def convertInputStep(self, particlesId, classesId):
writeSetOfParticles(self.inputParticles.get(),self.imgsFn,alignType=em.ALIGN_NONE)
if not self.randomInitialization:
if isinstance(self.initialClasses.get(), SetOfClasses2D):
writeSetOfClasses2D(self.initialClasses.get(),self.initialClassesFn, writeParticles=False)
else:
writeSetOfParticles(self.initialClasses.get(),self.initialClassesFn)
def convertInputStep(self, classesFn):
inputSet = self.inputSet.get()
if isinstance(inputSet, SetOfClasses2D):
writeSetOfClasses2D(inputSet, classesFn)
else:
writeSetOfParticles(inputSet, classesFn)
def convertStep(self, imgsFn):
from convert import writeSetOfClasses2D, writeSetOfParticles
imgSet = self.inputSet.get()
if isinstance(imgSet, SetOfClasses2D):
writeSetOfClasses2D(imgSet, self.imgsFn, writeParticles=False)
else:
writeSetOfParticles(imgSet, self.imgsFn)
def convertStep(self, imgsFn):
from convert import writeSetOfClasses2D, writeSetOfParticles
imgSet = self.inputSet.get()
if isinstance(imgSet, SetOfClasses2D):
writeSetOfClasses2D(imgSet, self.imgsFn, writeParticles=False)
else:
writeSetOfParticles(imgSet, self.imgsFn)
def convertInputStep(self, classesFn):
inputSet = self.inputSet.get()
if isinstance(inputSet, SetOfClasses2D):
writeSetOfClasses2D(inputSet, classesFn)
else:
writeSetOfParticles(inputSet, classesFn)
def convertInputStep(self):
writeSetOfParticles(self.inputParticles.get(), self.imgsFn)
if not self.randomInitialization:
if isinstance(self.initialClasses.get(), SetOfClasses2D):
writeSetOfClasses2D(self.initialClasses.get(), self.initialClassesFn, writeParticles=False)
else:
writeSetOfParticles(self.initialClasses.get(), self.initialClassesFn)
def convertInputStep(self, particlesId, classesId):
writeSetOfParticles(self.inputParticles.get(),
self.imgsFn,
alignType=em.ALIGN_NONE)
if not self.randomInitialization:
if isinstance(self.initialClasses.get(), SetOfClasses2D):
writeSetOfClasses2D(self.initialClasses.get(),
self.initialClassesFn,
writeParticles=False)
else:
writeSetOfParticles(self.initialClasses.get(),
self.initialClassesFn)
def convertStep(self, imgsFn):
from convert import writeSetOfClasses2D, writeSetOfParticles
imgSet = self.inputSet.get()
if isinstance(imgSet, SetOfClasses2D):
writeSetOfClasses2D(imgSet, self.imgsFn, writeParticles=True)
else:
writeSetOfParticles(imgSet, self.imgsFn)
from pyworkflow.em.convert import ImageHandler
img = ImageHandler()
fnVol = self._getTmpPath("volume.vol")
img.convert(self.inputVolume.get(), fnVol)
xdim=self.inputVolume.get().getDim()[0]
if xdim!=self._getDimensions():
self.runJob("xmipp_image_resize","-i %s --dim %d"%(fnVol,self._getDimensions()))
def convertStep(self, imgsFn):
from convert import writeSetOfClasses2D, writeSetOfParticles
imgSet = self.inputSet.get()
if isinstance(imgSet, SetOfClasses2D):
writeSetOfClasses2D(imgSet, self.imgsFn, writeParticles=True)
else:
writeSetOfParticles(imgSet, self.imgsFn)
from pyworkflow.em.convert import ImageHandler
img = ImageHandler()
fnVol = self._getTmpPath("volume.vol")
img.convert(self.inputVolume.get(), fnVol)
xdim = self.inputVolume.get().getDim()[0]
if xdim != self._getDimensions():
self.runJob("xmipp_image_resize",
"-i %s --dim %d" % (fnVol, self._getDimensions()))
def convertInputStep(self, classesFn):
inputSet = self.inputSet.get()
if isinstance(inputSet, SetOfClasses2D):
writeSetOfClasses2D(inputSet, classesFn, writeParticles=False)
else:
writeSetOfParticles(inputSet, classesFn)
if self.thereisRefVolume:
inputVolume = self.refVolume.get()
fnVolumes = self._getExtraPath('input_volumes.xmd')
row = XmippMdRow()
volumeToRow(inputVolume, row, alignType=ALIGN_NONE)
md = xmipp.MetaData()
row.writeToMd(md, md.addObject())
md.write(fnVolumes)
def convertInputStep(self, classesFn):
inputSet = self.inputSet.get()
if isinstance(inputSet, SetOfClasses2D):
writeSetOfClasses2D(inputSet, classesFn, writeParticles=False)
else:
writeSetOfParticles(inputSet, classesFn)
if self.thereisRefVolume:
inputVolume= self.refVolume.get()
fnVolumes = self._getExtraPath('input_volumes.xmd')
row = XmippMdRow()
volumeToRow(inputVolume, row, alignType = ALIGN_NONE)
md = xmipp.MetaData()
row.writeToMd(md, md.addObject())
md.write(fnVolumes)
def denoiseImages(self, inputId, inputClassesId):
# We start preparing writing those elements we're using as input to keep them untouched
imagesMd = self._getPath('images.xmd')
writeSetOfParticles(self.inputParticles.get(), imagesMd)
classesMd = self._getPath('classes.xmd')
writeSetOfClasses2D(self.inputClasses.get(), classesMd)
fnRoot = self._getExtraPath('pca')
fnRootDenoised = self._getExtraPath('imagesDenoised')
args = '-i Particles@%s --oroot %s --eigenvectors %d --maxImages %d' % (imagesMd, fnRoot, self.maxPCABases.get(), self.maxClasses.get())
self.runJob("xmipp_image_rotational_pca", args)
N=min(self.maxPCABases.get(), self.PCABases2Project.get())
args='-i %s -o %s.stk --save_metadata_stack %s.xmd --basis %s.stk %d'\
% (imagesMd, fnRootDenoised, fnRootDenoised, fnRoot, N)
self.runJob("xmipp_transform_filter", args)
self.outputMd = String('%s.stk' % fnRootDenoised)
def denoiseImages(self, inputId, inputClassesId):
# We start preparing writing those elements we're using as input to keep them untouched
imagesMd = self._getPath('images.xmd')
writeSetOfParticles(self.inputParticles.get(), imagesMd)
classesMd = self._getPath('classes.xmd')
writeSetOfClasses2D(self.inputClasses.get(), classesMd)
fnRoot = self._getExtraPath('pca')
fnRootDenoised = self._getExtraPath('imagesDenoised')
args = '-i Particles@%s --oroot %s --eigenvectors %d --maxImages %d' % (imagesMd, fnRoot, self.maxPCABases.get(), self.maxClasses.get())
self.runJob("xmipp_image_rotational_pca", args)
N=min(self.maxPCABases.get(), self.PCABases2Project.get())
args='-i %s -o %s.stk --save_metadata_stack %s.xmd --basis %s.stk %d'\
% (imagesMd, fnRootDenoised, fnRootDenoised, fnRoot, N)
self.runJob("xmipp_transform_filter", args)
self.outputMd = String('%s.stk' % fnRootDenoised)
