Merge pull request #337 from clEsperanto/stitching

Stitching

pyclesperanto_prototype/_tier3/__init__.py

@@ -56,6 +56,7 @@
 from ._standard_deviation_of_touching_neighbors_map import standard_deviation_of_touching_neighbors_map
 from ._standard_deviation_of_proximal_neighbors_map import standard_deviation_of_proximal_neighbors_map
 from ._standard_deviation_of_proximal_neighbors_map import standard_deviation_of_proximal_neighbors_map as standard_deviation_of_distal_neighbors_map
-
+from ._stitch_horizontally_linear_blending import stitch_horizontally_linear_blending
+from ._stitch_vertically_linear_blending import stitch_vertically_linear_blending
 from ._subtract_gaussian_background import subtract_gaussian_background
-from ._z_position_range_projection import z_position_range_projection
+from ._z_position_range_projection import z_position_range_projection

pyclesperanto_prototype/_tier3/_stitch_horizontally_linear_blending.py

@@ -0,0 +1,51 @@
+from .._tier0 import plugin_function
+from .._tier0 import create
+from .._tier0 import create_none
+from .._tier0 import Image
+from .._tier1 import paste
+
+@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant'])
+def stitch_horizontally_linear_blending(image1 : Image, image2 : Image, destination : Image = None, num_pixels_overlap:int=0) -> Image:
+    """Combines two images in X by linearly blending them in an overlapping region.
+
+    Parameters
+    ----------
+    image1 : Image
+    image2 : Image
+    destination : Image, optional
+    num_pixels_overlap : int, optional
+
+    Returns
+    -------
+    destination
+    """
+    from .._tier0 import create, asarray
+    from .._tier1 import set_ramp_x, crop
+    from .._tier1 import subtract_image_from_scalar
+    from .._tier2 import combine_horizontally
+
+    num_pixels_overlap = int(num_pixels_overlap)
+    image1_width = image1.shape[-1]
+    image2_width = image2.shape[-1]
+    image1_height = image1.shape[-2]
+    image2_height = image2.shape[-2]
+    image1_depth = 1 if len(image1.shape) == 2 else image1.shape[-3]
+    image2_depth = 1 if len(image2.shape) == 2 else image2.shape[-3]
+
+    # crop out left, right and the two overlapping parts
+    left_part = crop(image1, width=image1_width - num_pixels_overlap, height=image1_height, depth=image1_depth)
+    center_part1 = crop(image1, start_x=image1_width - num_pixels_overlap, width=num_pixels_overlap, height=image1_height, depth=image1_depth)
+    center_part2 = crop(image2, width=num_pixels_overlap, height=image2_height, depth=image2_depth)
+    right_part = crop(image2, start_x=num_pixels_overlap, width=image2_width - num_pixels_overlap, height=image2_height, depth=image2_depth)
+
+    # setup a gradient for the blending
+    gradient = create(center_part1.shape)
+    set_ramp_x(gradient)
+    gradient_right_left = (gradient + 1) / (gradient.shape[-1]+1)
+    gradient_left_right = subtract_image_from_scalar(gradient_right_left, scalar=1)
+
+    # compute the overlapping image by multiplying both images with the gradient
+    center_part = asarray(center_part1) * gradient_left_right + asarray(center_part2) * gradient_right_left
+
+    # combine images vertically
+    return combine_horizontally(combine_horizontally(left_part, center_part), right_part, destination)

pyclesperanto_prototype/_tier3/_stitch_vertically_linear_blending.py

@@ -0,0 +1,51 @@
+from .._tier0 import plugin_function
+from .._tier0 import create
+from .._tier0 import create_none
+from .._tier0 import Image
+from .._tier1 import paste
+
+@plugin_function(output_creator=create_none, categories=['combine', 'transform', 'in assistant'])
+def stitch_vertically_linear_blending(image1 : Image, image2 : Image, destination : Image = None, num_pixels_overlap:int=0) -> Image:
+    """Combines two images in Y by linearly blending them in an overlapping region.
+
+    Parameters
+    ----------
+    image1 : Image
+    image2 : Image
+    destination : Image, optional
+    num_pixels_overlap : int, optional
+
+    Returns
+    -------
+    destination
+    """
+    from .._tier0 import create, asarray
+    from .._tier1 import set_ramp_y, crop
+    from .._tier1 import subtract_image_from_scalar
+    from .._tier2 import combine_vertically
+
+    num_pixels_overlap = int(num_pixels_overlap)
+    image1_width = image1.shape[-1]
+    image2_width = image2.shape[-1]
+    image1_height = image1.shape[-2]
+    image2_height = image2.shape[-2]
+    image1_depth = 1 if len(image1.shape) == 2 else image1.shape[-3]
+    image2_depth = 1 if len(image2.shape) == 2 else image2.shape[-3]
+
+    # crop out left, right and the two overlapping parts
+    top_part = crop(image1, width=image1_width, height=image1_height - num_pixels_overlap, depth=image1_depth)
+    center_part1 = crop(image1, start_y=image1_height-num_pixels_overlap, width=image1_width, height=num_pixels_overlap, depth=image1_depth)
+    center_part2 = crop(image2, width=image2_width, height=num_pixels_overlap, depth=image2_depth)
+    bottom_part = crop(image2, start_y=num_pixels_overlap, width=image2_width, height=image2_height-num_pixels_overlap, depth=image2_depth)
+
+    # setup a gradient for the blending
+    gradient = create(center_part1.shape)
+    set_ramp_y(gradient)
+    gradient_right_left = (gradient + 1) / (gradient.shape[-2]+1)
+    gradient_left_right = subtract_image_from_scalar(gradient_right_left, scalar=1)
+
+    # compute the overlapping image by multiplying both images with the gradient
+    center_part = asarray(center_part1) * gradient_left_right + asarray(center_part2) * gradient_right_left
+
+    # combine images vertically
+    return combine_vertically(combine_vertically(top_part, center_part), bottom_part, destination)

