def data_prep_function(data, patch_centers, pixel_spacing, p_transform, p_transform_augment, **kwargs): x = data_transforms.transform_dsb_candidates(data=data, patch_centers=patch_centers, p_transform=p_transform, p_transform_augment=p_transform_augment, pixel_spacing=pixel_spacing) x = data_transforms.pixelnormHU(x) return x
def data_prep_function(data, patch_centers, pixel_spacing, p_transform, p_transform_augment, **kwargs): x = data_transforms.transform_dsb_candidates(data=data, patch_centers=patch_centers, p_transform=p_transform, p_transform_augment=p_transform_augment, pixel_spacing=pixel_spacing) x = data_transforms.pixelnormHU(x) return x
def data_prep_function(data, pixel_spacing, p_transform=p_transform): # TODO: MAKE SURE THAT DATA IS PREPROCESSED THE SAME WAY lung_mask = lung_segmentation.segment_HU_scan_elias(data) x, tf_matrix, lung_mask_out = data_transforms.transform_scan3d(data=data, pixel_spacing=pixel_spacing, p_transform=p_transform, lung_mask=lung_mask, p_transform_augment=None) x = data_transforms.pixelnormHU(x) return x, lung_mask_out, tf_matrix
def data_prep_function(data, pixel_spacing, p_transform=p_transform): # TODO: MAKE SURE THAT DATA IS PREPROCESSED THE SAME WAY lung_mask = lung_segmentation.segment_HU_scan(data) x, tf_matrix, lung_mask_out = data_transforms.transform_scan3d( data=data, pixel_spacing=pixel_spacing, p_transform=p_transform, lung_mask=lung_mask, p_transform_augment=None) x = data_transforms.pixelnormHU(x) return x, lung_mask_out, tf_matrix
def data_prep_function(data, patch_center, luna_annotations, pixel_spacing, luna_origin, p_transform, p_transform_augment, **kwargs): x, patch_annotation_tf, annotations_tf = data_transforms.transform_patch3d(data=data, luna_annotations=luna_annotations, patch_center=patch_center, p_transform=p_transform, p_transform_augment=p_transform_augment, pixel_spacing=pixel_spacing, luna_origin=luna_origin) x = data_transforms.pixelnormHU(x) y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere') return x, y
def data_prep_function(data, patch_center, pixel_spacing, luna_origin, p_transform, p_transform_augment, world_coord_system, **kwargs): x, patch_annotation_tf = data_transforms.transform_patch3d(data=data, luna_annotations=None, patch_center=patch_center, p_transform=p_transform, p_transform_augment=p_transform_augment, pixel_spacing=pixel_spacing, luna_origin=luna_origin, world_coord_system=world_coord_system) x = data_transforms.pixelnormHU(x) return x
def data_prep_function(data, pixel_spacing, p_transform=p_transform): # TODO: MAKE SURE THAT DATA IS PREPROCESSED THE SAME WAY #lung_mask = lung_segmentation.segment_HU_scan(data) x, tf_matrix = data_transforms.transform_scan3d(data=data, pixel_spacing=pixel_spacing, p_transform=p_transform_data_in, lung_mask=None, p_transform_augment=None) print('x.shape', x.shape) x = data_transforms.pixelnormHU(x) print('x.shape', x.shape) return x, tf_matrix
def data_prep_function(data, patch_center, luna_annotations, pixel_spacing, luna_origin, p_transform, p_transform_augment, **kwargs): x, patch_annotation_tf, annotations_tf = data_transforms.transform_patch3d(data=data, luna_annotations=luna_annotations, patch_center=patch_center, p_transform=p_transform, p_transform_augment=p_transform_augment, pixel_spacing=pixel_spacing, luna_origin=luna_origin) x = data_transforms.pixelnormHU(x) y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere') return x, y
def data_prep_function(data, pixel_spacing, p_transform=p_transform): # TODO: MAKE SURE THAT DATA IS PREPROCESSED THE SAME WAY #lung_mask = lung_segmentation.segment_HU_scan(data) x, tf_matrix = data_transforms.transform_scan3d(data=data, pixel_spacing=pixel_spacing, p_transform=p_transform_data_in, lung_mask=None, p_transform_augment=None) print 'x.shape', x.shape x = data_transforms.pixelnormHU(x) print 'x.shape', x.shape return x, tf_matrix
def data_prep_function(data, luna_annotations, pixel_spacing, luna_origin, p_transform=p_transform, p_transform_augment=None): # make sure the data is processed the same way x, annotations_tf, tf_matrix = data_transforms.transform_scan3d(data=data, pixel_spacing=pixel_spacing, p_transform=p_transform, luna_annotations=luna_annotations, p_transform_augment=None, luna_origin=luna_origin) x = data_transforms.pixelnormHU(x) y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere') return x, y, annotations_tf, tf_matrix
def data_prep_function(data, luna_annotations, pixel_spacing, luna_origin, p_transform=p_transform, p_transform_augment=None): # make sure the data is processed the same way x, annotations_tf, tf_matrix = data_transforms.transform_scan3d(data=data, pixel_spacing=pixel_spacing, p_transform=p_transform, luna_annotations=luna_annotations, p_transform_augment=None, luna_origin=luna_origin) x = data_transforms.pixelnormHU(x) y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere') return x, y, annotations_tf, tf_matrix
def data_prep_function(data, patch_center, pixel_spacing, luna_origin, p_transform, p_transform_augment, world_coord_system, **kwargs): x, patch_annotation_tf = data_transforms.transform_patch3d( data=data, luna_annotations=None, patch_center=patch_center, p_transform=p_transform, p_transform_augment=p_transform_augment, pixel_spacing=pixel_spacing, luna_origin=luna_origin, world_coord_system=world_coord_system) x = data_transforms.pixelnormHU(x) return x