TEST: Centaurz

.github/workflows/ci.yml

@@ -27,16 +27,16 @@ jobs:
       - name: Checkout xnat-docker-compose
         uses: actions/checkout@v3
         with:
-          repository: NrgXnat/xnat-docker-compose
-          ref: 1.8.1
+          repository: jhuguetn/xnat-docker-compose
+          ref: 1.8.10.5
           path: xnat-docker-compose
       - run: docker compose version
       - run: python --version
       - run: python -m pip install --upgrade pip
       - name: Install dependencies
         run: pip install -r requirements-dev.txt
       - name: Start xnat-docker-compose
-        run: docker compose up -d
+        run: docker compose --env-file default.env up -d
         working-directory: xnat-docker-compose
       - run: sleep 120
         if: ${{ matrix.python-version == '3.8' }}

pyxnat/core/derivatives/centaurz.py

@@ -0,0 +1,23 @@
+XNAT_RESOURCE_NAMES = ['CENTAURZ']
+
+
+def quantification_results(self):
+    import pandas as pd
+    from io import StringIO
+
+    f = self.file('centaurz_quantification_results.csv')
+    uri = f._uri
+    res = self._intf.get(uri).text
+    text = StringIO(res)
+    df = pd.read_csv(text)
+    return df
+
+
+def centaurz(self, optimization='harmonized'):
+    """Return the CenTauRz metric for the "Universal" region and given
+    optimization type. The default optimization ("harmonized") ensures
+    generalizability and robustness across tracers, scanners and projects."""
+    df = self.quantification_results()
+    q = 'region == "Universal" and measurement == "centaurz"'
+    q += f' and smoothing_type == "{optimization}"'
+    return float(df.query(q)['value'].iloc[0])

pyxnat/core/derivatives/dicom.py

@@ -13,7 +13,7 @@ def scandate(self):
     fd, fp = tempfile.mkstemp(suffix='.dcm')
     os.close(fd)
     f.get(dest=fp)
-    d = pydicom.read_file(fp)
+    d = pydicom.dcmread(fp)
 
     if hasattr(d, 'AcquisitionDate'):
         acquisition_date = d.AcquisitionDate

pyxnat/core/derivatives/pet_fdg.py

@@ -3,11 +3,7 @@
 
 def quantification_results(self):
     import pandas as pd
-    import sys
-    if sys.version_info[0] < 3:
-        from StringIO import StringIO
-    else:
-        from io import StringIO
+    from io import StringIO
 
     f = self.file('quantification_results.csv')
     uri = f._uri

pyxnat/tests/test_resource_functions.py

@@ -323,3 +323,16 @@ def test_bamos_arterial_stats():
     r = e1.resource('BAMOS_ARTERIAL')
     v = r.stats()
     assert isclose(sum(v['volume']), 32995.6548)
+
+
+def test_centaurz_quantification():
+    r = e1.resource('CENTAURZ')
+    c1 = r.centaurz()
+    c2 = r.centaurz(optimization='original')
+    q = 'region == "MesialTemporal" and smoothing_type == "{s_type}"'
+    rq1 = r.quantification_results().query(q.format(s_type="original"))
+    rq2 = r.quantification_results().query(q.format(s_type="harmonized"))
+    assert c1 > c2
+    assert not rq1.empty and not rq2.empty
+    assert rq1[rq1['measurement'] == 'suvr'].value.iloc[0] > 0.8
+    assert rq2[rq2['measurement'] == 'suvr_spm8'].value.iloc[0] < 0.8