sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4c38466e5235926127418a2624cdac2493a58e2ea94f520764b2afa6fbf74058 | Python | 16,858 | 434 | """
The implementation is based on Keras DDPM implementation: https://keras.io/examples/generative/ddpm/
"""
import os
import numpy as np
import keras
from keras import ops
from tsgm.types import Tensor as TensorLike
from tsgm.backend import get_backend
import typing as T
class GaussianDiffusion:
"""
Gaussia... |
945ea9cddbab9389d31cd3e4fc0ab33bca737bea92623857032174687c2e29fe | Python | 16,879 | 420 | ##
## CPCantalapiedra 2019
import os
from os.path import join as pjoin, isdir as pisdir, isfile as pisfile
import shutil
import subprocess
from sys import stderr as sys_stderr
from tempfile import mkdtemp, mkstemp
import uuid
from ...common import MMSEQS2, get_eggnog_mmseqs_db, ITYPE_CDS, ITYPE_PROTS, ITYPE_GENOME, I... |
d69bca6971e3caa42940d0319db60468bf42224b4392f10efe76d8c3ca4fe80c | Python | 16,908 | 418 | # Copyright (c) OpenMMLab. All rights reserved.
# Modified from https://github.com/MendelXu/SAN/blob/main/san/model/attn_helper.py # noqa: E501
# Copyright (c) 2023 MendelXu.
# Licensed under the MIT License
import warnings
from typing import Optional
import torch
from mmcv.cnn.bricks.transformer import BaseTransfor... |
5239723dc9268c39ad1e06861eeb9da91c8d4165061a10accbc6033064857c90 | Python | 16,931 | 459 | # Author: Huaxu Yu
# A module for data visualization.
# imports
import random
import numpy as np
import os
import re
from tqdm import tqdm
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
import matplotlib.transforms as transforms
from matplotlib.patches import Ellipse
import matplotlib.font_manag... |
6df631cc43e26db5a7491c1ee38a7c63c3dfe1273a4145161728df61fb4443f2 | Python | 16,934 | 362 | """TensorBoard callback for training visualization.
This is the TF v1 version. A subset of the functionality
also works with other backends.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import numpy as np
import warnings
from .. import ba... |
26db44ce85ca659b5b84aad1e57697cc0f3175ea50b700a5e6b84285f604d8cf | Python | 16,946 | 415 | #!/usr/bin/env python
#
# Utilities for labels
#
# Copyright (c) 2013 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
# TODO: for vert-disc: make it faster! currently the module display-voxel is very long
# (esp. when ran on PAM50). We can find an alternative approach by sweeping th... |
ca888b9ac50f202e1fac4042f3aa08716e199c3eccb68d03ea43715facb35e54 | Python | 16,961 | 319 | import numpy as np
import torch
import torch.nn.functional as F
import matplotlib.pyplot as plt
from matplotlib import colors
from matplotlib.patches import FancyArrowPatch
def generateShapes(gridsize, radius, imagesize):
"""Generate a list of shapes by morphing circles into squares and blobs.
Args:
g... |
0bae46403219f5189be4bbe10f0720592224c069a182402ca00a9c2538df0060 | Python | 16,967 | 377 | import networkx as nx
from networkx import connected_components
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider, Button
import time
import numpy as np
from copy import deepcopy
from CybORG import CybORG
from CybORG.Simulator.Scenarios.EnterpriseScenarioGenerator import SUBNET
from CybORG.Simulato... |
5a0839a8e346c3fd1d30ef5d8014a8df90cebcecf83a704b3e63eb3c5dbe1d23 | Python | 16,967 | 400 | """"Simulated DBTL cycles"""
from typing import Union, Optional, Tuple
import jax.numpy as jnp
import jax
import numpy as np
from jaxkineticmodel.load_sbml.sbml_model import SBMLModel
from jaxkineticmodel.utils import get_logger
import matplotlib.pyplot as plt
import pandas as pd
import scipy
import sklearn
import xg... |
a92148bbd3551fd1267ac58197ec1e4a77d4c883970dd7701f0d40ad3b8da112 | Python | 16,973 | 393 | import os
import tqdm
import torch
import numpy as np
import argparse
import json
import cv2
import scipy.io as sio
import matplotlib.colors as mcolors
import matplotlib.cm as cm
from scipy.interpolate import interp1d
from skimage import io
from nns.model import ISOSNet
from utils import fix_random_seeds
from tools.vis... |
93059ca6e6cebb7699dd32b0d4ddf89596bb6799924e98e046a06a6897e4b8c3 | Python | 16,986 | 430 | # -*- coding: utf-8 -*-
import json
from django.db import connection
from django.test import TestCase
import catmaid.state as state
from catmaid.tests.common import CatmaidTestCase
class StateCheckingTest(CatmaidTestCase):
"""This tests various aspects of the back-end state checks"""
# Work on regular test... |
1530971064fff3726a612dea057b868e18e584432f849e07f7ec40b48dec9583 | Python | 16,992 | 483 | # 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 types
import torch
import transformers
import torch.nn.functional as F
from torch import nn
from torch.nn import Cro... |
c5bf074e4ca8711bd20b522cefae986a58fd79c702bda5bed6684e9e17146c24 | Python | 17,004 | 403 | # coding=utf-8
# Copyright 2021 The IDEA Authors. 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 a... |
8b5f058f094e7aa66a8f09f504f638acad72d762cc11d3d5686cbcd5e05bc842 | Python | 17,007 | 478 | #!/usr/bin/env python3
import multigrid
multigrid.g_reuse_multigridop = False
from multigrid import (
Multigrid,
MultigridOp,
MultigridDecomp,
SparseOperator,
get_shift_csr,
ModNumpy,
ModTensorflow,
ModCupy,
)
from multigrid_plot import plot_3d, plot_grid, plot_grid_matrix
import numpy ... |
76dcb0644f99205f571c334c22764a5a7166e7fa620f22ad211ef4ff667285c5 | Python | 17,008 | 511 | import logging
from collections import Counter
from functools import partial
from itertools import combinations
from multiprocessing import Pool
import numpy as np
from rdkit import Chem
from rdkit.Chem import Fragments as frag_func
from tqdm import tqdm
from .scoring_func import *
def get_drug_chem(mol):
qed_s... |
9c60e275508a0427084d5ee2089d27dd0a86db40bf90c3b268e81c1cb8b5716c | Python | 17,010 | 453 | from __future__ import annotations
import torch
from torch import Tensor, nn
from chgnet.model.functions import (
MLP,
GatedMLP,
aggregate,
find_activation,
find_normalization,
)
class AtomConv(nn.Module):
"""A convolution Layer to update atom features."""
