Add check_bbox argument management

scilpy/io/streamlines.py

@@ -82,11 +82,28 @@ def ichunk(sequence, n):
 
 def is_argument_set(args, arg_name):
     # Check that attribute is not None
-    return not getattr(args, 'reference', None) is None
+    return not getattr(args, arg_name, None) is None
 
 
-def load_tractogram_with_reference(parser, args, filepath,
-                                   bbox_check=True, arg_name=None):
+def load_tractogram_with_reference(parser, args, filepath, arg_name=None):
+    """
+    Parameters
+    ----------
+    parser: Argument Parser
+        Used to print errors, if any.
+    args: Namespace
+        Parsed arguments. Used to get the 'ref' and 'bbox_check' args.
+        See scilpy.io.utils to add the arguments to your parser.
+    filepath: str
+        Path of the tractogram file.
+    arg_name: str, optional
+        Name of the reference argument. By default the args.ref is used. If
+        arg_name is given, then args.arg_name_ref will be used instead.
+    """
+    if is_argument_set(args, 'bbox_check'):
+        bbox_check = args.bbox_check
+    else:
+        bbox_check = True
 
     _, ext = os.path.splitext(filepath)
     if ext == '.trk':

scilpy/io/utils.py

@@ -198,6 +198,15 @@ def add_verbose_arg(parser):
                         help='If set, produces verbose output.')
 
 
+def add_bbox_arg(parser):
+    parser.add_argument('--no_bbox_check', dest='bbox_check',
+                        action='store_false',
+                        help='Activate to ignore validity of the bounding '
+                             'box during loading / saving of \n'
+                             'tractograms (ignores the presence of invalid '
+                             'streamlines).')
+
+
 def add_sh_basis_args(parser, mandatory=False):
     """Add spherical harmonics (SH) bases argument.
 
@@ -440,7 +449,8 @@ def verify_compatibility_with_reference_sft(ref_sft, files_to_verify,
     parser: argument parser
         Will raise an error if a file is not compatible.
     args: Namespace
-        Should contain a args.reference if any file is a .tck.
+        Should contain a args.reference if any file is a .tck, and possibly a
+        args.bbox_check (set to True by default).
     """
     save_ref = args.reference
 
@@ -455,8 +465,7 @@ def verify_compatibility_with_reference_sft(ref_sft, files_to_verify,
                     args.reference = None
                 else:
                     args.reference = save_ref
-                mask = load_tractogram_with_reference(parser, args, file,
-                                                      bbox_check=False)
+                mask = load_tractogram_with_reference(parser, args, file)
             else:  # should be a nifti file.
                 mask = file
             compatible = is_header_compatible(ref_sft, mask)

scilpy/segment/tractogram_from_roi.py

@@ -41,9 +41,11 @@ def compute_masks_from_bundles(gt_files, parser, args, inverse_mask=False):
     gt_files: list
         List of either StatefulTractograms or niftis.
     parser: ArgumentParser
-        Argument parser which handles the script's arguments.
+        Argument parser which handles the script's arguments. Used to print
+        parser errors, if any.
     args: Namespace
-        List of arguments passed to the script.
+        List of arguments passed to the script. Used for its 'ref' and
+        'bbox_check' arguments.
     inverse_mask: bool
         If true, returns the list of inversed masks instead.
 
@@ -74,7 +76,7 @@ def compute_masks_from_bundles(gt_files, parser, args, inverse_mask=False):
                 else:
                     args.reference = save_ref
                 gt_sft = load_tractogram_with_reference(
-                    parser, args, gt_bundle, bbox_check=False)
+                    parser, args, gt_bundle)
                 gt_sft.to_vox()
                 gt_sft.to_corner()
                 _, dimensions, _, _ = gt_sft.space_attributes
@@ -653,7 +655,7 @@ def segment_tractogram_from_roi(
     nc_sft = sft[all_nc_ids]
     if len(nc_sft) > 0 or not args.no_empty:
         save_tractogram(nc_sft, os.path.join(
-            args.out_dir, filename), bbox_valid_check=False)
+            args.out_dir, filename), bbox_valid_check=args.bbox_check)
 
     return (vb_sft_list, wpc_sft_list, ib_sft_list, nc_sft, ib_names,
             bundle_stats)

scripts/scil_apply_transform_to_tractogram.py

@@ -41,7 +41,8 @@
 import numpy as np
 
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.io.utils import (add_overwrite_arg,
+from scilpy.io.utils import (add_bbox_arg,
+                             add_overwrite_arg,
                              add_reference_arg,
                              add_verbose_arg,
                              assert_inputs_exist,
@@ -55,7 +56,9 @@ def _build_arg_parser():
                                 description=__doc__)
 
     p.add_argument('in_moving_tractogram',
-                   help='Path of the tractogram to be transformed.')
+                   help='Path of the tractogram to be transformed.\n'
+                        'Bounding box validity will not be checked (could '
+                        'contain invalid streamlines).')
     p.add_argument('in_target_file',
                    help='Path of the reference target file (trk or nii).')
     p.add_argument('in_transfo',
@@ -105,9 +108,9 @@ def main():
                                  args.in_transfo], args.in_deformation)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
+    args.bbox_check = False  # Adding manually bbox_check argument.
     moving_sft = load_tractogram_with_reference(parser, args,
-                                                args.in_moving_tractogram,
-                                                bbox_check=False)
+                                                args.in_moving_tractogram)
 
