From d8eda3bbfbe2df3ccc8eb1a5f35b6a62d1a86080 Mon Sep 17 00:00:00 2001
From: shaunwbell <shaun.w.bell@gmail.com>
Date: Fri, 26 Mar 2021 16:51:02 -0700
Subject: [PATCH] begin sbe parser (#20)

- add simple sbe39 parser w/wo pressure
- initial test start
---
 examples/16bsm2a_wpak_0000m.nc            | Bin 24830 -> 0 bytes
 examples/mtrduino_process.py              |  26 +++
 examples/sbe39_process.py                 |  29 +++
 src/EcoFOCIpy/io/mtr_parser.py            |  41 +++-
 src/EcoFOCIpy/io/sbe_parser.py            |  58 +++++-
 staticdata/instr_metaconfig/sbe39_cf.yaml |   4 +-
 staticdata/sbe39_wopress.cnv              | 204 ++++++++++++++++++++
 staticdata/sbe39_wpress.cnv               | 217 ++++++++++++++++++++++
 8 files changed, 574 insertions(+), 5 deletions(-)
 delete mode 100644 examples/16bsm2a_wpak_0000m.nc
 create mode 100644 examples/mtrduino_process.py
 create mode 100644 examples/sbe39_process.py
 create mode 100644 staticdata/sbe39_wopress.cnv
 create mode 100644 staticdata/sbe39_wpress.cnv

diff --git a/examples/16bsm2a_wpak_0000m.nc b/examples/16bsm2a_wpak_0000m.nc
deleted file mode 100644
index 30ca6ad9e7891066121af75dd11eb75e250c3b2f..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/examples/mtrduino_process.py b/examples/mtrduino_process.py
new file mode 100644
index 0000000..36bd8c3
--- /dev/null
+++ b/examples/mtrduino_process.py
@@ -0,0 +1,26 @@
+"""
+MTR 5K (Arduino) Example
+========================
+
+Demonstrate how to use the routines to process downloaded mtr data.
+
+Only for the 5k Arduino Series
+"""
+import yaml
+
+import EcoFOCIpy.io.mtr_parser as mtr_parser
+import EcoFOCIpy.io.ncCFsave as ncCFsave
+import EcoFOCIpy.metaconfig.load_config as load_config
+
+###############################################################
+# edit to point to wpak raw datafile (arg parse?)
+datafile = '../staticdata/'
+instrument = ''
+mooring_meta_file = '../staticdata/mooring_example.yaml'
+inst_meta_file = '../staticdata/instr_metaconfig/mtr.yaml'
+inst_shortname = 'mtr'
+###############################################################
+
+#init and load data
+mtr = mtr_parser.mtrduino()
+mtr_data = mtr.parse(filename=datafile,datetime_index=True) 
\ No newline at end of file
diff --git a/examples/sbe39_process.py b/examples/sbe39_process.py
new file mode 100644
index 0000000..2ad9730
--- /dev/null
+++ b/examples/sbe39_process.py
@@ -0,0 +1,29 @@
+"""
+SBE39 Example
+=============
+
+Demonstrate how to use the routines to process downloaded sbe39 cnv data
+
+* with pressure and without pressure
+
+"""
+import yaml
+
+import EcoFOCIpy.io.sbe_parser as sbe_parser
+import EcoFOCIpy.io.ncCFsave as ncCFsave
+import EcoFOCIpy.metaconfig.load_config as load_config
+
+###############################################################
+# edit to point to wpak raw datafile (arg parse?)
