# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors: Jose Gutierrez (jose.gutierrez@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 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'
# *
# **************************************************************************
"""
This module implement some wizards
"""
import os
from pwem.wizards import EmWizard
from pwem.viewers import CoordinatesObjectView
from pyworkflow.utils import makePath, cleanPath, readProperties
from appion.protocols import DogPickerProtPicking
from appion import Plugin
[docs]class DogPickerWizard(EmWizard):
_targets = [(DogPickerProtPicking, ['diameter', 'threshold'])]
[docs] def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print('must specify input micrographs')
return
project = autopickProt.getProject()
micfn = micSet.getFileName()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
# Get current values of the properties
# micfn = os.path.join(coordsDir, 'micrographs.xmd')
# writeSetOfMicrographs(micSet, micfn)
dogpickerProps = os.path.join(coordsDir, 'picker.conf')
f = open(dogpickerProps, "w")
args = {
"dogpicker": os.path.join(Plugin.getHome(), "ApDogPicker.py"),
"convert": 'emconvert',
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
"diameter": autopickProt.diameter,
"threshold": autopickProt.threshold,
"apix": micSet.getSamplingRate()
}
f.write("""
parameters = diameterA,threshold
diameterA.value = %(diameter)s
diameterA.label = Diameter in A
diameterA.help = Sampling rate is %(apix)s
threshold.value = %(threshold)s
threshold.label = Threshold
threshold.help = Threshold in standard deviations above the mean
autopickCommand = python2 %(dogpicker)s --thresh=%%(threshold) --diam=%%(diameterA) --apix=%(apix)s --image=%%(micrograph) --outfile=%(coordsDir)s/%%(micrographName).txt
convertCommand = %(convert)s --coordinates --from dogpicker --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
f.close()
process = CoordinatesObjectView(project, micfn, coordsDir, autopickProt,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=dogpickerProps).show()
process.wait()
# Check if the wizard changes were accepted or just canceled
myprops = readProperties(dogpickerProps)
if myprops['applyChanges'] == 'true':
form.setVar('diameter', myprops['diameterA.value'])
form.setVar('threshold', myprops['threshold.value'])