def _createCluster(self):
""" Create the cluster with the selected particles
from the cluster. This method will be called when
the button 'Create Cluster' is pressed.
"""
# Write the particles
prot = self.protocol
project = prot.getProject()
inputSet = prot.getInputParticles()
fnSqlite = prot._getTmpPath('cluster_particles.sqlite')
cleanPath(fnSqlite)
partSet = SetOfParticles(filename=fnSqlite)
partSet.copyInfo(inputSet)
for point in self.getData():
if point.getState() == Point.SELECTED:
particle = inputSet[point.getId()]
partSet.append(particle)
partSet.write()
partSet.close()
from protocol_batch_cluster import BatchProtNMACluster
newProt = project.newProtocol(BatchProtNMACluster)
clusterName = self.clusterWindow.getClusterName()
if clusterName:
newProt.setObjLabel(clusterName)
newProt.inputNmaDimred.set(prot)
newProt.sqliteFile.set(fnSqlite)
project.launchProtocol(newProt)
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(filename=self._getPath('micrographs_pairs.sqlite'))
print "self._dbName=%s" % self._dbName
modifiedSet = MicrographsTiltPair(filename=self._dbName, prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
outputU.append(untilted)
outputT.append(tilted)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output
def _createSubSetFromParticlesTiltPair(self, particlesTiltPair):
print 'create subset from particles tilt pair'
""" Create a subset of Micrographs Tilt Pair. """
output = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
inputU = particlesTiltPair.getUntilted()
inputT = particlesTiltPair.getTilted()
outputU = SetOfParticles(filename=self._getPath('particles_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('particles_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
modifiedSet = ParticlesTiltPair(filename=self._dbName, prefix=self._dbPrefix)
for pair, u, t in izip(modifiedSet, inputU, inputT):
if pair.isEnabled():
output.append(pair)
outputU.append(u)
outputT.append(t)
# Register outputs
output.setUntilted(outputU)
output.setTilted(outputT)
outputDict = {'outputParticlesTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(particlesTiltPair, output)
return output
def _createSubSetFromParticlesTiltPair(self, particlesTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = ParticlesTiltPair(
filename=self._getPath('particles_pairs.sqlite'))
inputU = particlesTiltPair.getUntilted()
inputT = particlesTiltPair.getTilted()
outputU = SetOfParticles(
filename=self._getPath('particles_untilted.sqlite'))
outputT = SetOfParticles(
filename=self._getPath('particles_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
modifiedSet = ParticlesTiltPair(filename=self._dbName,
prefix=self._dbPrefix)
for pair, u, t in izip(modifiedSet, inputU, inputT):
if pair.isEnabled():
output.append(pair)
outputU.append(u)
outputT.append(t)
# Register outputs
output.setUntilted(outputU)
output.setTilted(outputT)
outputDict = {'outputParticlesTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(particlesTiltPair, output)
return output
def _createCluster(self):
""" Create the cluster with the selected particles
from the cluster. This method will be called when
the button 'Create Cluster' is pressed.
