def readPartDocFile(self, reflist):
partlist = []
docfile = "part"+self.params['timestamp']+".doc"
if not os.path.isfile(docfile) or apFile.fileSize(docfile) < 50:
apDisplay.printWarning("Could not find doc file "+docfile+" to read particle angles")
lastdocfile = "iter%03d/part%s_it%06d.doc"%(self.lastiter, self.params['timestamp'], self.lastiter)
if not os.path.isfile(lastdocfile) or apFile.fileSize(lastdocfile) < 50:
apDisplay.printError("Could not find backup doc file")
apDisplay.printColor("Found a backup copy of docfile", "green")
shutil.copy(lastdocfile, docfile)
f = open(docfile, "r")
mininplane = 360.0
for line in f:
if line[:2] == ' ;':
continue
spidict = operations.spiderInLine(line)
origpartdict = self.spidict2partdict(spidict)
partdict = self.adjustPartDict(origpartdict, reflist)
if partdict['inplane'] < mininplane:
mininplane = partdict['inplane']
partlist.append(partdict)
apDisplay.printMsg("minimum inplane: "+str(mininplane))
for partdict in partlist:
partdict['inplane'] = partdict['inplane']-mininplane
apDisplay.printMsg("read rotation and shift parameters for "+str(len(partlist))+" particles")
if len(partlist) < 1:
apDisplay.printError("Did not find any particles in doc file: "+docfile)
return partlist
def readPickFile(pickfile): f = open(pickfile, "r") picklist = [] for line in f: sline = line.strip() if sline[0] == ";": continue spidict = operations.spiderInLine(line) x = spidict['floatlist'][0] y = spidict['floatlist'][1] picklist.append((x,y)) picks = numpy.asarray(picklist) return picks
def readPickFile(pickfile):
f = open(pickfile, "r")
picklist = []
for line in f:
sline = line.strip()
if sline[0] == ";":
continue
spidict = operations.spiderInLine(line)
x = spidict['floatlist'][0]
y = spidict['floatlist'][1]
picklist.append((x, y))
picks = numpy.asarray(picklist)
return picks
def readRefDocFile(self):
reflist = []
docfile = "ref"+self.params['timestamp']+".doc"
if not os.path.isfile(docfile):
apDisplay.printError("could not find doc file "+docfile+" to read reference angles")
f = open(docfile, "r")
mininplane = 360.0
for line in f:
if line[:2] == ' ;':
continue
spidict = operations.spiderInLine(line)
refdict = self.spidict2partdict(spidict)
if refdict['inplane'] < mininplane:
mininplane = refdict['inplane']
reflist.append(refdict)
for refdict in reflist:
refdict['inplane'] = refdict['inplane']-mininplane
apDisplay.printMsg("read rotation and shift parameters for "+str(len(reflist))+" references")
return reflist
def readPartDocFile(self):
partlist = []
docfile = "part"+self.timestamp+".doc"
if not os.path.isfile(docfile):
apDisplay.printError("could not find doc file "+docfile+" to read particle angles")
f = open(docfile, "r")
mininplane = 360.0
for line in f:
if line[:2] == ' ;':
continue
spidict = operations.spiderInLine(line)
partdict = self.spidict2partdict(spidict)
if partdict['inplane'] < mininplane:
mininplane = partdict['inplane']
partlist.append(partdict)
apDisplay.printMsg("minimum inplane: "+str(mininplane))
for partdict in partlist:
partdict['inplane'] = partdict['inplane']-mininplane
apDisplay.printMsg("read rotation and shift parameters for "+str(len(partlist))+" particles")
return partlist
def prepareEnvelope(self, scaleFactor=1.0):
"""
Original envelop mrc pixel size was 0.98 Angstroms, but may be better to say 1.04 Angstroms
Now converts a 1D array into the 2D spectra
"""
apDisplay.printMsg("Creating 2D envelop from 1D array")
envelope = self.params['envelopefile']
if envelope is None:
return
spi = open(envelope, 'r')
radialdata = []
for line in spi:
sline = line.strip()
if not sline or sline[0] == ";":
continue
spidict = operations.spiderInLine(line)
# second float column
radialvalue = spidict['floatlist'][1]
radialdata.append(radialvalue)
spi.close()
### create envelop in 2D
xdata = numpy.arange(0, len(radialdata), 1.0, dtype=numpy.float32)
rdata = numpy.array(radialdata, dtype=numpy.float32)
def funcrad(r, xdata=None, rdata=None):
return numpy.interp(r, xdata, rdata)
envshape = (4096, 4096)
envcalc = imagefun.fromRadialFunction(funcrad, envshape, xdata=xdata, rdata=rdata)
### scale envelope
if abs(scaleFactor - 1.0) > 0.01:
print "scaling envelope by", scaleFactor
envcalc = ndimage.zoom(envcalc, zoom=scaleFactor, mode='nearest')
### shift center of envelope to the edges
envamp = self.center(envcalc)
### mutliply real envelope function by image fft
self.envamp = (envamp - envamp.min()) / (envamp.max() - envamp.min())
apDisplay.printMsg("Successfully created 2D envelop from 1D array")
