def data_prep_function(data, patch_center, luna_annotations, pixel_spacing, luna_origin, p_transform,
p_transform_augment, **kwargs):
x = data_transforms.hu2normHU(data)
x, patch_annotation_tf, annotations_tf = data_transforms.transform_patch3d(data=x,
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)
return x, patch_annotation_tf
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, patch_center, pixel_spacing, luna_origin, p_transform,
p_transform_augment, **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)
x = data_transforms.hu2normHU(x)
return x
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.hu2normHU(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):
data_eq = utils_lung.histogram_equalization(data)
x, patch_annotation_tf = data_transforms.transform_patch3d(data=data_eq,
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.hu2normHU(x)
return x
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 = hu2normHU_wo_clipping(x)
return x
def data_prep_function(data, patch_center, pixel_spacing, luna_origin,
p_transform, p_transform_augment, world_coord_system,
**kwargs):
data_eq = utils_lung.histogram_equalization(data)
x, patch_annotation_tf = data_transforms.transform_patch3d(
data=data_eq,
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.hu2normHU(x)
return x
def data_prep_function(data, pid, 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)
bins, original_borders = rescale_params_hist_eq[pid]
x = data_transforms.apply_hist_eq_patch(x, bins, original_borders)
x = data_transforms.hu2normHU(x)
return x
}
for p in blob_files:
pid = utils_lung.extract_pid_filename(p, '.pkl')
blobs = utils.load_pkl(p)
blobs = np.asarray(sorted(blobs, key=lambda x: x[-1], reverse=True))
img, pixel_spacing = utils_lung.read_dicom_scan(pathfinder.DATA_PATH +
'/' + pid)
print pid
for blob in blobs[:10]:
patch_center = blob[:3]
p1 = blob[-1]
print p1
x, _ = data_transforms.transform_patch3d(data=img,
luna_annotations=None,
patch_center=patch_center,
p_transform=p_transform,
pixel_spacing=pixel_spacing,
luna_origin=None,
world_coord_system=False)
plot_slice_3d_3(input=x,
mask=x,
prediction=x,
axis=0,
pid='-'.join([str(pid), str(p1)]),
img_dir=outputs_img_path,
idx=np.array(x[0, 0].shape) / 2)
# print 'saved'
blob_files = sorted(glob.glob(outputs_path + '/*.pkl'))
p_transform = {'patch_size': (64, 64, 64),
'mm_patch_size': (64, 64, 64),
'pixel_spacing': (1., 1., 1.)
}
for p in blob_files:
pid = utils_lung.extract_pid_filename(p, '.pkl')
blobs = utils.load_pkl(p)
blobs = np.asarray(sorted(blobs, key=lambda x: x[-1], reverse=True))
img, pixel_spacing = utils_lung.read_dicom_scan(pathfinder.DATA_PATH + '/' + pid)
print pid
for blob in blobs[:10]:
patch_center = blob[:3]
p1 = blob[-1]
print p1
x, _ = data_transforms.transform_patch3d(data=img,
luna_annotations=None,
patch_center=patch_center,
p_transform=p_transform,
pixel_spacing=pixel_spacing,
luna_origin=None,
world_coord_system=False)
plot_slice_3d_3(input=x, mask=x, prediction=x,
axis=0, pid='-'.join([str(pid), str(p1)]),
img_dir=outputs_img_path, idx=np.array(x[0, 0].shape) / 2)
# print 'saved'
