def getSessionData(self):
sessiondata = None
if 'sessionname' in self.params and self.params['sessionname'] is not None:
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
if not sessiondata and 'stackid' in self.params:
from appionlib import apStack
sessiondata = apStack.getSessionDataFromStackId(self.params['stackid'])
if not sessiondata:
### works with only canonical session names
s = re.search('/([0-9][0-9][a-z][a-z][a-z][0-9][0-9][^/]*)/', self.params['rundir'])
if s:
self.params['sessionname'] = s.groups()[0]
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
return sessiondata
def getSessionData(self):
sessiondata = None
if "sessionname" in self.params and self.params["sessionname"] is not None:
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
if not sessiondata and "stackid" in self.params:
from appionlib import apStack
sessiondata = apStack.getSessionDataFromStackId(self.params["stackid"])
if not sessiondata:
### works with only canonical session names
s = re.search("/([0-9][0-9][a-z][a-z][a-z][0-9][0-9][^/]*)/", self.params["rundir"])
if s:
self.params["sessionname"] = s.groups()[0]
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
return sessiondata
def insertHipParamsData(self):
HipParams = appiondata.ApHipParamsData()
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
HipParams["session"] = sessiondata
HipParams["hipRun"] = self.params["HipRun"]
HipParams["numpart"] = self.params["numpart"]
HipParams["replen"] = self.params["replen"]
HipParams["diam"] = self.params["diameter"]
HipParams["diaminner"] = self.params["diaminner"]
HipParams["subunits"] = self.params["subunits"]
HipParams["xlngth"] = self.params["xlngth"]
HipParams["yht2"] = self.params["yht2"]
HipParams["padval"] = self.params["padval"]
HipParams["rescut"] = self.params["rescut"]
HipParams["filval"] = self.params["filval"]
HipParams["strong"] = os.path.join(self.params["rundir"], "strong.sa")
HipParams["range"] = os.path.join(self.params["rundir"], "range.sa")
HipParams["llbo"] = os.path.join(self.params["rundir"], "llbo.sa")
HipParams["final_stack"] = os.path.join(self.params["rundir"], "start.hed")
if self.params["commit"] is True:
HipParams.insert()
else:
print HipParams
self.params["HipParamsID"] = HipParams.dbid
print "self.params['HipParamsID']", self.params["HipParamsID"]
return
def onInit(self):
"""
standard appionScript
"""
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
if sessiondata:
### METHOD 1 : session already exists
apDisplay.printColor("Add images to an existing session", "cyan")
### what about linking an existing session with project id to a new project id
oldprojectid = apProject.getProjectIdFromSessionName(self.params['sessionname'])
if oldprojectid != self.params['projectid']:
apDisplay.printError("You cannot assign an existing session (PID %d) to a different project (PID %d)"%
(oldprojectid, self.params['projectid']))
else:
### METHOD 2 : create new session
apDisplay.printColor("Creating a new session", "cyan")
### die for now
apDisplay.printError("Uploading stack to a new session not allowed")
try:
directory = leginon.leginonconfig.mapPath(leginon.leginonconfig.IMAGE_PATH)
except AttributeError:
apDisplay.printWarning("Could not set directory")
directory = ''
userdata = None
sessiondata = self.createSession(userdata, self.params['sessionname'], self.params['description'], directory)
self.linkSessionProject(sessiondata, self.params['projectid'])
self.sessiondata = sessiondata
return
def insertHipParamsData(self):
HipParams = appiondata.ApHipParamsData()
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
HipParams['session'] = sessiondata
HipParams['hipRun'] = self.params['HipRun']
HipParams['numpart'] = self.params['numpart']
HipParams['replen'] = self.params['replen']
HipParams['diam'] = self.params['diameter']
HipParams['diaminner'] = self.params['diaminner']
HipParams['subunits'] = self.params['subunits']
HipParams['xlngth'] = self.params['xlngth']
HipParams['yht2'] = self.params['yht2']
HipParams['padval'] = self.params['padval']
HipParams['rescut'] = self.params['rescut']
HipParams['filval'] = self.params['filval']
HipParams['strong'] = os.path.join(self.params['rundir'], "strong.sa")
HipParams['range'] = os.path.join(self.params['rundir'], "range.sa")
HipParams['llbo'] = os.path.join(self.params['rundir'], "llbo.sa")
HipParams['final_stack'] = os.path.join(self.params['rundir'], "start.hed")
if self.params['commit'] is True:
HipParams.insert()
else:
print HipParams
self.params['HipParamsID'] = HipParams.dbid
print "self.params['HipParamsID']",self.params['HipParamsID']
return
def getStackIdFromSubStackName(substackname, sessionname, msg=True):
"""
For a given run name and session name find stack id
"""
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
stackrunq = appiondata.ApStackRunData()
stackrunq['session'] = sessiondata
stackq = appiondata.ApStackData()
stackq['substackname'] = substackname
runsinstackq = appiondata.ApRunsInStackData()
runsinstackq['stackRun'] = stackrunq
runsinstackq['stack'] = stackq
runsindatas = runsinstackq.query()
if not runsindatas:
return None
if len(runsindatas) == 1:
### simpe case
stackid = runsindatas[0]['stack'].dbid
else:
for runsindata in runsindatas:
print runsindata
apDisplay.printError("Found too many sub-stacks for specified criteria")
apDisplay.printMsg("Found stack id %d with substackname %s from session %s"%(stackid, substackname, sessionname))
return stackid
def getNumAlignRunsFromSession(sessionname):
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
stackrunq = appiondata.ApStackRunData()
stackrunq['session'] = sessiondata
runsinstackq = appiondata.ApRunsInStackData()
runsinstackq['stackRun'] = stackrunq
runsindatas = runsinstackq.query()
if not runsindatas:
return 0
alignidlist = []
for runsindata in runsindatas:
alignstackq = appiondata.ApAlignStackData()
alignstackq['stack'] = runsindata['stack']
alignstackdatas = alignstackq.query()
if not alignstackdatas:
continue
for alignstackdata in alignstackdatas:
alignrunid = alignstackdata['alignrun'].dbid
if not alignrunid in alignidlist:
alignidlist.append(alignrunid)
return len(alignidlist)
def checkPreviousTemplateRun(self):
### check if we have a previous selection run
selectrunq = appiondata.ApSelectionRunData()
selectrunq['name'] = self.params['runname']
selectrunq['session'] = sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
