def createSubset(log, inputFile, inputFileLabel, subsetFile, subsetFileLabel, outputFile):
mdInputFile = MetaData(inputFile)
mdSubsetFile = MetaData(subsetFile)
mdOutputFile = MetaData()
print inputFile, inputFileLabel, subsetFile, subsetFileLabel, outputFile
mdOutputFile.join2( mdInputFile
, mdSubsetFile
, str2Label(inputFileLabel)
, str2Label(subsetFileLabel)
, INNER_JOIN)
mdOutputFile.write(outputFile)
def joinMetaDatas(log,InputFile,UntiltedMetadata,TiltedMetadata):
mDInput=MetaData(InputFile)
mDstack = MetaData(UntiltedMetadata)
mDstack.removeLabel(MDL_MICROGRAPH)
mDstack.removeLabel(MDL_XCOOR)
mDstack.removeLabel(MDL_YCOOR)
mdPart1=MetaData()
mdPart1.join2(mDstack,mDInput,MDL_IMAGE_ORIGINAL,MDL_IMAGE,INNER_JOIN)
mdPart1.removeLabel(MDL_IMAGE_ORIGINAL)
mDstack = MetaData(TiltedMetadata)
mDstack.removeLabel(MDL_MICROGRAPH)
mDstack.removeLabel(MDL_XCOOR)
mDstack.removeLabel(MDL_YCOOR)
mDstack.renameColumn(MDL_IMAGE,MDL_IMAGE_TILTED)
mdJoined=MetaData()
mdJoined.join2(mDstack,mdPart1,MDL_IMAGE_ORIGINAL,MDL_IMAGE_TILTED,INNER_JOIN)
mdJoined.removeLabel(MDL_IMAGE_ORIGINAL)
mdJoined.write(InputFile)
def gatherPairs(log, WorkingDir, ExtraDir, ClassSelection, ClassFile, ExtractDir, PickingDir):
mdImages = getImagesMd(ExtractDir)
fnMicrographs = getProtocolFilename("micrographs", WorkingDir=ExtractDir)
mdTiltAngles = MetaData("micrographPairs@" + fnMicrographs)
mdU = getImagesMd(ExtractDir, "untilted")
mdUAux = MetaData()
mdUAux.setColumnValues(MDL_IMAGE, mdU.getColumnValues(MDL_IMAGE))
mdUAux.setColumnValues(MDL_MICROGRAPH, mdU.getColumnValues(MDL_MICROGRAPH))
mdT = getImagesMd(ExtractDir, "tilted")
mdTAux = MetaData()
mdTAux.setColumnValues(MDL_IMAGE_TILTED, mdT.getColumnValues(MDL_IMAGE))
mdTAux.setColumnValues(MDL_MICROGRAPH_TILTED, mdT.getColumnValues(MDL_MICROGRAPH))
fnExtractImages = os.path.join(ExtractDir, "images.xmd")
mdJoin1 = MetaData()
mdJoin2 = MetaData()
mdJoin3 = MetaData()
mdJoin4 = MetaData()
fixedMdClass = MetaData()
fnOut = join(ExtraDir, "rct_classes.xmd")
for classNo in ClassSelection:
MDclass = MetaData(getClassBlock(classNo, ClassFile))
if not MDclass.containsLabel(MDL_IMAGE_TILTED):
if MDclass.containsLabel(MDL_IMAGE_ORIGINAL):
fixedMdClass.join2(MDclass, mdImages, MDL_IMAGE_ORIGINAL, MDL_IMAGE, INNER_JOIN)
else:
fixedMdClass.join1(MDclass, mdImages, MDL_IMAGE, INNER_JOIN)
else:
fixedMdClass = MDclass
mdJoin1.join1(fixedMdClass, mdImages, MDL_IMAGE, LEFT_JOIN)
mdJoin2.join1(mdJoin1, mdUAux, MDL_IMAGE, LEFT_JOIN)
mdJoin3.join1(mdJoin2, mdTAux, MDL_IMAGE_TILTED, LEFT_JOIN)
mdJoin4.join1(mdJoin3, mdTiltAngles, MDL_MICROGRAPH, LEFT_JOIN)
fnClassOut = getClassBlock(classNo, fnOut)
mdJoin4.write(fnClassOut, MD_APPEND)