# **************************************************************************
# *
# * Authors: Pablo Conesa (pconesa@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
from matplotlib import cm
from pwem.viewers import EmPlotter
from pyworkflow.viewer import ProtocolViewer
import pwem.objects as emobj
from pyworkflow.protocol.params import LabelParam
from pwem.viewers.plotter import PLOT_PROJ_ANGLES, PLOT_PROJ_DIR, PLOT_EULER_ANGLES
[docs]class AngularDistributionViewer(ProtocolViewer):
""" Visualize particles, subtomograms with orientation information """
_label = "Angular distribution viewer"
_targets = [emobj.SetOfParticles, emobj.SetOfVolumes]
def _defineParams(self, form):
form.addSection(label='Visualization')
form.addParam(self.getParamName(self.doShowHeatMap), LabelParam,
label="Show heatmap")
form.addParam(self.getParamName(self.doShow2DPolar), LabelParam,
label="Show 2D polar plot")
form.addParam(self.getParamName(self.doShow3DPlot), LabelParam,
label="Show 3D plot")
from pwem.wizards import ColorScaleWizardBase
ColorScaleWizardBase.defineColorScaleParams(form, defaultHighest=20,
defaultLowest=0, defaultColorMap="Blues")
[docs] def getParamName(self, method):
return method.__name__ + "P"
def _getVisualizeDict(self):
return {self.getParamName(self.doShowHeatMap): self.doShowHeatMap,
self.getParamName(self.doShow2DPolar): self.doShow2DPolar,
self.getParamName(self.doShow3DPlot): self.doShow3DPlot,
}
[docs] def getColorMap(self):
cmap = cm.get_cmap(self.colorMap.get())
if cmap is None:
cmap = cm.jet
return cmap
[docs] @staticmethod
def plotAngularDistribution(emSet:emobj.EMSet, colormap, type):
plotter = EmPlotter(x=1, y=1, windowTitle='Projection direction distribution')
subtitle = "Color based on count of particles."
if type == PLOT_PROJ_ANGLES:
subtitle += "\nRadius = polar angle, rotation = azimuthal angle."
elif type == PLOT_PROJ_DIR:
subtitle += "\nRed line marks origin of coordinates."
plotter.plotAngularDistributionFromSet(emSet, "Projection direction distribution", type=type,
colormap=colormap, subtitle=subtitle)
return [plotter]
[docs] def doShowHeatMap(self, e):
return self.plotAngularDistribution(self.protocol, self.getColorMap(), PLOT_EULER_ANGLES)
[docs] def doShow2DPolar(self,e):
return self.plotAngularDistribution(self.protocol, self.getColorMap(), PLOT_PROJ_ANGLES)
[docs] def doShow3DPlot(self,e):
return self.plotAngularDistribution(self.protocol, self.getColorMap(), PLOT_PROJ_DIR)