Source code for spider.protocols.protocol_align_apsr

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se)
# *              Tapu Shaikh            (shaikh@ceitec.muni.cz)
# * 
# * 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 3 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'
# *
# **************************************************************************

from pyworkflow.utils.path import getLastFile

from .protocol_align_base import SpiderProtAlign

      
[docs]class SpiderProtAlignAPSR(SpiderProtAlign): """ This protocol wraps SPIDER AP SR command. Reference-free alignment (both translational and rotational) of an image series. See detailed description at: [[http://spider.wadsworth.org/spider_doc/spider/docs/man/apsr.html][SPIDER's AP SR online manual]] """ _label = 'align ap sr' def __init__(self, **args): SpiderProtAlign.__init__(self, 'mda/apsr4class.msa', 'apsr', **args) def _defineAlignParams(self, form): SpiderProtAlign._defineAlignParams(self, form) # Hide the center of gravity option from the GUI since it is not # used in this particular alignment method cgOption = form.getParam('cgOption') cgOption.config(condition='False') form.addParallelSection(threads=2, mpi=0)
[docs] def alignParticlesStep(self, innerRadius, outerRadius): """ Apply the selected filter to particles. Create the set of particles. """ self._params.update({ '[inner-rad]': innerRadius, '[outer-rad]': outerRadius, '[group_particles]': self._params['particlesSel'], '[unaligned]': self._params['particles'] + '@******', '[aligned_stack]': self._params['particlesAligned'], '[nummps]': self.numberOfThreads.get() }) self.runTemplate(self.getScript(), self.getExt(), self._params)
[docs] def getAverage(self): pattern = self._getPath(self.getAlignDir(), 'iteravg*.%s' % self.getExt()) return getLastFile(pattern)
def _summary(self): summary = list() summary.append('Radius range (px): *%s - %s*' % (self.innerRadius, self.outerRadius)) return summary def _methods(self): if hasattr(self, 'outputParticles'): msg = "Input particles %s were " % self.getObjectTag('inputParticles') msg += "initially subjected to reference-free alignment using SPIDER's " msg += "_AP SR_ command, using radii %s to %s pixels. " % ( self.innerRadius, self.outerRadius) msg += "Output particles: %s" % self.getObjectTag('outputParticles') else: msg = "Output not ready yet." return [msg] def _citations(self): return ['Penczek1992']