Merge pull request #34 from ioos/spike_test_initial_final_values_bugfix

spike test bugfix: first & last values are unknown
ioos · Mar 27, 2020 · c9c149e · c9c149e
2 parents e54b5e7 + fbbe296
commit c9c149e
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Showing 3 changed files with 25 additions and 5 deletions.
diff --git a/ioos_qc/qartod.py b/ioos_qc/qartod.py
@@ -508,6 +508,10 @@ def spike_test(inp : Sequence[N],
     with np.errstate(invalid='ignore'):
         flag_arr[diff > fail_threshold] = QartodFlags.FAIL
 
+    # test is undefined for first and last values
+    flag_arr[0] = QartodFlags.UNKNOWN
+    flag_arr[-1] = QartodFlags.UNKNOWN
+
     # If the value is masked or nan set the flag to MISSING
     flag_arr[diff.mask] = QartodFlags.MISSING
 

diff --git a/tests/test_config.py b/tests/test_config.py
@@ -108,7 +108,7 @@ def test_run_with_agg(self):
         }})
         inp = [-1, 0, 1, 2, 10, 3]
         expected_gross_range = np.array([4, 1, 1, 1, 1, 1])
-        expected_spike = np.array([1, 1, 1, 3, 3, 1])
+        expected_spike = np.array([2, 1, 1, 3, 3, 2])
         expected_agg = np.array([4, 1, 1, 3, 3, 1])
 
         r = qc.run(

diff --git a/tests/test_qartod.py b/tests/test_qartod.py
@@ -876,7 +876,7 @@ def test_spike(self):
 
         # First and last elements should always be good data, unless someone
         # has set a threshold to zero.
-        expected = [1, 4, 4, 4, 1, 3, 1, 1]
+        expected = [2, 4, 4, 4, 1, 3, 1, 2]
 
         inputs = [
             arr,
@@ -901,7 +901,7 @@ def test_spike_negative_vals(self):
 
         # First and last elements should always be good data, unless someone
         # has set a threshold to zero.
-        expected = [1, 4, 4, 4, 1, 3, 1, 1]
+        expected = [2, 4, 4, 4, 1, 3, 1, 2]
 
         inputs = [
             arr,
@@ -918,6 +918,22 @@ def test_spike_negative_vals(self):
                 expected
             )
 
+    def test_spike_initial_final_values(self):
+        """
+        The test is not defined for the initial and final values in the array
+        """
+        arr = [-100, -99, -99, -98]
+        expected = [2, 1, 1, 2]
+
+        npt.assert_array_equal(
+            qartod.spike_test(
+                inp=arr,
+                suspect_threshold=self.suspect_threshold,
+                fail_threshold=self.fail_threshold
+            ),
+            expected
+        )
+
     def test_spike_masked(self):
         """
         Test with missing data.
@@ -927,7 +943,7 @@ def test_spike_masked(self):
 
         # First and last elements should always be good data, unless someone
         # has set a threshold to zero.
-        expected = [1, 4, 4, 4, 1, 3, 1, 1, 9, 9, 4, 4, 4, 9]
+        expected = [2, 4, 4, 4, 1, 3, 1, 1, 9, 9, 4, 4, 4, 9]
 
         inputs = [
             arr,
@@ -955,7 +971,7 @@ def test_spike_realdata(self):
                -0.3932, -0.3383, -0.2804, -0.2347, -0.2134, -0.2347, -0.2926, -0.3597, -0.442, -0.509, 0, -0.5944,
                -0.57, -0.4267, -0.2926, -0.1585, -0.0945, -0.0762]
 
-        expected = [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1]
+        expected = [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 2]
 
         inputs = [
             arr,