def testSetupSlicerFreedman(self):
"""Test that setting up the slicer using bins=None works."""
dvmin = 0
dvmax = 1
dv = makeDataValues(1000, dvmin, dvmax, random=2234)
self.testslicer = OneDSlicer(sliceColName='testdata', bins=None)
self.testslicer.setupSlicer(dv)
# How many bins do you expect from optimal binsize?
from lsst.sims.maf.utils import optimalBins
bins = optimalBins(dv['testdata'])
np.testing.assert_equal(self.testslicer.nslice, bins)
def testSetupSlicerFreedman(self):
"""Test that setting up the slicer using bins=None works."""
dvmin = 0
dvmax = 1
dv = makeDataValues(1000, dvmin, dvmax, random=True)
self.testslicer = OneDSlicer(sliceColName='testdata', bins=None)
self.testslicer.setupSlicer(dv)
# How many bins do you expect from optimal binsize?
from lsst.sims.maf.utils import optimalBins
bins = optimalBins(dv['testdata'])
np.testing.assert_equal(self.testslicer.nslice, bins)
def __call__(self, metricValueIn, slicer, userPlotDict, fignum=None):
"""
Plot a histogram of metricValues (such as would come from a spatial slicer).
"""
# Adjust metric values by zeropoint or normVal, and use 'compressed' version of masked array.
plotDict = {}
plotDict.update(self.defaultPlotDict)
plotDict.update(userPlotDict)
metricValue = applyZPNorm(metricValueIn, plotDict)
metricValue = metricValue.compressed()
# Toss any NaNs or infs
metricValue = metricValue[np.isfinite(metricValue)]
# Determine percentile clipped X range, if set. (and xmin/max not set).
if plotDict['xMin'] is None and plotDict['xMax'] is None:
if plotDict['percentileClip']:
plotDict['xMin'], plotDict['xMax'] = percentileClipping(
metricValue, percentile=plotDict['percentileClip'])
# Set the histogram range values, to avoid cases of trying to histogram single-valued data.
# First we try to use the range specified by a user, if there is one. Then use the data if not.
# all of this only works if plotDict is not cumulative.
histRange = [plotDict['xMin'], plotDict['xMax']]
if histRange[0] is None:
histRange[0] = metricValue.min()
if histRange[1] is None:
histRange[1] = metricValue.max()
# Need to have some range of values on the histogram, or it will fail.
if histRange[0] == histRange[1]:
warnings.warn(
'Histogram range was single-valued; expanding default range.')
histRange[1] = histRange[0] + 1.0
# Set up the bins for the histogram. User specified 'bins' overrides 'binsize'.
# Note that 'bins' could be a single number or an array, simply passed to plt.histogram.
if plotDict['bins'] is not None:
bins = plotDict['bins']
elif plotDict['binsize'] is not None:
# If generating a cumulative histogram, want to use full range of data (but with given binsize).
# .. but if user set histRange to be wider than full range of data, then
# extend bins to cover this range, so we can make prettier plots.
if plotDict['cumulative']:
if plotDict['xMin'] is not None:
# Potentially, expand the range for the cumulative histogram.
bmin = np.min([metricValue.min(), plotDict['xMin']])
else:
bmin = metricValue.min()
if plotDict['xMax'] is not None:
bmax = np.max([metricValue.max(), plotDict['xMax']])
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax + plotDict['binsize'] / 2.0,
plotDict['binsize'])
# Otherwise, not cumulative so just use metric values, without potential expansion.
else:
bins = np.arange(histRange[0],
histRange[1] + plotDict['binsize'] / 2.0,
plotDict['binsize'])
# Catch edge-case where there is only 1 bin value
if bins.size < 2:
bins = np.arange(bins.min() - plotDict['binsize'] * 2.0,
bins.max() + plotDict['binsize'] * 2.0,
plotDict['binsize'])
else:
# If user did not specify bins or binsize, then we try to figure out a good number of bins.
bins = optimalBins(metricValue)
# Generate plots.
fig = plt.figure(fignum, figsize=plotDict['figsize'])
ax = fig.add_subplot(plotDict['subplot'])
# Check if any data falls within histRange, because otherwise histogram generation will fail.
if isinstance(bins, np.ndarray):
condition = ((metricValue >= bins.min()) &
(metricValue <= bins.max()))
else:
condition = ((metricValue >= histRange[0]) &
(metricValue <= histRange[1]))
plotValue = metricValue[condition]
if len(plotValue) == 0:
# No data is within histRange/bins. So let's just make a simple histogram anyway.
n, b, p = plt.hist(metricValue,
bins=50,
histtype='step',
cumulative=plotDict['cumulative'],
log=plotDict['logScale'],
label=plotDict['label'],
color=plotDict['color'])
else:
# There is data to plot, and we've already ensured histRange/bins are more than single value.
n, b, p = plt.hist(metricValue,
bins=bins,
range=histRange,
histtype='step',
log=plotDict['logScale'],
cumulative=plotDict['cumulative'],
label=plotDict['label'],
color=plotDict['color'])
hist_ylims = plt.ylim()
if n.max() > hist_ylims[1]:
plt.ylim(top=n.max())
if n.min() < hist_ylims[0] and not plotDict['logScale']:
plt.ylim(bottom=n.min())
