def compute(self, qlwell, qlwell_channel, well_channel_metric):
channel_num = qlwell_channel.channel_num
well_channel_metric.s2d_value = well_s2d_values( qlwell )[channel_num]
clusters = getClusters( qlwell )
high_fliers = high_flier_droplets( clusters, channel_num )
if ( high_fliers is not None ):
well_channel_metric.high_flier_value = high_fliers[1]
else:
well_channel_metric.high_flier_value = None
low_fliers = low_flier_droplets( clusters, channel_num )
if ( low_fliers is not None ):
well_channel_metric.low_flier_value = low_fliers[1]
else:
well_channel_metric.low_flier_value = None
singleRain = singleRain_droplets( clusters, channel_num )
if ( singleRain is not None ):
well_channel_metric.single_rain_value = singleRain[1]
well_channel_metric.single_rain_pct = singleRain[2] * 100
else:
well_channel_metric.single_rain_value = None
well_channel_metric.single_rain_pct = None
doubleRain = doubleRain_droplets( clusters, channel_num )
if ( doubleRain is not None ):
well_channel_metric.double_rain_value = doubleRain[1]
well_channel_metric.double_rain_pct = doubleRain[2] * 100
else:
well_channel_metric.double_rain_value = None
well_channel_metric.double_rain_pct = None
return well_channel_metric
def stats_for_qlp_well(well, compute_clusters=False, override_thresholds=None):
"""
Return statistics about a QLWell object read from a QLP file.
The QLWell object should have a populated `peaks` attribute (reading from QLBs won't work)
For parameter explanations and return values, see :func:`stats_for_qlp_well`.
"""
from pyqlb.nstats.peaks import cluster_1d, channel_amplitudes
from pyqlb.nstats.well import accepted_peaks, above_min_amplitude_peaks, well_channel_sp_values, well_cluster_peaks
from pyqlb.nstats.well import well_observed_positives_negatives, well_s2d_values, getClusters
from pyqlb.nstats.well import high_flier_droplets, low_flier_droplets, singleRain_droplets, doubleRain_droplets, diagonal_scatter
from numpy import mean as np_mean, std as np_std
if not override_thresholds:
override_thresholds = (None, None)
statistics = well_statistics(well, override_thresholds=override_thresholds)
accepted = len(accepted_peaks(well))
num_above_min = len(above_min_amplitude_peaks(well))
if num_above_min > 0 and accepted > 0:
if well.sum_amplitude_bins:
peaksets, boundaries, amps = revb_polydisperse_peaks(well, 0, threshold=override_thresholds[0])
poly_peaks = sum([len(p) for p in peaksets])
statistics[0].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
peaksets, boundaries, width_gates = polydisperse_peaks(well, 0, threshold=override_thresholds[0])
poly_peaks = sum([len(p) for p in peaksets])
statistics[0].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
statistics[0].revb_polydispersity_pct = 0
s, p_plus, p, p_minus = well_channel_sp_values(well, 0, override_threshold=override_thresholds[0])
statistics[0].s_value = s
statistics[0].p_plus = p_plus
statistics[0].p_plus_drops = int(p_plus*accepted) if p_plus is not None else None
statistics[0].p = p
statistics[0].p_drops = int(p*accepted) if p is not None else None
statistics[0].p_minus = p_minus
statistics[0].p_minus_drops = int(p_minus*accepted) if p_minus is not None else None
if num_above_min > 0 and accepted > 0:
if well.sum_amplitude_bins:
peaksets, boundaries, amps = revb_polydisperse_peaks(well, 1, threshold=override_thresholds[1])
poly_peaks = sum([len(p) for p in peaksets])
statistics[1].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
peaksets, boundaries, width_gates = polydisperse_peaks(well, 1, threshold=override_thresholds[1])
poly_peaks = sum([len(p) for p in peaksets])
statistics[1].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
statistics[1].revb_polydispersity_pct = 0
s, p_plus, p, p_minus = well_channel_sp_values(well, 1, override_threshold=override_thresholds[1])
statistics[1].s_value = s
statistics[1].p_plus = p_plus
statistics[1].p_plus_drops = int(p_plus*accepted) if p_plus is not None else None
statistics[1].p = p
statistics[1].p_drops = int(p*accepted) if p is not None else None
statistics[1].p_minus = p_minus
statistics[1].p_minus_drops = int(p_minus*accepted) if p_minus is not None else None
## compute s2d plots
s2d_vals = well_s2d_values( well, thresholds=override_thresholds)
statistics[0].s2d_value = s2d_vals[0] if s2d_vals is not None else None
statistics[1].s2d_value = s2d_vals[1] if s2d_vals is not None else None
## compute extra cluster metrics
clusters = getClusters( well, override_thresholds )
dscatter = diagonal_scatter( clusters )
statistics.diagonal_scatter = dscatter[1] if dscatter is not None else None
statistics.diagonal_scatter_pct = dscatter[2] *100 if dscatter is not None else None
for channel in [0,1]:
high_fliers = high_flier_droplets( clusters, channel )
statistics[channel].high_flier_value = high_fliers[1] if high_fliers is not None else None
statistics[channel].high_flier_pct = high_fliers[2] * 100 if high_fliers is not None else None
low_fliers = low_flier_droplets( clusters, channel )
statistics[channel].low_flier_value = low_fliers[1] if low_fliers is not None else None
statistics[channel].low_flier_pct = low_fliers[2] * 100 if low_fliers is not None else None
singleRain = singleRain_droplets( clusters, channel )
statistics[channel].single_rain_value = singleRain[1] if singleRain is not None else None
statistics[channel].single_rain_pct = singleRain[2] * 100 if singleRain is not None else None
doubleRain = doubleRain_droplets( clusters, channel )
statistics[channel].double_rain_value = doubleRain[1] if doubleRain is not None else None
statistics[channel].double_rain_pct = doubleRain[2] * 100 if doubleRain is not None else None
if compute_clusters:
clusters = well_cluster_peaks(well, override_thresholds)
else:
clusters = {'positive_peaks': {'positive_peaks': [], 'negative_peaks': []},
'negative_peaks': {'positive_peaks': [], 'negative_peaks': []}}
# cheap hack
statistics.alg_version = "%s.%s/%s.%s" % (well.statistics.peak_alg_major_version,
well.statistics.peak_alg_minor_version,
well.statistics.quant_alg_major_version,
well.statistics.quant_alg_minor_version)
statistics.ref_copy_num = well.ref_copy_num
statistics[0].decision_tree = well.channels[0].decision_tree_verbose
statistics[1].decision_tree = well.channels[1].decision_tree_verbose
# end cheap hack
# SNR
for chan in (0,1):
if override_thresholds[chan]:
# TODO add this to pyqlb.nstats.well instead
pos, neg = cluster_1d(accepted_peaks(well), chan, override_thresholds[chan])
else:
pos, neg, unknown = well_observed_positives_negatives(well, chan)
for attr, coll in (('positive_snr', pos),('negative_snr',neg)):
if len(pos) > 0:
amps = channel_amplitudes(coll, chan)
amp_mean = np_mean(amps)
amp_std = np_std(amps)
if amp_std > 0:
setattr(statistics[chan], attr, amp_mean/amp_std)
else:
setattr(statistics[chan], attr, 10000)
else:
setattr(statistics[chan], attr, 0)
for channel in [0,1]:
means,stds = total_events_amplitude_vals(well,channel)
statistics[channel].total_events_amplitude_mean = means if means is not None else None
statistics[channel].total_events_amplitude_stdev = stds if stds is not None else None
return statistics, clusters