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# import logging # logging.getLogger('pgen').addHandler(logging.NullHandler())
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from .main import ShapeOut2 # noqa: F401 from . import widgets # noqa: F401
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""" scanometrics.utils module: utility functions for statistics (stats.py) """
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# -*- coding: utf-8 -*- from .ensemble import SWA from .eval import KGCNMetric
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from .spec import * from .abs import * from .inmemory import * from .hdf import *
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from .io import write_h5, write_pkl, read_h5, _export_to_stc, _export_to_vol_stc
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""" Using __init__.py to organize the structure. """ __version__ = "1.2.9.1"
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import sys for line in sys.stdin: print("!ARTICLE") print(line.rstrip())
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import os # suppress tensorflow print out os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
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from .metrics import compute_mld, compute_ospa, compute_sd, compute_goodness_of_fit
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import torch device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
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from .cell import Cell from .mixed_layer import MixedLayer from .network import Network
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import sys import os sys.path.append(os.path.join(os.path.dirname(sys.argv[0]), "lib"))
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from evcouplings.mutate.calculations import * from evcouplings.mutate.protocol import *
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from .optimization import OptimizationProblem from .optimization import VariablesStitcher
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from .downselect_edges import DownselectEdges from .rattle_particles import RattleParticles
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from .topk_accuracy import accuracy_topk from .topk_accuracy import multitask_accuracy_topk
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from .viz import plot_n_sources, plot_amplitudes, plot_stc, plot_vol_stc, plot_cloud_sources
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from .cell import Cell from .network import ConvNetwork from .mixed_layer import MixedLayer
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from . import platform from . import dmd from . import neopixel from . import synchronizer
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from qbiome.network import Network Network('hypothesis_1_5.dot',outfile='network.png').get()
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from .t_loss import tLoss, tMSELoss, tCrossEntropyLoss, tLogSoftmax, t_log_softmax, t_softmax
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from trainers.neural_trainer import NeuralTrainer class CNNTrainer(NeuralTrainer): pass
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from trainers.neural_trainer import NeuralTrainer class LSTMTrainer(NeuralTrainer): pass
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from .regularizers import BlockRegularization, TikhonovRegularization, SmoothTimeRegularization
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from setuptools import setup setup( name='brand', version='0.0.0', packages=['brand'], )
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from inference.segment_brain_gauss import * from inference.segment_brain import segment_brain_normal
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from .compute_pvalues import compute_pvalues from .parse_input import parse_input from . import mapping
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# empty file -- turns directory into a package so # 'python -m unittest discover' works.
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""" Processing modules for ScanOMetrics """ from . import freesurfer, dldirect, fsl, pipeline_template
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# pyaging/data/__init__.py from ._data import download_example_data __all__ = ["download_example_data"]
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options = { 'yn_min_ms' : 20, 'yn_max_ms' : 120, 'alpha' : .3, 'ms' : 50, 'mew' : 2 }
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# flake8: noqa: F401 from .comp_lme4 import ComputeSignificance from .comp_stats import ComputeStatistics
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from setuptools import find_packages, setup setup( name='cellPLATO', packages=find_packages(), )
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""" This is a module to be used as a reference for building other modules """ def foo(): return 'foo'
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from .signal import ecgSignalSamplingPeriod, extractSignalFromImage, verticallyScaleECGSignal, zeroECGSignal
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from brand import Supervisor if __name__ == "__main__": supervisor = Supervisor() supervisor.main()
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import warnings from dynast.logging import logger logger.setLevel(9999) warnings.filterwarnings('ignore')
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import pandas as pd def read_pickle_file(file): pickle_data = pd.read_pickle(file) return pickle_data
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""" This is evcouplings """ __all__ = ["align", "compare", "couplings", "fold", "mutate", "visualize", "utils"]
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from .utils import index2mask, mask2index, np_groupby, np_scatter from .alignn import line_graph, dihedral_graph
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from .emulator import APEmulator, load_default_emulator_model __version__ = "0.9" __author__ = "Grandits et al."
