Source code for imod.protocols.protocol_auto3d

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * 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.
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# * 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 pyworkflow as pw
import pyworkflow.protocol.params as params

from tomo.protocols import ProtTomoReconstruct
from tomo.convert import writeTiStack


[docs]class ProtImodAuto3D(ProtTomoReconstruct): """ Simple protocol to do a quick Tomogram reconstruction with IMOD. (Sample scripts provided by Javi Chichon) """ _label = 'imod auto3d' # -------------------------- DEFINE param functions ----------------------- def _defineParams(self, form): form.addSection('Input') form.addParam('inputTiltSeries', params.PointerParam, pointerClass='TiltSeries,SetOfTiltSeries', important=True, label='Input Tilt-Series', help='Provide either a single TiltSeries or a ' 'SetOfTiltSeries that will be used for the quick ' 'reconstruction of Tomograms.') form.addParam('excludeList', params.StringParam, default='', label='Exclusion list', help='Provide tilt images IDs (usually starting at 1) ' 'that you want to exclude from the processing. ') form.addParam('bin', params.IntParam, default=2, label='Bin the input images', help='Binning of the input images.') form.addParam('zWidth', params.IntParam, label='Z width of the tomograph', help='???') form.addParam('rotationAngle', params.FloatParam, default=0.0, label='Tilt rotation angle (deg)', help='Angle from the vertical to the tilt axis in raw ' 'images.') group = form.addGroup('Fiducial markers') group.addParam('useRaptor', params.BooleanParam, default=True, label='Use RAPTOR for automatic markers tracking?', help='???') group.addParam('markersDiameter', params.IntParam, default=20, label='Markers diameter (nm)', help='Size of gold beads in nanometers.') group.addParam('markersNumber', params.IntParam, default=20, label='Number of markers to track', help='Number of markers that will be tracked by RAPTOR.') # --------------------------- STEPS functions ----------------------------
[docs] def processTiltSeriesStep(self, tsId): ts = self._tsDict.getTs(tsId) workingFolder = self._getTmpPath(tsId) prefix = os.path.join(workingFolder, tsId) pw.utils.makePath(workingFolder) # Write new stack discarding excluded tilts excludeList = map(int, self.excludeList.get().split()) tiList = self._tsDict.getTiList(tsId) tiList.sort(key=lambda ti: ti.getTiltAngle()) tsStack = prefix + '.st' writeTiStack(tiList, outputStackFn=tsStack, outputTltFn=prefix + '.rawtlt', excludeList=excludeList) here = os.path.abspath(os.path.dirname(__file__)) args = os.path.join(here, 'script_imod_auto3d.py') tomoName = self._getTomoName(tsId) args += ' --output %s ' % tomoName args += '%s --widthz %d --bin %d ' % (os.path.basename(tsStack), self.zWidth, self.bin) args += '--rotation_angle %s ' % self.rotationAngle if self.useRaptor: args += ('--raptor --markers_diameter %d --markers_number %d' % (self.markersDiameter, self.markersNumber)) self.runJob('python', args, cwd=workingFolder) tomoPath = os.path.join(workingFolder, tomoName) if os.path.exists(tomoPath): pw.utils.moveFile(tomoPath, self._getPath(tomoName)) else: print("ERROR: The expected tomogram for Tilt-Series %s " "was not properly generated. " % tsId) if not pw.utils.envVarOn('SCIPION_DEBUG_NOCLEAN'): pw.utils.cleanPath(workingFolder) self._tsDict.setFinished(tsId)