update doc for dockers

docs/pages/docker_cl_instructions.md

@@ -36,89 +36,67 @@ Now you can start working with the [gnssrefl code.](https://github.com/kristinem
 
 ### Kristine's Docker advice 
 
-I find Docker confusing!  I am sure if I used it more often, it would be easier. But here goes:
+I find Docker confusing!  I am sure if I used it more often, it would be easier. But here goes my recommendations:
 
 Open a window. You will be using linux commands. Make sure that you hit the return key after typing a command.
 
-ensure that you are using the latest docker 
+Ensure that you are using the latest docker : 
 
 `docker pull ghcr.io/kristinemlarson/gnssrefl:latest`
 
-make a directory where you plan to run the docker. I will call it local, i.e. `mkdir local`
+Make a directory where you plan to run the docker. I will call mine local, i.e. `mkdir local`
 
-cd into that directory, i.e. `cd local`
+Change into that directory,  `cd local`
 
 
 If you are new to linux, make sure you know the full name of this directory.  type `pwd` and see what
-come back.  I will pretend that what came back is `/usr/kristine/local` for this example
+come back.  I will pretend that what came back is `/usr/kristine/local` for my example
 
-If you want to use GNSS data that are stored in archives, you can go ahead and run the relevant commands provided above.
-If you want to use your own GNSS data, you have some options. For convenience, here I will only cover RINEX 2.11 users.  You have two choices:
+If you want to use GNSS data that are stored in archives, you can stop reading and just run the relevant commands provided above.
+If you want to use your own GNSS data, you have some options. For convenience, here I will only cover RINEX 2.11 users. 
+You first need to create the *local directory*, `mkdir refl_code` . Then you have two choices: 
 
-Your RINEX files can be in the so-called local directory. They will be deleted after you translate them.
-You will want to your RINEX files in 
+1. Your RINEX files can be stored in `/usr/kristine/local/refl_code`. They will be deleted after translation, so don't 
+put your only copy there.
 
-`/usr/kristine/local/refl_code`. 
-
-
-That means you should first make that directory and only then move or copy your RINEX files there.
-
-`mkdir refl_code` 
-
-
-or
-
-Your RINEX files can be stored in a the standard storage areas.  These will not be deleted after you translate them.
-For a RINEX file from the year 2023 and with a station name of abcd, these files should be stored in 
-
-`/usr/kristine/local/refl_code/2023/rinex/abcd` 
-
-This means you have to create the 2023 directory, the rinex directory and the abcd directory before you copy or move files.
+2. Your RINEX files can be stored in a the standard gnssrefl storage areas. Your RINEX files will *not* be deleted after you translate them.
+For a RINEX file from the year 2023 and with a station name of abcd, these files should be stored in the directory called `/usr/kristine/local/refl_code/2023/rinex/abcd`. This means you have to create those additional directories.  You can do that with an additional flag to the mkdir command, `mkdir -p refl_code/2023/rinex/abcd`.
 
 Now start your docker.   
 
 ```bash
 docker run -it -v $(pwd)/refl_code:/etc/gnssrefl/refl_code/  --name gnssrefl ghcr.io/kristinemlarson/gnssrefl:latest /bin/bash
 ```
 
-Yes, the command started the Docker, but it also told it to associate internally a directory it calls 
-
-`/etc/gnssrefl/refl_code` 
-
-with a physical directory on your machine called 
-
-`/usr/kristine/local/refl_code`
-
-Now you should be able to run the rinex2snr code with your own files. Example:
+In addition to starting the Docker, it also associates a directory 
+it calls `/etc/gnssrefl/refl_code` with a physical directory on your machine called `/usr/kristine/local/refl_code`
+Now that that is set up, you should be able to run differnt gnssrefl commands. Example:
 
 `rinex2snr abcd 2023 305 -nolook T`
 
-This should translate a file a RINEX file for you.  It will be stored in your Docker bucket as 
+The SNR output will be stored in your Docker bucket in the directory it calls `/etc/gnssrefl/refl_code/2023/snr/abcd`. 
+On your local machine it will live in `/usr/kristine/local/refl_code/2023/snr/abcd`
 
-`/etc/gnssrefl/refl_code/2023/snr/abcd` 
-
-on your local machine it will live in 
-
-`/usr/kristine/local/refl_code/2023/snr/abcd`
-
-When you run `quickLook` 
+Another example:
 
 `quickLook abcd 2023 305`
 
-It should put the files in 
-
-`/usr/kristine/local/refl_code/Files/abcd`
+This creates two png files (`quickLook_summary.png` and `quickLook_lsp.png`) that are 
+stored in `/usr/kristine/local/refl_code/Files/abcd`. The code should always print the location of 
+output files so you don't have to remember all these details.
 
-The names of the specific png files it created should be printed to the screen.
+When you run `gnssir` the output txt or csv files will go in `/etc/gnssrefl/refl_code/2023/results/abcd`
 
-You can change to different directories using two naming conventions.  
+You can change to different directories using either naming conventions.  
 
 `cd /etc/gnssrefl/refl_code/Files/abcd`
 
 or
 
 `cd $REFL_CODE/Files/abcd`
 
+I hope this helps. I have posted an issue on github to make sure this page is up to date with the current
+release of the software.
 
 ### Update Docker Image to newest version <a name="Update Docker"></a>
 

gnssrefl/sd_libs.py

@@ -32,7 +32,9 @@ def mjd_to_obstimes(mjd):
 def write_spline_output(splineout, iyear, th, spline, delta_out, station, txtdir,Hortho):
     """
     Writing the output of the spline fit to the final RH time series.
-    No output other than this text file.
+    No output other than this text file for year 2023 and station name ssss:
+
+    $REFL_CODE/Files/ssss/ssss_2023_spline_out.txt
 
     Parameters
     ----------