def runMaxlike(self):
stackdata = apStack.getOnlyStackData(self.params['stackid'])
apix = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
### process stack to local file
self.params['localstack'] = os.path.join(self.params['rundir'],
self.timestamp + ".hed")
proccmd = "proc2d " + stackfile + " " + self.params[
'localstack'] + " apix=" + str(apix)
if self.params['highpass'] > 1:
proccmd += " hp=" + str(self.params['highpass'])
if self.params['lowpass'] > 1:
proccmd += " lp=" + str(self.params['lowpass'])
apEMAN.executeEmanCmd(proccmd, verbose=True)
### convert stack into single spider files
self.partlistdocfile = apXmipp.breakupStackIntoSingleFiles(
self.params['localstack'])
### setup Xmipp command
aligntime = time.time()
xmippopts = (
" " + " -i " +
os.path.join(self.params['rundir'], self.partlistdocfile) +
" -nref 1 " + " -iter 10 " + " -o " +
os.path.join(self.params['rundir'], "part" + self.timestamp) +
" -fast -C 1e-18 ")
### angle step
if self.params['rotate'] is True:
xmippopts += " -psi_step 90 "
else:
xmippopts += " -psi_step 360 "
### convergence criteria
if self.params['converge'] == "fast":
xmippopts += " -eps 5e-3 "
elif self.params['converge'] == "slow":
xmippopts += " -eps 5e-8 "
else:
xmippopts += " -eps 5e-5 "
### mirrors
if self.params['mirror'] is True:
xmippopts += " -mirror "
if self.params['maxshift'] is not None:
xmippopts += " -max_shift %d " % (self.params['maxshift'])
### use single processor
xmippexe = apParam.getExecPath("xmipp_ml_align2d", die=True)
xmippcmd = xmippexe + " " + xmippopts
self.writeXmippLog(xmippcmd)
apEMAN.executeEmanCmd(xmippcmd, verbose=True, showcmd=True)
aligntime = time.time() - aligntime
apDisplay.printMsg("Alignment time: " +
apDisplay.timeString(aligntime))
### create a quick mrc
emancmd = "proc2d part" + self.timestamp + "_ref000001.xmp average.mrc"
apEMAN.executeEmanCmd(emancmd, verbose=True)
apFile.removeStack(self.params['localstack'])
apFile.removeFilePattern("partfiles/*")
def start(self):
### load parameters
runparams = self.readRunParameters()
### align references
self.alignReferences(runparams)
### create an aligned stack
self.createAlignedReferenceStack()
### read particles
self.lastiter = self.findLastIterNumber()
if self.params['sort'] is True:
self.sortFolder()
reflist = self.readRefDocFile()
partlist = self.readPartDocFile(reflist)
self.writePartDocFile(partlist)
### create aligned stacks
alignimagicfile = self.createAlignedStacks(partlist, runparams['localstack'])
apStack.averageStack(alignimagicfile)
### calculate resolution for each reference
apix = apStack.getStackPixelSizeFromStackId(runparams['stackid'])*runparams['bin']
self.calcResolution(partlist, alignimagicfile, apix)
### insert into databse
self.insertRunIntoDatabase(alignimagicfile, runparams)
self.insertParticlesIntoDatabase(runparams['stackid'], partlist)
apFile.removeStack(runparams['localstack'], warn=False)
rmcmd = "/bin/rm -fr partfiles/*"
apEMAN.executeEmanCmd(rmcmd, verbose=False, showcmd=False)
apFile.removeFilePattern("partfiles/*")
def runMaxlike(self):
stackdata = apStack.getOnlyStackData(self.params["stackid"])
apix = apStack.getStackPixelSizeFromStackId(self.params["stackid"])
stackfile = os.path.join(stackdata["path"]["path"], stackdata["name"])
### process stack to local file
self.params["localstack"] = os.path.join(self.params["rundir"], self.timestamp + ".hed")
proccmd = "proc2d " + stackfile + " " + self.params["localstack"] + " apix=" + str(apix)
if self.params["highpass"] > 1:
proccmd += " hp=" + str(self.params["highpass"])
if self.params["lowpass"] > 1:
proccmd += " lp=" + str(self.params["lowpass"])
apEMAN.executeEmanCmd(proccmd, verbose=True)
### convert stack into single spider files
self.partlistdocfile = apXmipp.breakupStackIntoSingleFiles(self.params["localstack"])
### setup Xmipp command
aligntime = time.time()
xmippopts = (
" "
+ " -i "
