def convertInputStep(self, particlesId, volId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
inputParticles = self.inputParticles.get()
inputVolume = self.inputVolume.get()
writeSetOfParticles(inputParticles, self._getExpParticlesFn())
img = ImageHandler()
img.convert(inputVolume, self._getInputVolFn())
if self._useSeveralClasses():
# Scale particles
Xdim = inputParticles.getXDim()
Ts = inputParticles.getSamplingRate()
newTs = self.targetResolution.get() * 0.4
newTs = max(Ts, newTs)
newXdim = Xdim * Ts / newTs
self.runJob(
"xmipp_image_resize",
"-i %s -o %s --save_metadata_stack %s --fourier %d" %
(self._getExpParticlesFn(),
self._getTmpPath('scaled_particles.stk'),
self._getTmpPath('scaled_particles.xmd'), newXdim))
# Scale volume
Xdim = inputVolume.getXDim()
if Xdim != newXdim:
self.runJob("xmipp_image_resize",
"-i %s --dim %d" %
(self._getInputVolFn(), newXdim),
numberOfMpi=1)
def convertInputStep(self, particlesId, volId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
inputParticles = self.inputParticles.get()
inputVolume = self.inputVolume.get()
writeSetOfParticles(inputParticles, self._getExpParticlesFn())
img = ImageHandler()
img.convert(inputVolume, self._getInputVolFn())
if self._useSeveralClasses():
# Scale particles
Xdim = inputParticles.getXDim()
Ts = inputParticles.getSamplingRate()
newTs = self.targetResolution.get() * 0.4
newTs = max(Ts, newTs)
newXdim = Xdim * Ts / newTs
self.runJob("xmipp_image_resize",
"-i %s -o %s --save_metadata_stack %s --fourier %d" %
(self._getExpParticlesFn(),
self._getTmpPath('scaled_particles.stk'),
self._getTmpPath('scaled_particles.xmd'),
newXdim))
# Scale volume
Xdim = inputVolume.getXDim()
if Xdim != newXdim:
self.runJob("xmipp_image_resize", "-i %s --dim %d"
% (self._getInputVolFn(), newXdim), numberOfMpi=1)
def convertInputStep(self, particlesId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.<
"""
writeSetOfParticles(self.inputTiltPair.get().getUntilted(), self._getPath('input_untilted_particles.xmd'))
writeSetOfParticles(self.inputTiltPair.get().getTilted(), self._getPath('input_tilted_particles.xmd'))
def convertInputStep(self, particlesId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
writeSetOfParticles(self.inputParticles.get(),
self._getPath('input_particles.xmd'))
def convertInputStep(self):
""" Read the input metadatata.
"""
# Get the converted input micrographs in Xmipp format
inputSet = self.input.get()
inputPath = self._getExtraPath('inputSet')
fnSet = inputPath+'.xmd'
writeSetOfParticles(inputSet, fnSet)
def convertInputStep(self, atomsFn):
# Write the modes metadata taking into account the selection
self.writeModesMetaData()
# Write a metadata with the normal modes information
# to launch the nma alignment programs
writeSetOfParticles(self.inputParticles.get(), self.imgsFn)
# Copy the atoms file to current working dir
copyFile(atomsFn, self.atomsFn)
def convertInputStep(self, atomsFn):
# Write the modes metadata taking into account the selection
self.writeModesMetaData()
# Write a metadata with the normal modes information
# to launch the nma alignment programs
writeSetOfParticles(self.inputParticles.get(), self.imgsFn)
# Copy the atoms file to current working dir
copyFile(atomsFn, self.atomsFn)
def convertInputStep(self):
""" convert to Xmipp image model"""
writeSetOfParticles(self.inputParticles.get(), self.inputFn,
alignType=ALIGN_NONE)
if self.inputParticles2.get() is not None:
writeSetOfParticles(self.inputParticles2.get(),
self._getSecondSetFn(),
alignType=ALIGN_NONE)
def convertInputStep(self, particlesId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
