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[Draft] Pass valid mask to OpenCV's template matching #202

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[Draft] Pass valid mask to OpenCV's template matching #202

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cfs-data Mar 19, 2026
4d2ad7d
Merge branch 'main' of https://github.com/NetherlandsForensicInstitut…
cfs-data Mar 22, 2026
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5 changes: 4 additions & 1 deletion packages/scratch-core/src/conversion/surface_comparison/cell_registration/coarse.py
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,7 @@ def _find_best_match(
score_map = _get_score_map(
comparison_array=rotated,
template=grid_cell.cell_data_filled,
template_mask=grid_cell.valid_mask,
)
score, x, y = _compute_best_score_from_maps(
score_map=score_map, fill_fraction_mask=fill_fraction_mask
Expand Down Expand Up @@ -237,7 +238,7 @@ def _compute_best_score_from_maps(


def _get_score_map(
comparison_array: FloatArray2D, template: FloatArray2D
comparison_array: FloatArray2D, template: FloatArray2D, template_mask: BinaryMask
) -> FloatArray2D:
"""
Compute a normalized cross-correlation score map for one reference cell.
Expand All @@ -248,12 +249,14 @@ def _get_score_map(

:param comparison_array: NaN-free float32-compatible comparison image, padded by a full cell on each side.
:param template: Reference grid cell whose ``cell_data`` is used as the template; must contain no NaN values.
:param template_mask: Mask with the pixel values that should be matched (i.e. no NaNs).
:returns: Float64 score map of shape ``(H - cell_height + 1, W - cell_width + 1)`` with values in ``[-1, 1]``.
"""

score_map = cv2.matchTemplate(
image=comparison_array.astype(np.float32),
templ=template.astype(np.float32),
method=cv2.TM_CCOEFF_NORMED,
mask=template_mask.astype(np.uint8),
)
return np.asarray(score_map, dtype=np.float64)
7 changes: 6 additions & 1 deletion packages/scratch-core/src/conversion/surface_comparison/models.py
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Expand Up @@ -9,7 +9,7 @@

from scipy.constants import mega

from container_models.base import ConfigBaseModel, FloatArray2D
from container_models.base import ConfigBaseModel, FloatArray2D, BinaryMask
from conversion.data_formats import Mark, MarkType


Expand Down Expand Up @@ -246,3 +246,8 @@ def fill_fraction(self) -> float:
def cell_data_filled(self) -> FloatArray2D:
"""Cell data where NaN values are replaced with the sentinel value."""
return np.nan_to_num(self.cell_data, nan=self.nan_fill_value, copy=True)

@cached_property
def valid_mask(self) -> BinaryMask:
"""Mask where the cell data has valid values (i.e. no NaNs)."""
return ~np.isnan(self.cell_data)
4 changes: 3 additions & 1 deletion packages/scratch-core/tests/conversion/surface_comparison/cell_registration/test_coarse.py
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Expand Up @@ -136,7 +136,9 @@ def test_get_score_map_self_match_peak_at_cell_top_left(self):

# Act
score_map = _get_score_map(
comparison_array=filled, template=grid_cell.cell_data_filled
comparison_array=filled,
template=grid_cell.cell_data_filled,
template_mask=grid_cell.valid_mask,
)

# Asserts
Expand Down
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