#------Directory paths needed

idl_paths=/data/kbah/from_home_kbah/ms2gt/tempcase/
input_data_path=/data/kbah/from_home_kbah/ms2gt/tempcase/inpout/
output_data_path=/data/kbah/from_home_kbah/ms2gt/tempcase/output/
ms2gt_path=/data/kbah/from_home_kbah/ms2gt/tempcase/

#1-----------

echo 'run the idlsave001.pro to read hdf and output seperate .dat var. files

 how to call idlsave :
 	idlsave001, input hdf file path, output .dat files path

#2 -------------
#move to the ms2gt directory

 	
 
 run the following sub routines:
 

 ./bin/extract_region -v 4 2600 900 0 220 2600 680 lat.dat   fixed_lat.dat
 ./bin/extract_region -v 4 2600 900 0 220 2600 680 lon.dat   fixed_lon.dat
 ./bin/extract_region -v 4 2600 900 0 220 2600 680 ctc.dat   fixed_ctc.dat
 ./bin/extract_region -v 4 2600 900 0 220 2600 680 ctc_scaled.dat  fixed_ctc_scaled.dat
 ./bin/extract_region -v 1 2600 900 0 220 2600 680 cloud_type.dat  fixed_cloud_type.dat
 ./bin/extract_region -v 1 2600 900 0 220 2600 680 conv_init.dat   fixed_conv_init.dat
 
  # you can now delete the non fixed .dat files (eg output/GOES-11_2011_074_2015_lat.dat) if you want to save space
 


#3 -------------
 # Run ll2cr on the fixed lat lon files to create the .img lat lon files  
  How to call ll2cr
  ./bin/ll2cr -v -f 2600 1 680 fixed_lat.dat fixed_lon.dat hawaii.gdp path_to_output_lat/lon_img_files eg:
 
  ./bin/ll2cr -v -f 2600 1 680 fixed_lat.dat fixed__lon.dat hawaii.gpd /data/kbah/from_home_kbah/ms2gt/tempcase/output/hawaii




#4 -------------
# Now run fornav on all the fixed .dat files and output new .dat files
	How to call fornav
  ./bin/fornav 1 -v  -m -t u1 -c 2 -D 1 2000 1 680 cols_img rows_img fixed_cloud_type.dat 321 225 extrated_projected_cloud_type.dat (path and name of the output .dat file) 
  
  #here is how to run it on each of the 6 files
./bin/fornav 1 -v  -m -t f4 -c 2 -D 1 2000 1 680 cols_img_file  rows_img_file  fixed_lat.dat_file 321 225 output_lat_filename.dat           
./bin/fornav 1 -v  -m -t f4 -c 2 -D 1 2000 1 680 cols_img_file  rows_img_file  fixed_lon.dat_file 321 225 output_lon_filename.dat
./bin/fornav 1 -v  -m -t f4 -c 2 -D 1 2000 1 680 cols_img_file  rows_img_file  fixed_ctc.dat_file 321 225 output_ctc_filename.dat
./bin/fornav 1 -v  -m -t f4 -c 2 -D 1 2000 1 680 cols_img_file  rows_img_file  fixed_ctc_scaled.dat_file 321 225 output_ctc_scaled_filename.dat           
./bin/fornav 1 -v  -m -t u1 -c 2 -D 1 2000 1 680 cols_img_file  rows_img_file  fixed_ci.dat_file 321 225 output_ci_filename.dat
./bin/fornav 1 -v  -m -t u1 -c 2 -D 1 2000 1 680 cols_img_file  rows_img_file  fixed_cloud_type.dat_file 321 225 output_cloud_type_filename.dat


#5 -------------
   cd ${idl_path} 
  #Run subsetdomain.pro, this will creat the out.ASCII files that will be converted to grib2 for each of the four products.
  How to call subsetdomain, where lat.dat (means the final output_lat.dat file from step 4 above etc)
  
  SUBSETDOMAIN, input_file_path, lat.dat, output_lon  ouput_c_type0,output_ci, output_ctc,  output_ctc_scaled
  
  
#Now you can delete all the .dat files and keep the .txt files created by subsetdomain above.