# Fill in axes labels and limits.
# Option to use 'scale' to turn y axis into area or other value.
def mjrFormatter(y, pos):
if not isinstance(plotDict['scale'], numbers.Number):
raise ValueError(
'plotDict["scale"] must be a number to scale the y axis.')
return plotDict['yaxisformat'] % (y * plotDict['scale'])
ax.yaxis.set_major_formatter(FuncFormatter(mjrFormatter))
# Set optional x, y limits.
if 'xMin' in plotDict:
plt.xlim(left=plotDict['xMin'])
if 'xMax' in plotDict:
plt.xlim(right=plotDict['xMax'])
if 'yMin' in plotDict:
plt.ylim(bottom=plotDict['yMin'])
if 'yMax' in plotDict:
plt.ylim(top=plotDict['yMax'])
# Set/Add various labels.
plt.xlabel(plotDict['xlabel'], fontsize=plotDict['fontsize'])
plt.ylabel(plotDict['ylabel'], fontsize=plotDict['fontsize'])
plt.title(plotDict['title'])
if plotDict['labelsize'] is not None:
plt.tick_params(axis='x', labelsize=plotDict['labelsize'])
plt.tick_params(axis='y', labelsize=plotDict['labelsize'])
# Return figure number
return fig.number
def setupSlicer(self, simData, maps=None):
"""
Set up bins in slicer.
"""
if self.sliceColName is None:
raise Exception('sliceColName was not defined when slicer instantiated.')
sliceCol = simData[self.sliceColName]
# Set bin min/max values.
if self.binMin is None:
self.binMin = sliceCol.min()
if self.binMax is None:
self.binMax = sliceCol.max()
# Give warning if binMin = binMax, and do something at least slightly reasonable.
if self.binMin == self.binMax:
warnings.warn('binMin = binMax (maybe your data is single-valued?). '
'Increasing binMax by 1 (or 2*binsize, if binsize set).')
if self.binsize is not None:
self.binMax = self.binMax + 2 * self.binsize
else:
self.binMax = self.binMax + 1
# Set bins.
# Using binsize.
if self.binsize is not None:
if self.bins is not None:
warnings.warn('Both binsize and bins have been set; Using binsize %f only.' %(self.binsize))
self.bins = np.arange(self.binMin, self.binMax+self.binsize/2.0, float(self.binsize), 'float')
# Using bins value.
else:
# Bins was a sequence (np array or list)
if hasattr(self.bins, '__iter__'):
self.bins = np.sort(self.bins)
# Or bins was a single value.
else:
if self.bins is None:
self.bins = optimalBins(sliceCol, self.binMin, self.binMax)
nbins = int(self.bins)
self.binsize = (self.binMax - self.binMin) / float(nbins)
self.bins = np.arange(self.binMin, self.binMax+self.binsize/2.0, self.binsize, 'float')
# Set nbins to be one less than # of bins because last binvalue is RH edge only
self.nslice = len(self.bins) - 1
# Set slicePoint metadata.
self.slicePoints['sid'] = np.arange(self.nslice)
self.slicePoints['bins'] = self.bins
# Add metadata from maps.
self._runMaps(maps)
# Set up data slicing.
self.simIdxs = np.argsort(simData[self.sliceColName])
simFieldsSorted = np.sort(simData[self.sliceColName])
# "left" values are location where simdata == bin value
self.left = np.searchsorted(simFieldsSorted, self.bins[:-1], 'left')
self.left = np.concatenate((self.left, np.array([len(self.simIdxs),])))
# Set up _sliceSimData method for this class.
if self.cumulative:
@wraps(self._sliceSimData)
def _sliceSimData(islice):
"""
Slice simData on oneD sliceCol, to return relevant indexes for slicepoint.
"""
#this is the important part. The ids here define the pieces of data that get
#passed on to subsequent slicers
#cumulative version of 1D slicing
idxs = self.simIdxs[0:self.left[islice+1]]
return {'idxs':idxs,
'slicePoint':{'sid':islice, 'binLeft':self.bins[0], 'binRight':self.bins[islice+1]}}
setattr(self, '_sliceSimData', _sliceSimData)
else:
@wraps(self._sliceSimData)
def _sliceSimData(islice):
"""
Slice simData on oneD sliceCol, to return relevant indexes for slicepoint.
