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 forceMrcHeader(array=None):
'''
Hack to force MRC header to something that frealign will accept.
This may only be necessary on 64-bit machine
'''
h=mrc.newHeader()
mrc.updateHeaderDefaults(h)
if array is not None:
mrc.updateHeaderUsingArray(h,array)
h['byteorder']=0x4144
return h
def forceMrcHeader(array=None):
'''
Hack to force MRC header to something that frealign will accept.
This may only be necessary on 64-bit machine
'''
h = mrc.newHeader()
mrc.updateHeaderDefaults(h)
if array is not None:
mrc.updateHeaderUsingArray(h, array)
h['byteorder'] = 0x4144
return h
def mrcHeader(box, nump):
header = mrc.newHeader()
mrc.updateHeaderDefaults(header)
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
hbytes = mrc.makeHeaderData(header)
return hbytes
def mrcHeader(box, nump):
#copied verbatim from EMAN2toFREALIGN.py
header = mrc.newHeader()
mrc.updateHeaderDefaults(header)
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
hbytes = mrc.makeHeaderData(header)
return hbytes
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)
