def add_bkg_ovv(im, proj=p):
"""
Receive the projected image (RGB) and add it to the overview
"""
# To handle cases where the projection was faster than subscribing,
# we get called at subscription. If we receive None, we just need
# to be a little bit more patient.
if im is None:
return
if isinstance(proj.stream, stream.OpticalStream):
bkg = self._bkg_opt
else:
bkg = self._bkg_sem
insert_tile_to_image(im, bkg)
logging.debug("Added overview projection %s", proj.name.value)
# Normally not necessary as the image will not change, and the
# projection + stream will go out of scope, which will cause
# the VA to be unsubscribed automatically. But it feels cleaner.
proj.image.unsubscribe(add_bkg_ovv)
del self._bkg_ovv_subs[proj]
# We could only do it when _bkg_ovv_subs is empty, as a sign it's
# the last one... but it could delay quite a bit, and could easily
# break if for some reason projection fails.
self._update_ovv()
def _onNewImage(self, _):
# update overview whenever the streams change, limited to a frequency of 1 Hz
if self.curr_s and self.curr_s.image.value is not None:
s = self.curr_s
img = s.image.value
logging.debug("Updating overview using image at %s", getBoundingBox(img))
if isinstance(s, acqstream.OpticalStream):
insert_tile_to_image(img, self.im_opt)
elif isinstance(s, acqstream.EMStream):
insert_tile_to_image(img, self.im_sem)
else:
logging.info("%s not added to overview image as it's not optical nor EM", s)
self._update_ovv()
def test_image_on_ovv(self):
""" Tests insert_tile_to_image function """
# Insert tile into image
ovv_im = model.DataArray(numpy.zeros((11, 11, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((3, 3, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (-3, 3)
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
# rectangle with edges (-4,4), (-2,4), (-4,2), (-4,2) should be white now
# (6,6) is the center, so this corresponds to a rectangle with top left at (2,2) (=(1,1) when counting from 0)
numpy.testing.assert_array_equal(ovv_im_new[1:4, 1:4, :], tile)
numpy.testing.assert_array_equal(ovv_im_new[5:, 5:, :],
numpy.zeros((6, 6, 3)))
# Test tile that goes beyond the borders of the image top left
ovv_im = model.DataArray(numpy.zeros((5, 5, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((2, 2, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (
-3, 3) # top-left corner, one pixel diagonal to start of ovv
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
self.assertEqual(ovv_im_new[0][0][0],
255) # first pixel white (all three dims), rest black
numpy.testing.assert_array_equal(
ovv_im.flatten()[3:], numpy.zeros(len(ovv_im.flatten()[3:])))
# Test tile that goes beyond the borders of the image bottom right
ovv_im = model.DataArray(numpy.zeros((5, 5, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((2, 2, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (
3, -3) # bottom-right corner, one pixel diagonal to end of ovv
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
self.assertEqual(ovv_im_new[4][4][0], 255)
numpy.testing.assert_array_equal(
ovv_im.flatten()[:-3], numpy.zeros(len(ovv_im.flatten()[3:])))
# Test tile that lies completely outside the overview image
ovv_im = model.DataArray(numpy.zeros((5, 5, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((2, 2, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (10, -10)
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
numpy.testing.assert_array_equal(ovv_im_new, numpy.zeros((5, 5, 3)))
def test_image_on_ovv(self):
""" Tests insert_tile_to_image function """
# Insert tile into image
ovv_im = model.DataArray(numpy.zeros((11, 11, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((3, 3, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (-3, 3)
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
# rectangle with edges (-4,4), (-2,4), (-4,2), (-4,2) should be white now
# (6,6) is the center, so this corresponds to a rectangle with top left at (2,2) (=(1,1) when counting from 0)
numpy.testing.assert_array_equal(ovv_im_new[1:4, 1:4, :], tile)
numpy.testing.assert_array_equal(ovv_im_new[5:, 5:, :], numpy.zeros((6, 6, 3)))
# Test tile that goes beyond the borders of the image top left
ovv_im = model.DataArray(numpy.zeros((5, 5, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((2, 2, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (-3, 3) # top-left corner, one pixel diagonal to start of ovv
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
self.assertEqual(ovv_im_new[0][0][0], 255) # first pixel white (all three dims), rest black
numpy.testing.assert_array_equal(ovv_im.flatten()[3:],
numpy.zeros(len(ovv_im.flatten()[3:])))
# Test tile that goes beyond the borders of the image bottom right
ovv_im = model.DataArray(numpy.zeros((5, 5, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((2, 2, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (3, -3) # bottom-right corner, one pixel diagonal to end of ovv
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
self.assertEqual(ovv_im_new[4][4][0], 255)
numpy.testing.assert_array_equal(ovv_im.flatten()[:-3],
numpy.zeros(len(ovv_im.flatten()[3:])))
# Test tile that lies completely outside the overview image
ovv_im = model.DataArray(numpy.zeros((5, 5, 3), dtype=numpy.uint8))
ovv_im.metadata[model.MD_PIXEL_SIZE] = (1, 1)
tile = model.DataArray(255 * numpy.ones((2, 2, 3), dtype=numpy.uint8))
tile.metadata[model.MD_POS] = (10, -10)
tile.metadata[model.MD_PIXEL_SIZE] = (1, 1)
ovv_im_new = insert_tile_to_image(tile, ovv_im)
numpy.testing.assert_array_equal(ovv_im_new, numpy.zeros((5, 5, 3)))
def _update_ovv(self):
""" Update the overview image with the currently active stream. """
if self.curr_s and self.curr_s.image.value is not None:
s = self.curr_s
img = s.image.value
if isinstance(s, acqstream.OpticalStream):
self.im_opt = insert_tile_to_image(img, self.im_opt)
elif isinstance(s, acqstream.EMStream):
self.im_sem = insert_tile_to_image(img, self.im_sem)
else:
logging.info("%s not added to overview image as it's not optical nor EM", s)
# Merge optical and sem overview images
self.ovv_im = merge_screen(self.im_opt, self.im_sem)
# Update display
self.upd_stream.update(self.ovv_im)
self.canvas.fit_view_to_content()
def _update_ovv(self):
""" Update the overview image with the currently active stream. """
if self.curr_s and self.curr_s.image.value is not None:
s = self.curr_s
img = s.image.value
if isinstance(s, acqstream.OpticalStream):
self.im_opt = insert_tile_to_image(img, self.im_opt)
elif isinstance(s, acqstream.EMStream):
self.im_sem = insert_tile_to_image(img, self.im_sem)
else:
logging.info("%s not added to overview image as it's not optical nor EM", s)
# Merge optical and sem overview images
self.ovv_im = merge_screen(self.im_opt, self.im_sem)
# Update display
self.upd_stream.update(self.ovv_im)
self.canvas.fit_view_to_content()