def _showFSC(self, paramName=None):
threshold = self.resolutionThreshold.get()
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xmipp.activateMathExtensions()
for ref3d in self._refsList:
xplotter = XmippPlotter(*gridsize, windowTitle='Resolution FSC')
legends = []
show = False
plot_title = 'Ref3D_%s' % ref3d
a = xplotter.createSubPlot(plot_title,
'frequency(1/A)',
'FSC',
yformat=False)
legends = []
for it in self._iterations:
file_name = self.protocol._getFileName('resolutionXmdFile',
iter=it,
ref=ref3d)
if exists(file_name):
show = True
legends.append('iter %d' % it)
self._plotFSC(a, file_name)
xplotter.showLegend(legends)
if show:
if threshold < self.maxFrc:
a.plot([self.minInv, self.maxInv], [threshold, threshold],
color='black',
linestyle='--')
a.grid(True)
else:
raise Exception("Set a valid iteration to show its FSC")
return [xplotter]
def _showFSC(self, paramName=None):
threshold = self.resolutionThreshold.get()
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xmipp.activateMathExtensions()
for ref3d in self._refsList:
xplotter = XmippPlotter(*gridsize, windowTitle='Resolution FSC')
legends = []
show = False
plot_title = 'Ref3D_%s' % ref3d
a = xplotter.createSubPlot(plot_title, 'frequency(1/A)', 'FSC', yformat=False)
legends = []
for it in self._iterations:
file_name = self.protocol._getFileName('resolutionXmdFile', iter=it, ref=ref3d)
if exists(file_name):
show = True
legends.append('iter %d' % it)
self._plotFSC(a, file_name)
xplotter.showLegend(legends)
if show:
if threshold < self.maxFrc:
a.plot([self.minInv, self.maxInv],[threshold, threshold], color='black', linestyle='--')
a.grid(True)
else:
raise Exception("Set a valid iteration to show its FSC")
return [xplotter]
def calculateDeviationsStep(self, it):
""" Calculate both angles and shifts devitations for all iterations
"""
SL = xmipp.SymList()
mdIter = xmipp.MetaData()
#for it in self.allIters():
mdIter.clear()
SL.readSymmetryFile(self._symmetry[it])
md1 = xmipp.MetaData(self.docFileInputAngles[it])
md2 = xmipp.MetaData(self.docFileInputAngles[it-1])
#ignore disabled,
md1.removeDisabled()
md2.removeDisabled()
#first metadata file may not have shiftx and shifty
if not md2.containsLabel(xmipp.MDL_SHIFT_X):
md2.addLabel(xmipp.MDL_SHIFT_X)
md2.addLabel(xmipp.MDL_SHIFT_Y)
md2.fillConstant(xmipp.MDL_SHIFT_X,0.)
md2.fillConstant(xmipp.MDL_SHIFT_Y,0.)
oldLabels=[xmipp.MDL_ANGLE_ROT,
xmipp.MDL_ANGLE_TILT,
xmipp.MDL_ANGLE_PSI,
xmipp.MDL_SHIFT_X,
xmipp.MDL_SHIFT_Y]
newLabels=[xmipp.MDL_ANGLE_ROT2,
xmipp.MDL_ANGLE_TILT2,
xmipp.MDL_ANGLE_PSI2,
xmipp.MDL_SHIFT_X2,
xmipp.MDL_SHIFT_Y2]
md2.renameColumn(oldLabels,newLabels)
md2.addLabel(xmipp.MDL_SHIFT_X_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_Y_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_DIFF)
mdIter.join1(md1, md2, xmipp.MDL_IMAGE, xmipp.INNER_JOIN)
