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 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 galaxy_disperse_revb(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import above_min_amplitude_peaks
from qtools.lib.mplot import galaxy_polydisperse_revb, cleanup, render as plt_render, empty_fig
from qtools.lib.nstats.peaks import revb_polydisperse_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
title = 'GalaxyPDB - %s, %s, %s' % (c.well.plate.plate.name, c.well.well_name, 'VIC' if channel_idx == 1 else 'FAM')
if hasattr(qlwell, 'sum_amplitude_bins') and len(qlwell.sum_amplitude_bins) > 0:
polydisperse_data = revb_polydisperse_peaks(qlwell, channel_idx, threshold=threshold)
poly_peaks, rain_boundaries, mean_amplitudes = polydisperse_data
pos_peaks, midhigh_peaks, midlow_peaks, neg_peaks = poly_peaks
pos, midhigh, midlow, neg = rain_boundaries
fam_mean, vic_mean = mean_amplitudes
fig = galaxy_polydisperse_revb(title, peaks, channel_idx, threshold,
pos, midhigh, midlow, neg,
pos_peaks, midhigh_peaks, midlow_peaks, neg_peaks,
min_amplitude_excluded=True,
sum_amplitude_bins=qlwell.sum_amplitude_bins, other_channel_mean=fam_mean if channel_idx == 1 else vic_mean)
else:
fig = empty_fig()
ax = fig.add_subplot(111, title=title)
ax.text(0.33,0.5, "No amplitude bins for this well.")
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def svilen(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import accepted_peaks
from pyqlb.nstats.peaks import cluster_2d, peak_times, fam_widths
from pyqlb.factory import QLNumpyObjectFactory
from qtools.lib.mplot import svilen, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
well_path = self.__well_path()
# oh shit
factory = QLNumpyObjectFactory()
raw_well = factory.parse_well(well_path)
crap, crap, gold, crap = cluster_2d(accepted_peaks(qlwell), c.fam_threshold,
c.vic_threshold)
times = peak_times(gold)
widths = fam_widths(gold)
title = "VIC+/FAM- droplet traces (accepted events)"
ranges = [(int(t-(w*2)), int(t+(w*2))) for t, w in zip(times, widths)]
if c.fam_threshold == 0 or c.vic_threshold == 0:
ranges = []
title = "%s (no events in quadrant)" % title
elif len(ranges) > 100:
ranges = ranges[:100]
title = "%s (truncated at first 100)" % title
fig = svilen(title, raw_well.samples, ranges, widths)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def bscore_trend(self, id=None, *args, **kwargs):
from qtools.lib.mplot import plot_bscore_rolling_window, cleanup, render as plt_render
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
fig = plot_bscore_rolling_window(qlwell, title="%s - %s" % (c.well.plate.plate.name, c.well.well_name))
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def conc_trend(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.mplot import plot_conc_rolling_window, cleanup, render as plt_render
response.content_type = 'image/png'
c.channel_num = int(channel_num)
qlwell = self.__qlwell_from_threshold_form(id)
chan = 'FAM' if c.channel_num == 0 else 'VIC'
fig = plot_conc_rolling_window(qlwell, c.channel_num, title="%s - %s (%s)" % (c.well.plate.plate.name, c.well.well_name, chan))
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def galaxy_sum_bins(self, id=None, *args, **kwargs):
from qtools.lib.mplot import galaxy_sum_width_bins, cleanup, render as plt_render
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
title = 'Sum Amps/Width Bins - %s, %s' % (c.well.plate.plate.name, c.well.well_name)
fig = galaxy_sum_width_bins(title, qlwell)
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def noreject(self, id=None, *args, **kwargs):
from qtools.lib.mplot import plot_gated_types, cleanup, render as plt_render
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
max_amplitudes = [self.form_result['max_fam_amplitude'], self.form_result['max_vic_amplitude']]
fig = plot_gated_types(qlwell,
max_amplitudes=max_amplitudes)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def nds(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import above_min_amplitude_peaks, NARROW_NORMALIZED_DROPLET_SPACING
from qtools.lib.mplot import nds, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
