sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cd589c1017043ffaaa38244461cfe8cf915054e70c00fa3ce6bb26b333701ca2 | Python | 8,926 | 213 | import os
import sys
import numpy as np
import scipy.sparse as sp
import pandas as pd
import torch
import snf
from sklearn.neighbors import kneighbors_graph
from utils import sparse_mx_to_torch_sparse_tensor, normalize, encode_onehot, prepare_data, diffusion_fun_improved_ppmi_dynamic_sparsity
from runR2 import... |
6c90245ad78533d7224281b38e7389de3d0ead09d29a3d5eba2f6c748259f055 | Python | 8,934 | 216 | import unittest
from datetime import datetime
import os.path
import numpy as np
from dateutil.tz import tzlocal, tzoffset
import numpy.testing as npt
import h5py
from pynwb import get_manager, NWBFile, TimeSeries
from pynwb.ecephys import ElectricalSeries, Clustering
from pynwb.ophys import OpticalChannel, TwoPhotonSe... |
95e4630ca468b83efeaae2f49888b9a18b6a37ae49643192b98f81b7bdecc8a2 | Python | 8,935 | 212 | """
Copyright (c) Meta Platforms, Inc. and 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 annotations
import bisect
from typing import TypeVar
import numpy as np
from omegaconf import DictConfig, OmegaCon... |
a1b091adcbfe26cb0e22c07c2a558d1e08701ad36636eb06ea349ba6f8cd11b5 | Python | 8,937 | 277 | # %%
# making new target data for a simple sensitivity analysis.
import SSN_model_funcs as ssn
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
# import matplotlib.patches as patches
import seaborn as sns
from importlib import reload
from scipy.signal import butter, lfilter
from scipy.ndimage impo... |
b33768fa7f2875615b4dcb281639b3d96109413bb9c259d2323f868dc59fc851 | Python | 8,939 | 207 | from torch.nn import Conv2d, Linear, BatchNorm2d
from torch import where, rand, topk, long, empty, zeros, no_grad, tensor
from math import sqrt
import torch
import sys
from torch.nn.init import calculate_gain
def get_layer_bound(layer, init, gain):
if isinstance(layer, Conv2d):
return sqrt(1 / (layer.in_c... |
e5c310fa6bc41dbf1ac2980aa83bb41a747bc076a1e87166767fc31eeef98e74 | Python | 8,939 | 268 | import numpy as np
import pytest
from datamate import set_root_context
from flyvis.datasets.sintel import MultiTaskSintel, RenderedSintel, sintel_meta
def test_rendering(mock_sintel_data, tmp_path_factory):
"""Test rendering with mocked Sintel data."""
with set_root_context(tmp_path_factory.mktemp("tmp")):
... |
e623a65c9a4896362f369af893263ebcc81e8fa58db3bd54a0585a04951d5bd6 | Python | 8,939 | 226 | import numpy as np
import brian2
#brian2.BrianLogger.log_level_debug()
import spinnaker2.neuron_models
import copy
# Leaky integrate and fire model
eqs_lif = '''
dv/dt = -v / tau + i_offset/dt: 1
v_th : 1
i_offset : 1
v_reset : 1
tau : second
'''
eqs_lif_curr_exp = '''
dI_syn_exc/dt = -I_syn_exc/tau_exc : 1
dI_syn_i... |
032f5eee234216a186f9efe5b29f959646a3f002549b61d88f9070a31db1fc0a | Python | 8,942 | 243 | from __future__ import annotations
from typing import Tuple, Optional, Sequence, Literal
import numpy as np
import scanpy as sc
from anndata import AnnData
import squidpy as sq
import pandas as pd
from ..preprocessing import FlowSigConfig
def _make_flow_adata(
adata: AnnData,
config: FlowSigConfig,
var_mas... |
2eef8017634edcc78ae5fbeff59cd191b40d5910731aef1bdd02dd9e2cebbd7c | Python | 8,947 | 260 | """KEGG data collector."""
import logging
from typing import Any, Dict, List, Optional
from src.api.kegg import KEGGClient
from src.models.pathway import Pathway
from src.models.genomic import Gene
from src.models.protein import Protein
from .base import BaseCollector
from config.config import settings
logger = log... |
554a7e6b1cdbad035de08c773fc55ecbdecce258b3733139c830bd329a0b809e | Python | 8,948 | 269 | """
Data structures for validation results.
This module defines the data structures used throughout the DataStateInspector
system to represent validation results, data checks, and suggestions.
