new version 3.4.0

CHANGELOG.md

@@ -3,6 +3,18 @@
 All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## 3.4.0
+fixed pretty major problem with default (rapid) orbits.  updated to new file names and 
+locations for GFZ analysis center.  I do not know when the old naming conventions will fail for ultra.
+
+also added Wuhan ultra rapid orbit downloads from Wuhan to download_orbits.
+It was previously added to rinex2snr 
+
+Changed spline output file in subdaily so that you can print out 999 at the gap values
+(times during large gaps were previously not written out at all).  per request, I also
+told people the time tags are in UTC in the file header. this is currently on the command line
+as gap_flag = T for putting in the gap flag.
+
 ## 3.3.1
 rinex2snr: Added BKG access to high-rate files that are more than 6 months old.
 This will allow parallel processing, though CDDIS does not (this is a restriction

README.md

@@ -1,4 +1,4 @@
-# gnssrefl v3.3.1 
+# gnssrefl v3.4.0 
 
 If you use this code in any presentation or publication, you are expected to cite either 
 this github repository or the gnssrefl DOI, which is given just below.

gnssrefl/sd_libs.py

@@ -939,7 +939,7 @@ def subdaily_resids_last_stage(station, year, th, biasCor_rh, spline_at_GPS, fs,
 
     return badpoints2
 
-def RH_ortho_plot2( station, H0, year,  txtdir, fs, time_rh, rh, gap_min_val,th,spline,delta_out,csvfile):
+def RH_ortho_plot2( station, H0, year,  txtdir, fs, time_rh, rh, gap_min_val,th,spline,delta_out,csvfile,gap_flag):
     """
 
     Makes a plot of the final spline fit to the data. Output time interval controlled by the user.
@@ -972,6 +972,8 @@ def RH_ortho_plot2( station, H0, year,  txtdir, fs, time_rh, rh, gap_min_val,th,
         how often spline is printed, in seconds
     csvfile : bool
         print out csv instead of plain txt
+    gap_flag : bool
+        whether to write 999 in file where there are gaps
     """
 
     firstpoint = float(th[0]); lastpoint = float(th[-1])
@@ -1014,6 +1016,7 @@ def RH_ortho_plot2( station, H0, year,  txtdir, fs, time_rh, rh, gap_min_val,th,
     fout = open(splinefileout,'w+')
     vn = station + ' gnssrefl v' + str(g.version('gnssrefl'))
     fout.write('{0:1s}  {1:30s}  \n'.format('%','station ' + vn))
+    fout.write('{0:1s}  {1:60s}  \n'.format('%','TIME TAGS ARE IN UTC/999 values mean there was a large gap and no spline value is available.'))
     fout.write('{0:1s}  {1:30s}  \n'.format('%','This is NOT observational data - be careful when interpreting it.'))
     fout.write('{0:1s}  {1:30s}  \n'.format('%','If the data are not well represented by the spline functions, you will '))
     fout.write('{0:1s}  {1:30s}  \n'.format('%','have a very poor representation of the data. I am also writing out station '))
@@ -1078,6 +1081,13 @@ def RH_ortho_plot2( station, H0, year,  txtdir, fs, time_rh, rh, gap_min_val,th,
                     fout.write('{0:15.7f}, {1:10.3f},{2:4.0f},{3:3.0f},{4:3.0f},{5:3.0f},{6:3.0f},{7:3.0f},{8:10.3f} \n'.format( mjd_new[i], rhout, theyear[i], xm[i], xd[i], xh[i], xmin[i], xs[i], H0-rhout))
                 else:
                     fout.write('{0:15.7f}  {1:10.3f} {2:4.0f} {3:3.0f} {4:3.0f} {5:3.0f} {6:3.0f} {7:3.0f} {8:10.3f} \n'.format(mjd_new[i], rhout, theyear[i], xm[i], xd[i], xh[i], xmin[i], xs[i], H0-rhout))
+            else:
+                if gap_flag: 
+                    rhout = spline_new[i]
+                    if csvfile:
+                        fout.write('{0:15.7f}, {1:10.3f},{2:4.0f},{3:3.0f},{4:3.0f},{5:3.0f},{6:3.0f},{7:3.0f},{8:10.3f} \n'.format( mjd_new[i], 999, theyear[i], xm[i], xd[i], xh[i], xmin[i], xs[i], 999))
+                    else:
+                        fout.write('{0:15.7f}  {1:10.3f} {2:4.0f} {3:3.0f} {4:3.0f} {5:3.0f} {6:3.0f} {7:3.0f} {8:10.3f} \n'.format(mjd_new[i], 999, theyear[i], xm[i], xd[i], xh[i], xmin[i], xs[i], 999))
 
 
     fout.close()

gnssrefl/subdaily.py

@@ -780,6 +780,8 @@ def rhdot_correction2(station,fname,fname_new,pltit,outlierV,outlierV2,**kwargs)
         a secondary knot value if you want the final output 
         to use a different one than the one used for outliers and 
         RH dot
+    gap_flag : bool, option
+        whether gaps are written as 999 in final output
 