a = self.inputParticles.get()
print a.printAll()
writeSetOfParticles(self.inputParticles.get(),
self._getPath('input_particles.xmd'))
def convertInputStep(self, particlesId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
writeSetOfParticles(self.inputParticles.get(),
self._getPath('input_particles.xmd'))
if self.doWiener.get():
params = ' -i %s' % self._getPath('input_particles.xmd')
params += ' -o %s' % self._getExtraPath(
'corrected_ctf_particles.stk')
params += ' --save_metadata_stack %s' % self._getExtraPath(
'corrected_ctf_particles.xmd')
params += ' --pad %s' % self.padding_factor.get()
params += ' --wc %s' % self.wiener_constant.get()
params += ' --sampling_rate %s' % self.inputParticles.get(
).getSamplingRate()
if self.inputParticles.get().isPhaseFlipped():
params += ' --phase_flipped '
if self.correctEnvelope:
params += ' --correct_envelope '
nproc = self.numberOfMpi.get()
nT = self.numberOfThreads.get()
self.runJob('xmipp_ctf_correct_wiener2d', params)
newTs, newXdim = self._getModifiedSizeAndSampling()
if self.doWiener.get():
params = ' -i %s' % self._getExtraPath(
'corrected_ctf_particles.xmd')
else:
params = ' -i %s' % self._getPath('input_particles.xmd')
params += ' -o %s' % self._getExtraPath('scaled_particles.stk')
params += ' --save_metadata_stack %s' % self._getExtraPath(
'scaled_particles.xmd')
params += ' --dim %d' % newXdim
self.runJob('xmipp_image_resize', params)
from pyworkflow.em.convert import ImageHandler
img = ImageHandler()
img.convert(self.inputVolumes.get(), self._getExtraPath("volume.vol"))
Xdim = self.inputVolumes.get().getDim()[0]
if Xdim != newXdim:
self.runJob("xmipp_image_resize","-i %s --dim %d"%\
(self._getExtraPath("volume.vol"),
newXdim), numberOfMpi=1)
def convertInputStep(self, particlesId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
writeSetOfParticles(self.inputParticles.get(),
self._getPath('input_particles.xmd'))
if self.doWiener.get():
params = ' -i %s' % self._getPath('input_particles.xmd')
params += ' -o %s' % self._getExtraPath('corrected_ctf_particles.stk')
params += ' --save_metadata_stack %s' % self._getExtraPath('corrected_ctf_particles.xmd')
params += ' --pad %s' % self.padding_factor.get()
params += ' --wc %s' % self.wiener_constant.get()
params += ' --sampling_rate %s' % self.inputParticles.get().getSamplingRate()
if self.inputParticles.get().isPhaseFlipped():
params += ' --phase_flipped '
if self.correctEnvelope:
params += ' --correct_envelope '
nproc = self.numberOfMpi.get()
nT=self.numberOfThreads.get()
self.runJob('xmipp_ctf_correct_wiener2d',
params)
newTs, newXdim = self._getModifiedSizeAndSampling()
if self.doWiener.get():
params = ' -i %s' % self._getExtraPath('corrected_ctf_particles.xmd')
else :
params = ' -i %s' % self._getPath('input_particles.xmd')
params += ' -o %s' % self._getExtraPath('scaled_particles.stk')
params += ' --save_metadata_stack %s' % self._getExtraPath('scaled_particles.xmd')
params += ' --fourier %d' % newXdim
self.runJob('xmipp_image_resize',params)
from pyworkflow.em.convert import ImageHandler
img = ImageHandler()
img.convert(self.inputVolumes.get(), self._getExtraPath("volume.vol"))
Xdim = self.inputVolumes.get().getDim()[0]
if Xdim!=newXdim:
self.runJob("xmipp_image_resize","-i %s --dim %d"%\
(self._getExtraPath("volume.vol"),
newXdim), numberOfMpi=1)
def convertInputStep(self, particlesId, classesId):
writeSetOfParticles(self.inputParticles.get(),
self._getFileName('input_particles'),
alignType=em.ALIGN_NONE)
if not self.randomInitialization:
if isinstance(self.initialClasses.get(), SetOfClasses2D):
