def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['start'] is None:
apDisplay.printError("a number of starting classes was not provided")
if self.params['end'] is None:
apDisplay.printError("a number of ending classes was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] is None:
self.params['numpart'] = npart
elif self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
self.boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.workingboxsize = math.floor(self.boxsize/self.params['bin'])
if not self.params['mask']:
self.params['mask'] = (self.boxsize/2)-2
self.workingmask = math.floor(self.params['mask']/self.params['bin'])
if self.params['mramethod'] == 'imagic':
self.imagicroot = apIMAGIC.checkImagicExecutablePath()
self.imagicversion = apIMAGIC.getImagicVersion(self.imagicroot)
def checksizes(self):
newnots = apFile.numImagesInStack(self.params['notstack'])
newtilts = apFile.numImagesInStack(self.params['tiltstack'])
stackdata1 = apStack.getOnlyStackData(self.params['stack1'], msg=False)
stackpath1 = os.path.join(stackdata1['path']['path'],
stackdata1['name'])
oldnots = apFile.numImagesInStack(stackpath1)
stackdata2 = apStack.getOnlyStackData(self.params['stack2'], msg=False)
stackpath2 = os.path.join(stackdata2['path']['path'],
stackdata2['name'])
oldtilts = apFile.numImagesInStack(stackpath2)
if newtilts != oldtilts:
apDisplay.printWarning(
"tilted stack are different sizes: %d vs. %d part" %
(newtilts, oldtilts))
else:
apDisplay.printMsg("tilted stack are the sames sizes: %d part" %
(newtilts))
if newnots != oldnots:
apDisplay.printWarning(
"untilted stack are different sizes: %d vs. %d part" %
(newnots, oldnots))
else:
apDisplay.printMsg("untilted stack are the sames sizes: %d part" %
(newnots))
def makeNewStack(oldstack, newstack, listfile=None, remove=False, bad=False):
if not os.path.isfile(oldstack):
apDisplay.printWarning("could not find old stack: "+oldstack)
if os.path.isfile(newstack):
if remove is True:
apDisplay.printWarning("removing old stack: "+newstack)
time.sleep(2)
apFile.removeStack(newstack)
else:
apDisplay.printError("new stack already exists: "+newstack)
apDisplay.printMsg("creating a new stack\n\t"+newstack+
"\nfrom the oldstack\n\t"+oldstack+"\nusing list file\n\t"+str(listfile))
emancmd = "proc2d "+oldstack+" "+newstack
if listfile is not None:
emancmd += " list="+listfile
apEMAN.executeEmanCmd(emancmd, verbose=True)
if bad is True and listfile is not None:
### run only if num bad particles < num good particles
newstacknumpart = apFile.numImagesInStack(newstack)
oldstacknumpart = apFile.numImagesInStack(oldstack)
if newstacknumpart > oldstacknumpart/2:
### create bad.hed stack with all bad particles
badstack = os.path.join(os.path.dirname(newstack), "bad.hed")
emancmd = "proc2d %s %s exclude=%s"%(oldstack, badstack, listfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
else:
apDisplay.printMsg("Rejecting more particles than keeping, not creating a bad stack")
return
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
if self.params['templatelist'] is None:
apDisplay.printError("template list was not provided")
if self.params['lastring'] is None:
apDisplay.printError("a last ring radius was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])/self.params['bin']
if self.params['lastring'] > boxsize/2-2:
apDisplay.printError("last ring radius is too big for boxsize "
+str(self.params['lastring'])+" > "+str(boxsize/2-2))
if self.params['lastring']+self.params['xysearch'] > boxsize/2-2:
apDisplay.printError("last ring plus xysearch radius is too big for boxsize "
+str(self.params['lastring']+self.params['xysearch'])+" > "+str(boxsize/2-2))
### convert / check template data
self.templatelist = self.params['templatelist'].strip().split(",")
if not self.templatelist or type(self.templatelist) != type([]):
apDisplay.printError("could not parse template list="+self.params['templatelist'])
self.params['numtemplate'] = len(self.templatelist)
apDisplay.printMsg("Found "+str(self.params['numtemplate'])+" templates")
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d"
%(self.params['clipsize'],self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
self.mpirun = self.checkMPI()
if self.mpirun is None:
apDisplay.printError("There is no MPI installed")
if self.params['nproc'] is None:
self.params['nproc'] = apParam.getNumProcessors()
if self.params['nproc'] < 2:
apDisplay.printError("Only the MPI version of CL2D is currently supported, must run with > 1 CPU")
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
if self.params['templatelist'] is None:
apDisplay.printError("template list was not provided")
if self.params['lastring'] is None:
apDisplay.printError("a last ring radius was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])/self.params['bin']
if self.params['lastring'] > boxsize/2-2:
apDisplay.printError("last ring radius is too big for boxsize "
+str(self.params['lastring'])+" > "+str(boxsize/2-2))
if self.params['lastring']+self.params['xysearch'] > boxsize/2-2:
apDisplay.printError("last ring plus xysearch radius is too big for boxsize "
+str(self.params['lastring']+self.params['xysearch'])+" > "+str(boxsize/2-2))
### convert / check template data
self.templatelist = self.params['templatelist'].strip().split(",")
if not self.templatelist or type(self.templatelist) != type([]):
apDisplay.printError("could not parse template list="+self.params['templatelist'])
self.params['numtemplate'] = len(self.templatelist)
apDisplay.printMsg("Found "+str(self.params['numtemplate'])+" templates")
def checkConflicts(self):
if self.params["stackid"] is None:
apDisplay.printError("stack id was not defined")
if self.params["description"] is None:
apDisplay.printError("run description was not defined")
if self.params["runname"] is None:
apDisplay.printError("run name was not defined")
maxparticles = 150000
if self.params["numpart"] > maxparticles:
apDisplay.printError(
"too many particles requested, max: " + str(maxparticles) + " requested: " + str(self.params["numpart"])
)
if self.params["initmethod"] not in self.initmethods:
apDisplay.printError(
"unknown initialization method defined: "
+ str(self.params["initmethod"])
+ " not in "
+ str(self.initmethods)
)
stackdata = apStack.getOnlyStackData(self.params["stackid"], msg=False)
stackfile = os.path.join(stackdata["path"]["path"], stackdata["name"])
if self.params["numpart"] > apFile.numImagesInStack(stackfile):
apDisplay.printError(
"trying to use more particles "
+ str(self.params["numpart"])
+ " than available "
+ str(apFile.numImagesInStack(stackfile))
)
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
#if self.params['description'] is None:
# apDisplay.printError("run description was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: "+str(self.fastmodes))
if not self.params['converge'] in self.convergemodes:
apDisplay.printError("converge mode must be on of: "+str(self.convergemodes))
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d"
%(self.params['clipsize'],self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
def appendParticleListToStackFile(partlist, mergestackfile, msg=True):
"""
takes a list of 2D numpy arrays and add to stack file
due to hack, we must re-number the stack later
"""
### initialization
t0 = time.time()
root = os.path.splitext(mergestackfile)[0]
mergeheaderfile = root + ".hed"
mergedatafile = root + ".img"
### merge data files
premergesize = apFile.fileSize(mergedatafile)
mergedata = file(mergedatafile, 'ab')
for partarray in partlist:
part32bit = numpy.asarray(partarray, dtype=numpy.float32)
mergedata.write(part32bit.tostring())
mergedata.close()
finalsize = apFile.fileSize(mergedatafile)
addsize = len(part32bit.tostring() * len(partlist))
if finalsize != addsize + premergesize:
apDisplay.printError(
"size mismatch %s vs. %s + %s = %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(addsize),
apDisplay.bytes(premergesize),
apDisplay.bytes(premergesize + addsize)))
elif msg is True:
apDisplay.printMsg(
"size match %s vs. %s + %s = %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(addsize),
