def insertOtrRun(self, volfile): ### setup resolutions fscresq = appiondata.ApResolutionData() fscresq['type'] = "fsc" fscresq['half'] = self.fscresolution fscresq['fscfile'] = "fscdata"+self.timestamp+".fsc" rmeasureq = appiondata.ApResolutionData() rmeasureq['type'] = "rmeasure" rmeasureq['half'] = self.rmeasureresolution rmeasureq['fscfile'] = None ### insert rct run data otrrunq = appiondata.ApOtrRunData() otrrunq['runname'] = self.params['runname'] tempstr = "" for cnum in self.classlist: tempstr += str(cnum)+"," classliststr = tempstr[:-1] otrrunq['classnums'] = classliststr otrrunq['numiter'] = self.params['numiters'] otrrunq['euleriter'] = self.params['refineiters'] otrrunq['maskrad'] = self.params['radius'] otrrunq['lowpassvol'] = self.params['lowpassvol'] otrrunq['highpasspart'] = self.params['highpasspart'] otrrunq['median'] = self.params['median'] otrrunq['description'] = self.params['description'] otrrunq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) otrrunq['alignstack'] = self.alignstackdata otrrunq['tiltstack'] = apStack.getOnlyStackData(self.params['tiltstackid']) otrrunq['numpart'] = self.numpart otrrunq['fsc_resolution'] = fscresq otrrunq['rmeasure_resolution'] = rmeasureq if self.params['commit'] is True: otrrunq.insert() ### insert 3d volume density densq = appiondata.Ap3dDensityData() densq['otrrun'] = otrrunq densq['path'] = appiondata.ApPathData(path=os.path.dirname(os.path.abspath(volfile))) densq['name'] = os.path.basename(volfile) densq['hidden'] = False densq['norm'] = True densq['symmetry'] = appiondata.ApSymmetryData.direct_query(25) densq['pixelsize'] = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin'] densq['boxsize'] = self.getBoxSize() densq['lowpass'] = self.params['lowpassvol'] densq['highpass'] = self.params['highpasspart'] densq['mask'] = self.params['radius'] #densq['iterid'] = self.params['numiters'] densq['description'] = self.params['description'] densq['resolution'] = self.fscresolution densq['rmeasure'] = self.rmeasureresolution densq['session'] = apStack.getSessionDataFromStackId(self.params['tiltstackid']) densq['md5sum'] = apFile.md5sumfile(volfile) if self.params['commit'] is True: densq.insert() return
def insertRefinementIterationData(self,
iteration,
package_table=None,
package_database_object=None,
reference_number=1):
''' fills in database entry for ApRefineIterData table '''
if not self.params['euleronly']:
### get resolution
try:
fscfile = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.fsc" \
% (self.params['timestamp'], iteration, reference_number))
fscRes = apRecon.getResolutionFromGenericFSCFile(
fscfile,
self.runparams['boxsize'],
self.runparams['apix'],
filtradius=3,
criterion=self.fscResCriterion)
apDisplay.printColor(
"FSC " + str(self.fscResCriterion) + " Resolution: " +
str(fscRes), "cyan")
resq = appiondata.ApResolutionData()
resq['half'] = fscRes
resq['fscfile'] = os.path.basename(fscfile)
except Exception, e:
apDisplay.printWarning(
"An error occured while reading fsc data: ")
print e
apDisplay.printWarning(
"The following FSC file does not exist or is unreadable: %s "
% (fscfile))
resq = None
def getResolutionData(self, avgpath, iternum):
evenvol = os.path.join(avgpath, "avglist3_%dp1.mrc"%(self.params['rescut']))
oddvol = os.path.join(avgpath, "avglist3_%dp2.mrc"%(self.params['rescut']))
evenhed = os.path.join(avgpath, "avglist3_%dp1.hed"%(self.params['rescut']))
oddhed = os.path.join(avgpath, "avglist3_%dp2.hed"%(self.params['rescut']))
emancmd1 = 'proc3d %s %s' % (evenvol, evenhed)
apEMAN.executeEmanCmd(emancmd1, verbose=True)
emancmd2 = 'proc3d %s %s' % (oddvol, oddhed)
apEMAN.executeEmanCmd(emancmd2, verbose=True)
fscfile = 'fsc.eotest.%d'%(iternum)
fscpath = os.path.join(avgpath, fscfile)
emancmd3 = 'proc3d %s %s fsc=%s' % (evenhed, oddhed, fscpath)
apEMAN.executeEmanCmd(emancmd3, verbose=True)
if not os.path.isfile(fscpath):
apDisplay.printWarning("Could not find FSC file: "+fscpath)
return None
f = open(fscpath, 'r')
xy = f.readlines()
lines = len(xy)
boxsize = (lines * 2.0)
f.close()
# calculate the resolution:
halfres = apRecon.calcRes(fscpath, boxsize, self.params['step'])
apDisplay.printColor("FSC 0.5 Resolution of %.3f Angstroms"%(halfres), "cyan")
# save to database
resq=appiondata.ApResolutionData()
resq['half'] = halfres
resq['fscfile'] = fscpath
return resq
def getResolutionData(self, iternum):
fscfile = 'fsc.eotest.%d'%(iternum)
fscpath = os.path.join(self.params['rundir'], "iter%03d"%(iternum), fscfile)
if not os.path.isfile(fscpath):
apDisplay.printWarning("Could not find FSC file: "+fscpath)
return None
# calculate the resolution:
halfres = apRecon.calcRes(fscpath, self.boxsize, self.apix)
apDisplay.printColor("FSC 0.5 Resolution of %.3f Angstroms"%(halfres), "cyan")
# save to database
resq=appiondata.ApResolutionData()
resq['half'] = halfres
resq['fscfile'] = fscfile
return resq
def getResolutionData(self, iteration):
fsc = 'fsc.eotest.'+iteration['num']
fscfile = os.path.join(self.params['rundir'],fsc)
if not os.path.isfile(fscfile):
apDisplay.printWarning("Could not find FSC file: "+fscfile)
iteration['fscfile'] = fscfile
if not fsc in self.params['fscs']:
return None
# calculate the resolution:
halfres = apRecon.calcRes(fscfile, self.params['boxsize'], self.params['apix'])
# save to database
resq=appiondata.ApResolutionData()
resq['half'] = halfres
resq['fscfile'] = fsc
return resq