writeSetOfClasses2D(self.initialClasses.get(),
self._getFileName('input_references'),
writeParticles=False)
else:
writeSetOfParticles(self.initialClasses.get(),
self._getFileName('input_references'))
def createOutputStep(self, fnOutputParts, inputSet, inputVol):
volTransformMatrix = np.matrix(inputVol.getTransform().getMatrix())
outputSet = self._createSetOfParticles()
for part in inputSet.iterItems():
partTransformMat = part.getTransform().getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = volTransformMatrix * partTransformMatrix
part.getTransform().setMatrix(newTransformMatrix)
outputSet.append(part)
outputSet.copyInfo(inputSet)
self._defineOutputs(outputParticles=outputSet)
writeSetOfParticles(outputSet, fnOutputParts)
def createOutputStep(self, fnOutputParts, inputSet, inputVol):
volTransformMatrix = np.matrix(inputVol.getTransform().getMatrix())
outputSet = self._createSetOfParticles()
for part in inputSet.iterItems():
partTransformMat = part.getTransform().getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = volTransformMatrix * partTransformMatrix
part.getTransform().setMatrix(newTransformMatrix)
outputSet.append(part)
outputSet.copyInfo(inputSet)
self._defineOutputs(outputParticles=outputSet)
writeSetOfParticles(outputSet, fnOutputParts)
def convertInputStep(self, particlesId, classesId):
writeSetOfParticles(self.inputParticles.get(),
self._getFileName('input_particles'),
alignType=em.ALIGN_NONE)
if not self.randomInitialization:
if isinstance(self.initialClasses.get(), SetOfClasses2D):
writeSetOfClasses2D(self.initialClasses.get(),
self._getFileName('input_references'),
writeParticles=False)
else:
writeSetOfParticles(self.initialClasses.get(),
self._getFileName('input_references'))
def convertInputStep(self, imagesMd):
# It is unusual to create the output in the convertInputStep,
# but just to avoid reading twice the sqlite with particles
inputSet = self.inputNmaDimred.get().getInputParticles()
partSet = self._createSetOfParticles()
partSet.copyInfo(inputSet)
tmpSet = SetOfParticles(filename=self.sqliteFile.get())
partSet.appendFromImages(tmpSet)
# Register outputs
partSet.setAlignmentProj()
self._defineOutputs(outputParticles=partSet)
self._defineTransformRelation(inputSet, partSet)
writeSetOfParticles(partSet, imagesMd)
def convertInputStep(self, imagesMd):
# It is unusual to create the output in the convertInputStep,
# but just to avoid reading twice the sqlite with particles
inputSet = self.inputNmaDimred.get().getInputParticles()
partSet = self._createSetOfParticles()
partSet.copyInfo(inputSet)
tmpSet = SetOfParticles(filename=self.sqliteFile.get())
partSet.appendFromImages(tmpSet)
# Register outputs
partSet.setAlignmentProj()
self._defineOutputs(outputParticles=partSet)
self._defineTransformRelation(inputSet, partSet)
writeSetOfParticles(partSet, imagesMd)
def _insertAllSteps(self):
inputParticlesMd = self._getExtraPath('input_particles.xmd')
inputParticles = self.inputParticles.get()
writeSetOfParticles(inputParticles, inputParticlesMd)
inputVol = self.inputVolume.get().getFileName()
referenceVol = self.referenceVolume.get().getFileName()
if not self.doAlignment.get():
self._insertFunctionStep('opticalFlowAlignmentStep',
inputVol, referenceVol, inputParticlesMd)
else:
fnAlignedVolFf = self._getExtraPath('aligned_inputVol_to_refVol_FF.vol')
fnAlnVolFfLcl = self._getExtraPath('aligned_FfAlnVol_to_refVol_lcl.vol')
fnInPartsNewAng = self._getExtraPath("inputParts_anglesModified.xmd")
self._insertFunctionStep('volumeAlignmentStep',
referenceVol, inputVol, fnAlignedVolFf,
fnAlnVolFfLcl, fnInPartsNewAng)
