def centerParticles(stack, mask=None, maxshift=None):
apDisplay.printMsg("Centering stack: "+stack)
stacksize = apFile.stackSize(stack)
freemem = mem.free()*1024 #convert memory to bytes
apDisplay.printMsg("file is %s, mem is %s"
%(apDisplay.bytes(stacksize), apDisplay.bytes(freemem)))
### from EMAN FAQ: need to have at least 3x as much ram as the size of the file
memsize = freemem/3.0
numfrac = int(math.ceil(stacksize/memsize))
apDisplay.printMsg("file is %s, will be split into %d fractions"
%(apDisplay.bytes(stacksize), numfrac))
for i in range(numfrac):
emancmd = "cenalignint "+stack
if numfrac > 1:
emancmd += " frac="+str(i)+"/"+str(numfrac)
if mask is not None:
emancmd += " mask="+str(mask)
if maxshift is not None:
emancmd += " maxshift="+str(maxshift)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
return
def initValues(self, stackfile, numrequest=None):
### check for stack
if not os.path.isfile(stackfile):
apDisplay.printError("stackfile does not exist: "+stackfile)
### amount of free memory on machine (converted to bytes)
self.freememory = mem.free()*1024
self.message("Free memory: %s"%(apDisplay.bytes(self.freememory)))
### box size of particle
self.boxsize = apFile.getBoxSize(stackfile)[0]
self.message("Box size: %d"%(self.boxsize))
### amount of memory used per particles (4 bytes per pixel)
self.memperpart = self.boxsize**2 * 4.0
self.message("Memory used per part: %s"%(apDisplay.bytes(self.memperpart)))
### maximum number particles that fit into memory
self.maxpartinmem = self.freememory/self.memperpart
self.message("Max particles in memory: %d"%(self.maxpartinmem))
### number particles to fit into memory
self.partallowed = int(self.maxpartinmem/20.0)
self.message("Particles allowed in memory: %d"%(self.partallowed))
### number particles in stack
numpart = apFile.numImagesInStack(stackfile)
if self.numpart is None or self.numpart > numpart:
self.numpart = numpart
if numrequest is not None and self.numpart > numrequest:
self.numpart = numrequest
self.message("Number of particles in stack: %d"%(self.numpart))
if self.numpart > self.partallowed:
numchucks = math.ceil(self.numpart/float(self.partallowed))
self.stepsize = int(self.numpart/numchucks)
else:
numchucks = 1
self.stepsize = self.numpart
self.message("Particle loop num chunks: %d"%(numchucks))
self.message("Particle loop step size: %d"%(self.stepsize))
def getParticlesPerCycle(self, stackfile):
"""
it more efficient to process X particles and write them to disk rather than
write each particle to disk each time.