title = 'NDS Histogram - %s - %s' % (c.well.plate.plate.name, c.well.well_name)
ok_peaks = above_min_amplitude_peaks(qlwell)
fig = nds(title, ok_peaks, NARROW_NORMALIZED_DROPLET_SPACING)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def outliers(self, id=None, *args, **kwargs):
from qtools.lib.nstats.peaks import total_events_amplitude_vals
from qtools.lib.mplot import plot_cluster_outliers, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
means0,stds0 = total_events_amplitude_vals(qlwell,0)
means1,stds1 = total_events_amplitude_vals(qlwell,1)
title = 'Outliers - Well:%s FAM:(Mean: %.0f, Stdev:%.0f) \n VIC/HEX:(Mean: %.0f, Stdev: %.0f)' % (c.well.well_name,means0,stds0,means1,stds1)
peaks = qlwell.peaks
fig = plot_cluster_outliers(title, peaks)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def width(self, id=None, *args, **kwargs):
from qtools.lib.mplot import plot_widths, cleanup, render as plt_render
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
# assume widths are same on channel 0 as on 1
fig = plot_widths(qlwell.peaks,
min_width_gate=qlwell.channels[0].statistics.min_width_gate,
max_width_gate=qlwell.channels[0].statistics.max_width_gate,
max_width=20,
background_rgbs=self.__get_1d_background_rgbs(qlwell))
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def amptime(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.mplot import amptime, cleanup, render as plt_render
response.content_type = 'image/png'
c.channel_num = int(channel_num)
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
peaks = qlwell.peaks
title = 'Intensity/Time - %s - %s, %s' % (c.well.plate.plate.name, c.well.well_name, 'VIC' if c.channel_num == 1 else 'FAM')
fig = amptime(title, peaks, 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
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
def amphist(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.mplot import plot_amp_hist, cleanup, render as plt_render
from pyqlb.nstats.well import accepted_peaks
response.content_type = 'image/png'
c.channel_num = int(channel_num)
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
peaks = accepted_peaks(qlwell)
fig = plot_amp_hist(peaks,
title='%s - %s' % (c.well.plate.plate.name, c.well.well_name),
channel_num=c.channel_num,
threshold=(c.vic_threshold if c.channel_num == 1 else c.fam_threshold))
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def cluster(self, id=None, *args, **kwargs):
from qtools.lib.mplot import plot_threshold_2d, cleanup, render as plt_render
from qtools.lib.nstats.peaks import accepted_peaks
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
max_amplitudes = [self.form_result['max_fam_amplitude'], self.form_result['max_vic_amplitude']]
boundaries = (-2000,-2000,max_amplitudes[1],max_amplitudes[0])
# to emulate current behavior -- include gated events
peaks = accepted_peaks(qlwell)
fig = plot_threshold_2d(peaks,
thresholds=(c.fam_threshold, c.vic_threshold),
boundaries=boundaries)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def temporal(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.mplot import temporal, cleanup, render as plt_render
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
channel = int(request.params.get("channel", 0))
if not request.params.get('threshold', None):
threshold = c.vic_threshold if channel == 1 else c.fam_threshold
else:
threshold = float(request.params.get('threshold'))
title = 'Temporal Width Lite - %s - %s' % (c.well.plate.plate.name, c.well.well_name)
fig = temporal(title, qlwell.peaks, threshold, qlwell.channels[channel].statistics.min_width_gate,
qlwell.channels[channel].statistics.max_width_gate, channel)
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def galaxy(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.nstats.peaks import above_min_amplitude_peaks
from pyqlb.nstats.well import well_static_width_gates
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
channel_idx = int(request.params.get("channel", 0))
from qtools.lib.mplot import galaxy, cleanup, render as plt_render
peaks = above_min_amplitude_peaks(qlwell)
title = 'Galaxy Lite - %s - %s, %s' % (c.well.plate.plate.name, c.well.well_name, 'VIC' if channel_idx == 1 else 'FAM')
