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'))