def random_sample(num_maps, sf, particles):
#subset_num = int (len(particles)*fraction)
num_part = int(len(particles))
num_proj = EMAN.fileCount("proj.img")[0]
for i in range(num_maps):
#print "Model %d" % (i)
#random.shuffle(particles)
directory = "model_%d" % (i)
os.mkdir(directory)
os.chdir(directory)
for files in ["start.hed","proj.hed"]:
#up_dir_file = "../"+file
cmd="lstcat.py "+files+" ../"+files
os.system(cmd)
os.link(files, files[:-3]+"img")
os.link("../"+sf,sf)
for c in range(num_proj):
clsfile="cls%04d.lst" % (c)
fp = file(clsfile,"w")
fp.write("#LST\n%d\tproj.hed\n" % (c) )
fp.close()
#for j in range(subset_num):
for j in range(num_part):
#p = int(particles[j][0])
#c = int(particles[j][1])
partt=random.choice(particles)
p = partt[0]
c = int(partt[1])
#print "Index %d/%d/%d\tParticle %d -> Class %d" % (j, subset_num, len(particles), p, c)
clsfile="cls%04d.lst" % (c)
fp = open(clsfile,"a")
fp.write(p)
fp.close()
os.chdir("..")
def parse_command_line():
usage="Usage: %prog <image filename> <output filename> [options]"
parser = OptionParser(usage=usage)
parser.add_option("--mode",metavar="['defocus', 'snr', 'ctfb', 'ctfamp']",dest="mode",type="choice",choices=['defocus', 'snr', 'ctfb', 'ctfamp'], help="ctf mode to plot. default to \"defocus\"", default="defocus")
parser.add_option("--sf",dest="sffile",type="string",help="structural factor file name", default="")
parser.add_option("--first",dest="first",type="int",help="first image to use. default to 0", default=0)
parser.add_option("--last",dest="last",type="int",help="last image to use. default to last image in the file", default=-1)
(options, args) = parser.parse_args()
if len(args) != 2:
parser.print_help()
sys.exit(-1)
else:
image = args[0]
output = args[1]
if options.mode in ['snr']:
if not options.sffile:
print "Error: --sf should be specified"
sys.exit(1)
elif not os.path.exists(options.sffile):
print "Error: sffile %s does not exist" % (options.sffile)
sys.exit(2)
imgnum = EMAN.fileCount(image)[0]
if options.last==-1: options.last=imgnum-1
if options.first>0 or options.last>0:
if not (0<=options.first<imgnum):
print "Error: --first=%d is out of correct range [0, %d]" % (options.first, imgnum-1)
sys.exit(3)
if not (options.first<=options.last<imgnum):
print "Error: --last=%d is out of correct range [%d, %d]" % (options.last, options.first, imgnum-1)
sys.exit(4)
return (options, image, output)
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 main():
(options, input_lstfiles) = parse_command_line()
ptcls = readLstFiles(input_lstfiles, nBest = options.nBest)
if options.ortLstFile:
ptcls_list = []
for p in ptcls:
ptcls_list += ptcls[p].items()
ptcls_list.sort()
fp = open(options.ortLstFile, 'w')
fp.write("#LST\n")
for p in ptcls_list:
fp.write("%d\t%s\teuler=%g,%g,%g\tcenter=%g,%g\n" % (p.imageIndex, p.imageFile, p.euler[0], p.euler[1], p.euler[2], p.center[0], p.center[1]))
fp.close()
cmd = "images2lst.py %s %s" % (options.ortLstFile, options.ortLstFile)
os.system(cmd)
if options.saveClsLst:
nProj = EMAN.fileCount(options.projFile)[0]
clses = [ 1 ]* nProj
for i in range(len(clses)): clses[i] = []
for p in ptcls:
solutions = ptcls[p].items()
for pi in solutions:
clses[pi.refid].append(pi)
import math
#digits = int(math.log10(nProj)+1)
digits = 4
for cls in range(len(clses)):
ptcls_list = clses[cls]
ptcls_list.sort()
clsfn = "%d" % (cls)
clsfn = "%s%s.lst" % (options.clsFileTag, clsfn.zfill(digits))
fp = open(clsfn,'w')
fp.write("#LST\n")
fp.write("%d\t%s\n" % (cls, options.projFile))
for p in ptcls_list:
fp.write("%d\t%s\t%s\n" % (p.imageIndex, p.imageFile, p.clsinfo))
fp.close()
if options.eotest:
clsfn = "%d" % (cls)
clsfn_even = "%s%s.even.lst" % (options.clsFileTag, clsfn.zfill(digits))
clsfn_odd = "%s%s.odd.lst" % (options.clsFileTag, clsfn.zfill(digits))
fp_even = open(clsfn_even,'w')
fp_even.write("#LST\n")
fp_even.write("%d\t%s\n" % (cls, options.projFile))
fp_odd = open(clsfn_odd,'w')
fp_odd.write("#LST\n")
fp_odd.write("%d\t%s\n" % (cls, options.projFile))
for p in ptcls_list:
if p.imageIndex%2:
fp_odd.write("%d\t%s\t%s\n" % (p.imageIndex, p.imageFile, p.clsinfo))
else:
fp_even.write("%d\t%s\t%s\n" % (p.imageIndex, p.imageFile, p.clsinfo))
fp_even.close()
fp_odd.close()
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 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 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 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 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 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 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 follow_lst_link(image, index, lstfiles, imagefiles):
if not (
imagefiles.has_key(image) or lstfiles.has_key(image)
): # it has not seen this image before and will find out
imgnum, imgtype = EMAN.fileCount(image)
if imgtype == "lst":
tmplst = []
fp = open(image, "r")
lines = fp.readlines()
fp.close()
if lines[0].startswith("#LST"):
line0 = 1
elif lines[0].startswith("#LSX"):
line0 = 3
for l in lines[line0:]:
tokens = l.split()
tmplst.append((tokens[1], int(tokens[0])))
lstfiles[image] = tmplst
else:
imagefiles[image] = imgnum
if imagefiles.has_key(image): # it has already known this image is a binary format image
if index >= imagefiles[image]:
print "Error: image file %s only has %d images, not enough for %d" % (image, imagefiles[image], index)
sys.exit(-1)
else:
return (image, index)
elif lstfiles.has_key(image): # it has already known this image is a list format image
if index >= len(lstfiles[image]):
print "Error: lst file %s only has images, not enough for %d" % (image, len(lstfiles[image]), index)
sys.exit(-1)
else:
return follow_lst_link(lstfiles[image][index][0], lstfiles[image][index][1], lstfiles, imagefiles)
else:
print "Something is wrong, need to debug this program and the image file"
sys.exit(-1)
def parse_command_line():
usage="Usage: %prog <Raw image filename 1> ... <Raw image filename n> <reference filename> [options]"
parser = OptionParser(usage=usage)
parser.add_option("--createconfigFile",dest="createconfigFile",type="string",help="use to create a configure file under a given directory and file name (Default file name is [./ccmlConfigFile.ini])", default="./ccmlConfigFile.ini")
parser.add_option("--configFile",dest="configFile",type="string",help="all/parts of the parameters can be read from this file. command line parameters have higher priority, but it will be enforced to use if an 'endforce' is followed by the corresponding values. (Default file name is [./ccmlConfigFile.ini])", default="./ccmlConfigFile.ini")
parser.add_option("--saveParms",dest="saveParms",type="string",help="if a file name is given, the actually parameters will be saved to the file. (default is not save if no name)", default="")
