def test_recon_fails_ok(self):
import IMAT.tomorec.reconstruction_command as cmd
cmd = cmd.ReconstructionCommand()
with self.assertRaises(ValueError):
cmd.do_recon('', cmd_line='')
import IMAT.tomorec.configs as cfgs
pre_conf = cfgs.PreProcConfig()
alg_conf = cfgs.ToolAlgorithmConfig()
post_conf = cfgs.PostProcConfig()
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
with self.assertRaises(ValueError):
cmd.do_recon(conf, cmd_line='irrelevant')
pre_conf.input_dir = self.test_input_dir
import IMAT.tomorec.io as tomoio
tomoio.make_dirs_if_needed(self.test_input_dir)
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
with self.assertRaises(ValueError):
cmd.do_recon(conf, cmd_line='irrelevant')
post_conf.output_dir = self.test_output_dir
tomoio.make_dirs_if_needed(self.test_output_dir)
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
# should fail because no images found in input dir
with self.assertRaises(RuntimeError):
cmd.do_recon(conf, cmd_line='irrelevant')
import os
self.assertTrue(os.path.exists(self.test_input_dir))
self.assertTrue(os.path.exists(os.path.join(self.test_output_dir,
'0.README_reconstruction.txt')))
self.assertTrue(os.path.exists(self.test_output_dir))
def test_normalize_flat_raises(self):
import IMAT.tomorec.reconstruction_command as cmd
cmd = cmd.ReconstructionCommand()
import IMAT.tomorec.configs as cfgs
pre_conf = cfgs.PreProcConfig()
alg_conf = cfgs.ToolAlgorithmConfig()
post_conf = cfgs.PostProcConfig()
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
# absolutely invalid data
with self.assertRaises(ValueError):
cmd.normalize_flat_dark([], pre_conf, np.ones((10, 23)), None)
# wrong data dimensions
with self.assertRaises(ValueError):
cmd.normalize_flat_dark(np.ones((3, 2)), pre_conf, np.ones((10, 23)), None)
# wrong dimensions of the flat image
with self.assertRaises(ValueError):
cmd.normalize_flat_dark(self.data_vol, pre_conf, np.ones((10, 23)), None)
# invalid configurations
with self.assertRaises(ValueError):
cmd.normalize_flat_dark(self.data_vol, alg_conf, None, None)
with self.assertRaises(ValueError):
cmd.normalize_flat_dark(self.data_vol, post_conf, None, None)
with self.assertRaises(ValueError):
cmd.normalize_flat_dark(self.data_vol, conf, None, None)
def __init__(self):
self._PREPROC_IMGS_SUBDIR_NAME = 'preproc_images'
self._OUT_README_FNAME = '0.README_reconstruction.txt'
self._OUT_SLICES_FILENAME_PREFIX='out_recon_slice'
self._OUT_HORIZ_SLICES_SUBDIR='out_recon_horiz_slice'
self.preproc_cfg = tomocfg.PreProcConfig()
self.alg_cfg = tomocfg.ToolAlgorithmConfig
self.postproc_cfg = tomocfg.PostProcConfig()
def test_config_post(self):
"""
Basic consistency check of the post-processing config and some default
values
"""
import IMAT.tomorec.configs as cfgs
post = cfgs.PostProcConfig()
self.assertEquals(post.output_dir, None)
self.assertEquals(post.circular_mask, 0.94)
def test_config_all(self):
"""
Basic consistency check of the tomographic reconstruction config and some
default values
"""
import IMAT.tomorec.configs as cfgs
pre_conf = cfgs.PreProcConfig()
alg_conf = cfgs.ToolAlgorithmConfig()
post_conf = cfgs.PostProcConfig()
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
self.assertEquals(conf.preproc_cfg, pre_conf)
self.assertEquals(conf.alg_cfg, alg_conf)
self.assertEquals(conf.postproc_cfg, post_conf)
print conf
def test_normalize_air_raises(self):
import IMAT.tomorec.reconstruction_command as cmd
cmd = cmd.ReconstructionCommand()
import IMAT.tomorec.configs as cfgs
pre_conf = cfgs.PreProcConfig()
alg_conf = cfgs.ToolAlgorithmConfig()
post_conf = cfgs.PostProcConfig()
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
normalized = cmd.normalize_air_region(self.data_vol, pre_conf)
np.testing.assert_allclose(normalized, self.data_vol,
err_msg="Epected normalized data volume not to changed")
# absolutely invalid data
with self.assertRaises(ValueError):
cmd.normalize_air_region([], pre_conf)
# wrong data dimensions
with self.assertRaises(ValueError):
cmd.normalize_air_region(np.ones((3, 2)), pre_conf)
# invalid configurations
with self.assertRaises(ValueError):
cmd.normalize_air_region(self.data_vol, alg_conf)
with self.assertRaises(ValueError):
cmd.normalize_air_region(self.data_vol, post_conf)
with self.assertRaises(ValueError):
cmd.normalize_air_region(self.data_vol, conf)
# wrong air-regions
pre_conf.normalize_air_region = [3]
with self.assertRaises(ValueError):
cmd.normalize_air_region(self.data_vol, pre_conf)
pre_conf.normalize_air_region = (3, 0, 100, 10)
with self.assertRaises(ValueError):
cmd.normalize_air_region(self.data_vol, pre_conf)
pre_conf.normalize_air_region = [3, 0, 100]
with self.assertRaises(ValueError):
cmd.normalize_air_region(self.data_vol, pre_conf)
def grab_postproc_options(args):
"""
Get post-processing (on the reconstructed volume) options from the command line
(through an argument parser)
@param parser :: arguments parsed already, set up with post-processing options
Returns:: a post-processing object set up according to the user inputs in the command line
"""
config = tomocfg.PostProcConfig()
config.output_dir = args.output_path
if args.circular_mask:
config.circular_mask = float(args.circular_mask)
if args.cut_off:
config.cut_off_level = float(args.cut_off)
if args.out_median_filter:
config.median_filter_size = float(args.out_median_filter)
return config
def test_rotate_raises(self):
import IMAT.tomorec.reconstruction_command as cmd
cmd = cmd.ReconstructionCommand()
import IMAT.tomorec.configs as cfgs
pre_conf = cfgs.PreProcConfig()
alg_conf = cfgs.ToolAlgorithmConfig()
post_conf = cfgs.PostProcConfig()
conf = cfgs.ReconstructionConfig(pre_conf, alg_conf, post_conf)
pre_conf.rotation = 1
# absolutely invalid data
with self.assertRaises(ValueError):
cmd.rotate_stack([], pre_conf)
# wrong data type or dimensions (for samples / flats / darks
with self.assertRaises(ValueError):
cmd.rotate_stack(np.ones((3, 2)), pre_conf)
with self.assertRaises(ValueError):
cmd.rotate_stack(self.data_vol, pre_conf, [1])
with self.assertRaises(ValueError):
cmd.rotate_stack(self.data_vol, pre_conf, None, np.zeros((3, 3)))
with self.assertRaises(ValueError):
cmd.rotate_stack(self.data_vol, pre_conf, None, [0, 1])
# invalid configurations
with self.assertRaises(ValueError):
cmd.rotate_stack(self.data_vol, None)
with self.assertRaises(ValueError):
cmd.rotate_stack(self.data_vol, [])
with self.assertRaises(ValueError):
cmd.rotate_stack(self.data_vol, conf)
