def build_universal_config(config_dir):
"""
Build uni_config.yaml in the config_dir
:param config_dir: directory where exp_description.yaml
:raise:
"""
config_yaml_filename = os.path.join(config_dir,'exp_description.yaml')
res=yamlutils.read_yaml(config_yaml_filename)[0]
# pprint(res)
if not 'frames' in res:
logging.error(str.format('Section FRAMES not found in config file {0}',config_yaml_filename))
raise AttributeError
uc = UniversalConfigBuilder()
#TODO: fix this hack
uc.add_section({'preprocess_config': res['preprocess_config']})
uc.add_section({'description': res['description']})
groups = get_groups(res['frames'])
start_data_angle=0
for group_name in natsorted(groups.keys()):
group = groups[group_name]
files,start_data_angle = get_files_in_group(group, root=config_dir, start_data_angle=start_data_angle)
for f in files:
uc.add_frame(group_name=group_name, frame_type=f['type'], file_name=f['name'],
image_format=f['image_format'], angle=f['angle'], exposure_time=f['exposure_time'],
rotation_angle=f['rotation_angle'])
uc.save2yaml(os.path.join(config_dir,'uni_config.yaml'))
def build_universal_config(config_dir):
"""
Build uni_config.yaml in the config_dir
:param config_dir: directory where exp_description.yaml
:raise:
"""
config_yaml_filename = os.path.join(config_dir,'exp_description.yaml')
res=yamlutils.read_yaml(config_yaml_filename)[0]
# pprint(res)
if not 'frames' in res:
logging.error(str.format('Section FRAMES not found in config file {0}',config_yaml_filename))
raise AttributeError
uc = UniversalConfigBuilder()
#TODO: fix this hack
uc.add_section({'preprocess_config': res['preprocess_config']})
uc.add_section({'description': res['description']})
files=get_files(config_dir)
for f in files:
uc.add_frame(group_name='0', frame_type=f['type'], file_name=f['name'],
image_format=f['image_format'], angle=f['angle'], exposure_time=f['exposure_time'],
rotation_angle=0)
#add dark type by value
if 'dark_value' in res['frames']:
uc.add_frame(group_name='0', frame_type='dark', file_name=res['frames']['dark_value'],
image_format='number', angle=0, exposure_time=1, rotation_angle=0)
uc.save2yaml(os.path.join(config_dir,'uni_config.yaml'))
def build_universal_config(config_dir):
"""
Build uni_config.yaml in the config_dir
:param config_dir: directory where exp_description.yaml
:raise:
"""
config_yaml_filename = os.path.join(config_dir,'exp_description.yaml')
res=yamlutils.read_yaml(config_yaml_filename)[0]
# pprint(res)
if not 'frames' in res:
logging.error(str.format('Section FRAMES not found in config file {0}',config_yaml_filename))
raise AttributeError
uc = UniversalConfigBuilder()
#TODO: fix this hack
uc.add_section({'preprocess_config': res['preprocess_config']})
uc.add_section({'description': res['description']})
data_dir=os.path.join(config_dir,'Data')
files=glob.glob(os.path.join(data_dir,'*.tif'))
for f_path in sorted(files):
fname=os.path.split(f_path)[-1]
f_prefix=fname.split('.')[0]
if f_prefix=='eb':
uc.add_frame(group_name='0',frame_type='empty',file_name=f_path,image_format='tiff',angle=0)
elif f_prefix=='dc':
uc.add_frame(group_name='0',frame_type='dark',file_name=f_path,image_format='tiff',angle=0)
else:
angle=float(f_prefix.replace(',','.'))
uc.add_frame(group_name='0',frame_type='data',file_name=f_path,image_format='tiff',angle=angle)
uc.save2yaml(os.path.join(config_dir,'uni_config.yaml'))
def get_profile_name(data_root):
"""
Get profile name from **exp_description.yaml** file
:param data_root:
:return:
"""
config_yaml_filename=os.path.join(data_root,'exp_description.yaml')
config=read_yaml(config_yaml_filename)[0]
tomo_profile=config['profile']
return tomo_profile
def preprocess_and_save_all_data(data_root, res_folder, tomo_profile=None):
"""
Preprocess all data (build universal config, normalize, shift, rotate, save to hdf5)
:param data_root:
:param res_folder:
:param tomo_profile:
:return:
:raise:
"""
if tomo_profile is None:
tomo_profile = get_profile_name(data_root)
if tomo_profile == 'amur':
from tomofrontend.profiles.amur_config import build_universal_config
elif tomo_profile == 'senin':
from tomofrontend.profiles.senin_config import build_universal_config
elif tomo_profile == 'mediana':
from tomofrontend.profiles.mediana_config import build_universal_config
else:
raise NameError, str.format('Unknown profile type {0}', tomo_profile)
build_universal_config(data_root)
config = read_yaml(os.path.join(data_root, 'uni_config.yaml'))[0]
image_process_config = config['preprocess_config']
frames_groups = config['frames']
normalized_data = get_normalized_frames(frames_groups, image_process_config)
op_ind = get_index_opposite_files(normalized_data)
data0 = normalized_data[op_ind[0]]['data']
data1 = numpy.fliplr(normalized_data[op_ind[1]]['data'])
data0 = my_filter(data0)
data1 = my_filter(data1)
sh_ang = find_shift_and_rotation(data0, data1, image_process_config, res_folder)
shift_val = sh_ang['shift']
angle_val = sh_ang['angle']
pixel_size = image_process_config['pixel_size']
fix_axis_position(angle_val, shift_val, normalized_data, pixel_size)
h5_postprocess_file = os.path.join(res_folder, 'postproc_data.h5')
save_frames_hdf5(normalized_data, h5_postprocess_file)
return h5_postprocess_file
def get_files(config_dir):
tomo_log=yamlutils.read_yaml(os.path.join(config_dir,'log.txt'))[0]
files=[]
data_files=tomo_log['---Data']
frames_folder='Data'
for f in data_files:
tmp_frame = get_frame(config_dir, f, frames_folder,'data')
files.append(tmp_frame)
empty_files=tomo_log['---Empty']
frames_folder='Background'
for f in empty_files:
tmp_frame = get_frame(config_dir, f, frames_folder,'empty')
files.append(tmp_frame)
return files
def test_yaml_reader():
test_yaml_filename = '/media/WD_ext4/bones/ikran/2012_02_02/F1-M2/exp_description.yaml'
res=yamlutils.read_yaml(test_yaml_filename)
pprint(list(res))
def load_tomo_config(self):
tomo_dir=self.get_full_path()
tomo_config = os.path.join(tomo_dir, 'original', 'exp_description.yaml')
self['config']=read_yaml(tomo_config)[0]