def runCLTomo(log, WorkingDir, params, nproc):
runJob(log,'xmipp_mpi_classify_CLTomo','%d %s'%(nproc,params))
levelFiles=glob.glob(WorkingDir+"/extra/results_classes_level*.xmd")
if levelFiles:
levelFiles.sort()
lastLevelFile=levelFiles[-1]
createLink(log,lastLevelFile,os.path.join(WorkingDir,'results.xmd'))
def postEvaluation(log,WorkingDir):
levelFiles=glob.glob(os.path.join(WorkingDir,"extra/level_??/level_classes_core.xmd"))
if levelFiles:
levelFiles.sort()
lastLevelFile=levelFiles[-1]
createLink(log,lastLevelFile,os.path.join(WorkingDir,'classes_core.xmd'))
levelFiles=glob.glob(os.path.join(WorkingDir,"extra/level_??/level_classes_stable_core.xmd"))
if levelFiles:
levelFiles.sort()
lastLevelFile=levelFiles[-1]
createLink(log,lastLevelFile,os.path.join(WorkingDir,'classes_stable_core.xmd'))
def postCl2d(log, WorkingDir, NumberOfReferences):
levelDirs=glob.glob(os.path.join(WorkingDir,"extra/level_??"))
createLink(log,os.path.join(WorkingDir,"extra/images.xmd"),os.path.join(WorkingDir,"images.xmd"))
if levelDirs:
levelDirs.sort()
lastLevelDir=levelDirs[-1]
fnLastLevelFile=os.path.join(lastLevelDir,"level_classes.xmd")
from protlib_xmipp import getMdSize
size = getMdSize("classes@"+fnLastLevelFile)
if size == NumberOfReferences:
createLink(log, fnLastLevelFile, os.path.join(WorkingDir,"classes.xmd"))
def rewriteClassBlock(log,WorkingDir,ExtraDir):
fnClassMetadata=os.path.join(ExtraDir,"kerdensom_classes.xmd")
fnClass="classes@%s"%fnClassMetadata
fnClassStack=os.path.join(ExtraDir,"classes.stk")
mD = MetaData(fnClass)
counter = 1
for id in mD:
mD.setValue(MDL_IMAGE,"%06d@%s"%(counter,fnClassStack),id)
counter += 1
mD.write(fnClass,MD_APPEND)
createLink(log,fnClassMetadata,os.path.join(WorkingDir,"classes.xmd"))
createLink(log,os.path.join(ExtraDir,"kerdensom_images.xmd"),os.path.join(WorkingDir,"images.xmd"))
def createAcquisition(log,InputFile,WorkingDir,DoResize,NewSize):
fnAcqIn = findAcquisitionInfo(InputFile)
if not fnAcqIn is None:
fnAcqOut = getProtocolFilename('acquisition', WorkingDir=WorkingDir)
if not DoResize:
createLink(log, fnAcqIn, fnAcqOut)
else:
md = MetaData(fnAcqIn)
id = md.firstObject()
Ts = md.getValue(MDL_SAMPLINGRATE, id)
(Xdim, Ydim, Zdim, Ndim, _) = MetaDataInfo(InputFile)
downsampling = float(Xdim)/NewSize;
md.setValue(MDL_SAMPLINGRATE,Ts*downsampling,id)
md.write(getProtocolFilename('acquisition', WorkingDir=WorkingDir))
def createResults(log
, CTFDatName
, DoCtfCorrection
, inDocfile
, listWithResultVolume
, resultsImages
, resultsClasses3DRef
, resultsClasses3DRefDefGroup
, resultsVolumes
, selFileName
, workingDir
):
''' Create standard output results_images, result_classes'''
from os import remove
from os.path import exists
#create metadata file with volume names
mdVolume = MetaData()
for resultVolume in listWithResultVolume:
objId = mdVolume.addObject()
mdVolume.setValue(MDL_IMAGE,resultVolume,objId)
#link also last iteration volumes
createLink(log,resultVolume,join(workingDir, basename(resultVolume)))
mdVolume.write(resultsVolumes)
#read file with results
allExpImagesinDocfile = FileName()
all_exp_images="all_exp_images"
allExpImagesinDocfile.compose(all_exp_images, inDocfile)
md = MetaData(allExpImagesinDocfile)
#read file with ctfs
mdOut = MetaData()
if DoCtfCorrection:
#read only image and ctf_model
mdOut = MetaData()
mdCTF = MetaData()
mdCTF.read(CTFDatName, [MDL_IMAGE, MDL_CTF_MODEL])
md.addIndex(MDL_IMAGE)
mdCTF.addIndex(MDL_IMAGE)
mdOut.joinNatural(md, mdCTF)
else:
mdOut = MetaData(md)#becareful with copy metadata since it only copies pointers
mdref3D = MetaData()
mdrefCTFgroup = MetaData()
mdref3D.aggregate(mdOut, AGGR_COUNT, MDL_REF3D, MDL_REF3D, MDL_COUNT)
mdrefCTFgroup.aggregate(mdOut, AGGR_COUNT, MDL_DEFGROUP, MDL_DEFGROUP, MDL_COUNT)
#total number Image
numberImages = mdOut.size()
#total number CTF
numberDefocusGroups = mdrefCTFgroup.size()
#total number volumes
numberRef3D = mdref3D.size()
fnResultImages=FileName()
fnResultClasses=FileName()
fnResultImages.compose("images",resultsImages)
comment = " numberImages=%d..................................................... "%numberImages
comment += " numberDefocusGroups=%d................................................."%numberDefocusGroups
comment += " numberRef3D=%d........................................................."%numberRef3D
#
mdAux1 = MetaData()
mdAux2 = MetaData()
mdAux1.read(selFileName,[MDL_IMAGE,MDL_ITEM_ID])
mdAux2.join1(mdOut, mdAux1, MDL_IMAGE, LEFT_JOIN)
mdAux2.setComment(comment)
mdAux2.write(fnResultImages)
#
#make query and store ref3d with all
for id in mdref3D:
ref3D = mdref3D.getValue(MDL_REF3D, id)
md.importObjects(mdOut, MDValueEQ(MDL_REF3D, ref3D))
fnResultClasses.compose(("images_ref3d%06d"%ref3D),resultsClasses3DRef)
md.write(fnResultClasses,MD_APPEND)
md2=MetaData()
for id in mdref3D:
ref3D = mdref3D.getValue(MDL_REF3D, id)
#a multiquey would be better but I do not know how to implement it in python
md.importObjects(mdOut, MDValueEQ(MDL_REF3D, ref3D))
for id in mdrefCTFgroup:
defocusGroup = mdrefCTFgroup.getValue(MDL_DEFGROUP, id)
md2.importObjects(md, MDValueEQ(MDL_DEFGROUP, defocusGroup))
fnResultClasses.compose(("images_ref3d%06d_defocusGroup%06d"%(ref3D,defocusGroup)),resultsClasses3DRefDefGroup)
md2.write(fnResultClasses,MD_APPEND)
