def createOutputStep(self):
micTiltPairs = self.getInputMicrographs()
# Get the converted input micrographs in Xmipp format
writeSetOfMicrographsPairs = Domain.importFromPlugin(
'xmipp3.convert', 'writeSetOfMicrographsPairs')
writeSetOfMicrographsPairs(micTiltPairs.getUntilted(),
micTiltPairs.getTilted(), self.micsFn)
uCoordSet, tCoordSet, anglesSet = self.readCoordinates()
# Create CoordinatesTiltPair object
coordsSet = self._createCoordinatesTiltPair(micTiltPairs,
uCoordSet,
tCoordSet,
anglesSet,
suffix='')
self._defineOutputs(outputCoordinatesTiltPair=coordsSet)
self._defineSourceRelation(self.inputMicrographsTiltedPair, coordsSet)
def _visualize(self, obj, **args):
fnCmd = self.protocol._getExtraPath("chimera_output.cxc")
self._getVols()
self._getPdbs()
dim = float()
sampling = float()
if len(self.vols) > 0:
if self.vols[0] is not None:
dim, sampling = self._getDimSamplingFromVol(self.vols[0])
elif self.vols[1] is not None:
dim, sampling = self._getDimSamplingFromVol(self.vols[1])
else:
# To show pdbs only
dim = 150.
sampling = 1.
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
with open(fnCmd, 'w') as f:
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
if len(self.vols) > 0:
for vol in self.vols:
sampling, volFileName, x, y, z = self._getXYZFromVol(vol)
f.write("open %s\n" % volFileName)
f.write("volume #2 style surface voxelSize %f\n"
"volume #2 origin %0.2f,%0.2f,%0.2f\n" %
(sampling, x, y, z))
for filename in self.pdbList:
f.write("open %s\n" % filename)
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera',
'Plugin',
doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(),
fnCmd + "&",
cwd=os.getcwd())
return []
def _validate(self):
validateMsgs = []
if self.mtfFile.hasValue() and not os.path.exists(self.mtfFile.get()):
validateMsgs.append("MTF file %s does not exist!" % self.mtfFile.get())
if self.defectFile.hasValue() and not os.path.exists(self.defectFile.get()):
validateMsgs.append("Defect file %s does not exist!" % self.defectFile.get())
if self.gainRot or self.gainFlip:
try:
from pwem import Domain
eman2 = Domain.importFromPlugin('eman2', doRaise=True)
except:
validateMsgs.append("EMAN2 plugin not found!\nTransforming gain image "
"requires EMAN2 plugin and binaries installed.")
return validateMsgs
def homoNoGoldStandardAlign(self, relion1, relion2):
"""test without Goldstandard and alignment"""
XmippProtVolumeHomogenizer = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtEnrich', doRaise=True)
protVolumeHomogenizer = self.newProtocol(
XmippProtVolumeHomogenizer, objLabel='volume homogenizer2')
protVolumeHomogenizer.referenceVolume.set(relion1.outputVolume)
protVolumeHomogenizer.inputVolume.set(relion2.outputVolume)
protVolumeHomogenizer.inputParticles.set(relion2.outputParticles)
protVolumeHomogenizer.doAlignment.set(True)
self.launchProtocol(protVolumeHomogenizer)
self.assertIsNotNone(
protVolumeHomogenizer.outputParticles.getFileName(),
"There was a problem with the homoNoGoldStandardAlign")
return protVolumeHomogenizer
def getDimensions(self, locationObj):
""" It will return a tuple with the images dimensions.
The tuple will contains:
(x, y, z, n) where x, y, z are image dimensions (z=1 for 2D) and
n is the number of elements if stack.
"""
if self.existsLocation(locationObj):
location = self._convertToLocation(locationObj)
fn = location[1]
ext = pwutils.getExt(fn).lower()
# Local import to avoid import loop between ImageHandler and Ccp4Header.
from pwem.convert import headers
if ext == '.png' or ext == '.jpg':
im = Image.open(fn)
x, y = im.size # (width,height) tuple
return x, y, 1, 1
elif headers.getFileFormat(fn) == headers.MRC:
header = headers.Ccp4Header(fn, readHeader=True)
return header.getXYZN()
elif ext == '.img':
# FIXME Since now we can not read dm4 format in Scipion natively
# or recent .img format
# we are opening an Eman2 process to read the dm4 file
from pwem import Domain
getImageDimensions = Domain.importFromPlugin(
'eman2.convert', 'getImageDimensions', doRaise=True)
return getImageDimensions(fn) # we are ignoring index here
elif ext in ['.eer', '.gain']:
tif = TiffFile(fn)
frames = len(tif.pages) # number of pages in the file
page = tif.pages[
0] # get shape and dtype of the image in the first page
x, y = page.shape
return x, y, frames, 1
else:
self._img.read(location, lib.HEADER)
return self._img.getDimensions()
else:
return None, None, None, None
def test_volume1_AtomStructCIF(self):
from pwem import Domain
XmippProtResolution3D = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtResolution3D', doRaise=True)
prot = self.newProtocol(XmippProtResolution3D)
prot.inputVolume.set(self.protImportHalf1.outputVolume)
prot.referenceVolume.set(self.protImportHalf2.outputVolume)
self.launchProtocol(prot)
protExp = self.newProtocol(emprot.ProtExportDataBases)
protExp.setObjLabel("export to DB\ndir1")
protExp.exportVolume.set(self.protImportHalf1.outputVolume)
protExp.exportFSC.set(prot.outputFSC)
protExp.exportAtomStruct.set(self._importAtomStructCIF())
protExp.filesPath.set(os.getcwd() + "/dir1")
self.launchProtocol(protExp)
# Check the files were generated properly.
# protExp._createFileNamesTemplates()
dirName = protExp.filesPath.get()
nameVolume = os.path.join(dirName, protExp.VOLUMENAME)
nameFsc = os.path.join(dirName, "fsc_%02d.xml" % 1)
nameAtomStruct = os.path.join(dirName, protExp.COORDINATEFILENAME)
self.assertTrue(os.path.exists(nameVolume))
self.assertTrue(os.path.exists(nameFsc))
self.assertTrue(os.path.exists(nameAtomStruct))
# Check if the files have the correct data
orig_list_x, orig_list_y = protExp.exportFSC.get().getData()
fo = open(nameFsc, "rU")
saved_x = []
orig_x = []
count = 0
for line in fo:
if line[0:3] == '<x>':
saved_x.append(int(float(line[3:-5]) * 1000))
orig_x.append(int(orig_list_x[count] * 1000))
count = count + 1
self.assertListEqual(orig_x, saved_x)
def test_halfmaps_mask(self):
""" If the input is a 3D map with half volumes associated
Save them to the output directory
Also create a mask and export it
"""
# first create the 3 3dmaps and the mask
self.import_volume_halfmaps()
# run the export protocol
from pwem import Domain
XmippProtResolution3D = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtResolution3D', doRaise=True)
prot = self.newProtocol(XmippProtResolution3D)
prot.inputVolume.set(self.half1)
prot.referenceVolume.set(self.half2)
self.launchProtocol(prot)
protExp = self.newProtocol(emprot.ProtExportDataBases)
protExp.setObjLabel("export to DB\ndir3")
protExp.exportVolume.set(self.volume)
protExp.additionalVolumesToExport.set(True)
protExp.exportAdditionalVolumes.set([
self.protImportHalf1.outputVolume,
self.protImportHalf2.outputVolume
])
protExp.exportFSC.set(prot.outputFSC)
protExp.masksToExport.set(True)
protExp.exportMasks.set([self.mask])
protExp.exportAtomStruct.set(self._importAtomStructCIF())
protExp.filesPath.set(os.getcwd() + "/dir3")
self.launchProtocol(protExp)