+datafile = '../staticdata/sbe39_wopress.cnv'
+instrument = 'SBE-39 1777'
+mooring_meta_file = '../staticdata/mooring_example.yaml'
+inst_meta_file = '../staticdata/instr_metaconfig/sbe39_cf.yaml'
+inst_shortname = 's39'
+###############################################################
+
+#init and load data
+sbe39_wop = sbe_parser.sbe39()
+(sbe39_wop_header,sbe39_wop_data) = sbe39_wop.parse(filename=datafile,
+                                                    return_header=True,
+                                                    datetime_index=True) 
\ No newline at end of file
diff --git a/src/EcoFOCIpy/io/mtr_parser.py b/src/EcoFOCIpy/io/mtr_parser.py
index 505f811..46f412e 100644
--- a/src/EcoFOCIpy/io/mtr_parser.py
+++ b/src/EcoFOCIpy/io/mtr_parser.py
@@ -2,7 +2,44 @@
 
 These include:
 
-* Version 3/4 (old version)
-* Version 5 (MTRduino)
+* Version 3/4 (old version) [ ]
+* Version 5 (MTRduino) [x]
 
 """
+import pandas as pd
+
+class mtrduino(object):
+    r""" MicroTemperature Recorders (MTR) - 5k / MTRduino generation
+    Collection of static methods to define MTR processing and conversion
+
+    It is assumed the data passed here is preliminarily processed and has calibration
+    functions already applied
+
+    ToDO:  Allow raw data to be passed"""
+
+    @staticmethod
+    def parse(filename=None, datetime_index=True, **kwargs):
+        r"""
+        Basic Method to open and read mtrduino raw converted csv files
+            
+            kwargs:
+                round_10min_interval - force small deviations to 10min intervals.  Actually rounds all so it
+                    is user responisbility to make sure values are representative first.
+
+        """
+        assert filename != None , 'Must provide a datafile'
+
+        rawdata = pd.read_csv(
+            filename, delimiter=",", parse_dates=["date_time"]
+        )
+
+        if datetime_index:
+            rawdata_df = rawdata_df.set_index(pd.DatetimeIndex(rawdata_df['date_time'])).drop(['date_time'],axis=1)
+
+        #previous algorithms rounded to 10min
+        ## all time manipulation should either be outside the instrument methods
+        ##  or optional via a method call... maybe not a flag like here??
+        if kwargs["round_10min_interval"]:
+            rawdata.index = rawdata.index.round("10min", inplace=True)
+
+        return rawdata_df
diff --git a/src/EcoFOCIpy/io/sbe_parser.py b/src/EcoFOCIpy/io/sbe_parser.py
index 47c5b56..66fbdfd 100644
--- a/src/EcoFOCIpy/io/sbe_parser.py
+++ b/src/EcoFOCIpy/io/sbe_parser.py
@@ -6,4 +6,60 @@
 Moored SBE (cnv files):
 * 16,19,26,37,39,56
 
-"""
\ No newline at end of file
+"""
+import pandas as pd
+import sys
+
+
+class sbe39(object):
+    r""" Seabird 39 Temperature (with optional pressure)
+        
+        Basic Method to open files.  Specific actions can be passes as kwargs for instruments
+
+        With or without header
+
+        With or without pressure - assume 4 cols = w/press, 3 cols = w/o press
+
+    """
+
+    @staticmethod
+    def parse(filename=None, return_header=True, datetime_index=True):
+        r"""
+        Basic Method to open and read sbe39 csv files
