add option to set ramp path in stitching.

Author: robert-graf

TPTBox/stitching/stitching.py

@@ -324,6 +324,7 @@ def main(  # noqa: C901
     is_segmentation: bool = False,
     dtype: type | str = float,
     save=True,
+    ramp_path=None,
 ):
     np.set_printoptions(precision=2, floatmode="fixed")
     if is_segmentation:
@@ -529,7 +530,8 @@ def main(  # noqa: C901
             occupancy_arr = occupancy_arr[ex_slice]
         assert output is not None
         nii_occ = set_array(nii_out, occupancy_arr)
-        output = output.replace(".nii.gz", "_ramps.nii.gz")
+        nii_occ.set_data_dtype(np.int8)
+        output = output.replace(".nii.gz", "_ramps.nii.gz").replace("_msk_", "_") if ramp_path is None else ramp_path
         if save:
             nib.save(nii_occ, output)  # type: ignore
             print("Saved ", output) if verbose else None

TPTBox/stitching/stitching_tools.py

@@ -22,6 +22,7 @@ def stitching(
     dtype: type = float,
     match_histogram=False,
     store_ramp=False,
+    ramp_path=None,
 ):
     out = str(out.file["nii.gz"]) if isinstance(out, BIDS_FILE) else str(out)
     files = [to_nii(bf).nii for bf in bids_files]
@@ -37,6 +38,7 @@ def stitching(
         kick_out_fully_integrated_images=kick_out_fully_integrated_images,
         is_segmentation=is_seg,
         dtype=dtype,
+        ramp_path=ramp_path,
     )