     transfo = load_matrix_in_any_format(args.in_transfo)
     deformation_data = None

scripts/scil_clean_qbx_clusters.py

@@ -27,7 +27,8 @@
 from dipy.io.utils import is_header_compatible
 
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.io.utils import (add_overwrite_arg,
+from scilpy.io.utils import (add_bbox_arg,
+                             add_overwrite_arg,
                              add_reference_arg,
                              add_verbose_arg,
                              assert_inputs_exist,
@@ -65,6 +66,7 @@ def _build_arg_parser():
     add_reference_arg(p)
     add_overwrite_arg(p)
     add_verbose_arg(p)
+    add_bbox_arg(p)
 
     return p
 
@@ -175,12 +177,11 @@ def keypress_callback(obj, _):
     concat_streamlines = []
 
     ref_bundle = load_tractogram_with_reference(
-        parser, args, args.in_bundles[0], bbox_check=False)
+        parser, args, args.in_bundles[0])
 
     for filename in args.in_bundles:
         basename = os.path.basename(filename)
-        sft = load_tractogram_with_reference(parser, args, filename,
-                                             bbox_check=False)
+        sft = load_tractogram_with_reference(parser, args, filename)
         if not is_header_compatible(ref_bundle, sft):
             return
         if len(sft) >= args.min_cluster_size:
@@ -240,32 +241,38 @@ def keypress_callback(obj, _):
     accepted_streamlines = save_clusters(sft_accepted_on_size,
                                          accepted_streamlines,
                                          args.out_accepted_dir,
-                                         filename_accepted_on_size)
+                                         filename_accepted_on_size,
+                                         args.bbox_check)
 
     accepted_sft = StatefulTractogram(accepted_streamlines,
                                       sft_accepted_on_size[0],
                                       Space.RASMM)
-    save_tractogram(accepted_sft, args.out_accepted, bbox_valid_check=False)
+    save_tractogram(accepted_sft, args.out_accepted,
+                    bbox_valid_check=args.bbox_check)
 
     # Save rejected clusters (by GUI)
     rejected_streamlines = save_clusters(sft_accepted_on_size,
                                          rejected_streamlines,
                                          args.out_rejected_dir,
-                                         filename_accepted_on_size)
+                                         filename_accepted_on_size,
+                                         args.bbox_check)
 
     # Save rejected clusters (by size)
     rejected_streamlines.extend(save_clusters(sft_rejected_on_size,
                                               range(len(sft_rejected_on_size)),
                                               args.out_rejected_dir,
-                                              filename_rejected_on_size))
+                                              filename_rejected_on_size,
+                                              args.bbox_check))
 
     rejected_sft = StatefulTractogram(rejected_streamlines,
                                       sft_accepted_on_size[0],
                                       Space.RASMM)
-    save_tractogram(rejected_sft, args.out_rejected, bbox_valid_check=False)
+    save_tractogram(rejected_sft, args.out_rejected,
+                    bbox_valid_check=args.bbox_check)
 
 
-def save_clusters(cluster_lists, indexes_list, directory, basenames_list):
+def save_clusters(cluster_lists, indexes_list, directory, basenames_list,
+                  bbox_check):
     output_streamlines = []
     for idx in indexes_list:
         streamlines = cluster_lists[idx].streamlines
@@ -277,7 +284,8 @@ def save_clusters(cluster_lists, indexes_list, directory, basenames_list):
                                          Space.RASMM)
             tmp_filename = os.path.join(directory,
                                         basenames_list[idx])
-            save_tractogram(tmp_sft, tmp_filename, bbox_valid_check=False)
+            save_tractogram(tmp_sft, tmp_filename,
+                            bbox_valid_check=bbox_check)
 
     return output_streamlines
 

scripts/scil_compute_seed_density_map.py

@@ -11,10 +11,11 @@
 from nibabel import Nifti1Image
 from nibabel.streamlines import detect_format, TrkFile
 import numpy as np
-from scilpy.io.utils import (
-    add_overwrite_arg,
-    assert_inputs_exist,
-    assert_outputs_exist)
+
+from scilpy.io.utils import (add_bbox_arg,
+                             add_overwrite_arg,
+                             assert_inputs_exist,
+                             assert_outputs_exist)
 
 
 def _build_arg_parser():
@@ -34,6 +35,7 @@ def _build_arg_parser():
                         'without a value, 1 is used.\n If a value is given, '
                         'will be used as the stored value.')
     add_overwrite_arg(p)
+    add_bbox_arg(p)
 
     return p
 
@@ -57,9 +59,9 @@ def main():
                      .format(args.binary, max_))
 
