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10-reassimilate.py~
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Rerun the assimilation routine using different assimilation params (in base_info.py)
"""
__author__ = "David Honegger"
__copyright__ = "Copyright 2016, Oregon State University"
__license__ = "GPL"
__version__ = "0.1"
__email__ = "dahonegger@gmail.com"
#########################################################
# David Honegger; dahonegger@gmail.com
# Logs:
# 1.0 04/22/2016 prepared for initial use
# 2.0
# 3.0
# 4.0
#########################################################
##### NOTE #####
# Much of this script is copy-pasted from 00-run_assim.py
# Not all imported packages and variables are used
################
# Import python packages to use
import os,sys
import glob
import pylab as pl
import netCDF4
import netcdftime
# Declare global access to some logical variables
global roms_swan
global asim_sar
global asim_wav
global asim_swf
global real_data
global uv_curv
# Declare global access to more variables
global base_dir
global inp_dir,local_inp
global scr_dir
global reassim
global mk_bathy
global adj_bathy
global do_run
global adj_mem
global do_assim_matlab
global do_pre_assim_sar
global do_pre_assim_wav
global do_assim_python
# Declare global access to even more variables
global mat2prior
global pre_wav_scr
global adj_wav_scr
global pre_swf_scr
global ocean_exe
global run_type
global roms_inp
global run_forwards
global logfile
global final_grd
global bry_file
##########################################
# Clean up from previous runs and import from:
# "base_info.py"; "__init__.py"; "assim_module.py"
##########################################
try:
os.system('rm base_info.pyc' )
except:
pass
if 'base_info' in sys.modules:
del(sys.modules["base_info"])
import base_info
#####
try:
os.system('rm __init__.pyc' )
except:
pass
if '__init__' in sys.modules:
del(sys.modules["__init__"])
from __init__ import *
#####
try:
os.system('rm assim_module.pyc' )
except:
pass
if 'assim_module' in sys.modules:
del(sys.modules["assim_module"])
from assim_module import *
##########################################
# Rename imported variables to global counterparts
##########################################
base_dir = base_info.base_dir
inp_dir = base_info.inp_dir
scr_dir = base_info.scr_dir
prior = base_info.prior
final_grd = base_info.grd
bry_file = base_info.bry
##########################################
# Rename imported variables to local counterparts
##########################################
# number of iterations
nstart = base_info.nstart
nend = base_info.nend
############ List of available servers #####
servers = base_info.servers
########### Type of operation (TWIN test or Real data assimilation) >>>
real_data = base_info.real_data # False: use synthetic data True: use read observation
uv_curv = base_info.uv_curv # to use curvilinear grid to extract align curve velocity
if not real_data:
uv_curv = False
############ Which model is going to be assimilated >>>>>>>>>>>>>>>>>>>>>>>>
asim_sar = base_info.asim_sar # 2. ROMS alone assimilation (waves=False)
asim_wav = base_info.asim_wav # 3. SWAN alone assimilation (change the option in
asim_sar2 = base_info.asim_sar2 #In case of assimilating a second SAR image
asim_swf = base_info.asim_swf #assimilate swift data
##############################################
# Make bathymetry parameters global
global equal_space
global N
global Li
global Lj
global Lz
global sar_err_reduction
global radar_err_reduction
global cov_hh_limit
##############################################
equal_space = base_info.equal_space
N = base_info.N
Li = base_info.Li
Lj = base_info.Lj
Lz = pl.array(base_info.Lz )
sar_err_reduction = pl.array(base_info.sar_err_reduction)
radar_err_reduction = pl.array(base_info.radar_err_reduction)
cov_hh_limit = pl.array(base_info.cov_hh_limit)
########################################################################
### Read in cut window #####
global ijxy
######### Read in script names #############
main_scr = base_info.main_scr
mk_bathy = base_info.mk_bathy
adj_bathy = base_info.adj_bathy
do_run = base_info.do_run
adj_mem = base_info.adj_mem
############################################
do_pre_assim_sar = base_info.do_pre_assim_sar
do_pre_assim_wav = base_info.do_pre_assim_wav
do_assim_python = base_info.do_assim_python
###########################################
mat2prior = base_info.mat2prior
#SWAN
pre_wav_scr = base_info.pre_wav_scr
adj_wav_scr = base_info.adj_wav_scr
#SWIFT
pre_swf_scr = base_info.pre_swf_scr
#
ocean_exe = base_info.ocean_exe
roms_inp = base_info.roms_inp
run_type = base_info.run_type
##########################################
if not real_data:
uv_curv = False
#############################################
####### THE ACTION IS HERE ##################
#############################################
# Reassimilate only final iteration, because reassimilation changes downstream iterations
# (Really, reassimilation only makes sense for zero-iteration assimilations)
itr = nend
# Output directory
base=base_dir+'/run_'+str(1000+itr)+'/'
# Load output subdirectories
dirs = load_dirs(itr,base)
##### PSEUDOCODE:
# copy everything from 06_mat2prior to 05_assimilate
comm = 'cp -rf '+base+'06_mat2prior/* '+base+'05_assimilate/'
os.system(comm)
# rerun preassimilation scripts
members_adj(dirs,nobs=0) # nobs is the number of data index in data nc file (0 for the first time index)
do_pre_assim_cur (itr, dirs)
if asim_sar2:
members_adj(dirs,nobs=1)
if asim_swf:
roms2swift(dirs)
do_pre_assim_swift(itr, dirs)
if asim_wav:
do_swan_adj(dirs)
do_pre_assim_wave(itr, dirs)
# rerun assimilation script
#sys.exit()
do_reassimilate_py(itr, dirs)
print 'Reassimilation done'
sys.exit()
### END OF SCRIPT ###
############## ORIGINAL 00- SCRIPT BELOW
for itr in range(nstart,nend+1):
logf('**** > Start iteration > ',str(itr)+' from > '+str(nend) ,logfile)
# check if we need to create new directory structure
base=base_dir+'/run_'+str(1000+itr)+'/'
if os.path.exists(base):
print 'assimilation directory exist'
sys.exit('I have to think what to do now !')
