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 _plotHistogram(self, param=None):
""" First we parse the MSA plt:
first column: cumulative percent.
second column: iteration number.
"""
iters = []
cumPercents = []
fn = self.protocol.getOutputPlt()
with open(fn) as f:
lines_after_2 = f.readlines()[2:]
for line in lines_after_2:
values = line.split()
cumPercents.append(float(values[0]))
iters.append(int(float(values[1])))
f.close()
width = 0.85
xplotter = EmPlotter()
a = xplotter.createSubPlot(
'Behaviour of sum of eigenvalues during analysis',
'Iteration number', '%')
a.bar(iters, cumPercents, width, color='b')
return [xplotter]
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 _createAngDist2D(self, it):
fnDir = self.protocol._getExtraPath("Iter%03d" % it)
fnAngles = join(fnDir, "angles.xmd")
view = None
if exists(fnAngles):
fnAnglesSqLite = join(fnDir, "angles.sqlite")
from pyworkflow.em.viewers import EmPlotter
if not exists(fnAnglesSqLite):
from pyworkflow.em.metadata.utils import getSize
self.createAngDistributionSqlite(
fnAnglesSqLite,
getSize(fnAngles),
itemDataIterator=self._iterAngles(fnAngles))
view = EmPlotter(x=1,
y=1,
mainTitle="Iteration %d" % it,
windowTitle="Angular distribution")
view.plotAngularDistributionFromMd(fnAnglesSqLite, 'iter %d' % it)
return view
def _createScatterPlot(self, rmax, colorzaxis=False):
gridsize = self._getGridSize(1)
xplotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
windowTitle='Tilt geometry plot')
plot_title = 'Tilt pair parameter plot'
a = xplotter.createSubPlot(plot_title,
'Tilt axis',
'Tilt angle',
projection='polar')
datap, r, theta, zaxis = self._getValues()
if colorzaxis:
a.scatter(theta, r, c=zaxis)
else:
a.scatter(theta, r)
a.set_rmax(rmax)
return xplotter
def _createAngDist2D(self, it):
nrefs = len(self._refsList)
nparts = self.protocol.inputParticles.get().getSize()
gridsize = self._getGridSize(nrefs)
if self.protocol.IS_REFINE:
data_angularDist = self.protocol._getFileName("output_par",
iter=it)
if exists(data_angularDist):
plotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
mainTitle="Iteration %d" % it,
windowTitle="Angular distribution")
title = 'iter %d' % it
sqliteFn = self.protocol._getFileName('projections', iter=it)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(it, data_angularDist))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
else:
return
else:
for ref3d in self._refsList:
data_angularDist = self.protocol._getFileName(
"output_par_class", iter=it, ref=ref3d)
if exists(data_angularDist):
plotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
mainTitle="Iteration %d" % it,
windowTitle="Angular distribution")
title = 'class %d' % ref3d
sqliteFn = self.protocol._getFileName('projectionsClass',
iter=it,
ref=ref3d)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(
it, data_angularDist))
plotter.plotAngularDistributionFromMd(sqliteFn, title)
return plotter
def main():
parser = argparse.ArgumentParser(prog='Scipion Plot')
parser.add_argument('--file', help='File to visualize', required=True)
parser.add_argument('--block', help='Block to visualize')
parser.add_argument('--type', help='Plot type')
parser.add_argument('--columns', help='Columns to plot')
parser.add_argument('--xcolumn', help='X Column to plot')
parser.add_argument('--orderColumn', help='Column to order')
parser.add_argument('--orderDir', help='Order direction(ASC, DESC)')
parser.add_argument('--bins',
help='If plot type is histogram, number of bins')
parser.add_argument('--colors', help='Colors to plot columns')
parser.add_argument('--styles', help='Styles to plot columns')