self._insertFunctionStep('opticalFlowAlignmentStep',
fnAlnVolFfLcl, referenceVol, fnInPartsNewAng)
self._insertFunctionStep('createOutputStep')
def volumeAlignmentStep (self, referenceVol, inputVol, fnAlignedVolFf,
fnAlnVolFfLcl, fnInPartsNewAng):
fnTransformMatFF = self._getExtraPath('transformation-matrix-FF.txt')
alignArgsFf = "--i1 %s --i2 %s --apply %s" % (referenceVol,
inputVol,
fnAlignedVolFf)
alignArgsFf += " --frm --copyGeo %s" % fnTransformMatFF
self.runJob('xmipp_volume_align', alignArgsFf, numberOfMpi = 1)
fnTransformMatLocal = self._getExtraPath('transformation-matrix-local.txt')
alignArgsLocal = "--i1 %s --i2 %s --apply %s" % (referenceVol,
fnAlignedVolFf,
fnAlnVolFfLcl)
alignArgsLocal += " --local --rot 0 0 1 --tilt 0 0 1"
alignArgsLocal += " --psi 0 0 1 -x 0 0 1 -y 0 0 1"
alignArgsLocal += " -z 0 0 1 --scale 1 1 0.005 --copyGeo %s" % fnTransformMatLocal
self.runJob('xmipp_volume_align', alignArgsLocal, numberOfMpi = 1)
#apply transformation matrix to input ratricles
transMatFromFileFF = np.loadtxt(fnTransformMatFF)
transformationArrayFF = np.reshape(transMatFromFileFF,(4,4))
transformMatrixFF = np.matrix(transformationArrayFF)
transMatFromFileLocal = np.loadtxt(fnTransformMatLocal)
transformationArrayLocal = np.reshape(transMatFromFileLocal,(4,4))
transformMatrixLocal = np.matrix(transformationArrayLocal)
transformMatrix = transformMatrixFF * transformMatrixLocal
print "Transformation matrix used to apply to the input particles =\n"
print transformMatrix
inputParts = self.inputParticles.get()
outputSet = self._createSetOfParticles()
for part in inputParts.iterItems():
partTransformMat = part.getTransform().getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = transformMatrix * partTransformMatrix
part.getTransform().setMatrix(newTransformMatrix)
outputSet.append(part)
outputSet.copyInfo(inputParts)
writeSetOfParticles(outputSet, fnInPartsNewAng)
def volumeAlignmentStep(self, referenceVol, inputVol, fnAlignedVolFf,
fnAlnVolFfLcl, fnInPartsNewAng):
fnTransformMatFF = self._getExtraPath('transformation-matrix-FF.txt')
alignArgsFf = "--i1 %s --i2 %s --apply %s" % (referenceVol, inputVol,
fnAlignedVolFf)
alignArgsFf += " --frm --copyGeo %s" % fnTransformMatFF
self.runJob('xmipp_volume_align', alignArgsFf, numberOfMpi=1)
fnTransformMatLocal = self._getExtraPath(
'transformation-matrix-local.txt')
alignArgsLocal = "--i1 %s --i2 %s --apply %s" % (
referenceVol, fnAlignedVolFf, fnAlnVolFfLcl)
alignArgsLocal += " --local --rot 0 0 1 --tilt 0 0 1"
alignArgsLocal += " --psi 0 0 1 -x 0 0 1 -y 0 0 1"
alignArgsLocal += " -z 0 0 1 --scale 1 1 0.005 --copyGeo %s" % fnTransformMatLocal
self.runJob('xmipp_volume_align', alignArgsLocal, numberOfMpi=1)
#apply transformation matrix to input ratricles
transMatFromFileFF = np.loadtxt(fnTransformMatFF)
transformationArrayFF = np.reshape(transMatFromFileFF, (4, 4))
transformMatrixFF = np.matrix(transformationArrayFF)
transMatFromFileLocal = np.loadtxt(fnTransformMatLocal)
transformationArrayLocal = np.reshape(transMatFromFileLocal, (4, 4))
transformMatrixLocal = np.matrix(transformationArrayLocal)
transformMatrix = transformMatrixFF * transformMatrixLocal
print "Transformation matrix used to apply to the input particles =\n"
print transformMatrix
inputParts = self.inputParticles.get()
outputSet = self._createSetOfParticles()
for part in inputParts.iterItems():
partTransformMat = part.getTransform().getMatrix()
partTransformMatrix = np.matrix(partTransformMat)
newTransformMatrix = transformMatrix * partTransformMatrix
part.getTransform().setMatrix(newTransformMatrix)
outputSet.append(part)
