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bugfix orthogonal interpolation #284

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bugfix orthogonal interpolation #284

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cd4f954
Ensure trig functions are positive for deskewing
pr4deepr Mar 10, 2023
e65f43e
reran notebooks
pr4deepr Mar 13, 2023
f9dc639
reran notebooks
pr4deepr Mar 13, 2023
595efd9
reran notebooks
pr4deepr Jun 8, 2023
dc1c641
Merge branch 'master' of https://github.com/clEsperanto/pyclesperanto…
pr4deepr Jun 8, 2023
a6fdaab
modified test to push numpy array instead of list
pr4deepr Jun 19, 2023
4b879f8
if negative angle rotate 180
pr4deepr Aug 11, 2023
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65 changes: 37 additions & 28 deletions demo/transforms/deskew.ipynb
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31 changes: 20 additions & 11 deletions demo/transforms/deskew_artifact_interpolation.ipynb
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17 changes: 10 additions & 7 deletions demo/transforms/deskew_x_test.ipynb
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@pr4deepr pr4deepr Jun 8, 2023 •
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@haesleinhuepf I think we ran some of the notebooks before we made some kernel changes, especially the flip z for backward compatbility
As far as I can tell, there are no breaking changes downstream..

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36 changes: 22 additions & 14 deletions demo/transforms/deskew_x_with_other_data.ipynb
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39 changes: 19 additions & 20 deletions demo/transforms/inverse_deskewing.ipynb
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8 changes: 4 additions & 4 deletions pyclesperanto_prototype/_tier8/_affine_transform_deskew_3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,10 +74,10 @@ def affine_transform_deskew_3d(source: Image, destination: Image = None,
# we invert the transform because we go from the target image to the source image to read pixels
transform_matrix = np.asarray(transform.copy().inverse())

# precalculate these functions that are dependent on deskewing angle
tantheta = np.float32(np.tan(deskewing_angle_in_degrees * np.pi/180))
sintheta = np.float32(np.sin(deskewing_angle_in_degrees * np.pi/180))
costheta = np.float32(np.cos(deskewing_angle_in_degrees * np.pi/180))
# precalculate these functions that are dependent on deskewing angle and ensure they are positive
tantheta = np.float32(np.absolute(np.tan(deskewing_angle_in_degrees * np.pi/180)))
sintheta = np.float32(np.absolute(np.sin(deskewing_angle_in_degrees * np.pi/180)))
costheta = np.float32(np.absolute(np.cos(deskewing_angle_in_degrees * np.pi/180)))

gpu_transform_matrix = push(transform_matrix)

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7 changes: 6 additions & 1 deletion pyclesperanto_prototype/_tier8/_deskew_y.py
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Expand Up @@ -48,9 +48,14 @@ def deskew_y(input_image: Image,
from ._AffineTransform3D import AffineTransform3D
from ._affine_transform import affine_transform
from ._affine_transform_deskew_3d import affine_transform_deskew_3d, DeskewDirection
from ._rotate import rotate

if angle_in_degrees<0:
input_image = rotate(input_image,angle_around_y_in_degrees=180,auto_size=True)

transform = AffineTransform3D()

# define affine transformation matrix
transform = AffineTransform3D()
transform._deskew_y(angle_in_degrees=angle_in_degrees, voxel_size_x=voxel_size_x, voxel_size_y=voxel_size_y,
voxel_size_z=voxel_size_z, scale_factor=scale_factor)

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7 changes: 6 additions & 1 deletion tests/test_skimage_imsave.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
def test_skimage_imsave():
import pyclesperanto_prototype as cle
image = cle.push([1, 2, 3])
import numpy as np

image = cle.push(np.asarray([
[1, 2],
[3, 4]
]))

from skimage.io import imsave
imsave('test.tif', image)
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