Ensure that the straightening.cache file is output to the PWD during template registration

spinalcordtoolbox/scripts/sct_label_vertebrae.py

@@ -307,13 +307,13 @@ def main(argv: Sequence[str]):
     cache_sig = cache_signature(
         input_files=[fname_in, fname_seg],
     )
-    fname_cache = "straightening.cache"
-    if (cache_valid(os.path.join(curdir, fname_cache), cache_sig)
+    if (cache_valid(os.path.join(curdir, "straightening.cache"), cache_sig)
             and os.path.isfile(os.path.join(curdir, "warp_curve2straight.nii.gz"))
             and os.path.isfile(os.path.join(curdir, "warp_straight2curve.nii.gz"))
             and os.path.isfile(os.path.join(curdir, "straight_ref.nii.gz"))):
         # if they exist, copy them into current folder
         printv('Reusing existing warping field which seems to be valid', verbose, 'warning')
+        copy(os.path.join(curdir, "straightening.cache"), 'straightening.cache')
         copy(os.path.join(curdir, "warp_curve2straight.nii.gz"), 'warp_curve2straight.nii.gz')
         copy(os.path.join(curdir, "warp_straight2curve.nii.gz"), 'warp_straight2curve.nii.gz')
         copy(os.path.join(curdir, "straight_ref.nii.gz"), 'straight_ref.nii.gz')
@@ -326,7 +326,7 @@ def main(argv: Sequence[str]):
             '-r', str(remove_temp_files),
             '-v', '0',
         ])
-        cache_save(os.path.join(path_output, fname_cache), cache_sig)
+        cache_save("straightening.cache", cache_sig)
 
     # resample to 0.5mm isotropic to match template resolution
     printv('\nResample to 0.5mm isotropic...', verbose)
@@ -467,6 +467,7 @@ def main(argv: Sequence[str]):
     generate_output_file(os.path.join(path_tmp, "segmentation_labeled.nii"), fname_seg_labeled)
     generate_output_file(os.path.join(path_tmp, "segmentation_labeled_disc.nii"), os.path.join(path_output, file_seg + '_labeled_discs' + ext_seg))
     # copy straightening files in case subsequent SCT functions need them
+    generate_output_file(os.path.join(path_tmp, "straightening.cache"), os.path.join(path_output, "straightening.cache"), verbose=verbose)
     generate_output_file(os.path.join(path_tmp, "warp_curve2straight.nii.gz"), os.path.join(path_output, "warp_curve2straight.nii.gz"), verbose=verbose)
     generate_output_file(os.path.join(path_tmp, "warp_straight2curve.nii.gz"), os.path.join(path_output, "warp_straight2curve.nii.gz"), verbose=verbose)
     generate_output_file(os.path.join(path_tmp, "straight_ref.nii.gz"), os.path.join(path_output, "straight_ref.nii.gz"), verbose=verbose)

spinalcordtoolbox/scripts/sct_register_to_template.py

@@ -529,9 +529,12 @@ def main(argv: Sequence[str]):
         cache_sig = cache_signature(
             input_files=cache_input_files,
         )
-        cachefile = os.path.join(curdir, "straightening.cache")
-        if cache_valid(cachefile, cache_sig) and os.path.isfile(fn_warp_curve2straight) and os.path.isfile(fn_warp_straight2curve) and os.path.isfile(fn_straight_ref):
+        if (cache_valid(os.path.join(curdir, "straightening.cache"), cache_sig)
+                and os.path.isfile(fn_warp_curve2straight)
+                and os.path.isfile(fn_warp_straight2curve)
+                and os.path.isfile(fn_straight_ref)):
             printv('Reusing existing warping field which seems to be valid', verbose, 'warning')
+            copy(os.path.join(curdir, "straightening.cache"), 'straightening.cache')
             copy(fn_warp_curve2straight, 'warp_curve2straight.nii.gz')
             copy(fn_warp_straight2curve, 'warp_straight2curve.nii.gz')
             copy(fn_straight_ref, 'straight_ref.nii.gz')
@@ -560,7 +563,7 @@ def main(argv: Sequence[str]):
                 sc_straight.discs_ref_filename = ftmp_template_label
 
             sc_straight.straighten()
-            cache_save(cachefile, cache_sig)
+            cache_save("straightening.cache", cache_sig)
 