# Check the files were generated properly.
# protExp._createFileNamesTemplates()
dirName = protExp.filesPath.get()
nameVolume = os.path.join(dirName, protExp.VOLUMENAME)
nameFsc = os.path.join(dirName, "fsc_%02d.xml" % 1)
nameAtomStruct = os.path.join(dirName, protExp.COORDINATEFILENAME)
self.assertTrue(os.path.exists(nameVolume))
self.assertTrue(os.path.exists(nameFsc))
self.assertTrue(os.path.exists(nameAtomStruct))
def _compareMicPairs(self, micFn, uSet, tSet):
# compare micFn input file and input micsSet
micMd = md.MetaData(micFn)
micFnDict = {}
inputMicsDict = {}
XmippMdRow = Domain.importFromPlugin('xmipp3', 'XmippMdRow')
for objId in micMd:
row = XmippMdRow()
row.readFromMd(micMd, objId)
micUFn = pwutils.removeBaseExt(row.getValue(md.MDL_MICROGRAPH))
micTFn = pwutils.removeBaseExt(row.getValue(md.MDL_MICROGRAPH_TILTED))
micFnDict[micUFn] = micTFn
for micU, micT in izip(uSet, tSet):
inputMicsDict[pwutils.removeBaseExt(micU.getFileName())] = pwutils.removeBaseExt(micT.getFileName())
for micKey in inputMicsDict:
if micKey not in micFnDict:
return False
return True
def relionRefine(self, protSubSetClass, vol, classid):
ProtRelionRefine3D = Domain.importFromPlugin('relion.protocols',
'ProtRelionRefine3D',
doRaise=True)
relionRefine = self.newProtocol(ProtRelionRefine3D,
objLabel='relion_%s' % classid,
doCTF=False, runMode=1,
memoryPreThreads=1,
maskDiameterA=424,
angularSamplingDeg=1,
localSearchAutoSamplingDeg=2,
symmetryGroup="c1",
numberOfMpi=3, numberOfThreads=1)
relionRefine.inputParticles.set(protSubSetClass.outputParticles)
relionRefine.referenceVolume.set(vol.outputVolume)
self.launchProtocol(relionRefine)
return relionRefine
def _readCoordinates(self, coordsDir, suffix=''):
micTiltPairs = self.inputMicrographsTiltedPair.get()
uSuffix = 'Untilted' + suffix
tSuffix = 'Tilted' + suffix
uSet = micTiltPairs.getUntilted()
tSet = micTiltPairs.getTilted()
# Create Untilted and Tilted SetOfCoordinates
readSetOfCoordinates = Domain.importFromPlugin('xmipp3.convert',
'readSetOfCoordinates')
uCoordSet = self._createSetOfCoordinates(uSet, suffix=uSuffix)
readSetOfCoordinates(coordsDir, uSet, uCoordSet)
uCoordSet.write()
tCoordSet = self._createSetOfCoordinates(tSet, suffix=tSuffix)
readSetOfCoordinates(coordsDir, tSet, tCoordSet)
tCoordSet.write()
boxSize = self._getBoxSize()
if boxSize:
uCoordSet.setBoxSize(boxSize)
tCoordSet.setBoxSize(boxSize)
return uCoordSet, tCoordSet
def _validate(self):
# Check base validation before the specific ones
errors = ProtAlignMovies._validate(self)
if self.doApplyDoseFilter and self.inputMovies.get():
inputMovies = self.inputMovies.get()
doseFrame = inputMovies.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append('Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
if self.doComputeMicThumbnail or self.doComputePSD:
try:
from pwem import Domain
eman2 = Domain.importFromPlugin('eman2', doRaise=True)
except:
errors.append(
"EMAN2 plugin not found!\nComputing thumbnails "
"or PSD requires EMAN2 plugin and binaries installed.")
return errors
def _displayModel(self, e=None):
# bildFileName = os.path.abspath(self.protocol._getTmpPath(
# "axis_output.bild"))
bildFileName = self.protocol._getTmpPath("axis_output.bild")
# Axis Dim
dim = 150.
sampling = 1.
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self.protocol._getTmpPath("chimera_output.cxc")
f = open(fnCmd, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
# reference axis model = 0
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
# f.write("open %s\n" % os.path.abspath(
# self.protocol.pdbFileToBeRefined.get().getFileName()))
f.write("open %s\n" %
self.protocol.pdbFileToBeRefined.get().getFileName())
if self.protocol.SYMMETRY.get() and \
os.path.exists(self.protocol.getSymmetrizedModelName()):
f.write("open %s\n" % self.protocol.getSymmetrizedModelName())
f.close()
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera',
'Plugin',
doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(),
fnCmd + "&",
cwd=os.getcwd())
return []
def _visualize(self, obj, **args):
# TODO if input volume is not mrc this will not work.
# Construct the coordinate file and visualization
bildFileName = os.path.abspath(
self.protocol._getExtraPath("axis.bild"))
dims = []
samplings = []
if len(self.protocol.inputVolumes) is 0:
if self.protocol.pdbFileToBeRefined.get().getVolume() is not None:
dim = self.protocol.pdbFileToBeRefined.get().getVolume(
).getDim()[0]
sampling = self.protocol.pdbFileToBeRefined.get().getVolume().\
getSamplingRate()
dims.append(dim)
samplings.append(sampling)
else:
for i in range(len(self.protocol.inputVolumes)):
dim = self.protocol.inputVolumes[i].get().getDim()[0]
sampling = self.protocol.inputVolumes[i].get().\
getSamplingRate()
dims.append(dim)
samplings.append(sampling)
if len(dims) != 0 and len(samplings) != 0:
Chimera.createCoordinateAxisFile(max(dims),
bildFileName=bildFileName,
sampling=max(samplings))
else:
dim = 150.
sampling = 1.
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self.protocol._getExtraPath("chimera.cxc")
f = open(fnCmd, 'w')
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n")
outputsVol = []
if len(self.protocol.inputVolumes) is 0:
if self.protocol.pdbFileToBeRefined.get().getVolume() is not None:
outputVol = self.protocol.pdbFileToBeRefined.get().getVolume()
outputsVol.append(outputVol)
else:
for i in range(len(self.protocol.inputVolumes)):
outputVol = self.protocol.inputVolumes[i].get()
outputsVol.append(outputVol)
count = 2
if len(outputsVol) != 0:
for outputVol in outputsVol:
outputVolFileName = os.path.abspath(
ImageHandler.removeFileType(outputVol.getFileName()))
x, y, z = outputVol.getOrigin(force=True).getShifts()
f.write("open %s\n" % outputVolFileName)
f.write("volume #%d style surface voxelSize %f\n"
"volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(count, outputVol.getSamplingRate(), count, x, y, z))
count += 1
# counter = 1
# template = self.protocol._getExtraPath(COOTPDBTEMPLATEFILENAME)
databasePath = self.protocol._getExtraPath(
OUTPUTDATABASENAMESWITHLABELS)
conn = sqlite3.connect(databasePath)
c = conn.cursor()
sql = 'SELECT fileName FROM %s where saved = 1 order by id' % \
DATABASETABLENAME
c.execute(sql)
for row in c:
pdbFileName = os.path.abspath(row[0])
if not pdbFileName.endswith(".mrc"):
f.write("open %s\n" % pdbFileName)
f.close()
conn.close()
# run in the background
chimeraPlugin = Domain.importFromPlugin('chimera',
'Plugin',
doRaise=True)
chimeraPlugin.runChimeraProgram(chimeraPlugin.getProgram(),
fnCmd + "&")
return []
def test_RefineEman(self):
print(magentaStr("\n==> Importing data - micrograph pairs:"))
protImportMicsPairs = self.newProtocol(ProtImportMicrographsTiltPairs,
patternUntilted=self.micsUFn,
patternTilted=self.micsTFn,
samplingRate=1.88,
voltage=200,
sphericalAberration=2.0)
self.launchProtocol(protImportMicsPairs)
self.assertIsNotNone(
protImportMicsPairs.outputMicrographsTiltPair,
"There was a problem with the import of mic pairs")
print(magentaStr("\n==> Importing data - coordinate pairs:"))
protImportCoords = self.newProtocol(
ProtImportCoordinatesPairs,
importFrom=1, # from eman
patternUntilted=self.patternU,
patternTilted=self.patternT,
boxSize=256)
protImportCoords.inputMicrographsTiltedPair.set(
protImportMicsPairs.outputMicrographsTiltPair)
self.launchProtocol(protImportCoords)
self.assertIsNotNone(
protImportCoords.outputCoordinatesTiltPair,
"There was a problem with the import of coord pairs")
print(magentaStr("\n==> Running xmipp3 - extract particles:"))
XmippProtExtractParticlesPairs = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtExtractParticlesPairs')
protExtractPairs = self.newProtocol(XmippProtExtractParticlesPairs,
downFactor=2.0,
boxSize=128,
doInvert=True)
protExtractPairs.inputCoordinatesTiltedPairs.set(
protImportCoords.outputCoordinatesTiltPair)
self.launchProtocol(protExtractPairs)
self.assertIsNotNone(
protExtractPairs.outputParticlesTiltPair,
"There was a problem with particle pair extraction")
print(magentaStr("\n==> Testing eman2 - tilt validate:"))
protValidate = self.newProtocol(
EmanProtTiltValidate,
symmetry="c4",
maxtilt=60.0,
delta=2.0,
shrink=2,
quaternion=True,
simcmpType=2, # frc
simcmpParams='maxres=60',
simalignType=7, # rotate_translate
simralignType=1, # refine
numberOfThreads=4)
protValidate.inputTiltPair.set(
protExtractPairs.outputParticlesTiltPair)
protValidate.inputVolume.set(self.protImportVol.outputVolume)
protValidate._createFilenameTemplates()
outputAngles = protValidate._getFileName('outputAngles')
self.launchProtocol(protValidate)
self.assertIsNotNone(outputAngles, "Missing some output files!")