"""
from dataclasses import dataclass, field
from datetime import datetime
from typing import List, Dict, Optional, Any, Lite... |
26da82525867360975bcc3457936740e7ab65cf06bb2dc45ff0044f5b5b686c2 | Python | 8,950 | 207 | # -*- coding: utf-8 -*-
"""
# # SCRIPT: THE FUNCTIONS OF IDENTIFYING REPLAY AND REACTIVATION IN TASK AND REST
# # PROJECT: FMRIREPLAY
# # WRITTEN BY QI HUANG 2022
# # CONTACT: STATE KEY LABORATORY OF COGNITIVE NEUROSCIENCE AND LEARNING, BEIJING NORMAL UNIVERSITY
"""
# get the number of scans of task for each run:
def... |
3745880e4c6ddd86837e19d3cbc060f396546922a0594c1de000ad5603449b28 | Python | 8,955 | 202 | # -*- coding: utf-8 -*-
# @Time :2024/6/6 9:56
# @Author :MENGLong Li
# @File :AbaqusModelCreate.py
# @Software:PyCharm
# from abqpy import *
import numpy as np
from abaqus import *
from abaqusConstants import *
from scipy.spatial import KDTree
import os
def output1(name, Location, element):
with open("%s... |
8a367dd4fb9e97cde0e5a0850a1b94fe6b11ba0bcd269c48cb45a39099e05efd | Python | 8,955 | 222 |
import torch
import torch.nn as nn
import math
# Function to initialize weights for convolutional and linear layers
def weights_init(m):
if isinstance(m, nn.Conv2d):
m.weight.data.normal_(
0, math.sqrt(2.0 / (m.kernel_size[0] * m.kernel_size[1] * m.out_channels))
)
if m.bias is... |
5d6b169698915621f4df3d45ff9a156729aa7b6027a4148dc49408747b00d77f | Python | 8,957 | 225 | import os
import numpy as np
import pandas as pd
import pickle
from matplotlib import pyplot as plt
import seaborn as sns
import statsmodels.api as sm
import pingouin as pg
from pcntoolkit.normative import estimate, predict, evaluate
from pcntoolkit.util.utils import compute_MSLL, create_design_matrix, calibration_des... |
de32f05db3d8260c9efd6968dcc1d51f07b6da38300795876081a24d43072fb1 | Python | 8,959 | 197 | # -*- coding: utf-8 -*-
"""
@author: Valeria Fascianelli
"""
import pickle
import numpy as np
import matplotlib.pyplot as plt
import random
from sklearn.preprocessing import PolynomialFeatures
import scipy.special
import statsmodels.api as sm
def get_multi_linear(correct_trials,rt,conditions):
number_cor... |
74b41c09e4aa56544c26aee81bc64669fc8ab5c97e34b2a4c00855016d258455 | Python | 8,961 | 244 | # coding=utf-8
# Copyright 2023 HuggingFace 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 ag... |
eaf8b334fcb199098bcc4634b13df2854be669bdc724421f8382b4f566cf35a6 | Python | 8,961 | 181 | import numpy as np
import pytest
import copy
import warnings
import re
def matching_import(pattern, module, globals):
"""
Imports only elements from a module that match the given regular expression
(credit: https://stackoverflow.com/a/17226922)
:param pattern: regular expression that describes the des... |
08e414c450ad5b4a473a90d16b2373b352d1bd6df4bcc798594d9c6254e9eb95 | Python | 8,962 | 288 | #!usr/bin/python
"""Rank genes on the precomputed integrated trajectory."""
# --------------------------------------------------------------
# Compute an integrated UMAP across all neuron subtypes:
# Updated: 03/01/22
# --------------------------------------------------------------
import re
import logging
from time im... |
1ecfe294fc88649a49fb5b0b96c270fecff9177d42454d6b3fbb1b5711275db8 | Python | 8,964 | 298 | import keras
from keras.utils.np_utils import to_categorical # used for converting labels to one-hot-encoding
from keras.models import Sequential
from keras.layers import Dense, Dropout, Flatten, Conv2D, MaxPool2D, BatchNormalization
from sklearn.model_selection import train_test_split
from scipy import stats
from skle... |
56271a187cbc9b643b28117fd65b4032b36a8324ceb444d6bcb5ed22af1f6930 | Python | 8,966 | 210 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
c69b24415c1da459b1950881af2fe26ac9c8e3f8fa018ba0ae32edb47b3b54e4 | Python | 8,973 | 267 | """HexScatter animation."""
from typing import List, Optional, Tuple, Union
import numpy as np
from matplotlib import colormaps as cm
from matplotlib.axes import Axes
from matplotlib.colors import Colormap
from matplotlib.figure import Figure
from flyvis import utils
from ..visualization import plots, plt_utils
fro... |
63a7ad4c05f0e3e93ec8d2a34d0d7d7930fa8d6f60479465cdcb719add87a08e | Python | 8,974 | 210 | from typing import List
import torch
def _movie_spatial_stimulus_contrib_gensig(spat_filt_w: torch.Tensor,
time_filt_applied: torch.Tensor) -> torch.Tensor:
'''
:param spat_filt_w: shape (1, n_basis_stim_spat)
:param multimovie_filtered_list: shape (n_basis_sti... |
b47060714f7b074dfa9f82602454f2f42859214374730781af4dd8ce5c94ef69 | Python | 8,978 | 273 | # type: ignore
# pylint: disable-all
# -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://w... |
628b0181a4e4a2a07d18aefe1eeb8a88a0b95ab109b792c0be2666c2eca90cb5 | Python | 8,982 | 306 | import copy
import json
import logging
import os
from typing import Any, Dict
import yaml
from ray.autoscaler._private.loader import load_function_or_class
logger = logging.getLogger(__name__)
# For caching provider instantiations across API calls of one python session
_provider_instances = {}
# Minimal config for... |
74810cfd794b97264acfc6ad89d6a06b31e25fd517e30945b05fce7a2c504c0a | Python | 8,982 | 330 | """This is the script for `ray microbenchmark`."""