+            
+            kwargs
+            truncate_seconds : boolean (truncates down to nearest minute)
+
+        """
+        assert filename != None , 'Must provide a datafile'
+
+        header = []
+
+        with open(filename) as fobj:
+            for k, line in enumerate(fobj.readlines()):
+                header = header + [line]
+                if "*END*" in line:
+                    headercount=k+4
+                    break
+
+
+        rawdata_df = pd.read_csv(filename, 
+                        delimiter=",", 
+                        parse_dates=True, 
+                        header=None, 
+                        skiprows=headercount)
+
+        if len(rawdata_df.columns) == 4:
+            rawdata_df.columns = ['temperature','pressure','date','time']
+        elif len(rawdata_df.columns) == 3:
+            rawdata_df.columns = ['temperature','date','time']
+        else:
+            sys.exit('Unknown number of columns in raw data')
+
+        rawdata_df["date_time"] = pd.to_datetime(rawdata_df["date"] + " " + rawdata_df["time"], format="%d %b %Y %H:%M:%S")
+
+        if datetime_index:
+            rawdata_df = rawdata_df.set_index(pd.DatetimeIndex(rawdata_df['date_time'])).drop(['date_time','DATE','TIME'],axis=1)        
+
+        return (rawdata_df,header)
+
diff --git a/staticdata/instr_metaconfig/sbe39_cf.yaml b/staticdata/instr_metaconfig/sbe39_cf.yaml
index f12b98b..ff01ec5 100644
--- a/staticdata/instr_metaconfig/sbe39_cf.yaml
+++ b/staticdata/instr_metaconfig/sbe39_cf.yaml
@@ -43,13 +43,13 @@ timeseries_id:
   long_name: "timeseries id"
   standard_name: ''
 #variables
-temp:
+temperature:
   epic_key: T_20
   generic_name: temp
   long_name: "Sea temperature in-situ ITS-90 scale"
   standard_name: sea_water_temperature
   units: degree_C
-pres: 
+pressure: 
   epic_key: P_1
   generic_name: pres
   units: decibar
diff --git a/staticdata/sbe39_wopress.cnv b/staticdata/sbe39_wopress.cnv
new file mode 100644
index 0000000..2f9530a
--- /dev/null
+++ b/staticdata/sbe39_wopress.cnv
@@ -0,0 +1,204 @@
+* Sea-Bird SBE39 Data File:
+* FileName = C:\Users\strausz.PMEL\Desktop\2016\bering_downloads\16bsm2a_sbe39_1777_21m.asc
+* Software Version 1.59
+* Temperature SN = 
+* Conductivity SN = 
+* System UpLoad Time = Oct 11 2016 21:04:04
+** real time:  205610
+** inst time: 205631
+* ds
+* SBE 39 V 2.2   SERIAL NO. 1777    11 Oct 2016  21:03:12
+* battery voltage = 8.6
+* not logging: received stop command
+* sample interval = 600 seconds
+* samplenumber = 23023, free = 576163
+* serial sync mode disabled
+* real-time output disabled
+* SBE 39 configuration = temperature only
+* binary upload does not include time
+* temperature = 21.23 deg C
+
+
+* S>
+* SBE39 V 2.2   01777
+* temperature:  02-dec-15
+*     TA0 = 7.411042e-05
+*     TA1 = 2.721709e-04
+*     TA2 = -2.270258e-06
+*     TA3 = 1.482924e-07
+
+
+* S> 
+*END*
+start time =  05 May 2016  00:00:00
+sample interval = 600 seconds
+start sample number = 1
+  8.2290, 05 May 2016, 00:00:00
+  8.1297, 05 May 2016, 00:10:00
+  8.1061, 05 May 2016, 00:20:00
+  8.2852, 05 May 2016, 00:30:00
+  8.4766, 05 May 2016, 00:40:00
+  9.0763, 05 May 2016, 00:50:00
