def createOutputStep(self):
imgSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
partSet.copyInfo(imgSet)
outImagesMd = self._getExtraPath('expanded_particles.star')
# remove repeating rlnImageId column
tableName = ''
if Plugin.IS_GT30():
tableName = 'particles'
mdOptics = Table(fileName=outImagesMd, tableName='optics')
mdOut = Table(fileName=outImagesMd, tableName=tableName)
mdOut.removeColumns("rlnImageId")
with open(outImagesMd, "w") as f:
mdOut.writeStar(f, tableName=tableName)
if Plugin.IS_GT30():
mdOptics.writeStar(f, tableName='optics')
reader = convert.createReader()
reader.readSetOfParticles(
outImagesMd, partSet,
alignType=ALIGN_PROJ,
postprocessImageRow=self._postprocessImageRow)
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(imgSet, partSet)
def test_removeColumns(self):
print("Checking removeColumns...")
dataFile = testfile('star', 'refine3d', 'run_it016_data.star')
table = Table(fileName=dataFile, tableName='particles')
expectedCols = [
'rlnCoordinateX',
'rlnCoordinateY',
'rlnAutopickFigureOfMerit',
'rlnClassNumber',
'rlnAnglePsi',
'rlnImageName',
'rlnMicrographName',
'rlnOpticsGroup',
'rlnCtfMaxResolution',
'rlnCtfFigureOfMerit',
'rlnDefocusU',
'rlnDefocusV',
'rlnDefocusAngle',
'rlnCtfBfactor',
'rlnCtfScalefactor',
'rlnPhaseShift',
'rlnGroupNumber',
'rlnAngleRot',
'rlnAngleTilt',
'rlnOriginXAngst',
'rlnOriginYAngst',
'rlnNormCorrection',
'rlnLogLikeliContribution',
'rlnMaxValueProbDistribution',
'rlnNrOfSignificantSamples',
'rlnRandomSubset'
]
colsToRemove = [
'rlnOriginXAngst',
'rlnOriginYAngst',
'rlnNormCorrection',
'rlnAnglePsi',
'rlnMaxValueProbDistribution'
]
# Check all columns were read properly
self.assertEqual(expectedCols, table.getColumnNames())
# Check also using hasAllColumns method
self.assertTrue(table.hasAllColumns(expectedCols))
table.removeColumns(colsToRemove)
self.assertEqual([c for c in expectedCols if c not in colsToRemove],
table.getColumnNames())
# Check also using hasAnyColumn method
self.assertFalse(table.hasAnyColumn(colsToRemove))
