plotter.createSubPlot(title, 'atom index', ylabel)
plotter.plotMdFile(mdFn, None, xmippLib.MDL_NMA_ATOMSHIFT)
return plotter
def createDistanceProfilePlot(protocol, modeNumber):
vectorMdFn = protocol._getExtraPath("distanceProfiles",
"vec%d.xmd" % modeNumber)
plotter = createShiftPlot(vectorMdFn,
"Atom shifts for mode %d" % modeNumber, "shift")
return plotter
def createVmdView(protocol, modeNumber):
vmdFile = protocol._getExtraPath("animations",
"animated_mode_%03d.vmd" % modeNumber)
return VmdView('-e "%s"' % vmdFile)
def showDistanceProfilePlot(protocol, modeNumber):
createDistanceProfilePlot(protocol, modeNumber).show()
def showVmdView(protocol, modeNumber):
createVmdView(protocol, modeNumber).show()
ProjectWindow.registerObjectCommand(OBJCMD_NMA_PLOTDIST,
showDistanceProfilePlot)
ProjectWindow.registerObjectCommand(OBJCMD_NMA_VMD, showVmdView)
DataView(volFn).show()
def showClassAvgProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_aptcl.hdf')
def showProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_proj.hdf')
def showInitialRandomVolume(volumeSet, volId):
showExtraFile(volumeSet, volId, '_init.hdf')
ProjectWindow.registerObjectCommand(OBJCMD_CLASSAVG_PROJS, showClassAvgProjs)
ProjectWindow.registerObjectCommand(OBJCMD_PROJS, showProjs)
ProjectWindow.registerObjectCommand(OBJCMD_INITVOL, showInitialRandomVolume)
class Refine2DViewer(ProtocolViewer):
""" Visualization of e2refine2d results. """
_targets = [EmanProtRefine2D, EmanProtRefine2DBispec]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_label = 'viewer refine 2d'
def _defineParams(self, form):
self._env = os.environ.copy()
form.addSection(label='Results per Iteration')
form.addParam('iterToShow',
if i == 0:
res['freq'] = [float(x) for x in line.split()]
elif i == 2:
res['amp'] = [float(x) for x in line.split()]
elif i == 3:
res['fit'] = [float(x) for x in line.split()]
elif i == 4:
res['quality'] = [float(x) for x in line.split()]
break
i += 1
return res
OBJCMD_CTFFIND4 = "CTFFind plot results"
ProjectWindow.registerObjectCommand(OBJCMD_CTFFIND4, createCtfPlot)
class CtffindViewer(Viewer):
""" Specific way to visualize SetOfCtf. """
_environments = [DESKTOP_TKINTER]
_targets = [CistemProtCTFFind]
def _visualize(self, prot, **kwargs):
outputCTF = getattr(prot, 'outputCTF', None)
if outputCTF is not None:
ctfView = CtfView(self._project, outputCTF)
viewParams = ctfView.getViewParams()
viewParams[showj.OBJCMDS] = "'%s'" % OBJCMD_CTFFIND4
return [ctfView]
# we only consider the 'doSaveUnweightedMic' flag if the
# weighted ones should be created.
return (self.doSaveAveMic and self.doSaveUnweightedMic)
def _createOutputWeightedMicrographs(self):
return (self.doSaveAveMic and self.doApplyDoseFilter)
def _getOutputMovieUnWtName(self, movie):
""" Returns the name of the output dose-weighted movie.