particles are read using a memory map (numpy.memmap), so we can pretend to
continuously read all into memory
"""
### amount of free memory on machine (converted to bytes)
freememory = mem.free()*1024
self.message("Free memory: %s"%(apDisplay.bytes(freememory)))
### box size of particle
self.boxsize = apFile.getBoxSize(stackfile)[0]
self.message("Box size: %d"%(self.boxsize))
### amount of memory used per particles (4 bytes per pixel)
memperpart = self.boxsize**2 * 4.0
self.message("Memory used per part: %s"%(apDisplay.bytes(memperpart)))
### maximum number particles that fit into memory
maxpartinmem = freememory/memperpart
self.message("Max particles in memory: %d"%(maxpartinmem))
### number particles to fit into memory
partallowed = int(maxpartinmem/20.0)
self.message("Particles allowed in memory: %d"%(partallowed))
### number particles in stack
numpart = self.params['last']
if numpart > partallowed:
numcycles = math.ceil(numpart/float(partallowed))
stepsize = int(numpart/numcycles)
else:
numcycles = 1
stepsize = numpart
self.message("Particle loop num cycles: %d"%(numcycles))
self.message("Particle loop step size: %d"%(stepsize))
return stepsize
def initValues(self, stackfile, numrequest=None):
### check for stack
if not os.path.isfile(stackfile):
apDisplay.printError("stackfile does not exist: " + stackfile)
### amount of free memory on machine (converted to bytes)
self.freememory = mem.free() * 1024
self.message("Free memory: %s" % (apDisplay.bytes(self.freememory)))
### box size of particle
self.boxsize = apFile.getBoxSize(stackfile)[0]
self.message("Box size: %d" % (self.boxsize))
### amount of memory used per particles (4 bytes per pixel)
self.memperpart = self.boxsize**2 * 4.0
self.message("Memory used per part: %s" %
(apDisplay.bytes(self.memperpart)))
### maximum number particles that fit into memory
self.maxpartinmem = self.freememory / self.memperpart
self.message("Max particles in memory: %d" % (self.maxpartinmem))
### number particles to fit into memory
self.partallowed = int(self.maxpartinmem / 20.0)
self.message("Particles allowed in memory: %d" % (self.partallowed))
### number particles in stack
numpart = apFile.numImagesInStack(stackfile)
if self.numpart is None or self.numpart > numpart:
self.numpart = numpart
if numrequest is not None and self.numpart > numrequest:
self.numpart = numrequest
self.message("Number of particles in stack: %d" % (self.numpart))
if self.numpart > self.partallowed:
numchucks = math.ceil(self.numpart / float(self.partallowed))
self.stepsize = int(self.numpart / numchucks)
else:
numchucks = 1
self.stepsize = self.numpart
self.message("Particle loop num chunks: %d" % (numchucks))
self.message("Particle loop step size: %d" % (self.stepsize))
def convertStackToXmippData(instack, outdata, maskpixrad, boxsize, numpart=None):
"""
From http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Img2Data
This program applies a mask to a set of images.
This set is given by a selfile.
After applying the mask the result is storaged as a vector in the following format:
The first line indicates the dimension of the vectors and the number of vectors.
The rest of the lines are the feature vectors.
Each line is a vector and each column is a vectors' component (pixels values inside the mask).
"""
apDisplay.printMsg("Convert stack file to Xmipp data file")
maskfile = "circlemask.spi"
operations.createMask(maskfile, maskpixrad, boxsize)
partlistdocfile = breakupStackIntoSingleFiles(instack, numpart=numpart)
convertcmd = "xmipp_convert_img2data -i %s -mask %s -o %s"%(partlistdocfile, maskfile, outdata)
proc = subprocess.Popen(convertcmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE,)
proc.wait()
outfilesize = apFile.fileSize(outdata)
partfilesize = apFile.fileSize(partlistdocfile)
if outfilesize < 2*partfilesize:
apDisplay.printError("Outdata conversion did not work, data file smaller than docfile, %s < %s"
%(apDisplay.bytes(outfilesize), apDisplay.bytes(partfilesize)))
