def checkConflicts(self):
if self.params['sessionname'] is None:
apDisplay.printError(
"Enter a session name (e.g. --session=06jul12a)")
if self.params['projectid'] is not None:
projid = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
if projid != self.params['projectid']:
apDisplay.printError(
"Project ID and Session name do not match")
if self.params['description'] is None:
apDisplay.printError("Enter a description of the initial model")
if self.params['chimeraonly'] is True:
self.params['commit'] = False
if self.params['newbox'] is not None and self.params['newbox'] % 8 != 0:
apDisplay.printWarning("Box size is not a multiple of 8")
### program requires either a model id or density id or filename
checkvalue = int(self.params['file'] is not None)
checkvalue += int(self.params['oldmodelid'] is not None)
checkvalue += int(self.params['densityid'] is not None)
if checkvalue != 1:
apDisplay.printError(
"Either provide a modelid or densityid or file, but not more than one of them"
)
elif self.params[
'oldmodelid'] is not None and self.params['newbox'] is None:
apDisplay.printError(
"Please specify either a new boxsize or scale for your model")
elif self.params['densityid'] is not None:
self.getDensityParams()
elif self.params['oldmodelid'] is not None:
self.getModelParams()
elif self.params['file'] is not None:
if not os.path.isfile(self.params['file']):
apDisplay.printError("could not find file: " +
self.params['file'])
if self.params['file'][-4:] != ".mrc":
apDisplay.printError("uploadModel.py only supports MRC files")
self.params['file'] = os.path.abspath(self.params['file'])
else:
apDisplay.printError(
"Please provide either a --modelid=112 or --file=initmodel.mrc"
)
### required only if now model id is provided
if self.params['newapix'] is None:
apDisplay.printError("Enter the pixel size of the model")
if self.params['symmetry'] is None:
apSymmetry.printSymmetries()
apDisplay.printError("Enter a symmetry ID, e.g. --symm=19")
self.params['symdata'] = apSymmetry.findSymmetry(
self.params['symmetry'])
if self.params['res'] is None:
apDisplay.printError("Enter the resolution of the initial model")
self.params['oldbox'] = apVolume.getModelDimensions(
self.params['file'])
if self.params['newbox'] is None:
self.params['newbox'] = self.params['oldbox']
if self.params['oldapix'] is None:
self.params['oldapix'] = self.params['newapix']
def start(self):
mrcfile = self.params['file']
### bin the volume
if self.params['bin'] is not None and self.params['bin'] > 1:
apDisplay.printMsg("Binning volume")
newmrcfile = os.path.join(os.getcwd(), "binned.mrc")
voldata = mrc.read(mrcfile)
voldata = imagefun.bin3(voldata, self.params['bin'])
mrc.write(voldata, newmrcfile)
del voldata
self.params['apix'] *= self.params['bin']
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### scale by mass
if self.params['mass'] is not None:
apDisplay.printMsg("Using scale by mass method")
newmrcfile = os.path.join(os.getcwd(), "setmass.mrc")
shutil.copy(self.params['file'], newmrcfile)
apChimera.setVolumeMass(newmrcfile, apix=self.params['apix'], mass=self.params['mass'])
self.params['contour'] = 1.0
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### print stats
box = apVolume.getModelDimensions(mrcfile)
apDisplay.printColor("Box: %d Apix: %.2f File: %s"%
(box, self.params['apix'], os.path.basename(mrcfile)), "green")
### animation
if self.params['type'] != "snapshot":
apDisplay.printMsg("Creating animation")
apChimera.renderAnimation(mrcfile, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.params['sym'],
color=self.params['color'], xvfb=self.params['xvfb'],
name=self.params['file'], silhouette=self.params['silhouette'])
### snapshot
if self.params['type'] != "animate":
apDisplay.printMsg("Creating snapshots")
apChimera.renderSnapshots(mrcfile, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.params['sym'],
color=self.params['color'], xvfb=self.params['xvfb'],
pdb=self.params['pdb'], name=self.params['file'],
silhouette=self.params['silhouette'])
### clean up
if self.params['mass'] is not None or self.params['bin'] is not None:
images = glob.glob(mrcfile+"*")
