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fix: consider only dimensions with size >1 for plane-coordinate #32

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fix: consider only dimensions with size >1 for plane-coordinate #32

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cf89bb7
fix: consider only dimensions with size >1 for plane-coordinate
FelixS90 Jul 27, 2024
855ad61
refactor: Remove trailing whitespace
FelixS90 Jul 27, 2024
eb1343c
Update test references
soyers Aug 6, 2024
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4 changes: 3 additions & 1 deletion pylibCZIrw/czi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -644,6 +644,8 @@ def _create_roi(

def _create_default_plane_coords(self) -> Dict[str, int]:
"""Generates a default plane coordinates dictionary with all indexes to 0.
This default plane coordinate contains all dimensions reported being used by
the CZI-document, but includes only dimensions for which the size is >1.

Returns
-------
Expand All @@ -653,7 +655,7 @@ def _create_default_plane_coords(self) -> Dict[str, int]:
return {
dim: 0
for dim, dim_index in self.CZI_DIMS.items()
if self._czi_reader.GetDimensionSize(_pylibCZIrw.DimensionIndex(dim_index)) > 0
if self._czi_reader.GetDimensionSize(_pylibCZIrw.DimensionIndex(dim_index)) > 1
}

def _create_plane_coords(
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14 changes: 7 additions & 7 deletions pylibCZIrw/tests/unit/test_czi_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -444,14 +444,14 @@ def test_create_roi_raises_error_on_incorrect_scene() -> None:
@pytest.mark.parametrize(
"GetDimensionSize, expected",
[
(dimension_sizes_test1, {"C": 0}),
(dimension_sizes_test1, {}),
(
dimension_sizes_test2,
{"C": 0, "I": 0, "R": 0, "V": 0},
{"C": 0, "R": 0, "V": 0},
),
(
dimension_sizes_test3,
{"Z": 0, "C": 0, "T": 0, "R": 0, "I": 0, "H": 0, "V": 0, "B": 0},
{"Z": 0, "C": 0, "T": 0, "R": 0, "I": 0, "V": 0, "B": 0},
),
],
)
Expand All @@ -469,17 +469,17 @@ def test_create_default_plane_coords(
@pytest.mark.parametrize(
"plane, GetDimensionSize, expected",
[
(None, dimension_sizes_test1, {"C": 0}),
({"C": 1, "Z": 3, "T": 4}, dimension_sizes_test1, {"C": 1}),
(None, dimension_sizes_test1, {}),
({"C": 1, "Z": 3, "T": 4}, dimension_sizes_test1, {}),
(
{"C": 5, "Z": 3, "T": 4, "B": 12},
dimension_sizes_test2,
{"C": 5, "I": 0, "R": 0, "V": 0},
{"C": 5, "R": 0, "V": 0},
),
(
None,
dimension_sizes_test3,
{"Z": 0, "C": 0, "T": 0, "R": 0, "I": 0, "H": 0, "V": 0, "B": 0},
{"Z": 0, "C": 0, "T": 0, "R": 0, "I": 0, "V": 0, "B": 0},
),
],
)
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