sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7d81533a565de80cbaf414891d8d3f9c2a5d0212c7d2eac5af935ea6043f155e | Python | 6,066 | 173 | import math
import sys
from ij import IJ
from sc.fiji.analyzeSkeleton import AnalyzeSkeleton_
BASIC_NAMES = [
"Branches",
"Junctions",
"End-point Voxels",
"Junction Voxels",
"Slab Voxels",
"Average branch length",
"Triple Points",
"Quadruple Points",
"Maximum Branch Length",
]
DETA... |
2636763523ef66811d950216a862715dd66026ddd83464d6e53beb608acf99cd | Python | 6,067 | 154 | import sys
sys.path.append('../TM2_segmentation')
import datetime
import json
import os
import numpy as np
import pandas as pd
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.callbacks import TensorBoard, LearningRateScheduler, ModelCheckpoint, ReduceLROnPlateau
from tensorflow.keras.models import ... |
fc1617cc2834cf325cb54f6f981448d1db36295805fca8ed9c1804e850311aa1 | Python | 6,067 | 184 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .multiheadattention import CustomMultiheadAttention
class ConvolvedAttention(nn.Module):
"""
Attention where the attention takes place over a window of finite size.
This is done for two reasons:
1. To reduce the computationa... |
7404fa490c0785e1a93b53b0b6f29932fa2e73b58b74b249fa3f7b11479dd683 | Python | 6,069 | 182 | """Round-47 secB_1 immunizer -- dataclass foreign-``__init__`` forged-flag recompute.
Sparse runnable reconstruction sets only captured fields and NEVER invokes ``__init__`` (that would
be the SEC1 construction-gadget RCE surface). So a dataclass output whose WINNING ``__init__`` is a
user-authored / foreign construct... |
04f7b1f668ce7d735b4acfdcfcdfcf7b02604e5b787fb1c00698007c19b95ba6 | Python | 6,070 | 176 | #################################################################################################################################################################
####################### Testing DeepRiPe #####################################################################################################################... |
655737006fc083cd988d40dd5da3143f20323553b06c2ffa390749946c45279e | Python | 6,070 | 175 | # ---
# jupyter:
# jupytext:
# formats: ipynb,py:light
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.14.5
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
# name: python3
# ---
# +
import o... |
75c8258dc3487e1d0857dc5d3c7ca471fac1a254282570fa57e56d71aada037e | Python | 6,070 | 179 | from __future__ import annotations
import typing as t
from jinja2.loaders import BaseLoader
from werkzeug.routing import RequestRedirect
from .blueprints import Blueprint
from .globals import _cv_app
from .sansio.app import App
if t.TYPE_CHECKING:
from .sansio.scaffold import Scaffold
from .wrappers import ... |
b192c423257232ad67ceed09f7f99a909ac3d665994a1665405cc19eaecc92a8 | Python | 6,070 | 210 | """
Sample implementations of visualization functions.
"""
import os
import matplotlib.pyplot as plt
import numpy as np
from skimage.measure import regionprops
from tqdm import tqdm
def draw_cell_area(
imgs=None, channel=None, seg_masks=None, savedir=None, configs=None, display=False
):
"""
Draw th... |
e6e4f33734d5ba98df16de2eaec99291017172cd61e471eef444389f16c6b287 | Python | 6,071 | 234 | from tempfile import NamedTemporaryFile, TemporaryDirectory
import numpy as np
import pandas as pd
import polars as pl
import seqpro as sp
import xarray as xr
from pytest_cases import fixture
import zarr
import seqdata as sd
@fixture # type: ignore
def gen_table():
"""Dummy dataset with AA, CC, GG, TT sequence... |
ee5bea656b55d7a59deabbf2d16c6521a57ccc17aadd49e894a702457ec38cec | Python | 6,071 | 103 | import numpy as np
import tensorflow as tf
#tfa.register_all()
'''
import numpy as np
from tensorflow.keras.models import Sequential
from tensorflow.keras.activations import get as get_activation
from tensorflow.keras.layers import SimpleRNNCell, RNN, Layer
class SimpleRNNCellWithLayerNorm(SimpleRNNCell):
def __ini... |
b7e7369744a3ea75dcd250f7b214db188214f77d81a3dee913709ac34d5a0248 | Python | 6,072 | 178 | """
Preprocessing code for image data.
Resizes and rescales data using MedPicPy and
then saves it as individual npy files for use in the training process.
Because some scans are 3D, the number of 2D
images can't be known ahead of time so
a function was added to MedPicPy that
loads the images individually
and fi... |
4dead3193f7475045373495bd830d669b3c8adb01f36d3ae24bd316eb1bfb74f | Python | 6,073 | 164 | #!/usr/bin/env python
"""Normalize sdists AND wheels in place so equal inputs give equal bytes.