for img in images:
newimg = re.sub(mrcfile, self.params['file'], img)
shutil.move(img, newimg)
apFile.removeFile(mrcfile)
def checkConflicts(self):
if self.params['sessionname'] is None:
apDisplay.printError("Enter a session name (e.g. --session=06jul12a)")
if self.params['projectid'] is not None:
projid = apProject.getProjectIdFromSessionName(self.params['sessionname'])
if projid != self.params['projectid']:
apDisplay.printError("Project ID and Session name do not match")
if self.params['description'] is None:
apDisplay.printError("Enter a description of the initial model")
if self.params['chimeraonly'] is True:
self.params['commit'] = False
if self.params['newbox'] is not None and self.params['newbox'] % 8 != 0:
apDisplay.printWarning("Box size is not a multiple of 8")
### program requires either a model id or density id or filename
checkvalue = int(self.params['file'] is not None)
checkvalue += int(self.params['oldmodelid'] is not None)
checkvalue += int(self.params['densityid'] is not None)
if checkvalue != 1:
apDisplay.printError("Either provide a modelid or densityid or file, but not more than one of them")
elif self.params['oldmodelid'] is not None and self.params['newbox'] is None:
apDisplay.printError("Please specify either a new boxsize or scale for your model")
elif self.params['densityid'] is not None:
self.getDensityParams()
elif self.params['oldmodelid'] is not None:
self.getModelParams()
elif self.params['file'] is not None:
if not os.path.isfile(self.params['file']):
apDisplay.printError("could not find file: "+self.params['file'])
if self.params['file'][-4:] != ".mrc":
apDisplay.printError("uploadModel.py only supports MRC files")
self.params['file'] = os.path.abspath(self.params['file'])
else:
apDisplay.printError("Please provide either a --modelid=112 or --file=initmodel.mrc")
### required only if now model id is provided
if self.params['newapix'] is None:
apDisplay.printError("Enter the pixel size of the model")
if self.params['symmetry'] is None:
apSymmetry.printSymmetries()
apDisplay.printError("Enter a symmetry ID, e.g. --symm=19")
self.params['symdata'] = apSymmetry.findSymmetry(self.params['symmetry'])
if self.params['res'] is None:
apDisplay.printError("Enter the resolution of the initial model")
self.params['oldbox'] = apVolume.getModelDimensions(self.params['file'])
if self.params['newbox'] is None:
self.params['newbox'] = self.params['oldbox']
if self.params['oldapix'] is None:
self.params['oldapix'] = self.params['newapix']
def start(self):
### start the outfile name
fileroot = os.path.splitext(self.params['filename'])[0]
fileroot += "-"+self.timestamp
filename = self.params['file'].split('/')[-1]
filepath = self.params['file'].strip(filename)
self.params['box'] = apVolume.getModelDimensions(self.params['file'])
if self.params['ampfile'] is not None:
### run amplitude correction
spifile = apVolume.MRCtoSPI(self.params['file'], self.params['rundir'])
tmpfile = apAmpCorrect.createAmpcorBatchFile(spifile, self.params)
apAmpCorrect.runAmpcor()
### check if spider was successful
fileroot += ".amp"
if not os.path.isfile(tmpfile) :
apDisplay.printError("amplitude correction failed")
### convert amplitude corrected file back to mrc
fileroot += ".amp"
a = spider.read(tmpfile)
outfile = os.path.join( self.params['rundir'], "ampl-fix.mrc" )
mrc.write(a, outfile)
curfile = outfile
elif self.params['bfactor'] is True:
outfile = os.path.join( self.params['rundir'], "bfactor-fix.mrc" )
outfile = apAmpCorrect.applyBfactor(self.params['file'], fscfile=self.params['fscfile'], apix=self.params['apix'], mass=self.params['mass'], outfile=outfile)
curfile = outfile
elif self.params['lrdw'] is True:
lrdwcmd = "s_diffmap2 %s %s %s %s"%(self.params['filepath'],self.params['filename'],self.params['ampx'],self.params['resol'])
proc = subprocess.Popen(lrdwcmd)
print lrdwcmd
else :
### just run proc3d
curfile = self.params['file']
emancmd = "proc3d "+self.params['file']+" "
emancmd = "proc3d "+curfile+" "
if self.params['median'] is not None:
data = mrc.read(curfile)
data = ndimage.median_filter(data, size=self.params['median'])
