUNet_raw
def convert_amos_task1(amos_base_dir: str, nnunet_dataset_id: int = 218):
"""
AMOS doesn't say anything abo... |
1beb11894e4639d728e97f60b405c9e2a2355b012ebc9dbc9ac7e6e85cff5fe8 | Python | 3,742 | 100 | # 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.
from .how2processor import (
ShardedHow2MetaProcessor,
ShardedVideoProcessor,
ShardedTextProcessor,
VariedLenAligner,
Over... |
8f64718df87c52599057b4e61b12564e8f7c8eafd65132c51fbac3493d471bb0 | Python | 3,742 | 104 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
from os.path import join
from os.path import expanduser
def get_config_name(input_type, output_type, dropout_sampling=False, tract_definition="TractQuerier+"):
if tract_definition ==... |
d7df37d8adecac0b6bae43a38e5ca36c587c8ade7a06fe549a86932b3ca87ff2 | Python | 3,742 | 106 | import unittest
from scipy.special import jnp_zeros
import numpy as np
from numpy.testing import assert_allclose
import mdt
from mot.configuration import CLRuntimeInfo
from mot.lib.kernel_data import Array
class test_VanGelderenCylindricalRestrictedSignal(unittest.TestCase):
def __init__(self, *args, **kwargs):
... |
f0ae1c63d1683a1238861bff82359a4244f3d7e11b242cd787f5578027359a01 | Python | 3,742 | 107 | from torch.utils.data import DataLoader
import torch
import lightning.pytorch as pl
from typing import Union, Optional
from pathlib import Path
from rinalmo.data.alphabet import Alphabet
from rinalmo.data.constants import *
from rinalmo.data.downstream.expression_level.dataset import ExpressionLevelDataset
from rina... |
9571addfb346b7c6c2d852964d1825fd66564269863f3e10a331657e71e036c0 | Python | 3,743 | 105 | import numpy as np
import torch
from fairseq.data.audio import rand_uniform
from fairseq.data.audio.dataset_transforms import (
AudioDatasetTransform,
register_audio_dataset_transform,
)
from fairseq.data.audio.waveform_transforms.noiseaugment import (
NoiseAugmentTransform,
)
_DEFAULTS = {
"rate": 0.... |
8acfe8a927f7c960523b783838d6d48dbff9ba4bc2e7f325fb673b391ce39b74 | Python | 3,744 | 64 | import torch
from transformers.deepspeed import HfTrainerDeepSpeedConfig
class KMAETrainerDeepSpeedConfig(HfTrainerDeepSpeedConfig):
"""
The ``KMAETrainerDeepSpeedConfig`` object is meant to be created during ``TrainingArguments`` object creation and has
the same lifespan as the latter.
Note: It is r... |
4bb1a37489e609e75f3b9234ec4a585fe21a35f537ce95655d1c9bf3ea70a70e | Python | 3,745 | 131 | """Tests for ``aestetik.utils.utils_clustering``.
Covers kmeans/bgm/leiden/louvain paths, the resolution-search helper,
and the spatial cluster-refinement code path including the multi-batch
branch.
"""
from __future__ import annotations
import numpy as np
import pytest
from aestetik.utils.utils_clustering import (
... |
8d1be7bb5876068deca21acb8ee4a976f51a2a6ca909c8c54bdfc9b98c2058ce | Python | 3,745 | 108 | # 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 torch
logger = logging.getLogger(__name__)
class NanDetector:
"""
Detects the first NaN or Inf in forward a... |
b3f1b5e32581c76b475ff996e16f572ece0650556fa221917ce079430eb0b1b3 | Python | 3,745 | 108 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import scipy.io as sio
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_pMFM_generate_simualted_fc_fcd(gpu_index=0):
... |
e6d0c9f1ac73ac3eb520319eceb584c6cf0a09d766beaa82f9500a7b1bdba4ec | Python | 3,745 | 98 | import numpy as np
def interpolant(t):
return t*t*t*(t*(t*6 - 15) + 10)
def interpolant1(t):
return t*t*(t*(t*6 - 15) + 10)
def interpolant2(t):
return t*(t*(t*6 - 15) + 10)
def generate_perlin_noise_2d(
shape, res, tileable=(False, False), interpolant=interpolant
):
"""Generate a 2D numpy a... |
580f188e28cce92fa7f46ba19f7b09c8a12fdfbfea3178def46faacf1c58a0e2 | Python | 3,746 | 128 | # _ _
# | | | |
# ___ __ _ __ _ ___| |_ ___ ___ | |___
# / __/ _` |/ _` / __| __/ _ \ / _ \| / __|
# | (_| (_| | (_| \__ \ || (_) | (_) | \__ \
# \___\__,_|\__,_|___/\__\___/ \___/|_|___/
'''
A Convergent Amino Acid Substitution identif... |
94702e1b70f5ec63d29e90098eacf867fd5f9a148d2d939d41bcaa60fc032f8d | Python | 3,750 | 104 | # 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.
