def checkConflicts(self):
self.rundata = apTomo.getFullTomoRunById(self.params["samplerunid"])
if self.rundata["method"] != "etomo":
apDisplay.printError("The fulltomoram run is not made for ETOMO manual reconstruction")
paramfile = os.path.join(self.rundata["path"]["path"], "%s_sample.params" % (self.rundata["runname"]))
sampleparams = apParam.readRunParameters(paramfile)
self.params["alignerid"] = sampleparams["alignerid"]
self.params["description"] = sampleparams["description"] + "\n" + self.params["description"]
self.params["method"] = self.rundata["method"]
self.params["runname"] = self.rundata["runname"]
self.params["rundir"] = self.rundata["path"]["path"]
def checkConflicts(self):
self.rundata = apTomo.getFullTomoRunById(self.params['samplerunid'])
if self.rundata['method'] != 'etomo':
apDisplay.printError(
'The fulltomoram run is not made for ETOMO manual reconstruction'
)
paramfile = os.path.join(
self.rundata['path']['path'],
'%s_sample.params' % (self.rundata['runname']))
sampleparams = apParam.readRunParameters(paramfile)
self.params['alignerid'] = sampleparams['alignerid']
self.params['description'] = sampleparams[
'description'] + '\n' + self.params['description']
self.params['method'] = self.rundata['method']
self.params['runname'] = self.rundata['runname']
self.params['rundir'] = self.rundata['path']['path']
def start(self):
### simple is written in Fortran, which cannot take inputs of certain length, therefore one needs
### to change to the directory to minimize the filename length, in particular for the stack
os.chdir(self.params['rundir'])
### stack needs to be centered
if self.params['no_center'] is False:
if os.path.isfile(os.path.join(self.params['rundir'], "ali.hed")):
apFile.removeStack(
os.path.join(self.params['rundir'], "ali.hed"))
centstack = os.path.join(self.params['rundir'], "ali.hed")
centcmd = "cenalignint %s > cenalignint.log" % (self.stack['file'])
apParam.runCmd(centcmd, "EMAN")
### process stack to local file
if self.params['timestamp'] is None:
apDisplay.printMsg("creating timestamp")
self.params['timestamp'] = self.timestamp
self.params['localstack'] = os.path.join(
self.params['rundir'], self.params['timestamp'] + ".spi")
if os.path.isfile(self.params['localstack']):
apFile.removeFile(self.params['localstack'])
if self.params['no_center'] is False:
proccmd = "proc2d " + centstack + " " + self.params[
'localstack'] + " apix=" + str(self.stack['apix'])
else:
proccmd = "proc2d " + self.stack['file'] + " " + self.params[
'localstack'] + " apix=" + str(self.stack['apix'])
if self.params['bin'] > 1 or self.params['clipsize'] is not None:
proccmd += " shrink=%d clip=%d,%d " % (self.params['bin'],
self.boxsize, self.boxsize)
proccmd += " last=" + str(self.params['numpart'] - 1)
proccmd += " spiderswap"
# if self.params['highpass'] is not None and self.params['highpass'] > 1:
# proccmd += " hp="+str(self.params['highpass'])
# if self.params['lowpass'] is not None and self.params['lowpass'] > 1:
# proccmd += " lp="+str(self.params['lowpass'])
apParam.runCmd(proccmd, "EMAN", verbose=True)
# if self.params['numpart'] != int(spider.getSpiderHeader(self.params['localstack'])[-2]):
# apDisplay.printError("Missing particles in stack")
### setup Simple command
aligntime = time.time()
simpleopts = (
"" + " stk=%s" % os.path.basename(self.params['localstack']) +
" box=%d" % self.boxsize + " nptcls=%d" % self.params['numpart'] +