 
     """
@@ -792,6 +794,9 @@ def rhdot_correction2(station,fname,fname_new,pltit,outlierV,outlierV2,**kwargs)
 
     val = kwargs.get('txtdir',[])
 
+    gap_flag = kwargs.get('gap_flag',False)
+    print('gap flag ', gap_flag)
+
     if len(val) == 0:
         txtdir = xdir + '/Files/'
     else:
@@ -971,7 +976,6 @@ def rhdot_correction2(station,fname,fname_new,pltit,outlierV,outlierV2,**kwargs)
     th_obs = sd.mjd_to_obstimes(mjd0 + th-th[0])
 
     if multiyear :
-        print('exiting')
         th_obs = sd.mjd_to_obstimes(th)
 
     fig=plt.figure(figsize=(10,6))
@@ -1182,7 +1186,7 @@ def rhdot_correction2(station,fname,fname_new,pltit,outlierV,outlierV2,**kwargs)
     # pick up the orthometric height from the gnssir_analysis json
     H0 = sd.find_ortho_height(station,extension)
     # this writes out spline file and makes plot .... 
-    sd.RH_ortho_plot2( station, H0, year, txtdir, fs, th[jj],biasCor_rh[jj],gap_min_val,th,spline,delta_out,writecsv)
+    sd.RH_ortho_plot2( station, H0, year, txtdir, fs, th[jj],biasCor_rh[jj],gap_min_val,th,spline,delta_out,writecsv,gap_flag)
     print('\nRMS with frequency biases and RHdot taken out (m) ', np.round(newsigma,3) , '\n' )
 
 

gnssrefl/subdaily_cl.py

@@ -48,11 +48,12 @@ def parse_arguments():
     parser.add_argument("-alt_sigma", default=None, type=str, help="boolean test for alternate Nievinski sigma definition. default is False")
     parser.add_argument("-gap_min_val", default=None, type=float, help="min gap (hours) allowed in splinefit output file. default is 6 hours")
     parser.add_argument("-knots2", default=None, type=int, help="Secondary knots value for final fit. default is to use original knots value.")
+    parser.add_argument("-gap_flag", default=None, type=str, help="if set to True/T, write 999 to spline fit for gaps")
 
     args = parser.parse_args().__dict__
 
     # convert all expected boolean inputs from strings to booleans
-    boolean_args = ['csv', 'plt', 'rhdot', 'testing','kplt','if_corr','hires_figs','apply_rhdot','alt_sigma']
+    boolean_args = ['csv', 'plt', 'rhdot', 'testing','kplt','if_corr','hires_figs','apply_rhdot','alt_sigma','gap_flag']
     args = str2bool(args, boolean_args)
 
     # only return a dictionary of arguments that were added from the user - all other defaults will be set in code below
@@ -66,7 +67,7 @@ def subdaily(station: str, year: int, txtfile_part1: str = '', txtfile_part2: st
         azim1: int=0, azim2: int = 360, peak2noise: float = 0, kplt: bool = False, 
         subdir: str = None, delta_out : int = None , if_corr: bool = True, knots_test: int = 0, 
              hires_figs : bool=False, apply_rhdot : bool=True, fs: int = 10, alt_sigma: bool= False, gap_min_val: float=6.0,
-             year_end: int=None, knots2 : int=None):
+             year_end: int=None, knots2 : int=None, gap_flag: bool = False):
     """
     Subdaily combines gnssir solutions and applies relevant corrections needed to measure water levels (tides). 
     As of January 2024, it will allow multiple years. You can also specify which day of year to start with, i.e.
@@ -211,6 +212,8 @@ def subdaily(station: str, year: int, txtfile_part1: str = '', txtfile_part2: st
         last year of analysis period.  
     knots2 : int, optional
         testing out allowing different knots for last spline
+    gap_flag : bool
+        whether you want gaps filled with 999 values in the final spline file 
     """
 
     print('<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
@@ -378,7 +381,7 @@ def subdaily(station: str, year: int, txtfile_part1: str = '', txtfile_part2: st
                                       if_corr=if_corr,knots_test=knots_test,
                                       hires_figs=hires_figs, apply_rhdot=apply_rhdot,fs=fs,
                                       gap_min_val=gap_min_val,year=year, extension=extension, 
-                                      knots2=knots2,csv=csv )
+                                      knots2=knots2,csv=csv,gap_flag=gap_flag)
        if plt:
            mplt.show()
 

setup.py

@@ -42,7 +42,7 @@
 ]
 setup(
     name="gnssrefl",
-    version="3.3.1",
+    version="3.4.0",
     author="Kristine Larson",
     author_email="[email protected]",
     description="A GNSS reflectometry software package ",