# go to directory 
  cd Downloads/

# download ALOS_preproc.tar.gz from Wiki or Rob's site
# http://www-rohan.sdsu.edu/~rmellors/RJM_InSAR_software.html
# http://www.sci.sdsu.edu/~rmellors/ALOS_preproc/ALOS_preproc.tar.gz
# make a directory for ALOS code
mkdir ALOS
# move package, unpack it
mv ALOS_preproc.tar.gz ALOS
cd ALOS
tar zxvf ALOS_preproc.tar.gz 
# run "make"
make
# check machine type
uname -p
# machine type of Intel Mac is "i386"
ls -l bin/i386/
# go to dir
cd bin/i386/
# check path
pwd

####
# edit SAR_CONFIG-gfortran_v3_1.txt
export MY_BIN=/Users/insar/Downloads/ALOS/bin/i386
# save and source again
cd ~/Downloads
source SAR_CONFIG-gfortran_v3_1.txt 
# check
ls $MY_BIN

# download ALOS scenes from course servers
#   PALSAR_090309_D447_3250.tgz
#   PALSAR_100125_D447_3250.tgz

# make subdirectory for Haiti, go to it
mkdir Haiti
cd Haiti/

# make subdirectory for first scene 2009-03-09
mkdir 090309
# move data file
mv ../PALSAR_090309_D447_3250.tgz 090309/
# go to dir and unpack
cd 090309/
tar xvf PALSAR_090309_D447_3250.tgz 

# move data and leader files up to date directory
mv RSP447_3250/IMG-HH-ALPSRP166373250-H1.0__D .
mv RSP447_3250/LED-ALPSRP166373250-H1.0__D .

#run "make_raw_alos.pl"
make_raw_alos.pl IMG 090309

# go back to Haiti directory, make second date subdirectory
cd ..
mkdir 100125
# go to dir, move files, unpack
cd 100125
mv ../../PALSAR_100125_D447_3250.tgz .
tar xvf PALSAR_100125_D447_3250.tgz 

# move data and leader files to date dir
mv RSP447_3250/IMG-HH-ALPSRP213343250-H1.0__D .
mv RSP447_3250/LED-ALPSRP213343250-H1.0__D .

#run "make_raw_alos.pl"
make_raw_alos.pl IMG 100125

# go back to Downloads dir
cd ~/Downloads
# create Haiti DEM from SRTM 3-arcsecond data
get_SRTM.pl Haiti.dem 18 19 -73 -72 1 3

# go back to "Haiti" dir
cd Haiti

# download co-0309-1001-8x16.proc from course server
###
# edit path to DEM in co-0309-1001-8x16.proc

###
# run "process_2pass.pl"
 process_2pass.pl co-0309-1001-8x16.proc&

# trouble-shooting
  576  cd int_090309_100125/
  577  mdx.pl 090309-100125_8rlks.cor&
  578  bg
  579  mdx.pl sim_3asec_8rlks.hgt&
  580  cd ../sim_3asec/
  581  vi Aik_resample.in 
  582  Aik_resample Aik_resample.in 
  583  mdx.pl sim_3asec_8rlks.hgt
  584  vi Aik_resample.in 
  585  Aik_resample Aik_resample.in 
  586  vi Aik_resample.in 
  587  Aik_resample Aik_resample.in 
  588  ls
  589  cd ..
  590  ls
  591  cd int_090309_100125/
  592  rm *ampmag*
  593  cd ..
  594  process_2pass.pl co-0309-1001-8x16.proc full_res&

#########
# download SNAPHU software 
#    from http://www-star.stanford.edu/sar_group/snaphu/
#    http://www-star.stanford.edu/sar_group/snaphu/snaphu-v1.4.2.tar.gz

# unpack
tar zxvf snaphu-v1.4.2.tar.gz
x snaphu-v1.4.2/
x snaphu-v1.4.2/bin/
x snaphu-v1.4.2/man/
x snaphu-v1.4.2/man/man1/
x snaphu-v1.4.2/man/man1/snaphu.1
x snaphu-v1.4.2/man/snaphu_man1.html
x snaphu-v1.4.2/man/snaphu_man1.txt
x snaphu-v1.4.2/src/
x snaphu-v1.4.2/src/snaphu.h
x snaphu-v1.4.2/src/snaphu.c
x snaphu-v1.4.2/src/snaphu_util.c
x snaphu-v1.4.2/src/snaphu_cs2parse.c
x snaphu-v1.4.2/src/Makefile
x snaphu-v1.4.2/src/snaphu_cs2types.h
x snaphu-v1.4.2/src/snaphu_cost.c
x snaphu-v1.4.2/src/snaphu_io.c
x snaphu-v1.4.2/src/snaphu_solver.c
x snaphu-v1.4.2/src/snaphu_cs2.c
x snaphu-v1.4.2/src/snaphu_tile.c
x snaphu-v1.4.2/README
x snaphu-v1.4.2/config/
x snaphu-v1.4.2/config/snaphu.conf.brief
x snaphu-v1.4.2/config/snaphu.conf.full

# go to directory and build
cd snaphu-v1.4.2
cd src

# build it
make

# copy executable to $MY_BIN
cd ../bin
cp snaphu $MY_BIN

### re-process with SNAPHU unwrapper
# go back to Haiti directory
cd ~/Downloads/Haiti
# edit "co-0309-1001-8x16.proc" to change to "unw_method=snaphu"
# (uncomment that line and comment the "#unw_method=old" line

# re-run processing
# use new "process_2pass_master.pl" script that knows how to run SNAPHU
# start at begin_filt or seismic step
process_2pass_master.pl co-0309-1001-8x16.proc seismic &