apDisplay.bytes(premergesize),
apDisplay.bytes(premergesize + addsize)))
### merge header files
premergenumpart = apFile.numImagesInStack(mergeheaderfile)
mergehead = open(mergeheaderfile, 'ab')
count = 0
for partarray in partlist:
count += 1
headerstr = makeHeaderStrFromArray(premergenumpart + count, partarray)
mergehead.write(headerstr)
mergehead.close()
numberStackFile(mergeheaderfile, msg=msg)
finalnumpart = apFile.numImagesInStack(mergeheaderfile)
addpart = len(partlist)
if finalnumpart != addpart + premergenumpart:
apDisplay.printError("size mismatch %d vs. %d + %d = %d" %
(finalnumpart, addpart, premergenumpart,
addpart + premergenumpart))
elif msg is True:
apDisplay.printMsg("size match %d vs. %d + %d = %d" %
(finalnumpart, addpart, premergenumpart,
addpart + premergenumpart))
return True
def checkConflicts(self):
apDisplay.printMsg("/bin/rm -f *.hed *.img *.doc *.vol *.mrc *.spi *.log *~ *.pickle *.hist *.proj *.xmp *.sel *.basis *.original; rm -fr volume*")
### check for missing and duplicate entries
#if self.params['alignid'] is None and self.params['clusterid'] is None:
# apDisplay.printError("Please provide either --cluster-id or --align-id")
if self.params['alignid'] is not None and self.params['clusterid'] is not None:
apDisplay.printError("Please provide only one of either --cluster-id or --align-id")
if self.params['modelstr'] is None and self.params['nvol'] is None:
apDisplay.printError("Please provide model numbers or number of volumes")
elif self.params['modelstr'] is not None:
modellist = self.params['modelstr'].split(",")
self.params['modelids'] = []
for modelid in modellist:
self.params['modelids'].append(int(modelid))
### get the stack ID from the other IDs
if self.params['alignid'] is not None:
self.alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignid'])
self.params['stackid'] = self.alignstackdata['stack'].dbid
elif self.params['clusterid'] is not None:
self.clusterstackdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterid'])
self.alignstackdata = self.clusterstackdata['clusterrun']['alignstack']
self.params['stackid'] = self.alignstackdata['stack'].dbid
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
#if self.params['description'] is None:
# apDisplay.printError("run description was not defined")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: "+str(self.fastmodes))
maxparticles = 150000
minparticles = 50
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
if self.params['numpart'] < minparticles:
apDisplay.printError("not enough particles requested, min: "
+ str(minparticles) + " requested: " + str(self.params['numpart']))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
### find number of processors
if self.params['nproc'] is None:
self.nproc = apParam.getNumProcessors()
else:
self.nproc = self.params['nproc']
self.mpirun = self.checkMPI()
def checkConflicts(self):
if self.params["stackid"] is None:
apDisplay.printError("Stack id was not defined")
if self.params["mandir"] is None:
apDisplay.printError("Directory containing mandatory files was not defined")
if self.params["description"] is None:
apDisplay.printError("Run description was not defined")
stackdata = apStack.getOnlyStackData(self.params["stackid"], msg=False)
stackfile = os.path.join(stackdata["path"]["path"], stackdata["name"])
if self.params["numpart"] is None:
self.params["numpart"] = apFile.numImagesInStack(stackfile)
apDisplay.printWarning("Number of particles not defined, processing full stack")
if self.params["numpart"] > apFile.numImagesInStack(stackfile):
apDisplay.printError(
"trying to use more particles "
+ str(self.params["numpart"])
+ " than available "
+ str(apFile.numImagesInStack(stackfile))
)
if self.params["replen"] is None:
apDisplay.printError("Helical repeat was not defined")
if self.params["subunits"] is None:
apDisplay.printError("Number of subunits was not defined")
if self.params["diameter"] is None:
apDisplay.printError("Filament diameter was not defined")
if self.params["diaminner"] is None:
apDisplay.printError("Inner filament diameter was not defined")
if self.params["rescut"] is None:
apDisplay.printError("Phase residual cutoff was not defined")
if self.params["filval"] is None:
apDisplay.printError("Filter value was not defined")
if self.params["bin"] is None:
self.params["bin"] = 1
apDisplay.printWarning("Binning factor was not defined, binning by one")
if self.params["cont"] is None:
apDisplay.printError("Must specify if a contrast change is needed")
if self.params["prehip"] is None:
apDisplay.printError("Must specify if prehip needs to be executed or not")
step = apStack.getStackPixelSizeFromStackId(self.params["stackid"])
self.params["step"] = step
onerep = math.floor(self.params["replen"] / step)
calcyht2 = math.floor(self.params["diameter"] / step)
boxsize = apStack.getStackBoxsize(self.params["stackid"])
self.params["boxsize"] = boxsize
if self.params["xlngth"] < onerep:
apDisplay.printError("Filament segment length can not be less than one helical repeat")
if self.params["xlngth"] > boxsize:
apDisplay.printError("Filament segment length can not be greater than stack box size")
if self.params["yht2"] < calcyht2:
apDisplay.printError("Filament box height can not be less than filament diameter")
if self.params["padval"] < self.params["xlngth"]:
apDisplay.printError("Pad value can not be less than the filament segment length")
if not self.checkval(self.params["yht2"]):
apDisplay.printError("Filament box height must be a power of two")
if not self.checkval(self.params["padval"]):
apDisplay.printError("Pad value must be a power of two")
def checkConflicts(self):
apDisplay.printMsg("/bin/rm -f *.hed *.img *.doc *.vol *.mrc *.spi *.log *~ *.pickle *.hist *.proj *.xmp *.sel *.basis *.original; rm -fr volume*")
### check for missing and duplicate entries
#if self.params['alignid'] is None and self.params['clusterid'] is None:
# apDisplay.printError("Please provide either --cluster-id or --align-id")
if self.params['alignid'] is not None and self.params['clusterid'] is not None:
apDisplay.printError("Please provide only one of either --cluster-id or --align-id")
if self.params['modelstr'] is None and self.params['nvol'] is None:
apDisplay.printError("Please provide model numbers or number of volumes")
elif self.params['modelstr'] is not None:
modellist = self.params['modelstr'].split(",")
self.params['modelids'] = []
for modelid in modellist:
self.params['modelids'].append(int(modelid))
### get the stack ID from the other IDs
if self.params['alignid'] is not None:
self.alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignid'])
self.params['stackid'] = self.alignstackdata['stack'].dbid
elif self.params['clusterid'] is not None:
self.clusterstackdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterid'])
self.alignstackdata = self.clusterstackdata['clusterrun']['alignstack']
self.params['stackid'] = self.alignstackdata['stack'].dbid
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
#if self.params['description'] is None:
# apDisplay.printError("run description was not defined")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: "+str(self.fastmodes))
maxparticles = 150000
minparticles = 50
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
if self.params['numpart'] < minparticles:
apDisplay.printError("not enough particles requested, min: "
+ str(minparticles) + " requested: " + str(self.params['numpart']))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
### find number of processors
if self.params['nproc'] is None:
self.nproc = apParam.getNumProcessors()
else:
self.nproc = self.params['nproc']
self.mpirun = self.checkMPI()
def checkConflicts(self):
### setup correct database after we have read the project id
if 'projectid' in self.params and self.params['projectid'] is not None:
apDisplay.printMsg("Using split database")
# use a project database
newdbname = apProject.getAppionDBFromProjectId(self.params['projectid'])
sinedon.setConfig('appiondata', db=newdbname)
apDisplay.printColor("Connected to database: '"+newdbname+"'", "green")