def readPartDocFile(self):
partlist = []
docfile = "part" + self.timestamp + ".doc"
if not os.path.isfile(docfile):
apDisplay.printError("could not find doc file " + docfile +
" to read particle angles")
f = open(docfile, "r")
mininplane = 360.0
for line in f:
if line[:2] == ' ;':
continue
spidict = operations.spiderInLine(line)
partdict = self.spidict2partdict(spidict)
if partdict['inplane'] < mininplane:
mininplane = partdict['inplane']
partlist.append(partdict)
apDisplay.printMsg("minimum inplane: " + str(mininplane))
for partdict in partlist:
partdict['inplane'] = partdict['inplane'] - mininplane
apDisplay.printMsg("read rotation and shift parameters for " +
str(len(partlist)) + " particles")
return partlist
def prepareEnvelope(self, scaleFactor=1.0):
"""
Original envelop mrc pixel size was 0.98 Angstroms, but may be better to say 1.04 Angstroms
Now converts a 1D array into the 2D spectra
"""
apDisplay.printMsg("Creating 2D envelop from 1D array")
envelope = self.params['envelopefile']
if envelope is None:
return
spi = open(envelope, 'r')
radialdata = []
for line in spi:
sline = line.strip()
if not sline or sline[0] == ";":
continue
spidict = operations.spiderInLine(line)
# second float column
radialvalue = spidict['floatlist'][1]
radialdata.append(radialvalue)
spi.close()
### create envelop in 2D
xdata = numpy.arange(0, len(radialdata), 1.0, dtype=numpy.float32)
rdata = numpy.array(radialdata, dtype=numpy.float32)
def funcrad(r, xdata=None, rdata=None):
return numpy.interp(r, xdata, rdata)
envshape = (4096, 4096)
envcalc = imagefun.fromRadialFunction(funcrad, envshape, xdata=xdata, rdata=rdata)
### scale envelope
if abs(scaleFactor - 1.0) > 0.01:
print "scaling envelope by", scaleFactor
envcalc = ndimage.zoom(envcalc, zoom=scaleFactor, mode='nearest')
### shift center of envelope to the edges
envamp = self.center(envcalc)
### mutliply real envelope function by image fft
self.envamp = (envamp - envamp.min()) / (envamp.max() - envamp.min())
apDisplay.printMsg("Successfully created 2D envelop from 1D array")
def canClassificationToDict(self):
### read the particle classification results from CAN
### output in spider format & save as a dictionary
pclass = {}
spitarf = "cls.spi.tar"
if not os.path.isfile(spitarf):
apDisplay.printError("no SPIDER cls tar file found")
spitar = tarfile.open(spitarf)
## revert when using python 2.5+
self.TarExtractall(spitar)
#spitar.extractall()
spitar.close()
spifiles = glob.glob("classes_class_*.spi")
if not spifiles:
apDisplay.printError("CAN did not create SPIDER cls files")
spifiles.sort()
# store classification in dictionary, defined by particle number
for spi in spifiles:
## get ref number from class file name
refn=int(os.path.splitext(spi)[0][-4:])
f = open(spi)
for l in f:
if l[:2] == ' ;':
continue
spidict = operations.spiderInLine(l)
p = int(spidict['floatlist'][0])
if p not in pclass:
pclass[p]=self.sortedAvgDict[refn]
else:
apDisplay.printError("particle %i has more than 1 classification,"
+" classified to reference %i and %i"%(p,pclass[p],refn))
f.close()
os.remove(spi)
return pclass
def runEoTest(self, alignstack, eulerfile):
evenvolfile = os.path.join(self.params['rundir'],
"evenvolume%s.spi" % (self.timestamp))
oddvolfile = os.path.join(self.params['rundir'],
"oddvolume%s.spi" % (self.timestamp))
eveneulerfile = os.path.join(self.params['rundir'],
"eveneulers%s.spi" % (self.timestamp))
oddeulerfile = os.path.join(self.params['rundir'],
"oddeulers%s.spi" % (self.timestamp))
evenpartlist = os.path.join(self.params['rundir'],
"evenparts%s.lst" % (self.timestamp))
oddpartlist = os.path.join(self.params['rundir'],
"oddparts%s.lst" % (self.timestamp))
### Create New Doc Files
of = open(oddeulerfile, "w")
ef = open(eveneulerfile, "w")
op = open(oddpartlist, "w")
ep = open(evenpartlist, "w")
inf = open(eulerfile, "r")
evenpart = 0
oddpart = 0
for line in inf:
spidict = operations.spiderInLine(line)
if spidict:
partnum = spidict['row']
if partnum % 2 == 0:
ep.write("%d\n" % (partnum - 1))
evenpart += 1
outline = operations.spiderOutLine(evenpart,
spidict['floatlist'])
ef.write(outline)
elif partnum % 2 == 1:
op.write("%d\n" % (partnum - 1))
oddpart += 1
outline = operations.spiderOutLine(oddpart,
spidict['floatlist'])
of.write(outline)
inf.close()
of.close()
ef.close()
op.close()
ep.close()
### Create stacks
evenstack = os.path.join(self.params['rundir'],
"evenstack%s.spi" % (self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap" % (alignstack, evenstack,
evenpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
oddstack = os.path.join(self.params['rundir'],
"oddstack%s.spi" % (self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap" % (alignstack, oddstack,
oddpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
### Create Volumes
backproject.backproject3F(evenstack, eveneulerfile, evenvolfile,
evenpart)
backproject.backproject3F(oddstack, oddeulerfile, oddvolfile, oddpart)
if not os.path.isfile(evenvolfile) or not os.path.isfile(oddvolfile):
apDisplay.printError("Even-Odd volume creation failed")
### Calculate FSC
apix = apStack.getStackPixelSizeFromStackId(
self.params['tiltstackid']) * self.params['tiltbin']
emancmd = "proc3d %s %s" % (evenvolfile, evenvolfile + ".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
emancmd = "proc3d %s %s" % (oddvolfile, oddvolfile + ".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
fscfile = os.path.join(self.params['rundir'],
"fscdata%s.fsc" % (self.timestamp))
emancmd = "proc3d %s %s fsc=%s" % (evenvolfile + ".mrc",
oddvolfile + ".mrc", fscfile)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
if not os.path.isfile(fscfile):
apDisplay.printError("Even-Odd fsc calculation failed")
boxsize = self.getBoxSize()
self.fscresolution = apRecon.getResolutionFromFSCFile(fscfile,
boxsize,
apix,
msg=True)
apDisplay.printColor(
("Final FSC resolution: %.5f" % (self.fscresolution)), "cyan")
for fname in (evenvolfile, oddvolfile, evenstack, oddstack,
eveneulerfile, oddeulerfile, evenpartlist, oddpartlist):
apFile.removeFile(fname)
def runEoTest(self, alignstack, eulerfile):
evenvolfile = os.path.join(self.params['rundir'], "evenvolume%s.spi"%(self.timestamp))
oddvolfile = os.path.join(self.params['rundir'], "oddvolume%s.spi"%(self.timestamp))
eveneulerfile = os.path.join(self.params['rundir'], "eveneulers%s.spi"%(self.timestamp))
oddeulerfile = os.path.join(self.params['rundir'], "oddeulers%s.spi"%(self.timestamp))
evenpartlist = os.path.join(self.params['rundir'], "evenparts%s.lst"%(self.timestamp))
oddpartlist = os.path.join(self.params['rundir'], "oddparts%s.lst"%(self.timestamp))
### Create New Doc Files
of = open(oddeulerfile, "w")
ef = open(eveneulerfile, "w")
op = open(oddpartlist, "w")
ep = open(evenpartlist, "w")
inf = open(eulerfile, "r")
evenpart = 0
oddpart = 0
for line in inf:
spidict = operations.spiderInLine(line)
if spidict:
partnum = spidict['row']
if partnum % 2 == 0:
ep.write("%d\n"%(partnum-1))
evenpart += 1
outline = operations.spiderOutLine(evenpart, spidict['floatlist'])
ef.write(outline)
elif partnum % 2 == 1:
op.write("%d\n"%(partnum-1))
oddpart += 1
outline = operations.spiderOutLine(oddpart, spidict['floatlist'])
of.write(outline)
inf.close()
of.close()
ef.close()
op.close()
ep.close()
### Create stacks
evenstack = os.path.join(self.params['rundir'], "evenstack%s.spi"%(self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap"%(alignstack,evenstack,evenpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
oddstack = os.path.join(self.params['rundir'], "oddstack%s.spi"%(self.timestamp))
emancmd = "proc2d %s %s list=%s spiderswap"%(alignstack,oddstack,oddpartlist)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
### Create Volumes
backproject.backproject3F(evenstack, eveneulerfile, evenvolfile, evenpart)
backproject.backproject3F(oddstack, oddeulerfile, oddvolfile, oddpart)
if not os.path.isfile(evenvolfile) or not os.path.isfile(oddvolfile):
apDisplay.printError("Even-Odd volume creation failed")
### Calculate FSC
apix = apStack.getStackPixelSizeFromStackId(self.params['tiltstackid'])*self.params['tiltbin']
emancmd = "proc3d %s %s"%(evenvolfile, evenvolfile+".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
emancmd = "proc3d %s %s"%(oddvolfile, oddvolfile+".mrc")
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
fscfile = os.path.join(self.params['rundir'], "fscdata%s.fsc"%(self.timestamp))
emancmd = "proc3d %s %s fsc=%s"%(evenvolfile+".mrc", oddvolfile+".mrc", fscfile)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
if not os.path.isfile(fscfile):
apDisplay.printError("Even-Odd fsc calculation failed")
boxsize = self.getBoxSize()
self.fscresolution = apRecon.getResolutionFromFSCFile(fscfile, boxsize, apix, msg=True)
apDisplay.printColor( ("Final FSC resolution: %.5f" % (self.fscresolution)), "cyan")
for fname in (evenvolfile, oddvolfile, evenstack, oddstack, eveneulerfile, oddeulerfile, evenpartlist, oddpartlist):
apFile.removeFile(fname)
