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20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,您的评价将有助于我们的系统推荐出更棒的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)
开发者ID:azazellochg,项目名称:scipion,代码行数:32,代码来源:protocol_multireference_alignability.py
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)
开发者ID:I2PC,项目名称:scipion,代码行数:26,代码来源:protocol_compare_reprojections.py
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))
开发者ID:azazellochg,项目名称:scipion,代码行数:7,代码来源:protocol_classify3d.py
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))
开发者ID:I2PC,项目名称:scipion,代码行数:7,代码来源:protocol_refine3d.py
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)
开发者ID:coocoky,项目名称:scipion,代码行数:32,代码来源:protocol_apply_alignment.py
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)
开发者ID:azazellochg,项目名称:scipion,代码行数:7,代码来源:convert.py
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)
开发者ID:I2PC,项目名称:scipion,代码行数:29,代码来源:protocol_autopick_v2.py
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))
开发者ID:I2PC,项目名称:scipion,代码行数:8,代码来源:protocol_ml2d.py
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)
开发者ID:I2PC,项目名称:scipion,代码行数:9,代码来源:convert.py
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)
开发者ID:azazellochg,项目名称:scipion,代码行数:10,代码来源:protocol_break_symmetry.py
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))
开发者ID:azazellochg,项目名称:scipion,代码行数:10,代码来源:protocol_projmatch.py
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)
开发者ID:denisfortun,项目名称:scipion,代码行数:55,代码来源:projmatch_steps.py
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)
开发者ID:I2PC,项目名称:scipion,代码行数:12,代码来源:protocol_subtract.py
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)
开发者ID:coocoky,项目名称:scipion,代码行数:12,代码来源:protocol_ctf_correct_wiener2d.py
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)
开发者ID:I2PC,项目名称:scipion,代码行数:13,代码来源:protocol_nma_alignment.py
示例16: _loadClassesInfo
def _loadClassesInfo(self, filename):
""" Read some information about the produced 2D classes
from the metadata file.
"""
self._classesInfo = {} # store classes info, indexed by class id
mdClasses = md.MetaData(filename)
for classNumber, row in enumerate(md.iterRows(mdClasses)):
index, fn = xmippToLocation(row.getValue(md.MDL_IMAGE))
# Store info indexed by id, we need to store the row.clone() since
# the same reference is used for iteration
self._classesInfo[classNumber+1] = (index, fn, row.clone())
开发者ID:I2PC,项目名称:scipion,代码行数:13,代码来源:protocol_ml2d.py
示例17: _loadClassesInfo
def _loadClassesInfo(self, iteration):
""" Read some information about the produced Relion 3D classes
from the *model.star file.
"""
self._classesInfo = {} # store classes info, indexed by class id
modelStar = md.MetaData('[email protected]' + self._getFileName('model', iter=iteration))
for classNumber, row in enumerate(md.iterRows(modelStar)):
index, fn = relionToLocation(row.getValue('rlnReferenceImage'))
# Store info indexed by id, we need to store the row.clone() since
# the same reference is used for iteration
self._classesInfo[classNumber+1] = (index, fn, row.clone())
开发者ID:azazellochg,项目名称:scipion,代码行数:13,代码来源:protocol_classify3d.py
示例18: createOutputStep
def createOutputStep(self):
outputSet = self._createSetOfParticles()
imgSet = self.inputSet.get()
imgFn = self._getExtraPath("anglesCont.xmd")
if isinstance(imgSet, SetOfClasses2D):
outputSet.copyInfo(imgSet.getImages())
else:
outputSet.copyInfo(imgSet)
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)
开发者ID:azazellochg,项目名称:scipion,代码行数:15,代码来源:protocol_compare_reprojections.py
示例19: createOutputStep
def createOutputStep(self):
outputVols = self._createSetOfVolumes()
for i, vol in enumerate(self._iterInputVols()):
volDir = self._getVolDir(i+1)
volume = vol.clone()
volPrefix = 'vol%03d_' % (i+1)
m_pruned = md.MetaData()
m_pruned.read(volDir+'/pruned_particles_alignability.xmd')
prunedMd = self._getExtraPath(volPrefix + 'pruned_particles_alignability.xmd')
moveFile(join(volDir, 'pruned_particles_alignability.xmd'), prunedMd)
m_volScore = md.MetaData()
m_volScore.read(volDir+'/validationAlignability.xmd')
validationMd = self._getExtraPath(volPrefix + 'validation_alignability.xmd')
moveFile(join(volDir, 'validationAlignability.xmd'), validationMd)
imgSet = self.inputParticles.get()
outImgSet = self._createSetOfParticles(volPrefix)
outImgSet.copyInfo(imgSet)
outImgSet.copyItems(imgSet,
updateItemCallback=self._setWeight,
itemDataIterator=md.iterRows(prunedMd, sortByLabel=md.MDL_ITEM_ID))
mdValidatoin = md.getFirstRow(validationMd)
weight = mdValidatoin.getValue(md.MDL_WEIGHT_PRECISION_ALIGNABILITY)
volume.weightAlignabilityPrecision = Float(weight)
weight = mdValidatoin.getValue(md.MDL_WEIGHT_ACCURACY_ALIGNABILITY)
volume.weightAlignabilityAccuracy = Float(weight)
weight = mdValidatoin.getValue(md.MDL_WEIGHT_PRECISION_MIRROR)
volume.weightMirror = Float(weight)
volume.cleanObjId() # clean objects id to assign new ones inside the set
outputVols.append(volume)
self._defineOutputs(outputParticles=outImgSet)
self.createPlot2D(volPrefix,m_pruned)
outputVols.setSamplingRate(volume.getSamplingRate())
self._defineOutputs(outputVolumes=outputVols)
开发者ID:I2PC,项目名称:scipion,代码行数:48,代码来源:protocol_multireference_alignability.py
示例20: createOutputStep
def createOutputStep(self):
inputSet = self.inputParticles.get()
# outputSet could be SetOfParticles, SetOfAverages or any future sub-class of SetOfParticles
className = inputSet.getClassName()
outputSet = self._createSetFromName(className)
outputSet.copyInfo(inputSet)
self._preprocessOutput(outputSet)
outputSet.copyItems(inputSet,
updateItemCallback=self._updateItem,
itemDataIterator=md.iterRows(self.outputMd, sortByLabel=md.MDL_ITEM_ID))
self._postprocessOutput(outputSet)
outputKey = className.replace('SetOf', 'output')
self._defineOutputs(**{outputKey: outputSet})
self._defineTransformRelation(inputSet, outputSet)
开发者ID:azazellochg,项目名称:scipion,代码行数:17,代码来源:protocol_process.py
注:本文中的pyworkflow.em.metadata.iterRows函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
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