Source code for dynamo.viewers.views_tkinter_tree

# **************************************************************************
# *
# * 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.
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# * 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.
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# * 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'
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# **************************************************************************

import os, threading
import numpy as np

import pyworkflow.config as conf
from pyworkflow import utils as pwutils
from pyworkflow.utils.process import runJob
from pyworkflow.gui.dialog import ToolbarListDialog

from dynamo import Plugin


[docs]class DynamoTomoDialog(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, **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.lanchDynamoForTomogram, args=(self.tomo,)) self.proc.start() self.after(1000, self.refresh_gui)
[docs] def lanchDynamoForTomogram(self, tomo): commandsFile = self.writeMatlabCode(tomo) args = ' %s' % commandsFile runJob(None, Plugin.getDynamoProgram(), args, env=Plugin.getEnviron())
[docs] def writeMatlabCode(self, tomo): # Initialization params codeFilePath = os.path.join(os.getcwd(), "DynamoPicker.m") catalogue = os.path.join(self.path, "tomos") # Write code to Matlab code file codeFid = open(codeFilePath, 'w') content = "catalogue_name='%s'\n" \ "c=dread(strcat(catalogue_name,'.ctlg'))\n" \ "n=cellfun(@(c) c.fullFileName,c.volumes,'UniformOutput',false)\n" \ "idt=find(cell2mat(cellfun(@(c) strcmp(c,'%s'),n,'UniformOutput',false)))\n" \ "eval(strcat('dtmslice @{%s}',num2str(idt)))\n" \ "modeltrack.loadFromCatalogue('handles',c,'full',true,'select',false)\n" \ "uiwait(dpkslicer.getHandles().figure_fastslicer)\n" \ "modeltrack.saveAllInCatalogue\n" \ "models = dread(dcmodels(catalogue_name,'i', idt))\n" \ "outFile='%s'\n" \ "savePath='%s'\n" \ "outPoints=[outFile '.txt']\n" \ "outAngles=['angles_' outFile '.txt']\n" \ "crop_points=[]\n" \ "crop_angles=[]\n" \ "model_id=0\n" \ "for model=models\n" \ "model_id=model_id+1\n" \ "if iscell(model)\n" \ "crop_points=[crop_points; [model{end}.points model_id*ones(length(model{end}.points),1)]]\n" \ "else\n" \ "crop_points=[crop_points; [model.points model_id*ones(length(model.points),1)]]\n" \ "end\n" \ "end\n" \ "if ~isempty(crop_points)\n" \ "writematrix(crop_points,fullfile(savePath,outPoints),'Delimiter',' ')\n" \ "end\n" \ "exit\n" % (catalogue, os.path.abspath(tomo.getFileName()), catalogue, pwutils.removeBaseExt(tomo.getFileName()), self.path) # "writematrix(crop_angles,fullfile(savePath,outAngles),'Delimiter',' ')\n" \ # "crop_angles=[crop_angles; [model{end}.crop_angles model_id*ones(length(model{end}.crop_angles),1)]]\n" \ # "crop_angles=[crop_angles; [model.crop_angles model_id*ones(length(model.crop_angles),1)]]\n" \ codeFid.write(content) codeFid.close() return codeFilePath