``python -m build`` under ``SOURCE_DATE_EPOCH`` produces a wheel whose
timestamps are deterministic, but two machine-dependent residuals remained
(grind r4 R86-1; grind r5 b10 R84-1, MEASURED): the sdist's gzip ENVELOPE
sto... |
3033ecdee2e1428d98d54249625e542038ae639e03b31cb98e5d0f3a055c4f68 | Python | 6,074 | 182 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Line(_BaseTraceHierarchyType):
_parent_path_str = "contourcarpet"
_path_s... |
eee370eac3c705bb0f178d41854c1d16e6a05e30faa45ca1884aecb69d6465f9 | Python | 6,074 | 147 | import os
import argparse
import torch
import torch.nn as nn
import torch.distributed as dist
import torch.optim
from tensorboardX import SummaryWriter
from gluoncv.torch.model_zoo import get_model
from gluoncv.torch.data import create_datasets, create_loaders
from gluoncv.torch.utils.model_utils import deploy_model,... |
b36e0df6945a61bc37c171a68e2b952c0786b9f76d23f7d5030a30b1b3313e1b | Python | 6,076 | 175 | """Regression tests for the Lightning ``LayerProfilerCallback`` teardown."""
from __future__ import annotations
import weakref
from pathlib import Path
from typing import Any
from unittest.mock import patch
import pytest
import torch
from torch import nn
pytest.importorskip("lightning")
from torchlens.callbacks.li... |
b9603e0fb1f2b9152c393fb89e18b7bef0833599cd117c18707310d3651111f4 | Python | 6,076 | 149 | # The triton fused matmul + sqrelu is faster for fp16 but slower for bf16, compared
# to naive implementation.
import fused_dense_lib as fused_dense_cuda
import torch
import torch.nn as nn
import torch.nn.functional as F
from flash_attn.utils.torch import custom_fwd, custom_bwd
from flash_attn.ops.activations import s... |
34e0174fd80a7dc5aa70eae0c0a72edcc5a61aa67a1628087bc17d50f7838061 | Python | 6,077 | 210 | """
misc_figs.py
This script contains functions defining miscellaneous figure panel analyses.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
from util import gen_util, logger_util
from analysis import misc_analys
from paper_fig_util import helper_fcts
TAB = " "
logger = log... |
43ee20c0bf55698411e91e2c9bd586f87e93470cf1f73f3aa7ceb6694d55d631 | Python | 6,077 | 155 | """
analyze ensemble results
"""
import sys
import os
import numpy as np
import glob
import pandas as pd
def get_ensemble_result(ensem_list, score_name, en_type='', conf_name=None):
if en_type == 'mean':
en_scores = [l[score_name] for l in ensem_list if score_name in l]
if len(en_scores) == 0:
... |
a4db4f4c5348c4ca7b0515d9ea1dc553d5b28a9b98a0e240dde954afd21f0305 | Python | 6,078 | 165 | # pylint: disable=all
"""Transforms for simple pose estimation."""
from __future__ import absolute_import
import random
import numpy as np
import mxnet as mx
from ..image import random_flip as random_flip_image
from ..pose import flip_joints_3d, get_affine_transform, affine_transform
from ....utils.filesystem import t... |
7c5aa0f59deec2208d6e21446e3ef5eca00bca1b5f7d0e6bb17573402627821c | Python | 6,080 | 133 | # -*- coding: utf-8 -*-
import tensorflow as tf
import numpy as np
import scipy.misc
import time
import os
import glob
import cv2
#reader = tf.train.NewCheckpointReader("./checkpoint/CGAN_120/CGAN.model-9")
def imread(path, is_grayscale=True):
"""
Read image using its path.
Default value is gray-scale, and ima... |
a9d0ec516268c92756adff49cf048bb359a9d1e619dca2716a45042cf6ae7742 | Python | 6,080 | 147 | import logging
import os
from pathlib import Path
import torch
import torch_geometric.transforms as T
from coeffnet.dataset.reaction import ReactionDataset as Dataset
from e3nn import o3
from torch_geometric.loader import DataLoader
import wandb
from cli_functions import (
create_timestamp,
get_basis_set_name... |
5ab3ac41fed5f8d5d017215e4e869a0d785489fcd4213d71660b4c9894bd2ce2 | Python | 6,081 | 202 | model = dict(
type='BYOL',
base_momentum=0.99,
backbone=dict(
type='ResNet',
depth=50,
in_channels=3,
out_indices=[4],
norm_cfg=dict(type='SyncBN'),
init_cfg=dict(type='Pretrained', checkpoint='torchvision://resnet50')),
neck=dict(
type='NonLinearN... |
e338c87098321ff53d26a95c277ac796bbde3601bf5cd1c163f480c438ff3205 | Python | 6,081 | 220 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Currentvalue(_BaseLayoutHierarchyType):
_parent_path_str = "layout.slider"
... |
a6dbec31d1a3ab8da9ce8638b24001545e37bb6c40b4b2655c0ba53e2f80d746 | Python | 6,083 | 152 | """Logic that powers autocompletion installed by ``pip completion``.
"""
import optparse
import os
import sys
from pip._internal.cli.main_parser import create_main_parser
from pip._internal.commands import commands_dict, get_summaries
from pip._internal.utils.misc import get_installed_distributions
def autocomplete... |
40f770a33e1248206af21b94fa7dfe0a25ceffee8a416bf6cce3036cf8ee386a | Python | 6,084 | 155 | # SOURCE: vendored from cubeyoung/Noise2Score @ main (models/networks.py, class UNet)
"""Noise2Score (NeurIPS 2021) -- Tweedie-formula score-based denoiser.
