def setupInitialModel(self):
modeldata = apModel.getModelFromId(self.params["modelid"])
modelfile = os.path.join(modeldata["path"]["path"], modeldata["name"])
modelsym = modeldata["symmetry"]["symmetry"]
apDisplay.printMsg("Current symmetry: %s" % (modeldata["symmetry"]["description"]))
# if icosahedral recon, rotate volume to 3DEM standard orientation
if modelsym.startswith("Icos (5 3 2)"):
tempfile = "temp.mrc"
emancmd = "proc3d %s %s icos5fTo2f" % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
if modelsym.startswith("Icos (5 3 2)") or modelsym.startswith("Icos (2 5 3)"):
tempfile = "temp.mrc"
emancmd = "proc3d %s %s rotspin=0,0,1,90" % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
outmodelfile = os.path.join(self.params["rundir"], "initmodel.hed")
apFile.removeStack(outmodelfile, warn=False)
emancmd = "proc3d %s %s clip=%d,%d,%d " % (modelfile, outmodelfile, self.boxsize, self.boxsize, self.boxsize)
# rescale initial model if necessary
scale = modeldata["pixelsize"] / self.apix
if abs(scale - 1.0) > 1e-3:
emancmd += "scale=%.4f " % (scale)
apEMAN.executeEmanCmd(emancmd, verbose=True)
apImagicFile.setImagic4DHeader(outmodelfile, machineonly=True)
return outmodelfile
def setupInitialModel(self):
modeldata = apModel.getModelFromId(self.params['modelid'])
modelfile = os.path.join(modeldata['path']['path'], modeldata['name'])
modelsym = modeldata['symmetry']['symmetry']
apDisplay.printMsg("Current symmetry: %s"%(modeldata['symmetry']['description']))
# if icosahedral recon, rotate volume to 3DEM standard orientation
if modelsym.startswith('Icos (5 3 2)'):
tempfile = "temp.mrc"
emancmd = 'proc3d %s %s icos5fTo2f' % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
if modelsym.startswith('Icos (5 3 2)') or modelsym.startswith('Icos (2 5 3)'):
tempfile = "temp.mrc"
emancmd = 'proc3d %s %s rotspin=0,0,1,90' % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
outmodelfile = os.path.join(self.params['rundir'], "initmodel.hed")
apFile.removeStack(outmodelfile, warn=False)
emancmd = "proc3d %s %s clip=%d,%d,%d " % (modelfile, outmodelfile, self.boxsize, self.boxsize, self.boxsize)
# rescale initial model if necessary
scale = modeldata['pixelsize']/self.apix
if abs(scale - 1.0) > 1e-3:
emancmd += "scale=%.4f "%(scale)
apEMAN.executeEmanCmd(emancmd, verbose=True)
apImagicFile.setImagic4DHeader(outmodelfile, machineonly=True)
return outmodelfile
def start(self):
self.iflag = 1
self.setIBLOW()
### get stack info
self.stackdata = apStack.getOnlyStackData(self.params['stackid'])
self.refinestackfile = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
apImagicFile.setImagic4DHeader(self.refinestackfile)
### copy stack or start job file
if self.params['cluster'] is False:
#create alias to stack data
pass
if self.params['cluster'] is True:
self.setupMultiNode()
if self.params['reconstackid'] is not None:
self.reconstackdata = apStack.getOnlyStackData(
self.params['stackid'])
self.reconstackfile = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
else:
self.reconstackfile = self.refinestackfile
### create initial model file
self.currentvol = os.path.basename(self.setupInitialModel())
### create parameter file
self.currentparam = os.path.basename(self.setupParticleParams())
apDisplay.printColor(
"Initial files:\n Stack: %s\n Volume: %s\n Params: %s\n" %
(os.path.basename(
self.refinestackfile), self.currentvol, self.currentparam),
"violet")
## run frealign for number for refinement cycles
for i in range(self.params['numiter']):
iternum = i + 1
if self.params['cluster'] is True:
self.multiNodeRun(iternum)
else:
self.singleNodeRun(iternum)
time.sleep(2)
### calculate FSC
#emancmd = 'proc3d %s %s fsc=fsc.eotest.%d' % (evenvol, oddvol, self.params['iter'])
#apEMAN.executeEmanCmd(emancmd, verbose=True)
if self.params['cluster'] is True:
self.prepareForCluster()
print "Done!"
def start(self):
self.iflag = 1
self.setIBLOW()
### get stack info
self.stackdata = apStack.getOnlyStackData(self.params["stackid"])
self.refinestackfile = os.path.join(self.stackdata["path"]["path"], self.stackdata["name"])
apImagicFile.setImagic4DHeader(self.refinestackfile)
### copy stack or start job file
if self.params["cluster"] is False:
# create alias to stack data
pass
if self.params["cluster"] is True:
self.setupMultiNode()
if self.params["reconstackid"] is not None:
self.reconstackdata = apStack.getOnlyStackData(self.params["stackid"])
self.reconstackfile = os.path.join(self.stackdata["path"]["path"], self.stackdata["name"])
else:
self.reconstackfile = self.refinestackfile
### create initial model file
self.currentvol = os.path.basename(self.setupInitialModel())
### create parameter file
self.currentparam = os.path.basename(self.setupParticleParams())
apDisplay.printColor(
"Initial files:\n Stack: %s\n Volume: %s\n Params: %s\n"
% (os.path.basename(self.refinestackfile), self.currentvol, self.currentparam),
"violet",
)
## run frealign for number for refinement cycles
for i in range(self.params["numiter"]):
iternum = i + 1
if self.params["cluster"] is True:
self.multiNodeRun(iternum)
else:
self.singleNodeRun(iternum)
time.sleep(2)
### calculate FSC
# emancmd = 'proc3d %s %s fsc=fsc.eotest.%d' % (evenvol, oddvol, self.params['iter'])
# apEMAN.executeEmanCmd(emancmd, verbose=True)
if self.params["cluster"] is True:
self.prepareForCluster()
print "Done!"