from typing import Dict, List, Optional, Tuple
import torch.nn as nn
from fairseq import utils
from torch import Tensor
class FairseqDecode... |
c6678d23ea5aa6dfe3671af86dee491c9880f734e456974d7444c7e3665c9794 | Python | 3,750 | 93 | import unittest
from unittest.mock import patch
from pyecharts import options as opts
from pyecharts.charts import Radar
v1 = [(4300, 10000, 28000, 35000, 50000, 19000)]
v2 = [(5000, 14000, 28000, 31000, 42000, 21000)]
class TestRadarChart(unittest.TestCase):
@patch("pyecharts.render.engine.write_utf8_html_file... |
428f48234fc28509ce71afbdeb09eaaf0eea5df36a14161d0c07854bff002a1b | Python | 3,752 | 104 | import numpy as np
import pytest
import torch
import torch.nn as nn
from moove.utils.segment_utils import segment_ml
from moove.models.ConvMLP import ConvMLP
class AlwaysSyllableModel(nn.Module):
"""Mock model that always predicts syllable (logit > 0)."""
def forward(self, x):
return torch.tensor([[5.... |
427e7229c8b8689aa932251bd0541dd9ed8b3a7fbe9d40bfe7e1d766ccbdb6ce | Python | 3,754 | 105 | import pandas as pd
from os.path import join
from config_path import PROSTATE_DATA_PATH
processed_dir = 'processed'
data_dir = 'raw_data'
processed_dir = join(PROSTATE_DATA_PATH, processed_dir)
data_dir = join(PROSTATE_DATA_PATH, data_dir)
def prepare_design_matrix_crosstable():
print('preparing mutations ...')... |
07608d93b8df8de115992cd01e6b071555ecf63167f095cce363791c441c982f | Python | 3,755 | 102 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import warnings
from dataclasses import dataclass, field
from functools import cached_property
import numpy as np
from pymatgen.core import Structure
from pymatgen.entries.compatibility import Compatibility, MaterialsProject2020Compatibility
fro... |
65116912c1391de6b0f3464c71119f33e043591d5a3017ae708a8d7419602b7b | Python | 3,755 | 91 | import os
import pandas as pd
import numpy as np
from neuron import h
# Dictionary mapping current types to their corresponding NEURON attributes
current_types = {
'nax': '_ref_ina_nax',
'nad': '_ref_ina_nad',
'car': '_ref_ica_car',
'kdr': '_ref_ik_kdr',
'kap': '_ref_ik_kap',
... |
65b4a753726bfaf599ca9e389905d50cfca46609ba3493200c7a020fed47e96f | Python | 3,755 | 98 | from __future__ import annotations
from typing import TYPE_CHECKING
import torch
from torch import nn
if TYPE_CHECKING:
from collections.abc import Callable
def _partial_freeze_hook_factory(freeze: int) -> Callable[[torch.Tensor], torch.Tensor]:
"""Factory for a hook that freezes the first ``freeze`` entri... |
4d7511a22363de250629e649dbf1619c907aa80a0f2d4f47b2d91fb67df7ef5c | Python | 3,758 | 105 | """
Integration tests for file_management/file_loader.py.
Verifies that loading example CSV and Excel files produces the expected
DataFrames — correct shape, column names, selected column, and time detection.
"""
from pathlib import Path
import pandas as pd
import pytest
from src.file_management.file_loader import l... |
c76017a8477212ca3c97d31721adb02deb7f3edb213a77ae90069b49c332705b | Python | 3,759 | 62 | # -*- coding: utf-8 -*-
"""
Created on Mon Mar 18 16:44:50 2024
@author: Satoru Muro
"""
import pyautogui
import time
import tkinter as tk
from tkinter import simpledialog
from tkinter import messagebox
import keyboard # keyboardモジュールをインポート
def ungroup_selected_objects():
try:
pyautogui.... |
e25edde625eab6e73339685a986c3076d13e5e12c54deeeae83ff781f3da7ef7 | Python | 3,759 | 129 | import argparse
import pandas as pd
# Find the best orientation for index barcodes based on multiple % Undetermined reads results.
#
# Works around any issues with bcl-convert, RunInfo.xml, isReverseComplement, and barcode orientations which
# "can be wrong in some cases due to software bugs."[0]
#
# See:
# - [0] h... |
ec4530c547ded5dc3725114861edc8cb68195cc52c1ea5c7b87c969e7f8c2dd7 | Python | 3,759 | 96 | def run_seg_cmd(
input_srr,
cmd,
cfg,
singularity_path=None,
singularity_mount=None,
singularity_home=None,
):
"""
Run a segmentation command with the given input SRR.
Args:
input_srr (str or list): Path to the input SRR file or a list
contain... |
60e19795e8ce46e7576fbc6d91a6f7dcbba4419f9f66797b7150f3b9f1f1a30e | Python | 3,764 | 126 | __author__ = 'heroico'
import numpy
import logging
import math
NONE="none"
FROM_PHENO="from_pheno"
FROM_REFERENCE="from_reference"
def normalizationScheme(scheme, covariances=None, weight_db_logic=None):
n = None
if scheme == NONE:
n = NoNormalization()
elif scheme == FROM_PHENO:
n = _Bet... |
f9b2f3c27234963e611479ace7b956ecd2dbfda136cf3f79c92ab7f4be8e5554 | Python | 3,764 | 105 | #!/usr/bin/env python3
"""Gera todos os inputs da campanha: 1784 perovskitas + 9 atomos isolados.