Noise2Score estimates the score function (gradient of log-density) of noisy observations
via amortized residual learning (AR-DAE), then applies Tweedie's formula ... |
428cee7f6011c09285e5af2393babbef59f73e50656d079347d82ec10cc8198a | Python | 6,085 | 147 | import os, sys
from datetime import datetime
import XML_Parse as xparse
import Apical_Basal_Classification as classify
import Branch_Number_per_Skeleton as bnps
import Euclidean_Distance as ed
import Skeleton_Visualization as sv
import File_Converter as sw
import pandas as pd
########################################... |
ec001c80e3fdba27126fd4c77b9e3fe96f543178afc1145db2754dfa0d001da7 | Python | 6,086 | 195 | """
===============================================================================
Clustering algorithm comparison
===============================================================================
A comparison of several clustering algorithms on low-dimensional synthetic
datasets, adapted to SPD matrices from [1]_.
The... |
3fbed660a55b12b32ac9ee88a740b1c2e047a1f803d037154e8f3af061c230fb | Python | 6,087 | 148 | """Param byte-witness gating regression suite (W6).
The named-parameter whole-storage byte-witness (r18/r19-A: forward-start snapshot +
forward-end ``torch.equal`` reconcile in ``buffer_writes``) is armed ONLY for
runnable-capable captures (``intervention_ready=True``) -- the exact predicate for
"this capture can prod... |
4597fd560ad8f796dffc07a7dadafcc8295ff9a651b7fca1dcbf0060699b0d97 | Python | 6,087 | 157 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Python wrapper for the plumed sum_hills program.
"""
# =======================================================... |
525e2b2ba0d3b4756540fea25bbc8668578cba8b96ce6bc1a7ad1212a7df567e | Python | 6,088 | 173 | # Copyright 2022 Deepfold Team
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... |
9f250abb28b9c9d10fefff61f8eb6d58dec16c2c507740efe8257d05753559d3 | Python | 6,089 | 181 | import argparse
import os
import subprocess
import warnings
from zipfile import ZipFile
import h5py
import yaml
from skl2onnx import convert_sklearn
from skl2onnx.common.data_types import FloatTensorType
warnings.filterwarnings("ignore")
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
SKLEARN_MODELS = [
"sklearn.ensem... |
1fa6cc33ac2499fc9fe57f895b4eaa758d778838a9b9840d2877b4c2378db89e | Python | 6,090 | 171 | #!/usr/bin/env python
"""
BASIL GUI for Oxford ASL - Main window
Currently this does not use any of the FSL python libraries. Possible improvements would be:
- Use props library to hold run options and use the signalling mechanisms to communicate
values. The built-in widget builder does not seem to be flexible e... |
2ac2e418bb4585b2f7e56f094c95f0d5b263fa8976779e8a523ec894a5fcec4d | Python | 6,090 | 170 | '''
Testing functionalities of models systems
author: obanmarcos
'''
import os
import os, sys
sys.path.append('/home/obanmarcos/Balseiro/DeepOPT/')
import lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_utilities as dlutils
from ... |
36874f507c6a0e9846ca4dcbc81205661dc39859c0b4cd3bde5ef35d91b5417f | Python | 6,090 | 133 | import os
import random
import numpy as np
import tensorflow as tf
from tensorflow.keras.layers import Dropout, Embedding, Input, Dense, GRU, SpatialDropout1D, Flatten
from tensorflow.keras.models import Model, Sequential
import utils
'''embed_dim = 128
ff_dim = 128
dropout = 0.1
n_train_batches = 50
batch_size = 1... |
d80cb29dcb898ab87104d457887134d4a4b40c29b226c86fdbc2197294de4175 | Python | 6,090 | 195 | """Deterministic scenario set for the producer parity harness.
Each scenario returns a fresh model + input + the capture callable so a run is
reproducible in-process and cross-process (fixed seeds, no external data).
The P0 skeleton carries the scenarios the design-of-record names for the
harness proofs; the P5 campai... |
03e6d7cce4db1bed7eb23c9c0f49bca36c950b77d9b5d58a3de5eb484d5f7819 | Python | 6,091 | 170 | """Memory Bank Wrapper"""
