Issue around absent either darks or flats

httomo/darks_flats.py

@@ -56,7 +56,7 @@ class DarksFlatsFileConfig(NamedTuple):
     """
 
     file: Path
-    data_path: str
+    data_path: Optional[str]
     image_key_path: Optional[str]
     ignore: bool = False
 
@@ -145,8 +145,12 @@ def get_separate(config: DarksFlatsFileConfig):
             ]
 
     if darks_config.file != flats_config.file:
-        darks = get_separate(darks_config)
-        flats = get_separate(flats_config)
+        darks = None
+        flats = None
+        if not darks_config.ignore:
+            darks = get_separate(darks_config)
+        if not flats_config.ignore:
+            flats = get_separate(flats_config)
         return darks, flats  # type: ignore
 
     return get_together_or_dummy()

httomo/runner/dataset.py

@@ -171,7 +171,7 @@ def slicing_dim(self) -> Literal[0, 1, 2]:
 
     def _empty_aux_array(self):
         empty_shape = list(self._data.shape)
-        empty_shape[self.slicing_dim] = 0
+        empty_shape[self.slicing_dim] = 1
         return np.empty_like(self._data, shape=empty_shape)
 
     @property

httomo/transform_loader_params.py

@@ -322,8 +322,8 @@ class DarksFlatsParam(TypedDict):
     Darks/flats configuration dict.
     """
 
-    file: str
-    data_path: str
+    file: Path
+    data_path: Optional[str]
     image_key_path: Optional[str]
     ignore: bool
 
@@ -426,25 +426,28 @@ def parse_config(
     data_config = DataConfig(in_file=input_file, data_path=str(data_path))
 
     darks_value = config.get("darks", None)
-    ignore_darks = False
-    if darks_value == "ignore":
-        ignore_darks = True  # ignore darks in the data
-        darks_value = None
-    if darks_value is not None and "image_key_path" not in darks_value:
-        darks_value["image_key_path"] = None
-    darks_config = parse_darks_flats(
-        data_config, image_key_path, darks_value, ignore=ignore_darks
-    )
+    if darks_value == "ignore" or darks_value is None:
+        darks_config = DarksFlatsFileConfig(
+            file=input_file, data_path=None, image_key_path=None, ignore=True
+        )
+    else:
+        if "image_key_path" not in darks_value:
+            darks_value["image_key_path"] = None
+        darks_config = parse_darks_flats(
+            data_config, image_key_path, darks_value, ignore=False
+        )
+
     flats_value = config.get("flats", None)
-    ignore_flats = False
-    if flats_value == "ignore":
-        ignore_flats = True  # ignore flats in the data
-        flats_value = None
-    if flats_value is not None and "image_key_path" not in flats_value:
-        flats_value["image_key_path"] = None
-    flats_config = parse_darks_flats(
-        data_config, image_key_path, flats_value, ignore=ignore_flats
-    )
+    if flats_value == "ignore" or flats_value is None:
+        flats_config = DarksFlatsFileConfig(
+            file=input_file, data_path=None, image_key_path=None, ignore=True
+        )
+    else:
+        if "image_key_path" not in flats_value:
+            flats_value["image_key_path"] = None
+        flats_config = parse_darks_flats(
+            data_config, image_key_path, flats_value, ignore=False
+        )
 
     return (
         data_config,

tests/runner/test_dataset_block.py

@@ -33,10 +33,10 @@ def test_full_block_for_global_data():
     np.testing.assert_array_equal(data, block.data)
     np.testing.assert_array_equal(angles, block.angles)
     np.testing.assert_array_equal(angles, block.angles_radians)
-    assert block.darks.shape == (0, 10, 10)
-    assert block.dark.shape == (0, 10, 10)
-    assert block.flats.shape == (0, 10, 10)
-    assert block.flat.shape == (0, 10, 10)
+    assert block.darks.shape == (1, 10, 10)
+    assert block.dark.shape == (1, 10, 10)
+    assert block.flats.shape == (1, 10, 10)
+    assert block.flat.shape == (1, 10, 10)
     assert block.darks.dtype == data.dtype
     assert block.flats.dtype == data.dtype
     assert block.dark.dtype == data.dtype