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 get_normalized_frames(frames_groups, image_process_config):
"""
Build normalized frames from groups of frames.
:param frames_groups:
:param image_process_config:
:return:
"""
normalized_data = []
for group_name in natsorted(frames_groups.keys()):
cur_group = frames_groups[group_name]
frames_by_type = build_grouped_by(cur_group, 'frame_type')
data_frames_by_angle = build_grouped_by(frames_by_type['data'], 'angle')
dark_frames_by_angle = build_grouped_by(frames_by_type['dark'], 'angle')
empty_frames_by_angle = build_grouped_by(frames_by_type['empty'], 'angle')
mean_dark_frame = get_mean_prepoces_frame(dark_frames_by_angle[dark_frames_by_angle.keys()[0]],
image_process_config)
mean_empty_frame = get_mean_prepoces_frame(empty_frames_by_angle[empty_frames_by_angle.keys()[0]],
image_process_config,dark_frame=mean_dark_frame)
for df_angle in data_frames_by_angle:
normalized_data.append(normalize_data_frames(data_frames_by_angle[df_angle],
mean_empty_frame, mean_dark_frame, image_process_config))
# pylab.figure()
# pylab.imshow(normalized_data[-1]['data'])
# pylab.colorbar()
# pylab.show()
return normalized_data
def get_files_in_group(group,root='.',start_data_angle=0):
"""
Get files in each group.
:param group:
:param root:
:param start_data_angle:
:return:
"""
files=[]
stop_data_angle=start_data_angle
for type_key in ['dark','data','empty']:
if type_key in group:
if 'filesnames' in group[type_key]:
if 'regexp' in group[type_key]['filesnames']:
cur_root=root
fname_pattern=group[type_key]['filesnames']['regexp']
if 'folder' in group:
cur_root=os.path.join(cur_root,group['folder'])
delta_angle=get_value(group,[type_key,],'angles_step')
exp_time=get_value(group,[type_key,],'exposure_time')
rotation_angle=get_value(group,[type_key,],'rotation_angle')
image_format=try_get_value(group,[type_key,],'image_format','fits')
frames_per_angle=try_get_value(group,[type_key,],'frames_per_angle',1)
tmp_files_names_list=glob.glob(os.path.join(cur_root,fname_pattern))
tmp_files_names_list=natsorted(tmp_files_names_list)
tmp_files_list=[]
for ef,f in enumerate(tmp_files_names_list):
if type_key=='data':
angle=start_data_angle+delta_angle*((ef-ef%frames_per_angle)/frames_per_angle)
stop_data_angle=start_data_angle+delta_angle*(((ef+1)-(ef+1)%frames_per_angle)/frames_per_angle)
else:
angle=0
td= {'name': f, 'angle': angle, 'exposure_time': exp_time, 'type': type_key,
'rotation_angle': rotation_angle, 'image_format': image_format}
tmp_files_list.append(td)
files.extend(tmp_files_list)
return files, stop_data_angle
def test_natsort(self):
self.assertEqual(natsort.natsorted(input_list), ref_list)
def get_files_list(self, file_pattern):
file_list=glob.glob(os.path.join(self.get_full_path(),file_pattern))
full_path=self.get_full_path()
file_list=[x[len(full_path)+1:] for x in file_list if x.find(full_path)==0 if os.path.isfile(x)]
return natsorted(file_list)
