Source code for emantomo.protocols.protocol_tomo_boxing

# **************************************************************************
# *
# * Authors:     Adrian Quintana (adrian@eyeseetea.com) [1]
# *
# * [1] EyeSeeTea Ltd, London, UK
# *
# * 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'
# *
# **************************************************************************

from pyworkflow import BETA
from pyworkflow.utils.properties import Message
from pyworkflow.gui.dialog import askYesNo
from pyworkflow.protocol.params import BooleanParam, PointerParam, EnumParam

from emantomo.convert import setCoords3D2Jsons, jsons2SetCoords3D
from emantomo.viewers.views_tkinter_tree import EmanDialog

from tomo.protocols import ProtTomoPicking
from tomo.viewers.views_tkinter_tree import TomogramsTreeProvider


[docs]class EmanProtTomoBoxing(ProtTomoPicking): """ Manual picker for Tomo. Uses EMAN2 e2spt_boxer.py. """ _label = 'tomo boxer' _devStatus = BETA def __init__(self, **kwargs): ProtTomoPicking.__init__(self, **kwargs) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): ProtTomoPicking._defineParams(self, form) form.addParam('selection', EnumParam, choices=['Yes', 'No'], default=1, label='Modify previous coordinates?', display=EnumParam.DISPLAY_HLIST, help='This option allows to add and/or remove coordinates to a previous SetOfCoordinates') form.addParam('inputCoordinates', PointerParam, label="Input Coordinates", condition='selection == 0', allowsNull=True, pointerClass='SetOfCoordinates3D', help='Select the previous SetOfCoordinates you want to modify') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): # Copy input coordinates to Extra Path if self.inputCoordinates.get(): self._insertFunctionStep('copyInputCoords') # Launch Boxing GUI self._insertFunctionStep('launchBoxingGUIStep', interactive=True) def _createOutput(self): jsons2SetCoords3D(self, self.inputTomograms.get(), self._getExtraPath()) # --------------------------- STEPS functions -----------------------------
[docs] def copyInputCoords(self): setCoords3D2Jsons(self.inputTomograms.get(), self.inputCoordinates.get(), self._getExtraPath())
[docs] def launchBoxingGUIStep(self): if self.getOutputsSize() >= 1: lastOutput = [output for _, output in self.iterOutputAttributes()][-1] setCoords3D2Jsons(self.inputTomograms.get(), lastOutput, self._getExtraPath()) tomoList = [tomo.clone() for tomo in self.inputTomograms.get().iterItems()] tomoProvider = TomogramsTreeProvider(tomoList, self._getExtraPath(), "json") self.dlg = EmanDialog(None, self._getExtraPath(), provider=tomoProvider,) # Open dialog to request confirmation to create output import tkinter as tk frame = tk.Frame() if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, frame): self._createOutput()
[docs] def getMethods(self, output): msg = 'User picked %d particles ' % output.getSize() msg += 'with a particle size of %s.' % output.getBoxSize() return msg
def _methods(self): methodsMsgs = [] if self.inputTomograms is None: return ['Input tomogram not available yet.'] methodsMsgs.append("Input tomograms imported of dims %s." %( str(self.inputTomograms.get().getDim()))) if self.getOutputsSize() >= 1: for key, output in self.iterOutputAttributes(): msg = self.getMethods(output) methodsMsgs.append("%s: %s" % (self.getObjectTag(output), msg)) else: methodsMsgs.append(Message.TEXT_NO_OUTPUT_CO) return methodsMsgs