Source code for xmipptomo.protocols.protocol_splitTS

# **************************************************************************
# *
# * Authors:     Federico P. de Isidro Gomez (fp.deisidro@cnb.csi.es) [1]
# *
# * [1] Centro Nacional de Biotecnologia, CSIC, Spain
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# *  All comments concerning this program package may be sent to the
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import os
import pyworkflow.utils.path as path
import pyworkflow.utils as pwutils
from pyworkflow.protocol import params
from pwem.protocols import EMProtocol
from tomo.protocols import ProtTomoBase
import tomo.objects as tomoObj


[docs]class XmippProtSplitTiltSeries(EMProtocol, ProtTomoBase): """ Wrapper protocol to Xmipp split Odd Even on tilt-series """ _label = 'split tilt-series' # --------------------------- DEFINE param functions ------------------------ def _defineParams(self, form): form.addSection(label='Input') form.addParam('inputSetOfTiltSeries', params.PointerParam, pointerClass='SetOfTiltSeries', important=True, label='Input set of tilt-series', help='Select a set of tilt-series to be split into two sets (odd and even).' 'It means, the set of tilt-series is split in two subsets.') # -------------------------- INSERT steps functions --------------------- def _insertAllSteps(self): for ts in self.inputSetOfTiltSeries.get(): self._insertFunctionStep('splitTiltSeries', ts.getObjId()) self._insertFunctionStep('convertXmdToStackStep', ts.getObjId()) self._insertFunctionStep('createOutputStep', ts.getObjId()) # --------------------------- STEPS functions -------------------------------
[docs] def splitTiltSeries(self, tsObjId): ts = self.inputSetOfTiltSeries.get()[tsObjId] tsId = ts.getTsId() tsFileName = ts.getFirstItem().getFileName() path.makePath(self._getExtraPath(tsId)) tsFileNameOdd = pwutils.removeExt(os.path.basename(tsFileName)) + "_odd.xmd" tsFileNameEven = pwutils.removeExt(os.path.basename(tsFileName)) + "_even.xmd" paramsOddEven = { 'inputImg': tsFileName, 'outputOdd': self._getExtraPath(os.path.join(tsId, tsFileNameOdd)), 'outputEven': self._getExtraPath(os.path.join(tsId, tsFileNameEven)), 'type': "images", } argsOddEven = "--img %(inputImg)s " \ "-o %(outputOdd)s " \ "-e %(outputEven)s " \ "--type %(type)s " self.runJob('xmipp_image_odd_even', argsOddEven % paramsOddEven)
[docs] def convertXmdToStackStep(self, tsObjId): ts = self.inputSetOfTiltSeries.get()[tsObjId] tsId = ts.getTsId() tsFileName = ts.getFirstItem().getFileName() tsFileNameOdd = pwutils.removeExt(os.path.basename(tsFileName)) + "_odd.xmd" tsFileNameEven = pwutils.removeExt(os.path.basename(tsFileName)) + "_even.xmd" tsFileNameOddMrc = pwutils.removeExt(os.path.basename(tsFileNameOdd)) + ".mrc" tsFileNameEvenMrc = pwutils.removeExt(os.path.basename(tsFileNameEven)) + ".mrc" paramsConvertOdd = { 'inputXmdOdd': self._getExtraPath(os.path.join(tsId, tsFileNameOdd)), 'outputMrcOdd': self._getExtraPath(os.path.join(tsId, tsFileNameOddMrc)), } argsConvertOdd = "-i %(inputXmdOdd)s " \ "-o %(outputMrcOdd)s " self.runJob('xmipp_image_convert', argsConvertOdd % paramsConvertOdd) paramsConvertEven = { 'inputXmdEven': self._getExtraPath(os.path.join(tsId, tsFileNameEven)), 'outputMrcEven': self._getExtraPath(os.path.join(tsId, tsFileNameEvenMrc)), } argsConvertEven = "-i %(inputXmdEven)s " \ "-o %(outputMrcEven)s " self.runJob('xmipp_image_convert', argsConvertEven % paramsConvertEven)
