use case updates

docs/use_cases/use_mchl.md

@@ -21,7 +21,7 @@
 <img src=../_static/MCHL.jpeg width=500>
 </p>
 
-**Archives:** CDDIS, BKG, GA
+**Archives:** CDDIS, BKG-IGS, GA
 
 Read the instructions for the [soil moisture code!](../pages/README_vwc.md)!
 

docs/use_cases/use_nwot.md

@@ -10,7 +10,8 @@ like to try to do so, that would be great. Please submit a PR.
 
 <HR>
 
-**Status:** this site is no longer supported and the equipment was removed.
+**Status:** The equipment has been installed and removed multiple times. As of spring 2020,
+it is no longer available.
 
 **Station name:** nwot
 
@@ -32,27 +33,26 @@ like to try to do so, that would be great. Please submit a PR.
 
 Station nwot was originally installed/designed by Jim Normandeau (UNAVCO) to support GPS reflections research 
 by Kristine Larson, Eric Small, Ethan Gutmann, Felipe Nievinski, and Mark Williams at the University of Colorado. 
-The site was hosted by the Niwot Ridge LTER. 
 
 nwot was deliberately made to be taller than the typical geodetic antenna so that it would never be 
-buried by snow. It is approximately 3 meters above 
-the bare soil surface.  Because it was installed to support testing GPS reflections, nwot has always tracked L2C.
+buried by snow. It is approximately 3 meters above the bare soil surface. Because it was 
+installed to support testing GPS reflections, nwot has always tracked L2C.
 nwot was also part of [PBO H2O](http://cires1.colorado.edu/portal/?station=nwot).
 
 <img src="https://www.unavco.org/data/gps-gnss/lib/images/station_images/NWOT.jpg" width=500>
 
-The site has generally not been used by geodesists and there is very little useful information 
+The site has not generally been used by geodesists and there is very little useful information 
 about when data are available at either UNAVCO or Nevada Reno (i.e. no time series).
 After the original receiver failed in spring 2015, a new receiver was installed in late 2016 by 
-Mark Raleigh (then at CIRES, now at the University Oregon). The receiver stopped transmitting 
+Mark Raleigh (then at CIRES, now at the University of Oregon). The receiver stopped transmitting 
 in 2020 and was removed in 2022. We will focus on the data between 2009-2015.
 
 ### Make a SNR File and run quickLook
 
 We will start by making a single SNR file. Here there are two options. The main 
 archive for this dataset only provides the high-quality
-L2C data in the highrate (1-sec) area. We do not need this sample rate for GPS reflectometry,
-so to speed things up, we strongly encourage you to use the "special" archive option.  Here
+L2C data in the highrate (1-sec) area. We do not need this sample rate for a GPS site that is 
+three meters tall. To speed things up, we strongly encourage you to use the "special" archive option.  Here
 the 1-sec data have been decimated to 15 seconds:
 
 <code>rinex2snr nwot 2014 270 -archive special</code>
@@ -61,7 +61,7 @@ If for any reason this command does not work, please use the direct command:
 
 <code>rinex2snr nwot 2014 270 -archive unavco -rate high -dec 15</code>
 
-Both L1 and L2C signals can be used at this site, though the L2C data are far superior in quality
+Both L1 and L2C signals can be used at this site, though the L2C data are **far superior** in quality
 to the L1 data. Use this **quickLook** command to get a sense of the quality of the 
 reflector height (RH) retrievals. First L1:
 

docs/use_cases/use_p041.md

@@ -1,5 +1,9 @@
 # Marshall, Colorado, USA
 
+This use case needs to be updated to include the use of the 
+[snowdepth](https://gnssrefl.readthedocs.io/en/latest/api/gnssrefl.snowdepth_cl.html) module.
+Please improve this use case by making a pull request with the relevant software calls.
+
 ## metadata
 
 [Warning](warning.md)
@@ -38,28 +42,16 @@ check the [Reflection Zone Mapping in the web app](https://gnss-reflections.org/
 In the linked page, the reflection zones from 5 to 25 degree elevation angles are plotted as 
 colored ellipses surrounding the station.  
 
-## Reproduce the Web App 
-
-p041 is one of the example cases for the [GNSS-IR webapp.](https://gnss-reflections.org/api?example=p041) 
-You can see from the title of the plot that the web app reproduces 
-results for the year 2019, day of year 150, and L1 frequency. You can make something that looks similar
-to this using these commands:
-
-<code>rinex2snr p041 2019 150</code>
-
-and
-
-<code>quickLook p041 2019 150</code>
-
 
 ## Take a Quick Look at the Data
 
-First make a SNR file:
+Translate a RINEX file:
 
 <code>rinex2snr p041 2020 132</code>
 
 
-Then use **quickLook** to analyze the reflection characteristics of the site [(For details on quickLook output)](../pages/quickLook.md).
+Then use **quickLook** to analyze the reflection characteristics of 
+the site [(For details on quickLook output)](../pages/quickLook.md).
 
