Fixes fill value

ion_functions/__init__.py

@@ -11,3 +11,6 @@
 #from data.vel_functions import nobska_mag_corr_east, nobska_mag_corr_north, nobska_mag_corr_up, vel_mag_correction
 
 from data.generic_functions import extract_parameter, magnetic_declination, ntp_to_unix_time
+
+
+fill_value = -9999999.

ion_functions/data/co2_functions.py

@@ -9,6 +9,7 @@
 
 import numpy as np
 import numexpr as ne
+from ion_functions import fill_value
 
 
 # wrapper functions to extract parameters from SAMI-II CO2 instruments (PCO2W)
@@ -88,7 +89,7 @@ def pco2_pco2wat(mtype, light, therm, ea434, eb434, ea620, eb620,
           pco2 = pco2_calc_pco2(light, therm, ea434, eb434, ea620, eb620,  
                     calt, cala, calb, calc, a434blnk, a620blnk)
      else:
-          pco2 = -99999999.
+          pco2 = fill_value
 
      return pco2
 

ion_functions/data/perf/test_co2_performance.py

@@ -2,6 +2,7 @@
 from ion_functions.data.perf.test_performance import PerformanceTestCase
 from ion_functions.data.co2_functions import pco2_thermistor, pco2_abs434_blank, pco2_abs620_blank, pco2_pco2wat
 import numpy as np
+from ion_functions import fill_value
 
 class TestCO2Performance(PerformanceTestCase):
     def setUp(self):
@@ -15,14 +16,14 @@ def setUp(self):
         self.cala = 0.0459
         self.calb = 0.6257
         self.calc = -1.5406
-        self.a434blnk = -99999999.
-        self.a620blnk = -99999999.
+        self.a434blnk = fill_value
+        self.a620blnk = fill_value
 
         # expected outputs
         self.therm = np.array([18.8526, 18.8765, 18.9245, 18.9485,
                           18.9485, 18.9485, 18.8765, 19.0686,
                           19.0686, 19.0446, 18.9725])
-        self.pco2 = np.array([-99999999., 294.1720, 311.3361, 319.0101,
+        self.pco2 = np.array([fill_value, 294.1720, 311.3361, 319.0101,
                          319.8925, 319.8950, 305.8104, 317.9661,
                          284.3676, 280.2324, 280.0354
                          ])

ion_functions/data/sfl_functions.py

@@ -5,7 +5,7 @@
 @author Christopher Wingard
 @brief Module containing Seafloor Properties related data-calculations.
 """
-
+from ion_functions import fill_value
 def sfl_trhph_vfltemp(V_s, V_c, a, b, c, d, e):
     """
     Description:
@@ -147,6 +147,7 @@ def sfl_trhph_chloride(V_R1, V_R2, V_R3, T):
 
     # reset NaN values generated in interpolation functions above to system
     # default of -99999999
-    Cl[np.isnan(Cl)] = -99999999.
+    Cl[np.isnan(Cl)] = fill_value
 
     return Cl
+

ion_functions/data/test/test_co2_functions.py

@@ -12,6 +12,7 @@
 
 import numpy as np
 from ion_functions.data import co2_functions as co2func
+from ion_functions import fill_value
 
 @attr('UNIT', group='func')
 class Testpco2FunctionsUnit(BaseUnitTestCase):
@@ -53,14 +54,14 @@ def test_co2_pco2wat(self):
         cala = 0.0459
         calb = 0.6257
         calc = -1.5406
-        a434blnk = -99999999.
-        a620blnk = -99999999.
+        a434blnk = fill_value
+        a620blnk = fill_value
 
         # expected outputs
         therm = np.array([18.8526, 18.8765, 18.9245, 18.9485,
                           18.9485, 18.9485, 18.8765, 19.0686,
                           19.0686, 19.0446, 18.9725])
-        pco2 = np.array([-99999999., 294.1720, 311.3361, 319.0101,
+        pco2 = np.array([fill_value, 294.1720, 311.3361, 319.0101,
                          319.8925, 319.8950, 305.8104, 317.9661,
                          284.3676, 280.2324, 280.0354
                          ])

ion_functions/data/test/test_sfl_functions.py

@@ -12,6 +12,7 @@
 
 import numpy as np
 from ion_functions.data import sfl_functions as sflfunc
+from ion_functions import fill_value
 
 @attr('UNIT', group='func')
 class TestSFLFunctionsUnit(BaseUnitTestCase):
@@ -84,14 +85,14 @@ def test_sfl_trhph_chloride(self):
         Implemented by Christopher Wingard, April 2013
         """
         test_array = np.array([
-            [0.906, 4.095, 4.095, 11.8, 4.530, 0.2208, -99999999., -99999999.],
-            [0.890, 4.095, 4.095, 15.9, 4.450, 0.2247, -99999999., -99999999.],
-            [0.891, 4.095, 4.095, 3.2, 4.455, 0.2245, -99999999., -99999999.],
-            [0.184, 0.915, 4.064, 67.7, 0.915, 1.0929, -99999999., -99999999.],
-            [0.198, 1.002, 4.095, 75.8, 1.002, 0.9980, -99999999., -99999999.],
-            [0.172, 0.857, 4.082, 97.5, 0.857, 1.1669, -99999999., -99999999.],
-            [0.183, 0.926, 4.076, 95.0, 0.926, 1.0799, -99999999., -99999999.],
-            [0.233, 1.182, 4.072, 96.2, 1.182, 0.8460, -99999999., -99999999.],
+            [0.906, 4.095, 4.095, 11.8, 4.530, 0.2208, fill_value, fill_value],
+            [0.890, 4.095, 4.095, 15.9, 4.450, 0.2247, fill_value, fill_value],
+            [0.891, 4.095, 4.095, 3.2, 4.455, 0.2245, fill_value, fill_value],
+            [0.184, 0.915, 4.064, 67.7, 0.915, 1.0929, fill_value, fill_value],
+            [0.198, 1.002, 4.095, 75.8, 1.002, 0.9980, fill_value, fill_value],
+            [0.172, 0.857, 4.082, 97.5, 0.857, 1.1669, fill_value, fill_value],
+            [0.183, 0.926, 4.076, 95.0, 0.926, 1.0799, fill_value, fill_value],
+            [0.233, 1.182, 4.072, 96.2, 1.182, 0.8460, fill_value, fill_value],
             [0.146, 0.747, 3.634, 116.8, 0.727, 1.3759, 0.19507, 195],
             [0.134, 0.681, 3.405, 272.8, 0.681, 1.4684, 0.10893, 109],
             [0.131, 0.673, 3.293, 325.8, 0.659, 1.5184, 0.12813, 128],

ion_functions/qc/qc_functions.py

@@ -12,7 +12,7 @@
 import numpy as np
 import numexpr as ne
 from scipy.interpolate import LinearNDInterpolator
-from ion_functions import utils
+from ion_functions import utils, fill_value
 
 # try to load the OOI logging module, using default Python logging module if
 # unavailable
@@ -23,7 +23,7 @@
     log = logging.getLogger('ion-functions')
 
 def is_fill(arr):
-    return np.atleast_1d(arr)[-1] == -9999
+    return np.atleast_1d(arr)[-1] == fill_value
 def is_none(arr):
     return arr is None or (np.atleast_1d(arr)[-1] == None)