(relative to micFolder)
"""
return self._getMovieRoot(movie) + '_aligned_movie.mrcs'
def showCartesianShiftsPlot(inputSet, itemId):
item = inputSet[itemId]
if item.hasAttribute('_xmipp_OFMeanX'):
meanX = [float(x) for x in item._xmipp_OFMeanX]
meanY = [float(y) for y in item._xmipp_OFMeanY]
plotter = createAlignmentPlot(meanX, meanY)
plotter.show()
else:
print("These items do not have OF alignment set. ")
ProjectWindow.registerObjectCommand(OBJCMD_MOVIE_ALIGNCARTESIAN,
showCartesianShiftsPlot)
# Just for backwards compatibility
ProtMovieAlignment = XmippProtOFAlignment
'CTF',
yformat=False)
a.invert_xaxis()
for i in range(1, 5):
_plotCurve(a, i, fn)
xplotter.showLegend([
'simulated CTF', 'equiphase avg.', 'equiphase avg. - bg',
'cross correlation'
])
a.grid(True)
xplotter.show()
OBJCMD_GCTF = "Display Ctf Analysis"
ProjectWindow.registerObjectCommand(OBJCMD_GCTF, createCtfPlot)
def _plotCurve(a, i, fn):
freqs = _getValues(fn, 0)
curv = _getValues(fn, i)
a.plot(freqs, curv)
def _getValues(fn, col):
f = open(fn)
values = []
for line in f:
if not line.startswith('Resolution', 2, 12):
column = line.split()
value = float(column[col])
def showExtraFile(volumeSet, volId, suffix):
vol = volumeSet[volId]
volFn = vol.getFileName().replace('.hdf', suffix)
vw.DataView(volFn).show()
def showClassAvgProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_aptcl.hdf')
def showProjs(volumeSet, volId):
showExtraFile(volumeSet, volId, '_proj.hdf')
def showInitialRandomVolume(volumeSet, volId):
showExtraFile(volumeSet, volId, '_init.hdf')
ProjectWindow.registerObjectCommand(OBJCMD_CLASSAVG_PROJS, showClassAvgProjs)
ProjectWindow.registerObjectCommand(OBJCMD_PROJS, showProjs)
ProjectWindow.registerObjectCommand(OBJCMD_INITVOL, showInitialRandomVolume)
class RefineEasyViewer(ProtocolViewer):
""" Visualization of Refine Easy."""
_targets = [EmanProtRefine]
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_label = 'viewer Refine Easy'
def _defineParams(self, form):
self._env = os.environ.copy()
form.addSection(label='Results per Iteration')
form.addParam('iterToShow', EnumParam,
legendName = ['rotational avg. No Astg',
'rotational avg.',
'CTF Fit',
'Cross Correlation',
'2sigma cross correlation of noise']
for i in range(1, 6):
_plotCurve(a, i, fn)
xplotter.showLegend(legendName)
a.grid(True)
xplotter.show()
OBJCMD_CTFFIND4 = "Display Ctf Fitting"
ProjectWindow.registerObjectCommand(OBJCMD_CTFFIND4, createCtfPlot)
class CtffindViewer(Viewer):
""" Specific way to visualize SetOfCtf after Gctf. """
_environments = [DESKTOP_TKINTER, WEB_DJANGO]
_targets = [ProtCTFFind]
def _visualize(self, prot, **kwargs):
outputCTF = getattr(prot, 'outputCTF', None)
if outputCTF is not None:
ctfView = CtfView(self._project, outputCTF)
viewParams = ctfView.getViewParams()
viewParams[showj.OBJCMDS] = "'%s'" % OBJCMD_CTFFIND4
return [ctfView]
return (self.doSaveAveMic and self.doSaveUnweightedMic)
def _createOutputWeightedMicrographs(self):
return (self.doSaveAveMic and self.doApplyDoseFilter)
def _getOutputMovieWtName(self, movie):
""" Returns the name of the output dose-weighted movie.
(relative to micFolder)
"""
return self._getMovieRoot(movie) + '_aligned_movie_DW.mrcs'
def showCartesianShiftsPlot(inputSet, itemId):
item = inputSet[itemId]
if item.hasAttribute('_xmipp_OFMeanX'):
meanX = [float(x) for x in item._xmipp_OFMeanX]
meanY = [float(y) for y in item._xmipp_OFMeanY]
plotter = createAlignmentPlot(meanX, meanY)
plotter.show()
else:
print "These items do not have OF alignment set. "
ProjectWindow.registerObjectCommand(OBJCMD_MOVIE_ALIGNCARTESIAN,
showCartesianShiftsPlot)
# Just for backwards compatibility
ProtMovieAlignment = XmippProtOFAlignment
a = xplotter.createSubPlot(plot_title, 'Resolution (Angstroms)', 'CTF',
yformat=False)
a.invert_xaxis()
for i in range(1, 5):
_plotCurve(a, i, fn)
xplotter.showLegend(['simulated CTF',
'equiphase avg.',
'equiphase avg. - bg',
'cross correlation'])
a.grid(True)
xplotter.show()
OBJCMD_GCTF = "Display Ctf Analysis"
ProjectWindow.registerObjectCommand(OBJCMD_GCTF, createCtfPlot)
def _plotCurve(a, i, fn):
freqs = _getValues(fn, 0)
curv = _getValues(fn, i)
a.plot(freqs, curv)
def _getValues(fn, col):
f = open(fn)
values = []
for line in f:
if not line.startswith('Resolution', 2, 12):
column = line.split()
value = float(column[col])