Source code for xmipp3.viewers.viewer_extract_asymmetric_unit
# **************************************************************************
# *
# * Authors: Roberto Marabini (roberto@cnb.csic.es), May 2013
# * Marta Martinez (mmmtnez@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 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 distutils.spawn import find_executable
from os.path import exists
import pyworkflow.protocol.params as params
from pwem.constants import SYM_I222
from pwem.emlib.image import ImageHandler
from pwem.objects import (SetOfVolumes)
from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO
from pwem.viewers import Chimera, ChimeraView, EmProtocolViewer
from xmipp3.protocols.protocol_extract_asymmetric_unit import XmippProtExtractUnit
from xmipp3.constants import (XMIPP_TO_SCIPION, XMIPP_I222)
VOLUME_SLICES = 1
VOLUME_CHIMERA = 0
[docs]class viewerXmippProtExtractUnit(EmProtocolViewer):
""" Visualize the input and output volumes of protocol XmippProtExtractUnit
by choosing Chimera (3D) or Xmipp visualizer (2D).
The axes of coordinates x, y, z will be shown by choosing Chimera"""
_label = 'viewer extract asymmetric unit'
_targets = [XmippProtExtractUnit]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
# ROB: I know that there is a nice chimera interface but it does not work
# in this case since I am interested in reading the MRC header. So I will
# use chimera as an external program
def _defineParams(self, form):
form.addSection(label='Visualization of input volume and extracted '
'asymmetric unit')
form.addParam('displayVol', params.EnumParam,
choices=['chimerax', 'slices'], default=VOLUME_CHIMERA,
display=params.EnumParam.DISPLAY_HLIST,
label='Display volume with',
help='*chimerax*: display volumes as surface with '
'ChimeraX.\n*slices*: display volumes as 2D slices '
'along z axis.\n')
def _getVisualizeDict(self):
return{
'displayVol': self._showVolumes,
}
def _validate(self):
if find_executable(Chimera.getProgram()) is None:
return ["chimerax is not available. Either install it or choose"
" option 'slices'. "]
return []
# =========================================================================
# Show Volumes
# =========================================================================
def _showVolumes(self, paramName=None):
if self.displayVol == VOLUME_CHIMERA:
return self._showVolumesChimera()
elif self.displayVol == VOLUME_SLICES:
return self._showVolumesXmipp()
def _createSetOfVolumes(self):
if not exists(self.protocol._getExtraPath('tmpVolumes.sqlite')):
tmpFileName = self.protocol._getExtraPath("tmpVolumes.sqlite")
_inputVol = self.protocol.inputVolumes.get()
_outputVol = self.protocol.outputVolume
setOfVolumes = SetOfVolumes(filename=tmpFileName)
setOfVolumes.append(_inputVol)
setOfVolumes.append(_outputVol)
setOfVolumes.write()
else:
tmpFileName = self.protocol._getExtraPath('tmpVolumes.sqlite')
setOfVolumes = SetOfVolumes(filename=tmpFileName)
return setOfVolumes
def _showVolumesChimera(self):
tmpFileNameCMD = self.protocol._getExtraPath("chimera.cxc")
f = open(tmpFileNameCMD, "w")
dim = self.protocol.inputVolumes.get().getDim()[0]
sampling = self.protocol.inputVolumes.get().getSamplingRate()
tmpFileName = os.path.abspath(self.protocol._getExtraPath("axis.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileName,
sampling=sampling)
f.write("open %s\n" % tmpFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
_inputVol = self.protocol.inputVolumes.get()
_outputVol = self.protocol.outputVolume
inputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_inputVol.getFileName()))
# input vol origin coordinates
x_input, y_input, z_input = _inputVol.getShiftsFromOrigin()
f.write("open %s\n" % inputVolFileName)
f.write("volume #2 style mesh level 0.001 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_inputVol.getSamplingRate(), x_input, y_input, z_input))
outputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_outputVol.getFileName()))
# output vol origin coordinates
x_output, y_output, z_output = _outputVol.getShiftsFromOrigin()
f.write("open %s\n" % outputVolFileName)
f.write("volume #3 style surface level 0.001 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_outputVol.getSamplingRate(), x_output, y_output, z_output))
cMap = ['red', 'yellow', 'green', 'cyan', 'blue']
d = {}
innerRadius = self.protocol.innerRadius.get()
d['outerRadius'] = self.protocol.outerRadius.get() * sampling
if innerRadius < 0:
innerRadius = 0
d['innerRadius'] = innerRadius * sampling
d['symmetry'] = Chimera.getSymmetry(XMIPP_TO_SCIPION[self.protocol.symmetryGroup.get()])
if self.protocol.symmetryGroup >= XMIPP_I222:
f.write("shape icosahedron mesh true radius %(outerRadius)d "
"orientation %(symmetry)s\n" % d)
step = (d['outerRadius'] - d['innerRadius']) / float(len(cMap) - 1)
f.write("color radial #3 center 0,0,0 palette -")
counter = 0
s = ""
for color in cMap:
s += "%d,%s:" % (d['innerRadius'] + counter * step, color)
counter += 1
f.write(s[:-1] + '\n')
f.close()
return [ChimeraView(tmpFileNameCMD)]
def _showVolumesXmipp(self):
setOfVolumes = self._createSetOfVolumes()
return [self.objectView(setOfVolumes)]