shipgrav 1.0.5__tar.gz → 1.0.7__tar.gz

{shipgrav-1.0.5 → shipgrav-1.0.7}/CHANGELOG

@@ -1,3 +1,18 @@
+v1.0.7
+
+2025-06-20  Hannah F Mark  <hmark@whoi.edu>
+    * add nav interpolation to the TN400 cross-coupling example script; fixes dropout section
+    * related: update documentation with new figure
+
+2024-12-25  Hannah F Mark  <hmark@whoi.edu>
+    * add option to decimate nav data, per file as it is being read
+
+v1.0.6
+
+2024-11-21  Hannah F Mark  <hmark@whoi.edu>
+
+    * another minor version bump after linking zenodo so release can get a DOI
+
 v1.0.5
 
 2024-11-20  Hannah F Mark  <hmark@whoi.edu>

{shipgrav-1.0.5 → shipgrav-1.0.7}/PKG-INFO

@@ -1,9 +1,10 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: shipgrav
-Version: 1.0.5
+Version: 1.0.7
 Summary: Functions for marine gravity data processing and reduction
 Author-email: "Hannah F. Mark" <hmark@whoi.edu>
 Maintainer-email: "Hannah F. Mark" <hmark@whoi.edu>
+License-File: LICENSE
 Keywords: UNOLS,gravimetry,marine gravity
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent

{shipgrav-1.0.5 → shipgrav-1.0.7}/example-scripts/dgs_ccp_calc.py

@@ -27,6 +27,7 @@ import shipgrav.grav as sgg
 import shipgrav.io as sgi
 import shipgrav.nav as sgn
 import tomli as tm
+from scipy.interpolate import interp1d
 from scipy.signal import filtfilt, firwin
 
 # %%
@@ -49,6 +50,24 @@ dgs_files = pooch.retrieve(url="https://zenodo.org/records/12733929/files/data.z
             members=['data/Thompson/TN400/gravimeter/DGS/AT1M-Grav-PROC_20220314-000001.Raw',
                     'data/Thompson/TN400/gravimeter/DGS/AT1M-Grav-PROC_20220313-000001.Raw']))
 
+nav_files = pooch.retrieve(url="https://service.rvdata.us/data/cruise/TN400/fileset/151457",
+        known_hash="76e66365c41d393510bb7ab9637305296282e9041415c1343faa171af28abf85",progressbar=True,
+        processor=pooch.Untar(
+            members=['TN400/151457/data/POSMV-V5-INGGA-RAW_20220313-000001.Raw',
+                    'TN400/151457/data/POSMV-V5-INGGA-RAW_20220314-000001.Raw']))
+
+# %%
+# read and sort the nav data
+gps_nav = sgi.read_nav(ship, nav_files)
+gps_nav.sort_values('time_sec', inplace=True)
+gps_nav.reset_index(inplace=True, drop=True)
+
+# %%
+# we happen to know that there are some weird nav dropouts in this dataset
+# so clean them up here
+bad_inds = np.where(np.diff(gps_nav['lon']) > 1)[0]
+gps_nav.drop(bad_inds, axis=0, inplace=True)
+
 # %%
 # read and sort the gravimeter data
 dgs_data = sgi.read_dgs_laptop(dgs_files, ship)
@@ -59,18 +78,25 @@ dgs_data['tsec'] = [e.timestamp()
 dgs_data['grav'] = dgs_data['rgrav'] + bias_dgs
 
 # %%
-# trim some bits that we happen to know are bad
-dgs_data = dgs_data.iloc[1000:]
+# sync data geographic coordinates to nav by interpolating with timestamps
+# (interpolators use posix timestamps, not datetimes)
+gps_lon_int = interp1d(gps_nav['time_sec'].values, gps_nav['lon'].values,
+                       kind='linear', fill_value='extrapolate')
+gps_lat_int = interp1d(gps_nav['time_sec'].values, gps_nav['lat'].values,
+                       kind='linear', fill_value='extrapolate')
+dgs_data['lon_new'] = gps_lon_int(dgs_data['tsec'].values)
+dgs_data['lat_new'] = gps_lat_int(dgs_data['tsec'].values)
+
 