"""
# Write the particles
prot = self.protocol
project = prot.getProject()
inputSet = prot.getInputParticles()
fnSqlite = prot._getTmpPath('cluster_particles.sqlite')
cleanPath(fnSqlite)
partSet = SetOfParticles(filename=fnSqlite)
partSet.copyInfo(inputSet)
for point in self.getData():
if point.getState() == Point.SELECTED:
particle = inputSet[point.getId()]
partSet.append(particle)
partSet.write()
partSet.close()
from protocol_batch_cluster import BatchProtNMACluster
newProt = project.newProtocol(BatchProtNMACluster)
clusterName = self.clusterWindow.getClusterName()
if clusterName:
newProt.setObjLabel(clusterName)
newProt.inputNmaDimred.set(prot)
newProt.sqliteFile.set(fnSqlite)
project.launchProtocol(newProt)
def _createSubSetFromMicrographsTiltPair(self, micrographsTiltPair):
""" Create a subset of Micrographs Tilt Pair. """
output = MicrographsTiltPair(
filename=self._getPath('micrographs_pairs.sqlite'))
modifiedSet = MicrographsTiltPair(filename=self._dbName,
prefix=self._dbPrefix)
inputU = micrographsTiltPair.getUntilted()
inputT = micrographsTiltPair.getTilted()
outputU = SetOfMicrographs(
filename=self._getPath('mics_untilted.sqlite'))
outputT = SetOfParticles(filename=self._getPath('mics_tilted.sqlite'))
outputU.copyInfo(inputU)
outputT.copyInfo(inputT)
for micPairI in modifiedSet:
untilted = micPairI.getUntilted()
tilted = micPairI.getTilted()
if micPairI.isEnabled():
micPairO = TiltPair()
micPairO.setUntilted(untilted)
micPairO.setTilted(tilted)
output.append(micPairO)
outputU.append(untilted)
outputT.append(tilted)
output.setUntilted(outputU)
output.setTilted(outputT)
# Register outputs
outputDict = {'outputMicrographsTiltPair': output}
self._defineOutputs(**outputDict)
self._defineTransformRelation(micrographsTiltPair, output)
return output
def getParticles(self, protImport, classid):
dbPartSet = protImport._getPath("particles_class-%d.sqlite" % classid)
class3D = protImport.outputClasses[classid]
if os.path.exists(dbPartSet):
os.remove(dbPartSet)
partSet = SetOfParticles(filename=dbPartSet)
partSet.copyInfo(class3D)
for part in class3D:
partSet.append(part)
partSet.write()
partSet.close()
protImportCls1 = self.newProtocol(
ProtImportParticles,
objLabel='particles class-%d' % classid,
importFrom=ProtImportParticles.IMPORT_FROM_SCIPION,
sqliteFile=dbPartSet,
magnification=10000,
samplingRate=7.08,
haveDataBeenPhaseFlipped=True)
self.launchProtocol(protImportCls1)
self.assertIsNotNone(protImportCls1.outputParticles.getFileName(),
"There was a problem with the import")
return protImportCls1
def createOutputStep(self):
# Create the SetOfImages object on the database
#imgSet = XmippSetOfParticles(self._getPath('images.xmd'))
fnImages = self._getOutputImgMd()
# Create output SetOfParticles
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputMics)
if self.doFlip:
# Check if self.inputMics are phase flipped.
if self.inputMics.isPhaseFlipped():
imgSet.setIsPhaseFlipped(False)
else:
imgSet.setIsPhaseFlipped(True)
#imgSet.setHasCTF(self.fnCTF is not None)
if self.downsampleType == OTHER:
imgSet.setSamplingRate(self.inputMics.getSamplingRate() *
self.downFactor.get())
imgSet.setCoordinates(self.inputCoords)
# Create a temporary set to read from the metadata file
# and later create the good one with the coordinates
# properly set. We need this because the .update is not
# working in the mapper when new attributes are added.
imgSet.setHasCTF(self.ctfRelations.hasValue())
auxSet = SetOfParticles(filename=':memory:')
auxSet.copyInfo(imgSet)
readSetOfParticles(fnImages, auxSet)
if self.downsampleType != SAME_AS_PICKING:
factor = self.samplingInput / self.samplingFinal
# For each particle retrieve micId from SetOFCoordinates and set it on the CTFModel
for img in auxSet:
#FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
coord = self.inputCoords[img.getObjId()]
if self.downsampleType != SAME_AS_PICKING:
x, y = coord.getPosition()
coord.setPosition(x * factor, y * factor)
ctfModel = img.getCTF()
if ctfModel is not None:
ctfModel.setObjId(coord.getMicId())
##img.setCTF(ctfModel)####JM
img.setMicId(coord.getMicId())
img.setCoordinate(coord)
imgSet.append(img)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=imgSet)
self._defineSourceRelation(self.inputCoordinates, imgSet)
if self.ctfRelations.hasValue():
self._defineSourceRelation(self.ctfRelations.get(), imgSet)
def createOutputStep(self):
# Create the SetOfImages object on the database
#imgSet = XmippSetOfParticles(self._getPath('images.xmd'))
fnImages = self._getOutputImgMd()
# Create output SetOfParticles
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputMics)
if self.doFlip:
# Check if self.inputMics are phase flipped.
if self.inputMics.isPhaseFlipped():
imgSet.setIsPhaseFlipped(False)
else:
imgSet.setIsPhaseFlipped(True)
#imgSet.setHasCTF(self.fnCTF is not None)
if self.downsampleType == OTHER:
imgSet.setSamplingRate(self.inputMics.getSamplingRate()*self.downFactor.get())
imgSet.setCoordinates(self.inputCoords)
# Create a temporary set to read from the metadata file
# and later create the good one with the coordinates
# properly set. We need this because the .update is not
# working in the mapper when new attributes are added.
imgSet.setHasCTF(self.ctfRelations.hasValue())
auxSet = SetOfParticles(filename=':memory:')
auxSet.copyInfo(imgSet)
readSetOfParticles(fnImages, auxSet)
if self.downsampleType != SAME_AS_PICKING:
factor = self.samplingInput / self.samplingFinal
# For each particle retrieve micId from SetOFCoordinates and set it on the CTFModel
for img in auxSet:
#FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
coord = self.inputCoords[img.getObjId()]
if self.downsampleType != SAME_AS_PICKING:
x, y = coord.getPosition()
coord.setPosition(x*factor, y*factor)
ctfModel = img.getCTF()
if ctfModel is not None:
ctfModel.setObjId(coord.getMicId())
##img.setCTF(ctfModel)####JM
img.setMicId(coord.getMicId())
img.setCoordinate(coord)
imgSet.append(img)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=imgSet)
self._defineSourceRelation(self.inputCoordinates, imgSet)
if self.ctfRelations.hasValue():
self._defineSourceRelation(self.ctfRelations.get(), imgSet)
def _allParticles(self, iterate=False):
# A handler function to iterate over the particles
inputSet = self.inputSet.get()
if self.isInputClasses():
iterParticles = inputSet.iterClassItems()
if iterate:
return iterParticles
else:
particles = SetOfParticles(filename=":memory:")
particles.copyInfo(inputSet.getFirstItem())
particles.copyItems(iterParticles)
return particles
else:
if iterate:
return inputSet.iterItems()
else:
return inputSet
def createOutputStep(self):
fnTilted = self._getExtraPath("images_tilted.xmd")
fnUntilted = self._getExtraPath("images_untilted.xmd")
# Create outputs SetOfParticles both for tilted and untilted
imgSetU = self._createSetOfParticles(suffix="Untilted")
imgSetU.copyInfo(self.uMics)
imgSetT = self._createSetOfParticles(suffix="Tilted")
imgSetT.copyInfo(self.tMics)
sampling = self.getMicSampling() if self._micsOther(
) else self.getCoordSampling()
if self._doDownsample():
sampling *= self.downFactor.get()
imgSetU.setSamplingRate(sampling)
imgSetT.setSamplingRate(sampling)
# set coords from the input, will update later if needed
imgSetU.setCoordinates(
self.inputCoordinatesTiltedPairs.get().getUntilted())
imgSetT.setCoordinates(
self.inputCoordinatesTiltedPairs.get().getTilted())
# Read untilted and tilted particles on a temporary object (also disabled particles)
imgSetAuxU = SetOfParticles(filename=':memory:')
imgSetAuxU.copyInfo(imgSetU)
readSetOfParticles(fnUntilted, imgSetAuxU, removeDisabled=False)
imgSetAuxT = SetOfParticles(filename=':memory:')
imgSetAuxT.copyInfo(imgSetT)
readSetOfParticles(fnTilted, imgSetAuxT, removeDisabled=False)
# calculate factor for coords scaling
factor = 1 / self.samplingFactor
if self._doDownsample():
factor /= self.downFactor.get()
coordsT = self.getCoords().getTilted()
# For each untilted particle retrieve micId from SetOfCoordinates untilted
for imgU, coordU in izip(imgSetAuxU, self.getCoords().getUntilted()):
# FIXME: Remove this check when sure that objIds are equal
id = imgU.getObjId()
if id != coordU.getObjId():
raise Exception(
'ObjIds in untilted img and coord are not the same!!!!')
