reformatting

reghbali · Mar 18, 2024 · e68b652 · e68b652
1 parent d68d48f
commit e68b652
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Showing 8 changed files with 35 additions and 51 deletions.
diff --git a/pyalfe/containers.py b/pyalfe/containers.py
@@ -6,7 +6,7 @@
 from pyalfe.data_structure import DefaultALFEDataDir, Modality
 from pyalfe.image_processing import Convert3DProcessor, NilearnProcessor
 from pyalfe.image_registration import GreedyRegistration, AntsRegistration
-from pyalfe.inference import NNUnet, NNUnetV2
+from pyalfe.inference import NNUnetV2
 from pyalfe.models import MODELS_PATH
 from pyalfe.pipeline import PyALFEPipelineRunner
 from pyalfe.tasks.initialization import Initialization
@@ -58,9 +58,7 @@ class Container(containers.DeclarativeContainer):
         NNUnetV2,
         model_dir=str(
             MODELS_PATH.joinpath(
-                'nnunetv2',
-                'Dataset502_SS',
-                'nnUNetTrainer__nnUNetPlans__3d_fullres'
+                'nnunetv2', 'Dataset502_SS', 'nnUNetTrainer__nnUNetPlans__3d_fullres'
             )
         ),
         folds=(2,),
@@ -84,7 +82,7 @@ class Container(containers.DeclarativeContainer):
             MODELS_PATH.joinpath(
                 'nnunetv2',
                 'Dataset503_Enhancement',
-                'nnUNetTrainer__nnUNetPlans__3d_fullres'
+                'nnUNetTrainer__nnUNetPlans__3d_fullres',
             )
         ),
         folds=(0,),
@@ -96,7 +94,7 @@ class Container(containers.DeclarativeContainer):
             MODELS_PATH.joinpath(
                 'nnunetv2',
                 'Dataset510_Tissue_W_Prior',
-                'nnUNetTrainer__nnUNetPlans__3d_fullres'
+                'nnUNetTrainer__nnUNetPlans__3d_fullres',
             )
         ),
         folds=(3,),

diff --git a/pyalfe/main.py b/pyalfe/main.py
@@ -10,7 +10,6 @@
 from pyalfe.models import MODELS_PATH, models_url
 from pyalfe.tools import C3D_PATH, GREEDY_PATH, c3d_url, greedy_url
 from pyalfe.utils import download_archive, extract_binary_from_archive
-from pyalfe.utils.archive import extract_tar
 
 DEFAULT_CFG = os.path.expanduser(os.path.join('~', '.config', 'pyalfe', 'config.ini'))
 # importlib.resources.files('pyalfe').joinpath('config.ini')
@@ -59,7 +58,6 @@ def download(assets):
             click.print(f'asset {asset} is not recognized.')
 
 
-
 @main.command()
 @click.argument('accession')
 @click.option(

diff --git a/pyalfe/tasks/quantification.py b/pyalfe/tasks/quantification.py
@@ -234,12 +234,12 @@ def get_lesion_stats(
                 stats[f'median_{modality_name}_signal'] = np.median(
                     modality_image[lesion_indices]
                 )
-                stats[
-                    f'five_percentile_{modality_name}_signal'
-                ] = np.percentile(modality_image[lesion_indices], 5)
-                stats[
-                    f'ninety_five_percentile_{modality_name}_signal'
-                ] = np.percentile(modality_image[lesion_indices], 95)
+                stats[f'five_percentile_{modality_name}_signal'] = np.percentile(
+                    modality_image[lesion_indices], 5
+                )
+                stats[f'ninety_five_percentile_{modality_name}_signal'] = np.percentile(
+                    modality_image[lesion_indices], 95
+                )
 
         if Modality.T1 in modality_images and Modality.T1Post in modality_images:
             t1_image = modality_images[Modality.T1]

diff --git a/pyalfe/tasks/registration.py b/pyalfe/tasks/registration.py
@@ -247,9 +247,7 @@ def run(self, accession):
             )
             return
         if not os.path.exists(t1trim_upsampled):
-            self.logger.info(
-                'T1 trim upsampled is missing. Skipping T1Registration'
-            )
+            self.logger.info('T1 trim upsampled is missing. Skipping T1Registration')
             return
 
         template = roi_dict['template']['source']

diff --git a/pyalfe/tasks/segmentation.py b/pyalfe/tasks/segmentation.py
@@ -131,7 +131,7 @@ def __init__(
         pipeline_dir: PipelineDataDir,
         modality_list: list[str],
         output_modality: str,
-        image_type_input: str= 'skullstripped',
+        image_type_input: str = 'skullstripped',
         image_type_output: str = 'abnormal_seg',
         image_type_mask: str = None,
         segmentation_dir: str = 'abnormalmap',
@@ -303,11 +303,11 @@ def __init__(
         inference_model: InferenceModel,
         image_processor: ImageProcessor,
         pipeline_dir: PipelineDataDir,
-        image_type_input: str= 'trim_upsampled',
-        image_type_output: str='tissue_seg',
-        template_name: str='Tissue',
+        image_type_input: str = 'trim_upsampled',
+        image_type_output: str = 'tissue_seg',
+        template_name: str = 'Tissue',
         overwrite: bool = True,
-        ):
+    ):
         super().__init__(inference_model, image_processor)
         self.pipeline_dir = pipeline_dir
         self.image_type_input = image_type_input
@@ -319,31 +319,27 @@ def __init__(
 
