def plotAll(self,
savefig=True,
outfileSuffix=None,
figformat='pdf',
dpi=600,
thumbnail=True,
closefigs=True):
"""
Make a few generically desired plots. This needs more flexibility in the future.
"""
plotHandler = PlotHandler(outDir=self.outDir,
resultsDb=self.resultsDb,
savefig=savefig,
figformat=figformat,
dpi=dpi,
thumbnail=thumbnail)
for b in self.bundleDict.values():
try:
b.plot(plotHandler=plotHandler,
outfileSuffix=outfileSuffix,
savefig=savefig)
except ValueError as ve:
message = 'Plotting failed for metricBundle %s.' % (b.fileRoot)
message += ' Error message: %s' % (ve.message)
warnings.warn(message)
if closefigs:
plt.close('all')
if self.verbose:
print('Plotting all metrics.')
def plotCurrent(self,
savefig=True,
outfileSuffix=None,
figformat='pdf',
dpi=600,
thumbnail=True,
closefigs=True):
plotHandler = PlotHandler(outDir=self.outDir,
resultsDb=self.resultsDb,
savefig=savefig,
figformat=figformat,
dpi=dpi,
thumbnail=thumbnail)
for b in self.currentBundleDict.itervalues():
b.plot(plotHandler=plotHandler,
outfileSuffix=outfileSuffix,
savefig=savefig)
for cb in b.childBundles.itervalues():
cb.plot(plotHandler=plotHandler,
outfileSuffix=outfileSuffix,
savefig=savefig)
if closefigs:
plt.close('all')
if self.verbose:
print 'Plotting complete.'
def plotCurrent(self, savefig=True, outfileSuffix=None, figformat='pdf', dpi=600, thumbnail=True,
closefigs=True):
"""Generate the plots for the currently active set of MetricBundles.
Parameters
----------
savefig : Optional[bool]
If True, save figures to disk, to self.outDir directory.
outfileSuffix : Optional[str]
Append outfileSuffix to the end of every plot file generated. Useful for generating
sequential series of images for movies.
figformat : Optional[str]
Matplotlib figure format to use to save to disk. Default pdf.
dpi : Optional[str]
DPI for matplotlib figure. Default 600.
thumbnail : Optional[bool]
If True, save a small thumbnail jpg version of the output file to disk as well.
This is useful for showMaf web pages. Default True.
closefigs : Optional[bool]
Close the matplotlib figures after they are saved to disk. If many figures are
generated, closing the figures saves significant memory. Default True.
"""
plotHandler = PlotHandler(outDir=self.outDir, resultsDb=self.resultsDb,
savefig=savefig, figformat=figformat, dpi=dpi, thumbnail=thumbnail)
for b in self.currentBundleDict.itervalues():
b.plot(plotHandler=plotHandler, outfileSuffix=outfileSuffix, savefig=savefig)
if closefigs:
plt.close('all')
if self.verbose:
print 'Plotting complete.'
def plotCurrent(self,
savefig=True,
outfileSuffix=None,
figformat='pdf',
dpi=600,
trimWhitespace=True,
thumbnail=True,
closefigs=True):
"""Generate the plots for the currently active set of MetricBundles.
Parameters
----------
savefig : bool, opt
If True, save figures to disk, to self.outDir directory.
outfileSuffix : str, opt
Append outfileSuffix to the end of every plot file generated. Useful for generating
sequential series of images for movies.
figformat : str, opt
Matplotlib figure format to use to save to disk. Default pdf.
dpi : int, opt
DPI for matplotlib figure. Default 600.
trimWhitespace : bool, opt
If True, trim additional whitespace from final figures. Default True.
thumbnail : bool, opt
If True, save a small thumbnail jpg version of the output file to disk as well.
This is useful for showMaf web pages. Default True.
closefigs : bool, opt
Close the matplotlib figures after they are saved to disk. If many figures are
generated, closing the figures saves significant memory. Default True.