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from .replay_buffer import make_reverb_dataset # noqa from .variable_container import VariableContainer # noqa
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from .aminoacids import * from .mods import * from .losses import * from .fragments import * from .pepmass import *
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from .glycans import * from .nglycans import * from .fragments import * from .gmass import * from .gpmass import *
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# sitecustomize.py import coverage import os if os.getenv("COVERAGE_PROCESS_START"): coverage.process_startup()
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__all__ = ['prediction_error', 'sparse_evaluation'] from .prediction_error import * from .sparse_evaluation import *
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from .io import Session, SessionCollection, parse_ma_directory, parse_ma_session, parse_tdt_directory, parse_tdt_session
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from .anova import anova from .remove_non_expressed import remove_non_expressed from .log_normalize import log_normalize
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# __init__.py import sys, os sys.path.append(os.path.join(os.path.dirname(__file__), '..', 'neuroxai')) import neuroxai
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from .aug_loss import * from .homography import * from .modules import * from .unsup_loss import * from .sl1loss import *
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# MOFTransformer version 2.0.0 from moftransformer.modules import module from moftransformer.modules.module import Module
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# -*- coding: utf-8 -*- """ Created on Wed Feb 7 19:38:09 2024 @author: tpisano """ #from dxr_inference import *
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# This file turns "img" into a Python module such that we can access # image files in this folder via importlib.resources.
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# from . import initialization # from . import config print('Finished running cellPLATO initialization and loaded config.')
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import pytest @pytest.fixture def mock_no_gpu(monkeypatch): monkeypatch.setattr("torch.cuda.is_available", lambda: False)
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from scanometrics.GUI.MainWindow import main as start_gui def main(): start_gui() if __name__ == "__main__": main()
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from .utils import optimizer_keys, optimizer_parameters, parameters_norm from .batch_train import train, test, train_one_epoch
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# -*- coding: utf-8 -*- from .io import pickle_dump, pickle_load, write_log, format_filename from .data_loader import load_data
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from .modules import * from .render_utils import * from .renderer import * from .render_models import * from .casmvsnet import *
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class MissingDataError(Exception): """ Error raised if variables contain missing values when forbidden """ pass
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# MOFTransformer version 2.0.0 from moftransformer.visualize.visualizer import PatchVisualizer __all__ = ["PatchVisualizer"]
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from distutils.core import setup from Cython.Build import cythonize setup( ext_modules = cythonize("linear_assignment.pyx") )
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# Copyright 2021 ETH Zurich, NVIDIA CORPORATION # SPDX-License-Identifier: BSD-3-Clause from .rollout_storage import RolloutStorage
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from .twixtools import read_twix, write_twix, del_from_mdb_list,\ construct_multiheader from .map_twix import map_twix, twix_array
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from xgb.xgboost_preprocess import load_and_preprocess_default_data from xgb.xgboost_preprocess import load_and_preprocess_custom_data
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from ._test import test from ._plot import plot try: from ._version import __version__ except ImportError: __version__ = "???"
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from ecgdigitize.signal.extraction.viterbi import * if __name__ == "__main__": print(list(interpolate(Point(0,0), Point(5,5))))
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# SPDX-FileCopyrightText: 2023-present Quentin Uhl <quentin.uhl@wanadoo.fr> # # SPDX-License-Identifier: Apache-2.0 __version__ = "1.0.7"
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from .e2data import ExportData # noqa: F401 from .e2filter import ExportFilter # noqa: F401 from .e2plot import ExportPlot # noqa: F401
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from .agent import Agent # noqa from .learner import Learner # noqa from .server import Server # noqa from .tester import Tester # noqa
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import yaml def load_config(config_path: str): with open(config_path, "r") as f: config = yaml.safe_load(f) return config
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# -*- coding: utf-8 -*- """ Created on Thu Dec 2 14:47:36 2021 @author: jeanbaptiste """ from . import acquisitions from . import microscope