+ os.path.join(self.params["rundir"], self.partlistdocfile)
+ " -nref 1 "
+ " -iter 10 "
+ " -o "
+ os.path.join(self.params["rundir"], "part" + self.timestamp)
+ " -fast -C 1e-18 "
)
### angle step
if self.params["rotate"] is True:
xmippopts += " -psi_step 90 "
else:
xmippopts += " -psi_step 360 "
### convergence criteria
if self.params["converge"] == "fast":
xmippopts += " -eps 5e-3 "
elif self.params["converge"] == "slow":
xmippopts += " -eps 5e-8 "
else:
xmippopts += " -eps 5e-5 "
### mirrors
if self.params["mirror"] is True:
xmippopts += " -mirror "
if self.params["maxshift"] is not None:
xmippopts += " -max_shift %d " % (self.params["maxshift"])
### use single processor
xmippexe = apParam.getExecPath("xmipp_ml_align2d", die=True)
xmippcmd = xmippexe + " " + xmippopts
self.writeXmippLog(xmippcmd)
apEMAN.executeEmanCmd(xmippcmd, verbose=True, showcmd=True)
aligntime = time.time() - aligntime
apDisplay.printMsg("Alignment time: " + apDisplay.timeString(aligntime))
### create a quick mrc
emancmd = "proc2d part" + self.timestamp + "_ref000001.xmp average.mrc"
apEMAN.executeEmanCmd(emancmd, verbose=True)
apFile.removeStack(self.params["localstack"])
apFile.removeFilePattern("partfiles/*")
def start(self):
aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
boxsize = aligndata['boxsize']
apix = aligndata['pixelsize']
maskpixrad = self.params['maskrad']/apix
if maskpixrad*2 > boxsize-2:
apDisplay.printError("Mask radius is too big for boxsize: %d > %d"%(maskpixrad*2,boxsize-2))
apDisplay.printMsg("Mask radius and boxsize: %.1f < %d"%(maskpixrad*2,boxsize-2))
self.instack = os.path.join(aligndata['path']['path'], aligndata['imagicfile'])
outdata = "stack.data"
apXmipp.convertStackToXmippData(self.instack, outdata, maskpixrad,
boxsize, numpart=self.params['numpart']-1)
self.runKerdenSOM(outdata)
if apFile.stackSize(self.instack) > 3.0*(1024**3):
# Big stacks use eman
self.createMontageByEMAN()
binned = None
else:
binned = self.createMontageInMemory(apix)
self.insertKerDenSOM(binned=binned)
apFile.removeFile(outdata)
apFile.removeFilePattern("*.cod")
def convertStackToXmippData(instack, outdata, maskpixrad, boxsize, numpart=None):
"""
From http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Img2Data
This program applies a mask to a set of images.
This set is given by a selfile.
After applying the mask the result is storaged as a vector in the following format:
The first line indicates the dimension of the vectors and the number of vectors.
The rest of the lines are the feature vectors.
Each line is a vector and each column is a vectors' component (pixels values inside the mask).
"""
apDisplay.printMsg("Convert stack file to Xmipp data file")
maskfile = "circlemask.spi"
operations.createMask(maskfile, maskpixrad, boxsize)
partlistdocfile = breakupStackIntoSingleFiles(instack, numpart=numpart)
convertcmd = "xmipp_convert_img2data -i %s -mask %s -o %s"%(partlistdocfile, maskfile, outdata)
proc = subprocess.Popen(convertcmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE,)
proc.wait()
outfilesize = apFile.fileSize(outdata)
partfilesize = apFile.fileSize(partlistdocfile)
if outfilesize < 2*partfilesize:
apDisplay.printError("Outdata conversion did not work, data file smaller than docfile, %s < %s"
%(apDisplay.bytes(outfilesize), apDisplay.bytes(partfilesize)))
apFile.removeFilePattern("partfiles/*")
return outdata
def close(self):
"""
hack to override appionScript close
"""
#apDisplay.printMsg("Waiting 10 seconds for threads to complete")
#time.sleep(10)
if self.params['keepall'] is False and self.params['limit'] is None:
pattern = os.path.join(self.params['rundir'], self.params['sessionname']+'*.dwn.mrc')
apFile.removeFilePattern(pattern)
appionScript.AppionScript.close(self)
def renderAnimation(density, contour=None, zoom=1.0, sym=None, color=None,
silhouette=False, xvfb=False, name=None):
"""
create several snapshots and merge into animated GIF
