sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
04bcfa845232d797692e68789ab3f20580432a9f64c6cdf409fd1aabde096bd9 | Python | 8,290 | 268 | """Tests of NPZ file functions"""
import shutil
import warnings
from pathlib import Path
import numpy as np
import pandas as pd
import pytest
import pynapple as nap
# look for tests folder
path = Path(__file__).parent
if path.name == "pynapple":
path = path / "tests"
path = path / "npzfilestest"
# Recursively ... |
d1222d47cccbe12511fed50e368426d9cdcbc64b69d7f96fec07261eb58ad3bb | Python | 8,290 | 203 | '''
This is a wrapper script that combines several functions:
- Picking loci from sumstats files based on Zscores and number of SNPs
- Generating LD matrices for these loci based on 1000 Genomes
- LD pruning those loci and intersecting the SNPs between the studies
- Running MsCAVIAR on all those loci
Essentially, the i... |
0a6ab68c96797e781221f7d59cb2700acba553d797fc83de08edbfe1900afa1f | Python | 8,291 | 247 | """Vendored code from scikit-image in order to limit the number of dependencies
Extracted from scikit-image/skimage/exposure/exposure.py
"""
import numpy as np
from warnings import warn
_integer_types = (
np.byte,
np.ubyte, # 8 bits
np.short,
np.ushort, # 16 bits
np.intc,
np.uintc, # 16 or... |
e041c85568aa34d0b11f12e77df460985f3aa7d558f76152651c4416d29fb7b4 | Python | 8,293 | 216 | """DeviceContext injection must work under ACTIVE logging, not just the fast path.
Bug DEVICE-CONTEXT-LOGGING: when a ``TorchFunctionMode`` device context (e.g.
``with torch.device("meta"):``, used internally by HuggingFace
``from_pretrained``) is active, factory functions like ``torch.zeros`` must
produce tensors on ... |
22efbcae288d69c301a849818249da596e5b4ee07e33d4e62cb682b170fc2da9 | Python | 8,294 | 236 | from unittest import mock
import pytest
from api.mocks import FakeAuthContext, FakeUserWithAuthDependency
from dependency_injector import providers
from fastapi import FastAPI, status
from fastapi.testclient import TestClient
from carbonserver.api.errors import UserException, get_http_exception
from carbonserver.api.... |
fb7377fa245512153bfaf4e48504616853708d1d78ef63d3a885145fbd313f56 | Python | 8,296 | 218 | """Fake quantization with learnable ranges, for quantization-aware training."""
from keras.src import backend
from keras.src import ops
from keras.src.api_export import keras_export
from keras.src.backend import KerasTensor
from keras.src.backend import any_symbolic_tensors
from keras.src.backend.common import standar... |
32bedd662415d060ddae79ff06fa4169022ce15d26e25c10faca806c7447404f | Python | 8,297 | 245 | from __future__ import annotations
from typing import Optional, Sequence
import torch
import torch.nn.functional as F
def activation_from_name(name: str) -> torch.nn.Module:
table = {
"ELU": torch.nn.ELU(),
"ReLU": torch.nn.ReLU(),
"LeakyReLU": torch.nn.LeakyReLU(0.01),
"GELU": t... |
c36af284f9cadecf818deb64c73a1468ceb66519645dd1c30b23c067bd78c768 | Python | 8,298 | 225 | """Echo narration benchmark rows (lane F28; snoop memo build row 9).
Measures, on real architectures (torchvision resnet18 with pretrained
weights; the real HF gpt2 checkpoint when cached, else the config-built
architecture), for SUCCESS and CRASH paths:
- baseline raw forward;
- the record substrate (no echo) and re... |
1687f6e04c60730cc0e2ea0878083292282ba4999891702bb5c5c54dce92f969 | Python | 8,299 | 221 | # Copyright (c) 2024 PaddlePaddle 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 app... |
d9126c8546ef1813b64fce1d323c0d76582d9061acae0adfcb7de7f5524ebc50 | Python | 8,302 | 301 | """
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJE... |
8c5424f592f5874f9b16e63cfdf3144dcf6f6a0dbbe1f2bc2ceb53fb88554797 | Python | 8,303 | 200 | import platform
import numpy as np
import vtk, slicer
import vtk.util.numpy_support as vtk_np
from slicer import vtkMRMLScalarVolumeNode
from slicer import vtkMRMLLabelMapVolumeNode
from Logic.BiomedisaParameter import BiomedisaParameter
from SegmentEditorCommon.Helper import Helper
import subprocess
import tempfile
fr... |
f7daa10d3e4f714fe8f4a0af13d0827c58349b0a49041ddd454a8a9e3a35f78a | Python | 8,307 | 226 | import numpy as np
import scipy
from scipy.cluster import hierarchy
from scipy.spatial.distance import squareform
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from scipy.spatial import distance
Z1_COLOR = (234.0/255, 29.0/255, 37.0/255)
Z5_COLOR = (43.0/255, 61.0/255, 150.0/255)
def read_le... |
38b355d72211267be844406127a45e2f2ae9f25f96bd3402499b436a778b30ac | Python | 8,308 | 203 | import numpy as np
import pickle
import matplotlib.pyplot as plt
from utilities import dataloading_utilities as dlutils
from utilities.folders import *
from torch.utils.data import DataLoader
from training import train_utilities as trutils
import os, sys
from config import *
sys.path.append(where_am_i())
from mode... |
2eb131b8da8e7c4b20f7c4e7cd7f46324f6717572511fe367ae93e5bb87392d3 | Python | 8,310 | 211 | """Wrapper for recording videos."""
import os
from typing import Callable, Optional
import gym
from gym import logger
from gym.wrappers.monitoring import video_recorder
def capped_cubic_video_schedule(episode_id: int) -> bool:
"""The default episode trigger.
