diff --git a/code_roscop.csv b/code_roscop.csv
index 44a1172bd8ad7efc30c6289e95b5f807f4661a98..7fff2b537b95529e853a8bdef2bd59974ae519fc 100644
--- a/code_roscop.csv
+++ b/code_roscop.csv
@@ -5,7 +5,7 @@ PROFILE;int32;profile number;;1;;;;;;%4d;99999;;;Station number, a station could
LATITUDE;float32;latitude of measurement;latitude;degrees_north;;;;;;;;Y;;;;;;WGS84;urn:ogc:crs:EPSG::4326
LONGITUDE;float32;longitude of measurement;longitude;degrees_east;;;;;;;;X;;;;;;WGS84;urn:ogc:crs:EPSG::4327
TIME;float64;time of measurement;time;days since 1950-01-01T00:00:00Z;Relative julian days with decimal part (as parts of the day);;;0.0;90000.0;%6.6f;;T;;;;;;;
-ETDD;float32;ellapsed time;;1;;;;0;90000;%9.5f;;;;;;;;;
+ETDD;float64;ellapsed time;;1;;;;0;90000;%9.5f;1E+36;;;;;;;;
DEPH;float32;depth of measurement;depth;meter;;;down;0;9000;%7.2f;1E+36;Z;;;;;;;urn:ogc:crs:EPSG::5831
DEPTH;float32;depth of measurement;depth;meter;;;down;0;9000;%7.2f;1E+36;Z;;;;;;;urn:ogc:crs:EPSG::5831
PRES;float32;sea water pressure;sea_water_pressure;decibar;;TIME DEPTH LATITUDE LONGITUDE;;0;9000;%7.2f;1E+36;;;Pressure (dbar) of the measurement;;;;;
@@ -21,13 +21,14 @@ WMSP;float32;wind speed - max aver per 2 mn;wind_speed;meter/second;;TIME DEPTH
WDIR;float32;wind direction rel. true north;wind_to_direction;degree;;TIME DEPTH LATITUDE LONGITUDE;;0;360;%5.1f;1E+36;;0.001;Horizontal wind speed;;;;;
ATMS;float32;atmospheric pressure - sea lev;air_pressure_at_sea_level;hectoPascal;;TIME DEPTH LATITUDE LONGITUDE;;940;1030;%8.3f;1E+36;;0.001;Atmospheric pressure at sea level;;;;;
RELH;float32;relative humidity;relative_humidity;%;;TIME DEPTH LATITUDE LONGITUDE;;0;100;%6.1f;1E+36;;0.001;Relative humidity;;;;;
-NSCT;float32;current north component;;cm/second;;TIME DEPTH LATITUDE LONGITUDE;;-100;100;%7.3f;1E+36;;0.01; Current north;;;;;
+NSCT;float32;current north component;;cm/second;;TIME DEPTH LATITUDE LONGITUDE;;-100;100;%7.3f;1E+36;;0.01;" Current north";;;;;
EWCT;float32;current east component;;cm/second;;TIME DEPTH LATITUDE LONGITUDE;;-100;100;%7.3f;1E+36;;0.02;Current east;;;;;
SSJT;float32;sea surface water jacket temperature;sea_water_temperature;degree_Celsius;;TIME DEPTH LATITUDE LONGITUDE;;-1.5;38;%6.3f;1E+36;;0.001;Ocean temperature;;;;;
SSTP;float32;sea surface water temperature;sea_water_temperature;degree_Celsius;;TIME DEPTH LATITUDE LONGITUDE;;-1.5;38;%6.3f;1E+36;;0.001;Sea surface Ocean temperature;;;;;
-SSPS;float32;sea surface practical salinity;sea_water_salinity ;pss;;TIME DEPTH LATITUDE LONGITUDE;;-1.5;38;%6.3f;1E+36;;0.001;Ocean salinity;;;;;
+SSPS;float32;sea surface practical salinity;"sea_water_salinity ";pss;;TIME DEPTH LATITUDE LONGITUDE;;-1.5;38;%6.3f;1E+36;;0.001;Ocean salinity;;;;;
