using tmpdir.join().strpath in tests with nibabel or other funcions that dont take path.local

Author: djarecka

nipype/algorithms/tests/test_errormap.py

@@ -11,7 +11,6 @@
 
 def test_errormap(tmpdir):
 
-    tempdir = tmpdir.strpath
     # Single-Spectual
     # Make two fake 2*2*2 voxel volumes
     volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]])  # John von Neumann's birthday
@@ -22,15 +21,15 @@ def test_errormap(tmpdir):
     img2 = nb.Nifti1Image(volume2, np.eye(4))
     maskimg = nb.Nifti1Image(mask, np.eye(4))
 
-    nb.save(img1, os.path.join(tempdir, 'von.nii.gz'))
-    nb.save(img2, os.path.join(tempdir, 'alan.nii.gz'))
-    nb.save(maskimg, os.path.join(tempdir, 'mask.nii.gz'))
+    nb.save(img1, tmpdir.join('von.nii.gz').strpath)
+    nb.save(img2, tmpdir.join('alan.nii.gz').strpath)
+    nb.save(maskimg, tmpdir.join('mask.nii.gz').strpath)
 
     # Default metric
     errmap = ErrorMap()
-    errmap.inputs.in_tst = os.path.join(tempdir, 'von.nii.gz')
-    errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz')
-    errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz')
+    errmap.inputs.in_tst = tmpdir.join('von.nii.gz').strpath
+    errmap.inputs.in_ref = tmpdir.join('alan.nii.gz').strpath
+    errmap.out_map = tmpdir.join('out_map.nii.gz').strpath
     result = errmap.run()
     assert result.outputs.distance == 1.125
 
@@ -45,7 +44,7 @@ def test_errormap(tmpdir):
     assert result.outputs.distance == 0.875
 
     # Masked
-    errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz')
+    errmap.inputs.mask = tmpdir.join('mask.nii.gz').strpath
     result = errmap.run()
     assert result.outputs.distance == 1.0
 
@@ -62,11 +61,11 @@ def test_errormap(tmpdir):
     msvolume2[:, :, :, 1] = volume1
     msimg2 = nb.Nifti1Image(msvolume2, np.eye(4))
 
-    nb.save(msimg1, os.path.join(tempdir, 'von-ray.nii.gz'))
-    nb.save(msimg2, os.path.join(tempdir, 'alan-ray.nii.gz'))
+    nb.save(msimg1, tmpdir.join('von-ray.nii.gz').strpath)
+    nb.save(msimg2, tmpdir.join('alan-ray.nii.gz').strpath)
 
-    errmap.inputs.in_tst = os.path.join(tempdir, 'von-ray.nii.gz')
-    errmap.inputs.in_ref = os.path.join(tempdir, 'alan-ray.nii.gz')
+    errmap.inputs.in_tst = tmpdir.join('von-ray.nii.gz').strpath
+    errmap.inputs.in_ref = tmpdir.join('alan-ray.nii.gz').strpath
     errmap.inputs.metric = 'sqeuclidean'
     result = errmap.run()
     assert result.outputs.distance == 5.5

nipype/algorithms/tests/test_modelgen.py

@@ -17,9 +17,8 @@
 
 
 def test_modelgen1(tmpdir):
-    tempdir = tmpdir.strpath
-    filename1 = os.path.join(tempdir, 'test1.nii')
-    filename2 = os.path.join(tempdir, 'test2.nii')
+    filename1 = tmpdir.join('test1.nii').strpath
+    filename2 = tmpdir.join('test2.nii').strpath
     Nifti1Image(np.random.rand(10, 10, 10, 200), np.eye(4)).to_filename(filename1)
     Nifti1Image(np.random.rand(10, 10, 10, 200), np.eye(4)).to_filename(filename2)
     s = SpecifyModel()
@@ -56,9 +55,8 @@ def test_modelgen1(tmpdir):
 
 
 def test_modelgen_spm_concat(tmpdir):
-    tempdir = tmpdir.strpath
-    filename1 = os.path.join(tempdir, 'test1.nii')
-    filename2 = os.path.join(tempdir, 'test2.nii')
+    filename1 = tmpdir.join('test1.nii').strpath
+    filename2 = tmpdir.join('test2.nii').strpath
     Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename1)
     Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename2)
 
@@ -97,7 +95,7 @@ def test_modelgen_spm_concat(tmpdir):
     npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0]))
 