def __runXmippProgram(cls, program, args):
""" Internal shortcut function to launch a Xmipp program. """
from pwem import Domain
xmipp3 = Domain.importFromPlugin('xmipp3')
xmipp3.Plugin.runXmippProgram(program, args)
def test_volume1_AtomStructPDB(self):
from pwem import Domain
XmippProtResolution3D = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtResolution3D', doRaise=True)
prot = self.newProtocol(XmippProtResolution3D)
prot.inputVolume.set(self.protImportHalf1.outputVolume)
prot.referenceVolume.set(self.protImportHalf2.outputVolume)
self.launchProtocol(prot)
protExp = self.newProtocol(emprot.ProtExportDataBases)
protExp.setObjLabel("export to DB\ndir2")
protExp.exportVolume.set(self.protImportHalf1.outputVolume)
protExp.exportFSC.set(prot.outputFSC)
# run Chimera rigid fit ti get a PDB file
extraCommands = ""
extraCommands += "scipionwrite #3 prefix DONOTSAVESESSION_\n"
extraCommands += "exit\n"
args = {
'extraCommands': extraCommands,
'inputVolume': self.protImportHalf1.outputVolume,
'pdbFileToBeRefined': self._importAtomStructCIF()
}
from pwem import Domain
ChimeraProtRigidFit = Domain.importFromPlugin('chimera.protocols',
'ChimeraProtRigidFit',
doRaise=True)
protChimera = self.newProtocol(ChimeraProtRigidFit, **args)
protChimera.setObjLabel('chimera fit\n volume and PDB\n save model')
self.launchProtocol(protChimera)
outputAttr = "DONOTSAVESESSION_Atom_struct__3_%06d" % protChimera.getObjId(
)
protExp.exportAtomStruct.set(getattr(protChimera, outputAttr))
protExp.filesPath.set(os.getcwd() + "/dir2")
self.launchProtocol(protExp)
# Check the files were generated properly.
# protExp._createFileNamesTemplates()
dirName = protExp.filesPath.get()
nameVolume = os.path.join(dirName, protExp.VOLUMENAME)
nameFsc = os.path.join(dirName, "fsc_%02d.xml" % 1)
nameAtomStruct = os.path.join(dirName, protExp.COORDINATEFILENAME)
self.assertTrue(os.path.exists(nameVolume))
self.assertTrue(os.path.exists(nameFsc))
self.assertTrue(os.path.exists(nameAtomStruct))
# Check if the files have the correct data
orig_list_x, orig_list_y = protExp.exportFSC.get().getData()
fo = open(nameFsc, "rU")
saved_x = []
orig_x = []
count = 0
for line in fo:
if line[0:3] == '<x>':
saved_x.append(int(float(line[3:-5]) * 1000))
orig_x.append(int(orig_list_x[count] * 1000))
count = count + 1
self.assertListEqual(orig_x, saved_x)
def __runXmippProgram(program, args):
""" Internal function to launch a Xmipp program. """
from pwem import Domain
xmipp3 = Domain.importFromPlugin('xmipp3', doRaise=True)
xmipp3.runXmippProgram(program, args)
def testRisosome(self):
# First, import a set of micrographs
print("Importing a set of micrographs...")
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=os.path.abspath(
self.proj.getTmpPath()),
filesPattern="*%s" % self.ext,
samplingRateMode=1,
magnification=79096,
scannedPixelSize=56,
voltage=300,
sphericalAberration=2.0,
dataStreaming=True,
fileTimeout=3,
timeout=60)
protImport.setObjLabel('import 20 mics (streaming)')
self.proj.launchProtocol(protImport, wait=False)
self._waitOutput(protImport, 'outputMicrographs')
# Now estimate CTF on the micrographs with ctffind
print("Performing CTFfind...")
ProtCTFFind = Domain.importFromPlugin('cistem.protocols',
'CistemProtCTFFind',
doRaise=True)
protCTF = self.newProtocol(ProtCTFFind,
minDefocus=12000,
maxDefocus=30000,
runMode=1,
numberOfMpi=1,
numberOfThreads=1)
protCTF.inputMicrographs.set(protImport.outputMicrographs)
protCTF.setObjLabel('CTF ctffind')
self.proj.launchProtocol(protCTF, wait=False)
self._waitOutput(protCTF, 'outputCTF')
# Now pick particles on the micrographs with Relion
print("Performing Relion Autopicking (LoG)...")
ProtRelionAutopickLoG = Domain.importFromPlugin(
'relion.protocols', 'ProtRelionAutopickLoG')
protPick = self.newProtocol(
ProtRelionAutopickLoG,
objLabel='Streaming relion - autopic (LoG)',
inputMicrographs=protImport.outputMicrographs,
boxSize=60,
minDiameter=260,
maxDiameter=380)
self.proj.launchProtocol(protPick, wait=False)
self._waitOutput(protPick, 'outputCoordinates')
ProtRelionExtractParticles = Domain.importFromPlugin(
'relion.protocols', 'ProtRelionExtractParticles', doRaise=True)
protExtract = self.newProtocol(ProtRelionExtractParticles,
objLabel='extract box=64',
boxSize=64,
doInvert=True)
protExtract.inputCoordinates.set(protPick.outputCoordinates)
protExtract.ctfRelations.set(protCTF.outputCTF)
self.launchProtocol(protExtract)
x, y, _ = protExtract.outputParticles.getDim()
self.assertEqual(
protExtract.outputParticles.getDim(), (64, 64, 1),
"Dimension of the particles should be 64 x 64 and it "
"is %d x %d" % (x, y))
def test_workflow(self):
#First, import a set of micrographs
print("Importing a set of micrographs...")
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=self.micsFn,
samplingRateMode=1, magnification=79096,
scannedPixelSize=56, voltage=300,
sphericalAberration=2.0)
protImport.setObjLabel('import 20 mics')
self.launchProtocol(protImport)
self.assertIsNotNone(protImport.outputMicrographs,
"There was a problem with the import")
print("Importing a volume...")
protImportVol = self.newProtocol(emprot.ProtImportVolumes, filesPath=self.vol,
samplingRate=7.08)
protImportVol.setObjLabel('import single vol')
self.launchProtocol(protImportVol)
self.assertIsNotNone(protImportVol.outputVolume, "There was a problem with the import")
print("Preprocessing the micrographs...")
xmippProtocols = Domain.importFromPlugin('xmipp3.protocols',
doRaise=True)
protPreprocess = self.newProtocol(xmippProtocols.XmippProtPreprocessMicrographs,
doCrop=True, cropPixels=25)
protPreprocess.inputMicrographs.set(protImport.outputMicrographs)
protPreprocess.setObjLabel('crop 50px')
self.launchProtocol(protPreprocess)
self.assertIsNotNone(protPreprocess.outputMicrographs,
"There was a problem with the downsampling")
print("Running Eman import coordinates...")
protPP = self.newProtocol(emprot.ProtImportCoordinates,
importFrom=emprot.ProtImportCoordinates.IMPORT_FROM_EMAN,
filesPath=self.crdsEmanDir,
filesPattern='info/*_info.json', boxSize=60)
protPP.inputMicrographs.set(protPreprocess.outputMicrographs)
protPP.setObjLabel('import from Eman boxing')
self.launchProtocol(protPP)
self.assertIsNotNone(protPP.outputCoordinates,
"There was a problem with the Eman import coordinates")
# Now estimate CTF on the micrographs with ctffind
print("Performing CTFfind...")
grigorieffLabProtocols = Domain.importFromPlugin(
'cistem.protocols',
doRaise=True)
protCTF = self.newProtocol(grigorieffLabProtocols.CistemProtCTFFind,
minDefocus=12000, maxDefocus=30000,
runMode=1, numberOfMpi=1, numberOfThreads=16)
protCTF.inputMicrographs.set(protPreprocess.outputMicrographs)
protCTF.setObjLabel('CTF ctffind')
self.launchProtocol(protCTF)
print("Run extract particles with <Same as picking> option")
protExtract = self.newProtocol(xmippProtocols.XmippProtExtractParticles,
boxSize=60,
downsampleType=emprot.SAME_AS_PICKING,
doRemoveDust=False,
doInvert=False,
doFlip=False, backRadius=28, runMode=1)
protExtract.inputCoordinates.set(protPP.outputCoordinates)
protExtract.ctfRelations.set(protCTF.outputCTF)
protExtract.setObjLabel('Extract particles')
self.launchProtocol(protExtract)
self.assertIsNotNone(protExtract.outputParticles,
"There was a problem with the extract particles")
print("Run CL2D")
protCL2D = xmippProtocols.XmippProtCL2D(numberOfClasses=32,
numberOfInitialClasses=4,
numberOfIterations=2,
numberOfMpi=16)
protCL2D.inputParticles.set(protExtract.outputParticles)
protCL2D.setObjLabel('CL2D')
self.launchProtocol(protCL2D)
self.assertIsNotNone(protCL2D.outputClasses,
"There was a problem with CL2D")
# Now estimate CTF on the micrographs with xmipp
print("Performing Xmipp CTF...")
