if m > max_abs_pressure:
max_abs_pressure = m
m_ind = [i for i, j in enumerate(data['pressure']) if j ==m] # this line finds the index of the max depth
#this loop here will take the readings only when the fish is going down
for j in names:
vars()[j] = []
for i in np.arange(1,float(m_ind[0])):
if data['pressure'][i]-data['pressure'][i-1] >0:
vars()[j].append(data[str(j)][i])
depth = sw.depth(pressure, xyzt['lat_DD.dd'])
c3515 = 42.9140
condr = [x/c3515 for x in cond]
salinity = sw.salt(condr, temp, pressure)
density = sw.dens(salinity, temp,pressure)
griddeddata=[]
for k in names2:
griddeddata = np.interp(grid_depth,depth,vars()[k],right=np.NaN)
griddeddata = griddeddata[0:]
vars()['grid_'+k][:,file[0]] = vars()['griddeddata']
f.close()
except:
failedloadfiles.append(str(file))
print ("Could not process " + file[1])
for k in names2:
vars()['grid_'+k][:,file[0]] = np.NaN
def parseScience(gliderTbdDir, fileType):
"""
Module: parseScience()
Date: 2012-11-27
Author: [email protected]
Modified: 2013-10-15
By: [email protected]
Inputs: None
Outputs: Inserts into SQLite database file
Purpose: Grabs a db cursor and calls dbd2asc for all non-parsed tbd
files. Looks for 'sci_' and splits sensor list. Finds pos
of sensors of interest so list can change if tbdlist.dat
changes. Uses pos of SOI to store values in correct field.
"""
cur = gliderlog.cursor()
curParsed = gliderlog.cursor()
sbdParsedStructure = 0
#
#Regex for lines beginning with m_present_time
#m_present_time structure: '1277271054.36734
pattMPresentTime = re.compile(r'1[0-9]{9}\.[0-9]{5}')
#
select = "select %sfile from %sFiles where parsed = 0 \
ORDER BY %sfile ASC" % (fileType, fileType, fileType)
cur.execute(select)
for(tbdFile) in cur:
if DEBUG > 0:
print "Running dbd2asc on %s/%s" % (gliderTbdDir, tbdFile[0])
command = "/opt/dinkum/dbd2asc -c /opt/glider_data_pipeline/cache \
%s/%s" % (gliderTbdDir, tbdFile[0])
p = subprocess.Popen(command, shell=True, stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True)
(sIn, sOut) = (p.stdin, p.stdout)
myBuffer = sOut.xreadlines()
#
curInsert = gliderlog.cursor()
curInsert.execute('begin')
for (line) in myBuffer:
#2011-06-02 rdc changed to sci_ to reflect new tbd file format
#Look to see if line starts with "sci_" -- assume that a list
#of sensors follows. Split into sensors, create tbdSensors
#table and store values in tbdSensorReadings.
if (line.startswith("sci_")):
#we need to split and create here, not print
sensorList = line.split()
if (DEBUG > 1):
print "sensorList: %s" % (sensorList)
if DEBUG > 1:
for (sensor) in sensorList:
print "Factored %s" % (sensor)
#Get order of sensors
m_present_timePos = sensorList.index('sci_m_present_time')
sci_water_tempPos = sensorList.index('sci_water_temp')
sci_water_condPos = sensorList.index('sci_water_cond')
sci_water_pressurePos = sensorList.index('sci_water_pressure')
sci_bbfl2s_chlor_scaledPos = sensorList.index('sci_bbfl2s_chlor_scaled')
if pattMPresentTime.search(line):
index = 0
matchobj = pattMPresentTime.search(line)
if matchobj:
if DEBUG > 1:
print "MATCH ON pattMPresentTime"
print "m_present_time: %s" % matchobj.group(0)
m_present_time = float(matchobj.group(0))
line = line.replace('NaN','nan')
sensorReadings = line.split()
if DEBUG > 1:
print sensorReadings
sci_water_cond = float(sensorReadings[sci_water_condPos])
sci_water_temp = float(sensorReadings[sci_water_tempPos])
sci_water_pressure = float(sensorReadings[sci_water_pressurePos])
sci_water_condRatio = (sci_water_cond*0.23302418791070513)
#Salinity and density calculations and db update
#
if (sci_water_condRatio > 0 and sci_water_temp > 0 and \
sci_water_pressure > 0):
calc_salinity = sw.salt(sci_water_condRatio, \
sci_water_temp, sci_water_pressure)
#get most recent position
#[TO DO] Fudge it for now -- add to plotValues
lon = -82
lat = 27
absSalinty = gsw.SA_Sstar_from_SP(calc_salinity, \
sci_water_pressure, lon, lat)[0]
calc_density = (gsw.rho(absSalinty, sci_water_temp, \
sci_water_pressure) - 1000)
else:
sci_water_condRatio = 'nan'
calc_salinity = 'nan'
calc_density = 'nan'
absSalinty = 'nan'
curInsert.execute("INSERT INTO plotValues(m_present_time,\
m_depth, m_water_depth, sci_water_temp, sci_water_cond, sci_water_pressure,\
calc_salinity, absSalinty, calc_density,sci_bbfl2s_chlor_scaled, sci_moteopd_corr1,\
sci_moteopd_corr2,sci_moteopd_corr3,sci_moteopd_corr4,sci_moteopd_corr5,\
sci_moteopd_corr6,sci_moteopd_corr7,sci_moteopd_corr8,sci_moteopd_corr9,\
sci_moteopd_corr10,sci_moteopd_corr11,m_avg_climb_rate,m_avg_dive_rate,m_lat, \
m_lon, m_tot_horz_dist, m_avg_speed,sci_moteopd_volt) \
VALUES(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)", \
(sensorReadings[m_present_timePos],'nan','nan',\
sensorReadings[sci_water_tempPos],sci_water_condRatio,\
sensorReadings[sci_water_pressurePos],calc_salinity, \
absSalinty, calc_density,sensorReadings[sci_bbfl2s_chlor_scaledPos],0,0,0,0,0,0,0,0,0,0,0 \
,'nan','nan','nan','nan','nan','nan',0))
curInsert.execute('commit')
curInsert.close()
select = "UPDATE %sFiles set parsed = '1' where %sfile = '%s'" \
% (fileType, fileType, tbdFile[0])
curParsed.execute(select)
curParsed.close()
cur.close()