rundatas = selectrunq.query(results=1)
if not rundatas:
return True
rundata = rundatas[0]
### check if we have a previous template run
templaterunq = appiondata.ApTemplateRunData(selectionrun=rundata)
templatedatas = templaterunq.query()
if not templatedatas:
return True
### make sure of using same number of templates
if len(self.params['templateIds']) != len(templatedatas):
apDisplay.printError("different number of templates from last run")
### make sure we have same rotation parameters
for i, templateid in enumerate(self.params['templateIds']):
templaterunq = appiondata.ApTemplateRunData()
templaterunq['selectionrun'] = rundata
templaterunq['template'] = appiondata.ApTemplateImageData.direct_query(templateid)
### this is wrong only check last template run not this run
queryresult = templaterunq.query(results=1)
if queryresult:
templatedata=queryresult[0]
return True
def checkConflicts(self):
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.sessiondata = sessiondata
if self.params['goodalignerid'] is None:
if self.params['tiltseriesnumber'] is None :
apDisplay.printError("There is no tilt series specified")
if self.params['runname'] is None:
apDisplay.printError("enter a run name")
if self.params['description'] is None:
apDisplay.printError("enter a description, e.g. --description='awesome data'")
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseriesnumber'],sessiondata)
self.params['tiltseries'] = tiltdata
if self.params['othertilt'] is not None:
othertiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['othertilt'],sessiondata)
self.params['othertiltseries'] = othertiltdata
else:
self.params['othertiltseries'] = None
if self.params['alignmethod'] == 'leginon':
self.params['cycle'] = 0
self.params['region'] = 100
else:
self.createParamsFromGoodAligner(self.params['goodalignerid'])
if self.params['goodcycle'] is None:
if self.params['goodstart'] or self.params['goodend']:
apDisplay.printError("Cannot specify reseting image range without knowing the cycle number to reset to")
elif self.params['goodcycle'] >= self.params['cycle']:
apDisplay.printError("Only older cycle can be used as the base to reset image origin to")
# Sampling is needed for protomo1 and 2, not imod
if self.params['sample'] is not None:
if self.params['sample'] < 1:
apDisplay.printError("Sampling factor (--sample) must be greater or equal to 1.")
def setRunDir(self):
"""
this function only runs if no rundir is defined at the command line
"""
if self.params['rundir'] is None:
if ('sessionname' in self.params and self.params['sessionname'] is not None ):
# command line users may use sessionname rather than expId
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.params['rundir'] = self.getDefaultBaseAppionDir(sessiondata,[self.processdirname,self.params['runname']])
else:
if ('expId' in self.params and self.params['expId']):
# expId should always be included from appionwrapper derived appionscript
sessiondata = apDatabase.getSessionDataFromSessionId(self.params['expId'])
self.params['rundir'] = self.getDefaultBaseAppionDir(sessiondata,[self.processdirname,self.params['runname']])
# The rest should not be needed with appionwrapper format
from appionlib import apStack
if ( self.params['rundir'] is None
and 'reconid' in self.params
and self.params['reconid'] is not None ):
self.params['stackid'] = apStack.getStackIdFromRecon(self.params['reconid'], msg=False)
if ( self.params['rundir'] is None
and 'stackid' in self.params
and self.params['stackid'] is not None ):
#auto set the run directory
stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
path = os.path.abspath(stackdata['path']['path'])
path = os.path.dirname(path)
path = os.path.dirname(path)
self.params['rundir'] = os.path.join(path, self.processdirname, self.params['runname'])
self.params['outdir'] = self.params['rundir']
def checkConflicts(self):
if self.params['sessionname'] is None:
apDisplay.printError("Enter a session name (e.g. --session=06mar12a)")
if self.params['pdbid'] is None and self.params['pdbfile'] is None:
apDisplay.printError("Specify a PDB id or PDB file")
if self.params['pdbid'] is not None and self.params['pdbfile'] is not None:
apDisplay.printError("Specify only one of PDB id or PDB file")
if self.params['pdbfile'] is not None and not os.path.isfile(self.params['pdbfile']):
apDisplay.printError("PDB file does not exist")
### PDB is case-insensitve, so make all caps for consistency
if self.params['pdbid'] is not None:
self.params['pdbid'] = self.params['pdbid'].upper()
if self.params['lowpass'] is None:
apDisplay.printError("Enter a lowpass value")
if self.params['apix'] is None:
apDisplay.printError("Specify a pixel size")
if self.params['lowpass'] < 1.5*self.params['apix']:
apDisplay.printWarning("Lowpass is less than pixelsize, overriding lp=1.5*apix")
self.params['lowpass'] = 1.5*self.params['apix']
if self.params['symmetry'] is None and self.params['pdbfile'] is not None:
apDisplay.printError("Please specify symmetry group")
elif self.params['symmetry'] is None:
apDisplay.printWarning("No symmetry specified using 'c1'")
self.params['symmetry'] = 'c1'
self.params['symdata'] = apSymmetry.findSymmetry(self.params['symmetry'])
self.sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
def insertHipIterData(self):
for i in range(3):
iternum = i + 1
apDisplay.printColor("\nUploading iteration %d of %d\n" % (iternum, 3), "green")
HipIter = appiondata.ApHipIterData()
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
HipIter["session"] = sessiondata
if iternum == 1:
avgpath = os.path.join(self.params["rundir"], "avgsnif1")
HipIter["chop1"] = os.path.join(avgpath, "chop1.dek")
elif iternum == 2:
avgpath = os.path.join(self.params["rundir"], "avgsnif1/avgsnif2")
HipIter["chop2"] = os.path.join(avgpath, "chop2.dek")
elif iternum == 3:
avgpath = os.path.join(self.params["rundir"], "avgsnif1/avgsnif2/avg3")
volumeMrcFile = os.path.join(avgpath, "avglist3_%dp.mrc" % (self.params["rescut"]))
apChimera.filterAndChimera(
volumeMrcFile,
res=10,
apix=self.params["step"],
chimtype="snapshot",
contour=1.0,
zoom=1,
sym="c9",
silhouette=True,
)
HipIter["hipRun"] = self.params["HipRun"]
HipIter["iteration"] = iternum
HipIter["iterpath"] = avgpath
HipIter["volumeDensity"] = volumeMrcFile
HipIter["resolution"] = self.getResolutionData(avgpath, iternum)
HipIter["rMeasure"] = self.getRMeasureData(volumeMrcFile)