"""
if isValidVolume(density) is False:
apDisplay.printError("Volume file is not valid")
### setup chimera params
if name is None:
os.environ['CHIMVOL'] = density
else:
### set chimera to use temp volume
os.environ['CHIMTEMPVOL'] = density
os.environ['CHIMVOL'] = name
os.environ['CHIMTYPE'] = 'animate'
if silhouette is True:
os.environ['CHIMSILHOUETTE'] = 'true'
else:
os.unsetenv('CHIMSILHOUETTE')
if sym is not None:
os.environ['CHIMSYM'] = sym
if contour is not None:
os.environ['CHIMCONTOUR'] = str(contour)
if color is not None:
colorstr = colorToString(color)
os.environ['CHIMCOLORS'] = colorstr
else:
colorstr = getColorString()
os.environ['CHIMCOLORS'] = colorstr
if zoom is not None:
os.environ['CHIMZOOM'] = str(zoom)
os.environ['CHIMIMGSIZE'] = "512"
### unused
#'CHIMBACK', 'CHIMIMGSIZE', 'CHIMIMGFORMAT', 'CHIMFILEFORMAT',
chimsnappath = getSnapPath()
apDisplay.printColor("running Chimera Animation for sym "+str(sym), "cyan")
runChimeraScript(chimsnappath, xvfb=xvfb)
image1 = os.environ['CHIMVOL']+".001.png"
if os.path.isfile(image1):
### merge into animated GIF
finalgif = density+".animate.gif"
imagemagickcmd1 = "convert -delay 10 -loop 15 "
images = glob.glob(density+".*[0-9][0-9].png")
images.sort()
imagestr = ""
for image in images:
imagestr += image+" "
imagemagickcmd1 += imagestr+finalgif
apFile.removeFile(finalgif)
proc = subprocess.Popen(imagemagickcmd1, shell=True)
proc.wait()
#if os.path.isfile(finalgif):
apFile.removeFilePattern(density+".*[0-9][0-9].png")
return
def createMontageByEMAN(self):
self.cluster_resolution = []
apDisplay.printMsg("Converting files")
### create crappy files
emancmd = ("proc2d " + self.instack +
" crap.mrc first=0 last=0 mask=1")
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
emancmd = ("proc2d crap.mrc crap.png")
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
files = glob.glob(self.timestamp + ".[0-9]*")
files.sort(self.sortFile)
montagecmd = ("montage -geometry +4+4 -tile %dx%d " %
(self.params['xdim'], self.params['ydim']))
stackname = "kerdenstack" + self.timestamp + ".hed"
count = 0
numclass = self.params['xdim'] * self.params['ydim']
i = 0
for listname in files:
i += 1
apDisplay.printMsg("%d of %d classes" % (i, len(files)))
#listname = self.timestamp+str(i)
if not os.path.isfile(listname) or apFile.fileSize(listname) < 1:
### create a ghost particle
emancmd = ("proc2d crap.mrc " + stackname + " ")
sys.stderr.write("skipping " + listname + "\n")
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
### create png
shutil.copy("crap.png", listname + ".png")
else:
### average particles
emancmd = ("proc2d %s %s list=%s average" %
(self.instack, stackname, listname))
apEMAN.executeEmanCmd(emancmd, showcmd=True, verbose=False)
### create mrc
emancmd = ("proc2d %s %s first=%d last=%d" %
(stackname, listname + ".mrc", count, count))
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
### create png
emancmd = ("proc2d %s %s" %
(listname + ".mrc", listname + ".png"))
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
### FIX ME: for now fill self.clsuter_sersolution with None, although it
### should be possible to calculate it if particle list exists like in createMontageInMemory
self.cluster_resolution.append(None)
montagecmd += listname + ".png "
count += 1
montagecmd += "montage.png"
apEMAN.executeEmanCmd(montagecmd, showcmd=True, verbose=False)
time.sleep(1)
apFile.removeFile("crap.mrc")
apFile.removeFile("crap.png")
apFile.removeFilePattern(self.timestamp + ".*.png")
def close(self):
"""
hack to override appionScript close
"""
#apDisplay.printMsg("Waiting 10 seconds for threads to complete")
#time.sleep(10)
if self.params['keepall'] is False and self.params['limit'] is None:
pattern = os.path.join(self.params['rundir'],
self.params['sessionname'] + '*.dwn.mrc')
apFile.removeFilePattern(pattern)
appionScript.AppionScript.close(self)
