def getTemplate(self):
"""
takes the spider file and creates an average template of all particles
"""
### create random keep list
templatedata = apTemplate.getTemplateFromId(self.params["templateid"])
templatepath = os.path.join(templatedata["path"]["path"], templatedata["templatename"])
if not os.path.isfile(templatepath):
apDisplay.printError("Could not find template: " + templatepath)
newpath = os.path.join(self.params["rundir"], "template.mrc")
shutil.copy(templatepath, newpath)
### needs to scale template by old apix to new apix
templatefile = self.processTemplate("template.mrc")
return templatefile
def getTemplate(self):
"""
takes the spider file and creates an average template of all particles
"""
### create random keep list
templatedata = apTemplate.getTemplateFromId(self.params['templateid'])
templatepath = os.path.join(templatedata['path']['path'],
templatedata['templatename'])
if not os.path.isfile(templatepath):
apDisplay.printError("Could not find template: " + templatepath)
newpath = os.path.join(self.params['rundir'], "template.mrc")
shutil.copy(templatepath, newpath)
### needs to scale template by old apix to new apix
templatefile = self.processTemplate("template.mrc")
return templatefile
def insertRefBasedRun(self, partlist, imagicstack, insert=False):
apDisplay.printMsg("committing results to DB")
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
uniquerun = alignrunq.query(results=1)
if uniquerun:
apDisplay.printError("Run name '"+runparams['runname']+"' and path already exist in database")
### setup ref based run
refrunq = appiondata.ApRefBasedRunData()
refrunq['runname'] = self.params['runname']
refrunq['xysearch'] = self.params['xysearch']
refrunq['xystep'] = self.params['xystep']
refrunq['first_ring'] = self.params['firstring']
refrunq['last_ring'] = self.params['lastring']
refrunq['num_iter'] = self.params['numiter']
refrunq['invert_templs'] = self.params['inverttemplates']
refrunq['num_templs'] = self.params['numtemplate']
#refrunq['csym', int),
refrunq['run_seconds'] = self.params['runtime']
### finish alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['refbasedrun'] = refrunq
alignrunq['hidden'] = False
alignrunq['bin'] = self.params['bin']
alignrunq['hp_filt'] = self.params['highpass']
alignrunq['lp_filt'] = self.params['lowpass']
alignrunq['runname'] = self.params['runname']
alignrunq['description'] = self.params['description']
### setup alignment stack
alignstackq = appiondata.ApAlignStackData()
alignstackq['alignrun'] = alignrunq
alignstackq['imagicfile'] = imagicstack
alignstackq['avgmrcfile'] = "average.mrc"
emancmd = "proc2d templatestack%02d.spi templatestack%02d.hed"%(self.params['numiter'],self.params['numiter'])
apEMAN.executeEmanCmd(emancmd)
alignstackq['refstackfile'] = ("templatestack%02d.hed"%(self.params['numiter']))
alignstackq['alignrun'] = alignrunq
alignstackq['iteration'] = self.params['numiter']
alignstackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### check to make sure files exist
imagicfile = os.path.join(self.params['rundir'], alignstackq['imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find stack file: "+imagicfile)
avgmrcfile = os.path.join(self.params['rundir'], alignstackq['avgmrcfile'])
if not os.path.isfile(avgmrcfile):
apDisplay.printError("could not find average mrc file: "+avgmrcfile)
refstackfile = os.path.join(self.params['rundir'], alignstackq['refstackfile'])
if not os.path.isfile(refstackfile):
apDisplay.printError("could not find reference stack file: "+refstackfile)
alignstackq['stack'] = self.stack['data']
alignstackq['boxsize'] = self.boxsize
alignstackq['pixelsize'] = self.stack['apix']*self.params['bin']
alignstackq['description'] = self.params['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = self.params['numpart']
if insert is True:
alignstackq.insert()
### insert reference data
reflist = []
for j in range(self.params['numiter']):
iternum = j+1
for i in range(len(self.templatelist)):
refnum = i+1
templateid = self.templatelist[i]
refq = appiondata.ApAlignReferenceData()
refq['refnum'] = refnum
refq['iteration'] = iternum
refq['template'] = apTemplate.getTemplateFromId(templateid)
refq['mrcfile'] = ("templateavg%02d-%02d.mrc"%(iternum,refnum))
refpath = os.path.join(self.params['rundir'], "templates")
refq['path'] = appiondata.ApPathData(path=os.path.abspath(refpath))
refq['alignrun'] = alignrunq
if refnum in self.resdict:
refq['ssnr_resolution'] = self.resdict[refnum]
if insert is True:
refq.insert()
if iternum == self.params['numiter']:
reflist.append(refq)
#refq['varmrcfile', str),
#refq['frc_resolution', float),
### insert particle data
apDisplay.printColor("Inserting particle alignment data, please wait", "cyan")
for partdict in partlist:
### see apSpider.alignment.alignStack() for more info
"""
partdict.keys()
'num': int(data[0]), #SPIDER NUMBERING: 1,2,3,...