HipIter["cutfit1"] = os.path.join(avgpath, "cutfit1.dek")
HipIter["cutfit2"] = os.path.join(avgpath, "cutfit2.dek")
HipIter["cutfit3"] = os.path.join(avgpath, "cutfit3.dek")
HipIter["avglist_file"] = os.path.join(avgpath, "avglist3_%dp.list" % (self.params["rescut"]))
f = open(HipIter["avglist_file"], "r")
lines = f.readlines()
f.close()
HipIter["final_numpart"] = len(lines)
HipIter["asymsu"] = int(
((self.params["boxsize"] * self.params["step"]) / self.params["replen"])
* self.params["subunits"]
* len(lines)
)
HipIter["avg_file"] = os.path.join(avgpath, "avglist3_%dp.avg" % (self.params["rescut"]))
HipIter["map_file"] = os.path.join(avgpath, "avglist3_%dp.map" % (self.params["rescut"]))
HipIter["mrc_file"] = os.path.join(avgpath, "avglist3_%dp.mrc" % (self.params["rescut"]))
HipIter["ll_file"] = os.path.join(avgpath, "pll.list")
HipIter["op_file"] = os.path.join(avgpath, "pop.list")
HipIter["output_file"] = os.path.join(avgpath, "avglist3_%dp.OUTPUT" % (self.params["rescut"]))
if self.params["commit"] is True:
HipIter.insert()
else:
print HipIter
self.params["HipIterID"] = HipIter.dbid
print "self.params['HipIterID']", self.params["HipIterID"]
return
def showAssessedMask(self,imgfile,imgdata): self.filename = imgfile image = pyami.mrc.read(imgfile) sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname']) maskassessname = self.params['checkmask'] mask,maskbin = apMask.makeInspectedMask(sessiondata,maskassessname,imgdata) overlay = apMask.overlayMask(image,mask) self.app.panel.setImage(overlay.astype(numpy.float32))
def getNumCtfRunsFromSession(sessionname):
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
ctfrunq = appiondata.ApAceRunData()
ctfrunq['session'] = sessiondata
ctfrundatas = ctfrunq.query()
if not ctfrundatas:
return 0
return len(ctfrundatas)
def getRecentSelectionIdFromSession(sessionname): sessiondata = apDatabase.getSessionDataFromSessionName(sessionname) selectq = appiondata.ApSelectionRunData() selectq['session'] = sessiondata selectdatas = selectq.query(results=1) if not selectdatas: return None return selectdatas[0].dbid
def getNumSelectionRunsFromSession(sessionname): sessiondata = apDatabase.getSessionDataFromSessionName(sessionname) selectq = appiondata.ApSelectionRunData() selectq['session'] = sessiondata selectdatas = selectq.query() if not selectdatas: return 0 return len(selectdatas)
def setRunDir(self):
#auto set the output directory
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
path = os.path.abspath(sessiondata['image path'])
pieces = path.split('leginon')
path = 'leginon'.join(pieces[:-1]) + 'appion' + pieces[-1]
path = re.sub("/rawdata","",path)
path = os.path.join(path, self.processdirname, self.params['runname'])
self.params['rundir'] = path
def getFrameType(self): # set how frames are saved depending on what is found in the basepath sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname']) if sessiondata['frame path']: # 3.0+ return ddinfo.getRawFrameType(sessiondata['frame path']) else: # pre-3.0 return ddinfo.getRawFrameType(sessiondata['image path'])
def setRunDir(self):
# auto set the output directory
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
path = os.path.abspath(sessiondata["image path"])
pieces = path.split("leginon")
path = "leginon".join(pieces[:-1]) + "appion" + pieces[-1]
path = re.sub("/rawdata", "", path)
path = os.path.join(path, self.processdirname, self.params["runname"])
self.params["rundir"] = path
def checkConflicts(self):
if self.params['sessionname'] is None:
apDisplay.printError("Enter a session name (e.g. --session=06mar12a)")
if self.params['emdbid'] is None:
apDisplay.printError("specify a emdb id")
if self.params['symmetry'] is None:
#apSymmetry.printSymmetries()
apDisplay.printError("Enter a symmetry group, e.g. --symm=c1")
self.params['symdata'] = apSymmetry.findSymmetry(self.params['symmetry'])
self.sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
def start(self):
### some of this should go in preloop functions
###do queries
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseries'],sessiondata)
tiltseriessettings= apTomo.getTomographySettings(sessiondata,tiltseriesdata)
tiltdata=apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
print "ordering list"
tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(tiltdata)
#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int
###set up files
seriesname=self.params['seriesname']
print type(seriesname)
# param_out=seriesname+'.param'
###insert protomo run params
print "first insert"
protomodata = apProTomo.insertProtomoParams(seriesname)
print "second insert"
alignrun = apTomo.insertTomoAlignmentRun(sessiondata,tiltseriessettings,None,protomodata,None,1,self.params['runname'],self.params['rundir'],self.params['description'])
###insert protomo alignment
###hack to get around need to parse protomo param file
#should read imgref from tlt file
refineparamdict={'alismp':None,'alibox_x':None,'alibox_y':None,'cormod':None,'imgref':None}
###
self.params['goodcycle']=None
if self.params['goodrange'] is None:
self.params['goodstart']=1
self.params['goodend']=len(tilts)
alignerdata = apProTomo.insertAlignIteration(alignrun, protomodata, self.params, refineparamdict,ordered_imagelist[refimg])
# read tlt file
print "third insert"
alignmentdict, geometrydict, seriesname = apProTomo.parseTilt(self.params['tltfile'])
# insert geometry model
modeldata = apProTomo.insertModel2(alignerdata, geometrydict)
#insert image alignments
for i,imagedata in enumerate(ordered_imagelist):
#Caution...assumes ordered_imagelist is in same order as tlt file
apProTomo.insertTiltAlignment(alignerdata,imagedata,i,alignmentdict[i+1],center=None)
print "fourth insert"
apTomo.insertTiltsInAlignRun(alignrun, tiltseriesdata,tiltseriessettings,True)
def setRunDir(self):
if self.params["sessionname"] is None:
apDisplay.printError("Please provide a sessionname or run directory")
else:
print self.params["sessionname"]
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
path = os.path.abspath(sessiondata["image path"])
path = re.sub("leginon", "appion", path)
path = re.sub("/rawdata", "", path)
path = os.path.join(path, self.processdirname, self.params["runname"])
self.params["rundir"] = path
def setRunDir(self):
if self.params['reconid'] is not None:
self.recondata = apRecon.getRefineRunDataFromID(self.params['reconid'])