+  8.9149, 05 May 2016, 01:00:00
+  9.0934, 05 May 2016, 01:10:00
+ 11.9529, 05 May 2016, 01:20:00
+ 12.4361, 05 May 2016, 01:30:00
+ 14.1294, 05 May 2016, 01:40:00
+ 12.8875, 05 May 2016, 01:50:00
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+  7.6283, 05 May 2016, 02:40:00
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+  5.1848, 05 May 2016, 12:00:00
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+  4.7733, 05 May 2016, 14:20:00
+  4.7788, 05 May 2016, 14:30:00
+  4.7932, 05 May 2016, 14:40:00
+  4.8262, 05 May 2016, 14:50:00
+  4.8414, 05 May 2016, 15:00:00
+  4.9209, 05 May 2016, 15:10:00
+  5.1120, 05 May 2016, 15:20:00
+  5.2432, 05 May 2016, 15:30:00
+  5.2809, 05 May 2016, 15:40:00
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+  5.3467, 05 May 2016, 16:40:00
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+  5.3904, 05 May 2016, 17:50:00
+  5.3910, 05 May 2016, 18:00:00
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+  5.3322, 05 May 2016, 18:40:00
+  5.3522, 05 May 2016, 18:50:00
+  5.3075, 05 May 2016, 19:00:00
+  5.3045, 05 May 2016, 19:10:00
+  5.2856, 05 May 2016, 19:20:00
+  5.3156, 05 May 2016, 19:30:00
+  5.3033, 05 May 2016, 19:40:00
+  5.3147, 05 May 2016, 19:50:00
+  5.3569, 05 May 2016, 20:00:00
+  5.1978, 05 May 2016, 20:10:00
+  5.2093, 05 May 2016, 20:20:00
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+  5.4355, 05 May 2016, 20:50:00
+  5.4800, 05 May 2016, 21:00:00
+  5.4778, 05 May 2016, 21:10:00
+  5.4599, 05 May 2016, 21:20:00
+  5.4757, 05 May 2016, 21:30:00
+  5.4571, 05 May 2016, 21:40:00
+  5.5096, 05 May 2016, 21:50:00
+  5.4864, 05 May 2016, 22:00:00
+  5.4631, 05 May 2016, 22:10:00
+  5.4860, 05 May 2016, 22:20:00
+  5.4740, 05 May 2016, 22:30:00
+  5.5130, 05 May 2016, 22:40:00
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+  5.4256, 05 May 2016, 23:30:00
+  5.4053, 05 May 2016, 23:40:00
+  5.3565, 05 May 2016, 23:50:00
+  5.3449, 06 May 2016, 00:00:00
+  5.2386, 06 May 2016, 00:10:00
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+  5.1892, 06 May 2016, 00:30:00
+  5.2889, 06 May 2016, 00:40:00
+  5.4054, 06 May 2016, 00:50:00
+  5.4813, 06 May 2016, 01:00:00
+  5.4264, 06 May 2016, 01:10:00
+  5.2134, 06 May 2016, 01:20:00
+  5.3266, 06 May 2016, 01:30:00
+  5.4210, 06 May 2016, 01:40:00
+  5.5686, 06 May 2016, 01:50:00
+  5.5257, 06 May 2016, 02:00:00
+  5.3876, 06 May 2016, 02:10:00
+  5.3468, 06 May 2016, 02:20:00
+  5.5345, 06 May 2016, 02:30:00
+  5.1555, 06 May 2016, 02:40:00
+  5.5858, 06 May 2016, 02:50:00
+  5.3153, 06 May 2016, 03:00:00
+  5.4245, 06 May 2016, 03:10:00
+  5.4083, 06 May 2016, 03:20:00
+  5.5367, 06 May 2016, 03:30:00
+  5.3333, 06 May 2016, 03:40:00
+  5.2527, 06 May 2016, 03:50:00
+  5.2081, 06 May 2016, 04:00:00
\ No newline at end of file
diff --git a/staticdata/sbe39_wpress.cnv b/staticdata/sbe39_wpress.cnv
new file mode 100644
index 0000000..4e072fe
--- /dev/null
+++ b/staticdata/sbe39_wpress.cnv
@@ -0,0 +1,217 @@
+* Sea-Bird SBE39 Data File:
+* FileName = C:\Users\strausz.PMEL\Desktop\2016\bering_downloads\16bsm2a_sbe39_992_39m.asc
+* Software Version 1.59
+* Temperature SN = 
