gnssrefl.phase_functions module

gnssrefl.phase_functions.apriori_file_exist(station, fr)

reads in the a priori RH results

  • station (string) – station name

  • fr (integer) – frequency

Return type:

boolean as to whether the apriori file exists

gnssrefl.phase_functions.convert_phase(station, year, year_end=None, plt2screen=True, fr=20, tmin=0.05, tmax=0.5, polyorder=-99, circles=False, subdir='', hires_figs=False)

Convert GPS phase to VWC. Using Clara Chew’s algorithm from Matlab write_vegcorrect_smc.m

  • station (str) – 4 char station name

  • year (int) – beginning year

  • year_end (int) – last year

  • plt2screen (boolean) – plots come to the screen

  • fr (integer) – frequency default is L2C (20)

  • tmin (float) – soil texture minimum

  • tmax (float) – soil texture maximum

  • polyorder (integer) – override on the polynomial order used in leveling

  • circles (boolean) – final plot using circles (instead of line)

  • subdir (str) – subdirectory for $REFL_CODE/Files

  • hires_figs (bool) – whether you want eps instead of png files created

gnssrefl.phase_functions.daily_phase_plot(station, fr, datetime_dates, tv, xdir, subdir, hires_figs)

makes a plot of daily averaged phase for vwc code

  • station (str) – 4 char station name

  • fr (int) – frequency of signal

  • datetime_dates – datetime values for phase points

  • tv (list of results) – cannot remember the format

  • xdir (str) – location of the results (environment variable REFL_CODE)

  • subdir (str) – subdirectory in Files

  • hires_figs (bool) – whether you want eps instead of png files

gnssrefl.phase_functions.help_debug(rt, xdir, station)

Takes the input of phase files, read by other functions, and writes out a file to help with debugging (comparion of matlab and python codes)

rtnumpy array of floats

contents of the phase files stored in a numpy array


where the otuput should be written


name of the station

gnssrefl.phase_functions.kinda_qc(satellite, rhtrack, meanaztrack, nvalstrack, amin, amax, y, t, new_phase, avg_date, avg_phase, warning_value, ftmp, remove_bad_tracks, k4, avg_exist)
  • satellite (int) – satellite number

  • rhtrack (float) – a priori reflector height

  • meanaztrack (float) – I think it is the azimuth of the track, degrees

  • nvalstrack (int) – not sure?

  • amin (int) – min az of this quadrant

  • amax (int) – max az of this quadrant

  • y (numpy array of ints) – year

  • t (numpy array of ints) – day of year

  • new_phase (numpy array of floats) – phase values for a given satellite track ??

  • avg_date (numpy array of floats) – y + doy/365.25 I think

  • avg_phase (numpy array of floats) – average phase, in degrees

  • warning_value (float) – phase noise value

  • ftmp (file ID) – for writing

  • remove_bad_tracks (bool) – whether you write out new tracks with bad ones removed

  • k4 (int) – number of tracks?

  • avg_exist (bool) – whether you have previous solution to compare to

gnssrefl.phase_functions.load_avg_phase(station, fr)

loads a previously computed daily average phase solution. this is NOT the same as the multi-track phase results. This file is now stored in station subdirectory in $REFL_CODE/Files/

  • station (str) – 4 character station ID, lowercase

  • fr (int) – frequency


  • avg_exist (bool) – whether the necessary file exists

  • avg_date (list of floats) – fractional year, i.e. year + doy/365.25

  • avg_phase (list of floats) – average phase for a given day

gnssrefl.phase_functions.load_phase_filter_out_snow(station, year1, year2, fr, snowmask)

Load all phase data and attempt to remove outliers from snow if snowmask provided.

  • station (str) – four character station name

  • year1 (int) – starting year

  • year2 (int) – ending year

  • fr (int) – frequency, i.e. 1 or 20

  • snowmask (str) – name/location of the snow mask file None if this value is not going to be used


  • dataexist (bool) – whether phase data were found

  • year (numpy array of int) – calendar years

  • doy (numpy array of int) – day of year

  • hr (numpy array of floats) – UTC hour of measurement

  • ph (numpy array of floats) – LS phase estimates

  • azdata (numpy array of floats) – average azimuth, degrees

  • ssat (numpy array of int) – satellite number

  • rh (numpy array of floats) – reflector height, meters

  • amp_lsp (numpy array of floats) – lomb scargle periodogram amplitude

  • amp_ls (numpy array of floats) – least squares amplitude

  • ap_rh (numpy array of floats) – apriori rh

  • results_trans (numpy array) – all phase results concatenated into numpy array plus column for quadrant and unwrapped phase

gnssrefl.phase_functions.load_sat_phase(station, year, year_end, freq)

Picks up the phase estimates from local (REFL_CODE) results section and returns most of the information from those files

  • station (str) – four character station name

  • year (integer) – beginning year

  • year_end (integer) – ending year

  • freq (integer) – GPS frequency (1,20 allowed)


  • dataexist (bool) – whether data found?