def createMontageByEMAN(self):
self.cluster_resolution = []
apDisplay.printMsg("Converting files")
### create crappy files
emancmd = ( "proc2d "+self.instack+" crap.mrc first=0 last=0 mask=1" )
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
emancmd = ( "proc2d crap.mrc crap.png" )
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
files = glob.glob(self.timestamp+".[0-9]*")
files.sort(self.sortFile)
montagecmd = ("montage -geometry +4+4 -tile %dx%d "%(self.params['xdim'], self.params['ydim']))
stackname = "kerdenstack"+self.timestamp+".hed"
count = 0
numclass = self.params['xdim']*self.params['ydim']
i = 0
for listname in files:
i += 1
apDisplay.printMsg("%d of %d classes"%(i,len(files)))
#listname = self.timestamp+str(i)
if not os.path.isfile(listname) or apFile.fileSize(listname) < 1:
### create a ghost particle
emancmd = ( "proc2d crap.mrc "+stackname+" " )
sys.stderr.write("skipping "+listname+"\n")
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
### create png
shutil.copy("crap.png", listname+".png")
else:
### average particles
emancmd = ("proc2d %s %s list=%s average"%
(self.instack, stackname, listname))
apEMAN.executeEmanCmd(emancmd, showcmd=True, verbose=False)
### create mrc
emancmd = ("proc2d %s %s first=%d last=%d"%
(stackname, listname+".mrc", count, count))
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
### create png
emancmd = ("proc2d %s %s"%
(listname+".mrc", listname+".png"))
apEMAN.executeEmanCmd(emancmd, showcmd=False, verbose=False)
### FIX ME: for now fill self.clsuter_sersolution with None, although it
### should be possible to calculate it if particle list exists like in createMontageInMemory
self.cluster_resolution.append(None)
montagecmd += listname+".png "
count +=1
montagecmd += "montage.png"
apEMAN.executeEmanCmd(montagecmd, showcmd=True, verbose=False)
time.sleep(1)
apFile.removeFile("crap.mrc")
apFile.removeFile("crap.png")
apFile.removeFilePattern(self.timestamp+".*.png")
def postLoopFunctions(self):
### Delete CTF corrected images
if self.params['keepall'] is False:
pattern = os.path.join(self.params['rundir'], self.params['sessionname']+'*.dwn.mrc')
apFile.removeFilePattern(pattern)
### remove Ace2 images
pattern = os.path.join(self.params['rundir'], self.params['sessionname']+'*mrc.corrected.mrc')
apFile.removeFilePattern(pattern)
### remove Spider images
if self.params['fliptype'] == 'spiderimage':
pattern = os.path.join(self.params['rundir'], self.params['sessionname']+'*_out.spi')
apFile.removeFilePattern(pattern)
pattern = os.path.join(self.params['rundir'], self.params['sessionname']+'*_tf.spi')
apFile.removeFilePattern(pattern)
if self.noimages is True:
return
stackpath = os.path.join(self.params['rundir'], self.params['single'])
### delete this after testing
apStack.averageStack(stack = stackpath)
### Create Stack Mean Plot
if self.params['commit'] is True and self.params['meanplot'] is True:
stackid = apStack.getStackIdFromPath(stackpath)
if stackid is not None:
apStackMeanPlot.makeStackMeanPlot(stackid)
apDisplay.printColor("Timing stats", "blue")
self.printTimeStats("Batch Boxer", self.batchboxertimes)
self.printTimeStats("Ctf Correction", self.ctftimes)
self.printTimeStats("Stack Merging", self.mergestacktimes)
self.printTimeStats("Mean/Std Read", self.meanreadtimes)
self.printTimeStats("DB Insertion", self.insertdbtimes)
def convertStackToXmippData(instack,
outdata,
maskpixrad,
boxsize,
numpart=None):
"""
From http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Img2Data
This program applies a mask to a set of images.
This set is given by a selfile.
After applying the mask the result is storaged as a vector in the following format:
The first line indicates the dimension of the vectors and the number of vectors.
The rest of the lines are the feature vectors.
Each line is a vector and each column is a vectors' component (pixels values inside the mask).