# Copyright (c) 2020. Lightly AG and its affiliates.
# All Rights Reserved
from typing import Optional, Sequence, Tuple, Union
import torch
from torch import Tensor
from torch.nn import Module
from lightly.models import utils
from lightly.utils import dist
class MemoryBankModule(Module):... |
3f6c8a9587580a22785e3a9bfb7350736618540e91092f6f0a401add45b0535c | Python | 6,092 | 181 | import io
import pathlib
import shutil
import sys
import tempfile
from unittest import mock
import pytest
import pyjibe
import pyjibe.head
data_path = pathlib.Path(__file__).parent / "data"
@pytest.mark.skipif(sys.version_info < (3, 8), reason="requires python>=3.8")
def test_init_print_version(qtbot):
"""I j... |
d2a833328a8749bccbbb50f656a38ad74a5d5ceea192b181fc4ca5dca9490420 | Python | 6,095 | 181 | import io
import pathlib
import shutil
import sys
import tempfile
from unittest import mock
import pytest
import pyjibe
import pyjibe.head
data_path = pathlib.Path(__file__).parent / "data"
@pytest.mark.skipif(sys.version_info < (3, 8), reason="requires python>=3.8")
def test_init_print_version(qtbot):
"""I j... |
d6ed8a79dd15433d3b4e231c779248918ec41bc9be7044db4824367c7e66c9c5 | Python | 6,096 | 130 | import torch
import numpy as np
def e_path_loss(model, calc, config, edges, edges_e, n_nodes, box, batch_size, beta, alpha=0.9, emax=10, L=5, device='cpu'):
err = torch.zeros(batch_size).to(device)
pred = model(x=config, edges=edges, n_nodes=n_nodes)
epots = calc.calculate(config*10, edges_e, box*10)
#... |
da634eccc772bae3cd2aa0399dd471d6a237000ac9e6a76bc8012233f151a401 | Python | 6,097 | 213 | import matplotlib.pyplot as plt
import numpy as np
from anndata import AnnData
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import proj3d
def local_plot(
adata: AnnData,
use_cluster: int,
use_label: str = "leiden",
reverse: bool = False,
cluster: int = 0,
data_alpha... |
34779b71853d07b77cf110fd3931d58ec88f6759dfe438dc92e722a51ff74c4f | Python | 6,100 | 158 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
d5c273c8bf74fe5c4fd10205be9ff7f4737a3887745e2053aa774da952fc2fd6 | Python | 6,102 | 162 | """
OIDC Authentication Provider Implementation
This module provides a generic OIDC authentication provider implementation.
It can work with any OIDC-compliant provider (Keycloak, Auth0, etc.).
"""
import logging
from typing import Any, Dict, Optional
from urllib.parse import urlencode
from authlib.integrations.star... |
3be6383741099d53d0bf037e407a0c8fa242f38453891febd7b4cf7ed95c13b0 | Python | 6,104 | 182 | #!/usr/bin/env python3
"""
File: visualise_replication_stats.py
Created: 2022/07/18
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source ... |
9f8222da84b79335cb762c131769b36fd678c203811384a25aac8a6f04c72780 | Python | 6,107 | 223 | from datetime import datetime
import numpy as np
import torch
import os
import time
from constants import get_args
from binary_motif_model import (
MotifModel,
load_model,
save_model,
MotifModelDataset,
evaluate_model,
)
from map_protein_name import (
get_map_protein,
get_rbns_name_psam_... |
d42268ad16aa6095b6b843145a51b215c307d83ca6c2b2e75dde46625f09a0d6 | Python | 6,108 | 166 | import re
from typing import Tuple
import pytest
import torch
from lightly.models.modules.memory_bank import MemoryBankModule
class TestNTXentLoss:
def test_init__negative_size(self) -> None:
with pytest.raises(ValueError):
MemoryBankModule(size=-1)
def test_forward_easy(self) -> None:
... |
06a20039d4d6d6b9c569a2f377a5c79fe6de1bc8fc054b15c13f31b072373a56 | Python | 6,109 | 117 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
79a35497f7e839fc2e6b43c36d1451bd8d39f054e6a1d6776ceb0db0225258c1 | Python | 6,109 | 172 | import json
import logging
import os
from functools import partial
from pathlib import Path
from typing import Union
import torch
from torch.hub import HASH_REGEX, download_url_to_file, urlparse
try:
from torch.hub import get_dir
except ImportError:
from torch.hub import _get_torch_home as get_dir
try:
fr... |
57b300a354ae6f2fb0ac0a8d8ef98813ff267bd579e8422c28914afc392a1fcb | Python | 6,110 | 166 | """Benchmark + correctness oracle for Ragged integer-array fancy-indexing (issue #69).
Proves the O(k) index-resolution candidate (a) matches the current O(n)
arange-based reference on every representative + edge case and (b) is flat in n
while the reference grows ~proportionally to n. Transitional harness (cf.
benchm... |
496799693923f95733e878175528a4701a6167e5d2ddf27ddb2ed46a697bcc54 | Python | 6,111 | 103 | #!/usr/bin/env python3
'''
This is a script which will generate a file of commands for gnina to use cnn_minimze to generate iterative training poses.
ASSUMPTIONS
i) assumes all receptors are PDB files IE end in .pdb
ii) Assumes all docked poses or outputs from gnina will be SDF files.
iii) The crystal ligand fi... |
c9f2aad0a43bfd019cb3e809adb0cdf227d7fb548512247a7d0c9c121e01c2c6 | Python | 6,111 | 167 | """Created on Thu Jan 30 13:47:15 2020.
