Source code for xmipptomo.protocols.protocol_roiIJ

# **************************************************************************
# *
# * 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 numpy as np

from pyworkflow.protocol.params import PointerParam
import pyworkflow.utils as pwutils
from pwem.viewers.showj import *
from pwem.protocols import ProtAnalysis2D

from tomo.objects import MeshPoint
from tomo.viewers.views_tkinter_tree import TomogramsTreeProvider, TomogramsDialog
from tomo.protocols.protocol_base import ProtTomoBase


[docs]class XmippProtRoiIJ(ProtAnalysis2D, ProtTomoBase): """ Tomogram ROI selection in IJ """ _label = 'imagej roi' def __init__(self, **kwargs): ProtAnalysis2D.__init__(self, **kwargs) # --------------------------- DEFINE param functions ---------------------- def _defineParams(self, form): form.addSection(label='General parameters') form.addParam('inputTomos', PointerParam, label="Input Tomograms", pointerClass='SetOfTomograms', help='Select tomograms.') # --------------------------- INSERT steps functions ---------------------- def _insertAllSteps(self): # Launch Boxing GUI self._insertFunctionStep('launchIJGUIStep', interactive=True) def _createOutput(self): inputTomos = self.inputTomos.get() outSet = self._createSetOfMeshes(inputTomos) for tomo in inputTomos.iterItems(): tomoName = pwutils.removeBaseExt(tomo.getFileName()) outFile = self._getExtraPath(tomoName + '.txt') if os.path.isfile(outFile): data = np.loadtxt(outFile, delimiter=',') for coord in data: mesh = MeshPoint() mesh.setPosition(coord[0], coord[1], coord[2]) mesh.setGroupId(coord[3]) mesh.setVolume(tomo) outSet.append(mesh) outSet.setPrecedents(inputTomos) self._defineOutputs(outputMeshes=outSet) self._defineSourceRelation(inputTomos, outSet) # --------------------------- STEPS functions -----------------------------
[docs] def launchIJGUIStep(self): tomoList = [tomo.clone() for tomo in self.inputTomos.get().iterItems()] tomoProvider = TomogramsTreeProvider(tomoList, self._getExtraPath(), 'txt') path = self._getExtraPath() self.dlg = TomogramsDialog(None, False, provider=tomoProvider, path=path) self._createOutput()
def _summary(self): summary = [] if not os.listdir(self._getExtraPath()): summary.append("Output ROIs not ready yet.") else: count = 0 for file in os.listdir(self._getExtraPath()): if file.endswith(".txt"): count += 1 summary.append("Rois defined for %d/%d files have been saved in Scipion (%s)." % ( count, self.inputTomos.get().getSize(), self._getExtraPath())) return summary def _methods(self): tomos = self.inputTomos.get() return [ "ROI selection and extraction using ImageJ", "A total of %d tomograms of dimensions %s were used" % (tomos.getSize(), tomos.getDimensions()), ]