# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch> # # SPDX-License-Identifier: GPL-3.0-or-later """Tests for NIH CXR-14 dataset.""" import importlib import pytest def id_function(val): if isinstance(val, dict): return str(val) return repr(val) @pytest.mark.parametrize( "split,lenghts", [ ("default.json.bz2", dict(train=98637, validation=6350, test=4054)), ("cardiomegaly.json", dict(train=40, validation=40)), ], ids=id_function, # just changes how pytest prints it ) def test_protocol_consistency( database_checkers, split: str, lenghts: dict[str, int] ): from mednet.config.data.nih_cxr14.datamodule import make_split database_checkers.check_split( make_split(split), lengths=lenghts, prefixes=("images/000",), possible_labels=(0, 1), ) testdata = [ ("default", "train", 14), ("default", "validation", 14), ("default", "test", 14), ("cardiomegaly", "train", 14), ("cardiomegaly", "validation", 14), ] @pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14") @pytest.mark.parametrize("name,dataset,num_labels", testdata) def test_loading(database_checkers, name: str, dataset: str, num_labels: int): datamodule = importlib.import_module( f".{name}", "mednet.config.data.nih_cxr14" ).datamodule datamodule.model_transforms = [] # should be done before setup() datamodule.setup("predict") # sets up all datasets loader = datamodule.predict_dataloader()[dataset] limit = 3 # limit load checking for batch in loader: if limit == 0: break database_checkers.check_loaded_batch( batch, batch_size=1, color_planes=1, prefixes=("images/000",), possible_labels=(0, 1), expected_num_labels=num_labels, expected_image_shape=(1, 1024, 1024), ) limit -= 1 @pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14") def test_loaded_image_quality(database_checkers, datadir): reference_histogram_file = str( datadir / "histograms/raw_data/histograms_nih_cxr14_default.json" ) datamodule = importlib.import_module( ".default", "mednet.config.data.nih_cxr14" ).datamodule datamodule.model_transforms = [] datamodule.setup("predict") database_checkers.check_image_quality(datamodule, reference_histogram_file)