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 start(self):
if self.params['method'] == 'any':
### startAny uses class averages
clusterstack, numimages = self.getClusterStack()
else:
### starticos, startoct, startcsym uses individual particles
clusterstack, numimages = self.getClusterParticles()
if self.params['method'] != 'any':
if self.params['numkeep'] is not None and numimages/10 < int(self.params['numkeep']):
apDisplay.printWarning("particle number of "+ self.params['numkeep']
+ " is greater than 10% of the number of selected classes")
elif self.params['numkeep'] is None:
self.params['numkeep'] = int(math.floor(numimages/20.0))+1
apDisplay.printWarning("numkeep was not defined, using %d particles"%(self.params['numkeep']))
nproc = apParam.getNumProcessors()
#construct command for each of the EMAN commonline method
if self.params['method'] == 'any':
startcmd = "startAny "+clusterstack+" proc="+str(nproc)
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['mask'] is not None:
startcmd +=" mask="+str(self.params['mask'])
else:
maskrad = math.floor(self.clusterstackdata['clusterrun']['boxsize']/2.0)
startcmd +=" mask=%d"%(maskrad)
if self.params['rounds'] is not None:
startcmd +=" rounds="+str(self.params['rounds'])
elif self.params['method'] == 'csym':
startcmd = "startcsym "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
elif self.params['method'] == 'oct':
startcmd = "startoct "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
elif self.params['method'] == 'icos':
startcmd = "starticos "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
apDisplay.printMsg("Creating 3D model with EMAN function: start"+self.params['method'])
apFile.removeFile("threed.0a.mrc")
apFile.removeFile("eman.log")
apEMAN.executeEmanCmd(startcmd, verbose=False, logfile="eman.log")
#apEMAN.executeEmanCmd(startcmd, verbose=True)
finalmodelname = "threed-%s-eman_start%s.mrc"%(self.timestamp, self.params['method'])
finalmodelpath = os.path.join(self.params['rundir'], finalmodelname)
apDisplay.printMsg("Final model name: "+finalmodelname)
finalmodel = "threed.0a.mrc"
if os.path.isfile(finalmodel):
emancmd = "proc3d %s %s norm=0,1 origin=0,0,0"%(finalmodel, finalmodelpath)
#shutil.move(finalmodel, finalmodelpath)
apEMAN.executeEmanCmd(emancmd, verbose=True)
if not apVolume.isValidVolume(finalmodelpath):
apDisplay.printError("Created volume is not valid")
else:
apDisplay.printError("No 3d model was created")
### upload it
self.uploadDensity(finalmodelpath)
### chimera imaging
apChimera.renderSnapshots(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
apChimera.renderAnimation(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
### remove stack
if apFile.stackSize(clusterstack)/1024**2 > 10:
### file bigger than 10MB
apFile.removeStack(clusterstack)
apFile.removeFile("threed.0a.mrc")
def start(self):
if self.params['method'] == 'any':
### startAny uses class averages
clusterstack, numimages = self.getClusterStack()
else:
### starticos, startoct, startcsym uses individual particles
clusterstack, numimages = self.getClusterParticles()
if self.params['method'] != 'any':
if self.params['numkeep'] is not None and numimages/10 < int(self.params['numkeep']):
apDisplay.printWarning("particle number of "+ self.params['numkeep']
+ " is greater than 10% of the number of selected classes")
elif self.params['numkeep'] is None:
self.params['numkeep'] = int(math.floor(numimages/20.0))+1
apDisplay.printWarning("numkeep was not defined, using %d particles"%(self.params['numkeep']))
nproc = apParam.getNumProcessors()
#construct command for each of the EMAN commonline method
if self.params['method'] == 'any':
startcmd = "startAny "+clusterstack+" proc="+str(nproc)
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['mask'] is not None:
startcmd +=" mask="+str(self.params['mask'])
else:
maskrad = math.floor(self.clusterstackdata['clusterrun']['boxsize']/2.0)
startcmd +=" mask=%d"%(maskrad)
if self.params['rounds'] is not None:
startcmd +=" rounds="+str(self.params['rounds'])
elif self.params['method'] == 'csym':
startcmd = "startcsym "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
startcmd +=" sym="+self.symmdata['eman_name']
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
elif self.params['method'] == 'oct':
startcmd = "startoct "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
elif self.params['method'] == 'icos':
startcmd = "starticos "+clusterstack+" "
startcmd +=" "+str(self.params['numkeep'])
if self.params['imask'] is not None:
startcmd +=" imask="+self.params['imask']
apDisplay.printMsg("Creating 3D model with EMAN function: start"+self.params['method'])
apFile.removeFile("threed.0a.mrc")
apFile.removeFile("eman.log")
apEMAN.executeEmanCmd(startcmd, verbose=False, logfile="eman.log")
#apEMAN.executeEmanCmd(startcmd, verbose=True)
finalmodelname = "threed-%s-eman_start%s.mrc"%(self.timestamp, self.params['method'])
finalmodelpath = os.path.join(self.params['rundir'], finalmodelname)
apDisplay.printMsg("Final model name: "+finalmodelname)
finalmodel = "threed.0a.mrc"
if os.path.isfile(finalmodel):
emancmd = "proc3d %s %s norm=0,1 origin=0,0,0"%(finalmodel, finalmodelpath)
#shutil.move(finalmodel, finalmodelpath)
apEMAN.executeEmanCmd(emancmd, verbose=True)
if not apVolume.isValidVolume(finalmodelpath):
apDisplay.printError("Created volume is not valid")
else:
apDisplay.printError("No 3d model was created")
### upload it
self.uploadDensity(finalmodelpath)
### chimera imaging
apChimera.renderSnapshots(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
apChimera.renderAnimation(finalmodelpath, contour=self.params['contour'],
zoom=self.params['zoom'], sym=self.symmdata['eman_name'])
### remove stack
if apFile.stackSize(clusterstack)/1024**2 > 10:
### file bigger than 10MB
apFile.removeStack(clusterstack)
apFile.removeFile("threed.0a.mrc")
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)
