sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b62e4458e81676a8341cc76752a1f1260a7abfbbeca4d2f06c63590dfbeb4463 | Python | 6,894 | 172 | #!/usr/bin/env python3
"""
Dx BJ — Sub-sampling + recording-length redo under proper per-fold
===================================================================
Two analyses re-run under the proper per-fold deployment-mode
pipeline:
A) HC sub-sampling: shrink each cohort's HC pool to fractions
{1.0, 0.7, 0.5,... |
d4c5b379a74641fedb7ca91edaf6a974900ac489df14271ebb8c8d0a1934994e | Python | 6,896 | 135 | """Label definition."""
from collections import namedtuple
# a label and all meta information
# Code inspired by Cityscapes https://github.com/mcordts/cityscapesScripts
Label = namedtuple(
"Label",
[
"name", # The identifier of this label, e.g. 'car', 'person', ... .
# We use them to uniquely... |
7bc5f2f679894cdef26535ff348bfeb56835d527d63f166413fa8f51183dd6cd | Python | 6,897 | 200 | # SOURCE: vendored from https://github.com/yihaosun1124/OfflineRL-Kit @ main (951302eed019)
# (offlinerlkit/nets/ensemble_linear.py + offlinerlkit/modules/dynamics_module.py,
# minimal changes: merged into one file, imports fixed)
"""COMBO (Conservative Offline Model-Based Optimization, Yu et al. 2021) -- the
distingu... |
04def0147b9f7c7779222ed6921c8efb6bc4c984fa878d920826190cb6b6bae6 | Python | 6,899 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
4749d9b68be2cd743a7fefc4880d96560f22035df4f5bfc321f56df19784a6ed | Python | 6,899 | 167 | """
Théo Gauvrit
Spetembre 2021
General script to compute PSD for different frequency bands from resting menbrane potential recordings.
Comparaison of two groups(ex: WT vs KO)
Compute the PSD with bands, plot the wlech periodogram.
"""
import os
import time
import matplotlib.pyplot as plt
import numpy as np
import pan... |
535fb11fb75079013cdec35c207a8a3ef5e9e23e5090af68728a9d92232d2cba | Python | 6,899 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
62c4a222bdf81c5256bc72e5a7b3bea98444d4d587d4d1200db8ee50d3be21ab | Python | 6,899 | 134 | from ovseg.preprocessing.SegmentationPreprocessing import SegmentationPreprocessing
from os.path import join
from os import environ
import argparse
import warnings
warnings.filterwarnings("ignore", category=UserWarning)
parser = argparse.ArgumentParser()
# first some arguments we need for the planning and saving
pars... |
65f5caa62528480392b0c44e46b5305d7e63bf8093ca712a7d30ce58fd32c336 | Python | 6,899 | 203 | from __future__ import annotations
from pathlib import Path
from types import SimpleNamespace
import pytest
from larvaworld.portal.datasets import import_adapter
from larvaworld.portal.datasets.models import ImportRequest, WorkspaceDatasetRecord
from larvaworld.portal.workspace import initialize_workspace, set_activ... |
d7b90a6a01ead65ced723e1b54795924491ef325baba08ba8b0805d81cf7b0d9 | Python | 6,899 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
a36b7831dab261ccd777618619fac8d3407fa91be93906b4bf517bf0ce72d853 | Python | 6,900 | 143 | import math,copy,random
import numpy as np
from rdkit import Chem
from rdkit.Chem import MolFromSmiles,MolToSmiles,CanonSmiles, AllChem
import torch
from torch_geometric.data import Data
from torch_geometric.utils import to_dense_adj
from torch_geometric.utils import add_self_loops
allowable_features = {
... |
1a662e4fd4805dc0100a3cfca02ccab1e5ba44aefa7150219af87cf2d0789db4 | Python | 6,901 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
659a24e00c7f843c13f88257146436884d769b02388650bc29557f86a4d170d6 | Python | 6,901 | 188 | #!/usr/bin/env python3
"""
Dx AG — Platt scaling for calibrated probability output.
The Dx AA tool outputs continuous LDA discriminant scores. Platt
scaling transforms these into calibrated P(AD | features) probabilities
via a logistic regression fit on (score, label) pairs from training
data.
For clinical deployment... |
a1128789cf06887774d5db975c83fe1141503411455c013de7d5260612edfe50 | Python | 6,901 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
cd3431c61924789aa8fef7b050f767d85b8f6249b27871fe1f1e4e1be53494b1 | Python | 6,901 | 242 | """
Methods for managing context and attributes
"""
from __future__ import annotations
import functools
import os
import sys
import time
from collections import Counter
from contextlib import contextmanager, redirect_stderr, redirect_stdout
from typing import Any, Callable, Iterable, Iterator
# from functools import... |
65762ec7da872eb094ea185820bd6503ad339b205e5ff03c8d8af7dbcadd9c20 | Python | 6,903 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
9305c8a7fecc120b032dc6b145fce5b96c04c14eb0f3b2febcafcdede04761fd | Python | 6,903 | 174 | """
Copyright (C) 2022 Giansalvo Gusinu
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribu... |
a0959bf9060a2fe991d2f5455f0f8f44c12070892b124a0869371d4fb3aaa27d | Python | 6,903 | 193 | from __future__ import annotations
import copy
from typing import Any, Optional
import numpy as np
import pandas as pd
from bream4.device_interfaces.devices.base_device import BaseDeviceInterface
from bream4.device_interfaces.devices.promethion import PromethionGrpcClient
from bream4.toolkit.procedure_components.dat... |
bfbad78d2ae7397c25673d005a2da181b89626adb734fbe04b60606427dfd3fe | Python | 6,905 | 170 | """G3 ceiling consolidation: one typed above-ceiling refusal at every door.
