# **************************************************************************
# *
# * Authors: Scipion Team
# *
# * 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
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# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
import threading
from os.path import abspath
from pyworkflow.gui.dialog import ToolbarListDialog
from pyworkflow.utils.path import removeBaseExt
from deepfinder import Plugin
[docs]class ParticleAnnotatorDialog(ToolbarListDialog):
"""
This class allows to call a deepfinder particle annotation subprocess for rach element of a list of Tomograms.
"""
tomo = None
proc = None
def __init__(self, parent, path, **kwargs):
self.path = path
self.provider = kwargs.get("provider", None)
self.prot = kwargs.get('prot', None)
ToolbarListDialog.__init__(self, parent,
"Particle Annotator Object Manager",
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:
self.tree.update()
[docs] def doubleClickOnTomogram(self, e=None):
self.tomo = e
self.proc = threading.Thread(target=self.launchParticleAnnotatorForTomogram, args=(self.tomo,))
self.proc.start()
self.after(1000, self.refresh_gui)
[docs] def launchParticleAnnotatorForTomogram(self, tomo):
print("\n==> Running Deepfinder Particle Annotator:")
tomoName = tomo.getFileName()
fname_objl = 'objl_annot_' + removeBaseExt(tomoName) + '.xml'
deepfinder_args = ' -t %s ' % abspath(tomoName)
deepfinder_args += '-o %s' % abspath(self.prot._getExtraPath(fname_objl))
deepfinder_args += ' -scipion' # hide unnecessary buttons from DeepFinder GUI
Plugin.runDeepFinder(self.prot, 'annotate', deepfinder_args)