import asyncio
import logging
import multiprocessing
import numpy as np
import ray
from ray._private.ray_client_microbenchmark import main as client_microbenchmark_main
from ray._private.ray_microbenchmark_helpers import timeit
logger = logging.getLogger(__name__)
... |
69a278520cabfae0b8af74703246b065b7c6935f91c31a958c723de0b9410413 | Python | 8,984 | 212 | import tempfile
import torch
from diffusers import (
DEISMultistepScheduler,
DPMSolverMultistepScheduler,
DPMSolverSinglestepScheduler,
UniPCMultistepScheduler,
)
from .test_schedulers import SchedulerCommonTest
class DPMSolverSinglestepSchedulerTest(SchedulerCommonTest):
scheduler_classes = (D... |
59bc5463f02045b8175e15cd85f0c0423341fccdffad450741f21950f765c251 | Python | 8,990 | 173 | #!/usr/bin/env python2.7
# tool_versions.py v1.1 Creates "SW" versions json string for a particular DX applet.
# Write request to stdout and verbose info to stderr. This allows easy use in dx app scripts.
import sys
import argparse
import json
import commands
# APP_TOOLS is a dict keyed by ap... |
96314c6d127df416bb0433b2f10752b92c8f6b07f5f34e25010f66278ff917f4 | Python | 8,991 | 241 | #!/usr/bin/python
"""Class for handling correlations in scdemon."""
# --------------------------------------------
# Class for handling correlations in scdemon:
# Updated: 07/02/21
# --------------------------------------------
from .utils_correlation import (
calculate_correlation,
calculate_correlation_estima... |
efed44b81ce89d986d9870589096b9bbdb577eb5afcc0336b3df3c710784f501 | Python | 8,992 | 317 | import argparse
import os
import shutil
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from PIL import Image
from torch.autograd import Variable
from torchvision import transforms
import cv2
import time
import argparse
from scipy.io import loadmat
from torch.nn import functional as F
... |
59855255a2a8c0cbfa2abfe77c8413797ba58458d2e52daf30130c550a4b2ea2 | Python | 8,993 | 254 | import functools
import numpy as np
from scipy.ndimage import uniform_filter
from skimage._shared import utils
from skimage._shared.filters import gaussian
from skimage._shared.utils import (
_supported_float_type, check_shape_equality, warn)
from skimage.util.arraycrop import crop
from skimage.util.dtype imp... |
1cc85e23c503f0c8dcf397420d0a86db2415a773002dbf4ddc0610961fc569f5 | Python | 8,994 | 249 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import glob
import json
import os.path as osp
import shutil
import subprocess
import torch
from mmengine.config import Config
from mmengine.fileio import dump
from mmengine.utils import mkdir_or_exist, scandir
def process_checkpoint(in_file, out_file):
... |
9c7804c432b00d5d77e905836844e7baf0eebb50d9c7cb42fa93f37107c47018 | Python | 8,994 | 320 | import argparse
import os
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from PIL import Image
from torch.autograd import Variable
from torchvision import transforms
import cv2
import time
import argparse
from torch.nn import functional as F
import csv
from DM import DMData
from... |
d217f2145a75e2fbc002882d4e8eaf8e87cad712be00833e0a60c3390b0f25ea | Python | 8,995 | 200 | import sys
from typing import TYPE_CHECKING, Iterable, List, Optional, Union
from ray.data._internal.object_extensions.arrow import raise_on_pickle_object_columns
from ray.data._internal.tensor_extensions.arrow import pyarrow_table_from_pydict
from ray.data._internal.util import _check_pyarrow_version
from ray.data.bl... |
2faa2f7a6acd350840022e074f8aff68be22ba3598bb1869ff9a1f79eafe8e5a | Python | 8,999 | 273 |
import numpy
import os
import yaml
import copy
import sklearn
import h5py
import shutil
import time
from matplotlib import pyplot
from scipy.spatial import distance
from collections import defaultdict
from tqdm.auto import tqdm, trange
BOUNDS = {
"Resolution" : {
"min" : -numpy.inf,
"max" : 140.,... |
ec511669b71063192995cc02edfdc36e16485598b7daabf463449b581ac04e61 | Python | 9,000 | 294 | import socket
import struct
import numpy as np
import pdb
import time
from tqdm import *
import matplotlib.pyplot as plt
from power_readout import *
import scipy.io
from scipy.optimize import fsolve
from awg import *
from channnel_shift import ChannelShifter
import pyautogui
import torch
def isnan(input... |
f499d68a77400864fa81ffed8ecb5f64c4f9d20925f0cc83d2cb4c0396cf4ab9 | Python | 9,009 | 261 | import warnings
warnings.filterwarnings("ignore")
import argparse
import json
# import matplotlib
# import matplotlib.pyplot as plt
import math
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
from torch import cuda
import sys, os
import random
import numpy as np
from sklea... |
6110a00b19c6d677543d5e6a59aef9ba7c7bc8459c46e1ccb095a5840ab89d55 | Python | 9,012 | 264 | ####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free softw... |
91b2eb3cddef4b7d2f981c46367997c9fffc832f3a5fa3379e741cd3e0aff891 | Python | 9,012 | 331 | import datetime