outputSet.copyInfo(inputParts)
writeSetOfParticles(outputSet, fnInPartsNewAng)
def _insertAllSteps(self):
inputParticlesMd = self._getExtraPath('input_particles.xmd')
inputParticles = self.inputParticles.get()
writeSetOfParticles(inputParticles, inputParticlesMd)
inputVol = self.inputVolume.get().getFileName()
referenceVol = self.referenceVolume.get().getFileName()
if not self.doAlignment.get():
self._insertFunctionStep('opticalFlowAlignmentStep', inputVol,
referenceVol, inputParticlesMd)
else:
fnAlignedVolFf = self._getExtraPath(
'aligned_inputVol_to_refVol_FF.vol')
fnAlnVolFfLcl = self._getExtraPath(
'aligned_FfAlnVol_to_refVol_lcl.vol')
fnInPartsNewAng = self._getExtraPath(
"inputParts_anglesModified.xmd")
self._insertFunctionStep('volumeAlignmentStep', referenceVol,
inputVol, fnAlignedVolFf, fnAlnVolFfLcl,
fnInPartsNewAng)
self._insertFunctionStep('opticalFlowAlignmentStep', fnAlnVolFfLcl,
referenceVol, fnInPartsNewAng)
self._insertFunctionStep('createOutputStep')
def _insertAllSteps(self):
self._createFilenameTemplates()
#convertInputStep
particlesMd = self._getFileName('input_xmd')
imgSet = self.inputParticles.get()
writeSetOfParticles(imgSet, particlesMd)
#for debugging purpose
debugging = False
inputNameRefVol = self.input3DReference.get().getFileName()
fnNewVol = self._getExtraPath('newVolume.vol')
fnNewImgStk = self._getExtraPath('newImages.stk')
fnNewImgMd = self._getExtraPath('newImages.xmd')
#do resizing
if self.doResize.get():
args = "-i %s " "-o %s --fourier %f " % (inputNameRefVol, fnNewVol,
self.newSize)
self.runJob("xmipp_image_resize", args)
args = "-i %s -o %s --fourier %f" % (particlesMd, fnNewImgStk,
self.newSize)
args += " --save_metadata_stack %s" % fnNewImgMd
args += " --keep_input_columns"
self.runJob("xmipp_image_resize", args)
oldSize = self.inputParticles.get().getDim()[0]
scaleFactor = oldSize / self.newSize.get()
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftX=shiftX*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args)
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftY=shiftY*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args)
#projections from reference volume
if self.doResize.get():
args = "-i %s -o %s" % (fnNewVol,
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % fnNewImgMd
else:
args = "-i %s -o %s" % (self.input3DReference.get().getFileName(),
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % particlesMd
args += " --sampling_rate %f --sym %s" % (self.angSampRate,
self.symmetryGroup.get())
args += " --min_tilt_angle 0 --max_tilt_angle 90"
args += " --compute_neighbors --angular_distance -1"
self.runJob("xmipp_angular_project_library",
args,
numberOfMpi=self.numberOfMpi.get() *
self.numberOfThreads.get())
numberOfParticles = getFloatListFromValues(
self.numberOfParticles.get())
fractionCounter = 0
maxNumberOfParticles = 0.5 * self.inputParticles.get().getSize()
for number in numberOfParticles:
if number <= maxNumberOfParticles:
for iteration in range(0, self.numberOfIterations.get()):
self._insertFunctionStep('reconstructionStep', number,
fractionCounter, iteration,
debugging, fnNewImgMd,
particlesMd)
fractionCounter += 1
self._insertFunctionStep('gatherResultsStep', debugging)
def convertInputStep(self):
writeSetOfParticles(self.inputParticles.get(), self.inputFn)
def convertInputStep(self):
particlesMd = self._getFileName('input_xmd')
imgSet = self.inputParticles.get()
#TODO: This only writes metadata what about binary file
#it should
writeSetOfParticles(imgSet, particlesMd)
def convertInputStep(self, particlesId):
""" Write the input images as a Xmipp metadata file.
