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2fbc5f8965a651b379762cf6e5aa5e1a8340b2606c9afe612a3883e5d4cf0987
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""" Module providing usefull math formulas. """ from .math import sigmoid, dirichlet, beta, poisson, average_every_n
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from .spherenet import SphereNet from .features import dist_emb, angle_emb, torsion_emb __all__ = [ 'SphereNet' ]
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"""Top-level package for Fimpy.""" __author__ = """Luigi Petrucco & Vilim Stih @portugueslab""" __version__ = "0.1.4"
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from django.contrib import admin # Register your models here. from .models import markers admin.site.register(markers)
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.databases package."""
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6
from os import walk, path from datetime import date from django.contrib import admin from django.conf import settings
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from sleepy.gui.tagging.model.datasource import DataSource from sleepy.gui.tagging.model.navigator import Navigator
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.utilities package."""
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.component package."""
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.pipelines package."""
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """openfl.utilities.fedcurv package."""
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from setuptools import setup, find_packages setup(name="src", version="0.0.1", packages=find_packages(include=["src"]))
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from .node_fm import NodeFM from .node_drop import NodeDrop from .edge_per import EdgePer from .augmenter import Augmenter
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#!/usr/bin/python3 x = input('a number = ') print('<'.encode()) for ch in x: print(ch.encode()) print('>'.encode())
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 from openfl.__version__ import __version__
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5
# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 from openfl.federated.plan.plan import Plan
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from .mmp import * from .precomputed import * from .scaffold import * from .tanimoto import * from .pair_generator import *
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## Wrapper for mace.cli.eval_configs.main ## from mace.cli.eval_configs import main if __name__ == "__main__": main()
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """openfl experimental workflow package."""
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from django.contrib import admin # Register your models here. from .models import tcgapatient admin.site.register(tcgapatient)
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from .trajectories_creation import produce_output_dict, trajectories_API __all__ = ["trajectories_API", "produce_output_dict"]
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from corgie.main import cli as corgie_command from corgie.worker import worker as corgie_worker from corgie.cli import *
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.component.assigner package."""
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"""idtracker.ai tools, which have a dedicated command line main entrypoint, can also be called from here as Python functions."""
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## Wrapper for mace.cli.preprocess_data.main ## from mace.cli.preprocess_data import main if __name__ == "__main__": main()
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from .fragmentation import find_exclusive_contours, fragmentation_API __all__ = ["fragmentation_API", "find_exclusive_contours"]
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from .bond_mapper import BondMapper from .fragment_filter import FragmentFilter from .fragment_reactions import FragmentReactions
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"""Sample size determination.""" from .interpolation import * from .linear_model import * from .univariate_correlations import *
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.utilities.optimizers package."""
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.component.aggregator package."""
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from __future__ import absolute_import import numpy as np from numpy.testing import assert_allclose from pycircstat import utils
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from .graphflow import GraphFlowModel from .graphflow_rl import GraphFlowModel_rl from .graphflow_con_rl import GraphFlowModel_con_rl
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# Copyright (C) 2020-2023 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """tests.openfl.component.collaborator package."""
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """openfl.experimental.workflow.protocols module."""
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from .fix_default_event_values import (fix_default_event_values, dir_fix_default_event_values)
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global LayerIndex global X global XI global t global mean_l global mean_L global Ml LayerIndex=0 X=[] XI=[] t=0 mean_l=0 mean_L=0 Ml=0
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from dataclasses import dataclass @dataclass(frozen=True) class ModelModeEnum: INFERENCE = "inference" TRAINING = "training"
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# Copyright 2025 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """This package contains utilities for verifying datasets."""
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from dataclasses import dataclass @dataclass class LeavingGroupsDTO: leaving_group_scaffold: str leaving_group_decoration: str
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""" HCI - Human Computer Interaction This module contains all the predefined Class and Functions to interact with the participants. """
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# SPDX-FileCopyrightText: 2022-present Chatipat Lorpaiboon <chatipat@uchicago.edu> # # SPDX-License-Identifier: MIT __version__ = "0.0.1"
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """openfl.experimental.workflow.interface.cli package."""