import numpy as np
import pandas as pd
import pytest
from visions.test.utils import (
contains,
convert,
get_contains_cases,
get_convert_cases,
get_inference_cases,
infers,
)
from data_profiling.config import Settings
from data_profiling.model.typeset import Prof... |
f8dc7e34c460cb49b3c40d457e09a3ef1627c9b796745110ba38ed204aa6d725 | Python | 9,013 | 195 | """
analysis/processing.py: part of expfactory package
functions for automatically cleaning and manipulating experiments by operating
on an expanalysis Result.data dataframe
"""
import pandas
import numpy
def drop_null_cols(df):
null_cols = df.columns[pandas.isnull(df).sum()==len(df)]
df.drop(null_cols,ax... |
5141e1944080d1eafccbd4cb2f47cc525a2301832ef5c07396274810b39762ce | Python | 9,015 | 314 | # Copyright 2021 Google Research. 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 applicable law... |
30f23dc8a05dd4ea81452c4eee88ca39f6468d831d5340f61b6ac8704ff322f6 | Python | 9,020 | 246 | import numpy as np
import pandas as pd
from anndata import AnnData
from typing import Union, Sequence
def get_top_nmf_genes(adata: AnnData,
gems: Union[str, Sequence[str]],
n_genes: int,
gene_type: str = 'all',
model_organism: str ... |
5f76d848283c55a21ea221345bc76d48cb1a488dde381637a4dea5a0651c53d4 | Python | 9,022 | 259 | import numpy as np
class PEKNNCRP():
'''a prediction error based 1NN
if PE is high, it make a decision between
- assigns new input to the cloest exisiting cluster
- or create a new cluster
else, it assigns new input to the previous cluster
use PEKNN to compute likelihood and combine w... |
cdb43c43fc58a2e1f1a8e43dd8dd8f682aee0d5d348d7265c473f5ced0445d91 | Python | 9,024 | 246 | import numpy as np
import pandas as pd
import scanpy as sc
from typing import Union, Sequence
def get_top_nmf_genes(adata: sc.AnnData,
gems: Union[str, Sequence[str]],
n_genes: int,
gene_type: str = 'all',
model_organism: str = 'hu... |
efb936a935dd88d1780aaeab183bd4b88c0bfde34da52b4598ab68e173712458 | Python | 9,027 | 237 | import asyncio
import logging
import os
import time
from collections import OrderedDict, defaultdict
from concurrent.futures import ThreadPoolExecutor
from datetime import datetime
from itertools import islice
from typing import Dict, List, Union
import aiohttp.web
import ray
import ray.dashboard.optional_utils as da... |
b25cd445b1b5123598c84563f20b0c96c809f74af1330690cff7150ff21e4e21 | Python | 9,038 | 207 | import pathlib
path = pathlib.Path.cwd()
if path.stem == 'tmb_survival':
cwd = path
else:
cwd = list(path.parents)[::-1][path.parts.index('tmb_survival')]
import sys
sys.path.append(str(cwd))
import numpy as np
from lifelines import CoxPHFitter
import pandas as pd
import pickle
from model import utils
from matp... |
de45385057b1081c3d4bf9933bde66d727046435016cde0e31c03803ae85b142 | Python | 9,038 | 245 | """HiveServer2 connection, schema, and row conversion helpers."""
import re
from contextlib import suppress
from typing import Any, Callable, Iterator, List, Optional, Tuple
import pyarrow as pa
from ray.data._internal.datasource_v2.formats.hive.hive_contract import (
HiveReadSpec,
)
_FETCH_ROWS = 1024
_DECIMAL... |
476cf35b8ef8bc17328f8feba90b41945c87b072118b366f0ba383935f3a1717 | Python | 9,039 | 278 | import numpy as np
import matplotlib.pyplot as plt
from .utils.tf import K, IS_TF_1, tf
if IS_TF_1:
from skimage.measure import compare_psnr, compare_ssim
else:
from skimage.metrics import structural_similarity as compare_ssim
from skimage.metrics import peak_signal_noise_ratio as compare_psnr
d... |
7a5c3b8753db9db0022b85d1f5ab1027c9b3a800966f862747fc62c4ffb340c9 | Python | 9,040 | 196 | import os
import neuron_morphology.swc_io as swc
from neuron_morphology.morphology import Morphology
from neuron_morphology.marker import Marker
from neuron_morphology.constants import *
test_pia_transform = {
"id": 611512262,
"tvr_00": -0.984586262715884,
"tvr_01": 0.174899660580482,
"tvr_02": 0.0,
... |
4bd572ad4a224b67852cdec743f8f6a22fe0ebfee836ae728f93861a35fabeac | Python | 9,042 | 238 | # Crystal structures are saved in 'mp-####.cif' files;
# Other properties are saved in 'mp-####.pickle' files;
import functools
import warnings
from abc import ABC, abstractmethod
from pathlib import Path
from typing import List
import io
import torch
import pickle
import ase
import numpy as np
from torch import tenso... |
95b381de78b076080101197429dc498a149819819c7ecf609affc3e48d05255c | Python | 9,042 | 211 | import pathlib
path = pathlib.Path.cwd()
if path.stem == 'tmb_survival':
cwd = path
else:
cwd = list(path.parents)[::-1][path.parts.index('tmb_survival')]
import sys
sys.path.append(str(cwd))
from matplotlib import pyplot as plt
import numpy as np
from tqdm import tqdm
import concurrent.futures
from model impor... |
830eeb03d8a1dd8599b12be1f95ff5c64d5c7c9021e3a9e1de94ff3216bb68a9 | Python | 9,044 | 219 | """Diagnostics for a stalled dashboard-agent asyncio event loop.
