def numberParticlesInStack(stackname, startnum=0, verbose=True):
### new faster methond
apImagicFile.numberStackFile(stackname, startnum=0)
return
# store the particle number in the stack header
# NOTE!!! CONFORMS TO EMAN CONVENTION, STARTS AT 0!!!
import EMAN
t0 = time.time()
apDisplay.printMsg("saving particle numbers to stack header")
n = EMAN.fileCount(stackname)[0]
im = EMAN.EMData()
i = 0
back = "\b\b\b\b\b\b\b"
while i < n:
j = startnum + i
im.readImage(stackname, i)
im.setNImg(j)
im.writeImage(stackname, i)
if verbose is True and i % 100 == 0:
sys.stderr.write(back + back + back + str(j) + " of " + str(n))
i += 1
sys.stderr.write("\n")
apDisplay.printMsg("finished in " + apDisplay.timeString(time.time() - t0))
return
def writeImageToImage(instack, inn, outstack, outn=-1, particles=0):
import EMAN
# copy an image from an input stack to another one
img = EMAN.EMData()
img.readImage(instack, inn)
img.setNImg(particles)
img.writeImage(outstack, outn)
return
def writeBlankImage(outfile, boxsize, place, type=None):
import EMAN
a = EMAN.EMData()
a.setSize(boxsize, boxsize)
a.zero()
if type == 'spider':
a.writeImage(outfile, place, EMAN.EMData.SINGLE_SPIDER)
else:
a.writeImage(outfile, place)
return
def writeStackParticlesToFile(stackname, filename):
import EMAN
# write out the particle numbers from imagic header to a file
# NOTE!!! CONFORMS TO EMAN CONVENTION, STARTS AT 0!!!
apDisplay.printMsg("saving list of saved particles to:")
apDisplay.printMsg(filename)
f = open(filename, 'w')
n = EMAN.fileCount(stackname)[0]
im = EMAN.EMData()
for i in range(n):
im.readImage(stackname, i)
f.write(str(im.NImg()) + "\n")
f.close()
return
def getClassInfo(classes):
import EMAN
# read a classes.*.img file, get # of images
imgnum, imgtype = EMAN.fileCount(classes)
img = EMAN.EMData()
img.readImage(classes, 0, 1)
# for projection images, get eulers
projeulers = []
for i in range(imgnum):
img.readImage(classes, i, 1)
e = img.getEuler()
alt = e.thetaMRC() * 180. / math.pi
az = e.phiMRC() * 180. / math.pi
phi = e.omegaMRC() * 180. / math.pi
eulers = [alt, az, phi]
if i % 2 == 0:
projeulers.append(eulers)
return projeulers
def makeClassAverages(lst, outputstack, e, mask):
import EMAN
#align images in class
print "creating class average from", lst, "to", outputstack
images = EMAN.readImages(lst, -1, -1, 0)
for image in images:
image.rotateAndTranslate()
if image.isFlipped():
image.hFlip()
#make class average
avg = EMAN.EMData()
avg.makeMedian(images)
#write class average
avg.setRAlign(e)
avg.setNImg(len(images))
avg.applyMask(mask, 0)
avg.writeImage(outputstack, -1)
def checkStackNumbering(stackname):
import EMAN
# check that the numbering is stored in the NImg parameter
apDisplay.printMsg("checking that original stack is numbered")
n = EMAN.fileCount(stackname)[0]
im = EMAN.EMData()
im.readImage(stackname, n - 1)
# if last particle is not numbered with same value as # of particles,
# renumber the entire stack
if n - 1 != im.NImg():
apDisplay.printWarning(
"Original stack is not numbered! numbering now...")
# check that the stack exists in a writable directory and is not read-only
if os.access(stackname, os.W_OK) is True:
numberParticlesInStack(stackname, startnum=0, verbose=True)
else:
apDisplay.printWarning(
"old stack header exists in a READ-only directory and cannot be numbered according to EMAN"
)
return
def makeClassAverages(lst, outputstack, classdata, params):
#align images in class
images = EMAN.readImages(lst, -1, -1, 0)
for image in images:
image.rotateAndTranslate()
if image.isFlipped():
image.hFlip()
#make class average
avg = EMAN.EMData()
avg.makeMedian(images)
#write class average
e = EMAN.Euler()
alt = classdata['euler1'] * math.pi / 180
az = classdata['euler2'] * math.pi / 180
phi = 0.0
e.setAngle(alt, az, phi)
avg.setRAlign(e)
avg.setNImg(len(images))
avg.applyMask(params['mask'], 0)
avg.writeImage(outputstack, -1)
# get eulers from proj.img file
import sys, os
from math import pi
try:
import EMAN
except ImportError:
print "EMAN module did not get imported"
if __name__ == "__main__":
if len(sys.argv) !=3:
print "Usage: getProjEulers.py <infile> <outfile>\n"
sys.exit(1)
projfile = sys.argv[1]
outfile = sys.argv[2]
out = open(outfile, "w")
count,imgtype = EMAN.fileCount(projfile)
imgs = EMAN.EMData()
imgs.readImage(projfile,0,1)
for i in range(count):
imgs.readImage(projfile,i,1)
e = imgs.getEuler()
alt = e.alt()*180./pi
az = e.az()*180./pi
phi = e.phi()*180./pi
out.write("%i\t%f\t%f\t%f\n" % (i,alt,az,phi))
out.close()