@author: martafradera
"""
import numpy as np
from neurogym.core import TrialEnv
from neurogym.utils import spaces
from neurogym.utils.ngym_random import TruncExp
# TODO: Need a more intuitive name
class ChangingEnvironment(TrialEnv):
"""Random Dots Motion tasks in which ... |
7d0e8ef60574cec87be9fe7f0d5e51d2bea29ef68daf871a4aadb2883266371f | Python | 6,112 | 161 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
40132108d35dcda790d78441f634739d7d4b221c1f8a02d2c973ed3ff21c81b2 | Python | 6,113 | 214 | # _*_coding:utf-8 _*_
# @Time : 2021/8/19 18:25
# @Author : XCH
# @FileName: 3_bilstm_wzt1bd.py.py
# @Software: PyCharm
#%%导入原始数据
## import data,moudle
import torch
import os
import numpy as np
from torch import nn
from torch import nn
from torch.autograd import Variable
torch.set_default_tensor_type... |
eb5b9962cd45b3a8a32ea54af2aef3bc6aedff24a76bc62657594a45cf42f792 | Python | 6,113 | 191 | from __future__ import annotations
from typing import TYPE_CHECKING, Callable, List, Optional
import torch
from PIL import Image
from lightly.transforms.multi_view_transform import MultiViewTransform
from lightly.transforms.torchvision_v2_compatibility import torchvision_transforms as T
if TYPE_CHECKING:
from m... |
027e7fdcf4fc8eac08c503cd363d9a89c456944125a311fe49848617b2202032 | Python | 6,114 | 170 | '''
Testing functionalities of models systems
author: obanmarcos
'''
import os
import os, sys
sys.path.append('/home/obanmarcos/Balseiro/DeepOPT/')
import pytorch_lightning as pl
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_utilities as dluti... |
35f96e5574627695deaa28c5b2bd9ac0b1a46e9e81d59a17de34b63792f06e61 | Python | 6,115 | 193 | """
=================================
Processing Remote Sensing Helpers
=================================
This file contains helper functions for handling remote sensing processes
"""
from math import ceil
import numpy as np
from numpy.lib.stride_tricks import sliding_window_view
from sklearn.base import BaseEstimat... |
06c5597c4f022a76d39ac451dd5563ade485b1f7d06741e1d7050bf54a7f35ba | Python | 6,118 | 137 | """
@Time: 4/8/2023 下午2:25
@Author: Heng Cai
@FileName: utils.py
@Copyright: 2020-2023 CarbonSilicon.ai
@Description:
"""
import torch as th
import MDAnalysis as mda
from torch.utils.data import DataLoader
from RTMScore.data.data import VSDataset
from RTMScore.model.utils import collate, run_an_eval_epoch
f... |
456d08358635982bfc61777f784d958ed02ae80f9e86812ee7a084cbd64b9a0a | Python | 6,118 | 134 | import sys
# setting path
sys.path.append('../TM2_segmentation')
from scipy.ndimage.filters import gaussian_filter
from skimage.transform import resize
import SimpleITK as sitk
import numpy as np
import pandas as pd
import tensorflow as tf
import glob, os, functools
import matplotlib.pyplot as plt
from contextlib i... |
439765d9236370a909a40c9c15a097b470bf0d1895e649daf87405e24db70a3b | Python | 6,119 | 188 | """Smoke tests for backward grad disk streaming."""
from __future__ import annotations
from pathlib import Path
import pytest
import safetensors # noqa: F401
import torch
from torch import nn
import torchlens as tl
from torchlens._io.manifest import Manifest
from torchlens.options import CaptureOptions
class _Ti... |
86df37b6002562fa302620dc2f22907f613f6a5ee409d9501f40f26fe4ced90a | Python | 6,120 | 154 | import sys
sys.path.append('../TM2_segmentation')
import datetime
import json
import os
import numpy as np
import pandas as pd
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.callbacks import TensorBoard, LearningRateScheduler, ModelCheckpoint, ReduceLROnPlateau
from tensorflow.keras.models import ... |
a1f1013520efb1b749213d2f51edfd42f3aeb8ef6e145357a054a139123eb77d | Python | 6,121 | 154 | """Lane F22 rsatoolbox convention matrix (neuro MEMO item 16, rows T6/T11/T12).
The entire provenance claim rests on a foreign package's behaviour across
the declared version range, so these rows are the BOTH-VERSIONS gate: the
suite must pass with rsatoolbox 0.1.5 (the declared floor) AND current
0.3.x installed. Pin... |
a4f0dc132c7b0d5cc6443093f4e56d571e230a99a25f7371ef006caa88abdf1b | Python | 6,121 | 193 | from typing import Optional, Tuple, Union
import numpy as np
import pyvista as pv
from pyvista import PolyData
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from ..utilities import add_model_labels
def _construct_line(
start_point: Union[list, tuple, np.ndarr... |
f1fe7c446f13b1f7547edfb79552897e49e1d2f2b6b059754545b6e122952cb1 | Python | 6,121 | 209 | """
====================================================================
Ensemble learning on functional connectivity
====================================================================
This example shows how to compute SPD matrices from functional
connectivity estimators and how to combine classification with
ensemb... |
b082e2a1d508b57f5aa7214589792d7811629d35bb863fef4837d6ef1ad9d228 | Python | 6,122 | 145 | import argparse
import glob
import os
import shutil
import tqdm
import mne
import numpy as np
from mp_dip.obci_readmanager.signal_processing.read_manager import ReadManager
from mp_dip.obci_readmanager.signal_processing.signal.data_generic_write_proxy import SamplePacket
from mp_dip.obci_readmanager.signal_processing.... |
1e7ddc91a8d44dc6b086820e25bc7ded832b0186da6e1a2f2b3d8cc43e7e8dac | Python | 6,123 | 142 | import os
import re
import tifffile
import cupy as cp
import numpy as np
import multiprocessing as mp
import concurrent.futures as cf
from .XCorrCpu import XCorrCpu
from .XCorrGpu import XCorrGpu
from tqdm.auto import tqdm
from matplotlib import pyplot as plt
from multiprocessing.pool import ThreadPool
def sampled_... |
3dba96b6a329fc9ca3353f2e150d10172a71749b71a9ca1c8dd216a0917139af | Python | 6,124 | 180 | # ---
# jupyter:
# jupytext:
# formats: ipynb,py:light
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.14.5
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
# name: python3
# ---
# +
from pat... |
4ba2575e793da9e81b0466a4aaa552911e0d819d01056cf6a40c37db9f5c090f | Python | 6,124 | 160 | """
Unit tests for adaptive background tracker ObjectModel.