This function will trigger recordings at the epis... |
5d28e8a7a28acd17f0c9ff75c80f78d29100c16bc186833c3b1ce645c2c3fae7 | Python | 8,310 | 198 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from ultralytics.utils import TESTS_RUNNING
from ultralytics.utils.torch_utils import model_info_for_loggers
try:
assert not TESTS_RUNNING # do not log pytest
import wandb as wb
assert hasattr(wb, "__version__") # verify package is not... |
45bc7702487cdcf5f74c04bb63cb877ea396843a2834d4aac0f2da6b99f23fd5 | Python | 8,315 | 149 | """Протокол B: «Когда выгодно учиться». Единая точка правды для конфигурации.
Мир B отличается от мира A ровно тремя вещами, и все три записаны здесь:
1. два типа еды, роли которых меняются в непредсказуемые моменты;
2. мир богаче (patch_threshold 0.0 и regrowth 0.008 вместо 0.35 и 0.004),
чтобы питательная п... |
ffd5ef89e264edf6dd71ed7cb76b9a7b5ff1a2f3643fca84558ebec9cdd50cb9 | Python | 8,317 | 216 | import pickle
import torch
import torch.nn.functional as F
from trainingUtils import NBLoss,_convert_mean_disp_to_counts_logits #,MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Encoder,Decoder,GaussianDecoder,VAE,CellStateEncoder,\
CellStateDecoder, CellStateVAE,... |
ab2497c8c3165f5d16e91a94049a7ea0337a5f7906fc52c8e871181d73bbd7e8 | Python | 8,318 | 168 | """Pascal ADE20K Semantic Segmentation Dataset."""
import os
from PIL import Image
import numpy as np
import mxnet as mx
from ..segbase import SegmentationDataset
class ADE20KSegmentation(SegmentationDataset):
"""ADE20K Semantic Segmentation Dataset.
Parameters
----------
root : string
Path to... |
08aab8a956daeddc3920c0bc922389fffd531239787b5b236955d341667a2103 | Python | 8,319 | 267 | from pathlib import Path
import os
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import torch
import torchvision.transforms as transforms
import torch.nn.functional as F
from tqdm import tqdm
from torchvision.models.resnet import resnet18 as Net
import warnings
warnings.f... |
d155b23da1638b0c09e9cfad91f134c7ddf456fa009513433ad1936becf74cf4 | Python | 8,321 | 334 | from sys import argv
def update_map_dic(line, map_dic, reg_nom_dex, regulator_type_dex, targ_nom_dex, targ_type_dex):
if line[reg_nom_dex] in map_dic[line[regulator_type_dex]]:
if line[targ_nom_dex] not in map_dic[line[regulator_type_dex]][line[reg_nom_dex]][line[targ_type_dex]]:
map_dic[lin... |
4a924c5f408e95a7710c5625338fe1211cd2d6a130d7f1c06b50f7b26730e757 | Python | 8,324 | 228 | import pickle as pkl
import networkx as nx
import numpy as np
import scipy.sparse as sp
import torch
from sklearn.metrics import roc_auc_score, average_precision_score
def sample_mask(idx, l):
"""Create mask."""
mask = np.zeros(l)
mask[idx] = 1
return np.array(mask, dtype=np.bool)
def load_data(dat... |
93b351c4068228cdbffa007f613e088d71c817bb5391f998703f2c59822f3e57 | Python | 8,324 | 180 | from operator import imod
import os
import torch
import torch.nn as nn
from torch.autograd import Variable
from torch.utils.data import DataLoader
import argparse
import time
import datetime
import os
import math
import tifffile as tiff
import numpy as np
import random
#################################################... |
9b8cbf9a3579ad0af1e1d96f306b65cee69a59380cbd3cc490348b8ff4401b9b | Python | 8,325 | 284 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from itertools import chain, repeat
from math import ceil, pi, sin
import random
import numpy as np
from .._data_obj import NDVar, Var, NestedEffect
from .._utils import intervals
from . import vector
# Keep local RNG independent of public RNG
RNG = random.Ra... |
b125b17ce2b244131fe6e924bb3b3260c147960175cf978c4c60a01c2846b27e | Python | 8,327 | 208 | #!/usr/bin/env python3
"""
Diagnostic J — two-model ensemble (decision-score averaging).
Two complementary LDA classifiers are trained per fold:
- Model A (LOO winner): 7D + aperiodic + topographic IAF + frontal asymmetry
- Model B (LOCO winner): 7D + alpha/theta peaks + topographic IAF + posterior asymmetry
For ... |
aee0972a6783bd7ce375a0913726b552f7418f0d0ed1a2babd5aa7e76d64b8d3 | Python | 8,328 | 189 | """
09: Fitting Models over Time
============================
Use extensions of the model object to fit power spectra across time.