imgT = imgSetAuxT[id]
coordT = coordsT[id]
# If both particles are enabled append them
if imgU.isEnabled() and imgT.isEnabled():
if self._micsOther() or self._doDownsample():
coordU.scale(factor)
coordT.scale(factor)
imgU.setCoordinate(coordU)
imgSetU.append(imgU)
imgT.setCoordinate(coordT)
imgSetT.append(imgT)
if self.doFlip:
imgSetU.setIsPhaseFlipped(self.ctfUntilt.hasValue())
imgSetU.setHasCTF(self.ctfUntilt.hasValue())
imgSetT.setIsPhaseFlipped(self.ctfTilt.hasValue())
imgSetT.setHasCTF(self.ctfTilt.hasValue())
imgSetU.write()
imgSetT.write()
# Define output ParticlesTiltPair
outputset = ParticlesTiltPair(
filename=self._getPath('particles_pairs.sqlite'))
outputset.setTilted(imgSetT)
outputset.setUntilted(imgSetU)
for imgU, imgT in izip(imgSetU, imgSetT):
outputset.append(TiltPair(imgU, imgT))
outputset.setCoordsPair(self.inputCoordinatesTiltedPairs.get())
self._defineOutputs(outputParticlesTiltPair=outputset)
self._defineSourceRelation(self.inputCoordinatesTiltedPairs, outputset)
def createOutputStep(self):
# Create the SetOfImages object on the database
#imgSet = XmippSetOfParticles(self._getPath('images.xmd'))
#Create images.xmd metadata
fnImages = self._getPath('images.xmd')
imgsXmd = xmipp.MetaData()
posFiles = glob(self._getExtraPath('*.pos'))
for posFn in posFiles:
xmdFn = self._getExtraPath(replaceBaseExt(posFn, "xmd"))
if exists(xmdFn):
md = xmipp.MetaData(xmdFn)
mdPos = xmipp.MetaData('particles@%s' % posFn)
mdPos.merge(md)
#imgSet.appendFromMd(mdPos)
imgsXmd.unionAll(mdPos)
else:
self.warning("The coord file %s wasn't used to extract! Maybe you are extracting over a subset of micrographs" % basename(posFn))
imgsXmd.write(fnImages)
# IF selected run xmipp_image_sort_by_statistics to add zscore info to images.xmd
if self.doSort:
args="-i %(fnImages)s --addToInput"
if self.rejectionMethod == REJECT_MAXZSCORE:
maxZscore = self.maxZscore.get()
args += " --zcut " + str(maxZscore)
elif self.rejectionMethod == REJECT_PERCENTAGE:
percentage = self.percentage.get()
args += " --percent " + str(percentage)
self.runJob("xmipp_image_sort_by_statistics", args % locals())
# Create output SetOfParticles
imgSet = self._createSetOfParticles()
imgSet.copyInfo(self.inputMics)
if self.doFlip:
# Check if self.inputMics are phase flipped.
if self.inputMics.isPhaseFlipped():
imgSet.setIsPhaseFlipped(False)
else:
imgSet.setIsPhaseFlipped(True)
#imgSet.setHasCTF(self.fnCTF is not None)
if self.downsampleType == OTHER:
imgSet.setSamplingRate(self.inputMics.getSamplingRate()*self.downFactor.get())
imgSet.setCoordinates(self.inputCoords)
# Create a temporary set to read from the metadata file
# and later create the good one with the coordinates
# properly set. We need this because the .update is not
# working in the mapper when new attributes are added.
imgSet.setHasCTF(self.ctfRelations.hasValue())
auxSet = SetOfParticles(filename=':memory:')
auxSet.copyInfo(imgSet)
readSetOfParticles(fnImages, auxSet)
# For each particle retrieve micId from SetOFCoordinates and set it on the CTFModel
for img in auxSet:
#FIXME: This can be slow to make a query to grab the coord, maybe use zip(imgSet, coordSet)???
