def setupInitialModel(self):
modeldata = apModel.getModelFromId(self.params["modelid"])
modelfile = os.path.join(modeldata["path"]["path"], modeldata["name"])
modelsym = modeldata["symmetry"]["symmetry"]
apDisplay.printMsg("Current symmetry: %s" % (modeldata["symmetry"]["description"]))
# if icosahedral recon, rotate volume to 3DEM standard orientation
if modelsym.startswith("Icos (5 3 2)"):
tempfile = "temp.mrc"
emancmd = "proc3d %s %s icos5fTo2f" % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
if modelsym.startswith("Icos (5 3 2)") or modelsym.startswith("Icos (2 5 3)"):
tempfile = "temp.mrc"
emancmd = "proc3d %s %s rotspin=0,0,1,90" % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
outmodelfile = os.path.join(self.params["rundir"], "initmodel.hed")
apFile.removeStack(outmodelfile, warn=False)
emancmd = "proc3d %s %s clip=%d,%d,%d " % (modelfile, outmodelfile, self.boxsize, self.boxsize, self.boxsize)
# rescale initial model if necessary
scale = modeldata["pixelsize"] / self.apix
if abs(scale - 1.0) > 1e-3:
emancmd += "scale=%.4f " % (scale)
apEMAN.executeEmanCmd(emancmd, verbose=True)
apImagicFile.setImagic4DHeader(outmodelfile, machineonly=True)
return outmodelfile
def setupInitialModel(self):
modeldata = apModel.getModelFromId(self.params['modelid'])
modelfile = os.path.join(modeldata['path']['path'], modeldata['name'])
modelsym = modeldata['symmetry']['symmetry']
apDisplay.printMsg("Current symmetry: %s"%(modeldata['symmetry']['description']))
# if icosahedral recon, rotate volume to 3DEM standard orientation
if modelsym.startswith('Icos (5 3 2)'):
tempfile = "temp.mrc"
emancmd = 'proc3d %s %s icos5fTo2f' % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
if modelsym.startswith('Icos (5 3 2)') or modelsym.startswith('Icos (2 5 3)'):
tempfile = "temp.mrc"
emancmd = 'proc3d %s %s rotspin=0,0,1,90' % (modelfile, tempfile)
apEMAN.executeEmanCmd(emancmd, verbose=True)
modelfile = tempfile
outmodelfile = os.path.join(self.params['rundir'], "initmodel.hed")
apFile.removeStack(outmodelfile, warn=False)
emancmd = "proc3d %s %s clip=%d,%d,%d " % (modelfile, outmodelfile, self.boxsize, self.boxsize, self.boxsize)
# rescale initial model if necessary
scale = modeldata['pixelsize']/self.apix
if abs(scale - 1.0) > 1e-3:
emancmd += "scale=%.4f "%(scale)
apEMAN.executeEmanCmd(emancmd, verbose=True)
apImagicFile.setImagic4DHeader(outmodelfile, machineonly=True)
return outmodelfile
def getModelParams(self): modeldata = apModel.getModelFromId(self.params['oldmodelid']) self.params['oldapix'] = float(modeldata['pixelsize']) if self.params['symmetry'] is None: self.params['symdata'] = modeldata['symmetry'] self.params['symmetry'] = self.params['symdata']['eman_name'] self.params['res'] = float(modeldata['resolution']) self.params['file'] = os.path.join(modeldata['path']['path'], modeldata['name'])
def __initializeModel(self,modelid,ismask=False):
self.model = {}
self.model['data'] = apModel.getModelFromId(modelid)
self.model['id'] = modelid
self.model['file'] = os.path.join(self.model['data']['path']['path'], self.model['data']['name'])
self.model['apix'] = self.model['data']['pixelsize']
self.model['format'] = self.model['data']['name'].split('.')[-1]
self.model['ismask'] = ismask
def getModelParams(self):
modeldata = apModel.getModelFromId(self.params['oldmodelid'])
self.params['oldapix'] = float(modeldata['pixelsize'])
if self.params['symmetry'] is None:
self.params['symdata'] = modeldata['symmetry']
self.params['symmetry'] = self.params['symdata']['eman_name']
self.params['res'] = float(modeldata['resolution'])
self.params['file'] = os.path.join(modeldata['path']['path'],
modeldata['name'])
def __initializeModel(self, modelid, ismask=False):
self.model = {}
self.model['data'] = apModel.getModelFromId(modelid)
self.model['id'] = modelid
self.model['file'] = os.path.join(self.model['data']['path']['path'],
