# **************************************************************************
# *
# * Authors: David Herreros (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 glob
import os
import threading
from pyworkflow import utils as pwutils
from pyworkflow.gui.dialog import ToolbarListDialog
from pyworkflow.utils.path import moveFile, cleanPath, copyFile
from pyworkflow.utils.process import runJob
import emantomo
from emantomo.convert import loadJson
[docs]class EmanDialog(ToolbarListDialog):
"""
This class extend from ListDialog to allow calling
an Eman subprocess from a list of Tomograms.
"""
def __init__(self, parent, path, **kwargs):
self.path = path
self.provider = kwargs.get("provider", None)
ToolbarListDialog.__init__(self, parent,
"Tomogram List",
allowsEmptySelection=False,
itemDoubleClick=self.doubleClickOnTomogram,
allowSelect=False,
**kwargs)
[docs] def refresh_gui(self):
if self.proc.is_alive():
self.after(1000, self.refresh_gui)
else:
outFile = '*%s_info.json' % pwutils.removeBaseExt(self.tomo.getFileName().split("__")[0])
jsonPath = os.path.join(self.path, "info", outFile)
jsonPath = glob.glob(jsonPath)[0]
# moveFile((files[0]), os.path.join(self.path, os.path.basename(files[0])))
# cleanPath(os.path.join(self.path, "info"))
jsonDict = loadJson(jsonPath)
self.tomo.count = len(jsonDict["boxes_3d"])
self.tree.update()
[docs] def doubleClickOnTomogram(self, e=None):
self.tomo = e
self.proc = threading.Thread(target=self.lanchEmanForTomogram, args=(self.tomo,))
self.proc.start()
self.after(1000, self.refresh_gui)
[docs] def lanchEmanForTomogram(self, tomo):
# self._moveCoordsToInfo(tomo)
program = emantomo.Plugin.getProgram("e2spt_boxer.py")
arguments = "%s" % os.path.abspath(tomo.getFileName())
runJob(None, program, arguments, env=emantomo.Plugin.getEnviron(), cwd=self.path)
def _moveCoordsToInfo(self, tomo):
fnCoor = '*%s_info.json' % pwutils.removeBaseExt(tomo.getFileName().split("__")[0])
pattern = os.path.join(self.path, fnCoor)
files = glob.glob(pattern)
if files:
infoDir = pwutils.join(os.path.abspath(self.path), 'info')
pathCoor = os.path.join(infoDir, os.path.basename(files[0]))
pwutils.makePath(infoDir)
copyFile(files[0], pathCoor)