def testGetVolumeField(self):
import numpy
cmd.load(self.datafile('emd_1155.ccp4'), 'map1')
fieldcopy = cmd.get_volume_field('map1')
field = cmd.get_volume_field('map1', copy=0)
self.assertEqual(field.shape, (141, 91, 281))
self.assertTrue(numpy.allclose(field, fieldcopy))
# data manipulation with copy=0
mean1 = field.mean()
field += 5.0
mean2 = cmd.get_volume_field('map1', copy=0)[:].mean()
self.assertAlmostEqual(mean1 + 5.0, mean2, delta=1e-2)
def testLoad_cube(self):
cmd.load(self.datafile('h2o-elf.cube'))
extent = cmd.get_extent('h2o-elf')
self.assertArrayEqual(
extent, [[-0.075, -0.075, -0.075], [5.925, 5.925, 5.925]],
delta=1e3)
field = cmd.get_volume_field('h2o-elf', copy=0)
self.assertEqual(field.shape, (40, 40, 40))
self.assertAlmostEqual(field.mean(), 0.06915, delta=1e-4)
def testLoad_cube(self):
cmd.load(self.datafile('h2o-elf.cube'))
extent = cmd.get_extent('h2o-elf')
self.assertArrayEqual(extent, [
[ -0.075, -0.075, -0.075],
[ 5.925, 5.925, 5.925]], delta=1e3)
field = cmd.get_volume_field('h2o-elf', copy=0)
self.assertEqual(field.shape, (40, 40, 40))
self.assertAlmostEqual(field.mean(), 0.06915, delta=1e-4)
def testLoad_map(self, ext, check_extent):
filename = self.datafile('emd_1155' + ext)
if not os.path.exists(filename):
self.skipTest("missing " + filename)
cmd.load(filename, 'map1')
field = cmd.get_volume_field('map1', copy=0)
self.assertEqual(field.shape, (141, 91, 281))
if check_extent:
extent = cmd.get_extent('map1')
self.assertArrayEqual(extent, [[0.0, 0.0, 0.0], [2296.0, 1476.0, 4592.0]], delta=1e-2)
def set_isoslider(self, mrc, setvalue=True):
self.grid = cmd.get_volume_field(mrc)
isomin = self.grid.min()
isomax = self.grid.max()
self.form.label_isomin.setText('%.4f' % isomin)
self.form.label_isomax.setText('%.4f' % isomax)
self.form.isoslider.setMinimum(self.iso_to_slider(isomin))
self.form.isoslider.setMaximum(self.iso_to_slider(isomax))
self.form.isoslider.setTickInterval(1)
if setvalue:
self.form.isoslider.setValue(
self.iso_to_slider(isomin + (isomax - isomin) / 2.))
self.form.isoval_edit.setText(str(self.isoslider_value))
def testLoad_map(self, ext, check_extent):
filename = self.datafile('emd_1155' + ext)
if not os.path.exists(filename):
self.skipTest("missing " + filename)
cmd.load(filename, 'map1')
field = cmd.get_volume_field('map1', copy=0)
self.assertEqual(field.shape, (141, 91, 281))
if check_extent:
extent = cmd.get_extent('map1')
self.assertArrayEqual(extent,
[[0.0, 0.0, 0.0], [2296.0, 1476.0, 4592.0]],
delta=1e-2)
def testCopyMap(self):
cmd.load(self.datafile('emd_1155.ccp4'), 'map1')
cmd.copy('map2', 'map1')
self.assertEqual(cmd.get_symmetry('map1'), cmd.get_symmetry('map2'))
self.assertArrayEqual(cmd.get_volume_field('map1'), cmd.get_volume_field('map2'))