Uso:
python3 gen_inputs.py # tudo
python3 gen_inputs.py --limit 8 # amostra, para teste local
python3 gen_inputs.py --only nome1,nome2
Saida:
inputs/<nome>.fdf um arquivo por est... |
a32da0c573a0ab0ba5636d92343cc4c46fb455105e77d8877a9571473a0ae019 | Python | 3,766 | 101 | from itertools import product
from typing import Any
import numpy as np
from torch.optim import Adam, SGD
from simulation_encoder.dataclass.config_schemas import (
HyperparameterDiscreteConfig,
HyperparameterRangeConfig,
)
def generate_hyperparameters(
continuous_params: HyperparameterRangeConfig, discr... |
aeca5afe20ed10974a0463e8f9ee964ed49072e103215a3e3fef66531b46d6ea | Python | 3,766 | 82 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# 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... |
7cd4d5a04d5ae9c860272fca7bb5e4c5f8d1c926912c2dcd578068c1041d69d1 | Python | 3,767 | 118 | # @license
# Copyright 2020 Google Inc.
# 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... |
e3e16eb37994565c19ed2bf063687745ebb2985c15f58ccd3c9bcfdfa309e588 | Python | 3,767 | 83 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# 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... |
1a63f99c586f056578ab343a9cbe4376cada39e0c9a036740d356ea216c82c03 | Python | 3,769 | 105 | # 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.
from dataclasses import dataclass
import math
from omegaconf import II
import torch
from fairseq import modules, utils
from fairseq.logging i... |
8aee9500118c7e04fe4909d2dc78a3d6e0ceba9dfb1624bb29fa28bfad77edf1 | Python | 3,769 | 124 | import tkinter as tk
from PIL import Image, ImageTk
import glob
import subprocess
import os
import sys
def saveICs (indices, path, f):
outfile = path + f
with open(outfile, 'w') as file:
for item in indices:
file.write("{},".format(item))
def handler (event):
if eve... |
c6ae032496caab83c0852156cd0f6bbbfe53846ffa51a21b2690e47fa20d2190 | Python | 3,769 | 126 | # extract 20% independent_test_set, do 5-fold split in remaining data
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from sklearn.model_selection import train_test_split
import os
from tqdm import tqdm
import random
from sklearn.model_selection import KFold
import argparse
import numpy as np
import csv
rand... |
eea8a3d016d85be9d537f8b0908c8303058771dbb28fb593bbbc559fb9e899d5 | Python | 3,770 | 96 | """A module you can import that does one thing: It makes Tensorflow shut up.
You can import this before you import tensorflow in your code, and some of the warning
messages will go away.
There is also a class (with context manager support) for capturing ALL stderr messages.
Use with caution since it can delete import... |
86c581782a607e5c138a8090bf122ebe9abf270ccd9de816e8ebf8bbdc7dbb98 | Python | 3,772 | 128 | import os
import subprocess
import glob
import shutil
from create_input_json import createInputJson
npx_directories = [r'N:\715093703_386129_20180627'
]
probe_type = '3A'
json_directory = r'C:\Users\svc_neuropix\Documents\json_files'
def copy_to_local(source, destination):
robocopy(source, destination)
... |
0b403e0186e6090a639066ee7734c274de88bd3fe5946c2bf6b21d3a22021348 | Python | 3,773 | 125 | import torch
from neurovfm.pipelines.encoder import EncoderPipeline
from neurovfm.systems.utils import NormalizationModule
class DummyEncoderModel(torch.nn.Module):
"""Minimal stand-in for VisionTransformer in encoder pipeline tests."""
def __init__(self, out_dim: int = 64):
super().__init__()
... |
9a2df716bd91d7eb1e1565aee7a3289c7afb32bcfe345368de4966a180d1fdb3 | Python | 3,773 | 90 | """Manages GO group headers and optionally sections containing GO group headers."""