parser.add_argument('--markers', help='Markers to plot columns')
parser.add_argument('--title', help='Plot title', default='')
parser.add_argument('--ytitle', help='Y axis title', default='')
parser.add_argument('--xtitle', help='X axis title', default='')
args = parser.parse_args()
plotfile = args.file
block = args.block if args.block else ''
type = args.type
columns = args.columns
xcolumn = args.xcolumn
orderColumn = args.orderColumn
orderDir = args.orderDir
bins = args.bins
colors = args.colors
styles = args.styles
markers = args.markers
title = args.title
xtitle = args.xtitle
ytitle = args.ytitle
Plotter.setBackend('TkAgg')
plotter = EmPlotter.createFromFile(plotfile, block, type, columns, colors,
styles, markers, xcolumn, ytitle,
xtitle, title, bins, orderColumn,
orderDir)
plotter.show(block=True)
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 _createAngDist2D(self, it):
nrefs = self._getNumberOfRefs()
gridsize = self._getGridSize(nrefs)
self.protocol._execEmanProcess(self.protocol._getRun(), it)
angularDist = self.protocol._getFileName("angles", iter=it)
if os.path.exists(angularDist):
xplotter = EmPlotter(x=gridsize[0],
y=gridsize[1],
mainTitle="Iteration %d" % it,
windowTitle="Angular distribution")
def plot(prefix):
nparts = self._getNumberOfParticles(it, prefix)
title = '%s particles' % prefix
sqliteFn = self.protocol._getFileName('projections',
iter=it,
half=prefix)
self.createAngDistributionSqlite(
sqliteFn,
nparts,
itemDataIterator=self._iterAngles(it, prefix))
xplotter.plotAngularDistributionFromMd(sqliteFn, title)
if self.showHalves.get() == HALF_EVEN:
plot('even')
elif self.showHalves.get() == HALF_ODD:
plot('odd')
elif self.showHalves.get() == FULL_MAP:
plot('full')
else:
for prefix in ['even', 'odd', 'full']:
plot(prefix)
return xplotter
else:
return
def _plotHistogram(self, param=None):
md = MetaData()
md.read(self.protocol._getFileName(FN_METADATA_HISTOGRAM))
x_axis = []
y_axis = []
for idx in md:
x_axis_ = md.getValue(MDL_X, idx)
y_axis_ = md.getValue(MDL_COUNT, idx)
x_axis.append(x_axis_)
y_axis.append(y_axis_)
plotter = EmPlotter()
plotter.createSubPlot("Resolutions Histogram", "Resolution (A)",
"# of Counts")
barwidth = (x_axis[-1] - x_axis[0]) / len(x_axis)
plotter.plotDataBar(x_axis, y_axis, barwidth)
return [plotter]
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 it %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 it %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 it %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 it %d' % it)
self._plotFSC(a, fscMask)
legends.append('masked map it %d' % it)
self._plotFSC(a, fscMaskTight)
legends.append('masked tight map it %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 _visualizeHistogram(self, e=None):
views = []
numberOfBins = self.visualizeHistogram.get()
if hasattr(self.protocol, "outputCTF"):
numberOfBins = min(numberOfBins, self.protocol.outputCTF.getSize())
plotter = EmPlotter()
plotter.createSubPlot("Resolution Discrepancies histogram",
"Resolution (A)", "# of Comparisons")
resolution = [ctf.getResolution() for ctf in
self.protocol.outputCTF]
plotter.plotHist(resolution, nbins=numberOfBins)
views.append(plotter)
if hasattr(self.protocol, "outputCTFDiscarded"):
numberOfBins = min(numberOfBins,
self.protocol.outputCTFDiscarded.getSize())
plotter = EmPlotter()
plotter.createSubPlot(
"Resolution Discrepancies histogram (discarded)",
"Resolution (A)", "# of Comparisons")
resolution = [ctf.getResolution() for ctf in
self.protocol.outputCTFDiscarded]
plotter.plotHist(resolution, nbins=numberOfBins)
views.append(plotter)
return views
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]