def __init__(
self,
... |
a715859c942212c6c6a57b0eb286902f56a37d298d7c71159514b7109d222d4a | Python | 17,037 | 507 | # -*- coding: utf-8 -*-
"""
Created on Jan 29 2024
@author: george.dickinson@gmail.com
This program is a Python script developed to analyze the motion of intracellular Piezo1 proteins labeled with a fluorescent tag.
It allows the user to load raw data from a series of image files and track the movement of individual ... |
7f8916903e387526e5b921139b59e38c611300f752c14c85aa5deae4d5bbd932 | Python | 17,041 | 360 |
from pathlib import Path
import shutil
import tarfile
import hydra
from omegaconf import DictConfig
import torch
import torchaudio
from functools import partial
from tqdm import tqdm
import urllib
import numpy as np
from datasets.audio_compress import LibriTTS
test_clean_path = "https://openslr.elda.org/resources/... |
af193bc430e966186271e5ae70f5ca690fd243aaac27af863edc583bbc037d2a | Python | 17,057 | 413 | import numpy as np
import hickle as hkl
from sklearn.preprocessing import normalize
from sklearn.neighbors import KNeighborsRegressor
from grid_cell.manifold_fitter import label_mesh
from sklearn.metrics import r2_score
import copy
from global_setting import *
def average_lattice_area(feamap):
'''
input:
f... |
8018c97a90dc9488107ca5dc77a240ef28b226d3aa6ba7c0180dc7921bfac5d2 | Python | 17,064 | 322 | #!/usr/bin/env python2.7
import os, sys
os.environ["OMP_NUM_THREADS"] = "1"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["VECLIB_MAXIMUM_THREADS"] = "1"
os.environ["NUMEXPR_NUM_THREADS"] = "1"
import argparse
import shlex
import shutil
import glob
import re
import traceba... |
4e8941f8a27fb05a7c05680eac3f01e8697e71c5cbc9b140163d0294de25bb0c | Python | 17,069 | 389 | import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import logging
import numpy as np
from PIL import Image
from diffusers.utils import make_image_grid
from dataclasses import dataclass
from tqdm.auto import tqdm
from initialization import extract_material_parameter
class Generator_ClsEmd_ligh... |
9c3a2f0f70141605f7c4042d6a5bea974c50546bd7642a21f6adcbf6e49fda9c | Python | 17,076 | 410 | # /// script
# requires-python = ">=3.10"
# dependencies = [
# "matplotlib",
# "numpy",
# "scipy",
# ]
# ///
"""Generate SVG figures for the PSTH significance explanation page.
The bootstrap and the consecutive-run filter mirror
src/guppy/analysis/psth_significance.py, and the significance bar is drawn ins... |
14f067348ee71064a24752b6b5ca19a580e2847e237fff53079397d33d4ac142 | Python | 17,083 | 444 | import logging
import os
import nibabel as nib
import numpy as np
import pandas as pd
from pyalfe.data_structure import PipelineDataDir, Tissue, Modality
from pyalfe.roi import roi_dict
from pyalfe.tasks import Task
try:
from radiomics import featureextractor
except ImportError:
featureextractor = None
cla... |
5f048281cd286cdbcd7b4441ee15db10d5c6220cc179b01265a400261b2b09ae | Python | 17,089 | 470 | # Copyright (c) 2021, EleutherAI
# This file is based on code by the authors denoted below and has been modified from its original version.
#
# Copyright (c) 2020, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complian... |
29b0ff465051b399f5956a3d933748b9487a22f110d454a9143b63e2601e69b5 | Python | 17,096 | 414 | # Copyright 2022 EleutherAI and The HuggingFace Inc. team. 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 r... |
c7bd1076ee5ee2683428c8589f21f0194f1c75dd1c43824f77ea845dc8f69da6 | Python | 17,100 | 491 | # Copyright DST Group. Licensed under the MIT license.
import queue
from threading import Thread, Event
import warnings
from typing import Any, Tuple, Union
import gym
import numpy as np
import pygame
from gym.utils import seeding
from CybORG.Simulator.SimulationController import SimulationController
from CybORG.Shar... |
da7d0c7fab02dccec5557a04f5f8bcf55f79dbfab4e4a9b47bb0ce947bd6d2bd | Python | 17,103 | 472 | """
Training Agents for GNODEVAE
This module implements agent classes that manage the training process for
GNODEVAE models. Agents combine environment setup, model training, and
evaluation metrics to provide a high-level interface for users.
