sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
d0152d459e9eed3235c44b64dda4b07c261713f25510ed7610d32de5648a3b43 | Python | 6,863 | 209 | """Integration tests for worker resilience — SIO disconnect vs. HTTP DELETE.
Verifies that removing eager `cleanup_worker()` from SIO `on_disconnect`
does not break the system:
- SIO disconnect preserves worker records (sweeper handles cleanup).
- HTTP DELETE (jobs.disconnect()) still cleans up correctly.
- Server res... |
2a2c70f27b8ab135d0cdbdd27ab5cc9222cb1ffb5810a55fadff47d0ffe0874b | Python | 6,866 | 183 | # Copyright (c) OpenMMLab. All rights reserved.
from typing import Optional, Tuple, Union
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule, build_activation_layer, build_norm_layer
from mmengine.model import BaseModule
from torch import Tensor
from mmseg.models.decode_heads.decode_head import BaseDe... |
a8187fb3530ddddcc22ce42400bb1017262e965600bea3c4c31622966b9a755e | Python | 6,868 | 175 | """EGNN model"""
from typing import Optional, Tuple
import torch
from torch import nn, Tensor
from .block import EquivariantBlock, SinusoidsEmbeddingNew
from .util_funcs import coord2diff, symmetrize_edge, get_ji_bond_index
class EGNN(nn.Module):
def __init__(
self,
in_node_nf: int = 8,
... |
b600ce294342388c68e3d4b12a7ea7aaafeb828d340074ae42a05b78749f3811 | Python | 6,868 | 232 | """Main Graupner-Brunel STDP example script"""
# pylint: disable=R0914
from __future__ import print_function
import pickle
import bluepyopt as bpop
import matplotlib.pyplot as plt
import numpy as np
import gbevaluator
import stdputil
cp_filename = 'checkpoints/checkpoint.pkl'
evaluator = gbevaluator.GraupnerBrunel... |
32ec106f8062162986df7fc9027b2b503be1fc939304841cf45f384f072027a4 | Python | 6,869 | 133 | # 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... |
7a0446044fb8696515999dfa2f4fa4d537024917f38b52b29da4ef314c955816 | Python | 6,871 | 198 | #!/usr/bin/env python
import argparse
import errno
import glob
import os
import platform
import shutil
import subprocess
import sys
from contextlib import contextmanager
# Monkey-patch the API inconsistency between Python2.X and 3.X.
if sys.platform.startswith("linux"):
sys.platform = "linux"
CONFIG = {
"USE... |
b8077a8e4b4ef15c5e4ee39d8a036ebcf8af0d34ec91010b6081a8bd978e6e05 | Python | 6,873 | 211 | import sys
import yaml
import hashlib
DEFINE = 'YAML_GEN_TESTS'
EVENT_COUNT = 5
def encode_stream(line):
for c in line:
if c == '\n':
yield '\\n'
elif c == '"':
yield '\\"'
elif c == '\t':
yield '\\t'
elif ord(c) < 0x20:
yield '\\x' +... |
06137e30a7a90eecbeb032760053f17c916a8322a9e758e5e2b362452804ada9 | Python | 6,875 | 178 | # SPDX-License-Identifier: BSD-3-Clause
import torch
import onnxruntime
import onnx
from onnx import numpy_helper
from PIL import Image
from torchvision import transforms
import numpy as np
import os
import urllib
# GitHub Repo | Model
MODELS = [
('pytorch/vision:v0.5.0', 'shufflenet_v2_x0_5'),
... |
96b53d636e4a9cfa89fe5dbe5ee53aa4643cb1233ba0f48d0861d3e5e88c9625 | Python | 6,875 | 175 | import numpy as np
from os.path import dirname
from collections import Counter
from copy import deepcopy
from math import log
from PIL import Image, ImageDraw, ImageFont, ImageChops
class Motif:
"""
The Motif class is a convenience class to compute and plot a position-weight matrix (PWM).
The only functio... |
29bffe37488fc43cfb4203cd0c449bcb779fe54c6b24b96150005f4bb5040480 | Python | 6,879 | 170 | """
Detection of the posterior edge of C2-C3 disc
The models have been trained as explained in (Gros et al. 2018, MIA, doi.org/10.1016/j.media.2017.12.001),
in section 2.1.2, except that the cords are not straightened for the C2-C3 disc detection task.
