def _doViewRawDeformation(self, components):
# components = map(int, self.displayRawDeformation.get().split())
components = map(int, components.split())
dim = len(components)
views = []
if dim > 0:
modeList = [m - 1 for m in components]
modeNameList = ['Mode %d' % m for m in components]
missingList = []
if missingList:
return [self.errorMessage("Invalid mode(s) *%s*\n." % (', '.join(missingList)),
title="Invalid input")]
# Actually plot
plotter = XmippNmaPlotter(data=self.getData())
baseList = [basename(n) for n in modeNameList]
if dim == 1:
self.getData().XIND = modeList[0]
plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.getData().YIND = modeList[1]
if dim == 2:
plotter.plotArray2D("%s vs %s" % tuple(baseList), *baseList)
elif dim == 3:
self.getData().ZIND = modeList[2]
plotter.plotArray3D("%s %s %s" % tuple(baseList), *baseList)
views.append(plotter)
return views
def _doViewRawDeformation(self, components):
# components = map(int, self.displayRawDeformation.get().split())
components = map(int, components.split())
dim = len(components)
views = []
if dim > 0:
modeList = []
modeNameList = []
missingList = []
for modeNumber in components:
found = False
md = xmipp.MetaData(self.protocol._getExtraPath('modes.xmd'))
for i, objId in enumerate(md):
modeId = md.getValue(xmipp.MDL_ORDER, objId)
if modeNumber == modeId:
modeNameList.append('Mode %d' % modeNumber)
modeList.append(i)
found = True
break
if not found:
missingList.append(str(modeNumber))
if missingList:
return [
self.errorMessage("Invalid mode(s) *%s*\n." %
(', '.join(missingList)),
title="Invalid input")
]
# Actually plot
plotter = XmippNmaPlotter(data=self.getData())
baseList = [basename(n) for n in modeNameList]
if dim == 1:
self.getData().XIND = modeList[0]
plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.getData().YIND = modeList[1]
if dim == 2:
plotter.plotArray2D("%s vs %s" % tuple(baseList),
*baseList)
elif dim == 3:
self.getData().ZIND = modeList[2]
plotter.plotArray3D("%s %s %s" % tuple(baseList),
*baseList)
views.append(plotter)
return views
def _doViewRawDeformation(self, components):
# components = map(int, self.displayRawDeformation.get().split())
components = map(int, components.split())
dim = len(components)
views = []
if dim > 0:
modeList = []
modeNameList = []
missingList = []
for modeNumber in components:
found = False
md = xmipp.MetaData(self.protocol._getExtraPath('modes.xmd'))
for i, objId in enumerate(md):
modeId = md.getValue(xmipp.MDL_ORDER, objId)
if modeNumber == modeId:
modeNameList.append('Mode %d' % modeNumber)
modeList.append(i)
found = True
break
if not found:
missingList.append(str(modeNumber))
if missingList:
return [self.errorMessage("Invalid mode(s) *%s*\n." % (', '.join(missingList)),
title="Invalid input")]
# Actually plot
plotter = XmippNmaPlotter(data=self.getData())
baseList = [basename(n) for n in modeNameList]
if dim == 1:
self.getData().XIND = modeList[0]
plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.getData().YIND = modeList[1]
if dim == 2:
plotter.plotArray2D("%s vs %s" % tuple(baseList), *baseList)
elif dim == 3:
self.getData().ZIND = modeList[2]
plotter.plotArray3D("%s %s %s" % tuple(baseList), *baseList)
views.append(plotter)
return views
def _doViewRawDeformation(self, components):
# components = map(int, self.displayRawDeformation.get().split())
components = map(int, components.split())
dim = len(components)
views = []
if dim > 0:
modeList = [m - 1 for m in components]
modeNameList = ['Mode %d' % m for m in components]
missingList = []
if missingList:
return [
self.errorMessage("Invalid mode(s) *%s*\n." %
(', '.join(missingList)),
title="Invalid input")
]
# Actually plot
plotter = XmippNmaPlotter(data=self.getData())
baseList = [basename(n) for n in modeNameList]
if dim == 1:
self.getData().XIND = modeList[0]
plotter.plotArray1D("Histogram for %s" % baseList[0],
"Deformation value", "Number of images")
else:
self.getData().YIND = modeList[1]
if dim == 2:
plotter.plotArray2D("%s vs %s" % tuple(baseList),
*baseList)
elif dim == 3:
self.getData().ZIND = modeList[2]
plotter.plotArray3D("%s %s %s" % tuple(baseList),
*baseList)
views.append(plotter)
return views
def createShiftPlot(mdFn, title, ylabel):
plotter = XmippNmaPlotter()
plotter.createSubPlot(title, 'atom index', ylabel)
plotter.plotMdFile(mdFn, None, xmipp.MDL_NMA_ATOMSHIFT)
return plotter
def createShiftPlot(mdFn, title, ylabel):
plotter = XmippNmaPlotter()
plotter.createSubPlot(title, 'atom index', ylabel)
plotter.plotMdFile(mdFn, None, xmipp.MDL_NMA_ATOMSHIFT)
return plotter