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 _createAngDist2D(self, it):
nrefs = len(self._refsList)
nparts = self.protocol.inputParticles.get().getSize()
gridsize = self._getGridSize(nrefs)
if self.protocol.IS_REFINE:
data_angularDist = self.protocol._getFileName("output_par", iter=it)
if exists(data_angularDist):
plotter = EmPlotter(x=gridsize[0], y=gridsize[1],
mainTitle="Iteration %d" % it, windowTitle="Angular distribution")
title = 'iter %d' % it
sqliteFn = self.protocol._getFileName('projections', iter=it)
self.createAngDistributionSqlite(sqliteFn, nparts, itemDataIterator=self._iterAngles(it, data_angularDist))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
else:
return
else:
for ref3d in self._refsList:
data_angularDist = self.protocol._getFileName("output_par_class", iter=it, ref=ref3d)
if exists(data_angularDist):
plotter = EmPlotter(x=gridsize[0], y=gridsize[1],
mainTitle="Iteration %d" % it, windowTitle="Angular distribution")
title = 'class %d' % ref3d
sqliteFn = self.protocol._getFileName('projectionsClass', iter=it, ref=ref3d)
self.createAngDistributionSqlite(sqliteFn, nparts, itemDataIterator=self._iterAngles(it, data_angularDist))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
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 _createAngDist2D(self, it):
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnAngles = join(fnDir,"angles.xmd")
view=None
if exists(fnAngles):
fnAnglesSqLite = join(fnDir,"angles.sqlite")
from pyworkflow.em.metadata.utils import getSize
from pyworkflow.em.plotter import EmPlotter
self.createAngDistributionSqlite(fnAnglesSqLite, getSize(fnAngles), itemDataIterator=self._iterAngles(fnAngles))
view = EmPlotter(x=1, y=1, mainTitle="Iteration %d" % it, windowTitle="Angular distribution")
view.plotAngularDistributionFromMd(fnAnglesSqLite, 'iter %d' % it)
return view
def _createAngDist2D(self, it):
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnAngles = join(fnDir,"angles.xmd")
view=None
if exists(fnAngles):
fnAnglesSqLite = join(fnDir,"angles.sqlite")
from pyworkflow.em.plotter import EmPlotter
if not exists(fnAnglesSqLite):
from pyworkflow.em.metadata.utils import getSize
self.createAngDistributionSqlite(fnAnglesSqLite, getSize(fnAngles), itemDataIterator=self._iterAngles(fnAngles))
view = EmPlotter(x=1, y=1, mainTitle="Iteration %d" % it, windowTitle="Angular distribution")
view.plotAngularDistributionFromMd(fnAnglesSqLite, 'iter %d' % it)
return view
def _createAngDist2D(self, it):
nrefs = len(self._refsList)
nparts = self.protocol.inputParticles.get().getSize()
gridsize = self._getGridSize(nrefs)
if self.protocol.IS_REFINE:
data_angularDist = self.protocol._getFileName("output_par",
iter=it)
if exists(data_angularDist):
plotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
mainTitle="Iteration %d" % it,
windowTitle="Angular distribution")
title = 'iter %d' % it
sqliteFn = self.protocol._getFileName('projections', iter=it)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(it, data_angularDist))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
else:
return
else:
for ref3d in self._refsList:
data_angularDist = self.protocol._getFileName(
"output_par_class", iter=it, ref=ref3d)
if exists(data_angularDist):
plotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
mainTitle="Iteration %d" % it,
windowTitle="Angular distribution")
title = 'class %d' % ref3d
sqliteFn = self.protocol._getFileName('projectionsClass',
iter=it,
ref=ref3d)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(
it, data_angularDist))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
