def saveData(self):
# be carefull save Data is runs in a different thread
# (callback of map_async)
self.pool.close()
self.pool.join()
self.parent().onFileClose()
writer = HdfWriter(self.dataFile.text())
try:
channels = self.cbar.checkedChannels()
proc = TiffProcessor(
self._files[0], self._regex, self.segdlg.segmentationParams(), self.cbar.checkedChannels()
)
colors = [self.cbar.colors[ch] for ch in channels.values()]
writer.setupFile(len(self._files), channels, colors)
writer.saveSettings(
self.segdlg.segmentationParams(), self.segdlg.featureGroups(), channels.values(), self.cbar.colors
)
for i, res_ in enumerate(self.results):
res = res_.get()
file_, image, image_objects, feature_names = res
# reconstruct the ObjectDict
objects = ObjectDict("multicolor")
objects.feature_names = feature_names
for obj in image_objects:
objects[obj.label] = obj
writer.saveData(objects, image, None, file_.file)
self.incrementProgress()
writer.flush()
finally:
writer.close()
self.finished.emit()
def import_images(files, outfile, params):
proc = TiffProcessor(files[0], None, params.seg_params, params.channels, params.gsize)
writer = HdfWriter(outfile)
colors = [params.colors[c] for c in params.channels.values()]
writer.setupFile(len(files), params.channels, colors)
writer.saveSettings(params.seg_params, params.feature_groups,
params.channels.values(), params.colors)
pool = Pool(processes=8)#, initializer=initfunc, initargs=("Hello world!", ))
fprm = zip(files, len(files)*[params])
results = list()
for fp in fprm:
#import pdb; pdb.set_trace()
results.append(pool.apply_async(process_image, fp, callback=callback))
pool.close()
pool.join()
for res, file_ in zip(results, files):
_, image, image_objects, feature_names = res.get()
# reconstruct the ObjectDict
objects = ObjectDict("multicolor")
objects.feature_names = feature_names
for obj in image_objects:
objects[obj.label] = obj
writer.saveData(objects, image, None, file_)
writer.flush()
def objects(self):
if self._objects is None:
odict = ObjectDict("multicolor")
for i, (name, container) in enumerate(self._containers.iteritems()):
for label, cobj in container.getObjects().iteritems():
obj = ImageObject(
name, cobj, container.getCrackCoordinates(label),
self.treatment, label)
if odict.has_key(label):
odict.concatenate(name, label, obj)
else:
# mulitchannel gallery image
obj.gallery_image = self._gallery_image(
obj.center, gallery_size=self.gsize)
odict[label] = obj
# set feature names extend with a prefix
try:
cn = name.split()[1]
odict.feature_names.extend(
["ch%s-%s" %(cn, n) for n in obj.feature_names])
except UnboundLocalError as e:
# empty image has no objects
pass
removed = odict.remove_incomplete()
if len(removed) > 0:
warnings.warn("%d objects have been removed" %len(removed))
self._objects = odict
return self._objects
def objects(self):
if self._objects is None:
odict = ObjectDict("multicolor")
for i, (name,
container) in enumerate(self._containers.iteritems()):
for label, cobj in container.getObjects().iteritems():
obj = ImageObject(name, cobj,
container.getCrackCoordinates(label),
self.treatment, label)
if odict.has_key(label):
odict.concatenate(name, label, obj)
else:
# mulitchannel gallery image
obj.gallery_image = self._gallery_image(
obj.center, gallery_size=self.gsize)
odict[label] = obj
# set feature names extend with a prefix
try:
cn = name.split()[1]
odict.feature_names.extend(
["ch%s-%s" % (cn, n) for n in obj.feature_names])
except UnboundLocalError as e:
# empty image has no objects
pass
removed = odict.remove_incomplete()
if len(removed) > 0:
warnings.warn("%d objects have been removed" % len(removed))
self._objects = odict
return self._objects