add odv output

odv.py

+# ascii.py
+# write hdr and data in ascii files
+
+import os
+import logging
+from re import S
+import tools
+import numpy as np
+from datetime import datetime
+    
+def writeDataProfile(dataFile, cfg, device, fe, r):
+    f = open(dataFile, 'w')
+
+    # write header, first line
+    f.write("{}  {}  {}  {}  {}  {}\n".format(cfg['cruise']['CYCLEMESURE'], 
+        cfg['cruise']['PLATEFORME'], cfg['cruise']['INSTITUTE'],
+        cfg[device]['typeInstrument'], cfg[device]['instrumentNumber'],
+        cfg['cruise']['PI']))
+
+    # write odv header
+    f.write(f"//ODV Spreadsheet file : {dataFile}\n")
+    f.write(f"//Data treated : {datetime.today().strftime('%Y-%m-%dT%H:%M:%SZ')}\n")
+    f.write("//<DataType>Profiles</DataType>\n")
+    f.write(f"//<InstrumentType>{cfg[device]['typeInstrument']}</InstrumentType>\n")
+    f.write(f"//<Source>{os.getcwd()}</Sources>\n")
+    f.write(f"//<Creator>{cfg['cruise']['CREATOR']}</Creator>\n")
+    f.write("//\n")
+    f.write("Cruise\tStation\tType\tmon/day/yr\thh:mm\tLongitude [degrees_east]\tLatitude [degrees_north]\tBot. Depth [m]")
+
+    # write variables and unit
+    for k in fe.keys:
+        f.write(f"  {k} [{fe.roscop[k]['units']}]")
+    f.write("\n")
+
+    type = 'C'
+    for i in range(fe.n):
+        # for each valid line in array (not _fillvalue)
+        
+        for m in range(fe.size[i+1]):
+            fmt = fe.roscop['PROFILE']['format']
+            f.write(f"%s\t{fmt}\t%s\t" % (cfg['cruise']['CYCLEMESURE'], fe['PROFILE'][i], type))
+            f.write(f"%s\t" % (tools.julian2format(fe['TIME'][i], "%Y-%m-%dT%H:%M:%S")))
+            f.write(f"%f\t" % (fe['LATITUDE'][i]))
+            f.write(f"%f\t" % (fe['LONGITUDE'][i]))
+            if fe.iskey('BATH'):
+                fmt = fe.roscop['BATH']['format']
+                f.write(f"{fmt}\t" % (fe['BATH'][i]))
+            else:
+                f.write("\t")
+            for k in fe.keys:        
+                if fe[k][i][m] != fe.roscop[k]['_FillValue']:
+                    fmt = fe.roscop[k]['format']
+                    f.write(f"{fmt}\t" % (fe[k][i][m]))
+                else:
+                    f.write("\t")
+            f.write("\n")
+    f.close()
+
+def writeProfile(cfg, device, fe, r):
+    if not os.path.exists(cfg['global']['odv']):
+        os.makedirs(cfg['global']['odv'])
+    
+    fileName = "{}/{}_{}_odv.txt".format(cfg['global']['odv'], 
+        cfg['cruise']['CYCLEMESURE'], device.lower())
+    print('writing data   file: {}'.format(fileName), end='', flush=True)
+    writeDataProfile(fileName, cfg, device.lower(), fe, r)
+    print(' done...')
+
+def writeDecimalDataTrajectory(dataFile, cfg, device, fe, r):
+    f = open(dataFile, 'w')
+
+    # write header, first line
+    f.write("{}  {}  {}  ".format(cfg['cruise']['CYCLEMESURE'], 
+        cfg['cruise']['PLATEFORME'], cfg['cruise']['INSTITUTE']))
+    if 'typeInstrument' in cfg[device]:
+        f.write(f"{cfg[device]['typeInstrument']}")
+    if 'instrumentNumber' in cfg[device]:
+        f.write(f"{cfg[device]['instrumentNumber']}")
+    if 'PI' in cfg['cruise']:
+        f.write(f"{cfg['cruise']['PI']}")
+    f.write("\n")
+
+    # write header, second line with physical parameter liste, fill with N/A if necessary
+    for k in fe.keys:
+        f.write(f"  {k}  ")
+    f.write("\n")
+    # write data
+    for n in range(fe.n):
+        for k in fe.keys: 
+            fmt = fe.roscop[k]['format']
+            if '_FillValue' in fe.roscop[k] and fe[k][n] == fe.roscop[k]['_FillValue']:
+                f.write('  1e+36 ')
+            else:
+                f.write(f" {fmt} " % (fe[k][n]))
+        f.write("\n")
+    f.close()
+
+def writeHumanDataTrajectory(dataFile, cfg, device, fe, r):
+    f = open(dataFile, 'w')
+
+    # write header, first line
+    f.write("{}  {}  {}  ".format(cfg['cruise']['CYCLEMESURE'], 
+        cfg['cruise']['PLATEFORME'], cfg['cruise']['INSTITUTE']))
+    if 'typeInstrument' in cfg[device]:
+        f.write(f"{cfg[device]['typeInstrument']}")
+    if 'instrumentNumber' in cfg[device]:
+        f.write(f"{cfg[device]['instrumentNumber']}")
+    if 'PI' in cfg['cruise']:
+        f.write(f"{cfg['cruise']['PI']}")
+    f.write("\n")
+
+    # write header, second line with physical parameter liste, fill with N/A if necessary
+    for k in fe.keys:
+        if k == 'DAYD':
+            f.write("    DATE      TIME   ")
+            continue
+        f.write(f"   {k}  ")
+    f.write("\n")
+    # write data
+    for n in range(fe.n):
+        for k in fe.keys: 
+            if k == 'LATITUDE':
+                f.write(f" {tools.Dec2dmc(fe[k][n],'N')} ")
+                continue
+            if k == 'LONGITUDE':
+                f.write(f" {tools.Dec2dmc(fe[k][n],'E')} ")
+                continue
+            if k == 'DAYD':
+                # use the format given in devide trajectory toml config file
+                dt = tools.julian2format(fe[k][n])
+                f.write(f" {dt} ")
+                continue
+            fmt = fe.roscop[k]['format']
+            if '_FillValue' in fe.roscop[k] and fe[k][n] == fe.roscop[k]['_FillValue']:
+                f.write('  1e+36 ')
+            else:
+                f.write(f" {fmt} " % (fe[k][n]))
+        f.write("\n")
+    f.close()
+
+
+def writeTrajectory(cfg, device, fe, r):
+    if not os.path.exists(cfg['global']['odv']):
+        os.makedirs(cfg['global']['odv'])
+    
+    # write ascii file with human read time and position
+    fileName = "{}/{}_{}_odv.txt".format(cfg['global']['odv'], 
+        cfg['cruise']['CYCLEMESURE'], device.lower())
+    print('writing file: {}'.format(fileName), end='', flush=True)
+    writeHumanDataTrajectory(fileName, cfg, device.lower(), fe, r, )
+    print(' done...')
+    
+    # write ascii file with decimal time and position
+    fileName = "{}/{}_{}_odv.txt".format(cfg['global']['odv'], 
+        cfg['cruise']['CYCLEMESURE'], device.lower())
+    print('writing file: {}'.format(fileName), end='', flush=True)
+    writeDecimalDataTrajectory(fileName, cfg, device.lower(), fe, r)
+    print(' done...')
+   
\ No newline at end of file

