def applyMaskStep(self):
import pyworkflow.em.packages.xmipp3 as xmipp3
from pyworkflow.em.packages.xmipp3.convert import getImageLocation
params = ' -i %s --mult %s -o %s' % (getImageLocation(self.inputVolume.get()),
getImageLocation(self.refMask.get()),
self._getFileName('volume_masked'))
self.runJob('xmipp_image_operate', params, env=xmipp3.getEnviron())
def applyMaskStep(self):
import pyworkflow.em.packages.xmipp3 as xmipp3
from pyworkflow.em.packages.xmipp3.convert import getImageLocation
params = ' -i %s --mult %s -o %s' % (getImageLocation(
self.inputVolume.get()), getImageLocation(
self.refMask.get()), self._getFileName('volume_masked'))
self.runJob('xmipp_image_operate', params, env=xmipp3.getEnviron())
def _insertAllSteps(self):
cutoffStr = ''
if self.cutoffMode == NMA_CUTOFF_REL:
cutoffStr = 'Relative %f' % self.rcPercentage.get()
else:
cutoffStr = 'Absolute %f' % self.rc.get()
maskArgs = ''
alignArgs = self._getAlignArgs()
ALIGN_ALGORITHM_EXHAUSTIVE_LOCAL = 1
self.alignmentAlgorithm = ALIGN_ALGORITHM_EXHAUSTIVE_LOCAL
volList = [vol.clone() for vol in self._iterInputVolumes()]
nVoli = 1
for voli in volList:
fnIn = getImageLocation(voli)
fnMask = self._insertMaskStep(fnIn)
suffix = "_%d" % nVoli
self._insertFunctionStep('convertToPseudoAtomsStep', fnIn, fnMask,
voli.getSamplingRate(), suffix)
fnPseudoAtoms = self._getPath("pseudoatoms_%d.pdb" % nVoli)
self._insertFunctionStep('computeModesStep', fnPseudoAtoms,
self.numberOfModes, cutoffStr)
self._insertFunctionStep('reformatOutputStep',
os.path.basename(fnPseudoAtoms))
self._insertFunctionStep(
'qualifyModesStep', self.numberOfModes,
self.collectivityThreshold.get(),
self._getPath("pseudoatoms_%d.pdb" % nVoli), suffix)
#rigid alignment
nVolj = 1
for volj in volList:
if nVolj != nVoli:
refFn = getImageLocation(voli)
inVolFn = getImageLocation(volj)
volId = volj.getObjId()
outVolFn = self._getPath(
'outputRigidAlignment_vol_%d_to_%d.vol' %
(nVolj, nVoli))
self._insertFunctionStep('alignVolumeStep', refFn, inVolFn,
outVolFn, maskArgs, alignArgs,
volId)
self._insertFunctionStep('elasticAlignmentStep', nVoli,
voli, nVolj)
nVolj += 1
nVoli += 1
self._insertFunctionStep('gatherResultsStep')
self._insertFunctionStep('managingOutputFilesStep')
def _insertAllSteps(self):
"""Insert all steps to calculate the resolution of a 3D reconstruction. """
self.inputVol = getImageLocation(self.inputVolume.get())
if self.referenceVolume.hasValue():
self.refVol = getImageLocation(self.referenceVolume.get())
if self.doFSC:
self._insertFunctionStep('calculateFscStep')
if self.doComputeBfactor:
self._insertFunctionStep('computeBfactorStep')
self._insertFunctionStep('createSummaryStep')
def _insertAllSteps(self):
"""Insert all steps to calculate the resolution of a 3D reconstruction. """
self.inputVol = getImageLocation(self.inputVolume.get())
if self.referenceVolume.hasValue():
self.refVol = getImageLocation(self.referenceVolume.get())
if self.doFSC:
self._insertFunctionStep('calculateFscStep')
if self.doComputeBfactor:
self._insertFunctionStep('computeBfactorStep')
self._insertFunctionStep('createSummaryStep')
def _insertAllSteps(self):
cutoffStr=''
if self.cutoffMode == NMA_CUTOFF_REL:
cutoffStr = 'Relative %f'%self.rcPercentage.get()
else:
cutoffStr = 'Absolute %f'%self.rc.get()
maskArgs = ''
alignArgs = self._getAlignArgs()
