Merge pull request #21 from steinermg/Issue_15346

Issue #15346 - Change in PCO2W/PHSEN thermistor functions and parser …

ion_functions/data/co2_functions.py

@@ -120,7 +120,7 @@ def pco2_blank(raw_blank):
     return blank
 
 
-def pco2_thermistor(traw):
+def pco2_thermistor(traw, sami_bits):
     """
     Description:
 
@@ -131,15 +131,17 @@ def pco2_thermistor(traw):
 
         2013-04-20: Christopher Wingard. Initial code.
         2014-02-19: Christopher Wingard. Updated comments.
+        2023-01-12: Mark Steiner. Add sami_bits arg to handle hardware upgrades
 
     Usage:
 
-        therm = pco2_thermistor(traw)
+        therm = pco2_thermistor(traw, sami_bits)
 
             where
 
         therm = converted thermistor temperature [degC]
         traw = raw thermistor temperature (CO2THRM_L0) [counts]
+        sami_bits = number of bits on the SAMI hardware
 
     References:
 
@@ -149,8 +151,16 @@ def pco2_thermistor(traw):
             OOI >> Controlled >> 1000 System Level >>
             1341-00490_Data_Product_SPEC_PCO2WAT_OOI.pdf)
     """
+    # reset inputs to arrays
+    traw = np.atleast_1d(traw)
+    sami_bits = np.atleast_1d(sami_bits)
+
     # convert raw thermistor readings from counts to degrees Centigrade
-    Rt = ne.evaluate('log((traw / (4096. - traw)) * 17400.)')
+    # conversion depends on whether the SAMI is older 12 bit or newer 14 bit hardware
+    if sami_bits[0] == 14:
+        Rt = ne.evaluate('log((traw / (16384. - traw)) * 17400.)')
+    else:
+        Rt = ne.evaluate('log((traw / (4096. - traw)) * 17400.)')
     InvT = ne.evaluate('0.0010183 + 0.000241 * Rt + 0.00000015 * Rt**3')
     therm = ne.evaluate('(1 / InvT) - 273.15')
     return therm
@@ -255,6 +265,7 @@ def pco2_calc_pco2(light, therm, ea434, eb434, ea620, eb620,
                     incorrectly calculated the blank correction. Applies additional
                     corrections to calculations to avoid errors thrown when running a
                     blank measurement.
+        2023-01-12: Mark Steiner. Arg therm in degrees C instead of counts
 
     Usage:
 
@@ -265,7 +276,7 @@ def pco2_calc_pco2(light, therm, ea434, eb434, ea620, eb620,
 
         pco2 = measured pco2 in seawater (PCO2WAT_L1) [uatm]
         light = array of light measurements
-        therm = PCO2W thermistor temperature (CO2THRM_L0) [counts]
+        therm = PCO2W thermistor temperature (CO2THRM_L1) [degrees C]
         ea434 = Reagent specific calibration coefficient
         eb434 = Reagent specific calibration coefficient
         ea620 = Reagent specific calibration coefficient
@@ -301,9 +312,6 @@ def pco2_calc_pco2(light, therm, ea434, eb434, ea620, eb620,
     Ratio434 = light[:, 6]     # 434nm Ratio
     Ratio620 = light[:, 7]     # 620nm Ratio
 
-    # Convert thermistor counts to degrees C
-    therm = pco2_thermistor(therm)
-
     # correct the absorbance ratios using the blanks
     AR434 = (Ratio434 / a434blank)
     AR620 = (Ratio620 / a620blank)

ion_functions/data/perf/test_co2_performance.py

@@ -17,6 +17,7 @@ def setUp(self):
         self.cala = 0.0459
         self.calb = 0.6257
         self.calc = -1.5406
+        self.sami_bits = 12
 
         self.light = np.zeros(14, dtype=np.int)
         self.mtype = int(s[5:7], 16)
@@ -125,7 +126,8 @@ def test_pco2_thermistor(self):
         # create 10000 data points
         data = np.ones(a_deca, dtype='int16')
         traw = data * self.traw
-        self.profile(stats, pco2_thermistor, traw)
+        sami_bits = data * self.sami_bits
+        self.profile(stats, pco2_thermistor, traw, sami_bits)
 
     def test_pco2_calc_pco2(self):
         stats = []

ion_functions/data/perf/test_ph_performance.py

@@ -29,6 +29,7 @@ def setUp(self):
         self.eb578 = 38913.
         self.ind_slp = 1.
         self.ind_off = 0.
+        self.sami_bits = 12
 