" smpd=%.3f" % self.apix + " ring2=%d" % self.params['ring2'] +
" ncls=%d" % self.params['ncls'] +
" minp=%d" % self.params['minp'] +
" nvars=%d" % self.params['nvars'] +
" nthr=%d" % self.params['nproc'])
if self.params['no_kmeans'] is True:
simpleopts += " kmeans=off"
if self.params['nran'] is not None:
simpleopts += "nran=%d" % self.params['nran']
### SIMPLE 2D clustering
apDisplay.printColor(
"Using " + str(self.params['nproc']) + " processors!", "green")
simpleexe = apParam.getExecPath("cluster", die=True)
simplecmd = "%s %s" % (simpleexe, simpleopts)
self.writeSimpleLog(simplecmd)
apParam.runCmd(simplecmd,
package="SIMPLE",
verbose=True,
showcmd=True,
logfile="cluster.std")
self.params['runtime'] = time.time() - aligntime
apDisplay.printMsg("Alignment & Classification time: " +
apDisplay.timeString(self.params['runtime']))
### SIMPLE spider to Fourier format
clsavgs = "cavgstk.spi"
if not os.path.isfile(os.path.join(self.params['rundir'], clsavgs)):
apDisplay.printError(
"class averages were not created! try rerunning with centering, more particles, or less ppc"
)
try:
nptcls = spider.getSpiderHeader(clsavgs)[-2]
except:
nptcls = self.params['ncls']
apDisplay.printWarning(
"class average file may not have been created! Please check existence of file cavgstk.spi"
)
projfile = "projs"
projext = ".fim"
simpleexe = apParam.getExecPath("spi_to_fim", die=True)
simpleopts = ("" + " stk=%s" % clsavgs + " box=%d" % self.boxsize +
" nptcls=%d" % nptcls + " smpd=%.3f" % self.apix +
" outbdy=%s" % projfile +
" msk=%d" % self.params['mask'])
simplecmd = "%s %s" % (simpleexe, simpleopts)
self.writeSimpleLog(simplecmd)
apParam.runCmd(simplecmd,
package="SIMPLE",
verbose=True,
showcmd=True,
logfile="spi_to_fim.std")
### SIMPLE origami, ab initio 3D reconstruction
refinetime = time.time()
simpleexe = apParam.getExecPath("origami", die=True)
simpleopts = (
"" + " fstk=%s" % projfile + projext +
" froms=%d" % self.params['froms'] +
" tos=%d" % self.params['tos'] + " lp=%d" % self.params['lp'] +
" hp=%d" % self.params['hp'] +
" maxits=%d" % self.params['maxits'] +
" msk=%d" % self.params['mask'] + " mw=%d" % self.params['mw'] +
" frac=%.3f" % self.params['frac'] +
" amsklp=%d" % self.params['amsklp'] +
" edge=%d" % self.params['edge'] + " trs=%d" % self.params['trs'] +
" nthr=%d" % self.params['nproc'])
simplecmd = "%s %s" % (simpleexe, simpleopts)
self.writeSimpleLog(simplecmd)
apParam.runCmd(simplecmd,
package="SIMPLE",
verbose=True,
showcmd=True,
logfile="origami.std")
refinetime = time.time() - refinetime
apDisplay.printMsg("Origami reconstruction time: " +
apDisplay.timeString(refinetime))
# '''
### minor post-processing
self.clearIntermediateFiles()
apParam.dumpParameters(
self.params,
"simple-" + self.params['timestamp'] + "-params.pickle")
### upload results
self.runparams = apParam.readRunParameters("simple-" +
self.params['timestamp'] +
"-params.pickle")
### create average of aligned and clustered stacks, convert to IMAGIC
alignedStackSpi = "inplalgnstk.spi"
alignedStack = "inplalgnstk.hed"
if os.path.isfile(alignedStack):
apFile.removeStack(alignedStack)
emancmd = "proc2d %s %s flip" % (alignedStackSpi, alignedStack)
apParam.runCmd(emancmd, "EMAN")
clusterStackSpi = "cavgstk.spi"
clusterStack = "cavgstk.hed"
if os.path.isfile(clusterStack):
apFile.removeStack(clusterStack)
