# **************************************************************************
# *
# * Authors: Yunior C. Fonseca Reyna (cfonseca@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 BETA
from tomo.objects import SetOfCTFTomoSeries
from .protocol_ctfEstimation_automatic import ProtImodAutomaticCtfEstimation
[docs]class ProtImodManualCtfEstimation(ProtImodAutomaticCtfEstimation):
"""
CTF estimation of a set of input tilt-series using the IMOD procedure.
Run the protocol through the interactive GUI. Defocus values are saved
to file and exit after autofitting. The program will not ask for confirmation before
removing existing entries in the defocus table. If run in interactive mode defocus values
MUST BE SAVED manually by the user.
More info:
https://bio3d.colorado.edu/imod/doc/man/ctfplotter.html
"""
_label = 'Manual CTF estimation (step 2)'
_devStatus = BETA
_interactiveMode = True
def __init__(self, **args):
ProtImodAutomaticCtfEstimation.__init__(self, **args)
def _insertAllSteps(self):
self.inputTiltSeries = None
self._insertFunctionStep(self.runCTFEtimationStep, interactive=True)
# --------------------------- STEPS functions ----------------------------
[docs] def runCTFEtimationStep(self):
from imod.viewers import ImodGenericViewer
self.inputSetOfTiltSeries = self._getSetOfTiltSeries()
view = ImodGenericViewer(None, self, self.inputSetOfTiltSeries,
displayAllButton=False, createSetButton=True,
isInteractive=True,
itemDoubleClick=True)
view.show()
[docs] def runAllSteps(self, obj):
objId = obj.getObjId()
self.convertInputStep(objId)
self.ctfEstimation(objId)
[docs] def createOutput(self):
suffix = self._getOutputSuffix(SetOfCTFTomoSeries)
outputSetName = self.OUTPUT_PREFIX + str(suffix)
setOfTiltseries = self._getSetOfTiltSeries()
for item in setOfTiltseries.iterItems(iterate=False):
self.createOutputStep(item.getObjId(), outputSetName)
self.closeOutputSetsStep()
def _summary(self):
summary = []
return summary
# ------------------ UTILS METHODS ------------------------------------
[docs] def getFilePath(self, ts, suffix="", extension=""):
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
return os.path.join(extraPrefix, ts.getFirstItem().parseFileName(suffix=suffix,
extension=extension))