def get_plate_image_url( qlbplate_id ):
# still using qlbplate is bad but hard to unwind without complete rename of all folders...
plate = Session.query(QLBPlate).get(qlbplate_id)
local = plate.plate.box2.fileroot in config['qlb.local_fileroots']
if local:
image_url = config['qlb.image_url']
else:
image_url = config['qlb.%s_image_url' % plate.plate.box2.fileroot]
image_source = QLBImageSource( image_url, isLocal = False )
plate_image_url = image_source.get_path( str( plate.id ) )
return plate_image_url
def command(self):
from qtools.lib.mplot import plot_cluster_2d, cleanup as plt_cleanup
app = self.load_wsgi_app()
image_root = app.config['qlb.image_store']
image_source = QLBImageSource(image_root)
# enforce config.ini
if len(self.args) < 2:
raise ValueError, self.__class_.usage
analysis_group_id = int(self.args[0])
if len(self.args) == 3:
reprocess_config = Session.query(ReprocessConfig).filter_by(code=self.args[1]).one()
reprocess_config_id = reprocess_config.id
else:
reprocess_config = None
reprocess_config_id = None
if reprocess_config:
data_root = app.config['qlb.reprocess_root']
storage = QLPReprocessedFileSource(data_root, reprocess_config)
else:
storage = QLStorageSource(app.config)
analysis_group = Session.query(AnalysisGroup).get(analysis_group_id)
if not analysis_group:
raise ValueError, "No analysis group for id %s" % analysis_group_id
plates = analysis_group.plates
for plate in plates:
# TODO: UGH THIS CODE INVARIANT SUCKS (should merge QLReprocessedFile/QLStorageSources)
if reprocess_config:
plate_path = storage.full_path(analysis_group, plate)
else:
plate_path = storage.plate_path(plate)
print "Reading %s" % plate_path
qlplate = get_plate(plate_path)
if not qlplate:
print "Could not read plate: %s" % plate.name
continue
print "Generating thumbnails for %s" % plate.name
for name, qlwell in sorted(qlplate.analyzed_wells.items()):
# TODO abstract into utility image generation function (thumbnail.py?)
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)
image_path = image_source.get_path('%s/%s_2d.png' % (plate.qlbplate.id, name))
print image_path
fig.savefig(image_path, format='png', dpi=72)
plt_cleanup(fig)