PCO2;float32;co2 part. pres in dry/wet gas;;microatmosphere;;TIME DEPTH LATITUDE LONGITUDE;;100;700;%7.3f;1E+36;;0.001;;;;;;
FLU2;float32;fluorescence;;milligram/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;1;%8.4f;1E+36;;0.001;;;;;;
+FLU3;float32;secondary fluorescence;;milligram/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;1;%8.4f;1E+36;;0.001;;;;;;
TUR1;float32;light diffusion coefficient;;m-1;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%6.3f;1E+36;;0.001;;;;;;
TUR2;float32;light attenuation coefficient;;m-1;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%6.3f;1E+36;;0.001;;;;;;
TUR3;float32;light transmission;;%;;TIME DEPTH LATITUDE LONGITUDE;;0;100;%6.2f;1E+36;;0.001;;;;;;
@@ -54,10 +55,10 @@ DOV1;float32;dissolved oxygen primary sensor voltage;;V;;TIME DEPTH LATITUDE LON
DOV2;float32;dissolved oxygen secondary sensor voltage;;V;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%6.4f;1E+36;;0.001;;;;;;
DVT1;float32;dissolved oxygen primary sensor dv/dt;;dv/dt;;TIME DEPTH LATITUDE LONGITUDE;;-1;1;%+7.5f;1E+36;;0.001;;;;;;
DVT2;float32;dissolved oxygen secondary sensor dv/dt;;dv/dt;;TIME DEPTH LATITUDE LONGITUDE;;-1;1;%+7.5f;1E+36;;0.002;;;;;;
-NTIW;float32;nitrite (no2-n) ;moles_of_nitrite_per_unit_mass_in_sea_water;micromole/kg;;TIME DEPTH LATITUDE LONGITUDE;;0;100;%7.3f;1E+36;;0.001;;;;;;
-NTRI;float32;nitrite (no2-n) ;moles_concentration_of_nitrite_in_sea_water;millimole/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%6.3f;1E+36;;0.001;;;;;;
-NTAW;float32;nitrate (no3-n) ;moles_of_nitrate_per_unit_mass_in_sea_water;micromole/kg;;TIME DEPTH LATITUDE LONGITUDE;;0;90;%5.2f;1E+36;;0.001;;;;;;
-NTRA;float32;nitrate (no3-n) ;moles_concentration_of_nitrate_in_sea_water;millimole/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;56;%6.3f;1E+36;;0.001;;;;;;
+NTIW;float32;"nitrite (no2-n) ";moles_of_nitrite_per_unit_mass_in_sea_water;micromole/kg;;TIME DEPTH LATITUDE LONGITUDE;;0;100;%7.3f;1E+36;;0.001;;;;;;
+NTRI;float32;"nitrite (no2-n) ";moles_concentration_of_nitrite_in_sea_water;millimole/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%6.3f;1E+36;;0.001;;;;;;
+NTAW;float32;"nitrate (no3-n) ";moles_of_nitrate_per_unit_mass_in_sea_water;micromole/kg;;TIME DEPTH LATITUDE LONGITUDE;;0;90;%5.2f;1E+36;;0.001;;;;;;
+NTRA;float32;"nitrate (no3-n) ";moles_concentration_of_nitrate_in_sea_water;millimole/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;56;%6.3f;1E+36;;0.001;;;;;;
NTZW;float32;nitrate + nitrite;moles_of_nitrate_and_nitrite_per_unit_mass_in_sea_water;micromole/kg;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%6.3f;1E+36;;0.001;;;;;;
NTRZ;float32;nitrate + nitrite;moles_concentration_of_nitrate_and_nitrite_in_sea_water;millimole/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;100;%6.2f;1E+36;;0.001;;;;;;
