Adding tests to dwi_reorder_philips

scripts/scil_dwi_reorder_philips.py

@@ -34,18 +34,18 @@ def _build_arg_parser():
 
     p.add_argument('in_dwi',
                    help='Input dwi file.')
-    p.add_argument('in_bvec',
-                   help='Input bvec FSL format.')
     p.add_argument('in_bval',
                    help='Input bval FSL format.')
+    p.add_argument('in_bvec',
+                   help='Input bvec FSL format.')
     p.add_argument('in_table',
                    help='Original philips table - first line is skipped.')
     p.add_argument('out_basename',
                    help='Basename output file.')
 
     p.add_argument('--json',
-                   help='If you json file, it will check if you need'
-                        ' to reorder your Philips dwi.')
+                   help='If you give a json file, it will check if you need '
+                        'to reorder your Philips dwi.')
 
     add_verbose_arg(p)
     add_overwrite_arg(p)

scripts/tests/test_dwi_reorder_philips.py

@@ -1,7 +1,85 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+import os
+import json
+import tempfile
+
+from dipy.io.gradients import read_bvals_bvecs
+import numpy as np
+
+from scilpy.io.fetcher import fetch_data, get_home, get_testing_files_dict
+
+# If they already exist, this only takes 5 seconds (check md5sum)
+fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+tmp_dir = tempfile.TemporaryDirectory()
+
 
 def test_help_option(script_runner):
     ret = script_runner.run('scil_dwi_reorder_philips.py', '--help')
     assert ret.success
+
+
+def test_reorder(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
+    in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
+    in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
+    table = np.ones((64, 4))
+    bval, bvec = read_bvals_bvecs(in_bval, in_bvec)
+    table[:, :3] = bvec
+    table[:, 3] = bval
+    tmp = np.copy(table[15])
+    table[15] = table[30]
+    table[30] = tmp
+    in_table = os.path.expanduser(tmp_dir.name) + "/in_table.txt"
+    np.savetxt(in_table, table, header="Test")
+    ret = script_runner.run('scil_dwi_reorder_philips.py', in_dwi, in_bval,
+                            in_bvec, in_table, 'out1', '-f')
+    assert ret.success
+
+
+def test_reorder_w_json_old_version(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
+    in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
+    in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
+    table = np.ones((64, 4))
+    bval, bvec = read_bvals_bvecs(in_bval, in_bvec)
+    table[:, :3] = bvec
+    table[:, 3] = bval
+    tmp = np.copy(table[15])
+    table[15] = table[30]
+    table[30] = tmp
+    in_table = os.path.expanduser(tmp_dir.name) + "/in_table.txt"
+    np.savetxt(in_table, table, header="Test")
+    in_json = os.path.expanduser(tmp_dir.name) + "/in_json.json"
+    info = {'SoftwareVersions': '5.5'}
+    with open(in_json, 'w') as f:
+        json.dump(info, f)
+    ret = script_runner.run('scil_dwi_reorder_philips.py', in_dwi, in_bval,
+                            in_bvec, in_table, 'out2', '--json', in_json)
+    assert ret.success
+
+
+def test_reorder_w_json_new_version(script_runner):
+    os.chdir(os.path.expanduser(tmp_dir.name))
+    in_dwi = os.path.join(get_home(), 'processing', 'dwi_crop.nii.gz')
+    in_bval = os.path.join(get_home(), 'processing', 'dwi.bval')
+    in_bvec = os.path.join(get_home(), 'processing', 'dwi.bvec')
+    table = np.ones((64, 4))
+    bval, bvec = read_bvals_bvecs(in_bval, in_bvec)
+    table[:, :3] = bvec
+    table[:, 3] = bval
+    tmp = np.copy(table[15])
+    table[15] = table[30]
+    table[30] = tmp
+    in_table = os.path.expanduser(tmp_dir.name) + "/in_table.txt"
+    np.savetxt(in_table, table, header="Test")
+    in_json = os.path.expanduser(tmp_dir.name) + "/in_json.json"
+    info = {'SoftwareVersions': '5.6'}
+    with open(in_json, 'w') as f:
+        json.dump(info, f)
+    ret = script_runner.run('scil_dwi_reorder_philips.py', in_dwi, in_bval,
+                            in_bvec, in_table, 'out3', '--json', in_json)
+    assert not ret.success