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import math as _math from numpy import pi def comb(n, k): return _math.factorial(n) // _math.factorial(k) // _math.factorial(n - k)
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from .vtkhandler import VTKHandler from .vtuhandler import VTUHandler from .vtphandler import VTPHandler from .stlhandler import STLHandler
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face_detection_path = 'faceDetection/haarcascade_frontalface_default.xml' emotion_model_path = 'modelTraining/_mini_XCEPTION.102-0.66.hdf5'
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """openfl version information.""" __version__ = "1.9.0.dev"
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class UserCancel(Exception): pass class NoNavigatorError(Exception): pass class NavigatorEmptyError(Exception): pass
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from ._base import ( AgainstEinsumTestCase, AgainstNumpyTestCase, AgainstScipyTestCase, BackendTestCase, DtypeTestCase, )
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#from sleepy.processing.core import FileProcessor from sleepy.processing.valley import Valley from sleepy.processing.signal import Signal
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from django.apps import AppConfig class CelsusConfig(AppConfig): default_auto_field = 'django.db.models.BigAutoField' name = 'celsus'
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from Engine.train import initiate if __name__ == "__main__": initiate("D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\test_train.yaml")
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class MutationError(Exception): pass class UniprotNotFoundError(Exception): pass class UniprotMultipleOutputError(Exception): pass
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"""The pydfc toolbox.""" from .similarity_assessment import SimilarityAssessment __all__ = ["SimilarityAssessment", "plotting", "analytical"]
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# Copyright 2025 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """This package contains utilities for PyTorch verifying datasets."""
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from .multinomial import MultinomialMetricTestData class CategoricalMetricTestData(MultinomialMetricTestData): xfails = ("log_after_exp",)
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# type: ignore __submodules__ = [] import lazy_loader __getattr__, __dir__, __all__ = lazy_loader.attach_stub(__name__, __file__) __all__ = []
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from geomstats.test_cases.geometry.base import VectorSpaceOpenSetTestCase class PoincareHalfSpaceTestCase(VectorSpaceOpenSetTestCase): pass
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from Engine.train import initiate if __name__ == "__main__": initiate("/home/tumor/LungTumorSegmentation/Resources/Student_Train/train.yaml")
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from .cli import * from .config_parse import * from .helpers import * from .logmon import * from .prior_registry import * from .hw_report import *
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# Copyright (C) 2025 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """You may copy this file as the starting point of your own model."""
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from Engine.inference import initiate if __name__ == "__main__": initiate("/home/tumor/LungTumorSegmentation/Resources/Evaluate/malvik.yaml")
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 from openfl.utilities.fedcurv.torch.fedcurv import FedCurv # NOQA
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"""Compatibility entry point for Proj2Proj training.""" from sparse_ct.example.proj2proj_train import main if __name__ == "__main__": main()
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from .contact_map_utils import * from .xpdb import SloppyStructureBuilder from .polypeptide_featurizers import * from .residue_featurizers import *
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"""Stuff that doesn't belong anywhere else NOTE> should be moved probably """ from .image import * from .helpers import * from .evaluate import *
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""" Fixed parameters to affect fontsizes """ fsize_ticks = fsize_legends = 8 fsize_xylabels = 9 fsize_misc = 10 fsize_titles = 11 fsize_panels = 12
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# Copyright 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 from openfl.component.collaborator.collaborator import Collaborator
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from .aug_dataset import DegreeTrans, AUG_trans, Subset, TripleSet __all__ = [ 'DegreeTrans', 'AUG_trans', 'Subset', 'TripleSet' ]
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from Engine.inference import initiate if __name__ == "__main__": initiate("/home/tumor/LungTumorSegmentation/Resources/Inference/malvik.yaml")
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""" Module for assessing performance. """ from .benchmark_decoder import benchmark_BCIdecoder from .benchmark_multitaper import benchmark_multitaper
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''' Protocol specific post-analysis Contains the standard analysis for the different procotols (time-frequency analysis, features importance...) '''
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from .filtering_condition_dto import FilteringConditionDTO from .reaction_dto import ReactionDTO from .reaction_outcome_dto import ReactionOutcomeDTO
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from .create_packages import * from .diversity_filter import * from .intrinsic_penalty import * from .inception import * from .reward_strategy import *
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from geomstats.test_cases.geometry.riemannian_metric import RiemannianMetricTestCase class QuotientMetricTestCase(RiemannianMetricTestCase): pass
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# Copyright (C) 2020-2025 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """You may copy this file as the starting point of your own model."""