Tests specifically for the boundary validation and size compatibility fixes
to prevent OpenCV size mismatch crashes.
"""
from unittest.mock import Mock, patch
import cv2
import numpy as np
import pytest
try:
from ethoscope.trackers.adaptive_bg_tracker ... |
b8bcc7f4cc35b89149017d003e788ea0524e6289199b737f4aa37a991fed3ae2 | Python | 6,128 | 166 | """Test functions for specparam.models.utils."""
from pytest import raises
import numpy as np
from specparam import SpectralGroupModel
from specparam.sim import sim_group_power_spectra
from specparam.metrics.definitions import METRICS
from specparam.modutils.errors import NoModelError, IncompatibleSettingsError
fro... |
0bbed24c17116e607a304fd0d0652f19cf76dad0d523ff6836775c197ec1ca09 | Python | 6,129 | 193 | import sys
import time
import pytest
from caper.caper_labels import CaperLabels
from caper.cromwell import Cromwell
from caper.cromwell_rest_api import CromwellRestAPI, has_wildcard, is_valid_uuid
from caper.wdl_parser import WDLParser
from .example_wdl import make_directory_with_wdls
@pytest.mark.parametrize(
... |
6fffb8e03851d24fa468e7edbb3326e4fe29af5cae285574d1ca0aa02c658772 | Python | 6,129 | 152 | __author__ = 'quentin'
import cv2
try:
from cv2.cv import CV_FOURCC as VideoWriter_fourcc
from cv2.cv import CV_AA as LINE_AA
except ImportError:
from cv2 import VideoWriter_fourcc
from cv2 import LINE_AA
from ethoscope.utils.description import DescribedObject
import os
class BaseDrawer(object):
... |
d71ed5e56d43629b73586cb0262743562bb9f86a9fd2a442778d7796c7ec257e | Python | 6,129 | 206 | """Load packaged image manifests and images."""
from functools import lru_cache
from pathlib import Path
import pandas as pd
from PIL import Image
from hobj.data.download import resolve_data_root
from hobj.types import ImageId
def _load_image_manifest(
*,
dataset_name: str,
required_columns: set[str],
... |
9fc925b831fa9abbf48612543d6bea1e4c8ac0c134a584ec446761e943945d33 | Python | 6,130 | 148 | import datasets
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn.feature_extraction.text import CountVectorizer
datasets.logging.set_verbosity_error()
def load_huggingface_dataset(
dataset_name: str,
subsample_frac: float = 1.0,
binary_classification: bool = False,
r... |
24f18134b2ab4e2fd52cfeda9c62403791955cede9001ac810602bce598291b3 | Python | 6,131 | 138 | """Absence pins for the removed top-level deprecation shims.
The moved-name ``__getattr__`` table, the paper-era API shims, and the
deprecated top-level wrapper functions were deleted by the 2026-08-19
shim-removal lane. Contract now: the historical top-level spellings raise
the typed ``facade_redirect`` ``FacadeTeach... |
1a35b4b1fc4c03668d2ca4de3a1e198e480a035ea2b6a5d260f9627858ac0609 | Python | 6,132 | 149 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import seaborn as sns
import re
import os
from mpl_toolkits.axisartist.parasite_axes import SubplotHost, HostAxes, ParasiteAxes
from sklearn.inspection import permutation_importance, plot_partial_dependence
from sc... |
22362a6a2a60dace7783f9df57cb6274dc9b2fdc366508c4f398c4815eee8da6 | Python | 6,133 | 185 | import logging
import zlib
from dataclasses import (
dataclass,
fields,
)
from struct import unpack
from urllib.parse import (
parse_qs,
unquote,
urlparse,
)
from galaxy.files.models import (
BaseFileSourceConfiguration,
BaseFileSourceTemplateConfiguration,
FilesSourceRuntimeContext,
)
... |
2251e5d7974153734304158e845583024ebbb53e4d98d5e0a1e7db2fd68cc58d | Python | 6,133 | 123 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
79177ef4b660a1f918d9284daf65ffdf67d3960aec46747f3138d98619e7b61d | Python | 6,133 | 170 | import logging
from collections.abc import (
Callable,
Iterable,
)
from sqlalchemy import (
and_,
false,
func,
or_,
select,
)
from galaxy.model import (
Group,
GroupRoleAssociation,
Role,
User,
UserRoleAssociation,
)
from galaxy.model.scoped_session import galaxy_scoped... |
0d25ca61d06d84ba124691b01b479e9fc6bf8797df7cf02a627044fb70e8c296 | Python | 6,134 | 163 | from sqlalchemy import (
false,
select,
)
from galaxy import model
from galaxy.exceptions import (
Conflict,
ObjectAttributeMissingException,
ObjectNotFound,
RequestParameterInvalidException,
)
from galaxy.managers.context import ProvidesAppContext
from galaxy.model import Group
from galaxy.mod... |
a522eadf87143349ff49cf6fa35b320fcda29954626529544259b10c97c9ff0d | Python | 6,134 | 139 | """F26: T-RELAY-W / T-RELAY-C -- the measured relay-fidelity pins.