 The default return is for the L1 frequency:
 
@@ -72,24 +64,24 @@ azimuth (x-axis) and QC metrics:
 
 <img src="../_static/new-qc-p041-l1.png" width="600">
 
-Now try looking at the periodogram for L2C:
+Now try looking at the periodogram for L2C by specifying frequency 20:
 
 <code>quickLook p041 2020 132 -fr 20</code>
 
 <img src="../_static/p041-l2c.x.png" width="600">
 <P>
 <img src="../_static/new-qc-p041-l2c.png" width="600">
 
-Note that there are more colors in the L1 plots than in the L2C plots. That is the result of 
-the fact that there are more L1 satellites than L2C satellites.
+Note that there are more colors in the L1 plots than in the L2C plots. That is 
+the result of there being more L1 transmitting satellite than L2C transmitting satellites.
 
 Now try L5:
 
 <CODE>quickLook p041 2020 132 -fr 5</code>
 
 <img src="../_static/p041-l5.png" width="600">
 
-The L5 signal has only been available on satellites launched after 2010, so there are 
+The L5 signal has only been available on satellites launched after 2010, so there are even 
 fewer satellite tracks than either L1 or L2C.
 
 The **quickLook** code has multiple options. For example, it is possible change the reflector height range:
@@ -101,10 +93,13 @@ If you have already made a file using only the GPS data, you will need the overw
 
 <code>rinex2snr p041 2020 132 -orb gnss -overwrite True</code>
 
-Beidou signals are tracked at this site, but unfortunately the data are not available in the RINEX 2.11 file.
-They are very likely available in the RINEX 3 file, so you are encouraged to look there.
+Beidou signals are tracked at this site, but unfortunately the data 
+are not available in the RINEX 2.11 file. They are very likely available in the 
+RINEX 3 file, so you are encouraged to look there. Contact Earthscope if you have 
+any trouble accessing data for this site.
 
-**quickLook** is meant to be a visual assessment of the spectral characteristics at a given site on a given day. For routine analysis, one must use **gnssir**.
+**quickLook** is meant to be a visual assessment of the 
+spectral characteristics at a given site on a given day. For routine analysis, one must use **gnssir**.
 
 ## Analyze the Data
 

docs/use_cases/warning.md

@@ -1,6 +1,6 @@
 # Warning
 
-We have updated our arc selection algoirthm. Most of hte uses cases were computed with our old algorithm.
+We have updated our arc selection algoirthm. Most of the uses cases were computed with our old algorithm.
 We have edited the prose in most use cases, but have not remade the figures.
 
 [Earthscope](https://www.earthscope.org) (previously UNAVCO) now requires that you have a formal account

gnssrefl/gnssir_input.py

@@ -124,68 +124,92 @@ def make_gnssir_input(station: str, lat: float=0, lon: float=0, height: float=0,
     ----------
     station : str
         4 character station ID.
+
     lat : float, optional
         latitude in degrees.
+
     lon : float, optional
         longitude in degrees.
+
     height : float, optional
         ellipsoidal height in meters.
+
     e1 : float, optional
         elevation angle lower limit in degrees. default is 5.
+
     e2 : float, optional
         elevation angle upper limit in degrees. default is 25.
+
     h1 : float, optional
         reflector height lower limit in meters. default is 0.5.
+
     h2 : float, optional
         reflector height upper limit in meters. default is 8.
+
     nr1 : float, optional
         noise region lower limit for QC in meters. default is None.
+
     nr2 : float, optional
         noise region upper limit for QC in meters. default is None.
+
     peak2noise : float, optional
         peak to noise ratio used for QC.
         default is 2.7 (just a starting point for water - should be 3 or 3.5 for snow or soil...)
+
     ampl : float, optional
         spectral peak amplitude for QC. default is 6.0
         this is receiver and elevation angle region dependent - so you need to change it based on your site 
+
     allfreq : bool, optional
         True requests all GNSS frequencies.
         default is False (defaults to use GPS frequencies).
+
     l1 : bool, optional
         set to True to use only GPS L1 frequency. default is False.
+
     l2c : bool, optional
         set to use only GPS L2C frequency. default is False.
+
     xyz : bool, optional
         set to True if using Cartesian coordinates instead of Lat/Long/Ht.
         default is False.
+
     refraction : bool, optional
         set to False to turn off refraction correction.
         default is True.
+
     extension : str, optional
         provide extension name so you can try different strategies. 
         Results will then go into $REFL_CODE/YYYY/results/ssss/extension
         Default is '' 
+
     ediff : float, optional
         quality control parameter (Degrees)
         Allowed min/max elevation angle diff from requested min/max elev angle
         default is 2
+
     delTmax : float, optional
         maximum allowed arc length (minutes)
         default is 75, which can be a bit long for tides
+
     frlist : list of integers
         avoids all the booleans - if you know the frequencies, enter them.
         e.g. 1 2 or 1 20 5 or 1 20 101 102
+
     azlist2 : list of floats
         Default is 0 to 360. list of azimuth limits as subquadrants are no longer required.
+
     ellist: list of floats
         min and max elevation angles to be used with the azimuth regions you listed, i.e.
         [5 10 6 11 7 12 8 13] would allow overlapping regions - all five degrees long 
         Default is empty list. 
+
     refr_model : int
         refraction model. we are keeping this as integer as it is written to a file withonly
         numbers in it.  1 is the default simple refraction (just correct elevation angles
         using standard bending models).  0 is no refraction correction.  As we add more
         models, they will receiver their own number. 
+
     Hortho : float
         station orthometric height, in meters. Currently only used in subdaily.  If not provided on the command line, 
         it will use ellipsoidal height and EGM96 to compute.