'template': int(abs(templatenum)), #SPIDER NUMBERING: 1,2,3,...
'mirror': checkMirror(templatenum),
'score': float(data[3]),
'rot': float(data[4]),
'xshift': float(data[5]),
'yshift': float(data[6]),
"""
alignpartq = appiondata.ApAlignParticleData()
alignpartq['ref'] = reflist[partdict['template']-1]
alignpartq['partnum'] = partdict['num']
alignpartq['alignstack'] = alignstackq
stackpartdata = apStack.getStackParticle(self.params['stackid'], partdict['num'])
alignpartq['stackpart'] = stackpartdata
alignpartq['xshift'] = partdict['xshift']
alignpartq['yshift'] = partdict['yshift']
alignpartq['rotation'] = partdict['rot']
alignpartq['score'] = partdict['score']
alignpartq['mirror'] = partdict['mirror']
if insert is True:
alignpartq.insert()
return
def insertRefBasedRun(self, partlist, imagicstack, insert=False):
apDisplay.printMsg("committing results to DB")
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
uniquerun = alignrunq.query(results=1)
if uniquerun:
apDisplay.printError("Run name '"+runparams['runname']+"' and path already exist in database")
### setup ref based run
refrunq = appiondata.ApRefBasedRunData()
refrunq['runname'] = self.params['runname']
refrunq['xysearch'] = self.params['xysearch']
refrunq['xystep'] = self.params['xystep']
refrunq['first_ring'] = self.params['firstring']
refrunq['last_ring'] = self.params['lastring']
refrunq['num_iter'] = self.params['numiter']
refrunq['invert_templs'] = self.params['inverttemplates']
refrunq['num_templs'] = self.params['numtemplate']
#refrunq['csym', int),
refrunq['run_seconds'] = self.params['runtime']
### finish alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['refbasedrun'] = refrunq
alignrunq['hidden'] = False
alignrunq['bin'] = self.params['bin']
alignrunq['hp_filt'] = self.params['highpass']
alignrunq['lp_filt'] = self.params['lowpass']
alignrunq['runname'] = self.params['runname']
alignrunq['description'] = self.params['description']
### setup alignment stack
alignstackq = appiondata.ApAlignStackData()
alignstackq['alignrun'] = alignrunq
alignstackq['imagicfile'] = imagicstack
alignstackq['avgmrcfile'] = "average.mrc"
emancmd = "proc2d templatestack%02d.spi templatestack%02d.hed"%(self.params['numiter'],self.params['numiter'])
apEMAN.executeEmanCmd(emancmd)
alignstackq['refstackfile'] = ("templatestack%02d.hed"%(self.params['numiter']))
alignstackq['alignrun'] = alignrunq
alignstackq['iteration'] = self.params['numiter']
alignstackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### check to make sure files exist
imagicfile = os.path.join(self.params['rundir'], alignstackq['imagicfile'])
if not os.path.isfile(imagicfile):
apDisplay.printError("could not find stack file: "+imagicfile)
avgmrcfile = os.path.join(self.params['rundir'], alignstackq['avgmrcfile'])
if not os.path.isfile(avgmrcfile):
apDisplay.printError("could not find average mrc file: "+avgmrcfile)
refstackfile = os.path.join(self.params['rundir'], alignstackq['refstackfile'])
if not os.path.isfile(refstackfile):
apDisplay.printError("could not find reference stack file: "+refstackfile)
alignstackq['stack'] = self.stack['data']
alignstackq['boxsize'] = self.boxsize
alignstackq['pixelsize'] = self.stack['apix']*self.params['bin']
alignstackq['description'] = self.params['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = self.params['numpart']
if insert is True:
alignstackq.insert()
### insert reference data
reflist = []
for j in range(self.params['numiter']):
iternum = j+1
