minor bug fixes

Author: robert-graf

TPTBox/core/bids_files.py

@@ -687,7 +687,7 @@ def get_changed_bids(
         auto_add_run_id=False,
         additional_folder: str | None = None,
         dataset_path: str | None = None,
-        make_parent=True,
+        make_parent=False,
         non_strict_mode=False,
     ):
         ds = dataset_path if dataset_path is not None else self.get_path_decomposed()[0]

TPTBox/core/nii_wrapper.py

@@ -985,7 +985,7 @@ def resample_from_to(self, to_vox_map:Image_Reference|Has_Grid|tuple[SHAPE,AFFIN
                     # padding after = remaining dst size after src
                     pad_after = dst_shape-shift-src_shape
                     pad = tuple((int(b), int(a)) for b, a in zip(pad_before, pad_after))
-                    ret = s.apply_pad(pad, mode=mode,inplace=inplace)
+                    ret = s.apply_pad(pad, mode=mode,inplace=inplace,verbose=verbose)
 
                     #TODO SET raise_error=False before committing
                     valid = ret.assert_affine(mapping,raise_error=True,origin_tolerance=0.0001,error_tolerance=0.0001,shape_tolerance=0)
@@ -1801,7 +1801,7 @@ def infect(self: NII, reference_mask: NII, inplace=False,verbose=True,axis:int|s
         """
         self.assert_affine(reference_mask)
         if _do_crop:
-            crop = reference_mask.compute_crop(0,5)
+            crop = reference_mask.compute_crop(0,5,raise_error=False)
             s = self.apply_crop(crop)
             reference_mask = reference_mask.apply_crop(crop)
         else:

TPTBox/segmentation/VibeSeg/inference_nnunet.py

@@ -227,7 +227,7 @@ def to_int(a: str, k: None | int = None):
                 try:
                     return enum_[a].value
                 except Exception:
-                    print("no ", enum_)
+                    pass
             if k is not None and k not in unknown_strings.values():
                 return k
             unknown_strings[a] = unknown_strings["max"]
@@ -247,7 +247,7 @@ def to_int(a: str, k: None | int = None):
         logger.print(f"{mapping=}")
         seg_nii.map_labels_(mapping)
     if out_file is not None and (not Path(out_file).exists() or override):
-        seg_nii.save(out_file)
+        seg_nii.set_dtype("smallest_uint").save(out_file)
     del nnunet
 
     torch.cuda.empty_cache()