coord = self.inputCoords[img.getObjId()]
ctfModel = img.getCTF()
if ctfModel is not None:
ctfModel.setObjId(coord.getMicId())
##img.setCTF(ctfModel)####JM
img.setMicId(coord.getMicId())
img.setCoordinate(coord)
imgSet.append(img)
self._storeMethodsInfo(fnImages)
self._defineOutputs(outputParticles=imgSet)
self._defineSourceRelation(self.inputCoords, imgSet)
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
give the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print "\n"
print "*" * 80
print "* Launching test: ", fileKey
print "*" * 80
is2D = alignType == ALIGN_2D
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile(fileKey + '_Gold_output.vol')
if PRINT_FILES:
print "BINARY DATA: ", stackFn
print "SET1: ", partFn1
print " MD: ", mdFn
print "SET2: ", partFn2
print "OUTPUT: ", outputFn
print "GOLD: ", goldFn
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
partSet.setAcquisition(
Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [numpy.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print "Parset", partFn1
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.writeSetOfParticles(partSet,
mdFn,
"/tmp",
alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
relion.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
relion.readSetOfVolumes(mdFn, partSet2, alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print "-" * 5
print img.getFileName(), img.getIndex()
print 'm1:\n', m1, relion.geometryFromMatrix(m1, False)
print 'm2:\n', m2, relion.geometryFromMatrix(m2, False)
# self.assertTrue(numpy.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))
def createOutputStep(self):
fnTilted = self._getExtraPath("images_tilted.xmd")
fnUntilted = self._getExtraPath("images_untilted.xmd")
# Create outputs SetOfParticles both for tilted and untilted
imgSetU = self._createSetOfParticles(suffix="Untilted")
imgSetU.copyInfo(self.uMics)
imgSetT = self._createSetOfParticles(suffix="Tilted")
imgSetT.copyInfo(self.tMics)
sampling = self.samplingMics if self._micsOther() else self.samplingInput
if self._doDownsample():
sampling *= self.downFactor.get()
imgSetU.setSamplingRate(sampling)
imgSetT.setSamplingRate(sampling)
# set coords from the input, will update later if needed
imgSetU.setCoordinates(self.inputCoordinatesTiltedPairs.get().getUntilted())
imgSetT.setCoordinates(self.inputCoordinatesTiltedPairs.get().getTilted())
# Read untilted and tilted particles on a temporary object (also disabled particles)
imgSetAuxU = SetOfParticles(filename=':memory:')
imgSetAuxU.copyInfo(imgSetU)
readSetOfParticles(fnUntilted, imgSetAuxU, removeDisabled=False)
imgSetAuxT = SetOfParticles(filename=':memory:')
imgSetAuxT.copyInfo(imgSetT)
readSetOfParticles(fnTilted, imgSetAuxT, removeDisabled=False)
# calculate factor for coords scaling
factor = 1 / self.samplingFactor
if self._doDownsample():
factor /= self.downFactor.get()
coordsT = self.inputCoordinatesTiltedPairs.get().getTilted()
# For each untilted particle retrieve micId from SetOfCoordinates untilted
for imgU, coordU in izip(imgSetAuxU, self.inputCoordinatesTiltedPairs.get().getUntilted()):
# FIXME: Remove this check when sure that objIds are equal
id = imgU.getObjId()
if id != coordU.getObjId():
raise Exception('ObjIds in untilted img and coord are not the same!!!!')
imgT = imgSetAuxT[id]
coordT = coordsT[id]
# If both particles are enabled append them
if imgU.isEnabled() and imgT.isEnabled():
if self._micsOther() or self._doDownsample():
coordU.scale(factor)
coordT.scale(factor)
imgU.setCoordinate(coordU)
imgSetU.append(imgU)
imgT.setCoordinate(coordT)
imgSetT.append(imgT)
imgSetU.write()
imgSetT.write()
# Define output ParticlesTiltPair
outputset = ParticlesTiltPair(filename=self._getPath('particles_pairs.sqlite'))
outputset.setTilted(imgSetT)
outputset.setUntilted(imgSetU)
for imgU, imgT in izip(imgSetU, imgSetT):
outputset.append(TiltPair(imgU, imgT))
outputset.setCoordsPair(self.inputCoordinatesTiltedPairs.get())
self._defineOutputs(outputParticlesTiltPair=outputset)
self._defineSourceRelation(self.inputCoordinatesTiltedPairs, outputset)
def launchTest(self, fileKey, mList, alignType=None, **kwargs):
""" Helper function to launch similar alignment tests
give the EMX transformation matrix.
