def createParticleDataFile(self, iteration, package_database_object):
''' puts all relevant particle information into a single text file that can be read by the uploader '''
os.chdir(self.projmatchpath)
### read particle info
paramfile = os.path.join(self.projmatchpath, "recon_it%03d_data.star"%(iteration))
parttree = self.parseParticleDataIterationFile(paramfile)
### write data in appion format to input file for uploading to the database
partdatafilepath = os.path.join(self.resultspath, "particle_data_%s_it%.3d_vol001.txt" % (self.params['timestamp'], iteration))
particledataf = open(partdatafilepath, "w")
particledataf.write("### column info: ")
particledataf.write("(1) particle number ")
particledataf.write("(2) phi ")
particledataf.write("(3) theta ")
particledataf.write("(4) omega ")
particledataf.write("(5) shiftx ")
particledataf.write("(6) shifty ")
particledataf.write("(7) mirror ")
particledataf.write("(8) 3D reference # ")
particledataf.write("(9) 2D class # ")
particledataf.write("(10) quality factor ")
particledataf.write("(11) kept particle ")
particledataf.write("(12) postRefine kept particle \n")
### add each particle to the file
count = 0
for partnum, partdict in parttree.items():
count += 1
if count % 500 == 0:
apDisplay.printMsg("Wrote %d particles to Particle Data File: %s"%(count,partdatafilepath))
phi, theta, omega = apEulerCalc.convertFrealignEulersTo3DEM(float(partdict['angleRot']), float(partdict['angleTilt']), float(partdict['anglePsi']))
particledataf.write("%.6d\t" % partnum) ### NOTE: IT IS IMPORTANT TO START WITH 1, OTHERWISE STACKMAPPING IS WRONG!!!
particledataf.write("%.6f\t" % phi)
particledataf.write("%.6f\t" % theta)
particledataf.write("%.6f\t" % omega)
particledataf.write("%.6f\t" % float(partdict['originX']))
particledataf.write("%.6f\t" % float(partdict['originY']))
particledataf.write("%.6d\t" % 0)
particledataf.write("%.6d\t" % 1)
particledataf.write("%.6d\t" % 0)
particledataf.write("%.6d\t" % 1)
# DOn't think this applies to Relion?
#if partdict['phase_residual'] > package_database_object['thresh']:
#particledataf.write("%.6f\t" % 1)
#else:
#particledataf.write("%.6f\t" % 1) #TODO: this should be false???
particledataf.write("%.6f\t" % 1)
particledataf.write("%.6f\n" % 1)
### close the new file
particledataf.close()
os.chdir(self.params['rundir'])
return
def createParticleDataFile(self, iteration, package_database_object):
''' puts all relevant particle information into a single text file that can be read by the uploader '''
os.chdir(self.projmatchpath)
### read particle info
paramfile = os.path.join(self.projmatchpath, "recon_it%03d_data.star"%(iteration))
parttree = self.parseParticleDataIterationFile(paramfile)
### write data in appion format to input file for uploading to the database
partdatafilepath = os.path.join(self.resultspath, "particle_data_%s_it%.3d_vol001.txt" % (self.params['timestamp'], iteration))
particledataf = open(partdatafilepath, "w")
particledataf.write("### column info: ")
particledataf.write("(1) particle number ")
particledataf.write("(2) phi ")
particledataf.write("(3) theta ")
particledataf.write("(4) omega ")
particledataf.write("(5) shiftx ")
particledataf.write("(6) shifty ")
particledataf.write("(7) mirror ")
particledataf.write("(8) 3D reference # ")
particledataf.write("(9) 2D class # ")
particledataf.write("(10) quality factor ")
particledataf.write("(11) kept particle ")
particledataf.write("(12) postRefine kept particle \n")
### add each particle to the file
count = 0
for partnum, partdict in parttree.items():
count += 1
if count % 500 == 0:
apDisplay.printMsg("Wrote %d particles to Particle Data File: %s"%(count,partdatafilepath))
phi, theta, omega = apEulerCalc.convertFrealignEulersTo3DEM(float(partdict['angleRot']), float(partdict['angleTilt']), float(partdict['anglePsi']))
particledataf.write("%.6d\t" % partnum) ### NOTE: IT IS IMPORTANT TO START WITH 1, OTHERWISE STACKMAPPING IS WRONG!!!
particledataf.write("%.6f\t" % phi)
particledataf.write("%.6f\t" % theta)
particledataf.write("%.6f\t" % omega)
particledataf.write("%.6f\t" % float(partdict['originX']))
particledataf.write("%.6f\t" % float(partdict['originY']))
particledataf.write("%.6d\t" % 0)
particledataf.write("%.6d\t" % 1)
particledataf.write("%.6d\t" % 0)
particledataf.write("%.6d\t" % 1)
# DOn't think this applies to Relion?
#if partdict['phase_residual'] > package_database_object['thresh']:
#particledataf.write("%.6f\t" % 1)
#else:
#particledataf.write("%.6f\t" % 1) #TODO: this should be false???
particledataf.write("%.6f\t" % 1)
particledataf.write("%.6f\n" % 1)
### close the new file
particledataf.close()
os.chdir(self.params['rundir'])
return