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
