Source code for xmipp3.protocols.protocol_reconstruct_fourier

# **************************************************************************
# *
# * Authors:     Roberto Marabini (roberto@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# *  e-mail address 'scipion@cnb.csic.es'
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from pwem.objects import Volume
from pwem.protocols import ProtReconstruct3D
import pyworkflow.protocol.params as params
import pyworkflow.protocol.constants as cons
from xmipp3.convert import writeSetOfParticles
from xmipp3.base import isXmippCudaPresent
import os


[docs]class XmippProtReconstructFourier(ProtReconstruct3D): """ Reconstruct a volume using Xmipp_reconstruct_fourier from a given set of particles. The alignment parameters will be converted to a Xmipp xmd file and used as direction projections to reconstruct. """ _label = 'reconstruct fourier' #--------------------------- DEFINE param functions -------------------------------------------- def _defineParams(self, form): form.addHidden(params.USE_GPU, params.BooleanParam, default=True, label="Use GPU for execution", help="This protocol has both CPU and GPU implementation.\ Select the one you want to use.") form.addHidden(params.GPU_LIST, params.StringParam, default='0', expertLevel=cons.LEVEL_ADVANCED, label="Choose GPU IDs", help="Add a list of GPU devices that can be used") form.addSection(label='Input') form.addParam('inputParticles', params.PointerParam, pointerClass='SetOfParticles', pointerCondition='hasAlignmentProj', label="Input particles", help='Select the input images from the project.') form.addParam('symmetryGroup', params.StringParam, default='c1', label="Symmetry group", help='See [[Xmipp Symmetry][http://www2.mrc-lmb.cam.ac.uk/Xmipp/index.php/Conventions_%26_File_formats#Symmetry]] page ' 'for a description of the symmetry format accepted by Xmipp') form.addParam('maxRes', params.FloatParam, default=-1, label="Maximum resolution (A)", help='Maximum resolution (in Angstrom) to consider \n' 'in Fourier space (default Nyquist).\n' 'Param *--maxres* in Xmipp.') line = form.addLine('Padding factor', expertLevel=cons.LEVEL_ADVANCED, help='Padding of the input images. Higher number will result in more precise interpolation in Fourier ' 'domain, but slower processing time and higher memory requirements.') line.addParam('pad_proj', params.IntParam, default=2, label='Projection') line.addParam('pad_vol', params.IntParam, default=2, label='Volume') form.addParam('legacy', params.BooleanParam, default=False, label="Legacy version", expertLevel=cons.LEVEL_ADVANCED, help="Use original CPU version of the algorithm. This should not be necessary, but it's present" " to ensure backward compatibility") form.addParam('approx', params.BooleanParam, default=True, label="Approximative version", expertLevel=cons.LEVEL_ADVANCED, help="If on, an approximation of the original algorithm will be used. This will result in" " faster processing times, but (slightly) less precise result") form.addParam('extraParams', params.StringParam, default='', expertLevel=cons.LEVEL_ADVANCED, label='Extra parameters: ', help='Extra parameters to *xmipp_(cuda_)reconstruct_fourier* program:\n' """ --iter () : Subtract projections of this map from the images used for reconstruction """) form.addParallelSection(threads=4, mpi=1) #--------------------------- INSERT steps functions -------------------------------------------- def _createFilenameTemplates(self): """ Centralize how files are called for iterations and references. """ myDict = { 'input_xmd': self._getExtraPath('input_particles.xmd'), 'output_volume': self._getPath('output_volume.vol') } self._updateFilenamesDict(myDict) def _insertAllSteps(self): self._createFilenameTemplates() self._insertFunctionStep('convertInputStep') self._insertReconstructStep() self._insertFunctionStep('createOutputStep') def _insertReconstructStep(self): #imgSet = self.inputParticles.get() params = ' -i %s' % self._getFileName('input_xmd') params += ' -o %s' % self._getFileName('output_volume') params += ' --sym %s' % self.symmetryGroup.get() maxRes = self.maxRes.get() if maxRes == -1: digRes = 0.5 else: digRes = self.inputParticles.get().getSamplingRate() / self.maxRes.get() params += ' --max_resolution %0.3f' %digRes params += ' --padding %0.3f %0.3f' % (self.pad_proj.get(), self.pad_vol.get()) params += ' --sampling %f' % self.inputParticles.get().getSamplingRate() params += ' %s' % self.extraParams.get() params += ' --fast' if self.approx.get() else '' if self.useGpu.get(): #AJ to make it work with and without queue system params += ' --thr %d' % self.numberOfThreads.get() if self.numberOfMpi.get()>1: N_GPUs = len((self.gpuList.get()).split(',')) params += ' -gpusPerNode %d' % N_GPUs params += ' -threadsPerGPU %d' % max(self.numberOfThreads.get(),4) count=0 GpuListCuda='' if self.useQueueForSteps() or self.useQueue(): GpuList = os.environ["CUDA_VISIBLE_DEVICES"] GpuList = GpuList.split(",") for elem in GpuList: GpuListCuda = GpuListCuda+str(count)+' ' count+=1 else: GpuListAux = '' for elem in self.getGpuList(): GpuListCuda = GpuListCuda+str(count)+' ' GpuListAux = GpuListAux+str(elem)+',' count+=1 os.environ["CUDA_VISIBLE_DEVICES"] = GpuListAux if self.numberOfMpi.get()==1: params += ' --device %s'%(GpuListCuda) if self.useGpu.get() else '' self._insertFunctionStep('reconstructStep', params) #--------------------------- STEPS functions --------------------------------------------
[docs] 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)
[docs] def reconstructStep(self, params): """ Create the input file in STAR format as expected by Xmipp. If the input particles comes from Xmipp, just link the file. """ if self.useGpu.get(): if self.numberOfMpi.get()>1: self.runJob('xmipp_cuda_reconstruct_fourier', params, numberOfMpi=len((self.gpuList.get()).split(','))+1) else: self.runJob('xmipp_cuda_reconstruct_fourier', params) else: if self.legacy.get(): self.runJob('xmipp_reconstruct_fourier', params) else: self.runJob('xmipp_reconstruct_fourier_accel', params)
[docs] def createOutputStep(self): imgSet = self.inputParticles.get() volume = Volume() volume.setFileName(self._getFileName('output_volume')) volume.setSamplingRate(imgSet.getSamplingRate()) self._defineOutputs(outputVolume=volume) self._defineSourceRelation(self.inputParticles, volume)
#--------------------------- INFO functions -------------------------------------------- def _validate(self): """ Should be overriden in subclasses to return summary message for NORMAL EXECUTION. """ errors = ProtReconstruct3D._validate(self) if self.useGpu.get() and self.legacy.get(): errors.append("Legacy version is not implemented for GPU") if self.approx.get() and self.legacy.get(): errors.append("Approximative version is not implemented for Legacy code") if not self.useGpu.get() and self.numberOfThreads.get() > 1: errors.append("CPU version can use only a single thread. Use MPI instead") if self.useGpu and not isXmippCudaPresent(): errors.append("You have asked to use GPU, but I cannot find Xmipp GPU programs in the path") return errors def _summary(self): """ Should be overriden in subclasses to return summary message for NORMAL EXECUTION. """ return []
#--------------------------- UTILS functions --------------------------------------------