diff --git a/Readme-python.txt b/Readme-python.txt
index db8f34faed27dd3e8c3295ed22e9365eb448dabf..8706c72a93921dd9ca5a126711a192b48c973a94 100644
--- a/Readme-python.txt
+++ b/Readme-python.txt
@@ -1,15 +1,9 @@
-Sous Windows, VSCode et Python 3.6
+Sous Windows, VSCode et Python 3.7.2
> pip3
Fatal error in launcher: Unable to create process using '"'
[ntird-us191-jg4:jgrelet]/c/git/python/pirata
> python3 -m pip install --upgrade pip
-Collecting pip
- Downloading https://files.pythonhosted.org/packages/d8/f3/413bab4ff08e1fc4828dfc59996d721917df8e8583ea85385d51125dceff/pip-19.0.3-py2.py3-none-any.whl (1.4MB)
- 100% |████████████████████████████████| 1.4MB 72kB/s
-Installing collected packages: pip
- Found existing installation: pip 9.0.1
- Uninstalling pip-9.0.1:
- Successfully uninstalled pip-9.0.1
+...
Successfully installed pip-19.0.3
[ntird-us191-jg4:jgrelet]/c/git/python/pirata
> pip install toml
@@ -56,4 +50,10 @@ Configuration du fichier setting.json de jgrelet:
Pour utiliser le bash de git, modifier la ligne:
"terminal.integrated.shell.windows": "C:\\MinGW\\msys\\1.0\\bin\\bash.exe",
par
- "terminal.integrated.shell.windows": "C:\\Program Files\\Git\\bin\\bash.exe",
\ No newline at end of file
+ "terminal.integrated.shell.windows": "C:\\Program Files\\Git\\bin\\bash.exe",
+
+Autoformatting
+----------------------
+> pip install autopep8
+Installer l'extension Python-autopep8
+Cmd+P choisir autopip
\ No newline at end of file
diff --git a/ctd.py b/ctd.py
index cc7ed393db152cb613edb72b03ca0982eedf4c10..7f057886f834d260d55f01799562ca88a04bf2c7 100644
--- a/ctd.py
+++ b/ctd.py
@@ -39,48 +39,53 @@ example:
$ python3 ctd.py --cycle_mesure=PIRATA-FR29 --institut=IRD --plateforme="THALASSA" --sn=09P01263 --type=SBE911+ --pi=BOURLES --date_debut=01/03/2019 --date_fin=04/04/2019 data/asc/fr29???.hdr --echo --local --ascii
"""
-import sys, re, getopt, string, fileinput, csv
+import sys
+import re
+import getopt
+import string
+import fileinput
+import csv
from datetime import datetime
# a lire dans la premier fichier
seasave_version = "7.21b"
# initialize constants
-VERSION = "V1.1 J Grelet - IRD - US191 IMAGO, Plouzane - March 2019"
-DEGREE = 176
-CODE = -1
-CONTEXTE = "PIRATA"
-TIMEZONE = "GMT"
-FORMAT_DATE = "DMY"
+VERSION = "V1.1 J Grelet - IRD - US191 IMAGO, Plouzane - March 2019"
+DEGREE = 176
+CODE = -1
+CONTEXTE = "PIRATA"
+TIMEZONE = "GMT"
+FORMAT_DATE = "DMY"
# initialize variables and options
# --------------------------------
-echo = False
-quiet = True
-xml = True
-ascii = False
-odv = False
-netcdf = False
-dtd = True
-debug = 0
-code_oopc = '0A'
-cycle_mesure = 'PIRATA-FR29'
-plateforme = 'THALASSA'
-institut = 'IRD'
-sn = '09P01263'
-type = 'SBE911+'
-pi = 'BOURLES'
-date_debut = '01/03/2019'
-date_fin = '04/04/2019'
-output_file = 'pirata-fr29'
-latitude = 0.
-latitude_str = ''
-longitude = 0.
+echo = False
+quiet = True
+xml = True
+ascii = False
+odv = False
+netcdf = False
+dtd = True
+debug = 0
+code_oopc = '0A'
+cycle_mesure = 'PIRATA-FR29'
+plateforme = 'THALASSA'
+institut = 'IRD'
+sn = '09P01263'
+type = 'SBE911+'
+pi = 'BOURLES'
+date_debut = '01/03/2019'
+date_fin = '04/04/2019'
+output_file = 'pirata-fr29'
+latitude = 0.