import collections as cx
from goatools.gosubdag.go_tasks import chk_goids
__copyright__ = "Copyright (C) 2016-2017, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
class HdrgosSections(object):
"""M... |
ab3c06871874060c46a58819ef7d2d791ac1abaa2a632b0dbfd2b71fecbd4ea1 | Python | 3,773 | 113 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from collections import defaultdict
from contextlib import nullcontext
from typing import Callable, Dict, List, Type, Union
import pytest
import torch
from mattergen.diffusion.corruption.sde_lib import SDE, VESDE, VPSDE
from mattergen.diffusion... |
b9cd2fde1bddf7bae678a9c97e67c959bed430cf1eeff47e9c2135c429e90c76 | Python | 3,773 | 94 | #!/usr/bin/env -S uv run
# /// script
# requires-python = ">=3.11"
# ///
import os
import pathlib
SCRIPT_DIR = os.path.abspath(os.path.dirname(__file__))
# Based on example here: https://blog.yaakov.online/zip64-go-big-or-go-home/
CONTENT = (
(
# --- Local File Header ---
b"\x50\x4b\x03\x04" # L... |
5a550d3a41f567509149032612f583890a7aaace68007f0977a66e66f2a9f52c | Python | 3,774 | 109 | from torch.utils.data import DataLoader
import torch
from sklearn.model_selection import KFold
import lightning.pytorch as pl
from typing import Union, Optional
from pathlib import Path
from rinalmo.data.alphabet import Alphabet
from rinalmo.data.constants import *
from rinalmo.data.downstream.translation_efficienc... |
e51941730c62444e97379319150b093c9b7f4945444de66a4dec09a7571713d2 | Python | 3,774 | 122 | """
Adapted from https://github.com/neuroailab/TDANN/tree/main/spacetorch/losses
"""
import numpy as np
from scipy.spatial.distance import cdist, pdist, squareform
from scipy.stats import pearsonr
from spacestream.utils.array_utils import lower_tri
from spacestream.utils.swapopt_utils import precompute_neighborhoods
... |
b001de5619db65aaf376c5e5bfdfde69e275219e1a946cf83144b510d5cd59a6 | Python | 3,775 | 123 | import itertools
import joblib
import numpy as np
import pandas as pd
import os
import unittest
import tempfile
import pathlib
from numpy import testing
from sklearn import datasets, preprocessing
#from matplotlib import pyplot
from mentor import _cluster as cluster
from mentor import _datasets as datasets
from mento... |
cebb2a911ea31c213dfa2e74a2cc4ddeec2fdbada611c95892d339a80bd6f3ba | Python | 3,775 | 134 | """Culture-collection accession shape, gating what a StrainInfo match may join.
`fix_missing_strains.py` is the only caller. `apiadapters.straininfo.
StrainInfoAdapterBase.retrieve_strain_models` joins a record StrainInfo
returns to whichever BRENDA strain shares its *first* matching designation,
with no organism cons... |
e506a7d0923497021eb00b219332cb266849c97ac19c2836693c84fcff07b3e5 | Python | 3,775 | 125 | #!/usr/bin/env python3
# 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.
from __future__ import absolute_import, division, print_function, unicode_literals
import argparse
import concurrent.f... |
96731b0d2e09214e28e3d24dec937f07dde8e3af70e48c4008a84fa16f5fa404 | Python | 3,777 | 119 | import os
import pytest
from sklearn.ensemble import RandomForestRegressor
from pgmpy.ci_tests import GCM
from pgmpy.factors.continuous import LinearGaussianCPD
from pgmpy.models import LinearGaussianBayesianNetwork
@pytest.fixture
def df_indep():
model_indep = LinearGaussianBayesianNetwork(
[
... |
0f2660c4f8ff219e48290eac78b06c277d8798aa35019715b86670b9cebe5d83 | Python | 3,778 | 83 | #! /usr/bin/env python
import os
import logging
from timeit import default_timer as timer
import metax
from metax import Logging
from metax import Exceptions
from metax import Utilities
from metax.predixcan import PrediXcanAssociation as PA
from metax.predixcan import Utilities as PrediXcanUtilities
def run(args, p... |
78ed56598a92ceb8a625e9a24b5e5e1ad20b14e3bef950d6a33d59585589af61 | Python | 3,780 | 101 | import os
from copy import deepcopy
from os.path import dirname
import numpy as np
from model.builders.prostate_models import build_pnet2
base_dirname = dirname(dirname(__file__))
print (base_dirname)
filename = os.path.basename(__file__)
task = 'classification_binary'
selected_genes = 'tcga_prostate_expressed_gene... |
531c7715ae79e2a3bf134856a996dcd802f20b89d5f7024d02e08267db0c0269 | Python | 3,782 | 130 | #!/usr/bin/env python
# Copyright (c) Facebook, Inc. and its 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 argparse
import contextlib
import sys
from collections import Counter
from multiprocessing imp... |
6542a5de7466fb02d27dea07a14d1f0b0c7c5ffadfddc8bd9dab565a8f13ca3c | Python | 3,782 | 103 | import torch
import torch.nn as nn
from torch.utils.data import Dataset, DataLoader
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.metrics import roc_auc_score
import warnings
warnings.filterwarnings('ignore')
from .encode_structure import *
from .model import *
from .utils import *
def g... |
93e15244236eb7ae03d70a3615240012dd30b91483fc1b559b9a29879de5e75f | Python | 3,784 | 121 | from __future__ import annotations
from matplotlib import cbook
from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg, NavigationToolbar2QT
from matplotlib.figure import Figure
from PySide6.QtCore import QSize
from PySide6.QtGui import QIcon, QPixmap
from PySide6.QtWidgets import QVBoxLayout, QWidget
from s... |
a3b94506916c4dbf948a9270ca3c9bb117bab905786e14adc3e9559f015757f2 | Python | 3,784 | 115 | """Shared fixtures and helpers for the token-label test package.