else:
dirs=create_dirs(itr,base)
# for the first time prior will be copied from inp directory
if itr==0:
os.system('cp '+local_inp+'/const/'+prior+' '+dirs[0]+'/prior.nc')
else:
#copy new_perior from previous iteration
new_prior=base_dir+'/run_'+str(1000+itr-1)+'/06_mat2prior/new_prior.nc'
os.system('cp '+' '+new_prior+' '+dirs[0]+'/prior.nc' )
###### >>>>>>>> Start ASSIMILATION <<<<<<<<< #############
#Assign constants from base_info file
try:
dep_ij=Lz[itr]
except:
dep_ij=Lz.min()
############################################################
try:
sar_err_reduce = sar_err_reduction[itr]
radar_err_reduce = radar_err_reduction[itr]
except:
sar_err_reduce = sar_err_reduction.max()
radar_err_reduce = radar_err_reduction.max()
############################################################
try:
cov_hh_limit_ij=cov_hh_limit[itr]
except:
cov_hh_limit_ij=cov_hh_limit.min()
############################################################
logf('>sar_err_reduce ',str(sar_err_reduce) ,logfile)
logf('>radar_err_reduce ',str(radar_err_reduce) ,logfile)
logf('>dep_ij ' ,str(dep_ij) ,logfile)
logf('>cov_hh_limit_ij ' ,str(cov_hh_limit_ij) ,logfile)
############################################################
#Taking care of whether flood or ebb data need to take into account
#Works only for SYN data now
############################################################
if real_data:
obs_syn=local_inp+'/obs/sar/'+'uASAR.nc'
obs_flood=local_inp+'/obs/sar/'+base_info.obs_flood
obs_ebb=local_inp+'/obs/sar/'+base_info.obs_ebb
else:
obs_syn=local_inp+'/obs/syn/'+'syn1nri_his.nc'
obs_flood=local_inp+'/obs/syn/'+base_info.obs_flood
obs_ebb=local_inp+'/obs/syn/'+base_info.obs_ebb
#############################################################
try:
tide_case=base_info.choose_tide[itr]
except:
tide_case=base_info.choose_tide[-1]
if tide_case=='ebb':
logf(' ', 'Taking ebb obs file.' ,logfile)
os.system('rm '+obs_syn)
os.system('ln -s '+obs_ebb+' '+obs_syn)
logf('assim obs file ',obs_ebb,logfile)
elif tide_case=='flood':
logf(' ', 'Taking flood obs file.' ,logfile)
os.system('rm '+obs_syn)
os.system('ln -s '+obs_flood+' '+obs_syn)
logf('assim obs file ',obs_flood ,logfile)
make_bathy(dirs,N,Li,Lj,dep_ij,equal_space)
#sys.exit()
bathy_adj(dirs,cov_hh_limit_ij)
#sys.exit()
##############################################################
#do_runs(dirs)
#do_runs_roms(dirs,servers,nrun=50)
do_runs_roms(dirs,servers)
next = check_runs(dirs[3],list=None)
members_adj(dirs,nobs=0) # nobs is the number of data index in data nc file (0 for the first time index)
do_pre_assim_cur (itr, dirs)
if asim_sar2:
members_adj(dirs,nobs=1)
if asim_swf:
roms2swift(dirs)
do_pre_assim_swift(itr, dirs)
if asim_wav:
pre_swan_run(dirs)
do_swan_run (dirs,servers)
#final check over all again (because there might be remaining)
next=check_runs(dirs[9],list=None)
do_swan_adj(dirs)
do_pre_assim_wave(itr, dirs)
#Matlab routine
#do_assimilate_matlab (dirs,sar_err_reduce,radar_err_reduce,asim_sar,asim_wav,asim_swf)
#PYTHON routine
do_assimilate_py(itr, dirs)
mk_new_prior(dirs)
logf(' > Finish this part ',' With Success < ' ,logfile)
sys.exit() #
for itr in [0,1,2,3,4,5]:
print 'Start forward run > ', itr,' from > ', nend
base = base_dir+'/run_'+str(1000+itr)+'/'
dirs = create_dirs(itr,base)
os.system('cp -f '+' '+dirs[6]+'/new_prior.nc'+' '+dirs[8]+'/grd.nc' )
do_forward_run(dirs,'tirigan')
#SWAN Forward RUN
for itr in [0,6]:#,4,5,6,7,8]:
print 'Start SWAN forward run > ', itr,' from > ', nend
base = base_dir+'/run_'+str(1000+itr)+'/'
dirs = create_dirs(itr,base)
do_forward_swan_run(dirs,'tirigan')
#SWAN Forward RUN adjust and netcdf output
for itr in [0,6]:#,4,5,6,7,8]:
base = base_dir + '/run_'+str(1000+itr) + '/'
dirs = create_dirs(itr,base)
logf('do_swan_adj()',' > Adjust forward swan run ..' ,logfile)
sij=str1=' '.join('%.0f' % n for n in ijxy)
os.system('cd '+dirs[11]+'; echo "'+ sij+ '" &> param.inp ' )
os.system('cp -f '+scr_dir+'/'+adj_wav_scr+' '+dirs[11])
os.system('cp -f '+scr_dir+'/base_info.py '+dirs[11])
os.system('cd '+dirs[11]+'; python '+adj_wav_scr +' '+ dirs[11] +'/08_forward/ >> log_'+adj_wav_scr+'.txt')
logf(' > Finish forward run too ',' With Success < ' ,logfile)
############## END of reg code ###########################################
sys.exit() # <--- do not remove this
##########################################################################
### >>> Here is some useful code snips
### not part of the code
### ready to paste in ipython
clean_runs = True
if clean_runs:
nstart1=1
nend1=20
for itr in range(nstart1,nend1+1):
print 'Start cleaning run > ', itr,' from > ', nend
base=base_dir+'/run_'+str(1000+itr)+'/'
dirs=create_dirs(itr,base)
clean_dirs(dirs)
sys.exit()
#not part of the code
#ready to paste in ipython
itr = 3
real_data = True # False: use synthetic data True: use read observation
asim_sar = True
asim_wav = True
asim_swf = True #assimilate swift data
tide_case = 'ebb'
#tide_case = 'flood'
############################################################
if real_data:
obs_syn=local_inp+'/obs/sar/'+'uASAR.nc'
obs_flood=local_inp+'/obs/sar/'+base_info.obs_flood
obs_ebb=local_inp+'/obs/sar/'+base_info.obs_ebb
else:
obs_syn=local_inp+'/obs/syn/'+'syn1nri_his.nc'
obs_flood=local_inp+'/obs/syn/'+base_info.obs_flood
obs_ebb=local_inp+'/obs/syn/'+base_info.obs_ebb
#############################################################
if tide_case=='ebb':
logf(' ', 'Taking ebb obs file.' ,logfile)
os.system('rm '+obs_syn)
os.system('ln -s '+obs_ebb+' '+obs_syn)
logf('assim obs file ',obs_ebb ,logfile)
elif tide_case=='flood':
logf(' ', 'Taking flood obs file.' ,logfile)
os.system('rm '+obs_syn)
os.system('ln -s '+obs_flood+' '+obs_syn)
logf('assim obs file ',obs_flood ,logfile)
#############################################################
base = base_dir+'/run_'+str(1000+itr)+'/'
dirs = create_dirs(itr,base)
#############################################
members_adj(dirs,nobs=0)
do_pre_assim_cur(itr, dirs)
pre_swan_run(dirs)
do_swan_run (dirs,servers)
next=check_runs(dirs[9],list=None)
do_swan_adj(dirs)
do_pre_assim_wave(itr, dirs)
roms2swift(dirs)
do_pre_assim_swift(itr, dirs)
do_assimilate_py (itr, dirs)
mk_new_prior(dirs)
##############################################################
#itr = 4
#obs_ebb = local_inp+'/obs/syn/'+base_info.obs_ebb
#os.system('rm '+obs_syn)
#os.system('ln -s '+obs_ebb+' '+obs_syn)
itr = 0
obs_flood=local_inp+'/obs/syn/'+base_info.obs_flood
os.system('rm '+obs_syn)
os.system('ln -s '+obs_flood+' '+obs_syn)
base = base_dir+'/run_'+str(1000+itr)+'/'
dirs = create_dirs(itr,base)
do_assimilate_py (itr, dirs)
mk_new_prior(dirs)
############################################################