apFile.removeFilePattern("partfiles/*")
return outdata
def centerParticles(stack, mask=None, maxshift=None):
apDisplay.printMsg("Centering stack: "+stack)
stacksize = apFile.stackSize(stack)
freemem = mem.free()*1024 #convert memory to bytes
apDisplay.printMsg("file is %s, mem is %s"
%(apDisplay.bytes(stacksize), apDisplay.bytes(freemem)))
### from EMAN FAQ: need to have at least 3x as much ram as the size of the file
memsize = freemem/3.0
numfrac = int(math.ceil(stacksize/memsize))
apDisplay.printMsg("file is %s, will be split into %d fractions"
%(apDisplay.bytes(stacksize), numfrac))
for i in range(numfrac):
emancmd = "cenalignint "+stack
if numfrac > 1:
emancmd += " frac="+str(i)+"/"+str(numfrac)
if mask is not None:
emancmd += " mask="+str(mask)
if maxshift is not None:
emancmd += " maxshift="+str(maxshift)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=True)
return
def readImagic(filename, first=1, last=None, msg=True):
"""
Rudimentary Imagic stack reader
Could be improved with more sophisticated error testing and header parsing
Currently only reads image data as floats
Currently reads header information for only first image in stack
"""
t0 = time.time()
if first < 1:
apDisplay.printError("particle numbering starts at 1")
if last is not None and first > last:
apDisplay.printError("requested first particle %d is greater than last particle %d"%(first,last))
if msg is True:
apDisplay.printMsg("reading stack from disk into memory: "+os.path.basename(filename))
if last is not None:
apDisplay.printMsg("particles %d through %d"%(first, last))
root=os.path.splitext(filename)[0]
headerfilename=root + ".hed"
datafilename=root + ".img"
### check file size, no more than 2 GB is possible
### it takes double memory on machine to read stack
filesize = apFile.fileSize(datafilename)
if first is None and last is None and filesize > bytelimit:
apDisplay.printError("Stack is too large to read %s"%(apDisplay.bytes(filesize)))
### read stack header
headerdict = readImagicHeader(headerfilename)
### determine amount of memory needed
partbytes = 4*headerdict['rows']*headerdict['lines']
if last is None:
last = headerdict['nimg']
elif last > headerdict['nimg']:
apDisplay.printWarning("requested particle %d from stack of length %d"%(last, headerdict['nimg']))
last = headerdict['nimg']
numpart = last - first + 1
if partbytes*numpart > filesize:
apDisplay.printError("requested particle %d from stack of length %d"%(last, filesize/partbytes))
if partbytes*numpart > bytelimit:
apDisplay.printError("Stack is too large to read %d particles, requesting %s"
%(numpart, apDisplay.bytes(partbytes*numpart)))
### read stack images
images = readImagicData(datafilename, headerdict, first, numpart)
stack = {'header': headerdict, 'images': images}
if msg is True:
apDisplay.printMsg("read %d particles equaling %s in size"%(numpart, apDisplay.bytes(partbytes*numpart)))
apDisplay.printMsg("finished in "+apDisplay.timeString(time.time()-t0))
return stack
def appendParticleListToStackFile(partlist, mergestackfile, msg=True):
"""
takes a list of 2D numpy arrays and add to stack file
due to hack, we must re-number the stack later
"""
### initialization
t0 = time.time()
root = os.path.splitext(mergestackfile)[0]
mergeheaderfile = root + ".hed"
mergedatafile = root + ".img"
### merge data files
premergesize = apFile.fileSize(mergedatafile)
mergedata = file(mergedatafile, 'ab')
for partarray in partlist:
part32bit = numpy.asarray(partarray, dtype=numpy.float32)
mergedata.write(part32bit.tostring())
mergedata.close()
finalsize = apFile.fileSize(mergedatafile)
addsize = len(part32bit.tostring() * len(partlist))
if finalsize != addsize + premergesize:
apDisplay.printError(
"size mismatch %s vs. %s + %s = %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(addsize),
apDisplay.bytes(premergesize),
apDisplay.bytes(premergesize + addsize)))
elif msg is True:
apDisplay.printMsg(