To train a new model:
- Install SCT v3.2.7 (https://github.com/sp... |
e7a8b0a59599f1b54b40975afccb3ff75271d9985ae3735d7dbf64d1e0639e6b | Python | 6,880 | 151 | import nibabel as nib
import matplotlib.pyplot as plt
from matplotlib.colors import LinearSegmentedColormap
import numpy as np
import pandas as pd
import openpyxl
from openpyxl.styles import Font, Alignment, PatternFill
# Define the colors for the colormap
colors = ["blue", "aquamarine", "yellow", "red"]
#... |
969a4a2ea91a7a500aab043f701cd28579b74e568d11dd7e32aca10ad94b4ea6 | Python | 6,882 | 169 | # resnet model
# when tuning start with learning rate->mini_batch_size ->
# momentum-> #hidden_units -> # learning_rate_decay -> #layers
import tensorflow.keras as keras
import tensorflow as tf
import numpy as np
import time
import matplotlib
from utils.utils import save_test_duration
matplotlib.use('agg')
import ... |
466490c290c431ce1a8c44e62c8f48023a77a78a0c7be30b0e1193b3dc424a93 | Python | 6,884 | 209 | from django.conf import settings
from django.db import connection
from django.http import JsonResponse
from django.utils.decorators import method_decorator
from django.views.decorators.cache import never_cache
from django.contrib.auth.decorators import login_required
from django.shortcuts import get_object_or_404
from... |
9f4095a15912ada32a2658516588126776fa025ab8141a6d8910ee3b27cd43f6 | Python | 6,886 | 128 | # -*- coding: utf-8 -*-
from django.test import TestCase
from django.contrib.auth import get_user_model
from django.http.request import QueryDict
from catmaid.control.common import get_request_bool, get_request_list
from catmaid.models import Project, Class, Relation, ClassInstance, \
ClassInstanceClassInstance
fr... |
75ba904573d93244c4c1ea3bc0d3064d7e6b0ff31551dbee7cfd6b4360338735 | Python | 6,887 | 124 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
dcf24d0e7bceb3de9107495b20c773718f4db5a2d0e0777f1cd71bedf80d5d77 | Python | 6,887 | 118 | import scipy
import numpy as np
from .gemsbindings import KvlMeshCollection, KvlTransform, KvlOptimizer, KvlCostAndGradientCalculator, KvlImage
def kvlWarpMesh(sourceMeshCollectionFileName, sourceDeformation, targetMeshCollectionFileName):
#
# Applies sourceDeformation to the reference node positions of the s... |
fdb19e094a34f5a1a0ea9bae4d4c5a40a182f44737eae1b620bce81b0674cbe4 | Python | 6,887 | 173 | #!/usr/bin/env python
#
# Generate QC report
#
# Copyright (c) 2019 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import os
import sys
from typing import Sequence
import textwrap
from spinalcordtoolbox.reports.qc import generate_qc
from spinalcordtoolbox.reports import qc2
from spinalc... |
e980b52ef82023c19235d74156636166aef2e6306098e81f8c8838b9b1890c67 | Python | 6,888 | 204 | """Panel controller for BrainGlobe access"""
from typing import Callable, Optional, Sequence, TYPE_CHECKING
from PyQt5 import QtCore
from magmap.brain_globe import bg_model
from magmap.io import libmag
if TYPE_CHECKING:
try:
from brainglobe_atlasapi import BrainGlobeAtlas
except ImportError:
... |
7fdfd475faccfe2ebb75bf4311f30e4917f388505fc7e603c0503464c8c0ea62 | Python | 6,889 | 204 | import time
import json
from collections import defaultdict
import torch
import torch.nn.functional as F
import torch.distributed as dist
import utils
def inference(data_loader, model, result_path, class_names, no_average,
output_topk, tb_writer=None, write_embeddings=False):
print('inference')
... |
6b237aa18602adb6145aa48f96dcf97bb1af102566cab06e213364715d9fc951 | Python | 6,890 | 225 | #*******************************************************#
# Classes used as configuration files
#*******************************************************#
class datasetConfig:
'''
Class for defining dataset parameters: shape, split ratio, augumentation etc.
'''
'''
Labes_csv_path: Root directory w... |
bb473b135474c2f2ad600508a442d8bf56acad07d5f143670d0780fdd3dcd51c | Python | 6,892 | 203 | from typing import List
from medperf.commands.association.utils import (
get_experiment_associations,
get_user_associations,
)
import medperf.config as config
from medperf.entities.interface import Entity
from medperf.entities.schemas import BenchmarkSchema
from medperf.account_management import get_medperf_us... |
0a2aa2c8abf5d8bee6d15bbc81017cd13ebcdd6d1c113043ad6d27270e843fad | Python | 6,894 | 211 | """
Copyright (c) 2016-2020, EPFL/Blue Brain Project
This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
This library is free software; you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License version 3.0 as published
by the Free Software Foundation.
... |
d7e073e959f0f683fdbd294fd399741e1e818d8729334ebad6273afa54ae4afc | Python | 6,894 | 155 | import torch
from torch.optim import lr_scheduler
import numpy as np
from data import read_config, get_datasets, get_generic_dataset
import models
from training import Trainer
import argparse
import sys, os, json
def parse_args():
# Get args
parser = argparse.ArgumentParser()
parser.add_argum... |
1ad6012d1a86ccad6c3a99079d3dfcf6ce401df9e1013dcdc45b884d792853d1 | Python | 6,899 | 160 | import json
from tqdm import tqdm
import argparse
def save_data(data,file_path):
with open(file_path, 'w', encoding='utf8') as f:
for line in data:
json_data=json.dumps(line,ensure_ascii=False)
f.write(json_data+'\n')
label2id={"打车": "0", "地图导航": "1", "免费W... |
06f8ecdb5876b30bf9e6febe1c0517117818d6e717d98185de6affa4cab48b6f | Python | 6,904 | 171 | '''Feature prediction with neural code conversion: prediction (test) script'''
import os
import glob
import numpy as np
import pandas as pd
import hdf5storage
import bdpy
from time import time
from bdpy.util import makedir_ifnot
from bdpy.dataform import load_array, save_array
from fastl2lir import FastL2LiR
# Main ##... |
7772a865961424a6815b64d6ed69e92c1ce9e1257df43c0ffac075d9249951cf | Python | 6,907 | 178 | import numpy as np
def create_experimental_stimulus(condition, dt, c_coh_gra, c_coh_pla, c_incoh_gra, c_incoh_pla,
test = 'NullMov', num_stim_dirs = 3, T = 48000, t0 = 0, t0adap = 6000, t0test = 36000,
duralt = 1500):
"""
Creates stimulus conditions to pass to neurons, according to experimental protocol.