Params:
fileKey: the file where to grab the input stack images.
mList: the matrix list of transformations
(should be the same length of the stack of images)
"""
print ("\n")
print ("*" * 80)
print ("* Launching test: ", fileKey)
print ("*" * 80)
is2D = alignType == ALIGN_2D
stackFn = self.dataset.getFile(fileKey)
partFn1 = self.getOutputPath(fileKey + "_particles1.sqlite")
mdFn = self.getOutputPath(fileKey + "_particles.star")
partFn2 = self.getOutputPath(fileKey + "_particles2.sqlite")
if self.IS_ALIGNMENT:
outputFn = self.getOutputPath(fileKey + "_output.mrcs")
outputFnRelion = self.getOutputPath(fileKey + "_output")
goldFn = self.dataset.getFile(fileKey + '_Gold_output_relion.mrcs')
else:
outputFn = self.getOutputPath(fileKey + "_output.vol")
goldFn = self.dataset.getFile(fileKey + '_Gold_output.vol')
if PRINT_FILES:
print("BINARY DATA: ", stackFn)
print("SET1: ", partFn1)
print(" MD: ", mdFn)
print("SET2: ", partFn2)
print("OUTPUT: ", outputFn)
print("GOLD: ", goldFn)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
partSet = SetOfParticles(filename=partFn1)
else:
partSet = SetOfVolumes(filename=partFn1)
partSet.setAlignment(alignType)
partSet.setAcquisition(Acquisition(voltage=300,
sphericalAberration=2,
amplitudeContrast=0.1,
magnification=60000))
# Populate the SetOfParticles with images
# taken from images.mrc file
# and setting the previous alignment parameters
aList = [numpy.array(m) for m in mList]
for i, a in enumerate(aList):
p = Particle()
p.setLocation(i + 1, stackFn)
p.setTransform(Transform(a))
partSet.append(p)
# Write out the .sqlite file and check that are correctly aligned
print ("Parset", partFn1)
partSet.printAll()
partSet.write()
# Convert to a Xmipp metadata and also check that the images are
# aligned correctly
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.writeSetOfParticles(partSet, mdFn,"/tmp", alignType=alignType)
partSet2 = SetOfParticles(filename=partFn2)
else:
relion.writeSetOfVolumes(partSet, mdFn, alignType=alignType)
partSet2 = SetOfVolumes(filename=partFn2)
# Let's create now another SetOfImages reading back the written
# Xmipp metadata and check one more time.
partSet2.copyInfo(partSet)
if alignType == ALIGN_2D or alignType == ALIGN_PROJ:
relion.readSetOfParticles(mdFn, partSet2, alignType=alignType)
else:
relion.readSetOfVolumes(mdFn, partSet2, alignType=alignType)
partSet2.write()
if PRINT_MATRIX:
for i, img in enumerate(partSet2):
m1 = aList[i]
m2 = img.getTransform().getMatrix()
print ("-" * 5)
print (img.getFileName(), img.getIndex())
print ('m1:\n', m1, relion.geometryFromMatrix(m1, False))
print ('m2:\n', m2, relion.geometryFromMatrix(m2, False))
# self.assertTrue(numpy.allclose(m1, m2, rtol=1e-2))
# Launch apply transformation and check result images
runRelionProgram(self.CMD % locals())
if SHOW_IMAGES:
runRelionProgram('scipion show %(outputFn)s' % locals())
if os.path.exists(goldFn):
self.assertTrue(
ImageHandler().compareData(goldFn, outputFn, tolerance=0.001),
"Different data files:\n>%s\n<%s" % (goldFn, outputFn))