ALIGN_ALGORITHM_EXHAUSTIVE_LOCAL = 1
self.alignmentAlgorithm = ALIGN_ALGORITHM_EXHAUSTIVE_LOCAL
volList = [vol.clone() for vol in self._iterInputVolumes()]
nVoli = 1
for voli in volList:
fnIn = getImageLocation(voli)
fnMask = self._insertMaskStep(fnIn)
suffix = "_%d"%nVoli
self._insertFunctionStep('convertToPseudoAtomsStep',
fnIn, fnMask, voli.getSamplingRate(), suffix)
fnPseudoAtoms = self._getPath("pseudoatoms_%d.pdb"%nVoli)
self._insertFunctionStep('computeModesStep', fnPseudoAtoms,
self.numberOfModes, cutoffStr)
self._insertFunctionStep('reformatOutputStep', os.path.basename(fnPseudoAtoms))
self._insertFunctionStep('qualifyModesStep', self.numberOfModes,
self.collectivityThreshold.get(),
self._getPath("pseudoatoms_%d.pdb"%nVoli), suffix)
#rigid alignment
nVolj = 1
for volj in volList:
if nVolj != nVoli:
refFn = getImageLocation(voli)
inVolFn = getImageLocation(volj)
volId = volj.getObjId()
outVolFn = self._getPath('outputRigidAlignment_vol_%d_to_%d.vol' % (nVolj, nVoli))
self._insertFunctionStep('alignVolumeStep', refFn, inVolFn, outVolFn,
maskArgs, alignArgs, volId)
self._insertFunctionStep('elasticAlignmentStep',nVoli, voli, nVolj)
nVolj += 1
nVoli += 1
self._insertFunctionStep('gatherResultsStep')
self._insertFunctionStep('managingOutputFilesStep')
def _insertAllSteps(self):
# Iterate through all input volumes and align them
# againt the reference volume
refFn = getImageLocation(self.inputReference.get())
maskArgs = self._getMaskArgs()
alignArgs = self._getAlignArgs()
alignSteps = []
for vol in self._iterInputVolumes():
volFn = getImageLocation(vol)
stepId = self._insertFunctionStep('alignVolumeStep', refFn, volFn, vol.outputName,
maskArgs, alignArgs, prerequisites=[])
alignSteps.append(stepId)
self._insertFunctionStep('createOutputStep', prerequisites=alignSteps)
def _insertAllSteps(self):
# Iterate throught all input volumes and align them
# againt the reference volume
refFn = getImageLocation(self.inputReference.get())
maskArgs = self._getMaskArgs()
alignArgs = self._getAlignArgs()
alignSteps = []
for vol in self._iterInputVolumes():
volFn = getImageLocation(vol)
stepId = self._insertFunctionStep('alignVolumeStep', refFn, volFn, vol.outputName,
maskArgs, alignArgs, prerequisites=[])
alignSteps.append(stepId)
self._insertFunctionStep('createOutputStep', prerequisites=alignSteps)
def _insertAllSteps(self):
convertId = self._insertFunctionStep("convertInputStep", self.inputParticles.get().getObjId())
deps = [] # store volumes steps id to use as dependencies for last step
commonParams = self._getCommonParams()
commonParamsRef = self._getCommonParamsRef()
sym = self.symmetryGroup.get()
for i, vol in enumerate(self._iterInputVols()):
volName = getImageLocation(vol)
volDir = self._getVolDir(i + 1)
sigStepId = self._insertFunctionStep(
"significantStep", volName, volDir, "exp_particles.xmd", commonParams, prerequisites=[convertId]
)
phanProjStepId = self._insertFunctionStep("phantomProject", volName, prerequisites=[convertId])
sigStepId = self._insertFunctionStep(
"significantStep", volName, volDir, "ref_particles.xmd", commonParamsRef, prerequisites=[phanProjStepId]
)
volStepId = self._insertFunctionStep("validationStep", volName, volDir, sym, prerequisites=[sigStepId])
deps.append(volStepId)
self._insertFunctionStep("createOutputStep", prerequisites=deps)
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
