def _gallery_image(self, center, gallery_size=50):
height, width, zslices, nchannels = self.image.shape
halfsize = int(np.floor(gallery_size/2.0))
xmin = center.x - halfsize
xmax = xmin + gallery_size
ymin = center.y - halfsize
ymax = ymin + gallery_size
if xmin < 0:
xmin = 0
xmax = gallery_size
elif xmax >= width:
xmin = width - gallery_size
xmax = width
if ymin < 0:
ymin = 0
ymax = gallery_size
elif ymax >= height:
ymin = height - gallery_size
ymax = height
zprojection = self.params.values()[0].zprojection
gimg = self.image[ymin:ymax, xmin:xmax, :, self._channel_idx]
gimg = zProjection(gimg, zprojection, self.zslice)
if gimg.dtype == np.dtype('uint8'):
return gimg
else:
return self.normalize(gimg, norm_min=np.floor(gimg.min()),
norm_max=np.ceil(gimg.max()))
def segmentation(self):
# needed for gallery images
self._channel_idx = self.channels.keys()
# the master (primary) channel is determined by the first item
# the segmentation parameters (OrderedDict)
# channels_r = OrderedDict([(v, k) for k, v in self.channels.items()])
# segment the master first
cname = self.channels[self.imaster]
image = zProjection(self.image[:, :, :, :].copy(),
self.params[cname].zprojection, self.zslice)
cnt = self.threshold(image[:, :, self.imaster], self.params[cname])
self._containers[cname] = cnt
label_image = self._containers[cname].img_labels.toArray()
self._filter(self._containers[cname], self.params[cname])
rbo = self.params[cname].remove_borderobjects
for i, name in self.channels.iteritems():
if i == self.imaster:
continue
self._containers[name] = self.seededRegion( \
image[:, :, i], label_image, *self.params[name],
remove_borderobjects=rbo)
self._filterByLabels()
def iterQImages(self, all_channels=True, normalize=True):
"""Iterator over to qimage converted images, one qimage per channel."""
if all_channels:
channels = range(self._reader.channels)
else:
channels = self.channels.keys()
zprojection = self.params.values()[0].zprojection
qimages = list()
for ci in channels:
image = zProjection(self.image[:, :, :, ci], zprojection,
self.zslice)
qimages.append(gray2qimage(image, normalize=normalize))
return qimages