     # Test case for variable number of events in separate runs, sometimes unique.
-    filename3 = os.path.join(tempdir, 'test3.nii')
+    filename3 = tmpdir.join('test3.nii').strpath
     Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename3)
     s.inputs.functional_runs = [filename1, filename2, filename3]
     info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]),
@@ -122,9 +120,8 @@ def test_modelgen_spm_concat(tmpdir):
 
 
 def test_modelgen_sparse(tmpdir):
-    tempdir = tmpdir.strpath
-    filename1 = os.path.join(tempdir, 'test1.nii')
-    filename2 = os.path.join(tempdir, 'test2.nii')
+    filename1 = tmpdir.join('test1.nii').strpath
+    filename2 = tmpdir.join('test2.nii').strpath
     Nifti1Image(np.random.rand(10, 10, 10, 50), np.eye(4)).to_filename(filename1)
     Nifti1Image(np.random.rand(10, 10, 10, 50), np.eye(4)).to_filename(filename2)
     s = SpecifySparseModel()

nipype/algorithms/tests/test_normalize_tpms.py

@@ -18,7 +18,6 @@
 
 
 def test_normalize_tpms(tmpdir):
-    tempdir = tmpdir.strpath
 
     in_mask = example_data('tpms_msk.nii.gz')
     mskdata = nb.load(in_mask, mmap=NUMPY_MMAP).get_data()
@@ -30,8 +29,8 @@ def test_normalize_tpms(tmpdir):
 
     for i in range(3):
         mapname = example_data('tpm_%02d.nii.gz' % i)
-        filename = os.path.join(tempdir, 'modtpm_%02d.nii.gz' % i)
-        out_files.append(os.path.join(tempdir, 'normtpm_%02d.nii.gz' % i))
+        filename = tmpdir.join('modtpm_%02d.nii.gz' % i).strpath
+        out_files.append(tmpdir.join('normtpm_%02d.nii.gz' % i).strpath)
 
         im = nb.load(mapname, mmap=NUMPY_MMAP)
         data = im.get_data()

nipype/interfaces/freesurfer/tests/test_model.py

@@ -17,9 +17,8 @@
 def test_concatenate(tmpdir):
     tmpdir.chdir()
 
-    tempdir = tmpdir.strpath
-    in1 = os.path.join(tempdir, 'cont1.nii')
-    in2 = os.path.join(tempdir, 'cont2.nii')
+    in1 = tmpdir.join('cont1.nii').strpath
+    in2 = tmpdir.join('cont2.nii').strpath
     out = 'bar.nii'
 
     data1 = np.zeros((3, 3, 3, 1), dtype=np.float32)
@@ -32,12 +31,12 @@ def test_concatenate(tmpdir):
 
     # Test default behavior
     res = model.Concatenate(in_files=[in1, in2]).run()
-    assert res.outputs.concatenated_file == os.path.join(tempdir, 'concat_output.nii.gz')
+    assert res.outputs.concatenated_file == tmpdir.join('concat_output.nii.gz').strpath
     assert np.allclose(nb.load('concat_output.nii.gz').get_data(), out_data)
 
     # Test specified concatenated_file
     res = model.Concatenate(in_files=[in1, in2], concatenated_file=out).run()
-    assert res.outputs.concatenated_file == os.path.join(tempdir, out)
+    assert res.outputs.concatenated_file == tmpdir.join(out).strpath
     assert np.allclose(nb.load(out, mmap=NUMPY_MMAP).get_data(), out_data)
 
     # Test in workflow
@@ -47,9 +46,9 @@ def test_concatenate(tmpdir):
                      name='concat')
     wf.add_nodes([concat])
     wf.run()
-    assert np.allclose(nb.load(os.path.join(tempdir,
-                                             'test_concatenate',
-                                             'concat', out)).get_data(),
+    assert np.allclose(nb.load(tmpdir.join(
+                                           'test_concatenate',
+                                            'concat', out).strpath).get_data(),
                        out_data)
 
     # Test a simple statistic

nipype/utils/tests/test_provenance.py

@@ -21,7 +21,6 @@ def test_provenance():
     assert 'echo hello' in provn
 
 def test_provenance_exists(tmpdir):
-    tempdir = tmpdir.strpath
     tmpdir.chdir()
     from nipype import config
     from nipype.interfaces.base import CommandLine
@@ -31,7 +30,7 @@ def test_provenance_exists(tmpdir):
     CommandLine('echo hello').run()
     config.set('execution', 'write_provenance', provenance_state)
     config.set('execution', 'hash_method', hash_state)
-    provenance_exists = os.path.exists(os.path.join(tempdir, 'provenance.provn'))
+    provenance_exists = os.path.exists(tmpdir.join('provenance.provn').strpath)
     assert provenance_exists
 
 def test_safe_encode():