Every "artifact is newer than this runtime" site raises
``ArtifactVersionAboveRuntimeError`` through the one ``above_ceiling_error``
chokepoint; runtime-axis refusals (torch major mismatch) are the distinct
``ArtifactRuntimeIncompatibleError``... |
3b056ad2776b46928580c8b3d9b210f106de928c230ad3ad114aaccbd6272741 | Python | 6,908 | 199 | import copy
import numpy as np
import pytest
from numpy.testing import assert_array_equal
from gym.spaces import Box, Dict, MultiDiscrete, Space, Tuple
from gym.vector.utils.spaces import batch_space, iterate
from tests.vector.utils import CustomSpace, assert_rng_equal, custom_spaces, spaces
expected_batch_spaces_4 ... |
3e9549dd361f05684e642c0c2a43dfa0edf592e8f7b4254bb5f67a7f19dc8963 | Python | 6,909 | 217 | """Tests for bdpy.task.callback."""
from __future__ import annotations
import unittest
from typing import Any, Callable
from bdpy.task import callback as callback_module
# NOTE: setup functions
def setup_fns() -> list[tuple[Callable, tuple[Any, ...], Any]]:
def f1(input_: Any) -> None:
pass
def f2... |
46cdfb820c1d1d11797de33de8874cfeee2f7b4e713b452373a954bc3454336b | Python | 6,909 | 189 | '''
TNS class : Soma
'''
import logging
import numpy as np
from scipy.spatial import ConvexHull # pylint: disable=no-name-in-module
from scipy.spatial.qhull import QhullError # pylint: disable=no-name-in-module
from tns.utils import TNSError
from tns.morphmath import rotation
from tns.morphmath.utils import norm
L... |
776b2cf124b9b2c1cbcdbd7d7cf27518ff75d1cc8462fcab7487573ad396d869 | Python | 6,909 | 179 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# 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 applicab... |
89879d03740c0b43041c482f68b8811d16beee224910ffef4b8fe09a020cb732 | Python | 6,909 | 218 | """Set of wrapper functions for gym environments taken from
https://github.com/Shmuma/ptan/blob/master/ptan/common/wrappers.py."""
import collections
import numpy as np
import torch
from pl_bolts.utils import _GYM_AVAILABLE, _OPENCV_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _GYM_AVAILABLE:
... |
f87e6bc21ceb8a3742c36a74c801bba3a8548fac53a4bbde703d951b7d9dfddf | Python | 6,909 | 168 | import subprocess
import torch
import pandas as pd
import numpy as np
import torch.nn as nn
import itertools
def get_aa_list():
aa_list = ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
return aa_list
def remove_nonstandard_aas(prot_seq):
aa_list = get_... |
9bd21febbecfcef9a5672cbb5158425063a75876270448d932b5aa1ce392bd3c | Python | 6,910 | 142 | #!/usr/bin/python3
import os
import sys
import argparse
import pandas as pd
import numpy as np
version = "0.1.5"
# converts count data to fpkm and tpm values
# remove anyheaders ...
#HTSEQ count footer is removed (last 5 lines)....
# prepare data
def prepare_data(**opt):
# check output directory exists, create ... |
7135ab6354f00471c903b3d9cf73beddaee73b11e918862988edbb401b01c375 | Python | 6,912 | 199 | model = dict(
type='RetinaNet',
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=dict(type='Pretrai... |
d9eb0890dcd4bb3d073df6a27ffce349392cb80c2df670422b427898df5932e9 | Python | 6,912 | 181 | """Smoke tests for face_rhythm.alignment_multisession.
These tests validate three invariants that the port must hold:
1. The module imports cleanly even when the optional ``romatch`` dependency
is not installed.
2. ``Aligner(...)`` can be instantiated with the notebook's canonical kwargs.
3. ``Aligner.fit_geometri... |
90e5c7066d96694294f0ccd021578107e150a313c8883e3fd2347b74b2e6171f | Python | 6,913 | 230 | '''
Functions related to saving and loading of signal arrays to and from files.
The numpy savetxt and loadtxt are used, in addition to a header containing the
json-serialized information about how the signal was extracted.
Imports
-------
numpy, wormdatamodel, pkg_resources, json
'''
import numpy as np
import wormdat... |
fd85f23833579e3ce9da7213172a0a20e4d8aa2901c9ddb4ef9326e59b7dbd77 | Python | 6,913 | 186 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
A transformer applying different transformers to different features.