+latitude_str = ''
+longitude = 0.
longitude_str = ''
-julian = 0
-epic_date = ''
-Pres = 0
-bottom_depth = 0
+julian = 0
+epic_date = ''
+Pres = 0
+bottom_depth = 0
# initialize datetime object
# --------------------------
@@ -94,10 +99,11 @@ dt = datetime
# -------------------------------------------------
re_station_number = re.compile(r"fr29(\d{3})")
-# extract CTD station start date
+# extract CTD station start date
# ------------------------------
re_ctd_upload_time = \
- re.compile(r"System UpLoad Time\s*=\s*(\w+)\s+(\d+)\s+(\d+)\s+(\d+):(\d+):(\d+)")
+ re.compile(
+ r"System UpLoad Time\s*=\s*(\w+)\s+(\d+)\s+(\d+)\s+(\d+):(\d+):(\d+)")
# extract CTD station latitude
# ----------------------------
@@ -105,7 +111,8 @@ re_latitude = re.compile(r"NMEA\s+Latitude\s*[:=]\s*(\d+)\s+(\d+.\d+)\s+(\w)")
# extract CTD station longitude
# -----------------------------
-re_longitude = re.compile(r"NMEA\s+Longitude\s*[:=]\s*(\d+)\s+(\d+.\d+)\s+(\w)")
+re_longitude = re.compile(
+ r"NMEA\s+Longitude\s*[:=]\s*(\d+)\s+(\d+.\d+)\s+(\w)")
# extract bottom depth at station position from echo sounder
# ------------------------------------------------------------
@@ -115,363 +122,384 @@ re_bottom_depth = re.compile(r"Bottom\sDepth\s*[:=]\s*(\d+)")
# display help using text inside """ """" at the beginning of the
# script with special attribute __doc__ and quit
# ---------------------------------------------------------------
+
+
def usage():
- print(__doc__)
- sys.exit()
+ print(__doc__)
+ sys.exit()
# ------------------------------------------------
# display version and quit
# ------------------------------------------------
+
+
def version():
- print("%s: %s" % (sys.argv[0], VERSION))
- sys.exit()
+ print("%s: %s" % (sys.argv[0], VERSION))
+ sys.exit()
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
# entete XML
-#------------------------------------------------------------------------------
-def entete_xml(fd):
- #my $today = &dateFormat(undef,"%d/%m/%Y");
- today = '06/03/2019'
-
- fd.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
- # les commentaires ne sont pas acceptes par XML Toolbox Matlab de Geodise
- if (dtd):
- #fd.write("<!DOCTYPE OCEANO SYSTEM \"M:\ACQUISIT\oceano.dtd\">\n')
- fd.write("<!DOCTYPE OCEANO SYSTEM \"/m/oceano.dtd\">\n")
- #fd.write("<!DOCTYPE OCEANO PUBLIC \"-//US191//DTD OCEANO//FR\" \
- # \"http://antea/acquisit/oceano.dtd\">\n')
- else:
- fd.write("<!DOCTYPE OCEANO PUBLIC \"-//US191//DTD OCEANO//FR\" \
- \"http://www.brest.ird.fr/us191/database/oceano.dtd\">\n")
-
- fd.write("<OCEANO TYPE=\"PROFIL\">\n")
- fd.write(" <ENTETE>\n")
- fd.write(" <PLATEFORME>\n")
- fd.write(" <LIBELLE>%s</LIBELLE>\n" % plateforme)
- fd.write(" </PLATEFORME>\n")
- fd.write(" <CYCLE_MESURE CONTEXTE=\"%s\" TIMEZONE=\"%s\" FORMAT=\"%s\">\n" %
- (CONTEXTE, TIMEZONE, FORMAT_DATE))
- fd.write(" <LIBELLE>%s</LIBELLE>\n" % cycle_mesure)
- fd.write(" <DATE_DEBUT>%s</DATE_DEBUT>\n" % date_debut)
- fd.write(" <DATE_FIN>%s</DATE_FIN>\n" % date_fin)
- fd.write(" <INSTITUT>%s</INSTITUT>\n" % institut)
- fd.write(" <RESPONSABLE>%s</RESPONSABLE>\n" % pi)
- fd.write(" <ACQUISITION LOGICIEL=\"SEASAVE\" VERSION=\"%s\"></ACQUISITION>\n" %
- seasave_version)
- fd.write(" <TRAITEMENT LOGICIEL=\"SBEDATAPROCESSING\" VERSION=\"%s\"></TRAITEMENT>\n" % seasave_version)
- fd.write(" <VALIDATION LOGICIEL=\"%s\" VERSION=\"%s\" DATE=\"%s\" OPERATEUR=\"%s\" CODIFICATION=\"OOPC\">\n" % (sys.argv[0], VERSION, today, pi))
- fd.write(" <CODE>%s</CODE>\n" % code_oopc)
- fd.write(" <COMMENTAIRE>Extraction realisee avant la post-calibration</COMMENTAIRE>\n")
- fd.write(" </VALIDATION>\n")
- fd.write(" </CYCLE_MESURE>\n")