+* Conductivity SN = 
+* System UpLoad Time = Oct 11 2016 21:16:46
+** realtime: 211510
+** inst time: 211432
+* ds
+* SBE 39 V 1.7a   SERIAL NO. 00992    11 Oct 2016  21:15:27
+* not logging: received stop command
+* sample interval = 600 seconds
+* samplenumber = 23024, free = 209992
+* serial sync mode disabled
+* real-time output disabled
+* SBE 39 configuration = temperature and pressure
+* binary upload does not include time
+* temperature = 21.03 deg C
+
+
+* S>
+* SBE39 V 1.7a   00992
+* temperature:  01-dec-15
+*     TA0 = 5.747298e-05
+*     TA1 = 2.686513e-04
+*     TA2 = -2.064612e-06
+*     TA3 = 1.407888e-07
+* pressure S/N 1345, range = 508 psia:  25-nov-15
+*     PA0 = 1.374140e+00
+*     PA1 = 2.409012e-02
+*     PA2 = 1.747798e-09
+*     PTHA0 = -6.215146e+01
+*     PTHA1 = 5.103617e-02
+*     PTHA2 = -8.432632e-08
+*     PTCA0 = -3.407050e+00
+*     PTCA1 = 3.609744e+00
+*     PTCA2 = -4.446806e-02
+*     PTCB0 = 2.499963e+01
+*     PTCB1 = -6.750000e-04
+*     PTCB2 = 0.000000e+00
+* rtc:  01-dec-15
+*     RTCA0 = 9.999772e-01
+*     RTCA1 = 1.563622e-06
+*     RTCA2 = -3.397688e-08
+
+
+* S> 
+*END*
+start time =  05 May 2016  00:00:15
+sample interval = 600 seconds
+start sample number = 1
+  8.0234,   -0.028, 05 May 2016, 00:00:15
+  7.9049,   -0.028, 05 May 2016, 00:10:15
+  7.9709,   -0.028, 05 May 2016, 00:20:15
+  8.0860,   -0.028, 05 May 2016, 00:30:15
+  8.1800,   -0.033, 05 May 2016, 00:40:15
+  8.4526,   -0.042, 05 May 2016, 00:50:15
+  8.7365,   -0.071, 05 May 2016, 01:00:15
+  9.7027,   -0.089, 05 May 2016, 01:10:15
+ 10.3345,   -0.099, 05 May 2016, 01:20:15
+ 10.4398,   -0.104, 05 May 2016, 01:30:15
+ 10.5201,   -0.104, 05 May 2016, 01:40:15
+ 10.1627,   -0.104, 05 May 2016, 01:50:15
+  9.9630,   -0.094, 05 May 2016, 02:00:15
+ 10.1234,   -0.094, 05 May 2016, 02:10:15
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+ 10.1087,   -0.089, 05 May 2016, 02:30:15
+ 10.0655,   -0.089, 05 May 2016, 02:40:15
+  9.8675,   -0.089, 05 May 2016, 02:50:15
+  9.5327,   -0.085, 05 May 2016, 03:00:15
+  9.4890,   -0.080, 05 May 2016, 03:10:15
+  9.5061,   -0.080, 05 May 2016, 03:20:15
+  9.3634,   -0.075, 05 May 2016, 03:30:15
+  9.1183,   -0.075, 05 May 2016, 03:40:15
+  9.4723,   -0.085, 05 May 2016, 03:50:15
+  6.8989,   -0.033, 05 May 2016, 04:00:15
+  6.4069,    0.057, 05 May 2016, 04:10:15
+  5.0831,   19.047, 05 May 2016, 04:20:15
+  5.0780,   22.288, 05 May 2016, 04:30:15
+  5.0649,   21.651, 05 May 2016, 04:40:15
+  5.0262,   22.392, 05 May 2016, 04:50:15
+  4.8558,   23.864, 05 May 2016, 05:00:15
+  4.6777,   36.692, 05 May 2016, 05:10:15
+  4.6760,   35.998, 05 May 2016, 05:20:15
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+  4.6939,   34.833, 05 May 2016, 05:40:15
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+  4.6519,   40.070, 05 May 2016, 06:00:15
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+  4.7542,   39.683, 06 May 2016, 00:00:15
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+  4.4225,   39.900, 06 May 2016, 03:10:15
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+  4.4372,   39.329, 06 May 2016, 03:30:15
\ No newline at end of file