"""
# ===================================... |
9e37276118241007db2291192e7b5ad09b563e237aeaf56812227d00b80eb4d0 | Python | 6,914 | 203 | import logging
import time
from ethoscope.hardware.interfaces.interfaces import BaseInterface
class WrongSerialPortError(Exception):
pass
class NoValidPortError(Exception):
pass
class SimpleLynxMotionInterface(BaseInterface):
_baud = 115200
_min_angle_pulse = (-90.,535.)
_max_angle_pulse = (90.,... |
3f280e786d1b39c92e8a906ba8efb412f8b3d1aaadefb6e9619fe4a7deffb9c6 | Python | 6,916 | 187 | import typing
from typing import List
import numpy as np
import pytest
import torch
import torch.nn.functional as F
from torch import Tensor
from lightly.loss import VICRegLLoss
class TestVICRegLLoss:
def test_forward(self) -> None:
torch.manual_seed(0)
criterion = VICRegLLoss()
global_v... |
ae4046bdfe0eb14a324a335f92a4aa679ed303cf7227bdcfe240dded9b0bb11d | Python | 6,917 | 202 | import os.path
import numpy as np
import data_prep
import pre_process
from Bio.Seq import Seq
import argparse
from tensorflow import keras
import modeling
def normalize_theta(theta):
"""
Converts unnormalized probabilities of categorical distributions
into the corresponding normalized probabilities.
"... |
eaab208d0eb407fcc89c2f94ba8ba3fb5bd84040ad6f8075e7d35d4d3d0e8612 | Python | 6,917 | 164 | # Author : John Tsang
# Date : December 7th, 2017
# Purpose : Implement the Diebold-Mariano Test (DM test) to compare
# forecast accuracy
# Input : 1) actual_lst: the list of actual values
# 2) pred1_lst : the first list of predicted values
# 3) pred2_lst : the second l... |
5ae6bf1bb043b53c28706b6572eb402e4ea653c1cc9a3c9e56d1fe54c9fbdf18 | Python | 6,918 | 167 | import datetime
import logging
import os
import socket
import threading
from sqlalchemy import (
and_,
delete,
select,
)
from galaxy.model import WorkerProcess
from galaxy.model.base import check_database_connection
from galaxy.util import now
log = logging.getLogger(__name__)
WEBAPP = "webapp" # Worke... |
696ed1e271af8b415abf69fb38a19094a8e3ed8d252f77efa717dd029382898a | Python | 6,918 | 230 | import math
import numpy as np
import torch
import torch.nn.functional as F
from matplotlib import cm
####
def crop_op(x, cropping, data_format="NCHW"):
"""Center crop image.
Args:
x: input image
cropping: the substracted amount
data_format: choose either `NCHW` or `NHWC`
... |
0323c2e4a9d0b9436dc1c2cca2e8dabe53bd9bfbbe7b7d6578125da4077f935d | Python | 6,919 | 210 | from pathlib import Path
import pandas as pd
from utils.metrics_ECPred import MacroAvg
from collections import Counter
def parse_special_case(ec_number):
if "No" in ec_number:
return "-1.-1.-1.-1" # We create a class for no alignement found and then no prediction of BLAST
if "EC:" in ec_number:
... |
16a9f5c1a7d9f6e8bf39292920f111e4b7a7db121e7d07bf3235ea5ba5e743df | Python | 6,919 | 179 | import copy
from keras.src import backend
from keras.src import ops
from keras.src.api_export import keras_export
from keras.src.layers.merging.base_merge import Merge
@keras_export("keras.layers.Concatenate")
class Concatenate(Merge):
"""Concatenates a list of inputs.
It takes as input a list of tensors, a... |
aef1f2cfadf8c9b87917cbec5cb9db418e36e0267081d418c2d17f3704c3e8ab | Python | 6,919 | 193 | """
BoAmps output handler for CodeCarbon.
Writes BoAmps-formatted JSON reports containing energy consumption data
from CodeCarbon runs, enriched with user-provided ML task context.
"""
import json
import os
from typing import Optional
from codecarbon.external.logger import logger
from codecarbon.output_methods.base_... |
f70a15cc262b08830ef1a787349d2c648a91d3b896a0aeeee8038c370de33222 | Python | 6,919 | 214 | import sys
import argparse
import logging
import time
def pase_info(seq):
info = {'SVLEN': 0, 'END': 0, "SVTYPE": '', "RE": 0, "CHR2": ''}
for i in seq.split(';'):
if i.split('=')[0] in ["SVLEN", "END", "RE"]:
try:
info[i.split('=')[0]] = abs(int(float(i.split('=')[1])))
except:
pass
if i.split('='... |
2907ef03eb9650635ad121e2d727ebc3ed46e743808c5283f9fb65de0ad2ef2f | Python | 6,921 | 205 | # -*- coding: utf-8 -*-
import math
# Based on Gale & Church 1993,
# "A Program for Aligning Sentences in Bilingual Corpora"
infinity = float("inf")
def erfcc(x):
"""Complementary error function."""