- fd.write(" <INSTRUMENT TYPE=\"%s\" NUMERO_SERIE=\"%s\">\n" % (type, sn))
- fd.write(" </INSTRUMENT>\n")
-
- #decode_con_file(fileName)
-
- fd.write(" </ENTETE>\n")
- fd.write(" <DATA>\n")
-
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
+
+
+def entete_xml(fd):
+ # my $today = &dateFormat(undef,"%d/%m/%Y");
+ today = '06/03/2019'
+
+ fd.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
+ # les commentaires ne sont pas acceptes par XML Toolbox Matlab de Geodise
+ if (dtd):
+ # fd.write("<!DOCTYPE OCEANO SYSTEM \"M:\ACQUISIT\oceano.dtd\">\n')
+ fd.write("<!DOCTYPE OCEANO SYSTEM \"/m/oceano.dtd\">\n")
+ # fd.write("<!DOCTYPE OCEANO PUBLIC \"-//US191//DTD OCEANO//FR\" \
+ # \"http://antea/acquisit/oceano.dtd\">\n')
+ else:
+ fd.write("<!DOCTYPE OCEANO PUBLIC \"-//US191//DTD OCEANO//FR\" \
+ \"http://www.brest.ird.fr/us191/database/oceano.dtd\">\n")
+
+ fd.write("<OCEANO TYPE=\"PROFIL\">\n")
+ fd.write(" <ENTETE>\n")
+ fd.write(" <PLATEFORME>\n")
+ fd.write(" <LIBELLE>%s</LIBELLE>\n" % plateforme)
+ fd.write(" </PLATEFORME>\n")
+ fd.write(" <CYCLE_MESURE CONTEXTE=\"%s\" TIMEZONE=\"%s\" FORMAT=\"%s\">\n" %
+ (CONTEXTE, TIMEZONE, FORMAT_DATE))
+ fd.write(" <LIBELLE>%s</LIBELLE>\n" % cycle_mesure)
+ fd.write(" <DATE_DEBUT>%s</DATE_DEBUT>\n" % date_debut)
+ fd.write(" <DATE_FIN>%s</DATE_FIN>\n" % date_fin)
+ fd.write(" <INSTITUT>%s</INSTITUT>\n" % institut)
+ fd.write(" <RESPONSABLE>%s</RESPONSABLE>\n" % pi)
+ fd.write(" <ACQUISITION LOGICIEL=\"SEASAVE\" VERSION=\"%s\"></ACQUISITION>\n" %
+ seasave_version)
+ fd.write(" <TRAITEMENT LOGICIEL=\"SBEDATAPROCESSING\" VERSION=\"%s\"></TRAITEMENT>\n" %
+ seasave_version)
+ fd.write(" <VALIDATION LOGICIEL=\"%s\" VERSION=\"%s\" DATE=\"%s\" OPERATEUR=\"%s\" CODIFICATION=\"OOPC\">\n" % (
+ sys.argv[0], VERSION, today, pi))
+ fd.write(" <CODE>%s</CODE>\n" % code_oopc)
+ fd.write(
+ " <COMMENTAIRE>Extraction realisee avant la post-calibration</COMMENTAIRE>\n")
+ fd.write(" </VALIDATION>\n")
+ fd.write(" </CYCLE_MESURE>\n")
+ fd.write(" <INSTRUMENT TYPE=\"%s\" NUMERO_SERIE=\"%s\">\n" % (type, sn))
+ fd.write(" </INSTRUMENT>\n")
+
+ # decode_con_file(fileName)
+
+ fd.write(" </ENTETE>\n")
+ fd.write(" <DATA>\n")
+
+# ------------------------------------------------------------------------------
# read code roscop file
-#------------------------------------------------------------------------------
+# ------------------------------------------------------------------------------
+
+
def codeRoscop(file):
- print("Code roscop file: %s" % code_roscop)
- with open(code_roscop, 'rt') as f:
- reader = csv.DictReader(f, delimiter=';')
- for row in reader:
- print("%s : %s : %s : %s : %s" % (row['key'], row['long_name'],
- row['standard_name'], row['units'], row['format']))
- sys.exit()
+ print("Code roscop file: %s" % code_roscop)
+ with open(code_roscop, 'rt') as f:
+ reader = csv.DictReader(f, delimiter=';')
+ for row in reader:
+ print("%s : %s : %s : %s : %s" % (row['key'], row['long_name'],
+ row['standard_name'], row['units'], row['format']))
+ sys.exit()
+
# display help with no arg on command-line
# ----------------------------------------
if len(sys.argv) == 1:
- usage()
+ usage()
# setting and get otpions
# -----------------------
try:
- # The return args consists of two elements: the first is a list of
- # (option, arg) pairs; the second is the list of program arguments
- # left after the option list was stripped
- # see optparse, a powerful library for parsing command-line options
- # The gnu version of getopt means that option and non-option
- # arguments may be intermixed
- # The -e is a simple flag, while -d, -o and -r require an argument.