The dashboard agent runs a single asyncio loop that serves metric ingestion,
event aggregation, and the ``POST /api/jobs/`` submit handler, so a stall in
that loop hangs job submission while the dashboard head stays healthy on its
own loop.
``EventLoopM... |
886af50b89b8b9f93894888c8b09bec4f3f9978c6a2fda6432395f14b26598fc | Python | 9,049 | 273 | """Function to plot cell-type annotation."""
from __future__ import annotations
import os
import matplotlib.backends.backend_pdf
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from sklearn.metrics import confusion_matrix
def _sample_report(adata, cell_type_key, score_ke... |
cb4aff0ba1c79d48e42ceaffe07bd202b755cffe8892a5658353dedf7f400812 | Python | 9,056 | 297 | # -*- coding: utf-8 -*-
"""
Created on Mon Jan 22 13:47:12 2024
@author: Leyang Xue
"""
import sys
import matplotlib.pyplot as plt
import numpy as np
from collections import Counter
# Add package path
packagepath = '../kcorePercolation' # Manually specify the path to your script
sys.path.append(packagepath)
from ut... |
4099be764baa565be65c1adc53e419d40482132c0cbd58c8dd3d53565fe1bb43 | Python | 9,058 | 230 | import warnings
from typing import Dict, List, Tuple, Union
import torch
from mmengine.model import BaseModel
from torch import Tensor
from lqit.common.structures import DataSample, OptSampleList, SampleList
from lqit.edit.structures import BatchPixelData
from lqit.registry import MODELS
from lqit.utils import OptMul... |
7906fe50fdc58db20e09acd90ab80559b7dbcf1ce3d0952a44a7aa313fc0d841 | Python | 9,065 | 124 | import os
import argparse
import easygrid
# Stages
MAKE_TEMPLATE_FILES = 'make_template_files'
TRAIN_MODELS = 'train_models'
SCORE_SUMSTATS = 'score_sumstats'
GATHER_SUMSTATS = 'gather_sumstats'
if __name__ == '__main__':
parser = argparse.ArgumentParser('Script to generate LD score regression scores and plot res... |
9956c3aa3ef9d0c54adeec3e3099a38b3ea30ac1c6f0e2319e473810d8b97efc | Python | 9,065 | 227 | # built-in dependencies
import os
from typing import Any, Dict, List, Optional, Union
import zipfile
import bz2
# 3rd party dependencies
import gdown
import requests # type: ignore[import-untyped]
# project dependencies
from deepface.commons import folder_utils
from deepface.commons.logger import Logger
from deepfac... |
194e6e7826101db463600f90bfda1e270eeb06eaf067ef01b2caf0787c5689ae | Python | 9,068 | 173 | import logging
from datetime import datetime
from transformers import BertForSequenceClassification
from agent.data.entities.config import DEV_LABEL, TEST_LABEL, EXTERNAL_LABEL, CTT3_LABEL, CTT3FR_LABEL, CTT3SIM_LABEL, CTT3HEALTH_LABEL
from agent.classifiers.transformer_classifier import transformer_classifier
from a... |
5fff34447d4e0e857a1a0200ef0eb1f6c040c3618bc2fee2bfc068134a22ee83 | Python | 9,068 | 213 | import numpy as np
from packaging.version import Version
from dipy.data import get_sphere, HemiSphere
from dipy.reconst.shm import real_sym_sh_mrtrix
from dipy.utils.optpkg import optional_package
from dipy.reconst.shm import sph_harm_ind_list
cvxpy, have_cvxpy, _ = optional_package("cvxpy")
sphere = get_sphere('symmet... |
52579bf2b1930efa6b6e09855f9cbbe33cc80be2c9cd23f077076066863c414d | Python | 9,070 | 235 | """Anthropic Messages API adapter helpers for OmicVerseLLMBackend.
Internal module — import from ``omicverse.utils.agent_backend`` instead.
"""
from __future__ import annotations
import json
import logging
from typing import Any, Dict, List, Optional
from .agent_backend_common import (
Usage,
ToolCall,
C... |
00799fae9090d97d513a891355dc1b1856a5b2808f8dafd16ce1382b5f9b009e | Python | 9,075 | 273 | # __worker_def_start__
import tempfile
from typing import Dict, Any
from starlette.requests import Request
from starlette.responses import StreamingResponse
import torch
from transformers import TextStreamer
import ray
from ray import serve
from ray.util.queue import Queue
from ray.runtime_env import RuntimeEnv
@ra... |
2613fa12226346eb5e7b5ce112260a5cfb7d751ad63623e9892fa1480cbd6703 | Python | 9,082 | 292 | """
This is the code for global-local transformer for brain age estimation
@email: heshengxgd@gmail.com
"""
import torch
import torch.nn as nn
import copy
import math
class convBlock(nn.Module):
def __init__(self,inplace,outplace,kernel_size=3,padding=1):
super().__init__()
self.relu =... |
5e5be219b0dc2e1ee1136f04316b264f5c38eb217cdcfba9ee8506f43626a3d1 | Python | 9,088 | 204 | from suite2p.extraction import dcnv
import numpy as np
import matplotlib.pyplot as plt
from sklearn.decomposition import PCA
from matplotlib import use
use('qt5agg')
import core.util as cu
#%% Param settings
# Spike detection parameter
ca_tau = 0.5 # Replace with the real tau time of your calcium indi... |
42af6c576597e6366ab306f0b51c470b44d3f27ef8155fe2f31fdfbefe8d6a64 | Python | 9,090 | 255 | # Vendored from `decoupler` (https://github.com/scverse/decoupler) by
# omicverse for in-tree GPU acceleration work. Original copyright by
# the decoupler authors, redistributed under decoupler's GPL-3.0
# license. Cross-module imports rewritten from `decoupler.*` to
# `omicverse.es.*` (see scripts/vendor_decoupler.py)... |
0cb3b685c2d7add8d0cb2376d2021ace6d551591a2a31bfbd44a0281efe187c7 | Python | 9,092 | 224 | ''' Scoring functions between a reference annotation (ground-truth) and hypotheses (e.g. ML output).
