def writeCoordsConfig(configFn, boxSize, state):
""" Write the config.xmd file needed for Xmipp picker.
Params:
configFn: The filename were to store the configuration.
boxSize: the box size in pixels for extraction.
state: picker state
"""
# Write config.xmd metadata
print("writeCoordsConfig: state=", state)
table = Table(columns=['particleSize', 'pickingState'])
table.addRow(int(boxSize), state)
table.write(configFn, tableName='properties')
def test_addColumns(self):
tmpOutput = '/tmp/sampling.star'
print("Checking addColumns to %s..." % tmpOutput)
dataFile = testfile('star', 'refine3d', 'run_it016_sampling.star')
table = Table(fileName=dataFile, tableName='sampling_directions')
expectedCols = ['rlnAngleRot',
'rlnAngleTilt',
'rlnAnglePsi',
'rlnExtraAngle1',
'rlnExtraAngle2',
'rlnAnotherConst'
]
self.assertEqual(expectedCols[:2], table.getColumnNames())
table.addColumns('rlnAnglePsi=0.0',
'rlnExtraAngle1=rlnAngleRot',
'rlnExtraAngle2=rlnExtraAngle1',
'rlnAnotherConst=1000')
self.assertEqual(expectedCols, table.getColumnNames())
# Check values
def _values(colName):
return table.getColumnValues(colName)
for v1, v2, v3 in zip(_values('rlnAngleRot'),
_values('rlnExtraAngle1'),
_values('rlnExtraAngle2')):
self.assertAlmostEqual(v1, v2)
self.assertAlmostEqual(v1, v3)
self.assertTrue(all(v == 1000 for v in _values('rlnAnotherConst')))
table.write(tmpOutput, tableName='sampling_directions')
