def test_full_reconstruction(self):
"""Check that a basic reconstruction completes and produces output tiff files."""
params = make_params()
params.reconstruction_type = 'full'
params.output_format = 'tiff_stack'
response = rec(params=params)
# import pdb; pdb.set_trace()
self.assertTrue(self.full_tiff_dir.exists())
def test_recon_output_dir(self):
"""Check that ``--reconstruction-type=try`` respects output
directory.
"""
params = make_params()
params.reconstruction_type = "try"
params.center_search_width = 10
params.output_folder = "{file_name_parent}/_rec"
params.parameter_file = os.devnull
response = rec(params=params)
self.assertTrue(self.output_dir.exists())
def test_extra_args_no_file(self):
"""Check for behavior if the file is or isn't present in the
extra_args yaml file.
"""
params = make_params()
params.reconstruction_type = "try"
params.center_search_width = 10
params.output_folder = "{file_name_parent}/_rec"
params.parameter_file = "/tmp/gweoiuwerw"
response = rec(params=params)
self.assertTrue(self.output_dir.exists())
def test_hdf_output(self):
params = make_params()
params.reconstruction_type = 'full'
params.output_format = "hdf5"
response = rec(params=params)
expected_hdf5path = self.output_hdf
# Check that tiffs are not saved and HDF5 file is saved
self.assertFalse(os.path.exists(self.full_tiff_dir))
self.assertTrue(os.path.exists(expected_hdf5path))
with h5py.File(expected_hdf5path, mode='r') as h5fp:
vol = h5fp['volume']
self.assertEqual(vol.shape, (64, 64, 64))
self.assertFalse(np.any(np.isnan(vol)))
def test_hdf_output_chunks(self):
# Test with multiple chunks to ensure they're all written
params = make_params()
params.reconstruction_type = 'full'
params.output_format = 'hdf5'
params.nsino_per_chunk = 16 # 4 chunks
response = rec(params=params)
expected_hdf5path = self.output_hdf
# Check that tiffs are not saved and HDF5 file is saved
self.assertFalse(os.path.exists(self.full_tiff_dir))
self.assertTrue(os.path.exists(expected_hdf5path))
with h5py.File(expected_hdf5path, mode='r') as h5fp:
vol = h5fp['volume']
self.assertEqual(vol.shape, (64, 64, 64))
self.assertFalse(np.any(np.isnan(vol)))
def run_rec(args):
log.warning('reconstruction start')
file_path = Path(args.file_name)
if str(args.file_format) in KNOWN_FORMATS:
if file_path.suffix == '.yaml':
# Load the list of files from a given YAML parameters file
log.info("Reconstructing files listed in: %s" % file_path)
file_list = file_io.yaml_file_list(file_path)
failed_files = []
for idx, this_fname in enumerate(file_list):
args.file_name = file_path.parent / this_fname
log.info("Reconstructing next file (%d/%d): %s",
idx, len(file_list), args.file_name)
try:
recon.rec(args)
except Exception as err:
# This file failed, but we can keep going and try the rest of the files
failed_files.append(this_fname)
# Log the exception and stacktrace
log.error(" *** reconstruction failed: %s", repr(err))
log_exception(log, err, fmt=" %s")
else:
config.update_config(args)
# Report list of failed files so it's not buried in the log
if len(failed_files) > 0:
log.error("Some tomograms could not be reconstructed: %s",
", ".join([str(f) for f in failed_files]))
elif file_path.is_file():
log.info("reconstructing a single file: %s" % args.file_name)
recon.rec(args)
config.update_config(args)
elif file_path.is_dir():
# Add a trailing slash if missing
top = os.path.join(args.file_name, '')
h5_file_list = list(filter(lambda x: x.endswith(('.h5', '.hdf', 'hdf5')), os.listdir(top)))
if (h5_file_list):
h5_file_list.sort()
log.info("found: %s" % h5_file_list)
index=0
for fname in h5_file_list:
args.file_name = top + fname
log.warning(" *** file %d/%d; %s" % (index, len(h5_file_list), fname))
index += 1
recon.rec(args)
config.update_config(args)
log.warning('reconstruction end')
else:
log.error("directory %s does not contain any file" % args.file_name)
else:
log.error("directory or File Name does not exist: %s" % args.file_name)
else:
# add here support for other file formats
log.error(" *** %s is not a supported file format" % args.file_format)
log.error("supported data formats are: %s, %s, %s, %s" % tuple(KNOWN_FORMATS))
def test_extra_args_no_rotation_axis(self):
"""Check for behavior if the file is or isn't present in the
extra_args yaml file.
"""
params = make_params()
params.reconstruction_type = "try"
params.center_search_width = 10
params.output_folder = "{file_name_parent}/_rec"
params.parameter_file = self.yaml_file
# Create the YAML file
opts = {
"test_tomogram.h5": {
"spam": "foo",
}
}
with open(self.yaml_file, mode='w') as fp:
fp.write(yaml.dump(opts))
response = rec(params=params)
self.assertTrue(self.output_dir.exists())
def test_slice_reconstruction(self):
"""Check that a basic reconstruction completes and produces output tiff files."""
params = make_params()
params.reconstruction_type = 'slice'
response = rec(params=params)
self.assertTrue(self.output_dir.exists())
def test_yaml_params(self):
params = make_params()
params.parameter_file = self.yaml_file
response = rec(params=params)