Key Classes:
- BaseAgent: Base class with common training functionality
- ag... |
928dd2675496e95c595d8641dd283dc364e475b6d7c86c22f7989628adaf2f6c | Python | 17,120 | 334 | """
Core functions dealing with centerline extraction from 3D data
Copyright (c) 2019 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import os
import logging
import numpy as np
from spinalcordtoolbox.image import Image, zeros_like, add_suffix, reorient_coordinates
from spinalcordtool... |
29c4a1c998f0d24fde4713855d755fa0386c355a641c6bac9f85928002ec1859 | Python | 17,122 | 406 | """
Image slice extractors for generating QC reports
Copyright (c) 2017 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
# TODO: Replace slice by spinalcordtoolbox.image.Slicer
import os
import logging
import math
import numpy as np
from scipy.ndimage import center_of_mass
from spina... |
3d8cf2ec870962d8b84133e8368de258a96c57ece79a8832d10f761b67026c0d | Python | 17,128 | 547 | """Tests for functions in data_utils.py.
"""
import os
import time
import sys
import tarfile
import threading
import signal
import shutil
import zipfile
from itertools import cycle
import multiprocessing as mp
import numpy as np
import pytest
import six
from six.moves.urllib.parse import urljoin
from six.moves.urllib.r... |
8a2560f33641748f05be5209c3f875ce4f7555a9740ccd518a0bb6caecc40339 | Python | 17,135 | 470 | import numpy as np
import matplotlib.pyplot as plt
import json
import collections
import pandas
import seaborn as sns
# súlyozott:
# /home/tarluca/Modellke_story/Luca_modell_rework/Results_from_NSG/prep_and_run_model_rework_weight3_R0/nsg_csomag_model_rework/results_ca1_results/last.csv
# nem súlyozott:
# /home/tarlu... |
4d5e68172884ffbde0fe298a8f7a5bf9b9f060a05db0834964c62f29fef920fe | Python | 17,147 | 342 | #!/usr/bin/env python3
"""
# split runs with "fMRI trigger" e.g. binarize the values and identify start stop indices
# ttl onsets
# convert each event into trial number
# do this based on two events: expect and actual
# TODO:
# * identify BIDS scheme for physio data
# * flag files without ANISO
# * flag files with l... |
0c9be8e1c7e777b0e00a4944395bf8ff8bd7a684c5c955a6774808a8c993461b | Python | 17,169 | 495 | #!/usr/bin/env python
from __future__ import print_function, division
import numpy as np
from rdkit import Chem
from rdkit import rdBase
from rdkit.Chem import AllChem
from rdkit import DataStructs
import rdkit.Chem.QED as QED
import scripts.sascorer as sascorer
import pickle
import pandas as pd
import tensorflow as ... |
6a5f87f3d40515489fb0ae139890fa4278ed93df61eaca3c0461db4a89e8dadb | Python | 17,183 | 450 | # -*- encoding: utf-8 -*-
'''
Copyright 2022 The International Digital Economy Academy (IDEA). CCNL team. 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.o... |
9a07c25562559d2b3e712201363292f93b8c1f4d251bb0a5935bc6e7a4e9b2d6 | Python | 17,185 | 473 | # -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import unicode_literals
import re
import inspect
import os
import shutil
import six
try:
import pathlib
except ImportError:
import pathlib2 as pathlib
import keras
from keras import backend as K
from keras.backend import numpy_back... |
4eacfe3b0aa1a16f328c226110dcbff426ed9e1f2a30b153d604178d3a6ad37f | Python | 17,194 | 495 | #!/usr/bin/env python
from __future__ import print_function, division
import numpy as np
from rdkit import Chem
from rdkit import rdBase
from rdkit.Chem import AllChem
from rdkit import DataStructs
import rdkit.Chem.QED as QED
import scripts.sascorer as sascorer
import pickle
import pandas as pd
import tensorflow as ... |
89278e89c7d825512334ffe03c1bb50558c70b8176a8ed49fec61156a60f0d0a | Python | 17,216 | 385 | # Generated by Django 2.1.7 on 2019-02-18 16:37
from django.db import migrations
forward = """
-- Obtain the foreign key constraint name in a particular column of a
-- specific relation to a target relation.
