# **************************************************************************
# *
# * Authors: Carlos Oscar Sanchez Sorzano (coss@cnb.csic.es), May 2013
# * Slavica Jonic (jonic@impmc.upmc.fr)
# * Ported to Scipion:
# * J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es), Nov 2014
# *
# * 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 2 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'
# *
# **************************************************************************
import os
from os.path import exists, join
from pyworkflow.protocol.params import (EnumParam, NumericRangeParam,
LabelParam, IntParam, FloatParam)
from pyworkflow.protocol.constants import LEVEL_ADVANCED
from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO
import pyworkflow.utils as pwutils
from pwem.viewers import (ObjectView, showj, EmProtocolViewer, ChimeraAngDist)
from pwem.emlib import (MDL_SAMPLINGRATE, MDL_ANGLE_ROT, MDL_ANGLE_TILT,
MDL_RESOLUTION_FREQ, MDL_RESOLUTION_FRC, MetaData)
from xmipp3.protocols.protocol_reconstruct_highres import XmippProtReconstructHighRes
from .plotter import XmippPlotter
ITER_LAST = 0
ITER_SELECTION = 1
ANGDIST_2DPLOT = 0
ANGDIST_CHIMERA = 1
ANGDIST_HEATMAP = 2
VOLUME_SLICES = 0
VOLUME_CHIMERA = 1
[docs]class XmippReconstructHighResViewer(EmProtocolViewer):
""" Visualize the output of protocol reconstruct highres """
_label = 'viewer reconstruct highres'
_targets = [XmippProtReconstructHighRes]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
def _defineParams(self, form):
form.addSection(label='Visualization')
form.addParam('viewIter', EnumParam, choices=['last', 'selection'], default=ITER_LAST,
display=EnumParam.DISPLAY_HLIST,
label="Iteration to visualize",
help="""
*last*: only the last iteration will be visualized.
*selection*: you may specify a range of iterations.
Examples:
"1,5-8,10" -> [1,5,6,7,8,10]
"2,6,9-11" -> [2,6,9,10,11]
"2 5, 6-8" -> [2,5,6,7,8]
""")
form.addParam('iterSelection', NumericRangeParam,
condition='viewIter==%d' % ITER_SELECTION,
label="Iteration list",
help="Write the iteration list to visualize.")
group = form.addGroup('Particles')
group.addParam('showOutputParticles', LabelParam, default=False, label='Display output particles')
group.addParam('showAngDist', EnumParam, choices=['2D plot', 'chimera', 'heatmap'],
display=EnumParam.DISPLAY_HLIST, default=ANGDIST_HEATMAP,
label='Display angular distribution',
help='*2D plot*: display angular distribution as interative 2D in matplotlib.\n'
'*chimera*: display angular distribution using Chimera with red spheres.')
group.addParam('spheresScale', IntParam, default=-1,
expertLevel=LEVEL_ADVANCED,
label='Spheres size')
group.addParam('plotHistogramAngularMovement', LabelParam, default=False,
label='Plot histogram with angular changes',
help="""Plot histogram with angular changes from one iteration to next.
Available from iteration 2""")
group = form.addGroup('Volumes')
group.addParam('displayVolume', EnumParam, choices=['Reference', 'Reconstructed', 'Filtered'],
default=1, display=EnumParam.DISPLAY_COMBO,
label='Display volume',
help='Displays selected volume')
group.addParam('showResolutionPlots', LabelParam, default=True,
label='Display resolution plots (FSC)')
group.addParam('resolutionThreshold', FloatParam, default=0.143,
expertLevel=LEVEL_ADVANCED,
label='Threshold in resolution plots')
def _getVisualizeDict(self):
self._load()
return {
'displayVolume' : self._showVolume,
'showOutputParticles' : self._showOutputParticles,
'plotHistogramAngularMovement' : self._plotHistogramAngularMovement,
'showAngDist': self._showAngularDistribution,
'showResolutionPlots': self._showFSC
}
def _validate(self):
if self.lastIter is None:
return ['There are not iterations completed.']
