FEAT: centaurz derivatives (pyxnat#206)

* FEAT: centaurz derivatives
* REF: Remove legacy Python 2 import
* REF: refine centaurz() to filter by region and optimization level
* REF: set default optimization to "harmonized"
* FEAT: CI test_centaurz
* REF: simplify and generalize centaurz quantification test

---------

Co-authored-by: anaharrismatnez <anaharrismar@gmail.com>

Author: jhuguetn

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/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