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# -*- coding: utf-8 -*- def test_compute_asymmetry_index(): # toDO pass def test_compute_odd_power_map(): # toDO pass
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- __all__ = [ "flim_processing", "flim_set_processing", "flim_visualization", ]
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from .chemprop import MPN from .data import MoleculeDatapoint, MoleculeDataset __all__ = ["MPN", "MoleculeDatapoint", "MoleculeDataset"]
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from diffxpy.testing import lrt, wald, wald_repeated, t_test, rank_test, two_sample, pairwise, \ versus_rest, partition, continuous_1d
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from brainscore_vision import metric_registry from .metric import AccuracyDistance metric_registry['accuracy_distance'] = AccuracyDistance
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# __init__.py #from .main import main print('import before') from . import main_procedure, filterling, plot_spots print('import done')
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"""Method for causal disentanglement of inter-cellular and intra-cellular gene regulation in spatial transcriptomics""" __version__ = "0.0.1"
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"""Local web viewer for MEA-NAP run bundles.""" from meanap.viewer.server import ViewerService, serve __all__ = ["ViewerService", "serve"]
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from .backend import Datumaro2DBackend __all__ = ["Datumaro2DBackend"]
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from brainscore_core.supported_data_standards.brainio.s3 import load_folder_from_s3, load_weight_file download_weights = load_folder_from_s3
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from .base import AbstractAssociator from .gamma import GammaAssociator from .pyocto import PyOctoAssociator from .real import REALAssociator
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from .logger import setup_logger from .seeds import setup_seed from .config import Config __all__ = ["setup_logger", "setup_seed", "Config"]
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"""Pose-JEPA pretraining infrastructure for kinescope. Data loaders, clip datasets, visualization utilities, and the pretraining script. """
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from typing import Literal __all__ = ['SIGNAL_TYPE'] SIGNAL_TYPE = Literal['df_f', 'spks', 'cascade_spks'] """Calcium imaging signal type"""
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#! /usr/bin/env python # aponteeduardo@gmail.com # copyright (C) 2017 '''' ''' __import__('pkg_resources').declare_namespace(__name__)
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# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
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HOST_TEMPLATE = 'https://celldetection.org/torch/models/{name}' HOSTED_MODELS = dict( ginoro='ginoro_CpnResNeXt101UNet-fbe875f1a3e5ce2c', )
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# This file is part of connectome-manipulator. # # SPDX-License-Identifier: Apache-2.0 # Copyright (c) 2024 Blue Brain Project/EPFL """init"""
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from __future__ import annotations from chemgraph.academy.dashboard.server import main if __name__ == '__main__': raise SystemExit(main())
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from .fno import TFNO, TFNO1d, TFNO2d, TFNO3d from .fno import FNO, FNO1d, FNO2d, FNO3d from .fno import SFNO from .base_model import get_model
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from brainscore_vision import benchmark_registry from .benchmark import DicarloKar2019OST benchmark_registry['Kar2019-ost'] = DicarloKar2019OST
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import warnings warnings.filterwarnings("ignore", message="RuntimeWarning") warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
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""" Imputations for time-series data. """ from .locf import locf from .moving_window import moving_window __all__ = ["locf", "moving_window"]
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""" This submodule contains MPI operations. For more information about MPI visit: https://mpi4py.readthedocs.io/en/stable/ """ from .mpi import *
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from brainscore_vision import benchmark_registry from .benchmark import Hebart2023Match benchmark_registry['Hebart2023-match'] = Hebart2023Match
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from brainscore_vision import benchmark_registry from .benchmark import Cowley2026V4PLS benchmark_registry['Cowley2026.V4-pls'] = Cowley2026V4PLS
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""" nelpy utils """ from . import decorators __all__ = ["decorators"] __version__ = "0.0.2" # should I maintain a separate version for this?
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from brainscore_vision import metric_registry from .metric import BakerAccuracyDelta metric_registry['baker_accuracy_delta'] = BakerAccuracyDelta
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__all__ = ["CziFile", "remote_reads_available"] from .CziFile import CziFile, remote_reads_available from ._version import __version__ # noqa F401
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# TODO # From supplement doc: # "exclude subsets of data based on criteria such as missing data, # outlier state values, incorrect behavior, etc."
