def getStackRunParams(self):
stackdata = self.getOriginalStackMadeByMakeStack()
stackruns = apStack.getStackRunsFromStack(stackdata)
# To Do: need to handle combined stack
stackrun = stackruns[0]
self.originalStackParamData = stackrun['stackParams']
self.stackrunlogparams = apScriptLog.getScriptParamValuesFromRunname(stackrun['stackRunName'],stackdata['path'],jobdata=None)
def convertToRefineStack(self):
'''
The stack is remaked without ctf correction and without invertion (ccd)
'''
newstackroot = os.path.join(self.params['rundir'],
os.path.basename(self.stack['file'])[:-4])
if self.params['paramonly'] is True:
print 'newstackroot', newstackroot
self.setFrealignStack(newstackroot)
return
# copy existing refined stack if possible
existing_refine_stack = apStack.getExistingRefineStack(
self.stack['data'],
'frealign',
False,
self.params['last'],
self.params['bin'],
lowpass=self.params['lowpass'],
highpass=self.params['highpass'])
try:
if existing_refine_stack:
if existing_refine_stack != os.path.join(
self.params['rundir'], newstackroot + '.mrc'):
shutil.copyfile(existing_refine_stack,
newstackroot + '.mrc')
new_partorderfile = os.path.join(self.params['rundir'],
'stackpartorder.list')
existing_partorderfile = os.path.join(
os.path.dirname(existing_refine_stack),
'stackpartorder.list')
# particle order list also need to be copied
if not os.path.isfile(new_partorderfile) and os.path.isfile(
existing_partorderfile):
shutil.copyfile(existing_partorderfile, new_partorderfile)
self.setFrealignStack(newstackroot)
return
except:
# make one from scratch if there is error
apDisplay.printMsg(
'Error copying existing refine stack, will regenerate')
if self.no_ctf_correction:
self.ImagicStackToFrealignMrcStack(self.stack['file'])
self.setFrealignStack(newstackroot)
return
# stack need to be remade without ctf correction
apDisplay.printWarning(
'Frealign needs a stack without ctf correction. A new stack is being made....'
)
stackdata = self.stack['data']
madestackdata = self.getOriginalStackMadeByMakeStack()
stackid = stackdata.dbid
stackruns = apStack.getStackRunsFromStack(madestackdata)
# To Do: need to handle combined stack
stackrun = stackruns[0]
stackpathname = os.path.basename(stackdata['path']['path'])
totalpart = apStack.getNumberStackParticlesFromId(stackid)
if not self.params['last']:
numpart = totalpart
else:
numpart = min(self.params['last'], totalpart)
newstackrunname = self.params['runname']
newstackrundir = self.params['rundir']
newstackimagicfile = os.path.join(newstackrundir, 'temp.hed')
# use first particle image to get presetname
oneparticle = apStack.getOneParticleFromStackId(stackid,
particlenumber=1)
preset = oneparticle['particle']['image']['preset']
if preset:
presetname = preset['name']
else:
presetname = 'manual'
# use first stack run to get parameters
paramdata = stackrun['stackParams']
# binning is combination of the original binning of the stack and the preparation binnning
bin = paramdata['bin'] * self.params['bin']
unbinnedboxsize = self.stack['boxsize'] * paramdata['bin']
lowpasstext = self.setArgText(
'lowpass', (self.params['lowpass'], paramdata['lowpass']), False)
highpasstext = self.setArgText(
'highpass', (self.params['highpass'], paramdata['highpass']), True)
partlimittext = self.setArgText('partlimit', (numpart, ), False)
#normalization
normtext = ''
if 'xmipp-norm' in paramdata.keys():
# myami-3.1 or before
normtext = self.setArgText('xmipp-normalize',
(paramdata['xmipp-norm'], ), True)
normtext = '--normalized ' + normtext
elif 'normalizemethod' in paramdata.keys():
# myami-3.2 or newer
normtext = '--normalize-method=%s' % (
paramdata['normalizemethod'], )
sessionid = int(self.params['expid'])
sessiondata = apDatabase.getSessionDataFromSessionId(sessionid)
sessionname = sessiondata['name']
projectid = self.params['projectid']
# The assumption is that the image is from ice grid and digital camera (black particles on white background
if 'reverse' in self.stackrunlogparams.keys():
reversetext = '--reverse'
else:
reversetext = ''
if 'defocpair' in self.stackrunlogparams.keys():
defoctext = '--defocpair'
else:
defoctext = ''
cmd = '''
makestack2.py --single=%s --fromstackid=%d %s %s %s %s %s --no-invert %s --boxsize=%d --bin=%d --description="frealign refinestack based on %s(id=%d)" --projectid=%d --preset=%s --runname=%s --rundir=%s --no-wait --no-commit --no-continue --session=%s --expId=%d --jobtype=makestack2
''' % (os.path.basename(newstackimagicfile), stackid, lowpasstext,
highpasstext, partlimittext, reversetext, defoctext, normtext,
unbinnedboxsize, bin, stackpathname, stackid, projectid, presetname,
newstackrunname, newstackrundir, sessionname, sessionid)
logfilepath = os.path.join(newstackrundir, 'frealignstackrun.log')
returncode = self.runAppionScriptInSubprocess(cmd, logfilepath)
if returncode > 0:
apDisplay.printError('Error in Frealign specific stack making')
self.ImagicStackToFrealignMrcStack(newstackimagicfile)
