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 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)