# **************************************************************************
# *
# * 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, EmanProtTomoExtraction, EmanProtTomoTempMatch
from .protocols import EmanProtTomoExtraction, EmanProtTSExtraction, EmanProtTomoTempMatch, EmanProtTomoResize
# class SparxGaussianPickerWizard(EmWizard):
# _targets = [(SparxGaussianProtPicking, ['boxSize',
# 'lowerThreshold', 'higherThreshold',
# 'gaussWidth'])]
#
# 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 emantomo --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'])
[docs]class EmanTomoTempMatchWizard(EmWizard):
_targets = [(EmanProtTomoTempMatch, ['boxSize'])]
[docs] def show(self, form):
tomoExtractProt = form.protocol
inputReference = tomoExtractProt.ref.get()
if not inputReference:
print('You must specify input reference volume')
return
boxSize = inputReference.getDim()[0]
form.setVar('boxSize', boxSize)
[docs]class EmanTomoResizeWizard(EmWizard):
_targets = [(EmanProtTomoResize, ['xDim', 'yDim', 'zDim'])]
[docs] def show(self, form):
tomoResizeProt = form.protocol
inputTomos = tomoResizeProt.inputTomograms.get()
if not inputTomos:
print('You must specify input tomograms first')
return
dim = inputTomos.getFirstItem().getDim()
form.setVar('xDim', dim[0])
form.setVar('yDim', dim[1])
form.setVar('zDim', dim[2])