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 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 __call__(self):
self.started.emit()
self.progressSetRange.emit(0, len(self.files))
writer = HdfWriter(self.outfile)
colors = [self.colors[ch] for ch in self.channels.values()]
writer.setupFile(self.metadata.n_images, self.channels, colors)
writer.saveSettings(self.seg_params, self.feature_groups,
self.channels.values(), self.colors)
try:
gsize = self.seg_params.values()[0].gallery_size
for i, (file_, treatment) in enumerate(self.files.iteritems()):
self.progressUpdate.emit(i + 1)
self.interruption_point()
self.thread().msleep(self.PYDELAY)
mp = LsmProcessor(file_, self.seg_params, self.channels, gsize,
treatment)
# first channel for primary segementation
mp.segmentation()
mp.calculateFeatures(self.feature_groups)
objects = mp.objects
# saveData ignores empty objects
image = mp.image[:, :, :, self.channels.keys()]
writer.saveData(objects, image, treatment)
self.contourImage.emit(tuple(mp.iterQImages()),
objects.contours)
self.progressSetRange.emit(0, 0)
self.progressUpdate.emit(-1)
writer.flush()
self.finished.emit()
except AbortQWorker:
pass
except HdfError as e:
self.error.emit(e)
traceback.print_exc()
raise
except Exception as e:
self.error.emit(e)
traceback.print_exc()
raise
finally:
writer.close()
def __call__(self):
self.started.emit()
self.progressSetRange.emit(0, len(self.files))
writer = HdfWriter(self.outfile)
colors = [self.colors[ch] for ch in self.channels.values()]
writer.setupFile(self.metadata.n_images, self.channels, colors)
writer.saveSettings(self.seg_params, self.feature_groups,
self.channels.values(), self.colors)
try:
gsize = self.seg_params.values()[0].gallery_size
for i, (file_, treatment) in enumerate(self.files.iteritems()):
self.progressUpdate.emit(i+1)
self.interruption_point()
self.thread().msleep(self.PYDELAY)
mp = LsmProcessor(file_, self.seg_params, self.channels, gsize,
treatment)
# first channel for primary segementation
mp.segmentation()
mp.calculateFeatures(self.feature_groups)
objects = mp.objects
# saveData ignores empty objects
image = mp.image[:, :, :, self.channels.keys()]
writer.saveData(objects, image, treatment)
self.contourImage.emit(tuple(mp.iterQImages()),
objects.contours)
self.progressSetRange.emit(0, 0)
self.progressUpdate.emit(-1)
writer.flush()
self.finished.emit()
except AbortQWorker:
pass
except HdfError as e:
self.error.emit(e)
traceback.print_exc()
raise
except Exception as e:
self.error.emit(e)
traceback.print_exc()
raise
finally:
writer.close()