def createCtfPlot(ctfSet, ctfId):
from pyworkflow.utils.path import removeExt
ctfModel = ctfSet[ctfId]
psdFn = ctfModel.getPsdFile()
fn = removeExt(psdFn) + "_avrot.txt"
gridsize = [1, 1]
xplotter = EmPlotter(x=gridsize[0], y=gridsize[1], windowTitle='CTF Fitting')
plot_title = "CTF Fitting"
a = xplotter.createSubPlot(plot_title, 'pixels^-1', 'CTF', yformat=False)
legendName = []
for i in range(1, 5):
_plotCurve(a, i, fn)
if i == 1:
legendName.append('rotational avg. No Astg')
elif i == 2:
legendName.append('rotational avg.')
elif i == 3:
legendName.append('CTF Fit')
elif i == 4:
legendName.append('Cross Correlation')
elif i == 5:
legendName.append('2sigma cross correlation of noise')
xplotter.showLegend(legendName)
a.grid(True)
xplotter.show()
def _showGuinier(self, volume):
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
guinierFn = volume + ".guinier"
d2 = self._getGuinierValue(guinierFn, 0)
legends = ["lnFweighted ln(F)", "corrected ln(F)", "model"]
xplotter = EmPlotter(*gridsize, windowTitle='Guinier Plots')
subPlot = xplotter.createSubPlot(basename(volume), 'd^-2(A^-2)', 'ln(F)', yformat=False)
for i, legend in enumerate(legends):
y = self._getGuinierValue(guinierFn, i+2)
subPlot.plot(d2, y)
xplotter.showLegend(legends)
subPlot.grid(True)
return xplotter
def _showFSC(self, paramName=None):
threshold = self.resolutionThresholdFSC.get()
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xplotter = EmPlotter(x=gridsize[0], y=gridsize[1], windowTitle='Resolution FSC')
if self.protocol.IS_REFINE:
plot_title = 'FSC'
a = xplotter.createSubPlot(plot_title, 'Angstroms^-1', 'FSC', yformat=False)
legends = []
show = False
for it in self._iterations:
parFn = self.protocol._getFileName('output_vol_par', iter=it)
if exists(parFn):
show = True
self._plotFSC(a, parFn)
legends.append('iter %d' % it)
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")
else:
for ref3d in self._refsList:
plot_title = 'class %s' % ref3d
a = xplotter.createSubPlot(plot_title, 'Angstroms^-1', 'FSC', yformat=False)
legends = []
for it in self._iterations:
parFn = self.protocol._getFileName('output_vol_par_class', iter=it, ref=ref3d)
if exists(parFn):
show = True
self._plotFSC(a, parFn)
legends.append('iter %d' % it)
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.resolutionThresholdFSC.get()
gridsize = self._getGridSize(1)
xplotter = EmPlotter(x=gridsize[0], y=gridsize[1], windowTitle='Resolution FSC')
plot_title = 'FSC'
a = xplotter.createSubPlot(plot_title, 'Angstroms^-1', 'FSC', yformat=False)
legends = []
show = False
for it in self._iterations:
if self.resolutionPlotsFSC.get() == FSC_UNMASK:
fscUnmask = self.protocol._getFileName('fscUnmasked',run=self.protocol._getRun(), iter=it)
if os.path.exists(fscUnmask):
show = True
self._plotFSC(a, fscUnmask)
legends.append('unmasked map iter %d' % it)
xplotter.showLegend(legends)
elif self.resolutionPlotsFSC.get() == FSC_MASK:
fscMask = self.protocol._getFileName('fscMasked',run=self.protocol._getRun(), iter=it)
if os.path.exists(fscMask):
show = True
self._plotFSC(a, fscMask)
legends.append('masked map iter %d' % it)
xplotter.showLegend(legends)
elif self.resolutionPlotsFSC.get() == FSC_MASKTIGHT:
fscMaskTight = self.protocol._getFileName('fscMaskedTight',run=self.protocol._getRun(), iter=it)
if os.path.exists(fscMaskTight):
show = True
self._plotFSC(a, fscMaskTight)
legends.append('masked tight map iter %d' % it)
