Source code for xmipp3.viewers.viewer_deep_micrograph_cleaner

# **************************************************************************
# *
# * Authors:     David Maluenda (
# *
# * 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
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# * 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
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# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
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import xmipp3
from pwem.objects import SetOfCoordinates
from pwem.viewers import  EmPlotter,  CoordinatesObjectView
from pyworkflow.protocol.params import IntParam, LabelParam, FloatParam
from pyworkflow.utils import cleanPath, makePath
from pyworkflow.viewer import DESKTOP_TKINTER, WEB_DJANGO, ProtocolViewer

from pwem import emlib
from xmipp3.convert import getXmippAttribute
from xmipp3.protocols.protocol_deep_micrograph_screen import XmippProtDeepMicrographScreen

[docs]class XmippDeepMicrographViewer(ProtocolViewer): """ Viewer for the 'Xmipp - deep Micrograph cleaner' protocols.\n Select those cooridantes with high (close to 1.0) 'zScoreDeepLearning2' value and save them. The Histogram may help you to decide a threshold. """ _label = 'viewer deep Micrograph cleaner' _environments = [DESKTOP_TKINTER, WEB_DJANGO] _targets = [XmippProtDeepMicrographScreen] def _defineParams(self, form): form.addSection(label='Visualization') form.addParam('noteViz', LabelParam, label="\n") form.addParam('visualizeHistogram', IntParam, default=100, label="Visualize Deep Scores Histogram (Bin size)", help="Plot a histogram of the 'goodRegionScore' " "to visualize setting of a good threshold.") form.addParam('visualizeCoordinates', FloatParam, default=0.8, label="Visualize good coordinates (threshold from 0 to 1)", help="Visualize the coordinates considered good according" " to the threshold indicated in the box.\n" "If you like the result, save the result" " with the '+Coordinates' button") def _getVisualizeDict(self): return {'visualizeCoordinates': self._visualizeCoordinates, 'visualizeHistogram': self._visualizeHistogram} def _visualizeCoordinates(self, e=None): views = [] outCoords = self.protocol.getOutput() if not outCoords: print(" > Not output found, yet."); return coordsViewerFn = self.protocol._getExtraPath('coordsViewer.sqlite') mdLabel = emlib.MDL_GOOD_REGION_SCORE if not getXmippAttribute(outCoords.getFirstItem(), mdLabel): print(" > outputCoordinates do NOT have 'MDL_GOOD_REGION_SCORE'!"); return cleanPath(coordsViewerFn) newOutput = SetOfCoordinates(filename=coordsViewerFn) newOutput.copyInfo(outCoords) newOutput.setMicrographs(outCoords.getMicrographs()) thres = self.visualizeCoordinates.get() for coord in outCoords: if getXmippAttribute(coord, mdLabel).get() > thres: newOutput.append(coord.clone()) newOutput.write() newOutput.close() #SetOfCoordinates does not implement __exit__, required for with micSet = newOutput.getMicrographs() # accessing mics to provide metadata file if micSet is None: raise Exception('visualize: SetOfCoordinates has no micrographs set.') fn = self.protocol._getExtraPath("allMics.xmd") xmipp3.convert.writeSetOfMicrographs(micSet, fn) tmpDir = self.protocol._getExtraPath('manualThresholding_%03d'%int(thres*100)) cleanPath(tmpDir) makePath(tmpDir) xmipp3.convert.writeSetOfCoordinates(tmpDir, newOutput) views.append(CoordinatesObjectView(self._project, fn, tmpDir, self.protocol, inTmpFolder=True)) return views def _visualizeHistogram(self, e=None): views = [] numberOfBins = self.visualizeHistogram.get() outCoords = self.protocol.getOutput() if outCoords: mdLabel = emlib.MDL_GOOD_REGION_SCORE if getXmippAttribute(outCoords.getFirstItem(), mdLabel): plotter = EmPlotter() plotter.createSubPlot("Deep micrograph score", "Deep micrograph score", "Number of Coordinates") cScores = [getXmippAttribute(coord, mdLabel).get() for coord in outCoords] plotter.plotHist(cScores, nbins=numberOfBins) views.append(plotter) else: print(" > 'outputCoordinates' don't have 'xmipp_zScoreDeepLearning2' label.") else: print(" > Output not ready yet.") return views