mrc.write(data, curfile)
emancmd+="apix=%s " %self.params['apix']
if self.params['lp'] is not None:
fileroot += (".lp%d" % ( int(self.params['lp']), ))
emancmd += "lp=%d " %self.params['lp']
if self.params['yflip'] is True:
fileroot += ".yflip"
emancmd +="yflip "
if self.params['invert'] is True:
fileroot += ".inv"
emancmd +="mult=-1 "
if self.params['viper'] is True:
fileroot += ".vip"
emancmd +="icos5fTo2f "
if self.params['mask'] is not None:
# convert ang to pixels
maskpix=int(self.params['mask']/self.params['apix'])
fileroot += (".m%d" % ( int(self.params['mask']), ))
emancmd += "mask=%d " %maskpix
self.params['mask'] = maskpix
if self.params['imask'] is not None:
# convert ang to pixels
maskpix=int(self.params['imask']/self.params['apix'])
fileroot += (".im%d" % ( int(self.params['imask']), ))
emancmd += "imask=%d " %maskpix
self.params['imask'] = maskpix
if self.params['norm'] is True:
fileroot += ".norm"
emancmd += "norm=0,1 "
### add output filename to emancmd string
fileroot += ".mrc"
self.params['name'] = fileroot
outfile = os.path.join(self.params['rundir'], fileroot)
emancmd = re.sub(" apix=",(" %s apix=" % outfile), emancmd)
apEMAN.executeEmanCmd(emancmd)
if self.params['description'] is None:
self.params['description'] = "Volume from recon with amplitude adjustment"
### clean up files created during amp correction
if self.params['ampfile'] is not None:
apFile.removeFile(spifile)
apFile.removeFile(tmpfile)
if self.params['commit'] is True:
symdata = apSymmetry.findSymmetry(self.params['sym'])
print symdata
symmetry = symdata['eman_name']
self.params['reconid'] = self.params['reconiterid']
self.insert3dDensity()
### render chimera images of model
apChimera.filterAndChimera(outfile, res=self.params['res'], apix=self.params['apix'], box=self.params['box'],
chimtype='snapshot', mass=self.params['mass'], contour=self.params['contour'],
zoom=self.params['zoom'], sym=symmetry)
def start(self):
self.params['outputstack'] = os.path.join(self.params['rundir'],
self.params['stackname'])
particles, self.params['refineiter'] = getParticleInfo(
self.params['reconid'], self.params['iter'])
stackdata = particles[0]['particle']['stack']
stack = os.path.join(stackdata['path']['path'], stackdata['name'])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params['sigma'] is not None:
cutoff = cstats[
'meanquality'] + self.params['sigma'] * cstats['stdquality']
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(
particles, rejectlst, cutoff)
if self.params['avgjump'] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params['rejectlst']:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open('keep.lst', 'w')
keepfile.write('#LST\n')
reject = open('reject.lst', 'w')
reject.write('#LST\n')
apDisplay.printMsg("Processing classes")
#loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open('clstmp.lst', 'w')
clsfile.write('#LST\n')
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(
str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
#loop through particles in class
nptcls = 0
for ptcl in classes[key]['particles']:
if ptcl['mirror']:
mirror = 1
else:
mirror = 0
rot = ptcl['euler3']
rot = rot * math.pi / 180
if ptcl['particle']['particleNumber'] not in rejectlst:
l = '%d\t%s\t%f,\t%f,%f,%f,%d\n' % (
ptcl['particle']['particleNumber'] - 1, stack,
ptcl['quality_factor'], rot, ptcl['shiftx'],
ptcl['shifty'], mirror)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' %
(ptcl['particle']['particleNumber'] - 1,
stack, ptcl['quality_factor'], rot,
ptcl['shiftx'], ptcl['shifty'], mirror))
#if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params['skipavg'] is False:
makeClassAverages('clstmp.lst', self.params['outputstack'],
classes[key], self.params)
if self.params['eotest'] is True:
self.makeEvenOddClasses('clstmp.lst', classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove('clstmp.lst')
# make 3d density file if specified:
if self.params['make3d'] is not None:
self.params['make3d'] = os.path.basename(self.params['make3d'])
outfile = os.path.join(self.params['rundir'],
self.params['make3d'])
apEMAN.make3d(self.params['stackname'],