[docs] def createOutputStep(self, tsObjId): ts = self.inputSetOfTiltSeries.get()[tsObjId] tsId = ts.getTsId() tsFileName = ts.getFirstItem().getFileName() """Output even set""" outputOddSetOfTiltSeries = self.getOutputEvenSetOfTiltSeries() tsFileNameEvenMrc = pwutils.removeExt(os.path.basename(tsFileName)) + "_even.mrc" evenTs = tomoObj.TiltSeries(tsId=tsId) evenTs.copyInfo(ts) outputOddSetOfTiltSeries.append(evenTs) dimCounter = 0 for index, tiltImage in enumerate(ts): if (index+1) % 2 == 0: dimCounter += 1 newTi = tomoObj.TiltImage() newTi.copyInfo(tiltImage, copyId=True) newTi.setLocation(dimCounter, self._getExtraPath(os.path.join(tsId, tsFileNameEvenMrc))) evenTs.append(newTi) evenTs.write() outputOddSetOfTiltSeries.update(evenTs) outputOddSetOfTiltSeries.write() self._store() """Output odd set""" outputOddSetOfTiltSeries = self.getOutputOddSetOfTiltSeries() tsFileNameOddMrc = pwutils.removeExt(os.path.basename(tsFileName)) + "_odd.mrc" oddTs = tomoObj.TiltSeries(tsId=tsId) oddTs.copyInfo(ts) outputOddSetOfTiltSeries.append(oddTs) dimCounter = 0 for index, tiltImage in enumerate(ts): if (index+1) % 2 == 1: dimCounter += 1 newTi = tomoObj.TiltImage() newTi.copyInfo(tiltImage, copyId=True) newTi.setLocation(dimCounter, self._getExtraPath(os.path.join(tsId, tsFileNameOddMrc))) oddTs.append(newTi) oddTs.write() outputOddSetOfTiltSeries.update(oddTs) outputOddSetOfTiltSeries.write() self._store()
# --------------------------- UTILS functions ----------------------------
[docs] def getOutputEvenSetOfTiltSeries(self): if not hasattr(self, "outputEvenSetOfTiltSeries"): outputEvenSetOfTiltSeries = self._createSetOfTiltSeries(suffix='Even') outputEvenSetOfTiltSeries.copyInfo(self.inputSetOfTiltSeries.get()) outputEvenSetOfTiltSeries.setDim(self.inputSetOfTiltSeries.get().getDim()) self._defineOutputs(outputEvenSetOfTiltSeries=outputEvenSetOfTiltSeries) self._defineSourceRelation(self.inputSetOfTiltSeries, outputEvenSetOfTiltSeries) return self.outputEvenSetOfTiltSeries
[docs] def getOutputOddSetOfTiltSeries(self): if not hasattr(self, "outputOddSetOfTiltSeries"): outputOddSetOfTiltSeries = self._createSetOfTiltSeries(suffix='Odd') outputOddSetOfTiltSeries.copyInfo(self.inputSetOfTiltSeries.get()) outputOddSetOfTiltSeries.setDim(self.inputSetOfTiltSeries.get().getDim()) self._defineOutputs(outputOddSetOfTiltSeries=outputOddSetOfTiltSeries) self._defineSourceRelation(self.inputSetOfTiltSeries, outputOddSetOfTiltSeries) return self.outputOddSetOfTiltSeries
# --------------------------- INFO functions ------------------------------ def _methods(self): methods = [] if hasattr(self, 'outputEvenSetOfTiltSeries'): methods.append("%d Tilt-series have been splitted in its corresponding odd and even subsets.\n" % (self.outputOddSetOfTiltSeries.getSize())) else: methods.append("Output classes not ready yet.") return methods def _summary(self): summary = [] if hasattr(self, 'outputEvenSetOfTiltSeries'): summary.append("Input Tilt-Series: %d.\nSets of even images: %d.\nSets of odd images: %d.\n" % (self.inputSetOfTiltSeries.get().getSize(), self.outputEvenSetOfTiltSeries.getSize(), self.outputOddSetOfTiltSeries.getSize())) else: summary.append("Output classes not ready yet.") return summary