path = self.recondata['path']['path']
if self.params['fulltomoid'] is not None:
self.tomodata = apTomo.getFullTomoData(self.params['fulltomoid'])
path = self.tomodata['path']['path']
if self.params['sessionname'] is not None:
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
path = self.getDefaultBaseAppionDir(self.sessiondata,[])
self.params['rundir'] = os.path.join(path,"misc")
def setRunDir(self):
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params["tiltseriesnumber"], sessiondata)
path = self.getDefaultBaseAppionDir(sessiondata, ["tomo"])
tiltseriespath = "tiltseries%d" % self.params["tiltseriesnumber"]
if self.params["full"]:
tomovolumepath = ""
else:
tomovolumepath = self.params["volume"]
intermediatepath = os.path.join(tiltseriespath, self.params["runname"], tomovolumepath)
self.params["rundir"] = os.path.join(path, intermediatepath)
self.params["aligndir"] = os.path.abspath(os.path.join(path, tiltseriespath, "align", self.params["runname"]))
def checkConflicts(self):
# check to make sure that incompatible parameters are not set
if self.params['diam'] is None or self.params['diam']==0:
apDisplay.printError("Please input the diameter of your particle (for display purposes only)")
# get list of input images, since wildcards are supported
if self.params['files'] is None:
apDisplay.printError("Please enter the image names with picked particle files")
if self.params['sessionname'] is None:
apDisplay.printError("Please enter Name of session to upload to, e.g., --session=09dec07a")
self.sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
def getHipRunData(self):
HipRun = appiondata.ApHipRunData()
HipRun["runname"] = self.params["runname"]
HipRun["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
HipRun["description"] = self.params["description"]
HipRun["REF|projectdata|projects|project"] = apProject.getProjectIdFromStackId(self.params["stackid"])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params["sessionname"])
HipRun["session"] = sessiondata
HipRun["apix"] = self.params["step"]
self.stackdata = apStack.getOnlyStackData(self.params["stackid"], msg=False)
HipRun["stack"] = self.stackdata
return HipRun
def getHipRunData(self):
HipRun = appiondata.ApHipRunData()
HipRun['runname'] = self.params['runname']
HipRun['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
HipRun['description'] = self.params['description']
HipRun['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid'])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
HipRun['session'] = sessiondata
HipRun['apix'] = self.params['step']
self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False)
HipRun['stack'] = self.stackdata
return HipRun
def setRunDir(self): sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname']) tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseriesnumber'],sessiondata) path = self.getDefaultBaseAppionDir(sessiondata,['tomo']) tiltseriespath = "tiltseries%d" % self.params['tiltseriesnumber'] if self.params['full']: tomovolumepath = "" else: tomovolumepath = self.params['volume'] intermediatepath = os.path.join(tiltseriespath,self.params['runname'],tomovolumepath) self.params['rundir'] = os.path.join(path,intermediatepath) self.params['aligndir'] = os.path.abspath(os.path.join(path,tiltseriespath,'align',self.params['runname']))
def insertFunctionRun(self):
if self.params is None:
params = self.defaultparams.copy()
if self.params['commit']==True:
sessionname = self.params['sessionname']
sessiondata = apDatabase.getSessionDataFromSessionName(sessionname)
paramdata =self.insertFunctionParams(self.params)
maskRdata=apMask.createMaskMakerRun(sessiondata,self.params['rundir'],self.params['runname'],paramdata)
maskRdata.insert()
else:
maskRdata = apMask.createMaskMakerRun(None,None,None,None)
return maskRdata
def start(self):
### some of this should go in preloop functions
###do queries
os.chdir(self.params['rundir'])
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseries'],sessiondata)
tiltdata = apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(tiltdata)
def insertHipRunData(self): HipRun = appiondata.ApHipRunData() HipRun['runname'] = self.params['runname'] HipRun['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) HipRun['description'] = self.params['description'] HipRun['REF|projectdata|projects|project'] = apProject.getProjectIdFromStackId(self.params['stackid']) sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname']) HipRun['session'] = sessiondata HipRun['apix'] = self.params['step'] self.stackdata = apStack.getOnlyStackData(self.params['stackid'], msg=False) HipRun['stack'] = self.stackdata if self.params['commit'] is True: HipRun.insert() else: print HipRun self.params['HipRunID'] = HipRun.dbid print "self.params['HipRunID']",self.params['HipRunID'] self.params['HipRun'] = HipRun return HipRun
def checkConflicts(self):
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
self.sessiondata = sessiondata
if self.params['goodalignerid'] is None:
if self.params['tiltseriesnumber'] is None:
apDisplay.printError("There is no tilt series specified")
if self.params['runname'] is None:
apDisplay.printError("enter a run name")
if self.params['description'] is None:
apDisplay.printError(
"enter a description, e.g. --description='awesome data'")
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
self.params['tiltseriesnumber'], sessiondata)
self.params['tiltseries'] = tiltdata
if self.params['othertilt'] is not None:
othertiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
self.params['othertilt'], sessiondata)
self.params['othertiltseries'] = othertiltdata
else:
self.params['othertiltseries'] = None
if self.params['alignmethod'] == 'leginon':
self.params['cycle'] = 0
self.params['region'] = 100
else:
self.createParamsFromGoodAligner(self.params['goodalignerid'])
if self.params['goodcycle'] is None:
if self.params['goodstart'] or self.params['goodend']:
apDisplay.printError(
"Cannot specify reseting image range without knowing the cycle number to reset to"
)
elif self.params['goodcycle'] >= self.params['cycle']:
apDisplay.printError(
"Only older cycle can be used as the base to reset image origin to"
)
# Sampling is needed for protomo1 and 2, not imod
if self.params['sample'] is not None:
if self.params['sample'] < 1:
apDisplay.printError(
"Sampling factor (--sample) must be greater or equal to 1."
