def _getOutParam(self):
if getVersion() == "1.3" or getVersion() == "1.4":
outParam = '--o '
else:
outParam = '--operate_out '
outParam += self._getFileName("preprocess_particles_preffix")
return outParam
def _getOutParam(self):
if getVersion() == "1.3" or getVersion() == "1.4":
outParam = '--o '
else:
outParam = '--operate_out '
outParam += self._getFileName("preprocess_particles_preffix")
return outParam
def _setArgs(self, args):
from pyworkflow.em.packages.relion.convert import getVersion
particles = self._sampleParticles()
if self.maskDiameterA <= 0:
maskDiameter = particles.getSamplingRate() * particles.getXDim()
else:
maskDiameter = self.maskDiameterA.get()
args.update({
'--i': self._getFileName('input_particles'),
'--particle_diameter': maskDiameter,
'--angpix': particles.getSamplingRate(),
'--min_z': self.minZ.get()
})
if getVersion() == "2.0":
args['--o'] = self._getFileName('output_star')
else:
args['--o'] = 'sorted'
#if inputReferences is a volume, convert it to mrc here
if self.isInputAutoRefine():
args['--ref'] = self._getFileName('input_refvol')
else:
args['--ref'] = self._getFileName('input_refs')
if self.doInvert:
args['--invert'] = ''
if self.ignoreCTFUntilFirstPeak:
args['--ctf_intact_first_peak'] = ''
if self.doCTF:
args['--ctf'] = ''
def testProtRelionRefine(self):
from pyworkflow.em.packages.relion.convert import getVersion
relNorm = self.newProtocol(ProtRelionPreprocessParticles)
relNorm.inputParticles.set(self.protImport.outputParticles)
relNorm.doNormalize.set(True)
self.launchProtocol(relNorm)
def _runRelionRefine(doGpu=False, label=''):
print label
relionRefine = self.newProtocol(ProtRelionRefine3D,
doCTF=False,
runMode=1,
memoryPreThreads=1,
maskDiameterA=340,
symmetryGroup="d6",
numberOfMpi=3,
numberOfThreads=2)
relionRefine.setObjLabel(label)
relionRefine.inputParticles.set(relNorm.outputParticles)
relionRefine.referenceVolume.set(self.protImportVol.outputVolume)
if getVersion() == "2.0":
relionRefine.doGpu.set(doGpu)
self.launchProtocol(relionRefine)
return relionRefine
def _checkAsserts(relionProt):
relionProt._initialize() # Load filename templates
dataSqlite = relionProt._getIterData(3)
outImgSet = em.SetOfParticles(filename=dataSqlite)
self.assertIsNotNone(relionNoGpu.outputVolume,
"There was a problem with Relion autorefine")
self.assertAlmostEqual(
outImgSet[1].getSamplingRate(),
relNorm.outputParticles[1].getSamplingRate(),
"The sampling rate is wrong",
delta=0.00001)
self.assertAlmostEqual(outImgSet[1].getFileName(),
relNorm.outputParticles[1].getFileName(),
"The particles filenames are wrong")
if getVersion() == "2.0":
relionNoGpu = _runRelionRefine(False, "Relion auto-refine No GPU")
_checkAsserts(relionNoGpu)
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
relionGpu = _runRelionRefine(True, "Relion auto-refine GPU")
_checkAsserts(relionGpu)
else:
relionProt = _runRelionRefine(label="Run Relion auto-refine")
_checkAsserts(relionProt)
def testProtRelionClassify3D(self):
from pyworkflow.em.packages.relion.convert import getVersion
relionNormalize = self.newProtocol(ProtRelionPreprocessParticles)
relionNormalize.inputParticles.set(self.protImport.outputParticles)
relionNormalize.doNormalize.set(True)
self.launchProtocol(relionNormalize)
def _runRelionClassify3D(doGpu=False, label=''):
print label
relion3DClass = self.newProtocol(ProtRelionClassify3D,
numberOfClasses=3,
numberOfIterations=4,
doCTF=False,
runMode=1,
maskDiameterA=320,
numberOfMpi=2,
numberOfThreads=2)
relion3DClass.setObjLabel(label)
relion3DClass.inputParticles.set(relionNormalize.outputParticles)
