def _visualizeAvgPMAX(self):
addRelionLabels()
mdIters = MetaData()
iterations = range(self.firstIter(), self._visualizeLastIteration+1)
labels = [MDL_AVGPMAX, MDL_PMAX]
colors = ['g', 'b']
prefixes = self._getPrefixes()
for it in iterations: # range (firstIter,self._visualizeLastIteration+1): #alwaya list all iteration
objId = mdIters.addObject()
mdIters.setValue(MDL_ITER, it, objId)
for i, prefix in enumerate(prefixes):
fn = 'model_general@'+ self.getFilename(prefix + 'model', iter=it)
md = MetaData(fn)
pmax = md.getValue(MDL_AVGPMAX, md.firstObject())
mdIters.setValue(labels[i], pmax, objId)
fn = self.getFilename('all_avgPmax_xmipp')
mdIters.write(fn)
#self.display2D(fn, extraParams='--label_relion') //do not display table since labels are confussing
xplotter = XmippPlotter()
xplotter.createSubPlot("Avg PMax per Iterations", "Iterations", "Avg PMax")
for label, color in zip(labels, colors):
xplotter.plotMd(mdIters, MDL_ITER, label, color)
if len(prefixes) > 1:
xplotter.showLegend(prefixes)
xplotter.show(True)
def _visualizeLikelihood(self):
for it in self._visualizeIterations:
fn = self._getIterSortedData(it)
md = MetaData(fn)
self.display2D(fn)
xplotter = XmippPlotter(windowTitle="max Likelihood particles sorting Iter_%d"%it)
xplotter.createSubPlot("Particle sorting: Iter_%d" % it, "Particle number", "maxLL")
xplotter.plotMd(md, False, mdLabelY=MDL_LL)
xplotter.show(True)
def run(self):
from xmipp import MetaData, str2Label
from protlib_gui_figure import XmippPlotter
md = MetaData(self.getParam('-i'))
if self.checkParam('--xlabel'):
xlabel = self.getParam('--xlabel')
mdLabelX = str2Label(xlabel)
else:
xlabel = ""
mdLabelX = None
if self.checkParam('--xtitle'):
xlabel = self.getParam('--xtitle')
ylabels = self.getParam('--ylabel').split()
if self.checkParam('--ytitle'):
ylabel = self.getParam('--ytitle')
else:
ylabel = ylabels[0]
colors, lenColors = self.getList('--colors',
['g', 'b', 'r', 'y', 'c', 'm', 'k'])
markers, lenMarkers = self.getList('--markers')
styles, lenStyles = self.getList('--style')
if self.checkParam('--nbins'):
nBins = self.getIntParam('--nbins')
else:
nBins = None
title = self.getParam('--title')
xplotter = XmippPlotter()
xplotter.createSubPlot(title, xlabel, ylabel)
for i, l in enumerate(ylabels):
c = colors[i % lenColors]
m = markers[i % lenMarkers]
if m == "none":
m = None
s = styles[i % lenStyles]
if s == "none":
s = None
xplotter.plotMd(md,
mdLabelX,
str2Label(l),
color=c,
marker=m,
linestyle=s,
nbins=nBins) # if nbins is present do an histogram
legendLocation = self.getParam('--legend')
if legendLocation != 'none':
xplotter.showLegend(ylabels, loc=legendLocation.replace('_', ' '))
xplotter.show()
def run(self):
from xmipp import MetaData, str2Label
from protlib_gui_figure import XmippPlotter
md = MetaData(self.getParam('-i'))
if self.checkParam('--xlabel'):
xlabel = self.getParam('--xlabel')
mdLabelX = str2Label(xlabel)
else:
xlabel = ""
mdLabelX = None
if self.checkParam('--xtitle'):
xlabel = self.getParam('--xtitle')
ylabels = self.getParam('--ylabel').split()
if self.checkParam('--ytitle'):
ylabel = self.getParam('--ytitle')
else:
ylabel = ylabels[0]
colors, lenColors = self.getList('--colors', ['g', 'b', 'r', 'y', 'c', 'm', 'k'])
markers, lenMarkers = self.getList('--markers')
styles, lenStyles = self.getList('--style')
if self.checkParam('--nbins'):
nBins = self.getIntParam('--nbins')
else:
nBins = None
title = self.getParam('--title')
xplotter = XmippPlotter()
xplotter.createSubPlot(title, xlabel, ylabel)
for i, l in enumerate(ylabels):
c = colors[i % lenColors]
m = markers[i % lenMarkers]
if m == "none":
m = None
s = styles[i % lenStyles]
if s == "none":
s = None
xplotter.plotMd(md, mdLabelX, str2Label(l), color=c, marker=m, linestyle=s, nbins=nBins)#if nbins is present do an histogram
legendLocation = self.getParam('--legend')
if legendLocation != 'none':
xplotter.showLegend(ylabels, loc=legendLocation.replace('_', ' '))
xplotter.show()
def visualize(self):
fn = self.getFilename('images')
if exists(fn):
from protlib_utils import runShowJ
if getattr(self, 'TiltPairs', False):
runShowJ(fn,extraParams="--mode metadata --render first")
else:
runShowJ(fn)
from protlib_gui_figure import XmippPlotter
from xmipp import MDL_ZSCORE
md = MetaData(fn)
if md.containsLabel(MDL_ZSCORE):
#MD.sort(MDL_ZSCORE)
xplotter = XmippPlotter(windowTitle="Zscore particles sorting")
xplotter.createSubPlot("Particle sorting", "Particle number", "Zscore")
xplotter.plotMd(md, False, mdLabelY=MDL_ZSCORE)
xplotter.show()