outfile,
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" %
(outfile, outfile, self.params['mask']))
if self.params['eotest'] is True:
apEMAN.make3d(self.params['oddstack'],
"odd.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.make3d(self.params['evenstack'],
"even.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg('inserting density into database')
symdata = apSymmetry.findSymmetry(self.params['sym'])
if not symdata:
apDisplay.printError('no symmetry associated with this model')
modq = appiondata.Ap3dDensityData()
modq['session'] = apStack.getSessionDataFromStackId(
self.params['stackid'])
modq['name'] = self.params['make3d']
modq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
modq['boxsize'] = box
modq['mask'] = self.params['mask']
modq['pixelsize'] = apix
fscres = apRecon.getResolutionFromFSCFile('fsc.eotest',
box,
apix,
msg=True)
modq['resolution'] = fscres
modq['rmeasure'] = apRecon.runRMeasure(apix, outfile)
modq['md5sum'] = apFile.md5sumfile(outfile)
modq['maxjump'] = self.params['avgjump']
modq['sigma'] = self.params['sigma']
modq['hard'] = self.params['hard']
modq['symmetry'] = symdata
modq['refineIter'] = self.params['refineiter']
if self.params['commit'] is True:
modq.insert()
apChimera.filterAndChimera(outfile,
res=fscres,
apix=apix,
box=box,
chimtype='snapshot',
zoom=self.params['zoom'],
sym=self.params['sym'],
mass=self.params['mass'])
else:
apDisplay.printError(
'no 3d volume was generated - check the class averages:')
apDisplay.printError(self.params['stackname'])
apDisplay.printError(
'hard may be set too high, or avg euler jump set too low for the # of particles'
)
stackstr = str(stackdata.dbid)
reconstr = str(self.params['reconid'])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n" +
"subStack.py --projectid=" + str(self.params['projectid']) +
" -s " + stackstr + " \\\n " + " -k " +
os.path.join(self.params['rundir'], "keep.lst") + " \\\n " +
" -d 'recon " + reconstr + " sitters' -n sitters" + reconstr +
" -C ", "purple")
def start(self):
self.params["outputstack"] = os.path.join(self.params["rundir"], self.params["stackname"])
particles, self.params["refineiter"] = getParticleInfo(self.params["reconid"], self.params["iter"])
stackdata = particles[0]["particle"]["stack"]
stack = os.path.join(stackdata["path"]["path"], stackdata["name"])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params["sigma"] is not None:
cutoff = cstats["meanquality"] + self.params["sigma"] * cstats["stdquality"]
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(particles, rejectlst, cutoff)
if self.params["avgjump"] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params["rejectlst"]:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open("keep.lst", "w")
keepfile.write("#LST\n")
reject = open("reject.lst", "w")
reject.write("#LST\n")
apDisplay.printMsg("Processing classes")
# loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open("clstmp.lst", "w")
clsfile.write("#LST\n")
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
# loop through particles in class
nptcls = 0
for ptcl in classes[key]["particles"]:
if ptcl["mirror"]:
mirror = 1
else:
mirror = 0
rot = ptcl["euler3"]
rot = rot * math.pi / 180
if ptcl["particle"]["particleNumber"] not in rejectlst:
l = "%d\t%s\t%f,\t%f,%f,%f,%d\n" % (
ptcl["particle"]["particleNumber"] - 1,
stack,
ptcl["quality_factor"],
rot,
ptcl["shiftx"],
ptcl["shifty"],
mirror,
)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write(
"%d\t%s\t%f,\t%f,%f,%f,%d\n"
% (
ptcl["particle"]["particleNumber"] - 1,
stack,
ptcl["quality_factor"],
rot,
ptcl["shiftx"],
ptcl["shifty"],
mirror,
)
)
# if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params["skipavg"] is False:
makeClassAverages("clstmp.lst", self.params["outputstack"], classes[key], self.params)
if self.params["eotest"] is True:
self.makeEvenOddClasses("clstmp.lst", classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove("clstmp.lst")
# make 3d density file if specified:
if self.params["make3d"] is not None:
self.params["make3d"] = os.path.basename(self.params["make3d"])