from pyworkflow.em.packages.xmipp3.convert import getImageLocation
xmipp.gaussianFilter(self.rightImage, getImageLocation(self.lastObj),
self.getFreqSigma(), self.dim)
def _insertAllSteps(self):
#divide work in several threads
numberOfThreads = self.numberOfThreads.get() - 1
if numberOfThreads == 0:
numberOfThreads = 1
partSet = self.inputParticles.get()
nPart = len(partSet)
numberOfThreads = min(numberOfThreads, nPart)
samplingRate = partSet.getSamplingRate()
inputVolume = getImageLocation(self.inputVolume.get())
mdFn = self._getInputParticlesFn()
convertId = self._insertFunctionStep('convertInputStep', inputVolume)
deps = [convertId]
# Create xmipp metadata
# partSet
#writeSetOfParticles(partSet, mdFn, blockName="images")
groupSize = nPart / numberOfThreads
groupRemainder = nPart % numberOfThreads
depsOutPut = []
for thread in range(0, numberOfThreads):
start = long(thread * groupSize + 1)
end = long(thread * groupSize + groupSize)
if thread == (numberOfThreads - 1):
end += groupRemainder
idStep = self._insertFunctionStep('projectStep',
start,
end,
samplingRate,
thread,
prerequisites=deps)
depsOutPut.append(idStep)
self._insertFunctionStep('createOutputStep', prerequisites=depsOutPut)
def _insertAllSteps(self):
#divide work in several threads
numberOfThreads = self.numberOfThreads.get()-1
if numberOfThreads == 0:
numberOfThreads = 1
partSet = self.inputParticles.get()
nPart = len(partSet)
numberOfThreads = min(numberOfThreads, nPart)
samplingRate = partSet.getSamplingRate()
inputVolume = getImageLocation(self.inputVolume.get())
mdFn = self._getInputParticlesFn()
convertId = self._insertFunctionStep('convertInputStep',
inputVolume)
deps = [convertId]
# Create xmipp metadata
# partSet
#writeSetOfParticles(partSet, mdFn, blockName="images")
groupSize = nPart/numberOfThreads
groupRemainder = nPart%numberOfThreads
depsOutPut=[]
for thread in range(0, numberOfThreads):
start = long(thread * groupSize+1)
end = long(thread * groupSize+groupSize)
if thread == (numberOfThreads-1):
end += groupRemainder
idStep = self._insertFunctionStep('projectStep', start, end,
samplingRate, thread,
prerequisites=deps)
depsOutPut.append(idStep)
self._insertFunctionStep('createOutputStep', prerequisites=depsOutPut)
def _computeRightPreview(self):
""" This function should compute the right preview
using the self.lastObj that was selected
"""
from pyworkflow.em.packages.xmipp3.convert import getImageLocation
xmipp.gaussianFilter(self.rightImage, getImageLocation(self.lastObj),
self.getFreqSigma(), self.dim)
def _insertAllSteps(self):
self._insertFunctionStep('copyInput')
self._insertFunctionStep('coarseSearch')
self._insertFunctionStep('fineSearch')
self._insertFunctionStep('symmetrize')
self._insertFunctionStep('createOutput')
self.fnVol = getImageLocation(self.inputVolume.get())
self.fnVolSym = self._getPath('volume_symmetrized.vol')
[self.height, _, _] = self.inputVolume.get().getDim()
def _insertAllSteps(self):
self._insertFunctionStep('copyInput')
self._insertFunctionStep('coarseSearch')
self._insertFunctionStep('fineSearch')
self._insertFunctionStep('symmetrize')
self._insertFunctionStep('createOutput')
self.fnVol = getImageLocation(self.inputVolume.get())
self.fnVolSym=self._getPath('volume_symmetrized.vol')
[self.height,_,_]=self.inputVolume.get().getDim()