SL.computeDistance(mdIter,False,False,False)
xmipp.activateMathExtensions()
#operate in sqlite
shiftXLabel = xmipp.label2Str(xmipp.MDL_SHIFT_X)
shiftX2Label = xmipp.label2Str(xmipp.MDL_SHIFT_X2)
shiftXDiff = xmipp.label2Str(xmipp.MDL_SHIFT_X_DIFF)
shiftYLabel = xmipp.label2Str(xmipp.MDL_SHIFT_Y)
shiftY2Label = xmipp.label2Str(xmipp.MDL_SHIFT_Y2)
shiftYDiff = xmipp.label2Str(xmipp.MDL_SHIFT_Y_DIFF)
shiftDiff = xmipp.label2Str(xmipp.MDL_SHIFT_DIFF)
#timeStr = str(dtBegin)
operateString = shiftXDiff+"="+shiftXLabel+"-"+shiftX2Label
operateString += "," + shiftYDiff+"="+shiftYLabel+"-"+shiftY2Label
mdIter.operate(operateString)
operateString = shiftDiff+"=sqrt(" \
+shiftXDiff+"*"+shiftXDiff+"+" \
+shiftYDiff+"*"+shiftYDiff+");"
mdIter.operate(operateString)
iterFile = self._mdDevitationsFn(it)
mdIter.write(iterFile,xmipp.MD_APPEND)
self._setLastIter(it)
def calculateDeviationsStep(self, it):
""" Calculate both angles and shifts devitations for all iterations
"""
SL = xmipp.SymList()
mdIter = xmipp.MetaData()
#for it in self.allIters():
mdIter.clear()
SL.readSymmetryFile(self._symmetry[it])
md1 = xmipp.MetaData(self.docFileInputAngles[it])
md2 = xmipp.MetaData(self.docFileInputAngles[it-1])
#ignore disabled,
md1.removeDisabled()
md2.removeDisabled()
#first metadata file may not have shiftx and shifty
if not md2.containsLabel(xmipp.MDL_SHIFT_X):
md2.addLabel(xmipp.MDL_SHIFT_X)
md2.addLabel(xmipp.MDL_SHIFT_Y)
md2.fillConstant(xmipp.MDL_SHIFT_X,0.)
md2.fillConstant(xmipp.MDL_SHIFT_Y,0.)
oldLabels=[xmipp.MDL_ANGLE_ROT,
xmipp.MDL_ANGLE_TILT,
xmipp.MDL_ANGLE_PSI,
xmipp.MDL_SHIFT_X,
xmipp.MDL_SHIFT_Y]
newLabels=[xmipp.MDL_ANGLE_ROT2,
xmipp.MDL_ANGLE_TILT2,
xmipp.MDL_ANGLE_PSI2,
xmipp.MDL_SHIFT_X2,
xmipp.MDL_SHIFT_Y2]
md2.renameColumn(oldLabels,newLabels)
md2.addLabel(xmipp.MDL_SHIFT_X_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_Y_DIFF)
md2.addLabel(xmipp.MDL_SHIFT_DIFF)
mdIter.join1(md1, md2, xmipp.MDL_IMAGE, xmipp.INNER_JOIN)
SL.computeDistance(mdIter,False,False,False)
xmipp.activateMathExtensions()
#operate in sqlite
shiftXLabel = xmipp.label2Str(xmipp.MDL_SHIFT_X)
shiftX2Label = xmipp.label2Str(xmipp.MDL_SHIFT_X2)
shiftXDiff = xmipp.label2Str(xmipp.MDL_SHIFT_X_DIFF)
shiftYLabel = xmipp.label2Str(xmipp.MDL_SHIFT_Y)
shiftY2Label = xmipp.label2Str(xmipp.MDL_SHIFT_Y2)
shiftYDiff = xmipp.label2Str(xmipp.MDL_SHIFT_Y_DIFF)
shiftDiff = xmipp.label2Str(xmipp.MDL_SHIFT_DIFF)
#timeStr = str(dtBegin)
operateString = shiftXDiff+"="+shiftXLabel+"-"+shiftX2Label
operateString += "," + shiftYDiff+"="+shiftYLabel+"-"+shiftY2Label
mdIter.operate(operateString)
operateString = shiftDiff+"=sqrt(" \
+shiftXDiff+"*"+shiftXDiff+"+" \
+shiftYDiff+"*"+shiftYDiff+");"
mdIter.operate(operateString)
iterFile = self._mdDevitationsFn(it)
mdIter.write(iterFile,xmipp.MD_APPEND)
self._setLastIter(it)
