def _analyzeTrackway(self, trackway, sitemap):
"""
@param trackway:
@param sitemap:
@return:
"""
self.entries = dict(lp=[], rp=[], lm=[], rm=[])
super(SimulationCsvExporterStage, self)._analyzeTrackway(
trackway=trackway,
sitemap=sitemap
)
csv = CsvWriter(
autoIndexFieldName='Index',
fields=[
'lp_name', 'lp_uid', 'lp_x', 'lp_dx', 'lp_y', 'lp_dy',
'rp_name', 'rp_uid', 'rp_x', 'rp_dx', 'rp_y', 'rp_dy',
'lm_name', 'lm_uid', 'lm_x', 'lm_dx', 'lm_y', 'lm_dy',
'rm_name', 'rm_uid', 'rm_x', 'rm_dx', 'rm_y', 'rm_dy'
]
)
length = max(
len(self.entries['lp']),
len(self.entries['rp']),
len(self.entries['lm']),
len(self.entries['rm']),
)
for index in range(length):
items = []
for limb_id, entries in self.entries.items():
if index < len(entries):
items += entries[index].items()
else:
items += self._create_entry(limb_id).items()
csv.addRow(dict(items))
path = self.owner.settings.fetch('EXPORT_DATA_PATH')
if path is None:
path = self.owner.getLocalPath('Simulation', 'data', isFile=True)
path = FileUtils.makeFilePath(path, trackway.name, 'source.csv')
directory = os.path.dirname(path)
if not os.path.exists(directory):
os.makedirs(directory)
if csv.save(path):
print('[SAVED]:', path)
else:
print('[ERROR]: Unable to save CSV at "{}"'.format(path))
def _addQuartileEntry(self, label, trackway, data):
if not data or len(data) < 4:
return
if label not in self._quartileStats:
csv = CsvWriter()
csv.path = self.getPath(
'%s-Quartiles.csv' % label.replace(' ', '-'),
isFile=True)
csv.autoIndexFieldName = 'Index'
csv.addFields(
('name', 'Name'),
('normality', 'Normality'),
('unweightedNormality', 'Unweighted Normality'),
('unweightedLowerBound', 'Unweighted Lower Bound'),
('unweightedLowerQuart', 'Unweighted Lower Quartile'),
('unweightedMedian', 'Unweighted Median'),
('unweightedUpperQuart', 'Unweighted Upper Quartile'),
('unweightedUpperBound', 'Unweighted Upper Bound'),
('lowerBound', 'Lower Bound'),
('lowerQuart', 'Lower Quartile'),
('median', 'Median'),
('upperQuart', 'Upper Quartile'),
('upperBound', 'Upper Bound'),
('diffLowerBound', 'Diff Lower Bound'),
('diffLowerQuart', 'Diff Lower Quartile'),
('diffMedian', 'Diff Median'),
('diffUpperQuart', 'Diff Upper Quartile'),
('diffUpperBound', 'Diff Upper Bound') )
self._quartileStats[label] = csv
csv = self._quartileStats[label]
dd = mstats.density.Distribution(data)
unweighted = mstats.density.boundaries.unweighted_two(dd)
weighted = mstats.density.boundaries.weighted_two(dd)
#-----------------------------------------------------------------------
# PLOT DENSITY
# Create a density plot for each value
p = MultiScatterPlot(
title='%s %s Density Distribution' % (trackway.name, label),
xLabel=label,
yLabel='Probability (AU)')
x_values = mstats.density.ops.adaptive_range(dd, 10.0)
y_values = dd.probabilities_at(x_values=x_values)
p.addPlotSeries(
line=True,
markers=False,
label='Weighted',
color='blue',
data=zip(x_values, y_values)
)
temp = mstats.density.create_distribution(
dd.naked_measurement_values(raw=True)
)
x_values = mstats.density.ops.adaptive_range(dd, 10.0)
y_values = dd.probabilities_at(x_values=x_values)
p.addPlotSeries(
line=True,
markers=False,
label='Unweighted',
color='red',
data=zip(x_values, y_values)
)
if label not in self._densityPlots:
self._densityPlots[label] = []
self._densityPlots[label].append(
p.save(self.getTempFilePath(extension='pdf')))
