def start(self):
self.setFileName()
scale = float(self.params['oldapix'])/self.params['newapix']
mrcname = os.path.join(self.params['rundir'], self.params['name']+".mrc")
origmodel = self.params['file']
if os.path.isfile(mrcname):
apDisplay.printError("File exists")
if (abs(self.params['oldapix'] - self.params['newapix']) > 1.0e-2 or
abs(self.params['oldbox'] - self.params['newbox']) > 1.0e-1):
### rescale old model to a new size
apDisplay.printWarning("rescaling original model to a new size")
scale = float(self.params['oldapix'])/self.params['newapix']
apDisplay.printMsg("rescaling model by scale factor of %.4f"%(scale))
apVolume.rescaleVolume(origmodel, mrcname,
self.params['oldapix'], self.params['newapix'], self.params['newbox'])
else:
### simple upload, just copy file to models folder
apDisplay.printMsg("copying original model to a new location: "+mrcname)
shutil.copyfile(origmodel, mrcname)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['newapix'])
### render chimera images of model
contour = self.params['contour']
if self.params['mass'] is not None:
apChimera.setVolumeMass(mrcname, self.params['newapix'], self.params['mass'])
contour = 1.0
apChimera.renderSnapshots(mrcname, contour=contour,
zoom=self.params['zoom'], sym=self.params['symdata']['eman_name'])
self.insertModel(mrcname)
def preprocessModelWithProc3d(self, rescale=True):
'''
Use EMAN proc3d to scale initial or mask model to that of the refinestack and format
'''
extname = self.proc3dFormatConversion()
if self.model['ismask'] is False:
modelname = "initmodel"
else:
modelname = "maskvol"
outmodelfile = os.path.join(
self.params['rundir'],
"%s%04d.%s" % (modelname, self.model['id'], extname))
apFile.removeStack(outmodelfile, warn=False)
if rescale:
apVolume.rescaleVolume(self.model['file'],
outmodelfile,
self.model['apix'],
self.stack['apix'],
self.stack['boxsize'],
spider=self.modelspidersingle)
symmetry_description = self.model['data']['symmetry']['symmetry']
if 'Icos' in symmetry_description:
self.convertRefineModelIcosSymmetry(modelname, extname,
outmodelfile,
self.stack['apix'])
self.model['file'] = outmodelfile
self.model['apix'] = self.stack['apix']
self.model['format'] = extname
return outmodelfile
def rescaleModel(modelid, outfile, newbox=None, newapix=None, spider=None): """ take an existing model id and rescale it """ modeldata = getModelFromId(modelid) modelapix = modeldata['pixelsize'] modelfile = os.path.join(modeldata['path']['path'], modeldata['name']) apVolume.rescaleVolume(modelfile, outfile, modelapix, newapix, newbox, spider=spider) return
def rescaleModel(modelid, outfile, newbox=None, newapix=None, spider=None):
"""
take an existing model id and rescale it
"""
modeldata = getModelFromId(modelid)
modelapix = modeldata['pixelsize']
modelfile = os.path.join(modeldata['path']['path'], modeldata['name'])
apVolume.rescaleVolume(modelfile,
outfile,
modelapix,
newapix,
newbox,
spider=spider)
return
def start(self):
self.setFileName()
scale = float(self.params['oldapix']) / self.params['newapix']
mrcname = os.path.join(self.params['rundir'],
self.params['name'] + ".mrc")
origmodel = self.params['file']
if os.path.isfile(mrcname):
apDisplay.printError("File exists")
if (abs(self.params['oldapix'] - self.params['newapix']) > 1.0e-2 or
abs(self.params['oldbox'] - self.params['newbox']) > 1.0e-1):
### rescale old model to a new size
apDisplay.printWarning("rescaling original model to a new size")
scale = float(self.params['oldapix']) / self.params['newapix']
apDisplay.printMsg("rescaling model by scale factor of %.4f" %
(scale))
apVolume.rescaleVolume(origmodel, mrcname, self.params['oldapix'],
self.params['newapix'],
self.params['newbox'])
else:
### simple upload, just copy file to models folder
apDisplay.printMsg("copying original model to a new location: " +
mrcname)
shutil.copyfile(origmodel, mrcname)
if self.params['viper2eman'] is True:
apVolume.viper2eman(mrcname, mrcname, apix=self.params['newapix'])
### render chimera images of model
contour = self.params['contour']
if self.params['mass'] is not None:
apChimera.setVolumeMass(mrcname, self.params['newapix'],
self.params['mass'])
contour = 1.0
apChimera.renderSnapshots(mrcname,
contour=contour,
zoom=self.params['zoom'],
sym=self.params['symdata']['eman_name'])
self.insertModel(mrcname)
def preprocessModelWithProc3d(self, rescale=True): ''' Use EMAN proc3d to scale initial or mask model to that of the refinestack and format ''' extname = self.proc3dFormatConversion() if self.model['ismask'] is False: modelname = "initmodel" else: modelname = "maskvol" outmodelfile = os.path.join(self.params['rundir'], "%s%04d.%s" % (modelname,self.model['id'],extname)) apFile.removeStack(outmodelfile, warn=False) if rescale: apVolume.rescaleVolume(self.model['file'], outmodelfile, self.model['apix'], self.stack['apix'], self.stack['boxsize'], spider=self.modelspidersingle) symmetry_description = self.model['data']['symmetry']['symmetry'] if 'Icos' in symmetry_description: self.convertRefineModelIcosSymmetry(modelname,extname,outmodelfile,self.stack['apix']) self.model['file'] = outmodelfile self.model['apix'] = self.stack['apix'] self.model['format'] = extname return outmodelfile