### get stack data
self.stack = {}
if self.params['stackid'] is not None:
self.stack['data'] = apStack.getOnlyStackData(self.params['stackid'])
self.stack['apix'] = apStack.getStackPixelSizeFromStackId(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'])
else:
self.stack['data'] = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
self.stack['apix'] = self.stack['pixelsize']
self.stack['boxsize'] = self.stack['boxsize']
self.stack['file'] = self.stack['imagicfile']
### check conflicts
if self.params['stackid'] is None and self.params['alignstackid'] is None:
apDisplay.printError("stack id OR alignstack id was not defined")
if self.params['stackid'] is not None and self.params['alignstackid'] is not None:
apDisplay.printError("either specify stack id OR alignstack id, not both")
if self.params['generations'] is None:
apDisplay.printError("number of generations was not provided")
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
if self.params['numpart'] > apFile.numImagesInStack(self.stack['file']):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(self.stack['file'])))
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(self.stack['file'])
boxsize = apStack.getStackBoxsize(self.params['stackid'])
if self.params['ou'] is None:
self.params['ou'] = (boxsize / 2.0) - 2
self.clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d"
%(self.params['clipsize'],self.clipsize))
self.clipsize = self.params['clipsize']
self.mpirun = self.checkMPI()
if self.mpirun is None:
apDisplay.printError("There is no MPI installed")
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("Stack id was not defined")
if self.params['mandir'] is None:
apDisplay.printError("Directory containing mandatory files was not defined")
if self.params['description'] is None:
apDisplay.printError("Run description was not defined")
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
apDisplay.printWarning("Number of particles not defined, processing full stack")
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])+" than available "+str(apFile.numImagesInStack(stackfile)))
if self.params['replen'] is None:
apDisplay.printError("Helical repeat was not defined")
if self.params['subunits'] is None:
apDisplay.printError("Number of subunits was not defined")
if self.params['diameter'] is None:
apDisplay.printError("Filament diameter was not defined")
if self.params['diaminner'] is None:
apDisplay.printError("Inner filament diameter was not defined")
if self.params['rescut'] is None:
apDisplay.printError("Phase residual cutoff was not defined")
if self.params['filval'] is None:
apDisplay.printError("Filter value was not defined")
if self.params['bin'] is None:
self.params['bin'] = 1
apDisplay.printWarning("Binning factor was not defined, binning by one")
if self.params['cont'] is None:
apDisplay.printError("Must specify if a contrast change is needed")
if self.params['prehip'] is None:
apDisplay.printError("Must specify if prehip needs to be executed or not")
step = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
self.params['step'] = step
onerep = math.floor(self.params['replen'] / step)
calcyht2 = math.floor(self.params['diameter'] / step)
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.params['boxsize'] = boxsize
if self.params['xlngth'] < onerep:
apDisplay.printError("Filament segment length can not be less than one helical repeat")
if self.params['xlngth'] > boxsize:
apDisplay.printError("Filament segment length can not be greater than stack box size")
if self.params['yht2'] < calcyht2:
apDisplay.printError("Filament box height can not be less than filament diameter")
if self.params['padval'] < self.params['xlngth']:
apDisplay.printError("Pad value can not be less than the filament segment length")
if not self.checkval(self.params['yht2']):
apDisplay.printError("Filament box height must be a power of two")
if not self.checkval(self.params['padval']):
apDisplay.printError("Pad value must be a power of two")
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['numrefs'] is None:
apDisplay.printError("a number of classes was not provided")
maxparticles = 500000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: " +
str(maxparticles) + " requested: " +
str(self.params['numpart']))
self.stackdata = apStack.getOnlyStackData(self.params['stackid'],
msg=False)
stackfile = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
# check for virtual stack
self.params['virtualdata'] = None
if not os.path.isfile(stackfile):
vstackdata = apStack.getVirtualStackParticlesFromId(
self.params['stackid'])
npart = len(vstackdata['particles'])
self.params['virtualdata'] = vstackdata
else:
npart = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > npart:
apDisplay.printError("trying to use more particles " +
str(self.params['numpart']) +
" than available " +
str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(
boxsize / float(self.params['bin'] * 2))) * 2
if self.params['clipsize'] is not None:
if self.params['clipsize'] > self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d" %
(self.params['clipsize'], self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
self.mpirun = self.checkMPI()
if self.mpirun is None:
apDisplay.printError("There is no MPI installed")
if self.params['nproc'] is None:
self.params['nproc'] = self.params['nodes'] * self.params['ppn']
if self.params['nproc'] < 2:
apDisplay.printError(
"Only the MPI version of CL2D is currently supported, must run with > 1 CPU"
)
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
### convert / check template data
if self.params['templatelist'] is None:
apDisplay.printError("template list was not provided")
self.templatelist = self.params['templatelist'].strip().split(",")
if not self.templatelist or type(self.templatelist) != type([]):
apDisplay.printError("could not parse template list=" +
self.params['templatelist'])
self.params['numtemplate'] = len(self.templatelist)
apDisplay.printMsg("Found " + str(self.params['numtemplate']) +
" templates")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: " +
str(self.fastmodes))
if not self.params['converge'] in self.convergemodes:
apDisplay.printError("converge mode must be on of: " +
str(self.convergemodes))
maxparticles = 150000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: " +
str(maxparticles) + " requested: " +
str(self.params['numpart']))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles " +
str(self.params['numpart']) +
" than available " +
str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(
boxsize / float(self.params['bin'] * 2))) * 2
if self.params['clipsize'] is not None:
if self.params['clipsize'] >= self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d" %
(self.params['clipsize'], self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
def initValues(self, stackfile, numrequest=None):
### check for stack
if not os.path.isfile(stackfile):
apDisplay.printError("stackfile does not exist: " + stackfile)
### amount of free memory on machine (converted to bytes)
self.freememory = mem.free() * 1024
self.message("Free memory: %s" % (apDisplay.bytes(self.freememory)))
### box size of particle
self.boxsize = apFile.getBoxSize(stackfile)[0]
self.message("Box size: %d" % (self.boxsize))
### amount of memory used per particles (4 bytes per pixel)
self.memperpart = self.boxsize**2 * 4.0
self.message("Memory used per part: %s" %
(apDisplay.bytes(self.memperpart)))
### maximum number particles that fit into memory
self.maxpartinmem = self.freememory / self.memperpart
self.message("Max particles in memory: %d" % (self.maxpartinmem))
### number particles to fit into memory
self.partallowed = int(self.maxpartinmem / 20.0)
self.message("Particles allowed in memory: %d" % (self.partallowed))
### number particles in stack
numpart = apFile.numImagesInStack(stackfile)
if self.numpart is None or self.numpart > numpart:
self.numpart = numpart
if numrequest is not None and self.numpart > numrequest:
self.numpart = numrequest
self.message("Number of particles in stack: %d" % (self.numpart))
if self.numpart > self.partallowed:
numchucks = math.ceil(self.numpart / float(self.partallowed))
self.stepsize = int(self.numpart / numchucks)
else:
numchucks = 1
self.stepsize = self.numpart
self.message("Particle loop num chunks: %d" % (numchucks))
self.message("Particle loop step size: %d" % (self.stepsize))
def convertSpiderStack(self, spiderstack):
"""
takes the stack file and creates a spider file ready for processing
"""
emancmd = "proc2d "
if not os.path.isfile(spiderstack):
apDisplay.printError("stackfile does not exist: " + spiderstack)
emancmd += spiderstack + " "
imagicstack = os.path.join(self.params['rundir'], "alignstack.hed")
apFile.removeFile(imagicstack, warn=True)
emancmd += imagicstack + " "
starttime = time.time()
apDisplay.printColor(
"Running spider stack conversion this can take a while", "cyan")
apEMAN.executeEmanCmd(emancmd, verbose=True)
apDisplay.printColor(
"finished eman in " +
apDisplay.timeString(time.time() - starttime), "cyan")
numpart = apFile.numImagesInStack(imagicstack)
if numpart != self.params['numpart']:
apDisplay.printError(
"The number of particles returned is different from the number requested"
)
return imagicstack
def getClassification(self, classdoc, classname):
D = {}
tmp = {}
fh = open(classdoc)
nclasses = apFile.numImagesInStack(classname)
### all classes, assuming that some of them were discarded by the minp parameter
for i in range(self.params['ncls']):
tmp[(i + 1)] = []
for line in fh:
params = line.strip().split()
particleNumber = int(params[0])
classNumber = int(float(params[2]))
tmp[classNumber].append(particleNumber)
fh.close()
### rename the dictionary
i = 1
for oldkey, val in tmp.iteritems(): ### ascending order
if len(val) > 0:
D[i] = val
# print oldkey, i, val
i += 1
return D
def start(self):
### copy stack to rundir
newstack = os.path.join(self.params['rundir'], "start.hed")
if os.path.isfile(newstack):
apDisplay.printError("Stack already exists")
emancmd = "proc2d %s %s" % (self.params['stackfile'], newstack)
if self.params['normalize'] is True:
emancmd += " edgenorm"
apEMAN.executeEmanCmd(emancmd)
### set final parameters
boxsize = apFile.getBoxSize(newstack)
apDisplay.printMsg("Boxsize: %i" % boxsize[0])
if not boxsize or boxsize <= 0:
apDisplay.printError("Could not determine stack size")
else:
self.boxsize = boxsize[0]
self.numpart = apFile.numImagesInStack(newstack)
apDisplay.printMsg("Num part: %i" % self.numpart)
if not self.numpart or self.numpart <= 0:
apDisplay.printError("Could not determine number of particles")
if self.numpart <= 1:
apDisplay.printError("Not enough particles to upload")
apStack.averageStack(newstack)
#self.params['commit'] = False
self.createStackData()
def initValues(self, stackfile, numrequest=None):
### check for stack
if not os.path.isfile(stackfile):
apDisplay.printError("stackfile does not exist: "+stackfile)
### amount of free memory on machine (converted to bytes)
self.freememory = mem.free()*1024
self.message("Free memory: %s"%(apDisplay.bytes(self.freememory)))
### box size of particle
self.boxsize = apFile.getBoxSize(stackfile)[0]
self.message("Box size: %d"%(self.boxsize))
### amount of memory used per particles (4 bytes per pixel)
self.memperpart = self.boxsize**2 * 4.0
self.message("Memory used per part: %s"%(apDisplay.bytes(self.memperpart)))
### maximum number particles that fit into memory
self.maxpartinmem = self.freememory/self.memperpart
self.message("Max particles in memory: %d"%(self.maxpartinmem))
### number particles to fit into memory
self.partallowed = int(self.maxpartinmem/20.0)
self.message("Particles allowed in memory: %d"%(self.partallowed))
### number particles in stack
numpart = apFile.numImagesInStack(stackfile)
if self.numpart is None or self.numpart > numpart:
self.numpart = numpart
if numrequest is not None and self.numpart > numrequest:
self.numpart = numrequest
self.message("Number of particles in stack: %d"%(self.numpart))
if self.numpart > self.partallowed:
numchucks = math.ceil(self.numpart/float(self.partallowed))
self.stepsize = int(self.numpart/numchucks)
else:
numchucks = 1
self.stepsize = self.numpart
self.message("Particle loop num chunks: %d"%(numchucks))
self.message("Particle loop step size: %d"%(self.stepsize))
def useClusterForTemplate(self):
apDisplay.printMsg("Using clustering stack to make templates")
clusterstackdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterid'])
self.params['apix'] = clusterstackdata['clusterrun']['alignstack']['pixelsize']
stackfile = os.path.join(clusterstackdata['path']['path'], clusterstackdata['avg_imagicfile'])
self.params['templatelist'] = []
stackid = clusterstackdata['clusterrun']['alignstack']['stack'].dbid
sessiondata = apStack.getSessionDataFromStackId(stackid)
self.params['sessionname'] = sessiondata['name']
### check to see if stackimagenum is within the boundary of the stack
numpart = apFile.numImagesInStack(stackfile)
for i in self.params['imgnums'].split(","):
partnum = int(i)
if partnum > numpart or partnum < 0:
apDisplay.printError("'imgnums' is NOT within the boundary of the stack: %d > %d"%(partnum,numpart))
apDisplay.printMsg("Extracting image %d from cluster stack" % partnum)
templatename = "cluster%d-average%d.mrc"%(self.params['clusterid'],partnum)
abstemplatepath= os.path.join(clusterstackdata['path']['path'], templatename)
### run proc2d with params['stackimgnum']
emancmd = "proc2d %s %s first=%d last=%d" % (stackfile, abstemplatepath, partnum, partnum)
### create template
apDisplay.printMsg("creating "+templatename)
apEMAN.executeEmanCmd(emancmd)
if os.path.isfile(abstemplatepath):
self.params['templatelist'].append(abstemplatepath)
def getNumAlignedParticles(self):
t0 = time.time()
self.alignstackdata = appiondata.ApAlignStackData.direct_query(self.params['alignstackid'])
oldalignedstack = os.path.join(self.alignstackdata['path']['path'], self.alignstackdata['imagicfile'])
numpart = apFile.numImagesInStack(oldalignedstack)
apDisplay.printMsg("numpart="+str(numpart)+" in "+apDisplay.timeString(time.time()-t0))
return numpart
def getClassification(self, classdoc, classname):
D = {}
tmp = {}
fh = open(classdoc)
nclasses = apFile.numImagesInStack(classname)
### all classes, assuming that some of them were discarded by the minp parameter
for i in range(self.params['ncls']):
tmp[(i+1)] = []
for line in fh:
params = line.strip().split()
particleNumber = int(params[0])
classNumber = int(float(params[2]))
tmp[classNumber].append(particleNumber)
fh.close()
### rename the dictionary
i = 1
for oldkey, val in tmp.iteritems(): ### ascending order
if len(val) > 0:
D[i] = val
# print oldkey, i, val
i += 1
return D
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['rad'] is None:
apDisplay.printError("no particle radius set")
if self.params['modelid'] is None:
apDisplay.printError("model id was not defined")
if self.params['lastring'] is None:
apDisplay.printError("a last ring radius was not provided")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if self.params['incr'] is None:
apDisplay.printError("angular increments are not specified")
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
numstackp = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > numstackp:
apDisplay.printError("trying to use more particles "+str(numstackp)
+" than available "+str(numstackp))
elif self.params['numpart'] == 0:
apDisplay.printWarning("using all "+str(numstackp)+" particles")
self.params['numpart'] = numstackp
boxsize = apStack.getStackBoxsize(self.params['stackid'])
if self.params['lastring'] > boxsize/2-2:
apDisplay.printError("last ring radius is too big for boxsize "
+str(self.params['lastring'])+" > "+str(boxsize/2-2))
if self.params['lastring']+self.params['xysearch'] > boxsize/2-2:
apDisplay.printError("last ring plus xysearch radius is too big for boxsize "
+str(self.params['lastring']+self.params['xysearch'])+" > "+str(boxsize/2-2))
if (self.params['xysearch'] % self.params['xystep']) > 0:
apDisplay.printError("translational search (xy-search) must be divisible by search step (xy-step)")
def start(self):
"""
This is the core of your function.