emancmd = "proc2d %s %s flip" % (clusterStackSpi, clusterStack)
apParam.runCmd(emancmd, "EMAN")
# apStack.averageStack(alignedStack)
### parse alignment and classification results
if self.params['no_center'] is False:
self.alignD = self.getAlignParameters(centparams="cenalignint.log")
else:
self.alignD = self.getAlignParameters()
if self.params['no_kmeans'] is False:
self.classD = self.getClassification("kmeans.spi", clusterStack)
else:
self.classD = self.getClassification("hcl.spi", clusterStack)
### upload to database
self.insertSIMPLEAlignParamsIntoDatabase()
self.insertAlignStackRunIntoDatabase(alignedStack, clusterStack)
self.calcResolution(alignedStack)
self.insertAlignParticlesIntoDatabase()
self.insertClusterRunIntoDatabase()
self.insertClusterStackIntoDatabase(clusterStack, len(self.classD))
self.insertSIMPLEOrigamiParamsIntoDatabase()
def start(self):
### simple is written in Fortran, which cannot take inputs of certain length, therefore one needs
### to change to the directory to minimize the filename length, in particular for the stack
os.chdir(self.params['rundir'])
### stack needs to be centered
if self.params['no_center'] is False:
if os.path.isfile(os.path.join(self.params['rundir'], "ali.hed")):
apFile.removeStack(os.path.join(self.params['rundir'], "ali.hed"))
centstack = os.path.join(self.params['rundir'], "ali.hed")
centcmd = "cenalignint %s > cenalignint.log" % (self.stack['file'])
apParam.runCmd(centcmd, "EMAN")
### process stack to local file
if self.params['timestamp'] is None:
apDisplay.printMsg("creating timestamp")
self.params['timestamp'] = self.timestamp
self.params['localstack'] = os.path.join(self.params['rundir'], self.params['timestamp']+".spi")
if os.path.isfile(self.params['localstack']):
apFile.removeFile(self.params['localstack'])
if self.params['no_center'] is False:
proccmd = "proc2d "+centstack+" "+self.params['localstack']+" apix="+str(self.stack['apix'])
else:
proccmd = "proc2d "+self.stack['file']+" "+self.params['localstack']+" apix="+str(self.stack['apix'])
if self.params['bin'] > 1 or self.params['clipsize'] is not None:
proccmd += " shrink=%d clip=%d,%d " % (self.params['bin'], self.boxsize, self.boxsize)
proccmd += " last="+str(self.params['numpart']-1)
proccmd += " spiderswap"
# if self.params['highpass'] is not None and self.params['highpass'] > 1:
# proccmd += " hp="+str(self.params['highpass'])
# if self.params['lowpass'] is not None and self.params['lowpass'] > 1:
# proccmd += " lp="+str(self.params['lowpass'])
apParam.runCmd(proccmd, "EMAN", verbose=True)
# if self.params['numpart'] != int(spider.getSpiderHeader(self.params['localstack'])[-2]):
# apDisplay.printError("Missing particles in stack")
### setup Simple command
aligntime = time.time()
simpleopts = (""
+" stk=%s" % os.path.basename(self.params['localstack'])
+" box=%d" % self.boxsize
+" nptcls=%d" % self.params['numpart']
+" smpd=%.3f" % self.apix
+" ring2=%d" % self.params['ring2']
+" ncls=%d" % self.params['ncls']
+" minp=%d" % self.params['minp']
+" nvars=%d" % self.params['nvars']
+" nthr=%d" % self.params['nproc']
)
if self.params['no_kmeans'] is True:
simpleopts += " kmeans=off"
if self.params['nran'] is not None:
simpleopts += "nran=%d" % self.params['nran']
### SIMPLE 2D clustering
apDisplay.printColor("Using "+str(self.params['nproc'])+" processors!", "green")
simpleexe = apParam.getExecPath("cluster", die=True)