"""
apDisplay.printMsg("Convert stack file to Xmipp data file")
maskfile = "circlemask.spi"
operations.createMask(maskfile, maskpixrad, boxsize)
partlistdocfile = breakupStackIntoSingleFiles(instack, numpart=numpart)
convertcmd = "xmipp_convert_img2data -i %s -mask %s -o %s" % (
partlistdocfile, maskfile, outdata)
proc = subprocess.Popen(
convertcmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
proc.wait()
outfilesize = apFile.fileSize(outdata)
partfilesize = apFile.fileSize(partlistdocfile)
if outfilesize < 2 * partfilesize:
apDisplay.printError(
"Outdata conversion did not work, data file smaller than docfile, %s < %s"
% (apDisplay.bytes(outfilesize), apDisplay.bytes(partfilesize)))
apFile.removeFilePattern("partfiles/*")
return outdata
def postLoopFunctions(self): pattern = os.path.join(self.params['rundir'], self.params['sessionname']+'*.corrected.mrc') apFile.removeFilePattern(pattern) ctfdb.printCtfSummary(self.params, self.imgtree)
def renderAnimation(density,
contour=None,
zoom=1.0,
sym=None,
color=None,
silhouette=False,
xvfb=False,
name=None):
"""
create several snapshots and merge into animated GIF
"""
if isValidVolume(density) is False:
apDisplay.printError("Volume file is not valid")
### setup chimera params
if name is None:
os.environ['CHIMVOL'] = density
else:
### set chimera to use temp volume
os.environ['CHIMTEMPVOL'] = density
os.environ['CHIMVOL'] = name
os.environ['CHIMTYPE'] = 'animate'
if silhouette is True:
os.environ['CHIMSILHOUETTE'] = 'true'
else:
os.unsetenv('CHIMSILHOUETTE')
if sym is not None:
os.environ['CHIMSYM'] = sym
if contour is not None:
os.environ['CHIMCONTOUR'] = str(contour)
if color is not None:
colorstr = colorToString(color)
os.environ['CHIMCOLORS'] = colorstr
else:
colorstr = getColorString()
os.environ['CHIMCOLORS'] = colorstr
if zoom is not None:
os.environ['CHIMZOOM'] = str(zoom)
os.environ['CHIMIMGSIZE'] = "512"
### unused
#'CHIMBACK', 'CHIMIMGSIZE', 'CHIMIMGFORMAT', 'CHIMFILEFORMAT',
chimsnappath = getSnapPath()
apDisplay.printColor("running Chimera Animation for sym " + str(sym),
"cyan")
runChimeraScript(chimsnappath, xvfb=xvfb)
image1 = os.environ['CHIMVOL'] + ".001.png"
if os.path.isfile(image1):
### merge into animated GIF
finalgif = density + ".animate.gif"
imagemagickcmd1 = "convert -delay 10 -loop 15 "
images = glob.glob(density + ".*[0-9][0-9].png")
images.sort()
imagestr = ""
for image in images:
imagestr += image + " "
imagemagickcmd1 += imagestr + finalgif
apFile.removeFile(finalgif)
proc = subprocess.Popen(imagemagickcmd1, shell=True)
proc.wait()
#if os.path.isfile(finalgif):
apFile.removeFilePattern(density + ".*[0-9][0-9].png")
return
def start(self):
self.stack = {}
self.stack['data'] = apStack.getOnlyStackData(self.params['stackid'])
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
self.stack['part'] = apStack.getOneParticleFromStackId(self.params['stackid'])
self.stack['boxsize'] = apStack.getStackBoxsize(self.params['stackid'])
self.stack['file'] = os.path.join(self.stack['data']['path']['path'], self.stack['data']['name'])
### test insert to make sure data is not overwritten
self.params['runtime'] = 0
#self.checkDuplicateRefBasedRun()
### set box size
self.boxsize = int(math.floor(self.stack['boxsize']/self.params['bin']/2.0))*2
### convert stack to spider
spiderstack = self.createSpiderFile()
### create template stack
templatestack = self.createTemplateStack()
### run the alignment
aligntime = time.time()
usestack = spiderstack
oldpartlist = None
for i in range(self.params['numiter']):
iternum = i+1
apDisplay.printColor("\n\nITERATION "+str(iternum), "green")
alignedstack, partlist = self.runAlignmentGPU(
usestack, templatestack, spiderstack,
self.params['xysearch'], self.params['xystep'],
self.params['firstring'], self.params['lastring'],
iternum=iternum, oldpartlist=oldpartlist)
oldpartlist = partlist
usestack = alignedstack
templatestack = self.updateTemplateStack(alignedstack, partlist, iternum)