'''
__author__ = "Jonathan Dan, Una Pale"
__email__ = "jonathan.dan at epfl.ch"
import numpy as np
from .annotations import Annotation
class Scoring:
"""" Base class for different scoring methods. The class pro... |
8eef8d895b01cc4d4a8a2221fc7ef64064ca7221606082f08f9e57303ed0b206 | Python | 9,095 | 216 | import numpy as np
import pkg_resources
from os.path import join
from packaging.version import Version
from dipy.data import get_sphere, HemiSphere
from dipy.reconst.shm import real_sym_sh_mrtrix
from dipy.utils.optpkg import optional_package
from dipy.reconst.shm import sph_harm_ind_list
cvxpy, have_cvxpy, _ = optiona... |
a705282ab6de91e2177314a452305bf6054d9f69a66e17e20ad484843d1e250e | Python | 9,105 | 312 | """JASPAR API client for transcription factor binding profiles."""
import logging
from typing import Any, Dict, List, Optional
from .base import BaseAPIClient
from ..config import settings
logger = logging.getLogger(__name__)
class JASPARClient(BaseAPIClient):
"""Client for JASPAR REST API.
JASPAR is ... |
f2d1667175534a6a03bc828941359f6df4650a2f64618f8d6ce16cefece9f254 | Python | 9,105 | 233 |
import numpy
class RewardCalculator:
"""
Base class for the reward calculator
"""
def __init__(self, objs, *args, **kwargs):
"""
Instantiates the `RewardCalculator`
:param objs: A `dict` of objective
"""
self.objectives = objs
def evaluate(self, sted_image... |
391bd131a51edf54a152159fff6ae2bb965af59192d303ac58c0648a62010343 | Python | 9,106 | 163 | import os
import click
import torch
import itertools
import numpy as np
import pandas as pd
from Bio import SeqIO
from scripts.model import SPIRED_Fitness_Union
from scripts.utils_train_valid import getDataTest
amino_acid_list = list("ARNDCQEGHILKMFPSTWYV")
amino_acid_dict = {}
for index, value in enumerat... |
b7f34d7f60a5148abf4cb4c0ed07d93e64b1e0d34e7f90b23359eb4b5ab30388 | Python | 9,107 | 312 | """JASPAR API client for transcription factor binding profiles."""
import logging
from typing import Any, Dict, List, Optional
from ..base import BaseAPIClient
from ...config import settings
logger = logging.getLogger(__name__)
class JASPARClient(BaseAPIClient):
"""Client for JASPAR REST API.
JASPAR i... |
50a9b6794ff4c6a52e338d09799dc55607a7457f5d995a2f4a76b7be63ed91ff | Python | 9,109 | 228 | import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from easydict import EasyDict as edict
import sys
sys.path.append('.')
from BioMime.utils.params import coeff_a, coeff_b
from NeuroMotion.MNPoollib.mn_params import DEPTH, ANGLE, MS_AREA, NUM_MUS, mn_default_settings
class MotoneuronPoolStatus:
... |
4fdf3c4b618de9b35de38f67b4baadd163196b9e0345fa16f50845f7c71acf28 | Python | 9,111 | 237 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
ba9ebd940bcf62111852daa3bc68d5881f0eafa93627075d2705d47895b9a841 | Python | 9,113 | 258 | """Pseudo-bulk aggregation and bulk-style DE for single-EV proteomics.
Single-EV proteomic atlases hold 10^4-10^6 vesicles; collapsing the per-EV
signal to a sample x protein matrix recovers a classic "bulk" measurement on
which moderated-t / OLS differential expression can be run for biomarker
discovery.