protCTF2 = self.newProtocol(xmippProtocols.XmippProtCTFMicrographs,
doInitialCTF=True,
minDefocus=12000, maxDefocus=30000,
runMode=1, numberOfMpi=1, numberOfThreads=16)
protCTF2.ctfRelations.set(protCTF.outputCTF)
protCTF2.inputMicrographs.set(protPreprocess.outputMicrographs)
protCTF2.setObjLabel('CTF xmipp')
self.launchProtocol(protCTF2)
print("Running Xmipp Import Coordinates")
protPP2 = self.newProtocol(emprot.ProtImportCoordinates,
importFrom=emprot.ProtImportCoordinates.IMPORT_FROM_XMIPP,
filesPath=self.crdsXmippDir,
filesPattern='*.pos', boxSize=60)
protPP2.inputMicrographs.set(protPreprocess.outputMicrographs)
protPP2.setObjLabel('Xmipp Import Coords')
self.launchProtocol(protPP2)
self.assertIsNotNone(protPP2.outputCoordinates,
"There was a problem with the Xmipp import coordinates")
print("Run extract particles with <Same as picking> option")
protExtract2 = self.newProtocol(xmippProtocols.XmippProtExtractParticles,
boxSize=60,
downsampleType=emprot.SAME_AS_PICKING,
doRemoveDust=False, doInvert=True,
doFlip=False, backRadius=28, runMode=1)
protExtract2.inputCoordinates.set(protPP2.outputCoordinates)
protExtract2.ctfRelations.set(protCTF2.outputCTF)
protExtract2.setObjLabel('Extract particles')
self.launchProtocol(protExtract2)
self.assertIsNotNone(protExtract2.outputParticles,
"There was a problem with the extract particles")
print("Run Relion Classification2d")
relionProtocols = Domain.importFromPlugin('relion.protocols',
doRaise=True)
prot2D = relionProtocols.ProtRelionClassify2D(regularisationParamT=2,
numberOfMpi=4,
numberOfThreads=4)
prot2D.numberOfClasses.set(50)
prot2D.numberOfIterations.set(25)
prot2D.inputParticles.set(protExtract2.outputParticles)
prot2D.setObjLabel('relion 2D')
self.launchProtocol(prot2D)
self.assertIsNotNone(prot2D.outputClasses, "There was a problem with Relion 2D:\n" + (prot2D.getErrorMessage() or "No error set"))
print("Run Relion Refine")
proRef = relionProtocols.ProtRelionRefine3D()
proRef.inputParticles.set(protExtract2.outputParticles)
proRef.referenceVolume.set(protImportVol.outputVolume)
proRef.setObjLabel('relion Refine')
self.launchProtocol(proRef)
self.assertIsNotNone(proRef.outputVolume, "There was a problem with Relion Refine:\n" + (proRef.getErrorMessage() or "No error set"))
self.assertIsNotNone(proRef.outputParticles, "There was a problem with Relion Refine:\n" + (proRef.getErrorMessage() or "No error set"))
def test_workflow(self):
# First, import a set of micrographs
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=self.micsFn,
samplingRate=1.237, voltage=300)
self.launchProtocol(protImport)
self.assertIsNotNone(protImport.outputMicrographs,
"There was a problem with the import")
# self.validateFiles('protImport', protImport)
# Import a set of volumes
print("Import Volume")
protImportVol = self.newProtocol(emprot.ProtImportVolumes, filesPath=self.vol1,
samplingRate=9.896)
self.launchProtocol(protImportVol)
self.assertIsNotNone(protImportVol.getFiles(),
"There was a problem with the import")
# self.validateFiles('protImportVol', protImportVol)
# Perform a downsampling on the micrographs
print("Downsampling...")
XmippProtPreprocessMicrographs = Domain.importFromPlugin(
'xmipp3.protocols',
'XmippProtPreprocessMicrographs',
doRaise=True)
protDownsampling = self.newProtocol(XmippProtPreprocessMicrographs,
doDownsample=True, downFactor=5,
doCrop=False, runMode=1)
protDownsampling.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protDownsampling)
self.assertIsNotNone(protDownsampling.outputMicrographs,
"There was a problem with the downsampling")
# self.validateFiles('protDownsampling', protDownsampling)
# Estimate CTF on the downsampled micrographs
print("Performing CTFfind...")
ProtCTFFind = Domain.importFromPlugin('cistem.protocols',
'CistemProtCTFFind', doRaise=True)
protCTF = self.newProtocol(ProtCTFFind, numberOfThreads=4,
minDefocus=22000, maxDefocus=25000)
protCTF.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protCTF)
self.assertIsNotNone(protCTF.outputCTF,
"There was a problem with the CTF estimation")
# self.validateFiles('protCTF', protCTF)
print("Running Eman import coordinates...")
protPP = self.newProtocol(emprot.ProtImportCoordinates,
importFrom=emprot.ProtImportCoordinates.IMPORT_FROM_EMAN,
filesPath=self.crdsDir,
filesPattern='*_info.json', boxSize=110)
protPP.inputMicrographs.set(protDownsampling.outputMicrographs)
self.launchProtocol(protPP)
self.assertIsNotNone(protPP.outputCoordinates,
"There was a problem with the Eman import coordinates")
print("<Run extract particles with Same as picking>")
XmippProtExtractParticles = Domain.importFromPlugin(
'xmipp3.protocols',
'XmippProtExtractParticles')
SAME_AS_PICKING = Domain.importFromPlugin('xmipp3.constants',
'SAME_AS_PICKING')
protExtract = self.newProtocol(XmippProtExtractParticles, boxSize=110,
downsampleType=SAME_AS_PICKING,
doFlip=True, doInvert=True, runMode=1)
protExtract.inputCoordinates.set(protPP.outputCoordinates)
protExtract.ctfRelations.set(protCTF.outputCTF)
self.launchProtocol(protExtract)
self.assertIsNotNone(protExtract.outputParticles,
"There was a problem with the extract particles")
# self.validateFiles('protExtract', protExtract)
print("Run Preprocess particles")
XmippProtCropResizeParticles = Domain.importFromPlugin(
'xmipp3.protocols',
'XmippProtCropResizeParticles')
protCropResize = self.newProtocol(XmippProtCropResizeParticles,
doResize=True, resizeOption=1,
resizeDim=110)
protCropResize.inputParticles.set(protExtract.outputParticles)
self.launchProtocol(protCropResize)
self.assertIsNotNone(protCropResize.outputParticles,
"There was a problem with resize/crop the particles")
print("Run ML2D")
XmippProtML2D = Domain.importFromPlugin('xmipp3.protocols',
'XmippProtML2D')
protML2D = self.newProtocol(XmippProtML2D, numberOfClasses=8, maxIters=2,
numberOfMpi=2, numberOfThreads=2)
protML2D.inputParticles.set(protCropResize.outputParticles)
self.launchProtocol(protML2D)
self.assertIsNotNone(protML2D.outputClasses,
"There was a problem with ML2D")
# self.validateFiles('protML2D', protML2D)
# #FIXME: Check the initial model with EMAn and restore the next step
# return
print("Run Initial Model")
EmanProtInitModel = Domain.importFromPlugin('eman2.protocols',
'EmanProtInitModel',
doRaise=True)
protIniModel = self.newProtocol(EmanProtInitModel, numberOfIterations=1,
numberOfModels=2,
shrink=5, symmetry='icos',
numberOfThreads=3)
protIniModel.inputSet.set(protML2D.outputClasses)
self.launchProtocol(protIniModel)
self.assertIsNotNone(protIniModel.outputVolumes,
"There was a problem with Initial Model")
def _visualize(self, obj, **kwargs):
cls = type(obj)
if issubclass(cls, emobj.Volume):
fn = emlib.image.ImageHandler.locationToXmipp(obj)
self._addObjView(obj, fn,
{RENDER: 'image',
SAMPLINGRATE: obj.getSamplingRate()})
elif issubclass(cls, emobj.Image):
fn = emlib.image.ImageHandler.locationToXmipp(obj)
self._addObjView(obj, fn)
elif issubclass(cls, emobj.SetOfPDBs):
fn = obj.getFileName()
labels = 'id _filename '
self._addObjView(obj, fn, {ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: "no"})
elif issubclass(cls, emobj.SetOfMovies):
fn = obj.getFileName()
# Enabled for the future has to be available
labels = ('id _filename _samplingRate _acquisition._dosePerFrame '
'_acquisition._doseInitial ')
moviesView = self._addObjView(obj, fn, {ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: "no"})
# For movies increase the JVM memory by 1 GB, just in case
moviesView.setMemory(getJvmMaxMemory() + 1)
elif issubclass(cls, emobj.SetOfMicrographs):
self._views.append(MicrographsView(self._project, obj, **kwargs))
elif issubclass(cls, emobj.MicrographsTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
renderLabels = '_untilted._filename _tilted._filename'
self._addObjView(obj, obj.getFileName(), {ORDER: labels,
VISIBLE: labels,
MODE: MODE_MD,
RENDER: renderLabels})
elif issubclass(cls, emobj.ParticlesTiltPair):
labels = 'id enabled _untilted._filename _tilted._filename'
renderLabels = '_untilted._filename _tilted._filename'
self._addObjView(obj, obj.getFileName(), {ORDER: labels,
VISIBLE: labels,
RENDER: renderLabels,
MODE: MODE_MD})
elif issubclass(cls, emobj.SetOfCoordinates):
# FIXME: Remove dependency on xmipp3 plugin to visualize coordinates
xmipp3 = Domain.importFromPlugin('xmipp3',
errorMsg="xmipp3 plugin is required "
"now to visualize coordinates.")
micSet = obj.getMicrographs() # accessing mics to provide metadata file
if micSet is None:
raise Exception('visualize: SetOfCoordinates has no micrographs set.')