aligntime = time.time() - aligntime
apDisplay.printMsg("Alignment time: "+apDisplay.timeString(aligntime))
### remove large, worthless stack
spiderstack = os.path.join(self.params['rundir'], "start.spi")
apDisplay.printMsg("Removing un-aligned stack: "+spiderstack)
apFile.removeFile(spiderstack, warn=True)
### convert aligned stack to imagic
finalspistack = "aligned.spi"
shutil.move(alignedstack, finalspistack)
imagicstack = "aligned.hed"
apFile.removeStack(imagicstack)
emancmd = "proc2d "+finalspistack+" "+imagicstack
apEMAN.executeEmanCmd(emancmd, verbose=True)
### average stack
apStack.averageStack(imagicstack)
### calculate resolution for each reference
apix = self.stack['apix']*self.params['bin']
self.calcResolution(partlist, imagicstack, apix)
if self.params['commit'] is True:
apDisplay.printMsg("committing results to DB")
self.params['runtime'] = aligntime
self.insertRefBasedRun(partlist, imagicstack, insert=True)
else:
apDisplay.printWarning("not committing results to DB")
### remove temporary files
apFile.removeFilePattern("alignments/alignedstack*.spi")
apFile.removeFile(finalspistack)
def createKerdenSOMPlots(self):
apFile.removeFilePattern(
os.path.join(self.params['rundir'],
self.spectraTemporalFilesMask + ".png"))
#logging.debug('Inside createKerdenSOMPlots')
apDisplay.printMsg("Create Plots")
codeVectorFileName = os.path.join(self.params['rundir'],
self.timestamp + '.cod')
f1 = open(codeVectorFileName, 'r')
#Read first line, I need number of harmonic plus size
line = f1.readline()
splitline = line.split()
numberHarmonic = int(splitline[0])
xx = int(splitline[2])
yy = int(splitline[3])
numberCodevectors = xx * yy
xmin = int(self.params['spectralowharmonic'])
xmax = int(self.params['spectrahighharmonic'])
#array with x and y values
xvalues = []
#fill x array with harmonic number
for colNo in pylab.arange(xmin, xmax + 1):
xvalues.append(colNo)
#figure size in inches
pylab.rcParams['figure.figsize'] = 1, 1
pylab.rc("lines", linewidth=1.5)
pylab.rc(('xtick', 'ytick', 'axes'), labelsize=4.0) #fontsize
#read code vector
#compute y maximum
ymax = 0.
ymin = 150.
for rowNo in range(numberCodevectors):
line = f1.readline()
splitLine = line.split()
for colNo in pylab.arange(numberHarmonic):
yval = float(splitLine[colNo])
if ymax < yval:
ymax = yval
if ymin > yval:
ymin = yval
f1.close()
ymax = math.ceil(ymax) + 1
print "ymax ", ymax
ymin = max(math.floor(ymin) - 1, 0)
print "ymin ", ymin
f1 = open(codeVectorFileName, 'r')
#skip first line
line = f1.readline()
for rowNo in range(numberCodevectors):
line = f1.readline()
splitLine = line.split()
#print line
data = []
for colNo in pylab.arange(numberHarmonic):
data.append(float(splitLine[colNo]))
print xvalues
print data
#clear previous plot
pylab.clf()
lines = pylab.plot(xvalues, data)
pylab.ylim(ymin, ymax)
pylab.xlim(xmin, xmax)
pylab.xlabel('fold symmetry')
pylab.ylabel('likelihood')
pylab.xticks(xvalues)
basefilename = os.path.join(
self.params['rundir'],
self.spectraTemporalFiles % (int(rowNo / yy), rowNo % xx))
pylab.savefig(basefilename + ".png", dpi=256, format='png')
def start(self):
#get aligned stack id
aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
xSizeVoxel = aligndata['boxsize']
#get averaged image
avgmrc = os.path.join(aligndata['path']['path'], aligndata["avgmrcfile"])
avg = mrc.read(avgmrc)
tmpSpiderFile="average.xmp"
spider.write(avg, tmpSpiderFile)
self.runFindCenter(tmpSpiderFile,xSizeVoxel)
#get aligned stack
alignStack = os.path.join(aligndata['path']['path'], aligndata["imagicfile"])
tempFileNameforSpectra=self.runMakeSpectra(alignStack)
#kerdensom will work with spectra output
self.runKerdenSOM(tempFileNameforSpectra)
self.createMontageInMemory()
self.insertRotKerDenSOM()
#apFile.removeFile(outdata)
apFile.removeFilePattern("*.cod")
apFile.removeFilePattern("*.err")
apFile.removeFilePattern("*.his")
apFile.removeFilePattern("*.inf")
