dcm2nii: fix fcomment & add tests

Author: casperdcl

amypet/dcm2nii.py

@@ -18,10 +18,10 @@
 log = logging.getLogger(__name__)
 
 
-def run(dcmpth, fcomment="", timestamp=True):
+def run(dcmpth, fcomment="converted-from-DICOM_", timestamp=True):
     dcmpth = Path(dcmpth)
     assert dcmpth.is_dir()
     log.info("convert")
-    res = nimpa.dcm2nii(dcmpth, fcomment=fcomment, timestamp=timestamp)
+    res = nimpa.dcm2nii(dcmpth, fprefix=fcomment, timestamp=timestamp)
     log.debug("output file:%s", res)
     return res

tests/test_dcm2nii.py

@@ -0,0 +1,14 @@
+from pathlib import Path
+
+import pytest
+
+
+@pytest.mark.timeout(30 * 60) # 30m
+def test_dcm2nii(datain):
+    dcmpth = Path(datain['mumapDCM'])
+    assert not list(dcmpth.glob('test_dcm2nii_*.nii*'))
+    dcm2nii = pytest.importorskip("amypet.dcm2nii")
+    dcm2nii.run(datain['mumapDCM'], fcomment="test_dcm2nii_")
+    assert list(dcmpth.glob('test_dcm2nii_*.nii*'))
+    for f in dcmpth.glob('test_dcm2nii_*.nii*'):
+        f.unlink()