- # The option definition string is "ed:r:".
- # To mix option and non-option arguments on the command line in any order,
- # use gnu_getopt() instead getopt
- # ------------------------------------------------------------------
- options, args = getopt.gnu_getopt(sys.argv[1:], 'ed:qo:hvr:',
- ['echo', 'debug=', 'quiet', 'output=', 'help', 'version', 'roscop=',
- 'cycle_mesure=', 'plateforme=', 'date_debut=', 'date_fin=',
- 'institut=', 'code_oopc=', 'pi=', 'ascii', 'xml', 'odv',
- 'netcdf', 'all', 'local', 'secondary', 'sn=', 'type='])
+ # The return args consists of two elements: the first is a list of
+ # (option, arg) pairs; the second is the list of program arguments
+ # left after the option list was stripped
+ # see optparse, a powerful library for parsing command-line options
+ # The gnu version of getopt means that option and non-option
+ # arguments may be intermixed
+ # The -e is a simple flag, while -d, -o and -r require an argument.
+ # The option definition string is "ed:r:".
+ # To mix option and non-option arguments on the command line in any order,
+ # use gnu_getopt() instead getopt
+ # ------------------------------------------------------------------
+ options, args = getopt.gnu_getopt(sys.argv[1:], 'ed:qo:hvr:',
+ ['echo', 'debug=', 'quiet', 'output=', 'help', 'version', 'roscop=',
+ 'cycle_mesure=', 'plateforme=', 'date_debut=', 'date_fin=',
+ 'institut=', 'code_oopc=', 'pi=', 'ascii', 'xml', 'odv',
+ 'netcdf', 'all', 'local', 'secondary', 'sn=', 'type='])
# if bad option, display an error message and usage
# -------------------------------------------------
except getopt.GetoptError as err:
- print(str(err))
- usage()
+ print(str(err))
+ usage()
# iterate over options list
# -------------------------
for option, arg in options:
- if option in ('-e', '--echo'):
- echo = True
- elif option in ('-q', '--quiet'):
- quiet = False
- elif option in ('-d', '--debug'):
- debug = int(arg)
- elif option in ('-o', '--output'):
- outputfile = arg
- elif option in ('-h', '--help'):
- usage()
- elif option in ('-v', '--version'):
- version()
- elif option in ('-r', '--roscop'):
- code_roscop = arg
- codeRoscop(code_roscop)
- elif option == '--cycle_mesure':
- cycle_mesure = arg
- elif option == '--plateforme':
- plateforme = arg
- elif option == '--date_debut':
- date_debut = arg
- elif option == '--date_fin':
- date_fin = arg
- elif option == '--institut':
- institut = arg
- elif option == '--code_oopc':
- code_oopc = arg
- elif option == '--pi':
- pi = arg
- elif option == '--ascii':
- ascii = True
- elif option == '--xml':
- xml = True
- elif option == '--odv':
- odv = True
- elif option == '--netcdf':
- netcdf = True
- elif option == '--all':
- ascii = xml = odv = netcdf = True
+ if option in ('-e', '--echo'):
+ echo = True
+ elif option in ('-q', '--quiet'):
+ quiet = False
+ elif option in ('-d', '--debug'):
+ debug = int(arg)
+ elif option in ('-o', '--output'):
+ outputfile = arg
+ elif option in ('-h', '--help'):
+ usage()
+ elif option in ('-v', '--version'):
+ version()
+ elif option in ('-r', '--roscop'):
+ code_roscop = arg
+ codeRoscop(code_roscop)
+ elif option == '--cycle_mesure':
+ cycle_mesure = arg
+ elif option == '--plateforme':
+ plateforme = arg
+ elif option == '--date_debut':
+ date_debut = arg
+ elif option == '--date_fin':
+ date_fin = arg
+ elif option == '--institut':
+ institut = arg
+ elif option == '--code_oopc':
+ code_oopc = arg
+ elif option == '--pi':
+ pi = arg
+ elif option == '--ascii':
+ ascii = True
+ elif option == '--xml':
+ xml = True
+ elif option == '--odv':
+ odv = True
+ elif option == '--netcdf':
+ netcdf = True
+ elif option == '--all':
+ ascii = xml = odv = netcdf = True
# for debug only, display arg list
# --------------------------------
if debug == 1:
- print("Args: %s\t%s\t%s\t%s\t%s\t%s\t%s\n" % \
- (cycle_mesure, plateforme, date_debut, date_fin, institut,
- code_oopc, pi))
+ print("Args: %s\t%s\t%s\t%s\t%s\t%s\t%s\n" %
+ (cycle_mesure, plateforme, date_debut, date_fin, institut,
+ code_oopc, pi))
# open ascii files
# ----------------
-if ascii:
- hdr_file = open( output_file + '.ctd', "w")
- ascii_file = open( output_file + '_ctd', "w")
-
- # write header to ascii files
- # ---------------------------------
- hdr_file.write("//%s %s %s %s %s %s\n" % \
- (cycle_mesure, plateforme, institut, type, sn, pi))
- hdr_file.write("St Date Time Latitude Longitude Depth\n")