apFile.removeFilePattern("*.vs")
apFile.removeFilePattern("*.xmp")
apFile.removeFile(tempFileNameforSpectra)
def start(self):
#get aligned stack id
aligndata = appiondata.ApAlignStackData.direct_query(
self.params['alignstackid'])
xSizeVoxel = aligndata['boxsize']
#get averaged image
avgmrc = os.path.join(aligndata['path']['path'],
aligndata["avgmrcfile"])
avg = mrc.read(avgmrc)
tmpSpiderFile = "average.xmp"
spider.write(avg, tmpSpiderFile)
self.runFindCenter(tmpSpiderFile, xSizeVoxel)
#get aligned stack
alignStack = os.path.join(aligndata['path']['path'],
aligndata["imagicfile"])
tempFileNameforSpectra = self.runMakeSpectra(alignStack)
#kerdensom will work with spectra output
self.runKerdenSOM(tempFileNameforSpectra)
self.createMontageInMemory()
self.insertRotKerDenSOM()
#apFile.removeFile(outdata)
apFile.removeFilePattern("*.cod")
apFile.removeFilePattern("*.err")
apFile.removeFilePattern("*.his")
apFile.removeFilePattern("*.inf")
apFile.removeFilePattern("*.vs")
apFile.removeFilePattern("*.xmp")
apFile.removeFile(tempFileNameforSpectra)
def createMontageInMemory(self, apix):
self.cluster_resolution = []
apDisplay.printMsg("Converting files")
### Set binning of images
boxsize = apImagicFile.getBoxsize(self.instack)
bin = 1
while boxsize/bin > 200:
bin+=1
binboxsize = boxsize/bin
### create averages
files = glob.glob(self.timestamp+".[0-9]*")
files.sort(self.sortFile)
montage = []
montagepngs = []
i = 0
for listname in files:
i += 1
apDisplay.printMsg("%d of %d classes"%(i,len(files)))
pngfile = listname+".png"
if not os.path.isfile(listname) or apFile.fileSize(listname) < 1:
### create a ghost particle
sys.stderr.write("skipping "+listname+"\n")
blank = numpy.ones((binboxsize, binboxsize), dtype=numpy.float32)
### add to montage stack
montage.append(blank)
self.cluster_resolution.append(None)
### create png
apImage.arrayToPng(blank, pngfile)
else:
### read particle list
partlist = self.readListFile(listname)
### average particles
partdatalist = apImagicFile.readParticleListFromStack(self.instack, partlist, boxsize, msg=False)
partdataarray = numpy.asarray(partdatalist)
finaldata = partdataarray.mean(0)
if bin > 1:
finaldata = apImage.binImg(finaldata, bin)
### add to montage stack
montage.append(finaldata)
res = apFourier.spectralSNR(partdatalist, apix)
self.cluster_resolution.append(res)
### create png
apImage.arrayToPng(finaldata, pngfile)
### check for png file
if os.path.isfile(pngfile):
montagepngs.append(pngfile)
else:
apDisplay.printError("failed to create montage")
stackname = "kerdenstack"+self.timestamp+".hed"
apImagicFile.writeImagic(montage, stackname)
### create montage
montagecmd = ("montage -geometry +4+4 -tile %dx%d "%(self.params['xdim'], self.params['ydim']))
for monpng in montagepngs:
montagecmd += monpng+" "
montagecmd += "montage.png"
apEMAN.executeEmanCmd(montagecmd, showcmd=True, verbose=False)
time.sleep(1)
apFile.removeFilePattern(self.timestamp+".*.png")
return bin
def createKerdenSOMPlots(self):
apFile.removeFilePattern(os.path.join(self.params['rundir'],self.spectraTemporalFilesMask + ".png"))
#logging.debug('Inside createKerdenSOMPlots')
apDisplay.printMsg("Create Plots")
codeVectorFileName = os.path.join(self.params['rundir'], self.timestamp+'.cod')
f1=open(codeVectorFileName,'r')
#Read first line, I need number of harmonic plus size
line=f1.readline()
splitline = line.split()
numberHarmonic = int(splitline[0])
xx = int(splitline[2])
yy = int(splitline[3])
numberCodevectors = xx * yy
xmin = int(self.params['spectralowharmonic'])
xmax = int(self.params['spectrahighharmonic'])
#array with x and y values
xvalues=[]
#fill x array with harmonic number
for colNo in pylab.arange(xmin,xmax+1):
xvalues.append(colNo)
#figure size in inches
pylab.rcParams['figure.figsize'] = 1, 1
pylab.rc("lines", linewidth=1.5)
pylab.rc(('xtick','ytick','axes'), labelsize=4.0)#fontsize
#read code vector
#compute y maximum
ymax = 0.
