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Consider layer transform metadata when applying transform #85

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merged 3 commits into from
Nov 27, 2023
Merged

Consider layer transform metadata when applying transform #85

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ee19c12
Add failing test for issue #80
jni Nov 4, 2023
711f126
Consider layer transform metadata when applying transform
jni Nov 26, 2023
bb06c28
Use correct path for labels zarr
jni Nov 27, 2023
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20 changes: 18 additions & 2 deletions src/affinder/_tests/test_affinder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import napari
import pytest
from scipy import ndimage as ndi
from pathlib import Path


layer0_pts = np.array([[140.38371886,
Expand All @@ -21,8 +22,9 @@
# get reference and moving layer types
im0 = data.camera()
im1 = transform.rotate(im0[100:, 32:496], 60)
labels0 = zarr.open('./src/affinder/_tests/labels0.zarr', mode='r')
labels1 = zarr.open('./src/affinder/_tests/labels1.zarr', mode='r')
this_dir = Path(__file__).parent.absolute()
labels0 = zarr.open(this_dir / 'labels0.zarr', mode='r')
labels1 = zarr.open(this_dir / 'labels1.zarr', mode='r')


def make_vector_border(layer_pts):
Expand Down Expand Up @@ -126,6 +128,20 @@ def test_apply_affine():
np.testing.assert_allclose(res_layer[0], ref_im)


def test_apply_affine_with_scale():
ref_im = np.random.random((5, 5))
mov_im = ndi.zoom(ref_im, 2, order=0)

ref_layer = napari.layers.Image(ref_im, scale=(0.2, 0.2))
mov_layer = napari.layers.Image(mov_im, scale=(0.4, 0.4))
mov_layer.affine = np.array([[0.25, 0, 0], [0, 0.25, 0], [0, 0, 1]])

widget = apply_affine()
res_layer = widget(ref_layer, mov_layer)

np.testing.assert_allclose(res_layer[0], ref_im)


def test_apply_affine_nonimage():
ref_im = np.random.random((5, 5))
mov_pts = np.random.random((5, 2))
Expand Down
19 changes: 18 additions & 1 deletion src/affinder/apply_tf.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from magicgui import magic_factory
from skimage import transform
from napari.utils.transforms import CompositeAffine
import numpy as np


Expand Down Expand Up @@ -62,8 +63,24 @@ def apply_affine(
'Only image transforms supported at this point.'
)

reference_meta = CompositeAffine(
scale=reference_layer.scale,
translate=reference_layer.translate,
rotate=reference_layer.rotate,
shear=reference_layer.shear,
)
moving_meta = CompositeAffine(
scale=moving_layer.scale,
translate=moving_layer.translate,
rotate=moving_layer.rotate,
shear=moving_layer.shear,
)
# Find the transformation relative to the reference image
affine = np.linalg.inv(reference_layer.affine) @ moving_layer.affine
affine = (
np.linalg.inv(reference_meta)
@ np.linalg.inv(reference_layer.affine) @ moving_layer.affine
@ moving_meta
)

# Apply the transformation
transformed = _apply_affine_image(
Expand Down
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