def create_rois(im):
rgba = [
(255, 255, 255, 128),
(0, 128, 0, 128),
]
labels = [
'Chromosomes',
'Cell',
]
# Separate ROI for each channel and time
mask_files, filenames = get_mask_files(im)
mask_files = get_label_files_in_t_order(im, filenames)
rois = []
for t in range(im.getSizeT()):
maskim = imread(mask_files[t])
assert maskim.shape[0] == im.getSizeZ() * 2
assert maskim.min() == 0
for c in range(2):
roi = omero.model.RoiI()
nshapes = 0
for z in range(im.getSizeZ()):
maskzc = maskim[c * im.getSizeZ() + z]
shapes = masks_from_label_image(maskzc,
rgba=rgba[c],
z=z,
t=t,
text=labels[c],
raise_on_no_mask=False)
for s in shapes:
roi.addShape(s)
nshapes += len(shapes)
print('%s[t=%d] mask:%s shapes:%d' %
(im.name, t, os.path.basename(mask_files[t]), nshapes))
rois.append(roi)
return rois
def test_masks_from_label_image(self, label_image, args):
masks = masks_from_label_image(label_image, **args)
expected = (
# w, h, x, y, bytes
(2, 2, 1, 1, np.array([224], dtype=np.uint8)),
(2, 3, 2, 0, np.array([72], dtype=np.uint8)),
)
assert len(masks) == 2
for i, mask in enumerate(masks):
assert unwrap(mask.getWidth()) == expected[i][0]
assert unwrap(mask.getHeight()) == expected[i][1]
assert unwrap(mask.getX()) == expected[i][2]
assert unwrap(mask.getY()) == expected[i][3]
assert np.array_equal(mask.getBytes(), expected[i][4])
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
def create_rois(mask_path):
masks = masks_from_label_image(
imread(mask_path), rgba=(255, 255, 255, 128))
rois = []
log.debug('Creating %d ROIs' % len(masks))
for mask in masks:
roi = omero.model.RoiI()
roi.addShape(mask)
rois.append(roi)
return rois
def create_rois(im, seg_im):
print("Processing {} - {}".format(im.name, seg_im.shape))
assert im.getSizeX() == seg_im.shape[1]
assert im.getSizeY() == seg_im.shape[0]
rois = []
n_shapes = 0
shapes = masks_from_label_image(seg_im, rgba=RGBA, raise_on_no_mask=False)
if len(shapes) > 0:
n_shapes += len(shapes)
for s in shapes:
roi = omero.model.RoiI()
roi.addShape(s)
rois.append(roi)
print("{} masks created.".format(n_shapes))
return rois
def test_masks_from_label_image(self, label_image, args):
im = self.conn.createImageFromNumpySeq(iter([label_image]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
masks = masks_from_label_image(px, **args)
masks = self.save_and_return_masks(im, masks)
# The rest of this is more or less the same as the unit test
expected = (
# w, h, x, y, bytes
(2, 2, 1, 1, np.array([224], dtype=np.uint8)),
(2, 3, 2, 0, np.array([72], dtype=np.uint8)),
)
assert len(masks) == 2
for i, mask in enumerate(masks):
assert unwrap(mask.getWidth()) == expected[i][0]
assert unwrap(mask.getHeight()) == expected[i][1]
assert unwrap(mask.getX()) == expected[i][2]
assert unwrap(mask.getY()) == expected[i][3]
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8),
expected[i][4])
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None