def produceXmippOutputs(log, inputDataStar,
outputImages, outputClasses, outputVolumes,
classLabel, classTemplate):
""" After Relion have finished, produce the files expected by Xmipp.
Params:
inputDataStar: the filename of the last data.star images file.
outputImages: the filename to write the images as expected by xmipp.
outputClasses: the filename to write the classes and images as expected by xmipp.
outputVolumes: filename to write a list of produced volumes.
classLabel: either MDL_REF or MDL_REF3D
"""
addRelionLabels()
# Write output images
md = MetaData(inputDataStar)
md.write(outputImages)
# Create the classes metadata
iteration = getIteration(inputDataStar)
# If iteration is not None, means that is a classification
# since for refinenment, the final images should not have iteration
if iteration is not None:
createClassesFromImages(inputDataStar, outputClasses, iteration,
classLabel, classTemplate)
# Write volumes (the same as classes block)
md.read('classes@' + outputClasses)
if outputVolumes.endswith('.xmd'): # do not write volumes.xmd for 2d
md.write('volumes@' + outputVolumes)
else:
volFn = inputDataStar.replace('data.star', 'class001.mrc')
md.clear()
md.setValue(MDL_IMAGE, volFn, md.addObject())
if outputVolumes.endswith('.xmd'): # do not write volumes.xmd for 2d
md.write('volumes@' + outputVolumes)
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 _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 _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 _getIterAngularDist(self, it):
""" Return the .star file with the classes angular distribution
for this iteration. If the file not exists, it will be written.
"""
data_angularDist = self.getFilename('angularDist_xmipp', iter=it)
addRelionLabels()
if not xmippExists(data_angularDist):
self._writeIterAngularDist(it)
return data_angularDist
def _getIterSortedData(self, it):
""" Sort the it??.data.star file by the maximum likelihood. """
addRelionLabels()
data_sorted = self.getFilename('data_sorted_xmipp', iter=it)
if not xmippExists(data_sorted):
print "Sorting particles by likelihood iteration %03d" % it
fn = 'images@'+ self.getFilename('data', iter=it)
md = MetaData(fn)
md.sort(MDL_LL, False)
md.write('images_sorted@' + data_sorted)
return data_sorted
def _getIterClasses(self, it):
""" Return the .star file with the classes for this iteration.
If the file doesn't exists, it will be created.
"""
addRelionLabels()
data_star = self.getFilename('data', iter=it)
data_classes = self.getFilename('classes_xmipp', iter=it)
if not xmippExists(data_classes):
createClassesFromImages(data_star, data_classes, it,
self.ClassLabel, self.ClassFnTemplate)
return data_classes
def _visualizeTableChange(self):
mdIters = MetaData()
labels = self._getChangeLabels()
iterations = range(self.firstIter(), self._visualizeLastIteration+1)
addRelionLabels()
print " Computing average changes in offset, angles, and class membership"
for it in iterations:
print "Computing data for iteration; %03d"% (it)
objId = mdIters.addObject()
mdIters.setValue(MDL_ITER, it, objId)
#agregar por ref3D
fn = self.getFilename('optimiser', iter=it )
md = MetaData(fn)
firstId = md.firstObject()
for label in labels:
mdIters.setValue(label, md.getValue(label, firstId), objId)
fn = self.getFilename('all_changes_xmipp')
mdIters.write(fn)
self.display2D(fn, extraParams='--label_relion')