def rain_split(qlwell, channel_num=0, threshold=None, pct_boundary=0.3, split_all_peaks=False):
"""
Splits between rain and non-rain. If you want the well's auto threshold to be used,
use None as a threshold parameter (the default).
If you do not want a threshold to be calculated, use '0'. (little unclear from the spec)
Returns tuple (rain, non-rain)
"""
if threshold is None:
threshold = qlwell.channels[channel_num].statistics.threshold
ok_peaks = accepted_peaks(qlwell)
prain, rain, nrain, p_thresh, mh_thresh, ml_thresh, l_thresh = \
rain_pvalues_thresholds(ok_peaks, channel_num=channel_num, threshold=threshold, pct_boundary=pct_boundary)
if split_all_peaks:
peaks = qlwell.peaks
else:
peaks = ok_peaks
# this would be useful as a standalone, but for efficiency's sake will cut out for now
rain_condition_arr = [channel_amplitudes(peaks, channel_num) > p_thresh]
if mh_thresh and ml_thresh:
rain_condition_arr.append(np.logical_and(channel_amplitudes(peaks, channel_num) > ml_thresh,
channel_amplitudes(peaks, channel_num) < mh_thresh))
rain_condition_arr.append(channel_amplitudes(peaks, channel_num) < l_thresh)
rain_condition = reduce(np.logical_or, rain_condition_arr)
nonrain_condition = np.logical_not(rain_condition)
rain = np.extract(rain_condition, peaks)
nonrain = np.extract(nonrain_condition, peaks)
return rain, nonrain
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 revb_extracluster_peaks(well, channel_num, threshold=None, pct_boundary=0.3, exclude_min_amplitude_peaks=True):
"""
Return the peaks that are outside the clusters.
A superset of polydispersity peaks, meant primarily for dye wells,
where there should be no biological basis for rain.
Returns a 3-tuple: peaks, rain gates, width gates
"""
if not threshold:
threshold = well.channels[channel_num].statistics.threshold
if not threshold:
threshold = None
if exclude_min_amplitude_peaks:
peaks = above_min_amplitude_peaks(well)
else:
peaks = well.peaks
# get rain_pvalues
p_plus, p, p_minus, pos, middle_high, middle_low, neg = \
rain_pvalues_thresholds(peaks,
channel_num=channel_num,
threshold=threshold,
pct_boundary=pct_boundary)
binned_peaks = bin_peaks_by_amplitude(peaks, well.sum_amplitude_bins)
extra_peaks = np.ndarray([0], dtype=peak_dtype(2))
for bin, (min_gate, max_gate, boundary) in zip(binned_peaks, well.sum_amplitude_bins):
if middle_high and middle_low:
extra_peaks = np.hstack([extra_peaks, np.extract(np.logical_not(
np.logical_or(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > min_gate,
channel_widths(bin, channel_num) < max_gate,
channel_amplitudes(bin, channel_num) > middle_high,
channel_amplitudes(bin, channel_num) < pos)),
reduce(np.logical_and,
(channel_widths(bin, channel_num) > min_gate,
channel_widths(bin, channel_num) < max_gate,
channel_amplitudes(bin, channel_num) > neg,
channel_amplitudes(bin, channel_num) < middle_low))
)
), bin)])
else:
extra_peaks = np.hstack([extra_peaks, np.extract(np.logical_not(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > min_gate,
channel_widths(bin, channel_num) < max_gate,
channel_amplitudes(bin, channel_num) > neg,
channel_amplitudes(bin, channel_num) < pos)
)
), bin)])
return (extra_peaks,
(pos, middle_high, middle_low, neg),
(np.mean(fam_amplitudes(peaks)), np.mean(vic_amplitudes(peaks))))
def temporal_galaxy(self, id=None, channel_num=0, *args, **kwargs):
from qtools.lib.nstats.peaks import above_min_amplitude_peaks
from pyqlb.nstats.peaks import peak_times, channel_amplitudes, channel_widths
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
c.channel_num = int(channel_num)
ok_peaks = above_min_amplitude_peaks(qlwell)
c.taw = zip(peak_times(ok_peaks), channel_amplitudes(ok_peaks, c.channel_num), channel_widths(ok_peaks, c.channel_num))
if c.channel_num == 0:
c.channel_name = 'FAM'
else:
c.channel_name = 'VIC'
return render('/well/temporal_galaxy.html')
def extracluster_peaks(well, channel_num, threshold=None, pct_boundary=0.3, exclude_min_amplitude_peaks=True):
"""
Return the peaks that are outside the clusters.