tests/test_stitch_horizontally_linear_blending.py

@@ -0,0 +1,80 @@
+import pyclesperanto_prototype as cle
+import numpy as np
+
+
+def test_stitch_horizontally_linear_blending_overlap0():
+    test1 = cle.push(np.asarray([
+        [1, 1],
+        [1, 1]
+    ]))
+    test2 = cle.push(np.asarray([
+        [2, 2, 2],
+        [2, 2, 2]
+    ]))
+
+    reference = cle.push(np.asarray([
+        [1, 1, 2, 2, 2],
+        [1, 1, 2, 2, 2]
+    ]))
+
+    result = cle.stitch_horizontally_linear_blending(test1, test2)
+
+    a = cle.pull(result)
+    b = cle.pull(reference)
+
+    print(a)
+    print(b)
+
+    assert (np.allclose(a, b, 0.01))
+
+def test_stitch_horizontally_linear_blending_overlap1():
+    test1 = cle.push(np.asarray([
+        [1, 1],
+        [1, 1]
+    ]))
+    test2 = cle.push(np.asarray([
+        [2, 2, 2],
+        [2, 2, 2]
+    ]))
+
+    reference = cle.push(np.asarray([
+        [1, 1.5, 2, 2],
+        [1, 1.5, 2, 2]
+    ]))
+
+    result = cle.stitch_horizontally_linear_blending(test1, test2, num_pixels_overlap=1)
+
+    a = cle.pull(result)
+    b = cle.pull(reference)
+
+    print(a)
+    print(b)
+
+    assert (np.allclose(a, b, 0.01))
+
+
+def test_stitch_horizontally_linear_blending_overlap2():
+    test1 = cle.push(np.asarray([
+        [1, 1, 1],
+        [1, 1, 1]
+    ]))
+    test2 = cle.push(np.asarray([
+        [2, 2, 2],
+        [2, 2, 2]
+    ]))
+
+    reference = cle.push(np.asarray([
+        [1, 1.33, 1.67, 2],
+        [1, 1.33, 1.67, 2]
+    ]))
+
+    result = cle.stitch_horizontally_linear_blending(test1, test2, num_pixels_overlap=2)
+
+    a = cle.pull(result)
+    b = cle.pull(reference)
+
+    print(a)
+    print(b)
+
+    assert (np.allclose(a, b, 0.01))
+

tests/test_stitch_vertically_linear_blending.py

@@ -0,0 +1,96 @@
+import pyclesperanto_prototype as cle
+import numpy as np
+
+
+def test_stitch_vertically_linear_blending_overlap0():
+    test1 = cle.push(np.asarray([
+        [1, 1],
+        [1, 1],
+        [1, 1]
+    ]))
+    test2 = cle.push(np.asarray([
+        [2, 2],
+        [2, 2],
+        [2, 2]
+    ]))
+
+    reference = cle.push(np.asarray([
+        [1, 1],
+        [1, 1],
+        [1, 1],
+        [2, 2],
+        [2, 2],
+        [2, 2],
+    ]))
+
+    result = cle.stitch_vertically_linear_blending(test1, test2)
+
+    a = cle.pull(result)
+    b = cle.pull(reference)
+
+    print(a)
+    print(b)
+
+    assert (np.allclose(a, b, 0.01))
+
+
+def test_stitch_vertically_linear_blending_overlap1():
+    test1 = cle.push(np.asarray([
+        [1, 1],
+        [1, 1],
+        [1, 1]
+    ]))
+    test2 = cle.push(np.asarray([
+        [2, 2],
+        [2, 2],
+        [2, 2]
+    ]))
+
+    reference = cle.push(np.asarray([
+        [1, 1],
+        [1, 1],
+        [1.5, 1.5],
+        [2, 2],
+        [2, 2],
+    ]))
+
+    result = cle.stitch_vertically_linear_blending(test1, test2, num_pixels_overlap=1)
+
+    a = cle.pull(result)
+    b = cle.pull(reference)
+
+    print(a)
+    print(b)
+
+    assert (np.allclose(a, b, 0.01))
+
+
+def test_stitch_vertically_linear_blending_overlap2():
+    test1 = cle.push(np.asarray([
+        [1, 1],
+        [1, 1],
+        [1, 1]
+    ]))
+    test2 = cle.push(np.asarray([
+        [2, 2],
+        [2, 2],
+        [2, 2]
+    ]))
+
+    reference = cle.push(np.asarray([
+        [1, 1],
+        [1.33, 1.33],
+        [1.67, 1.67],
+        [2, 2],
+    ]))
+
+    result = cle.stitch_vertically_linear_blending(test1, test2, num_pixels_overlap=2)
+
+    a = cle.pull(result)
+    b = cle.pull(reference)
+
+    print(a)
+    print(b)
+
+    assert (np.allclose(a, b, 0.01))
+