z = abs(x)
t = 1 / (1 + 0.5 * z)
r = t * math.exp(-z * z -
1.26551223 + t *
... |
2fb4ac609747c3510276d64511e542633d872daf36a93b07662e22f0e8501365 | Python | 6,922 | 211 | # type: ignore[override]
from typing import Any, Callable
from pytorch_lightning import LightningDataModule
from torch.utils.data import DataLoader
from pl_bolts.utils import _TORCHVISION_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _TORCHVISION_AVAILABLE:
from torchvision import transforms ... |
4bcb3ef443a9b9a7711d154062ef54d259ce32058323ec42730df22d445c2ebb | Python | 6,922 | 171 | from typing import Callable, List, Optional, Tuple, Union
import numpy as np
from anndata import AnnData
from ..configuration import SKM
from ..errors import SegmentationError
from ..logging import logger_manager as lm
@SKM.check_adata_is_type(SKM.ADATA_AGG_TYPE)
def select_qc_regions(
adata: AnnData,
regio... |
e2a9dd82e9c1b6598a9f8fa4a267eb181fe0fa4a47a0bdb5fec82cd14286ffbf | Python | 6,922 | 157 | #!/usr/bin/env python3
import os
import sys
import pandas as pd
import random
from random import shuffle
from collections import Counter
from collections import defaultdict
import argparse
# the following line is to deal with the case that self-defined module
# in the submission directory are not found when submit... |
415da3230e775a5b8c66d2900166ad8700eea409cf58cd3e4c7738112960df7d | Python | 6,924 | 184 | import argparse
import os
import numpy as np
import torch
import pytorch_lightning as pl
from pytorch_lightning.callbacks import ModelCheckpoint, EarlyStopping
from pytorch_lightning.loggers import WandbLogger
from torch_geometric.loader import DataLoader as GeometricDataLoader
from pathlib import Path
# Imports from ... |
ca9c24b51091e43beb665ca960304d89fe8b84b667ce2f94bdf6c3c24b546f4a | Python | 6,924 | 201 | import os
import random
import shutil
from collections import OrderedDict
import numpy as np
import torch
import torch.nn as nn
from imgaug import imgaug as ia
from termcolor import colored
from torch.autograd import Variable
####
def convert_pytorch_checkpoint(net_state_dict):
variable_name_list = list(net_stat... |
f9c39f98f99c22e08b3a19ab87b27fce346bcec4986cbedc9bb1cd5b0ebb3d60 | Python | 6,926 | 195 | #!/usr/bin/env python
#
# Copyright 2006, Google Inc.
# 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 source code must retain the above copyright
# notice, this list... |
32466bd3bac44aae8166583c1dbd0aacd16f59cde6a2e4da368d7cf9d320b1b8 | Python | 6,927 | 182 | """
===============================================================================
Artifact Correction by AJDC-based Blind Source Separation
===============================================================================
Blind source separation (BSS) based on approximate joint diagonalization of
Fourier cospectra (AJ... |
f28d6792a7f6229ff81469ec0986dfec884ba45c728ce172f30dc56e1eb094e3 | Python | 6,927 | 182 | """
===============================================================================
Artifact Correction by AJDC-based Blind Source Separation
===============================================================================
Blind source separation (BSS) based on approximate joint diagonalization of
Fourier cospectra (AJ... |
4660c9e511a8ace591658bfb35a9cfad435bd9bf8019cb9d76ff3d2377c2ba23 | Python | 6,930 | 207 | """Compile all public Python fences and execute the corrected flagship workflows."""
from __future__ import annotations
import ast
import importlib
import re
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.options import CaptureOp... |
4b8cf79b0d839dc4001ff91030dd98030a04c06cb02c12393c6235f76f716b5e | Python | 6,930 | 222 | from collections import defaultdict
import numpy as np
import seqpro as sp
from pytest_cases import parametrize_with_cases
from seqpro._modifiers import _align_axes, _slice_kmers, reverse_complement
from seqpro._utils import cast_seqs, check_axes
def test_align_axes():
arr1 = np.random.randint(0, 5, (3, 2, 7))
... |
1f80477a59ff40fe1b5b3c0700cf5110bb778b98f378f78615069237fb90d338 | Python | 6,933 | 146 | """Read and write files of queued and running jobs on behalf of remote job runners."""
import os
import re
import shutil
from galaxy import (
exceptions,
util,
)
from galaxy.config import GalaxyAppConfiguration
from galaxy.job_execution.setup import JobWorkingDirectory
from galaxy.model import (
Job,
... |
0100f135a35e055c88e4c9fc790a29a597986649d734f1b1c8f97dc6cd7f5445 | Python | 6,934 | 234 | from tempfile import TemporaryDirectory
import numpy as np
import polars as pl
import pandas as pd
import seqpro as sp
import xarray as xr
from pytest import fixture
import pickle
import seqdata as sd
import zarr
def read_fasta(file_path):
"""
Reads a FASTA file and returns a dictionary of sequences.