A superset of polydispersity peaks, meant primarily for dye wells,
where there should be no biological basis for rain.
Returns a 3-tuple: peaks, rain gates, width gates
"""
if not threshold:
threshold = well.channels[channel_num].statistics.threshold
if not threshold:
threshold = None
if exclude_min_amplitude_peaks:
peaks = above_min_amplitude_peaks(well)
else:
peaks = well.peaks
# get rain_pvalues
p_plus, p, p_minus, pos, middle_high, middle_low, neg = \
rain_pvalues_thresholds(peaks,
channel_num=channel_num,
threshold=threshold,
pct_boundary=pct_boundary)
min_gate, max_gate = well_static_width_gates(well)
if middle_high and middle_low:
extracluster_peaks = np.extract(np.logical_not(
np.logical_or(
reduce(np.logical_and,
(channel_widths(peaks, channel_num) > min_gate,
channel_widths(peaks, channel_num) < max_gate,
channel_amplitudes(peaks, channel_num) > middle_high,
channel_amplitudes(peaks, channel_num) < pos)),
reduce(np.logical_and,
(channel_widths(peaks, channel_num) > min_gate,
channel_widths(peaks, channel_num) < max_gate,
channel_amplitudes(peaks, channel_num) > neg,
channel_amplitudes(peaks, channel_num) < middle_low))
)
), peaks)
else:
extracluster_peaks = np.extract(np.logical_not(
reduce(np.logical_and,
(channel_widths(peaks, channel_num) > min_gate,
channel_widths(peaks, channel_num) < max_gate,
channel_amplitudes(peaks, channel_num) > neg,
channel_amplitudes(peaks, channel_num) < pos)
)
), peaks)
return (extracluster_peaks,
(pos, middle_high, middle_low, neg),
(min_gate, max_gate))
def gap_air(qlwell, channel_num=0, threshold=None, pct_boundary=0.3, gap_size=10000, gap_buffer=250, max_amp=1000):
"""
Return the air (gap rain < max_amp) in the gaps between non-rain droplets.
:param channel_num: The channel on which to detect air droplets.
:param threshold: The threshold dividing positives and negatives (used to detect 'rain')
:param pct_boundary: The percentage outside of which a droplet is classified as rain.
:param gap_size: The minimum size (in samples) of a gap. Default 0.1s.
:param gap_buffer: The distance a droplet must be from the main population to be considered an
air droplet, in samples. Default 0.0025s.
:param max_amp: The maximum color-corrected amplitude of an air droplet. Default 1000 RFU.
"""
rain, nonrain = rain_split(qlwell,
channel_num=channel_num,
threshold=threshold,
pct_boundary=pct_boundary,
split_all_peaks=True)
low_amp = np.extract(channel_amplitudes(rain, channel_num) < max_amp, rain)
times = peak_times(nonrain)
if nonrain is None or len(nonrain) < 2:
return np.ndarray([0], dtype=peak_dtype(2))
intervals = np.ediff1d(times, to_begin=0, to_end=0)
big_intervals = intervals > gap_size
# find beginning of gaps with extract
beginnings = [b+gap_buffer for b in np.extract(big_intervals[1:], times)]
ends = [e-gap_buffer for e in np.extract(big_intervals[:-1], times)]
gap_intervals = zip(beginnings, ends)
gap_intervals.insert(0, (0, times[0]-gap_buffer))
gap_intervals.append((times[-1]+gap_buffer, times[-1]*100))
# count the rain in the intervals
gap_drops = np.extract(reduce(np.logical_or, [np.logical_and(peak_times(low_amp) > b,
peak_times(low_amp) < e) for b, e in gap_intervals]),
low_amp)
return gap_drops
def stats_for_qlp_well(well, compute_clusters=False, override_thresholds=None):
"""
Return statistics about a QLWell object read from a QLP file.