"""
plotHandler = PlotHandler(outDir=self.outDir,
resultsDb=self.resultsDb,
savefig=savefig,
figformat=figformat,
dpi=dpi,
trimWhitespace=trimWhitespace,
thumbnail=thumbnail)
for b in self.currentBundleDict.values():
try:
b.plot(plotHandler=plotHandler,
outfileSuffix=outfileSuffix,
savefig=savefig)
except ValueError as ve:
message = 'Plotting failed for metricBundle %s.' % (b.fileRoot)
message += ' Error message: %s' % (ve)
warnings.warn(message)
if closefigs:
plt.close('all')
if self.verbose:
print('Plotting complete.')
def plot(self, plotHandler=None, plotFunc=None, outfileSuffix=None, savefig=False):
"""
Create all plots available from the slicer. plotHandler holds the output directory info, etc.
"""
# Generate a plotHandler if none was set.
if plotHandler is None:
plotHandler = PlotHandler(savefig=savefig)
# Make plots.
if plotFunc is not None:
if isinstance(plotFunc, BasePlotter):
plotFunc = plotFunc
else:
plotFunc = plotFunc()
plotHandler.setMetricBundles([self])
# The plotDict will be automatically accessed when the plotHandler calls the plotting method.
madePlots = {}
if plotFunc is not None:
# We haven't updated plotHandler to know about these kinds of plots yet.
# and we want to automatically set some values for the ylabel for metricVsH.
tmpDict = {}
if plotFunc.plotType == 'MetricVsH':
if 'ylabel' not in self.plotDict:
tmpDict['ylabel'] = self.metric.name
fignum = plotHandler.plot(plotFunc, plotDicts=tmpDict, outfileSuffix=outfileSuffix)
madePlots[plotFunc.plotType] = fignum
else:
for plotFunc in self.plotFuncs:
# We haven't updated plotHandler to know about these kinds of plots yet.
# and we want to automatically set some values for the ylabel for metricVsH.
tmpDict = {}
if plotFunc.plotType == 'MetricVsH':
if 'ylabel' not in self.plotDict:
tmpDict['ylabel'] = self.metric.name
fignum = plotHandler.plot(plotFunc, plotDicts=tmpDict, outfileSuffix=outfileSuffix)
madePlots[plotFunc.plotType] = fignum
return madePlots
def plot(self,
plotHandler=None,
plotFunc=None,
outfileSuffix=None,
savefig=False):
"""
Create all plots available from the slicer. plotHandler holds the output directory info, etc.
"""
# Generate a plotHandler if none was set.
if plotHandler is None:
plotHandler = PlotHandler(savefig=savefig)
# Make plots.
if plotFunc is not None:
if isinstance(plotFunc, BasePlotter):
plotFunc = plotFunc
else:
plotFunc = plotFunc()
plotHandler.setMetricBundles([self])
# The plotDict will be automatically accessed when the plotHandler calls the plotting method.
madePlots = {}
if plotFunc is not None:
# We haven't updated plotHandler to know about these kinds of plots yet.
# and we want to automatically set some values for the ylabel for metricVsH.
tmpDict = {}
if plotFunc.plotType == 'MetricVsH':
if 'ylabel' not in self.plotDict:
tmpDict['ylabel'] = self.metric.name
fignum = plotHandler.plot(plotFunc,
plotDicts=tmpDict,
outfileSuffix=outfileSuffix)
madePlots[plotFunc.plotType] = fignum
else:
for plotFunc in self.plotFuncs:
# We haven't updated plotHandler to know about these kinds of plots yet.
# and we want to automatically set some values for the ylabel for metricVsH.
tmpDict = {}
if plotFunc.plotType == 'MetricVsH':
if 'ylabel' not in self.plotDict:
tmpDict['ylabel'] = self.metric.name
fignum = plotHandler.plot(plotFunc,
plotDicts=tmpDict,
outfileSuffix=outfileSuffix)
madePlots[plotFunc.plotType] = fignum
return madePlots