- ascii_file.write("//%s %s %s %s %s %s\n" % \
- (cycle_mesure, plateforme, institut, type, sn, pi))
- ascii_file.write("PRFL PRES TEMP PSAL DENS SVEL DOX2 FLU2 TUR3 NAVG\n")
+if ascii:
+ hdr_file = open(output_file + '.ctd', "w")
+ ascii_file = open(output_file + '_ctd', "w")
+
+ # write header to ascii files
+ # ---------------------------------
+ hdr_file.write("//%s %s %s %s %s %s\n" %
+ (cycle_mesure, plateforme, institut, type, sn, pi))
+ hdr_file.write("St Date Time Latitude Longitude Depth\n")
+ ascii_file.write("//%s %s %s %s %s %s\n" %
+ (cycle_mesure, plateforme, institut, type, sn, pi))
+ ascii_file.write(
+ "PRFL PRES TEMP PSAL DENS SVEL DOX2 FLU2 TUR3 NAVG\n")
# open xml file
# -------------
if xml:
- xml_file = open( output_file + '_ctd.xml', "w")
-
- # write header to xml files
- # ---------------------------------
- entete_xml(xml_file)
- xml_file.write("PRFL PRES TEMP PSAL DENS SVEL DOX2 FLU2 TUR3 NAVG\n")
-
-if echo:
- # display selected output format
- # ------------------------------
- print("Output: ")
- if (ascii): print("ASCII ")
- if (xml) : print("XML ")
- if (odv) : print("ODV ")
-
- # display header
- # --------------
- print("\n//%s %s %s %s %s %s" % \
- (cycle_mesure, plateforme, institut, type, sn, pi))
- print(" File St Date Time Latitude Longitude Depth Bottom", end='')
-
-# iterate over file list getting with getopt.gnu_getopt
+ xml_file = open(output_file + '_ctd.xml', "w")
+
+ # write header to xml files
+ # ---------------------------------
+ entete_xml(xml_file)
+ xml_file.write(
+ "PRFL PRES TEMP PSAL DENS SVEL DOX2 FLU2 TUR3 NAVG\n")
+
+if echo:
+ # display selected output format
+ # ------------------------------
+ print("Output: ")
+ if (ascii):
+ print("ASCII ")
+ if (xml):
+ print("XML ")
+ if (odv):
+ print("ODV ")
+
+ # display header
+ # --------------
+ print("\n//%s %s %s %s %s %s" %
+ (cycle_mesure, plateforme, institut, type, sn, pi))
+ print(" File St Date Time Latitude Longitude Depth Bottom", end='')
+
+# iterate over file list getting with getopt.gnu_getopt
# ----------------------------------------------------
for fileName in args:
- # display processed filename
- # suppress '\n' character written at the end with a comma
- # -------------------------------------------------------
- if echo: print("\n%s" % (fileName), end='')
-
- # extract station number from file name using compiled regexp
- # -----------------------------------------------------------
- if re_station_number.search(fileName):
- station = int(re_station_number.search(fileName).group(1))
+ # display processed filename
+ # suppress '\n' character written at the end with a comma
+ # -------------------------------------------------------
+ if echo:
+ print("\n%s" % (fileName), end='')
- # open current file
- # TODOS: add some tests on file existence
- # ---------------------------------------
- file = open( fileName, "r", encoding = "ISO-8859-1")
+ # extract station number from file name using compiled regexp
+ # -----------------------------------------------------------
+ if re_station_number.search(fileName):
+ station = int(re_station_number.search(fileName).group(1))
- # read each line of current file
- # ------------------------------
- for line in file.readlines():
+ # open current file
+ # TODOS: add some tests on file existence
+ # ---------------------------------------
+ file = open(fileName, "r", encoding="ISO-8859-1")
- # extract CTD station start date
+ # read each line of current file
# ------------------------------
- if re_ctd_upload_time.search(line):
- (month, day, year, hour, minute, second) = \
- re_ctd_upload_time.search(line).groups()
-
- # format date and time to "May 09 2011 16:33:53"
- # -----------------------------------------------
- dateTime = "%s/%s/%s %s:%s:%s" % (day, month, year, hour, minute, second)
-
- # dateTime conversion to "09/05/2011 16:33:53"
- # --------------------------------------------
- dateTime = "%s" % \
- (dt.strptime(dateTime, "%d/%b/%Y %H:%M:%S").strftime("%d/%m/%Y %H:%M:%S"))
- # conversion to "20110509163353"
- # --------------------------------------------
- epic_date = "%s" % \
- (dt.strptime(dateTime, "%d/%m/%Y %H:%M:%S").strftime("%Y%m%d%H%M%S"))
-
- # conversion to julian day
- # ------------------------
- julian = float((dt.strptime(dateTime, "%d/%m/%Y %H:%M:%S").strftime("%j"))) \
- + ((float(hour) * 3600.) + (float(minute) * 60.) + float(second) ) / 86400.