)
def checkConflicts(self):
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
self.sessiondata = sessiondata
if self.params['tiltseriesnumber'] is None:
apDisplay.printError("There is no tilt series specified")
if self.params['runname'] is None:
apDisplay.printError("enter a run name")
if self.params['description'] is None:
apDisplay.printError(
"enter a description, e.g. --description='awesome data'")
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
self.params['tiltseriesnumber'], sessiondata)
self.params['tiltseries'] = tiltdata
if self.params['othertilt'] is not None:
othertiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
self.params['othertilt'], sessiondata)
self.params['othertiltseries'] = othertiltdata
else:
self.params['othertiltseries'] = None
def insertRun(self):
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
pathq = appiondata.ApPathData(path=self.params['rundir'])
pmparamq = appiondata.ApParticleMovieParamsData()
paramlist = pmparamq.keys()
for p in paramlist:
if p.lower() in self.params:
pmparamq[p] = self.params[p.lower()]
else:
print "missing", p.lower()
pmrunq = appiondata.ApParticleMovieRunData(
path=pathq,
movieRunName=self.params['runname'],
session=sessiondata,
movieParams=pmparamq,
selectionrun=self.selectiondata)
r = pmrunq.insert()
self.rundata = pmrunq
def start(self):
###do queries
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseries'],sessiondata)
tiltseriessettings= apTomo.getTomographySettings(sessiondata,tiltseriesdata)
tiltdata=apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
print "ordering list"
tilts,ordered_imagelist,ordered_mrc_files,refimg = apTomo.orderImageList(tiltdata)
#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int
###set up files
seriesname='series'+str(self.params['tiltseries'])
tiltfilename=seriesname+'.tlt'
param_out=seriesname+'.param'
maxtilt=max([abs(tilts[0]),abs(tilts[-1])])
apDisplay.printMsg("highest tilt angle is %f" % maxtilt)
self.params['cos_alpha']=math.cos(maxtilt*math.pi/180)
self.params['raw_path']=os.path.join(self.params['rundir'],'raw')
rawexists=apParam.createDirectory(self.params['raw_path'])
apDisplay.printMsg("copying raw images")
newfilenames=apProTomo.getImageFiles(ordered_imagelist,self.params['raw_path'], link=False)
#get alignment data
alignerdata = apTomo.getAlignerdata(self.params['alignerid'])
imgshape = apTomo.getTomoImageShape(ordered_imagelist[0])
imgcenter = {'x':self.imgshape[1]/2,'y':self.imgshape[0]/2}
specimen_euler, azimuth, origins, rotations = apTomo.getAlignmentFromDB(alignerdata,imgcenter)
#write protomo2 tilt file
outtltfile='series.tlt'
seriesname='series'
apProTomo.writeTiltFile2(outfilename, seriesname, specimen_eulers, azimuth, referenceimage ):
def setRunDir(self):
"""
this function only runs if no rundir is defined at the command line
"""
if self.params['rundir'] is None:
if ('sessionname' in self.params
and self.params['sessionname'] is not None):
# command line users may use sessionname rather than expId
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
self.params['rundir'] = self.getDefaultBaseAppionDir(
sessiondata, [self.processdirname, self.params['runname']])
else:
if ('expId' in self.params and self.params['expId']):
# expId should always be included from appionwrapper derived appionscript
sessiondata = apDatabase.getSessionDataFromSessionId(
self.params['expId'])
self.params['rundir'] = self.getDefaultBaseAppionDir(
sessiondata,
[self.processdirname, self.params['runname']])
# The rest should not be needed with appionwrapper format
from appionlib import apStack
if (self.params['rundir'] is None and 'reconid' in self.params
and self.params['reconid'] is not None):
self.params['stackid'] = apStack.getStackIdFromRecon(
self.params['reconid'], msg=False)
if (self.params['rundir'] is None and 'stackid' in self.params
and self.params['stackid'] is not None):
#auto set the run directory
stackdata = apStack.getOnlyStackData(self.params['stackid'],
msg=False)
path = os.path.abspath(stackdata['path']['path'])
path = os.path.dirname(path)
path = os.path.dirname(path)
self.params['rundir'] = os.path.join(path, self.processdirname,
self.params['runname'])
self.params['outdir'] = self.params['rundir']
def onInit(self):
"""
standard appionScript
"""
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
if sessiondata:
### METHOD 1 : session already exists
apDisplay.printColor("Add images to an existing session", "cyan")
### what about linking an existing session with project id to a new project id
oldprojectid = apProject.getProjectIdFromSessionName(
self.params['sessionname'])
if oldprojectid != self.params['projectid']:
apDisplay.printError(
"You cannot assign an existing session (PID %d) to a different project (PID %d)"
% (oldprojectid, self.params['projectid']))
else:
### METHOD 2 : create new session
apDisplay.printColor("Creating a new session", "cyan")
### die for now
apDisplay.printError(
"Uploading stack to a new session not allowed")
try:
directory = leginon.leginonconfig.mapPath(
leginon.leginonconfig.IMAGE_PATH)
except AttributeError:
apDisplay.printWarning("Could not set directory")
directory = ''
userdata = None
sessiondata = self.createSession(userdata,
self.params['sessionname'],
self.params['description'],
directory)
self.linkSessionProject(sessiondata, self.params['projectid'])
self.sessiondata = sessiondata
return
def eliminateMaskedParticles(self, particles, imgdata):
newparticles = []
eliminated = 0
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
if self.params['defocpair']:
imgdata = apDefocalPairs.getTransformedDefocPair(imgdata, 2)
maskimg, maskbin = apMask.makeInspectedMask(sessiondata,
self.params['maskassess'],
imgdata)
if maskimg is not None:
for prtl in particles:
binnedcoord = (int(prtl['ycoord'] / maskbin),
int(prtl['xcoord'] / maskbin))
if maskimg[binnedcoord] != 0:
eliminated += 1
else:
newparticles.append(prtl)
apDisplay.printMsg("%i particle(s) eliminated due to masking" %
eliminated)
else:
apDisplay.printMsg("no masking")
newparticles = particles
return newparticles
