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20x alignment fixes and tests #32

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Merged
merged 1 commit into from
Jul 27, 2022
Merged

20x alignment fixes and tests #32

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4 changes: 2 additions & 2 deletions camera_alignment_core/alignment_utils/segment_rings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ def __init__(
self.thresh = (0.5, 99.5)

def dot_2d_slice_by_slice_wrapper(
self, struct_img: np.typing.NDArray[np.uint16], s2_param: List
self, struct_img: np.typing.NDArray[np.float32], s2_param: List
) -> np.typing.NDArray[np.bool_]:
"""
https://github.com/AllenCell/aics-segmentation/blob/main/aicssegmentation/core/seg_dot.py
Expand Down Expand Up @@ -197,7 +197,7 @@ def segment_rings_dot_filter(
thresh: filter parameter after optimization

"""
img = np.zeros((1, img_2d.shape[0], img_2d.shape[1]), dtype=np.uint16)
img = np.zeros((1, img_2d.shape[0], img_2d.shape[1]), dtype=np.float32)
img[0, :, :] = img_2d

thresh = None
Expand Down
3 changes: 3 additions & 0 deletions camera_alignment_core/tests/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,9 @@
# Taken from /allen/aics/microscopy/PRODUCTION/OpticalControl/ArgoLight/Argo_QC_Daily/ZSD1/ZSD1_argo_100X_SLF-015_20210624 # noqa E501
ZSD_100x_OPTICAL_CONTROL_IMAGE_URL = "https://s3.us-west-2.amazonaws.com/public-dev-objects.allencell.org/camera-alignment-core/optical-controls/argo_ZSD1_100X_SLF-015_20210624.czi" # noqa E501

# Taken from //allen/aics/microscopy/PRODUCTION/OpticalControl/ArgoLight/Argo_QC_Daily/ZSD1/ZSD1_argo_20X_SLG-506_20220510/ZSD1_argo_20X_SLG-506_20220510.czi # noqa E501
ZSD_20x_OPTICAL_CONTROL_IMAGE_URL = "https://s3.us-west-2.amazonaws.com/public-dev-objects.allencell.org/camera-alignment-core/optical-controls/ZSD1_argo_20X_SLG-506_20220510.czi" # noqa E501

# FMS ID: 0023c446cd384dc3947c90dc7a76f794; 303.38 MB
GENERIC_OME_TIFF_URL = "https://s3.us-west-2.amazonaws.com/public-dev-objects.allencell.org/camera-alignment-core/images/3500003897_100X_20200306_1r-Scene-30-P89-G11.ome.tiff" # noqa E501

Expand Down
32 changes: 32 additions & 0 deletions camera_alignment_core/tests/test_alignment_core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
ALIGNED_ZSD1_IMAGE_URL,
ARGOLIGHT_OPTICAL_CONTROL_IMAGE_URL,
UNALIGNED_ZSD1_IMAGE_URL,
ZSD_20x_OPTICAL_CONTROL_IMAGE_URL,
ZSD_100x_OPTICAL_CONTROL_IMAGE_URL,
get_test_image,
)
Expand Down Expand Up @@ -66,6 +67,37 @@ def test_generate_alignment_matrix(self):
actual_alignment_matrix - expected_matrix
)

def test_generate_alignment_matrix_20x(self):
# Arrange
optical_control_image, _ = get_test_image(ZSD_20x_OPTICAL_CONTROL_IMAGE_URL)
optical_control_image_data = optical_control_image.get_image_data("CZYX", T=0)

expected_matrix = numpy.array(
[
[1.00122588e00, -3.02161488e-03, 1.91048540e00],
[3.02161488e-03, 1.00122588e00, -4.75823245e00],
[0.00000000e00, 0.00000000e00, 1.00000000e00],
]
)

# Act
(actual_alignment_matrix, _,) = generate_alignment_matrix(
optical_control_image_data,
reference_channel=2, # TaRFP
shift_channel=3, # CMDRP
magnification=Magnification.TWENTY.value,
px_size_xy=optical_control_image.physical_pixel_sizes.X,
)

# Assert
assert actual_alignment_matrix.shape == expected_matrix.shape

# Due to inherent challenges with floating point precision across different environments,
# compare actual vs expected elementwise with a (very) small epsilon (i.e., allowed error margin)
assert numpy.allclose(actual_alignment_matrix, expected_matrix, atol=1e-14), (
actual_alignment_matrix - expected_matrix
)

def test_generate_alignment_matrix_reproducability(self):
# Arrange
optical_control_image, _ = get_test_image(ZSD_100x_OPTICAL_CONTROL_IMAGE_URL)
Expand Down