def convertStackToMrc(self):
stackdata = apStackData.getOnlyStackData(self.params['stackid'])
stackfile = os.path.join(stackdata['path']['path'],stackdata['name'])
stackbaseroot = os.path.basename(stackfile).split('.')[0]
stackroot = os.path.join(stackdata['path']['path'],stackdata['name'][:-4])
apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s.mrc'% (stackroot,stackbaseroot))
self.stackfile = stackbaseroot+'.mrc'
apIMAGIC.convertImagicStackToMrcStack(stackroot,self.stackfile)
def convertStackToMrc(self):
stackdata = apStackData.getOnlyStackData(self.params["stackid"])
stackfile = os.path.join(stackdata["path"]["path"], stackdata["name"])
stackbaseroot = os.path.basename(stackfile).split(".")[0]
stackroot = os.path.join(stackdata["path"]["path"], stackdata["name"][:-4])
apDisplay.printMsg(
"converting %s from default IMAGIC stack format to MRC as %s.mrc" % (stackroot, stackbaseroot)
)
self.stackfile = stackbaseroot + ".mrc"
apIMAGIC.convertImagicStackToMrcStack(stackroot, self.stackfile)
def ImagicStackToMrcStack(self,stackfile):
stackroot = stackfile[:-4]
stackbaseroot = os.path.basename(stackfile).split('.')[0]
apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s.mrc'% (stackroot,stackbaseroot))
apIMAGIC.convertImagicStackToMrcStack(stackroot,stackbaseroot+'.mrc')
# clean up non-mrc stack in rundir which may be left from preprocessing such as binning
tmpstackdir = os.path.dirname(stackfile)
stackext = os.path.basename(stackfile).split('.')[-1]
if stackext != 'mrc' and tmpstackdir == self.params['rundir']:
os.remove(stackfile)
if stackext == 'hed':
imgfilepath = stackfile.replace('hed','img')
os.remove(imgfilepath)
def ImagicStackToFrealignMrcStack(self,stackfile):
stackroot = stackfile[:-4]
stackbaseroot = os.path.basename(stackfile).split('.')[0]
apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s.mrc'% (stackroot,stackbaseroot))
apIMAGIC.convertImagicStackToMrcStack(stackroot,stackbaseroot+'.mrc')
# clean up non-mrc stack in rundir which may be left from preprocessing such as binning
tmpstackdir = os.path.dirname(stackfile)
stackext = os.path.basename(stackfile).split('.')[-1]
if stackext != 'mrc' and tmpstackdir == self.params['rundir']:
os.remove(stackfile)
if stackext == 'hed':
imgfilepath = stackfile.replace('hed','img')
os.remove(imgfilepath)
def ImagicStackToMrcStack(self, oldstackfile):
'''
Convert IMAGIC Stack into MRC stack with extension .mrcs
'''
self.stackErrorCheck(oldstackfile)
stackroot = oldstackfile[:-4]
mrcstackfile = os.path.join(self.params['rundir'], 'particles.mrcs')
apDisplay.printMsg('converting %s from default IMAGIC stack format to MRC as %s'% (stackroot, mrcstackfile))
apIMAGIC.convertImagicStackToMrcStack(stackroot, mrcstackfile)
# clean up non-mrc stack in rundir which may be left from preprocessing such as binning
if not 'mrc' in oldstackfile and os.path.dirname(oldstackfile) == self.params['rundir']:
#apFile.removeStack(oldstackfile)
pass
def ImagicStackToMrcStack(self, oldstackfile):
'''
Convert IMAGIC Stack into MRC stack with extension .mrcs
'''
self.stackErrorCheck(oldstackfile)
stackroot = oldstackfile[:-4]
mrcstackfile = os.path.join(self.params['rundir'], 'particles.mrcs')
apDisplay.printMsg(
'converting %s from default IMAGIC stack format to MRC as %s' %
(stackroot, mrcstackfile))
apIMAGIC.convertImagicStackToMrcStack(stackroot, mrcstackfile)
# clean up non-mrc stack in rundir which may be left from preprocessing such as binning
if not 'mrc' in oldstackfile and os.path.dirname(
oldstackfile) == self.params['rundir']:
#apFile.removeStack(oldstackfile)
pass