simplecmd = "%s %s" % (simpleexe, simpleopts)
self.writeSimpleLog(simplecmd)
apParam.runCmd(simplecmd, package="SIMPLE", verbose=True, showcmd=True, logfile="cluster.std")
self.params['runtime'] = time.time() - aligntime
apDisplay.printMsg("Alignment & Classification time: "+apDisplay.timeString(self.params['runtime']))
### SIMPLE spider to Fourier format
clsavgs = "cavgstk.spi"
if not os.path.isfile(os.path.join(self.params['rundir'], clsavgs)):
apDisplay.printError("class averages were not created! try rerunning with centering, more particles, or less ppc")
try:
nptcls = spider.getSpiderHeader(clsavgs)[-2]
except:
nptcls = self.params['ncls']
apDisplay.printWarning("class average file may not have been created! Please check existence of file cavgstk.spi")
projfile = "projs"
projext = ".fim"
simpleexe = apParam.getExecPath("spi_to_fim", die=True)
simpleopts = (""
+" stk=%s" % clsavgs
+" box=%d" % self.boxsize
+" nptcls=%d" % nptcls
+" smpd=%.3f" % self.apix
+" outbdy=%s" % projfile
+" msk=%d" % self.params['mask']
)
simplecmd = "%s %s" % (simpleexe, simpleopts)
self.writeSimpleLog(simplecmd)
apParam.runCmd(simplecmd, package="SIMPLE", verbose=True, showcmd=True, logfile="spi_to_fim.std")
### SIMPLE origami, ab initio 3D reconstruction
refinetime = time.time()
simpleexe = apParam.getExecPath("origami", die=True)
simpleopts = (""
+" fstk=%s" % projfile+projext
+" froms=%d" % self.params['froms']
+" tos=%d" % self.params['tos']
+" lp=%d" % self.params['lp']
+" hp=%d" % self.params['hp']
+" maxits=%d" % self.params['maxits']
+" msk=%d" % self.params['mask']
+" mw=%d" % self.params['mw']
+" frac=%.3f" % self.params['frac']
+" amsklp=%d" % self.params['amsklp']
+" edge=%d" % self.params['edge']
+" trs=%d" % self.params['trs']
+" nthr=%d" % self.params['nproc']
)
simplecmd = "%s %s" % (simpleexe, simpleopts)
self.writeSimpleLog(simplecmd)
apParam.runCmd(simplecmd, package="SIMPLE", verbose=True, showcmd=True, logfile="origami.std")
refinetime = time.time() - refinetime
apDisplay.printMsg("Origami reconstruction time: "+apDisplay.timeString(refinetime))
# '''
### minor post-processing
self.clearIntermediateFiles()
apParam.dumpParameters(self.params, "simple-"+self.params['timestamp']+"-params.pickle")
### upload results
self.runparams = apParam.readRunParameters("simple-"+self.params['timestamp']+"-params.pickle")
### create average of aligned and clustered stacks, convert to IMAGIC
alignedStackSpi = "inplalgnstk.spi"
alignedStack = "inplalgnstk.hed"
if os.path.isfile(alignedStack):
apFile.removeStack(alignedStack)
emancmd = "proc2d %s %s flip" % (alignedStackSpi, alignedStack)
apParam.runCmd(emancmd, "EMAN")
clusterStackSpi = "cavgstk.spi"
clusterStack = "cavgstk.hed"
if os.path.isfile(clusterStack):
apFile.removeStack(clusterStack)
emancmd = "proc2d %s %s flip" % (clusterStackSpi, clusterStack)
apParam.runCmd(emancmd, "EMAN")
# apStack.averageStack(alignedStack)
### parse alignment and classification results
if self.params['no_center'] is False:
self.alignD = self.getAlignParameters(centparams="cenalignint.log")
else:
self.alignD = self.getAlignParameters()
if self.params['no_kmeans'] is False:
self.classD = self.getClassification("kmeans.spi", clusterStack)
else:
self.classD = self.getClassification("hcl.spi", clusterStack)
### upload to database
self.insertSIMPLEAlignParamsIntoDatabase()
self.insertAlignStackRunIntoDatabase(alignedStack, clusterStack)