self.model['data']['name'])
self.model['apix'] = self.model['data']['pixelsize']
self.model['format'] = self.model['data']['name'].split('.')[-1]
self.model['ismask'] = ismask
def getRunData(self): ### setup refinement run jobdata = apDatabase.getJobDataFromPathAndType(self.params['rundir'], "runfrealign") runq = appiondata.ApRefineRunData() runq['runname'] = self.params['runname'] runq['package'] = "Frealign" runq['description'] = self.params['description'] runq['hidden'] = False runq['num_iter'] = self.numiter runq['stack'] = apStack.getOnlyStackData(self.params['stackid']) runq['initialModel'] = apModel.getModelFromId(self.params['modelid']) runq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) runq['job'] = jobdata return runq
def getRunData(self): ### setup refinement run jobdata = apDatabase.getJobDataFromPathAndType(self.params['rundir'], "runfrealign") runq = appiondata.ApRefineRunData() runq['runname'] = self.params['runname'] runq['package'] = "Frealign" runq['description'] = self.params['description'] runq['hidden'] = False runq['num_iter'] = self.numiter runq['stack'] = apStack.getOnlyStackData(self.params['stackid']) runq['initialModel'] = apModel.getModelFromId(self.params['modelid']) runq['path'] = appiondata.ApPathData(path=os.path.abspath(self.params['rundir'])) runq['job'] = jobdata return runq
def getRunData(self):
### setup refinement run
jobdata = apDatabase.getJobDataFromPathAndType(self.params["rundir"], "runfrealign")
runq = appiondata.ApRefineRunData()
runq["runname"] = self.params["runname"]
runq["package"] = "Frealign"
runq["description"] = self.params["description"]
runq["hidden"] = False
runq["num_iter"] = self.numiter
runq["stack"] = apStack.getOnlyStackData(self.params["stackid"])
runq["initialModel"] = apModel.getModelFromId(self.params["modelid"])
runq["path"] = appiondata.ApPathData(path=os.path.abspath(self.params["rundir"]))
runq["job"] = jobdata
return runq
def start(self):
self.params["nproc"] = 6
### get info about the model
if self.params["modelid"] is not None:
apDisplay.printMsg("Information about model id %d" % (self.params["modelid"]))
modeldata = apModel.getModelFromId(self.params["modelid"])
apDisplay.printMsg("\tboxsize %d pixels" % (modeldata["boxsize"]))
apDisplay.printMsg("\tpixelsize %.3f Angstroms" % (modeldata["pixelsize"]))
apDisplay.printMsg("\n\n")
self.getModel()
inputlines = self.createFastFreeHandInputLineTemplate()
free_hand_scripts = self.writeMultipleFreeHandTestShells(inputlines, self.params["nproc"])
print free_hand_scripts
# self.runMultipleFreeHandTest(free_hand_scripts)
merged_outfile = self.mergeResults()
plot = plotFreeHandTestResult(merged_outfile, self.params["angSearch"], self.params["scoringtype"])
plot.plotResult()
def start(self):
self.params['nproc'] = 6
### get info about the model
if self.params['modelid'] is not None:
apDisplay.printMsg("Information about model id %d"%(self.params['modelid']))
modeldata = apModel.getModelFromId(self.params['modelid'])
apDisplay.printMsg("\tboxsize %d pixels"%(modeldata['boxsize']))
apDisplay.printMsg("\tpixelsize %.3f Angstroms"%(modeldata['pixelsize']))
apDisplay.printMsg("\n\n")
self.getModel()
inputlines = self.createFastFreeHandInputLineTemplate()
free_hand_scripts = self.writeMultipleFreeHandTestShells(inputlines,self.params['nproc'])
print free_hand_scripts
#self.runMultipleFreeHandTest(free_hand_scripts)
merged_outfile = self.mergeResults()
plot = plotFreeHandTestResult(merged_outfile,self.params['angSearch'],self.params['scoringtype'])
plot.plotResult()
def getModel(self):
modeldata = apModel.getModelFromId(self.params['modelid'])
self.modelfile = 'initmodel.mrc'
def getModel(self):
modeldata = apModel.getModelFromId(self.params["modelid"])
self.modelfile = "initmodel.mrc"
def getModel(self):
modeldata = apModel.getModelFromId(self.params['modelid'])
self.modelfile = 'initmodel.mrc'
