# **************************************************************************
# *
# * Authors: Estrella Fernandez Gimenez (me.fernandez@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
import tempfile
from distutils.spawn import find_executable
from os.path import exists, join
import pyworkflow.protocol.params as params
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_volume_adjust_sub import XmippProtVolSubtraction, XmippProtVolAdjust
VOLUME_SLICES = 1
VOLUME_CHIMERA = 0
[docs]class XmippProtVolSubtractionViewer(EmProtocolViewer):
""" Visualize the input and output volumes of protocol XmippProtVolumeSubtraction
by choosing Chimera (3D) or Xmipp visualizer (2D).
The axes of coordinates x, y, z will be shown by choosing Chimera"""
_label = 'viewer volumes subtraction'
_targets = [XmippProtVolSubtraction, XmippProtVolAdjust]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
def _defineParams(self, form):
form.addSection(label='Visualization volumes subtraction output')
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):
tmpFileName = join(tempfile.gettempdir(), 'tmpVolumes_adjust.sqlite')
if exists(tmpFileName):
os.remove(tmpFileName)
_outputVol = self.protocol.outputVolume
setOfVolumes = SetOfVolumes(filename=tmpFileName)
setOfVolumes.append(_outputVol)
setOfVolumes.write()
return setOfVolumes
def _showVolumesChimera(self):
tmpFileNameCMD = join(tempfile.gettempdir(), "vol_adjust_chimera.cxc")
f = open(tmpFileNameCMD, "w")
dim = self.protocol.outputVolume.getDim()[0]
sampling = self.protocol.outputVolume.getSamplingRate()
tmpFileName = os.path.abspath(join(tempfile.gettempdir(), "axis_vol_adjust.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
_outputVol = self.protocol.outputVolume
outputVolFileName = os.path.abspath(ImageHandler.removeFileType(
_outputVol.getFileName()))
# output vol origin coordinates
x_output, y_output, z_output = self.protocol.outputVolume.getShiftsFromOrigin()
f.write("open %s\n" % outputVolFileName)
f.write("volume #2 voxelSize %f origin "
"%0.2f,%0.2f,%0.2f\n"
% (_outputVol.getSamplingRate(), x_output/sampling, y_output/sampling, z_output/sampling))
f.close()
return [ChimeraView(tmpFileNameCMD)]
def _showVolumesXmipp(self):
setOfVolumes = self._createSetOfVolumes()
return [self.objectView(setOfVolumes)]