outfile = os.path.join(self.params["rundir"], self.params["make3d"])
apEMAN.make3d(
self.params["stackname"],
outfile,
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" % (outfile, outfile, self.params["mask"]))
if self.params["eotest"] is True:
apEMAN.make3d(
self.params["oddstack"],
"odd.mrc",
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.make3d(
self.params["evenstack"],
"even.mrc",
sym=self.params["sym"],
mode=self.params["mode"],
hard=self.params["hard"],
)
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params["stackid"])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg("inserting density into database")
symdata = apSymmetry.findSymmetry(self.params["sym"])
if not symdata:
apDisplay.printError("no symmetry associated with this model")
modq = appiondata.Ap3dDensityData()
modq["session"] = self.params["sessionname"]
modq["name"] = self.params["make3d"]
modq["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
modq["boxsize"] = box
modq["mask"] = self.params["mask"]
modq["pixelsize"] = apix
fscres = apRecon.getResolutionFromFSCFile("fsc.eotest", box, apix, msg=True)
modq["resolution"] = fscres
modq["rmeasure"] = apRecon.runRMeasure(apix, outfile)
modq["md5sum"] = apFile.md5sumfile(outfile)
modq["maxjump"] = self.params["avgjump"]
modq["sigma"] = self.params["sigma"]
modq["hard"] = self.params["hard"]
modq["symmetry"] = symdata
modq["refineIter"] = self.params["refineiter"]
if self.params["commit"] is True:
modq.insert()
apChimera.filterAndChimera(
outfile,
res=fscres,
apix=apix,
box=box,
chimtype="snapshot",
zoom=self.params["zoom"],
sym=self.params["sym"],
mass=self.params["mass"],
)
else:
apDisplay.printError("no 3d volume was generated - check the class averages:")
apDisplay.printError(self.params["stackname"])
apDisplay.printError("hard may be set too high, or avg euler jump set too low for the # of particles")
stackstr = str(stackdata.dbid)
reconstr = str(self.params["reconid"])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n"
+ "subStack.py --projectid="
+ str(self.params["projectid"])
+ " -s "
+ stackstr
+ " \\\n "
+ " -k "
+ os.path.join(self.params["rundir"], "keep.lst")
+ " \\\n "
+ " -d 'recon "
+ reconstr
+ " sitters' -n sitters"
+ reconstr
+ " -C ",
"purple",
)
def start(self):
mrcfile = self.params['file']
### bin the volume
if self.params['bin'] is not None and self.params['bin'] > 1:
apDisplay.printMsg("Binning volume")
newmrcfile = os.path.join(os.getcwd(), "binned.mrc")
voldata = mrc.read(mrcfile)
voldata = imagefun.bin3(voldata, self.params['bin'])
mrc.write(voldata, newmrcfile)
del voldata
self.params['apix'] *= self.params['bin']
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### scale by mass
if self.params['mass'] is not None:
apDisplay.printMsg("Using scale by mass method")
newmrcfile = os.path.join(os.getcwd(), "setmass.mrc")
shutil.copy(self.params['file'], newmrcfile)
apChimera.setVolumeMass(newmrcfile,
apix=self.params['apix'],
mass=self.params['mass'])
self.params['contour'] = 1.0
if os.path.isfile(newmrcfile):
mrcfile = newmrcfile
### print stats
box = apVolume.getModelDimensions(mrcfile)
apDisplay.printColor(
"Box: %d Apix: %.2f File: %s" %
(box, self.params['apix'], os.path.basename(mrcfile)), "green")
### animation
if self.params['type'] != "snapshot":
apDisplay.printMsg("Creating animation")
apChimera.renderAnimation(mrcfile,
contour=self.params['contour'],
zoom=self.params['zoom'],
sym=self.params['sym'],
color=self.params['color'],
xvfb=self.params['xvfb'],
name=self.params['file'],
silhouette=self.params['silhouette'])
### snapshot
if self.params['type'] != "animate":
apDisplay.printMsg("Creating snapshots")
apChimera.renderSnapshots(mrcfile,
contour=self.params['contour'],
zoom=self.params['zoom'],
sym=self.params['sym'],
color=self.params['color'],
xvfb=self.params['xvfb'],
pdb=self.params['pdb'],
name=self.params['file'],
silhouette=self.params['silhouette'])
### clean up
if self.params['mass'] is not None or self.params['bin'] is not None:
images = glob.glob(mrcfile + "*")
for img in images:
newimg = re.sub(mrcfile, self.params['file'], img)
shutil.move(img, newimg)
apFile.removeFile(mrcfile)
