Source code for xmipp3.viewers.viewer_analyze_local_ctf

# **************************************************************************
# *
# * Authors:     Estrella Fernandez Gimenez
# *              Carlos Oscar Sanchez Sorzano
# *
# * 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 numpy as np
from pwem import emlib
from os.path import exists

from pyworkflow.viewer import (ProtocolViewer, DESKTOP_TKINTER, WEB_DJANGO)
from pyworkflow.protocol.params import IntParam, LabelParam
from pwem.viewers import ObjectView, showj

from xmipp3.protocols.protocol_analyze_local_ctf import XmippProtAnalyzeLocalCTF
from .plotter import XmippPlotter


[docs]class XmippAnalyzeLocalCTFViewer(ProtocolViewer): """ Visualization of the output of analyze_local_ctf protocol """ _label = 'viewer analyze local defocus' _targets = [XmippProtAnalyzeLocalCTF] _environments = [DESKTOP_TKINTER, WEB_DJANGO] def __init__(self, **kwargs): ProtocolViewer.__init__(self, **kwargs) self._data = None
[docs] def getData(self): if self._data is None: self._data = self.loadData() return self._data
def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('displayR2', LabelParam, default=False, label='Display micrograph R2') form.addParam('displayLocalDefocus', IntParam, default=1, label='Display local defocus of micrograph:', help="""Type the ID of the micrograph to see particle local defocus of the selected micrograph. It is possible that not all the micrographs are available""") def _getVisualizeDict(self): return {'displayR2' : self._viewR2, 'displayLocalDefocus': self._viewLocalDefocus, } def _viewLocalDefocus(self, paramName=None): """display a 3D view of where the particles are placed in the micrograph taking as height the value estimated for local defocues""" views=[] fnDefoci="%s"%(self.protocol._getExtraPath("micrographDefoci.xmd")) if exists(fnDefoci): try: mdPoints = emlib.MetaData("mic_%d@%s"%(self.displayLocalDefocus.get(),fnDefoci)) x = mdPoints.getColumnValues(emlib.MDL_XCOOR) y = mdPoints.getColumnValues(emlib.MDL_YCOOR) defocusA = mdPoints.getColumnValues(emlib.MDL_CTF_DEFOCUSA) residuals = mdPoints.getColumnValues(emlib.MDL_CTF_DEFOCUS_RESIDUAL) title="Micrograph %d defocus"%self.displayLocalDefocus.get() xplotter = XmippPlotter(windowTitle=title) a = xplotter.createSubPlot(title, 'x', 'y', projection='3d') a.set_zlabel('Defocus') a.scatter(x, y, defocusA, c='r', marker='o') a.scatter(x, y, np.asarray(defocusA)-np.asarray(residuals), c='b', marker='^') legends = ['Avg. defocus','Adjusted defocus'] xplotter.showLegend(legends, loc=1) views.append(xplotter) except Exception as e: print(e) return views def _viewR2(self, paramName=None): views = [] if hasattr(self.protocol, "outputMicrographs"): obj = self.protocol.outputMicrographs fn = obj.getFileName() labels = 'id _filename _xmipp_ctfDefocusR2' views.append(ObjectView(self._project, obj.strId(), fn, viewParams={showj.ORDER: labels, showj.VISIBLE: labels, showj.RENDER: None, showj.MODE: showj.MODE_MD})) return views