CREATE OR REPLACE FUNCTION get_fk_constraint_name(relname text, colname text, targetrelname text)
... |
633b1f53c2f2b17a08e084272c384dff8c2ca9b95f2c02c82f50722002e4dfe1 | Python | 17,243 | 410 | from typing import Any, Union
import torch
import torchaudio
from auraloss.utils import apply_reduction
from auraloss.perceptual import FIRFilter
from auraloss.freq import SpectralConvergenceLoss, STFTMagnitudeLoss
reduce_map = {
'mean': lambda x: torch.mean(x),
'sum': lambda x: torch.sum(x),
'none': lambda... |
df9054b12aab31117d5fe5b52dd9f54afee2ec3e3efb0dfafcf1f946b19e649f | Python | 17,247 | 478 | from torch import nn
import torch
from torch_geometric.nn import global_max_pool, global_mean_pool
from torch.nn import Module, Linear, MSELoss, ModuleList #BCEWithLogitsLoss
from torch.nn.functional import relu
#from torch import sigmoid
from torch.utils.data import WeightedRandomSampler
import pytorch_lightning as pl... |
98ff70d389c840b8087f29312cc0b3b0d5551b212aeb49f84edb9e312f905c98 | Python | 17,264 | 524 | from rest_framework import status
from medperf.tests import MedPerfTest
from parameterized import parameterized, parameterized_class
class ResultsTest(MedPerfTest):
def generic_setup(self):
# setup users
data_owner = "data_owner"
model_owner = "model_owner"
bmk_owner = "bmk_owner... |
280f26a29e1a1a8172e645b1820402813376e494e6810bb20c04affe33384fe3 | Python | 17,312 | 643 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import glob
import datalad.api as dl
import pandas as pd
from zoo_bids.functions import find_root
path_project = find_root(project_name='zoo-bids')
path_participants = os.path.join(path_project, 'participants.tsv')
path_quest = os.path.join(path_project, 'input'... |
569b649cdc5ce087360a35dbf9bf310fb3d60a7d6be5a2b6a37ea025f662f358 | Python | 17,333 | 551 | import os
from dash import Dash, html, dcc, dash_table
import plotly.graph_objects as go
import plotly.express as px
import dash_bootstrap_components as dbc
import pandas as pd
from medperf import config
from medperf.utils import sanitize_path
from .get_data import get_data
from .utils import get_reports_path
from t... |
a7e320c3e29092503ff267bf4d595008ee77eb1159c8a38766fe8024722f8d79 | Python | 17,352 | 496 | """Base layers for model."""
from typing import Tuple, Optional
from torch import nn, Tensor
import torch
import math
from .util_funcs import unsorted_segment_sum, coord2diff, coord2cross
from .core import MLP
class GCL(nn.Module):
def __init__(
self,
node_nf: int = 8,
hidden_nf: int = 2... |
1d97a31c36423e6dc6f0119c2f91660cbfbb5b55e54bb4b89db5b6ce40176c68 | Python | 17,353 | 339 | """Generate stubbed testing data from the full testing_data directory.
Run from the project root:
python scripts/create_stubbed_testing_data.py
Stub durations are hard-coded per session. For sessions with TTL events, the
duration was chosen to capture at least 5 complete TTL pulses (rising and
falling edges both ... |
125b0dfeba718b865e54e92d8e8e02e626ce32d509d8dbf47e40df756a673c0e | Python | 17,373 | 586 | import os
import csv
import random
from functools import partialmethod
import torch
import torch.nn.functional as F
from torch.autograd import Variable
import numpy as np
from pandas import read_csv
from sklearn.metrics import (
precision_recall_fscore_support,
precision_recall_curve,
roc_auc_score,
bal... |
6b63aa89c820871e7a6aef1177a0f9420428f869bf6015b656188b603b0fdfd0 | Python | 17,381 | 433 | # Author: Hauxu Yu
# A module to summarize the premade data processing workflows.
# Import modules
import os
import multiprocessing
import pickle
from copy import deepcopy
import pandas as pd
import numpy as np
from importlib.metadata import version
from scipy.stats import zscore
import time
from .raw_data_utils imp... |
509167eaf176e58fc6e5e1a6efb8f00e5214f384189b7f6a3ad022a6ce39d68d | Python | 17,385 | 304 | """processingpipeline.py functions to aid in analyses done for (Fickling et al., 2025)
author: Logan James Fickling github.com/LoganJF
TODO: format_20min_exps_to_15mins isn't strictly necessary as a function as the variable length can be used instead
TODO:cluster.py should have the sklearn clustering stuff instead
"... |
2c4d5447ee7d6f3819e386f2a184e1bd7399b456e926735b35a5a46ed862fadc | Python | 17,400 | 408 | """Main alignment class"""
import logging
import time
import typing as ty
import warnings
import numpy as np
from .utilities import check_xy, convert_peak_values_to_index, generate_function, shift, time_loop
METHODS = ["pchip", "zero", "slinear", "quadratic", "cubic", "linear"]
LOGGER = logging.getLogger(__name__)
... |
cae78d498c0014d3938b04bc6147fa712e78ab23ae66a365cf1e3bf52477718d | Python | 17,402 | 530 | # library path
import os, sys
# lib_path = os.path.abspath(
# '/vol/biomedic/users/aa16914/software/SimpleITK/SimpleITK-build/SimpleITK-build/Wrapping/Python/')
# sys.path.insert(1, lib_path)
import SimpleITK as sitk
import numpy as np
import math as mt
# ssim
from scipy.ndimage import uniform_fil... |
0f1fc30f74709c6ac98a75d45f8d87c618a99a6f5aab2277a1c8b173d0b4cad0 | Python | 17,405 | 423 | """Tests for NwbRecordingExtractor and its private helper functions."""
import numpy as np
import pytest
from pynwb import TimeSeries
from guppy.extractors.nwb_recording_extractor import (
NwbRecordingExtractor,
_core_events_split_column,
_find_nwb_file,
_parse_event_name,
_read_ndx_event,
_re... |
64ddccd213c016249d19dbd4327791746b8d6282fe18250396a8b5c0cb536a7e | Python | 17,407 | 317 | """NCATS GARD (Genetic and Rare Diseases) rare-disease registry data handler.
