def save_tracks_to_file(nc_outfile,iyear,MPA_SOURCE):
nc_ofid = Dataset(nc_outfile, 'w')
# write run info to track file
nc_ofid.mpa_source = MPA_SOURCE
nc_ofid.iyear = iyear
nc_ofid.NUM_LARVAE = NUM_LARVAE
nc_ofid.RELEASE_WINDOW = RELEASE_WINDOW
nc_ofid.STARTDAY = STARTDAY
nc_ofid.DT = DT
nc_ofid.KMX = KMX
nc_ofid.KMY = KMY
nc_ofid.KMZ = KMZ
nc_ofid.VERTICAL_INTERP = str(VERTICAL_INTERP)
nc_ofid.ANIMATE = str(ANIMATE)
nc_ofid.DEATH = str(DEATH)
nc_ofid.BEHAVIOUR = BEHAVIOUR # behaviour index
# # 1 is standard Larrson et al behaviour
# # 2 is modified Larsson et al with small swimming speeds
nc_ofid.TARGETDEPTH = TARGETDEPTH # target depth
nc_ofid.SWIMSLOW = SWIMSLOW #initial swimming speed
nc_ofid.SWIMFAST = SWIMFAST # max swimming speed
nc_ofid.SWIMSTART = SWIMSTART #age in days at which start swimming
nc_ofid.SWIMMAX = SWIMMAX #average age in days at which max swimming speed is reached
nc_ofid.DESCENDAGE = DESCENDAGE # average age at which probability of heading down starts
# to increase
nc_ofid.DESCENDAGERANGE = DESCENDAGERANGE # now fully heading down
nc_ofid.MINSETTLEAGE = MINSETTLEAGE # minimum age at which can settle given suitable
# habitat
nc_ofid.DEADAGE = DEADAGE # Average age at which dead
nl = len(larvae_dead) + len(larvae_outofarea) + len(larvae_group)
if DEATH:
maxt = int((DEADAGE + 1) * SECONDS_IN_DAY / DT)
else:
maxt = int((NRUNDAYS + 1) * SECONDS_IN_DAY / DT)
time = nc_ofid.createDimension('time', maxt)
nlarvae = nc_ofid.createDimension('nlarvae', nl)
lon = nc_ofid.createVariable('longitude','f8',('nlarvae','time',))
lat = nc_ofid.createVariable('latitude','f8',('nlarvae','time',))
dep = nc_ofid.createVariable('depth','f8',('nlarvae','time',))
bed = nc_ofid.createVariable('at bed','i',('nlarvae','time',))
temp = nc_ofid.createVariable('temperature','f8',('nlarvae','time',))
sal = nc_ofid.createVariable('salinity','f8',('nlarvae','time',))
rt = nc_ofid.createVariable('release day','i',('nlarvae',))
fate = nc_ofid.createVariable('fate','S1',('nlarvae',))
i = 0
for larva in larvae_dead:
x, y = larva.get_track()
z, b = larva.get_depth_history()
t = larva.get_temperature_history()
s = larva.get_salinity_history()
release_time = larva.get_release_day()
state = 'D'
lon[i,0:len(x)] = x[0:len(x)]
lat[i,0:len(y)] = y[0:len(y)]
dep[i,0:len(z)] = z[0:len(z)]
bed[i,0:len(z)] = b[0:len(z)]
temp[i,0:len(t)] = t[0:len(t)]
sal[i,0:len(t)] = s[0:len(t)]
rt[i] = release_time
fate[i] = state
i = i + 1
for larva in larvae_outofarea:
x, y = larva.get_track()
z, b = larva.get_depth_history()
t = larva.get_temperature_history()
release_time = larva.get_release_day()
state = 'L'
lon[i,0:len(x)] = x[0:len(x)]
lat[i,0:len(y)] = y[0:len(y)]
dep[i,0:len(z)] = z[0:len(z)]
bed[i,0:len(z)] = b[0:len(z)]
temp[i,0:len(t)] = t[0:len(t)]
sal[i,0:len(t)] = s[0:len(t)]
rt[i] = release_time
fate[i] = state
i = i + 1
for larva in larvae_group:
x, y = larva.get_track()
z, b = larva.get_depth_history()
t = larva.get_temperature_history()
release_time = larva.get_release_day()
state = 'A'
lon[i,0:len(x)] = x[0:len(x)]
lat[i,0:len(y)] = y[0:len(y)]
dep[i,0:len(z)] = z[0:len(z)]
bed[i,0:len(z)] = b[0:len(z)]
temp[i,0:len(t)] = t[0:len(t)]
sal[i,0:len(t)] = s[0:len(t)]
rt[i] = release_time
fate[i] = state
i = i + 1
nc_ofid.close()