for i in range(len(self.templatelist)):
refnum = i+1
templateid = self.templatelist[i]
refq = appiondata.ApAlignReferenceData()
refq['refnum'] = refnum
refq['iteration'] = iternum
refq['template'] = apTemplate.getTemplateFromId(templateid)
refq['mrcfile'] = ("templateavg%02d-%02d.mrc"%(iternum,refnum))
refpath = os.path.join(self.params['rundir'], "templates")
refq['path'] = appiondata.ApPathData(path=os.path.abspath(refpath))
refq['alignrun'] = alignrunq
if refnum in self.resdict:
refq['ssnr_resolution'] = self.resdict[refnum]
if insert is True:
refq.insert()
if iternum == self.params['numiter']:
reflist.append(refq)
#refq['varmrcfile', str),
#refq['frc_resolution', float),
### insert particle data
apDisplay.printColor("Inserting particle alignment data, please wait", "cyan")
for partdict in partlist:
### see apSpider.alignment.alignStack() for more info
"""
partdict.keys()
'num': int(data[0]), #SPIDER NUMBERING: 1,2,3,...
'template': int(abs(templatenum)), #SPIDER NUMBERING: 1,2,3,...
'mirror': checkMirror(templatenum),
'score': float(data[3]),
'rot': float(data[4]),
'xshift': float(data[5]),
'yshift': float(data[6]),
"""
alignpartq = appiondata.ApAlignParticleData()
alignpartq['ref'] = reflist[partdict['template']-1]
alignpartq['partnum'] = partdict['num']
alignpartq['alignstack'] = alignstackq
stackpartdata = apStack.getStackParticle(self.params['stackid'], partdict['num'])
alignpartq['stackpart'] = stackpartdata
alignpartq['xshift'] = partdict['xshift']
alignpartq['yshift'] = partdict['yshift']
alignpartq['rotation'] = partdict['rot']
alignpartq['score'] = partdict['score']
alignpartq['mirror'] = partdict['mirror']
if insert is True:
alignpartq.insert()
return
def insertEdIterRun(self, insert=False):
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
uniquerun = alignrunq.query(results=1)
if uniquerun:
apDisplay.printError("Run name '" + runparams['runname'] +
"' and path already exist in database")
### setup ed-iter run
editrunq = appiondata.ApEdIterRunData()
editrunq['runname'] = self.params['runname']
editrunq['radius'] = self.params['partrad']
editrunq['num_iter'] = self.params['numiter']
#editrunq['freealigns'] = self.params['freealigns'] ### no longer an option
editrunq['invert_templs'] = self.params['inverttemplates']
editrunq['num_templs'] = self.params['numtemplate']
#editrunq['csym', int),
editrunq['run_seconds'] = self.runtime
### finish alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['editerrun'] = editrunq
alignrunq['hidden'] = False
alignrunq['bin'] = self.params['bin']
alignrunq['hp_filt'] = self.params['highpass']
alignrunq['lp_filt'] = self.params['lowpass']
alignrunq['runname'] = self.params['runname']
alignrunq['description'] = self.params['description']
### setup aligned stack
alignstackq = appiondata.ApAlignStackData()
alignstackq['alignrun'] = alignrunq
alignstackq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
# stack of aligned particles
alignstackq['imagicfile'] = "alignstack.hed"
# final class averages
alignstackq['refstackfile'] = "avg.hed"
# averaged results
alignstackq['avgmrcfile'] = "average.mrc"
# check to be sure dbpaths to files are correct
refstackfile = os.path.join(
self.params['rundir'],
alignstackq['refstackfile']) #final averages
if not os.path.isfile(refstackfile):
apDisplay.printError("could not find reference stack file: " +
refstackfile)
avgmrcfile = os.path.join(self.params['rundir'],
alignstackq['avgmrcfile']) #averaged results