Argu... |
e151d4d49da2df97e18a0d05c9e1e211f0ae8fde86704943d731a5f30e91c18e | Python | 6,907 | 174 | from nilearn.image import load_img
import numpy as np
import nibabel as nib
from nilearn.plotting import plot_img
def get_axial_slices(nii_file_path, num_slices):
"""
Calculate axial cut coordinates (in world space) for a NIfTI file using Nilearn.
:param nii_file_path: Path to the NIfTI (.nii) ... |
68889daa89bd1fd0de7c8dd8298e0ea5a54fd8f50e13f7eaba50776971281c1e | Python | 6,908 | 212 | #!/usr/bin/env python
# coding: utf-8
import os.path as op
import random
import time
import matplotlib.pyplot as plt
import numpy
import sklearn
import torch
import torch.nn.functional as nn_func
from sklearn import preprocessing
from sklearn.metrics import adjusted_rand_score
from torch.nn import Linear
from torch_g... |
e3e17e52f23a85794205ef098d072c2d3f4f28a096e01013c9085dbba559d3db | Python | 6,908 | 236 | """Test fixtures for zndraw-auth."""
from collections.abc import AsyncGenerator
from typing import Annotated
import pytest
from fastapi import Depends, FastAPI
from httpx import ASGITransport, AsyncClient
from pydantic import BaseModel
from sqlalchemy import text
from sqlalchemy.ext.asyncio import async_sessionmaker,... |
8f8144590e47d7cf4cb0f634d52cc70037aa21cb80ea5cd24a6063368146b589 | Python | 6,909 | 225 | """Tests for application configuration."""
import os
from pathlib import Path
import pytest
from httpx import AsyncClient
from zndraw.config import Settings
class TestStorageUri:
"""Test storage URI configuration."""
def test_default_storage_is_memory(self) -> None:
"""Default storage should be me... |
9f97764246a15800b44be5c8ffc885c6794d1f2826b93419465024152d37246a | Python | 6,909 | 198 | import os
import numpy as np
import pandas as pd
import math
import random
from datetime import datetime
import pickle
from utils import pkl_load, pad_nan_to_target
from scipy.io.arff import loadarff
from sklearn.preprocessing import StandardScaler, MinMaxScaler
def load_UCR(dataset):
train_file = os.path.join('da... |
aacf94341e8a4bfbc8a0c5f7f2a4703f3e450778502e69bf8f02ae6878dd3f17 | Python | 6,909 | 210 | """
Basic interface between the UI and the processing module
@author: Andrei Istudor andrei.istudor@hu-berlin.de
"""
import socket
from sys import argv
from os import path
import time
import subprocess
# from main import processVideo
from ProcessVideo import ProcessVideo
from Logger import Logger
# def setNon... |
61a1ec63872057477d8abf00ce081c87545c616ef2d02e8a84d54e14426bf6ba | Python | 6,915 | 189 | # tests/test_router_task_submit.py
"""Tests for task submission endpoint using shared fixtures."""
from unittest.mock import AsyncMock, MagicMock
from conftest import make_room_address
from zndraw_joblib.exceptions import ProblemDetail
from zndraw_joblib.registry import InternalRegistry
from zndraw_joblib.schemas im... |
7c7036c7b3b716ae27491fe6307ff2e17757e5d0a23666a1e1a91753ab57f3e4 | Python | 6,915 | 155 |
# We now have data that has been PLS'ed/CCA'ed with fMRI as the informing variable
# I may be missing import statements, so add if you find something I missed
import os
import pandas as pd
import numpy as np
from tqdm import tqdm
CURR_PATH = '/Users/karinsaltoun/dblabs/asymm_pat_age_progression'
os.chdir(CURR_PATH)... |
2d6ecf31eb367f1488d370f7f42704a49c70f7c884e5636a7078512f326b9b10 | Python | 6,918 | 191 | import os
import datetime
import shutil
import math
import random
from transforms.spatial import Preprocessing
from sklearn import metrics
from dataset_info import label_info
import numpy as np
import torch
from sklearn.metrics import classification_report
from copy import deepcopy
class ModelEMA:
""" Model Expon... |
ce668e3c1a441793c4ff2a6b59cd217bff478e9d21521bc595352fe8ec18d79b | Python | 6,919 | 189 | from rest_framework import status
from medperf.tests import MedPerfTest
from parameterized import parameterized, parameterized_class
class BenchmarkTest(MedPerfTest):
def generic_setup(self):
# setup users
bmk_owner = "bmk_owner"
prep_mlcube_owner = "prep_mlcube_owner"
ref_model_... |
818b24c437b85d543bc3c69f7ca2df063c903b1c8094bf823959dcc74f1e2c7b | Python | 6,924 | 209 | # src/zndraw_joblib/dependencies.py
import hashlib
import json
from typing import Annotated, Any, Protocol, runtime_checkable
from uuid import UUID
from fastapi import Depends, Path, Request
from fastapi_users.authentication import JWTStrategy
from zndraw_socketio import AsyncServerWrapper
from zndraw_joblib.exceptio... |
c1f8e86ccee6c87e3ddfc864f2865bbeaf2ba86a4404e555a37792f169f5e130 | Python | 6,925 | 176 | """Regression checks for the chemicals compendium.
