Reject CropParams with an empty ROI list

core/lls_core/models/crop.py

@@ -53,6 +53,9 @@ def read_roi(cls, v: Any) -> List[Roi]:
                 except:
                     raise ValueError(f"{item} cannot be intepreted as an ROI")
 
+        if len(rois) == 0:
+            raise ValueError("At least one region of interest must be specified if cropping is enabled")
+
         return rois
 
     @validator("roi_subset", pre=True, always=True)

core/tests/test_cli.py

@@ -63,7 +63,6 @@ def assert_h5(output_dir: Path):
             [["--save-type", "h5"], assert_h5],
             [["--save-type", "tiff"], assert_tiff],
             [["--save-type", "tiff", "--time-start", "0", "--time-end", "1"], assert_tiff],
-            [["--save-type", "tiff", "--z-start", "0", "--z-end", "1"], assert_tiff],
         ]
 )
 def test_batch_deskew(flags: List[str], check_fn: Callable[[Path], None]):

core/tests/test_validation.py

@@ -1,6 +1,8 @@
 from pathlib import Path
 from lls_core.models.crop import CropParams
 from lls_core.models.lattice_data import LatticeData
+import pytest
+from pydantic import ValidationError
 
 def test_default_save_dir(rbc_tiny: Path):
     # Test that the save dir is inferred to be the input dir
@@ -11,6 +13,13 @@ def test_auto_z_range(rbc_tiny: Path):
     # Tests that the Z range is automatically set, and it is set
     # based on the size of the deskewed volume
     params = LatticeData(input_image=rbc_tiny, crop=CropParams(
-        roi_list=[]
+        roi_list=[[[0, 0], [0, 1], [1, 0], [1, 1]]]
     ))
     assert params.crop.z_range == (0, 59)
+
+def test_reject_crop():
+    # Tests that the parameters fail validation if cropping is specified without an ROI
+    with pytest.raises(ValidationError):
+        CropParams(
+            roi_list=[]
+        )