def test_read_surface_and_save_as_stack(self): img = ImageStack(filename='', load=False) img.data = np.zeros([10, 100, 100]) img.data[2:7, 10:-10, 10:-10] = 1 voxel_size = [4, 0.3824, 0.3824] img.extract_surfaces('data/test_data/surfaces/', voxel_size=voxel_size, reconstruct=False) surf = Surface(filename='data/test_data/surfaces/_Cell00001.csv') for coord in ['x', 'y', 'z']: self.assertIsNotNone(surf.__dict__[coord]) surf.save_as_stack(filename='data/test_data/stack.tif', voxel_size=0.5) self.assertEqual(os.path.exists('data/test_data/stack.tif'), True) self.assertEqual(os.path.exists('data/test_data/stack.txt'), True) shutil.rmtree('data/test_data/')
def convert_to_tiff(**kwargs): """ Save the surface as a 3D image stack. Keyword arguments ----------------- *inputfolder* : str Directory with the input surface. *item* : str File name of the input surface. *outputfolder* : str Directory to save the output 3D stack. """ inputfolder = kwargs.get('inputfolder') outputfolder = kwargs.get('outputfolder', inputfolder + '../stacks/') filename = kwargs.get('item') surface = Surface(filename=inputfolder + filename, **kwargs) surface.save_as_stack(outputfolder + filename + '.tif', voxel_size=kwargs.get('voxel_size'))