os.rename(newstackimagicfile[:-4] + '.mrc', newstackroot + '.mrc')
self.setFrealignStack(newstackroot)
# use the same complex equation as in eman clip
clipsize = self.calcClipSize(self.stack['boxsize'], self.params['bin'])
self.stack['boxsize'] = clipsize / self.params['bin']
self.stack['apix'] = self.stack['apix'] * self.params['bin']
#clean up
rmfiles = glob.glob("*.box")
for rmfile in rmfiles:
apFile.removeFile(rmfile)
def convertToRefineStack(self):
'''
The stack is remaked without ctf correction and without invertion (ccd)
'''
newstackroot = os.path.join(self.params['rundir'],os.path.basename(self.stack['file'])[:-4])
if self.params['paramonly'] is True:
print 'newstackroot',newstackroot
self.setFrealignStack(newstackroot)
return
# copy existing refined stack if possible
existing_refine_stack = apStack.getExistingRefineStack(self.stack['data'],'frealign',False,self.params['last'],self.params['bin'],lowpass=self.params['lowpass'],highpass=self.params['highpass'])
if existing_refine_stack:
if existing_refine_stack != os.path.join(self.params['rundir'],newstackroot+'.mrc'):
shutil.copyfile(existing_refine_stack,newstackroot+'.mrc')
new_partorderfile = os.path.join(self.params['rundir'],'stackpartorder.list')
existing_partorderfile = os.path.join(os.path.dirname(existing_refine_stack),'stackpartorder.list')
# particle order list also need to be copied
if not os.path.isfile(new_partorderfile) and os.path.isfile(existing_partorderfile):
shutil.copyfile(existing_partorderfile,new_partorderfile)
self.setFrealignStack(newstackroot)
return
if self.no_ctf_correction:
self.ImagicStackToFrealignMrcStack(self.stack['file'])
self.setFrealignStack(newstackroot)
return
# stack need to be remade without ctf correction
apDisplay.printWarning('Frealign needs a stack without ctf correction. A new stack is being made....')
stackdata = self.stack['data']
madestackdata = self.getOriginalStackMadeByMakeStack()
stackid = stackdata.dbid
stackruns = apStack.getStackRunsFromStack(madestackdata)
# To Do: need to handle combined stack
stackrun = stackruns[0]
stackpathname = os.path.basename(stackdata['path']['path'])
totalpart = apStack.getNumberStackParticlesFromId(stackid)
if not self.params['last']:
numpart = totalpart
else:
numpart = min(self.params['last'],totalpart)
newstackrunname = self.params['runname']
newstackrundir = self.params['rundir']
newstackimagicfile = os.path.join(newstackrundir,'temp.hed')
# use first particle image to get presetname
oneparticle = apStack.getOneParticleFromStackId(stackid, particlenumber=1)
preset =oneparticle['particle']['image']['preset']
if preset:
presetname = preset['name']
else:
presetname = 'manual'
# use first stack run to get parameters
paramdata = stackrun['stackParams']
# binning is combination of the original binning of the stack and the preparation binnning
bin = paramdata['bin']*self.params['bin']
unbinnedboxsize = self.stack['boxsize']*paramdata['bin']
lowpasstext = self.setArgText('lowpass',(self.params['lowpass'],paramdata['lowpass']),False)
highpasstext = self.setArgText('highpass',(self.params['highpass'],paramdata['highpass']),True)
partlimittext = self.setArgText('partlimit',(numpart,),False)
xmipp_normtext = self.setArgText('xmipp-normalize',(paramdata['xmipp-norm'],),True)
sessionid = int(self.params['expid'])
sessiondata = apDatabase.getSessionDataFromSessionId(sessionid)
sessionname = sessiondata['name']
projectid = self.params['projectid']
# The assumption is that the image is from ice grid and digital camera (black particles on white background
if 'reverse' in self.stackrunlogparams.keys():
reversetext = '--reverse'
else:
reversetext = ''
if 'defocpair' in self.stackrunlogparams.keys():
defoctext = '--defocpair'
else:
defoctext = ''
cmd = '''
makestack2.py --single=%s --fromstackid=%d %s %s %s %s %s --no-invert --normalized %s --boxsize=%d --bin=%d --description="frealign refinestack based on %s(id=%d)" --projectid=%d --preset=%s --runname=%s --rundir=%s --no-wait --no-commit --no-continue --session=%s --expId=%d --jobtype=makestack2
''' % (os.path.basename(newstackimagicfile),stackid,lowpasstext,highpasstext,partlimittext,reversetext,defoctext,xmipp_normtext,unbinnedboxsize,bin,stackpathname,stackid,projectid,presetname,newstackrunname,newstackrundir,sessionname,sessionid)
logfilepath = os.path.join(newstackrundir,'frealignstackrun.log')
returncode = self.runAppionScriptInSubprocess(cmd,logfilepath)
if returncode > 0:
apDisplay.printError('Error in Frealign specific stack making')
self.ImagicStackToFrealignMrcStack(newstackimagicfile)
os.rename(newstackimagicfile[:-4]+'.mrc',newstackroot+'.mrc')
self.setFrealignStack(newstackroot)
# use the same complex equation as in eman clip
clipsize = self.calcClipSize(self.stack['boxsize'],self.params['bin'])
self.stack['boxsize'] = clipsize / self.params['bin']
self.stack['apix'] = self.stack['apix'] * self.params['bin']
#clean up
rmfiles = glob.glob("*.box")
for rmfile in rmfiles:
apFile.removeFile(rmfile)