"""
###################################################################################################
# sphinx_gallery_thumbnail_number = 2
# Import the time & event model objects
fro... |
23c07a1d1b5570b2300c8afa50b67544eed0119675a26986924da974be9ff6a6 | Python | 8,333 | 242 | """
===============================================================================
Compare covariance and kernel estimators with different time windows
===============================================================================
Comparison of covariance estimators for different EEG signal lengths and their
impact ... |
2a55a121bcfc4b88591c03691bc7bd8f2ec9a9577e6ba199f44bca1d67ce0d47 | Python | 8,335 | 146 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
b6d754fce09ebd68af2ff971eff25a9cfdca4a8f3ff09b7a6fdef8942a0845dd | Python | 8,336 | 185 | import os
import pandas as pd
from interfile import Interfile
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib import font_manager
palette = ["#0f8b8d", "#a3f3f5", "#a8201a", "#f6c9c6", "#ec9a29", "#f7d3a1", "#662e9b", "#c3a0e3"]
ecat_dir = r"E:\preclinical_data\raw_pet\headers"
if not os.path.i... |
c309272872872fea064711801dc312385b80926d031077933e1d4b820d5c0f6a | Python | 8,336 | 419 | """
Color sequences and scales from CARTO's CartoColors
Learn more at https://github.com/CartoDB/CartoColor
CARTOColors are made available under a Creative Commons Attribution license: https://creativecommons.org/licenses/by/3.0/us/
"""
from ._swatches import _swatches
def swatches(template=None):
return _swat... |
03917ee597af22103da86baa147af0b35ef31cdd0811aa5d3a759828c2db85d2 | Python | 8,337 | 200 | import numpy as np
import torch as ch
import sys
class EnvelopeExtraction(ch.nn.Module):
"""
Base class for envelope extraction functions.
Extracts the envelope of a time-signal.
"""
def __init__(self, signal_size, sr,
use_rfft, pad_factor):
"""
Base class for eac... |
ae93891a70c2a7ebc90cc038ad21d11b7f6b360991f5f11bd120cecd0d89a10f | Python | 8,337 | 279 | import ctypes
import logging
import os
import re
from datetime import datetime, timedelta
import numpy as np
from .exceptions import OTFError
from .util import load_lib
logger = logging.getLogger(__name__)
try:
import pathlib as plib
plib.Path()
except (ImportError, AttributeError):
import pathlib2 as... |
d3cc382825989ea6b5f7ba12b734c6dc7ff08f57a3bd92394baf5f2fe0443856 | Python | 8,337 | 277 | #!/usr/bin/env python3
"""
axtToSyn.py
Generates elongated synteny blocks from a pairwise alignment .axt file.
You can specify a min lastz alignment score to filter .axt file by
the last filed. The min block length only considers elongated blocks
larger than this length.
Jake VanCampen
vancampen@ohsu.edu
"""
import... |
2081afb16c25de6eac2b2a9827fcc49698682a0834a92e4ff3445809897abc26 | Python | 8,338 | 208 | """Manager for a user's favorites: tools, curated tool tags, and EDAM
operations/topics, plus the user-visible ordering across all of them.
The favorites payload is persisted as a JSON document inside
``user.preferences["favorites"]`` (a Text column). This manager owns its
schema — validation, deduplication, and the `... |
33ad01e696d21a666f71ce7b26bf417b2423618f9419a975ce04089d9991709e | Python | 8,338 | 253 | #!/usr/bin/ python
import numpy as np
import re
import gridData, glob, struct
import sys, argparse, os, subprocess
def parse_args(argv=None):
parser=argparse.ArgumentParser(description='Script for generating the jobs that need to be run for visualization. Generates types files & a text file that needs to be run. Can... |
bcb7603fe432ea15d6393e02642308576cd9e9ea37bb977c8ca53f2a0188e705 | Python | 8,340 | 223 | #!/usr/bin/env python3
import argparse
import os
import subprocess
"""
Install deseq-clip
==================
conda install -c bioconda pysam
conda install -c bioconda htseq
pip install htseq-clip
Or directly by:
conda install -c bioconda htseq-clip
Test call
=========
python htsc_create_sliding_windows.py --gff... |
5f726a4564140143ee2b7e1627486cf6a73eb49bae97b79672424706b8955321 | Python | 8,342 | 205 | """
amplification_03.py - adaptive signal amplification for impaired EEG
deficit = (baseline_rms - trial_rms) / baseline_rms
factor = clip(1.0 + deficit * GAIN, AMP_MIN, AMP_MAX)
Only trials below the baseline are amplified. Labels are never touched.
Two reference modes
-------------------
population The b... |
fdd400c9b4742530fdc046278a691f1b35ab72ebdc279a5ee341d4a4ffb5f75b | Python | 8,342 | 256 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import sys
import pwd
import pdb
import grp
INPUT_PATH = "SimBoost/data/davis_cv2.csv"
LOG_DIR = "logs/"
uid = pwd.getp... |
b27a8664d1bf85bb2ae831af651e10ca87c15c28796f4c44977ed5909676de97 | Python | 8,343 | 200 | # ---
# 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... |
1ee988a90f7a02d1bd3d526ba9232eafe2bbb782d0884ae6e382df85f54501e0 | Python | 8,344 | 221 | """Segment-run prefix search tests for the v2 collapse optimizer.