mdFn = getattr(micSet, '_xmippMd', None)
if mdFn:
fn = mdFn.get()
else: # happens if protocol is not an xmipp one
fn = self._getTmpPath(micSet.getName() + '_micrographs.xmd')
xmipp3.convert.writeSetOfMicrographs(micSet, fn)
tmpDir = self._getTmpPath(obj.getName())
pwutils.cleanPath(tmpDir)
pwutils.makePath(tmpDir)
# FIXME: (JMRT) We are always writing the SetOfCoordinates and removing
# the tmpDir, we need to take into account if the user have pick
# some particles in the tmpDir and have not save them, that now
# will loose all picked particles.
# A possible solution could be to alert that changes have not been
# written during modification of tmpDir or create a new Xmipp picking
# protocol to continue picking later without loosing the coordinates.
xmipp3.convert.writeSetOfCoordinates(tmpDir, obj)
self._views.append(CoordinatesObjectView(self._project, fn,
tmpDir, self.protocol,
inTmpFolder=True))
elif issubclass(cls, emobj.SetOfParticles):
fn = obj.getFileName()
labels = ('id enabled _index _filename _xmipp_zScore _xmipp_cumulativeSSNR '
'_sampling _xmipp_scoreByVariance _xmipp_scoreEmptiness '
'_ctfModel._defocusU _ctfModel._defocusV _ctfModel._defocusAngle '
'_transform._matrix')
self._addObjView(obj, fn, {ORDER: labels,
VISIBLE: labels,
SORT_BY: '_xmipp_zScore asc',
RENDER: '_filename'})
elif issubclass(cls, emobj.SetOfVolumes):
fn = obj.getFileName()
labels = 'id enabled comment _filename '
self._addObjView(obj, fn, {MODE: MODE_MD,
ORDER: labels,
VISIBLE: labels,
RENDER: '_filename'})
elif issubclass(cls, emobj.SetOfClasses2D):
self._views.append(ClassesView(self._project, obj.strId(),
obj.getFileName(), **kwargs))
elif issubclass(cls, emobj.SetOfClasses3D):
self._views.append(Classes3DView(self._project, obj.strId(),
obj.getFileName()))
elif issubclass(cls, emobj.SetOfImages):
self._views.append(ObjectView(self._project, obj.strId(),
obj.getFileName(), **kwargs))
elif issubclass(cls, emobj.SetOfCTF):
self._views.append(CtfView(self._project, obj))
elif issubclass(cls, emobj.CoordinatesTiltPair):
# FIXME: Remove dependency on xmipp3 plugin to visualize coordinates
xmipp3 = Domain.importFromPlugin('xmipp3',
errorMsg="xmipp3 plugin is required "
"now to visualize coordinates.")
tmpDir = self._getTmpPath(obj.getName())
pwutils.makePath(tmpDir)
mdFn = os.path.join(tmpDir, 'input_micrographs.xmd')
xmipp3.convert.writeSetOfMicrographsPairs(
obj.getUntilted().getMicrographs(),
obj.getTilted().getMicrographs(), mdFn)
# TODO: Review this if ever a non Xmipp CoordinatesTiltPair is available
xmipp3.convert.writeSetOfCoordinates(tmpDir, obj.getUntilted())
xmipp3.convert.writeSetOfCoordinates(tmpDir, obj.getTilted())
launchTiltPairPickerGUI(mdFn, tmpDir, self.protocol)
elif issubclass(cls, emprot.ProtParticlePicking):
if obj.getOutputsSize() >= 1:
self._visualize(obj.getCoords())
elif issubclass(cls, emprot.ProtImportMovies):
movs = obj.outputMovies
self._visualize(movs)
gainFn = movs.getGain()
if gainFn is not None:
if os.path.exists(gainFn):
self._views.append(DataView(gainFn))
return self._views
try:
from itertools import izip
except:
izip = zip
import urllib.request
import os
import pyworkflow.tests as tests
from pwem.protocols import ProtImportParticles, ProtSplitSet, ProtUnionSet
from pwem.emlib.image import ImageHandler
from pwem import Domain
from emxlib.protocols import ProtEmxExport
XmippProtExtractParticles = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtExtractParticles')
XmippProtFilterParticles = Domain.importFromPlugin('xmipp3.protocols',
'XmippProtFilterParticles')
XmippProtApplyAlignment = Domain.importFromPlugin('xmipp3.protocols',
'XmippProtApplyAlignment')
XmippProtReconstructFourier = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtReconstructFourier')
class TestEmxWeb(tests.BaseTest):
"""test emx web page """
@classmethod
def setUpClass(cls):
tests.setupTestProject(cls)
# cls.baseUrl = "http://i2pc.cnb.csic.es/emx/resourcesEmx/Tests/"
cls.baseUrl = "http://heisenberg.cnb.csic.es:8080/emx/resourcesEmx/Tests/"
def readCoordinates(self):
micTiltPairs = self.getInputMicrographs()
ci = self.getImportClass()
uSet = micTiltPairs.getUntilted()
tSet = micTiltPairs.getTilted()
# Create Untilted and Tilted SetOfCoordinates
uCoordSet = self._createSetOfCoordinates(uSet, suffix='Untilted')
tCoordSet = self._createSetOfCoordinates(tSet, suffix='Tilted')
anglesSet = self._createSetOfAngles()
def _importCoords(uCoordSet, tCoordSet):
for micU, micT in izip(uSet, tSet):
coordFnU, coordFnT = self.getMatchingCoord(micU, micT)
if coordFnU and coordFnT:
def addCoordinateU(coord):
coord.setMicrograph(micU)
self.correctCoordinatePosition(coord)
uCoordSet.append(coord)
ci.importCoordinates(coordFnU,
addCoordinate=addCoordinateU)
def addCoordinateT(coord):
coord.setMicrograph(micT)
self.correctCoordinatePosition(coord)
tCoordSet.append(coord)
ci.importCoordinates(coordFnT,
addCoordinate=addCoordinateT)
def addAngles(ang):
anglesSet.append(ang)
if self.importFrom.get() == self.IMPORT_FROM_EMAN:
ci.importAngles(coordFnT, addAngles=addAngles)
_importCoords(uCoordSet, tCoordSet)
boxSize = self.boxSize.get()
uCoordSet.setBoxSize(boxSize)
tCoordSet.setBoxSize(boxSize)
uCoordSet.write()
tCoordSet.write()
if self.importFrom.get() == self.IMPORT_FROM_XMIPP:
readAnglesFromMicrographs = Domain.importFromPlugin(
'xmipp3.convert', 'readAnglesFromMicrographs')
if exists(self.xmippMdFn.get()):
checkAngles = self._compareMicPairs(self.xmippMdFn, uSet, tSet)
if checkAngles:
readAnglesFromMicrographs(self.xmippMdFn, anglesSet)
else:
self.warning('Angles for some micrographs were not found, '
'skipping angles import')
else:
self.warning(
'Micrograph xmd file not provided, so tilt angles will '
'not be imported')
anglesSet.write()
return uCoordSet, tCoordSet, anglesSet
def testXmippRCTWorkflowBasic(self):
# First, import a set of micrographs
protImport = self.newProtocol(emprot.ProtImportMicrographsTiltPairs,
patternUntilted=self.micsUFn,
patternTilted=self.micsTFn,
samplingRate=2.28, voltage=100,
sphericalAberration=2.9)
self.launchProtocol(protImport)
self.assertIsNotNone(protImport.outputMicrographsTiltPair,
"There was a problem with the import")
# self.validateFiles('protImportRCT', protImport)
# Then simulate a particle picking
print("Running fake particle picking...")
from pwem import Domain
XmippProtParticlePickingPairs = Domain.importFromPlugin(
'xmipp3.protocols',
'XmippProtParticlePickingPairs',
doRaise=True)
protPicking = self.newProtocol(XmippProtParticlePickingPairs,
importFolder=self.allCrdsDir)
protPicking.inputMicrographsTiltedPair.set(protImport.outputMicrographsTiltPair)
self.proj.launchProtocol(protPicking, wait=True)
self.assertIsNotNone(protPicking.outputCoordinatesTiltPair,
"There was a problem with the faked picking")
# self.validateFiles('protPicking', protPicking)
# Extract particles
print("Run extract particles with Same as picking")
XmippProtExtractParticlesPairs = Domain.importFromPlugin(
'xmipp3.protocols',
'XmippProtExtractParticlesPairs')
SAME_AS_PICKING = Domain.importFromPlugin('xmipp3.constants',
'SAME_AS_PICKING')
protExtract = self.newProtocol(XmippProtExtractParticlesPairs,
downFactor=2,
boxSize=60,
doInvert=False,
downsampleType=SAME_AS_PICKING)
protExtract.inputCoordinatesTiltedPairs.set(protPicking.outputCoordinatesTiltPair)
self.proj.launchProtocol(protExtract, wait=True)
# self.validateFiles('protExtract', protExtract)
self.assertIsNotNone(protExtract.outputParticlesTiltPair,
"There was a problem with the extract particles")
# Classify using Xmipp CL2D
print("Run CL2D")
XmippProtCL2D = Domain.importFromPlugin('xmipp3.protocols',
'XmippProtCL2D')
protCL2D = self.newProtocol(XmippProtCL2D,
numberOfClasses=10,
numberOfInitialClasses=1,
numberOfIterations=3, numberOfMpi=2)
protCL2D.inputParticles.set(protExtract.outputParticlesTiltPair.getUntilted())
self.launchProtocol(protCL2D)
self.assertIsNotNone(protCL2D.outputClasses,
"There was a problem with CL2D")
# self.validateFiles('protCL2D', protCL2D)
# Random Conical Tilt
print("Run Random Conical Tilt")
XmippProtRCT = Domain.importFromPlugin('xmipp3.protocols',
'XmippProtRCT')
protRCT = self.newProtocol(XmippProtRCT)
protRCT.inputParticlesTiltPair.set(protExtract.outputParticlesTiltPair)
protRCT.inputParticles.set(protCL2D.outputClasses)
self.proj.launchProtocol(protRCT, wait=True)
# self.validateFiles('protExtract', protExtract)
self.assertIsNotNone(protRCT.outputVolumes, "There was a problem with the RCT")
def test_pattern(self):
""" Import several Particles from a given pattern.
