fix: consider only dimensions with size >1 for plane-coordinate (#28)

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Re-write of #16 due to changes in infrastructure.

Fixes #10

---------

Co-authored-by: Soyer, Sebastian <[email protected]>
Co-authored-by: soyers <[email protected]>

pylibCZIrw/czi.py

@@ -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
         -------
@@ -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(

pylibCZIrw/tests/unit/test_czi_reader.py

@@ -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},
         ),
     ],
 )
@@ -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},
         ),
     ],
 )

requirements_test.txt

@@ -1,13 +1,5 @@
 # Used for testing
 mypy
-types-all
-pylint==2.17.7
-pylint-runner==0.6.0
-flake8
-flake8-docstrings
-flake8-bugbear
-bandit
-black
 check-python-versions
 tox==3.27.1
 tox-current-env