self.calcResolution(alignedStack)
self.insertAlignParticlesIntoDatabase()
self.insertClusterRunIntoDatabase()
self.insertClusterStackIntoDatabase(clusterStack, len(self.classD))
self.insertSIMPLEOrigamiParamsIntoDatabase()
def start(self):
# self.insertCL2DJob()
self.stack = {}
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
self.stack['part'] = apStack.getOneParticleFromStackId(self.params['stackid'])
if self.params['virtualdata'] is not None:
self.stack['file'] = self.params['virtualdata']['filename']
else:
self.stack['file'] = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
### process stack to local file
if self.params['timestamp'] is None:
apDisplay.printMsg("creating timestamp")
self.params['timestamp'] = self.timestamp
self.params['localstack'] = os.path.join(self.params['rundir'], self.params['timestamp']+".hed")
if os.path.isfile(self.params['localstack']):
apFile.removeStack(self.params['localstack'])
a = proc2dLib.RunProc2d()
a.setValue('infile',self.stack['file'])
a.setValue('outfile',self.params['localstack'])
a.setValue('apix',self.stack['apix'])
a.setValue('bin',self.params['bin'])
a.setValue('last',self.params['numpart']-1)
if self.params['lowpass'] is not None and self.params['lowpass'] > 1:
a.setValue('lowpass',self.params['lowpass'])
if self.params['highpass'] is not None and self.params['highpass'] > 1:
a.setValue('highpass',self.params['highpass'])
if self.params['invert'] is True:
a.setValue('invert',True)
# clip not yet implemented
# if self.params['clipsize'] is not None:
# clipsize = int(self.clipsize)*self.params['bin']
# if clipsize % 2 == 1:
# clipsize += 1 ### making sure that clipped boxsize is even
# a.setValue('clip',clipsize)
if self.params['virtualdata'] is not None:
vparts = self.params['virtualdata']['particles']
plist = [int(p['particleNumber'])-1 for p in vparts]
a.setValue('list',plist)
#run proc2d
a.run()
if self.params['numpart'] != apFile.numImagesInStack(self.params['localstack']):
apDisplay.printError("Missing particles in stack")
### 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)
+" -codes "+str(self.params['numrefs'])
+" -iter "+str(self.params['maxiter'])
+" -o "+os.path.join(self.params['rundir'], "part"+self.params['timestamp'])
)
if self.params['fast']:
xmippopts += " -fast "
if self.params['correlation']:
xmippopts += " -useCorrelation "
if self.params['classical']:
xmippopts += " -classicalMultiref "
if self.params['align']:
xmippopts += " -alignImages "
### use multi-processor command
apDisplay.printColor("Using "+str(self.params['nproc'])+" processors!", "green")
xmippexe = apParam.getExecPath("xmipp_mpi_class_averages", die=True)
mpiruncmd = self.mpirun+" -np "+str(self.params['nproc'])+" "+xmippexe+" "+xmippopts
self.writeXmippLog(mpiruncmd)
apParam.runCmd(mpiruncmd, package="Xmipp", verbose=True, showcmd=True, logfile="xmipp.std")
self.params['runtime'] = time.time() - aligntime
apDisplay.printMsg("Alignment time: "+apDisplay.timeString(self.params['runtime']))
### minor post-processing
self.createReferenceStack()
self.parseOutput()
self.clearIntermediateFiles()
# self.readyUploadFlag()
apParam.dumpParameters(self.params, "cl2d-"+self.params['timestamp']+"-params.pickle")
### upload results ... this used to be two separate operations, I'm combining into one
self.runparams = apParam.readRunParameters("cl2d-"+self.params['timestamp']+"-params.pickle")