def convertInputStep(self, volName):
# Read volume and convert to DOUBLE
self.vol = xmipp.Image(volName)
self.vol.convert2DataType(xmipp.DT_DOUBLE)
# Mask volume if needed
if self.refMask.get() is not None:
maskName = getImageLocation(self.refMask.get())
self.mask = xmipp.Image(maskName)
self.mask.convert2DataType(xmipp.DT_DOUBLE)
self.vol.inplaceMultiply(self.mask)
padding = 2
maxFreq = 0.5
splineDegree = 3
###
self.fourierProjectVol = xmipp.FourierProjector(
self.vol, padding, maxFreq, splineDegree)
###
partSet = self.inputParticles.get()
nPart = len(partSet)
numberOfTasks = min(nPart, max(self.numberOfThreads.get() - 1, 1))
taskSize = nPart / numberOfTasks
md = xmipp.MetaData()
# Convert angles and shifts from volume system of coordinates to
# projection system of coordinates
mdCount = 0
for index, part in enumerate(partSet):
objId = md.addObject()
imgRow = XmippMdRow()
particleToRow(part, imgRow)
shifts, angles = geometryFromMatrix(
part.getTransform().getMatrix(), True)
imgRow.setValue(xmipp.MDL_SHIFT_X, -shifts[0])
imgRow.setValue(xmipp.MDL_SHIFT_Y, -shifts[1])
imgRow.setValue(xmipp.MDL_SHIFT_Z, 0.)
imgRow.setValue(xmipp.MDL_ANGLE_ROT, angles[0])
imgRow.setValue(xmipp.MDL_ANGLE_TILT, angles[1])
imgRow.setValue(xmipp.MDL_ANGLE_PSI, angles[2])
imgRow.writeToMd(md, objId)
# Write a new metadata every taskSize number of elements
# except in the last chunk where we want to add also the
# remainder and the condition is the last element
if ((index % taskSize == taskSize - 1
and mdCount < numberOfTasks - 1) or index == nPart - 1):
md.write(self._getInputParticlesSubsetFn(mdCount))
md.clear()
mdCount += 1
x, y, _ = partSet.getDim()
xmipp.createEmptyFile(self._getProjGalleryFn(), x, y, 1, nPart)
def _insertMaskStep(self, fnVol, prefix=''):
""" Check the mask selected and insert the necessary steps.
Return the mask filename if needed.
"""
fnMask = ''
if self.maskMode == NMA_MASK_THRE:
fnMask = self._getExtraPath('mask%s.vol' % prefix)
maskParams = '-i %s -o %s --select below %f --substitute binarize' % (fnVol, fnMask, self.maskThreshold.get())
self._insertRunJobStep('xmipp_transform_threshold', maskParams)
elif self.maskMode == NMA_MASK_FILE:
fnMask = getImageLocation(self.volumeMask.get())
return fnMask
def convertInputStep(self, volName):
# Read volume and convert to DOUBLE
self.vol = xmipp.Image(volName)
self.vol.convert2DataType(xmipp.DT_DOUBLE)
# Mask volume if needed
if self.refMask.get() is not None:
maskName = getImageLocation(self.refMask.get())
self.mask = xmipp.Image(maskName)
self.mask.convert2DataType(xmipp.DT_DOUBLE)
self.vol.inplaceMultiply(self.mask)
padding = 2
maxFreq = 0.5
splineDegree = 3
###
self.fourierProjectVol = xmipp.FourierProjector(self.vol, padding, maxFreq, splineDegree)
###
partSet = self.inputParticles.get()
nPart = len(partSet)
numberOfTasks = min(nPart, max(self.numberOfThreads.get()-1, 1))
taskSize = nPart / numberOfTasks
md = xmipp.MetaData()
# Convert angles and shifts from volume system of coordinates to
# projection system of coordinates
mdCount = 0
for index, part in enumerate(partSet):
objId = md.addObject()
imgRow = XmippMdRow()
particleToRow(part, imgRow)
shifts, angles = geometryFromMatrix(part.getTransform().getMatrix(), True)
imgRow.setValue(xmipp.MDL_SHIFT_X,-shifts[0])
imgRow.setValue(xmipp.MDL_SHIFT_Y,-shifts[1])
imgRow.setValue(xmipp.MDL_SHIFT_Z,0.)
