def main(args):
"""Iterate over the folders:
- check that the folder is valid
- check if the file exists (overwrite if the
--overwrite option was specified)
- analyse the header to save the parameters in the attributes of the
hdf5 dataset
- write the data as an hdf5 dataset
- remove the folder (unless --keep is true)
"""
output_names = []
for folder_name in args.folder:
if not os.path.isdir(folder_name):
print("make_hdf5.py: not a folder:", folder_name)
continue
print("make_hdf5.py: converting", folder_name)
files = glob(os.path.join(folder_name, "*.raw"))
output_name = os.path.normpath(folder_name) + ".hdf5"
output_names.append(output_name)
if not os.path.exists(output_name) or args.overwrite:
output_file = h5py.File(output_name, 'w')
else:
print()
print("""make_hdf5.py: file {0} exists.
Run with the --overwrite (-o) flag
if you want to overwrite it.""".format(output_name))
print(progress_bar(1))
print()
continue
group = output_file.create_group("raw_images")
n_files = len(files)
for i, input_file_name in enumerate(files):
print(progress_bar((i + 1) / n_files), end="\r")
(_, exposure_time, min_x, max_x, min_y,
max_y) = analyse_header(input_file_name)
image_name = os.path.splitext(os.path.basename(input_file_name))[0]
image = read_data(input_file_name)
dataset = group.create_dataset(image_name, data=image)
dataset.attrs['exposure_time'] = exposure_time
dataset.attrs['min_x'] = min_x
dataset.attrs['min_y'] = min_y
dataset.attrs['max_x'] = max_x
dataset.attrs['max_y'] = max_y
if not args.keep:
print("make_hdf5.py: removing", folder_name)
shutil.rmtree(folder_name)
output_file.close()
print()
print("make_hdf5.py: written", output_name)
print("make_hdf5.py: done!")
return output_names
def dont_start(self):
"""Hook for doing some operation when no calculation has to be
performed.
"""
print("base_analyser: result already saved in file.")
print(progress_bar(1))
def calculate_images(self):
"""Calculate the three signals from the phase stepping curves and
the flat parameters with the get_signals utility function.
"""
if not self.exists_in_file:
images = get_signals(self.images, self.flat_parameters,
self.n_periods)
(self.absorption_image, self.differential_phase_image,
self.dark_field_image) = images
else:
print("dpc_radiography: result already saved in file.")
print(progress_bar(1))
def analyse_histogram(self, i, hist):
"""base version just prints the progress bar advancement for
the index i"""
print(progress_bar((i + 1) / self.n_images), end='')
def dont_start(self):
print("projection_stack: result already saved in file.")
print(progress_bar(1))