Moved verbatim from ``tests/test_collapse_optimizer.py`` (at its size cap).
The linearized ``_longest_legal_segment_prefix`` search is checked against the
naive forward prefix scan it replaced (a differential oracle kept verbatim),
and its probe/recount... |
8821c4a3f2c6dd71cd42b41c242b88cfe7085cd4449db27e64483ce0f0ea814a | Python | 8,344 | 205 | import pickle
import torch
import numpy as np
import matplotlib.pyplot as plt
import networkx as nx
from torch_geometric.data import Data
from torch_geometric.utils import to_networkx
from model import EMGNN
from gnn_explainer import GNNExplainer
from captum.attr import Saliency, IntegratedGradients
from captum_custom ... |
4e5ae2b1e96898ca500d9a53014870664f9709d6db4ba910d468ce3181e857f3 | Python | 8,345 | 198 | #################################################################################################################################################################
####################### Training MulitRBP ####################################################################################################################... |
797c0430a79c152e98cf052318112344a4d22378f759602454842e80a5a89fb9 | Python | 8,349 | 176 | # -*- coding: utf-8 -*-
"""
Created on 23/09/2022 at 17:47
This is the Updated Version for easy access for multiple choses.
23/09/22 -> Possible To Choose to record detected events.
-> "_ImpPlot=True" Plots the Impedance Plot
-> "_SRT_Plot=True" Plots the Semi Real Time Data different cl... |
1496ef655360666ed9190c53ecd5e18b197d5e10155ef94c8f783b9038c1675f | Python | 8,353 | 211 | from __future__ import absolute_import
import os
import numpy as np
import tensorflow as tf
import argparse
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
import sys
import h5py
import time
import threading
from tqdm import tqdm
from tensorflow.python.platform import resource_loader
from .utils_dna... |
138f9d479673e9f92584741c1ae623357edb1c451adc5fb794e3bbe592bd5db7 | Python | 8,355 | 207 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import sys
import pwd
import pdb
import csv
import re
import math
import time
de... |
8136006f834a796bc05bcc20844b953e7fc035c35dc3ba38ccad1874399f0129 | Python | 8,358 | 268 | # -*- coding: utf-8 -*-
#
# mord documentation build configuration file, created by
# sphinx-quickstart on Tue Jan 6 09:55:06 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... |
1dce826964a16eb7894a7494ca98f80565dc7ac6e7d0ed437bbed039f7ea4d4e | Python | 8,361 | 176 | # -*- coding: utf-8 -*-
"""
Created on 23/09/2022 at 17:47
This is the Updated Version for easy access for multiple choses.
23/09/22 -> Possible To Choose to record detected events.
-> "_ImpPlot=True" Plots the Impedance Plot
-> "_SRT_Plot=True" Plots the Semi Real Time Data different cl... |
6ab49863e856d943037186149abd2e65c963ae9a14c7f6d48c1c05cd0dbf2dd0 | Python | 8,361 | 201 | """Hypothesis/discharge battery (L7a memo sec 3/9.4).
Covers: corroboration on identical geometry, refutation on a planted shape
divergence, the graph-mismatch verdict without row comparison, typed
precondition refusals, the POSITIONAL-JOIN pins (repeated identical ops and
recurrent passes under digest equality), G4 n... |
8c920d9e07a232ad7e276d056e60438abb9ee81a88cf4e459884977b725d99ef | Python | 8,363 | 273 | """Regression tests for two-pass logging with in-place operations."""
import pytest
import torch
import torch.nn as nn
import torchlens as tl
from torchlens.backends.torch.aliasing import detect_torch_alias_contract
from torchlens.ir.intervention import FunctionEventInput
from torchlens.options import CaptureOptions
... |
c9cacb0a1442c82388ee2b4e0f9aa4367f1aba503ad60c206b38b990b3f9e9b7 | Python | 8,363 | 210 | """Module that contain iterator used for dynamic data."""
from itertools import cycle
from torchtext.data import batch as torchtext_batch
from bioseq2seq.inputters import str2sortkey, max_tok_len, OrderedIterator
from bioseq2seq.inputters.corpus import get_corpora, build_corpora_iters,\
DatasetAdapter
from bioseq2... |
0f9dd6558a9c80a492bd5f8ca3996138ead2fb99b0f024374733fbef828e6391 | Python | 8,366 | 243 | """Tests for built-in attention recipe behavior."""
from __future__ import annotations
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens import trace as trace_fn
from torchlens.semantic import MissingFacetError
pytest.importorskip("transformers")
class DistilBertSdpaAttention(n... |
b109936e3339f9d1307a789dafddcd5ebf89d2b5eb481115bf94fac598f7ec75 | Python | 8,366 | 230 | """C03: tl.site() structural selector + live site-key minting (Build 0a/0c).
