def _createAngDist2D(self):
# Common variables to use
nparts = self.protocol._getInputParticles().getSize()
title = "Angular Distribution"
plotter = EmPlotter(windowTitle=title)
sqliteFn = self.protocol._getFileName('projections')
if not os.path.exists(sqliteFn):
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=iterAngles(
self.protocol._getFileName('anglesFn')))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
def _createAngDist2D(self, it, heatmap):
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnAngles = join(fnDir,"angles.xmd")
view=None
if exists(fnAngles):
fnAnglesSqLite = join(fnDir,"angles.sqlite")
from pwem.viewers import EmPlotter
if not exists(fnAnglesSqLite):
from pwem.emlib.metadata import getSize
self.createAngDistributionSqlite(fnAnglesSqLite, getSize(fnAngles), itemDataIterator=self._iterAngles(fnAngles))
view = EmPlotter(x=1, y=1, mainTitle="Iteration %d" % it, windowTitle="Angular distribution")
if heatmap:
axis = view.plotAngularDistributionFromMd(fnAnglesSqLite, '', histogram=True)
view.getFigure().colorbar(axis)
else:
view.plotAngularDistributionFromMd(fnAnglesSqLite, '')
return view
def _displayAngDist(self, *args):
iterations = self._getIterations()
nparts = self.protocol.inputParticles.get().getSize()
views = []
if self.displayAngDist == ANGDIST_2DPLOT:
for it in iterations:
if it == 1:
print(
"Orientations for the first iteration cannot be plotted. "
"Skipping..")
continue
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)
vol = self.protocol.outputVolume
volOrigin = vol.getOrigin(force=True).getShifts()
samplingRate = vol.getSamplingRate()
views.append(
ChimeraAngDist(volumes[0],
self.protocol._getTmpPath(),
voxelSize=samplingRate,
volOrigin=volOrigin,
angularDistFile=anglesSqlite,
format="spider"))
return views