GARD is a flat registry of rare-disease terms distributed by NCATS as a single CSV (UTF-8 with
BOM, CRLF line endings) with four columns -- ``ID``, ``DisplayName``, ``Synonyms``, ``URL``:
* ``ID`` -- a ``GARD:NNNNNNN`` CURIE (zero-padded to... |
97124a3918036c86b860abc0edc4a28202a4e8fc05ec5bde516a5ddc0761d7cb | Python | 17,414 | 444 | # Third Party Imports
import tensorflow
try:
# Third Party Imports
from tensorflow.python.data.ops.readers import TFRecordDatasetV
except:
from tensorflow.python.data.ops.readers import TFRecordDatasetV1 as TFRecordDataset
# Standard Library Imports
import os
from math import pi
# Third Party Imports
im... |
db1be21067edc9796e0e6602de808f820de5aa93fcc15cf0e8f616da06e00c48 | Python | 17,421 | 403 | import pymonetdb
import uuid
from prov.model import ProvDocument
from prov.dot import prov_to_dot
import os
import sys
import json
import argparse
import re
def run(args_list=None):
parser = argparse.ArgumentParser(description="Generate W3C document")
group = parser.add_mutually_exclusive_group(required=True... |
5f7ed98681f1d389a5ed2886577c08c053e559d6419bf42aeb57e1535ceac50e | Python | 17,423 | 429 | # -*- encoding: utf-8 -*-
'''
Copyright 2022 The International Digital Economy Academy (IDEA). CCNL team. 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.o... |
334ca739b0ed49d7e9617ac190af56d1e72ac6b323dae36982242a1527044a51 | Python | 17,434 | 383 | #!/usr/bin/env python
#
# Apply transformations. This function is a wrapper for sct_WarpImageMultiTransform
#
# Copyright (c) 2014 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
# TODO: display message at the end
# TODO: interpolation methods
import sys
import os
import functools
from t... |
b4f9b2a53a3f41983ab07810bfa6eda885a0ebfc6e36a489acb78870d1dfbd57 | Python | 17,436 | 450 | # Copyright (c) OpenMMLab. All rights reserved.
import math
import warnings
import torch
import torch.nn as nn
import torch.utils.checkpoint as cp
from mmcv.cnn import Conv2d, build_activation_layer, build_norm_layer
from mmcv.cnn.bricks.drop import build_dropout
from mmcv.cnn.bricks.transformer import MultiheadAttent... |
8135649c8ef469f56b9391204074413ab08c8163eee887f1797f9ecd5b215d12 | Python | 17,438 | 431 | import os,torch,json
import datetime, warnings
import tensorboardX
import numpy as np
import torch.nn as nn
from utils.config import opt
from model import ScaleDense
from model.ranking_loss import rank_difference_loss
from load_data import IMG_Folder,Integer_Multiple_Batch_Size
from prediction_first_stage import test
f... |
e44183a907f094d3c1da93e9433f617158957cf0a928d26ae91b2f1c38cd1f29 | Python | 17,464 | 395 | from pathlib import Path
import numpy as np
import pytest
from guppy.analysis.io_utils import (
check_storeslistfile,
check_TDT,
decide_naming_convention,
fetchCoords,
find_files,
get_control_and_signal_channel_names,
get_coords,
is_channel_label,
is_continuous_label,
is_covari... |
f028c296f74a0edd07353b9b3da0f206d6fff03298f7e0fb9fd81060ba62af05 | Python | 17,479 | 438 | #!/usr/bin/env python
"""
MetaWIBELE: check_install module
Check the installation of MetaWIBELE package and dependent tools
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Softwar... |
e85cce4d8852a0cae1033129b7d79feef78d8d485008c3d2ad6786cd08a9d6cd | Python | 17,488 | 451 | import os
import numpy as np
import copy
import scipy
from collections.abc import Iterable
from . import warning
from .geom import resample, apply_warp
from .transform import Transformable, LinearTransform, Geometry, LIA
class ArrayContainerTemplate:
'''
Internal, abstract template responsible for handling ... |
a0f4d7b508968a82337e484e915b5ea49df6d3a74114533e34fbd4de2bb1c869 | Python | 17,505 | 441 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
# pyre-strict
# pyre-ignore-all-errors[58]
import typing
import unittest
import numpy as np
import torch
from fvcore.nn import (
sigmoid_focal_loss,
sigmoid_focal_loss_jit,
sigmoid_focal_loss_star,
sigmoid_focal_loss_star_jit,
)
... |
df5ed5731b7c2c146a074b52afac4e625c49fed7ac7d34737d302a1947c21b92 | Python | 17,599 | 503 | # Interface with AWS
# Author: David Young, 2018, 2020
"""Connect MagellanMapper with AWS such as S3 and EC2.
