Start implementing parenchymal_mask = intracranial_mask - csf_mask

Author: cdaversin

src/mritk/cli.py

@@ -84,7 +84,7 @@ def setup_parser():
     looklocker.add_arguments(looklocker_parser, extra_args_cb=add_extra_arguments)
 
     masks_parser = subparsers.add_parser(
-        "mask", help="Generate CSF and intracranial masks.", formatter_class=parser.formatter_class
+        "mask", help="Generate CSF, intracranial and parenchymal masks.", formatter_class=parser.formatter_class
     )
     masks.add_arguments(masks_parser, extra_args_cb=add_extra_arguments)
 

src/mritk/masks.py

@@ -158,6 +158,32 @@ def intracranial_mask(segmentation: Segmentation, csf_mask: MRIData) -> MRIData:
 
     return mri_data
 
+def parenchymal_mask(intracranial_mask: MRIData, csf_mask: MRIData):
+    """
+    I/O wrapper for generating and saving an parenchymal mask from
+    previously generated intracranial and CSF masks
+
+    Loads the masks, verifies they share the same physical coordinate space, and
+    compute the difference intracranial - CSF
+
+    Args:
+        intracranial_mask (MRIData): The intracranial mask (MRIData), \
+        generated by the intracranial mask module.
+        csf_mask (MRIData): The CSF mask (MRIData), generated by the csf mask module.
+
+    Returns:
+        MRIData: An MRIData object containing the parenchymal mask.
+    """
+
+    # Validate spatial alignment before array operations
+    assert_same_space(intracranial_mask, csf_mask)
+
+    # Parenchymal mask is intracrnial mask - CSF = intracranial && !CSF
+    diff_mask = np.logical_and(intracranial_mask.data, np.logical_not(csf_mask.data))
+    mri_data = MRIData(data=diff_mask, affine=intracranial_mask.affine)
+
+    return mri_data
+
 
 def add_arguments(
     parser: argparse.ArgumentParser,
@@ -195,9 +221,28 @@ def add_arguments(
     )
     intracranial_mask_parser.add_argument("-o", "--output", type=Path, help="Desired output path for the resulting mask")
 
+
+    parenchymal_mask_parser = subparser.add_parser(
+        "parenchymal", help="Compute parenchymal mask", formatter_class=parser.formatter_class
+    )
+    parenchymal_mask_parser.add_argument(
+        "--csf-mask-path",
+        type=Path,
+        help="Path to the CSF mask NIfTI file, generated by \
+        the csf mask module, i.e. mritk mask csf",
+    )
+    parenchymal_mask_parser.add_argument(
+        "--intracranial-mask-path",
+        type=Path,
+        help="Path to the intracranial mask NIfTI file, generated by \
+        the csf mask module, i.e. mritk mask intracranial",
+    )
+    parenchymal_mask_parser.add_argument("-o", "--output", type=Path, help="Desired output path for the resulting mask")
+
     if extra_args_cb is not None:
         extra_args_cb(csf_mask_parser)
         extra_args_cb(intracranial_mask_parser)
+        extra_args_cb(parenchymal_mask_parser)
 
 
 def dispatch(args):
@@ -213,5 +258,11 @@ def dispatch(args):
             csf_mask=MRIData.from_file(args.pop("csf_mask_path"), dtype=np.single),
         )
         intracranial_mask_data.save(args.pop("output"), dtype=np.uint8)
+    elif command == "parenchymal":
+        parenchymal_mask_data = parenchymal_mask(
+            intracranial_mask=MRIData.from_file(args.pop("intracranial_mask_path"), dtype=np.single),
+            csf_mask=MRIData.from_file(args.pop("csf_mask_path"), dtype=np.single),
+        )
+        parenchymal_mask_data.save(args.pop("output"), dtype=np.uint8)
     else:
         raise ValueError(f"Unknown mask command: {command}")