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