def _load(self):
""" Load selected iterations and classes 3D for visualization mode. """
self.firstIter = 1
self.lastIter = self.protocol.getLastFinishedIter()
if self.viewIter.get() == ITER_LAST:
self._iterations = [self.lastIter]
else:
self._iterations = pwutils.getListFromRangeString(self.iterSelection.get())
from matplotlib.ticker import FuncFormatter
self._plotFormatter = FuncFormatter(self._formatFreq)
def _showFSC(self, paramName=None):
xplotter = XmippPlotter(windowTitle="FSC")
a = xplotter.createSubPlot("FSC", "Frequency (1/A)", "FSC")
legends = []
for it in self._iterations:
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnFSC = join(fnDir,"fsc.xmd")
if exists(fnFSC):
legends.append('Iter %d' % it)
self._plotFSC(a, fnFSC)
xplotter.showLegend(legends)
a.plot([self.minInv, self.maxInv],[self.resolutionThreshold.get(), self.resolutionThreshold.get()], color='black', linestyle='--')
a.grid(True)
views = []
views.append(xplotter)
return views
def _plotFSC(self, a, fnFSC):
md = MetaData(fnFSC)
resolution_inv = [md.getValue(MDL_RESOLUTION_FREQ, f) for f in md]
frc = [md.getValue(MDL_RESOLUTION_FRC, f) for f in md]
self.maxFrc = max(frc)
self.minInv = min(resolution_inv)
self.maxInv = max(resolution_inv)
a.plot(resolution_inv, frc)
a.xaxis.set_major_formatter(self._plotFormatter)
a.set_ylim([-0.1, 1.1])
def _formatFreq(self, value, pos):
""" Format function for Matplotlib formatter. """
inv = 999
if value:
inv = 1/value
return "1/%0.2f" % inv
def _showVolume(self, paramName=None):
choice = self.displayVolume.get()
views=[]
for it in self._iterations:
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
if choice == 0:
if self.protocol.alignmentMethod==self.protocol.GLOBAL_ALIGNMENT:
fnDir = join(fnDir,'globalAssignment')
else:
fnDir = join(fnDir,'localAssignment')
fnVolume = join(fnDir,"volumeRef01.vol")
elif choice == 1:
fnVolume = join(fnDir,"volumeAvg.mrc")
elif choice == 2:
fnVolume = join(fnDir,"volumeAvgFiltered.mrc")
if exists(fnVolume):
samplingRate=self.protocol.readInfoField(fnDir,"sampling",MDL_SAMPLINGRATE)
views.append(ObjectView(self._project, None, fnVolume, viewParams={showj.RENDER: 'image', showj.SAMPLINGRATE: samplingRate}))
return views
def _showOutputParticles(self, paramName=None):
views = []
if hasattr(self.protocol, "outputParticles"):
obj = self.protocol.outputParticles
fn = obj.getFileName()
labels = 'id enabled _filename _xmipp_zScore _xmipp_cumulativeSSNR '
labels += '_ctfModel._defocusU _ctfModel._defocusV _xmipp_shiftX _xmipp_shiftY _xmipp_tilt _xmipp_scale _xmipp_maxCC _xmipp_weight'
labels += " _xmipp_cost _xmipp_weightContinuous2 _xmipp_angleDiff0 _xmipp_weightJumper0 _xmipp_angleDiff _xmipp_weightJumper _xmipp_angleDiff2 _xmipp_weightJumper2"
labels += "_xmipp_weightSSNR _xmipp_maxCCPerc _xmipp_costPerc _xmipp_continuousScaleX _xmipp_continuousScaleY _xmipp_continuousX _xmipp_continuousY _xmipp_continuousA _xmipp_continuousB"
views.append(ObjectView(self._project, obj.strId(), fn,
viewParams={showj.ORDER: labels,
showj.VISIBLE: labels,
showj.MODE: showj.MODE_MD,
showj.RENDER:'_filename'}))
return views
def _plotHistogramAngularMovement(self, paramName=None):
views = []
for it in self._iterations:
fnDir = self.protocol._getExtraPath("Iter%03d"%it)
fnAngles = join(fnDir,"angles.xmd")
if it>1:
from pwem import emlib
xplotter = XmippPlotter(windowTitle="Angular difference")
a = xplotter.createSubPlot("Angular difference", "Angle", "Count")
xplotter.plotMdFile(fnAngles,emlib.MDL_ANGLE_DIFF,emlib.MDL_ANGLE_DIFF,nbins=100)
views.append(xplotter)
return views
#===============================================================================
# showAngularDistribution
#===============================================================================
def _showAngularDistribution(self, paramName=None):
views = []
if self.showAngDist == ANGDIST_CHIMERA:
for it in self._iterations:
angDist = self._createAngDistChimera(it)
if angDist is not None:
views.append(angDist)
elif self.showAngDist == ANGDIST_2DPLOT or self.showAngDist == ANGDIST_HEATMAP:
for it in self._iterations:
angDist = self._createAngDist2D(it, heatmap=self.showAngDist == ANGDIST_HEATMAP)
if angDist is not None:
views.append(angDist)
return views
def _iterAngles(self, fnAngles):
md=MetaData(fnAngles)
for objId in md:
rot = md.getValue(MDL_ANGLE_ROT, objId)
tilt = md.getValue(MDL_ANGLE_TILT, objId)
yield rot, tilt
def _createAngDistChimera(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 pwem.emlib.metadata import getSize
self.createAngDistributionSqlite(fnAnglesSqLite, getSize(fnAngles),
itemDataIterator=self._iterAngles(fnAngles))
vol = os.path.join(fnDir, "volumeAvg.mrc")
extraFilesPath = self.protocol._getExtraPath()
volOrigin = self.protocol.outputVolume.getShiftsFromOrigin()
radius = self.spheresScale.get()
view = ChimeraAngDist(vol, extraFilesPath,
angularDistFile=fnAngles,
spheresDistance=radius,
voxelSize=self.protocol.outputVolume.getSamplingRate(),
volOrigin=volOrigin,
showProjection=True)
return view
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