# **************************************************************************
# *
# * Authors: Grigory Sharov (gsharov@mrc-lmb.cam.ac.uk)
# *
# * MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * 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'
# *
# **************************************************************************
import os
import pyworkflow.protocol.params as params
from pyworkflow.constants import BETA
from pwem.protocols import ProtAnalysis3D
from pwem.objects import Volume
from pwem.emlib.image import ImageHandler
from sidesplitter import Plugin
from ..convert import convertMask
[docs]class ProtSideSplitter(ProtAnalysis3D):
"""
Protocol for mitigating local over-fitting by filtering.
Find more information at https://github.com/StructuralBiology-ICLMedicine/SIDESPLITTER
"""
_label = 'local filter'
_devStatus = BETA
def _createFilenameTemplates(self):
""" Centralize how files are called. """
myDict = {'half1': self._getExtraPath("half1_unfil.mrc"),
'half2': self._getExtraPath("half2_unfil.mrc"),
'mask': self._getExtraPath("mask.mrc"),
'outHalf1Fn': self._getExtraPath('half1_unfil_sidesplitter.mrc'),
'outHalf2Fn': self._getExtraPath('half2_unfil_sidesplitter.mrc'),
}
self._updateFilenamesDict(myDict)
# --------------------------- DEFINE param functions ----------------------
def _defineParams(self, form):
form.addSection(label='Input')
form.addParam('protRefine', params.PointerParam,
important=True,
pointerClass="ProtRefine3D",
label='Select a previous refinement protocol',
help='Select any previous refinement protocol to get the '
'3D half maps. Note that the refinement protocol '
'must use gold-standard method.')
form.addParam('mask', params.PointerParam,
allowsNull=True,
pointerClass="VolumeMask",
label='Volume mask',
help="Provide the mask used in 3D refinement.")
form.addParam('doSNRWeighting', params.BooleanParam,
expertLevel=params.LEVEL_ADVANCED,
default=False,
label='Use SNR-weighted spectrum',
help='Outputs the SNR weighted spectrum rather '
'than matching input spectrum / grey-scale.')
form.addParallelSection(threads=1, mpi=0)
# --------------------------- INSERT steps functions ----------------------
def _insertAllSteps(self):
self._createFilenameTemplates()
self._insertFunctionStep('convertInputStep')
self._insertFunctionStep('runSideSplitterStep')
self._insertFunctionStep('createOutputStep')
# --------------------------- STEPS functions -----------------------------
[docs] def runSideSplitterStep(self):
""" Call SIDESPLITTER with the appropriate parameters. """
args = self._getArgs()
param = ' '.join(['%s %s' % (k, str(v)) for k, v in args.items()])
program = Plugin.getProgram()
cmd = 'export OMP_NUM_THREADS=%d; ' % self.numberOfThreads.get()
cmd += program
self.runJob(cmd, param, env=Plugin.getEnviron(),
cwd=self._getExtraPath(),
numberOfThreads=1)
[docs] def createOutputStep(self):
inputVol = self.protRefine.get().outputVolume
ps = inputVol.getSamplingRate()
vol = Volume()
vol.setSamplingRate(ps)
vol.setObjLabel('Filtered half-map 1')
vol.setFileName(self._getFileName('outHalf1Fn'))
vol2 = Volume()
vol2.setSamplingRate(ps)
vol2.setObjLabel('Filtered half-map 2')
vol2.setFileName(self._getFileName('outHalf2Fn'))
outputs = {'outputVolume1': vol,
'outputVolume2': vol2}
self._defineOutputs(**outputs)
self._defineSourceRelation(inputVol, vol)
self._defineSourceRelation(inputVol, vol2)
# --------------------------- INFO functions ------------------------------
def _summary(self):
summary = []
if hasattr(self, 'outputVolume1'):
summary.append("Created locally filtered half-maps.")
else:
summary.append("Output is not ready")
return summary
def _validate(self):
errors = []
return errors
# --------------------------- UTILS functions -----------------------------
def _getArgs(self):
""" Prepare the args dictionary."""
args = {'--v1': os.path.basename(self._getFileName('half1')),
'--v2': os.path.basename(self._getFileName('half2'))}
if self.mask.hasValue():
args['--mask'] = os.path.basename(self._getFileName('mask'))
if self.doSNRWeighting:
args['--spectrum'] = ' '
return args