The tokenizer is built in-process from an inline vocabulary, because the
assertions are about *offsets* and stubbing those would test the stub. Each
word becomes one token per character, which gives exact control over which
tokens cover which characters.... |
1d10c5c14013d16cec88bc97a7aa5b999ebd5837cc2d8f3db72f898d67bf1335 | Python | 3,785 | 105 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_mfm_test_desikan_main(gpu_index=0):
torch.cuda.set_device(gpu_inde... |
019c29ba9ccf824b14c49cb91622f1047cc5dc1077dcdc304f8e2577eda21d6e | Python | 3,786 | 108 | """Function that gets an instance of a model,
given its name and a configuration as a dict."""
from __future__ import annotations
import inspect
from typing import Callable
import lightning
from . import registry
def get(
name: str,
config: dict,
input_shape: tuple[int, int, int],
num_classes: int... |
1c56ae201ac8da1e485d7b1215e5d235eb48a75a8ae9e2f6ad7729c053695381 | Python | 3,786 | 135 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2020 Daisuke Matsuyoshi
# Released under the GNU AGPLv3
# https://opensource.org/licenses/AGPL-3.0
"""
API for DTI-NODDI
"""
__author__ = "Daisuke Matsuyoshi @dicemt"
import os
import os.path
import re
import numpy as np
import nibabel as nib
from dti_n... |
84bffc70fd17113bb99aaf1525467378799aad42876826cc4b7b86b2fabf081b | Python | 3,788 | 105 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_mfm_test_desikan_main(gpu_index=0):
torch.cuda.set_device(gpu_inde... |
94e26db0179da06d6d13dea279c284400e8def774c3d3e30e22e092e1de8835f | Python | 3,789 | 91 | """Collect GO paths."""
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import collections as cx
import sys
from itertools import tee
class GoPaths(object):
"""Class for helping traverse GO paths."""
adjdir = {
None: lambda go_... |
d16af9fa29e6612d112a5978d185d9fce2b27d11596a9cd9fb8ab935873a2d4c | Python | 3,789 | 108 | import matplotlib.pyplot as plt
import numpy as np
import igraph as ig
import networkx as nx
import os
import sys
from weighted_rc import weighted_rich_club
abspath = os.path.abspath(__file__)
dname = os.path.dirname(abspath)
os.chdir(dname)
sys.path.append('..\\src\\')
from read_graph import read_graph
datapath = ".... |
243c709c98243570481b1b1efd72c4af10659458d5a9b4059d8ce08f7b8794b5 | Python | 3,791 | 107 | import pandas as pd
from sklearn.model_selection import train_test_split
import torch
from torch.utils.data import DataLoader, Dataset
class PointDataset(Dataset):
"""Dataset for a single time point from sequence data"""
def __init__(self, sequences: dict, time_point_idx: int):
self.sequences = seque... |
ceb0a24eb210f8feabcd6931bd1a22c34d8654f190cd51304b5e25a0e2b05cc9 | Python | 3,792 | 112 | import os
import torch
import matplotlib.pyplot as plt
class Plotter:
"""Class for creating and saving plots"""
def __init__(self, results_dir: str = "results/", experiment_key: str = ""):
self.experiment_key = experiment_key
self.results_dir = results_dir
self.results_path = os.path... |
bcd8a11bb989886b8c5b75bce0d51987b8184a5a79b8bb7f3ec48f5e5627b128 | Python | 3,793 | 100 | # 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.
from fairseq import utils
from fairseq.criterions import LegacyFairseqCriterion, register_criterion
from torch import nn
@register_criterion... |
7c9ce550884d6ec5835adae73c83cd8ee4d19e092465a410d7b5346d21563921 | Python | 3,794 | 117 | # 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 os
from mmpt.utils import recursive_config
class BaseJob(object):
def __init__(self, yaml_file, dryrun=False):
self.yaml_... |
0c25d5540d93b0a9cf77478118c165253d7cd8686f9b2ebd0068c9d58a8c98f9 | Python | 3,795 | 89 | import functools
import torch
import torch.nn as nn
import torch.nn.functional as F
import math
class route_func(nn.Module):
r"""CondConv: Conditionally Parameterized Convolutions for Efficient Inference
https://papers.nips.cc/paper/8412-condconv-conditionally-parameterized-convolutions-for-efficient-inference... |
f54babac62d1f4fb700aefd41ad0a089ee0ee29a733246ee7b88a660534726fc | Python | 3,795 | 119 | from __future__ import annotations
from src.core.app_settings_manager import AppSettingsManager
def test_app_settings_manager_instantiates_without_gui_state():
manager = AppSettingsManager(app_type="telemetry_photom_opto")
assert manager.display_duration_box_var is True
assert manager.num_instances_box_... |
e971006214d0030dc50b8d6f648a02e74208f5c08449c66e9afb59b29eead340 | Python | 3,796 | 97 | # 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.
"""
Use this script in order to build symmetric alignments for your translation
dataset.