  • results (numpy array of floats) – basically one variable with everything in the original columns from the daily phase files

gnssrefl.phase_functions.low_pct(amp, basepercent)

emulated amp_normK code from PBO H2O inputs are the amplitudes and a percentage used to define the bottom level. returns normalized amplitudes

this is meant to be used by individual tracks (I think) in this case they are the top values, not the bottom … ugh

gnssrefl.phase_functions.make_snow_filter(station, medfilter, ReqTracks, year1, year2)

Runs daily_avg code to make a snow mask file. This is so you have some idea of when the soil moisture products are contaminated by snow. Make a file with these years and doys saved. The user can edit if they feel the suggestsions are poor (i.e. days in the summer might show up as “snow”)

If snow mask file exists, it does not overwrite it.

  • station (str) – 4 ch station name

  • medfilter (float) – how much you allow the individual tracks to deviate from the daily median (meters)

  • ReqTracks (int) – number of tracks to compute trustworthy daily average

  • year1 (int) – starting year

  • year2 (int) – ending year


  • snowmask_exists (bool) – whether file was created

  • snow_file (str) – name of the snow mask file

  • Creates output file into a file $REFL_CODE/Files/{ssss}/snowmask_{ssss}.txt

  • where ssss is the station name

gnssrefl.phase_functions.normAmp(amp, basepercent)

emulated amp_normK code from PBO H2O inputs are the amplitudes and a percentage used to define the bottom level. returns normalized amplitudes this is meant to be used by individual tracks (I think) in this case they are the top values, not the bottom … ugh


calculates oldstyle quadrants from PBO H2O

  • azim (float) – azimuth, dgrees

  • q (int) – old quadrant system used in pboh2o

gnssrefl.phase_functions.phase_tracks(station, year, doy, snr_type, fr_list, e1, e2, pele, plot, screenstats, compute_lsp, gzip)

This does the main work of estimating phase and other parameters from the SNR files it uses tracks that were predefined by the code

  • name (station) – 4 char id, lowercase

  • year (int) – calendar year

  • doy (int) – day of year

  • snr_type (int) – SNR file extension (i.e. 99, 66 etc)

  • fr_list (list of integers) – frequency, [1], [20] or [1,20]

  • e1 (float) – min elevation angle (degrees)

  • e2 (float) – max elevation angle (degrees)

  • pele (list of floats) – elevation angle limits for the polynomial removal. units: degrees

  • screenstats (bool) – whether statistics are printed to the screen

  • compute_lsp (bool) – this is always true for now

  • gzip (bool) – whether you want SNR files gzipped after running the code

  • track. (Only GPS frequencies are allowed because this relies on the repeating ground) –

gnssrefl.phase_functions.read_apriori_rh(station, fr)

read the track dependent a priori reflector heights needed for phase & thus soil moisture.

  • station (str) – four character ID, lowercase

  • fr (int) – frequency (e.g. 1,20)


results – column 1 is just a number (1,2,3,4, etc)

column 2 is RH in meters

column 3 is satellite number

column 4 is azimuth of the track (degrees)

column 5 is number of values used in average

column 6 is minimum azimuth degrees for the quadrant

column 7 is maximum azimuth degrees for the quadrant

Return type:

numpy array

gnssrefl.phase_functions.rename_vals(year_sat_phase, doy, hr, phase, azdata, ssat, amp_lsp, amp_ls, rh, ap_rh, ii)

this is just trying to clean up send indices ii - and return renamed variables.