profile.py

@@ -18,6 +18,7 @@ import tools
 from physical_parameter import Roscop
 from notanorm import SqliteDb 
 import ascii
+import odv
 import netcdf
 
 # define SQL station table
@@ -87,6 +88,8 @@ class Profile:
         self.encoding = "ISO-8859-1"
         self.n = 0
         self.m = 0
+        # for each profile, store the indice of the max value
+        self.size = {}
         self.lineHeader = 0
         self.db = SqliteDb(self.__dbname) 
 
@@ -110,6 +113,13 @@ class Profile:
     # def encoding(self, encoding):
     #     self.__encoding = encoding
 
+    def iskey(self, key):
+        ''' return true ik key is in dict self.__data '''
+        if key in self.__data:
+            return True
+        else:
+            return False
+
     # overloading operators
     def __getitem__(self, key):
         ''' overload r[key] '''
@@ -190,6 +200,7 @@ class Profile:
             query = self.db.query(f"SELECT COUNT({self.keys[0]}) FROM data where station_id = {i}")
             #print(query)
             size = int(query[0][f"COUNT({self.keys[0]})"])
+            self.size[i] = size
             if size > m:
                 m = size
         
@@ -506,13 +517,18 @@ class Profile:
         self.set_regex(cfg, ti, 'header')
 
         self.read_files(cfg, ti)
-        #return fe
+
         # write ASCII hdr and data files
         ascii.writeProfile(cfg, ti, self, self.roscop)
 
+        # write ODV file
+        if cfg['global']['odv']:
+            odv.writeProfile(cfg, ti, self, self.roscop)
+
         # write the NetCDF file
         netcdf.writeProfile(cfg, ti, self, self.roscop)
 
+
 # for testing in standalone context
 # ---------------------------------
 if __name__ == "__main__":