diff --git a/ascii.py b/ascii.py
index df700d3160c08dcfeee629e62b19b9820af7aac4..446c398b8f691b1522e38ee9cd7be0fe03972736 100644
--- a/ascii.py
+++ b/ascii.py
@@ -7,7 +7,7 @@ import tools
import numpy as np
from datetime import datetime
-def writeHeaderProfile(hdrFile, cfg, device, fe, r):
+def writeHeaderProfile(hdrFile, cfg, device, fe):
f = open(hdrFile, 'w')
# first line, header ex:
# PIRATA-FR30 THALASSA IRD SBE911+ 09P-1263 BOURLES
@@ -76,7 +76,7 @@ def writeHeaderProfile(hdrFile, cfg, device, fe, r):
f.close()
-def writeDataProfile(dataFile, cfg, device, fe, r):
+def writeDataProfile(dataFile, cfg, device, fe):
f = open(dataFile, 'w')
# write header, first line
@@ -130,23 +130,23 @@ def writeDataProfile(dataFile, cfg, device, fe, r):
f.write("\n")
f.close()
-def writeProfile(cfg, device, fe, r):
+def writeProfile(cfg, device, fe):
if not os.path.exists(cfg['global']['ASCII']):
os.makedirs(cfg['global']['ASCII'])
fileName = "{}/{}.{}".format(cfg['global']['ASCII'],
cfg['cruise']['CYCLEMESURE'], device.lower())
- writeHeaderProfile(fileName, cfg, device.lower(), fe, r, )
+ writeHeaderProfile(fileName, cfg, device.lower(), fe)
print('writing header file: {}'.format(fileName), end='', flush=True)
print(' done...')
fileName = "{}/{}_{}".format(cfg['global']['ASCII'],
cfg['cruise']['CYCLEMESURE'], device.lower())
print('writing data file: {}'.format(fileName), end='', flush=True)
- writeDataProfile(fileName, cfg, device.lower(), fe, r)
+ writeDataProfile(fileName, cfg, device.lower(), fe)
print(' done...')
-def writeDecimalDataTrajectory(dataFile, cfg, device, fe, r):
+def writeDecimalDataTrajectory(dataFile, cfg, device, fe):
f = open(dataFile, 'w')
# write header, first line
@@ -175,7 +175,7 @@ def writeDecimalDataTrajectory(dataFile, cfg, device, fe, r):
f.write("\n")
f.close()
-def writeHumanDataTrajectory(dataFile, cfg, device, fe, r):
+def writeHumanDataTrajectory(dataFile, cfg, device, fe):
f = open(dataFile, 'w')
# write header, first line
@@ -219,7 +219,7 @@ def writeHumanDataTrajectory(dataFile, cfg, device, fe, r):
f.close()
-def writeTrajectory(cfg, device, fe, r):
+def writeTrajectory(cfg, device, fe):
if not os.path.exists(cfg['global']['ASCII']):
os.makedirs(cfg['global']['ASCII'])
@@ -227,13 +227,13 @@ def writeTrajectory(cfg, device, fe, r):
fileName = "{}/{}.{}".format(cfg['global']['ASCII'],
cfg['cruise']['CYCLEMESURE'], device.lower())
print('writing file: {}'.format(fileName), end='', flush=True)
- writeHumanDataTrajectory(fileName, cfg, device.lower(), fe, r, )
+ writeHumanDataTrajectory(fileName, cfg, device.lower(), fe)
print(' done...')
# write ascii file with decimal time and position
fileName = "{}/{}_{}".format(cfg['global']['ASCII'],
cfg['cruise']['CYCLEMESURE'], device.lower())
print('writing file: {}'.format(fileName), end='', flush=True)
- writeDecimalDataTrajectory(fileName, cfg, device.lower(), fe, r)
+ writeDecimalDataTrajectory(fileName, cfg, device.lower(), fe)
print(' done...')
\ No newline at end of file
diff --git a/config.toml b/config.toml
index 4258a6e8ab1a9acc3a6e7f56b6cabb5fb6a47972..a751db1468af8bb2dfa22438f780f1d8a013ad32 100644
--- a/config.toml
+++ b/config.toml
@@ -279,7 +279,7 @@ julianOrigin = 1
[tsg.header]
isHeader = '^[*#]+\s+'
- endHeader = '^[*]END[*]'
+ endHeader = '^[*]END[*]$'
DATETIME = 'System UpLoad Time\s*=\s*(\w+)\s+(\d+)\s+(\d+)\s+(\d+):(\d+):(\d+)'
[tsg.split]
diff --git a/netcdf.py b/netcdf.py
index 76b11d8b83c4bd4ea7cbb48aae97940919167098..0bba2507859dfcfc060d50c19c33b7bd14efa359 100644
--- a/netcdf.py
+++ b/netcdf.py
@@ -37,7 +37,7 @@ def writeGlobalAttributes(nc, cfg, device, type):
nc.Netcdf_version = "3.6"
-def writeProfile(cfg, device, fe, r):
+def writeProfile(cfg, device, fe):
# ncvars is a dictionary that store a NETCDF variable for each physical parameter key
ncvars = {}
@@ -81,7 +81,7 @@ def writeProfile(cfg, device, fe, r):
print(f"Define variable : {key}")
# for each variables get the attributes dictionary from Roscop
- hash = r[key]
+ hash = fe.roscop[key]
# _FillValue attribute must be set when variable is created
# (using fill_value keyword to createVariable)
if '_FillValue' in hash:
@@ -131,7 +131,7 @@ def writeProfile(cfg, device, fe, r):
nc.close()
print('done...')