"""
def checkOutputs(prot):
t0 = time.time()
while not (prot.isFinished() or prot.isFailed()):
# Time out 6 minutes, just in case
tdelta = time.time() - t0
if tdelta > 6*60:
break
time.sleep(10)
prot = self._updateProtocol(prot)
# Check if the protocol is still launched
if prot.isLaunched():
continue
elif prot.isScheduled():
continue
if prot.hasAttribute("outputCTF"):
ctfSet = emobj.SetOfCTF(filename=prot._getPath(CTF_SQLITE))
baseFn = prot._getPath(CTF_SQLITE)
self.assertTrue(os.path.isfile(baseFn))
counter = 0
if ctfSet.getSize() > counter:
counter += 1
for ctf in ctfSet:
self.assertNotEqual(ctf._resolution.get(), None)
self.assertNotEqual(ctf._fitQuality.get(), None)
self.assertNotEqual(ctf.isEnabled(), None)
self.assertNotEqual(ctf._defocusU.get(), None)
self.assertNotEqual(ctf._defocusV.get(), None)
self.assertNotEqual(ctf._defocusRatio.get(), None)
if ctf.getPhaseShift():
self.assertNotEqual(ctf.getPhaseShift(), None)
self.assertIsNotNone(prot.outputCTF,
"Error: outputCTF is not produced "
"in %s." % prot.getClassName())
self.assertEqual(prot.outputCTF.getSize(), MICS)
# Simulate streaming with create stream data protocol
kwargs = {'xDim': 4096,
'yDim': 4096,
'nDim': MICS,
'samplingRate': 1.25,
'creationInterval': 15,
'delay': 0,
'setof': emprot.SET_OF_RANDOM_MICROGRAPHS} # SetOfMicrographs
# create mic in streaming mode
protStream = self.newProtocol(emprot.ProtCreateStreamData, **kwargs)
protStream.setObjLabel('create Stream Mic')
self.proj.launchProtocol(protStream, wait=False)
# 1st ctf - ctffind4 in streaming
ProtCTFFind = Domain.importFromPlugin('cistem.protocols',
'CistemProtCTFFind', doRaise=True)
protCTF = self.newProtocol(ProtCTFFind)
protCTF.inputMicrographs.set(protStream)
protCTF.inputMicrographs.setExtended('outputMicrographs')
protCTF.findPhaseShift.set(True)
protCTF.numberOfThreads.set(4)
self.proj.scheduleProtocol(protCTF)
# 2nd ctf - Xmipp CTF
kwargs = {'ctfDownFactor': 2,
'numberOfThreads': 4
}
XmippProtCTFMicrographs = Domain.importFromPlugin(
'xmipp3.protocols.protocol_ctf_micrographs',
'XmippProtCTFMicrographs', doRaise=True)
protCTF2 = self.newProtocol(XmippProtCTFMicrographs, **kwargs)
protCTF2.inputMicrographs.set(protStream)
protCTF2.inputMicrographs.setExtended('outputMicrographs')
self.proj.scheduleProtocol(protCTF2)
# 3rd ctf - Gctf
protCTF3 = None
try:
# check if box has nvidia cuda libs.
pynvml.nvmlInit() # fails if not GPU attached
ProtGctf = Domain.importFromPlugin('gctf.protocols', 'ProtGctf',
doRaise=True)
protCTF3 = ProtGctf()
protCTF3.inputMicrographs.set(protStream)
protCTF3.inputMicrographs.setExtended('outputMicrographs')
protCTF3.ctfDownFactor.set(2)
self.proj.scheduleProtocol(protCTF3)
except pynvml.NVMLError as err:
print("Cannot find GPU."
"I assume that no GPU is connected to this machine")
# Check first ctf output - Ctffind
checkOutputs(protCTF)
# Check 2nd ctf output - Xmipp
checkOutputs(protCTF2)
# If GPU and therefore GCTF protocl
if protCTF3 is not None:
checkOutputs(protCTF3)
def test_workflow(self):
try:
from itertools import izip
except ImportError:
izip = zip
# First, import a set of micrographs
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=self.micsFn,
samplingRate=1.237, voltage=300)
self.launchProtocol(protImport)
self.assertIsNotNone(protImport.outputMicrographs,
"There was a problem with the import")
# self.validateFiles('protImport', protImport)
# Import a set of volumes
print("Import Volume")
protImportVol = self.newProtocol(emprot.ProtImportVolumes, filesPath=self.vol1,
samplingRate=9.896)
self.launchProtocol(protImportVol)
self.assertIsNotNone(protImportVol.getFiles(),
"There was a problem with the import")
# self.validateFiles('protImportVol', protImportVol)
# Perform a downsampling on the micrographs
print("Downsampling...")
XmippProtPreprocessMicrographs = Domain.importFromPlugin('xmipp3.protocols',
'XmippProtPreprocessMicrographs',
doRaise=True)
protDownsampling = self.newProtocol(XmippProtPreprocessMicrographs,
doDownsample=True, downFactor=5,
doCrop=False, runMode=1)
protDownsampling.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protDownsampling)
self.assertIsNotNone(protDownsampling.outputMicrographs,
"There was a problem with the downsampling")
# self.validateFiles('protDownsampling', protDownsampling)
# Estimate CTF on the downsampled micrographs
print("Performing CTFfind...")
ProtCTFFind = Domain.importFromPlugin('cistem.protocols',
'CistemProtCTFFind', doRaise=True)
protCTF = self.newProtocol(ProtCTFFind, numberOfThreads=4,
minDefocus=22000, maxDefocus=25000)
protCTF.inputMicrographs.set(protDownsampling.outputMicrographs)
self.launchProtocol(protCTF)
self.assertIsNotNone(protCTF.outputCTF,
"There was a problem with the CTF estimation")
valuesList = [[24000, 24000], [22548, 22518], [23058, 23029]]
for ctfModel, values in izip(protCTF.outputCTF, valuesList):
self.assertAlmostEquals(ctfModel.getDefocusU(), values[0], delta=1000)
self.assertAlmostEquals(ctfModel.getDefocusV(), values[1], delta=1000)
self.assertAlmostEquals(ctfModel.getMicrograph().getSamplingRate(),
6.185, delta=0.001)
# self.validateFiles('protCTF', protCTF)
print("Running Eman import coordinates...")
protPP = self.newProtocol(emprot.ProtImportCoordinates,
importFrom=emprot.ProtImportCoordinates.IMPORT_FROM_EMAN,
filesPath=self.crdsDir,
filesPattern='*_info.json', boxSize=110)
protPP.inputMicrographs.set(protDownsampling.outputMicrographs)
self.launchProtocol(protPP)
self.assertIsNotNone(protPP.outputCoordinates,
"There was a problem with the Eman import coordinates")
# Extract the SetOfParticles.
print("Run extract particles with other downsampling factor")
XmippProtExtractParticles = Domain.importFromPlugin(
'xmipp3.protocols',
'XmippProtExtractParticles')
OTHER = Domain.importFromPlugin('xmipp3.constants', 'OTHER')
protExtract = self.newProtocol(XmippProtExtractParticles,
boxSize=64,
downsampleType=OTHER,
downFactor=8.0,
doFlip=False, runMode=1, doInvert=False)
protExtract.inputCoordinates.set(protPP.outputCoordinates)
protExtract.ctfRelations.set(protCTF.outputCTF)
protExtract.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protExtract)
self.assertIsNotNone(protExtract.outputParticles,
"There was a problem with the extract particles")
def test_workflow(self):
#First, import a set of micrographs
print("Importing a set of micrographs...")
