improve documentation for local coordinate file

docs/pages/file_structure.md

@@ -22,6 +22,24 @@ we strongly encourage you to use them. And never use an elevation mask on your r
 completely unncessary for positioning (which allows masking to be done at the software level) and 
 are extremely harmful to GNSS-IR.
 
+## Where should I store station coordinates? (as of version 3.6.4)
+
+The software comes with a long list (almost 20,000) of station coordinates taken from the University 
+of Nevada Reno. If you are analyzing any of those stations, you should not have to enter
+any coordinates (use **query_unr** to see if your station is included). 
+
+If you are analyzing your own data, eventually you will need to tell the software 
+where your stations are. This location does not have to be super precise, within a few meters
+is perfectly acceptable, as it is primarily used for the refraction correction. The better your
+site coordinates, the better your reflection zone maps would be, however. Previously you 
+input this information (latitude, longitude, and ellipsoidal
+height) at the **gnssir_input** station). There is now another option. If you create a plain
+txt file iwth the name llh_local.txt and store it in the $REFL_CODE/input directory, the code will
+use this as your *a priori* station coordinates. The format of this file is station latitude longitude
+and height, with units of degrees, degrees, and meters. You can add comment lines with a percent sign.
+This file is read in the *query_coordinate_file* function in gps.py. The file is read by **nmea2snr**, so 
+that means you won't have to enter station coordinates on the command line when using **nmea2snr**.
+
 ## How do I analyze my own GNSS data?
 
 To analyze your own GNSS data you must comply with the software expectations for how the 

docs/pages/snr_simulation.m

@@ -1,3 +1,4 @@
+exit
 clear all
 close all
 clc

docs/use_cases/use_vlis.md

@@ -51,7 +51,7 @@ answer should pop up in about 10 seconds. The writing in magenta are comments I
 point out various things.
 
 <p align=center>
-<img src=../_static/vlis-default.png width=800/>
+<img src=../_static/vlis-default.jpg width=800/>
 </p>
 
 So what's going on here? (If you have never used this site before, I recommend you give a 
@@ -76,7 +76,7 @@ right answer (10 meters) and the tidal range (plus/minus two meters).
 Make sure your RINEX file is loaded and hit submit.
 
 <p align=center>
-<img src=../_static/vlis-better-choices.png width=800/>
+<img src=../_static/vlis-better-choices.jpg width=800/>
 </p>
 
 Now you can see a broad swath of "successful" retrievals in the azimuth range you chose. The RH 

gnssrefl/gnssir_cl.py

@@ -71,6 +71,7 @@ def gnssir(station: str, year: int, doy: int, snr: int = 66, plt: bool = False,
 
     beta version of parallel processing is now onine. If you set -par to an integer between 2 and 10,
     it should substantially speed up your processing. Big thank you to AaryanRampal for getting this up and running.
+
         
     Examples
     --------

gnssrefl/gnssir_input.py

@@ -88,17 +88,19 @@ def make_gnssir_input(station: str, lat: float=0, lon: float=0, height: float=0,
 
     Note: you can keep using your old json files - you just need to add this new -azlist2 setting manually.
 
-    Latitude, longitude, and height are assumed to be stored in the UNR database.  If they are not, you should
-    set them manually.
+    Latitude, longitude, and height are assumed to be stored in either the UNR database we provide with
+    gnssrefl or in your local coordinate file. See the instructions in the file formats section of gnssrefl for 
+    information about the format, name, and location of that local coordinate file.  
 
     Originally we had refraction as a boolean, i.e. on or off. This was stored in the gnssir 
     analysis description json. The code however, uses a 1 for a simple non-time-varying 
     Bennett correction and 0 for no correction.
 
     From version 1.8.4 we begin to implement more refraction models.  Model 1 (Bennett) will continue to be 
-    the default.  The model number is written (as an integer) to the LSP results file so that people can keep track easily of whether
-    they are inadvertently mixing files with different strategies. And that is why it is an integer, because
-    all results in the LSP results files are numbers.  Going forward, we are adding a time-varying capability.
+    the default.  The model number is written (as an integer) to the LSP results file so that people can 
+    keep track easily of whether they are inadvertently mixing files with different strategies. And that 
+    is why it is an integer, because all results in the LSP results files are numbers.  Going forward, 
+    we are adding a time-varying capability.
 
         Model 1: Bennett, non-time-varying
 
@@ -132,7 +134,8 @@ def make_gnssir_input(station: str, lat: float=0, lon: float=0, height: float=0,
 
     gnssir_input p041 -lat 39.9494 -lon -105.19426 -height 1728.85  -l2c T -e1 5 -e2 15
         uses only L2C GPS data between elevation angles of 5 and 15 degrees.
-        user input lat/long/height
+        user input lat/long/height. The lat/long/height can also be entered into a local
+        coordinate file.  See documentation in the file formats section.
 
     gnssir_input p041  -h1 0.5 -h2 10 -e1 5 -e2 25
         uses UNR database, only GPS data between elevation angles of 5-25 degrees and reflector heights of 0.5-10 meters

gnssrefl/nmea2snr_cl.py

@@ -79,6 +79,10 @@ def nmea2snr( station: str, year: int, doy: int, snr: int = 66, year_end: int=No
     As for March 16, 2024, this code has been changed to use gnssrefl standards for inputs and outputs.
     The code, in principle, now looks for final, rapid, and ultra rapid orbits from GFZ, in that order.
 
+    As of version 3.6.4 you no longer have to enter station coordinates on the command line. 
+    You just need to follow the instructions in the file formats documentation to set up a list of the locations of 
+    your local stations. 
+
     Parameters
     ----------
     station : str

gnssrefl/refl_zones_cl.py

@@ -37,8 +37,10 @@ def reflzones(station: str, azim1: int=0, azim2: int=360, lat: float=None, lon:
     This module creates “stand-alone” Fresnel Zones maps for google Earth. At a minimum 
     it requires a four station character name as input. The output is a KML file.
 
-    If the station is in the UNR database, those latitude, longitude, and ellipsoidal 
-    height values are used. You may override those values with the optional inputs.
+    If the station is in either your local coordinate file or in the UNR database that comes with gnssrefl, 
+    those latitude, longitude, and ellipsoidal height values are used. For information on the local
+    coordinate file see the file formats section of the documentation.
+    You may override those stored values with the optional lat lon height inputs.
 
     The output file will be stored in REFL_CODE/Files/kml unless you specify an output name. In that case
     it will go into your working directory