Merge pull request #130 from BillMills/CSIRO-translation

Translating CSIRO tests

qctests/CSIRO_gradient.py → qctests/CSIRO_constant_bottom.py

@@ -1,6 +1,6 @@
 """
-Implements the gradient test of DOI: 10.1175/JTECHO539.1
-All questionable features result in a flag, in order to minimize false negatives
+Implements CSIRO's constant-bottom check
+All questionable features result in a flag, in order to minimize false negatives 
 """
 
 import numpy
@@ -14,29 +14,23 @@ def test(p):
 
     # Get temperature values from the profile.
     t = p.t()
-    # Get depth values (m) from the profile.
+    # depths
     d = p.z()
     # is this an xbt?
     isXBT = p.probe_type() == 2
-
-    assert len(t.data) == len(d.data), 'Number of temperature measurements does not equal number of depth measurements.'
+    latitude = p.latitude()
 
     # initialize qc as a bunch of falses;
-    # implies all measurements pass when a gradient can't be calculated, such as at edges & gaps in data:
     qc = numpy.zeros(len(t.data), dtype=bool)
 
     # check for gaps in data
     isTemperature = (t.mask==False)
     isDepth = (d.mask==False)
     isData = isTemperature & isDepth
 
-    for i in range(0,len(t.data)-1):
-        if isData[i] & isData[i+1]:
-
-            gradient = (d.data[i+1] - d.data[i]) / (t.data[i+1] - t.data[i]) 
-
-            # gradient flag
-            if gradient > -0.4 and gradient < 12.5:
-                qc[i] = True
+    # constant temperature at bottom of profile, for latitude > -40 and bottom two depths at least 30m apart:
+    if isData[-1] and isData[-2] and isXBT:
+        if t.data[-1] == t.data[-2] and latitude > -40 and d.data[-1] - d.data[-2] > 30:
+            qc[-1] = True
 
-    return qc
+    return qc

qctests/CSIRO_long_gradient.py

@@ -0,0 +1,52 @@
+"""
+Implements CSIRO's long gradient check
+All questionable features result in a flag, in order to minimize false negatives 
+"""
+
+import numpy
+
+def test(p):
+    """
+    Runs the quality control check on profile p and returns a numpy array
+    of quality control decisions with False where the data value has
+    passed the check and True where it failed.
+    """
+
+    # depths
+    d = p.z()
+    # temperatures
+    t = p.t()
+
+    # initialize qc as a bunch of falses;
+    qc = numpy.zeros(len(t.data), dtype=bool)
+
+    # check for gaps in data
+    isDepth = (d.mask==False)
+    isTemperature = (t.mask==False)
+    isData = isTemperature & isDepth
+
+    on_inv = False # are we currently in an inversion?
+
+    for i in range(0, p.n_levels()-1 ):
+        if isData[i] and isData[i+1]:
+            # not interested below 5m:
+            if d.data[i] < 5: continue
+
+            if t.data[i+1] > t.data[i] and not on_inv:
+                # entering an inversion
+                start_inv_temp = t.data[i]
+                start_inv_depth = d.data[i]
+                potential_flag = i
+                on_inv = True
+
+            if t.data[i+1] < t.data[i] and on_inv:
+                # exiting the inversion
+                end_inv_temp = t.data[i]
+                end_inv_depth = d.data[i]
+                on_inv = False
+                gradlong = (end_inv_depth - start_inv_depth) / (end_inv_temp - start_inv_depth)
+
+                if abs(gradlong) < 4:
+                    qc[potential_flag] = True
+
+    return qc

qctests/CSIRO_short_gradient.py

@@ -0,0 +1,37 @@
+"""
+Implements CSIRO's short gradient check
+All questionable features result in a flag, in order to minimize false negatives 
+"""
+
+import numpy
+
+def test(p):
+    """
+    Runs the quality control check on profile p and returns a numpy array
+    of quality control decisions with False where the data value has
+    passed the check and True where it failed.
+    """
+
+    # depths
+    d = p.z()
+    # temperatures
+    t = p.t()
+
+    # initialize qc as a bunch of falses;
+    qc = numpy.zeros(len(t.data), dtype=bool)
+
+    # check for gaps in data
+    isDepth = (d.mask==False)
+    isTemperature = (t.mask==False)
+    isData = isTemperature & isDepth
+
+    for i in range(0, p.n_levels()-1 ):
+        if isData[i] and isData[i+1]:
+            deltaD = (d.data[i+1] - d.data[i]) 
+            deltaT = (t.data[i+1] - t.data[i])
+            gradshort = deltaD / deltaT 
+            if (deltaT > 0.5 and deltaD < 30) or abs(gradshort) < 0.4 or (gradshort > 0 and gradshort < 12.5):
+                if abs(deltaT) > 0.4:
+                    qc[i] = True
+
+    return qc