These pin the PANEL-MEASURED losses (trackers memo 3.2/3.3) at the measured
vendor versions, so a future vendor release that FIXES any of them fails
visibly and the published fidelity table gets revised. They run only where
the relay-test extra is inst... |
eb7fcfd556080196c6328365dae153ff373bc02e89fcbb3a0c75fdec37d648bb | Python | 6,137 | 153 | """Package-scoped R0 fixtures: one build+trace per (family, impl) per R0 block.
The deep sweep runs many assertions against each captured trace; caching the
capture keeps the whole R0 gate at seconds (memo section 10 PR row). Models
are ~100-225k params, inputs are 8 tokens -- the cache is a few MB.
The cache is PACK... |
2b3b0ed40be58078816f1d2705fe7e0c2346ac54867cf7eba40e42f0c557c560 | Python | 6,140 | 146 | """Round-26 security regression: exec/spawn/install denylist completion.
A comprehensive audit found two defense-in-depth gaps in the default-deny
callable/import resolution for attacker-controllable ``.tlspec`` bundles:
* E1 (MEDIUM): the hard module denylists (``_DENIED_MODULES`` in
``torchlens.utils._callable_sa... |
93bb2e767f3b33064b8e1e662e7c1ef80fe8b32ad0ddafdb8c08b8ebac3f52d4 | Python | 6,141 | 144 | '''
A MPNN for finetuning on the LSF dataset.
'''
import torch
import torch.nn as nn
import logging
logger = logging.getLogger(__name__)
from NMR_Pretrain_Net import NMR_MPNN
device = "cuda" if torch.cuda.is_available() else "cpu"
class LSF_MPNN(nn.Module):
'''
The LSF selectivity prediction layers to be use... |
2332790e43a545c4ff842265306cf4f33d6c139372f1d4ec0f003d5a302f3808 | Python | 6,143 | 183 | #!/usr/bin/env python
# coding: utf-8
# position_decoder.ipynb
#
# Script to create a position decoder using multinomial logistic regression
#
# MGC 7/15/2019
# FKM 7/31/2019
# In[171]:
# packages
import sys,os
#import pandas
import math
import glob
import pickle
from scipy import io
import numpy as np
from numpy... |
8d32e0eadd527622695a0976ed578f5084d104272247651398241bd4fa7c38e9 | Python | 6,143 | 164 | from typing import Sequence
import torch
from pytorch_lightning import Callback, LightningModule, Trainer
from torch import Tensor, nn
from pl_bolts.utils import _MATPLOTLIB_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _MATPLOTLIB_AVAILABLE:
from matplotlib import pyplot as plt
from matp... |
ba3a9d5e997380915fe2f88cefb02203ac3b2af465932500452ebf49309c890e | Python | 6,145 | 195 | import os
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
import math
import argparse
import re
import sys
import unicodedata
from itertools import product
import numpy as np
import pandas as pd
import tensorflow as tf
from joblib import dump, load
from tensorflow.keras import Input
from tensorflow.keras.layers import (
... |
335384b118f6b302f39fc5580504822b3fec55038dd439128b608c730b546809 | Python | 6,146 | 149 | import argparse
import subprocess
from carbontracker.tracker import CarbonTracker
from carbontracker import parser
from carbontracker.report import generate_report_from_log, REPORTLAB_AVAILABLE
import ast
import os
def parse_logs(log_dir):
parser.print_aggregate(log_dir=log_dir)
def generate_report(log_file, ou... |
3f963decd18fc98255d7fa0c8de44ae2a10583108a470da976a620eb23ba8126 | Python | 6,146 | 165 | #!/usr/bin/env python3
import sys, os
import msprime
import pyslim
import tskit
import numpy as np
helpMsg = '''
usage: $./swp_IwM_init.py <sc_min> <sc_max> <genbp_min> <genbp_max> <out_pref>
Put genbp minmax as `-1` to dynamically tune mutgen
'''
N_B = 30281
N_C = 10100
N_BC = 33980
N_ABC = 11593
... |
fc8d0ea421b597f35d55076bd52c129a8e27a3e0819f6ee15368d2acd8d75c6d | Python | 6,146 | 216 | # Copyright 2023 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... |
7f7673b4a670e0592abef6d81cbc5c7132b407a947b90ffa5979adb6b1323ca4 | Python | 6,148 | 230 | """
Main Script containing the following steps:
- perform similarity network fusion and diffusion map embedding in PNC
- train ML model on PNC embeddings with supervised Domain Adaptation
- HBN *no diagnosis* data enhances prediction of embedding in unseen HBN data
Author: Dominik Kraft
"""
import time
import pandas a... |
555649f21e049b9292346f3d141e5d1928c30408f44b8cab31e5c8c1bfd5a3e1 | Python | 6,150 | 124 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
