def test_setup_logging(self):
theargs = Parameters()
theargs.loglevel = 'DEBUG'
shift_fidfilemarkers._setup_logging(theargs)
self.assertEqual(shift_fidfilemarkers.logger.getEffectiveLevel(),
logging.DEBUG)
theargs.loglevel = 'INFO'
shift_fidfilemarkers._setup_logging(theargs)
self.assertEqual(shift_fidfilemarkers.logger.getEffectiveLevel(),
logging.INFO)
theargs.loglevel = 'WARNING'
shift_fidfilemarkers._setup_logging(theargs)
self.assertEqual(shift_fidfilemarkers.logger.getEffectiveLevel(),
logging.WARNING)
theargs.loglevel = 'ERROR'
shift_fidfilemarkers._setup_logging(theargs)
self.assertEqual(shift_fidfilemarkers.logger.getEffectiveLevel(),
logging.ERROR)
theargs.loglevel = 'CRITICAL'
shift_fidfilemarkers._setup_logging(theargs)
self.assertEqual(shift_fidfilemarkers.logger.getEffectiveLevel(),
logging.CRITICAL)
def test_rotate_markers_file_outfile_set_to_none(self):
temp_dir = tempfile.mkdtemp()
try:
markerfile = os.path.join(temp_dir, '3Dmarkers.txt')
markers = MarkersList()
markers.add_marker(1, 2, 3, 4)
markers.write_markers_to_file(markerfile)
theargs = Parameters()
theargs.outfile = None
theargs.angle = 90
theargs.width = 10
theargs.height = 10
theargs.markerfile = markerfile
rotate_3dmarkers.rotate_markers_file(theargs)
origfile = markerfile + '.orig'
self.assertTrue(os.path.isfile(origfile))
fac = MarkersFrom3DMarkersFileFactory(origfile)
markers = fac.get_markerslist()
m = markers.get_markers()[0]
self.assertEqual(m.get_index(), 1)
self.assertEqual(m.get_x(), 2)
self.assertEqual(m.get_y(), 3)
self.assertEqual(m.get_z(), 4)
self.assertTrue(os.path.isfile(markerfile))
fac = MarkersFrom3DMarkersFileFactory(markerfile)
markers = fac.get_markerslist()
m = markers.get_markers()[0]
self.assertEqual(m.get_index(), 1)
self.assertEqual(m.get_x(), 7)
self.assertEqual(m.get_y(), 2)
self.assertEqual(m.get_z(), 4)
finally:
shutil.rmtree(temp_dir)
def test_setup_logging(self):
theargs = Parameters()
theargs.loglevel = 'DEBUG'
create_tiltseries._setup_logging(theargs)
self.assertEqual(create_tiltseries.logger.getEffectiveLevel(),
logging.DEBUG)
theargs.loglevel = 'INFO'
create_tiltseries._setup_logging(theargs)
self.assertEqual(create_tiltseries.logger.getEffectiveLevel(),
logging.INFO)
theargs.loglevel = 'WARNING'
create_tiltseries._setup_logging(theargs)
self.assertEqual(create_tiltseries.logger.getEffectiveLevel(),
logging.WARNING)
theargs.loglevel = 'ERROR'
create_tiltseries._setup_logging(theargs)
self.assertEqual(create_tiltseries.logger.getEffectiveLevel(),
logging.ERROR)
theargs.loglevel = 'CRITICAL'
create_tiltseries._setup_logging(theargs)
self.assertEqual(create_tiltseries.logger.getEffectiveLevel(),
logging.CRITICAL)
def _get_valid_args_for_constructor(self):
theargs = Parameters()
theargs.outputdirectory = 'out'
theargs.inputmrcfile = 'input'
theargs.begintilt = '-60'
theargs.endtilt = '60'
theargs.tiltshift = '2'
theargs.cores = '1'
theargs.mpiexec = ''
theargs.nummarkers = '20'
theargs.bottommarkersize = '7'
theargs.topmarkersize = '9'
theargs.markernoise = '1'
theargs.aparam = '0.98'
theargs.markera = '0.2'
theargs.shrinkage = '1'
theargs.projmaxangle = '2'
theargs.numrotations = '2'
theargs.etspecbin = '/./foo'
theargs.rotationangles = ''
return theargs