Attributes:
"""
import os
from pprint import pprint
import boto3
import boto3.session
import botocore
from boto3.exceptions import RetriesExceededError, S3UploadFailedError
from botocore.exceptions import Cl... |
8de8a1d99320aa53461f4ba06e03d788c8a08ce2b3cfcfa67e9fc125c14bcb4b | Python | 17,623 | 482 |
import copy
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import GCNConv, GATConv, global_mean_pool, global_max_pool, TAGConv
from torch_geometric.nn import global_add_pool, SAGPooling, ASAPooling
from torch_geometric.nn.aggr import AttentionalAggregatio... |
46cf98a6b4b223770d89d5d3dbc4640fdf37743b23b7d5ffbe266b06199d1042 | Python | 17,640 | 432 | import pandas as pd
import numpy as np
import zipfile
import torch
from functools import lru_cache
import os
def return_top(srs):
concs,counts = np.unique(srs, return_counts = True)
top_counts = counts.argsort().argsort()
return (concs[top_counts <=4], )
class SynergyDataset():
def __init__(self, root ... |
9e16b54520af5db42b8511c0648ff0f2fb847fa8f1205db0726fafe406dd2b43 | Python | 17,648 | 369 | import numpy as np
import pytest
from guppy.analysis.timestamp_correction import (
applyCorrection_ttl,
correct_timestamps,
decide_naming_and_applyCorrection_ttl,
pair_timeline_label,
timestampCorrection,
)
def test_apply_correction_ttl_tdt_mode_all_above_rec_start_subtracts_only_rec_start():
... |
acbf2b58187a28e25d7ef38c85852b3013377ab1614295afa12873e9f7f4a8c0 | Python | 17,670 | 421 | ##
## CPCantalapiedra 2020
import errno, os, shutil, psutil
from sys import stderr
import time
from os.path import exists as pexists
from os.path import join as pjoin
from .utils import colorify
from .common import silent_rm, sort_seeds_file, \
ITYPE_GENOME, ITYPE_META, ITYPE_PROTS, ITYPE_CDS, get_data_path
from ... |
3a7cbb841497ae9d75fba0606db71f44b6fa643c5881693cee634c66128d5e9b | Python | 17,674 | 428 | from pathlib import Path
import struct
import numpy as np
from scipy.spatial.distance import cdist
import torch as th
from torch.utils.data import Dataset, DataLoader, WeightedRandomSampler
import time
import pandas as pd
import sys
from torch_geometric.utils import remove_self_loops
import torch
from joblib import Par... |
41d059ff002a6a19cdc9b9dbec97a5995cfc79fbb7670f5b60715bfba43737f5 | Python | 17,680 | 364 | '''
Loads pretrained VGAE and MLP models and tests them on a dataset.
If num_epochs > 0, then the models are fine-tuned on the dataset.
Authors: Hanna M. Tolle
Date: 2025-01-04
License: BSD 3-Clause
'''
import sys
sys.path.append('graphTRIP/')
from sacred import Experiment
from experiments.ingredients.data_ingredien... |
9d6293fade3836f1fae619b44b84719ada24565b6b1f478966523efecb3181f4 | Python | 17,698 | 384 | import os, torch, random
import numpy as np
import pandas as pd
from torch import nn
import torch.nn.functional as F
from sklearn.preprocessing import MinMaxScaler
import matplotlib.pyplot as plt
import argparse
from sklearn.metrics import roc_curve, precision_recall_curve, auc
from sklearn.metrics import roc_auc_score... |
8449f4114b90fd2115614a920863b9115a5034e0764254a90d916d2ac9eb1ea4 | Python | 17,701 | 470 | '''
This script is adapted from the toolkit of below CVPR paper.
If you find the functions in this script are helpful to you (for the challenge and beyond), please kindly cite the original paper:
Riqiang Gao, Bin Lou, Zhoubing Xu, Dorin Comaniciu, and Ali Kamen.
"Flexible-cm gan: Towards precise 3d dose prediction ... |
4d431dbac6901122d7dca7d33440f04e7192bebe81bc590b3c750b5628cd5e7a | Python | 17,706 | 460 | """Main module.
Holds the `BayesianOptimization` class, which handles the maximization of a
function over a specific target space.
"""
from __future__ import annotations
import json
from collections import deque
from os import PathLike
from pathlib import Path
from typing import TYPE_CHECKING, Any
from warnings impo... |
f1c844db5f4567a7cd11d02718e44b224b3b938fcbe6d589f94c3a7a1b9a5134 | Python | 17,710 | 376 | '''
In order to get mouse move event when left mouse button is pressed, we need to override a few pyqtgraph classes.