P... |
571809e99a4120b3a982308ce4431ef17dc676a80c54566813093a4976f04928 | Python | 6,939 | 216 | import configparser
import os
from pathlib import Path
from typing import Dict, List, Optional, Tuple, Union
from codecarbon.external.logger import logger
CONFIG_FILE_NAME = ".codecarbon.config"
CONFIG_SECTION = "codecarbon"
def clean_env_key(k: str) -> str:
"""
Clean up an environment variable key: remove ... |
b27e6a7f2dcfa52b2d14885188a0ccac8b1b13a21bb0a993c21001c4c893d7f4 | Python | 6,940 | 222 | """Evaluation procedures for semantic segmentation.
For dataset with `n` classes, we treat the index `n` as the ignored class.
When compute IoUs, this ignored class is considered.
However, IoU(ignored) doesn't influence mIoU.
"""
from functools import partial
from multiprocessing import Pool
from typing import Abstra... |
e0a0868f72fb77eb9f2e2e2bbd9a30898468d7f9cffe4219cf3eb345cfee9447 | Python | 6,942 | 202 | import os,sys,re
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
#from bioseq2seq.bin.batcher import train_test_val_split,filter_by_length
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from collections import defaultdict
from ushuffle impo... |
ebc00d88f1c9b287d0396dec6404964a32e7077eaea507c1bc6d00dd482ddbe4 | Python | 6,943 | 172 | from fastapi import HTTPException
from carbonserver.api.errors import NotAllowedError, NotAllowedErrorEnum, UserException
from carbonserver.api.infra.api_key_utils import generate_api_key, get_api_key_hash
from carbonserver.api.infra.repositories.repository_projects_tokens import (
SqlAlchemyRepository as ProjectT... |
7160861999c8e8298301927d1dc1902d6cd0612138c4eb64e9da4bd106ad793a | Python | 6,945 | 232 | # %%
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import cv2
from globals import path, sessions, subjects, folder_spots_noboth, colours_types
import os
from plotting import prettifySpinesTicks, removeSpines
mc = "black"
plt.rcParams.update(
{
"font.size": 40,
"axes.labelco... |
92fd91012c06bfb25e4f15cf327abe040cc8442555567570a236ed3377bfa5f3 | Python | 6,945 | 178 | #!/usr/bin/env python3
import os
import numpy as np
import h5py
from snudda.utils import SnuddaLoad
class DegreeDistribution:
def __init__(self, network_file):
self.network_loader = SnuddaLoad(network_file=network_file, load_synapses=True)
self.network_file = self.network_loader.network_file
... |
be78b30e7e6fd396b916305737b2b0427c6a4d69edc6619d1457435da2e3b94c | Python | 6,945 | 170 | """
The `trendline_functions` module contains functions which are called by Plotly Express
when the `trendline` argument is used. Valid values for `trendline` are the names of the
functions in this module, and the value of the `trendline_options` argument to PX
functions is passed in as the first argument to these func... |
9b78c615b86ab3c13b07f31d7e1cc661ee449ee20e2a06f588fee8d6250ad6e5 | Python | 6,946 | 175 | import argparse
import datetime
import shutil
import sys
import os
import random
from logging import getLogger
from collections import OrderedDict
import numpy as np
import pytorch_lightning as pl
import torch
from omegaconf import OmegaConf
import wandb
from src.modeling.modeling_base_model import BetaConfig
from .lo... |
067eb13e63b5d19741d0abd83d14c4160894775d62b557d63a9a1043d2342054 | Python | 6,947 | 211 | from __future__ import annotations
import json
import time
from typing import TYPE_CHECKING
from typing import Final
import numpy as np
from loguru import logger
from numpy.typing import NDArray
from .._shape import Shape
from ._geometry import shape_to_xyxy_bbox
from ._osam_session import OsamSession
from ._shape_b... |
73fd4d20dc487ecd1c33a82717b161074a59acfd30a818f56947b7229b95cb95 | Python | 6,948 | 179 | import pickle
import json
import numpy as np
import os,sys
from collections import OrderedDict
import torch
import biovec
from tape import ProteinBertModel, TAPETokenizer
import warnings
warnings.filterwarnings("ignore")
def generate_Y(dataset_path):
affinity = open(dataset_path+'/affinity.tsv','r').readlines()
... |
e24577e42e9553ec8d06eff69fd24d36ad5fe193539236eea73649dd63ab3d2e | Python | 6,948 | 123 | from Utilities.common_packages import np
'''
NOTE:
Returns emperical EMCCD cumulative density function
'''
def getEMCCDExperimentalCDF():
pmf = np.array([1.09863281e-08, 2.19726563e-08, 2.24609375e-07, 9.36279297e-07,
4.07592773e-06, 1.59155273e-05, 5.57116699e-05, 1.79609375e-04,
5.28302002e-04, 1.4... |
f5c6e9b2ffd11bf4bc374f484325d10f80335dcc5571fc1f38d9a996e65c5855 | Python | 6,948 | 211 | # Copyright 2023 Blue Brain Project, EPFL.