imgRow.setValue(xmipp.MDL_ANGLE_ROT,angles[0])
imgRow.setValue(xmipp.MDL_ANGLE_TILT,angles[1])
imgRow.setValue(xmipp.MDL_ANGLE_PSI,angles[2])
imgRow.writeToMd(md, objId)
# Write a new metadata every taskSize number of elements
# except in the last chunk where we want to add also the
# remainder and the condition is the last element
if ((index % taskSize == taskSize-1 and
mdCount < numberOfTasks-1) or index == nPart-1):
md.write(self._getInputParticlesSubsetFn(mdCount))
md.clear()
mdCount += 1
x, y, _ = partSet.getDim()
xmipp.createEmptyFile(self._getProjGalleryFn(), x, y, 1, nPart)
def _insertAllSteps(self):
convertId = self._insertFunctionStep(
'convertInputStep',
self.inputParticles.get().getObjId())
deps = [
] # store volumes steps id to use as dependencies for last step
commonParams = self._getCommonParams()
commonParamsRef = self._getCommonParamsRef()
sym = self.symmetryGroup.get()
for i, vol in enumerate(self._iterInputVols()):
volName = getImageLocation(vol)
volDir = self._getVolDir(i + 1)
pmStepId = self._insertFunctionStep('projectionLibraryStep',
volName,
volDir,
self.angularSampling.get(),
prerequisites=[convertId])
sigStepId1 = self._insertFunctionStep('significantStep',
volName,
volDir,
'exp_particles.xmd',
commonParams,
prerequisites=[pmStepId])
phanProjStepId = self._insertFunctionStep(
'phantomProject', prerequisites=[sigStepId1])
sigStepId2 = self._insertFunctionStep(
'significantStep',
volName,
volDir,
'ref_particles.xmd',
commonParamsRef,
prerequisites=[phanProjStepId])
if (not (self.pseudoSymmetryGroup.get() == '')):
sym = self.pseudoSymmetryGroup.get()
volStepId = self._insertFunctionStep('alignabilityStep',
volName,
volDir,
sym,
prerequisites=[sigStepId2])
deps.append(volStepId)
self._insertFunctionStep('createOutputStep', prerequisites=deps)
def _insertMaskStep(self, fnVol, prefix=''):
""" Check the mask selected and insert the necessary steps.
Return the mask filename if needed.
"""
fnMask = ''
if self.maskMode == NMA_MASK_THRE:
fnMask = self._getExtraPath('mask%s.vol' % prefix)
maskParams = '-i %s -o %s --select below %f --substitute binarize' % (
fnVol, fnMask, self.maskThreshold.get())
self._insertRunJobStep('xmipp_transform_threshold', maskParams)
elif self.maskMode == NMA_MASK_FILE:
fnMask = getImageLocation(self.volumeMask.get())
return fnMask
def copyDeformationsStep(self, deformationMd):
copyFile(deformationMd, self.imgsFn)
# We need to update the image name with the good ones
# and the same with the ids.
inputSet = self.inputParticles.get()
mdImgs = md.MetaData(self.imgsFn)
for objId in mdImgs:
imgPath = mdImgs.getValue(md.MDL_IMAGE, objId)
index, fn = xmippToLocation(imgPath)
# Conside the index is the id in the input set
particle = inputSet[index]
mdImgs.setValue(md.MDL_IMAGE, getImageLocation(particle), objId)
mdImgs.setValue(md.MDL_ITEM_ID, long(particle.getObjId()), objId)
mdImgs.write(self.imgsFn)
def copyDeformationsStep(self, deformationMd):
copyFile(deformationMd, self.imgsFn)