"size match %s vs. %s + %s = %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(addsize),
apDisplay.bytes(premergesize),
apDisplay.bytes(premergesize + addsize)))
### merge header files
premergenumpart = apFile.numImagesInStack(mergeheaderfile)
mergehead = open(mergeheaderfile, 'ab')
count = 0
for partarray in partlist:
count += 1
headerstr = makeHeaderStrFromArray(premergenumpart + count, partarray)
mergehead.write(headerstr)
mergehead.close()
numberStackFile(mergeheaderfile, msg=msg)
finalnumpart = apFile.numImagesInStack(mergeheaderfile)
addpart = len(partlist)
if finalnumpart != addpart + premergenumpart:
apDisplay.printError("size mismatch %d vs. %d + %d = %d" %
(finalnumpart, addpart, premergenumpart,
addpart + premergenumpart))
elif msg is True:
apDisplay.printMsg("size match %d vs. %d + %d = %d" %
(finalnumpart, addpart, premergenumpart,
addpart + premergenumpart))
return True
def appendStackFileToStackFile(stackfile, mergestackfile, msg=True):
"""
takes two stack files and merges them into second file
"""
### initialization
t0 = time.time()
root = os.path.splitext(mergestackfile)[0]
mergeheaderfile = root + ".hed"
mergedatafile = root + ".img"
root = os.path.splitext(stackfile)[0]
stackheaderfile = root + ".hed"
stackdatafile = root + ".img"
### merge data files
addnumpart = apFile.numImagesInStack(stackheaderfile)
addsize = apFile.fileSize(stackdatafile)
premergenumpart = apFile.numImagesInStack(mergeheaderfile)
premergesize = apFile.fileSize(mergedatafile)
fout = file(mergedatafile, 'ab')
fin = file(stackdatafile, 'rb')
shutil.copyfileobj(fin, fout, 65536)
fin.close()
fout.close()
finalsize = apFile.fileSize(mergedatafile)
if finalsize != addsize + premergesize:
apDisplay.printError(
"size mismatch %s vs. %s + %s = %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(addsize),
apDisplay.bytes(premergesize),
apDisplay.bytes(premergesize + addsize)))
### merge header files
fout = file(mergeheaderfile, 'ab')
fin = file(stackheaderfile, 'rb')
shutil.copyfileobj(fin, fout, 65536)
fin.close()
fout.close()
numberStackFile(mergeheaderfile, msg=msg)
finalnumpart = apFile.numImagesInStack(mergeheaderfile)
if finalnumpart != addnumpart + premergenumpart:
apDisplay.printError("size mismatch %d vs. %d + %d = %d" %
(finalnumpart, addnumpart, premergenumpart,
addnumpart + premergenumpart))
def setIBLOW(self):
"""
IBLOW expands the volume in memory,
larger is faster, but needs more mem;
can be 1, 2 or 4
"""
self.iblow = 4
if self.calcMemNeeded() > 4e9:
self.iblow = 2
if self.calcMemNeeded() > 4e9:
self.iblow = 1
### more than 40GB need then die
if self.calcMemNeeded() > 40e9:
apDisplay.printError("%s of memory is required which is too much, reduce box size or recons per processor"
%(apDisplay.bytes(self.calcMemNeeded())))
apDisplay.printMsg("IBLOW set to %d, requiring %s memory"
%(self.iblow, apDisplay.bytes(self.calcMemNeeded())))
def setIBLOW(self):
"""
IBLOW expands the volume in memory,
larger is faster, but needs more mem;
can be 1, 2 or 4
"""
self.iblow = 4
if self.calcMemNeeded() > 4e9:
self.iblow = 2
if self.calcMemNeeded() > 4e9:
self.iblow = 1
### more than 40GB need then die
if self.calcMemNeeded() > 40e9:
apDisplay.printError("%s of memory is required which is too much, reduce box size or recons per processor"
%(apDisplay.bytes(self.calcMemNeeded())))
apDisplay.printMsg("IBLOW set to %d, requiring %s memory"
%(self.iblow, apDisplay.bytes(self.calcMemNeeded())))
def convertStackToXmippData(instack,
outdata,
maskpixrad,
boxsize,
numpart=None):
"""
From http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Img2Data
This program applies a mask to a set of images.
This set is given by a selfile.
After applying the mask the result is storaged as a vector in the following format:
The first line indicates the dimension of the vectors and the number of vectors.
The rest of the lines are the feature vectors.
Each line is a vector and each column is a vectors' component (pixels values inside the mask).