def uploadTemplateStack(self, insert=False): sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname']) uploadq = appiondata.ApTemplateStackData() uploadq['REF|projectdata|projects|project'] = self.params['projectid'] if self.params['clusterId'] is not None: uploadq['clusterstack'] = appiondata.ApClusteringStackData.direct_query(self.params['clusterId']) elif self.params['alignId'] is not None: uploadq['alignstack'] = appiondata.ApAlignStackData.direct_query(self.params['alignId']) elif self.params['templatestack'] is not None: uploadq['origfile'] = self.params['templatestack']+".hed" uploadq['templatename'] = self.params['runname']+".hed" if self.params['templatetype'] == "clsavg": uploadq['cls_avgs'] = True if self.params['templatetype'] == "forward_proj": uploadq['forward_proj'] = True uploadq['description'] = self.params['description'] uploadq['session'] = sessiondata uploadq['apix'] = self.params['apix'] uploadq['boxsize'] = self.params['boxsize'] uploadq['numimages'] = self.numimages uploadq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) if insert is True: uploadq.insert()
def getFrameType(self):
# set how frames are saved depending on what is found in the basepath
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
return ddinfo.getRawFrameType(sessiondata['image path'])
def uploadData(self, ctfpartlist):
### read mean /stdev for uploading
self.getPartMeanTree(os.path.join(self.params['rundir'], self.params['finalstack']), ctfpartlist)
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
if self.params['projectid'] is not None:
projectnum = self.params['projectid']
else:
projectnum = apProject.getProjectIdFromSessionName(self.params['sessionname'])
### create synthetic stack object ... not saving global params like runname, session, project, description, etc. here; that's in ApStackData
syntheticq = appiondata.ApSyntheticStackParamsData()
### get number of fakestack runs
numentries = len(syntheticq)
syntheticq['modelid'] = appiondata.ApInitialModelData.direct_query(self.params['modelid'])
syntheticq['boxsize'] = self.params['box']
syntheticq['apix'] = self.params['apix']
syntheticq['projcount'] = self.params['projcount']
syntheticq['projstdev'] = self.params['projstdev']
syntheticq['shiftrad'] = self.params['shiftrad']
syntheticq['rotang'] = self.params['rotang']
syntheticq['flip'] = self.params['flip']
syntheticq['kilovolts'] = self.params['kv']
syntheticq['spher_aber'] = self.params['cs']
syntheticq['defocus_x'] = self.params['df1']
syntheticq['defocus_y'] = self.params['df2']
syntheticq['randomdef'] = self.params['randomdef']
if self.params['randomdef'] is True:
syntheticq['randomdef_std'] = self.params['randomdef_std']
syntheticq['astigmatism'] = self.params['astigmatism']
syntheticq['snr1'] = self.params['snr1']
syntheticq['snrtot'] = self.params['snrtot']
syntheticq['envelope'] = os.path.basename(self.params['envelopefile'])
syntheticq['ace2correct'] = self.params['ace2correct']
syntheticq['ace2correct_rand'] = self.params['ace2correct_rand']
if self.params['ace2correct_rand'] is True:
syntheticq['ace2correct_std'] = self.params['ace2correct_std']
syntheticq['ace2estimate'] = self.params['ace2estimate']
syntheticq['lowpass'] = self.params['lpfilt']
syntheticq['highpass'] = self.params['hpfilt']
syntheticq['norm'] = self.params['norm']
### fill stack parameters
stparamq = appiondata.ApStackParamsData()
stparamq['boxSize'] = self.params['box']
stparamq['bin'] = 1
stparamq['fileType'] = "imagic"
stparamq['defocpair'] = 0
stparamq['lowpass'] = self.params['lpfilt']
stparamq['highpass'] = self.params['hpfilt']
stparamq['norejects'] = 1
if self.params['invert'] is True:
stparamq['inverted'] = 1
else:
stparamq['inverted'] = 0
if self.params['ace2correct'] is True or self.params['ace2correct_rand'] is True:
stparamq['phaseFlipped'] = 1
stparamq['fliptype'] = "ace2part"
else:
stparamq['phaseFlipped'] = 0
stparamq['normalized'] = self.params['norm']
paramslist = stparamq.query()
### create a stack object
stackq = appiondata.ApStackData()
stackq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir']))
### see if stack already exists in the database (just checking path & name)
uniqstackdatas = stackq.query(results=1)
### create a stackRun object
runq = appiondata.ApStackRunData()
runq['stackRunName'] = self.params['runname']
runq['session'] = sessiondata
### see if stack run already exists in the database (just checking runname & session)
uniqrundatas = runq.query(results=1)
### finish stack object
stackq['name'] = self.params['finalstack']
stackq['description'] = self.params['description']
stackq['hidden'] = 0
stackq['pixelsize'] = self.params['apix'] * 1e-10
stackq['boxsize'] = self.params['box']
self.stackdata = stackq
### finish stackRun object
runq['stackParams'] = stparamq
runq['syntheticStackParams'] = syntheticq
self.stackrundata = runq
### create runinstack object
rinstackq = appiondata.ApRunsInStackData()
rinstackq['stackRun'] = runq
### if not in the database, make sure run doesn't already exist
if not uniqstackdatas and not uniqrundatas:
if self.params['commit'] is True:
apDisplay.printColor("Inserting stack parameters into database", "cyan")
rinstackq['stack'] = stackq
rinstackq.insert()
else:
apDisplay.printWarning("NOT INSERTING stack parameters into database")
elif uniqrundatas and not uniqstackdatas:
apDisplay.printError("Weird, run data without stack already in the database")
else:
rinstack = rinstackq.query(results=1)
prevrinstackq = appiondata.ApRunsInStackData()
prevrinstackq['stackRun'] = uniqrundatas[0]
prevrinstackq['stack'] = uniqstackdatas[0]
prevrinstack = prevrinstackq.query(results=1)
## if no runinstack found, find out which parameters are wrong:
if not rinstack:
for i in uniqrundatas[0]:
print "r =======",i,"========"
if uniqrundatas[0][i] != runq[i]:
apDisplay.printError("the value for parameter '"+str(i)+"' is different from before")
else:
print i,uniqrundatas[0][i],runq[i]
for i in uniqrundatas[0]['stackParams']:
print "p =======",i,"========"
if uniqrundatas[0]['stackParams'][i] != stparamq[i]:
apDisplay.printError("the value for parameter '"+str(i)+"' is different from before")
else:
print i, uniqrundatas[0]['stackParams'][i], stparamq[i]
for i in uniqstackdatas[0]:
print "s =======",i,"========"
if uniqstackdatas[0][i] != stackq[i]:
apDisplay.printError("the value for parameter '"+str(i)+"' is different from before")
else:
print i,uniqstackdatas[0][i],stackq[i]
for i in prevrinstack[0]:
print "rin =======",i,"========"
if prevrinstack[0][i] != rinstackq[i]:
print i,prevrinstack[0][i],rinstackq[i]
apDisplay.printError("the value for parameter '"+str(i)+"' is different from before")
else:
print i,prevrinstack[0][i],rinstackq[i]
apDisplay.printError("All parameters for a particular stack must be identical! \n"+\
"please check your parameter settings.")
