def readSetOfParticles(self, starFile, partSet, **kwargs):
""" Convert a star file into a set of particles.
Params:
starFile: the filename of the star file
partsSet: output particles set
Keyword Arguments:
blockName: The name of the data block (default particles)
alignType: alignment type
removeDisabled: Remove disabled items
"""
self._preprocessImageRow = kwargs.get('preprocessImageRow', None)
self._alignType = kwargs.get('alignType', ALIGN_NONE)
self._postprocessImageRow = kwargs.get('postprocessImageRow', None)
self._optics = OpticsGroups.fromStar(starFile)
self._pixelSize = getattr(self._optics.first(), 'rlnImagePixelSize',
1.0)
self._invPixelSize = 1. / self._pixelSize
partsReader = Table.Reader(starFile, tableName='particles')
firstRow = partsReader.getRow()
self._setClassId = hasattr(firstRow, 'rlnClassNumber')
self._setCtf = partsReader.hasAllColumns(self.CTF_LABELS[:3])
particle = Particle()
if self._setCtf:
particle.setCTF(CTFModel())
self._setAcq = kwargs.get("readAcquisition", True)
acq = Acquisition()
acq.setMagnification(kwargs.get('magnification', 10000))
extraLabels = kwargs.get('extraLabels', []) + PARTICLE_EXTRA_LABELS
self.createExtraLabels(particle, firstRow, extraLabels)
self._rowToPart(firstRow, particle)
partSet.setSamplingRate(self._pixelSize)
partSet.setAcquisition(acq)
self._optics.toImages(partSet)
partSet.append(particle)
for row in partsReader:
self._rowToPart(row, particle)
partSet.append(particle)
partSet.setHasCTF(self._setCtf)
partSet.setAlignment(self._alignType)
def test_iterRows(self):
print("Checking iterRows...")
dataFile = testfile('star', 'refine3d', 'run_it016_data.star')
table = Table(fileName=dataFile, tableName='particles')
# Let's open again the same file for iteration
with open(dataFile) as f:
tableReader = Table.Reader(f, tableName='particles')
for c1, c2 in zip(table.getColumns(), tableReader.getColumns()):
self.assertEqual(c1, c2, "Column c1 (%s) differs from c2 (%s)"
% (c1, c2))
for r1, r2 in zip(table, tableReader):
self.assertEqual(r1, r2)
# Now try directly with iterRows function
for r1, r2 in zip(table,
Table.iterRows(dataFile, tableName='particles')):
self.assertEqual(r1, r2)
defocusSorted = sorted(float(r.rlnDefocusU) for r in table)
for d1, row in zip(defocusSorted,
Table.iterRows(dataFile,
tableName='particles',
key=lambda r: r.rlnDefocusU)):
self.assertAlmostEqual(d1, row.rlnDefocusU)
# Test sorting by imageName column, also using getColumnValues and sort()
imageIds = table.getColumnValues('rlnImageName')
imageIds.sort()
# Check sorted iteration give the total amount of rows
rows = [r for r in Table.iterRows(dataFile,
tableName='particles',
key='rlnImageName')]
self.assertEqual(len(imageIds), len(rows))
for id1, row in zip(imageIds,
Table.iterRows(dataFile,
tableName='particles',
key='rlnImageName')):
self.assertEqual(id1, row.rlnImageName)
def getIter():
""" Test a function to get an iterator. """
return Table.iterRows(dataFile,
tableName='particles', key='rlnImageName')
iterByIds = getIter()
for id1, row in zip(imageIds, iterByIds):
self.assertEqual(id1, row.rlnImageName)
def test_readSetOfParticlesAfterCtf(self):
if not Plugin.IS_GT30():
print("Skipping test (required Relion > 3.1)")
return
starFile = self.ds.getFile(
"CtfRefine/job023/particles_ctf_refine.star")
partsReader = Table.Reader(starFile, tableName='particles')
firstRow = partsReader.getRow()
partsSet = self.__readParticles(starFile)
first = partsSet.getFirstItem()
ogLabels = ['rlnBeamTiltX', 'rlnBeamTiltY']
extraLabels = ['rlnCtfBfactor', 'rlnCtfScalefactor', 'rlnPhaseShift']
for l in extraLabels:
value = getattr(first, '_%s' % l)
self.assertIsNotNone(value, "Missing label: %s" % l)
self.assertAlmostEqual(getattr(firstRow, l), value)
fog = OpticsGroups.fromImages(partsSet).first()
self.assertTrue(all(hasattr(fog, l) for l in ogLabels))
# Also test writing and preserving extra labels
outputStar = self.getOutputPath('particles.star')
print(">>> Writing to particles star: %s" % outputStar)
starWriter = convert.createWriter()
starWriter.writeSetOfParticles(partsSet, outputStar)
fog = OpticsGroups.fromStar(outputStar).first()
self.assertTrue(all(hasattr(fog, l) for l in ogLabels))
partsReader = Table.Reader(outputStar, tableName='particles')
firstRow = partsReader.getRow()
for l in extraLabels:
value = getattr(first, '_%s' % l)
self.assertIsNotNone(value, "Missing label: %s" % l)
self.assertAlmostEqual(getattr(firstRow, l), value)