This script depends on fast_align and mosesdecoder too... |
eab44facc22fc0c211c7b2c02f1890546e5cd351f3028cd42e7ce2094e4ccf29 | Python | 3,796 | 105 | from copy import deepcopy
import numpy as np
def get_shape_must_be_divisible_by(net_numpool_per_axis):
return 2 ** np.array(net_numpool_per_axis)
def pad_shape(shape, must_be_divisible_by):
"""
pads shape so that it is divisible by must_be_divisible_by
:param shape:
:param must_be_divisible_by:
... |
6b8d5cc2df35a804d2a7d9eee45f8c18bb4734e6308e971e7c251f319d456ce8 | Python | 3,799 | 122 | # 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 os
import typing as tp
import unittest
from tempfile import TemporaryDirectory
from fairseq.binarizer import BinarizeSummary, FileBin... |
c4fac2f87ec1f1776d5f1df1308c0abe36769dd4a931e9486813240abb55d8f1 | Python | 3,800 | 116 | from os.path import join
import pandas as pd
from config_path import *
def get_reactome_pathway_names():
'''
:return: dataframe of pathway ids and names
'''
reactome_pathways_df = pd.read_csv(
join(REACTOM_PATHWAY_PATH, 'ReactomePathways.txt'), sep=' ',
header=None)
reactome_path... |
fd8be9d60f0218e219bc01a5e1c6465679595bb0bd3d19c7f338a1967bef1ec0 | Python | 3,802 | 99 | # 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 math
import torch
from torch.nn.modules.loss import _Loss
class LatentLayersKLLoss(_Loss):
def __init__(self, args):
sup... |
32522fd92910e9457aa5f54de0328bff1b8fca5b49d7a7069748ac9b1de205ce | Python | 3,803 | 81 | """Helper functions for loading pretrained gene embeddings."""
from pathlib import Path
from typing import Dict, Tuple
import torch
from scanpy import AnnData
import numpy as np
import pandas as pd
EMBEDDING_DIR = Path('model_files/protein_embeddings')
MODEL_TO_SPECIES_TO_GENE_EMBEDDING_PATH = {
'ESM2': {
... |
28fa7d4f4b10803473af35237450ba3fd9fdf510b207d00ef63bca0b03441acc | Python | 3,804 | 110 | import numpy as np
from .model_functions import SimpleModelCLFunction
from .parameters import CurrentObservationParam, CurrentModelSignalParam, NoiseStdFreeParameter
from mot.library_functions import log_bessi0, normal_logpdf
__author__ = 'Robbert Harms'
__date__ = "2014-08-05"
__license__ = "LGPL v3"
__maintainer__ ... |
ae9999784e7474342a47686538c46af0afaa817847fd6d5765094f340c640ea9 | Python | 3,808 | 129 | """Fetch the BRENDA data blobs from the Hugging Face Hub and verify them.
Both paths come from ``brenda_references.data_paths``, the one place that
decides where the blobs live, so the download lands exactly where every
reader looks for it. Resolving them here instead would put them in the
checkout while a non-editabl... |
3e00738f4d6356c412310df683bea67fcca9f74283ecaade98991d67a694bb4e | Python | 3,813 | 126 | #!/usr/bin/env python3
"""Generate a jobs.sh file for SLURM array job submission.
This is step 1 of the SLURM workflow for reproducing the SymmNet paper figure.
Each line of the output file contains one `python main_salnet.py ...` command,
one per dataset × algo × seed combination. Already-completed runs (those with a... |
63959137f48b9830ba33773686061d6f4f6274dc6398fcd9b2a9eb93034318fd | Python | 3,813 | 118 | # -*- coding: utf-8 -*-
"""
@Time:Created on 2019/5/20 20:49
@author: LiFan Chen
@Filename: main_glu.py
@Software: PyCharm
"""
import torch
import numpy as np
import random
import os
import time
from model_glu import *
import timeit
def load_tensor(file_name, dtype):
return [dtype(d).to(device) for d in np.load(f... |
82917a4ec805190ffc5937488355eaec67ee3fa1e8fb1495da3667d5f0e7fe0b | Python | 3,813 | 101 | # @license
# Copyright 2016 Google Inc.
# 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... |
c9af983eb726474c8445b6aae6753bb31288cf5ab6f4162063507156348e058d | Python | 3,814 | 119 | import numpy as np
graph_file = 'hcpl_graph.npz'
b0_file = 'hcpl_b0.nii.gz'
output_file = 'hcpl_odf.nii.gz'
import os
import scipy.ndimage as ndi
''' ----------------------------------------
Create graph or read from file if exists
----------------------------------------'''
if (os.path.isfi... |
de98ed06ffbd69d947e9fbf9db8b2f51ef893003b796ba7156eae90d62c97e3d | Python | 3,814 | 92 | # -*- coding: UTF-8 -*-
"""
@Project: iDCF
@File : main.py
@IDE : PyCharm
@Author : hjguo
@Date : 2025/7/9 11:35
@Doc : Main function. Add model interpretability analysis
"""
import os
import torch
import numpy as np
import pandas as pd
import random
from iDCF.utils import load_data, load_data_from_path, load... |
42846e8870343a56e984e91736d77e90c08b372ec6f5bf055b4c274b5b6fec4f | Python | 3,815 | 118 | #### ::: mutate seqs ::: ####
import os
import sys
sys.path.append('../motif')
import pandas as pd
import numpy as np
import argparse
import motif_utils as utils
def mutate(seq, start, end, target=None):
"""
Mutate input sequence at specified position.