apDisplay.printWarning("Stack already exists in database! Will try and appending new particles to stack")
### create a fake selection run
# selectq = appiondata.ApSelectionRunData()
# selectq['session'] = sessiondata
# selectq['name'] = "fakerun"
# self.selectq = selectq
if self.params['commit'] is True:
apDisplay.printColor("Inserting fake selection parameters into the database", "cyan")
# selectq.insert()
else:
apDisplay.printWarning("NOT INSERTING fake selection parameters into the database")
partNumber = 0
### loop over the particles and insert
if self.params['commit'] is True:
apDisplay.printColor("inserting particle parameters into database", "cyan")
else:
apDisplay.printWarning("NOT INSERTING particle parameters into database")
for i in range(len(ctfpartlist)):
partNumber += 1
partfile = ctfpartlist[i]
partmeandict = self.partmeantree[i]
partq = appiondata.ApParticleData()
# partq['selectionrun'] = selectq
partq['xcoord'] = partNumber
stpartq = appiondata.ApStackParticleData()
### check unique params
stpartq['stack'] = self.stackdata
stpartq['stackRun'] = self.stackrundata
stpartq['particleNumber'] = partNumber
stpartdata = stpartq.query(results=1)
if stpartdata:
apDisplay.printError("trying to insert a duplicate particle")
stpartq['particle'] = partq
stpartq['mean'] = partmeandict['mean']
stpartq['stdev'] = partmeandict['stdev']
if self.params['commit'] is True:
stpartq.insert()
return
def getSessionDataByName(name): sessiondata = apDatabase.getSessionDataFromSessionName(name) return sessiondata
def uploadTomo(params):
if not params['commit']:
apDisplay.printWarning("not commiting tomogram to database")
return
apDisplay.printMsg("Commiting tomogram to database")
sessiondata = apDatabase.getSessionDataFromSessionName(
params['sessionname'])
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
params['tiltseriesnumber'], sessiondata)
runname = params['runname']
name = params['name']
if params['full']:
fullbin = params['bin']
else:
fullbin = 1
subbin = params['bin']
alignrun = insertTomoAlignmentRun(sessiondata, None, None, None, None,
fullbin, runname, params['aligndir'],
'manual alignment from upload')
# only tilt series in one alignrun for now
insertTiltsInAlignRun(alignrun, tiltdata, None, True)
alignerdata = insertAlignerParams(alignrun, params)
firstimagedata = getFirstImage(tiltdata)
path = os.path.abspath(params['rundir'])
description = params['description']
if params['full']:
thickness = params['shape'][0] * fullbin
uploadfile = params['zprojfile']
projectimagedata = uploadZProjection(runname, firstimagedata,
uploadfile)
fullrundata = insertFullTomoRun(sessiondata, path, runname, 'upload')
return insertFullTomogram(sessiondata, tiltdata, alignerdata,
fullrundata, name, description,
projectimagedata, thickness, None, fullbin,
[])
else:
projectimagedata = None
fulltomopath = params['rundir'].replace('/' + params['volume'], '')
dummyname = 'dummy'
dummydescription = 'fake full tomogram for subtomogram upload'
thickness = params['shape'][0] * subbin
fullrundata = insertFullTomoRun(sessiondata, fulltomopath, runname,
'upload')
fulltomogram = insertFullTomogram(sessiondata, tiltdata, alignerdata,
fullrundata, dummyname,
dummydescription, projectimagedata,
thickness, None, fullbin, [])
apix = apDatabase.getPixelSize(firstimagedata)
tomoq = appiondata.ApTomogramData()
tomoq['session'] = sessiondata
tomoq['tiltseries'] = tiltdata
results = tomoq.query()
index = len(results) + 1
pixelsize = 1e-10 * apix * subbin
runname = params['volume']
shape = map((lambda x: x * subbin), params['shape'])
dimension = {'x': shape[2], 'y': shape[1], 'z': shape[0]}
subtomorundata = insertSubTomoRun(sessiondata, None, None, runname,
params['invert'], subbin)
return insertSubTomogram(fulltomogram, subtomorundata, None, 0,
dimension, path, name, index, pixelsize,
description)
def insertHipParticleData(self):
self.particleNumber = 0
alldir = os.listdir(self.params['rundir'])
ems_list = []
for file in alldir:
if re.search(".ems.out", file):
ems_list.append(file)
ems_list.sort()
avgdir = os.listdir(os.path.join(self.params['rundir'],"avgsnif1/avgsnif2/avg3"))
fhlxavg_list = []
for file in avgdir:
if re.search("f.hlxavg_dek", file):
fhlxavg_list.append(file)
fhlxavg_list.sort()
nhlxavg_list = []
for file in avgdir:
if re.search("n.hlxavg_dek", file):
nhlxavg_list.append(file)
nhlxavg_list.sort()
for i in range(len(ems_list)):
filename = ems_list[i]
### Will the filenames always be part000000.ext with apXmipp.breakStackIntoSingleFiles?? This is a risky way to get the file prefix. Find a better way!