The address law's structural lane: a ``site`` WHERE term is valid in EVERY
lane -- post hoc against ``op.site_key``, and during a live capture against
the streaming minter armed by the ``tl.trace`` entry. The parity pin is the
verification su... |
8b624dd103307c6eabc67cba3b6a2b70b50608330dc471e1be4501a570227417 | Python | 8,367 | 215 | """Spec rule identity follows the full, current content of tensor arguments (F4).
Rule ids, ``action_repr`` and ``spec_digest`` used to render tensor arguments
through ``repr``, which torch truncates above 1000 elements and which was
computed once at construction. Two model-width steering vectors differing in
one elem... |
9590349e4e27d33114652bd85da6e631a11aebb7e4204f239b66e5daa2105ba2 | Python | 8,367 | 277 | import numpy as np
#import time, sys
#from swan import pycwt
import itertools as itt
import operator as op
from functools import partial
from scipy import ndimage
from . import core
from .core import ifnot, coords
from functools import reduce
def locations(shape):
"""locations from a given shape (Cartesian prod... |
1d82488fe5db260068fe7406a89be4193637c571e005e8e0b0a86addb68075c5 | Python | 8,370 | 241 | """
===============================================================================
Compare covariance and kernel estimators
===============================================================================
Comparison of covariance estimators for different EEG signal lengths and their
impact on classification [1]_. Kern... |
7e5179519c8e5d57db463577aa50c659c3e68156130f01fe06cb23584baaacce | Python | 8,370 | 274 | """Tests for the provisional public structural-hash API."""
from __future__ import annotations
import subprocess
import sys
import textwrap
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.options import CaptureOptions
class _ResidualModel(nn.Module):
"""Small model with a... |
c241dddf83e61671973e94bd4b71227481642c4837aa26831090b090eb7283b5 | Python | 8,374 | 201 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 3 10:25:08 2020
@author: Audrey Mazancieux
This script performes analyses of pupil dilation during the local global task.
Ii includes:
- preprocess the data
- epoch data around event of interest
- plot the result gathering all sess... |
f34024d09c3d35f985545aa6287e8a8bf1d54062c4b54aacaba0f8dad05cfbbd | Python | 8,375 | 180 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""Shared helpers for operating on lists of track objects across trackers.
These functions are intentionally generic: they only touch attributes that every track
implementation exposes (`track_id`, `frame_id`, `start_frame`, `xyxy`, `mean`, `covarianc... |
d5da667423a10e8249e1628fbfdbb18cb281f2b38a50c7bffb166de30eec65b9 | Python | 8,378 | 237 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from pathlib import Path
from pickle import dump, HIGHEST_PROTOCOL, Unpickler
from itertools import chain
import os
from typing import Any
from .._data_obj import Dataset, NDVar, Var, SourceSpaceBase, ismodelobject
from .._types import PathArg
from .._utils impo... |
6fe0e283e35ab328fc2f1d1b2f2a423b88de16a53cdcbb92667b3cb1d6d48ab1 | Python | 8,384 | 214 | """LIFECYCLE PURITY -- the C06 row gate.
The chassis contracts (checks 4.2), each tested as evidence, not style:
- every hook handle is removed on EVERY exit path (success, exception,
context-manager unwind);
- zero user-RNG consumption: a bitwise same-seed observed run equals the
unobserved control (losses, para... |
a51da6862c23291a1c61d9901eedd648452a39ffb194d0f2202fba42eb53069a | Python | 8,384 | 465 | from typing import List
import math
from matplotlib.patches import Rectangle
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
# * matplot color introduction
# https://matplotlib.org/stable/tutorials/colors/colormaps.html
# https://matplotlib.org/stable/tutorials/colors/colormapnorms.html
# * color... |
d48110766d65ae2c6b837f018c6cfac09d358b144a0af3cfb1da14784916a1b2 | Python | 8,384 | 265 | from __future__ import annotations
from typing import Callable, Type, Any, Iterable, TypeVar, Generic
from typing_extensions import Annotated, ParamSpec
from collections import defaultdict
from functools import wraps
_P = ParamSpec("_P")
_Unused = Annotated[None, "unused"]
def _is_unused(fn: Callable) -> bool:
... |
dd692bf5a74fc7a6790fd686c1ae726b0b67fa420473fbade42e7c720474aea1 | Python | 8,384 | 195 | '''
TNS class : Grower object that contains the grower functionality.
'''
import logging
from copy import deepcopy
import numpy as np
from scipy.spatial import cKDTree
from morphio import SectionType
from tns.generate.grower import NeuronGrower
from tns.morphmath import sample
from tns.astrocyte.tree import TreeGrow... |
2f407d92c3e350962c86cdbcc82435147b6f31de0fe756b5bb60f4c271b0fcf0 | Python | 8,387 | 325 | import itertools
from typing import Optional
import anndata
from matplotlib import cm, colors
from .scatters import scatters
from .utils import _convert_to_geo_dataframe
# DEFAULT COLORS from
# https://github.com/scikit-image/scikit-image/blob/8faf62d677e73f5911cfc5232d5de02f1da7486b/skimage/color/colorlabel.py
DEFA... |
04b98438398d5b4876be66ff0f7f082c37f200dd958b0d6fc0e12e151aab35d6 | Python | 8,388 | 222 | """PointNet++ with Multi-Scale Grouping (MSG).