threshold = c.vic_threshold if channel_idx == 1 else c.fam_threshold
min_width_gate, max_width_gate = well_static_width_gates(qlwell)
fig = galaxy(title, peaks, threshold, min_width_gate, max_width_gate, channel_idx)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def widthbin(self, id=None, *args, **kwargs):
from qtools.lib.nstats.peaks import above_min_amplitude_peaks
from qtools.lib.mplot import plot_cluster_widthbins, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
title = 'Width Bins - %s, %s' % (c.well.plate.plate.name, c.well.well_name)
min_gate = qlwell.channels[0].statistics.min_width_gate
max_gate = qlwell.channels[0].statistics.max_width_gate
peaks = above_min_amplitude_peaks(qlwell)
fam_threshold = qlwell.channels[0].statistics.threshold
vic_threshold = qlwell.channels[1].statistics.threshold
fig = plot_cluster_widthbins(title, peaks, qlwell.sum_amplitude_bins, min_gate, max_gate,
fam_threshold=fam_threshold, vic_threshold=vic_threshold)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def cluster2d(self, id=None, *args, **kwargs):
from qtools.lib.mplot import plot_cluster_2d, cleanup, render as plt_render
from qtools.lib.nstats.peaks import accepted_peaks
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
max_amplitudes = [self.form_result['max_fam_amplitude'], self.form_result['max_vic_amplitude']]
boundaries = (-2000,-2000,max_amplitudes[1],max_amplitudes[0])
# to emulate current behavior -- include gated events
peaks = accepted_peaks(qlwell)
threshold_fallback = qlwell.clustering_method == QLWell.CLUSTERING_TYPE_THRESHOLD
fig = plot_cluster_2d(peaks,
thresholds=(c.fam_threshold, c.vic_threshold),
boundaries=boundaries,
use_manual_clusters=not well_channel_automatic_classification(qlwell),
highlight_thresholds=threshold_fallback)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def galaxy_extra_region(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import above_min_amplitude_peaks
from qtools.lib.mplot import graph_extracluster_by_region, cleanup, render as plt_render
from qtools.lib.nstats.peaks import revb_extracluster_peaks_by_region
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 = revb_extracluster_peaks_by_region(qlwell, channel_idx, threshold=threshold)
peaks_by_region, rain_gates, means = extra_data
title = "GalaxyEXR - %s, %s, %s" % (c.well.plate.plate.name, c.well.well_name, 'VIC' if channel_idx == 1 else 'FAM')
fig = graph_extracluster_by_region(title, peaks, channel_idx, threshold,
peaks_by_region, rain_gates,
sum_amplitude_bins=qlwell.sum_amplitude_bins,
other_channel_mean=means[channel_idx])
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def threshold(self, id=None, show_only_gated=True, *args, **kwargs):
from qtools.lib.mplot import plot_fam_vic_peaks, cleanup, render as plt_render
from qtools.lib.nstats.peaks import accepted_peaks
response.content_type = 'image/png'
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
max_amplitudes = [self.form_result['max_fam_amplitude'], self.form_result['max_vic_amplitude']]
# to emulate current behavior -- include gated events
if show_only_gated != 'False':
peaks = accepted_peaks(qlwell)
else:
peaks = qlwell.peaks
fig = plot_fam_vic_peaks(peaks, thresholds=(c.fam_threshold, c.vic_threshold),
max_amplitudes=max_amplitudes,
background_rgbs=self.__get_1d_background_rgbs(qlwell))
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def dg_trend(self, prop, view, dg_id):
from qtools.lib.mplot import dg_vacuum_time, dg_vacuum_runs, dg_pressure_time, dg_pressure_runs, dg_spike_runs, dg_spike_time
from qtools.lib.mplot import cleanup, render as plt_render
if id is None:
abort(404)
dg = Session.query(DropletGenerator).get(int(dg_id))
if not dg:
abort(404)
func_map = dict([(('vacuum', 'time'), dg_vacuum_time),
(('vacuum', 'runs'), dg_vacuum_runs),
(('pressure', 'time'), dg_pressure_time),
(('pressure', 'runs'), dg_pressure_runs),
(('spike', 'runs'), dg_spike_runs),
(('spike', 'time'), dg_spike_time)])
good_runs = get_good_dg_runs(int(dg_id))
fig = func_map[(prop, view)](dg.name, good_runs)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def fft(self, id=None):