#-----------------------------------------------------------------------
# NORMALITY
# Calculate the normality of the weighted and unweighted
# distributions as a test against how well they conform to
# the Normal distribution calculated from the unweighted data.
#
# The unweighted Normality test uses a basic bandwidth detection
# algorithm to create a uniform Gaussian kernel to populate the
# DensityDistribution. It is effectively a density kernel
# estimation, but is aggressive in selecting the bandwidth to
# prevent over-smoothing multi-modal distributions.
if len(data) < 8:
normality = -1.0
unweightedNormality = -1.0
else:
result = NumericUtils.getMeanAndDeviation(data)
mean = result.raw
std = result.rawUncertainty
normality = mstats.density.ops.overlap(
dd,
mstats.density.create_distribution([mean], [std])
)
rawValues = []
for value in data:
rawValues.append(value.value)
ddRaw = mstats.density.create_distribution(rawValues)
unweightedNormality = mstats.density.ops.overlap(
ddRaw,
mstats.density.create_distribution([mean], [std])
)
# Prevent divide by zero
unweighted = [
0.00001 if NumericUtils.equivalent(x, 0) else x
for x in unweighted
]
csv.addRow({
'index':trackway.index,
'name':trackway.name,
'normality':normality,
'unweightedNormality':unweightedNormality,
'unweightedLowerBound':unweighted[0],
'unweightedLowerQuart':unweighted[1],
'unweightedMedian' :unweighted[2],
'unweightedUpperQuart':unweighted[3],
'unweightedUpperBound':unweighted[4],
'lowerBound':weighted[0],
'lowerQuart':weighted[1],
'median' :weighted[2],
'upperQuart':weighted[3],
'upperBound':weighted[4],
'diffLowerBound':abs(unweighted[0] - weighted[0])/unweighted[0],
'diffLowerQuart':abs(unweighted[1] - weighted[1])/unweighted[1],
'diffMedian' :abs(unweighted[2] - weighted[2])/unweighted[2],
'diffUpperQuart':abs(unweighted[3] - weighted[3])/unweighted[3],
'diffUpperBound':abs(unweighted[4] - weighted[4])/unweighted[4]
})
class SimpleGaugeStage(CurveOrderedAnalysisStage):
"""A class for..."""
#===============================================================================
# C L A S S
_GAUGE_DATA_NT = namedtuple('GAUGE_DATA_NT', ['abs', 'width', 'pace', 'stride'])
#_______________________________________________________________________________
def __init__(self, key, owner, **kwargs):
"""Creates a new instance of SimpleGaugeStage."""
super(SimpleGaugeStage, self).__init__(
key, owner,
label='Simple Track Gauge',
**kwargs)
self._paths = []
self._errorTracks = []
self._ignoreTracks = []
self._trackwayGauges = None
self._count = 0
self._trackwayCsv = None
#===============================================================================
# P R O T E C T E D
#_______________________________________________________________________________
def _preAnalyze(self):
self._trackwayGauges = self._GAUGE_DATA_NT([], [], [], [])
self._paths = []
self._errorTracks = []
self._ignoreTracks = []
self._count = 0
self._trackwayCsv = CsvWriter(
path=self.getPath('Trackway-Gauge-Averages.csv'),
autoIndexFieldName='Index',
fields=[
('name', 'Name'),
('count', 'Pes Count'),
('abs', 'Absolute'),
('absUnc', 'Abs Unc'),
('stride', 'Stride Norm'),
('strideUnc', 'Stride Unc'),
('pace', 'Pace Norm'),
('paceUnc', 'Pace Unc'),
('width', 'Width Norm'),
('widthUnc', 'Width Unc')])
#_______________________________________________________________________________
def _analyzeSitemap(self, sitemap):
self._createDrawing(sitemap, 'SIMPLE-GAUGE', 'Simple-Gauge')
super(SimpleGaugeStage, self)._analyzeSitemap(sitemap)
self._saveDrawing(sitemap)
#_______________________________________________________________________________
def _analyzeTrackway(self, trackway, sitemap):
bundle = self.owner.getSeriesBundle(trackway)
if not bundle.isReady:
# Skip trackways that have incomplete series
return
data = self._collectGaugeData(bundle, trackway, sitemap)
if data['gauges'].abs:
self._processGaugeData(bundle, trackway, data)
#_______________________________________________________________________________
def _collectGaugeData(self, bundle, trackway, sitemap):
""" Collects the trackway gauge data by generating projections for each series and then
iterating over every track in the trackway and extracting the gauge information from
the CurveSeries projection data.