"""
apDisplay.printMsg("Convert stack file to Xmipp data file")
maskfile = "circlemask.spi"
operations.createMask(maskfile, maskpixrad, boxsize)
partlistdocfile = breakupStackIntoSingleFiles(instack, numpart=numpart)
convertcmd = "xmipp_convert_img2data -i %s -mask %s -o %s" % (
partlistdocfile, maskfile, outdata)
proc = subprocess.Popen(
convertcmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
proc.wait()
outfilesize = apFile.fileSize(outdata)
partfilesize = apFile.fileSize(partlistdocfile)
if outfilesize < 2 * partfilesize:
apDisplay.printError(
"Outdata conversion did not work, data file smaller than docfile, %s < %s"
% (apDisplay.bytes(outfilesize), apDisplay.bytes(partfilesize)))
apFile.removeFilePattern("partfiles/*")
return outdata
def setupMultiNode(self):
self.mainjobfile = "frealign.run.job"
mainf = open(self.mainjobfile, "w")
# mainf.write("#PBS -l nodes=%d:ppn=%d\n"%(self.params['nodes'], self.params['ppn']))
memrequest = self.calcMemNeeded()
apDisplay.printMsg("requesting %s of memory" % (apDisplay.bytes(memrequest)))
# mainf.write("#PBS -l mem=%s\n"%(apDisplay.clusterBytes(memrequest)))
# mainf.write("#PBS -m e\n")
# mainf.write("#PBS -r n\n")
# mainf.write("#PBS -j oe\n")
# mainf.write("\n")
### if local cluster
# mainf.write("cd %s\n"%(self.params['rundir']))
### elseif remote cluster
mainf.write("tar -xkf %s.tar\n" % (self.params["runname"]))
mainf.write("\n")
def setupMultiNode(self):
self.mainjobfile = 'frealign.run.job'
mainf = open(self.mainjobfile, 'w')
#mainf.write("#PBS -l nodes=%d:ppn=%d\n"%(self.params['nodes'], self.params['ppn']))
memrequest = self.calcMemNeeded()
apDisplay.printMsg("requesting %s of memory"%(apDisplay.bytes(memrequest)))
#mainf.write("#PBS -l mem=%s\n"%(apDisplay.clusterBytes(memrequest)))
#mainf.write("#PBS -m e\n")
#mainf.write("#PBS -r n\n")
#mainf.write("#PBS -j oe\n")
#mainf.write("\n")
### if local cluster
#mainf.write("cd %s\n"%(self.params['rundir']))
### elseif remote cluster
mainf.write("tar -xkf %s.tar\n"%(self.params['runname']))
mainf.write("\n")
def readImagic(filename, first=1, last=None, msg=True):
"""
Rudimentary Imagic stack reader
Could be improved with more sophisticated error testing and header parsing
Currently only reads image data as floats
Currently reads header information for only first image in stack
"""
t0 = time.time()
if first < 1:
apDisplay.printError("particle numbering starts at 1")
if last is not None and first > last:
apDisplay.printError(
"requested first particle %d is greater than last particle %d" %
(first, last))
if msg is True:
apDisplay.printMsg("reading stack from disk into memory: " +
os.path.basename(filename))
if last is not None:
apDisplay.printMsg("particles %d through %d" % (first, last))
root = os.path.splitext(filename)[0]
headerfilename = root + ".hed"
datafilename = root + ".img"
### check file size, no more than 2 GB is possible
### it takes double memory on machine to read stack
filesize = apFile.fileSize(datafilename)
if first is None and last is None and filesize > bytelimit:
apDisplay.printError("Stack is too large to read %s" %
(apDisplay.bytes(filesize)))
