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