-
- # we use julian day with origine 0
- # --------------------------------
- julian -= 1
-
- # extract latitude conversion
- # --------------------------------------------
- if re_latitude.search(line):
- (lat_deg, lat_min, lat_hemi) = re_latitude.search(line).groups()
-
- # format latitude to string
- # -------------------------
- latitude_str = "%s%c%s %s" % (lat_deg, DEGREE, lat_min, lat_hemi)
-
- # transform to decimal using ternary operator
- # -------------------------------------------
- latitude = float(lat_deg) + (float(lat_min) / 60.) if lat_hemi == 'N' else \
- (float(lat_deg) + (float(lat_min) / 60.)) * -1
-
- # extract longitude conversion
- # --------------------------------------------
- if re_longitude.search(line):
- (lon_deg, lon_min, lon_hemi) = re_longitude.search(line).groups()
-
- # format longitude to string
- # -------------------------
- longitude_str = "%s%c%s %s" % (lon_deg, DEGREE, lon_min, lon_hemi)
-
- # transform to decimal using ternary operator
- # -------------------------------------------
- longitude = float(lon_deg) + (float(lon_min) / 60.) if lon_hemi == 'E' \
- else (float(lon_deg) + (float(lon_min) / 60.)) * -1
-
- # extract bottom depth
- # --------------------------------------------
- if re_bottom_depth.search(line):
- bottom_depth = re_bottom_depth.search(line).group(1)
-
- # close header file
- # -----------------
- file.close()
-
- # display header information in console
- # -------------------------------------
- if echo: print(" %03d %s %s %s %5.0f %5.0f" % \
- (station, dateTime, latitude_str, longitude_str, float(Pres),
- float(bottom_depth)), end = '')
-
- # write station header to ascii files
- # -----------------------------------
- if ascii:
- hdr_file.write("%03d %s %s %s %5.0f\n" % \
- (station, dateTime, latitude_str, longitude_str, float(Pres)))
-
- # write station header in decimal with PRES = -1, and 5 decimals
- # --------------------------------------------------------------
- ascii_file.write("%3d %4d %9.5f %8.5f %9.5f %s 1e36 1e36 1e36 1e36\n" % \
- (station, CODE, julian, latitude, longitude, epic_date))
-
- # write station header in decimal with PRES = -1, and 5 decimals
- # --------------------------------------------------------------
- xml_file.write("%3d %4d %9.5f %8.5f %9.5f %s 1e36 1e36 1e36 1e36\n" % \
- (station, CODE, julian, latitude, longitude, epic_date))
-
- # substitute .hdr or .HDR in fileName with .asc
- # ---------------------------------------------
- fileName = re.sub(r'\.(?i)hdr$', '.asc', fileName)
-
- # we don't use __builtin__ readline method of file object that haven't
- # method to get read line number
- # --------------------------------------------------------------------
- file = fileinput.input(fileName, openhook=fileinput.hook_encoded("ISO-8859-1"))
-
- # iterate over the lines of opened file "fileName"
- # ------------------------------------------------
- for line in file:
-
- # skip header line
- # ----------------
- if file.isfirstline():
- continue
- else:
-
- # extract data
- # ------------
- (scan,TimeJ,Pres,Depth,T0,T1,C0,C1,v1,v2,v1dt,v2dt,Xmiss,FlC,Aqua,Ox0,Ox1,S0,S1,sigmateta0, \
- sigmateta1,sndvel0,sndvel1,nbin,flag) = line.split()
-
- # write data to ascii file
- # ------------------------
- if ascii:
- ascii_file.write( \
- "%3d %4d %6.5g %6.5g %6.3f %7.2f %7.6g %6.4g %7.6g %3d\n" % \
- (station, float(Pres), float(T0), float(S0), float(sigmateta0), \
- float(sndvel0), float(Ox0), float(FlC), float(Xmiss), int(nbin)))
-
- # write data to xml file
- # ------------------------
- if xml:
- xml_file.write( \