 # %%
 # calculate corrections for FAA
 ellipsoid_ht = np.zeros(len(dgs_data))  # we are working at sea level
-lat_corr = sgg.wgs_grav(dgs_data['lat']) + \
-    sgg.free_air_second_order(dgs_data['lat'], ellipsoid_ht)
-eotvos_corr = sgg.eotvos_full(dgs_data['lon'].values, dgs_data['lat'].values,
+lat_corr = sgg.wgs_grav(dgs_data['lat_new']) + \
+    sgg.free_air_second_order(dgs_data['lat_new'], ellipsoid_ht)
+eotvos_corr = sgg.eotvos_full(dgs_data['lon_new'].values, dgs_data['lat_new'].values,
                               ellipsoid_ht, sampling)
 tide_corr = sgg.longman_tide_prediction(
-    dgs_data['lon'], dgs_data['lat'], dgs_data['date_time'])
+    dgs_data['lon_new'], dgs_data['lat_new'], dgs_data['date_time'])
 
 dgs_data['faa'] = dgs_data['grav'] - lat_corr + eotvos_corr + tide_corr
 dgs_data['full_field'] = dgs_data['grav'] + eotvos_corr + tide_corr
@@ -79,7 +105,7 @@ dgs_data['full_field'] = dgs_data['grav'] + eotvos_corr + tide_corr
 # calculate kinematic variables and corrections for tilt correction
 # (maybe not strictly necessary? depends who you ask)
 gps_vn, gps_ve = sgn.latlon_to_EN(
-    dgs_data['lon'].values, dgs_data['lat'].values)
+    dgs_data['lon_new'].values, dgs_data['lat_new'].values)
 gps_vn = sampling*gps_vn
 gps_ve = sampling*gps_ve
 
@@ -102,6 +128,8 @@ cross_in_plat = acc_cross*up_vecs[1, :]
 long_in_plat = acc_long*up_vecs[0, :]
 level_error = lat_corr - igf_in_plat - long_in_plat + cross_in_plat
 
+dgs_data = dgs_data.iloc[2:]  # the first two points' FAA has some edge effect
+
 # %%
 # calculate cross-coupling coefficients
 _, model = sgg.calc_cross_coupling_coefficients(dgs_data['faa'].values, dgs_data['vcc'].values, dgs_data['ve'].values,
@@ -118,6 +146,7 @@ dgs_data['faa_ccp'] = dgs_data['faa'] + model.params.ve*dgs_data['ve'] + \
     model.params.al*dgs_data['al'] + \
     model.params.ax*dgs_data['ax']
 
+# filter FAA
 taps = 2*240
 freq = 1./240
 # we resampled to the specified sampling rate when reading the data
@@ -128,12 +157,25 @@ B = firwin(taps, wn, window='blackman')  # approx equivalent to matlab fir1
 ffaa = filtfilt(B, 1, dgs_data['faa'])
 cfaa = filtfilt(B, 1, dgs_data['faa_ccp'])
 
+# %%
+# load satellite data for comparison
+sat_path = pooch.retrieve(url="https://zenodo.org/records/12733929/files/data.zip", 
+        known_hash="md5:83b0411926c0fef9d7ccb2515bb27cc0", progressbar=True, 
+        processor=pooch.Unzip(
+            members=['data/Thompson/TN400/sandwell_tracked.llg']))
+sat_grav = np.loadtxt(sat_path[0], usecols=(3,),
+                      delimiter=',', skiprows=1)
+sat_grav = sat_grav[2:]
+
+
 # %%
 plt.figure(figsize=(11, 4.8))
 plt.plot(dgs_data.iloc[taps:-taps//2]['date_time'],
          ffaa[taps:-taps//2], label='no ccp')
 plt.plot(dgs_data.iloc[taps:-taps//2]['date_time'],
          cfaa[taps:-taps//2], label='with ccp')
+plt.plot(dgs_data.iloc[taps:-taps//2]['date_time'],
+         sat_grav[taps:-taps//2], label='satellite')
 plt.xlabel('Timestamp')
 plt.ylabel('Free air anomaly [mGal]')
 plt.legend(fontsize=8)

{shipgrav-1.0.5 → shipgrav-1.0.7}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "shipgrav"
-version = "1.0.5"
+version = "1.0.7"
 authors = [
     {name = "Hannah F. Mark", email = "hmark@whoi.edu"},
 ]

{shipgrav-1.0.5 → shipgrav-1.0.7}/shipgrav/__init__.py

@@ -62,7 +62,7 @@ Navigation data
 
 Which navigation data should you use to process gravimeter data?
 
-In an ideal world, the gravimeter pulls navigation info from the ship's feed and synchronizes it perfectly with acquisition such that the output files have the correct geographic coordinates in them at the start. In practice, this synchronization doesn't always work as expected (see ``example-scripts/dgs_raw_comp.py`` for a case where the serial files do not have GPS info). So, we like to take the timestamped navigation data directly from the ship's feed and match up the gravimeter timestamps to obtain more accurate coordinates.
+In an ideal world, the gravimeter pulls navigation info from the ship's feed and synchronizes it perfectly with acquisition such that the output files have the correct geographic coordinates in them at the start. In practice, this synchronization doesn't always work as expected (see ``example-scripts/dgs_raw_comp.py`` for a case where the serial files do not have GPS info). So, we like to take the timestamped navigation data directly from the ship's feed and match up the gravimeter timestamps to obtain more accurate coordinates. Using navigation from a feed separate from the gravimeter is **highly recommended**.
 