         # N.B. DO NOT UPDATE VARIABLE ftmp_seg BECAUSE TEMPORARY USED LATER
         # re-define warping field using non-cropped space (to avoid issue #367)
@@ -801,6 +804,7 @@ def main(argv: Sequence[str]):
     generate_output_file(os.path.join(path_tmp, "anat2template.nii.gz"), fname_anat2template, verbose=verbose)
     if ref == 'template':
         # copy straightening files in case subsequent SCT functions need them
+        generate_output_file(os.path.join(path_tmp, "straightening.cache"), os.path.join(path_output, "straightening.cache"), verbose=verbose)
         generate_output_file(os.path.join(path_tmp, "warp_curve2straight.nii.gz"), os.path.join(path_output, "warp_curve2straight.nii.gz"), verbose=verbose)
         generate_output_file(os.path.join(path_tmp, "warp_straight2curve.nii.gz"), os.path.join(path_output, "warp_straight2curve.nii.gz"), verbose=verbose)
         generate_output_file(os.path.join(path_tmp, "straight_ref.nii.gz"), os.path.join(path_output, "straight_ref.nii.gz"), verbose=verbose)

testing/cli/test_cli_sct_label_vertebrae.py

@@ -26,6 +26,11 @@ def test_sct_label_vertebrae_consistent_disc(tmp_path):
     assert fp == []
     assert fn == []
 
+    # Ensure that the straightening files are correctly generated in the output directory
+    for file in ["straightening.cache", "straight_ref.nii.gz",
+                 "warp_straight2curve.nii.gz", "warp_curve2straight.nii.gz"]:
+        assert os.path.isfile(tmp_path/file)
+
 
 @pytest.mark.sct_testing
 @pytest.mark.usefixtures("run_in_sct_testing_data_dir")

testing/cli/test_cli_sct_register_to_template.py

@@ -70,38 +70,44 @@ def test_sct_register_to_template_non_rpi_data(tmp_path, template_lpi):
     (os.path.join(__sct_dir__, 'data/PAM50/template/PAM50_cord.nii.gz'),
      ['-ldisc', 't2/labels.nii.gz', '-ref', 'subject'])
 ])
-def test_sct_register_to_template_dice_coefficient_against_groundtruth(fname_gt, remaining_args):
+def test_sct_register_to_template_dice_coefficient_against_groundtruth(fname_gt, remaining_args, tmp_path):
     """Run the CLI script and verify transformed images have expected attributes."""
     fname_seg = 't2/t2_seg-manual.nii.gz'
     dice_threshold = 0.9
-    sct_register_to_template.main(argv=['-i', 't2/t2.nii.gz', '-s', fname_seg] + remaining_args)
+    sct_register_to_template.main(argv=['-i', 't2/t2.nii.gz', '-s', fname_seg, '-ofolder', str(tmp_path)]
+                                  + remaining_args)
+
+    # Straightening files are only generated for `-ref template`. They should *not* exist for `-ref subject`.
+    for file in ["straightening.cache", "straight_ref.nii.gz",
+                 "warp_straight2curve.nii.gz", "warp_curve2straight.nii.gz"]:
+        assert os.path.isfile(tmp_path/file) == (False if 'subject' in remaining_args else True)
 
     # apply transformation to binary mask: template --> anat
     sct_apply_transfo.main(argv=[
         '-i', fname_gt,
         '-d', fname_seg,
-        '-w', 'warp_template2anat.nii.gz',
-        '-o', 'test_template2anat.nii.gz',
+        '-w', str(tmp_path/'warp_template2anat.nii.gz'),
+        '-o', str(tmp_path/'test_template2anat.nii.gz'),
         '-x', 'nn',
         '-v', '0'])
 
     # apply transformation to binary mask: anat --> template
     sct_apply_transfo.main(argv=[
         '-i', fname_seg,
         '-d', fname_gt,
-        '-w', 'warp_anat2template.nii.gz',
-        '-o', 'test_anat2template.nii.gz',
+        '-w', str(tmp_path/'warp_anat2template.nii.gz'),
+        '-o', str(tmp_path/'test_anat2template.nii.gz'),
         '-x', 'nn',
         '-v', '0'])
 
     # compute dice coefficient between template segmentation warped to anat and segmentation from anat
     im_seg = Image(fname_seg)
-    im_template_seg_reg = Image('test_template2anat.nii.gz')
+    im_template_seg_reg = Image(str(tmp_path/'test_template2anat.nii.gz'))
     dice_template2anat = compute_dice(im_seg, im_template_seg_reg, mode='3d', zboundaries=True)
     assert dice_template2anat > dice_threshold
 
     # compute dice coefficient between anat segmentation warped to template and segmentation from template
-    im_seg_reg = Image('test_anat2template.nii.gz')
+    im_seg_reg = Image(str(tmp_path/'test_anat2template.nii.gz'))
     im_template_seg = Image(fname_gt)
     dice_anat2template = compute_dice(im_seg_reg, im_template_seg, mode='3d', zboundaries=True)
     assert dice_anat2template > dice_threshold