Merge pull request nipreps#403 from davhunt/master

TEST/RF: Separate LTA length fixing and add doctest

niworkflows/conftest.py

@@ -6,6 +6,7 @@
 import pandas as pd
 import pytest
 import tempfile
+import pkg_resources
 
 from .utils.bids import collect_data
 
@@ -22,6 +23,7 @@ def add_np(doctest_namespace):
     doctest_namespace['Path'] = Path
     doctest_namespace['datadir'] = data_dir
     doctest_namespace['bids_collect_data'] = collect_data
+    doctest_namespace['test_data'] = pkg_resources.resource_filename('niworkflows', 'tests/data')
 
     tmpdir = tempfile.TemporaryDirectory()
     doctest_namespace['tmpdir'] = tmpdir.name

niworkflows/interfaces/freesurfer.py

@@ -205,19 +205,7 @@ def _post_run_hook(self, runtime):
             if not isdefined(lta_file):
                 continue
 
-            lines = Path(lta_file).read_text().splitlines(keepends=True)
-
-            fixed = False
-            newfile = []
-            for line in lines:
-                if line.startswith('filename = ') and len(line.strip("\n")) >= 255:
-                    fixed = True
-                    newfile.append('filename = path_too_long\n')
-                else:
-                    newfile.append(line)
-
-            if fixed:
-                Path(lta_file).write_text(''.join(newfile))
+            fix_lta_length(lta_file)
 
         runtime = super(TruncateLTA, self)._post_run_hook(runtime)
         return runtime
@@ -326,6 +314,53 @@ def _run_interface(self, runtime):
         return runtime
 
 
+def fix_lta_length(lta_file):
+    """ Fix the length of the filename field in an LTA file if too long.
+
+    Updates file in place.
+
+    Examples
+    --------
+
+    No changes are made to a valid transform file:
+
+    >>> valid_transform = Path(test_data) / 'valid_transform.lta'
+    >>> orig_contents = valid_transform.read_text()
+    >>> fix_lta_length(valid_transform)
+    False
+    >>> valid_transform.read_text() == orig_contents
+    True
+
+    Invalid transform files are files with > 255 characters in any line:
+
+    >>> invalid_transform = Path(test_data) / 'long_path_transform.lta'
+    >>> orig_contents = invalid_transform.read_text()
+    >>> any(len(line) > 255 for line in orig_contents.splitlines(keepends=True))
+    True
+    >>> local_copy = Path('invalid.lta')
+    >>> local_copy.write_text(orig_contents)
+    2120
+    >>> fix_lta_length(local_copy)
+    True
+    >>> local_copy.read_text() == orig_contents
+    False
+    """
+    lines = Path(lta_file).read_text().splitlines(keepends=True)
+
+    fixed = False
+    newfile = []
+    for line in lines:
+        if line.startswith('filename = ') and len(line.strip("\n")) >= 255:
+            fixed = True
+            newfile.append('filename = path_too_long\n')
+        else:
+            newfile.append(line)
+
+    if fixed:
+        Path(lta_file).write_text(''.join(newfile))
+    return fixed
+
+
 def inject_skullstripped(subjects_dir, subject_id, skullstripped):
     mridir = op.join(subjects_dir, subject_id, 'mri')
     t1 = op.join(mridir, 'T1.mgz')

niworkflows/tests/data/long_path_transform.lta

@@ -0,0 +1,31 @@
+# transform file /N/dc2/scratch/davhunt/workflows/5d6705bee0ae0618d1ededa8/5d6db5f2e0ae06ba6cee3710/fmripworkdir/fmriprep_wf/single_subject_TTTEMPSUB_wf/func_preproc_ses_SSSES_task_balloonanalogrisktask_run_1_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta
+# created by davhunt on Mon Sep  2 22:46:17 2019
+
+type      = 0 # LINEAR_VOX_TO_VOX
+nxforms   = 1
+mean      = 0.0000 0.0000 0.0000
+sigma     = 10000.0000
+1 4 4
+3.124938726425171e+00 -6.231633014976978e-03 2.379096671938896e-02 2.793729782104492e+01 
+1.451765652745962e-02 -1.255382895469666e+00 -3.662998914718628e+00 2.176610260009766e+02 
+1.317331008613110e-02 2.861747980117798e+00 -1.606821179389954e+00 3.680672836303711e+01 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999403953552e-01 
+src volume info
+valid = 1  # volume info valid
+filename = /N/dc2/scratch/davhunt/workflows/5d6705bee0ae0618d1ededa8/5d6db5f2e0ae06ba6cee3710/fmripworkdir/fmriprep_wf/single_subject_TTTEMPSUB_wf/func_preproc_ses_SSSES_task_balloonanalogrisktask_run_1_wf/bold_reg_wf/bbreg_wf/mri_coreg/ref_bold_corrected_trans_masked.nii.gz
+volume = 64 64 33
+voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = -2.068481445312500e+00 3.198078918457031e+01 -4.065056610107422e+01
+dst volume info
+valid = 1  # volume info valid
+filename = /N/dc2/scratch/davhunt/workflows/5d6705bee0ae0618d1ededa8/5d6db5f2e0ae06ba6cee3710/fmripout/freesurfer/sub-TTTEMPSUB/mri/brainmask.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -9.999999403953552e-01
+zras   = 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
+cras   = -3.000000000000000e+00 2.999969482421875e+00 -8.000038146972656e+00
+subject sub-TTTEMPSUB

niworkflows/tests/data/valid_transform.lta

@@ -0,0 +1,31 @@
+# transform file /N/dc2/scratch/davhunt/workflows/5d6705bee0ae0618d1ededa8/5d6db5f2e0ae06ba6cee3710/fmripworkdir/fmriprep_wf/single_subject_TTTEMPSUB_wf/func_preproc_ses_SSSES_task_balloonanalogrisktask_run_1_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta
+# created by davhunt on Mon Sep  2 22:46:17 2019
+
+type      = 0 # LINEAR_VOX_TO_VOX
+nxforms   = 1
+mean      = 0.0000 0.0000 0.0000
+sigma     = 10000.0000
+1 4 4
+3.124938726425171e+00 -6.231633014976978e-03 2.379096671938896e-02 2.793729782104492e+01 
+1.451765652745962e-02 -1.255382895469666e+00 -3.662998914718628e+00 2.176610260009766e+02 
+1.317331008613110e-02 2.861747980117798e+00 -1.606821179389954e+00 3.680672836303711e+01 
+0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 9.999999403953552e-01 
+src volume info
+valid = 1  # volume info valid
+filename = path_too_long
+volume = 64 64 33
+voxelsize = 3.125000000000000e+00 3.125000000000000e+00 4.000000000000000e+00
+xras   = -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00
+zras   = 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00
+cras   = -2.068481445312500e+00 3.198078918457031e+01 -4.065056610107422e+01
+dst volume info
+valid = 1  # volume info valid
+filename = /N/dc2/scratch/davhunt/workflows/5d6705bee0ae0618d1ededa8/5d6db5f2e0ae06ba6cee3710/fmripout/freesurfer/sub-TTTEMPSUB/mri/brainmask.mgz
+volume = 256 256 256
+voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00
+xras   = -9.999999403953552e-01 0.000000000000000e+00 0.000000000000000e+00
+yras   = 0.000000000000000e+00 0.000000000000000e+00 -9.999999403953552e-01
+zras   = 0.000000000000000e+00 9.999999403953552e-01 0.000000000000000e+00
+cras   = -3.000000000000000e+00 2.999969482421875e+00 -8.000038146972656e+00
+subject sub-TTTEMPSUB