Two kinds of assertions live here:
EXPECTED_IN_CHEMICALS / NOT_IN_CHEMICALS
— ID-presence checks: is a CURIE in the chemicals intermediate ID file?
— These depend on existing vocab fixtures (mesh_pipeline_outputs,
umls_pipeline_outputs, …) — only writ... |
5cc65022159d6e4461141357e6998056cd89826ae0adbc4ef37dbf2d5b7d1e54 | Python | 6,930 | 183 | import h5py
import os
import numpy as np
import networkx as nx
import pickle as pkl
import scipy.sparse as sp
from datetime import datetime
from pathlib import Path
def load_hdf_data(path, network_name='network', feature_name='features'):
"""Load a GCN input HDF5 container and return its content.
... |
d58dd75e926bbbb7b5f7ce92d3fc70f28960ac5bf8c3ea15a57023d63d95f397 | Python | 6,934 | 216 | from zetapy import getZeta, zetatest
from joblib import Parallel, delayed
from myphdlib.general.toolkit import psth2
# from myphdlib.pipeline.main import ModuleBase
import numpy as np
# TODO
# [ ] Recompute the visual response amplitudes and compute respone amplitudes to saccades
# [ ] Measure the latency to the very ... |
5bffb9bb16ab07907469781f0a456e2ff111bad9a7f1ea1bae7b97471e898b53 | Python | 6,935 | 248 | import pytest
import numpy as np
from numpy.testing import assert_allclose
from keras import backend as K
from keras import activations
from keras.layers.core import Dense
def get_standard_values():
"""A set of floats used for testing the activations.
"""
return np.array([[0, 0.1, 0.5, 0.9, 1.0]], dtype... |
3b80a652f14489383df703dcbb9322af7def1338b3b3ae48d70b2051a0fa2970 | Python | 6,939 | 167 | """Context-Aware Implicit Neural Representations to Compress Earth Systems Model Data
DEVELOPED AT:
Department of Chemical Engineering
University of Utah, Salt Lake City,
Utah 84112, USA
DIRECTOR: Prof. Salah A Faroughi
DEVELOPED BY:
... |
9ea01f28e1117ca2a02a3ff3455e8b21fdddfa73ce6b80c26c4d48306562d388 | Python | 6,940 | 235 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import json
import seaborn as sns
class DefaultTracking():
"""Expects to get a dict with a value for each epoch in form
{measure1:[val1, val2, ...], measure2:[val1, val2, ...], ...}
"""
values = None
def set_d... |
017dbec4fa6358a7ef99e84aa1efa72310743963773a8670f50de2394d089083 | Python | 6,943 | 193 | # Copyright (c) OpenMMLab. All rights reserved.
from unittest.mock import patch
import pytest
import torch
from mmengine.structures import PixelData
from mmseg.models.decode_heads.decode_head import BaseDecodeHead
from mmseg.structures import SegDataSample
from .utils import to_cuda
@patch.multiple(BaseDecodeHead, ... |
a6512fd9176514dc64e91330aad5cc0fda1116caf0d4844898b32dc0ca88fff8 | Python | 6,945 | 175 | #!/home/preclineu/hansav/.conda/envs/py38/bin/python
"""
Created on Thu Aug 29 11:16:53 2024
@author: hansav
"""
"""
####################
#Elastic Net Regression classification BDI score --> PERMUTATION
####################
"""
import pandas as pd
import numpy as np
import os
import sys
from pcntoolkit.dataio.file... |
10c878ca2cf0d92f38eacaa7198c2d56e8e86b8261e30d36eb117ad6f7449860 | Python | 6,947 | 193 | # Copyright DST Group. Licensed under the MIT license.
from ipaddress import IPv4Address, IPv4Network
from typing import Optional
from networkx import shortest_path, NetworkXNoPath, NodeNotFound
from networkx.classes.function import nodes, induced_subgraph
from CybORG.Shared import Observation, CybORGLogger
from CybO... |
9ec222065eff38cfa31a24731e35c4ee31b3ab28d4827dd3523eefc94393bf36 | Python | 6,949 | 242 | import urllib.parse
from io import BytesIO
from pathlib import Path
from typing import IO, Any, cast
import pytest
from cwl_utils.types import CWLObjectType
from ruamel.yaml.comments import CommentedMap
from schema_salad.sourceline import cmap
from cwltool.builder import content_limit_respected_read
from cwltool.comm... |
022cbb7ffb362d47543c567e065cc16053d583ce40618a2a15fa5c780fe871fe | Python | 6,952 | 193 | import torch
from torch.nn import Module
from torch.nn import functional as F
from models.graph import NodeEdgeNet
from models.transition import ContigousTransition, GeneralCategoricalTransition
from .common import *
from .diffusion import *
class BondPredictor(Module):
def __init__(
self,
confi... |
c33d8eeadefe2b339efa67ef5603259f02650e41353cdd6ecbc893a740902e9b | Python | 6,955 | 164 | import time
import argparse
from types import SimpleNamespace
from pathlib import Path
import torch
from eval_utils import load_model
# It only takes effect on the model parameters guided by conditions.
def generation(model, ld_kwargs, num_batches_to_sample, num_samples_per_z,
batch_size=512, d... |
174b85f5fccd8e771362452ab493bb11eaa76598999db6653031fdb1f5a482dc | Python | 6,959 | 210 | #!/usr/bin/env python
# coding: utf-8
# In[45]:
import torch
import pickle
import os
import ipdb
import os.path as osp
import numpy as np
import pandas as pd
from torch_geometric.data import Data
from torch_geometric.data import InMemoryDataset
from torch_sparse import coalesce
def load_dataset(path='../data/raw... |
bb6e6a23c0f63164a84b9e40e188df806f82b20f498f0953fff15139abc1b581 | Python | 6,965 | 207 | """Can a DLPack-adopted grid be fed straight into a 3D CNN?