"""
idxs = self.simIdxs[self.left[islice]:self.left[islice+1]]
return {'idxs':idxs,
'slicePoint':{'sid':islice, 'binLeft':self.bins[islice], 'binRight':self.bins[islice+1]}}
setattr(self, '_sliceSimData', _sliceSimData)
def setupSlicer(self, simData, maps=None):
"""
Set up bins in slicer.
"""
if self.sliceColName is None:
raise Exception(
'sliceColName was not defined when slicer instantiated.')
sliceCol = simData[self.sliceColName]
# Set bin min/max values.
if self.binMin is None:
self.binMin = sliceCol.min()
if self.binMax is None:
self.binMax = sliceCol.max()
# Give warning if binMin = binMax, and do something at least slightly reasonable.
if self.binMin == self.binMax:
warnings.warn(
'binMin = binMax (maybe your data is single-valued?). '
'Increasing binMax by 1 (or 2*binsize, if binsize set).')
if self.binsize is not None:
self.binMax = self.binMax + 2 * self.binsize
else:
self.binMax = self.binMax + 1
# Set bins.
# Using binsize.
if self.binsize is not None:
if self.bins is not None:
warnings.warn(
'Both binsize and bins have been set; Using binsize %f only.'
% (self.binsize))
self.bins = np.arange(self.binMin,
self.binMax + self.binsize / 2.0,
float(self.binsize), 'float')
# Using bins value.
else:
# Bins was a sequence (np array or list)
if hasattr(self.bins, '__iter__'):
self.bins = np.sort(self.bins)
# Or bins was a single value.
else:
if self.bins is None:
self.bins = optimalBins(sliceCol, self.binMin, self.binMax)
nbins = int(self.bins)
self.binsize = (self.binMax - self.binMin) / float(nbins)
self.bins = np.arange(self.binMin,
self.binMax + self.binsize / 2.0,
self.binsize, 'float')
# Set nbins to be one less than # of bins because last binvalue is RH edge only
self.nslice = len(self.bins) - 1
# Set slicePoint metadata.
self.slicePoints['sid'] = np.arange(self.nslice)
self.slicePoints['bins'] = self.bins
# Add metadata from maps.
self._runMaps(maps)
# Set up data slicing.
self.simIdxs = np.argsort(simData[self.sliceColName])
simFieldsSorted = np.sort(simData[self.sliceColName])
# "left" values are location where simdata == bin value
self.left = np.searchsorted(simFieldsSorted, self.bins[:-1], 'left')
self.left = np.concatenate((self.left, np.array([
len(self.simIdxs),
])))
# Set up _sliceSimData method for this class.
if self.cumulative:
@wraps(self._sliceSimData)
def _sliceSimData(islice):
"""
Slice simData on oneD sliceCol, to return relevant indexes for slicepoint.
"""
#this is the important part. The ids here define the pieces of data that get
#passed on to subsequent slicers
#cumulative version of 1D slicing
idxs = self.simIdxs[0:self.left[islice + 1]]
return {
'idxs': idxs,
'slicePoint': {
'sid': islice,
'binLeft': self.bins[0],
'binRight': self.bins[islice + 1]
}
}
setattr(self, '_sliceSimData', _sliceSimData)
else:
@wraps(self._sliceSimData)
def _sliceSimData(islice):
"""
Slice simData on oneD sliceCol, to return relevant indexes for slicepoint.
"""
idxs = self.simIdxs[self.left[islice]:self.left[islice + 1]]
return {
'idxs': idxs,
'slicePoint': {
'sid': islice,
'binLeft': self.bins[islice],
'binRight': self.bins[islice + 1]
}
}
setattr(self, '_sliceSimData', _sliceSimData)
def __call__(self, metricValueIn, slicer, userPlotDict, fignum=None):
"""
Plot a histogram of metricValues (such as would come from a spatial slicer).