def start(self):
t0 = time.time()
self.checkAnalysisRun()
# get stack parameters
if self.params['alignid'] is not None:
self.alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignid'])
stackpixelsize = self.alignstackdata['pixelsize']
stack_box_size = self.alignstackdata['boxsize']
self.params['boxsize'] = stack_box_size / int(self.params['bin'])
self.params['apix'] = stackpixelsize * int(self.params['bin'])
orig_path = self.alignstackdata['path']['path']
orig_file = self.alignstackdata['imagicfile']
linkingfile = orig_path+"/"+orig_file
linkingfile = linkingfile.replace(".hed", "")
else:
apDisplay.printError("stack not in the database")
# link stack file to working directory
if not os.path.isfile(linkingfile+".hed"):
apDisplay.printError("stackfile does not exist: "+linkingfile+".img")
else:
if not os.path.isfile(os.path.join(str(self.params['rundir']), "start.img")):
apDisplay.printMsg("copying aligned stack into working directory for operations with IMAGIC")
# shutil.copyfile(linkingfile+".img", str(self.params['rundir'])+"/start.img")
# shutil.copyfile(linkingfile+".hed", str(self.params['rundir'])+"/start.hed")
lnkcmd1 = "ln -s "+linkingfile+".img "+os.path.join(self.params['rundir'], "start.img")
lnkcmd2 = "ln -s "+linkingfile+".hed "+os.path.join(self.params['rundir'], "start.hed")
proc = subprocess.Popen(lnkcmd1, shell=True)
proc.wait()
proc = subprocess.Popen(lnkcmd2, shell=True)
proc.wait()
### header bug
apImagicFile.setImagic4DHeader(os.path.join(self.params['rundir'], "start.hed"))
else:
apDisplay.printColor("aligned stack already exists in working directory", "green")
### NEED TO CONVERT FILTERING PARAMETERS TO IMAGIC FORMAT BETWEEN 0-1
if self.params['lpfilt'] is not None:
self.params['lpfilt_imagic'] = 2 * float(self.params['apix']) / int(self.params['lpfilt'])
else:
self.params['lpfilt_imagic'] = False
if float(self.params['lpfilt_imagic']) > 1:
self.params['lpfilt_imagic'] = 1 # imagic cannot perform job when lowpass > 1
if self.params['hpfilt'] is not None:
self.params['hpfilt_imagic'] = 2 * float(self.params['apix']) / int(self.params['hpfilt'])
else:
self.params['hpfilt_imagic'] = False
print self.params
print "... aligned stack pixel size: "+str(self.params['apix'])
print "... aligned stack box size: "+str(self.params['boxsize'])
apDisplay.printColor("Running IMAGIC .batch file: See imagicMultivariateStatisticalAnalysis.log for details", "cyan")
### create imagic batch file
filename = self.createImagicBatchFile()
### execute batch file that was created
aligntime = time.time()
proc = subprocess.Popen('chmod 775 '+filename, shell=True)
proc.wait()
apParam.runCmd(filename, package="IMAGIC")
logfile = open(os.path.join(self.params['rundir'], "imagicMultivariateStatisticalAnalysis.log"))
apIMAGIC.checkLogFileForErrors(os.path.join(self.params['rundir'], "imagicMultivariateStatisticalAnalysis.log"))
if not os.path.isfile(os.path.join(self.params['rundir'], "eigenimages.hed")):
apDisplay.printError("IMAGIC did not run and did not create eigenimages")
aligntime = time.time() - aligntime
### remove copied stack
# while os.path.isfile(os.path.join(self.params['rundir'], "start.img")):
# apFile.removeStack(os.path.join(self.params['rundir'], "start.img"))
### normalize eigenimages
eigenimages = os.path.join(self.params['rundir'], "eigenimages.img")
emancmd = "proc2d "+str(eigenimages)+" "+str(eigenimages)+" inplace"
apParam.runCmd(emancmd, package="EMAN")
### upload alignment
imagicstack = os.path.join(self.params['rundir'], "start.hed")
inserttime = time.time()
if self.params['commit'] is True:
self.insertAnalysis(imagicstack, runtime=aligntime, insert=True)
else:
apDisplay.printWarning("not committing results to DB")
inserttime = time.time() - inserttime
apDisplay.printMsg("Alignment time: "+apDisplay.timeString(aligntime))
apDisplay.printMsg("Database Insertion time: "+apDisplay.timeString(inserttime))