* :func:`ps... |
e455fc89a22df487f86b118c13bac3c72e5e0eb71020a6abdc691b8cb1131fd5 | Python | 9,114 | 241 | # -*- coding: UTF-8 -*-
from datetime import datetime
import argparse
import logging
import os
import sys
root_dir = os.path.abspath(os.path.dirname(__file__))
sys.path.append(root_dir)
sys.path.append(os.path.join(root_dir, "models"))
from models.FCN import FCNs,VGGNet
from models.UNet_5 import UNet
from models.segn... |
0554a431ed0cbf9079bc17ac1369a8c4a97ff179a7480633ba473aab0a39d757 | Python | 9,115 | 200 | #------------------------------------------------------------------------------------------------------------------------
#Author: Brandon S Coventry
# Date: 08/23/2022
# Purpose: This program is a modified port of my previous heirarchical linear regression programs, updated for pymc (v4)
# Revision History: Based ... |
8b2b7dd3a3d7f5ccebe0b66f7fdbb122cbbd0ef2014a793dadafc85a1970dc75 | Python | 9,116 | 284 | from typing import Tuple, Union
import pandas as pd
import numpy as np
import torch.nn.functional as F # noqa
from torch import (
nn,
from_numpy,
Tensor,
no_grad,
nan_to_num
)
from python.utils import custom_logger
from config import (
TARGETS,
FORECAST_HORIZON,
NEEDED_OUTPUT_COLUMNS,
... |
e379fcf1f75296b4c098b82a588b13ff1cd23ace438f0ee1e4ff317b7fafdec7 | Python | 9,118 | 219 | ####################################################################################################
# Copyright (c) 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free softw... |
26c95fc760ca90139bc97dbeb50a8115b7fe1c1616f07a0cc35c9f63758a7fd9 | Python | 9,120 | 263 | import warnings
warnings.filterwarnings("ignore")
import argparse
import json
# import matplotlib
# import matplotlib.pyplot as plt
import math
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
from torch import cuda
import sys, os
import random
import numpy as np
from sklea... |
3fe7ba18db5c4490cc99cd740d510045f56447398b0ca9f77c1841ba56803022 | Python | 9,125 | 236 | """Combines json files into a single .tsv table for analysis."""
import argparse
import json
import logging
import os
import pathlib
import sys
import pandas as pd
logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s: %(message)s")
def parse_args(args_list=None):
"""Parse command-line args... |
7d53b8a9017011d00b05bd2724a222e064aaa120f665ebeaaa93f81bd5dbffa2 | Python | 9,125 | 197 | import matplotlib.pyplot as plt
import numpy as np
def plot_signal(config, data, key, on, off=None, ax=None, xlabel=True, ylabel=True, twinx_label=True, labelsize=14, fontsize=24):
if ax == None:
ax = plt.gca()
if off == None:
off = on + config.window
if config.sampling_freq == None:
... |
ff565fba730fdd275db41d0426816dfb5a685867548640e4c9e6fe13f2c985f8 | Python | 9,125 | 230 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 19 11:18:43 2022
@author: sam
BRANCHED FROM 04.19.22
"""
import os
import numpy as np
import tensorflow as tf
import keras
from keras import backend as K
import matplotlib.pyplot as plt
def fit_script_stage123(folder,connectivity, noise=1e-4,syn_f... |
10029d7445a60910d72138597592ac9bfc856032fd6603531d00b3ace6cd7b34 | Python | 9,126 | 261 | """
Module defining a custom combo box containing checkable items.
***
built as part of the Russell Ray Lab Breathing And Physiology Analysis Pipeline
***
Breathe Easy - an automated waveform analysis pipeline
Copyright (C) 2022
Savannah Lusk, Andersen Chang,
Avery Twitchell-Heyne, Shaun Fattig,
Christopher Scott ... |
2511e929fee511ec7f5c8544a91c1a763df65d3a8f80f717f68ded8b085ae984 | Python | 9,128 | 362 | import pytest
import ray
from ray.dag import (
PARENT_CLASS_NODE_KEY,
PREV_CLASS_METHOD_CALL_KEY,
InputNode,
MultiOutputNode,
)
@ray.remote
class Counter:
def __init__(self, init_value=0):
self.i = init_value
def inc(self):
self.i += 1
def get(self):
return self.... |
2a873a108dd2b36a893e077c4e1cb4ad7abe76165cc7ca15320b7ec1ea0592ad | Python | 9,139 | 215 | import numpy as np
import os
import utils
import pandas as pd
import random
import torch
import torchvision
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torch.utils.data import Dataset, DataLoader
from torchvision import datasets, transforms
from torchvision.transforms import T... |
77040b2a3154e9c733d04f22b4710f50039af5e39083171a794ff8794b4a5cbf | Python | 9,140 | 239 | # Modified from https://github.com/open-mmlab/mmdetection/tree/3.x/
import argparse
import copy
import os
import os.path as osp
from mmdet.engine.hooks.utils import trigger_visualization_hook
from mmdet.registry import RUNNERS
from mmengine.config import Config, DictAction
from mmengine.dist import get_dist_info
from ... |
39e53d661ebc09a41d772f500d40f9173fee676eed3ab15c792557737816570c | Python | 9,141 | 261 | import logging
import os
from collections import deque
import numpy as np
from pfrl.experiments.evaluator import Evaluator, save_agent
def train_agent_batch(
agent,
env,
steps,
outdir,
checkpoint_freq=None,
log_interval=None,
max_episode_len=None,
step_offset=0,
evaluator=None,
... |
4450831a875817d99dfae3bb3664ad66450a319251ec98ade110f639440488c6 | Python | 9,147 | 216 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from typing import Any
from django.contrib.auth.models import Group
from rest_framework import status
from cvat.apps.engine.tests.utils import ApiTestBase
from cvat.apps.iam.models import User
class TestQualityRequirementApiForDeletedAttributes(A... |
32aefdabae93b55c63adf19677093572ebf2c50c4a11d636dd001b4caa10f55e | Python | 9,151 | 226 | """Pseudobulk aggregation of single-cell data.