"""
# Adjust metric values by zeropoint or normVal, and use 'compressed' version of masked array.
plotDict = {}
plotDict.update(self.defaultPlotDict)
plotDict.update(userPlotDict)
if plotDict['zp'] is not None:
metricValue = metricValueIn.compressed() - plotDict['zp']
elif plotDict['normVal'] is not None:
metricValue = metricValueIn.compressed() / plotDict['normVal']
else:
metricValue = metricValueIn.compressed()
# Determine percentile clipped X range, if set. (and xmin/max not set).
if plotDict['xMin'] is None and plotDict['xMax'] is None:
if plotDict['percentileClip']:
plotDict['xMin'], plotDict['xMax'] = percentileClipping(metricValue,
percentile=plotDict['percentileClip'])
# Determine range for histogram. Note that if xmin/max are None, this will just be [None, None].
histRange = [plotDict['xMin'], plotDict['xMax']]
# Should we use log scale on y axis? (if 'auto')
if plotDict['logScale'] == 'auto':
plotDict['logScale'] = False
if np.min(histRange) > 0:
if (np.log10(np.max(histRange) - np.log10(np.min(histRange))) > 3):
plotDict['logScale'] = True
# If binsize was specified, set up an array of bins for the histogram.
if plotDict['binsize'] is not None:
# If generating cumulative histogram, want to use full range of data (but with given binsize).
# .. but if user set histRange to be wider than full range of data, then
# extend bins to cover this range, so we can make prettier plots.
if plotDict['cumulative'] is not False:
if histRange[0] is not None:
bmin = np.min([metricValue.min(), histRange[0]])
else:
bmin = metricValue.min()
if histRange[1] is not None:
bmax = np.max([metricValue.max(), histRange[1]])
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax + plotDict['binsize'] / 2.0, plotDict['binsize'])
# Catch edge-case where there is only 1 bin value
if bins.size < 2:
bins = np.arange(bmin, bmax + plotDict['binsize'], plotDict['binsize'])
# Else try to set up bins using min/max values if specified, or full data range.
else:
if histRange[0] is not None:
bmin = histRange[0]
else:
bmin = metricValue.min()
if histRange[1] is not None:
bmax = histRange[1]
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax + plotDict['binsize'], plotDict['binsize'])
# Otherwise, determine number of bins, if neither 'bins' or 'binsize' were specified.
else:
if plotDict['bins'] is None:
bins = optimalBins(metricValue)
else:
bins = plotDict['bins']
# Generate plots.
fig = plt.figure(fignum)
if plotDict['cumulative'] is not False:
# If cumulative is set, generate histogram without using histRange (to use full range of data).
n, b, p = plt.hist(metricValue, bins=bins, histtype='step', log=plotDict['logScale'],
cumulative=plotDict['cumulative'], label=plotDict['label'],
color=plotDict['color'])
else:
# Plot non-cumulative histogram.
# First, test if data falls within histRange, because otherwise histogram generation will fail.
if np.min(histRange) is not None:
if (histRange[0] is None) and (histRange[1] is not None):
condition = (metricValue <= histRange[1])
elif (histRange[1] is None) and (histRange[0] is not None):
condition = (metricValue >= histRange[0])
else:
condition = ((metricValue >= histRange[0]) & (metricValue <= histRange[1]))
plotValue = metricValue[condition]
else:
plotValue = metricValue
# If there is only one value to histogram, need to set histRange, otherwise histogram will fail.
rangePad = 20.
if (np.unique(plotValue).size == 1) & (np.min(histRange) is None):
warnings.warn('Only one metric value, making a guess at a good histogram range.')
histRange = [plotValue.min() - rangePad, plotValue.max() + rangePad]
if (plotValue.min() >= 0) & (histRange[0] < 0):
# Reset histogram range if it went below 0.
histRange[0] = 0.
if 'binsize' in plotDict:
bins = np.arange(histRange[0], histRange[1], plotDict['binsize'])
else:
bins = np.arange(histRange[0], histRange[1], (histRange[1] - histRange[0]) / 50.)
# If there is no data within the histogram range, we will generate an empty plot.
# If there is data, make the histogram.
if plotValue.size > 0:
# Generate histogram.
if np.min(histRange) is None:
histRange = None
n, b, p = plt.hist(plotValue, bins=bins, histtype='step', log=plotDict['logScale'],
cumulative=plotDict['cumulative'], range=histRange,
label=plotDict['label'], color=plotDict['color'])
# Fill in axes labels and limits.
# Option to use 'scale' to turn y axis into area or other value.
def mjrFormatter(y, pos):
return plotDict['yaxisformat'] % (y * plotDict['scale'])
ax = plt.gca()
ax.yaxis.set_major_formatter(FuncFormatter(mjrFormatter))
# Set y limits.
if 'yMin' in plotDict:
if plotDict['yMin'] is not None:
plt.ylim(ymin=plotDict['yMin'])
else:
# There is a bug in histype='step' that can screw up the ylim.
# Comes up when running allSlicer.Cfg.py
try:
if plt.axis()[2] == max(n):
plt.ylim([n.min(), n.max()])
except UnboundLocalError:
# This happens if we were generating an empty plot (no histogram).
# But in which case, the above error was probably not relevant. So skip it.
pass
if 'yMax' in plotDict:
plt.ylim(ymax=plotDict['yMax'])
# Set x limits.
if plotDict['xMin'] is not None:
plt.xlim(xmin=plotDict['xMin'])
if plotDict['xMax'] is not None:
plt.xlim(xmax=plotDict['xMax'])
# Set/Add various labels.
plt.xlabel(plotDict['xlabel'], fontsize=plotDict['fontsize'])
plt.ylabel(plotDict['ylabel'], fontsize=plotDict['fontsize'])
plt.title(plotDict['title'])
if plotDict['labelsize'] is not None:
plt.tick_params(axis='x', labelsize=plotDict['labelsize'])
plt.tick_params(axis='y', labelsize=plotDict['labelsize'])
# Return figure number
return fig.number
def plotHistogram(self, metricValueIn, title=None, xlabel=None, units=None, ylabel=None,
fignum=None, label=None, addLegend=False, legendloc='upper left',
bins=None, binsize=None, cumulative=False,
xMin=None, xMax=None, yMin=None, yMax=None,
logScale='auto',
scale=1.0, yaxisformat='%.3f', color='b',
zp=None, normVal=None, percentileClip=None, **kwargs):
"""Plot a histogram of metricValue, labelled by metricLabel.
title = the title for the plot (default None)
fignum = the figure number to use (default None - will generate new figure)
label = the label to use in the figure legend (default None)
addLegend = flag for whether or not to add a legend (default False)
legendloc = location for legend (default 'upper left')
bins = bins for histogram (numpy array or # of bins)
binsize = size of bins to use. Will override "bins" if both are set.
(default None, uses Freedman-Diaconis rule to set binsize)
cumulative = make histogram cumulative (default False) (<0 value makes cumulative the 'less than' way).
xMin/Max = histogram range (default None, set by matplotlib hist)
yMin/Max = histogram y range
scale = scale y axis by 'scale' (i.e. to translate to area)
zp = zeropoing to subtract off metricVals
normVal = normalization value to divide metric values by (overrides zp).
"""
# Adjust metric values by zeropoint or normVal, and use 'compressed' version of masked array.
if zp:
metricValue = metricValueIn.compressed() - zp
elif normVal:
metricValue = metricValueIn.compressed()/normVal
else:
metricValue = metricValueIn.compressed()
# Determine percentile clipped X range, if set. (and xmin/max not set).
if xMin is None and xMax is None:
if percentileClip:
xMin, xMax = percentileClipping(metricValue, percentile=percentileClip)
# Determine range for histogram. Note that if xmin/max are None, this will just be [None, None].
histRange = [xMin, xMax]
# Should we use log scale on y axis? (if 'auto')
if logScale == 'auto':
logScale = False
if np.min(histRange) > 0:
if (np.log10(np.max(histRange)-np.log10(np.min(histRange))) > 3 ):
logScale = True
# If binsize was specified, set up an array of bins for the histogram.
if binsize is not None:
# If generating cumulative histogram, want to use full range of data (but with given binsize).
# .. but if user set histRange to be wider than full range of data, then
# extend bins to cover this range, so we can make prettier plots.
if cumulative is not False:
if histRange[0] is not None:
bmin = np.min([metricValue.min(), histRange[0]])
else:
bmin = metricValue.min()
if histRange[1] is not None:
bmax = np.max([metricValue.max(), histRange[1]])
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax+binsize/2.0, binsize)
# Else try to set up bins using min/max values if specified, or full data range.
else:
if histRange[0] is not None:
bmin = histRange[0]
else:
bmin = metricValue.min()
if histRange[1] is not None:
bmax = histRange[1]
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax+binsize/2.0, binsize)
# Otherwise, determine number of bins, if neither 'bins' or 'binsize' were specified.
else:
if bins is None:
bins = optimalBins(metricValue)
# Generate plots.
fig = plt.figure(fignum)
if cumulative is not False:
# If cumulative is set, generate histogram without using histRange (to use full range of data).
n, b, p = plt.hist(metricValue, bins=bins, histtype='step', log=logScale,
cumulative=cumulative, label=label, color=color)
else:
# Plot non-cumulative histogram.
# First, test if data falls within histRange, because otherwise histogram generation will fail.
if np.min(histRange) is not None:
if (histRange[0] is None) and (histRange[1] is not None):
condition = (metricValue <= histRange[1])
elif (histRange[1] is None) and (histRange[0] is not None):
condition = (metricValue >= histRange[0])
else:
condition = ((metricValue >= histRange[0]) & (metricValue <= histRange[1]))
plotValue = metricValue[condition]
else:
plotValue = metricValue
# If there is only one value to histogram, need to set histRange, otherwise histogram will fail.
rangePad = 20.