test_dlpack_paths.py checks the protocol -- capsules, ownership, rejection.
This file checks the thing the protocol exists for: that the tensor coming out
the other side is a first-class input to torch's Conv3d and to the models in
nearl.models, with no copy,... |
9b5155c524bea53416d953b5700e04900e6d4637e6a002b7a14aa0e199b7f2d5 | Python | 6,966 | 201 | import numpy as np
import pytest
import torch
from ase import Atoms
from ase.build import molecule
from e3nn import o3
from mace.modules.blocks import RealAgnosticInteractionBlock
from mace.tools import AtomicNumberTable
from hydromace.interface import HydroMACE
from hydromace.tools import (
assign_num_hydrogens_a... |
aa91bed5827b0785227774476aa82bbf10f26413dad95b93401054683f53ce42 | Python | 6,966 | 201 | #!/usr/bin/env python
#
# Compute MT saturation map and T1 map from a PD-weigthed, a T1-weighted and MT-weighted FLASH images
#
# Reference paper:
# Helms G, Dathe H, Kallenberg K, Dechent P. High-resolution maps of magnetization transfer with inherent correction
# for RF inhomogeneity and T1 relaxation obtained ... |
e169b1a7272fe9632a0d9496203e77bc1ba533deeb01ebf153d17611ae5c239e | Python | 6,967 | 170 | # Once we generate the compendium files, we need to convert them into the
# Knowledge Graph Exchange (KGX, https://github.com/biolink/kgx) format.
# This file provides code for doing that, based on the code from
# https://github.com/NCATSTranslator/NodeNormalization/blob/68096b2f16e6c2eedb699178ace71cea98dc794f/node_no... |
a7ef2a7c6980f8ac3b786ca18482c3f2d10c929b34922ce98b9403f8ffdb0854 | Python | 6,972 | 193 | from luna.paths import LunaPaths
from luna import candidate_info, dataset
from luna.ct import Ct
from luna.prepcache import LunaPrepCacheApp
from torch.utils.data import DataLoader
from Utils.models import *
from Utils.TrainModelLUNA import *
from Utils.config import *
from tqdm import tqdm
import matplotlib.pyplot as ... |
d56e8d7eec3274d2409d1fb226a6d10594e96531010b426b099bbf3f73b272fa | Python | 6,972 | 170 |
from typing import Optional, Sequence
import torch._dynamo.guards
from models.helpers import generic_scan, generic_scan_with_states, spike_grad_injection_function
import torch
import torch.nn.functional as F
from torch.nn import Module
from torch import Tensor
from torch.nn.parameter import Parameter
from module.tau... |
0cd8702fba92972e2b34802d1c690f11e5ec4686e3633ba24569234788c1bdb1 | Python | 6,975 | 198 | """Preprocessing functions to extract gfp peaks."""
from typing import Optional, Union
import numpy as np
from mne import BaseEpochs, pick_info
from mne.io import BaseRaw
from mne.io.pick import _picks_to_idx
from numpy.typing import NDArray
from scipy.signal import find_peaks
import matplotlib.pyplot as plt
... |
19263da7b547eec1c6336caf4d6b06566bbc2f4855339703a16edaaeae02726f | Python | 6,975 | 202 | # /// script
# requires-python = ">=3.11"
# dependencies = [
# "requests>=2.30.0",
# ]
# ///
"""
Script for downloading and building HDF5 on Windows
This does not support MPI, nor non-Windows OSes
This script may not completely clean up after itself, it is designed to run in a
CI environment which thrown away eac... |
5113e7d119e98081391a57547c98bbc5ad8e1d8b3f6e39cf7aeb5c7e04853392 | Python | 6,978 | 158 | import logging
from collections import defaultdict
import jsonlines
from src.babel_utils import glom
from src.categories import GENE
from src.metadata.provenance import write_concord_metadata
from src.prefixes import NCBIGENE, UNIPROTKB
from src.util import LoggingUtil
logger = LoggingUtil.init_logging(__name__, lev... |
ad571f3779aa04794c6a7fc52b95f91f6b61cf8ba8bd05a67ef989f4815ecf3b | Python | 6,978 | 236 | import os
import pytest
import medperf.config as config
from medperf.entities.cube import Cube
from medperf.containers.runners.runner import Runner
from medperf.tests.entities.utils import (
setup_cube_fs,
setup_cube_comms,
setup_cube_comms_downloads,
)
from medperf.exceptions import InvalidEntityError
fro... |
be6e10e2aa172f996daaf5e3a86e427a3e66e0fefed69fbe85364e88e4a613df | Python | 6,979 | 168 | import json
import pytest
from guppy.frontend.group_labeling import (
