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
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# * 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
# * 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
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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, label='Display local defocus of micrograph:', allowsNull=True, 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. Please check the ID of the micrographs in the output set of micrographs of this protocol.""") 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 defocus""" 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