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from ._contact_communication import contact_communication, cluster_communication from ._cell_shape_modeling import cell_shape_modeling, cellshape_GT
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# -*- coding: utf-8 -*- def test_find_intersection(): # Todo: # finder = IntersectionFinder(...) # finder.find_intersection() pass
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#! /usr/bin/env python import jellyfish import sys mf = jellyfish.ReadMerFile(sys.argv[1]) for mer, count in mf: print("%s %d" % (mer, count))
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from ._model import DestVISpatial, CustomTrainingPlan from ._module import HSTDeconv __all__ = ["DestVISpatial", "CustomTrainingPlan", "HSTDeconv"]
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from .normalizer_base import Normalizer from .percentile_normalizer import PercentileNormalizer from .windowing_normalizer import WindowingNormalizer
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# Copyright (C) 2021-2022 Intel Corporation # # SPDX-License-Identifier: MIT from .core import ImageManifestManager, VideoManifestManager, is_manifest
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"""ChemGraph Command Line Interface. Entry point:: chemgraph = "chemgraph.cli:main" """ from chemgraph.cli.main import main __all__ = ["main"]
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# prsedm/extensions/__init__.py from .score_dm import gen_dm from .SQL import get_snp_db, get_dm_sql __all__ = ["gen_dm", "get_snp_db", "get_dm_sql"]
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import doctest import retnext.modules def load_tests(loader, tests, ignore): tests.addTests(doctest.DocTestSuite(retnext.modules)) return tests
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"""Compatibility launcher for the browser-based interface.""" from .browser_app import main __all__ = ["main"] if __name__ == "__main__": main()
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__version__ = '1.2.7' from . SpaGCN import * from . util import * from . calculate_moran_I import * from . calculate_adj import * from . ez_mode import *
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r"""Visualization package.""" from .graph import visualize_graph from .influence import influence __all__ = [ 'visualize_graph', 'influence', ]
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# -*- coding: utf-8 -*- from .evaluate import Evaluate from .predict import Predict from .train import Train __all__ = ['Evaluate', 'Predict', 'Train']
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from . import plots as pl from . import train as tr from . import utils as tl from .pca import dPCA, scPCA __all__ = ["scPCA", "dPCA", "tl", "tr", "pl"]
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__version__='0.1.1' from .constants import * from .transform import * from .gncc import * from .grid_search import grid_search from .preprocess import *
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from .dpca import dpca_guide, dpca_model from .scpca import scpca_guide, scpca_model __all__ = ["scpca_model", "scpca_guide", "dpca_model", "dpca_guide"]
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from .data_preprocessing import formulate_HRCHYCytoCommunity_input_from_anndata_singlecell,compute_knn,formulate_HRCHYCytoCommunity_input_from_anndata_spot
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from .base_reducer import BaseReducer class DoNothingReducer(BaseReducer): def forward(self, loss_dict, embeddings, labels): return loss_dict
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from .perlin_stimulus import PerlinStimulus from .util import generate_frames from .easy import zebra_noise Perl = PerlinStimulus # Backward compatibility
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from django.dispatch import Signal internal_ai_agent_function_call_signal = Signal()
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""" Utilities for handling PLS results generated using the Matlab PLS toolbox """ __all__ = ["import_matlab_result"] from .io import import_matlab_result
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"""Tests for use with the `pytest` library. To run all tests from command line: `pip install pytest` then: `pytest` from the nems-lite base directory. """
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT """Adapters for external representations, imported separately from the data model."""
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import pytest import brainscore_vision @pytest.mark.private_access def test_existence(): assert brainscore_vision.load_dataset('Kar2019') is not None
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# Copyright (c) OpenMMLab. All rights reserved. from .metrics import metrics, eval_metrics, pre_eval_to_metrics from .eval_hooks import EvalHook, DistEvalHook
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from setuptools import setup, find_packages setup( name='bce', version='0.1', packages=find_packages(where='src'), package_dir={'': 'src'}, )
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import pytest from brainscore_vision import load_dataset @pytest.mark.private_access def test_existence(): assert load_dataset('David2004') is not None
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import pytest from brainscore_vision import load_dataset @pytest.mark.private_access def test_existence(): assert load_dataset('Cichy2019') is not None
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import doctest import retnext.transforms def load_tests(loader, tests, ignore): tests.addTests(doctest.DocTestSuite(retnext.transforms)) return tests
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from .loss_functions import LOSS_FUNCTIONS from .neural_net import NeuralNet from .sinkhorn import Sinkhorn, marginals_and_transport_plan from .utils import *
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from __future__ import annotations class CloudStorageMissingError(Exception): pass
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"""Volumetric parcellations. For more information see :ref:`parcellations`. """ from pathlib import Path path = Path(__file__).parent directory = str(path)
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import numpy as np X_RANGE = np.linspace(-0.5, 0.5, 101, dtype=np.float32) Y_RANGE = np.linspace(-1.0, 1.0, 101, dtype=np.float32) THETA_RANGE = range(0, 360)
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class Defaults: expected_dims = ('presentation', 'neuroid') stimulus_coord = 'stimulus_id' neuroid_dim = 'neuroid' neuroid_coord = 'neuroid_id'
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from django.dispatch import Signal request_succeeded = Signal() request_failed = Signal()
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#!/usr/bin/env python """ Simple script to add a prefix to every line in a file. """ import sys for line in sys.stdin: print(sys.argv[1] + line, end=" ")
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import h5py import pathlib import matplotlib matplotlib.use('Qt5Agg') import matplotlib.pyplot as plt if __name__ == '__main__': result_path = pathlib.Path()
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import pytest import brainscore_vision @pytest.mark.private_access def test_existence(): assert brainscore_vision.load_dataset('Kuzovkin2018') is not None
