本文整理汇总了Python中pyworkflow.em.metadata.iterRows函数的典型用法代码示例。如果您正苦于以下问题：Python iterRows函数的具体用法？Python iterRows怎么用？Python iterRows使用的例子？那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。
在下文中一共展示了iterRows函数的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: createOutputStep
def createOutputStep(self):
outputVols = self._createSetOfVolumes()
imgSet = self.inputParticles.get()
for i, vol in enumerate(self._iterInputVols()):
volume = vol.clone()
volDir = self._getVolDir(i + 1)
volPrefix = "vol%03d_" % (i + 1)
validationMd = self._getExtraPath(volPrefix + "validation.xmd")
moveFile(join(volDir, "validation.xmd"), validationMd)
clusterMd = self._getExtraPath(volPrefix + "clusteringTendency.xmd")
moveFile(join(volDir, "clusteringTendency.xmd"), clusterMd)
outImgSet = self._createSetOfParticles(volPrefix)
outImgSet.copyInfo(imgSet)
outImgSet.copyItems(
imgSet,
updateItemCallback=self._setWeight,
itemDataIterator=md.iterRows(clusterMd, sortByLabel=md.MDL_ITEM_ID),
)
mdValidatoin = md.MetaData(validationMd)
weight = mdValidatoin.getValue(md.MDL_WEIGHT, mdValidatoin.firstObject())
volume.weight = Float(weight)
volume.clusterMd = String(clusterMd)
volume.cleanObjId() # clean objects id to assign new ones inside the set
outputVols.append(volume)
self._defineOutputs(outputParticles=outImgSet)
outputVols.setSamplingRate(volume.getSamplingRate())
self._defineOutputs(outputVolumes=outputVols)示例2: createOutputStep
def createOutputStep(self):
fnImgs = self._getExtraPath('images.stk')
if os.path.exists(fnImgs):
cleanPath(fnImgs)
outputSet = self._createSetOfParticles()
imgSet = self.inputSet.get()
imgFn = self._getExtraPath("anglesCont.xmd")
self.newAssignmentPerformed = os.path.exists(self._getExtraPath("angles.xmd"))
self.samplingRate = self.inputSet.get().getSamplingRate()
if isinstance(imgSet, SetOfClasses2D):
outputSet = self._createSetOfClasses2D(imgSet)
outputSet.copyInfo(imgSet.getImages())
elif isinstance(imgSet, SetOfAverages):
outputSet = self._createSetOfAverages()
outputSet.copyInfo(imgSet)
else:
outputSet = self._createSetOfParticles()
outputSet.copyInfo(imgSet)
if not self.newAssignmentPerformed:
outputSet.setAlignmentProj()
outputSet.copyItems(imgSet,
updateItemCallback=self._processRow,
itemDataIterator=md.iterRows(imgFn, sortByLabel=md.MDL_ITEM_ID))
self._defineOutputs(outputParticles=outputSet)
self._defineSourceRelation(self.inputSet, outputSet)示例3: _fillClassesFromIter
def _fillClassesFromIter(self, clsSet, iteration):
""" Create the SetOfClasses3D from a given iteration. """
self._loadClassesInfo(iteration)
dataStar = self._getFileName('data', iter=iteration)
clsSet.classifyItems(updateItemCallback=self._updateParticle,
updateClassCallback=self._updateClass,
itemDataIterator=md.iterRows(dataStar, sortByLabel=md.RLN_IMAGE_ID))示例4: _fillDataFromIter
def _fillDataFromIter(self, imgSet, iteration):
outImgsFn = self._getFileName('data', iter=iteration)
imgSet.setAlignmentProj()
imgSet.copyItems(self._getInputParticles(),
updateItemCallback=self._createItemMatrix,
itemDataIterator=md.iterRows(outImgsFn,
sortByLabel=md.RLN_IMAGE_ID))示例5: createOutputStep
def createOutputStep(self):
particles = self.inputParticles.get()
# Generate the SetOfAlignmet
alignedSet = self._createSetOfParticles()
alignedSet.copyInfo(particles)
inputMd = self._getPath('aligned_particles.xmd')
alignedSet.copyItems(particles,
updateItemCallback=self._updateItem,