CREATE_NEW_GROUP,
EDIT_EXISTING_GROUP,
GroupLabelingPage,
save_group_definition,
)
from guppy.utils.utils import GROUP_MEMBERS_FILENAME, read_group_members
@pytest.fixture
def member_run_folder(tmp_path):
"""A usable group mem... |
2283a557c904f3efc7ebda085e155846168672aed14554d95976bdd69e1a66f2 | Python | 6,980 | 196 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# Borrowed from https://github.com/facebookresearch/segment-anything
from typing import List, Tuple
import torch
from to... |
a3bd94f4cec8f568545c19b054df7e44556bb73f30c6242e7ab22f254beec57d | Python | 6,982 | 197 | _base_ = ['../_base_/default_runtime.py', '../_base_/datasets/cityscapes.py']
crop_size = (512, 1024)
data_preprocessor = dict(
type='SegDataPreProcessor',
mean=[123.675, 116.28, 103.53],
std=[58.395, 57.12, 57.375],
bgr_to_rgb=True,
pad_val=0,
seg_pad_val=255,
size=crop_size,
test_cfg=... |
18badae7a83580b9ad27eaa8992fef0e318d884a9c5de6b2ffd2b8fb1348ea42 | Python | 6,983 | 206 | #!/usr/bin/env python2.7
import os, sys
import argparse
import math
import ctypes
import warnings
import multiprocessing as mp
from multiprocessing import Lock, Value, Pool
import numpy as np
import scipy.spatial
from Utils import *
def kclustering(data, restarts, threshold, seed=None, lord=1, j=1, LB=1, UB=None... |
f7908751d4ee0b114a893397f5540b7190ad54152055589d17f3350345ea6a3d | Python | 6,986 | 178 | """Contract tests for orchestrate_read_raw_data error enrichment."""
import shutil
import time
from pathlib import Path
import pytest
from guppy.extractors.base_recording_extractor import BaseRecordingExtractor
from guppy.orchestration.read_raw_data import orchestrate_read_raw_data
from guppy.utils.progress import S... |
7030bae2aaf9c548885b40cda1d2578dbf9cdcf23594f04290d4a292d3c7de8b | Python | 6,987 | 162 | import argparse
import os
from torch.autograd import Variable
import torch
from time import time
from models import Converter
import numpy as np
from bdpy.dataform import save_array
from bdpy.util import makedir_ifnot
from utils import fastl2lir_parameter, test_fastl2lir_revise
import itertools, bdpy
from utils import ... |
bfd760531f2a5815aa42e46ef4d5d9afc1c0722ed6304332beaa7f2805cd24e8 | Python | 6,987 | 162 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
a420d5ddae16c53fb39310c7d1454cc5b93938a4aae4f665dfdb5e627d60b3c1 | Python | 6,988 | 310 | import torch
import torch.nn as nn
import torch.nn.functional as F
import pdb
class DoubleConv(nn.Module):
"""(convolution => [BN] => ReLU) * 2"""
def __init__(self, in_channels, out_channels, mid_channels=None):
super().__init__()
if not mid_channels:
mid_channels = out_cha... |
15678ad3502e2f7bafe07fd799fc861d6212e2b8e96578309e463e8a72fd9f66 | Python | 6,991 | 242 | import os
import re
import numpy as np
import pathlib as pl
from scipy.signal import find_peaks
# Number of samples in a single LabJack dat file
NSAMPLES = 12000
# Number of channels sampled by the LabJack
NCHANNELS = 9
class LabJackError(Exception):
pass
def readDataFile(dat, line_length_range=(94, np.inf)):
... |
742a018eaa4635f8ed27e5908fabc9d7383e056c7aa4f30b772f0609ea42f015 | Python | 6,992 | 205 | # 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... |
7e66e353293810775d97a7f4410d0f9169a5e6261987dc18c8499c0fb124b904 | Python | 7,000 | 159 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
acbaf4d13651eff2b78b1b3906f21d3e4eb6e2b7ce983a011c97d08b7c080df4 | Python | 7,009 | 184 | '''
These functions are rather specific to Amod's deeplearning code
and should probably be either moved or completely deleted. It might
make sense to develop some more universal normalization utility functions.
'''
import numpy as np
def piecewise_linear_normalize(in_img_data, ref_img_data):
'''Function to piece... |
bad9bf4cc431eebbe39beb9dd6da77f0cb8a33f77b69bb88d1146df4cc46e1df | Python | 7,009 | 238 | #*******************************************************#
# Classes used as configuration files
#*******************************************************#
class datasetConfig:
'''
Class for defining dataset parameters: shape, split ratio, augumentation etc.