``ov.single.pseudobulk`` collapses a single-cell AnnData into per-sample
(optionally per-sample-per-celltype) pseudobulk profiles — the correct unit
for cohort-level differential expression with DESeq2 / edgeR / limma
(``ov.bulk.pyDEG``).
The API mirrors :func:`decoupler... |
98b11003b3434d9da5492e0dc56960087def09c4d554b7a54166c57abe221225 | Python | 9,151 | 228 | from dataclasses import dataclass
from typing import TYPE_CHECKING, Optional
from ray.data._internal.datasource_v2.interfaces.pushdown import (
ListFilesPushdown,
SupportsColumnPruning,
SupportsFilterPushdown,
SupportsLimitPushdown,
SupportsPartitionPruning,
)
from ray.data._internal.planner.plan_e... |
bbf8d19b1ad95e33dd8d6627b541af131e964bd2a3fe6721fd9d7a7355cd10c0 | Python | 9,152 | 236 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .swin_transformer import SwinTransformer,SwinTransformerBlock, BasicLayer, PatchMerging, PatchEmbed
from timm.models.layers import DropPath, to_2tuple, trunc_normal_
from sleep_models.hypResnet import HypResnet
class Mlp(nn.Module):
de... |
c19d8f90b8f889d87bce68eb0d5c14c80ff4e1c9208ecc206007e630945fd13c | Python | 9,153 | 308 | # Copyright 2026 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
9770c392b5762a312ba63ea8e91bfc128c6e36ca367eaa1fc29eb51d836b12a1 | Python | 9,162 | 292 | """
This script simulates the structure-function mapping hypothesis for a varied
number of angles (using the parameter 'phbins'). The results are plotted and
saved. The saved figure is used in figure 4 (panel 'T') of the manuscript.
"""
from utils.grid_funcs import (
gridpop_clustering,
gridpop_conj,
gridpo... |
7c897ccfa85838f42bdf29a92a7802d72a752f73acceee1a6fac0eccad59a0ac | Python | 9,163 | 313 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""aihwkit example 20: MNIST training with PyTorch Distributed Data Parallel (DDP).
MNIST training example based on the paper:
https://www.frontiersin.org/artic... |
bb3354da2ae12dc4a3d1b43955052066348436f6e6d91727d8af457ce391d562 | Python | 9,164 | 325 | """Utility functions for the project."""
import logging
from functools import cache
import numpy as np
import pandas as pd
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.Descriptors import ExactMolWt
from scipy.stats import linregress, pearsonr, spearmanr
from sklearn.metrics import mean_absolu... |
954972a09fa2224f5632de708ad5d498343e13bcc9069274fe97926ddfd61593 | Python | 9,165 | 256 | from dataclasses import dataclass
from pathlib import Path
from typing import Any, Iterable, Sequence
import numpy as np
import pandas as pd
from numpy.typing import NDArray
from siapy.core import logger
from siapy.core.exceptions import InvalidInputError, InvalidTypeError
from .pixels import CoordinateInput, Pixels... |
7e3f4cb4813b72e16d1159df3f524a0e16c7a4f93f53a1c7394bc495458fda30 | Python | 9,166 | 272 | import random
from tkinter import W
import brainrender as b
import numpy as np
from brainrender.actors import Point
from brainrender import _utils
#Find cell coordinates
import csv as c
file = open("CN_neuron_coordinates_allcells.csv")
csvreader = c.reader(file)
# Skip first line to get to get to data
next(csvreade... |
0b89e6892e6a2f7edefa25a8e8e342e043694727a7c94123fb77b6640c6ed141 | Python | 9,170 | 227 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#... |
b76696b6f4b4444c3267529c0a8a177f44c73c04b848ee3c53f3afd8d652ab46 | Python | 9,171 | 295 | """RegulomeDB API client."""
import logging
from typing import Any, Dict, List, Optional
from .base import BaseAPIClient
from ..config import settings
logger = logging.getLogger(__name__)
class RegulomeDBClient(BaseAPIClient):
"""Client for RegulomeDB regulatory variants API.
RegulomeDB is a database... |
5a91115c60b0caf941df50b7804aa40bb2415f346260bf984304d4f20e3eecec | Python | 9,173 | 295 | """RegulomeDB API client."""
import logging
from typing import Any, Dict, List, Optional
from ..base import BaseAPIClient
from ...config import settings
logger = logging.getLogger(__name__)
class RegulomeDBClient(BaseAPIClient):
"""Client for RegulomeDB regulatory variants API.
RegulomeDB is a databa... |
63237789c52291d1b835918c2dc538166ef79b38b0b36c1dd7054bc9498ccdab | Python | 9,178 | 267 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#... |
43311dffb87ad0b86d5ae69ba480d2a4c07cc68da7f0da9bfc4276ead46f7302 | Python | 9,179 | 215 | import os
from GNNSubNet import GNNSubNet as gnn
import ensemble_gnn as egnn
from sklearn.metrics import balanced_accuracy_score
from sklearn.metrics import accuracy_score
from sklearn.metrics.cluster import normalized_mutual_info_score
from pickle import dump
from typing import Union
def getGraphs(model: egnn.ensem... |
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