     def run(self, accession):
         t1_image_path = self.pipeline_dir.get_output_image(
-                accession,
-                Modality.T1,
-                image_type=self.image_type_input,
-                )
+            accession,
+            Modality.T1,
+            image_type=self.image_type_input,
+        )
         tissue_prior_path = self.pipeline_dir.get_output_image(
             accession,
             Modality.T1,
             resampling_origin=self.template_name,
             resampling_target=Modality.T1,
-            sub_dir_name=roi_dict[self.template_name]['sub_dir']
+            sub_dir_name=roi_dict[self.template_name]['sub_dir'],
         )
         pred_path = self.pipeline_dir.get_output_image(
-            accession,
-            Modality.T1,
-            image_type=f'{self.image_type_output}_pred'
+            accession, Modality.T1, image_type=f'{self.image_type_output}_pred'
         )
 
         if self.overwrite or not os.path.exists(pred_path):
             self.predict([t1_image_path, tissue_prior_path], pred_path)
 
         seg_path = self.pipeline_dir.get_output_image(
-            accession,
-            Modality.T1,
-            image_type=self.image_type_output
+            accession, Modality.T1, image_type=self.image_type_output
         )
-        
+
         if self.overwrite or not os.path.exists(seg_path):
-            self.post_process(pred_path, seg_path)
+            self.post_process(pred_path, seg_path)
diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py
@@ -1,6 +1,5 @@
 import importlib.resources
 import os
-import pathlib
 import shutil
 from unittest import TestCase
 
@@ -11,9 +10,8 @@
 from pyalfe.main import run
 from tests.utils import download_and_extract
 
-class TestIntegration(TestCase):
-
 
+class TestIntegration(TestCase):
     def setUp(self) -> None:
         self.test_dir = os.path.join('/tmp', 'integration_test')
 
@@ -22,7 +20,9 @@ def tearDown(self) -> None:
 
     def test_run(self):
 
-        test_data_url = 'https://github.com/reghbali/pyalfe-test-data/archive/master.zip'
+        test_data_url = (
+            'https://github.com/reghbali/pyalfe-test-data/archive/master.zip'
+        )
         test_data_dir_name = 'pyalfe-test-data-main'
         accession = 'UPENNGBM0000511'
 
@@ -39,9 +39,7 @@ def test_run(self):
             Modality.ADC,
         ]
         targets = [Modality.T1Post, Modality.FLAIR]
-        pipeline_dir = DefaultALFEDataDir(
-            output_dir=output_dir, input_dir=input_dir
-        )
+        pipeline_dir = DefaultALFEDataDir(output_dir=output_dir, input_dir=input_dir)
 
         download_and_extract(test_data_url, self.test_dir)
 

diff --git a/tests/unit/test_tasks.py b/tests/unit/test_tasks.py
@@ -189,17 +189,15 @@ def test_run(self):
         input_path = self.pipeline_dir.get_output_image(
             accession, Modality.T1, image_type=task.image_type_input
         )
-        prior_path =  self.pipeline_dir.get_output_image(
+        prior_path = self.pipeline_dir.get_output_image(
             accession,
             Modality.T1,
             resampling_origin=task.template_name,
             resampling_target=Modality.T1,
-            sub_dir_name=roi_dict[task.template_name]['sub_dir']
+            sub_dir_name=roi_dict[task.template_name]['sub_dir'],
         )
         output_path = self.pipeline_dir.get_output_image(
-            accession,
-            Modality.T1,
-            image_type=task.image_type_output
+            accession, Modality.T1, image_type=task.image_type_output
         )
         shutil.copy(
             os.path.join('tests', 'data', 'brats10', 'BraTS19_2013_10_1_t1.nii.gz'),
@@ -464,13 +462,12 @@ def test_run(self):
             accession, Modality.T1, image_type='trim_upsampled'
         )
         shutil.copy(
-            os.path.join('tests', 'data', 'brainomics02', 'anat_t1.nii.gz'),
-            input_image
+            os.path.join('tests', 'data', 'brainomics02', 'anat_t1.nii.gz'), input_image
         )
         Convert3DProcessor.binarize(input_image, input_mask)
         shutil.copy(
             os.path.join('tests', 'data', 'brainomics02', 'anat_t1.nii.gz'),
-            input_image_trim_upsampled
+            input_image_trim_upsampled,
         )
         task.run(accession)
 

diff --git a/tests/utils.py b/tests/utils.py
@@ -32,4 +32,3 @@ def download_and_extract(url: str, dest_dir: str, archive_name: str = None):
         file.write(response.content)
 
     shutil.unpack_archive(archive_file_path, dest_dir)
-
Original file line number	Diff line number	Diff line change
Expand Up		@@ -32,4 +32,3 @@ def download_and_extract(url: str, dest_dir: str, archive_name: str = None):
		file.write(response.content)

		shutil.unpack_archive(archive_file_path, dest_dir)