"""
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
original_stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
filtered_stackfile = os.path.join(self.params['rundir'], self.timestamp+".hed")
apFile.removeStack(filtered_stackfile, warn=False)
apix = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
boxsize = apStack.getStackBoxsize(self.params['stackid'])
emancmd = "proc2d %s %s apix=%.3f "%(original_stackfile, filtered_stackfile, apix)
if self.params['lowpass'] is not None:
emancmd += " lp=%.3f "%(self.params['lowpass'])
if self.params['highpass'] is not None:
emancmd += " hp=%.3f "%(self.params['highpass'])
if self.params['bin'] is not None and self.params['bin'] > 1:
## determine a multiple of the bin that is divisible by 2 and less than the boxsize
clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2*self.params['bin']
emancmd += " shrink=%d clip=%d,%d "%(self.params['bin'], clipsize, clipsize)
emancmd += " last=%d "%(self.params['numpart']-1)
apEMAN.executeEmanCmd(emancmd, verbose=True, showcmd=True)
### confirm that it worked
if self.params['numpart'] != apFile.numImagesInStack(filtered_stackfile):
apDisplay.printError("Missing particles in stack")
### run the radon transform code
self.radonAlign(filtered_stackfile)
### insert info into database
self.commitToDatabase()
def fillSimilarityMatrix(self, alignedstack):
### Get initial correlation values
### this is really, really slow
similarfile = "similarities.dat"
simstack = similarityStack()
simstack.similarfile = similarfile
simstack.start(alignedstack)
if not os.path.isfile(similarfile):
apDisplay.printError("Failed to create similarity file")
simf = open(similarfile, 'r')
simlist = []
count = 0
for line in simf:
count += 1
sline = line.strip()
slist = sline.split()
ccval = float(slist[2])
simlist.append(ccval)
simf.close()
apDisplay.printMsg("There are %d lines in the sim file: %s"%(count, similarfile))
numpart = apFile.numImagesInStack(alignedstack)
if count != numpart*(numpart-1):
### we have a valid file already
apDisplay.printError("There are only %d lines need to have %d"%(count, numpart*(numpart-1)))
return similarfile, simlist
def start(self):
### copy stack to rundir
newstack = os.path.join(self.params['rundir'], "start.hed")
if os.path.isfile(newstack):
apDisplay.printError("Stack already exists")
emancmd = "proc2d %s %s"%(self.params['stackfile'], newstack)
if self.params['normalize'] is True:
emancmd += " edgenorm"
apEMAN.executeEmanCmd(emancmd)
### set final parameters
boxsize = apFile.getBoxSize(newstack)
apDisplay.printMsg("Boxsize: %i"%boxsize[0])
if not boxsize or boxsize <= 0:
apDisplay.printError("Could not determine stack size")
else:
self.boxsize = boxsize[0]
self.numpart = apFile.numImagesInStack(newstack)
apDisplay.printMsg("Num part: %i"%self.numpart)
if not self.numpart or self.numpart <= 0:
apDisplay.printError("Could not determine number of particles")
if self.numpart <= 1:
apDisplay.printError("Not enough particles to upload")
apStack.averageStack(newstack)
#self.params['commit'] = False
self.createStackData()
def useClusterForTemplate(self):
apDisplay.printMsg("Using clustering stack to make templates")
clusterstackdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterid'])
self.params['apix'] = clusterstackdata['clusterrun']['alignstack']['pixelsize']
stackfile = os.path.join(clusterstackdata['path']['path'], clusterstackdata['avg_imagicfile'])
self.params['templatelist'] = []
stackid = clusterstackdata['clusterrun']['alignstack']['stack'].dbid
sessiondata = apStack.getSessionDataFromStackId(stackid)
self.params['sessionname'] = sessiondata['name']
### check to see if stackimagenum is within the boundary of the stack
numpart = apFile.numImagesInStack(stackfile)
for i in self.params['imgnums'].split(","):
partnum = int(i)
if partnum > numpart or partnum < 0:
apDisplay.printError("'imgnums' is NOT within the boundary of the stack: %d > %d"%(partnum,numpart))
apDisplay.printMsg("Extracting image %d from cluster stack" % partnum)
templatename = "cluster%d-average%d.mrc"%(self.params['clusterid'],partnum)
abstemplatepath= os.path.join(clusterstackdata['path']['path'], templatename)
### run proc2d with params['stackimgnum']
emancmd = "proc2d %s %s first=%d last=%d" % (stackfile, abstemplatepath, partnum, partnum)
### create template
apDisplay.printMsg("creating "+templatename)
apEMAN.executeEmanCmd(emancmd)
if os.path.isfile(abstemplatepath):
self.params['templatelist'].append(abstemplatepath)
def start(self):
print self.params
if self.params['clusterId'] is not None:
self.clusterdata = appiondata.ApClusteringStackData.direct_query(self.params['clusterId'])
self.useClusterForTemplateStack()
elif self.params['alignId'] is not None:
self.aligndata = appiondata.ApAlignStackData.direct_query(self.params['alignId'])
self.useClusterForTemplateStack()
else:
apDisplay.printMsg("Using local file: '"+str(self.params['templatestack'])+"' to upload template")
# copy templates to final location
if str(self.params['templatestack'])[-4:] == ".img" or str(self.params['templatestack'])[-4:] == ".hed":
self.params['templatestack'] = self.params['templatestack'][:-4]
if str(self.params['runname'])[-4:] == ".img" or str(self.params['runname'])[-4:0] == ".hed":
self.params['runname'] = self.params['runname'][:-4]
shutil.copyfile(str(self.params['templatestack'])+".img", os.path.join(self.params['rundir'], str(self.params['runname'])+".img"))
shutil.copyfile(str(self.params['templatestack'])+".hed", os.path.join(self.params['rundir'], str(self.params['runname'])+".hed"))
self.numimages = apFile.numImagesInStack(os.path.join(self.params['rundir'], str(self.params['runname'])+".hed"))
# insert templates to database
if self.params['commit'] is True:
self.uploadTemplateStack(insert=True)
else:
apDisplay.printWarning("not committing results to DB")
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if self.params['partrad'] is None:
apDisplay.printError("particle radius was not defined")
### deal with particles
maxparticles = 150000
self.stackdata = apStack.getOnlyStackData(self.params['stackid'],
msg=False)
stackfile = os.path.join(self.stackdata['path']['path'],
self.stackdata['name'])
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: " +
str(maxparticles) + " requested: " +
str(self.params['numpart']))
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles " +
str(self.params['numpart']) +
" than available " +
str(apFile.numImagesInStack(stackfile)))
### get num processors
if self.params['nproc'] is None:
self.params['nproc'] = apParam.getNumProcessors()
### convert / check template data
if self.params['templatelist'] is None:
apDisplay.printError("template list was not provided")
self.templatelist = self.params['templatelist'].strip().split(",")
if not self.templatelist or type(self.templatelist) != type([]):
apDisplay.printError("could not parse template list=" +
self.params['templatelist'])
self.params['numtemplate'] = len(self.templatelist)
apDisplay.printMsg("Found " + str(self.params['numtemplate']) +
" templates")
### convert / check template data
if self.params['orientref'] is None:
apDisplay.printError("reference for orientation was not provided")
def checksizes(self):
newnots = apFile.numImagesInStack(self.params['notstack'])
newtilts = apFile.numImagesInStack(self.params['tiltstack'])
stackdata1 = apStack.getOnlyStackData(self.params['stack1'], msg=False)
stackpath1 = os.path.join(stackdata1['path']['path'], stackdata1['name'])
oldnots = apFile.numImagesInStack(stackpath1)
stackdata2 = apStack.getOnlyStackData(self.params['stack2'], msg=False)
stackpath2 = os.path.join(stackdata2['path']['path'], stackdata2['name'])
oldtilts = apFile.numImagesInStack(stackpath2)
if newtilts != oldtilts:
apDisplay.printWarning("tilted stack are different sizes: %d vs. %d part"%(newtilts,oldtilts))
else:
apDisplay.printMsg("tilted stack are the sames sizes: %d part"%(newtilts))
if newnots != oldnots:
apDisplay.printWarning("untilted stack are different sizes: %d vs. %d part"%(newnots,oldnots))
else:
apDisplay.printMsg("untilted stack are the sames sizes: %d part"%(newnots))
def appendStackFileToStackFile(stackfile, mergestackfile, msg=True):
"""
takes two stack files and merges them into second file
"""
### initialization
t0 = time.time()
root = os.path.splitext(mergestackfile)[0]
mergeheaderfile = root + ".hed"
mergedatafile = root + ".img"
root = os.path.splitext(stackfile)[0]
stackheaderfile = root + ".hed"
stackdatafile = root + ".img"
### merge data files
addnumpart = apFile.numImagesInStack(stackheaderfile)
addsize = apFile.fileSize(stackdatafile)
premergenumpart = apFile.numImagesInStack(mergeheaderfile)
premergesize = apFile.fileSize(mergedatafile)
fout = file(mergedatafile, 'ab')
fin = file(stackdatafile, 'rb')
shutil.copyfileobj(fin, fout, 65536)
fin.close()
fout.close()
finalsize = apFile.fileSize(mergedatafile)
if finalsize != addsize + premergesize:
apDisplay.printError(
"size mismatch %s vs. %s + %s = %s" %
(apDisplay.bytes(finalsize), apDisplay.bytes(addsize),
apDisplay.bytes(premergesize),
apDisplay.bytes(premergesize + addsize)))
### merge header files
fout = file(mergeheaderfile, 'ab')
fin = file(stackheaderfile, 'rb')
shutil.copyfileobj(fin, fout, 65536)
fin.close()
fout.close()
numberStackFile(mergeheaderfile, msg=msg)
finalnumpart = apFile.numImagesInStack(mergeheaderfile)
if finalnumpart != addnumpart + premergenumpart:
apDisplay.printError("size mismatch %d vs. %d + %d = %d" %
(finalnumpart, addnumpart, premergenumpart,
addnumpart + premergenumpart))
def numberStackFile(oldheadfile, startnum=0, msg=True):
"""
Takes an Imagic Stack header file and numbers the particles
based on
http://www.imagescience.de/formats/formats.htm
"""
if msg is True:
apDisplay.printMsg("saving particle numbers to stack header")
t0 = time.time()
newheadfile = (os.path.splitext(oldheadfile)[0] + "-temp.hed")
numimg = apFile.numImagesInStack(oldheadfile)
#print numimg
numimg_fbyte = intToFourByte(numimg - 1)
of = open(oldheadfile, 'rb')
nf = open(newheadfile, 'wb')
i = startnum
while i < numimg:
imgnum_fbyte = intToFourByte(i)
data = of.read(1024)
### start new string
headerstr = ""
### first image number
headerstr += intToFourByte(i)
### number of images, less one
headerstr += numimg_fbyte
### always 0,1 ???
headerstr += intToFourByte(0)
headerstr += intToFourByte(1)
### creation date: day, month, year, hour, min, sec
headerstr += intToFourByte(time.localtime()[2])
headerstr += intToFourByte(
time.localtime()[1]) #eman always uses month-1?