#TODO missing contrst amplitude ROB
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=self.micsFn,
samplingRateMode=1, magnification=79096,
scannedPixelSize=56, voltage=300,
sphericalAberration=2.0)
protImport.setObjLabel('import 20 mics')
self.launchProtocol(protImport)
self.assertIsNotNone(protImport.outputMicrographs,
"There was a problem with the import")
print("Importing a volume...")
protImportVol = self.newProtocol(emprot.ProtImportVolumes,
filesPath=self.vol, samplingRate=7.08)
protImportVol.setObjLabel('import single vol')
self.launchProtocol(protImportVol)
self.assertIsNotNone(protImportVol.outputVolume,
"There was a problem with the import")
print("Preprocessing the micrographs...")
xmippProtocols = Domain.importFromPlugin('xmipp3.protocols',
doRaise=True)
protPreprocess = self.newProtocol(xmippProtocols.XmippProtPreprocessMicrographs,
doCrop=True, cropPixels=25)
protPreprocess.inputMicrographs.set(protImport.outputMicrographs)
protPreprocess.setObjLabel('crop 50px')
self.launchProtocol(protPreprocess)
self.assertIsNotNone(protPreprocess.outputMicrographs,
"There was a problem with the downsampling")
print("Running Eman import coordinates...")
protPP = self.newProtocol(emprot.ProtImportCoordinates,
importFrom=emprot.ProtImportCoordinates.IMPORT_FROM_EMAN,
filesPath=self.crdsEmanDir,
filesPattern='info/*_info.json', boxSize=60)
protPP.inputMicrographs.set(protPreprocess.outputMicrographs)
protPP.setObjLabel('import from Eman boxing')
self.launchProtocol(protPP)
self.assertIsNotNone(protPP.outputCoordinates,
"There was a problem with the Eman import coordinates")
# Now estimate CTF on the micrographs with ctffind
print("Performing CTFfind...")
grigorieffLabProtocols = Domain.importFromPlugin(
'cistem.protocols',
doRaise=True)
protCTF = self.newProtocol(grigorieffLabProtocols.CistemProtCTFFind,
minDefocus=12000, maxDefocus=30000,
runMode=1, numberOfMpi=1, numberOfThreads=16)
protCTF.inputMicrographs.set(protPreprocess.outputMicrographs)
protCTF.setObjLabel('CTF ctffind')
self.launchProtocol(protCTF)
print("Run extract particles with <Same as picking> option")
protExtract = self.newProtocol(xmippProtocols.XmippProtExtractParticles,
boxSize=60,
downsampleType=emprot.SAME_AS_PICKING,
doRemoveDust=False,
doInvert=False,
doFlip=False, backRadius=28, runMode=1)
protExtract.inputCoordinates.set(protPP.outputCoordinates)
protExtract.ctfRelations.set(protCTF.outputCTF)
protExtract.setObjLabel('Extract particles')
self.launchProtocol(protExtract)
self.assertIsNotNone(protExtract.outputParticles,
"There was a problem with the extract particles")
def test1(self):
# Import a set of micrographs
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=self.micsFn,
samplingRate=1.237,
voltage=300)
self.launchProtocol(protImport)
self.assertIsNotNone(protImport.outputMicrographs,
"There was a problem with the import")
# Create pure noise micrographs (to force a Discarded consensus set)
protStream = self.newProtocol(
emprot.ProtCreateStreamData,
xDim=9216,
yDim=9441,
nDim=3,
samplingRate=1.237,
setof=2, # 2 -> SetOfRandomMicrographs
creationInterval=1)
self.proj.launchProtocol(protStream, wait=False)
# Computes the CTF with Xmipp
XmippProtCTFMicrographs = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtCTFMicrographs', doRaise=True)
protCTF1 = self.newProtocol(XmippProtCTFMicrographs)
protCTF1.inputMicrographs.set(protImport.outputMicrographs)
self.proj.launchProtocol(protCTF1, wait=False)
# Computes the CTF with CTFFind4
ProtCTFFind = Domain.importFromPlugin('cistem.protocols',
'CistemProtCTFFind',
doRaise=True)
protCTF2 = self.newProtocol(ProtCTFFind)
protCTF2.inputMicrographs.set(protImport.outputMicrographs)
self.proj.launchProtocol(protCTF2, wait=False)
self._waitOutput(protStream, "outputMicrographs")
# Computes the CTF with CTFFind4 for the noise mics
protCTF3 = self.newProtocol(ProtCTFFind)
protCTF3.inputMicrographs.set(protStream.outputMicrographs)
self.proj.launchProtocol(protCTF3, wait=False)
# Computes the Consensus of GOOD CTFs
self._waitOutput(protCTF1, "outputCTF")
self._waitOutput(protCTF2, "outputCTF")
XmippProtCTFConsensus = Domain.importFromPlugin(
'xmipp3.protocols', 'XmippProtCTFConsensus', doRaise=True)
protCTFcons = self.newProtocol(XmippProtCTFConsensus,
objLabel='default (pass)',
useDefocus=False,
useAstigmatism=False,
useResolution=False,
calculateConsensus=True,
averageDefocus=False,
includeSecondary=False)
protCTFcons.inputCTF.set(protCTF1.outputCTF)
protCTFcons.inputCTF2.set(protCTF2.outputCTF)
self.launchProtocol(protCTFcons)
protCTF1.outputCTF.load() # Needed to update the setSize
self.checkCTFs(protCTFcons,
refMics=protImport.outputMicrographs,
refCTFs=protCTF1.outputCTF)
# Computes the Consensus comparing a good CTF to a RANDOM one
self._waitOutput(protCTF3, "outputCTF")
protCTFcons2 = self.newProtocol(XmippProtCTFConsensus,
objLabel='default (block)',
useDefocus=False,
useAstigmatism=False,
useResolution=False,
calculateConsensus=True,
averageDefocus=False,
includeSecondary=False)
protCTFcons2.inputCTF.set(protCTF1.outputCTF)
protCTFcons2.inputCTF2.set(protCTF3.outputCTF)
self.launchProtocol(protCTFcons2)
self.checkCTFs(protCTFcons2,
refMics=protImport.outputMicrographs,
refCTFs=protCTF1.outputCTF,
label="Discarded")
# Averaging CTF parameters
protCTFcons3 = self.newProtocol(XmippProtCTFConsensus,
objLabel='defocus average',
useDefocus=False,
useAstigmatism=False,
useResolution=False,
calculateConsensus=True,
averageDefocus=True)
protCTFcons3.inputCTF.set(protCTF1.outputCTF)
protCTFcons3.inputCTF2.set(protCTF2.outputCTF)
self.launchProtocol(protCTFcons3)
protCTF1.outputCTF.load() # Needed to update the set
protCTF2.outputCTF.load() # Needed to update the set
ctfAveraged = {
'defocusU': 24140.0898,
'defocusV': 23569.0801,
'defocusAngle': 58.3429
}
self.checkCTFs(protCTFcons3,
refMics=protImport.outputMicrographs,
refCTFs=protCTF1.outputCTF,
avgCTF=ctfAveraged)
# merging Metadata columns
protCTFcons4 = self.newProtocol(XmippProtCTFConsensus,
objLabel='metadata merge',
useDefocus=False,
useAstigmatism=False,
useResolution=False,
calculateConsensus=True,
includeSecondary=True)
protCTFcons4.inputCTF.set(protCTF2.outputCTF)
protCTFcons4.inputCTF2.set(protCTF1.outputCTF)
self.launchProtocol(protCTFcons4)
protCTF1.outputCTF.load() # Needed to update the set
protCTF2.outputCTF.load() # Needed to update the set
self.checkCTFs(protCTFcons4,
refMics=protImport.outputMicrographs,
refCTFs=protCTF2.outputCTF,
MDmerging=True)
def testXmippWorkflow(self):
# First, import a set of micrographs
protImport = self.newProtocol(emprot.ProtImportMicrographs,
filesPath=self.micsFn,
samplingRate=1.237,
voltage=300)
self.launchProtocol(protImport)
self.assertSetSize(protImport.outputMicrographs, 3)
self.assertIsNotNone(protImport.outputMicrographs.getFileName(),
"There was a problem with the import")
self.validateFiles('protImport', protImport)
# Import a set of volumes
print("Import Volume")
protImportVol = self.newProtocol(emprot.ProtImportVolumes,
filesPath=self.vol1,
samplingRate=9.896)
self.launchProtocol(protImportVol)
self.assertIsNotNone(protImportVol.getFiles(),
"There was a problem with the import")
# self.validateFiles('protImportVol', protImportVol)
# Perform a downsampling on the micrographs
print("Downsampling...")
xmippProtcols = Domain.importFromPlugin('xmipp3.protocols',
doRaise=True)
protDownsampling = self.newProtocol(
xmippProtcols.XmippProtPreprocessMicrographs,
doDownsample=True,
downFactor=5,
doCrop=False,
runMode=1)
protDownsampling.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protDownsampling)
self.assertSetSize(protDownsampling.outputMicrographs, 3)
self.assertIsNotNone(protDownsampling.outputMicrographs,
"There was a problem with the downsampling")
self.validateFiles('protDownsampling', protDownsampling)
print("Importing coordinates")
protPP = self.newProtocol(
emprot.ProtImportCoordinates,
importFrom=emprot.ProtImportCoordinates.IMPORT_FROM_XMIPP,
filesPath=self.allCrdsDir,
filesPattern='*.pos',
boxSize=110)
protPP.inputMicrographs.set(protDownsampling.outputMicrographs)
self.launchProtocol(protPP)
self.protDict['protPicking'] = protPP
self.assertSetSize(
protPP.outputCoordinates, 143 + 138 + 122 + 110 + 138 + 122,
"There was a problem with the import of coordinates")
# Now estimate CTF on the downsampled micrographs
print("Performing CTF...")