Qi, Yi, Su & Guibas (Stanford), NeurIPS 2017, arXiv:1706.02413.
Source: https://github.com/charlesq34/pointnet2
PointNet++ MSG is a variant of PointNet++ where each Set Abstraction (SA)
layer groups neighbors at MULTIPLE radii simultaneously and concatenates the
per-scal... |
7c4710be0dd0ff25f397b02669a7cabbc5163d5c3233c4bec327be945afbf429 | Python | 8,388 | 269 | """Tests for the xcp_d.cli.parser_utils module."""
from argparse import ArgumentParser, ArgumentTypeError
from pathlib import Path
import pytest
from xcp_d.cli import parser_utils
def test_int_or_auto():
"""Test parser_utils._int_or_auto."""
with pytest.raises(
ArgumentTypeError,
match="Arg... |
aef182538f2d79e4e6855761863c24539931d263d2fd4a263fe556e00e56be63 | Python | 8,388 | 282 | import datetime
import errno
import os
import time
from collections import defaultdict, deque
import torch
import torch.distributed as dist
class SmoothedValue:
"""Track a series of values and provide access to smoothed values over a
window or the global series average.
"""
def __init__(self, window... |
d57f93e5a7550f4e4a72dae933d5ca14d5e87e56d2ca00b2e3cdf15eb4de6343 | Python | 8,388 | 153 | # -*- coding: utf-8 -*-
"""Собрать docs/ для GitHub Pages: страницы + SEO + разрешение ИИ-ботов.
Главная (index): ЖИВОЙ эксперимент (live.html, использует engine.js +
ancestors.json). about.html: объяснение проекта. sim.html: точная запись
Python-движка. Кросс-ссылки относительные; в каждую страницу вставляется
богаты... |
69f08ec90f1d7592e27dd9ecd5e550f49272d0e8bc118cc770877759788fdcfc | Python | 8,390 | 231 | #!/usr/bin/env python3
"""
File: plot_sample_size_simulations.py
Created: 2023/07/15
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... |
f34b4a82ed13f638f5d1362c11243a1bc7a8a1632cada246e131e51675c5cd09 | Python | 8,390 | 215 | import logging
from urllib.parse import unquote_plus
from pydantic import BaseModel
from galaxy.datatypes.display_applications.util import (
decode_dataset_user,
encode_dataset_user,
)
from galaxy.datatypes.registry import Registry
from galaxy.exceptions import MessageException
from galaxy.managers.context im... |
61af07e15a25cbb50c74efe80f9f4258e1b6b7d8fa073605aab8733020ef312a | Python | 8,391 | 211 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import sys
import pwd
import pdb
import grp
INPUT_PATH = "SimBoost/data/davis_cv.csv"
LOG_DIR = "logs2/"
PATIENCE = 3
#... |
2776c482664ccb2a9f869a25529d0e7c2f107f7134ac1d49dfaac75f847871f9 | Python | 8,393 | 222 | # -*- coding: utf-8 -*-
"""
Created on Fri May 12 15:23:40 2017
@author: Rong Chen
# """
import os
import gc
import logging
from reportlab.lib import colors
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.Graphics import GenomeDiagram
from Bio.Graphics.GenomeDiagram import CrossLink
from PyPDF2 impor... |
aeebb3c0736fe87336fdbb116d92a40819ee01c8f91fdca05199dd1f283a9f78 | Python | 8,393 | 212 | import csv
import os
from collections import namedtuple
from typing import Any, Callable, List, Optional, Type, Union, Tuple
import PIL
from sklearn import datasets
import torch
import numpy as np
import pandas as pd
from torchvision.datasets.utils import download_file_from_google_drive, check_integrity, verify_str_a... |
235b940dc9253268391896901887ba02acfdd54aeb337b61d624bb647a870810 | Python | 8,394 | 219 | """Tests for collect_confounds using simulated BIDS derivatives."""
import os
from pathlib import Path
import pytest
import yaml
from bids.layout import BIDSLayout
from niworkflows.utils.testing import generate_bids_skeleton
import xcp_d.utils.bids as xbids
from xcp_d.data import load as load_data
def _load_confou... |
7c5ec5492031c926d99f05dec045c9601cb890b8280fac865c773c688417ff90 | Python | 8,396 | 201 | #!/usr/bin/python3
#-*-coding:utf-8-*-
# Copyright (c) 2022 PaddlePaddle 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... |
e68a1785c91a23f0d0b323e24d0e1ad23cd3c3849bf8c99325ca6a4fd055ab6b | Python | 8,397 | 162 | import tensorflow as tf
from tensorflow.keras.metrics import Accuracy, CategoricalAccuracy, Precision, Recall, Mean
from tensorflow_addons.metrics import F1Score, CohenKappa
from tensorflow.python.keras import backend
class ComplexAccuracy(Accuracy):
def __init__(self, name='complex_accuracy', dtype=tf.complex64... |
85ce81cd59317056170795882d908910a58b0c84d4ac4d5eea3426e85bb9eff6 | Python | 8,398 | 205 | """Producer-side SSE helper: fans events out across Galaxy processes.