-def writeTrajectory(cfg, device, fe, r):
+def writeTrajectory(cfg, device, fe):
# ncvars is a dictionary that store a NETCDF variable for each physical parameter key
ncvars = {}
@@ -171,7 +171,7 @@ def writeTrajectory(cfg, device, fe, r):
print(f"Define variable : {key}")
# for each variables get the attributes dictionary from Roscop
- hash = r[key]
+ hash = fe.roscop[key]
# _FillValue attribute must be set when variable is created
# (using fill_value keyword to createVariable)
if '_FillValue' in hash:
diff --git a/odv.py b/odv.py
index 204e02e4177da00431f178a66d557b834d5d8c54..d22ec8e238368556aa0d6b55468d4257292732c7 100644
--- a/odv.py
+++ b/odv.py
@@ -7,105 +7,103 @@ from re import S
import tools
import numpy as np
from datetime import datetime
-
-def writeProfile(cfg, device, fe, r):
+
+def writeHeader(cfg, device, dataType):
+ '''Specifying * for Type (dataType) lets ODV make the choice.
+ If Bot. Depth values are not available, you should leave this field empty.'''
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)
- f = open(fileName, 'w')
+ fd = open(fileName, 'w')
# write odv header
- f.write(f"//ODV Spreadsheet file : {fileName}\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.lower()]['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\tyyyy-mm-ddThh:mm:ss.sss\tLongitude [degrees_east]\tLatitude [degrees_north]\tBot. Depth [m]")
+ fd.write(f"//ODV Spreadsheet file : {fileName}\n")
+ fd.write(f"//Data treated : {datetime.today().strftime('%Y-%m-%dT%H:%M:%SZ')}\n")
+ fd.write(f"//<DataType>{dataType}</DataType>\n")
+ fd.write(f"//<InstrumentType>{cfg[device.lower()]['typeInstrument']}</InstrumentType>\n")
+ fd.write(f"//<Source>{os.getcwd()}</Sources>\n")
+ fd.write(f"//<Creator>{cfg['cruise']['CREATOR']}</Creator>\n")
+ fd.write("//\n")
+ fd.write(f"Cruise\tStation\tType\tyyyy-mm-ddThh:mm:ss.sss\tLongitude [degrees_east]\tLatitude [degrees_north]\tBot. Depth [m]")
+ return fd
+
+def writeProfile(cfg, device, fe):
+
+ # You should use B for stations with less than about 250 samples (e.g., bottle data) and C for stations
+ # with more than about 250 samples (e.g., CTD, XBT, etc.)
+ if cfg[device.lower()] == 'btl':
+ stationType = 'B'
+ else:
+ stationType = 'C'
- # write variables and unit
+ # write header and return file descriptor
+ fd = writeHeader(cfg, device, 'Profiles')
+ # write following variables and unit
for k in fe.keys:
- f.write(f"\t{k} [{fe.roscop[k]['units']}]")
- f.write("\n")
+ fd.write(f"\t{k} [{fe.roscop[k]['units']}]")
+ fd.write("\n")
- if cfg[device.lower()] == 'btl':
- type = 'B'
- else:
- 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" % (cfg['cruise']['CYCLEMESURE'], fe['PROFILE'][i], type))
- f.write(f"\t%s" % (tools.julian2format(fe['TIME'][i], "%Y-%m-%dT%H:%M:%S")))
+ fd.write(f"%s\t{fmt}\t%s" % (cfg['cruise']['CYCLEMESURE'], fe['PROFILE'][i], stationType))
+ fd.write(f"\t%s" % (tools.julian2format(fe['TIME'][i], "%Y-%m-%dT%H:%M:%S")))
fmt = fe.roscop['LONGITUDE']['format']
- f.write(f"\t{fmt}" % (fe['LONGITUDE'][i]))
+ fd.write(f"\t{fmt}" % (fe['LONGITUDE'][i]))
fmt = fe.roscop['LATITUDE']['format']
- f.write(f"\t{fmt}" % (fe['LATITUDE'][i]))
- if fe.iskey('BATH'):
+ fd.write(f"\t{fmt}" % (fe['LATITUDE'][i]))
+ if fe.iskey('BATH') and not np.isnan(fe['BATH'][i]):
fmt = fe.roscop['BATH']['format']
- f.write(f"\t{fmt}" % (fe['BATH'][i]))
+ fd.write(f"\t{fmt}" % (fe['BATH'][i]))
else:
- f.write("\t")
- for k in fe.keys:
- if fe[k][i][m] != fe.roscop[k]['_FillValue']:
+ fd.write("\t")
+ for k in fe.keys:
+ if not np.isnan(fe[k][i][m]):
+ #if fe[k][i][m] != fe.roscop[k]['_FillValue']:
fmt = fe.roscop[k]['format']
- f.write(f"\t{fmt}" % (fe[k][i][m]))
+ fd.write(f"\t{fmt}" % (fe[k][i][m]))
else:
- f.write("\t")
- f.write("\n")
- f.close()
+ fd.write("\t")
+ fd.write("\n")
+ fd.close()
print(' done...')