#options
parser.add_option("--sym",dest="sym",type="string",help="set symmetry of the particle, (default is \"icos\")",default="icos")
parser.add_option("--rMask",dest="rMask",type="int",help="Mask will be applied to image center. The radial size = rMask, [half image size]",default=0)
parser.add_option("--rMask1",dest="rMask1",type="int",help="Mask will be applied to solved particle center. The radial size = rMask1, [rMask]",default=0)
parser.add_option("--startNum",dest="startNumOfRawImages",type="int",help="The starting image number",default=0)
parser.add_option("--endNum",dest="endNumOfRawImages",type="int",help="The ending image number, (0 is default, all images)",default=0)
parser.add_option("--numOfRefImages",dest="numOfRefImages",type="int",help="Number of projection images to use for calculating orientation, (5 is default)",default=5)
parser.add_option("--scatteringFactorFile",dest="sfFileName",type="string",help="File name for scattering factor of raw images",default="")
parser.add_option("--phasecorrected",dest="phasecorrected",action="store_true",help="if the particle images already phase flipped. default to false", default=0)
parser.add_option("--overSample",dest="FFTOverSampleScale",type="int",help="Scale of over sample FFT, (1 is default, NO over sample)",default=1)
parser.add_option("--pftStepSize",dest="pftStepSize",type="float",help="Angular step size for creating pseudo PFT, (0.1 degree is default)",default=0.1)
parser.add_option("--radialStepSize",dest="deltaR",type="float",help="Radial step size for collecting data on common line, (1.0 is default)",default=1.0)
parser.add_option("--radialStartPoint",dest="RMin",type="int",help="Radial start point for collecting data on common line, (5 is default)",default=5)
parser.add_option("--radialEndPoint",dest="RMax",type="int",help="Radial end point for collecting data on common line, (35 is default)",default=35)
#parser.add_option("--maskRadius",dest="maskR",type="int",help="Mask radius to remove background pixels at large radius (default to half of image size)",default=0)
parser.add_option("--orientationSearchRange",dest="orientationSearchRange",type="float",help="Maximum orientation deviation from a given one, (36.0 is default)",default=36.0)
parser.add_option("--centerSearchRange",dest="centerSearchRange",type="float",help="Maximum center deviation from a given one, (15.0 is default)",default=15.0)
parser.add_option("--maxIteration",dest="maxNumOfIteration",type="int",help="Maximum iteration, (1000 is default for coarse search, 150 for refinement)",default=150)
parser.add_option("--numOfRandomJump",dest="numOfRandomJump",type="int",help="iteration of beginning random jump, (50 is default for coarse search, 20 for refinement)",default=20)
parser.add_option("--numOfFastShrink",dest="numOfFastShrink",type="int",help="iteration of ending fast shrink, (150 is default for coarse search, 80 for refinement)",default=80)
parser.add_option("--numOfStartConfigurations",dest="numOfStartConfigurations",type="int",help="starting configurations, (10 is default)",default=10)
parser.add_option("--searchMode",dest="searchMode",type="int",help="Mode to handle a raw image, (0 is default)",default=0)
parser.add_option("--scalingMode",dest="scalingMode",type="int",help="Mode to handle a raw image, (0 is default)",default=0)
parser.add_option("--residualMode",dest="residualMode",type="int",help="Mode to calculate residual, (2 is default)",default=2)
parser.add_option("--weightMode",dest="weightMode",type="int",help="Weighting function mode to calculate residual, default to 1",default=1)
parser.add_option("--iniParameterFile",dest="rawImageIniParmFN",type="string",help="File name for initial orientation and center of raw images",default="")
parser.add_option("--refEulerConvention",dest="refEulerConvention",type="choice",choices=["eman","mrc"],help='Spcify an euler convention of the refence orientation. choices are ["eman","mrc"]. default to "eman"',default="eman")
parser.add_option("--iniCenterOrientationMode",dest="iniCenterOrientationMode",type="choice",choices=["random","headerfile","iniparmfile"],help='mode to initialize particle center and orientation. choices are ["random","headerfile","iniparmfile"]. default to "random"',default="random")
parser.add_option("--refCenterOrientationMode",dest="refCenterOrientationMode",type="string",help="mode to set reference center and orientation of the particle [copy from ini]",default="")
parser.add_option("--zScoreCriterion",dest="zScoreCriterion",type="float",help="The criterion of stopping run, (6.0 is default)",default=6.0)
parser.add_option("--residualCriterion",dest="residualCriterion",type="float",help="The criterion of stopping run, (default: no residual criterion)",default=-1.0)
parser.add_option("--solutionCenterDiffCriterion",dest="solutionCenterDiffCriterion",type="float",help="The criterion of stopping run, (default: no solution center diff criterion)",default=-1.0)
parser.add_option("--solutionOrientationDiffCriterion",dest="solutionOrientationDiffCriterion",type="float",help="The criterion of stopping run, (default: no solution orientation diff criterion)",default=-1.0)
parser.add_option("--numConsistentRun",dest="numConsistentRun",type="int",help="number of runs with consistent orienttion/center to accept as success. default to 2", default=2)
parser.add_option("--maxNumOfRun",dest="maxNumOfRun",type="int",help="Maximum number of re-search, (5 is default)",default=5)
parser.add_option("--updateHeader", dest="updataHeader",type="int", help="Write the calculated result to the header file, (default is O, NO update)",default=0)
parser.add_option("--solutionFile",dest="solutionFile",type="string",help="File name for outputing results, (default is Raw image filename + \"-OrientationCenter.dat\")",default="")
parser.add_option("--mrcSolutionFile",dest="mrcSolutionFile",type="string",help="File name for outputing results in MRC format, (default is Raw image filename + \"-MRC-OrientationCenter.dat\") ",default="")
parser.add_option("--listFile",dest="listFile",type="string",help="File name for listing good particles in EMAN LST format",default="")
parser.add_option("--scoreFile",dest="scoreFile",type="string",help="File name for the defocus and residual values of good particles in EMAN LST format",default="")
parser.add_option("--verbose", dest="verbose",type="int", help="verbose level [0-5], (default is O, no screen print out)",default=0)
parser.add_option("--nolog",dest="nolog",action="store_true",help="don't log the command in .emanlog", default=0)
if(len(sys.argv) > 1) : #for creating configure file