from qtools.lib.mplot import cleanup, render as plt_render
# make it better?
if not deps_loaded:
abort(500)
if not id:
abort(404)
well = Session.query(QLBWell).get(id)
if not well:
abort(404)
file = well.file
if not file:
abort(404)
storage = QLStorageSource(config)
path = storage.qlbwell_path(well)
wellobj = get_well(path)
fam_samples = wellobj.samples[:,0][::FFT_DOWNSAMPLE].astype('float')
vic_samples = wellobj.samples[:,1][::FFT_DOWNSAMPLE].astype('float')
# normalize to 0->1
fam_samples /= np.max(fam_samples)
vic_samples /= np.max(vic_samples)
Sf = np.fft.fft(fam_samples)
numpy.fft.fftpack._fft_cache = {}
ff = np.fft.fftfreq(len(Sf), d=FFT_DOWNSAMPLE/wellobj.data_acquisition_params.sample_rate)
# only consider positive half of frequency domain, normalize by num of samples
Yf = abs(Sf[0:len(ff)/2])/len(fam_samples)
# make X-axis in terms of Hz
Wf = int((len(ff)/2)/max(ff)) # group by 1 Hz
Sv = np.fft.fft(vic_samples)
numpy.fft.fftpack._fft_cache = {}
fv = np.fft.fftfreq(len(Sv), d=FFT_DOWNSAMPLE/wellobj.data_acquisition_params.sample_rate)
Yv = abs(Sv[0:len(fv)/2])/len(vic_samples)
Wv = int((len(fv)/2)/max(fv)) # group by 1 Hz
# find peaks
fam_peak_indices = fft.find_peak_indices(Yf, Wf*2) # group by 2Hz
vic_peak_indices = fft.find_peak_indices(Yv, Wv*2) # group by 2Hz
ftops = ff.take(fam_peak_indices)[0:10]
vtops = fv.take(vic_peak_indices)[0:10]
fig = plt.figure()
fig.set_figwidth(8)
fig.set_figheight(6)
plt.subplot(211)
plt.title('FAM Channel FFT (0-150Hz)')
plt.plot(ff[0:len(ff)/2], Yf)
plt.axis([-10, 150, -0.002, 0.04])
plt.text(70, 0.03, "Top Peaks (2 Hz windows):", weight='bold')
for i, val in enumerate(ftops):
plt.text(70 if i < 5 else 90, 0.027-(0.003*(i % 5)), "%.2f" % val, size=10)
# todo render text func?
plt.subplot(212)
plt.title('VIC Channel FFT (0-150Hz)')
plt.plot(fv[0:len(fv)/2], Yv)
plt.axis([-10, 150, -0.002, 0.04])
plt.text(70, 0.03, "Top Peaks (2 Hz windows):", weight='bold')
for i, val in enumerate(vtops):
plt.text(70 if i < 5 else 90, 0.027-(0.003*(i % 5)), "%.2f" % val, size=10)
# fft leaves cache-- not good for threaded server
imgdata = self.__render(fig)
cleanup(fig)
del fig, wellobj, fam_samples, vic_samples, Sf, ff, Yf, Wf, Sv, fv, Yv, Wv, ftops, vtops
gc.collect()
return imgdata