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
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