configFileName = ""
if (sys.argv[1] == "--createconfigFile" ) or (sys.argv[1] == "--createconfigFile=" ) : configFileName = "./ccmlConfigFile.ini" #default value
elif re.match("--createconfigFile=",sys.argv[1]) : #if specified
splitPosition = re.match("--createconfigFile=",sys.argv[1]).end()
configFileName = sys.argv[1][splitPosition:]
if configFileName != "" : createConfigureFile(configFileName) #create the configure file, then quite the program
(options, args)=parser.parse_args() #this is first parse the command line inputs, later a pseudo command line option will be parsed
allAdoptedOptions = {} #make a dictionary for saving the final adopted options which combines the command line options and the options form configure file
for aArg in sys.argv[1:] :
if re.match('--.*.=', aArg) :
splitPosition = re.match('--.*.=', aArg).end()
allAdoptedOptions[aArg[2:(splitPosition-1)]] = aArg[splitPosition:]
elif re.match('--.*.', aArg) :
allAdoptedOptions[aArg[2:]] = ""
if not os.path.exists(options.configFile) : #check if the default or given configure file is exist or not
if options.configFile != "./ccmlConfigFile.ini" :
print "The configure file : %s does NOT exist, QUIT the program!!!" % (options.configFile)
sys.exit(-1)
else :
config = ConfigParser.ConfigParser()
config.optionxform = str #output case-sensitive options
config.read(options.configFile)
tempListCommandParms = []
tempListArgs = []
tempRefImg = ""
tempListOptions = []
rawImgEnforced = False
refImgEnforced = False
tempListOptions.append("--%s=%s" % ("configFile",options.configFile)) #set value for configFile option
for section in config.sections(): #parse the configure file
for option in config.options(section):
#print option, " = ", config.get(section, option)
values = config.get(section, option).replace(","," ").split()
if len(values)==0 : continue # if give nothing, it will be ignored
if values[0][0] == ";" or values[0][0] == "#" : continue #sometimes, no value given, the parse will take comments as its value
enforced = False
if len(values) > 1 and re.search('enforce', values[-1]) : enforced = True #detect if this value will be enforced to replace the command line value
if re.search('option',section.lower()) :
if ((values[0].lower == 'yes') or (values[0].lower == 'true')) : values[0]='True'
if ((values[0].lower == 'no') or (values[0].lower == 'false')) : values[0]='False'
if not allAdoptedOptions.has_key(option) : allAdoptedOptions[option] = values[0] #if not specified in command line, add this option
elif enforced : allAdoptedOptions[option] = values[0] #if enforced, this option will replce the corresponding command line's value
if re.search('require',section.lower()) : #for required arguments in configure file
if re.match('raw.*.image.*.file', string.join(option.split(), sep=" ").lower()) : #remove all unneccessary spaces and convert to lower cases
if enforced :
rawImgEnforced = True
tempListArgs = values[:-1]
else : tempListArgs = values #raw images could be in multiple files
if re.match('ref.*.image.*.file', string.join(option.split(), sep=" ").lower()) :
if enforced : refImgEnforced = True
tempRefImg = values[0] #for reference image
argsFinal = []
if len(args) == 0 :
argsFinal = tempListArgs
argsFinal.append(tempRefImg)
if len(args) == 1 :
if not rawImgEnforced:
argsFinal = args
argsFinal.append(tempRefImg)
else :
argsFinal = tempListArgs
argsFinal.append(tempRefImg)
if len(args) >= 2 :
if rawImgEnforced and refImgEnforced :
argsFinal = tempListArgs
argsFinal.append(tempRefImg)
elif (not rawImgEnforced) and refImgEnforced :
argsFinal = args[:-1]
argsFinal.append(tempRefImg)
elif rawImgEnforced and (not refImgEnforced) :
argsFinal = tempListArgs
argsFinal.append(args[-1])
else : argsFinal = args
args = argsFinal #copy the final args to the args, the adopted options is already in list, allAdoptedOptions
adoptedArguments = [] #all actually adopted paramemters
#adoptedArguments = args #copy all the required argument to the list
for i in range(len(args)) : adoptedArguments += glob.glob(args[i]) #check if the raw and ref images exist and extend the pattern file name to all real names
for anOption in allAdoptedOptions : #it combines the both comand line options and the options from configure file
if allAdoptedOptions[anOption] == "False" : continue #if it is False, does not space
if allAdoptedOptions[anOption] == "True" or allAdoptedOptions[anOption] == "" : adoptedArguments.append("--" + anOption) #for the option take no value, just specifiy it as True
else : adoptedArguments.append("--" + anOption + "=" + str(allAdoptedOptions[anOption]))
#print adoptedArguments
(options, args)=parser.parse_args(adoptedArguments) # parse the adoptedArguments by command line parser
if len(args) < 2:
parser.print_help()
sys.exit(-1)
if options.saveParms != "" :
commandtime = time
t = commandtime.localtime()
timeStr = "# Command start time %s/%s/%s %s:%s:%s\n" % (t[1],t[2],t[0],t[3],t[4],t[5])
commandStr = sys.argv[0] #save all actually used paramemters
for aArg in args : commandStr += (" " + aArg)
#for anOption in options.__dict__ : commandStr += (" --" + anOption + "=" + str(options.__dict__[anOption])) #output all internal used parameters
for anOption in allAdoptedOptions :
if allAdoptedOptions[anOption] == "False" : continue #if it is False, does not space
if allAdoptedOptions[anOption] == "True" or allAdoptedOptions[anOption] == "" : commandStr += (" --" + anOption) #for the option take no value, just specifiy it as True
else : commandStr += (" --" + anOption + "=" + str(allAdoptedOptions[anOption])) #output all input parameters
commandStr += "\n"
f=open(options.saveParms, "a")
f.write(timeStr)
f.write(commandStr)
f.close()
for key in parser.option_list[1:]: #this omits the -h/--help option
eval_string = "options.%s" % (key.dest)
value = eval(eval_string)
if value == None:
if (options.verbose > 0) :
print "The option %s must be specified on the command line" % (key)
sys.exit(-1)
#remove the input string's spaces, some string may need to convert to lower cases
options.sfFileName = options.sfFileName.replace(" ", "")
options.rawImageIniParmFN = options.rawImageIniParmFN.replace(" ", "")
options.solutionFile = options.solutionFile.replace(" ", "")
options.mrcSolutionFile = options.mrcSolutionFile.replace(" ", "")
options.iniCenterOrientationMode = options.iniCenterOrientationMode.lower().replace(" ", "")
options.refCenterOrientationMode = options.refCenterOrientationMode.lower().replace(" ", "")
options.refEulerConvention = options.refEulerConvention.lower().replace(" ", "")
#if options.solutionFile == "":
# options.solutionFile = os.path.splitext(args[0])[0] + "-OrientationCenter.dat"
#if options.mrcSolutionFile == "":
