Пример #1
0
    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
Пример #2
0
 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
Пример #3
0
    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