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 save_preproc_images(self, output_dir, preproc_data, preproc_cfg, out_dtype='uint16'):
"""
Save (pre-processed) images from a data array to image files.
@param output_dir :: where results are being saved, including the pre-proc images/slices
@param preproc_data :: data volume with pre-processed images
@param preproc_cfg :: pre-processing configuration set up for a reconstruction
@param out_dtype :: dtype used for the pixel type/depth in the output image files
"""
print " * Pre-processed images (preproc_data) dtype:", preproc_data.dtype
min_pix = np.amin(preproc_data)
max_pix = np.amax(preproc_data)
print " with min_pix: {0}, max_pix: {1}".format(min_pix, max_pix)
if preproc_cfg.save_preproc_imgs:
preproc_dir = os.path.join(output_dir, self._PREPROC_IMGS_SUBDIR_NAME)
print "* Saving pre-processed images into: {0}".format(preproc_dir)
tomoio.make_dirs_if_needed(preproc_dir)
for idx in range(0, preproc_data.shape[0]):
# rescale_intensity has issues with float64=>int16
tomoio.write_image(preproc_data[idx, :, :], min_pix, max_pix,
os.path.join(preproc_dir, 'out_preproc_proj_image' + str(idx).zfill(6)),
img_format=preproc_cfg.out_img_format, dtype=out_dtype)
else:
print "* NOTE: not saving pre-processed images..."
