def MRCtoSPI(infile, rundir):
# convert file to spider file
tmpspifile = apParam.randomString(8) + ".spi"
tmpspifile = os.path.join(rundir, tmpspifile)
emancmd = "proc3d %s %s spidersingle" % (infile, tmpspifile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
return tmpspifile
def imagicToMrc(params, msg=True):
# convert imagic stack to mrc "stack"
outstack = os.path.join(params['rundir'],'start.mrc')
params['stackfile']=outstack
# if mrc stack exists, don't overwrite
# TO DO: check if existing stack is correct
if os.path.exists(outstack):
apDisplay.printWarning(outstack + " exists, not overwriting")
return
# first get stack info
stackdata = apStack.getOnlyStackData(params['stackid'], msg=False)
stackfile = os.path.splitext(os.path.join(stackdata['path']['path'],stackdata['name']))
# make sure to use the 'img' file, which contains the binary data
stackimg = stackfile[0]+'.img'
# get box size
box = apStack.getStackBoxsize(params['stackid'], msg=False)
nump = apStack.getNumberStackParticlesFromId(params['stackid'])
## create a new MRC header
header = mrc.newHeader()
mrc.updateHeaderDefaults(header)
# fill with stack params
header['nx']=box
header['ny']=box
header['nz']=nump
header['mode']=2
header['mx']=box
header['my']=box
header['mz']=nump
header['xlen']=box
header['ylen']=box
header['zlen']=nump
header['amin']=0.0
header['amax']=0.0
header['amean']=0.0
header['rms']=0.0
header['xorigin']=0.0
header['yorigin']=0.0
header['zorigin']=0.0
# write header to temporary file
hbytes = mrc.makeHeaderData(header)
tmpheadername = apParam.randomString(8)+'.mrc'
f = open(tmpheadername,'w')
f.write(hbytes)
f.close()
if msg is True:
apDisplay.printMsg('saving MRC stack file:')
apDisplay.printMsg(os.path.join(params['rundir'],outstack))
catcmd = "cat %s %s > %s" % (tmpheadername, stackimg, outstack)
print catcmd
proc = subprocess.Popen(catcmd, shell=True)
proc.wait()
os.remove(tmpheadername)
def MRCtoSPI(infile, rundir): # convert file to spider file tmpspifile = apParam.randomString(8)+".spi" tmpspifile = os.path.join(rundir,tmpspifile) emancmd = "proc3d %s %s spidersingle" %(infile,tmpspifile) apEMAN.executeEmanCmd(emancmd, verbose=True) return tmpspifile
def exclude_classes_from_frealign9_parfiles(inparfilebase, outlist, minocc,
*classlist):
'''
inparfilebase is the base name of the parameter file, w/ iteration number, but w/o class number
e.g. for parameter file input_20_r1.par, inparfilebase is input_20
classlist refers to a list with class numbers (starting with 1), e.g. [0,1,4]
outlist is a list containing the particle numbers within the relevant classes (starts with 0)
'''
if minocc < 50:
apDisplay.printWarning(
"minimum occupancy is < 50% ... are you sure you want to include these particles?"
)
combined = []
outbase = apParam.randomString(10)
for i in classlist:
parfile = "%s_r%d.par" % (inparfilebase, i)
exclude_class_from_frealign9_parfile(parfile,
"%s_%d.lst" % (outbase, i),
minocc=minocc)
f = open("%s_%d.lst" % (outbase, i), "r")
lines = f.readlines()
f.close()
os.remove("%s_%d.lst" % (outbase, i))
stripped = [int(l.strip()) for l in lines]
combined.extend(stripped)
combined.sort()
### check for duplicates
last = -1
for i in reversed(range(0, len(combined))):
if combined[i] == combined[i - 1]:
tmp = combined.pop(i)
### write to file
outlistf = open(outlist, "w")
for i in combined:
outlistf.write("%d\n" % i)
outlistf.close()
def exclude_classes_from_frealign9_parfiles(inparfilebase, outlist, minocc, *classlist):
'''
inparfilebase is the base name of the parameter file, w/ iteration number, but w/o class number
e.g. for parameter file input_20_r1.par, inparfilebase is input_20
classlist refers to a list with class numbers (starting with 1), e.g. [0,1,4]
outlist is a list containing the particle numbers within the relevant classes (starts with 0)
'''
if minocc < 50:
apDisplay.printWarning("minimum occupancy is < 50% ... are you sure you want to include these particles?")
combined = []
outbase = apParam.randomString(10)
for i in classlist:
parfile = "%s_r%d.par" % (inparfilebase, i)
exclude_class_from_frealign9_parfile(parfile, "%s_%d.lst" % (outbase,i), minocc=minocc)
f = open("%s_%d.lst" % (outbase,i), "r")
lines = f.readlines()
f.close()
os.remove("%s_%d.lst" % (outbase,i))
stripped = [int(l.strip()) for l in lines]
combined.extend(stripped)
combined.sort()
### check for duplicates
last = -1
for i in reversed(range(0,len(combined))):
if combined[i] == combined[i-1]:
tmp = combined.pop(i)
### write to file
outlistf = open(outlist, "w")
for i in combined:
outlistf.write("%d\n" %i)
outlistf.close()
def imagicToMrc(params, msg=True):
# convert imagic stack to mrc "stack"
outstack = os.path.join(params['rundir'], 'start.mrc')
params['stackfile'] = outstack
# if mrc stack exists, don't overwrite
# TO DO: check if existing stack is correct
if os.path.exists(outstack):
apDisplay.printWarning(outstack + " exists, not overwriting")
return
# first get stack info
stackdata = apStack.getOnlyStackData(params['stackid'], msg=False)
stackfile = os.path.splitext(
os.path.join(stackdata['path']['path'], stackdata['name']))
# make sure to use the 'img' file, which contains the binary data
stackimg = stackfile[0] + '.img'
# get box size
box = apStack.getStackBoxsize(params['stackid'], msg=False)
nump = apStack.getNumberStackParticlesFromId(params['stackid'])
## create a new MRC header
header = mrc.newHeader()
mrc.updateHeaderDefaults(header)
# fill with stack params
header['nx'] = box
header['ny'] = box
header['nz'] = nump
header['mode'] = 2
header['mx'] = box
header['my'] = box
header['mz'] = nump
header['xlen'] = box
header['ylen'] = box
header['zlen'] = nump
header['amin'] = 0.0
header['amax'] = 0.0
header['amean'] = 0.0
header['rms'] = 0.0
header['xorigin'] = 0.0
header['yorigin'] = 0.0
header['zorigin'] = 0.0
# write header to temporary file
hbytes = mrc.makeHeaderData(header)
tmpheadername = apParam.randomString(8) + '.mrc'
f = open(tmpheadername, 'w')
f.write(hbytes)
f.close()
if msg is True:
apDisplay.printMsg('saving MRC stack file:')
apDisplay.printMsg(os.path.join(params['rundir'], outstack))
catcmd = "cat %s %s > %s" % (tmpheadername, stackimg, outstack)
print catcmd
proc = subprocess.Popen(catcmd, shell=True)
proc.wait()
os.remove(tmpheadername)