This is due to the fact that the GraphicsScene class only emits the position of the mouse without any information
whether a button is pressed or not. Theoretically this could be a bit of resource hog, ho... |
93a16f796fd250f5049a64242fb8cddd2a5ad9f53e950cd0924a7735bb102b80 | Python | 17,718 | 716 | from __future__ import annotations
import copy
from datetime import datetime
from typing import TYPE_CHECKING, Any, Generic, Literal, TypeVar
from uuid import UUID
from pydantic import BaseModel, ConfigDict, Field
from zndraw.access import GroupRole, ShareAccess, Visibility
def deep_merge(base: dict, override: dic... |
33793d11cf6301de6926f2394e6eaaeae8cef21f7368789767cd543bdaa3354a | Python | 17,772 | 609 | from __future__ import annotations
import csv
import os
from ast import literal_eval
from itertools import zip_longest
from pathlib import Path
from typing import Any, Callable, Mapping, Optional, Sequence, Union
import dateutil.parser
import numpy as np
import pandas as pd
from omegaconf import OmegaConf
from ..dat... |
943888aaa558c3e63a545e75ed5739a5483ddb158e07c3f80a36d76ed36feebe | Python | 17,777 | 423 | import warnings
from pytorch_lightning import LightningModule
from fengshen.models import transformer_utils
import torch
import torch.utils.checkpoint
from torch import nn
import torch.nn.functional as F
from dataclasses import dataclass
from typing import Optional, Tuple
from transformers.file_utils import *
from t... |
e6de9b973278db0663fbf9078911d3665b675722f461d8ba429d29077e092f9e | Python | 17,794 | 496 | import torch
import logging
import merlinth
from merlinth.layers import ComplexConv2d, ComplexConv3d
from merlinth.layers.complex_act import cReLU
from merlinth.layers.module import ComplexModule
def complex2real(z, channel_last=False, separate_echo_dim=False):
stack_dim = -1 if channel_last else 1
if separat... |
451fd121a0f9bf59afdb2dac08a46292611aeea119ed9ea86685e01aa27b2df6 | Python | 17,798 | 353 | """
Model class
"""
import numpy as np
import pandas as pd
# Imports from the stroke_outcome package:
from stroke_outcome.continuous_outcome import Continuous_outcome
import stroke_outcome.outcome_utilities as outcome_utilities
class Model(object):
"""
Model class
Attributes
----------
scenario... |
32ca97dfe7c07cf52e2a6132e4fae417db5a94a376662bef9c58b25fa169056c | Python | 17,800 | 472 | #!/usr/bin/env python
"""
MeteWIBELE: finalize characterization module
1) combine all functional and taxonomic annotations
2) format outputs
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation fi... |
a77f2e023049db9daa5e7c2730c78fe0303b597f63fd7569bba7126c146b829c | Python | 17,852 | 482 | '''
Unit test for the high level vds interface for eiger
https://support.hdfgroup.org/HDF5/docNewFeatures/VDS/HDF5-VDS-requirements-use-cases-2014-12-10.pdf
'''
import os
import os.path as osp
import shutil
import tempfile
import numpy as np
from numpy.testing import assert_array_equal
import pytest
import h5py as h5... |
6e5a046c05e5ed3ce2044bb585ba68fc3a557c5a47c8946689213557c769bbcb | Python | 17,871 | 360 | #!/usr/bin/env python
# encoding: utf-8
# %% libraries _________________________________________________________________________________________
import argparse
import datetime
import glob
import itertools
import json
import logging
import os
import sys
from os.path import join
from pathlib import Path
from statistics... |
275c0e36017e2ac0cecbc71739f5f24d99c27d0de27dbba2def8df69d277ab41 | Python | 17,906 | 405 | # coding=utf-8
# Copyright 2022 EleutherAI The HuggingFace Inc. team. 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
#... |
1515c14b3b57a90536b94b9a6d2ebe3838f65ac2a28e08ff76dc65482e27f15d | Python | 17,920 | 448 | import glob
import yaml
import torch
import numpy as np
import gc
from sklearn.metrics import precision_recall_curve
from data.t2star_loader import *
from dl_utils.config_utils import import_module
from projects.moco_t2star.utils import *
from projects.line_detection_t2star.utils import process_kspace_linedet
def gpu... |
de674b0a646fc7c5713ec8f61b52c0888f827d14de8713455cb12aee303e7eb1 | Python | 17,929 | 412 | ##################################################################
# Performing step 2 CytoCommunity in CRC simulation dataset
# Reproducibility for Figure.3C
##################################################################
import torch
import torch.nn.functional as F
from torch.nn import Linear
from torch_geometric... |
1356f229306c9ae347779b9afbd45f8af3876753215750edefeff09a2dfdb67f | Python | 17,950 | 431 | # -*- coding: utf-8 -*-
from collections import defaultdict
import numpy as np
import networkx as nx
from typing import Any, Dict, DefaultDict, List, Set
from catmaid.models import (ClassInstance, ClassInstanceClassInstance, Relation,
Review, Treenode, TreenodeConnector, TreenodeClassInstance )
class Neuron... |
75ff296b8ae29b646a6f5f7f56fe69e7c44d9b190e6b314b609b327653c4b28e | Python | 17,970 | 381 | # Generate events files for task-narratives
# This script reads raw behavior data files from d_beh for task-narratives, extracts time stamps and design information, and stores them in new *events.tsv files accompanying BOLD files.
# For more information, please see README.md and the associated paper (Jung et al., 202... |
6a6535fc1065d463db735b9d3a92373eb784ab74d0d6d9bc46c3ad783b9cae20 | Python | 17,972 | 476 | import torch
import torch.nn as nn
import torch.nn.functional as F
from einops import rearrange
import pdb
def conv3x3(in_planes, out_planes, stride=1):
return nn.Conv2d(in_planes, out_planes, kernel_size=3, stride=stride, padding=1, bias=False)
def conv1x1(in_planes, out_planes, stride=1):
return nn.Conv2d(... |
6ea49de3d683a64250c14117679983b2df9d113e83e811e58c823d6da26883a1 | Python | 17,980 | 534 | """
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.
