def _appendRctImages(self, particles):
blockMd = "class%06d_images@%s" % (particles.getObjId(),
self.rctClassesFn)
classMd = xmipp.MetaData()
uImages = self.inputParticlesTiltPair.get().getUntilted()
tImages = self.inputParticlesTiltPair.get().getTilted()
sangles = self.inputParticlesTiltPair.get().getCoordsPair().getAngles()
uMics = self.inputParticlesTiltPair.get().getCoordsPair().getMicsPair(
).getUntilted()
tMics = tImages.getCoordinates().getMicrographs()
scaleFactor = uImages.getSamplingRate() / particles.getSamplingRate()
for img in particles:
imgId = img.getObjId()
uImg = uImages[imgId]
tImg = tImages[imgId]
if uImg is None or tImg is None:
print ">>> Warning, for id %d, tilted or untilted particle was not found. Ignored." % imgId
else:
objId = classMd.addObject()
pairRow = XmippMdRow()
pairRow.setValue(xmipp.MDL_IMAGE, getImageLocation(uImg))
uCoord = uImg.getCoordinate()
micId = uCoord.getMicId()
uMic = uMics[micId]
angles = sangles[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH, uMic.getFileName())
pairRow.setValue(xmipp.MDL_XCOOR, uCoord.getX())
pairRow.setValue(xmipp.MDL_YCOOR, uCoord.getY())
pairRow.setValue(xmipp.MDL_ENABLED, 1)
pairRow.setValue(xmipp.MDL_ITEM_ID, long(imgId))
pairRow.setValue(xmipp.MDL_REF, 1)
alignment = img.getTransform()
# Scale alignment by scaleFactor
alignment.scale(scaleFactor)
alignmentToRow(alignment, pairRow, alignType=ALIGN_2D)
pairRow.setValue(xmipp.MDL_IMAGE_TILTED,
getImageLocation(tImg))
tMic = tMics[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH_TILTED,
tMic.getFileName())
(angleY, angleY2, angleTilt) = angles.getAngles()
pairRow.setValue(xmipp.MDL_ANGLE_Y, float(angleY))
pairRow.setValue(xmipp.MDL_ANGLE_Y2, float(angleY2))
pairRow.setValue(xmipp.MDL_ANGLE_TILT, float(angleTilt))
pairRow.writeToMd(classMd, objId)
classMd.write(blockMd, xmipp.MD_APPEND)
def _appendRctImages(self, particles):
blockMd = "class%06d_images@%s" % (particles.getObjId(),
self.rctClassesFn)
classMd = xmipp.MetaData()
partPairs = self.inputParticlesTiltPair.get()
uImages = partPairs.getUntilted()
tImages = partPairs.getTilted()
sangles = partPairs.getCoordsPair().getAngles()
micPairs = partPairs.getCoordsPair().getMicsPair()
uMics = micPairs.getUntilted()
tMics = micPairs.getTilted()
scaleFactor = uImages.getSamplingRate() / particles.getSamplingRate()
for img in particles:
imgId = img.getObjId()
uImg = uImages[imgId]
tImg = tImages[imgId]
if uImg is None or tImg is None:
print (">>> Warning, for id %d, tilted or untilted particle "
"was not found. Ignored." % imgId)
else:
objId = classMd.addObject()
pairRow = XmippMdRow()
pairRow.setValue(xmipp.MDL_IMAGE, getImageLocation(uImg))
uCoord = uImg.getCoordinate()
micId = uCoord.getMicId()
uMic = uMics[micId]
angles = sangles[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH, uMic.getFileName())
pairRow.setValue(xmipp.MDL_XCOOR, uCoord.getX())
pairRow.setValue(xmipp.MDL_YCOOR, uCoord.getY())
pairRow.setValue(xmipp.MDL_ENABLED, 1)
pairRow.setValue(xmipp.MDL_ITEM_ID, long(imgId))
pairRow.setValue(xmipp.MDL_REF, 1)
alignment = img.getTransform()
# Scale alignment by scaleFactor
alignment.scale(scaleFactor)
alignmentToRow(alignment, pairRow, alignType=ALIGN_2D)
pairRow.setValue(xmipp.MDL_IMAGE_TILTED, getImageLocation(tImg))
tMic = tMics[micId]
pairRow.setValue(xmipp.MDL_MICROGRAPH_TILTED, tMic.getFileName())
(angleY, angleY2, angleTilt) = angles.getAngles()
pairRow.setValue(xmipp.MDL_ANGLE_Y, float(angleY))
pairRow.setValue(xmipp.MDL_ANGLE_Y2, float(angleY2))
pairRow.setValue(xmipp.MDL_ANGLE_TILT, float(angleTilt))
pairRow.writeToMd(classMd, objId)
classMd.write(blockMd, xmipp.MD_APPEND)
def _applyBfactor(self, e=None):
bFactorFile = self.protocol._getPath('bfactor.txt')
f = open(bFactorFile)
values = map(float, f.readline().split())
f.close()
self.protocol.setStepsExecutor() # set default execution
vol = self.protocol.inputVolume.get()
volPath = getImageLocation(vol)
maxres = 1. / sqrt(values[2])
args = '-i %s ' % volPath
pixelSize = vol.getSamplingRate()
args += '--sampling %f ' % pixelSize
args += '--maxres %f ' % maxres
args += '--adhoc %f ' % -values[4]
volName = os.path.basename(volPath)
volOut = self.protocol._getPath(volName)