         # raw data strings provided by the DPS
         raw_strings = np.array([
@@ -75,7 +76,8 @@ def test_ph_thermistor(self):
 
         # create 12000 data points
         traw = np.repeat(self.traw, 2000)
-        self.profile(stats, ph_thermistor, traw)
+        sami_bits = np.repeat(self.sami_bits, 2000)
+        self.profile(stats, ph_thermistor, traw, sami_bits)
 
     def test_ph_434_intensity(self):
         stats = []

ion_functions/data/ph_functions.py

@@ -39,13 +39,21 @@ def ph_578_intensity(light):
 
 # functions to convert thermistor and battery measurements from counts to
 # applicable engineering units
-def ph_thermistor(traw):
+def ph_thermistor(traw, sami_bits):
     """
     Function to convert the thermistor data (ABSTHRM_L0) from counts to degrees
     Centigrade for the pH instrument.
     """
+    # reset inputs to arrays
+    traw = np.atleast_1d(traw)
+    sami_bits = np.atleast_1d(sami_bits)
+
     # convert raw thermistor readings from counts to degrees Centigrade
-    Rt = ne.evaluate('(traw / (4096.0 - traw)) * 17400.0')
+    # conversion depends on whether the SAMI is older 12 bit or newer 14 bit hardware
+    if sami_bits[0] == 14:
+        Rt = ne.evaluate('(traw / (16384.0 - traw)) * 17400.0')
+    else:
+        Rt = ne.evaluate('(traw / (4096.0 - traw)) * 17400.0')
     lRt = np.log(Rt) 
     InvT = ne.evaluate('0.0010183 + 0.000241 * lRt + 0.00000015 * lRt**3')
     therm = ne.evaluate('(1.0 / InvT) - 273.15')

ion_functions/data/test/test_co2_functions.py

@@ -73,6 +73,7 @@ def setUp(self):
 
         self.a434blnk = np.ones(14) * a434blnk
         self.a620blnk = np.ones(14) * a620blnk
+        self.sami_bits = np.ones(14) * 12
 
     def test_pco2_pco2wat(self):
         """
@@ -96,7 +97,7 @@ def test_pco2_pco2wat(self):
         # calculate pco2.
 
         ### bulk case ###
-        tout = co2func.pco2_thermistor(self.traw)
+        tout = co2func.pco2_thermistor(self.traw, self.sami_bits)
         pco2out = co2func.pco2_pco2wat(self.mtype, self.light, self.traw,
                                        fill_value, fill_value, fill_value, fill_value,
                                        self.calt, self.cala, self.calb, self.calc,
@@ -108,7 +109,7 @@ def test_pco2_pco2wat(self):
         ### single record case ###
         indx = 0
         for mtype in self.mtype:
-            tout = co2func.pco2_thermistor(self.traw[indx])
+            tout = co2func.pco2_thermistor(self.traw[indx], self.sami_bits)
             pco2out = co2func.pco2_pco2wat(mtype, self.light[indx, :], self.traw[indx],
                                            fill_value, fill_value, fill_value, fill_value,
                                            self.calt[indx], self.cala[indx],

ion_functions/data/test/test_ph_functions.py

@@ -39,6 +39,7 @@ def setUp(self):
         self.eb578 = 38502.
         self.ind_slp = 0.9698
         self.ind_off = 0.2484
+        self.sami_bits = 12
         self.salinity = np.array([30., 30., 30., 30., 30.,
                                   32., 32., 32., 32., 32.,
                                   35., 35., 35., 35., 35.])
@@ -235,7 +236,7 @@ def test_ph_singles(self):
             bout[iRec] = ph.ph_battery(self.braw[iRec])
             a434[iRec, :] = ph.ph_434_intensity(self.light[iRec, :])
             a578[iRec, :] = ph.ph_578_intensity(self.light[iRec, :])
-            tout[iRec] = ph.ph_thermistor(self.traw[iRec])
+            tout[iRec] = ph.ph_thermistor(self.traw[iRec], self.sami_bits)
             pout[iRec] = ph.ph_calc_phwater(self.ref[iRec, :], self.light[iRec, :],
                                             tout[iRec], self.ea434, self.eb434,
                                             self.ea578, self.eb578, self.ind_slp,
@@ -252,7 +253,7 @@ def test_ph_multiples(self):
         in a single block.
         """
         bout = ph.ph_battery(self.braw)
-        tout = ph.ph_thermistor(self.traw)
+        tout = ph.ph_thermistor(self.traw, self.sami_bits)
         a434 = ph.ph_434_intensity(self.light)  # no unit tests, just checking to see if they work
         print a434
         a578 = ph.ph_578_intensity(self.light)