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['innerRadius'] = self.protocol.innerRadius.get() * 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)]