def galaxy_extra(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import above_min_amplitude_peaks
from qtools.lib.mplot import galaxy_extracluster, cleanup, render as plt_render
from qtools.lib.nstats.peaks import extracluster_peaks
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
channel_idx = int(request.params.get("channel", 0))
peaks = above_min_amplitude_peaks(qlwell)
threshold = c.vic_threshold if channel_idx == 1 else c.fam_threshold
extra_data = extracluster_peaks(qlwell, channel_idx, threshold=threshold)
extra_peaks, rain_boundaries, width_gates = extra_data
pos, midhigh, midlow, neg = rain_boundaries
min_gate, max_gate = width_gates
title = 'GalaxyEX - %s, %s, %s' % (c.well.plate.plate.name, c.well.well_name, 'VIC' if channel_idx == 1 else 'FAM')
fig = galaxy_extracluster(title, peaks, channel_idx, threshold, min_gate, max_gate,
pos, midhigh, midlow, neg,
extra_peaks,
min_amplitude_excluded=True)
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def compute(self, qlwell, qlwell_channel, well_channel_metric):
# only return for >= 1000 peaks
if len(qlwell.peaks) < 1000:
return well_channel_metric
data = extracluster_peaks(qlwell, qlwell_channel.channel_num,
threshold=qlwell_channel.statistics.threshold)
peaks, rain_gates, width_gates = data
# have to worry about min amplitude peaks here
# found in well_metric but don't have access to wm in compute()
above_min_amp_peaks = above_min_amplitude_peaks(qlwell)
if len(above_min_amp_peaks) == 0:
well_channel_metric.extracluster = 0
else:
well_channel_metric.extracluster = float(len(peaks))/len(above_min_amp_peaks)
if hasattr(qlwell, 'sum_amplitude_bins') and len(qlwell.sum_amplitude_bins) > 0:
data = revb_extracluster_peaks(qlwell, qlwell_channel.channel_num,
threshold=qlwell_channel.statistics.threshold)
peaks, rain_gates, mean_amps = data
if len(above_min_amp_peaks) == 0:
well_channel_metric.revb_extracluster = 0
else:
well_channel_metric.revb_extracluster = float(len(peaks))/len(above_min_amp_peaks)
else:
well_channel_metric.revb_extracluster = None
return well_channel_metric