# options.mrcSolutionFile = os.path.splitext(args[0])[0] + "-MRC-OrientationCenter.dat"
#numOfRawImages = EMAN.fileCount(args[0])[0]
#if options.endNumOfRawImages < 1:
# options.endNumOfRawImages = numOfRawImages
numOfRefImages = EMAN.fileCount(args[-1])[0]
if options.numOfRefImages > numOfRefImages:
options.numOfRefImages = numOfRefImages
if options.startNumOfRawImages < 0:
options.startNumOfRawImages = 0
if (options.searchMode) == 0 : # coarse search
# set default values
if options.numOfRandomJump == 20 : options.numOfRandomJump = 1000
if options.numOfFastShrink == 50 : options.numOfFastShrink = 300
if options.maxNumOfIteration == 150 : options.maxNumOfIteration = 2500
# check if the given values are less than mins
if options.numOfRandomJump < 500 : options.numOfRandomJump = 500
if options.numOfFastShrink <150 : options.numOfFastShrink = 150
if options.maxNumOfIteration < (options.numOfRandomJump + options.numOfFastShrink + 500) :
options.maxNumOfIteration = (options.numOfRandomJump + options.numOfFastShrink + 500)
if options.maxNumOfIteration < 1500 : options.maxNumOfIteration = 1500
elif (options.searchMode) == 1 : # refinement
if options.rawImageIniParmFN == "" :
if (options.verbose > 0) : print "\n\n\tFor refinement, you need to give a file name which specifies orientation and center of each image\n"
#sys.exit(0)
# check if the given values are less than mins
if options.numOfRandomJump < 20 : options.numOfRandomJump = 20
if options.numOfFastShrink < 50 : options.numOfFastShrink = 50
if options.maxNumOfIteration < (options.numOfRandomJump + options.numOfFastShrink + 50) :
options.maxNumOfIteration = (options.numOfRandomJump + options.numOfFastShrink + 50)
if options.maxNumOfIteration < 120 : options.maxNumOfIteration = 120
if options.orientationSearchRange > 36 : options.orientationSearchRange = 36
if options.centerSearchRange > 100 : options.centerSearchRange = 100
if options.zScoreCriterion < 0 : options.zScoreCriterion = 0
allInputParameters = "-------------------------------------------------------------------------\n"
allInputParameters += "--------------- All input parameters are listed as follows --------------\n"
allInputParameters += "-------------------------------------------------------------------------\n"
allInputParameters += "%40s :: %s \n" % ("Raw image file name",args[0:-1])
allInputParameters += "%40s :: %s \n" % ("Reference image file name",args[-1])
if options.sfFileName != "" : allInputParameters += "%40s :: %s \n" % ("Scattering factor file name",options.sfFileName)
if options.searchMode == 1 : allInputParameters += "%40s :: %s \n" % ("Raw image initial parameter file name", options.rawImageIniParmFN)
allInputParameters += "%40s :: %s \n" % ("Starting number of raw images", options.startNumOfRawImages)
allInputParameters += "%40s :: %s \n" % ("Ending number of raw images", options.endNumOfRawImages)
allInputParameters += "%40s :: %s \n" % ("Number of reference images", options.numOfRefImages)
allInputParameters += "%40s :: %d \n" % ("Mask radius (pixels)", options.rMask)
allInputParameters += "%40s :: %s \n" % ("Scale of over sample FFT", options.FFTOverSampleScale)
allInputParameters += "%40s :: %s \n" % ("Maximum number of iteration", options.maxNumOfIteration)
allInputParameters += "%40s :: %s \n" % ("Iteration number of random jump", options.numOfRandomJump)
allInputParameters += "%40s :: %s \n" % ("Iteration number of fast shrink", options.numOfFastShrink)
allInputParameters += "%40s :: %s \n" % ("Center search range", options.centerSearchRange)
allInputParameters += "%40s :: %s \n" % ("Orientation search range", options.orientationSearchRange)
allInputParameters += "%40s :: %s \n" % ("Radial Step size of a common line", options.deltaR)
allInputParameters += "%40s :: %s \n" % ("Radial start point of a common line", options.RMin)
allInputParameters += "%40s :: %s \n" % ("Radial end point of a common line", options.RMax)
allInputParameters += "%40s :: %s \n" % ("Mode to handle a raw image", options.searchMode)
allInputParameters += "%40s :: %s \n" % ("Mode to calculate residual", options.residualMode)
allInputParameters += "%40s :: %s \n" % ("Weighting mode to calculate residual", options.weightMode)
allInputParameters += "%40s :: %s \n" % ("Maximum number of re-run", options.maxNumOfRun)
allInputParameters += "%40s :: %s%s \n" % ("The criteria of discriminating data", "z score = ", options.zScoreCriterion)
if options.residualCriterion > 0 : allInputParameters += "%40s :: %s%s \n" % ("", "residual threshold = ", options.residualCriterion)
else : allInputParameters += "%40s :: %s \n" % ("", "residual threshold = N/A")
if options.solutionCenterDiffCriterion > 0 : allInputParameters += "%40s :: %s%s \n" % ("", "center difference = ", options.solutionCenterDiffCriterion)
else : allInputParameters += "%40s :: %s \n" % ("", "center difference = N/A")
if options.solutionOrientationDiffCriterion > 0 : allInputParameters += "%40s :: %s%s \n" % ("", "orientation difference = ", options.solutionOrientationDiffCriterion)
else : allInputParameters += "%40s :: %s \n" % ("", "orientation difference = N/A")
printOnScreen = allInputParameters
printOnScreen += "-------------------------------------------------------------------------\n"
printOnScreen += "%40s :: %s \n" % ("Solution file name", options.solutionFile)
printOnScreen += "-------------------------------------------------------------------------\n"
writeToSolutionFile = allInputParameters
writeToSolutionFile += "-------------------------------------------------------------------------\n\n"
writeToSolutionFile += "%6s%8s%7s%7s%7s%7s%10s%34s%16s%24s%9s%12s\n" % ("######","X","Y","Alt","Az","Phi","residual"," sigma Z Z-crti Run# Status","ref center", "ref orientation", "XY diff","angle diff")
writeToSolutionFile += "------------------------------------------------------------------------------------------------------------------------\n"
if options.verbose > 0 and (not mpi or (mpi and mpi.rank==0)) : #print out the input parameters on screen
print "%s " % (printOnScreen)
if options.solutionFile and options.startNumOfRawImages == 0 : #write the input parameters to the solution file
solutionFile = open(options.solutionFile, "w")
solutionFile.write("%s" % (writeToSolutionFile))
solutionFile.close()
return (options,args)
def main():
(options, input_imagefiles, output_lstfile) = parse_command_line()
lstfiles = {}
imagefiles = {}
alllines = []
if options.removeDuplicates:
import sets
seenImages = sets.Set()
for imagefile in input_imagefiles:
if os.path.exists(imagefile):
imgnum, imgtype = EMAN.fileCount(imagefile)
if not imgnum:
print 'WARNING: file "%s" is empty' % (imagefile)
continue
else:
print "%s: %d images" % (imagefile, imgnum)
if imgtype == "lst":
fp = open(imagefile, "r")
lines = fp.readlines()
if lines[0].startswith("#LST"):
line0 = 1
elif lines[0].startswith("#LSX"):
line0 = 3
if len(lines) > line0:
for l in lines[line0:]:
tokens = l.split(None, 2)
realimg, realindex = follow_lst_link(tokens[1], int(tokens[0]), lstfiles, imagefiles)
if len(tokens) > 2:
line = "%d\t%s\t%s" % (realindex, realimg, tokens[2])
else:
line = "%d\t%s\n" % (realindex, realimg)
if options.removeDuplicates and isDuplicate(seenImages, realimg, realindex):
print "%s: particle %d is a duplicate image, ignored" % (realimg, realindex)
else:
alllines += [line]
else:
print 'WARNING: lst file "%s" is empty' % (imagefile)
fp.close()
else:
d = EMAN.EMData()
for i in range(imgnum):
d.readImage(imagefile, i, 1)
line = "%d\t%s\t%g\t%g\t%g\t%g\t%g\n" % (
i,
imagefile,
d.alt() * 180.0 / pi,
d.az() * 180.0 / pi,
d.phi() * 180.0 / pi,
d.get_center_x(),
d.get_center_y(),
)
if options.removeDuplicates and isDuplicate(seenImages, imagefile, i):
print "%s: particle %d is a duplicate image, ignored" % (imagefile, i)
else:
alllines += [line]
else:
print 'WARNING: file "%s" does not exists' % (imagefile)
if len(alllines):
maxlen = 0
for l in alllines:
if len(l) > maxlen:
maxlen = len(l)
lstfp = open(output_lstfile, "w")
lstfp.write("#LSX\n#If you edit this file, you MUST rerun lstfast.py on it before using it!\n# %d\n" % (maxlen))
for l in alllines:
l = l.strip()
lstfp.write(l + " " * (maxlen - len(l) - 1) + "\n")
lstfp.close()
#!/usr/bin/env python import sys, os from math import pi import EMAN if len(sys.argv) != 3: print "%s: convert image orientation and center (in EMAN convention) stored in the image headers into a text file in MRC/IMIRS format/convention" % (sys.argv[0]) print "Usage: %s <input image file> <output ortcen file>" % (sys.argv[0]) sys.exit(1) imagefile = sys.argv[1] output_ortcen_file = sys.argv[2] imgnum, imgtype = EMAN.fileCount(imagefile) img = EMAN.EMData() img.readImage(imagefile, 0, 1) # read Header only imagesize = img.xSize() imagefile_prefix = os.path.splitext(output_ortcen_file)[0] outFile = open(output_ortcen_file, "w") e5fto2f = EMAN.Euler(1.0172219678978513677, pi, -pi/2) # rotation from 2fold to 5fold for i in range(imgnum): print "Working on image %d/%d\r" % (i, imgnum) , img.readImage(imagefile, i, 1) e = img.getEuler() e2 = e * e5fto2f; # use 2-fold view instead of 5-fold view as orientation origin
def getNumParticlesInStack(stackname):
import EMAN
numparticles = EMAN.fileCount(stackname)[0]
return numparticles
# create new list file with only good particles
if params['clean'] is True:
f = open(fsp, 'r')
lines = f.readlines()
f.close()
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
#!/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
if o in ("", "--tree"):
tree=a
if o in ("", "--treemem"):
treemem=a
indices = []
members = {}
if tree:
for l in open(tree,"r"):
indices.append(int(l.split()[0]))
if treemem:
mem = l.split()[1:]
members[indices[-1]] = []
for m in mem: members[indices[-1]].append(int(m))
else:
indices = range(EMAN.fileCount(sys.argv[1])[0])
img = EMAN.EMData()
pdb = open(sys.argv[2],"w")
for i in indices:
img.readImage(sys.argv[1],i,nodata=1)
alt=img.alt()
az=img.az()
phi=img.phi()
x=r*sin(alt)*cos(az)
y=r*sin(alt)*sin(az)
z=r*cos(alt)
#!/usr/bin/env python # by Wen Jiang 2005-12-9 # $Id: ctfcopy.py,v 1.1 2005/12/09 00:23:32 wjiang Exp $ import sys import EMAN usage = "Usage: %s <input image> <output image>" % (sys.argv[0]) if len(sys.argv) != 3: print usage sys.exit(1) n1 = EMAN.fileCount(sys.argv[1])[0] n2 = EMAN.fileCount(sys.argv[2])[0] if n1 != n2: print "ERROR: %d in %s != %d in %s" % (n1, sys.argv[1], n2, sys.argv[2]) sys.exit(1) d1 = EMAN.EMData() d2 = EMAN.EMData() for i in range(n1): d1.readImage(sys.argv[1],i,1) d2.readImage(sys.argv[2],i,1) if d1.hasCTF(): ctf = d1.getCTF() print "%d\t%g,%g,%g,%g,%g,%g,%g,%g,%g,%g,%g" % (i, ctf[0], ctf[1], ctf[2], ctf[3], ctf[4], ctf[5], ctf[6], ctf[7], ctf[8], ctf[9], ctf[10])
#!/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 main():
if sys.argv[-1].startswith("usefs="): sys.argv = sys.argv[:-1] # remove the runpar fileserver info
(options,args) = parse_command_line()
if not options.nolog and (not mpi or (mpi and mpi.rank==0)): EMAN.appinit(sys.argv)
inputParm = EMAN.ccmlInputParm()
sf = EMAN.XYData()
if options.sfFileName != "" :
readsf = sf.readFile(options.sfFileName)
if ((readsf == -1) and (options.verbose > 0)) :
print "The file of scattering factor does NOT exist"
inputParm.scateringFactor = sf
startNumOfRawImages = options.startNumOfRawImages
#endNumOfRawImages = options.endNumOfRawImages
refImageFileName = args[-1]
numOfRefImages = options.numOfRefImages
solutionFile = options.solutionFile
# write log info to .emanlog file so that eman program can browse the history
if not options.nolog and (not mpi or (mpi and mpi.rank==0)):
pid = EMAN.LOGbegin(sys.argv)
for f in args[0:-1]: EMAN.LOGInfile(pid,f)
EMAN.LOGReffile(pid,args[-1])
if options.solutionFile: EMAN.LOGOutfile(pid,options.solutionFile)
if options.listFile: EMAN.LOGOutfile(pid,options.listFile)
if options.mrcSolutionFile: EMAN.LOGOutfile(pid,options.mrcSolutionFile)
inputParm.sym = options.sym
inputParm.FFTOverSampleScale = options.FFTOverSampleScale
inputParm.pftStepSize = options.pftStepSize
inputParm.deltaR = options.deltaR
inputParm.RMin = options.RMin
inputParm.RMax = options.RMax
inputParm.searchMode = options.searchMode
inputParm.scalingMode = options.scalingMode
inputParm.residualMode = options.residualMode
inputParm.weightMode = options.weightMode
# inputParm.rawImageFN will be set later
inputParm.refImagesFN = refImageFileName
inputParm.rawImageIniParmFN = options.rawImageIniParmFN
inputParm.rawImagePhaseCorrected = options.phasecorrected
inputParm.maxNumOfRun = options.maxNumOfRun
inputParm.zScoreCriterion = options.zScoreCriterion
inputParm.residualCriterion = options.residualCriterion
inputParm.solutionCenterDiffCriterion = options.solutionCenterDiffCriterion
inputParm.solutionOrientationDiffCriterion = options.solutionOrientationDiffCriterion/180.0*pi
inputParm.maxNumOfIteration = options.maxNumOfIteration
inputParm.numOfRandomJump = options.numOfRandomJump
inputParm.numOfFastShrink = options.numOfFastShrink
inputParm.numOfStartConfigurations = options.numOfStartConfigurations
inputParm.orientationSearchRange = options.orientationSearchRange/180.0*pi
inputParm.centerSearchRange = options.centerSearchRange
inputParm.numOfRefImages = options.numOfRefImages
inputParm.refEulerConvention = options.refEulerConvention
#maskR = options.maskR
#if (maskR<=0): maskR = refImageSizeY/2
inputParm.verbose = options.verbose