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from typing import Callable, Tuple, Type, Union import torch LayerType = Union[str, Callable, Type[torch.nn.Module]] PadType = Union[str, int, Tuple[int, int]]
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"""Objects and methods to evaluate accuracy of causal models.""" from .evaluator import evaluate, evaluate_bootstrap __all__ = ["evaluate", "evaluate_bootstrap"]
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from .Submodules import * from .AberrantExpression import * from .AberrantSplicing import * from .MonoallelicExpression import * from .RNAVariantCalling import *
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT from enum import Enum class SourceDataType(Enum): images = "images" video = "video"
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# Copyright (c) OpenMMLab. All rights reserved. from .encoding import Encoding from .wrappers import Upsample, resize __all__ = ['Upsample', 'resize', 'Encoding']
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# Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license """Optimizers for Ultralytics model training.""" from .muon import MuSGD __all__ = ["MuSGD"]
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import pytest import brainscore_vision @pytest.mark.private_access def test_existence(): assert brainscore_vision.load_dataset('Rajalingham2020') is not None
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r1 = 3.2e-3 # l/mmol/ms T01 = 4500 # ms R01 = 1.0 / T01 def compute_c(T1): return (1.0 / T1 - R01) / r1 def compute_T1(c): return 1.0 / (R01 + c * r1)
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from bism.targets.affinities import affinities from bism.targets.local_shape_descriptors import lsd _valid_targets = { 'lsd': lsd, 'affinities': affinities }
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# coding: utf-8 # file generated by setuptools_scm # don't change, don't track in version control version = '1.1.dev260054000' version_tuple = (1, 1, 'dev260054000')
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""" Current whole-genome alignment often result in large unaligned regions. This result in large HDRs/notals, even though the actual sequence is quite comparable. """
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from app import MainApp from service.router import users, topics MainApp.app.include_router(users.router) MainApp.app.include_router(topics.router) app = MainApp.app
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from __future__ import absolute_import from .classification import accuracy from .ranking import cmc, mean_ap __all__ = [ 'accuracy', 'cmc', 'mean_ap' ]
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import pytest import brainscore_vision def test_has_identifier(): model = brainscore_vision.load_model('hmax_v3_adj') assert model.identifier == 'hmax_v3_adj'
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# import self-written scripts to get random positions and manage exp import exp_utils LOCATION='mockup' if __name__ == '__main__': exp_utils.run_exp(LOCATION)
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from importlib.metadata import version, PackageNotFoundError try: __version__ = version("encore-toolkit") except PackageNotFoundError: __version__ = "unknown"
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from .threshold_reducer import ThresholdReducer class AvgNonZeroReducer(ThresholdReducer): def __init__(self, **kwargs): super().__init__(low=0, **kwargs)
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from ._cellgraph import * from ._assgraph import * from ._dataset import * from ._model import * from ._classifier import * from ._scoring import * from ._utils import *
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Python
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from .cci import * from .hotspot import * from .utility import * from . import methods from . import data from . import plot from . import hmrf from . import benchmarks
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Python
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# import self-written scripts to get random positions and manage exp import exp_utils LOCATION='scanner' if __name__ == '__main__': exp_utils.run_exp(LOCATION)
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Python
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- __all__ = [ "shared", "visualization", "parameters", "files_io", "image", "flim", "utils", ]
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Python
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# -*- coding: utf-8 -*- """ """ import math import matplotlib.pyplot as plt import networkx as nx import numpy as np import pandas as pd import pygsp import scipy as sc
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import pytest import brainscore_vision def test_has_identifier(): model = brainscore_vision.load_model('hmax_v3_adj2') assert model.identifier == 'hmax_v3_adj2'
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Python
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# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT # Force execution of fixture definitions from .fixtures import * # pylint: disable=wildcard-import
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Python
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#!/usr/bin/env python # -*- coding: utf-8 -*- from setuptools import setup requirements = [ "pandas", "imageio", ] setup( install_requires=requirements, )
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Python
170
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from setuptools import setup, find_packages setup( name='stroketriage', version='0.1.0', packages=find_packages(where='src'), package_dir={'': 'src'}, )
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Python
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- def test_help_option(script_runner): ret = script_runner.run(['scil_data_download', '--help']) assert ret.success
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Python
171
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from .physiodicom import PhysioDicom from .ecg import HeartRate from .phaseresp import PhaseRespWave from .bidsphysio import (write_json, make_bids_stub, save_bids_physio)
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Python
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12
# -*- coding: utf-8 -*- """ """ import pygsp import numpy as np import networkx as nx import pandas as pd import matplotlib.pyplot as plt import math import scipy as sc
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Python
172
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import importlib def get_instance(mod_name, class_name): mod = importlib.import_module(mod_name) prototype = getattr(mod, class_name) return prototype
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Python
172
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from functools import update_wrapper from .densedepth_head import DenseDepthHead, DepthBaseDecodeHead from .densedepth_head24 import DenseDepthHead24, DepthBaseDecodeHead
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Python
173
6
# Copyright (C) CVAT.ai Corporation # # SPDX-License-Identifier: MIT # Force execution of fixture definitions from sdk.fixtures import * # pylint: disable=wildcard-import