if not os.path.isfile(avgmrcfile):
apDisplay.printError("could not find average mrc file: " +
avgmrcfile)
alignstackq['stack'] = self.stack['data']
alignstackq['iteration'] = self.params['numiter']
alignstackq['boxsize'] = math.floor(self.stack['boxsize'] /
self.params['bin'])
alignstackq['pixelsize'] = self.stack['apix'] * self.params['bin']
alignstackq['description'] = self.params['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = self.params['numpart']
if insert is True:
alignstackq.insert(
) #alignstackq contains alignrunq which contains editrunq
### setup data from each iteration
apDisplay.printColor(
"Inserting average and variance images from each iteration, please wait",
"cyan")
reflist = []
for j in range(self.params['numiter']):
iternum = j + 1
for i in range(len(self.templatelist)):
refnum = i + 1
templateid = self.templatelist[i]
refq = appiondata.ApAlignReferenceData()
refq['refnum'] = refnum
refq['iteration'] = iternum
refq['template'] = apTemplate.getTemplateFromId(templateid)
refpath = os.path.join(self.params['rundir'], "templates")
refq['path'] = appiondata.ApPathData(
path=os.path.abspath(refpath))
refq['alignrun'] = alignrunq
#refq['frc_resolution'] = #(float)
avgname = os.path.join(self.params['rundir'],
"r%02d/avg%03d" % (iternum, refnum))
varname = os.path.join(self.params['rundir'],
"r%02d/var%03d" % (iternum, refnum))
if os.path.isfile(avgname + ".spi"):
emancmd = "proc2d " + avgname + ".spi " + avgname + ".mrc"
apEMAN.executeEmanCmd(emancmd)
refq['mrcfile'] = (avgname + ".mrc")
emancmd = "proc2d " + varname + ".spi " + varname + ".mrc"
apEMAN.executeEmanCmd(emancmd)
refq['varmrcfile'] = (varname + ".mrc")
if insert is True:
refq.insert()
if iternum == self.params['numiter']:
reflist.append(refq)
else:
reflist.append(None)
### insert particle data
apDisplay.printColor("Inserting particle alignment data, please wait",
"cyan")
partlist = self.readApshDocFile("apshdoc.spi", "apshdoc.pickle")
for partdict in partlist:
alignpartq = appiondata.ApAlignParticleData()
alignpartq['ref'] = reflist[partdict['template'] - 1]
alignpartq['partnum'] = partdict['num']
alignpartq['alignstack'] = alignstackq
stackpartdata = apStack.getStackParticle(self.params['stackid'],
partdict['num'])
alignpartq['stackpart'] = stackpartdata
alignpartq['rotation'] = partdict['rot']
alignpartq['xshift'] = partdict['xshift']
alignpartq['yshift'] = partdict['yshift']
alignpartq['mirror'] = partdict['mirror']
alignpartq['score'] = partdict['score']
if insert is True:
alignpartq.insert() #insert each particle
return
def insertEdIterRun(self, insert=False):
### setup alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['runname'] = self.params['runname']
alignrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
uniquerun = alignrunq.query(results=1)
if uniquerun:
apDisplay.printError("Run name '"+runparams['runname']+"' and path already exist in database")
### setup ed-iter run
editrunq = appiondata.ApEdIterRunData()
editrunq['runname'] = self.params['runname']
editrunq['radius'] = self.params['partrad']
editrunq['num_iter'] = self.params['numiter']
#editrunq['freealigns'] = self.params['freealigns'] ### no longer an option
editrunq['invert_templs'] = self.params['inverttemplates']
editrunq['num_templs'] = self.params['numtemplate']
#editrunq['csym', int),
editrunq['run_seconds'] = self.runtime
### finish alignment run
alignrunq = appiondata.ApAlignRunData()
alignrunq['editerrun'] = editrunq
alignrunq['hidden'] = False