relion3DClass.referenceVolume.set(self.protImportVol.outputVolume)
if getVersion() == "2.0":
relion3DClass.doGpu.set(doGpu)
self.launchProtocol(relion3DClass)
return relion3DClass
def _checkAsserts(relionProt):
self.assertIsNotNone(
relionProt.outputClasses, "There was a "
"problem with "
"Relion 3D classify")
for class3D in relionProt.outputClasses:
self.assertTrue(class3D.hasAlignmentProj())
if getVersion() == "2.0":
relionNoGpu = _runRelionClassify3D(False,
"Relion classify3D No GPU")
_checkAsserts(relionNoGpu)
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
relionGpu = _runRelionClassify3D(True, "Relion classify3D GPU")
_checkAsserts(relionGpu)
else:
relionProt = _runRelionClassify3D(label="Run Relion classify3D")
_checkAsserts(relionProt)
def testRelion2D(self):
from pyworkflow.em.packages.relion.convert import getVersion
def _runRelionClassify2D(doGpu=False, label=''):
prot2D = self.newProtocol(ProtRelionClassify2D,
doCTF=False,
maskDiameterA=340,
numberOfMpi=4,
numberOfThreads=1)
prot2D.numberOfClasses.set(4)
prot2D.numberOfIterations.set(3)
prot2D.inputParticles.set(self.protNormalize.outputParticles)
prot2D.setObjLabel(label)
if getVersion() == "2.0":
prot2D.doGpu.set(doGpu)
self.launchProtocol(prot2D)
return prot2D
def _checkAsserts(relionProt):
self.assertIsNotNone(
relionProt.outputClasses, "There was a problem with "
"Relion 2D classify")
partsPixSize = self.protNormalize.outputParticles.getSamplingRate()
classsesPixSize = relionProt.outputClasses.getImages(
).getSamplingRate()
self.assertAlmostEquals(
partsPixSize, classsesPixSize,
"There was a problem with the sampling rate "
"of the particles")
for class2D in relionProt.outputClasses:
self.assertTrue(class2D.hasAlignment2D())
if getVersion() == "2.0":
relionNoGpu = _runRelionClassify2D(False,
"Relion classify2D No GPU")
_checkAsserts(relionNoGpu)
environ = Environ(os.environ)
cudaPath = environ.getFirst(('RELION_CUDA_LIB', 'CUDA_LIB'))
if cudaPath is not None and os.path.exists(cudaPath):
relionGpu = _runRelionClassify2D(True, "Relion classify2D GPU")
_checkAsserts(relionGpu)
else:
relionProt = _runRelionClassify2D(label="Run Relion classify2D")
_checkAsserts(relionProt)
def _runRelionClassify2D(doGpu=False, label=''):
prot2D = self.newProtocol(ProtRelionClassify2D,
doCTF=False,
maskDiameterA=340,
numberOfMpi=4,
numberOfThreads=1)
prot2D.numberOfClasses.set(4)
prot2D.numberOfIterations.set(3)
prot2D.inputParticles.set(self.protNormalize.outputParticles)
prot2D.setObjLabel(label)
if getVersion() == "2.0":
prot2D.doGpu.set(doGpu)
self.launchProtocol(prot2D)
return prot2D
def _runRelionRefine(doGpu=False, label=''):
print label
relionRefine = self.newProtocol(ProtRelionRefine3D,
doCTF=False,
runMode=1,
memoryPreThreads=1,
maskDiameterA=340,
symmetryGroup="d6",
numberOfMpi=3,
numberOfThreads=2)
relionRefine.setObjLabel(label)
relionRefine.inputParticles.set(relNorm.outputParticles)
relionRefine.referenceVolume.set(self.protImportVol.outputVolume)
if getVersion() == "2.0":
relionRefine.doGpu.set(doGpu)
self.launchProtocol(relionRefine)
return relionRefine
def _runRelionClassify3D(doGpu=False, label=''):
print label
relion3DClass = self.newProtocol(ProtRelionClassify3D,
numberOfClasses=3,
numberOfIterations=4,
doCTF=False,
runMode=1,
maskDiameterA=320,
numberOfMpi=2,
numberOfThreads=2)
relion3DClass.setObjLabel(label)
relion3DClass.inputParticles.set(relionNormalize.outputParticles)
relion3DClass.referenceVolume.set(self.protImportVol.outputVolume)
if getVersion() == "2.0":
relion3DClass.doGpu.set(doGpu)
self.launchProtocol(relion3DClass)
return relion3DClass