  • year_sat_sat

  • doy

  • hr

  • phase

  • azdata

  • ssat

  • amp_lsp

  • amp_ls

  • rh

  • ap_rh

  • ii


  • y (numpy array of int) – year

  • t (numpy array of int) – day of year

  • h (numpy array of floats) – hour of the day (UTC)

  • x (numpy array of floats) – phase, degrees

  • azd (numpy array of floats) – azimuth for the track

  • s (numpy array of int)

  • amps_lsp (numpy array of floats) – LSP amplitude

  • amps_ls (numpy array of floats) – least squares amplitude

  • rhs (numpy array of floats) – estimated RH (m)

  • ap_rhs (numpy array of floats) – a priori RH (m)

gnssrefl.phase_functions.save_vwc_plot(fig, pngfile)
  • fig (matplotlib figure) – the figure definition you define when you open a figure

  • pngfile (str) – name of the png file to be saved

gnssrefl.phase_functions.set_parameters(station, minvalperday, tmin, tmax, min_req_pts_track, fr, year, year_end, subdir, plt, auto_removal, warning_value)

station (str) – 4 character station name


  • minvalperday (int) – number of phase values required each day

  • tmin (float) – min soil texture

  • tmax (float) – max soil texture

  • min_req_pts_track (int) – minimum number of phase values per year per track

  • freq (int) – frequency to use (1,20 allowed)

  • year_end (int) – last year to analyze

  • subdir (str) – name for subdirectory used in subdirectory of REFL_CODE/Files

  • plt (bool) – whether you want plots to come to the screen

  • auto_removal (bool) – whther tracks should be removed when they fail QC

  • warning_value (float) – phase RMS needed to trigger warning

  • plot_legend (bool) – whether to plot PRN numbers on the phase & amplitude results

gnssrefl.phase_functions.test_func(x, a, b, rh_apriori)

This is least squares for estimating a sine wave given a fixed frequency, freqLS

gnssrefl.phase_functions.test_func_new(x, a, b, rh_apriori, freq)

This is least squares for estimating a sine wave given a fixed frequency, freqLS now freq is input so it is not hardwired for L2

  • x (numpy array of floats) – sine(elevation angle) I think

  • a (float) – amplitude - estimated

  • b (float) – phase - estimated

  • rh_apriori (float) – reflector height (m)

  • freq (int) – frequency

gnssrefl.phase_functions.vwc_plot(station, t_datetime, vwcdata, plot_path, circles)

makes a plot of volumetric water content

  • station (string) – 4 ch station name

  • t_datetime (datetime) – observation times for measurements

  • vwcdata (numpy array of floats (I think)) – volumetric water content

  • plot_path (Saves a plot to) – full name of the plot file

  • circles (boolean) – circles in the plot. default is a line (really .-)

  • plot_path

gnssrefl.phase_functions.write_all_phase(v, fname)

writes out preliminary phase values and other metrics for advanced vegetation option. This is in the hope that it can be used in clara chew’s dissertation algorithm.

File is written to $REFL_CODE/Files/station/station_all_phase.txt I think

  • v (numpy of floats as defined in vwc_cl) – TBD year, doy, phase, azimuth, satellite number estimated RH, LSP amplitude, LS amplitude, UTC hours raw LSP amp, raw LS amp

  • fname (str) – name of the output file

  • filestatus (int) – 1, open the file 2, write to file (well, really any value)

  • rhtrack (float) – apriori reflector height for the given track, meters



Return type:


gnssrefl.phase_functions.write_avg_phase(station, phase, fr, year, year_end, minvalperday, vxyz, subdir)

creates output file for average phase results

  • station (string) –

  • phase (numpy list (float)) – phase values

  • fr (int) – frequency

  • year (int) – first year evaluated

  • year_end (int) – last year evaluated

  • minvalperday (int) – required number of satellite tracks to trust the daily average

  • compilation (vxyz is from some other) –

  • subdir (str) – subdirectory for results


tv – year doy - day of year meanph - mean phase value in degrees nvals - number of values that went into the average

Return type:

numpy array with elements

gnssrefl.phase_functions.write_out_raw_phase(v, fname)

write daily phase values used in vwc to a new consolidated file I added columns for quadrant and unwrapped phase

  • v (numpy array) – phase results read for multiple years. could be with snow filter applied

  • fname (str) – filename for output


newv – original variable v with columns added for quadrant (1-4) and unwrapped phase

Return type:

numpy array

gnssrefl.phase_functions.write_phase_for_advanced(filename, vxyz)

Writes out a file of interim phase results for advanced models developed by Clara Chew

File generally written to $REFL_CODE/Files/<station>/all_phase.txt

  • filename (str) – name for output file

  • vxyz (numpy array of floats) – as defined in