PHOW;float32;phosphate (po4-p);moles_of_phosphate_per_unit_mass_in_sea_water;micromole/kg;;TIME DEPTH LATITUDE LONGITUDE;;0;10;%5.3f;1E+36;;0.001;;;;;;
@@ -65,7 +66,7 @@ PHOS;float32;phosphate (po4-p);moles_phosphate_of_nitrate_in_sea_water;millimole
PHPT;float32;total pheophytin;;milligramm/m3;;TIME DEPTH LATITUDE LONGITUDE;;0;99;%5.2f;1E+36;;0.01;;;;;;
WETT;float32;wet bulb temperature;;degree_Celsius;;TIME DEPTH LATITUDE LONGITUDE;;0;90;%5.1f;1E+36;;0.001;;;;;;
HEIG;float32;atmospheric height;;meter;;TIME DEPTH LATITUDE LONGITUDE;up;0;40000;%8.2f;1E+36;;0.1;;;;;;urn:ogc:crs:EPSG::5829
-NAVG;int32;averaged data cycle number;;1;;;;0;999;%3.0f;99999;;;;;;;;
+NAVG;int32;averaged data cycle number;;1;;;;0;999;%3d;9999;;;;;;;;
BOTL;int32;sea water sample bottle number;;1;;;;1;36;%3d;99999;;;;;;;;
-TYPECAST;int32;type of cast: unknow=0, phy=1, bio=2, geo=3;;1;;;;0.0;9.0;%1d;99999;;;;;;;;
-BATH;float32;bathymetric depth;;meter;;;;0;11000;%6.1f;1E+36;;0.1;;;;;;
+TYPECAST;int32;type of cast: unknow=0, phy=1, bio=2, geo=3;;1;;;;0;9;%1d;99999;;;;;;;;
+BATH;float32;bathymetric depth;;meter;;;;0;11000;%6.1f;1E+36;;0.1;;;;;;
\ No newline at end of file
diff --git a/file_extractor.py b/file_extractor.py
index c0390f02eb52137b93e6df719a377bbd1272be68..13545ab86815e897cfbbd3459ef5a61571e520fd 100644
--- a/file_extractor.py
+++ b/file_extractor.py
@@ -29,11 +29,12 @@ class FileExtractor:
'''
# constructor with values by defaul
- def __init__(self, fname, keys, separator=None):
+ def __init__(self, fname, roscop, keys, separator=None):
# attibutes
# public:
self.fname = fname
self.keys = keys
+ self.roscop = roscop
self.n = 0
self.m = 0
self.lineHeader = 0
@@ -44,7 +45,7 @@ class FileExtractor:
self.__data = {}
self.__regex = {}
# replace this constante with roscop fill value
- self.__FillValue = 1e36
+ #self.__FillValue = 1e36
# overloading operators
def __getitem__(self, key):
@@ -82,11 +83,9 @@ class FileExtractor:
# first pass on file(s)
d = cfg[ti.lower()]['header']
- #print(d, end='\n')
+ # fill the __regex dict with compiled regex
for key in d.keys():
- print("{}: {}".format(key, d[key]))
self.__regex[key] = re.compile(d[key])
- print(end='\n')
def first_pass(self):
'''
@@ -105,6 +104,8 @@ class FileExtractor:
with fileinput.input(
file, openhook=fileinput.hook_encoded("ISO-8859-1")) as f:
lineData = 0
+ lineHeader = 0
+ isHeader = True
filesRead += 1
for line in f:
# header detection, skip header lines
@@ -116,7 +117,7 @@ class FileExtractor:
elif 'endHeader' in self.__regex:
if self.__regex['endHeader'].match(line):
lineHeader += 1
- isHeader = False
+ isHeader = False
else:
lineHeader += 1
continue
@@ -163,12 +164,19 @@ class FileExtractor:
# initialize arrays, move at the end of firstPass ?
for key in variables_1D:
- self.__data[key] = np.ones((self.n)) * self.__FillValue
+ #self.__data[key] = np.ones((self.n)) * self.__FillValue
+ if '_FillValue' in self.roscop[key]:
+ self.__data[key] = np.full((self.n, self.roscop[key]['_FillValue']))
+ else:
+ self.__data[key] = np.empty(self.n)
for key in self.keys:
# mult by __fillValue next
# the shape parameter has to be an int or sequence of ints
- self.__data[key] = np.ones((self.n, self.m)) * self.__FillValue
+ if '_FillValue' in self.roscop[key]:
+ self.__data[key] = np.full([self.n, self.m], self.roscop[key]['_FillValue'])
+ else:
+ self.__data[key] = np.empty([self.n, self.m])
for file in self.fname:
with fileinput.input(
@@ -177,78 +185,87 @@ class FileExtractor:
for line in f:
if f.filelineno() < self.lineHeader + 1:
# read and decode header
- if self.__regex['DATETIME'].search(line):
- (month, day, year, hour, minute, second) = \
- self.__regex['DATETIME'].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
- print("{:07.4f} : {} / {}".format(julian, dateTime, epic_date))
- self.__data['TIME'][n] = julian
-
- if self.__regex['DATE'].search(line):
- (month, day, year) = \
- self.__regex['DATE'].search(line).groups()
- if self.__regex['TIME'].search(line):
- (hour, minute, second) = \
- self.__regex['TIME'].search(line).groups()
+ for k in self.__regex.keys():
+ # key is DATETIME
+ if k == "DATETIME" and self.__regex[k].search(line):
+ (month, day, year, hour, minute, second) = \
+ self.__regex[k].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
+ self.__data['TIME'][n] = julian
+ # key is DATE
+ if k == "DATE" and self.__regex[k].search(line):
+ if device.lower() == 'ladcp':
+ (year, month, day) = \
+ self.__regex[k].search(line).groups()
+ else:
+ (month, day, year) = \
+ self.__regex[k].search(line).groups()
+ # key is TIME
+ if k == "TIME" and self.__regex[k].search(line):
+ (hour, minute, second) = \
+ self.__regex[k].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/%m/%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
- print("{:07.4f} : {} / {}".format(julian, dateTime, epic_date))
- self.__data['TIME'][n] = julian
-
- if self.__regex['LATITUDE'].search(line):
- (lat_deg, lat_min, lat_hemi) = self.__regex['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
- print("{:07.4f} : {}".format(latitude, latitude_str))
- self.__data['LATITUDE'][n] = latitude
-
- if self.__regex['LONGITUDE'].search(line):
- (lon_deg, lon_min, lon_hemi) = self.__regex['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
- print("{:07.4f} : {}".format(longitude, longitude_str))
- self.__data['LONGITUDE'][n] = longitude
+ # 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/%m/%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
+ self.__data['TIME'][n] = julian
+ # key is LATITUDE
+ if k == "LATITUDE" and self.__regex[k].search(line):
+ if device.lower() == 'ladcp':
+ [latitude] = self.__regex[k].search(line).groups()
+ else:
+ (lat_deg, lat_min, lat_hemi) = self.__regex[k].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
+ self.__data['LATITUDE'][n] = latitude
+ # key is LONGITUDE
+ if k == "LONGITUDE" and self.__regex[k].search(line):