'''
'''
Labes_csv_path: Root directory w... |
f3012247bedca4b88ed8837b0e00ae61c0531fa0c4e517afff10fd2b4a680779 | Python | 7,009 | 191 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import itertools
from multiprocessing import Pool
import os
import shutil
import numpy as np
from dmriqcpy.analysis.stats import stats_mean_in_tissues
from dmriqcpy.io.report import Report
from dmriqcpy.io.utils import (add_online_arg, add_overwrite_arg,... |
0c3682b748f9ad4d37e167184233f1a2af4bb2bbf99e1a8a8fd2b3bc51458b02 | Python | 7,010 | 156 | import os
from freesurfer.samseg.SamsegLesion import SamsegLesion
from freesurfer.samseg.SamsegLongitudinal import SamsegLongitudinal
from .SamsegUtility import *
class SamsegLongitudinalLesion(SamsegLongitudinal):
def __init__(self,
imageFileNamesList,
atlasDir,
savePath,
userMode... |
12f7260d741a1bec71692d464f173b4132507bb0ea63b3c1724521ddc70bb2bc | Python | 7,015 | 204 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import argparse
import imageio
import os
import sys
import numpy as np
import tensorflow as tf
from tensorflow.contrib.slim.python.slim.nets import inception
from geomstats.invariant_metric import InvariantMe... |
09d5ba175f159e5bb1c659fac142d6e6194cd6522bd327856af0ecf6c6200186 | Python | 7,025 | 272 | ##
## CPCantalapiedra 2020
import os, subprocess, sys
def run(cmd):
'''
Runs eggnog-mapper with the arguments specified.
Replaces leading ./emapper.py with the current Python interpreter so
that tests always run inside the active venv.
'''
if cmd.startswith("./emapper.py"):
cmd = sys.e... |
cfeee7581fe17c8be7b2b525bcb0d4c6107ca702979812a5d47ae8ad524ae7ad | Python | 7,025 | 219 | from functools import partial
import numpy as np
import torch
from tqdm import tqdm
from neuralpredictors.measures import modules
from neuralpredictors.training import (
early_stopping,
MultipleObjectiveTracker,
LongCycler,
)
from nnfabrik.utility.nn_helpers import set_random_seed
from ..utility import sc... |
563ba8114476f77e1a160d2aba9b84b474caacbcfe8c78361359b17875a4cc3a | Python | 7,026 | 220 | import logging
import traceback
import os
import platform
import re
import socket
import subprocess
import sys
import tarfile
from importlib import metadata
import psutil
import yaml
from medperf import config
def get_system_information():
try:
# Get basic system information
system_info = {
... |
afe7ce2e1f9adc3ee666c0616779e82e7b9a0468d411a39928b4d9dbc8f6efed | Python | 7,026 | 207 | """
Processing of raw geographic data for model
"""
import pandas as pd
class Geoprocessing(object):
"""
Processing of raw geographic data for model.
"""
def __init__(self, limit_to_england=False):
"""
Initialise geographic class.
Attributes
----------
admi... |
5d0b4541d825edfce2c2d17784671375c4668cf34e65fa54818107421882c963 | Python | 7,027 | 244 | #!/usr/bin/env python
"""
Module for calculations related to the SO(3) group
"""
import sys
import numpy as np
import torch
from typing import Tuple, Union, TypeVar
Tensor = TypeVar('torch.tensor')
def taitbryan_to_matrix(
angles: Union[Tensor, np.ndarray]
) -> Union[Tensor, np.ndarray]:
"""
Takes ... |
4ba26f4969919fd08bbd2d38aa10d7e0113508dab0d778c7ded8fa934a585c6f | Python | 7,038 | 229 | """CLI commands for visual preset operations."""
from __future__ import annotations
import fnmatch
import pathlib # noqa: TC003 — Typer evals annotations at runtime
from typing import TYPE_CHECKING, Annotated
import typer
from zndraw.schemas import Preset, PresetRule
from .connection import (
PasswordOpt,
... |
0dd9f50770428f94082961c9645909a187bde39813e8818bf634d08f208b7901 | Python | 7,040 | 230 | """
Benchmark the 3 modes:
1. Static feature: AtomType
2. Marching Observers
3. Probability Density Flow
"""
import argparse
import json
import os
import time
from collections import OrderedDict
import h5py as h5
import nearl
import nearl.features
import nearl.featurizer
import nearl.io
# from nearl.io import Traje... |
72d689d00bfd9b00012dc3271ff765639e13b0c65fd9eb5d44a5d47145a5e50d | Python | 7,047 | 128 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
0b2682e3c5598f3df2566e9013f9a6e761e782dc00f78d0ba53dff12a0c9e7f6 | Python | 7,051 | 221 | """
DeepEtoProfile entry point: pheno_ui.py
- Defines the :class:`pheno_ui` class
- The __main__ method intatiates this class with the number of processing tasks passed as parameter (default = 1) and shows the dialog
"""
"""
@author: Andrei Istudor andrei.istudor@gmail.com
"""
__version__ = 0.1
import os
im... |
b90ffb4c4de03a792a95a11af70c63a8dc59cc10936b939f37fbe5f0142f4f80 | Python | 7,051 | 187 | import torch
import torch.nn as nn
def weights_init(m):
if isinstance(m, nn.Linear):
torch.nn.init.xavier_uniform_(m.weight)
torch.nn.init.zeros_(m.bias)
class PINNet(nn.Module):
def __init__(self,input_size, pathway, num_fc):
super(PINNet, self).__init__()
... |
51db2ff5f96bab2744566e44b6e7e2ee6387f4e436b7ca18e7a07ced67ba1ed6 | Python | 7,053 | 185 | import abc
# import sklearn.metrics
import numpy as np
import tensorflow as tf
import os
import sys
import pandas as pd
def pairwise_dist (A, B):
"""
Computes pairwise distances between each elements of A and each elements of B.