itemDataIterator=md.iterRows(inputMd, sortByLabel=md.MDL_ITEM_ID))
# Remove alignment 2D
alignedSet.setAlignment(em.ALIGN_NONE)
# Define the output average
avgFile = self._getExtraPath("average.xmp")
imgh = ImageHandler()
avgImage = imgh.computeAverage(alignedSet)
avgImage.write(avgFile)
avg = em.Particle()
avg.setLocation(1, avgFile)
avg.copyInfo(alignedSet)
self._defineOutputs(outputAverage=avg)
self._defineSourceRelation(self.inputParticles, avg)
self._defineOutputs(outputParticles=alignedSet)
self._defineSourceRelation(self.inputParticles, alignedSet)示例6: readCoordinates
def readCoordinates(mic, fileName, coordsSet):
for row in md.iterRows(fileName):
coord = rowToCoordinate(row)
coord.setX(coord.getX())
coord.setY(coord.getY())
coord.setMicrograph(mic)
coordsSet.append(coord)示例7: createOutputStep
def createOutputStep(self):
micSet = self.getInputMicrographs()
outputCoordinatesName = 'outputCoordinates'
outputSuffix = ''
# If in optimization phase, let's create a subset of the micrographs
if self.isRunOptimize():
outputSuffix = '_subset'
outputCoordinatesName = 'outputCoordinatesSubset'
micSubSet = self._createSetOfMicrographs(suffix=outputSuffix)
micSubSet.copyInfo(micSet)
# Use previously written star file for reading the subset of micrographs,
for row in md.iterRows(self._getPath('input_micrographs.star')):
mic = micSet[row.getValue('rlnImageId')]
micSubSet.append(mic)
self._defineOutputs(outputMicrographsSubset=micSubSet)
self._defineTransformRelation(self.getInputMicrographsPointer(),
micSubSet)
micSet = micSubSet
coordSet = self._createSetOfCoordinates(micSet)
template = self._getExtraPath("%s_autopick.star")
starFiles = [template % pwutils.removeBaseExt(mic.getFileName())
for mic in micSet]
readSetOfCoordinates(coordSet, starFiles, micSet)
self._defineOutputs(**{outputCoordinatesName: coordSet})
self._defineSourceRelation(self.getInputMicrographsPointer(),
coordSet)示例8: _fillClassesFromIter
def _fillClassesFromIter(self, clsSet, iteration):
""" Create the SetOfClasses2D from a given iteration. """
self._loadClassesInfo(self._getIterMdClasses(iteration))
dataXmd = self._getIterMdImages(iteration)
clsSet.classifyItems(updateItemCallback=self._updateParticle,
updateClassCallback=self._updateClass,
itemDataIterator=md.iterRows(dataXmd,
sortByLabel=md.MDL_ITEM_ID))示例9: readCoordinates
def readCoordinates(mic, fileName, coordsSet):
if os.path.exists(fileName):
mdCoords = md.MetaData()
mdCoords.readPlain(fileName, "xcoor ycoor xSize ySize")
for row in md.iterRows(mdCoords):
coord = em.Coordinate(x = row.getValue("xcoor") + row.getValue("xSize")/2,
y = row.getValue("ycoor") + row.getValue("ySize")/2)
coord.setMicrograph(mic)
coordsSet.append(coord)示例10: createOutputStep
def createOutputStep(self):
imgSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
partSet.copyInfo(imgSet)
partSet.copyItems(imgSet,
updateItemCallback=self._createItemMatrix,
itemDataIterator=md.iterRows(self.outputMd.get(), sortByLabel=md.MDL_ITEM_ID))
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(imgSet, partSet)示例11: _fillParticlesFromIter
def _fillParticlesFromIter(self, partSet, iteration):
import pyworkflow.em.metadata as md
imgSet = self.inputParticles.get()
imgFn = "[email protected]" + self._getFileName('docfileInputAnglesIters', iter=iteration, ref=1)
partSet.copyInfo(imgSet)
partSet.setAlignmentProj()
partSet.copyItems(imgSet,
