def getTomoDirs(WorkingDir, tomogram): """ Give the tomogram filename, return the root and prefix to store the result files. """ tomoBaseName = removeBasenameExt(tomogram) tomoDir = join(WorkingDir, tomoBaseName) tomoRoot = join(tomoDir, tomoBaseName) return tomoBaseName, tomoDir, tomoRoot
def summary(self): md = self.getTomogramMd() size = md.size() message = [] if size > 1: message.append("Alignment of <%d> tomograms" % size) elif size == 1: message.append("Alignment of <%s> tomogram" % removeBasenameExt(md.getValue(xmipp.MDL_TOMOGRAMMD, md.firstObject()))) return message
def __init__(self, scriptname, project): ProtParticlesBase.__init__(self, protDict.preprocess_particles.name, scriptname, project) self.Import = 'from protocol_preprocess_particles import *' (self.InputDir,file)=split(self.InSelFile) baseFile = removeBasenameExt(file) self.OutStack = self.getFilename('images_stk') self.OutMetadata = self.getFilename('images') self.TiltPair = exists(os.path.join(self.InputDir,'images_untilted.xmd')) and self.InSelFile.find('images.xmd')!=-1 if self.TiltPair: self.InputUntilted=self.InSelFile.replace(".xmd","_untilted.xmd") self.InputTilted=self.InSelFile.replace(".xmd","_tilted.xmd") self.OutUntiltedStack=self.getFilename('images_untilted_stk') self.OutUntiltedMetadata=self.getFilename('images_untilted') self.OutTiltedStack=self.getFilename('images_tilted_stk') self.OutTiltedMetadata=self.getFilename('images_tilted') self.OutStack=self.OutUntiltedStack