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 _visualizeDisplayResolutionPlotsSSNR(self):
names = []
windowTitle = {}
prefixes = self._getPrefixes()
n = len(prefixes) * self._visualizeNrefs
gridsize = self._getGridSize(n)
addRelionLabels()
activateMathExtensions()
xplotter = XmippPlotter(*gridsize)
for prefix in prefixes:
for ref3d in self._visualizeRef3Ds:
plot_title = 'Resolution SSNR %s, for Class %s' % (prefix, ref3d)
a = xplotter.createSubPlot(plot_title, 'Armstrongs^-1', 'log(SSNR)', yformat=False)
blockName = 'model_class_%d@' % ref3d
legendName = []
for it in self._visualizeIterations:
file_name = blockName + self.getFilename(prefix + 'model', iter=it)
#file_name = self.getFilename('ResolutionXmdFile', iter=it, ref=ref3d)
self._plotSSNR(a, file_name)
legendName.append('iter %d' % it)
xplotter.showLegend(legendName)
a.grid(True)
xplotter.show(True)
def _visualizeDisplayResolutionPlotsFSC(self):
self.ResolutionThreshold = float(self.parser.getTkValue('ResolutionThreshold'))
n = self._visualizeNrefs * len(self._getPrefixes())
gridsize = self._getGridSize(n)
activateMathExtensions()
addRelionLabels()
xplotter = XmippPlotter(*gridsize, windowTitle='Resolution FSC')
for prefix in self._getPrefixes():
for ref3d in self._visualizeRef3Ds:
plot_title = prefix + 'class %s' % ref3d
a = xplotter.createSubPlot(plot_title, 'Armstrongs^-1', 'FSC', yformat=False)
legends = []
blockName = 'model_class_%d@' % ref3d
for it in self._visualizeIterations:
model_star = blockName + self.getFilename(prefix + 'model', iter=it)
if self._plotFSC(a, model_star):
legends.append('iter %d' % it)
xplotter.showLegend(legends)
if self.ResolutionThreshold < self.maxFrc:
a.plot([self.minInv, self.maxInv],[self.ResolutionThreshold, self.ResolutionThreshold], color='black', linestyle='--')
a.grid(True)
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):
if self.ExperimentalSAXS=="":
fnInt=self.workingDirPath("pseudoatoms00.int")
else:
fnInt=self.workingDirPath("pseudoatoms00.fit")
import numpy
x=numpy.loadtxt(fnInt,skiprows=1)
xplotter = XmippPlotter(*[1,1],windowTitle="SAXS Curves")
a = xplotter.createSubPlot('SAXS curves', 'Armstrongs^-1', 'log(SAXS)', yformat=False)
a.plot(x[:,0], numpy.log(x[:,1]))
a.plot(x[:,0], numpy.log(x[:,2]))
if self.ExperimentalSAXS=="":
xplotter.showLegend(['SAXS in solution','SAXS in vacuo'])
else:
xplotter.showLegend(['Experimental SAXS','SAXS from volume'])
xplotter.draw()
xplotter.show()