The QLWell object should have a populated `peaks` attribute (reading from QLBs won't work)
For parameter explanations and return values, see :func:`stats_for_qlp_well`.
"""
from pyqlb.nstats.peaks import cluster_1d, channel_amplitudes
from pyqlb.nstats.well import accepted_peaks, above_min_amplitude_peaks, well_channel_sp_values, well_cluster_peaks
from pyqlb.nstats.well import well_observed_positives_negatives, well_s2d_values, getClusters
from pyqlb.nstats.well import high_flier_droplets, low_flier_droplets, singleRain_droplets, doubleRain_droplets, diagonal_scatter
from numpy import mean as np_mean, std as np_std
if not override_thresholds:
override_thresholds = (None, None)
statistics = well_statistics(well, override_thresholds=override_thresholds)
accepted = len(accepted_peaks(well))
num_above_min = len(above_min_amplitude_peaks(well))
if num_above_min > 0 and accepted > 0:
if well.sum_amplitude_bins:
peaksets, boundaries, amps = revb_polydisperse_peaks(well, 0, threshold=override_thresholds[0])
poly_peaks = sum([len(p) for p in peaksets])
statistics[0].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
peaksets, boundaries, width_gates = polydisperse_peaks(well, 0, threshold=override_thresholds[0])
poly_peaks = sum([len(p) for p in peaksets])
statistics[0].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
statistics[0].revb_polydispersity_pct = 0
s, p_plus, p, p_minus = well_channel_sp_values(well, 0, override_threshold=override_thresholds[0])
statistics[0].s_value = s
statistics[0].p_plus = p_plus
statistics[0].p_plus_drops = int(p_plus*accepted) if p_plus is not None else None
statistics[0].p = p
statistics[0].p_drops = int(p*accepted) if p is not None else None
statistics[0].p_minus = p_minus
statistics[0].p_minus_drops = int(p_minus*accepted) if p_minus is not None else None
if num_above_min > 0 and accepted > 0:
if well.sum_amplitude_bins:
peaksets, boundaries, amps = revb_polydisperse_peaks(well, 1, threshold=override_thresholds[1])
poly_peaks = sum([len(p) for p in peaksets])
statistics[1].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
peaksets, boundaries, width_gates = polydisperse_peaks(well, 1, threshold=override_thresholds[1])
poly_peaks = sum([len(p) for p in peaksets])
statistics[1].revb_polydispersity_pct = 100*float(poly_peaks)/num_above_min
else:
statistics[1].revb_polydispersity_pct = 0
s, p_plus, p, p_minus = well_channel_sp_values(well, 1, override_threshold=override_thresholds[1])
statistics[1].s_value = s
statistics[1].p_plus = p_plus
statistics[1].p_plus_drops = int(p_plus*accepted) if p_plus is not None else None
statistics[1].p = p
statistics[1].p_drops = int(p*accepted) if p is not None else None
statistics[1].p_minus = p_minus
statistics[1].p_minus_drops = int(p_minus*accepted) if p_minus is not None else None
## compute s2d plots
s2d_vals = well_s2d_values( well, thresholds=override_thresholds)
statistics[0].s2d_value = s2d_vals[0] if s2d_vals is not None else None
statistics[1].s2d_value = s2d_vals[1] if s2d_vals is not None else None
## compute extra cluster metrics
clusters = getClusters( well, override_thresholds )
dscatter = diagonal_scatter( clusters )
statistics.diagonal_scatter = dscatter[1] if dscatter is not None else None
statistics.diagonal_scatter_pct = dscatter[2] *100 if dscatter is not None else None
for channel in [0,1]:
high_fliers = high_flier_droplets( clusters, channel )
statistics[channel].high_flier_value = high_fliers[1] if high_fliers is not None else None
