def createChimeraVolumeSnapshot(self, volume, iteration, reference_number=1):
""" create chimera snapshot images of volume """
if self.params["snapfilter"]:
resolution = self.params["snapfilter"]
else:
newfscfile = os.path.join(
self.resultspath,
"recon_%s_it%.3d_vol%.3d.fsc" % (self.params["timestamp"], iteration, reference_number),
)
try:
resolution = apRecon.getResolutionFromGenericFSCFile(
newfscfile, self.runparams["boxsize"], self.runparams["apix"]
)
except:
apDisplay.printWarning("Failed to get resolution from generic FSC file: " + newfscfile)
resolution = 30
apDisplay.printWarning("Running Chimera Snapshot with resolution: %d " % resolution)
apChimera.filterAndChimera(
volume,
resolution,
self.runparams["apix"],
self.runparams["boxsize"],
"snapshot",
self.params["contour"],
self.params["zoom"],
sym="c1",
mass=self.params["mass"],
)
def createChimeraVolumeSnapshot(self,
volume,
iteration,
reference_number=1):
''' create chimera snapshot images of volume '''
if self.params['snapfilter']:
resolution = self.params['snapfilter']
else:
newfscfile = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.fsc" \
% (self.params['timestamp'], iteration, reference_number))
try:
resolution = apRecon.getResolutionFromGenericFSCFile(
newfscfile, self.runparams['boxsize'],
self.runparams['apix'])
except:
apDisplay.printWarning(
"Failed to get resolution from generic FSC file: " +
newfscfile)
resolution = 30
apDisplay.printWarning(
"Running Chimera Snapshot with resolution: %d " % resolution)
apChimera.filterAndChimera(volume,
resolution,
self.runparams['apix'],
self.runparams['boxsize'],
'snapshot',
self.params['contour'],
self.params['zoom'],
sym='c1',
mass=self.params['mass'])
def createChimeraVolumeSnapshot(self,
volume,
iteration,
reference_number=1):
''' create chimera snapshot images of volume '''
if self.params['snapfilter']:
resolution = self.params['snapfilter']
else:
newfscfile = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.fsc" \
% (self.params['timestamp'], iteration, reference_number))
try:
resolution = apRecon.getResolutionFromGenericFSCFile(
newfscfile,
self.runparams['boxsize'],
self.runparams['apix'],
filtradius=3,
criterion=self.fscResCriterion)
except:
apDisplay.printWarning(
"Failed to get resolution from generic FSC file: " +
newfscfile)
resolution = 30
apDisplay.printWarning(
"Running Chimera Snapshot with resolution: %d " % resolution)
# TODO: need to work this out.
# symmetry was hard coded to 'c1'. why?
try:
symmetry = self.runparams['symmetry']
except Exception, e:
symmetry = self.runparams['symmetry'].split()[0]
symmetry = apSymmetry.findSymmetry(symmetry)
def insertRefinementIterationData(self,
iteration,
package_table=None,
package_database_object=None,
reference_number=1):
''' fills in database entry for ApRefineIterData table '''
if not self.params['euleronly']:
### get resolution
try:
fscfile = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.fsc" \
% (self.params['timestamp'], iteration, reference_number))
fscRes = apRecon.getResolutionFromGenericFSCFile(
fscfile,
self.runparams['boxsize'],
self.runparams['apix'],
filtradius=3,
criterion=self.fscResCriterion)
apDisplay.printColor(
"FSC " + str(self.fscResCriterion) + " Resolution: " +
str(fscRes), "cyan")
resq = appiondata.ApResolutionData()
resq['half'] = fscRes
resq['fscfile'] = os.path.basename(fscfile)
except Exception, e:
apDisplay.printWarning(
"An error occured while reading fsc data: ")
print e
apDisplay.printWarning(
"The following FSC file does not exist or is unreadable: %s "
% (fscfile))
resq = None
def insertRefinementIterationData(self, iteration, package_table=None, package_database_object=None, reference_number=1):
''' fills in database entry for ApRefineIterData table '''
if not self.params['euleronly']:
### get resolution
try:
fscfile = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.fsc" \
% (self.params['timestamp'], iteration, reference_number))
fscRes = apRecon.getResolutionFromGenericFSCFile(fscfile, self.runparams['boxsize'], self.runparams['apix'],filtradius=3, criterion=self.fscResCriterion)
apDisplay.printColor("FSC " + str(self.fscResCriterion) + " Resolution: "+str(fscRes), "cyan")
resq = appiondata.ApResolutionData()
resq['half'] = fscRes
resq['fscfile'] = os.path.basename(fscfile)
except Exception, e:
apDisplay.printWarning("An error occured while reading fsc data: ")
print e
apDisplay.printWarning("The following FSC file does not exist or is unreadable: %s " % (fscfile))
resq = None
def createChimeraVolumeSnapshot(self, volume, iteration, reference_number=1):
''' create chimera snapshot images of volume '''
if self.params['snapfilter']:
resolution = self.params['snapfilter']
else:
newfscfile = os.path.join(self.resultspath, "recon_%s_it%.3d_vol%.3d.fsc" \
% (self.params['timestamp'], iteration, reference_number))
try:
resolution = apRecon.getResolutionFromGenericFSCFile(newfscfile, self.runparams['boxsize'], self.runparams['apix'],filtradius=3, criterion=self.fscResCriterion)
except:
apDisplay.printWarning("Failed to get resolution from generic FSC file: "+newfscfile)
resolution = 30
apDisplay.printWarning("Running Chimera Snapshot with resolution: %d " % resolution)
# TODO: need to work this out.
# symmetry was hard coded to 'c1'. why?
try:
symmetry = self.runparams['symmetry']
except Exception, e:
symmetry = self.runparams['symmetry'].split()[0]
symmetry = apSymmetry.findSymmetry( symmetry )
def insertRefinementIterationData(
self, iteration, package_table=None, package_database_object=None, reference_number=1
):
""" fills in database entry for ApRefineIterData table """
if not self.params["euleronly"]:
### get resolution
try:
fscfile = os.path.join(
self.resultspath,
"recon_%s_it%.3d_vol%.3d.fsc" % (self.params["timestamp"], iteration, reference_number),
)
fscRes = apRecon.getResolutionFromGenericFSCFile(
fscfile, self.runparams["boxsize"], self.runparams["apix"]
)
apDisplay.printColor("FSC 0.5 Resolution: " + str(fscRes), "cyan")
resq = appiondata.ApResolutionData()
resq["half"] = fscRes
resq["fscfile"] = os.path.basename(fscfile)
except Exception, e:
print e
apDisplay.printWarning("FSC file does not exist or is unreadable")
resq = None
