Source code for xmipp3.viewers.plotter

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * 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
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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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"""
This module implement the classes to create plots on xmipp.
"""

from pwem.viewers import EmPlotter


[docs]class XmippPlotter(EmPlotter): ''' Class to create several plots with Xmipp utilities''' def __init__(self, x=1, y=1, mainTitle="", **kwargs): EmPlotter.__init__(self, x, y, mainTitle, **kwargs)
[docs] def plotMdAngularDistribution(self, title, md, color='blue'): '''Create an special type of subplot, representing the angular distribution of weight projections. A metadata should be provided containing labels: MDL_ANGLE_ROT, MDL_ANGLE_TILT, MDL_WEIGHT ''' from math import radians from pwem.emlib import MDL_ANGLE_ROT, MDL_ANGLE_TILT, MDL_WEIGHT rot = [radians(md.getValue(MDL_ANGLE_ROT, objId)) for objId in md] tilt = [md.getValue(MDL_ANGLE_TILT, objId) for objId in md] weight = [md.getValue(MDL_WEIGHT, objId) for objId in md] self.plotAngularDistribution(title, rot, tilt, weight)
def _prepareDataForPlot(self, md, mdLabelX, mdLabelY): """ plot metadata columns mdLabelX and mdLabelY if nbins is in args then and histogram over y data is made """ if mdLabelX: xx = [] else: xx = range(1, md.size() + 1) yy = [] for objId in md: if mdLabelX: xx.append(md.getValue(mdLabelX, objId)) yy.append(md.getValue(mdLabelY, objId)) return xx, yy
[docs] def plotScatterMd(self, md, mdLabelX, mdLabelY, color='g', **args): """ scatterplot metadata columns mdLabelX and mdLabelY if nbins is in args then and histogram over y data is made """ xx, yy= self._prepareDataForPlot( md, mdLabelX, mdLabelY) try: self.plotScatter(xx, yy, color, **args) except AttributeError: return
[docs] def plotMd(self, md, mdLabelX, mdLabelY, color='g', **args): """ plot metadata columns mdLabelX and mdLabelY if nbins is in args then and histogram over y data is made """ xx, yy= self._prepareDataForPlot( md, mdLabelX, mdLabelY) nbins = args.pop('nbins', None) if nbins is None: self.plotData(xx, yy, color, **args) else: self.plotHist(yy, nbins, color, **args)
[docs] def plotMdFile(self, mdFilename, mdLabelX, mdLabelY, color='g', **args): """ plot metadataFile columns mdLabelX and mdLabelY if nbins is in args then and histogram over y data is made """ from pwem.emlib import MetaData md = MetaData(mdFilename) self.plotMd(md, mdLabelX, mdLabelY, color=color,**args)