def _displayAngDist(self, *args):
#print "_displayAngDist...."
iterations = self._getIterations()
nparts = self.protocol.inputParticles.get().getSize()
views = []
if self.displayAngDist == ANGDIST_2DPLOT:
#print " self.displayAngDist == ANGDIST_2DPLO "
for it in iterations:
anglesSqlite = self._getFinalPath('angular_dist_%03d.sqlite' %
it)
title = 'Angular distribution iter %03d' % it
plotter = EmPlotter(x=1, y=1, windowTitle=title)
self.createAngDistributionSqlite(
anglesSqlite,
nparts,
itemDataIterator=self._iterAngles(it))
plotter.plotAngularDistributionFromMd(anglesSqlite, title)
views.append(plotter)
else:
it = iterations[-1]
print "Using last iteration: ", it
anglesSqlite = self._getFinalPath('angular_dist_%03d.sqlite' % it)
self.createAngDistributionSqlite(
anglesSqlite, nparts, itemDataIterator=self._iterAngles(it))
volumes = self.getVolumeNames(it)
views.append(
em.ChimeraClientView(
volumes[0],
showProjection=True,
angularDistFile=anglesSqlite,
spheresDistance=2)) #self.spheresScale.get()))
return views
def _createAngDistChimera(self, it):
nparts = self.protocol.inputParticles.get().getSize()
radius = self.spheresScale.get()
volumes = self._getVolumeNames()
if len(volumes) > 1:
raise Exception(
"Please, select a single volume to show it's angular distribution"
)
else:
if self.protocol.IS_REFINE:
data_angularDist = self.protocol._getFileName("output_par",
iter=it)
if exists(data_angularDist):
sqliteFn = self.protocol._getFileName('projections',
iter=it)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(
it, data_angularDist))
view = em.ChimeraClientView(volumes[0],
showProjection=True,
angularDistFile=sqliteFn,
spheresDistance=radius)
else:
for ref3d in self._refsList:
data_angularDist = self.protocol._getFileName(
"output_par_class", iter=it, ref=ref3d)
if exists(data_angularDist):
sqliteFn = self.protocol._getFileName(
'projectionsClass', iter=it, ref=ref3d)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(
it, data_angularDist))
view = em.ChimeraClientView(volumes[0],
showProjection=True,
angularDistFile=sqliteFn,
spheresDistance=radius)
return view
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volumes = self._getVolumeNames()
if len(volumes) > 1:
cmdFile = self.protocol._getExtraPath('chimera_volumes.cmd')
f = open(cmdFile, 'w+')
for volFn in volumes:
# We assume that the chimera script will be generated
# at the same folder than relion volumes
vol = volFn.replace(':mrc', '')
localVol = os.path.basename(vol)
if exists(vol):
f.write("open %s\n" % localVol)
f.write('tile\n')
f.close()
view = em.ChimeraView(cmdFile)
else:
view = em.ChimeraClientView(volumes[0])
return [view]
def _showVolumesChimera(self):
""" Create a chimera script to visualize selected volumes. """
volumes = self.getVolumeNames()
if len(volumes) > 1:
cmdFile = self._getFinalPath('chimera_volumes.cmd')
f = open(cmdFile, 'w+')
for vol in volumes:
# We assume that the chimera script will be generated
# at the same folder than spider volumes
localVol = os.path.basename(vol)
if os.path.exists(vol):
f.write("open spider:%s\n" % localVol)
f.write('tile\n')
f.close()
view = em.ChimeraView(cmdFile)
else:
#view = CommandView('xmipp_chimera_client --input "%s" --mode projector 256 &' % volumes[0])
#view = em.ChimeraClientView(volumes[0])
view = em.ChimeraClientView(
volumes[0], showProjection=True
) #, angularDistFile=sqliteFn, spheresDistance=radius)
return [view]