@param bundle: TrackSeriesBundle
@param trackway: Tracks_Trackway
@param sitemap: Tracks_Sitemap
@return: dict """
trackway.cache.set('data', {'points':[], 'gauges':self._GAUGE_DATA_NT([], [], [], [])})
for key, series in bundle.items():
series.cache.set('referenceWidth', series.averageTrackWidth)
if series.count < 2:
continue
curve = CurveSeries(stage=self, series=series)
try:
curve.compute()
except Exception as err:
self.logger.writeError([
'[ERROR]: Failed to compute track curve projection',
'TRACKWAY: %s' % trackway.name,
'SERIES: %s[%s]' % (series.fingerprint, series.count) ], err)
raise
curve.draw(sitemap.cache.get('drawing'), drawPairs=False)
series.cache.set('curve', curve)
super(SimpleGaugeStage, self)._analyzeTrackway(trackway=trackway, sitemap=sitemap)
for key, series in bundle.items():
series.cache.remove('referenceWidth')
return trackway.cache.extract('data')
#_______________________________________________________________________________
def _processGaugeData(self, bundle, trackway, data):
pesCount = bundle.leftPes.count + bundle.rightPes.count
record = {'name':trackway.name, 'count':pesCount}
gaugeData = data['gauges']
try:
value = NumericUtils.getWeightedMeanAndDeviation(gaugeData.abs)
record['abs'] = value.value
record['absUnc'] = value.uncertainty
self._trackwayGauges.abs.append((pesCount, value))
except ZeroDivisionError:
return
widthValue = NumericUtils.getWeightedMeanAndDeviation(gaugeData.width)
record['width'] = widthValue.value
record['widthUnc'] = widthValue.uncertainty
self._trackwayGauges.width.append((pesCount, widthValue))
if gaugeData.pace:
value = NumericUtils.getWeightedMeanAndDeviation(gaugeData.pace)
record['pace'] = value.value
record['paceUnc'] = value.uncertainty
self._trackwayGauges.pace.append((pesCount, value))
else:
record['pace'] = ''
record['paceUnc'] = ''
if gaugeData.stride:
value = NumericUtils.getWeightedMeanAndDeviation(gaugeData.stride)
record['stride'] = value.value
record['strideUnc'] = value.uncertainty
self._trackwayGauges.stride.append((pesCount, value))
else:
record['stride'] = ''
record['strideUnc'] = ''
self._trackwayCsv.addRow(record)
plot = ScatterPlot(
data=data['points'],
title='%s Width-Normalized Gauges (%s)' % (trackway.name, widthValue.label),
xLabel='Track Position (m)',
yLabel='Gauge (AU)')
self._paths.append(plot.save(self.getTempFilePath(extension='pdf')))
analysisTrackway = trackway.getAnalysisPair(self.analysisSession)
analysisTrackway.simpleGauge = widthValue.raw
analysisTrackway.simpleGaugeUnc = widthValue.rawUncertainty
#_______________________________________________________________________________
def _analyzeTrack(self, track, series, trackway, sitemap):
if series.count < 1 or not track.pes:
return
segmentPair = None
segmentSeries = None
skipped = 0
for key, otherSeries in series.bundle.items():
if not otherSeries.pes:
continue
if otherSeries == series or otherSeries.left == series.left or otherSeries.count < 2:
# If the series isn't suitable for comparison then mark this as a skipped attempt
# and continue.
skipped += 1
continue
segment = otherSeries.cache.get('curve').getTrackSegment(track)
if segment is None:
continue
for pair in segment.pairs:
if pair['track'] != track:
continue
if segmentPair is None or pair['line'].length.raw < segmentPair['line'].length.raw:
# Store the shortest of the available gauge lengths
segmentPair = pair
segmentSeries = otherSeries
break
if skipped == 4:
# If skipped is 4 it means that no suitable series existed for calculating a gauge
# value and the method should abort quietly
self._ignoreTracks.append(track)
return
if segmentPair is None:
self._errorTracks.append(track)
return
color = 'blue' if segmentSeries.pes == series.pes else 'orange'
data = trackway.cache.get('data')
gauges = data['gauges']
line = segmentPair['line']
sitemap.cache.get('drawing').lineSegment(
line, stroke=color, stroke_width=1, stroke_opacity='0.5')
length = line.length
gauges.abs.append(length)
analysisTrack = track.getAnalysisPair(self.analysisSession)
analysisTrack.simpleGauge = line.length.raw
analysisTrack.simpleGaugeUnc = line.length.rawUncertainty
widthNormGauge = NumericUtils.divideValueUncertainties(
numeratorValue=length,
denominatorValue=series.cache.get('referenceWidth'))
gauges.width.append(widthNormGauge)
point = PositionValue2D(
x=analysisTrack.curvePosition, xUnc=0.0,
y=widthNormGauge.value, yUnc=widthNormGauge.uncertainty)
data['points'].append(point)
if analysisTrack.paceLength:
gauges.pace.append(NumericUtils.divideValueUncertainties(
length, analysisTrack.paceLengthValue))
if analysisTrack.strideLength:
gauges.stride.append(NumericUtils.divideValueUncertainties(
length, analysisTrack.strideLengthValue))
self._count += 1
#_______________________________________________________________________________
def _postAnalyze(self):
self.logger.write('%s gauge calculated tracks' % self._count)
self._trackwayCsv.save()
csv = CsvWriter(
path=self.getPath('Simple-Gauge-Errors.csv', isFile=True),
autoIndexFieldName='Index',
fields=[
('uid', 'UID'),
('fingerprint', 'Fingerprint') ])
for track in self._errorTracks:
csv.createRow(uid=track.uid, fingerprint=track.fingerprint)
csv.save()
if self._errorTracks:
self.logger.write('Failed to calculate gauge for %s tracks' % len(self._errorTracks))
csv = CsvWriter(
path=self.getPath('Simple-Gauge-Ignores.csv', isFile=True),
autoIndexFieldName='Index',
fields=[
('uid', 'UID'),
('fingerprint', 'Fingerprint') ])
for track in self._ignoreTracks:
csv.createRow(uid=track.uid, fingerprint=track.fingerprint)
csv.save()
if self._ignoreTracks:
self.logger.write('%s tracks lacked suitability for gauge calculation' % len(
self._ignoreTracks))
plotData = [
('stride', 'red', 'AU', 'Stride-Normalized Weighted'),
('pace', 'green', 'AU', 'Pace-Normalized Weighted'),
('width', 'blue', 'AU', 'Width-Normalized Weighted'),
('abs', 'purple', 'm', 'Absolute Unweighted') ]
for data in plotData:
out = []
source = ListUtils.sortListByIndex(
source=getattr(self._trackwayGauges, StringUtils.toStr2(data[0])),
index=0,
inPlace=True)
for item in source:
out.append(PositionValue2D(x=len(out), y=item[1].value, yUnc=item[1].uncertainty))
self._plotTrackwayGauges(out, *data[1:])
self.mergePdfs(self._paths, 'Gauges.pdf')
#_______________________________________________________________________________
def _plotTrackwayGauges(self, points, color, unit, heading):
histData = []
for p in points:
histData.append(p.yValue.value)
plot = Histogram(
data=histData,
title='%s Trackway Gauges' % heading,
xLabel='Averaged Trackway Gauge (%s)' % unit,
yLabel='Frequency',
color=color)
self._paths.insert(0, plot.save(self.getTempFilePath(extension='pdf')))
plot = ScatterPlot(
data=ListUtils.sortObjectList(points, 'y', inPlace=True),
title='%s Trackway Gauges' % heading,
xLabel='Trackway Pes Count (#)',
yLabel='Averaged Trackway Gauge (%s)' % unit,
color=color)
self._paths.insert(0, plot.save(self.getTempFilePath(extension='pdf')))