Args:
A, [m,d] matrix
B, [n,d] matrix
Returns:
D, [m,n] matri... |
ec5e2024cda4db47b607d87a41d7451f1bb65cd8a2b891830496c60ec8aa4eba | Python | 7,053 | 175 | """Tests for the build-report archiver (``releases/scripts/archive_build.py``).
The two behaviours worth pinning are the ones that protect the repository from a bad archive: the
size cap that keeps a 200 MB DuckDB dump out of git, and the check that the prefix report is stamped
with the release it is being filed under... |
0403e149ec8b19e758b72872b9d8ef7fb4b93cfa8d93565bbb96b934232e3aaf | Python | 7,055 | 170 | """Tests for cwltool.load_tool."""
import logging
import urllib.parse
from pathlib import Path
import pytest
from cwl_utils.types import CWLObjectType
from schema_salad.exceptions import ValidationException
from cwltool.context import LoadingContext, RuntimeContext
from cwltool.errors import WorkflowException
from c... |
d7a8ae50b16e3002edcc050e04956177f0574b4e0069283509bc8fc25ad9107d | Python | 7,057 | 179 | from pathlib import Path
import numpy as np
import pandas as pd
import panel as pn
import pytest
from guppy.analysis.io_utils import PSTH_SIGNIFICANCE_DIRNAME
from guppy.frontend.psth_significance_view import (
PsthSignificanceView,
build_psth_significance_view,
describe_comparison,
metric_label_for,
... |
8eee0d15919a071da7560e2644e8213c82e792a379d30826e313cb892928e7d7 | Python | 7,059 | 166 | """
Configurator.py
Default class for configuring DL experiments
"""
import copy
import logging
import torch
from dl_utils.config_utils import check_config_file, import_module, set_seed
class DLConfigurator(object):
"""
DL Configurator
- parametrization of deep learning via 'config.yaml'
- ... |
d09dec77a32198aee9ade204295c93b70979346889643c4d3aa0e01063cd9fae | Python | 7,061 | 179 | import os
import torch
import random
import numpy as np
import torch.nn as nn
import torch.nn.functional as F
from utils import *
from const import *
from random import shuffle
from model import *
from sklearn import metrics
from dataset import MyTestDataset
from torch_geometric.loader import DataLoader
from sklearn.m... |
73de9c900d6236949c37c6222db0cc3922abada0ac4b8a23d1007f8188f8544d | Python | 7,062 | 208 | import numpy as np
import torch.nn.functional as F
import torch
import random
import pickle
from tqdm import tqdm
from pathlib import Path
import os
def set_seed(seed):
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed(seed)
random.seed(seed)
torch.backends.cudnn.deterministic = ... |
9910966e0c6af05fb0f73b1a48db1f1bd2742f57ac976715d8a1c854d986d77b | Python | 7,064 | 184 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import os
import shutil
import numpy as np
import pandas as pd
from dmriqcpy.analysis.utils import (dwi_protocol, read_protocol,
identify_shells,
build_ms_from_shell_idx)
from dmri... |
af67f22825bb939d87f8e4ce630d94dfa1f6d85f7022dde212ebeef92d96a61c | Python | 7,065 | 189 | # -*- coding: utf-8 -*-
import logging
import requests
from django import forms
from django.core.exceptions import ValidationError
from django.contrib import messages
from django.shortcuts import redirect
from formtools.wizard.views import SessionWizardView
from catmaid.control.common import is_valid_host
from catmai... |
25fad5ee664fb280a464ea87d591cd2b74f4999f4f225d4847ff100b4bcdb3eb | Python | 7,067 | 183 | from __future__ import annotations
from typing import Any
import numpy as np
from scipy.optimize import linear_sum_assignment
from soccertrack import BBoxDataFrame
from soccertrack.utils.utils import list2dict
def mota_score(bboxes_track: BBoxDataFrame, bboxes_gt: BBoxDataFrame) -> dict[str, Any]:
"""Calculates... |
fb90d00c2ee24aa857bfdd221fb98a75e55cf7ceeb43b50c1be2be718ea4535d | Python | 7,068 | 160 | import numpy as np
import tensorflow as tf
import time
import datetime
import os
import sys
import h5py
from pathlib import Path
import evidential_deep_learning as edl
from .util import normalize, gallery
class Ensemble:
def __init__(self, models, opts, dataset="", learning_rate=1e-3, tag=""):
self.mse = ... |
fd572de371d060fd4b4b9da68324869e770eb371b19871ee432a1f10bbd81db0 | Python | 7,068 | 175 | # SPDX-License-Identifier: Apache-2.0
import torch
import onnxruntime
import onnx
from onnx import numpy_helper
from transformers import GPT2Model, GPT2LMHeadModel, GPT2Tokenizer
import numpy as np
import os
# Transformers has a unified API
# for 8 transformer architectures and 30 pretrained weights.
# Mode... |
15e57d894ee45cc253584c8eec8768b2fd8e64503b2204778d88bc0a4fcb2093 | Python | 7,069 | 183 | # coding=utf-8
# Copyright 2021 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... |
5efc8b4c3ef8e0a42551c59ea84ff3d40f53143d55e5b4f5498bf1480424dbee | Python | 7,074 | 233 | import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import matplotlib.ticker as ticker
import numpy as np
EV_list = [
25,
100,
# 500,
# 1000,
]
# avg of 100 runs
optimal_mean = [
-20_556,
-108_539,
-2_764_761,
-11_034_490
]
optimal_std = [
6_191,
24_080,
... |
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