def readParamsFromOptimiserFile(self, iternum):
"""
read the recon_it000_optimiser.star file to get iteration parameters,
such as symmetry and phase residual cutoff
"""
iterparams = {'iternum': iternum,}
#recondir = os.path.join(self.params['rundir'], "recon")
recondir = self.params['rundir']
optimiserfile = "recon_it%03d_optimiser.star"%(iternum)
optimiserfilepath = os.path.join(recondir, optimiserfile)
# Create a dictionary of parameters found in the optimiser file
paramdict = {}
### parse optimiser file to populate dictionary
f = starFile.StarFile( optimiserfilepath )
f.read()
dataBlock = f.getDataBlock("data_optimiser_general")
paramdict = dataBlock.getLabelDict()
header = f.getHeader()
# Parse the header for the command line options used to run relion
sheader = header.strip()
bits = sheader.split("--")
for bit in bits:
params = bit.split()
key = params[0]
if len(params) > 1 :
value = params[1]
paramdict[key] = value
else:
paramdict[key] = True
if 'ini_high' not in paramdict:
paramdict['ini_high'] = 0
iterparams['ctf'] = self.convertBool(paramdict['_rlnDoCorrectCtf']) if paramdict['_rlnDoCorrectCtf'] else False
iterparams['ctf_intact_first_peak'] = self.convertBool(paramdict['_rlnDoIgnoreCtfUntilFirstPeak']) if paramdict['_rlnDoIgnoreCtfUntilFirstPeak'] else False
iterparams['ctf_corrected_ref'] = self.convertBool(paramdict['_rlnRefsAreCtfCorrected']) if paramdict['_rlnRefsAreCtfCorrected'] else False
iterparams['offset_step'] = int(paramdict['offset_step'])
iterparams['auto_local_healpix_order'] = int(paramdict['_rlnAutoLocalSearchesHealpixOrder'])
iterparams['healpix_order'] = int(paramdict['healpix_order'])
iterparams['offset_range'] = int(paramdict['offset_range'])
iterparams['ini_high'] = int(paramdict['ini_high'])
iterparams['sym'] = paramdict['sym']
### convert symetry to Appion
symtext = apFrealign.convertFrealignSymToAppionSym(iterparams['sym'])
symmdata = apSymmetry.findSymmetry(symtext)
apDisplay.printMsg("Found symmetry %s with id %s"%(symmdata['eman_name'], symmdata.dbid))
iterparams['symmdata'] = symmdata
return iterparams
def readParamsFromOptimiserFile(self, iternum):
"""
read the recon_it000_optimiser.star file to get iteration parameters,
such as symmetry and phase residual cutoff
"""
iterparams = {'iternum': iternum,}
#recondir = os.path.join(self.params['rundir'], "recon")
recondir = self.params['rundir']
optimiserfile = "recon_it%03d_optimiser.star"%(iternum)
optimiserfilepath = os.path.join(recondir, optimiserfile)
# Create a dictionary of parameters found in the optimiser file
paramdict = {}
### parse optimiser file to populate dictionary
f = starFile.StarFile( optimiserfilepath )
f.read()
dataBlock = f.getDataBlock("data_optimiser_general")
paramdict = dataBlock.getLabelDict()
header = f.getHeader()
# Parse the header for the command line options used to run relion
sheader = header.strip()
bits = sheader.split("--")
for bit in bits:
params = bit.split()
key = params[0]
if len(params) > 1 :
value = params[1]
paramdict[key] = value
else:
paramdict[key] = True
if 'ini_high' not in paramdict:
paramdict['ini_high'] = 0
iterparams['ctf'] = self.convertBool(paramdict['_rlnDoCorrectCtf']) if paramdict['_rlnDoCorrectCtf'] else False
iterparams['ctf_intact_first_peak'] = self.convertBool(paramdict['_rlnDoIgnoreCtfUntilFirstPeak']) if paramdict['_rlnDoIgnoreCtfUntilFirstPeak'] else False
iterparams['ctf_corrected_ref'] = self.convertBool(paramdict['_rlnRefsAreCtfCorrected']) if paramdict['_rlnRefsAreCtfCorrected'] else False
iterparams['offset_step'] = int(paramdict['offset_step'])
iterparams['auto_local_healpix_order'] = int(paramdict['_rlnAutoLocalSearchesHealpixOrder'])
iterparams['healpix_order'] = int(paramdict['healpix_order'])
iterparams['offset_range'] = int(paramdict['offset_range'])
iterparams['ini_high'] = int(paramdict['ini_high'])
iterparams['sym'] = paramdict['sym']
### convert symetry to Appion
symtext = apFrealign.convertFrealignSymToAppionSym(iterparams['sym'])
symmdata = apSymmetry.findSymmetry(symtext)
apDisplay.printMsg("Found symmetry %s with id %s"%(symmdata['eman_name'], symmdata.dbid))
iterparams['symmdata'] = symmdata
return iterparams
def readParamsFromCombineFile(self, iternum):
"""
read the combine file to get iteration parameters,
such as symmetry and phase residual cutoff
"""
iterparams = {
'iternum': iternum,
}
recondir = os.path.join(self.params['rundir'], "recon")
combinefile = "iter%03d/frealign.iter%03d.proc%03d.sh" % (
iternum, iternum, iternum)
conbinefilepath = os.path.join(recondir, combinefile)
apDisplay.printMsg("Reading combine file %s for parameters" %
(conbinefilepath))
f = open(conbinefilepath, "r")
### locate start
for line in f:
if line.startswith("### START FREALIGN ###"):
break
### parse file
cards = []
for line in f:
cards.append(line.strip())
if line.startswith("EOF"):
break
f.close()
### get lots of info from card #1
data = cards[1].split(",")
#print data
iterparams['cform'] = data[0]
iterparams['iflag'] = int(data[1])
iterparams['fmag'] = self.convertBool(data[2])
iterparams['fdef'] = self.convertBool(data[3])
iterparams['fastig'] = self.convertBool(data[4])
iterparams['fpart'] = self.convertBool(data[5])
iterparams['iewald'] = float(data[6])
iterparams['fbeaut'] = self.convertBool(data[7])
iterparams['fcref'] = self.convertBool(data[8])
iterparams['fbfact'] = self.convertBool(data[9])
iterparams['fmatch'] = self.convertBool(data[10])
iterparams['ifsc'] = self.convertBool(data[11])
iterparams['fstat'] = self.convertBool(data[12])
iterparams['iblow'] = int(data[13])
### get lots of info from card #2
data = cards[2].split(",")
#print data
iterparams['mask'] = float(data[0])
iterparams['imask'] = float(data[1])
iterparams['wgh'] = float(data[3])
iterparams['xstd'] = float(data[4])
iterparams['pbc'] = float(data[5])
iterparams['boff'] = float(data[6])
iterparams['dang'] = float(data[7]) ### only used for recon search
iterparams['itmax'] = int(data[8])
iterparams['ipmax'] = int(data[9])
### get symmetry info from card #5
apDisplay.printMsg("Found Frealign symmetry %s in card 5" %
(cards[5], ))
symtext = apFrealign.convertFrealignSymToAppionSym(cards[5])
print symtext
symmdata = apSymmetry.findSymmetry(symtext)
apDisplay.printMsg("Found symmetry %s with id %s" %
(symmdata['eman_name'], symmdata.dbid))
iterparams['symmdata'] = symmdata
### get threshold info from card #6
data = cards[6].split(",")
#print data
iterparams['target'] = float(data[2])
iterparams['thresh'] = float(data[3])
iterparams['cs'] = float(data[4])
### get limit info from card #7
data = cards[7].split(",")
#print data
iterparams['rrec'] = float(data[0])
iterparams['highpass'] = float(data[1])
iterparams['lowpass'] = float(data[2])
iterparams['rbfact'] = float(data[4])
#print iterparams
return iterparams
def readParamsFromCombineFile(self, iternum):
"""
read the combine file to get iteration parameters,
such as symmetry and phase residual cutoff
"""
iterparams = {'iternum': iternum,}
recondir = os.path.join(self.params['rundir'], "recon")
combinefile = "iter%03d/frealign.iter%03d.proc%03d.sh"%(iternum, iternum, iternum)
conbinefilepath = os.path.join(recondir, combinefile)
apDisplay.printMsg("Reading combine file %s for parameters"%(conbinefilepath))
f = open(conbinefilepath, "r")
### locate start
for line in f:
if line.startswith("### START FREALIGN ###"):
break
### parse file
cards = []
for line in f:
cards.append(line.strip())
if line.startswith("EOF"):
break
f.close()
### get lots of info from card #1
data = cards[1].split(",")
#print data
iterparams['cform'] = data[0]
iterparams['iflag'] = int(data[1])
iterparams['fmag'] = self.convertBool(data[2])
iterparams['fdef'] = self.convertBool(data[3])
iterparams['fastig'] = self.convertBool(data[4])
iterparams['fpart'] = self.convertBool(data[5])
iterparams['iewald'] = float(data[6])
iterparams['fbeaut'] = self.convertBool(data[7])
iterparams['fcref'] = self.convertBool(data[8])
iterparams['fbfact'] = self.convertBool(data[9])
iterparams['fmatch'] = self.convertBool(data[10])
iterparams['ifsc'] = self.convertBool(data[11])
iterparams['fstat'] = self.convertBool(data[12])
iterparams['iblow'] = int(data[13])
### get lots of info from card #2
data = cards[2].split(",")
#print data
iterparams['mask'] = float(data[0])
iterparams['imask'] = float(data[1])
iterparams['wgh'] = float(data[3])
iterparams['xstd'] = float(data[4])
iterparams['pbc'] = float(data[5])
iterparams['boff'] = float(data[6])
iterparams['dang'] = float(data[7]) ### only used for recon search
iterparams['itmax'] = int(data[8])
iterparams['ipmax'] = int(data[9])
### get symmetry info from card #5
apDisplay.printMsg("Found Frealign symmetry %s in card 5"%(cards[5], ))
symtext = apFrealign.convertFrealignSymToAppionSym(cards[5])
print symtext
symmdata = apSymmetry.findSymmetry(symtext)
apDisplay.printMsg("Found symmetry %s with id %s"%(symmdata['eman_name'], symmdata.dbid))
iterparams['symmdata'] = symmdata
### get threshold info from card #6
data = cards[6].split(",")
#print data
iterparams['target'] = float(data[2])
iterparams['thresh'] = float(data[3])
iterparams['cs'] = float(data[4])
### get limit info from card #7
data = cards[7].split(",")
#print data
iterparams['rrec'] = float(data[0])
iterparams['highpass'] = float(data[1])
iterparams['lowpass'] = float(data[2])
iterparams['rbfact'] = float(data[4])
#print iterparams
return iterparams