b7edd2cb2c34eb03d2d1b126fa3f87cd6bf6793e8ee422f447396b7e3e964236 | Python | 6,150 | 185 | from typing import List
import numpy as np
import seqpro as sp
from hypothesis import given, note
from hypothesis import strategies as st
from seqpro.rag import Ragged
seq = st.text(
alphabet=st.characters(codec="ascii", min_codepoint=32, max_codepoint=126),
min_size=1,
)
seqs = st.lists(seq, min_size=1, max_... |
92ed7b2c78bb4d0bdebca9abec32838744df84079812c87e20fdc7b2081bea48 | Python | 6,152 | 162 | import re
import shutil
import string
import pathlib
import mimetypes
import dataclasses
import unicodedata
from typing import Optional
from pyasjp.api import ASJP
from pycldf.sources import Source
from clldutils.path import md5
import pylexibank
from pyasjp.models import MEANINGS_ALL
def slug(s):
"""Condensed ... |
153ed1ca54b9c47836db01abd7c47d3263875ba45336a9e7c3e706a93a9c0974 | Python | 6,153 | 184 | """Forward-load CI gate: the previous release's wheel loads the new goldens.
Ecosystem MEMO 3.4 / G8: on every persistence train, install the PREVIOUS
release's torchlens wheel and analysis-load the new train's golden artifacts
under it. This is the only mechanism that catches a same-stamp drift break
(two writers sha... |
903593203b2efec36544cf9b80cd6e19c5840155c4414b96fdb99413c6d55ad3 | Python | 6,153 | 161 | #!/usr/bin/env python3
"""
File: calc_genotype_info.py
Created: 2021/06/14
Last Changed: 2022/02/10
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this sourc... |
fdfc8db813a6f25c2e34de3196caa52cf0fccc6fe833ae0b6b5b41f199fc4b9a | Python | 6,153 | 184 | """
Food and odor sources placed in the arena.
Provides the point and patch sources the agents feed from and navigate towards,
together with the odor they emit into the environment's value grids.
"""
from __future__ import annotations
from typing import Any
import numpy as np
import param
from ...param import Class... |
3e58e8fcf1cd52764959d25553101eb00e593a3f865e208dd87d62fff7e5cb30 | Python | 6,154 | 168 | # pylint: disable=W0611, W0612, F0401, R0914, C0302
"""Settings tests of eFEL"""
"""
Copyright (c) 2015, Blue Brain Project/EPFL
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of... |
761321748ed8494360c8e0d7f2a62a70b4d6f1f818318ea62d193f9f76eda107 | Python | 6,154 | 197 | """Functions to convert spiking data to different representations."""
import numpy as np
from spiketools.utils.data import smooth_data
from spiketools.utils.checks import check_time_bins
###################################################################################################
##############################... |
76a376527de322eacbe0df82b33c3338284cd4a314578e312f47cd6c05dff52b | Python | 6,155 | 174 | # -*- coding: utf-8 -*-
"""
Created on Sun May 15 15:02:10 2022
@author: Chenyong
"""
import math
import json
import pandas as pd
import numpy as np
import json
import datetime
import position_util
# from skmob.tessellation import tilers
import geopandas as gpd
import matplotlib.pyplot as plt
from math import sqrt, sin... |
77fe1073dc30721d0d93c02ca4fe56b8271ea97c2d1c0ae43c2b9b7d6269857c | Python | 6,155 | 134 | # SOURCE: vendored from frankligy/DeepImmuno @ df42ac5b6bddfe531268335e2dcb496559cd488b
# https://raw.githubusercontent.com/frankligy/DeepImmuno/df42ac5b6bddfe531268335e2dcb496559cd488b/extension/deepimmuno-gan-train.py
#
# Li & Mansour et al. (Cell Reports Methods 2021) "Deep learning-based
# prediction of immunogenic... |
88012555725299999c05ca3b3813f465e788625e1f1801d941e7e57052911a07 | Python | 6,155 | 178 | #!/usr/bin/env python
import argparse
import json
import os
import shutil
import subprocess
import sys
import tarfile
import time
from urllib.request import urlopen
import wget
def rmtree_tolerant(path, retries=5, delay=2):
"""Remove ``path`` recursively, tolerating the transient "Directory not
empty" (OSEr... |
a22524b556a251a34467b37f72fa9bef7ea1fd230151030b16c7c61d740f18bb | Python | 6,155 | 165 | import torch
import numpy as np
from .._utils import _k_largest_index_argsort
from .._ism import _naive_ism
from .._utils import _model_to_device
def best_k_muts(
model: torch.nn.Module,
X: np.ndarray,
k: int = 1,
device: str = "cpu"
) -> np.ndarray:
"""
Find and return the k highest scorin... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.