self.filep = filename[0:10]
self.particleNumber += 1
HipParticle = appiondata.ApHipParticleData()
HipParticle['hipRun'] = self.params['HipRun']
for file in fhlxavg_list:
if re.search(self.filep, file):
f = open(os.path.join(self.params['rundir'], "avgsnif1/avgsnif2/avg3", file), 'r')
lines = f.readlines()
keyline = lines[2]
pzr_list = keyline.split()
f.close()
HipParticle['far_phi'] = pzr_list[2]
HipParticle['far_z'] = pzr_list[3]
HipParticle['far_rscale'] = pzr_list[4]
HipParticle['far_ampscale'] = lines[-1]
for file in nhlxavg_list:
if re.search(self.filep, file):
f = open(os.path.join(self.params['rundir'], "avgsnif1/avgsnif2/avg3", file), 'r')
lines = f.readlines()
keyline = lines[2]
pzr_list = keyline.split()
f.close()
HipParticle['ner_phi'] = pzr_list[2]
HipParticle['ner_z'] = pzr_list[3]
HipParticle['ner_rscale'] = pzr_list[4]
HipParticle['ner_ampscale'] = lines[-1]
f = open(ems_list[i], 'r')
lines = f.readlines()
lastline = lines[-1]
tsr_list = lastline.split()
f.close()
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
HipParticle['session'] = sessiondata
HipParticle['filename'] = self.filep
HipParticle['stack'] = self.stackdata
HipParticle['mrc_file'] = os.path.join(self.params['rundir'], self.filep + ".mrc")
HipParticle['s_file'] = os.path.join(self.params['rundir'], self.filep + ".s")
HipParticle['dft_file'] = os.path.join(self.params['rundir'], self.filep + ".dft")
HipParticle['colb_file'] = os.path.join(self.params['rundir'], self.filep + ".colb")
HipParticle['ner_file'] = os.path.join(self.params['rundir'], self.filep + ".ner")
HipParticle['far_file'] = os.path.join(self.params['rundir'], self.filep + ".far")
HipParticle['fft_file'] = os.path.join(self.params['rundir'], self.filep + ".fft")
self.stackrundata = appiondata.ApStackRunData()
HipParticle['stackRun'] = self.stackrundata
HipParticle['particleNumber'] = self.particleNumber
HipParticle['tilt'] = tsr_list[0]
HipParticle['shift'] = tsr_list[1]
HipParticle['resid'] = tsr_list[2]
HipParticledata = HipParticle.query(results=1)
if HipParticledata:
apDisplay.printError("trying to insert a duplicate particle")
if self.params['commit'] is True:
HipParticle.insert()
self.params['HipParticleID'] = HipParticle.dbid
print "self.params['HipParticleID']",self.params['HipParticleID']
return
def getImageShapeFromTiltSeries(self):
sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname'])
tiltdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(self.params['tiltseriesnumber'],sessiondata)
firstimagedata = apTomo.getFirstImage(tiltdata)
self.imageshape = apTomo.getTomoImageShape(firstimagedata)
def setRunDir(self):
#auto set the run directory
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
path = os.path.abspath(sessiondata['image path'])
self.params['rundir'] = path
def start(self):
### some of this should go in preloop functions
###do queries
sessiondata = apDatabase.getSessionDataFromSessionName(
self.params['sessionname'])
self.sessiondata = sessiondata
tiltseriesdata = apDatabase.getTiltSeriesDataFromTiltNumAndSessionId(
self.params['tiltseries'], sessiondata)
tiltseriessettings = apTomo.getTomographySettings(
sessiondata, tiltseriesdata)
tiltdata = apTomo.getImageList([tiltseriesdata])
description = self.params['description']
apDisplay.printMsg("getting imagelist")
print "ordering list"
tilts, ordered_imagelist, ordered_mrc_files, refimg = apTomo.orderImageList(
tiltdata)
#tilts are tilt angles, ordered_imagelist are imagedata, ordered_mrc_files are paths to files, refimg is an int
###set up files
seriesname = self.params['seriesname']
print type(seriesname)
# param_out=seriesname+'.param'
###insert protomo run params
print "first insert"
protomodata = apProTomo.insertProtomoParams(seriesname)
print "second insert"
alignrun = apTomo.insertTomoAlignmentRun(sessiondata,
tiltseriessettings, None,
protomodata, None, 1,
self.params['runname'],
self.params['rundir'],
self.params['description'])
###insert protomo alignment
###hack to get around need to parse protomo param file
#should read imgref from tlt file
refineparamdict = {
'alismp': None,
'alibox_x': None,
'alibox_y': None,
'cormod': None,
'imgref': None
}
###
self.params['goodcycle'] = None
if self.params['goodrange'] is None:
self.params['goodstart'] = 1
self.params['goodend'] = len(tilts)
alignerdata = apProTomo.insertAlignIteration(alignrun, protomodata,
self.params,
refineparamdict,
ordered_imagelist[refimg])
# read tlt file
print "third insert"
alignmentdict, geometrydict, seriesname = apProTomo.parseTilt(
self.params['tltfile'])
# insert geometry model
modeldata = apProTomo.insertModel2(alignerdata, geometrydict)
#insert image alignments
for i, imagedata in enumerate(ordered_imagelist):
#Caution...assumes ordered_imagelist is in same order as tlt file
apProTomo.insertTiltAlignment(alignerdata,
imagedata,
i,
alignmentdict[i + 1],
center=None)
print "fourth insert"
apTomo.insertTiltsInAlignRun(alignrun, tiltseriesdata,
tiltseriessettings, True)
def setRunDir(self): #auto set the output directory sessiondata = apDatabase.getSessionDataFromSessionName(self.params['sessionname']) self.params['rundir'] = self.getDefaultBaseAppionDir(sessiondata,['templatestacks',self.params['runname']])