+ if device.lower() == 'ladcp':
+ [longitude] = self.__regex[k].search(line).groups()
+ else:
+ (lon_deg, lon_min, lon_hemi) = self.__regex[k].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
+ self.__data['LONGITUDE'][n] = longitude
continue
# split the line, remove leading and trailing space before
diff --git a/netcdf.py b/netcdf.py
index 37935e16d52a63201d16692f6e10956fba1f6d74..1b577f470483e765c19dab64fb145758cc1a2289 100644
--- a/netcdf.py
+++ b/netcdf.py
@@ -1,10 +1,9 @@
import logging
from netCDF4 import Dataset
from numpy import arange, dtype
-from physical_parameter import Roscop
-def writeNetCDF(fileName, fe, variables_1D):
+def writeNetCDF(fileName, fe, r, variables_1D):
# ncvars is a dictionary that store a netcdf variable for each physical parameter key
ncvars = {}
@@ -14,9 +13,6 @@ def writeNetCDF(fileName, fe, variables_1D):
variables = variables_1D.copy()
dims_2D = ['TIME', 'DEPTH']
- # move to main after tests
- r = Roscop("code_roscop.csv")
-
# create netcdf file
nc = Dataset(fileName, "w", format="NETCDF3_CLASSIC")
logging.debug(' ' + nc.data_model)
@@ -49,13 +45,14 @@ def writeNetCDF(fileName, fe, variables_1D):
hash.pop('_FillValue')
else:
fillvalue = None
+
# create the variable
if any(key in item for item in variables_1D):
ncvars[key] = nc.createVariable(
key, dtype(hash['types']).char, (key,), fill_value=fillvalue)
else:
ncvars[key] = nc.createVariable(
- key, dtype(hash['types']).char, dims_2D, fill_value=fillvalue)
+ key, dtype(hash['types']).char, dims_2D, fill_value=fillvalue)
# remove from the dictionary
hash.pop('types')
# create dynamically variable attributes
@@ -71,10 +68,8 @@ def writeNetCDF(fileName, fe, variables_1D):
# write the ncvars
for key in variables:
if any(key in item for item in variables_1D):
- #print("Key: {}, {}".format(key,fe[key]))
ncvars[key][:] = fe[key]
else:
- #print("Key: {}, {}".format(key,fe[key]))
ncvars[key][:, :] = fe[key]
# close the netcdf file
diff --git a/oceano.py b/oceano.py
index 5558b314e20a3dc2db04d6ab0408a4e731107f6e..b0232582bceebaf5fe7cb63d638cbd7fcaa0e9fe 100644
--- a/oceano.py
+++ b/oceano.py
@@ -10,6 +10,7 @@ from configparser import ConfigParser
import os
import distutils.util as du
import netcdf
+from physical_parameter import Roscop
# typeInstrument is a dictionary as key: files extension
typeInstrument = {'CTD': ('cnv', 'CNV'), 'XBT': (
@@ -21,6 +22,8 @@ filesBrowsePosition_column = 1
# initialize filename use to save GUI configuration
configfile = 'oceano.cfg'
+# move to main after tests
+r = Roscop("code_roscop.csv")
def processArgs():
parser = argparse.ArgumentParser(
@@ -41,7 +44,7 @@ def processArgs():
default='tests/test.toml')
parser.add_argument('-i', '--instrument', nargs='?', choices=ti.keys(),
help='specify the instrument that produce files, eg CTD, XBT, TSG, LADCP')
- parser.add_argument('-k', '--keys', nargs='+', default=['PRES', 'TEMP', 'PSAL'],
+ parser.add_argument('-k', '--keys', nargs='+',
help='display dictionary for key(s), (default: %(default)s)')
parser.add_argument('-g', '--gui', action='store_true',
help='use GUI interface')
@@ -130,12 +133,17 @@ def process(args, cfg, ti):
n, m: array size
'''
+ print('processing...')