protCTF = self.newProtocol(xmippProtcols.XmippProtCTFMicrographs,
numberOfThreads=4,
minDefocus=2.2,
maxDefocus=2.5) # Defocus is in microns
protCTF.inputMicrographs.set(protDownsampling.outputMicrographs)
self.launchProtocol(protCTF)
self.assertSetSize(protCTF.outputCTF, 3)
self.assertIsNotNone(protCTF.outputCTF,
"There was a problem with the CTF estimation")
# After CTF estimation, the output micrograph should have CTF info
self.validateFiles('protCTF', protCTF)
print("Run extract particles with other downsampling factor")
protExtract = self.newProtocol(xmippProtcols.XmippProtExtractParticles,
boxSize=64,
downsampleType=emprot.OTHER,
doFlip=True,
downFactor=8,
runMode=1,
doInvert=True)
protExtract.inputCoordinates.set(protPP.outputCoordinates)
protExtract.ctfRelations.set(protCTF.outputCTF)
protExtract.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protExtract)
self.assertIsNotNone(protExtract.outputParticles,
"There was a problem with the extract particles")
self.validateFiles('protExtract', protExtract)
print("Run Extract Coordinates without applying shifts")
protExtractCoords = self.newProtocol(emprot.ProtExtractCoords)
protExtractCoords.inputParticles.set(protExtract.outputParticles)
protExtractCoords.inputMicrographs.set(protImport.outputMicrographs)
self.launchProtocol(protExtractCoords)
# The size of the set of coordinates must be the same as the input set of particles
self.assertSetSize(
protExtractCoords.outputCoordinates,
size=protExtract.outputParticles.getSize(),
msg="There was a problem with the coordinates extraction")
# Check if the scaling factor is being calculated and applied correctly
scale = protExtract.outputParticles.getSamplingRate(
) / protImport.outputMicrographs.getSamplingRate()
inParticleCoord = protExtract.outputParticles.getFirstItem(
).getCoordinate()
x, y = inParticleCoord.getPosition()
self.assertAlmostEqual(
protExtractCoords.outputCoordinates.getFirstItem().getPosition(),
(int(x * scale), int(y * scale)))
print("Run Screen Particles")
protScreen = self.newProtocol(xmippProtcols.XmippProtScreenParticles,
autoParRejection=xmippProtcols.
XmippProtScreenParticles.REJ_MAXZSCORE,
maxZscore=3.0)
protScreen.inputParticles.set(protExtract.outputParticles)
self.launchProtocol(protScreen)
self.assertSetSize(protScreen.outputParticles,
msg="There was a problem with Screen Particles")
print("Run ML2D")
protML2D = self.newProtocol(xmippProtcols.XmippProtML2D,
numberOfClasses=1,
maxIters=4,
doMlf=True,
numberOfMpi=2,
numberOfThreads=1)
protML2D.inputParticles.set(protScreen.outputParticles)
self.launchProtocol(protML2D)
self.assertIsNotNone(protML2D.outputClasses,
"There was a problem with ML2D")
self.validateFiles('protML2D', protML2D)
print("Run CL2D")
protCL2D = self.newProtocol(xmippProtcols.XmippProtCL2D,
numberOfClasses=2,
numberOfInitialClasses=1,
numberOfIterations=4,
numberOfMpi=2)
protCL2D.inputParticles.set(protExtract.outputParticles)
self.launchProtocol(protCL2D)
self.assertIsNotNone(protCL2D.outputClasses,
"There was a problem with CL2D")
self.validateFiles('protCL2D', protCL2D)
print("Run Only Align2d")
protOnlyAlign = self.newProtocol(xmippProtcols.XmippProtCL2DAlign,
maximumShift=5,
numberOfIterations=2,
numberOfMpi=2,
numberOfThreads=1,
useReferenceImage=False)
protOnlyAlign.inputParticles.set(protExtract.outputParticles)
self.launchProtocol(protOnlyAlign)
self.assertIsNotNone(protOnlyAlign.outputParticles,
"There was a problem with Only align2d")
self.validateFiles('protOnlyAlign', protOnlyAlign)
print("Run Extract Coordinates applying shifts")
protExtractCoordsShifts = self.newProtocol(emprot.ProtExtractCoords,
applyShifts=True)
protExtractCoordsShifts.setObjLabel(
'Extract Coordinates applying shifts')
inputParticles = protOnlyAlign.outputParticles
inputMics = protDownsampling.outputMicrographs
protExtractCoordsShifts.inputParticles.set(inputParticles)
protExtractCoordsShifts.inputMicrographs.set(inputMics)
self.launchProtocol(protExtractCoordsShifts)
# The size of the set of coordinates must be the same as the input set of particles
outputParticles = protExtractCoordsShifts.outputCoordinates
self.assertSetSize(
outputParticles,
size=protExtract.outputParticles.getSize(),
msg="There was a problem with the coordinates extraction")
# Check if the scaling factor is being calculated and applied correctly
scale = inputParticles.getSamplingRate(
) / protDownsampling.outputMicrographs.getSamplingRate()
inParticleCoord = inputParticles.getFirstItem().getCoordinate()
shifts = protExtractCoordsShifts.getShifts(
inputParticles.getFirstItem().getTransform(),
inputParticles.getAlignment())
x, y = inParticleCoord.getPosition()
xCoor, yCoor = x - int(shifts[0]), y - int(shifts[1])
self.assertAlmostEqual(
protExtractCoordsShifts.outputCoordinates.getFirstItem().
getPosition(), (int(xCoor * scale), int(yCoor * scale)))
print("Run kerdensom")
ProtKerdensom = self.newProtocol(xmippProtcols.XmippProtKerdensom,
useMask=False,
SomXdim=2,
SomYdim=2,
SomReg0=800,
SomReg1=400,
SomSteps=2)
ProtKerdensom.inputParticles.set(protOnlyAlign.outputParticles)
self.launchProtocol(ProtKerdensom)
self.assertIsNotNone(ProtKerdensom.outputClasses,
"There was a problem with kerdensom")
# self.validateFiles('ProtKerdensom', ProtKerdensom)
print("Run Rotational Spectra")
xmippProtRotSpectra = self.newProtocol(
xmippProtcols.XmippProtRotSpectra,
SomXdim=2,
SomYdim=2,
spectraInnerRadius=4,
spectraOuterRadius=24)
xmippProtRotSpectra.inputParticles.set(protOnlyAlign.outputParticles)
self.launchProtocol(xmippProtRotSpectra)
self.assertIsNotNone(xmippProtRotSpectra.outputClasses,
"There was a problem with Rotational Spectra")
def testRisosome(self):
print("Importing 2D averages (subset of 4)")
ih = emlib.image.ImageHandler()
classesFn = self.ds.getFile('import/classify2d/extra/'
'relion_it015_classes.mrcs')
outputName = 'input_averages.mrcs'
inputTmp = os.path.abspath(self.proj.getTmpPath())
outputFn = self.proj.getTmpPath(outputName)
for i, index in enumerate([5, 16, 17, 18, 24]):
ih.convert((index, classesFn), (i + 1, outputFn))
protAvgs = self.newProtocol(emprot.ProtImportAverages,
objLabel='avgs - 5',
filesPath=inputTmp,
filesPattern=outputName,
samplingRate=7.08)
self.launchProtocol(protAvgs)
# First, import a set of micrographs
print("Importing a set of micrographs...")
protImport = self.newProtocol(emprot.ProtImportMicrographs,
objLabel='import 20 mics (streaming)',
filesPath=os.path.abspath(
self.proj.getTmpPath()),
filesPattern="*%s" % self.ext,
samplingRateMode=1,
magnification=79096,
scannedPixelSize=56,
voltage=300,
sphericalAberration=2.0,
dataStreaming=True,
fileTimeout=10,
timeout=60)
self.proj.launchProtocol(protImport, wait=False)
self._waitOutput(protImport, 'outputMicrographs')
# Now estimate CTF on the micrographs with ctffind
print("Performing CTFfind...")
ProtCTFFind = Domain.importFromPlugin('cistem.protocols',
'CistemProtCTFFind',
doRaise=True)
protCtf = self.newProtocol(
ProtCTFFind,
objLabel='ctffind',
inputMicrographs=protImport.outputMicrographs,
minDefocus=12000,
maxDefocus=30000,
slowSearch=False)
self.proj.launchProtocol(protCtf, wait=False)
self._waitOutput(protCtf, 'outputCTF')
self._waitUntilMinSize(protCtf.outputCTF)
# Select some good averages from the iterations mrcs a
ProtRelion2Autopick = Domain.importFromPlugin('relion.protocols',
'ProtRelion2Autopick')
relion_RUN_COMPUTE = Domain.importFromPlugin('relion', 'RUN_COMPUTE')
protPick = self.newProtocol(
ProtRelion2Autopick,
objLabel='autopick refs',
inputMicrographs=protImport.outputMicrographs,
ctfRelations=protCtf.outputCTF,
runType=relion_RUN_COMPUTE,
inputReferences=protAvgs.outputAverages,
numberOfMpi=2)
self.launchProtocol(protPick)