def _load_data(self, channel):
dtable = HmmDataTable()
# XXX read region names from hdf not from settings
mask = "%s__%s" % (channel, self.ecopts.regionnames[channel])
c = 2
if self.ecopts.write_gallery:
c += 1
thread = QThread.currentThread()
with Ch5File(self.ch5file, mode="r") as ch5:
layout = ch5.layout(self.plate)
mappings = PlateMapping(layout)
thread.statusUpdate(min=0, max=ch5.numberSites(self.plate) + c)
for site in ch5.iterSites():
ws = "%s_%02d" % (site.well, int(site.site))
thread.statusUpdate(text="loading plate: %s, file: %s" %
(site.plate, ws))
thread.increment.emit()
thread.interruption_point()
QtCore.QCoreApplication.processEvents()
if not ch5.hasClassifier(mask):
continue
# make dtable aware of all positions, sometime they contain
# no tracks and I don't want to ignore them
dtable.add_position(ws, mappings[ws])
if not ch5.hasEvents(site):
continue
objidx = ch5.events(site, self.ecopts.ignore_tracking_branches)
tracks = np.asarray(ch5.predictions(site, mask))[objidx]
try:
probs = ch5.probabilities(site, mask)[objidx, :]
except KeyError as e:
probs = None
site.mask = mask
dtable.add_tracks(tracks, ws, mappings[ws], objidx, site,
probs)
if dtable.is_empty():
raise RuntimeError(
"No data found for plate '%s' and channel '%s' " %
(self.plate, channel))
return dtable, self._load_classdef(mask)
def __call__(self):
self._makedirs()
mappings = PlateMapping([splitext(basename(f))[0] for f in self.files])
if self.ecopts.position_labels:
mpfile = join(self.ecopts.mapping_dir, "%s.txt" %self.plate)
mappings.read(mpfile)
for channel in self.ecopts.regionnames.keys():
dtable, cld = self._load_data(mappings, channel)
msg = 'performing error correction on channel %s' %channel
self.interruption_point(msg)
# error correction
if self.ecopts.hmm_algorithm == self.ecopts.HMM_BAUMWELCH:
hmm = HmmSklearn(dtable, channel, cld, self.ecopts)
else:
hmm = HmmTde(dtable, channel, cld, self.ecopts)
data = hmm()
# plots and export
report = HmmReport(data, self.ecopts, cld, self._hmm_dir)
prefix = "%s_%s" %(channel.title(), self.ecopts.regionnames[channel])
sby = self.ecopts.sortby.replace(" ", "_")
self.interruption_point("plotting overview")
report.overview(join(self._hmm_dir, '%s-%s.pdf' %(prefix, sby)))
report.close_figures()
self.interruption_point("plotting bar- and boxplots")
report.bars_and_boxes(join(self._hmm_dir, '%s-%s_boxbars.pdf'
%(prefix, sby)))
report.close_figures()
self.interruption_point("plotting hmm model")
report.hmm_model(join(self._hmm_dir, "%s-%s_model.pdf")
%(prefix, sby))
if self.ecopts.write_gallery:
self.interruption_point("plotting image gallery")
try:
# replace image_gallery_png with image_gallery_pdf
fn = join(self._gallery_dir,
'%s-%s_gallery.png' %(prefix, sby))
with cellh5.ch5open(self.ch5file, 'r') as ch5:
report.image_gallery_png(ch5, fn, self.ecopts.n_galleries,
self.ecopts.resampling_factor,
self.ecopts.size_gallery_image)
report.close_figures()
except Exception as e: # don't stop error corection
with open(join(self._gallery_dir, '%s-%s_error_readme.txt'
%(prefix, sby)), 'w') as fp:
traceback.print_exc(file=fp)
fp.write("Check if gallery images exist!")