updateItemCallback=self._createItemMatrix,
itemDataIterator=md.iterRows(imgFn, sortByLabel=md.MDL_ITEM_ID))示例12: runCreateOutputStep
def runCreateOutputStep(self):
import pyworkflow.em.metadata as md
''' Create standard output results_images, result_classes'''
#creating results files
imgSet = self.inputParticles.get()
lastIter = self.numberOfIterations.get()
if self.numberOfReferences != 1:
inDocfile = self._getFileName('docfileInputAnglesIters', iter=lastIter)
ClassFnTemplate = '%(rootDir)s/reconstruction_Ref3D_%(ref)03d.vol'
allExpImagesinDocfile = xmipp.FileName()
all_exp_images="all_exp_images"
allExpImagesinDocfile.compose(all_exp_images, inDocfile)
dataClasses = self._getFileName('sqliteClasses')
createClassesFromImages(imgSet, str(allExpImagesinDocfile), dataClasses,
SetOfClasses3D, xmipp.MDL_REF3D, ClassFnTemplate, lastIter)
classes = self._createSetOfClasses3D(imgSet)
clsSet = SetOfClasses3D(dataClasses)
classes.appendFromClasses(clsSet)
volumes = self._createSetOfVolumes()
volumes.setSamplingRate(imgSet.getSamplingRate())
for refN in self.allRefs():
volFn = self._getFileName('reconstructedFileNamesIters', iter=lastIter, ref=refN)
vol = Volume()
vol.setFileName(volFn)
volumes.append(vol)
self._defineOutputs(outputVolumes=volumes)
self._defineOutputs(outputClasses=classes)
self._defineSourceRelation(self.inputParticles, volumes)
self._defineSourceRelation(self.inputParticles, classes)
else:
volFn = self._getFileName('reconstructedFileNamesIters', iter=lastIter, ref=1)
vol = Volume()
vol.setFileName(volFn)
vol.setSamplingRate(imgSet.getSamplingRate())
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputParticles, vol)
#create set of images
imgSetOut = self._createSetOfParticles()
imgFn = "[email protected]" + self._getFileName('docfileInputAnglesIters', iter=lastIter, ref=1)
imgSetOut.copyInfo(imgSet)
imgSetOut.setAlignmentProj()
imgSetOut.copyItems(imgSet,
updateItemCallback=self._createItemMatrix,
itemDataIterator=md.iterRows(imgFn))
self._defineOutputs(outputParticles=imgSetOut)
self._defineSourceRelation(self.inputParticles, imgSetOut)示例13: createOutputStep
def createOutputStep(self):
imgSet = self._getInputParticles()
outImgSet = self._createSetOfParticles()
outImgsFn = self._getFileName('output_star')
outImgSet.copyInfo(imgSet)
outImgSet.setAlignmentProj()
outImgSet.copyItems(imgSet,
updateItemCallback=self._updateItem,
itemDataIterator=md.iterRows(outImgsFn))
self._defineOutputs(outputParticles=outImgSet)
self._defineTransformRelation(imgSet, outImgSet)示例14: createOutputStep
def createOutputStep(self):
imgSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
imgFn = self._getPath('corrected_ctf_particles.xmd')
partSet.copyInfo(imgSet)
partSet.copyItems(imgSet,
updateItemCallback=self._updateLocation,
itemDataIterator=md.iterRows(imgFn, sortByLabel=md.MDL_ITEM_ID))
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(imgSet, partSet)示例15: createOutputStep
def createOutputStep(self):
inputSet = self.inputParticles.get()
partSet = self._createSetOfParticles()
pdbPointer = self.inputModes.get()._pdbPointer
partSet.copyInfo(inputSet)
partSet.copyItems(inputSet,
updateItemCallback=self._updateParticle,
itemDataIterator=md.iterRows(self.imgsFn, sortByLabel=md.MDL_ITEM_ID))
self._defineOutputs(outputParticles=partSet)
self._defineSourceRelation(pdbPointer, partSet)
self._defineTransformRelation(self.inputParticles, partSet)