# check if no file selected or cancel button pressed
logging.debug("File(s): {}, config: {}, Keys: {}".format(
args.files, args.config, args.keys))
- # fileExtractor
- fe = FileExtractor(args.files, args.keys)
+ # if physical parameters are not given from cmd line, option -k, use the toml <device>.split values
+ if args.keys == None:
+ args.keys = cfg['split'][device.lower()].keys()
+
+ # extract header and data from files
+ fe = FileExtractor(args.files, r, args.keys)
# prepare (compile) each regular expression inside toml file under section [<device=ti>.header]
fe.set_regex(cfg, ti)
@@ -273,11 +281,11 @@ if __name__ == "__main__":
parser.print_help(sys.stderr)
sys.exit(1)
- keys = cfg['split'][device.lower()].keys()
# in command line mode (console)
fe = process(args, cfg, device)
#print("Dimensions: {} x {}".format(fe.m, fe.n))
#print(fe.disp())
# write the NetCDF file
- netcdf.writeNetCDF( "netcdf/OS_{}_{}.nc".format(cfg['cruise']['cycleMesure'], device), fe,variables_1D)
+ ncfile = "netcdf/OS_{}_{}.nc".format(cfg['cruise']['cycleMesure'], device)
+ netcdf.writeNetCDF( ncfile, fe, r, variables_1D)
diff --git a/physical_parameter.py b/physical_parameter.py
index 03da9e18faf1acf040c00d5f6b88658a560a570c..fb92c2434d4ce2161baf4f5cb5492740b0df274e 100644
--- a/physical_parameter.py
+++ b/physical_parameter.py
@@ -82,9 +82,14 @@ class Roscop:
# use the second line with key string to convert each numeric type into float
if theKey != 'string':
if self['string'][k] == 'numeric':
- row[k] = float(row[k])
- logging.debug(
- " {} -> {}, {} = {}".format(theKey, k, type(row[k]), row[k]))
+ if 'float' in row['types']:
+ row[k] = float(row[k])
+ elif 'int' in row['types']:
+ row[k] = int(row[k])
+ else:
+ print('invalid type {}: {}'.format(theKey, k))
+ #logging.debug(
+ # " {} -> {}, {} = {}".format(theKey, k, type(row[k]), row[k]))
self.__hash[theKey] = row
return
diff --git a/tests/test.toml b/tests/test.toml
index cfbcc73b940dacfac002e9257acb12c5be4f6b4e..79544cb122faa7b7b48d63b3f3eab3ddf05f0fc8 100644
--- a/tests/test.toml
+++ b/tests/test.toml
@@ -24,7 +24,6 @@ instrumentNumber = "09P1263"
[ctd.header]
isHeader = '^[*#]'
-isDevice = '^\*\s+(Sea-Bird)'
DATETIME = 'System UpLoad Time\s*=\s*(\w+)\s+(\d+)\s+(\d+)\s+(\d+):(\d+):(\d+)'
LATITUDE = 'NMEA\s+Latitude\s*[:=]\s*(\d+)\s+(\d+\.\d+)\s+(\w)'
LONGITUDE = 'NMEA\s+Longitude\s*[:=]\s*(\d+)\s+(\d+.\d+)\s+(\w)'
@@ -82,7 +81,6 @@ comment = "Extract from .colcor files"
[ladcp]
cruisePrefix = "fr29"
stationPrefixLength = 3
-skipHeader = 10
acquisitionSoftware = "BBTALK"
acquisitionVersion = 3.04
processingSoftware = "MATLAB-VISBECK"
@@ -94,19 +92,26 @@ downSn = "24543"
title_summary = "IFM-GEOMAR/LDEO Matlab LADCP-Processing system adapted by FM/PR/JG"
comment = "Extract from .lad files"
+ [ladcp.header]
+ endHeader = 'Columns'
+ DATE = 'Date\s*=\s*(\d+)/(\d+)/(\d+)'
+ TIME = 'Start_Time\s*=\s*(\d+)[:hH](\d+):(\d+)'
+ LATITUDE = 'Latitude\s*[:=]\s*([-+]?\d+\.\d+)'
+ LONGITUDE = 'Longitude\s*[:=]\s*([-]?\d+.\d+)'
+
[split]
[split.ctd]
- ETDD = 2
- PRES = 3
- DEPTH = 4
- TEMP = 5
- PSAL = 18
- DENS = 20
- SVEL = 22
- DOX2 = 16
- FLU2 = 14
- FLU3 = 15
- TUR3 = 13
+ ETDD = 1
+ PRES = 2
+ DEPTH = 3
+ TEMP = 4
+ PSAL = 17
+ DENS = 19
+ SVEL = 21
+ DOX2 = 15
+ FLU2 = 13
+ FLU3 = 14
+ TUR3 = 12
NAVG = 23
[split.ctdAll]
@@ -174,4 +179,4 @@ comment = "Extract from .lad files"
DEPTH = 0
SSJT = 1
SSTP = 2
- SSPS = 3
\ No newline at end of file
+ SSPS = 3