report.export_hmm(join(self._hmm_dir, "%s-%s_hmm.csv"
%(prefix, sby)),
self.ecopts.sortby)
def __call__(self):
self._makedirs()
mappings = PlateMapping([splitext(basename(f))[0] for f in self.files])
if self.ecopts.position_labels:
mpfile = join(self.ecopts.mapping_dir, "%s.txt" % self.plate)
mappings.read(mpfile)
for channel in self.ecopts.regionnames.keys():
dtable, cld = self._load_data(mappings, channel)
msg = 'performing error correction on channel %s' % channel
self.interruption_point(msg)
# error correction
if self.ecopts.hmm_algorithm == self.ecopts.HMM_BAUMWELCH:
hmm = HmmSklearn(dtable, channel, cld, self.ecopts)
else:
hmm = HmmTde(dtable, channel, cld, self.ecopts)
data = hmm()
# plots and export
report = HmmReport(data, self.ecopts, cld, self._hmm_dir)
prefix = "%s_%s" % (channel.title(),
self.ecopts.regionnames[channel])
sby = self.ecopts.sortby.replace(" ", "_")
self.interruption_point("plotting overview")
report.overview(join(self._hmm_dir, '%s-%s.pdf' % (prefix, sby)))
report.close_figures()
self.interruption_point("plotting bar- and boxplots")
report.bars_and_boxes(
join(self._hmm_dir, '%s-%s_boxbars.pdf' % (prefix, sby)))
report.close_figures()
self.interruption_point("plotting hmm model")
report.hmm_model(
join(self._hmm_dir, "%s-%s_model.pdf") % (prefix, sby))
if self.ecopts.write_gallery:
self.interruption_point("plotting image gallery")
try:
# replace image_gallery_png with image_gallery_pdf
fn = join(self._gallery_dir,
'%s-%s_gallery.png' % (prefix, sby))
with cellh5.ch5open(self.ch5file, 'r') as ch5:
report.image_gallery_png(
ch5, fn, self.ecopts.n_galleries,
self.ecopts.resampling_factor,
self.ecopts.size_gallery_image)
report.close_figures()
except Exception as e: # don't stop error corection
with open(
join(self._gallery_dir,
'%s-%s_error_readme.txt' % (prefix, sby)),
'w') as fp:
traceback.print_exc(file=fp)
fp.write("Check if gallery images exist!")
report.export_hmm(
join(self._hmm_dir, "%s-%s_hmm.csv" % (prefix, sby)),
self.ecopts.sortby)
# replace image_gallery_png with image_gallery_pdf
fn = join(self._gallery_dir,
'%s-%s_gallery.png' %(prefix, sby))
with cellh5.ch5open(self.ch5file, 'r') as ch5:
report.image_gallery_png(ch5, fn, self.ecopts.n_galleries,
self.ecopts.resampling_factor,
self.ecopts.size_gallery_image)
report.close_figures()
except Exception as e: # don't stop error corection
with open(join(self._gallery_dir, '%s-%s_error_readme.txt'
%(prefix, sby)), 'w') as fp:
traceback.print_exc(file=fp)
fp.write("Check if gallery images exist!")
report.export_hmm(join(self._hmm_dir, "%s-%s_hmm.csv"
%(prefix, sby)),
self.ecopts.sortby)
if __name__ == "__main__":
path_in = '/Users/hoefler/demo_data/ibb/mappings/input.txt'
path_out = '/Users/hoefler/demo_data/ibb/mappings/output.txt'
positons = ["018", "028", "051", "067"]
pm = PlateMapping(positons)
pm.read(path_in)
pm['018']['OligoID'] = "just made up"
pm.save(path_out)
with cellh5.ch5open(self.ch5file, 'r') as ch5:
report.image_gallery_png(
ch5, fn, self.ecopts.n_galleries,
self.ecopts.resampling_factor,
self.ecopts.size_gallery_image)
report.close_figures()
except Exception as e: # don't stop error corection
with open(
join(self._gallery_dir,
'%s-%s_error_readme.txt' % (prefix, sby)),
'w') as fp:
traceback.print_exc(file=fp)
fp.write("Check if gallery images exist!")
report.export_hmm(
join(self._hmm_dir, "%s-%s_hmm.csv" % (prefix, sby)),
self.ecopts.sortby)
if __name__ == "__main__":
path_in = '/Users/hoefler/demo_data/ibb/mappings/input.txt'
path_out = '/Users/hoefler/demo_data/ibb/mappings/output.txt'
positons = ["018", "028", "051", "067"]
pm = PlateMapping(positons)
pm.read(path_in)
pm['018']['OligoID'] = "just made up"
pm.save(path_out)
