def xmippNormStack(self, inStackPath, outStackPath):
### convert stack into single spider files
selfile = apXmipp.breakupStackIntoSingleFiles(inStackPath)
### setup Xmipp command
xmippexe = apParam.getExecPath("xmipp_normalize", die=True)
apDisplay.printMsg("Using Xmipp to normalize particle stack")
normtime = time.time()
xmippopts = ( " "
+" -i %s"%os.path.join(self.params['rundir'],selfile)
+" -method Ramp "
+" -background circle %i"%(self.stack['boxsize']/self.params['bin']*0.4)
+" -remove_black_dust"
+" -remove_white_dust"
+" -thr_black_dust -%.2f"%(self.params['xmipp-norm'])
+" -thr_white_dust %.2f"%(self.params['xmipp-norm'])
)
xmippcmd = xmippexe+" "+xmippopts
apParam.runCmd(xmippcmd, package="Xmipp", verbose=True, showcmd=True)
normtime = time.time() - normtime
apDisplay.printMsg("Xmipp normalization time: "+apDisplay.timeString(normtime))
### recombine particles to a single imagic stack
tmpstack = "tmp.xmippStack.hed"
apXmipp.gatherSingleFilesIntoStack(selfile,tmpstack)
apFile.moveStack(tmpstack,outStackPath)
### clean up directory
apFile.removeFile(selfile)
apFile.removeDir("partfiles")
def start(self):
# Path of the stack
stackdata = apStack.getOnlyStackData(self.params['stackid'])
fn_oldstack = os.path.join(stackdata['path']['path'],
stackdata['name'])
# Convert the stack to Xmipp
apXmipp.breakupStackIntoSingleFiles(fn_oldstack)
# Run sort junk
cmd = "xmipp_sort_by_statistics -i partlist.sel"
apDisplay.printColor(cmd, "cyan")
proc = subprocess.Popen(cmd, shell=True)
proc.wait()
# Create sorted stack
apXmipp.gatherSingleFilesIntoStack("sort_junk.sel", "sorted.hed")
# Create average MRC
apStack.averageStack("sorted.hed")
# Remove intermediate stuff
#os.unlink("partlist.sel")
#shutil.rmtree("partfiles")
# Upload results
self.uploadResults()
time.sleep(1)
return
def xmippNormStack(self, inStackPath, outStackPath):
### convert stack into single spider files
selfile = apXmipp.breakupStackIntoSingleFiles(inStackPath)
### setup Xmipp command
xmippexe = apParam.getExecPath("xmipp_normalize", die=True)
apDisplay.printMsg("Using Xmipp to normalize particle stack")
normtime = time.time()
xmippopts = (" " +
" -i %s" % os.path.join(self.params['rundir'], selfile) +
" -method Ramp " + " -background circle %i" %
(self.stack['boxsize'] / self.params['bin'] * 0.4) +
" -remove_black_dust" + " -remove_white_dust" +
" -thr_black_dust -%.2f" % (self.params['xmipp-norm']) +
" -thr_white_dust %.2f" % (self.params['xmipp-norm']))
xmippcmd = xmippexe + " " + xmippopts
apParam.runCmd(xmippcmd, package="Xmipp", verbose=True, showcmd=True)
normtime = time.time() - normtime
apDisplay.printMsg("Xmipp normalization time: " +
apDisplay.timeString(normtime))
### recombine particles to a single imagic stack
tmpstack = "tmp.xmippStack.hed"
apXmipp.gatherSingleFilesIntoStack(selfile, tmpstack)
apFile.moveStack(tmpstack, outStackPath)
### clean up directory
apFile.removeFile(selfile)
apFile.removeDir("partfiles")
def start(self):
# Path of the stack
stackdata = apStack.getOnlyStackData(self.params['stackid'])
fn_oldstack = os.path.join(stackdata['path']['path'], stackdata['name'])
# Convert the stack to Xmipp
apXmipp.breakupStackIntoSingleFiles(fn_oldstack)
# Run sort junk
cmd = "xmipp_sort_by_statistics -i partlist.sel"
apDisplay.printColor(cmd, "cyan")
proc = subprocess.Popen(cmd, shell=True)
proc.wait()
# Create sorted stack
apXmipp.gatherSingleFilesIntoStack("sort_junk.sel","sorted.hed")
# Create average MRC
apStack.averageStack("sorted.hed")
# Remove intermediate stuff
#os.unlink("partlist.sel")
#shutil.rmtree("partfiles")
# Upload results
self.uploadResults()
time.sleep(1)
return
def applyEnvelopeAndCTF(self, stack):
### get defocus lists
numpart = self.params['projcount']
cut = int(numpart/80.0)+1
apDisplay.printMsg("%d particles per dot"%(cut))
if len(self.deflist1) == 0:
self.getListOfDefoci(numpart)
### break up particles
partlistdocfile = apXmipp.breakupStackIntoSingleFiles(stack, filetype="mrc")
t0 = time.time()
apDisplay.printMsg("Applying CTF and Envelop to particles")
### apply CTF using ACE2
ctfapplydocfile = self.applyCTFToDocFile(partlistdocfile)
### apply Envelop using ACE2
envelopdocfile = self.applyEnvelopToDocFile(ctfapplydocfile)
### correct CTF using ACE2
if self.params['ace2correct'] is True or self.params['ace2correct_rand'] is True:
ctfcorrectdocfile = self.correctCTFToDocFile(envelopdocfile)
else:
ctfcorrectdocfile = envelopdocfile
timeper = (time.time()-t0)/float(numpart)
apDisplay.printColor("Total time %s"%(apDisplay.timeString(time.time()-t0)), "green")