Kept in its own module (separate from ``galaxy.managers.sse``) because the
dispatcher depends on ``galaxy.queue_worker`` and ``galaxy.queues``, while
``queue_worker`` in turn depends on the connection types in ``sse``. Splitting
the producer (``SSEE... |
9ff07c2290496012d90fb259b6074d24ea8d90bd946bc70f6dfef747c6a8dc10 | Python | 8,400 | 153 | # -*- coding: utf-8 -*-
"""Собрать docs/ для GitHub Pages: страницы + SEO + разрешение ИИ-ботов.
Главная (index) — ЖИВОЙ эксперимент (live.html, использует engine.js +
ancestors.json). about.html — объяснение проекта. sim.html — точная запись
Python-движка. Кросс-ссылки относительные; в каждую страницу вставляется
бог... |
84ecac82961eb233db8d65c8e86336ec834dc3a043494b85450bd52cfca0769c | Python | 8,401 | 237 | import os
import json
import rclpy
from rclpy.node import Node
from rclpy.parameter import Parameter
from std_msgs.msg import Bool, Int32, Float32MultiArray, String
import torch
import numpy as np
import pandas as pd
from scene_classifier_code import SceneClassificationModel
from retinal_sampling.sampling_code impor... |
778c58ff8f0a443ef25d6a48989d9ac1210072b95a699b6682605a527b93750b | Python | 8,402 | 184 | """
Author: Derek van Tilborg -- TU/e -- 22-05-2022
A collection of data-prepping functions
- split_data(): split ChEMBL csv into train/test taking similarity and cliffs into account. If you want
to process your own data, use this function
- process_data(): ... |
edad543b25ea9d63af7e4d546f88cf0ddeeb552c9da3ad9929ee4828ae983c43 | Python | 8,403 | 234 | import numpy as np
from scipy import stats
from sklearn.metrics import r2_score, mean_squared_error
def common_part_of_commuters(values1, values2):
"""
Compute the common part of commuters for two pairs of fluxes.
:param values1: the values for the first array
:type values1: numpy array
:param v... |
fcd3f70ef34f67a90d86d01c439460df4d627f1c10ffed66efad293daf2703e0 | Python | 8,403 | 194 | """int4 handlers for the projection family (`Dense`, `EinsumDense`)."""
import math
from keras.src import ops
from keras.src.quantizers.modes.common import apply_bias_activation
from keras.src.quantizers.modes.int4.block_size import int4_scheme
from keras.src.quantizers.modes.int4.block_size import is_grouped
from ke... |
3bfcae98c0c03bbec54ebad966f7f32e387e9086abd0be7b70d85a45021ede94 | Python | 8,404 | 205 | '''
Script to run the model from commandline to be used on biolib.
'''
import argparse
import torch
import utils
from write_markdown_output import write_fancy_output
from concurrent.futures import ProcessPoolExecutor
import os
import json
from tqdm.auto import tqdm
MODEL_LIST_ESM1B = [
'checkpoints_esm1b/0/1/model... |
9404e6ffc17726d313fce32f8ea6caa051424018f9a73f69ef7fda72e1a43482 | Python | 8,407 | 234 | import itertools
from pathlib import Path
import numpy as np
from numpy.random import default_rng
_eps = 10 ** (-5)
class DCBM:
def __init__(self, n=None, model_order_K=None, p_in=None, p_out=None, seed=0):
assert isinstance(n, int) and n > 1
assert isinstance(model_order_K, int) and model_order... |
0515781be85942751b86279a4dce8a0bc90efe2d57318c5146655d092a301d79 | Python | 8,408 | 264 | """
Process-level cache for hardware detection and setup.
Reuses the outcome of the first tracker hardware probe so additional runs on
the same device (same process) skip repeated powermetrics, cpuinfo, and GPU
detection work.
"""
from __future__ import annotations
import threading
from dataclasses import dataclass,... |
5ae36df92f67e44e7b83ee4d9377814d88d828d28c37c178af13e8c6d73cffe4 | Python | 8,409 | 224 | import os
import random
import torch
import json
import itertools
from collections import defaultdict
import numpy as np
from src.utils.util import device
from src.data.tokenize import tokenize_pet_txt, tokenize_pet_mlm_txt
class MultiRCReader(object):
'''
MultiRC reads MultiRC dataset
'''
def __ini... |
7fa03d4fd3111d60560620d21bc06daccbc58fa880b3c1a326a9c8c1ddf22544 | Python | 8,411 | 244 | #!/usr/bin/env python3
"""
File: plot_start_vs_end.py
Created: 2021/05/18
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 tree.
"""
... |
a5dab251c7993e5b8e375cdca5f51ad6e35b2ba6f45fc920e097496a82cde092 | Python | 8,411 | 241 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=None),
neck=d... |
e6ff91d016e25cd215bf998e12a878371ef3045e0733d9121f738f444962de63 | Python | 8,412 | 252 | """
Use to easily handle various plugin UI components.
Can be inherited to customize the class.
Use with the plugin_form, plugin_table, and plugin_popup modules.