alignrunq['bin'] = self.params['bin']
alignrunq['hp_filt'] = self.params['highpass']
alignrunq['lp_filt'] = self.params['lowpass']
alignrunq['runname'] = self.params['runname']
alignrunq['description'] = self.params['description']
### setup aligned stack
alignstackq = appiondata.ApAlignStackData()
alignstackq['alignrun'] = alignrunq
alignstackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
# stack of aligned particles
alignstackq['imagicfile'] = "alignstack.hed"
# final class averages
alignstackq['refstackfile'] = "avg.hed"
# averaged results
alignstackq['avgmrcfile'] = "average.mrc"
# check to be sure dbpaths to files are correct
refstackfile = os.path.join(self.params['rundir'], alignstackq['refstackfile']) #final averages
if not os.path.isfile(refstackfile):
apDisplay.printError("could not find reference stack file: "+refstackfile)
avgmrcfile = os.path.join(self.params['rundir'], alignstackq['avgmrcfile']) #averaged results
if not os.path.isfile(avgmrcfile):
apDisplay.printError("could not find average mrc file: "+avgmrcfile)
alignstackq['stack'] = self.stack['data']
alignstackq['iteration'] = self.params['numiter']
alignstackq['boxsize'] = math.floor(self.stack['boxsize']/self.params['bin'])
alignstackq['pixelsize'] = self.stack['apix']*self.params['bin']
alignstackq['description'] = self.params['description']
alignstackq['hidden'] = False
alignstackq['num_particles'] = self.params['numpart']
if insert is True:
alignstackq.insert() #alignstackq contains alignrunq which contains editrunq
### setup data from each iteration
apDisplay.printColor("Inserting average and variance images from each iteration, please wait", "cyan")
reflist = []
for j in range(self.params['numiter']):
iternum = j+1
for i in range(len(self.templatelist)):
refnum = i+1
templateid = self.templatelist[i]
refq = appiondata.ApAlignReferenceData()
refq['refnum'] = refnum
refq['iteration'] = iternum
refq['template'] = apTemplate.getTemplateFromId(templateid)
refpath = os.path.join(self.params['rundir'], "templates")
refq['path'] = appiondata.ApPathData(path=os.path.abspath(refpath))
refq['alignrun'] = alignrunq
#refq['frc_resolution'] = #(float)
avgname = os.path.join(self.params['rundir'], "r%02d/avg%03d"%(iternum,refnum) )
varname = os.path.join(self.params['rundir'], "r%02d/var%03d"%(iternum,refnum) )
if os.path.isfile(avgname+".spi"):
emancmd = "proc2d "+avgname+".spi "+avgname+".mrc"
apEMAN.executeEmanCmd(emancmd)
refq['mrcfile'] = (avgname+".mrc")
emancmd = "proc2d "+varname+".spi "+varname+".mrc"
apEMAN.executeEmanCmd(emancmd)
refq['varmrcfile'] = (varname+".mrc")
if insert is True:
refq.insert()
if iternum == self.params['numiter']:
reflist.append(refq)
else:
reflist.append(None)
### insert particle data
apDisplay.printColor("Inserting particle alignment data, please wait", "cyan")
partlist = self.readApshDocFile("apshdoc.spi","apshdoc.pickle")
for partdict in partlist:
alignpartq = appiondata.ApAlignParticleData()
alignpartq['ref'] = reflist[partdict['template']-1]
alignpartq['partnum'] = partdict['num']
alignpartq['alignstack'] = alignstackq
stackpartdata = apStack.getStackParticle(self.params['stackid'], partdict['num'])
alignpartq['stackpart'] = stackpartdata
alignpartq['rotation'] = partdict['rot']
alignpartq['xshift'] = partdict['xshift']
alignpartq['yshift'] = partdict['yshift']
alignpartq['mirror'] = partdict['mirror']
alignpartq['score'] = partdict['score']
if insert is True:
alignpartq.insert() #insert each particle
return