- "%3d %4d %6.5g %6.5g %6.3f %7.2f %7.6g %6.4g %7.6g %3d\n" % \
- (station, float(Pres), float(T0), float(S0), float(sigmateta0), \
- float(sndvel0), float(Ox0), float(FlC), float(Xmiss), int(nbin)))
-
-
- # close current file
- # ------------------
- file.close()
+ for line in file.readlines():
+
+ # extract CTD station start date
+ # ------------------------------
+ if re_ctd_upload_time.search(line):
+ (month, day, year, hour, minute, second) = \
+ re_ctd_upload_time.search(line).groups()
+
+ # format date and time to "May 09 2011 16:33:53"
+ # -----------------------------------------------
+ dateTime = "%s/%s/%s %s:%s:%s" % (day,
+ month, year, hour, minute, second)
+
+ # dateTime conversion to "09/05/2011 16:33:53"
+ # --------------------------------------------
+ dateTime = "%s" % \
+ (dt.strptime(dateTime, "%d/%b/%Y %H:%M:%S").strftime("%d/%m/%Y %H:%M:%S"))
+ # conversion to "20110509163353"
+ # --------------------------------------------
+ epic_date = "%s" % \
+ (dt.strptime(dateTime, "%d/%m/%Y %H:%M:%S").strftime("%Y%m%d%H%M%S"))
+
+ # conversion to julian day
+ # ------------------------
+ julian = float((dt.strptime(dateTime, "%d/%m/%Y %H:%M:%S").strftime("%j"))) \
+ + ((float(hour) * 3600.) + (float(minute) * 60.) + float(second)) / \
+ 86400.
+
+ # we use julian day with origine 0
+ # --------------------------------
+ julian -= 1
+
+ # extract latitude conversion
+ # --------------------------------------------
+ if re_latitude.search(line):
+ (lat_deg, lat_min, lat_hemi) = re_latitude.search(line).groups()
+
+ # format latitude to string
+ # -------------------------
+ latitude_str = "%s%c%s %s" % (lat_deg, DEGREE, lat_min, lat_hemi)
+
+ # transform to decimal using ternary operator
+ # -------------------------------------------
+ latitude = float(lat_deg) + (float(lat_min) / 60.) if lat_hemi == 'N' else \
+ (float(lat_deg) + (float(lat_min) / 60.)) * -1
+
+ # extract longitude conversion
+ # --------------------------------------------
+ if re_longitude.search(line):
+ (lon_deg, lon_min, lon_hemi) = re_longitude.search(line).groups()
+
+ # format longitude to string
+ # -------------------------
+ longitude_str = "%s%c%s %s" % (lon_deg, DEGREE, lon_min, lon_hemi)
+
+ # transform to decimal using ternary operator
+ # -------------------------------------------
+ longitude = float(lon_deg) + (float(lon_min) / 60.) if lon_hemi == 'E' \
+ else (float(lon_deg) + (float(lon_min) / 60.)) * -1
+
+ # extract bottom depth
+ # --------------------------------------------
+ if re_bottom_depth.search(line):
+ bottom_depth = re_bottom_depth.search(line).group(1)
+
+ # close header file
+ # -----------------
+ file.close()
+
+ # display header information in console
+ # -------------------------------------
+ if echo:
+ print(" %03d %s %s %s %5.0f %5.0f" %
+ (station, dateTime, latitude_str, longitude_str, float(Pres),
+ float(bottom_depth)), end='')
+
+ # write station header to ascii files
+ # -----------------------------------
+ if ascii:
+ hdr_file.write("%03d %s %s %s %5.0f\n" %
+ (station, dateTime, latitude_str, longitude_str, float(Pres)))
+
+ # write station header in decimal with PRES = -1, and 5 decimals
+ # --------------------------------------------------------------
+ ascii_file.write("%3d %4d %9.5f %8.5f %9.5f %s 1e36 1e36 1e36 1e36\n" %
+ (station, CODE, julian, latitude, longitude, epic_date))
+
+ # write station header in decimal with PRES = -1, and 5 decimals
+ # --------------------------------------------------------------
+ xml_file.write("%3d %4d %9.5f %8.5f %9.5f %s 1e36 1e36 1e36 1e36\n" %