self.apix = apStack.getStackPixelSizeFromStackId(self.runparams['stackid'])*self.runparams['bin']
self.Nlevels=len(glob.glob("part"+self.params['timestamp']+"_level_??_.hed"))
### create average of aligned stacks & insert aligned stack info
lastLevelStack = "part"+self.params['timestamp']+"_level_%02d_.hed"%(self.Nlevels-1)
apStack.averageStack(lastLevelStack)
self.boxsize = apFile.getBoxSize(lastLevelStack)[0]
self.insertCL2DParamsIntoDatabase()
if self.runparams['align'] is True:
self.insertAlignStackRunIntoDatabase("alignedStack.hed")
self.calcResolution(self.Nlevels-1)
self.insertAlignParticlesIntoDatabase(level=self.Nlevels-1)
### loop over each class average stack & insert as clustering stacks
self.insertClusterRunIntoDatabase()
for level in range(self.Nlevels):
### NOTE: RESOLUTION CAN ONLY BE CALCULATED IF ALIGNED STACK EXISTS TO EXTRACT / READ THE PARTICLES
if self.params['align'] is True:
self.calcResolution(level)
partdict = self.getClassificationAtLevel(level)
for classnum in partdict:
self.insertClusterStackIntoDatabase(
"part"+self.params['timestamp']+"_level_%02d_.hed"%level,
classnum+1, partdict[classnum], len(partdict))
def start(self):
# self.insertCL2DJob()
self.stack = {}
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
self.stack['part'] = apStack.getOneParticleFromStackId(self.params['stackid'])
self.stack['boxsize'] = apStack.getStackBoxsize(self.params['stackid'])
if self.params['virtualdata'] is not None:
self.stack['file'] = self.params['virtualdata']['filename']
else:
self.stack['file'] = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
### process stack to local file
if self.params['timestamp'] is None:
apDisplay.printMsg("creating timestamp")
self.params['timestamp'] = self.timestamp
self.params['localstack'] = os.path.join(self.params['rundir'], self.params['timestamp']+".hed")
if os.path.isfile(self.params['localstack']):
apFile.removeStack(self.params['localstack'])
a = proc2dLib.RunProc2d()
a.setValue('infile',self.stack['file'])
a.setValue('outfile',self.params['localstack'])
a.setValue('apix',self.stack['apix'])
a.setValue('bin',self.params['bin'])
a.setValue('last',self.params['numpart']-1)
if self.params['lowpass'] is not None and self.params['lowpass'] > 1:
a.setValue('lowpass',self.params['lowpass'])
if self.params['highpass'] is not None and self.params['highpass'] > 1:
a.setValue('highpass',self.params['highpass'])
if self.params['invert'] is True:
a.setValue('invert',True)
# clip not yet implemented
# if self.params['clipsize'] is not None:
# clipsize = int(self.clipsize)*self.params['bin']
# if clipsize % 2 == 1:
# clipsize += 1 ### making sure that clipped boxsize is even
# a.setValue('clip',clipsize)
if self.params['virtualdata'] is not None:
vparts = self.params['virtualdata']['particles']
plist = [int(p['particleNumber'])-1 for p in vparts]
a.setValue('list',plist)
#run proc2d
a.run()
if self.params['numpart'] != apFile.numImagesInStack(self.params['localstack']):
apDisplay.printError("Missing particles in stack")
### setup Xmipp command
aligntime = time.time()
xmippopts = (" -i "+os.path.join(self.params['rundir'], self.params['localstack'])
+" --nref "+str(self.params['numrefs'])
+" --iter "+str(self.params['maxiter'])
+" --odir "+str(self.params['rundir'])
+" --oroot "+ "part"+str(self.params['timestamp'])
+" --classifyAllImages"
)
if self.params['correlation']:
xmippopts += " --distance correlation"
if self.params['classical']:
xmippopts += " --classicalMultiref"
### use multi-processor command
apDisplay.printColor("Using "+str(self.params['nproc'])+" processors!", "green")
xmippexe = apParam.getExecPath(self.execFile, die=True)
mpiruncmd = self.mpirun+" -np "+str(self.params['nproc'])+" "+xmippexe+" "+xmippopts
self.writeXmippLog(mpiruncmd)
apParam.runCmd(mpiruncmd, package="Xmipp 3", verbose=True, showcmd=True, logfile="xmipp.std")
self.params['runtime'] = time.time() - aligntime
apDisplay.printMsg("Alignment time: "+apDisplay.timeString(self.params['runtime']))
### post-processing
# Create a stack for the class averages at each level
Nlevels=glob.glob("level_*")
for level in Nlevels:
digits = level.split("_")[1]
apParam.runCmd("xmipp_image_convert -i "+level+"/part"+self.params['timestamp']+"*xmd -o part"
+self.params['timestamp']+"_level_"+digits+"_.hed", package="Xmipp 3", verbose=True)
if self.params['align']:
apParam.runCmd("xmipp_transform_geometry -i images.xmd -o %s_aligned.stk --apply_transform" % self.params['timestamp'], package="Xmipp 3", verbose=True)
apParam.runCmd("xmipp_image_convert -i %s_aligned.xmd -o alignedStack.hed" % self.params['timestamp'], package="Xmipp 3", verbose=True)
apFile.removeFile("%s_aligned.xmd" % self.params['timestamp'])
apFile.removeFile("%s_aligned.stk" % self.params['timestamp'])
self.parseOutput()
apParam.dumpParameters(self.params, "cl2d-"+self.params['timestamp']+"-params.pickle")
### upload results ... this used to be two separate operations, I'm combining into one
self.runparams = apParam.readRunParameters("cl2d-"+self.params['timestamp']+"-params.pickle")
self.apix = apStack.getStackPixelSizeFromStackId(self.runparams['stackid'])*self.runparams['bin']
self.Nlevels=len(glob.glob("part"+self.params['timestamp']+"_level_??_.hed"))
### create average of aligned stacks & insert aligned stack info
lastLevelStack = "part"+self.params['timestamp']+"_level_%02d_.hed"%(self.Nlevels-1)
apStack.averageStack(lastLevelStack)
self.boxsize = apFile.getBoxSize(lastLevelStack)[0]
self.insertCL2DParamsIntoDatabase()
if self.runparams['align'] is True:
self.insertAlignStackRunIntoDatabase("alignedStack.hed")
self.calcResolution(self.Nlevels-1)
self.insertAlignParticlesIntoDatabase(level=self.Nlevels-1)
### loop over each class average stack & insert as clustering stacks
self.insertClusterRunIntoDatabase()
for level in range(self.Nlevels):
### NOTE: RESOLUTION CAN ONLY BE CALCULATED IF ALIGNED STACK EXISTS TO EXTRACT / READ THE PARTICLES
if self.params['align'] is True:
self.calcResolution(level)
partdict = self.getClassificationAtLevel(level)
for classnum in partdict:
self.insertClusterStackIntoDatabase(
"part"+self.params['timestamp']+"_level_%02d_.hed"%level,
classnum+1, partdict[classnum], len(partdict))
self.clearIntermediateFiles()
def start(self):
# self.insertCL2DJob()
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'])
### process stack to local file
if self.params['timestamp'] is None:
apDisplay.printMsg("creating timestamp")
self.params['timestamp'] = self.timestamp
self.params['localstack'] = os.path.join(
self.params['rundir'], self.params['timestamp'] + ".hed")
if os.path.isfile(self.params['localstack']):
apFile.removeStack(self.params['localstack'])
proccmd = "proc2d " + self.stack['file'] + " " + self.params[
