Source code for emantomo.viewers.viewers_data

# **************************************************************************
# *
# * Authors:     David Herreros Calero (dherreros@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

import pyworkflow.viewer as pwviewer
from pyworkflow.gui.dialog import askYesNo
from pyworkflow.utils.properties import Message
import pyworkflow.utils as pwutils

import pwem.viewers.views as vi
import tomo.objects
from tomo.viewers.views_tkinter_tree import TomogramsTreeProvider
from tomo.protocols.protocol_import_coordinates import ProtImportCoordinates3D

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



[docs]class EmanDataViewer(pwviewer.Viewer): """ Wrapper to visualize different type of objects with the Xmipp program xmipp_showj """ _environments = [pwviewer.DESKTOP_TKINTER] _targets = [ ProtImportCoordinates3D, tomo.objects.SetOfCoordinates3D ] def __init__(self, **kwargs): pwviewer.Viewer.__init__(self, **kwargs) self._views = [] def _getObjView(self, obj, fn, viewParams={}): return vi.ObjectView( self._project, obj.strId(), fn, viewParams=viewParams) def _visualize(self, obj, **kwargs): views = [] cls = type(obj) if issubclass(cls, tomo.objects.SetOfCoordinates3D): outputCoords = obj tomoList = [item.clone() for item in outputCoords.getPrecedents().iterItems()] path = os.path.join(self.protocol._getExtraPath(), '..') tomoProvider = TomogramsTreeProvider(tomoList, path, 'json',) setCoords3D2Jsons(outputCoords.getPrecedents(), outputCoords, path) setView = EmanDialog(self._tkRoot, path, provider=tomoProvider) import tkinter as tk frame = tk.Frame() if askYesNo(Message.TITLE_SAVE_OUTPUT, Message.LABEL_SAVE_OUTPUT, frame): jsons2SetCoords3D(self.protocol, outputCoords.getPrecedents(), path) pwutils.cleanPattern(os.path.join(path, '*json')) elif issubclass(cls, ProtImportCoordinates3D): if obj.getOutputsSize() >= 1: for _, out in obj.iterOutputAttributes(tomo.objects.SetOfCoordinates3D): lastOutput = out self._visualize(lastOutput) return views