# See the top-level LICENSE file for details.
#
# SPDX-License-Identifier: Apache-2.0
from nmodl.ode import differentiate2c, integrate2c, make_symbol
from nmodl.ode import transform_expression, discretize_derivative
import pytest
import sympy as sp
def _equivalent(
lhs... |
02392005ce98a433702c668bb640a933ad6f48c963be52f645d89f88d45e6c51 | Python | 6,952 | 148 | '''
Data driven CNN model for neural system identification
Author: Santiago Cadena
Last update: April 2019
'''
import numpy as np
import os
from scipy import stats
import tensorflow as tf
import hashlib
import inspect
import random
from tensorflow.contrib import layers
from tensorflow import losses
from cnn_sys_ident... |
a2ff25374ddc8f01024a82b565ca8829e1f637077ac9b1bed541f64c04b671c3 | Python | 6,952 | 186 | """Gallery gates (row 0.6): fingerprints, fork isolation, consume-not-construct.
The galleries are the substrate every matrix shares (memo 0.6); these gates
prove the economics rules actually enforce -- the fingerprint detects
mutation, forks isolate, and no cell constructs its own products.
"""
from __future__ impor... |
5fa14ce065c87ce3453b9d1a7895db4d092cd777164151b93dd1c80dea7af193 | Python | 6,953 | 250 | """
sess_stim_df_util.py
This module contains the functions needed to generate the stimulus dataframe
for Allen Institute OpenScope experiments for the Credit Assignment Project.
Authors: Colleen Gillon
Date: October, 2018
Note: this code uses python 3.7.
"""
import numpy as np
import pynwb
from util import gen_... |
13dfbc2b424cfcef34c46f0197a992d08f44cd13161d8236d8af3c9288b63481 | Python | 6,954 | 204 | ### This code displays and image, then it grabs the position of the pixel when you click on the image
# It saves the positions in a csv file
from tkinter import *
from tkinter import filedialog as tkfd
import numpy as np
from PIL import Image, ImageDraw, ImageTk
import csv
import os
import sys
counter = 0
library = ... |
c96b34b4d3d66c32adec7b0c88f279228f730571513647ed389fc40e1b397774 | Python | 6,957 | 214 | """
Simple scikit-learn interface for finetuning a single linear layer on top of LLM embeddings.
"""
from numpy.typing import ArrayLike
import numpy as np
from scipy.special import softmax
from sklearn.base import BaseEstimator, ClassifierMixin, RegressorMixin
from sklearn.linear_model import LogisticRegressionCV, Ridg... |
b2f8a0d70f38897350bcb45f87a63340c98f50078e385c7d34dfcc6808b30c52 | Python | 6,959 | 169 | """Entry self-test for the shared replay comparator (R75-4).
``tensor_nanequal`` is the single judge behind every per-op replay verdict
AND capture-side alias/mutation bookkeeping, with no oracle above it: a
degradation making it vacuously true would blind the whole forward-replay
tripwire while the suite stays green ... |
4c59ab29608e6af4c642f904caaff7503f4040854989ca86de103a9b193e5f28 | Python | 6,960 | 175 | """L6 DNA CANARY (D7 evidence) — lands immediately after stage 2.
Two live-trace demos judging the do()-verb lock (design memo sec 5):
DEMO 1 — zero-ablation via ``do()``: downstream deltas real; FireRecords +
state ``REPLAY_PROPAGATED`` + ``last_run`` honest; the nonfinite-gate
(ABORTED_NONFINITE settlement) behavio... |
6279fcdff47c2ac1b5345ddd8fa760efb57cfce893050386ac25d9c9aa9390d4 | Python | 6,961 | 228 | from functools import partial
from pathlib import Path
from textwrap import dedent
from typing import List, Optional, Union
import numpy as np
import polars as pl
import zarr
from numcodecs import Blosc, VLenBytes
from tqdm import tqdm
from seqdata._io.utils import _df_to_xr_zarr
from seqdata.types import FlatReader,... |
aff9530003cba0ae9b0be08bd95f16c6c0c7f7998702b849b461fa1e441fa739 | Python | 6,961 | 159 | import numpy as np
import torch as ch
import scipy.signal as signal
try:
from scipy.signal import kaiser
except ImportError:
from scipy.signal.windows import kaiser
class DownsampleEnvelopes(ch.nn.Module):
"""
Base class for downsampling operations for the cochlear envelopes.
"""
def __init__(s... |
bb6c4f88aa4a005ddb668776265c08fe20cc184f937bff9525cadb2d3e0a4aa8 | Python | 6,961 | 320 | from gym.envs.registration import load_env_plugins as _load_env_plugins
from gym.envs.registration import make, register, registry, spec
# Hook to load plugins from entry points
_load_env_plugins()
# Classic
# ----------------------------------------
register(
id="CartPole-v0",
entry_point="gym.envs.classic... |
428370d97a8f4463d7441f9ab467c9618db4a6df183b1b3510d517efad93c80d | Python | 6,962 | 167 | import os
import sys
from robustness import datasets
from robustness.attacker import AttackerModel
from robustness.model_utils import make_and_restore_model
from model_analysis_folders.all_model_info import IMAGENET_PATH
from robustness.imagenet_models.clip import clip
import torch
from PIL import Image
sys.path.appen... |
43f4f6789259f4cf45278335d2a05307ba7dae2a1e6c77834647f5eaee909e6b | Python | 6,962 | 204 | from typing import Any
import torch
import numpy as np
import pandas as pd
from .metrics import MetricManager
from tqdm import tqdm
import os
import os.path as osp
import json
import matplotlib.pyplot as plt
class GNNTrainer():
"""
Class to train and validate GNN models. It can also run predictions
with t... |
b5ad5b55067d2b5bc3ebf82e8d9eaac3e56a5d141be8c672316e1960f877c940 | Python | 6,962 | 211 | """Functions to help segmentation benchmarking, specifically to compare
two sets of segmentation labels.
"""
from typing import Optional, Tuple
import numpy as np
import pandas as pd
from anndata import AnnData
from scipy import sparse
from sklearn import metrics
from ..configuration import SKM
from ..logging import ... |
225d4f76c6384e6d9a6cd2be159f8c67e44e66122f38fcae90ac1a13a58fdfc5 | Python | 6,964 | 187 | """
test_canonical_pipeline.py — Smoke tests for the deposit.
Three tests, each fast (< 1 minute total):
1. test_build_trained_model_reproduces_paper_numbers
Runs build_trained_model.py against the bundled feature JSONs and
asserts the four paper headline numbers are within tolerance.
2. test_rank_norm... |
a8ed3dc701445911644c154b79178fc1e81c17291394a683b70217bab579d6a0 | Python | 6,964 | 202 |
# meshAttributes.py
#
# Created on: August 1, 2019
# Authors: An Qu
# {an.qu} <at> yale.edu
#
import numpy as np
from sklearn.preprocessing import normalize
def triangleMeshAttributes(vertices, faces, returnList):
'''
This function can be used for calculating th... |
87a0f2fff23af4677bc7d6b16648b455888535f9efaa1c85787ce5247a609f87 | Python | 6,966 | 175 | __author__ = "quentin"
import datetime
import logging
import time
import traceback
from .tracking_unit import TrackingUnit
class Monitor:
def __init__(
self,
camera,
tracker_class,
rois=None,
reference_points=None,
stimulators=None,
time_offset=0,
... |
b365fd714d4833e54e9c6e12da2dd4af411a6fc4aef854292f3bb0a79c2efbb5 | Python | 6,966 | 148 | '''
Finetuning on the top 4 atom GRU 4 linear layer network.
'''
import torch
import torch.nn as nn
import logging
logger = logging.getLogger(__name__)
from neural_nets.NMR_4ll_Net import NMR_MPNN
import collections
device = "cuda" if torch.cuda.is_available() else "cpu"
import os
def gen_states(model_state_dict):
... |
55f8429e27a09376ee3d83c28fb724fef1b3ed3ac4dad083510be6c40dbc86bb | Python | 6,967 | 198 | """Cold-import subprocess matrix: the A10 row gate.
One fresh interpreter per matrix run proves, with no test-session state:
- ``import torchlens`` imports no appliance/integration namespace, no
semantic package, and no foreign extra package;
- a ``hasattr``/``dir()`` probe sweep across the root and every facade
... |
60480a04f3b30891a12462624315f5851cf25e8f98bc2435b2843a0ff76c2004 | Python | 6,968 | 185 | #!/usr/bin/env python3
"""
File: filter_gte_file.py
Created: 2021/10/28
Last Changed: 2021/11/10
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 source t... |
4621fe81638363706a7feaa08c1288882adb10471ae0fe83c674006cbcd5a4f0 | Python | 6,969 | 184 | """Fabrication pins (W1-FAB, memo L2/L5, sec 8.1 items 5-6), RED-first.
The generalized rule (D6): weights-free, a value comparison that cannot
answer resolves to ``unknown``, never ``changed``; no record and no
completeness-witness flag may rest on an ``unknown``. Fail-closed in the
HONEST direction: absence of a wri... |
43f5c7d83ef0d52005db91f8cdd2a354d491978c2e44eb0c94f2a0a884d16194 | Python | 6,970 | 227 | """
Behaviorl-epoch-related plotting
"""
from __future__ import annotations
from typing import Any, Optional, Sequence
import copy
from .. import plot, reg, util, funcs
__all__: list[str] = [
"plot_single_bout",
"plot_bouts",
# 'plot_stridesNpauses',
]
def plot_single_bout(
x0: Sequence[float],
... |
e277abdd25ac8c56fede7ec9a13bb9fa41e3050c401a46807c665df54eb3d092 | Python | 6,970 | 192 | import os
import sys
import abc
import math
import yaml
import torch
from torch.utils.tensorboard import SummaryWriter
from config.default_hparas import default_hparas
from src.util import human_format, Timer
class BaseSolver():
'''
Prototype Solver for all kinds of tasks
Arguments
config - yaml-s... |
d0d5ceecd117533169c924cdbb01ea5bb0ee74b7b1c4b22855f73f0e4dea0ee7 | Python | 6,971 | 191 | from __future__ import annotations
import typing as t
from . import typing as ft
from .globals import current_app
from .globals import request
F = t.TypeVar("F", bound=t.Callable[..., t.Any])
http_method_funcs = frozenset(
["get", "query", "post", "head", "options", "delete", "put", "trace", "patch"]
)
class ... |
8e00fc32770c94dc9c9c5ee2bef31406525d161833da8103b58c780d64f5f9b5 | Python | 6,972 | 175 | """Round-11 security regression: duplicate container-type resolver RCE.
