def test_initialize(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = self._get_valid_args_for_constructor()
subdir = os.path.join(temp_dir, 'foo')
theargs.outputdirectory = subdir
theargs.numrotations = ''
theargs.rotationangles = '45,90,135'
ts = TiltSeriesCreator(theargs)
ts.initialize()
self.assertTrue(os.path.isdir(subdir))
self.assertTrue(os.getcwd().endswith('foo'))
self.assertEqual(ts._rotationangles, [0.0, 45.0, 90.0, 135.0])
finally:
shutil.rmtree(temp_dir)
def test_get_methods(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = self._get_valid_args_for_constructor()
subdir = os.path.join(temp_dir, 'foo')
theargs.outputdirectory = subdir
theargs.numrotations = '4'
ts = TiltSeriesCreator(theargs)
ts._workdir = temp_dir
self.assertEqual(ts._get_warpz_dir(),
os.path.join(temp_dir,
TiltSeriesCreator.WARPZ_DIR_NAME))
self.assertEqual(ts._get_marker_dir(),
os.path.join(temp_dir,
TiltSeriesCreator.MARKER_DIR_NAME))
self.assertEqual(ts._get_projection_dir(),
os.path.join(temp_dir,
TiltSeriesCreator.
PROJECTION_DIR_NAME))
self.assertEqual(ts._get_tracking_dir(),
os.path.join(temp_dir,
TiltSeriesCreator.TRACKING_DIR_NAME))
self.assertEqual(ts._get_result_dir(),
os.path.join(subdir,
TiltSeriesCreator.RESULT_DIR_NAME))
finally:
shutil.rmtree(temp_dir)
def create_tiltseries(theargs):
"""Rotates 3DMarkers.txt file
"""
logger.info('Creating tilt series')
if theargs.cores is None:
try:
cpucount = multiprocessing.cpu_count()
except NotImplementedError:
logger.exception('Unable to obtain cpu count from '
'multiprocessing.cpu_count() defaulting to 1')
cpucount = 1
theargs.cores = cpucount
logger.debug('Cores to use set to ' + str(theargs.cores))
ts = TiltSeriesCreator(theargs)
ts.initialize()
ts.prepare_mrc_for_tiltseries_generation()
ts.create_tiltseries()