headerstr += intToFourByte(time.localtime()[0])
headerstr += intToFourByte(time.localtime()[3])
headerstr += intToFourByte(time.localtime()[4])
headerstr += intToFourByte(time.localtime()[5])
### append other header info, 4 character per item
headerstr += data[10 * 4:61 * 4]
### first image number, EMAN does this
headerstr += intToFourByte(i)
### append other header info, 4 character per item
headerstr += data[62 * 4:]
#print ""
#print "old=", fourByteToInt(data[0:4]), fourByteToInt(data[4:8]), fourByteToInt(data[8:12])
#print "new=", fourByteToInt(headerstr[0:4]), fourByteToInt(headerstr[4:8]), fourByteToInt(headerstr[8:12])
nf.write(headerstr)
i += 1
if not os.path.isfile(newheadfile):
apDisplay.printError("failed to number particles in stack file")
apFile.removeFile(oldheadfile)
shutil.move(newheadfile, oldheadfile)
if msg is True:
apDisplay.printMsg("completed %d particles in %s" %
(numimg, apDisplay.timeString(time.time() - t0)))
return True
def fillSimilarityMatrix(stackfile):
### Get initial correlation values
### this is really, really slow
numpart = apFile.numImagesInStack(stackfile)
similarfile = "similarities.dat"
if os.path.isfile(similarfile):
simf = open(similarfile, 'r')
simlist = []
count = 0
for line in simf:
count += 1
sline = line.strip()
slist = sline.split()
ccval = float(slist[2])
simlist.append(ccval)
simf.close()
apDisplay.printMsg("There are %d lines in the sim file: %s"%(count, similarfile))
if count == numpart*(numpart-1):
### we have a valid file already
return similarfile, simlist
### read data and estimate time
imagicdict = apImagicFile.readImagic(stackfile)
partarray = imagicdict['images']
numpart = partarray.shape[0]
boxsize = partarray.shape[1]
#timeper = 27.0e-9
timeper = 17.0e-9
apDisplay.printMsg("Computing CC values in about %s"
%(apDisplay.timeString(timeper*numpart**2*boxsize**2)))
### Computing CC values
simf = open(similarfile, 'w')
cctime = time.time()
simlist = []
for i in range(0, numpart):
if i % 100 == 99:
sys.stderr.write(".")
for j in range(i+1, numpart):
ccval = self.getCCValue(partarray[i],partarray[j])
str1 = "%05d %05d %.10f\n" % (i+1, j+1, ccval)
simf.write(str1)
str2 = "%05d %05d %.10f\n" % (j+1, i+1, ccval)
simf.write(str2)
simlist.append(ccval)
sys.stderr.write("\n")
simf.close()
del partarray
del imagicdict['images']
apDisplay.printMsg("CC calc time: %s :: %s per part :: %s per part per pixel"
%(apDisplay.timeString(time.time()-cctime),
apDisplay.timeString((time.time()-cctime)/numpart**2),
apDisplay.timeString((time.time()-cctime)/numpart**2/boxsize**2)))
return similarfile, simlist
def appendToStack(self, stackdata):
addfile = os.path.join( stackdata['path']['path'], stackdata['name'] )
addnumpart = apFile.numImagesInStack(addfile)
orignumpart = apFile.numImagesInStack(self.combinefile)
cmd = "proc2d "+addfile+" "+self.combinefile
apDisplay.printMsg("adding "+str(addnumpart)+" particles to "+str(orignumpart)+" particles")
apEMAN.executeEmanCmd(cmd, verbose=True, showcmd=True)
newnumpart = apFile.numImagesInStack(self.combinefile)
apDisplay.printMsg("added "+str(addnumpart)+" particles from stackid="+str(stackdata.dbid)+" to "
+str(orignumpart)+" particles giving a new combined stack of "+str(newnumpart)+" particles")
if addnumpart + orignumpart < newnumpart:
apDisplay.printError("Error in stack merging, too few particles added")
return
def numberStackFile(oldheadfile, startnum=0):
"""
Takes an Imagic Stack header file and numbers the particles
based on
http://www.imagescience.de/formats/formats.htm
"""
apDisplay.printMsg("saving particle numbers to stack header")
t0 = time.time()
newheadfile = (os.path.splitext(oldheadfile)[0]+"-temp.hed")
numimg = apFile.numImagesInStack(oldheadfile)
#print numimg
numimg_fbyte = intToFourByte(numimg-1)
of = open(oldheadfile, 'rb')
nf = open(newheadfile, 'wb')
i = startnum
while i < numimg:
imgnum_fbyte = intToFourByte(i)
data = of.read(1024)
### start new string
headerstr = ""
### first image number
headerstr += intToFourByte(i)
### number of images, less one
headerstr += numimg_fbyte
### always 0,1 ???
headerstr += intToFourByte(0)
headerstr += intToFourByte(1)
### creation date: day, month, year, hour, min, sec
headerstr += intToFourByte(time.localtime()[2])
headerstr += intToFourByte(time.localtime()[1]) #eman always uses month-1?
headerstr += intToFourByte(time.localtime()[0])
headerstr += intToFourByte(time.localtime()[3])
headerstr += intToFourByte(time.localtime()[4])
headerstr += intToFourByte(time.localtime()[5])
### append other header info, 4 character per item
headerstr += data[10*4:61*4]
### first image number, EMAN does this
headerstr += intToFourByte(i)
### append other header info, 4 character per item
headerstr += data[62*4:]
#print ""
#print "old=", fourByteToInt(data[0:4]), fourByteToInt(data[4:8]), fourByteToInt(data[8:12])
#print "new=", fourByteToInt(headerstr[0:4]), fourByteToInt(headerstr[4:8]), fourByteToInt(headerstr[8:12])
nf.write(headerstr)
i += 1
if not os.path.isfile(newheadfile):
apDisplay.printError("failed to number particles in stack file")
apFile.removeFile(oldheadfile)
shutil.move(newheadfile, oldheadfile)
apDisplay.printMsg("completed %d particles in %s"%(numimg, apDisplay.timeString(time.time()-t0)))
return True
def wrtieEvenParticles(self, stackfile, outfile=None):
numpart = apFile.numImagesInStack(stackfile)
evenPartList = 2 * numpy.arange(numpart / 2) + 2
self.stacksToMerge = []
if outfile is None:
root = os.path.splitext(stackfile)[0]
outfile = root + ".even.hed"
self.start(stackfile, partlist=evenPartList)
mergeStacks(self.stacksToMerge, outfile, self.msg)
for tempstackfile in self.stacksToMerge:
apFile.removeStack(tempstackfile, warn=self.msg)
return outfile
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
### convert / check template data
if self.params['templatelist'] is None:
apDisplay.printError("template list was not provided")
self.templatelist = self.params['templatelist'].strip().split(",")
if not self.templatelist or type(self.templatelist) != type([]):
apDisplay.printError("could not parse template list="+self.params['templatelist'])
self.params['numtemplate'] = len(self.templatelist)
apDisplay.printMsg("Found "+str(self.params['numtemplate'])+" templates")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if not self.params['fastmode'] in self.fastmodes:
apDisplay.printError("fast mode must be on of: "+str(self.fastmodes))
if not self.params['converge'] in self.convergemodes:
apDisplay.printError("converge mode must be on of: "+str(self.convergemodes))
maxparticles = 150000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "
+ str(maxparticles) + " requested: " + str(self.params['numpart']))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
boxsize = apStack.getStackBoxsize(self.params['stackid'])
self.clipsize = int(math.floor(boxsize/float(self.params['bin']*2)))*2
if self.params['clipsize'] is not None:
if self.params['clipsize'] >= self.clipsize:
apDisplay.printError("requested clipsize is too big %d > %d"
%(self.params['clipsize'],self.clipsize))
self.clipsize = self.params['clipsize']
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
def makeNewStack(oldstack, newstack, listfile=None, remove=False, bad=False):
"""
selects particular particles from a stack
"""
if not os.path.isfile(oldstack):
apDisplay.printWarning("could not find old stack: " + oldstack)
if os.path.isfile(newstack):
if remove is True:
apDisplay.printWarning("removing old stack: " + newstack)
time.sleep(2)
apFile.removeStack(newstack)
else:
apDisplay.printError("new stack already exists: " + newstack)
apDisplay.printMsg("creating a new stack\n\t" + newstack +
"\nfrom the oldstack\n\t" + oldstack + "\n")
a = proc2dLib.RunProc2d()
a.setValue('infile', oldstack)
a.setValue('outfile', newstack)
if listfile is not None:
a.setValue('list', listfile)
a.run()
if bad is True and listfile is not None:
### run only if num bad particles < num good particles
newstacknumpart = apFile.numImagesInStack(newstack)
oldstacknumpart = apFile.numImagesInStack(oldstack)
if newstacknumpart > oldstacknumpart / 2:
### create bad.hed stack with all bad particles
badstack = os.path.join(os.path.dirname(newstack), "bad.hed")
emancmd = "proc2d %s %s exclude=%s" % (oldstack, badstack,
listfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
else:
apDisplay.printMsg(
"Rejecting more particles than keeping, not creating a bad stack"
)
return
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
if self.params['partrad'] is None:
apDisplay.printError("particle radius was not defined")
### deal with particles
maxparticles = 150000
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(self.stackdata['path']['path'], self.stackdata['name'])
if self.params['numpart'] is None:
self.params['numpart'] = apFile.numImagesInStack(stackfile)
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: "+str(maxparticles)+" requested: "+str(self.params['numpart']))
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles "+str(self.params['numpart'])
+" than available "+str(apFile.numImagesInStack(stackfile)))
### get num processors
if self.params['nproc'] is None:
self.params['nproc'] = apParam.getNumProcessors()
### convert / check template data
if self.params['templatelist'] is None:
apDisplay.printError("template list was not provided")
self.templatelist = self.params['templatelist'].strip().split(",")
if not self.templatelist or type(self.templatelist) != type([]):
apDisplay.printError("could not parse template list="+self.params['templatelist'])
self.params['numtemplate'] = len(self.templatelist)
apDisplay.printMsg("Found "+str(self.params['numtemplate'])+" templates")
### convert / check template data
if self.params['orientref'] is None:
apDisplay.printError("reference for orientation was not provided")
def stackToEmanMrc(stackfile):
numpart = apFile.numImagesInStack(stackfile)
partlist = []
for i in range(numpart):
mrcfile = "eman%02d.mrc" % (i)
emancmd = "proc2d %s %s first=%d last=%d" % (stackfile, mrcfile, i, i)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=False)
if not os.path.isfile(mrcfile):
print "Failed to create MRC"
sys.exit(1)
part = mrc.read(mrcfile)
apFile.removeFile(mrcfile)
partlist.append(part)
return partlist
def checkConflicts(self):
if self.params['stackid'] is None:
apDisplay.printError("stack id was not defined")
if self.params['description'] is None:
apDisplay.printError("run description was not defined")
if self.params['runname'] is None:
apDisplay.printError("run name was not defined")
maxparticles = 150000
if self.params['numpart'] > maxparticles:
apDisplay.printError("too many particles requested, max: " +
str(maxparticles) + " requested: " +
str(self.params['numpart']))
if self.params['initmethod'] not in self.initmethods:
apDisplay.printError("unknown initialization method defined: " +
str(self.params['initmethod']) + " not in " +
str(self.initmethods))
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
if self.params['numpart'] > apFile.numImagesInStack(stackfile):
apDisplay.printError("trying to use more particles " +
str(self.params['numpart']) +
" than available " +
str(apFile.numImagesInStack(stackfile)))
def stackToEmanMrc(stackfile):
numpart = apFile.numImagesInStack(stackfile)
partlist = []
for i in range(numpart):
mrcfile = "eman%02d.mrc"%(i)
emancmd = "proc2d %s %s first=%d last=%d"%(stackfile, mrcfile, i, i)
apEMAN.executeEmanCmd(emancmd, verbose=False, showcmd=False)
if not os.path.isfile(mrcfile):
print "Failed to create MRC"
sys.exit(1)
part = mrc.read(mrcfile)
apFile.removeFile(mrcfile)
partlist.append(part)
return partlist
def useStackForTemplate(self):
apDisplay.printMsg("Using stack to make templates")
sessiondata = apStack.getSessionDataFromStackId(self.params['stackid'])
self.params['sessionname'] = sessiondata['name']
self.params['apix'] = apStack.getStackPixelSizeFromStackId(
self.params['stackid'])
stackdata = apStack.getOnlyStackData(self.params['stackid'])
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
self.params['templatelist'] = []
if self.params['avgstack'] is True:
### averaging all particles together
apDisplay.printMsg("Averaging all images in stack")
templatename = "stack%d-average.mrc" % (self.params['stackid'])
oldtemplatepath = os.path.join(stackdata['path']['path'],
"average.mrc")
abstemplatepath = os.path.join(stackdata['path']['path'],
templatename)
if os.path.isfile(oldtemplatepath):
shutil.copy(oldtemplatepath, abstemplatepath)
else:
### average all images using proc2d
emancmd = "proc2d %s %s average" % (stackfile, abstemplatepath)
apEMAN.executeEmanCmd(emancmd)
if os.path.isfile(abstemplatepath):
self.params['templatelist'] = [abstemplatepath]
elif self.params['imgnums'] is not None:
### check to see if stackimagenum is within the boundary of the stack
numpart = apFile.numImagesInStack(stackfile)
for i in self.params['imgnums'].split(","):
partnum = int(i)
if partnum > numpart or partnum < 0:
apDisplay.printError(
"'imgnums' is NOT within the boundary of the stack: %d > %d"
% (partnum, numpart))
apDisplay.printMsg("Extracting image %d from stack" % partnum)
templatename = "stack%d-particle%d.mrc" % (
self.params['stackid'], partnum)
abstemplatepath = os.path.join(self.params['rundir'],
templatename)
### run proc2d with params['stackimgnum']
emancmd = "proc2d %s %s first=%d last=%d" % (
stackfile, abstemplatepath, partnum, partnum)
### create template
apDisplay.printMsg("creating " + templatename)
apEMAN.executeEmanCmd(emancmd)
if os.path.isfile(abstemplatepath):
self.params['templatelist'].append(abstemplatepath)
def makeNewStack(oldstack, newstack, listfile=None, remove=False, bad=False):
"""
selects particular particles from a stack
"""
if not os.path.isfile(oldstack):
apDisplay.printWarning("could not find old stack: "+oldstack)
if os.path.isfile(newstack):
if remove is True:
apDisplay.printWarning("removing old stack: "+newstack)
time.sleep(2)
apFile.removeStack(newstack)
else:
apDisplay.printError("new stack already exists: "+newstack)
apDisplay.printMsg("creating a new stack\n\t"+newstack+
"\nfrom the oldstack\n\t"+oldstack+"\n")
a = proc2dLib.RunProc2d()
a.setValue('infile',oldstack)
a.setValue('outfile',newstack)
if listfile is not None:
a.setValue('list',listfile)
a.run()
if bad is True and listfile is not None:
### run only if num bad particles < num good particles
newstacknumpart = apFile.numImagesInStack(newstack)
oldstacknumpart = apFile.numImagesInStack(oldstack)
if newstacknumpart > oldstacknumpart/2:
### create bad.hed stack with all bad particles
badstack = os.path.join(os.path.dirname(newstack), "bad.hed")
emancmd = "proc2d %s %s exclude=%s"%(oldstack, badstack, listfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
else:
apDisplay.printMsg("Rejecting more particles than keeping, not creating a bad stack")
return
def appendToStack(self, stackdata):
addfile = os.path.join(stackdata['path']['path'], stackdata['name'])
addnumpart = apFile.numImagesInStack(addfile)
orignumpart = apFile.numImagesInStack(self.combinefile)
cmd = "proc2d " + addfile + " " + self.combinefile
