# **************************************************************************
# *
# * 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, jsonFilesFromSet
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
tomos = outputCoords.getPrecedents()
volIds = outputCoords.aggregate(["MAX", "COUNT"], "_volId", ["_volId"])
volIds = [(d['_volId'], d["COUNT"]) for d in volIds]
tomoList = []
for objId in volIds:
tomogram = tomos[objId[0]].clone()
tomogram.count = objId[1]
tomoList.append(tomogram)
path = self.protocol._getExtraPath()
info_path = self.protocol._getExtraPath('info')
tomoProvider = TomogramsTreeProvider(tomoList, info_path, 'json',)
if not os.path.exists(info_path):
pwutils.makePath(info_path)
json_files, _ = jsonFilesFromSet(tomos, info_path)
_ = setCoords3D2Jsons(json_files, outputCoords)
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(), info_path)
elif issubclass(cls, ProtImportCoordinates3D):
if obj.getOutputsSize() >= 1:
for _, out in obj.iterOutputAttributes(tomo.objects.SetOfCoordinates3D):
lastOutput = out
self._visualize(lastOutput)
return views