def extract_time_and_grid_information(root_name, settings, queue_com, name):
"""
Extract the time and grid information from the micrograph names.
Arguments:
root_name - Name to extract information from.
settings - TranSPHIRE settings.
queue_com - Queue for communication.
name - Name of the process.
Returns:
hole_number, spot1_number, spot2_number, date, time
"""
message = None
if settings['Input']['Software'] == 'Just Stack':
hole = 0
grid_number = 0
spot1 = 0
spot2 = 0
date = 0
time = 0
elif settings['Input']['Software'] == 'Latitude S':
if settings['Input']['Camera'] in ('Falcon2', 'Falcon3'):
message = '\n'.join([
'Falcon2/Falcon3 is not supported for Software {0}.'.format(
settings['Input']['Software']),
'Please contact the TranSPHIRE authors!'
])
elif settings['Input']['Camera'] in ('K2', 'K3'):
search_results = re.search(
r'(?P<date>\d{8})_(?P<project>.*)_A(?P<atlas>\d{3,})_G(?P<grid>\d{3,})_H(?P<hole>\d{3,})_D(?P<spot>\d{3,})',
root_name)
grid_number = '{0}_{1}'.format(search_results.group('atlas'),
search_results.group('grid'))
hole = search_results.group('hole')
spot1 = search_results.group('spot')
spot2 = ''
date = search_results.group('date')
with open('{0}.gtg'.format(root_name), 'rb') as read:
reader = DigitalMicrographReader(read)
reader.parse_file()
time = datetime.datetime.strptime(
reader.tags_dict['DataBar']['Acquisition Time'],
'%I:%M:%S %p').strftime('%H%M%S')
else:
message = '\n'.join([
'Camera {0} for Software {1} not known!'.format(
settings['Input']['Camera'],
settings['Input']['Software']),
'Please contact the TranSPHIRE authors!'
])
elif settings['Input']['Software'] == 'EPU >=1.8':
if settings['Input']['Camera'] == 'Falcon2' \
or settings['Input']['Camera'] == 'Falcon3' \
or settings['Input']['Camera'] in ('K2', 'K3'):
*skip, grid, skip, old_file = \
os.path.realpath(root_name).split('/')
grid_number = grid.split('_')[1]
*skip, hole, skip, spot1, spot2, date, time = old_file.split('_')
del skip
else:
message = '\n'.join([
'Camera {0} for Software {1} not known!'.format(
settings['Input']['Camera'],
settings['Input']['Software']),
'Please contact the TranSPHIRE authors!'
])
elif settings['Input']['Software'] == 'EPU >=1.9':
if settings['Input']['Camera'] == 'Falcon2' \
or settings['Input']['Camera'] == 'Falcon3' \
or settings['Input']['Camera'] in ('K2', 'K3'):
*skip, grid, skip, old_file = \
os.path.realpath(root_name).split('/')
grid_number = grid.split('_')[1]
*skip, hole, skip, spot1, spot2, date, time = old_file.split('_')
del skip
elif settings['Input']['Camera'] in ('K2', 'K3'):
*skip, grid, skip, old_file = \
os.path.realpath(root_name).split('/')
grid_number = grid.split('_')[1]
*skip, hole, skip, spot1, spot2, date, time = old_file.split('_')
del skip
else:
message = '\n'.join([
'Camera {0} for Software {1} not known!'.format(
settings['Input']['Camera'],
settings['Input']['Software']),
'Please contact the TranSPHIRE authors!'
])
else:
message = '\n'.join([
'Software {0} not known!'.format(settings['Input']['Software']),
'Please contact the TranSPHIRE authors!'
])
if message is None:
pass
else:
queue_com['error'].put(message, name)
raise IOError(message)
return hole, grid_number, spot1, spot2, date, time
def _load_file(self, fname):
with open(fname, "rb") as f:
dm = DigitalMicrographReader(f)
dm.parse_file()
self.imdict = dm.get_image_dictionaries()
return [ImageObject(imdict, fname) for imdict in self.imdict]
def _load_file(self, fname):
with open(fname, "rb") as f:
dm = DigitalMicrographReader(f)
dm.parse_file()
self.imdict = dm.get_image_dictionaries()
return [ImageObject(imdict, fname) for imdict in self.imdict]