### read stack header
headerdict = readImagicHeader(headerfilename)
### determine amount of memory needed
partbytes = 4 * headerdict['rows'] * headerdict['lines']
if last is None:
last = headerdict['nimg']
elif last > headerdict['nimg']:
apDisplay.printWarning(
"requested particle %d from stack of length %d" %
(last, headerdict['nimg']))
last = headerdict['nimg']
numpart = last - first + 1
if partbytes * numpart > filesize:
apDisplay.printError("requested particle %d from stack of length %d" %
(last, filesize / partbytes))
if partbytes * numpart > bytelimit:
apDisplay.printError(
"Stack is too large to read %d particles, requesting %s" %
(numpart, apDisplay.bytes(partbytes * numpart)))
### read stack images
images = readImagicData(datafilename, headerdict, first, numpart)
stack = {'header': headerdict, 'images': images}
if msg is True:
apDisplay.printMsg("read %d particles equaling %s in size" %
(numpart, apDisplay.bytes(partbytes * numpart)))
apDisplay.printMsg("finished in " +
apDisplay.timeString(time.time() - t0))
return stack
def mergeStacks(stacklist, mergestack):
### initialization
t0 = time.time()
apFile.removeStack(mergestack)
root=os.path.splitext(mergestack)[0]
mergeheader = root+".hed"
mergedata = root+".img"
### merge data files
fout = file(mergedata, 'wb')
numpart = 0
totalsize = 0
for stackfile in stacklist:
stackdatafile = os.path.splitext(stackfile)[0]+ ".img"
### size checks
npart = apFile.numImagesInStack(stackdatafile)
size = apFile.fileSize(stackdatafile)
apDisplay.printMsg("%d particles in %s (%s)"%(npart, stackdatafile, apDisplay.bytes(size)))
totalsize += size
numpart += npart
fin = file(stackdatafile, 'rb')
shutil.copyfileobj(fin, fout, 65536)
fin.close()
fout.close()
if numpart < 1:
apDisplay.printError("found %d particles"%(numpart))
apDisplay.printMsg("found %d particles"%(numpart))
finalsize = apFile.fileSize(mergedata)
if finalsize != totalsize:
apDisplay.printError("size mismatch %s vs. %s"%(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
apDisplay.printMsg("size match %s vs. %s"%(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
### merge header files
#apDisplay.printError("not finished")
mergehead = open(mergeheader, 'wb')
partnum = 1
totalsize = 0
for stackfile in stacklist:
headerfilename = os.path.splitext(stackfile)[0]+ ".hed"
headfile = open(headerfilename, 'rb')
### size checks
size = apFile.fileSize(headerfilename)
apDisplay.printMsg("%s (%d kB)"%(headerfilename, size/1024))
totalsize += size
#apDisplay.printMsg("%d\t%s"%(npart, stackfile))
i = 0
npart = apFile.numImagesInStack(stackfile)
while i < npart:
#print i, npart, partnum
### read old header
data = headfile.read(1024)
### start new string
headerstr = ""
### first image number
headerstr += intToFourByte(partnum)
### number of images, less one
headerstr += intToFourByte(numpart-partnum)
### always 0,1 ???
headerstr += intToFourByte(0)
headerstr += intToFourByte(1)
### creation date: day, month, year, hour, min, sec
headerstr += intToFourByte(time.localtime()[2])
headerstr += intToFourByte(time.localtime()[1]) #eman always uses month-1?
