From fbbe29673b09ebdcaefc0b6e1e7bf0273adfa52d Mon Sep 17 00:00:00 2001
From: Jessica Austin <jessica@axiomalaska.com>
Date: Wed, 25 Mar 2020 17:16:10 -0800
Subject: [PATCH] spike test bugfix: first & last values are unknown

if abs(arr[0])>threshold, then the test was failing. but it's not really
    defined for the first or last values in the array. so always set
    those flags to QC unknown
---
 ioos_qc/qartod.py    |  4 ++++
 tests/test_config.py |  2 +-
 tests/test_qartod.py | 24 ++++++++++++++++++++----
 3 files changed, 25 insertions(+), 5 deletions(-)

diff --git a/ioos_qc/qartod.py b/ioos_qc/qartod.py
index db54f3f..ba91fb3 100644
--- 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
index ff97257..fab04df 100644
--- 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
index 9e019cb..ad13aef 100644
--- 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,