If target is not None, returns the mutated seq.... |
8d92c927fab4e43a8c371855a98a2f1283a1cb63b7adbce6f273bfe041c6e12f | Python | 3,816 | 89 | import os
import json
import sys
def add_intended_for_field(base_dir, subject, session):
# Construct the subject and session identifiers
subject = f"sub-{subject}"
session = f"ses-{session}"
# Define the field map directory
fmap_dir = os.path.join(base_dir, subject, session, 'fmap')
# Define ... |
457ae2eb8c81a8c39edc4a85259253f9bffcfec89eea5cea6e920c129d09feff | Python | 3,817 | 111 | import numpy as np
import cv2
import time
import numba
from msi_visual.normalization import spatial_total_ion_count, total_ion_count, median_ion
class TOP3:
def __init__(self, low=99.9, norm_percentile=99.9):
self.low = low
self.norm_percentile = norm_percentile
def __repr__(self)... |
ea740852eab78a63ece13653decde45e754c154a8fed4237755f9bdcbe7fdec0 | Python | 3,818 | 97 | from kneed import KneeLocator
import pickle
from matplotlib import pyplot as plt
import numpy as np
highlight_rank = 3
with open("performance_metrics/objective_function.pkl", "rb") as f:
objective_function = pickle.load(f)
with open("performance_metrics/similarity_metric.pkl", "rb") as f:
similarity_metric =... |
306f7c3d8a122cdd2e44d4547185546844eb37063ec89d6b62f0d1c9d09f540b | Python | 3,819 | 112 | from os.path import join
import numpy as np
import pandas as pd
import seaborn as sns
from matplotlib import pyplot as plt, ticker
from config_path import PROSTATE_LOG_PATH
from setup import saving_dir
custom_rcParams = {
'figure.figsize': (8, 3),
'font.family': 'Arial',
'font.size': 14,
'font.weight... |
97fdcfc369a39e79f27e4ddb9dda042347f7bc1a50e083159668a5637ccac6bd | Python | 3,821 | 79 | """Load the three Paper-#2 FTIR datasets into the shared `SpectralDataset` interface.
Design choices (see spec §4–5):
- `y` = the AUTHENTIC fraction (main-food %), single target. This makes the existing detection
engine (`classification_from_tahini`, threshold scan) apply unchanged, and RMSE/R²/MAE/RPD are
numeric... |
ef8f61deb698c43cd816b44626896172861131653d3351a3d8ea368fa30c117d | Python | 3,821 | 117 | from __future__ import annotations
import dataclasses
from subprocess import CalledProcessError
from typing import TYPE_CHECKING
from typing import Literal
import pbs_installer as pbi
from poetry.core.constraints.version import Version
from poetry.config.config import Config
from poetry.console.exceptions import C... |
702a452e60274d9f88b59c9dcdac69f07e2d1f9841be49c4e5db93683c3cde98 | Python | 3,825 | 105 | import math
from itertools import combinations
import numpy as np
import pandas as pd
from scipy import stats
from tqdm import tqdm
from pgmpy.base import DAG
from pgmpy.ci_tests import get_ci_test
from pgmpy.global_vars import config
from pgmpy.metrics import BaseUnsupervisedMetric
class FisherC(BaseUnsupervisedMe... |
cf652c16e7dd8ef13f63b620acc8597daf5caffa52cf19ce669cff8b08307706 | Python | 3,827 | 89 | # Copyright 2021 DeepMind Technologies Limited
#
# 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 agr... |
9d5ff295cf8c0565bde01ad6a3ae438f8f8da49fd3298a255380bca4f2fbb8ae | Python | 3,829 | 120 | import pandas as pd
from scipy.spatial.distance import jensenshannon
import matplotlib
matplotlib.use("TkAgg")
def kmer_frequency_analysis(sequences, k=3):
def generate_kmers(seq, k):
return [seq[i:i + k] for i in range(len(seq) - k + 1)]
kmer_counts = {}
total_kmers = 0
for seq... |
e9943eb7bae83d2a460b5c639b27caf0f3b94ec84d0d1123e60059d25c8f287e | Python | 3,829 | 117 | """Configuration loader.
Single entry point for parameters (`config/params.yaml`) and data locations
(`config/paths.yaml`). Also the single source of the random seed, so every
stochastic step in the package is reproducible.
