def test_cross_outside_canvas_raises_index_error(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(width=3, height=3)
with self.assertRaises(IndexError):
canvas.draw_cross(position=(1, 3), color=(1, 1, 1), radius=1)
with self.assertRaises(IndexError):
canvas.draw_cross(position=(3, 1), color=(1, 1, 1), radius=1)
def test_draw_cross_in_lower_right_corner(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(width=3, height=3)
canvas.draw_cross(position=(2, 2), color=(1, 1, 1), radius=1)
layer = np.array([[0, 0, 0], [0, 0, 1], [0, 1, 1]], dtype=np.uint8)
expected = np.dstack([layer, layer, layer])
self.assertTrue(np.array_equal(canvas, expected))
def test_mask_region(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(3, 3)
region = np.zeros((3, 3), dtype=bool)
region[1, 1] = True
canvas.mask_region(region, color=(0, 1, 0))
self.assertEqual(np.sum(canvas), 1)
self.assertTrue(canvas[1, 1, 1])
def test_blank_canvas(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(width=4, height=5)
self.assertTrue(isinstance(canvas, Canvas))
self.assertTrue(isinstance(canvas, np.ndarray))
self.assertEqual(canvas.shape, (5, 4, 3))
self.assertEqual(canvas.dtype, np.uint8)
self.assertEqual(np.sum(canvas), 0)
def test_draw_line_float_input(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(3, 3)
layer = np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]], dtype=np.uint8)
expected = np.dstack([layer, layer, layer])
canvas.draw_line((0.2, 0.3), (1.9, 2.2), color=(1, 1, 1))
self.assertTrue(np.array_equal(canvas, expected))
def test_draw_line_color(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(3, 3)
layer = np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]], dtype=np.uint8)
expected = np.dstack([layer, layer*2, layer*3])
canvas.draw_line((0, 0), (2, 2), color=(1, 2, 3))
self.assertTrue(np.array_equal(canvas, expected))
def test_text_at_outside_image(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(width=6, height=6)
layer = np.array([
[0, 0, 0, 0, 0, 0],
[0, 0, 1, 1, 0, 0],
[0, 1, 0, 0, 1, 0],
[0, 1, 1, 1, 1, 0],
[0, 1, 0, 0, 0, 0],
[0, 1, 1, 0, 0, 0]], dtype=np.uint8)
expected = np.dstack([layer, layer, layer])
canvas.text_at("e", (1, 0), color=(1, 1, 1), antialias=False)
self.assertTrue(np.array_equal(canvas, expected))
def test_text_at_antialias(self):
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(width=6, height=6)
layer = np.array(
[[0, 38, 209, 233, 75, 0],
[0, 182, 77, 48, 212, 0],
[0, 239, 255, 255, 249, 0],
[0, 239, 21, 0, 0, 0],
[0, 176, 145, 10, 0, 0],
[0, 31, 192, 246, 213, 0]], dtype=np.uint8)
expected = np.dstack([layer, layer, layer])
canvas.text_at("e", (0, 0), color=(255, 255, 255), antialias=True)
self.assertTrue(np.array_equal(canvas, expected))
def test_create_annotation_image_from_scratch(self):
from jicbioimage.illustrate import Canvas
# Create an empty canvas.
canvas = Canvas.blank_canvas(50, 75)
# Draw a cross on it, centered on pixel 10,15.
canvas.draw_cross(position=(10, 15), radius=1, color=(1, 0, 0))
self.assertEqual(np.sum(canvas), 5)
self.assertEqual(canvas[10, 15, 0], 1)
self.assertEqual(canvas[9, 15, 0], 1)
self.assertEqual(canvas[11, 15, 0], 1)
self.assertEqual(canvas[10, 14, 0], 1)
self.assertEqual(canvas[10, 16, 0], 1)
def generate_annotation(segmentation):
areas = [
segmentation.region_by_identifier(i).area
for i in segmentation.identifiers
]
imin = min(areas)
imax = max(areas)
ydim, xdim = segmentation.shape
canvas = Canvas.blank_canvas(width=xdim, height=ydim)
for i in segmentation.identifiers:
region = segmentation.region_by_identifier(i)
area = region.area
color = get_normalised_rgb(area, imin, imax)
canvas.mask_region(region.inner.inner, color)
return canvas
def write_zslice(zslice, cellinfo, fpath, intensity_method):
"""Write PNG z-slice."""
ydim, xdim = zslice.shape
imin, imax = min_max_cell_intensity(cellinfo, intensity_method)
canvas = Canvas.blank_canvas(width=xdim, height=ydim)
for i, props in enumerate(cellinfo):
cell_intenistity = intensity_method(props)
color = get_normalised_rgb_from_cell_intensity(cell_intenistity,
imin, imax)
region = zslice == props["cell_id"]
if np.sum(region) == 0:
continue
canvas.mask_region(region, color)
with open(fpath, "wb") as fh:
fh.write(canvas.png())
def test_draw_cross_on_rectangular_canvas(self):
# This used to fail when there was an issue confusing the y, x axis.
from jicbioimage.illustrate import Canvas
canvas = Canvas.blank_canvas(width=3, height=30)
canvas.draw_cross(position=(25, 1), color=(1, 1, 1), radius=1)
self.assertEqual(np.sum(canvas), 15)