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is f... |
932e5691af0af936972d83b3a834d6e83e3a55ec71aaa123c865e3d96794b427 | Python | 8,413 | 253 | """
Computing in the thymic Q framework.
"""
import os
import tempfile
import click
import delegator
import numpy as np
import pandas as pd
# These are our "lvj" columns, which are the most common indices for
# probabilities and sequences in what follows.
lvj = ['length', 'v_gene', 'j_gene']
def bound(x, m):
"... |
875e988c75bfebb7af1b59001eb53b7c8e129cb51758903998365c777472f796 | Python | 8,415 | 212 | #!/usr/bin/env python
import argparse
import json
from cp_common_functions import (get_json_value,
get_pipeline_lines,
get_total_number_of_modules,
INDENTATION, update_module_count,
... |
bb9b56234a6e985fa5c464752ea590b5119050f3c56a5203e7dc9c8c218df431 | Python | 8,415 | 226 | from typing import Dict, List, Optional, Tuple, Union
from PIL.Image import Image
from torch import Tensor
from lightly.transforms.gaussian_blur import GaussianBlur
from lightly.transforms.multi_view_transform import MultiViewTransform
from lightly.transforms.rotation import random_rotation_transform
from lightly.tra... |
c59702b74fa5ff80d0bfc9ff07456ce46509365e93d838078e2d5114bb42678d | Python | 8,415 | 239 | """Capture-floor release-at-emission oracles (F20 W1a, brainpipe memo s3.3).
The brainpipe panel's central discovery: an instrumented forward that saves
nothing peaked at 27x the bare forward because capture bookkeeping pinned
every live intermediate for the whole pass. These oracles pin the fix at the
mechanism level... |
40e05bbc028bd874a0751d6d90474c906d5f6003e38c252aa928d769cf23401f | Python | 8,417 | 202 | import tensorflow
from tensorflow.keras.models import Sequential
from tensorflow.keras.models import Model
from tensorflow.keras.layers import BatchNormalization
from tensorflow.keras.layers import Conv2D
from tensorflow.keras.layers import MaxPooling2D
from tensorflow.keras.layers import Activation
from tensorflow.ke... |
725b082ddc4782c3b51c5ae88ffdd45a202e044f7b5a71970ad1e4f417ef3017 | Python | 8,418 | 240 | import numpy as np
import scipy
from scipy.cluster import hierarchy
from scipy.spatial.distance import squareform
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from scipy.spatial import distance
import pandas as pd
# used to plot heatmap in Supp Figure 2D
# input is matrix of Hi-C contacts or... |
c2db3023cd2e449e6776e4e9a882014503ada04485ebf160ae664d1b7d4dac31 | Python | 8,419 | 230 | import os
import json
import random
import numpy as np
import itertools
import torch
from collections import defaultdict
from src.data.tokenize import tokenize_pet_txt, tokenize_pet_mlm_txt
from src.utils.util import device
class RTEReader(object):
'''
RTEReader reads BoolQ dataset
'''
def __init__(s... |
3d0029e5c9113c4878f1163f2371b9be3f31cdfdf417967e6911d2629c18e8a6 | Python | 8,420 | 256 | import math
import numpy as np
import pickle
import time
from manfit_our import manfit_our
from manfit_cf18 import manfit_cf18
from manfit_km17 import manfit_km17
import matplotlib.pyplot as plt
import scipy.io
from torusUnif import torusUnif
from pdtorus import pdtorus
# xiayq @ 12/01/2022
# xiayq0121@zu... |
065445879aebbf1ef0b656e7b489cf6804ab157329500acb5a9b11142bd8357c | Python | 8,425 | 253 | # -*- coding: utf-8 -*-
"""
This file preprocesses data to speed up regression. Specifically, it creates columns of exogeneous variables that will later get used in fitting other units.
------------------
Instead of doing an exhaustive search over Markov parameters, we will specify a single mapping of past values t... |
fd8f1048b9c6569ce3df91a784cca3651589590322d263d235c8cdf0e29ba9be | Python | 8,427 | 180 | """
BASIL GUI for Oxford ASL - Input data/acquisition options
Copyright (C) 2020 University of Oxford
"""
import wx
import wx.grid
from . import get_nvols, OptionError
from .widgets import TabPage, NumberChooser, NumberList
class AslInputOptions(TabPage):
"""
Tab page containing input data options
"""
... |
1a7d5eac1c90107c180056676204a7d1a4702a38dcf343aa295cf5f4cb68dfad | Python | 8,429 | 173 | """08. Finetune a pretrained detection model
============================================
Fine-tuning is commonly used approach to transfer previously trained model to a new dataset.
It is especially useful if the targeting new dataset is relatively small.
Finetuning from pre-trained models can help reduce the risk o... |
ac55577d9a6132cd2a5079a1533f8362f78cdfd1f8580cdc36745acddc9be391 | Python | 8,429 | 217 | # AUTOGENERATED! DO NOT EDIT! File to edit: nbs/Uniprot_integration.ipynb (unless otherwise specified).
__all__ = ['extract_note', 'extract_note_end', 'resolve_unclear_position', 'extract_positions', 'preprocess_uniprot',
'uniprot_feature_dict']
# Cell
import re
import pandas as pd
import numpy as np
# C... |
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