Usage
-----
>>> from musicnarr import get_params, get_paths, get_rng
>>> p = get_params()
>>> ... |
c3692aeece6f8e5323421940ba7d301cc563ef7cccfe0a227c08eb541cc7a717 | Python | 3,830 | 89 | import jax
import jax.numpy as jnp
import pytest
from oneqmc.geom import (
masked_pairwise_diffs,
masked_pairwise_distance,
masked_pairwise_self_distance,
)
@pytest.mark.parametrize("shape_x", [(10,), (10, 2)])
@pytest.mark.parametrize("shape_y", [(10,), (10, 4)])
def test_masked_pairwise_distance(shape_... |
4c22674d06d6db29a0e18ba297e1bf1ab01d3e18a557f77c20783cbd0f565961 | Python | 3,831 | 130 | import re
import logging
import os
import io
import gzip
import pandas
from . import Expression
from ..misc import Math
########################################################################################################################
class ExpressionManager(Expression.ExpressionManager):
def __init__(self,... |
b02a5d65e716d3c453537ee3b705c225416ceaa5d5c2b708074b191a91b1eac7 | Python | 3,832 | 119 | #!/usr/bin/env python
from __future__ import annotations
import argparse
import subprocess
import sys
from pathlib import Path
from typing import List, Optional
ROOT = Path(__file__).resolve().parent
PYTHON = sys.executable
def run_script(script: str, extra: Optional[List[str]] = None) -> None:
command = [PYTHO... |
02e2c82613e4aa810295e8b0940605231b7ff6c7b8e34fb2bf1245882f6225eb | Python | 3,833 | 93 | from copy import deepcopy
import numpy as np
def merge(dict1, dict2):
keys = np.unique(list(dict1.keys()) + list(dict2.keys()))
keys = np.unique(keys)
res = {}
for k in keys:
all_configs = []
if dict1.get(k) is not None:
all_configs += list(dict1[k])
if dict2.get(k)... |
3ae101f427bd8d321d040f5de00501d8edd8534758e6b153dfbdfef7d0e65b76 | Python | 3,834 | 117 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Reads nd2 images and extracts layers of interest"""
from pprint import pprint
from PIL import Image
import numpy as np
import nd2
from nd2.structures import Volume
from utils.types import MetaLike_ND2
def _process_volume(vol: Volume) -> dict:
"""Processs volume... |
6ff7659ffdf7bb8fbb9d944d613345563c78eafa84870b5691bc344be620dd3c | Python | 3,834 | 90 | import os
import textwrap
import yaml
import argparse
from parcellate.cfg import *
from parcellate.data import purge_bad_nii
from parcellate.util import CFG_FILENAME, join
from parcellate.model import parcellate
if __name__ == '__main__':
argparser = argparse.ArgumentParser('Compute a subject-specific brain parce... |
60d3b1d0a0eecd8acb129f5b99ca7b10b79960316fd1c73b0b329384d1355895 | Python | 3,836 | 78 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2024 Broad Institute
#
# 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 u... |
991ac42204ee777050376aee973af3b9f245c9c7e4dfd928b722544f08feeb2f | Python | 3,839 | 60 | """Canonical medical sources for SegCT/MRI, independent of the input format."""
from pathlib import Path
import nibabel as nib
import numpy as np
import pydicom
from pydicom.pixels import apply_modality_lut
from instant3d_bridge import Instant3DBridgeError, nifti_fingerprint
from volume_geometry import dicom_datasets... |
221fa1bebb0e1a0b8ded4008cff896c12e7c8d8b05c2252cefc18ea1ad0854e3 | Python | 3,840 | 82 | """Extract pinned Microsoft x64 redistributables without installing them.
Input: https://aka.ms/vs/18/release/14.50.35719/VC_redist.x64.exe
The installer also contains ARM64 payloads. Select only the amd64 minimum CAB.
Never collect runtime DLLs from this build machine's System32 directory.
"""
from __future__ import ... |
23642758067ec1ba4ea44bb0182c283fde2bf37baee0c0065141f7c6f8e925c4 | Python | 3,843 | 77 | from dynamic_network_architectures.architectures.unet import PlainConvUNet, ResidualEncoderUNet
from dynamic_network_architectures.building_blocks.helper import get_matching_instancenorm, convert_dim_to_conv_op
from dynamic_network_architectures.initialization.weight_init import init_last_bn_before_add_to_0
from nnunet... |
7e519a60e302c1937b6b01e59ea27f77aa7f8be7563c3a99edf7ae4522508b39 | Python | 3,846 | 109 | #!/usr/bin/env python
"""
This script will query a SMRTLink instance based on a provided set
of credentials, and pull a variety of run metrics for longitudinal
tracking. Notably, if an output file of the same name exists, it
will filter results by existing metrics to enable it to run quickly
as new runs are introduced... |
d66be30e831248c94d289317998c4223a840fe68281071fc03e76d6d5f669cfd | Python | 3,846 | 90 | import torch
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
class nnUNetTrainer_5epochs(nnUNetTrainer):
def __init__(self, plans: dict, configuration: str, fold: int, dataset_json: dict,
device: torch.device = torch.device('cuda')):
"""used for debugging plans et... |
99fa4a8b12375f9da7623dcb959731ff80d54009e37a81ace4ad58c54eba3cba | Python | 3,850 | 89 | import sys
import types
import unittest
import numpy as np
if 'parmed' not in sys.modules:
parmed = types.ModuleType('parmed')
parmed.__version__ = 'stub'
sys.modules['parmed'] = parmed
from GMXMMPBSA.amber_outputs import DecompOut
from GMXMMPBSA.output_file import _combine_entropy
from GMXMMPBSA.utils i... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.