# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors: Jose Luis Vilas (jlvilas@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 pyworkflow import VERSION_2_0
from pyworkflow.utils import getExt
from pyworkflow.protocol.params import (PointerParam, BooleanParam, FloatParam,
LEVEL_ADVANCED)
from pwem.protocols import ProtAnalysis3D
RADIAL_RESOLUTION_FN = 'radial_FSC_resolution.xmd'
[docs]class XmippProtResolutionAlignment(ProtAnalysis3D):
"""
Given two half maps the protocol estimates if the reconstruction presents angular
alignment errors. To do that, a set of directional FSC along all possible directions
are estimated. The result is a curve Resolution-radius. If this curve presents a slope
then the map present angular assignment errors, but it the graph is flat (horizontal), the map
is error free. Note that this protocol generates a plot, not a Scipion object. Its result
can only be visualized.
"""
_label = 'resolution alignment'
_lastUpdateVersion = VERSION_2_0
def __init__(self, **args):
ProtAnalysis3D.__init__(self, **args)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('halfVolumesFile', BooleanParam, default=False,
label="Are the half volumes stored with the input volume?",
help='Usually, the half volumes are stored as properties of '
'the input volume. If this is not the case, set this to '
'False and specify the two halves you want to use.')
form.addParam('inputHalves', PointerParam, pointerClass='Volume',
label="Input Half Maps",
condition='halfVolumesFile',
help='Select a half maps for determining its '
' resolution anisotropy and resolution.')
form.addParam('half1', PointerParam, pointerClass='Volume',
condition="not halfVolumesFile",
label="Half Map 1", important=True,
help='Select one map for determining the '
'directional FSC resolution.')
form.addParam('half2', PointerParam, pointerClass='Volume',
condition="not halfVolumesFile",
label="Half Map 2", important=True,
help='Select the second map for determining the '
'directional FSC resolution.')
form.addParam('mask', PointerParam, pointerClass='VolumeMask',
allowsNull=True,
label="Mask",
help='The mask determines which points are specimen'
' and which are not')
form.addParam('helicalReconstruction', BooleanParam, default=False,
label="Is a the protein a helix",
help='blablabla')
form.addParam('limRadius', BooleanParam, default=True,
expertLevel=LEVEL_ADVANCED,
label="Limit the protein radius",
help='blablabla')
form.addParam('usedirectionalfsc', BooleanParam, default=True,
expertLevel=LEVEL_ADVANCED,
label="use directional fsc",
help='blablabla')
form.addParam('coneAngle', FloatParam, default=17.0,
expertLevel=LEVEL_ADVANCED,
label="Cone Angle",
help='Angle between the axis of the cone and the generatrix. '
'An angle of 17 degrees is the best angle (see publication'
'Vilas 2021) to measuare directional FSCs')
form.addParam('threshold', FloatParam, expertLevel=LEVEL_ADVANCED,
default=0.143,
label="FSC Threshold",
help='Threshold for the fsc. By default the standard 0.143. '
'Other common thresholds are 0.5 and 0.3.')
form.addParallelSection(threads=4, mpi=0)
# --------------------------- INSERT steps functions --------------------------------------------
def _insertAllSteps(self):
self._insertFunctionStep(self.convertInputStep)
self._insertFunctionStep(self.angularResolutionAlignmentStep)
[docs] def angularResolutionAlignmentStep(self):
"""
This function runs the algorithm to detect misalignment
"""
fndir = self._getExtraPath("fsc")
os.mkdir(fndir)
params = ' --half1 "%s"' % self.vol1Fn
params += ' --half2 "%s"' % self.vol2Fn
params += ' -o %s' % self._getExtraPath(RADIAL_RESOLUTION_FN)
if self.halfVolumesFile:
params += ' --sampling %f' % self.inputHalves.get().getSamplingRate()
else:
params += ' --sampling %f' % self.half1.get().getSamplingRate()
if self.helicalReconstruction.get():
params += ' --helix '
if self.mask.hasValue():
params += ' --mask "%s"' % self.maskFn
if self.limRadius.get():
params += ' --limit_radius '
if self.usedirectionalfsc.get():
params += ' --directional_resolution '
params += ' --anglecone %f' % self.coneAngle.get()
params += ' --threshold %s' % self.threshold.get()
params += ' --threads %s' % self.numberOfThreads.get()
self.runJob('xmipp_angular_resolution_alignment', params)
# --------------------------- INFO functions ------------------------------
def _methods(self):
messages = []
ARTICLE_URL = 'Pending on publication'
messages.append('Information about the method/article in ' + ARTICLE_URL)
return messages
def _validate(self):
errors = []
if self.halfVolumesFile.get():
if not self.inputHalves.get():
errors.append("You need to select the Associated halves")
else:
if not self.half1.get():
errors.append("You need to select the half1")
if not self.half2.get():
errors.append("You need to select the half2")
return errors
def _summary(self):
summary = []
summary.append("This protocol does not produce Scipion Objects as output. Click on Analyze results to visualize the results")
return summary