verbose = options.verbose
#verboseSolution = options.verboseSolution
updataHeader = options.updataHeader
solutionFile = options.solutionFile
mrcSolutionFile = options.mrcSolutionFile
iniCenterOrientationMode = options.iniCenterOrientationMode
refCenterOrientationMode = options.refCenterOrientationMode
rawImages = []
if not mpi or (mpi and mpi.rank==0):
for imgfile in args[0:-1]:
imgnum = EMAN.fileCount(imgfile)[0]
for i in range(imgnum): rawImages.append((imgfile, i))
if mpi: rawImages = mpi.bcast(rawImages)
endNumOfRawImages = options.endNumOfRawImages
if endNumOfRawImages <=0 or endNumOfRawImages > len(rawImages):
endNumOfRawImages = len(rawImages)
numRawImages = endNumOfRawImages - startNumOfRawImages
if mpi:
ptclset = range(startNumOfRawImages + mpi.rank, endNumOfRawImages, mpi.size)
else:
ptclset = range(startNumOfRawImages, endNumOfRawImages)
solutions = []
rMask = options.rMask #mask size is given
if options.rMask <= 0 : rMask = refImageSizeY/2 #mask size = half image size
rMask1 = options.rMask1 #output tnf mask size is given
if options.rMask1 <= 0 : rMask1 = rMask #output tnf mask size = half image size
inputParm.rMask = rMask
inputParm.rMask1 = rMask1
rawImage = EMAN.EMData()
rawImage.getEuler().setSym(inputParm.sym) #set the symmetry of the raw partile
inputParm.rawImageFN = rawImages[0][0] #give the initial raw particle filename
print "start to prepare------"
rawImage.crossCommonLineSearchPrepare(inputParm) #prepare, create pseudo PFT of ref images
print "end to prepare------"
inputParm.rawImage = rawImage
#for rawImgSN in ptclset:
for index in range(len(ptclset)):
rawImgSN = ptclset[index]
inputParm.rawImageFN = rawImages[rawImgSN][0]
inputParm.thisRawImageSN = rawImages[rawImgSN][1]
if mpi: print "rank %d: %d in %d-%d (%d in %d-%d)" % (mpi.rank, rawImgSN, startNumOfRawImages, endNumOfRawImages, index, 0, len(ptclset))
#rawImage.readImage(rawImages[rawImgSN][0], rawImages[rawImgSN][1])
#rawImage.applyMask(rMask, 6) #apply mask type 6 [edge mean value] to raw image, center will be image center
#rawImage.getEuler().setSym("icos")
#if rawImage.hasCTF() == 1:
#ctfParm = rawImage.getCTF()
#inputParm.zScoreCriterion = options.zScoreCriterion + atan(abs(ctfParm[0])-1.5)/(pi/4) +0.59 #adjust zScore criterion -0.6 --> +1.2, 1.5, 2.0
#inputParm.numOfRefImages = int(min(numOfRefImages, max(numOfRefImages*exp(-(abs(ctfParm[0])/2.0-0.15))+0.5, 5.0))) # adjust maxNumOfRun, the min is 2
inputParm.thisRawImageSN = rawImgSN
solutionCenterDiffCriterion = inputParm.solutionCenterDiffCriterion
solutionOrientationDiffCriterion = inputParm.solutionOrientationDiffCriterion
#initialize Center And Orientation by ont of the following modes
if iniCenterOrientationMode == "iniparmfile" :
inputParm.initializeCenterAndOrientationFromIniParmFile() # need to set "refEulerConvention"
elif iniCenterOrientationMode == "headerfile" :
inputParm.initializeCenterAndOrientationFromParticle() # need to set "refEulerConvention"
else :
inputParm.initializeCenterAndOrientationFromRandom() # default is random orientation and physical center
#set the refence Center And Orientation by ont of the following modes
if refCenterOrientationMode == "iniparmfile" : inputParm.setRefCenterAndOrientationFromIniParmFile() # need to set "refEulerConvention"
elif refCenterOrientationMode == "headerfile" : inputParm.setRefCenterAndOrientationFromParticle() # need to set "refEulerConvention"
else : inputParm.setRefCenterAndOrientationFromInitializedParms() # default is copy the initial center and orientation
rawImage.crossCommonLineSearchReadRawParticle(inputParm) #create pseudo PFT of raw image
maxNumOfRun = inputParm.maxNumOfRun
outputParmList = []
numOfRun = 0
passAllConsistencyCriteria = 0
while (numOfRun < maxNumOfRun) or (len(outputParmList) < 2):
if (iniCenterOrientationMode != "iniparmfile") and (iniCenterOrientationMode != "headerfile") :
inputParm.initializeCenterAndOrientationFromRandom() # default is random orientation and physical center
if (refCenterOrientationMode != "iniparmfile") and (refCenterOrientationMode != "headerfile") :
inputParm.setRefCenterAndOrientationFromInitializedParms() # default is copy the initial center and orientation
numOfRun = numOfRun + 1
print "numOfRun = ", numOfRun
############################################################################
############ execute cross common line search for reference ################
############################################################################
outputParm = rawImage.crossCommonLineSearch(inputParm)
############################################################################
# pass criteria check
outputParmList.append(outputParm) #if passed criteria, e.g. zscore, residualThreshold, etc
############################################################################
outputParmList.sort(lambda x, y: cmp(x.residual, y.residual))
############################################################################
########################## consistency check ###############################
############################################################################
#passConsistencyCriteria = 0
finalOutputParmList = []
lowestResidualList = []
lengthOfList = len(outputParmList)
if lengthOfList < 2 : continue
for i in range(lengthOfList-1):
thisOutputParm = outputParmList[i]
numOfPairsPassConsistencyCheck = 0
for j in range(i+1,lengthOfList):
refOutputParm = outputParmList[j]
tmpOutputParm = EMAN.ccmlOutputParm() #create a new output parm object
tmpOutputParm.rawImageSN = thisOutputParm.rawImageSN #copy all paramenters
tmpOutputParm.residual = thisOutputParm.residual
tmpOutputParm.sigma = thisOutputParm.sigma
tmpOutputParm.verbose = thisOutputParm.verbose
tmpOutputParm.zScore = thisOutputParm.zScore
tmpOutputParm.zScoreCriterion = thisOutputParm.zScoreCriterion
tmpOutputParm.passAllCriteria = 0
tmpOutputParm.setCalculatedCenterAndOrientation(thisOutputParm.cx,thisOutputParm.cy,thisOutputParm.q)
tmpOutputParm.setRefCenterAndOrientation(refOutputParm.cx, refOutputParm.cy, refOutputParm.q)
tmpOutputParm.calculateDifferenceWithRefParm() #calculated the difference
centerDiff = tmpOutputParm.centerDiff
orientationDiff = tmpOutputParm.orientationDiff
##### FLIP CASE : if no consistency found, try flip this orientation
if ((centerDiff > solutionCenterDiffCriterion) or (orientationDiff > solutionOrientationDiffCriterion)) :
quatFlip = EMAN.Quaternion(refOutputParm.q.getEuler().alt(), refOutputParm.q.getEuler().az(), refOutputParm.q.getEuler().phi()+pi)
tmpOutputParm.setRefCenterAndOrientation(refOutputParm.cx, refOutputParm.cy, quatFlip)
tmpOutputParm.calculateDifferenceWithRefParm() #calculated the difference
centerDiff = tmpOutputParm.centerDiff