'localstack'] + " apix=" + str(self.stack['apix'])
if self.params['bin'] > 1 or self.params['clipsize'] is not None:
clipsize = int(self.clipsize) * self.params['bin']
if clipsize % 2 == 1:
clipsize += 1 ### making sure that clipped boxsize is even
proccmd += " shrink=%d clip=%d,%d " % (self.params['bin'],
clipsize, clipsize)
proccmd += " last=" + str(self.params['numpart'] - 1)
if self.params['highpass'] is not None and self.params['highpass'] > 1:
proccmd += " hp=" + str(self.params['highpass'])
if self.params['lowpass'] is not None and self.params['lowpass'] > 1:
proccmd += " lp=" + str(self.params['lowpass'])
apParam.runCmd(proccmd, "EMAN", verbose=True)
if self.params['numpart'] != apFile.numImagesInStack(
self.params['localstack']):
apDisplay.printError("Missing particles in stack")
### 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) +
" -codes " + str(self.params['numrefs']) + " -iter " +
str(self.params['maxiter']) + " -o " + os.path.join(
self.params['rundir'], "part" + self.params['timestamp']))
if self.params['fast']:
xmippopts += " -fast "
if self.params['correlation']:
xmippopts += " -useCorrelation "
if self.params['classical']:
xmippopts += " -classicalMultiref "
if self.params['align']:
xmippopts += " -alignImages "
### use multi-processor command
apDisplay.printColor(
"Using " + str(self.params['nproc']) + " processors!", "green")
xmippexe = apParam.getExecPath("xmipp_mpi_class_averages", die=True)
mpiruncmd = self.mpirun + " -np " + str(
self.params['nproc']) + " " + xmippexe + " " + xmippopts
self.writeXmippLog(mpiruncmd)
apParam.runCmd(mpiruncmd,
package="Xmipp",
verbose=True,
showcmd=True,
logfile="xmipp.std")
self.params['runtime'] = time.time() - aligntime
apDisplay.printMsg("Alignment time: " +
apDisplay.timeString(self.params['runtime']))
### minor post-processing
self.createReferenceStack()
self.parseOutput()
self.clearIntermediateFiles()
# self.readyUploadFlag()
apParam.dumpParameters(
self.params, "cl2d-" + self.params['timestamp'] + "-params.pickle")
### upload results ... this used to be two separate operations, I'm combining into one
self.runparams = apParam.readRunParameters("cl2d-" +
self.params['timestamp'] +
"-params.pickle")
self.apix = apStack.getStackPixelSizeFromStackId(
self.runparams['stackid']) * self.runparams['bin']
self.Nlevels = len(
glob.glob("part" + self.params['timestamp'] + "_level_??_.hed"))
### create average of aligned stacks & insert aligned stack info
lastLevelStack = "part" + self.params[
'timestamp'] + "_level_%02d_.hed" % (self.Nlevels - 1)
apStack.averageStack(lastLevelStack)
self.boxsize = apFile.getBoxSize(lastLevelStack)[0]
self.insertCL2DParamsIntoDatabase()
if self.runparams['align'] is True:
self.insertAlignStackRunIntoDatabase("alignedStack.hed")
self.calcResolution(self.Nlevels - 1)
self.insertAlignParticlesIntoDatabase(level=self.Nlevels - 1)
### loop over each class average stack & insert as clustering stacks
self.insertClusterRunIntoDatabase()
for level in range(self.Nlevels):
### NOTE: RESOLUTION CAN ONLY BE CALCULATED IF ALIGNED STACK EXISTS TO EXTRACT / READ THE PARTICLES
if self.params['align'] is True:
self.calcResolution(level)
partdict = self.getClassificationAtLevel(level)
for classnum in partdict:
self.insertClusterStackIntoDatabase(
"part" + self.params['timestamp'] +
"_level_%02d_.hed" % level, classnum + 1,
partdict[classnum], len(partdict))
