示例#1
0
 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)
示例#2
0
 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))
示例#3
0
 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])
示例#4
0
 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)
示例#5
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))
示例#6
0
 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))
示例#7
0
 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))
示例#8
0
 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))
示例#9
0
    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())
示例#12
0
 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)