headerstr += intToFourByte(time.localtime()[0])
headerstr += intToFourByte(time.localtime()[3])
headerstr += intToFourByte(time.localtime()[4])
headerstr += intToFourByte(time.localtime()[5])
### append other header info, 4 character per item
headerstr += data[10*4:60*4]
### number of z slices
headerstr += intToFourByte(1)
### first image number, EMAN does this
headerstr += intToFourByte(partnum)
### append other header info, 4 character per item
headerstr += data[62*4:68*4]
headerstr += intToFourByte(33686018)
headerstr += data[69*4:]
mergehead.write(headerstr)
partnum += 1
i += 1
mergehead.close()
apDisplay.printMsg("wrote %d particles"%(numpart))
finalsize = apFile.fileSize(mergeheader)
if finalsize != totalsize:
apDisplay.printError("size mismatch %s vs. %s"%(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
apDisplay.printMsg("size match %s vs. %s"%(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
apDisplay.printMsg("finished stack merge in "+apDisplay.timeString(time.time()-t0))
def mergeStacks(stacklist, mergestack, msg=True):
### initialization
t0 = time.time()
apFile.removeStack(mergestack, warn=msg)
root = os.path.splitext(mergestack)[0]
mergeheader = root + ".hed"
mergedata = root + ".img"
### merge data files
fout = file(mergedata, 'wb')
numpart = 0
totalsize = 0
for stackfile in stacklist:
stackdatafile = os.path.splitext(stackfile)[0] + ".img"
### size checks
npart = apFile.numImagesInStack(stackdatafile)
size = apFile.fileSize(stackdatafile)
if msg is True:
apDisplay.printMsg("%d particles in %s (%s)" %
(npart, stackdatafile, apDisplay.bytes(size)))
totalsize += size
numpart += npart
fin = file(stackdatafile, 'rb')
shutil.copyfileobj(fin, fout, 65536)
fin.close()
fout.close()
if numpart < 1:
apDisplay.printError("found %d particles" % (numpart))
if msg is True:
apDisplay.printMsg("found %d particles" % (numpart))
finalsize = apFile.fileSize(mergedata)
if finalsize != totalsize:
apDisplay.printError(
"size mismatch %s vs. %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
if msg is True:
apDisplay.printMsg(
"size match %s vs. %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
### merge header files
#apDisplay.printError("not finished")
mergehead = open(mergeheader, 'wb')
partnum = 1
totalsize = 0
for stackfile in stacklist:
headerfilename = os.path.splitext(stackfile)[0] + ".hed"
headfile = open(headerfilename, 'rb')
### size checks
size = apFile.fileSize(headerfilename)
if msg is True:
apDisplay.printMsg("%s (%d kB)" % (headerfilename, size / 1024))
totalsize += size
#apDisplay.printMsg("%d\t%s"%(npart, stackfile))
i = 0
npart = apFile.numImagesInStack(stackfile)
while i < npart:
#print i, npart, partnum
### read old header
data = headfile.read(1024)
### start new string
headerstr = ""
### first image number
headerstr += intToFourByte(partnum)
### number of images, less one
headerstr += intToFourByte(numpart - partnum)
### always 0,1 ???
headerstr += intToFourByte(0)
headerstr += intToFourByte(1)
### creation date: day, month, year, hour, min, sec
headerstr += intToFourByte(time.localtime()[2])
headerstr += intToFourByte(
time.localtime()[1]) #eman always uses month-1?
headerstr += intToFourByte(time.localtime()[0])
headerstr += intToFourByte(time.localtime()[3])
headerstr += intToFourByte(time.localtime()[4])
headerstr += intToFourByte(time.localtime()[5])
### append other header info, 4 character per item
headerstr += data[10 * 4:60 * 4]
### number of z slices
headerstr += intToFourByte(1)
### first image number, EMAN does this
headerstr += intToFourByte(partnum)
### append other header info, 4 character per item
headerstr += data[62 * 4:68 * 4]
headerstr += intToFourByte(33686018)
headerstr += data[69 * 4:]
mergehead.write(headerstr)
partnum += 1
i += 1
mergehead.close()
if msg is True:
apDisplay.printMsg("wrote %d particles to file %s" %
(numpart, mergestack))
finalsize = apFile.fileSize(mergeheader)
if finalsize != totalsize:
apDisplay.printError(
"size mismatch %s vs. %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
if msg is True:
apDisplay.printMsg(
"size match %s vs. %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(totalsize)))
apDisplay.printMsg(
"finished stack merge of %s in %s" %
(mergestack, apDisplay.timeString(time.time() - t0)))