xplotter.showLegend(legends)
elif self.resolutionPlotsFSC.get() == FSC_ALL:
fscUnmask = self.protocol._getFileName('fscUnmasked',run=self.protocol._getRun(), iter=it)
fscMask = self.protocol._getFileName('fscMasked',run=self.protocol._getRun(), iter=it)
fscMaskTight = self.protocol._getFileName('fscMaskedTight',run=self.protocol._getRun(), iter=it)
if os.path.exists(fscUnmask):
show = True
self._plotFSC(a, fscUnmask)
legends.append('unmasked map iter %d' % it)
self._plotFSC(a, fscMask)
legends.append('masked map iter %d' % it)
self._plotFSC(a, fscMaskTight)
legends.append('masked tight map iter %d' % it)
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 createCtfPlot(ctfSet, ctfId):
ctfModel = ctfSet[ctfId]
psdFn = ctfModel.getPsdFile()
fn = removeExt(psdFn) + "_avrot.txt"
gridsize = [1, 1]
xplotter = EmPlotter(x=gridsize[0], y=gridsize[1], windowTitle='CTF Fitting')
plot_title = "CTF Fitting"
a = xplotter.createSubPlot(plot_title, 'pixels^-1', 'CTF', yformat=False)
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()
def createCtfPlot(ctfSet, ctfId):
ctfModel = ctfSet[ctfId]
psdFn = ctfModel.getPsdFile()
fn = pwutils.removeExt(psdFn) + "_EPA.txt"
gridsize = [1, 1]
xplotter = EmPlotter(x=gridsize[0], y=gridsize[1],
windowTitle='CTF Fitting')
plot_title = "CTF Fitting"
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()
def createCtfPlot(ctfSet, ctfId):
ctfModel = ctfSet[ctfId]
psdFn = ctfModel.getPsdFile()
fn = removeExt(psdFn) + "_avrot.txt"
gridsize = [1, 1]
xplotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
windowTitle='CTF Fitting')
plot_title = "CTF Fitting"
a = xplotter.createSubPlot(plot_title, 'pixels^-1', 'CTF', yformat=False)
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()
def _showSSNR(self, paramName=None):
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xplotter = EmPlotter(x=gridsize[0], y=gridsize[1])
for ref3d in self._refsList:
plot_title = 'Resolution SSNR, for Class %s' % ref3d
a = xplotter.createSubPlot(plot_title, 'Angstroms^-1', 'sqrt(SSNR)', yformat=False)
legendName = []
for it in self._iterations:
if self.protocol.IS_REFINE:
fn = self.protocol._getFileName('output_vol_par', iter=it)
else:
fn = self.protocol._getFileName('output_vol_par_class', iter=it, ref=ref3d)
if exists(fn):
self._plotSSNR(a, fn)
legendName.append('iter %d' % it)
xplotter.showLegend(legendName)
a.grid(True)
return [xplotter]
def _showFSC(self, paramName=None):
threshold = self.resolutionThresholdFSC.get()
iterations = self._getIterations()
groups = self._getGroups()
if self.groupFSC == 0: # group by iterations
files = [(it, self._getFinalPath('fscdoc_%02d.stk' % it)) for it in iterations]
legendPrefix = 'iter'
else:
it = iterations[-1]
legendPrefix = 'group'
def group(f): # retrieve the group number
return int(f.split('_')[-1].split('.')[0])
groupFiles = glob(self._getFinalPath('fscdoc_%02d_???.stk' % it))
groupFiles.sort()
files = [(group(f), f) for f in groupFiles if group(f) in groups]
if not files: #empty files
return [self.errorMessage("Please select valid groups to display",
title="Wrong groups selection")]
plotter = EmPlotter(x=1, y=1, windowTitle='Resolution FSC')
a = plotter.createSubPlot("FSC", 'Angstroms^-1', 'FSC', yformat=False)
#fscFile = self._getFinalPath('fscdoc_%02d.stk' % iterations[0])
legends = []
for it, fscFile in files:
if os.path.exists(fscFile):
self._plotFSC(a, fscFile)
