Add test for mask_default_cube

scilpy/image/tests/test_volume_operations.py

@@ -10,7 +10,8 @@
 
 from scilpy.image.volume_operations import (flip_volume, crop_volume,
                                             apply_transform, compute_snr,
-                                            resample_volume, register_image)
+                                            resample_volume, register_image,
+                                            mask_data_with_default_cube)
 from scilpy.io.fetcher import fetch_data, get_testing_files_dict, get_home
 from scilpy.utils.util import compute_nifti_bounding_box
 
@@ -165,3 +166,13 @@ def test_resample_volume():
     resampled_img = resample_volume(moving3d_img, res=(2, 2, 2), interp='nn')
 
     assert_equal(resampled_img.get_fdata(), ref3d)
+
+
+def test_mask_data_with_default_cube():
+    data = np.ones((12, 12, 12))
+    out = mask_data_with_default_cube(data)
+    assert np.array_equal(data.shape, out.shape)
+    assert out[0, 0, 0] == 0
+    assert out[-1, -1, -1] == 0
+    assert out[6, 6, 6] == 1
+

scilpy/image/volume_operations.py

@@ -535,16 +535,17 @@ def resample_volume(img, ref=None, res=None, iso_min=False, zoom=None,
     return nib.Nifti1Image(data2.astype(data.dtype), affine2)
 
 
-def crop_data_with_default_cube(data):
-    """ Crop data with a default cube
-    Cube: data.shape/3 centered
+def mask_data_with_default_cube(data):
+    """Masks data outside a default cube (Cube: data.shape/3 centered)
 
     Parameters
     ----------
-    data : 3D ndarray
-        Volume data.
+    data :  np.ndarray
+        Volume data, 3D.
+
     Returns
     -------
+    data: np.ndarray
         Data masked
     """
     shape = np.array(data.shape[:3])

scripts/scil_tractogram_fix_trk.py

@@ -55,7 +55,7 @@
 import nibabel as nib
 import numpy as np
 
-from scilpy.image.volume_operations import crop_data_with_default_cube
+from scilpy.image.volume_operations import mask_data_with_default_cube
 from scilpy.io.utils import (add_bbox_arg,
                              add_verbose_arg,
                              add_overwrite_arg,
@@ -210,8 +210,8 @@ def main():
                 # Sometimes DSI studio has quite a lot of skull left
                 # Dipy Median Otsu does not work with FA/GFA
                 if args.auto_crop:
-                    moving_data = crop_data_with_default_cube(moving_data)
-                    static_data = crop_data_with_default_cube(static_data)
+                    moving_data = mask_data_with_default_cube(moving_data)
+                    static_data = mask_data_with_default_cube(static_data)
 
                 # Since DSI Studio register to AC/PC and does not save the
                 # transformation We must estimate the transformation,