-def writeTrajectory(cfg, device, fe, r):
- if not os.path.exists(cfg['global']['odv']):
- os.makedirs(cfg['global']['odv'])
+def writeTrajectory(cfg, device, fe):
- fileName = "{}/{}_{}_odv.txt".format(cfg['global']['odv'],
- cfg['cruise']['CYCLEMESURE'], device.lower())
- print('writing data file: {}'.format(fileName), end='', flush=True)
- f = open(fileName, 'w')
-
- # write odv header
- f.write(f"//ODV Spreadsheet file : {fileName}\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.lower()]['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\tyyyy-mm-ddThh:mm:ss.sss\tLongitude [degrees_east]\tLatitude [degrees_north]\tBot. Depth [m]")
-
+ # write header and return file descriptor
+ fd = writeHeader(cfg, device, 'Trajectories')
# write variables and unit
for k in fe.keys:
if k == 'ID' or k == 'DAYD' or k == 'LATITUDE' or k == 'LONGITUDE':
continue
else:
- f.write(f"\t{k} [{fe.roscop[k]['units']}]")
- f.write("\n")
+ fd.write(f"\t{k} [{fe.roscop[k]['units']}]")
+ fd.write("\n")
- type = 'B'
+ # If Bot. Depth values are not available, you should leave this field empty,
+ # usually the case for trajectory
+ stationType = ''
for i in range(fe.n):
# Trajectory data of this form have exactly one sample per station. The number of stations
# equals the number of observation along the trajectory, which is usually large.
fmt = "%06d"
- f.write(f"%s\t{fmt}\t%s" % (cfg['cruise']['CYCLEMESURE'], i+1, type))
- f.write(f"\t%s" % (tools.julian2format(fe['DAYD'][i], "%Y-%m-%dT%H:%M:%S")))
+ fd.write(f"%s\t{fmt}\t%s" % (cfg['cruise']['CYCLEMESURE'], i+1, stationType))
+ fd.write(f"\t%s" % (tools.julian2format(fe['DAYD'][i], "%Y-%m-%dT%H:%M:%S")))
fmt = fe.roscop['LONGITUDE']['format']
- f.write(f"\t{fmt}" % (fe['LONGITUDE'][i]))
+ fd.write(f"\t{fmt}" % (fe['LONGITUDE'][i]))
fmt = fe.roscop['LATITUDE']['format']
- f.write(f"\t{fmt}" % (fe['LATITUDE'][i]))
- if fe.iskey('BATH'):
+ fd.write(f"\t{fmt}" % (fe['LATITUDE'][i]))
+ if fe.iskey('BATH') and not np.isnan(fe['BATH'][i]):
fmt = fe.roscop['BATH']['format']
- f.write(f"\t{fmt}" % (fe['BATH'][i]))
+ fd.write(f"\t{fmt}" % (fe['BATH'][i]))
else:
- f.write("\t")
+ fd.write("\t")
for k in fe.keys:
if k == 'ID' or k == 'DAYD' or k == 'LATITUDE' or k == 'LONGITUDE':
@@ -113,11 +111,11 @@ def writeTrajectory(cfg, device, fe, r):
else:
if fe[k][i] != fe.roscop[k]['_FillValue']:
fmt = fe.roscop[k]['format']
- f.write(f"\t{fmt}" % (fe[k][i]))
+ fd.write(f"\t{fmt}" % (fe[k][i]))
else:
- f.write("\t")
- f.write("\n")
- f.close()
+ fd.write("\t")
+ fd.write("\n")
+ fd.close()
print(' done...')
diff --git a/profile.py b/profile.py
index 85a8069f53c01b35a5a3ca8e4b1fd270907104ac..0734402d673199de1499377e3a97400a928d32b8 100644
--- a/profile.py
+++ b/profile.py
@@ -519,14 +519,14 @@ class Profile:
self.read_files(cfg, ti)
# write ASCII hdr and data files
- ascii.writeProfile(cfg, ti, self, self.roscop)
+ ascii.writeProfile(cfg, ti, self)
# write ODV file
if cfg['global']['odv']:
- odv.writeProfile(cfg, ti, self, self.roscop)
+ odv.writeProfile(cfg, ti, self)
# write the NetCDF file
- netcdf.writeProfile(cfg, ti, self, self.roscop)
+ netcdf.writeProfile(cfg, ti, self)
# for testing in standalone context