legends.append('%s %d' % (legendPrefix, it))
else:
print "Missing file: ", fscFile
if threshold < self.maxfsc:
a.plot([self.minInv, self.maxInv],[threshold, threshold],
color='black', linestyle='--')
plotter.showLegend(legends)
a.grid(True)
return [plotter]
def createCtfPlot(ctfSet, ctfId):
ctfModel = ctfSet[ctfId]
psdFn = ctfModel.getPsdFile()
fn = pwutils.removeExt(psdFn) + "_EPA.txt"
gridsize = [1, 1]
xplotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
windowTitle='CTF Fitting')
plot_title = "CTF Fitting"
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()
def _showFSC(self, paramName=None):
threshold = self.resolutionThresholdFSC.get()
gridsize = self._getGridSize(1)
xplotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
windowTitle='Resolution FSC')
plot_title = 'FSC'
a = xplotter.createSubPlot(plot_title,
'Angstroms^-1',
'FSC',
yformat=False)
legends = []
show = False
for it in self._iterations:
if self.resolutionPlotsFSC.get() == FSC_UNMASK:
fscUnmask = self.protocol._getFileName(
'fscUnmasked', run=self.protocol._getRun(), iter=it)
if os.path.exists(fscUnmask):
show = True
self._plotFSC(a, fscUnmask)
legends.append('unmasked map iter %d' % it)
xplotter.showLegend(legends)
elif self.resolutionPlotsFSC.get() == FSC_MASK:
fscMask = self.protocol._getFileName(
'fscMasked', run=self.protocol._getRun(), iter=it)
if os.path.exists(fscMask):
show = True
self._plotFSC(a, fscMask)
legends.append('masked map iter %d' % it)
xplotter.showLegend(legends)
elif self.resolutionPlotsFSC.get() == FSC_MASKTIGHT:
fscMaskTight = self.protocol._getFileName(
'fscMaskedTight', run=self.protocol._getRun(), iter=it)
if os.path.exists(fscMaskTight):
show = True
self._plotFSC(a, fscMaskTight)
legends.append('masked tight map iter %d' % it)
xplotter.showLegend(legends)
elif self.resolutionPlotsFSC.get() == FSC_ALL:
fscUnmask = self.protocol._getFileName(
'fscUnmasked', run=self.protocol._getRun(), iter=it)
fscMask = self.protocol._getFileName(
'fscMasked', run=self.protocol._getRun(), iter=it)
fscMaskTight = self.protocol._getFileName(
'fscMaskedTight', run=self.protocol._getRun(), iter=it)
if os.path.exists(fscUnmask):
show = True
self._plotFSC(a, fscUnmask)
legends.append('unmasked map iter %d' % it)
self._plotFSC(a, fscMask)
legends.append('masked map iter %d' % it)
self._plotFSC(a, fscMaskTight)
legends.append('masked tight map iter %d' % it)
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.resolutionThresholdFSC.get()
nrefs = len(self._refsList)
gridsize = self._getGridSize(nrefs)
xplotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
windowTitle='Resolution FSC')
if self.protocol.IS_REFINE:
plot_title = 'FSC'
a = xplotter.createSubPlot(plot_title,
'Angstroms^-1',
'FSC',
yformat=False)
legends = []
show = False
for it in self._iterations:
parFn = self.protocol._getFileName('output_vol_par', iter=it)
if exists(parFn):
show = True
self._plotFSC(a, parFn)
legends.append('iter %d' % it)
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")
else:
for ref3d in self._refsList:
plot_title = 'class %s' % ref3d
a = xplotter.createSubPlot(plot_title,
'Angstroms^-1',
'FSC',
yformat=False)
legends = []
for it in self._iterations:
parFn = self.protocol._getFileName('output_vol_par_class',
iter=it,
ref=ref3d)
if exists(parFn):
show = True
self._plotFSC(a, parFn)
legends.append('iter %d' % it)
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]