#!/usr/bin/env python
# this will save the particle stack number into the header of a stack.
# use this if you want to run cenalignint, and keep track of the particles.
# NOTE!!! CONFORMS TO EMAN CONVENTION, STARTS AT 0!!!!
import sys
try:
import EMAN
except ImportError:
print "EMAN module did not get imported"
if __name__ == "__main__":
if len(sys.argv) < 2:
print "usage: renumber.py [filename]"
sys.exit()
filename = sys.argv[1]
n = EMAN.fileCount(filename)[0]
im = EMAN.EMData()
for i in range(n):
im.readImage(filename, i)
im.setNImg(i)
im.writeImage(filename, i)
print i
def start(self):
self.params['outputstack'] = os.path.join(self.params['rundir'],
self.params['stackname'])
particles, self.params['refineiter'] = getParticleInfo(
self.params['reconid'], self.params['iter'])
stackdata = particles[0]['particle']['stack']
stack = os.path.join(stackdata['path']['path'], stackdata['name'])
classes, cstats = determineClasses(particles)
rejectlst = []
if self.params['sigma'] is not None:
cutoff = cstats[
'meanquality'] + self.params['sigma'] * cstats['stdquality']
apDisplay.printMsg("Cutoff = " + str(cutoff))
rejectlst = self.removePtclsByQualityFactor(
particles, rejectlst, cutoff)
if self.params['avgjump'] is not None:
rejectlst = self.removePtclsByJumps(particles, rejectlst)
if self.params['rejectlst']:
rejectlst = removePtclsByLst(rejectlst, self.params)
classkeys = classes.keys()
classkeys.sort()
classnum = 0
totalptcls = 0
keepfile = open('keep.lst', 'w')
keepfile.write('#LST\n')
reject = open('reject.lst', 'w')
reject.write('#LST\n')
apDisplay.printMsg("Processing classes")
#loop through classes
for key in classkeys:
# file to hold particles of this class
clsfile = open('clstmp.lst', 'w')
clsfile.write('#LST\n')
classnum += 1
if classnum % 10 == 1:
apDisplay.printMsg(
str(classnum) + " of " + (str(len(classkeys))))
images = EMAN.EMData()
#loop through particles in class
nptcls = 0
for ptcl in classes[key]['particles']:
if ptcl['mirror']:
mirror = 1
else:
mirror = 0
rot = ptcl['euler3']
rot = rot * math.pi / 180
if ptcl['particle']['particleNumber'] not in rejectlst:
l = '%d\t%s\t%f,\t%f,%f,%f,%d\n' % (
ptcl['particle']['particleNumber'] - 1, stack,
ptcl['quality_factor'], rot, ptcl['shiftx'],
ptcl['shifty'], mirror)
keepfile.write(l)
clsfile.write(l)
totalptcls += 1
nptcls += 1
else:
reject.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' %
(ptcl['particle']['particleNumber'] - 1,
stack, ptcl['quality_factor'], rot,
ptcl['shiftx'], ptcl['shifty'], mirror))
#if ptcl['quality_factor']>cstats['meanquality']+3*cstats['stdquality']:
# high.write('%d\t%s\t%f,\t%f,%f,%f,%d\n' % (ptcl['particle']['particleNumber']-1,
# stack,ptcl['quality_factor'],rot,ptcl['shiftx'],ptcl['shifty'],mirror))
clsfile.close()
if nptcls < 1:
continue
if self.params['skipavg'] is False:
makeClassAverages('clstmp.lst', self.params['outputstack'],
classes[key], self.params)
if self.params['eotest'] is True:
self.makeEvenOddClasses('clstmp.lst', classes[key])
apDisplay.printMsg("\n")
reject.close()
keepfile.close()
os.remove('clstmp.lst')
# make 3d density file if specified:
if self.params['make3d'] is not None:
self.params['make3d'] = os.path.basename(self.params['make3d'])
outfile = os.path.join(self.params['rundir'],
self.params['make3d'])
apEMAN.make3d(self.params['stackname'],
outfile,
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d %s %s mask=%d norm" %
(outfile, outfile, self.params['mask']))
if self.params['eotest'] is True:
apEMAN.make3d(self.params['oddstack'],
"odd.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.make3d(self.params['evenstack'],
"even.mrc",
sym=self.params['sym'],
mode=self.params['mode'],
hard=self.params['hard'])
apEMAN.executeEmanCmd("proc3d odd.mrc even.mrc fsc=fsc.eotest")
if os.path.exists(outfile):
# run rmeasure
apix = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
box = apVolume.getModelDimensions(outfile)
apDisplay.printMsg('inserting density into database')
symdata = apSymmetry.findSymmetry(self.params['sym'])
if not symdata:
apDisplay.printError('no symmetry associated with this model')
modq = appiondata.Ap3dDensityData()
modq['session'] = apStack.getSessionDataFromStackId(
self.params['stackid'])
modq['name'] = self.params['make3d']
modq['path'] = appiondata.ApPathData(
path=os.path.abspath(self.params['rundir']))
modq['boxsize'] = box
modq['mask'] = self.params['mask']
modq['pixelsize'] = apix
fscres = apRecon.getResolutionFromFSCFile('fsc.eotest',
box,
apix,
msg=True)
modq['resolution'] = fscres
modq['rmeasure'] = apRecon.runRMeasure(apix, outfile)
modq['md5sum'] = apFile.md5sumfile(outfile)
modq['maxjump'] = self.params['avgjump']
modq['sigma'] = self.params['sigma']
modq['hard'] = self.params['hard']
modq['symmetry'] = symdata
modq['refineIter'] = self.params['refineiter']
if self.params['commit'] is True:
modq.insert()
apChimera.filterAndChimera(outfile,
res=fscres,
apix=apix,
box=box,
chimtype='snapshot',
zoom=self.params['zoom'],
sym=self.params['sym'],
mass=self.params['mass'])
else:
apDisplay.printError(
'no 3d volume was generated - check the class averages:')
apDisplay.printError(self.params['stackname'])
apDisplay.printError(
'hard may be set too high, or avg euler jump set too low for the # of particles'
)
stackstr = str(stackdata.dbid)
reconstr = str(self.params['reconid'])
apDisplay.printColor(
"Make a new stack with only non-jumpers:\n" +
"subStack.py --projectid=" + str(self.params['projectid']) +
" -s " + stackstr + " \\\n " + " -k " +
os.path.join(self.params['rundir'], "keep.lst") + " \\\n " +
" -d 'recon " + reconstr + " sitters' -n sitters" + reconstr +
" -C ", "purple")
fsp = fsp.split('.')[0] + '.good.lst'
f = open(fsp, 'w')
for l in lines:
d = l.strip().split()
if len(d) < 3:
f.write(l)
continue
if d[3][-1] == '1':
f.write(l)
f.close()
n = EMAN.fileCount(fsp)[0]
classnamepath = fsp.split('.')[0] + '.dir'
if not os.path.exists(classnamepath):
os.mkdir(classnamepath)
b = EMAN.EMData()
b.readImage(fsp, 0)
e = b.getEuler()
a = EMAN.EMData()
if format == "eman" or format == "imagic":
outname = "aligned.hed"
else:
outname = "aligned.spi"
startn = 1
if params['noproj'] is True:
startn = 0
print "creating aligned stack"
for i in range(startn, n):
a.readImage(fsp, i)
rap = float(s[1])
elif (s[0] == 'norm'):
norm = int(s[1])
elif (s[0] == 'searchx'):
searchx = int(s[1])
elif (s[0] == 'searchy'):
searchy = int(s[1])
elif (s[0] == 'searchz'):
searchz = int(s[1])
else:
print("Unknown argument " + a)
exit(1)
print target, probe
targetMRC = EMAN.EMData()
targetMRC.readImage(argv[1], -1)
targetMean = targetMRC.Mean()
targetSigma = targetMRC.Sigma()
print "Target Information"
print " mean: %f" % (targetMean)
print " sigma: %f" % (targetSigma)
target_xsize = targetMRC.xSize()
target_ysize = targetMRC.ySize()
target_zsize = targetMRC.zSize()
if (target_xsize != target_ysize != target_zsize) or (target_xsize % 2 == 1):
print "The density map must be even and cubic. Terminating."
sys.exit()
box = target_xsize
