From 624133bd9d294957634b5b1a1411f6546d25e270 Mon Sep 17 00:00:00 2001 From: clementpoiret Date: Tue, 29 Oct 2024 13:02:38 +0100 Subject: [PATCH] chore: bump to v1.2.2 --- hsf/__init__.py | 2 +- tests/test_hsf.py | 107 +++++++++++++++++++--------------------------- 2 files changed, 45 insertions(+), 64 deletions(-) diff --git a/hsf/__init__.py b/hsf/__init__.py index 3f262a6..bc86c94 100644 --- a/hsf/__init__.py +++ b/hsf/__init__.py @@ -1 +1 @@ -__version__ = '1.2.1' +__version__ = "1.2.2" diff --git a/tests/test_hsf.py b/tests/test_hsf.py index a79e7eb..fb33221 100644 --- a/tests/test_hsf.py +++ b/tests/test_hsf.py @@ -17,7 +17,7 @@ def test_version(): - assert __version__ == '1.2.1' + assert __version__ == "1.2.2" # SETUP FIXTURES @@ -51,26 +51,22 @@ def config(models_path): "pattern": "sub*_tse.nii.gz", "mask_pattern": None, "output_dir": "hsf_outputs", - "overwrite": False + "overwrite": False, }, "hardware": { "engine": "onnxruntime", "engine_settings": { - "execution_providers": [[ - "CUDAExecutionProvider", { - "device_id": 0, - "gpu_mem_limit": 2147483648 - } - ], "CPUExecutionProvider"], - "batch_size": - 1 - } - }, - "roiloc": { - "roi": "hippocampus", - "contrast": "t2", - "margin": [2, 0, 2] + "execution_providers": [ + [ + "CUDAExecutionProvider", + {"device_id": 0, "gpu_mem_limit": 2147483648}, + ], + "CPUExecutionProvider", + ], + "batch_size": 1, + }, }, + "roiloc": {"roi": "hippocampus", "contrast": "t2", "margin": [2, 0, 2]}, "augmentation": { "flip": { "axes": ["LR"], @@ -87,30 +83,24 @@ def config(models_path): "elastic": { "num_control_points": 4, "max_displacement": 4, - "locked_borders": 0 + "locked_borders": 0, }, }, "multispectrality": { "pattern": None, "same_space": True, - "registration": { - "type_of_transform": "AffineFast" - } + "registration": {"type_of_transform": "AffineFast"}, }, "segmentation": { "ca_mode": "1/2/3", "models_path": str(models_path), "models": { "model.onnx": { - "url": - "https://zenodo.org/record/6457484/files/arunet_3.0.0_single.onnx?download=1", - "xxh3_64": "71edec9011f7f304" + "url": "https://zenodo.org/record/6457484/files/arunet_3.0.0_single.onnx?download=1", + "xxh3_64": "71edec9011f7f304", } }, - "segmentation": { - "test_time_augmentation": True, - "test_time_num_aug": 5 - } + "segmentation": {"test_time_augmentation": True, "test_time_num_aug": 5}, }, } @@ -122,9 +112,9 @@ def deepsparse_inference_engines(models_path): """Tests that models can be loaded using DeepSparse""" settings = DictConfig({"num_cores": 0, "batch_size": 2}) - engines = hsf.engines.get_inference_engines(models_path, - engine_name="deepsparse", - engine_settings=settings) + engines = hsf.engines.get_inference_engines( + models_path, engine_name="deepsparse", engine_settings=settings + ) return list(engines) @@ -167,16 +157,13 @@ def test_roiloc(models_path): mri, mask = hsf.roiloc_wrapper.get_mri(mris[0], mask_pattern="mask.nii.gz") assert isinstance(mask, ants.ANTsImage) - mri, mask = hsf.roiloc_wrapper.get_mri(mris[0], - mask_pattern="no_mask.nii.gz") + mri, mask = hsf.roiloc_wrapper.get_mri(mris[0], mask_pattern="no_mask.nii.gz") assert isinstance(mri, ants.ANTsImage) assert mask is None - _, right, left = hsf.roiloc_wrapper.get_hippocampi(mri, { - "contrast": "t2", - "margin": [2, 0, 2], - "roi": "hippocampus" - }, mask) + _, right, left = hsf.roiloc_wrapper.get_hippocampi( + mri, {"contrast": "t2", "margin": [2, 0, 2], "roi": "hippocampus"}, mask + ) assert isinstance(right, ants.ANTsImage) assert isinstance(left, ants.ANTsImage) @@ -200,47 +187,41 @@ def test_segment(models_path, config, deepsparse_inference_engines): n_engines=1, engines=deepsparse_inference_engines, ca_mode=ca_mode, - batch_size=2) + batch_size=2, + ) hsf.segment.save_prediction(mri, pred) def test_multispectrality(models_path): """Tests that we can co-locate hippocampi in another contrast.""" - config = DictConfig({ - "files": { - "output_dir": str(models_path) - }, - "multispectrality": { - "pattern": "sub0_tse.nii.gz", - "same_space": False, - "registration": { - "type_of_transform": "AffineFast" - } + config = DictConfig( + { + "files": {"output_dir": str(models_path)}, + "multispectrality": { + "pattern": "sub0_tse.nii.gz", + "same_space": False, + "registration": {"type_of_transform": "AffineFast"}, + }, } - }) + ) - mri = hsf.roiloc_wrapper.load_from_config(models_path, - "sub0_tse.nii.gz")[0] - second_contrast = hsf.multispectrality.get_second_contrast( - mri, "sub0_tse.nii.gz") + mri = hsf.roiloc_wrapper.load_from_config(models_path, "sub0_tse.nii.gz")[0] + second_contrast = hsf.multispectrality.get_second_contrast(mri, "sub0_tse.nii.gz") registered = hsf.multispectrality.register( - mri, second_contrast, - DictConfig({"multispectrality": { - "same_space": True - }})) + mri, second_contrast, DictConfig({"multispectrality": {"same_space": True}}) + ) registered = hsf.multispectrality.register(mri, second_contrast, config) img = ants.image_read(str(mri), reorient="LPI") - locator, _, _ = hsf.roiloc_wrapper.get_hippocampi(img, { - "contrast": "t2", - "margin": [2, 0, 2], - "roi": "hippocampus" - }, None) + locator, _, _ = hsf.roiloc_wrapper.get_hippocampi( + img, {"contrast": "t2", "margin": [2, 0, 2], "roi": "hippocampus"}, None + ) _, _ = hsf.multispectrality.get_additional_hippocampi( - mri, registered, locator, config) + mri, registered, locator, config + ) def test_uncertainty():