# **************************************************************************
# *
# * 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
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_deep_align import XmippProtDeepAlign
ANGDIST_2DPLOT = 0
ANGDIST_HEATMAP = 1
[docs]class XmippDeepAlignViewer(EmProtocolViewer):
""" Visualize the output of protocol reconstruct highres """
_label = 'viewer deep align'
_targets = [XmippProtDeepAlign]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
def _defineParams(self, form):
form.addSection(label='Visualization')
group = form.addGroup('Particles')
group.addParam('showOutputParticles', LabelParam, default=False, label='Display output particles')
group.addParam('showAngDist', EnumParam, choices=['2D plot', 'heatmap'],
display=EnumParam.DISPLAY_HLIST, default=ANGDIST_2DPLOT,
label='Display angular distribution',
help='*2D plot*: display angular distribution as interative 2D in matplotlib.')
group.addParam('spheresScale', IntParam, default=-1,
expertLevel=LEVEL_ADVANCED,
label='Spheres size')
def _getVisualizeDict(self):
return {
'showOutputParticles': self._showOutputParticles,
'showAngDist': self._showAngularDistribution
}
def _showOutputParticles(self, paramName=None):
views = []
if hasattr(self.protocol, "outputParticles"):
obj = self.protocol.outputParticles
fn = obj.getFileName()
labels = 'id enabled _filename '
labels += '_ctfModel._defocusU _ctfModel._defocusV _xmipp_shiftX _xmipp_shiftY _xmipp_angleTilt '
labels += ' _xmipp_angleRot _xmipp_anglePsi _xmipp_maxCC _xmipp_weight '
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
# ===============================================================================
# showAngularDistribution
# ===============================================================================
def _showAngularDistribution(self, paramName=None):
views = []
angDist = self._createAngDist2D(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 _createAngDist2D(self, heatmap):
fnDir = self.protocol._getExtraPath()
fnAngles = join(fnDir, "outConesParticles.xmd")
view = None
if not exists(fnAngles):
fnAngles = join(fnDir,"outputParticles.xmd")
if exists(fnAngles):
fnAnglesSqLite = join(fnDir, "outConesParticles.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, windowTitle="Angular distribution")
if heatmap:
axis = view.plotAngularDistributionFromMd(fnAnglesSqLite, '', histogram=True)
view.getFigure().colorbar(axis)
else:
view.plotAngularDistributionFromMd(fnAnglesSqLite, '')
return view