args += '-o %s ' % volOut
self.protocol.runJob('xmipp_volume_correct_bfactor', args)
#args = '-i %s -o %s' % (volPath, self.protocol._getPath(volName))
#self.protocol.runJob('xmipp_image_convert', args)
volSet = self.protocol._createSetOfVolumes()
volSet.setSamplingRate(pixelSize)
newVol = vol.clone()
newVol.setObjId(None)
newVol.setLocation(volOut)
volSet.append(newVol)
volSet.write()
self.objectView(volSet).show()
def _applyBfactor(self, e=None):
bFactorFile = self.protocol._getPath('bfactor.txt')
f = open(bFactorFile)
values = map(float, f.readline().split())
f.close()
self.protocol.setStepsExecutor() # set default execution
vol = self.protocol.inputVolume.get()
volPath = getImageLocation(vol)
maxres = 1. / sqrt(values[2])
args = '-i %s ' % volPath
pixelSize = vol.getSamplingRate()
args += '--sampling %f ' % pixelSize
args += '--maxres %f ' % maxres
args += '--adhoc %f ' % -values[4]
volName = os.path.basename(volPath)
volOut = self.protocol._getPath(volName)
args += '-o %s ' % volOut
self.protocol.runJob('xmipp_volume_correct_bfactor', args)
#args = '-i %s -o %s' % (volPath, self.protocol._getPath(volName))
#self.protocol.runJob('xmipp_image_convert', args)
volSet = self.protocol._createSetOfVolumes()
volSet.setSamplingRate(pixelSize)
newVol = vol.clone()
newVol.setObjId(None)
newVol.setLocation(volOut)
volSet.append(newVol)
volSet.write()
self.objectView(volSet).show()
def _reconstructImages(self, particles, deps):
""" Function to insert the step needed to reconstruct a class (or setOfParticles) """
classNo = particles.getObjId()
blockMd = "class%06d_images@%s" % (classNo, self.rctClassesFn)
classNameIn = blockMd
classNameOut = self._getExtraPath("rct_images_%06d.xmd" % classNo)
classVolumeOut = self._getPath("rct_%06d.vol" % classNo)
if particles.hasRepresentative():
classImage = getImageLocation(particles.getRepresentative())
else:
classImage = None
reconStep = self._insertFunctionStep('reconstructClass', classNameIn, classNameOut, classImage, classVolumeOut, prerequisites=[deps])
return reconStep
def _reconstructImages(self, particles, deps):
""" Function to insert the step needed to reconstruct a
class (or setOfParticles) """
classNo = particles.getObjId()
blockMd = "class%06d_images@%s" % (classNo, self.rctClassesFn)
classNameIn = blockMd
classNameOut = self._getExtraPath("rct_images_%06d.xmd" % classNo)
classVolumeOut = self._getPath("rct_%06d.vol" % classNo)
if particles.hasRepresentative():
classImage = getImageLocation(particles.getRepresentative())
else:
classImage = None
reconStep = self._insertFunctionStep('reconstructClass',
classNameIn,
classNameOut,
classImage,
classVolumeOut,
prerequisites=[deps])
return reconStep
def _insertAllSteps(self):
""" Mainly prepare the command line for call cl2d align program"""
# Convert input images if necessary
self.imgsFn = self._getExtraPath('images.xmd')
self._insertFunctionStep('convertInputStep')
# Prepare arguments to call program: xmipp_classify_CL2D
self._params = {'imgsFn': self.imgsFn,
'extraDir': self._getExtraPath(),
'maxshift': self.maximumShift.get(),
'iter': self.numberOfIterations.get(),
}
args = '-i %(imgsFn)s --odir %(extraDir)s --nref 1 --iter %(iter)d --maxShift %(maxshift)d'
if self.useReferenceImage:
args += " --ref0 " + getImageLocation(self.referenceImage.get())
else:
args += " --nref0 1"
self._insertRunJobStep("xmipp_classify_CL2D", args % self._params)
self._insertFunctionStep('createOutputStep')
def _insertAllSteps(self):
""" Mainly prepare the command line for call cl2d align program"""
# Convert input images if necessary
self.imgsFn = self._getExtraPath('images.xmd')
self._insertFunctionStep('convertInputStep')
# Prepare arguments to call program: xmipp_classify_CL2D
self._params = {'imgsFn': self.imgsFn,
'extraDir': self._getExtraPath(),
'maxshift': self.maximumShift.get(),
'iter': self.numberOfIterations.get(),
}
args = '-i %(imgsFn)s --odir %(extraDir)s --nref 1 --iter %(iter)d --maxShift %(maxshift)d'
if self.useReferenceImage:
args += " --ref0 " + getImageLocation(self.referenceImage.get())
else:
args += " --nref0 1"
self._insertRunJobStep("xmipp_classify_CL2D", args % self._params)
self._insertFunctionStep('createOutputStep')
