Add pre-processing flag and functions applicable to fMOST datastes (#61)

* Add pre-processing functions for fMOST datasets * Add command-line option for pre-processing * Add opencv to dependencies * Corrections for CI/CD * Docstrings, refactoring * Save pre-processed image in brainreg output directory * Replace opencv connected components by skimage label and regionprops * Add test to check background removal * Corrections for PR review * Format code with black * remove fmost preprocessing Co-authored-by: Adam Tyson <[email protected]>
brainglobe · Nov 16, 2022 · 2b9474a · 2b9474a
1 parent c9ef993
commit 2b9474a
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Showing 4 changed files with 30 additions and 4 deletions.
diff --git a/brainreg/backend/niftyreg/run.py b/brainreg/backend/niftyreg/run.py
@@ -42,6 +42,7 @@ def run_niftyreg(
     DATA_ORIENTATION,
     ATLAS_ORIENTATION,
     niftyreg_args,
+    preprocessing_args,
     scaling,
     load_parallel,
     sort_input_file,
@@ -78,7 +79,7 @@ def run_niftyreg(
         paths.downsampled_brain_path,
     )
 
-    target_brain = preprocess.filter_image(target_brain)
+    target_brain = preprocess.filter_image(target_brain, preprocessing_args)
     save_nii(
         target_brain, atlas.resolution, niftyreg_paths.downsampled_filtered
     )

diff --git a/brainreg/cli.py b/brainreg/cli.py
@@ -28,6 +28,7 @@ def register_cli_parser():
     parser = pixel_parser(parser)
     parser = geometry_parser(parser)
     parser = misc_parse(parser)
+    parser = preprocessing_parser(parser)
 
     return parser
 
@@ -177,6 +178,24 @@ def geometry_parser(parser):
     return parser
 
 
+def preprocessing_parser(parser):
+    preprocessing_opt_parser = parser.add_argument_group(
+        "Pre-processing options"
+    )
+
+    preprocessing_opt_parser.add_argument(
+        "--pre-processing",
+        dest="preprocessing",
+        type=str,
+        default="default",
+        required=False,
+        help="Pre-processing method to be applied before registration. "
+        "Possible values: skip, default.",
+    )
+
+    return parser
+
+
 def prep_registration(args):
     logging.debug("Making registration directory")
     ensure_directory_exists(args.brainreg_directory)
@@ -219,6 +238,7 @@ def main():
         paths,
         args.voxel_sizes,
         arg_groups["NiftyReg registration backend options"],
+        arg_groups["Pre-processing options"],
         sort_input_file=args.sort_input_file,
         n_free_cpus=args.n_free_cpus,
         additional_images_downsample=additional_images_downsample,

diff --git a/brainreg/main.py b/brainreg/main.py
@@ -17,6 +17,7 @@ def main(
     paths,
     voxel_sizes,
     niftyreg_args,
+    preprocessing_args,
     n_free_cpus=2,
     sort_input_file=False,
     additional_images_downsample=None,
@@ -70,6 +71,7 @@ def main(
             data_orientation,
             atlas.metadata["orientation"],
             niftyreg_args,
+            preprocessing_args,
             scaling,
             load_parallel,
             sort_input_file,

diff --git a/brainreg/utils/preprocess.py b/brainreg/utils/preprocess.py
@@ -5,15 +5,18 @@
 from tqdm import trange
 
 
-def filter_image(brain):
+def filter_image(brain, preprocessing_args=None):
     """
     Filter a 3D image to allow registration
     :return: The filtered brain
     :rtype: np.array
     """
     brain = brain.astype(np.float64, copy=False)
-    for i in trange(brain.shape[-1], desc="filtering", unit="plane"):
-        brain[..., i] = filter_plane(brain[..., i])
+    if preprocessing_args and preprocessing_args.preprocessing == "skip":
+        pass
+    else:  # default pre-processing
+        for i in trange(brain.shape[-1], desc="filtering", unit="plane"):
+            brain[..., i] = filter_plane(brain[..., i])
     brain = scale_and_convert_to_16_bits(brain)
     return brain