particlesId: is only need to detect changes in
input particles and cause restart from here.
"""
writeSetOfParticles(self.partSet, self._getMdParticles())
def _insertAllSteps(self):
self._createFilenameTemplates()
#convertInputStep
particlesMd = self._getFileName('input_xmd')
imgSet = self.inputParticles.get()
writeSetOfParticles(imgSet, particlesMd)
#for debugging purpose
debugging = False
inputNameRefVol = self.input3DReference.get().getFileName()
fnNewVol = self._getExtraPath('newVolume.vol')
fnNewImgStk = self._getExtraPath('newImages.stk')
fnNewImgMd = self._getExtraPath('newImages.xmd')
#do resizing
if self.doResize.get():
args = "-i %s ""-o %s --fourier %f " % (inputNameRefVol,
fnNewVol,
self.newSize)
self.runJob("xmipp_image_resize", args)
args = "-i %s -o %s --fourier %f" % (particlesMd,
fnNewImgStk,
self.newSize)
args += " --save_metadata_stack %s" % fnNewImgMd
args += " --keep_input_columns"
self.runJob("xmipp_image_resize", args)
oldSize = self.inputParticles.get().getDim()[0]
scaleFactor = float(self.newSize.get())/float(oldSize)
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftX=shiftX*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args, numberOfMpi=1)
args = "-i %s" % fnNewImgMd
args += " --operate modify_values 'shiftY=shiftY*%f'" % scaleFactor
self.runJob('xmipp_metadata_utilities', args, numberOfMpi=1)
#projections from reference volume
if self.doResize.get():
args = "-i %s -o %s" % (fnNewVol,
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % fnNewImgMd
else:
args = "-i %s -o %s" % (self.input3DReference.get().getFileName(),
self._getExtraPath('Ref_Projections.stk'))
args += " --experimental_images %s" % particlesMd
args += " --sampling_rate %f --sym %s" % (self.angSampRate,
self.symmetryGroup.get())
args += " --min_tilt_angle 0 --max_tilt_angle 90"
args += " --compute_neighbors --angular_distance -1"
self.runJob("xmipp_angular_project_library",
args,
numberOfMpi = self.numberOfMpi.get() * self.numberOfThreads.get())
numberOfParticles = getFloatListFromValues(self.numberOfParticles.get())
fractionCounter = 0
maxNumberOfParticles = 0.5 * self.inputParticles.get().getSize()
for number in numberOfParticles:
if number <= maxNumberOfParticles:
for iteration in range(0,self.numberOfIterations.get()):
self._insertFunctionStep('reconstructionStep', number,
fractionCounter, iteration,
debugging, fnNewImgMd,
particlesMd)
fractionCounter+=1
self._insertFunctionStep('gatherResultsStep', debugging)