ymin = 150.
for rowNo in range(numberCodevectors):
line=f1.readline()
splitLine=line.split()
for colNo in pylab.arange(numberHarmonic):
yval = float(splitLine[colNo])
if ymax < yval:
ymax = yval
if ymin > yval:
ymin = yval
f1.close()
ymax = math.ceil(ymax)+1
print "ymax ", ymax
ymin = max(math.floor(ymin)-1,0)
print "ymin ", ymin
f1=open(codeVectorFileName,'r')
#skip first line
line=f1.readline()
for rowNo in range(numberCodevectors):
line=f1.readline()
splitLine=line.split()
#print line
data = []
for colNo in pylab.arange(numberHarmonic):
data.append(float(splitLine[colNo]))
print xvalues
print data
#clear previous plot
pylab.clf()
lines = pylab.plot(xvalues, data)
pylab.ylim(ymin, ymax)
pylab.xlim(xmin, xmax)
pylab.xlabel('fold symmetry')
pylab.ylabel('likelihood')
pylab.xticks(xvalues)
basefilename = os.path.join(self.params['rundir'], self.spectraTemporalFiles%(int(rowNo/yy),rowNo%xx))
pylab.savefig(basefilename+".png", dpi=256, format='png')
def start(self):
self.stack = {}
self.stack['data'] = apStack.getOnlyStackData(self.params['stackid'])
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
self.stack['part'] = apStack.getOneParticleFromStackId(self.params['stackid'])
self.stack['boxsize'] = apStack.getStackBoxsize(self.params['stackid'])
self.stack['file'] = os.path.join(self.stack['data']['path']['path'], self.stack['data']['name'])
### test insert to make sure data is not overwritten
self.params['runtime'] = 0
#self.checkDuplicateRefBasedRun()
### set box size
self.boxsize = int(math.floor(self.stack['boxsize']/self.params['bin']/2.0))*2
### convert stack to spider
spiderstack = self.createSpiderFile()
### create template stack
templatestack = self.createTemplateStack()
### run the alignment
aligntime = time.time()
usestack = spiderstack
oldpartlist = None
for i in range(self.params['numiter']):
iternum = i+1
apDisplay.printColor("\n\nITERATION "+str(iternum), "green")
alignedstack, partlist = self.runAlignmentGPU(
usestack, templatestack, spiderstack,
self.params['xysearch'], self.params['xystep'],
self.params['firstring'], self.params['lastring'],
iternum=iternum, oldpartlist=oldpartlist)
oldpartlist = partlist
usestack = alignedstack
templatestack = self.updateTemplateStack(alignedstack, partlist, iternum)
aligntime = time.time() - aligntime
apDisplay.printMsg("Alignment time: "+apDisplay.timeString(aligntime))
### remove large, worthless stack
spiderstack = os.path.join(self.params['rundir'], "start.spi")
apDisplay.printMsg("Removing un-aligned stack: "+spiderstack)
apFile.removeFile(spiderstack, warn=True)
### convert aligned stack to imagic
finalspistack = "aligned.spi"
shutil.move(alignedstack, finalspistack)
imagicstack = "aligned.hed"
apFile.removeStack(imagicstack)
emancmd = "proc2d "+finalspistack+" "+imagicstack
apEMAN.executeEmanCmd(emancmd, verbose=True)
### average stack
apStack.averageStack(imagicstack)
### calculate resolution for each reference
apix = self.stack['apix']*self.params['bin']
self.calcResolution(partlist, imagicstack, apix)
if self.params['commit'] is True:
apDisplay.printMsg("committing results to DB")
self.params['runtime'] = aligntime
self.insertRefBasedRun(partlist, imagicstack, insert=True)
else:
apDisplay.printWarning("not committing results to DB")
### remove temporary files
apFile.removeFilePattern("alignments/alignedstack*.spi")
apFile.removeFile(finalspistack)
def postLoopFunctions(self):
pattern = os.path.join(self.params['rundir'],
self.params['sessionname'] + '*.corrected.mrc')
apFile.removeFilePattern(pattern)
ctfdb.printCtfSummary(self.params, self.imgtree)