statistics[channel].high_flier_pct = high_fliers[2] * 100 if high_fliers is not None else None
low_fliers = low_flier_droplets( clusters, channel )
statistics[channel].low_flier_value = low_fliers[1] if low_fliers is not None else None
statistics[channel].low_flier_pct = low_fliers[2] * 100 if low_fliers is not None else None
singleRain = singleRain_droplets( clusters, channel )
statistics[channel].single_rain_value = singleRain[1] if singleRain is not None else None
statistics[channel].single_rain_pct = singleRain[2] * 100 if singleRain is not None else None
doubleRain = doubleRain_droplets( clusters, channel )
statistics[channel].double_rain_value = doubleRain[1] if doubleRain is not None else None
statistics[channel].double_rain_pct = doubleRain[2] * 100 if doubleRain is not None else None
if compute_clusters:
clusters = well_cluster_peaks(well, override_thresholds)
else:
clusters = {'positive_peaks': {'positive_peaks': [], 'negative_peaks': []},
'negative_peaks': {'positive_peaks': [], 'negative_peaks': []}}
# cheap hack
statistics.alg_version = "%s.%s/%s.%s" % (well.statistics.peak_alg_major_version,
well.statistics.peak_alg_minor_version,
well.statistics.quant_alg_major_version,
well.statistics.quant_alg_minor_version)
statistics.ref_copy_num = well.ref_copy_num
statistics[0].decision_tree = well.channels[0].decision_tree_verbose
statistics[1].decision_tree = well.channels[1].decision_tree_verbose
# end cheap hack
# SNR
for chan in (0,1):
if override_thresholds[chan]:
# TODO add this to pyqlb.nstats.well instead
pos, neg = cluster_1d(accepted_peaks(well), chan, override_thresholds[chan])
else:
pos, neg, unknown = well_observed_positives_negatives(well, chan)
for attr, coll in (('positive_snr', pos),('negative_snr',neg)):
if len(pos) > 0:
amps = channel_amplitudes(coll, chan)
amp_mean = np_mean(amps)
amp_std = np_std(amps)
if amp_std > 0:
setattr(statistics[chan], attr, amp_mean/amp_std)
else:
setattr(statistics[chan], attr, 10000)
else:
setattr(statistics[chan], attr, 0)
for channel in [0,1]:
means,stds = total_events_amplitude_vals(well,channel)
statistics[channel].total_events_amplitude_mean = means if means is not None else None
statistics[channel].total_events_amplitude_stdev = stds if stds is not None else None
return statistics, clusters
def revb_polydisperse_peaks(well, channel_num, threshold=None, pct_boundary=0.3, exclude_min_amplitude_peaks=True):
"""
Computes polydispersity for a well which has amplitude bins defined.
Returns a 3-tuple (4-tuple, 4-tuple, 2-tuple). The first 4-tuple is:
* positive droplets, with widths above the width gate set for that droplet's amplitude bin.
* middle rain, with widths above the bin width gate.
* middle rain, with width below the bin width gate.
* negative rain, with width below the bin width gate.
The second 4-tuple is:
* positive rain boundary
* middle rain upper boundary (can be None)
* middle rain lower boundary (can be None)
* negative rain boundary
The third 2-tuple is:
* mean FAM amplitude
* mean VIC amplitude
This is for being able to draw approximate single-channel polydispersity graphs
down the line (this does beg the question, is there a better 2D definition of
polydispersity?)
Will raise an error if amplitude bins are not defined on the well.
"""
if not hasattr(well, 'sum_amplitude_bins') or len(well.sum_amplitude_bins) == 0:
raise ValueError("No amplitude bins for this well.")