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__version__ = "4" from .utils import PROBE_DIR, DOWNLOADS_DIR from .run_kilosort import run_kilosort from .parameters import DEFAULT_SETTINGS
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from typing import Union from os import PathLike import torch PathType = Union[str, PathLike[str]] DeviceType = Union[torch.device, str, None]
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from .dqn_agent import DQNAgentCallback # noqa from .lr import PrintLR, cosine_schedule # noqa from .sac_agent import SACAgentCallback # noqa
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import os os.environ['CUDA_VISIBLE_DEVICES']="/The directory where the source code is located/radiation_mapping/openmc_library/cross_sections.xml"
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# pyaging/__init__.py from . import data, logger, models, utils from . import predict as pred from . import preprocess as pp __version__ = "0.5.7"
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"""Module with visualization functions.""" from .viz import plot_lda_results, plot_validation_curve, plot_permutation_score, Aesthetics # noqa: F401
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from ._IsmrmrdRawTestData import IsmrmrdRawTestData from ._DicomTestImage import DicomTestImage from ._PulseqRadialTestSeq import PulseqRadialTestSeq
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from .image import ( Stack, Volume, Slice, Image, save_slices, load_slices, load_stack, load_volume, load_mask, )
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#!/usr/bin/env python __version__ = '1.0' import os, sys from Bio import Seq for seq in sys.argv[1:]: print(Seq.Seq(seq).reverse_complement())
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"""Initialization for `paccmann.models` submodule.""" from .core import paccmann_model_fn from .model_specifications import MODEL_SPECIFICATION_FACTORY
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import sys docid = sys.argv[1] header = sys.stdin.readline().strip() print(header + ' docid') for l in sys.stdin: print(l.strip() + ' ' + docid)
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"""Density Compensation Calculation.""" from mrpro.algorithms.dcf.dcf_voronoi import dcf_1d, dcf_2d3d_voronoi __all__ = ['dcf_1d', 'dcf_2d3d_voronoi']
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# -*- coding: utf-8 -*- """Top-level package for tractify.""" __author__ = """Salim Mansour""" __email__ = 'Salim.Mansour@camh.ca' __version__ = '0.1.0'
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"""Gradec: Meta-analytic gradient decoding.""" from . import decode, fetcher, segmentation __all__ = [ "segmentation", "decode", "fetcher", ]
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python scaling_with_autoresponses.py && python scaling_with_autoresponses_trends.py python wt_unc31_timescales_differences.py python show_non_asymmetry.py
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"""Coil Sensitivity Estimation.""" from mrpro.algorithms.csm.walsh import walsh from mrpro.algorithms.csm.inati import inati __all__ = ['inati', 'walsh']
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# from .csd_profile import gauss_1d_mono, gauss_1d_dipole # from .csd_profile import gauss_2d_large, gauss_2d_small # from .csd_profile import gauss_3d_small
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#! /usr/bin/python3 # -*- coding: utf-8 -*- # @FileName: main.py # @Author: Li Chengxin # @Time: 2023/7/19 1:45 from SCTrack import sctrack sctrack.main()
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from .actor import Actor # noqa from .actor_critic import ActorCritic # noqa from .critic import MultiCritic # noqa from .dueling import DuelingDQN # noqa
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from rl_games.networks.tcnn_mlp import TcnnNetBuilder from rl_games.algos_torch import model_builder model_builder.register_network('tcnnnet', TcnnNetBuilder)
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from .sesame import Sesame from .dipoles import Dipole from .emp_pdf import EmpPdf from .particles import Particle __all__ = ['Sesame'] __version__ = '0.0.3'
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Python
161
9
# -*- coding: utf-8 -*- """ Created on Thu Dec 2 14:48:21 2021 @author: jeanbaptiste """ from . import experiment from . import processors from . import series
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Python
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import sys for line in sys.stdin: ix = 1 for word in line.split(): print(str(ix) + '\t' + word + '\t_\t_\t_\t_\t_\t_\t_') ix += 1 print('')
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Python
163
9
import numpy as np import sklearn import tensorflow as tf def test_imports(): print(tf.__version__) print(sklearn.__version__) print(np.__version__)
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Python
163
7
from .det import det from .ep import ep from .es_sd import es_sd from .es_mu import es_mu from .esw_star import esw_star from .ges import ges from .nsi import nsi
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Python
164
6
__all__ = ['models', 'losses', 'predict_model', 'train_model'] from .models import * from .losses import * from .predict_model import * from .train_model import *
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Python
165
7
from importlib.metadata import version import pyaging def test_package_version_matches_installed_metadata(): assert version("pyaging") == pyaging.__version__