orientationDiff = tmpOutputParm.orientationDiff
tmpOutputParm.setRefCenterAndOrientation(refOutputParm.cx, refOutputParm.cy, refOutputParm.q) #set back the exact orientation of reference
#Save the configurations with lowest residuals
if (i<3) and (j==i+1) : lowestResidualList.append(tmpOutputParm)
#make the good/answers list
if ((centerDiff < solutionCenterDiffCriterion) and (orientationDiff < solutionOrientationDiffCriterion)) :
numOfPairsPassConsistencyCheck += 1
if numOfPairsPassConsistencyCheck == 1 : #save to the final list
tmpOutputParm.passAllCriteria = 1
finalOutputParmList.append(tmpOutputParm)
if i==0 and numOfPairsPassConsistencyCheck >= options.numConsistentRun: #if the first one, check whether it has 3 pair of consistencies
passAllConsistencyCriteria = 1
break
if i>0 : break #if not the first one, find one pair of consistency, then break
#no break here, just for saving all possible solutions
if passAllConsistencyCriteria and len(finalOutputParmList) >= options.numConsistentRun: break #if 3 consistent pair orientations were found, then stop
rawImage.crossCommonLineSearchReleaseParticle(inputParm) # release the memory related to this raw particle
# if no consistency found, keep the lowest ones as output
if len(finalOutputParmList) == 0 : finalOutputParmList = lowestResidualList
for i in range(len(finalOutputParmList)) :
if passAllConsistencyCriteria : finalOutputParmList[i].passAllCriteria = 1
else : finalOutputParmList[i].passAllCriteria = 0
if options.solutionFile:
for i in range(len(finalOutputParmList)) : finalOutputParmList[i].outputResult(solutionFile)
outputParm = finalOutputParmList[0] #just use the lowest residual as regular output
if outputParm.passAllCriteria: passfail = "pass"
else: passfail = "fail"
print "Final result: euler=%g\t%g\t%g\tcenter=%g\t%g\tresidue=%g\t%s" % (outputParm.alt*180/pi, outputParm.az*180/pi, outputParm.phi*180/pi, outputParm.cx, outputParm.cy, outputParm.residual, passfail)
if options.scoreFile:
rawImage.readImage(rawImages[rawImgSN][0], rawImages[rawImgSN][1], 1) # read header only
if rawImage.hasCTF():
defocus = rawImage.getCTF()[0]
else:
defocus = 0
solution = (rawImages[rawImgSN][0], rawImages[rawImgSN][1], outputParm.alt, outputParm.az, outputParm.phi, \
outputParm.cx, outputParm.cy, defocus, outputParm.residual, outputParm.passAllCriteria)
solutions.append( solution )
sys.stdout.flush()
rawImage.crossCommonLineSearchFinalize(inputParm) #finalize, i.e. delete memories
if mpi:
if options.verbose:
print "rank %d: done and ready to output" % (mpi.rank)
sys.stdout.flush()
mpi.barrier()
#print "rank %d: %s" % (mpi.rank, solutions)
if mpi.rank==0:
for r in range(1,mpi.size):
msg, status = mpi.recv(source = r, tag = r)
solutions += msg
def ptcl_cmp(x, y):
eq = cmp(x[0], y[0])
if not eq: return cmp(x[1],y[1])
else: return eq
solutions.sort(ptcl_cmp)
else:
mpi.send(solutions, 0, tag = mpi.rank)
if not mpi or (mpi and mpi.rank==0):
if options.scoreFile:
sFile = open(options.scoreFile, "w")
sFile.write("#LST\n")
for i in solutions:
if i[-1]:
sFile.write("%d\t%s\tdefocus=%g\tresidual=%g\n" % (i[1], i[0], i[7], i[8]))
sFile.close()
if options.listFile:
lFile = open(options.listFile, "w")
lFile.write("#LST\n")
for i in solutions:
if i[-1]:
lFile.write("%d\t%s\t%g\t%g\t%g\t%g\t%g\n" % (i[1], i[0], i[2]*180.0/pi, i[3]*180.0/pi, i[4]*180.0/pi, i[5], i[6]))
lFile.close()
if options.mrcSolutionFile:
outFile = open(options.mrcSolutionFile, "w")
for i in solutions:
if i[-1]:
#rawImage.readImage(i[0], i[1], 1)
rawImage.readImage(i[0], i[1])
thisEu = EMAN.Euler(i[2], i[3], i[4])
thisEu.convertToMRCAngle()
alt = thisEu.alt_MRC()*180.0/pi
az = thisEu.az_MRC()*180.0/pi
phi = thisEu.phi_MRC()*180.0/pi
cx = i[5]
cy = i[6]
dx = cx - rawImage.xSize()/2
dy = cy - rawImage.ySize()/2
rawImage.applyMask(rMask1,6,dx,dy,0) #apply mask type 4 [outside=0] to raw image, center will be the solved center
#tnfFileName = "%s-%d.tnf" % (os.path.basename(os.path.splitext(rawImages[rawImgSN][0])[0]), rawImages[rawImgSN][1])
prefix = os.path.dirname(options.mrcSolutionFile).replace(" ", "")
if prefix != "" : prefix = prefix + "/"
tnfFileName = "%s%s-%d.tnf" % (prefix,os.path.basename(os.path.splitext(i[0])[0]), i[1])
rawFFT = rawImage.doFFT()
rawFFT.writeImage(tnfFileName,0) #tnf file no header information, it is a pure FFT of raw image file
outFile.write("%s\n" % (os.path.abspath(tnfFileName)))
outFile.write(" %d, %.4f, %.4f, %.4f, %.4f, %.4f, 0.0\n" % (0, alt, az, phi, cy, cx))
outFile.close()
if updataHeader:
for i in solutions:
rawImage.readImage(i[0], i[1], 1)
if options.verbose:
cx = rawImage.get_center_x()
cy = rawImage.get_center_y()
alt = rawImage.alt()
az = rawImage.az()
phi = rawImage.phi()
print "Update header: %s %d\t%7.5f %7.5f %7.2f %7.2f %7.2f => %7.5f %7.5f %7.2f %7.2f %7.2f" % \
(i[0], i[1], alt*180.0/pi, az*180.0/pi, phi*180.0/pi, cx, cy, i[2]*180.0/pi, i[3]*180.0/pi, i[4]*180.0/pi, i[5], i[6])
rawImage.setRAlign(i[2], i[3], i[4])
rawImage.set_center_x(i[5])
rawImage.set_center_y(i[6])
imgtype = EMAN.EMData.ANY
rawImage.writeImage(i[0], i[1], imgtype, 1)
if not options.nolog and (not mpi or (mpi and mpi.rank==0)): EMAN.LOGend()
def parse_command_line():
usage = "Usage: %prog <raw image filename> <ref 3D map> [options]"
parser = OptionParser(usage=usage)
parser.add_option("--mask", dest="mask", type="int", help="mask radius. default to half image size", default=0)
parser.add_option("--verbose", dest="verbose", type="int", help="verbose level [0-2]. default to 1", default=1)
parser.add_option(
"--phasecorrected",
dest="phasecorrected",
action="store_true",
help="if the particle images already phase flipped. default to false",
default=0,
)
parser.add_option("--sf", dest="sffile", type="string", help="structural factor ile name", default="")
parser.add_option(
"--startSym", dest="startSym", type="string", help="starting symmetry, default to icos", default="icos"
)
parser.add_option("--endSym", dest="endSym", type="string", help="ending symmetry, default to c1", default="c1")
parser.add_option("--first", dest="first", type="int", help="first image index", default=0)
parser.add_option("--last", dest="last", type="int", help="last image index", default=0)
parser.add_option(
"--shrink", dest="shrink", type="float", help="shrink factor, can only be 1.5 or >1 integer", default=1
)
parser.add_option(
"--score",
metavar="['ncccmp', 'lcmp', 'pcmp', 'fsccmp', 'wfsccmp']",
dest="scorefunc",
type="choice",
choices=["ncccmp", "lcmp", "pcmp", "fsccmp", "wfsccmp"],
help='scoring function to use. default to "fsccmp"',
default="fsccmp",
)
parser.add_option(
"--projection", dest="projection", type="string", help="output projection image filename", default=""