r10 hardened the container-type resolver in ``torchlens/ir/container.py`` into a strict
default-deny, never-import gate. But a PARALLEL resolver survived in
``torchlens/data_classes/op.py``: the public inspection property ``Op.multi_output_type``
... |
fb5dfb11c9bad7d90164e07a8e2bea76fcfe3bcc1c0d73d1e149c5e9f8946faf | Python | 6,973 | 168 |
#%%
import dataprocessing
import numpy as np
from tensorflow.keras.layers import Dense, Conv2D, MaxPooling2D, Flatten,Input,Concatenate,Reshape,UpSampling2D,PReLU
from tensorflow.keras.models import *
from tensorflow.keras.optimizers import Adam,SGD,RMSprop,Adagrad,Adadelta,Adamax
from tensorflow.python.keras.u... |
aaa56725ad4bfae27e0f862d068ebbd514cdf6a060a22ced193151127a3a32d2 | Python | 6,974 | 185 | """W051-MECH regression pins for AUD-CODE 3.12 (a) and (c): flops_report.
(a) The model door ran its one capture under eval + ``no_grad``, which flips
``nn.MultiheadAttention`` / ``nn.TransformerEncoderLayer`` onto the fused
fast path (``_native_multi_head_attention`` / ``_transformer_encoder_layer_fwd``)
-- one opaqu... |
c35b3ae6da553da338d57247ae2b453b9ea797b18b5aa53be6c9f90dc4bd5004 | Python | 6,976 | 132 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
478e305baf8763ae17b6aa2d5dafc559261239094d08ff9f04af183a9b57bb75 | Python | 6,977 | 182 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
599813b85ae252f615ad8aee807a5cc5611124d905097e7bc2a3a3da1935a5ce | Python | 6,977 | 175 | """Edge substitution into a NON-LAST pass of a multi-pass child (AUD-CODE 1.2).
Before the fix the edge door committed ``{child.layer_label: new_out}`` and
``{child.layer_label: [fire_record]}`` -- the BARE label, which
``layer_dict_all_keys`` resolves to the LAST pass -- then ``push_from``
pushed the addressed pass's... |
6eacb200fe860c210f1e5a50d1a4c0c66f6f931c24acffc0d688104a127556b3 | Python | 6,977 | 193 | """
=================================
Frequency Band Selection Helpers
=================================
This file contains helper functions for the frequency band selection example
"""
import numpy as np
from mne import Epochs, events_from_annotations
from pyriemann.estimation import Covariances
from pyriemann.cla... |
e9702374a10893a5ca8bb1f2acf0c504900a7fc6164db869137d859950a1def1 | Python | 6,982 | 180 | """Video models: C3D (3D-conv action recognition) and DCVC (deep contextual video codec).
C3D -- Tran et al., ICCV 2015, "Learning Spatiotemporal Features with 3D Convolutional
Networks", arXiv:1412.0767. Source: github.com/facebookarchive/C3D.
DISTINCTIVE primitive: 3x3x3 3D convolutions over a video clip (T x H x ... |
974a423565f4da472d30b3c55ccedfc3689faaa6b82df7fea4ccd0e7f4435c67 | Python | 6,984 | 224 | # coding=utf-8
# Copyright 2025 The Google Research Authors.
#
# 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 applicab... |
3c6405003d4a50c968a052babb02f7bd9bf98c1c99ca7f9baa9887bceadbf4b9 | Python | 6,985 | 207 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft
# Licensed under the MIT License.
# Written by Bin Xiao (leoxiaobin@gmail.com)
# Modified by Bowen Cheng (bcheng9@illinois.edu)
# ------------------------------------------------------------------------------
fro... |
4489c104313f07f49d47562a06aff970aa715c7b2e61173bddf25d00308a4e62 | Python | 6,989 | 192 | """
=================================
Frequency Band Selection Helpers
=================================
This file contains helper functions for the frequency band selection example
"""
import numpy as np
from mne import Epochs, events_from_annotations
from pyriemann.estimation import Covariances
from pyriemann.cla... |
7c7c050c010e709fe1c387b51781eb624248ea108328b8f81773d39a172aa6a8 | Python | 6,991 | 177 | """Vizmech wave-2 item 15: cluster caption placement from member geometry (D18b).
Captions were emitted ``labelloc=b`` and INHERITED the graph-level
``labeljust=left``: a fixed corner of the cluster box, up to 1121.9 pt from
the nearest member (p90 732.6 pt over 1066 measured clusters). Pins here:
- every module clus... |
9fd389617c4304f27ff88520226c0db6257efb7d689cbbda6d97cea41a6d9d06 | Python | 6,991 | 227 | from __future__ import annotations
import time
from threading import Thread
import pytest
import env # noqa: F401
from pybind11_tests import callbacks as m
from pybind11_tests import detailed_error_messages_enabled
def test_callbacks():
from functools import partial
def func1():
return "func1"
... |
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