示例#1
0
    def cluster_csv(self, id=None, show_only_gated=True, *args, **kwargs):
        from pyqlb.nstats.well import accepted_peaks
        qlwell = self.__qlwell_from_threshold_form(id)

        if show_only_gated != 'False':
            peaks = accepted_peaks(qlwell)
        else:
            peaks = qlwell.peaks

        from pyqlb.nstats.peaks import fam_amplitudes, fam_widths, vic_amplitudes, vic_widths, peak_times
        from pyqlb.nstats.well import well_observed_cluster_assignments

        response.headers['Content-Type'] = 'text/csv'
        h.set_download_response_header(request, response, "%s_%s%s.csv" % \
            (str(c.well.plate.plate.name), str(c.well.well_name), '' if show_only_gated != 'False' else '_all'))
        out = StringIO.StringIO()
        csvwriter = csv_pkg.writer(out)
        csvwriter.writerow(['Plate',c.well.plate.plate.name])
        csvwriter.writerow(['Well',c.well.well_name])
        csvwriter.writerow([])
        csvwriter.writerow(['Time','FAMAmplitude','FAMWidth','VICAmplitude','VICWidth','Cluster'])
        csvwriter.writerow([])

        pts = peak_times(peaks)
        fas = fam_amplitudes(peaks)
        fws = fam_widths(peaks)
        vas = vic_amplitudes(peaks)
        vws = vic_widths(peaks)
        cls = well_observed_cluster_assignments(qlwell, peaks)

        for row in zip(pts, fas, fws, vas, vws, cls):
            csvwriter.writerow(row)
        csv = out.getvalue()
        out.close()
        return csv
示例#2
0
    def peak_csv(self, id=None, show_only_gated=True, *args, **kwargs):
        from qtools.lib.nstats.peaks import accepted_peaks
        qlwell = self.__qlwell_from_threshold_form(id)

        if show_only_gated != 'False':
            peaks = accepted_peaks(qlwell)
        else:
            peaks = qlwell.peaks

        from pyqlb.nstats.peaks import fam_amplitudes, fam_widths, fam_quality, vic_amplitudes, vic_widths, vic_quality, peak_times

        response.headers['Content-Type'] = 'text/csv'
        h.set_download_response_header(request, response, "%s_%s%s.csv" % \
            (str(c.well.plate.plate.name), str(c.well.well_name), '' if show_only_gated != 'False' else '_all'))
        out = StringIO.StringIO()
        csvwriter = csv_pkg.writer(out)
        csvwriter.writerow(['Plate',c.well.plate.plate.name])
        csvwriter.writerow(['Well',c.well.well_name])
        csvwriter.writerow([])
        csvwriter.writerow(['FAMThreshold',qlwell.channels[0].statistics.threshold])
        csvwriter.writerow(['VICThreshold',qlwell.channels[1].statistics.threshold])
        csvwriter.writerow(['WidthGate',qlwell.channels[0].statistics.min_width_gate,qlwell.channels[0].statistics.max_width_gate])
        csvwriter.writerow(['MinQualityGate',qlwell.channels[0].statistics.min_quality_gate])
        csvwriter.writerow([])
        csvwriter.writerow(['Time','FAMAmplitude','FAMWidth','FAMQuality','VICAmplitude','VICWidth','VICQuality'])
        csvwriter.writerow([])

        pts = peak_times(peaks)
        fas = fam_amplitudes(peaks)
        fws = fam_widths(peaks)
        fqs = fam_quality(peaks)
        vas = vic_amplitudes(peaks)
        vws = vic_widths(peaks)
        vqs = vic_quality(peaks)

        for row in zip(pts, fas, fws, fqs, vas, vws, vqs):
            csvwriter.writerow(row)
        csv = out.getvalue()
        out.close()
        return csv