)
parser.add_option(
"--update_rawimage",
dest="update_rawimage",
type="string",
help="output image file name for the updated raw images",
default="",
)
parser.add_option(
"--cmplstfile",
dest="cmplstfile",
type="string",
help="output the lst file for comparing raw images and projections",
default="",
)
parser.add_option(
"--ortlstfile",
dest="ortlstfile",
type="string",
help="output the lst file for the new orientation/center parameters",
default="",
)
parser.add_option(
"--nocmdlog", dest="nocmdlog", action="store_true", help="don't log command, disabled by default", default=0
)
(options, args) = parser.parse_args()
if len(args) != 2:
parser.print_help()
sys.exit(-1)
if options.sffile and not os.path.exists(options.sffile):
print 'ERROR: sffile "%s" does not exist' % (options.sffile)
sys.exit()
if options.cmplstfile and not options.projection:
print '"--projection" options must be set for "--cmplstfile" to work'
options.cmplstfile = ""
if options.mask <= 0:
d = EMAN.EMData()
d.readImage(args[0], 0) # header only
imagesize = d.ySize()
options.mask = imagesize / 2
if options.first < 0 or options.last <= 0 or options.first >= options.last:
imgnum = EMAN.fileCount(args[0])
if options.first < 0:
options.first = 0
if options.last <= 0 or options.first >= options.last:
options.first = imgnum
return (options, args[0], args[1])
# create new list file with only good particles
if params['clean'] is True:
f=open(fsp,'r')
lines=f.readlines()
f.close()
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
def getNumParticlesInStack(stackname):
import EMAN
numparticles = EMAN.fileCount(stackname)[0]
return numparticles
def main():
(options, rawimage) = parse_command_line()
pid = EMAN.LOGbegin(sys.argv)
EMAN.LOGInfile(pid, rawimage)
imagenum = EMAN.fileCount(rawimage)[0]
for iter in range(options.iters):
projfile = "proj.%d.hdf" % (iter+1)
cmplstfile = "cmp.%d.lst" % (iter+1)
ortlstfile = "ort.%d.lst" % (iter+1)
mapfile = "threed.%da.mrc" % (iter)
mapfile2 = "threed.%da.mrc" % (iter+1)
if options.eotest:
mapfile2e = "threed.%da.e.mrc" % (iter+1)
mapfile2o = "threed.%da.o.mrc" % (iter+1)
subsetlste = "ort.%d.e.lst" % (iter+1)
subsetlsto = "ort.%d.o.lst" % (iter+1)
fscfile = "fsc.%d.txt" % (iter+1)
else:
mapfile2e = None
mapfile2o = None
subsetlste = None
subsetlsto = None
fscfile = None
if not os.path.exists(mapfile):
print "ERROR: cannot find 3D map \"%s\"" % (mapfile)
sys.exit()
else:
d = EMAN.EMData()
d.readImage(rawimage,0,1) # read header
rnx = d.xSize()
rny = d.ySize()
d.readImage(mapfile,-1,1) # read header
mnx = d.xSize()
mny = d.ySize()
mnz = d.zSize()
if rnx!=mnx or rny!=mny:
print "ERROR: raw images (%s) sizes (%dx%d) are different from the 3D map (%s) sizes (%dx%dx%d)" % (rawimage, rnx, rny, mapfile, mnx, mny, mnz)
sys.exit()
if not os.path.exists(cmplstfile):
runpar_file = "runpar.%d.ortcen.txt" % (iter+1)
n = imagenum/options.batchsize
if imagenum%n: n+=1
if n<options.cpus:
n=options.cpus
options.batchsize=imagenum/n+1
if options.batchsize==1:
n = imagenum
options.batchsize=1
num_tries = 0
max_tries = 3
while not os.path.exists(ortlstfile) and num_tries < max_tries:
runparfp = open(runpar_file, "w")
num_tries += 1
todo_num = 0
sublstfiles = []
cmpsublstfiles = []
for i in range(n):
cmplstfile_tmp = "cmp.%d.%d.lst" % (iter+1, i)
ortlstfile_tmp = "ort.%d.%d.lst" % (iter+1, i)
startNum = i * options.batchsize
endNum = (i+1) * options.batchsize
if startNum>=imagenum: break
if endNum>imagenum: endNum=imagenum
sublstfiles.append(ortlstfile_tmp)
cmpsublstfiles.append(cmplstfile_tmp)
if os.path.exists(ortlstfile_tmp): continue
else: todo_num += 1
cmd = "symrelax.py %s %s " % (rawimage, mapfile)
if options.sffile: cmd += "--sf=%s " % ( options.sffile )
if options.phasecorrected: cmd += "--phasecorrected "
cmd += "--verbose=%d " % (options.verbose )
cmd += "--mask=%d " % (options.mask)
cmd += "--startSym=%s " % (options.startSym)
cmd += "--endSym=%s " % (options.endSym)
cmd += "--first=%d --last=%d " % (startNum, endNum)
cmd += "--shrink=%d " % (options.shrink)
cmd += "--ortlstfile=%s " % (ortlstfile_tmp)
cmd += "--score=%s " % (options.scorefunc)
if options.saveprojection:
cmd += "--projection=%s " % (projfile)
cmd += "--cmplstfile=%s " % (cmplstfile_tmp)
if i: cmd += "--nocmdlog "
if i == 0: print cmd
runparfp.write("%s\n" % (cmd))
runparfp.close()
if todo_num:
cmd = "runpar proc=%d,%d file=%s" % (options.cpus, options.cpus, runpar_file)
print cmd
os.system(cmd)
#now merge all sublst file
# first test if all jobs are done properly
done = 1
for lstfile_tmp in sublstfiles:
if not os.path.exists(lstfile_tmp): done = 0
if done:
EMAN.merge_lstfiles(sublstfiles, ortlstfile, delete_lstfiles = 1)
# pool the cmplstfiles
if options.saveprojection:
EMAN.merge_lstfiles(cmpsublstfiles, cmplstfile, delete_lstfiles = 1)
if not os.path.exists(ortlstfile) or (os.path.exists(ortlstfile) and os.path.getsize(ortlstfile)<=5):
print "ERROR: raw image new orientation results lst file \"%s\" is not generated properly" % (ortlstfile)
sys.exit()
if not os.path.exists(mapfile2):
reconstruction_by_make3d(ortlstfile, mapfile2, options=options, mapfile2e=mapfile2e, mapfile2o=mapfile2o, fscfile=fscfile)
if not (os.path.exists(mapfile2) and os.path.getsize(mapfile2)):
print "ERROR: 3D map \"%s\" is not generated properly" % (mapfile2)
sys.exit()
EMAN.LOGend()
nbasis=20
mask=-1
for i in argv[3:] :
# s=i.split('=')
s=string.split(i,'=')
if (s[0]=="n") : nbasis=int(s[1])
elif (s[0]=="mask") : mask=int(s[1])
else:
print "Unknown argument ",i
exit(1)
EMAN.LOGbegin(argv)
n=EMAN.fileCount(argv[1])
if (n<2) :
print("Umm... I'd really be happier if the input file had at least 2 images...")
sys.exit(1)
nbasis=min(n,nbasis)
print "%d source images to consider\nGenerating %d basis images\n"%(n,nbasis)
basis=[EMAN.EMData()] # the actual basis vectors
basisn=[0] # list of the input image number used to generate each basis vector
basis[0].readImage(argv[1],0)
basis[0].realFilter(30) # 'true' normalization. We'll use this a lot
nx=basis[0].xSize()
da=atan2(1.0,nx/2.0) # da represents 1 pixel at the edge of the image
orig=EMAN.EMData()
# 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()
for i in argv[3:] :
# s=i.split('=')
s=string.split(i,'=')
if (s[0]=="maxbend") : maxbend=float(s[1])
else:
print "Unknown argument ",i
exit(1)
d=EMAN.EMData()
# get info from first 'particle' image
d.readImage(argv[1],0,1)
nx=d.xSize()
ny=d.ySize()
nptcl=EMAN.fileCount(argv[1])[0]
# Get references
refs=EMAN.readImages(argv[2],-1,-1)
nxr=refs[0].xSize()
nyr=refs[0].ySize()
nref=len(refs)
# initialize class files
for im in refs:
ind=refs.index(im)
try:
unlink("cls%04d.hed"%ind)
unlink("cls%04d.img"%ind)
except:
pass