qctests/CSIRO_surface_spikes.py

@@ -0,0 +1,38 @@
+"""
+Implements CSIRO's surface spike check
+All questionable features result in a flag, in order to minimize false negatives 
+"""
+
+import numpy
+
+def test(p):
+    """
+    Runs the quality control check on profile p and returns a numpy array
+    of quality control decisions with False where the data value has
+    passed the check and True where it failed.
+    """
+
+    # depths
+    d = p.z()
+    # is this an xbt?
+    isXBT = p.probe_type() == 2
+
+    # initialize qc as a bunch of falses;
+    qc = numpy.zeros(len(d.data), dtype=bool)
+
+    # check for gaps in data
+    isDepth = (d.mask==False)
+
+    if not isXBT:
+        return qc
+
+    # flag any level that is shallower than 4m and is followed by a level shallower than 8m.
+    for i in range(p.n_levels()):
+        if isDepth[i]:
+            if d.data[i] < 4 and i < p.n_levels()-1: #only interested in depths less than 4m and not at the bottom of the profile.
+                if d.data[i+1] < 8:
+                    qc[i] = True
+            else:
+                break
+
+    return qc

qctests/CSIRO_wire_break.py

@@ -24,9 +24,8 @@ def test(p):
     isTemperature = (t.mask==False)
 
     # wire breaks at bottom of profile:
-    i = len(t.data)-1
-    if isTemperature[i] and isXBT:
-        if t.data[i] < -2.8 or t.data[i] > 36:
-            qc[i] = True
+    if isTemperature[-1] and isXBT:
+        if t.data[-1] < -2.8 or t.data[-1] > 36:
+            qc[-1] = True
 
     return qc

tests/CSIRO_constant_bottom_validation.py

@@ -0,0 +1,43 @@
+import qctests.CSIRO_constant_bottom
+import util.testingProfile
+import numpy
+
+##### CSIRO_constant_bottom ---------------------------------------------------
+
+def test_CSIRO_constant_bottom():
+    '''
+    Spot-check the nominal behavior of the CSIRO constant bottom test.
+    '''
+
+    # nominal
+    p = util.testingProfile.fakeProfile([0,0,0], [0,100,200], latitude=0, longitude=0, probe_type=2) 
+    qc = qctests.CSIRO_constant_bottom.test(p)
+    truth = numpy.zeros(3, dtype=bool)
+    truth[2] = True
+
+    assert numpy.array_equal(qc, truth), 'failed to flag a constant temperature at bottom of profile' 
+
+    # inappropriate probe type
+    p = util.testingProfile.fakeProfile([0,0,0], [0,100,200], latitude=0, longitude=0, probe_type=1) 
+    qc = qctests.CSIRO_constant_bottom.test(p)
+    truth = numpy.zeros(3, dtype=bool)
+
+    assert numpy.array_equal(qc, truth), 'flagged a constant temperature for an inappropriate probe type' 
+
+    # inappropriate latitude
+    p = util.testingProfile.fakeProfile([0,0,0], [0,100,200], latitude=-41, longitude=0, probe_type=2) 
+    qc = qctests.CSIRO_constant_bottom.test(p)
+
+    assert numpy.array_equal(qc, truth), 'flagged a constant temperature for an inappropriate latitude' 
+
+    # inappropriate depth difference
+    p = util.testingProfile.fakeProfile([0,0,0], [0,100,100], latitude=0, longitude=0, probe_type=2) 
+    qc = qctests.CSIRO_constant_bottom.test(p)
+
+    assert numpy.array_equal(qc, truth), 'flagged a constant temperature for an inappropriate depth distance'
+
+    # not at bottom of profile
+    p = util.testingProfile.fakeProfile([0,0, -1], [100,200,300], latitude=0, longitude=0, probe_type=2) 
+    qc = qctests.CSIRO_constant_bottom.test(p)
+
+    assert numpy.array_equal(qc, truth), 'flagged a constant temperature not at the bottom of the profile'