if (np.unique(plotValue).size == 1) & (np.min(histRange) is None):
warnings.warn('Only one metric value, making a guess at a good histogram range.')
histRange = [plotValue.min()-rangePad, plotValue.max()+rangePad]
if (plotValue.min() >= 0) & (histRange[0] < 0):
# Reset histogram range if it went below 0.
histRange[0] = 0.
bins=np.arange(histRange[0], histRange[1], binsize)
# If there is no data within the histogram range, we will generate an empty plot.
# If there is data, make the histogram.
if plotValue.size > 0:
# Generate histogram.
if np.min(histRange) is None:
histRange = None
n, b, p = plt.hist(plotValue, bins=bins, histtype='step', log=logScale,
cumulative=cumulative, range=histRange, label=label, color=color)
# Fill in axes labels and limits.
# Option to use 'scale' to turn y axis into area or other value.
def mjrFormatter(y, pos):
return yaxisformat % (y * scale)
ax = plt.gca()
ax.yaxis.set_major_formatter(FuncFormatter(mjrFormatter))
# Set y limits.
if yMin is not None:
plt.ylim(ymin=yMin)
else:
# There is a bug in histype='step' that can screw up the ylim. Comes up when running allSlicer.Cfg.py
try:
if plt.axis()[2] == max(n):
plt.ylim([n.min(),n.max()])
except UnboundLocalError:
# This happens if we were generating an empty plot (no histogram).
# But in which case, the above error was probably not relevant. So skip it.
pass
if yMax is not None:
plt.ylim(ymax=yMax)
# Set x limits.
if xMin is not None:
plt.xlim(xmin=xMin)
if xMax is not None:
plt.xlim(xmax=xMax)
# Set/Add various labels.
if not xlabel:
xlabel = units
if xlabel is not None:
plt.xlabel(xlabel)
if ylabel is not None:
plt.ylabel(ylabel)
if addLegend:
plt.legend(fancybox=True, prop={'size':'smaller'}, loc=legendloc)
if title!=None:
plt.title(title)
# Return figure number (so we can reuse this if desired).
return fig.number
def __call__(self, metricValueIn, slicer, userPlotDict, fignum=None):
"""
Plot a histogram of metricValues (such as would come from a spatial slicer).
"""
# Adjust metric values by zeropoint or normVal, and use 'compressed' version of masked array.
plotDict = {}
plotDict.update(self.defaultPlotDict)
plotDict.update(userPlotDict)
if plotDict['zp'] is not None:
metricValue = metricValueIn.compressed() - plotDict['zp']
elif plotDict['normVal'] is not None:
metricValue = metricValueIn.compressed() / plotDict['normVal']
else:
metricValue = metricValueIn.compressed()
# Determine percentile clipped X range, if set. (and xmin/max not set).
if plotDict['xMin'] is None and plotDict['xMax'] is None:
if plotDict['percentileClip']:
plotDict['xMin'], plotDict['xMax'] = percentileClipping(metricValue,
percentile=plotDict['percentileClip'])
# Determine range for histogram. Note that if xmin/max are None, this will just be [None, None].
histRange = [plotDict['xMin'], plotDict['xMax']]
# Should we use log scale on y axis? (if 'auto')
if plotDict['logScale'] == 'auto':
plotDict['logScale'] = False
if np.min(histRange) > 0:
if (np.log10(np.max(histRange) - np.log10(np.min(histRange))) > 3):
plotDict['logScale'] = True
# If binsize was specified, set up an array of bins for the histogram.
if plotDict['binsize'] is not None:
# If generating cumulative histogram, want to use full range of data (but with given binsize).
# .. but if user set histRange to be wider than full range of data, then
# extend bins to cover this range, so we can make prettier plots.
if plotDict['cumulative'] is not False:
if histRange[0] is not None:
bmin = np.min([metricValue.min(), histRange[0]])
else:
bmin = metricValue.min()
if histRange[1] is not None:
bmax = np.max([metricValue.max(), histRange[1]])
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax + plotDict['binsize'] / 2.0, plotDict['binsize'])
# Catch edge-case where there is only 1 bin value
if bins.size < 2:
bins = np.arange(bmin, bmax + plotDict['binsize'], plotDict['binsize'])
# Else try to set up bins using min/max values if specified, or full data range.
else:
if histRange[0] is not None:
bmin = histRange[0]
else:
bmin = metricValue.min()
if histRange[1] is not None:
bmax = histRange[1]
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax + plotDict['binsize'], plotDict['binsize'])
# Otherwise, determine number of bins, if neither 'bins' or 'binsize' were specified.
else:
if plotDict['bins'] is None:
bins = optimalBins(metricValue)
else:
bins = plotDict['bins']
# Generate plots.
fig = plt.figure(fignum)
if plotDict['cumulative'] is not False:
# If cumulative is set, generate histogram without using histRange (to use full range of data).
n, b, p = plt.hist(metricValue, bins=bins, histtype='step', log=plotDict['logScale'],
cumulative=plotDict['cumulative'], label=plotDict['label'],
color=plotDict['color'])
else:
# Plot non-cumulative histogram.
# First, test if data falls within histRange, because otherwise histogram generation will fail.
if np.min(histRange) is not None:
if (histRange[0] is None) and (histRange[1] is not None):
condition = (metricValue <= histRange[1])
elif (histRange[1] is None) and (histRange[0] is not None):
condition = (metricValue >= histRange[0])
else:
condition = ((metricValue >= histRange[0]) & (metricValue <= histRange[1]))
plotValue = metricValue[condition]
else:
plotValue = metricValue
# If there is only one value to histogram, need to set histRange, otherwise histogram will fail.
rangePad = 20.
if (np.unique(plotValue).size == 1) & (np.min(histRange) is None):
warnings.warn('Only one metric value, making a guess at a good histogram range.')
histRange = [plotValue.min() - rangePad, plotValue.max() + rangePad]
if (plotValue.min() >= 0) & (histRange[0] < 0):
# Reset histogram range if it went below 0.
histRange[0] = 0.
if 'binsize' in plotDict:
bins = np.arange(histRange[0], histRange[1], plotDict['binsize'])
else:
bins = np.arange(histRange[0], histRange[1], (histRange[1] - histRange[0]) / 50.)
# If there is no data within the histogram range, we will generate an empty plot.
# If there is data, make the histogram.
if plotValue.size > 0:
# Generate histogram.
if np.min(histRange) is None:
histRange = None
n, b, p = plt.hist(plotValue, bins=bins, histtype='step', log=plotDict['logScale'],
cumulative=plotDict['cumulative'], range=histRange,
label=plotDict['label'], color=plotDict['color'])
# Fill in axes labels and limits.
# Option to use 'scale' to turn y axis into area or other value.
def mjrFormatter(y, pos):
return plotDict['yaxisformat'] % (y * plotDict['scale'])
ax = plt.gca()
ax.yaxis.set_major_formatter(FuncFormatter(mjrFormatter))
# Set y limits.
if 'yMin' in plotDict:
if plotDict['yMin'] is not None:
plt.ylim(ymin=plotDict['yMin'])
else:
# There is a bug in histype='step' that can screw up the ylim.
# Comes up when running allSlicer.Cfg.py
try:
if plt.axis()[2] == max(n):
plt.ylim([n.min(), n.max()])
except UnboundLocalError:
# This happens if we were generating an empty plot (no histogram).
# But in which case, the above error was probably not relevant. So skip it.
pass
if 'yMax' in plotDict:
plt.ylim(ymax=plotDict['yMax'])
# Set x limits.
if plotDict['xMin'] is not None:
plt.xlim(xmin=plotDict['xMin'])
if plotDict['xMax'] is not None:
plt.xlim(xmax=plotDict['xMax'])
# Set/Add various labels.
plt.xlabel(plotDict['xlabel'], fontsize=plotDict['fontsize'])
plt.ylabel(plotDict['ylabel'], fontsize=plotDict['fontsize'])
plt.title(plotDict['title'])
if plotDict['labelsize'] is not None:
plt.tick_params(axis='x', labelsize=plotDict['labelsize'])
plt.tick_params(axis='y', labelsize=plotDict['labelsize'])
# Return figure number
return fig.number
def __call__(self, metricValueIn, slicer, userPlotDict, fignum=None):
"""
Plot a histogram of metricValues (such as would come from a spatial slicer).
"""
# Adjust metric values by zeropoint or normVal, and use 'compressed' version of masked array.
plotDict = {}
plotDict.update(self.defaultPlotDict)
plotDict.update(userPlotDict)
metricValue = applyZPNorm(metricValueIn, plotDict)
metricValue = metricValue.compressed()
# Toss any NaNs or infs
metricValue = metricValue[np.isfinite(metricValue)]
# Determine percentile clipped X range, if set. (and xmin/max not set).
if plotDict['xMin'] is None and plotDict['xMax'] is None:
if plotDict['percentileClip']:
plotDict['xMin'], plotDict['xMax'] = percentileClipping(metricValue,
percentile=plotDict['percentileClip'])
# Set the histogram range values, to avoid cases of trying to histogram single-valued data.
# First we try to use the range specified by a user, if there is one. Then use the data if not.
# all of this only works if plotDict is not cumulative.
histRange = [plotDict['xMin'], plotDict['xMax']]
if histRange[0] is None:
histRange[0] = metricValue.min()
if histRange[1] is None:
histRange[1] = metricValue.max()
# Need to have some range of values on the histogram, or it will fail.
if histRange[0] == histRange[1]:
warnings.warn('Histogram range was single-valued; expanding default range.')