apDisplay.printColor("Time per particle %s"%(apDisplay.timeString(timeper)), "green")
### write corrected particle list to doc file
ctfpartlist = []
ctfpartlistfile = os.path.join(self.params['rundir'], "ctfpartlist.lst")
inf = open(ctfcorrectdocfile, 'r')
outf = open(ctfpartlistfile, "w")
for line in inf:
### get filename
filename = line.strip().split()[0]
if not os.path.isfile(filename):
apDisplay.printError("CTF and envelop apply failed")
ctfpartlist.append(filename)
outf.write(filename+"\t1\n")
inf.close()
outf.close()
### merge individual files into a common stack
ctfstack = os.path.join(self.params['rundir'], "ctfstack.hed")
apXmipp.gatherSingleFilesIntoStack(ctfpartlistfile, ctfstack, filetype="mrc")
if self.params['pad'] is True:
emancmd = "proc2d %s %s.clip.hed clip=%d,%d" % (ctfstack, ctfstack[:-4], self.params['box'], self.params['box'])
apParam.runCmd(emancmd, "EMAN")
shutil.move("%s.clip.hed" % ctfstack[:-4], "%s.hed" % ctfstack[:-4])
shutil.move("%s.clip.img" % ctfstack[:-4], "%s.img" % ctfstack[:-4])
return ctfstack, ctfpartlist
def applyEnvelopeAndCTF(self, stack):
### get defocus lists
numpart = self.params['projcount']
cut = int(numpart/80.0)+1
apDisplay.printMsg("%d particles per dot"%(cut))
if len(self.deflist1) == 0:
self.getListOfDefoci(numpart)
### break up particles
partlistdocfile = apXmipp.breakupStackIntoSingleFiles(stack, filetype="mrc")
t0 = time.time()
apDisplay.printMsg("Applying CTF and Envelop to particles")
### apply CTF using ACE2
ctfapplydocfile = self.applyCTFToDocFile(partlistdocfile)
### apply Envelop using ACE2
envelopdocfile = self.applyEnvelopToDocFile(ctfapplydocfile)
### correct CTF using ACE2
if self.params['ace2correct'] is True or self.params['ace2correct_rand'] is True:
ctfcorrectdocfile = self.correctCTFToDocFile(envelopdocfile)
else:
ctfcorrectdocfile = envelopdocfile
timeper = (time.time()-t0)/float(numpart)
apDisplay.printColor("Total time %s"%(apDisplay.timeString(time.time()-t0)), "green")
apDisplay.printColor("Time per particle %s"%(apDisplay.timeString(timeper)), "green")
### write corrected particle list to doc file
ctfpartlist = []
ctfpartlistfile = os.path.join(self.params['rundir'], "ctfpartlist.lst")
inf = open(ctfcorrectdocfile, 'r')
outf = open(ctfpartlistfile, "w")
for line in inf:
### get filename
filename = line.strip().split()[0]
if not os.path.isfile(filename):
apDisplay.printError("CTF and envelop apply failed")
ctfpartlist.append(filename)
outf.write(filename+"\t1\n")
inf.close()
outf.close()
### merge individual files into a common stack
ctfstack = os.path.join(self.params['rundir'], "ctfstack.hed")
apXmipp.gatherSingleFilesIntoStack(ctfpartlistfile, ctfstack, filetype="mrc")
if self.params['pad'] is True:
emancmd = "proc2d %s %s.clip.hed clip=%d,%d" % (ctfstack, ctfstack[:-4], self.params['box'], self.params['box'])
apParam.runCmd(emancmd, "EMAN")
shutil.move("%s.clip.hed" % ctfstack[:-4], "%s.hed" % ctfstack[:-4])
shutil.move("%s.clip.img" % ctfstack[:-4], "%s.img" % ctfstack[:-4])
return ctfstack, ctfpartlist
def createReferenceStack(self):
# Create a stack for the class averages at each level
Nlevels=len(glob.glob("part"+self.params['timestamp']+"_level_??_.sel"))
for level in range(Nlevels):
stack=[]
for f in glob.glob("part"+self.params['timestamp']+"_level_%02d_[0-9]*.xmp"%level):
stack.append(spider.read(f))
apImagicFile.writeImagic(stack, "part"+self.params['timestamp']+"_level_%02d_.hed"%level)
if self.params['align']:
apXmipp.gatherSingleFilesIntoStack("partlist.sel","alignedStack.hed")
return
def createReferenceStack(self):
# Create a stack for the class averages at each level
Nlevels = len(
glob.glob("part" + self.params['timestamp'] + "_level_??_.sel"))
for level in range(Nlevels):
stack = []
for f in glob.glob("part" + self.params['timestamp'] +
"_level_%02d_[0-9]*.xmp" % level):
stack.append(spider.read(f))
apImagicFile.writeImagic(
stack,
"part" + self.params['timestamp'] + "_level_%02d_.hed" % level)
if self.params['align']:
apXmipp.gatherSingleFilesIntoStack("partlist.sel",
"alignedStack.hed")
return
def putFilesInStack(self):
selfile = os.path.join(self.params["rundir"], "selfile.list")
stackfile = os.path.join(self.params["rundir"], "start.hed")
apXmipp.gatherSingleFilesIntoStack(selfile, stackfile, filetype="mrc")
return stackfile
def putFilesInStack(self):
selfile = os.path.join(self.params['rundir'], "selfile.list")
stackfile = os.path.join(self.params['rundir'], "start.hed")
apXmipp.gatherSingleFilesIntoStack(selfile, stackfile, filetype="mrc")
return stackfile