     # Load files and data. TRKs can have 'same' as reference
-    # Can handle streamlines outside of bbox
+    # Can handle streamlines outside of bbox, if asked by user.
     sft = load_tractogram(args.tractogram_filename, 'same',
-                          bbox_valid_check=False)
+                          bbox_valid_check=args.bbox_check)
 
     # IMPORTANT
     # Origin should be center when creating the seeds (see below, we

scripts/scil_convert_tractogram.py

@@ -12,8 +12,9 @@
 from dipy.io.streamline import save_tractogram
 
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.io.utils import (add_overwrite_arg, add_reference_arg,
-                             assert_inputs_exist, assert_outputs_exist)
+from scilpy.io.utils import (add_bbox_arg, add_overwrite_arg,
+                             add_reference_arg, assert_inputs_exist,
+                             assert_outputs_exist)
 
 
 def _build_arg_parser():
@@ -30,6 +31,7 @@ def _build_arg_parser():
 
     add_reference_arg(p)
     add_overwrite_arg(p)
+    add_bbox_arg(p)
 
     return p
 
@@ -48,9 +50,8 @@ def main():
 
     assert_outputs_exist(parser, args, args.output_name)
 
-    sft = load_tractogram_with_reference(parser, args, args.in_tractogram,
-                                         bbox_check=False)
-    save_tractogram(sft, args.output_name, bbox_valid_check=False)
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
+    save_tractogram(sft, args.output_name, bbox_valid_check=args.bbox_check)
 
 
 if __name__ == "__main__":

scripts/scil_decompose_connectivity.py

@@ -46,7 +46,8 @@
 
 from scilpy.image.labels import get_data_as_labels
 from scilpy.io.streamlines import load_tractogram_with_reference
-from scilpy.io.utils import (add_overwrite_arg,
+from scilpy.io.utils import (add_bbox_arg,
+                             add_overwrite_arg,
                              add_processes_arg,
                              add_verbose_arg,
                              add_reference_arg,
@@ -228,6 +229,7 @@ def _build_arg_parser():
     add_processes_arg(p)
     add_verbose_arg(p)
     add_overwrite_arg(p)
+    add_bbox_arg(p)
 
     return p
 
@@ -274,9 +276,13 @@ def main():
 
     logging.info('*** Loading streamlines ***')
     time1 = time.time()
-    sft = load_tractogram_with_reference(parser, args, args.in_tractogram,
-                                         bbox_check=False)
-    sft.remove_invalid_streamlines()
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
+
+    # If loaded with invalid (bbox_check False), remove invalid streamlines
+    # before continuing.
+    if not args.bbox_check:
+        sft.remove_invalid_streamlines()
+
     time2 = time.time()
     logging.info('    Loading {} streamlines took {} sec.'.format(
         len(sft), round(time2 - time1, 2)))

scripts/scil_extract_ushape.py

@@ -70,8 +70,7 @@ def main():
         parser.error('Min-Max ufactor "{},{}" '.format(args.minU, args.maxU) +
                      'must be between -1 and 1.')
 
-    sft = load_tractogram_with_reference(
-        parser, args, args.in_tractogram)
+    sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
 
     ids_c = detect_ushape(sft, args.minU, args.maxU)
     ids_l = np.setdiff1d(np.arange(len(sft.streamlines)), ids_c)

scripts/scil_fix_dsi_studio_trk.py

@@ -41,7 +41,8 @@
 import nibabel as nib
 import numpy as np
 
-from scilpy.io.utils import (add_overwrite_arg,
+from scilpy.io.utils import (add_bbox_arg,
+                             add_overwrite_arg,
                              assert_inputs_exist,
                              assert_outputs_exist)
 from scilpy.utils.streamlines import (transform_warp_sft,
@@ -82,10 +83,9 @@ def _build_arg_parser():
     invalid.add_argument('--remove_invalid', action='store_true',
                          help='Remove the streamlines landing out of the '
                               'bounding box.')
-    invalid.add_argument('--keep_invalid', action='store_true',
-                         help='Keep the streamlines landing out of the '
-                              'bounding box.')
+
     add_overwrite_arg(p)
+    add_bbox_arg(p)
 
     return p
 
@@ -122,7 +122,7 @@ def main():
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram(args.in_dsi_tractogram, 'same',
-                          bbox_valid_check=False)
+                          bbox_valid_check=args.bbox_check)
 
     # LPS -> RAS convention in voxel space
     sft.to_vox()
@@ -143,7 +143,7 @@ def main():
         elif args.remove_invalid:
             sft_flip.remove_invalid_streamlines()
         save_tractogram(sft_flip, args.out_tractogram,
-                        bbox_valid_check=not args.keep_invalid)
+                        bbox_valid_check=args.bbox_check)
     else:
         static_img = nib.load(args.in_native_fa)
         static_data = static_img.get_fdata()
@@ -206,7 +206,7 @@ def main():
         elif args.remove_invalid:
             new_sft.remove_invalid_streamlines()
         save_tractogram(new_sft, args.out_tractogram,
-                        bbox_valid_check=not args.keep_invalid)
+                        bbox_valid_check=args.bbox_check)
 
 
 if __name__ == "__main__":