histRange[1] = histRange[0] + 1.0
# Set up the bins for the histogram. User specified 'bins' overrides 'binsize'.
# Note that 'bins' could be a single number or an array, simply passed to plt.histogram.
if plotDict['bins'] is not None:
bins = plotDict['bins']
elif plotDict['binsize'] is not None:
# If generating a cumulative histogram, want to use full range of data (but with given binsize).
# .. but if user set histRange to be wider than full range of data, then
# extend bins to cover this range, so we can make prettier plots.
if plotDict['cumulative']:
if plotDict['xMin'] is not None:
# Potentially, expand the range for the cumulative histogram.
bmin = np.min([metricValue.min(), plotDict['xMin']])
else:
bmin = metricValue.min()
if plotDict['xMax'] is not None:
bmax = np.max([metricValue.max(), plotDict['xMax']])
else:
bmax = metricValue.max()
bins = np.arange(bmin, bmax + plotDict['binsize'] / 2.0, plotDict['binsize'])
# Otherwise, not cumulative so just use metric values, without potential expansion.
else:
bins = np.arange(histRange[0], histRange[1] + plotDict['binsize'] / 2.0, plotDict['binsize'])
# Catch edge-case where there is only 1 bin value
if bins.size < 2:
bins = np.arange(bins.min() - plotDict['binsize'] * 2.0,
bins.max() + plotDict['binsize'] * 2.0, plotDict['binsize'])
else:
# If user did not specify bins or binsize, then we try to figure out a good number of bins.
bins = optimalBins(metricValue)
# Generate plots.
fig = plt.figure(fignum, figsize=plotDict['figsize'])
ax = fig.add_subplot(plotDict['subplot'])
# Check if any data falls within histRange, because otherwise histogram generation will fail.
if isinstance(bins, np.ndarray):
condition = ((metricValue >= bins.min()) & (metricValue <= bins.max()))
else:
condition = ((metricValue >= histRange[0]) & (metricValue <= histRange[1]))
plotValue = metricValue[condition]
if len(plotValue) == 0:
# No data is within histRange/bins. So let's just make a simple histogram anyway.
n, b, p = plt.hist(metricValue, bins=50, histtype='step', cumulative=plotDict['cumulative'],
log=plotDict['logScale'], label=plotDict['label'],
color=plotDict['color'])
else:
# There is data to plot, and we've already ensured histRange/bins are more than single value.
n, b, p = plt.hist(metricValue, bins=bins, range=histRange,
histtype='step', log=plotDict['logScale'],
cumulative=plotDict['cumulative'],
label=plotDict['label'], color=plotDict['color'])
hist_ylims = plt.ylim()
if n.max() > hist_ylims[1]:
plt.ylim(ymax = n.max())
if n.min() < hist_ylims[0] and not plotDict['logScale']:
plt.ylim(ymin = n.min())
# Fill in axes labels and limits.
# Option to use 'scale' to turn y axis into area or other value.
def mjrFormatter(y, pos):
if not isinstance(plotDict['scale'], numbers.Number):
raise ValueError('plotDict["scale"] must be a number to scale the y axis.')
return plotDict['yaxisformat'] % (y * plotDict['scale'])
ax.yaxis.set_major_formatter(FuncFormatter(mjrFormatter))
# Set optional x, y limits.
if 'xMin' in plotDict:
plt.xlim(xmin=plotDict['xMin'])
if 'xMax' in plotDict:
plt.xlim(xmax=plotDict['xMax'])
if 'yMin' in plotDict:
plt.ylim(ymin=plotDict['yMin'])
if 'yMax' in plotDict:
plt.ylim(ymax=plotDict['yMax'])
# Set/Add various labels.
plt.xlabel(plotDict['xlabel'], fontsize=plotDict['fontsize'])
plt.ylabel(plotDict['ylabel'], fontsize=plotDict['fontsize'])
plt.title(plotDict['title'])
if plotDict['labelsize'] is not None:
plt.tick_params(axis='x', labelsize=plotDict['labelsize'])
plt.tick_params(axis='y', labelsize=plotDict['labelsize'])
# Return figure number
return fig.number