if not threshold:
threshold = well.channels[channel_num].statistics.threshold
if not threshold:
threshold = None
if exclude_min_amplitude_peaks:
peaks = above_min_amplitude_peaks(well)
else:
peaks = well.peaks
p_plus, p, p_minus, pos, middle_high, middle_low, neg = \
rain_pvalues_thresholds(peaks,
channel_num=channel_num,
threshold=threshold,
pct_boundary=pct_boundary)
binned_peaks = bin_peaks_by_amplitude(peaks, well.sum_amplitude_bins)
pos_peaks = np.ndarray([0], dtype=peak_dtype(2))
midhigh_peaks = np.ndarray([0], dtype=peak_dtype(2))
midlow_peaks = np.ndarray([0], dtype=peak_dtype(2))
neg_peaks = np.ndarray([0], dtype=peak_dtype(2))
for bin, (min_gate, max_gate, boundary) in zip(binned_peaks, well.sum_amplitude_bins):
pos_peaks = np.hstack([pos_peaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) > pos)),
bin)])
if middle_high and middle_low:
midhigh_peaks = np.hstack([midhigh_peaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
reduce(np.logical_and,
(channel_amplitudes(bin, channel_num) < middle_high,
channel_amplitudes(bin, channel_num) > middle_low)))),
bin)])
midlow_peaks = np.hstack([midlow_peaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
reduce(np.logical_and,
(channel_amplitudes(bin, channel_num) < middle_high,
channel_amplitudes(bin, channel_num) > middle_low)))),
bin)])
neg_peaks = np.hstack([neg_peaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) < neg)),
bin)])
return ((pos_peaks, midhigh_peaks, midlow_peaks, neg_peaks),
(pos, middle_high, middle_low, neg),
(np.mean(fam_amplitudes(peaks)), np.mean(vic_amplitudes(peaks))))
def revb_extracluster_peaks_by_region(well, channel_num, threshold=None, pct_boundary=0.3, exclude_min_amplitude_peaks=True):
"""
Return the peaks that are not desired (outside clusters)
and separate them by region. The region order is:
-- positive large peaks
-- positive rain
-- positive small peaks
-- positive wide peaks (directly above positive cluster)
-- positive narrow peaks (directly below positive cluster)
-- middle large peaks
-- middle rain
-- middle small peaks
-- negative large peaks
-- negative rain
-- negative small peaks
-- negative wide peaks (directly above positive cluster)
-- negative narrow peaks (directly below positive cluster)
Returns this 9-tuple, then rain gates, then mean of FAM and VIC.
"""
extra_peaks, rain_gates, means = \
revb_extracluster_peaks(well, channel_num,
threshold=threshold,
pct_boundary=pct_boundary,
exclude_min_amplitude_peaks=exclude_min_amplitude_peaks)
pos_gate, midhigh_gate, midlow_gate, neg_gate = rain_gates
binned_peaks = bin_peaks_by_amplitude(extra_peaks, well.sum_amplitude_bins)
plpeaks = np.ndarray([0], dtype=peak_dtype(2))
prpeaks = np.ndarray([0], dtype=peak_dtype(2))
pspeaks = np.ndarray([0], dtype=peak_dtype(2))
pwpeaks = np.ndarray([0], dtype=peak_dtype(2))
pnpeaks = np.ndarray([0], dtype=peak_dtype(2))
mlpeaks = np.ndarray([0], dtype=peak_dtype(2))
mrpeaks = np.ndarray([0], dtype=peak_dtype(2))
mspeaks = np.ndarray([0], dtype=peak_dtype(2))
nlpeaks = np.ndarray([0], dtype=peak_dtype(2))
nrpeaks = np.ndarray([0], dtype=peak_dtype(2))
nspeaks = np.ndarray([0], dtype=peak_dtype(2))
nwpeaks = np.ndarray([0], dtype=peak_dtype(2))
nnpeaks = np.ndarray([0], dtype=peak_dtype(2))
for bin, (min_gate, max_gate, boundary) in zip(binned_peaks, well.sum_amplitude_bins):
plpeaks = np.hstack([plpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) > pos_gate)
), bin)])
prpeaks = np.hstack([prpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) >= min_gate,
channel_widths(bin, channel_num) <= max_gate,
channel_amplitudes(bin, channel_num) > pos_gate)
), bin)])
pspeaks = np.hstack([pspeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) > pos_gate)
), bin)])
if midhigh_gate and midlow_gate:
mlpeaks = np.hstack([mlpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) < midhigh_gate,
channel_amplitudes(bin, channel_num) > midlow_gate)
), bin)])
mrpeaks = np.hstack([mrpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) >= min_gate,
channel_widths(bin, channel_num) <= max_gate,
channel_amplitudes(bin, channel_num) < midhigh_gate,
channel_amplitudes(bin, channel_num) > midlow_gate)
), bin)])
mspeaks = np.hstack([mspeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) < midhigh_gate,
channel_amplitudes(bin, channel_num) > midlow_gate)
), bin)])
# this means there are positives
pwpeaks = np.hstack([pwpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) >= midhigh_gate,
channel_amplitudes(bin, channel_num) <= pos_gate)
), bin)])
pnpeaks = np.hstack([pnpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) >= midhigh_gate,
channel_amplitudes(bin, channel_num) <= pos_gate)
), bin)])
nwpeaks = np.hstack([nwpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) >= neg_gate,
channel_amplitudes(bin, channel_num) <= midlow_gate)
), bin)])
nnpeaks = np.hstack([nnpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) >= neg_gate,
channel_amplitudes(bin, channel_num) <= midlow_gate)
), bin)])
else:
nwpeaks = np.hstack([nwpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) >= neg_gate,
channel_amplitudes(bin, channel_num) <= pos_gate)
), bin)])
nnpeaks = np.hstack([nnpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) >= neg_gate,
channel_amplitudes(bin, channel_num) <= pos_gate)
), bin)])
nlpeaks = np.hstack([nlpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) > max_gate,
channel_amplitudes(bin, channel_num) < neg_gate)
), bin)])
nrpeaks = np.hstack([nrpeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) >= min_gate,
channel_widths(bin, channel_num) <= max_gate,
channel_amplitudes(bin, channel_num) < neg_gate)
), bin)])
pbpeaks = np.hstack([pspeaks, np.extract(
reduce(np.logical_and,
(channel_widths(bin, channel_num) < min_gate,
channel_amplitudes(bin, channel_num) >= midhigh_gate,
channel_amplitudes(bin, channel_num) <= pos_gate)
), bin)])
return ((plpeaks, prpeaks, pspeaks,
pwpeaks, pnpeaks,
mlpeaks, mrpeaks, mspeaks,
nlpeaks, nrpeaks, nspeaks,
nwpeaks, nnpeaks),
rain_gates,
means)
def polydisperse_peaks(well, channel_num, threshold=None, pct_boundary=0.3, exclude_min_amplitude_peaks=True):
"""
Returns a 3-tuple (4-tuple, 4-tuple, 2-tuple). The first 4-tuple is:
* positive rain above the width gates.
* middle rain above the width gates.
* middle rain below the width gates.
* negative rain below the width gates.
The second 4-tuple is:
* positive rain boundary
* middle rain upper boundary (can be None)
* middle rain lower boundary (can be None)
* negative rain boundary
The last 2-tuple is:
* computed min width gate
* computed max width gate
Positives & negatives are computed on the specified channel number.
"""
if not threshold:
threshold = well.channels[channel_num].statistics.threshold
if not threshold:
threshold = None
# filter out min_amplitude_peaks
if exclude_min_amplitude_peaks:
peaks = above_min_amplitude_peaks(well)
else:
peaks = well.peaks
p_plus, p, p_minus, pos, middle_high, middle_low, neg = \
rain_pvalues_thresholds(peaks,
channel_num=channel_num,
threshold=threshold,
pct_boundary=pct_boundary)
min_gate, max_gate = well_static_width_gates(well)
pos_peaks = np.extract(
reduce(np.logical_and,
(channel_widths(peaks, channel_num) > max_gate,
channel_amplitudes(peaks, channel_num) > pos)),
peaks)
if middle_high and middle_low:
midhigh_peaks = np.extract(
reduce(np.logical_and,
(channel_widths(peaks, channel_num) > max_gate,
reduce(np.logical_and,
(channel_amplitudes(peaks, channel_num) < middle_high,
channel_amplitudes(peaks, channel_num) > middle_low)))),
peaks)
midlow_peaks = np.extract(
reduce(np.logical_and,
(channel_widths(peaks, channel_num) < min_gate,
reduce(np.logical_and,
(channel_amplitudes(peaks, channel_num) < middle_high,
channel_amplitudes(peaks, channel_num) > middle_low)))),
peaks)
else:
midhigh_peaks = np.ndarray([0],dtype=peak_dtype(2))
midlow_peaks = np.ndarray([0],dtype=peak_dtype(2))
neg_peaks = np.extract(
reduce(np.logical_and,
(channel_widths(peaks, channel_num) < min_gate,
channel_amplitudes(peaks, channel_num) < neg)),
peaks)
return ((pos_peaks, midhigh_peaks, midlow_peaks, neg_peaks),
(pos, middle_high, middle_low, neg),
(min_gate, max_gate))
def total_events_amplitude_vals(well,ch):
peaks = well.peaks
return (np.mean(channel_amplitudes(peaks, ch)), np.std(channel_amplitudes(peaks, ch)))