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from Engine.inference import initiate if __name__ == "__main__": initiate("D:\\Repos\\LungTumorSegmentation\\Resources\\Test\\test_inference.yaml")
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# Copyright (C) 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """You may copy this file as the starting point of your own model."""
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# Copyright (C) 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 def collaborator_private_attrs(index): return {"index": index + 1}
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# Copyright (C) 2020-2021 Intel Corporation # SPDX-License-Identifier: Apache-2.0 """You may copy this file as the starting point of your own model."""
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from Engine.evaluate import initiate if __name__ == "__main__": initiate("D:\\Repos\\LungTumorSegmentation\\Resources\\Windows_Files\\win_eval.yaml")
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''' Protocol templates Contains some basic protocols for training and testing. Google Glass visual feedback is supported through USB communication. '''
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# Copyright (C) 2020-2024 Intel Corporation # SPDX-License-Identifier: Apache-2.0 def collaborator_private_attrs(index): return {"index": index + 1}
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# nequip package version file # See Python packaging guide # https://packaging.python.org/guides/single-sourcing-package-version/ __version__ = "0.19.1"
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"""Static feature configuration for the SanPy package.""" # DO_KYMOGRAPH_ANALYSIS = False """Whether optional kymograph analysis features are enabled."""
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import sys if sys.version_info[1] > 7: raise Exception('Requires Python 3.7 or lower') from sleepy.gui.core import Gui gui = Gui() gui.run()
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from reinvent.models.transformer.transformer import TransformerModel class Mol2MolModel(TransformerModel): _model_type = "Mol2Mol" _version = 1
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from .optimize_evoked import optimize_evoked from .general_optimization import ( Optimizer, generate_opt_history_table, _update_params, )
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name_dict = { 'all_names': ['B. wickershamorum', 'P. bethaniensis', 'P. carolinus', 'P. forresti', 'P. frontalis', 'P. knulli', 'P. obscurellus'], }
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from django.conf.urls import url from . import views from django.urls import path, include urlpatterns = [ url(r'^$', views.listing, name='listing'), ]
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from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_16.yaml")
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from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_75.yaml")
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4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_32.yaml")
4748813305aa2c2b6443085750869e36d728cf63085f439a621cdaafefe0f245
Python
158
4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_us.yaml")
7e7348500b239de09ba4d6db34fc90b18ccf414777bcac9f50db337aae2f747d
Python
158
4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_50.yaml")
9262852880527c1b4da43dff5fd22e3b582d48eb8f6304cd2441ce6204b3787e
Python
158
4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_1/train_25.yaml")
9a53e2be59fff30c2f46a6ec6536d7f14f6f99dde860f374958b91dbc7a0c9c7
Python
158
6
from reinvent.models.transformer.transformer import TransformerModel class PepinventModel(TransformerModel): _model_type = "Pepinvent" _version = 1
e2515e378aa782bce3496d4a8ad0e2d76badbf14ad590fc32dac49ae0fffc4ce
Python
158
4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_ud.yaml")
e3e32f963ed7c6a5889c47c690fc27f775ee258f8e9a4370e9a9e64881104eff
Python
158
4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_48.yaml")
f838cd7cbf8c3cf936d0168d2614c7e4a12b13905c8b7a557eb7d8a8c6ddf7da
Python
158
4
from Engine.train import initiate if __name__ == "__main__": initiate("/cluster/work/sosevle/LungTumorSegmentation/Resources/Idun_Train_2/train_64.yaml")
4279c52dee13aacdca3545520359dc7085e495c01bf156d243b146dfda2bcdbc
Python
159
9
from dataclasses import dataclass @dataclass class FilteringConditionDTO: name: str min: float = None max: float = None equals: float = None