apDisplay.printMsg("adding " + str(addnumpart) + " particles to " +
str(orignumpart) + " particles")
apEMAN.executeEmanCmd(cmd, verbose=True, showcmd=True)
newnumpart = apFile.numImagesInStack(self.combinefile)
apDisplay.printMsg("added " + str(addnumpart) +
" particles from stackid=" + str(stackdata.dbid) +
" to " + str(orignumpart) +
" particles giving a new combined stack of " +
str(newnumpart) + " particles")
if addnumpart + orignumpart < newnumpart:
apDisplay.printError(
"Error in stack merging, too few particles added")
return
def postProcessParticleStack(self, imgdata, imgstackfile, boxedpartdatas, parttree_length):
### phase flipping
t0 = time.time()
if self.params['phaseflipped'] is True:
if self.params['fliptype'] == 'emantilt':
### ctf correct individual particles with tilt using Eman
imgstackfile = self.tiltPhaseFlipParticles(imgdata, imgstackfile, boxedpartdatas)
self.ctftimes.append(time.time()-t0)
elif self.params['fliptype'] == 'emanpart':
### ctf correct individual particles using Eman
imgstackfile = self.phaseFlipParticles(imgdata, imgstackfile)
self.ctftimes.append(time.time()-t0)
else:
apDisplay.printMsg("phase flipped whole image already")
else:
apDisplay.printMsg("not phase flipping particles")
numpart = apFile.numImagesInStack(imgstackfile)
apDisplay.printMsg(str(numpart)+" particles were boxed out from "+self.shortname)
if parttree_length != numpart:
apDisplay.printError("There is a mismatch in the number of particles expected and that were boxed")
### rectangular box masking
if self.params['boxmask'] is not None:
# create a stack of rectangular masks, which will be applied to
# the particles as they are added to the final stack
pixsz = apDatabase.getPixelSize(imgdata)*self.params['bin']
boxsz = self.boxsize/self.params['bin']
bxmask = int(self.params['bxmask']/pixsz)
bymask = int(self.params['bymask']/pixsz)
if self.params['bimask'] > 0:
bimask = int(self.params['bimask']/pixsz)
else: bimask = None
falloff = self.params['falloff']/pixsz
# adjust masks for falloff
bxmask -= falloff/2
bymask = (bymask/2)-(falloff/2)
self.params['boxmaskf'] = os.path.splitext(imgstackfile)[0]+"-mask.hed"
apBoxer.boxMaskStack(self.params['boxmaskf'], boxedpartdatas, boxsz,
bxmask, bymask, falloff, bimask, norotate=self.params['rotate'])
return imgstackfile
def postLoop(self):
if len(self.stackarray) > 0:
stackroot = self.outstackfile[:-4]
stackname = "%s-%d.hed"%(stackroot, self.imgnum)
apDisplay.printMsg("writing single particles to file "+stackname)
self.stacklist.append(stackname)
apFile.removeStack(stackname, warn=False)
apImagicFile.writeImagic(self.stackarray, stackname, msg=False)
### merge stacks
apFile.removeStack(self.outstackfile, warn=False)
apImagicFile.mergeStacks(self.stacklist, self.outstackfile)
filepart = apFile.numImagesInStack(self.outstackfile)
if filepart != self.imgnum:
apDisplay.printError("number merged particles (%d) not equal number expected particles (%d)"%
(filepart, numpart))
for stackname in self.stacklist:
apFile.removeStack(stackname, warn=False)
### summarize
apDisplay.printColor("merged %d particles in %s"%(self.imgnum, apDisplay.timeString(time.time()-self.starttime)), "cyan")
def start(self):
self.writeParams()
stackdata = apStack.getOnlyStackData(self.params["stackid"], msg=False)
stackpath = os.path.abspath(stackdata["path"]["path"])
stackfile = os.path.join(stackpath, "start.hed")
self.params["localstack"] = os.path.join(stackpath, self.timestamp + ".hed")
proccmd = "proc2d " + stackfile + " " + self.params["localstack"] + " apix=" + str(self.params["step"])
if self.params["bin"] > 1:
proccmd += " shrink=%d" % int(self.params["bin"])
proccmd += " last=" + str(self.params["numpart"] - 1)
apParam.runCmd(proccmd, "EMAN", verbose=True)
if self.params["numpart"] != apFile.numImagesInStack(self.params["localstack"]):
apDisplay.printError("Missing particles in stack")
apXmipp.breakupStackIntoSingleFiles(self.params["localstack"], filetype="mrc")
if self.params["prehip"] == "yes":
if self.params["rise"] is not None:
self.writeLLBO1()
elif self.params["ll1"] is not None:
self.writeLLBO2()
elif self.params["rise"] is None and self.params["ll1"] is None:
apDisplay.printError(
"You must specify either rise and twist or (1,0) and (0,1) layer lines to run preHIP"
)
apDisplay.printMsg("now running s_prehip to set up input files")
apDisplay.printMsg(
"Make sure the layer line/bessel order assignment is correct. If it is not, you may need to adjust some of the input variables."
)
cmd = "s_prehip"
proc = subprocess.Popen(cmd)
proc.wait()
else:
apDisplay.printMsg("now running s_hip2: Phoelix programs")
cmd = "s_hip2"
proc = subprocess.Popen(cmd)
proc.wait()
# apParam.runCmd(cmd, package="Phoelix")
self.putFilesInStack()
self.insertHipRunData()
self.insertHipParamsData()
self.insertHipIterData()
self.insertHipParticleData()
def useStackForTemplate(self):
apDisplay.printMsg("Using stack to make templates")
sessiondata = apStack.getSessionDataFromStackId(self.params['stackid'])
self.params['sessionname'] = sessiondata['name']
self.params['apix'] = apStack.getStackPixelSizeFromStackId(self.params['stackid'])
stackdata = apStack.getOnlyStackData(self.params['stackid'])
stackfile = os.path.join(stackdata['path']['path'], stackdata['name'])
self.params['templatelist'] = []
if self.params['avgstack'] is True:
### averaging all particles together
apDisplay.printMsg("Averaging all images in stack")
templatename = "stack%d-average.mrc"%(self.params['stackid'])
oldtemplatepath = os.path.join(stackdata['path']['path'], "average.mrc")
abstemplatepath = os.path.join(stackdata['path']['path'], templatename)
if os.path.isfile(oldtemplatepath):
shutil.copy(oldtemplatepath, abstemplatepath)
else:
### average all images using proc2d
emancmd = "proc2d %s %s average" % (stackfile, abstemplatepath)
apEMAN.executeEmanCmd(emancmd)
if os.path.isfile(abstemplatepath):
self.params['templatelist'] = [abstemplatepath]
elif self.params['imgnums'] is not None:
### check to see if stackimagenum is within the boundary of the stack
numpart = apFile.numImagesInStack(stackfile)
for i in self.params['imgnums'].split(","):
partnum = int(i)
if partnum > numpart or partnum < 0:
apDisplay.printError("'imgnums' is NOT within the boundary of the stack: %d > %d"%(partnum,numpart))
apDisplay.printMsg("Extracting image %d from stack" % partnum)
templatename = "stack%d-particle%d.mrc"%(self.params['stackid'],partnum)
abstemplatepath= os.path.join(self.params['rundir'], templatename)
### run proc2d with params['stackimgnum']
emancmd = "proc2d %s %s first=%d last=%d" % (stackfile, abstemplatepath, partnum, partnum)
### create template
apDisplay.printMsg("creating "+templatename)
apEMAN.executeEmanCmd(emancmd)
if os.path.isfile(abstemplatepath):
self.params['templatelist'].append(abstemplatepath)
def getParticleParams(self):
apDisplay.printColor("now getting particle shift / rotation / correlation parameters", "cyan")
f = open(os.path.join(self.params['rundir'], "outparams.plt"), "r")
lines = f.readlines()
strip = [line.strip() for line in lines]
split = [params.split() for params in strip]
params = []
for list in split:
numberlist = [eval(p) for p in list]
### figure out if the particle is mirrored, based on which reference it belongs to
numrefs = apFile.numImagesInStack(os.path.join(self.params['rundir'], "references.hed"))
half = numrefs / 2
if numberlist[4] > half and self.params['mirror'] is True:
mirror = 1
else:
mirror = 0
numberlist.append(mirror)
params.append(numberlist)
return params