tests/CSIRO_long_gradient_validation.py

@@ -0,0 +1,34 @@
+import qctests.CSIRO_long_gradient
+import util.testingProfile
+import numpy
+
+##### CSIRO_long_gradient ---------------------------------------------------
+
+def test_CSIRO_long_gradient():
+    '''
+    Spot-check the nominal behavior of the CSIRO long gradient test.
+    '''
+
+    # nominal
+    p = util.testingProfile.fakeProfile([20,10,15,15,15,10], [0,5,10,15,20,25]) 
+    qc = qctests.CSIRO_long_gradient.test(p)
+    truth = numpy.zeros(6, dtype=bool)
+    truth[1] = True
+
+    assert numpy.array_equal(qc, truth), 'failed to flag a nominal long inversion'
+
+    # gradlong too large
+    p = util.testingProfile.fakeProfile([20,10,15,15,15,10], [0,10,20,30,40,50]) 
+    qc = qctests.CSIRO_long_gradient.test(p)
+    truth = numpy.zeros(6, dtype=bool)
+
+    assert numpy.array_equal(qc, truth), 'should not flag a long inversion with such a large gradient'   
+
+    # too shallow
+    p = util.testingProfile.fakeProfile([20,10,15,15,15,10], [0,1,6,11,16,21]) 
+    qc = qctests.CSIRO_long_gradient.test(p)
+    truth = numpy.zeros(6, dtype=bool)
+
+    print truth, qc
+
+    assert numpy.array_equal(qc, truth), 'should not flag a long inversion that begins at < 5m' 

tests/CSIRO_short_gradient_validation.py

@@ -0,0 +1,30 @@
+import qctests.CSIRO_short_gradient
+import util.testingProfile
+import numpy
+
+##### CSIRO_short_gradient ---------------------------------------------------
+
+def test_CSIRO_short_gradient():
+    '''
+    Spot-check the nominal behavior of the CSIRO short gradient test.
+    '''
+
+    # nominal
+    p = util.testingProfile.fakeProfile([0,1], [0,10]) 
+    qc = qctests.CSIRO_short_gradient.test(p)
+    truth = numpy.zeros(2, dtype=bool)
+    truth[0] = True
+
+    assert numpy.array_equal(qc, truth), 'failed to flag a gradient at small delta-temp and delta-depth'
+
+    p = util.testingProfile.fakeProfile([0,10], [0,100]) 
+    qc = qctests.CSIRO_short_gradient.test(p)
+
+    assert numpy.array_equal(qc, truth), 'failed to flag a gradient outside of delta temp and depth ranges, but inside gradshort ranges'     
+
+    # temperature change too small
+    p = util.testingProfile.fakeProfile([0,0.1], [0,0.2]) 
+    qc = qctests.CSIRO_short_gradient.test(p)
+    truth = numpy.zeros(2, dtype=bool)
+
+    assert numpy.array_equal(qc, truth), 'flagged a gradient even though its temperature change was too small to consider' 

tests/CSIRO_surface_spikes.py

@@ -0,0 +1,33 @@
+import qctests.CSIRO_surface_spikes
+import util.testingProfile
+import numpy
+
+##### CSIRO_surface_spikes ---------------------------------------------------
+
+def test_CSIRO_surface_spikes():
+    '''
+    Spot-check the nominal behavior of the CSIRO CSIRO_surface_spikes test.
+    '''
+
+    # nominal
+    p = util.testingProfile.fakeProfile([0,0,0], [1,2,3], probe_type=2) 
+    qc = qctests.CSIRO_surface_spikes.test(p)
+    truth = numpy.zeros(3, dtype=bool)
+    truth[0] = True
+    truth[1] = True
+
+    assert numpy.array_equal(qc, truth), 'failed to flag a collection of shallow profiles' 
+
+    # inappropriate probe type
+    p = util.testingProfile.fakeProfile([0,0,0], [1,2,3], probe_type=1) 
+    qc = qctests.CSIRO_surface_spikes.test(p)
+    truth = numpy.zeros(3, dtype=bool)
+
+    assert numpy.array_equal(qc, truth), 'flagged shallow profiles for an inappropriate probe type' 
+
+    # no cluster
+    p = util.testingProfile.fakeProfile([0,0,0], [1,20,30], probe_type=1) 
+    qc = qctests.CSIRO_surface_spikes.test(p)
+    truth = numpy.zeros(3, dtype=bool)
+
+    assert numpy.array_equal(qc, truth), 'flagged shallow profile without a cluster'