def air_hist(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.nstats.peaks import gap_air
from pyqlb.nstats.well import accepted_peaks
from pyqlb.nstats.peaks import color_uncorrected_peaks, channel_amplitudes, peak_times
from qtools.lib.mplot import air_hist, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
c.channel_num = int(channel_num)
threshold = c.vic_threshold if c.channel_num == 1 else c.fam_threshold
cutoff = request.params.get('cutoff', 500)
# can detect air on either channel (especially if VICs super low)
# but always report VIC amplitude
air_drops = gap_air(qlwell, c.channel_num, threshold=threshold)
uncorrected_air = color_uncorrected_peaks(air_drops, qlwell.color_compensation_matrix)
# count number of accepted peak times
air_drop_times = peak_times(air_drops)
accepted_times = peak_times(accepted_peaks(qlwell))
num_air_accepted = len([t for t in air_drop_times if t in accepted_times])
# always gate on VIC
air_amps = channel_amplitudes(uncorrected_air, 1)
title = 'Air Droplet Histogram - %s, %s (%s)' % (c.well.plate.plate.name, c.well.well_name, 'VIC' if c.channel_num == 1 else 'FAM')
fig = air_hist(title, air_amps, cutoff=cutoff, num_accepted=num_air_accepted)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def compute(self, qlwell, well_metric):
if qlwell.sample_name not in self.test_well_names:
return well_metric
air_drops = gap_air(qlwell, self.channel_num,
max_amp=self.air_max_threshold,
threshold=qlwell.channels[self.channel_num].statistics.threshold or None)
# Rev A: droplets would not be there if below min amplitude
# Rev B: droplets will have min amplitude flag if they were below 500
# in the VIC channel
accepted_times = peak_times(accepted_peaks(qlwell))
air_times = peak_times(air_drops)
well_metric.air_droplets = len([t for t in air_times if t in accepted_times])
well_metric.air_droplets_threshold = qlwell.channels[1].statistics.trigger_min_amplitude
def air_plot(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.nstats.peaks import gap_air
from qtools.lib.mplot import airtime, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
c.channel_num = int(channel_num)
threshold = c.vic_threshold if c.channel_num == 1 else c.fam_threshold
#cutoff = request.params.get('cutoff', 500)
air_drops = gap_air(qlwell, c.channel_num, threshold=threshold)
title = 'Air - %s - %s, %s' % (c.well.plate.plate.name, c.well.well_name, 'VIC' if c.channel_num == 1 else 'FAM')
fig = airtime(title, qlwell.peaks, air_drops, c.vic_threshold if c.channel_num == 1 else c.fam_threshold, c.channel_num)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata