def test_get_beta_plate_metrics(self):
cnv_metrics = get_beta_plate_metrics(self.cnv_dbplate, self.cnv_qlplate)
# assert some stuff
assert len([wm for wm in cnv_metrics.well_metrics if wm.expected_cnv is not None]) == 21
assert len([wm for wm in cnv_metrics.well_metrics if wm.expected_cnv == 6]) == 3
assert len([wm for wm in cnv_metrics.well_metrics if wm.expected_cnv == 2]) == 6
assert (
len([wm for wm in cnv_metrics.well_metrics if wm.well_channel_metrics[0].auto_threshold_expected is False])
== 3
)
assert (
len([wm for wm in cnv_metrics.well_metrics if wm.well_channel_metrics[1].auto_threshold_expected is False])
== 3
)
# copied verbatim from TestMetricsMethods
wd = cnv_metrics.well_metric_name_dict
assert wd["A01"].expected_cnv == 1
assert wd["A02"].expected_cnv is None
assert wd["B01"].expected_cnv == 2
assert wd["B02"].expected_cnv == 2
assert wd["F02"].expected_cnv == 3
assert wd["F01"].expected_cnv == 6
assert wd["E02"].expected_cnv == 4
assert wd["E03"].expected_cnv == 5
assert wd["A01"].cnv > 0.9
assert wd["A01"].cnv < 1.1
assert wd["A02"].cnv is None
assert wd["B01"].cnv > 1.8
assert wd["B01"].cnv < 2.2
assert wd["B02"].cnv > 1.8
assert wd["B02"].cnv < 2.2
assert wd["F02"].cnv > 2.8
assert wd["F02"].cnv < 3.2
assert wd["F01"].cnv > 5.7
assert wd["F01"].cnv < 6.3
assert wd["E02"].cnv > 3.8
assert wd["E02"].cnv < 4.2
assert wd["E03"].cnv > 4.8
assert wd["E03"].cnv < 5.2
assert len([wm for wm in cnv_metrics.well_metrics if wm.well_channel_metrics[0].threshold == 0]) == 3
assert len([wm for wm in cnv_metrics.well_metrics if wm.well_channel_metrics[1].threshold == 0]) == 3
duplex_metrics = get_beta_plate_metrics(self.duplex_dbplate, self.duplex_qlplate)
assert (
len([wm for wm in duplex_metrics.well_metrics if wm.well_channel_metrics[0].expected_concentration == 0])
== 4
)
assert (
len([wm for wm in duplex_metrics.well_metrics if wm.well_channel_metrics[1].expected_concentration == 1000])
== 24
)
assert (
len(
[
wm
for wm in duplex_metrics.well_metrics
if wm.well_channel_metrics[0].auto_threshold_expected is False
]
)
== 4
)
assert (
len(
[
wm
for wm in duplex_metrics.well_metrics
if wm.well_channel_metrics[1].auto_threshold_expected is False
]
)
== 0
)
# copied verbatim from test_compute_conc_metrics
wd = duplex_metrics.well_metric_name_dict
assert wd["A01"].well_channel_metrics[0].expected_concentration == 0
assert wd["A01"].well_channel_metrics[1].expected_concentration == 1000
assert wd["B02"].well_channel_metrics[0].expected_concentration == 125
assert wd["B02"].well_channel_metrics[1].expected_concentration == 1000
assert wd["C03"].well_channel_metrics[0].expected_concentration == 250
assert wd["C03"].well_channel_metrics[1].expected_concentration == 1000
assert wd["D04"].well_channel_metrics[0].expected_concentration == 500
assert wd["D04"].well_channel_metrics[1].expected_concentration == 1000
assert wd["A05"].well_channel_metrics[0].expected_concentration == 1020
assert wd["A05"].well_channel_metrics[1].expected_concentration == 1000
assert wd["B06"].well_channel_metrics[0].expected_concentration == 2000
assert wd["B06"].well_channel_metrics[1].expected_concentration == 1000
assert wd["B02"].well_channel_metrics[0].concentration > 118
assert wd["B02"].well_channel_metrics[0].concentration < 119
assert wd["B02"].well_channel_metrics[1].concentration > 978
assert wd["B02"].well_channel_metrics[1].concentration < 979
fpfn_metrics = get_beta_plate_metrics(self.fpfn_dbplate, self.fpfn_qlplate)
assert (
len([wm for wm in fpfn_metrics.well_metrics if wm.well_channel_metrics[1].false_positive_peaks is not None])
== 2
)
assert (
len([wm for wm in fpfn_metrics.well_metrics if wm.well_channel_metrics[1].false_negative_peaks is not None])
== 1
)
assert (
len([wm for wm in fpfn_metrics.well_metrics if wm.well_channel_metrics[0].auto_threshold_expected is False])
== 24
)
assert (
len([wm for wm in fpfn_metrics.well_metrics if wm.well_channel_metrics[1].auto_threshold_expected is False])
== 19
)
# copied verbatim from test_compute_false_positives
wd = fpfn_metrics.well_metric_name_dict
assert wd["F03"].well_channel_metrics[1].false_positive_peaks == 0
assert wd["F06"].well_channel_metrics[1].false_positive_peaks == 6
assert wd["E03"].well_channel_metrics[1].false_negative_peaks == 61
red_metrics = get_beta_plate_metrics(self.red_dbplate, self.red_qlplate)
# copied verbatim from test_compute_lod_false_positives
wd = red_metrics.well_metric_name_dict
assert (
len([well for name, well in wd.items() if well.well_channel_metrics[0].false_positive_peaks is None]) == 21
)
assert (
len([well for name, well in wd.items() if well.well_channel_metrics[0].false_positive_peaks is not None])
== 3
)
assert (
len([wm for wm in red_metrics.well_metrics if wm.well_channel_metrics[0].auto_threshold_expected is False])
== 12
)
assert (
len([wm for wm in red_metrics.well_metrics if wm.well_channel_metrics[1].auto_threshold_expected is False])
== 21
)
assert wd["E10"].well_channel_metrics[0].false_positive_peaks == 5
assert wd["E11"].well_channel_metrics[0].false_positive_peaks == 5
assert wd["E12"].well_channel_metrics[0].false_positive_peaks == 5
# since RED has both expected conc and false positives, just test expected conc
assert wd["E07"].well_channel_metrics[0].expected_concentration == 0
assert wd["E07"].well_channel_metrics[1].expected_concentration == 0
assert wd["E10"].well_channel_metrics[0].expected_concentration == 0
assert wd["E10"].well_channel_metrics[1].expected_concentration is None
assert wd["F08"].well_channel_metrics[0].expected_concentration == 0.1
assert wd["F08"].well_channel_metrics[1].expected_concentration is None
assert wd["F12"].well_channel_metrics[0].expected_concentration == 0.5
assert wd["F12"].well_channel_metrics[1].expected_concentration is None
assert wd["G09"].well_channel_metrics[0].expected_concentration == 1
assert wd["G09"].well_channel_metrics[1].expected_concentration is None
assert wd["G11"].well_channel_metrics[0].expected_concentration == 5
assert wd["G11"].well_channel_metrics[1].expected_concentration is None
assert wd["H07"].well_channel_metrics[0].expected_concentration == 10
assert wd["H07"].well_channel_metrics[1].expected_concentration is None
assert wd["H10"].well_channel_metrics[0].expected_concentration == 10
assert wd["H10"].well_channel_metrics[1].expected_concentration is None
def write_images_stats_for_plate(dbplate, qlplate, image_source, overwrite=False, override_plate_type=None):
"""
Write plate metrics to the database and thumbnails to local storage,
as dictated by image_source.
Metrics will be related to the supplied dbplate (Plate model)
qlplate is a QLPlate object derived from reading the QLP file.
"""
if image_source.subdir_exists(str(dbplate.id)):
if not overwrite:
return
else:
image_source.make_subdir(str(dbplate.id))
max_amplitudes = (24000, 12000)
show_only_gated = False # keep default behavior
if qlplate:
for well_name, qlwell in sorted(qlplate.analyzed_wells.items()):
# TODO: common lib?
if well_channel_automatic_classification(qlwell, 0):
fig = plot_fam_peaks(qlwell.peaks,
threshold=qlwell.channels[0].statistics.threshold,
max_amplitude=max_amplitudes[0])
else:
fig = plot_fam_peaks(qlwell.peaks,
threshold=qlwell.channels[0].statistics.threshold,
threshold_color='red',
max_amplitude=max_amplitudes[0],
background_rgb=MANUAL_THRESHOLD_FAM_BGCOLOR)
fig.savefig(image_source.get_path('%s/%s_%s.png' % (dbplate.id, well_name, 0)), format='png', dpi=72)
plt_cleanup(fig)
if well_channel_automatic_classification(qlwell, 1):
fig = plot_vic_peaks(qlwell.peaks,
threshold=qlwell.channels[1].statistics.threshold,
max_amplitude=max_amplitudes[1])
else:
fig = plot_vic_peaks(qlwell.peaks,
threshold=qlwell.channels[1].statistics.threshold,
threshold_color='red',
max_amplitude=max_amplitudes[1],
background_rgb=MANUAL_THRESHOLD_VIC_BGCOLOR)
fig.savefig(image_source.get_path('%s/%s_%s.png' % (dbplate.id, well_name, 1)), format='png', dpi=72)
plt_cleanup(fig)
if qlwell.clusters_defined:
threshold_fallback = qlwell.clustering_method == QLWell.CLUSTERING_TYPE_THRESHOLD
fig = plot_cluster_2d(qlwell.peaks,
width=60,
height=60,
thresholds=[qlwell.channels[0].statistics.threshold,
qlwell.channels[1].statistics.threshold],
boundaries=[0,0,12000,24000],
show_axes=False,
antialiased=True,
unclassified_alpha=0.5,
use_manual_clusters=not well_channel_automatic_classification(qlwell),
highlight_thresholds=threshold_fallback)
fig.savefig(image_source.get_path('%s/%s_2d.png' % (dbplate.id, well_name)), format='png', dpi=72)
plt_cleanup(fig)
pm = [pm for pm in dbplate.plate.metrics if pm.reprocess_config_id is None]
for p in pm:
Session.delete(p)
plate = dbplate_tree(dbplate.plate.id)
# override plate_type if supplied (another artifact of bad abstraction)
if override_plate_type:
plate.plate_type = override_plate_type
# this relies on apply_template/apply_setup working correctly on plate addition
# verify on DR 10005 plate that this works
if plate.plate_type and plate.plate_type.code in beta_plate_types:
plate_metrics = get_beta_plate_metrics(plate, qlplate)
else:
plate_metrics = process_plate(plate, qlplate)
Session.add(plate_metrics)