# We need to update the image name with the good ones
# and the same with the ids.
inputSet = self.inputParticles.get()
md = xmipp.MetaData(self.imgsFn)
for objId in md:
imgPath = md.getValue(xmipp.MDL_IMAGE, objId)
index, fn = xmippToLocation(imgPath)
# Conside the index is the id in the input set
particle = inputSet[index]
md.setValue(xmipp.MDL_IMAGE, getImageLocation(particle), objId)
md.setValue(xmipp.MDL_ITEM_ID, long(particle.getObjId()), objId)
md.write(self.imgsFn)
def _insertAllSteps(self):
convertId = self._insertFunctionStep('convertInputStep',
self.inputParticles.get().getObjId())
deps = [] # store volumes steps id to use as dependencies for last step
commonParams = self._getCommonParams()
commonParamsRef = self._getCommonParamsRef()
sym = self.symmetryGroup.get()
for i, vol in enumerate(self._iterInputVols()):
volName = getImageLocation(vol)
volDir = self._getVolDir(i+1)
pmStepId = self._insertFunctionStep('projectionLibraryStep',
volName, volDir,self.angularSampling.get(),
prerequisites=[convertId])
sigStepId1 = self._insertFunctionStep('significantStep',
volName, volDir,
'exp_particles.xmd',
commonParams,
prerequisites=[pmStepId])
phanProjStepId = self._insertFunctionStep('phantomProject',
prerequisites=[sigStepId1])
sigStepId2 = self._insertFunctionStep('significantStep',
volName, volDir,
'ref_particles.xmd',
commonParamsRef,
prerequisites=[phanProjStepId])
if ( not (self.pseudoSymmetryGroup.get() == '') ):
sym = self.pseudoSymmetryGroup.get()
volStepId = self._insertFunctionStep('alignabilityStep',
volName, volDir,
sym,
prerequisites=[sigStepId2])
deps.append(volStepId)
self._insertFunctionStep('createOutputStep',
prerequisites=deps)
def significantStep(self, isTilt):
if isTilt == 1:
params = ' -i %s' % self._getPath('input_tilted_particles.xmd')
outputDir = self._getExtraPath("tilted")
elif isTilt == 0:
params = ' -i %s' % self._getPath('input_untilted_particles.xmd')
outputDir = self._getExtraPath("untilted")
firstImage = self.inputTiltPair.get().getUntilted().getFirstItem()
maxShift = 0.35 * firstImage.getDim()[0]
params += ' --sym %s' % self.symmetryGroup.get()
params += ' --alpha0 %f --alphaF %f' % ((1-self.alpha.get())/100,(1-self.alpha.get())/100)
params += ' --angularSampling %f' % self.angularSampling.get()
params += ' --dontReconstruct'
params += ' --iter 1'
params += ' --initvolumes %s' % getImageLocation(self.inputVolume.get())
params += ' --useForValidation 3'
params += ' --maxShift %f' % maxShift
params += ' --odir %s' % outputDir
makePath(outputDir)
self.runJob('xmipp_reconstruct_significant', params)
def _insertAllSteps(self):
inputVol = self.inputStructure.get()
fnIn = getImageLocation(inputVol)
fnMask = self._insertMaskStep(fnIn)
self._insertFunctionStep('convertToPseudoAtomsStep', fnIn, fnMask, inputVol.getSamplingRate())
self._insertFunctionStep('createOutputStep')
def _getSecondVolumeFn(self):
if self._isSingleInput():
return getImageLocation(self.inputVolumes2.get())
else:
return self._getSecondSetFn()
def _getSecondVolumeFn(self):
if self._isSingleInput():
return getImageLocation(self.inputVolumes2.get())
else:
return self._getSecondSetFn()
