Add --keep-mask

README.md

@@ -76,6 +76,13 @@ Arguments to pass to `inflate_to_sphere_implicit`. The default value `(200, 200)
 should work for fetal brains. While it shouldn't be necessary, increasing the
 values shouldn't do any harm, and would help compensate for larger brain sizes.
 
+#### `--keep-mask`
+
+Copy input mask file to output directory.
+
+`--keep-mask` is a workaround for using `pl-fetal-cp-surface-extract` as part of a
+_ChRIS_ pipeline. It eliminates the need for an extra _ts_ plugin step.
+
 ## Local Usage
 
 To get started with local command-line usage, use [Apptainer](https://apptainer.org/)

extract_cp/__main__.py

@@ -26,6 +26,8 @@
 parser.add_argument('--inflate_to_sphere_implicit', dest='inflate_to_sphere_implicit', type=str, default='200,200',
                     help='Parameters for inflate_to_sphere_implicit. Larger values are necessary '
                          'for larger brain size.')
+parser.add_argument('-k', '--keep-mask', dest='keep_mask', action='store_true',
+                    help='Copy input mask file to output directory')
 parser.add_argument('--no-fail', dest='no_fail', action='store_true',
                     help='Exit normally even when failed to process a subject')
 parser.add_argument('-V', '--version', action='version',

extract_cp/extract_surface.py

@@ -1,4 +1,5 @@
 import os
+import shutil
 from pathlib import Path
 from typing import Optional, Sequence, BinaryIO
 from civet.extraction.hemisphere import Side, HemisphereMask
@@ -22,6 +23,8 @@ def extract_surface(mask: Path, surface: Path, params: Parameters):
                 .adapt_object_mesh(*params.adapt_object_mesh)\
                 .interpolate_with_sphere(chosen_side, *params.inflate_to_sphere_implicit)\
                 .save(surface, shell=__curry_log(log))
+        if params.keep_mask:
+            shutil.copy(mask, surface.with_name(mask.name))
         logger.info('Completed {}', surface)
     except Exception as e:
         logger.exception('Failed to process {}', mask)

extract_cp/params.py

@@ -15,6 +15,7 @@ class Parameters:
     mincmorph_iterations: int
     adapt_object_mesh: tuple[int, int, int]
     inflate_to_sphere_implicit: tuple[int, int]
+    keep_mask: bool
 
     def __post_init__(self):
         if not len(self.adapt_object_mesh) == 3:
@@ -28,13 +29,15 @@ def new(
             side: SideStr,
             mincmorph_iterations: int,
             adapt_object_mesh: str,
-            inflate_to_sphere_implicit: str
+            inflate_to_sphere_implicit: str,
+            keep_mask: bool
     ) -> 'Parameters':
         return cls(
             side=side,
             mincmorph_iterations=mincmorph_iterations,
             adapt_object_mesh=_str2ints(adapt_object_mesh),
-            inflate_to_sphere_implicit=_str2ints(inflate_to_sphere_implicit)
+            inflate_to_sphere_implicit=_str2ints(inflate_to_sphere_implicit),
+            keep_mask=keep_mask
         )
 
     @classmethod
@@ -43,7 +46,8 @@ def from_obj(cls, options) -> 'Parameters':
             side=options.side,
             mincmorph_iterations=options.mincmorph_iterations,
             adapt_object_mesh=options.adapt_object_mesh,
-            inflate_to_sphere_implicit=options.inflate_to_sphere_implicit
+            inflate_to_sphere_implicit=options.inflate_to_sphere_implicit,
+            keep_mask=options.keep_mask
         )
 
 

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='extract_cp',
-    version='1.0.0',
+    version='1.1.0',
     description='Fetal brain MRI CP surface extraction using CIVET marching-cubes',
     author='Jennings Zhang',
     author_email='Jennings.Zhang@childrens.harvard.edu',