---
This code borrows heavily from the DimeNet implementation as part of
pytorch-geometric: https://github.com/rusty1s/pytorch_geometric. Licens... |
834624aa3944779a90b3db441fb8d9d6bb871902a990c12f3ffd99c6ad083ed6 | Python | 17,987 | 561 | """Shared functions and other definitions."""
import collections
from cwl_utils.types import (
CWLDirectoryType,
CWLFileType,
CWLObjectType,
CWLOutputType,
is_directory,
is_file,
is_file_or_directory,
)
try:
import fcntl
except ImportError:
# Guard against `from .utils import ...`... |
52db618bbab8764958d37b9755acd1806c9fde01ee70bde13da40ff2bcaa516d | Python | 18,021 | 528 | import os
import pickle
import copy
import pandas as pd
import numpy as np
import torch
from torch.utils.data import DataLoader
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.Polypeptide import one_to_index, index_to_one
from tqdm.auto import tqdm
from rde.utils.protein.constants import num_chi_angles
from rde.u... |
483833d133493dc9ec40d0b3f6c83247952af89ff77f54678519cee78b0d21ff | Python | 18,032 | 459 | """
Information Resource (InfoRes) utilities
"""
import re
from typing import Optional, Tuple, Callable, Dict, List, Any
from kgx.utils.kgx_utils import knowledge_provenance_properties, column_types
from kgx.error_detection import ErrorType, MessageLevel
from kgx.config import get_logger
log = get_logger()
class In... |
fe1e8e571ae904ad032514a2d3b80f7a2db3d5f857c90e683bb930a8274696c0 | Python | 18,045 | 493 | import argparse
import math
import os
import random
import shutil
import time
import warnings
import numpy as np
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.optim
import torch.utils.data
import torch.utils.data.distributed
import torchvision.models as m... |
aac52f1e93122a27819694c52fd8e831cea3f2b6e24d41c38f98e21751d058e6 | Python | 18,054 | 466 | # -*- coding: utf-8 -*-
from collections import defaultdict
import json
from typing import Any, DefaultDict, List, Optional, Union
from django.db import connection
from django.http import HttpRequest, Http404, JsonResponse, HttpResponse
from django.shortcuts import get_object_or_404
from rest_framework.decorators i... |
d877ed7913dffddc6ad8cb1ea4b070c33099a133dd85e5333b52ecd7b70ee21b | Python | 18,059 | 397 | #-*- coding: utf-8 -*-
#setting##############################################
n_jobs=16 #並列処理の数
t_n_jobs=16
PARAMETER_DIR='/Volumes/Siena/CP/parameter'
#n_jobs=40 #並列処理の数
#t_n_jobs='cuda'
#PARAMETER_DIR='/home/takeiyuuichi/Dropbox (MEG)/CP/parameter'
set_environment='main'
SET_EVENTID=[2,3]
event_id = dict(control=2... |
20034f2bfcbdcb841b19a4a5e66dad911fe3d5c8401c8717268ea666b753b7c9 | Python | 18,062 | 447 | from typing import Tuple
from unittest import result
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
import seaborn as sns
from lmfit.models import PowerLawModel
from sklearn import linear_model
from uncertainties import ufloat, unumpy
from uncertainties.umath import *
import lmfit
from... |
c31e9d7bca36c585da3de69e51917120c41af2f684b4ceaee8623ce844df950c | Python | 18,084 | 376 | #! /usr/bin/env python3
# ################################################################
# Copyright (c) 2016-present, Przemyslaw Skibinski, Yann Collet, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under both the BSD-style license (found in the
# LICENSE file in the root directory of this ... |
03141259f6f47f1e10ac5767fcc2e88a36334f487c49f3fdb25920a97e956c06 | Python | 18,085 | 418 | from typing import Union
import sympy as sp
import libsbml
import jax.numpy as jnp
import numpy as np
import pandas as pd
import re
import collections
import os
from jaxkineticmodel.utils import get_logger
from jaxkineticmodel.load_sbml.jax_kinetic_model import NeuralODE
from jaxkineticmodel.load_sbml.sympy_converter ... |
04f93c39c088483405529d3782b5397b654bf171d74026249756c2755a50657a | Python | 18,088 | 499 | import inspect
import time
from dataclasses import dataclass
import jax
import optax
from jaxkineticmodel.load_sbml.sbml_model import SBMLModel
from scipy.stats import qmc
import logging
from jaxkineticmodel.building_models import JaxKineticModelBuild as jkm
import numpy as np
import jax.numpy as jnp
import equinox
im... |
13ae41cf5b070112710a16386c7b6cbb74563fd0dda01e0d9f75908b0520960d | Python | 18,094 | 367 | #!/usr/bin/env python
# encoding: utf-8
# %% libraries _________________________________________________________________________________________
import argparse
import datetime
import glob
import itertools
import json
import logging
import os
import sys
from os.path import join
from pathlib import Path
from statistics... |
a98c548429ccf6717491f2c52dab574850c8a2f62652d96978a464b40b6d2fb9 | Python | 18,126 | 504 | import enum
import logging
from dataclasses import dataclass
from typing import Mapping
import ase
import torch
import torch.nn.functional as F
from simgen.calculators import MaceSimilarityCalculator
from torch import nn
from torch_scatter import scatter_logsumexp, scatter_max, scatter_sum
from tqdm import tqdm
from ... |
21f8a545569ee56224a21a73b6f1491479929fd1f37cc1187458a7e61bf3b5a0 | Python | 18,128 | 546 | """
Module to define base classes.
"""
import sys
import traceback
from abc import ABC, abstractmethod
from datetime import timedelta
from os import makedirs
from os.path import exists as pexists, join as pjoin
from pathlib import Path
from shutil import copyfile
from timeit import default_timer as timer
import num... |
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