# **************************************************************************
# *
# * 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'
# *
# **************************************************************************
import os
from pwem.wizards.wizard import EmWizard
from pwem.viewers import CoordinatesObjectView
from pyworkflow.utils import makePath, cleanPath, readProperties
from . import Plugin
from .convert import writeSetOfMicrographs
from .protocols import SparxGaussianProtPicking
[docs]class SparxGaussianPickerWizard(EmWizard):
_targets = [(SparxGaussianProtPicking, ['boxSize',
'lowerThreshold', 'higherThreshold',
'gaussWidth'])]
[docs] def show(self, form):
autopickProt = form.protocol
micSet = autopickProt.getInputMicrographs()
if not micSet:
print('You must specify input micrographs')
return
# ensuring a valid boxSize
if autopickProt.boxSize.get() is None:
autopickProt.boxSize.set(100)
project = autopickProt.getProject()
coordsDir = project.getTmpPath(micSet.getName())
cleanPath(coordsDir)
makePath(coordsDir)
micMdFn = os.path.join(coordsDir, "micrographs.xmd")
writeSetOfMicrographs(micSet, micMdFn)
pickerProps = os.path.join(coordsDir, 'picker.conf')
params = ['boxSize', 'lowerThreshold', 'higherThreshold', 'gaussWidth']
program = Plugin.getBoxerCommand(boxerVersion='old')
extraParams = "invert_contrast=%s:use_variance=%s:%s" % (
autopickProt.doInvert,
autopickProt.useVarImg,
autopickProt.extraParams)
args = {
"params": ','.join(params),
"preprocess": "emprogram %s" % Plugin.getProgram('sxprocess.py'),
"picker": "emprogram %s" % program,
"convert": "emconvert",
'coordsDir': coordsDir,
'micsSqlite': micSet.getFileName(),
"boxSize": autopickProt.boxSize,
"lowerThreshold": autopickProt.lowerThreshold,
"higherThreshold": autopickProt.higherThreshold,
"gaussWidth": autopickProt.gaussWidth,
"extraParams": extraParams
}
with open(pickerProps, "w") as f:
f.write("""
parameters = %(params)s
boxSize.value = %(boxSize)s
boxSize.label = Box Size
boxSize.help = Box size in pixels
lowerThreshold.value = %(lowerThreshold)s
lowerThreshold.label = Lower Threshold
lowerThreshold.help = Lower Threshold
higherThreshold.help = Higher Threshold
higherThreshold.value = %(higherThreshold)s
higherThreshold.label = Higher Threshold
gaussWidth.help = Width of the Gaussian kernel used
gaussWidth.value = %(gaussWidth)s
gaussWidth.label = Gauss Width
runDir = %(coordsDir)s
preprocessCommand = %(preprocess)s demoparms --makedb=thr_low=%%(lowerThreshold):thr_hi=%%(higherThreshold):boxsize=%%(boxSize):gauss_width=%%(gaussWidth):%(extraParams)s
autopickCommand = %(picker)s --gauss_autoboxer=demoparms --write_dbbox --boxsize=%%(boxSize) --norm=normalize.ramp.normvar %%(micrograph)
convertCommand = %(convert)s --coordinates --from eman2 --to xmipp --input %(micsSqlite)s --output %(coordsDir)s
""" % args)
process = CoordinatesObjectView(project, micMdFn, coordsDir, autopickProt,
mode=CoordinatesObjectView.MODE_AUTOMATIC,
pickerProps=pickerProps).show()
process.wait()
myprops = readProperties(pickerProps)
if myprops['applyChanges'] == 'true':
for param in params:
form.setVar(param, myprops[param + '.value'])