+ (station, CODE, julian, latitude, longitude, epic_date))
+
+ # substitute .hdr or .HDR in fileName with .asc
+ # ---------------------------------------------
+ fileName = re.sub(r'\.(?i)hdr$', '.asc', fileName)
+
+ # we don't use __builtin__ readline method of file object that haven't
+ # method to get read line number
+ # --------------------------------------------------------------------
+ file = fileinput.input(
+ fileName, openhook=fileinput.hook_encoded("ISO-8859-1"))
+
+ # iterate over the lines of opened file "fileName"
+ # ------------------------------------------------
+ for line in file:
+
+ # skip header line
+ # ----------------
+ if file.isfirstline():
+ continue
+ else:
+
+ # extract data
+ # ------------
+ (scan, TimeJ, Pres, Depth, T0, T1, C0, C1, v1, v2, v1dt, v2dt, Xmiss, FlC, Aqua, Ox0, Ox1, S0, S1, sigmateta0,
+ sigmateta1, sndvel0, sndvel1, nbin, flag) = line.split()
+
+ # write data to ascii file
+ # ------------------------
+ if ascii:
+ ascii_file.write(
+ "%3d %4d %6.5g %6.5g %6.3f %7.2f %7.6g %6.4g %7.6g %3d\n" %
+ (station, float(Pres), float(T0), float(S0), float(sigmateta0),
+ float(sndvel0), float(Ox0), float(FlC), float(Xmiss), int(nbin)))
+
+ # write data to xml file
+ # ------------------------
+ if xml:
+ xml_file.write(
+ "%3d %4d %6.5g %6.5g %6.3f %7.2f %7.6g %6.4g %7.6g %3d\n" %
+ (station, float(Pres), float(T0), float(S0), float(sigmateta0),
+ float(sndvel0), float(Ox0), float(FlC), float(Xmiss), int(nbin)))
+
+ # close current file
+ # ------------------
+ file.close()
# end of loop over files
# ----------------------
if echo:
- print("\n")
+ print("\n")
# close files
# -----------
-if ascii:
- hdr_file.close()
- ascii_file.close()
-
+if ascii:
+ hdr_file.close()
+ ascii_file.close()
+
if xml:
- xml_file.write(" </DATA>\n")
- xml_file.write("</OCEANO>\n")
- xml_file.close()
+ xml_file.write(" </DATA>\n")
+ xml_file.write("</OCEANO>\n")
+ xml_file.close()
diff --git a/roscop/roscop.py b/roscop/roscop.py
index 2568da126691d4200cd17ea6878c1f3600407cfe..e76f8548f8ac63c7c38c87a95d3da2c5cb55a6a3 100644
--- a/roscop/roscop.py
+++ b/roscop/roscop.py
@@ -2,35 +2,46 @@
code roscop
"""
-import csv, shelve,sys
+import csv
+import shelve
+import sys
-# class roscop
+
+class db:
+ def __setattr__(self, name, value):
+ self.__dict__[name] = value
+
+# class roscop
# ------------
+
+
class Roscop:
# constructor with values by default
- def __init__(self, file):
- self.file = file
-
- # call by print()
- def __repr__(self):
- return "class Roscop, file: {}".format(self.file)
-
- # read code roscop file
- def read(self):
- print("Code roscop file: %s" % self.file)
- with open(self.file, 'rt') as f:
- reader = csv.DictReader(f, delimiter=';')
- print(reader.fieldnames)
- for row in reader:
- for key in reader.fieldnames:
- print("%s:" % row[key], end='')
- print()
- return
+ def __init__(self, file):
+ self.file = file
+
+ # call by print()
+ def __repr__(self):
+ #print("%s:" % row[key], end='')
+ # print()
+ return "class Roscop, file: {}".format(self.file)
+
+ # read code roscop file
+ def read(self):
+ print("Code roscop file: %s" % self.file)
+ with open(self.file, 'rt') as f:
+ reader = csv.DictReader(f, delimiter=';')
+ for row in reader:
+ d = db()
+ for key in reader.fieldnames:
+ d.key = row[key]
+ return
+
# for testing in standalone context
-# ---------------------------------
+# ---------------------------------
if __name__ == "__main__":
- from roscop import Roscop
- r = Roscop("code_roscop.csv").read()
- print(r)
\ No newline at end of file
+ from roscop import Roscop
+ r = Roscop("code_roscop.csv").read()
+ print(r)