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'