 The database file included in shipgrav lists the navigation talkers that we expect are good to use for specific UNOLS vessels. Find the files that contain those feeds, and you should be able to read in timestamped coordinates from them.
 
@@ -94,10 +94,10 @@ The data files can be downloaded from R2R and Zenodo, and the scripts will do th
    :height: 250px
    :align: center
 
-``dgs_ccp_calc.py`` reads DGS files from R/V Thompson cruise TN400, calculates the FAA and various kinematic variables, and fits for cross-coupling coefficients. The cross-coupling correction is applied and the data are plotted with and without correction.
+``dgs_ccp_calc.py`` reads DGS files from R/V Thompson cruise TN400, calculates the FAA and various kinematic variables, and fits for cross-coupling coefficients. The cross-coupling correction is applied and the data are plotted with and without correction. Satellite-derived FAA is also plotted
 
 .. image:: _static/TN400_ccp.png
-   :alt: FAA for TN400, with and without cross-coupling correction applied.
+   :alt: FAA for TN400, with and without cross-coupling correction applied; and satellite-derived FAA.
    :height: 250px
    :align: center
 

{shipgrav-1.0.5 → shipgrav-1.0.7}/shipgrav/database.toml

@@ -5,6 +5,7 @@ Revelle = {'dgs'=968888.6465, 'bgm'=855240.81987}
 NBP = {'dgs'=968634.2514, 'bgm'=-999}
 Ride = {'dgs'=968895.7718, 'bgm'=-999}
 Langseth = {'dgs'=-999, 'bgm'=854974.4}
+Sikuliaq = {'dgs'=969538.8152, 'bgm'=-999}
 
 [nav-talkers]
 Atlantis = 'GPGGA'

{shipgrav-1.0.5 → shipgrav-1.0.7}/shipgrav/io.py

@@ -17,7 +17,7 @@ from tqdm import tqdm
 ########################################################################
 
 
-def read_nav(ship, pathlist, sampling=1, talker=None, ship_function=None, progressbar=True):
+def read_nav(ship, pathlist, sampling=1, talker=None, ship_function=None, decimate=0, progressbar=True):
     """ Read navigation strings from .GPS (or similar) files.
 
     Ships have different formats and use different talkers for preferred
@@ -38,6 +38,8 @@ def read_nav(ship, pathlist, sampling=1, talker=None, ship_function=None, progre
         This function should return arrays of lon, lat, and timestamps.
         Look at _navcoords() and navdate_Atlantis() (and similar functions) for examples.
     :type ship_function: function, optional
+    :param decimate: integer skip for decimating data, default 0 returns all points
+    :type decimate: int, optional
     :param progressbar: display progress bar while list of files is read
     :type progressbar: bool
 
@@ -119,6 +121,12 @@ def read_nav(ship, pathlist, sampling=1, talker=None, ship_function=None, progre
         lon_out = np.interp(sec_time, sec_time[idx], lon[idx])
         lat_out = np.interp(sec_time, sec_time[idx], lat[idx])
 
+        # decimate if we're doing that
+        if decimate:
+            sec_time = sec_time[::decimate]
+            lon_out = lon_out[::decimate]
+            lat_out = lat_out[::decimate]
+
         timetime = np.append(timetime, sec_time)
         lonlon = np.append(lonlon, lon_out)
         latlat = np.append(latlat, lat_out)
@@ -325,14 +333,16 @@ def _navcoords(allnav, talker):
         post = subnav[i].split(talker)[-1].lstrip().split(',')
         if post[0] == '':
             post = post[1:]  # correct for spacing in some files
-
-        lat[i] = int(post[1][:2]) + float(post[1][2:]) / \
-            60  # convert to decimal degrees
-        if post[2] == 'S':
-            lat[i] = -lat[i]         # handle coordinate sign
-        lon[i] = int(post[3][:3]) + float(post[3][3:])/60
-        if post[4] == 'W':
-            lon[i] = -lon[i]
+        if post[1] == '' or post[3] == '':  # no coords, nav dropped out?
+            lat[i] = np.nan; lon[i] = np.nan
+        else:
+            lat[i] = int(post[1][:2]) + float(post[1][2:]) / \
+                60  # convert to decimal degrees
+            if post[2] == 'S':
+                lat[i] = -lat[i]         # handle coordinate sign
+            lon[i] = int(post[3][:3]) + float(post[3][3:])/60
+            if post[4] == 'W':
+                lon[i] = -lon[i]
 
     return lon, lat
 
@@ -560,6 +570,8 @@ def read_dgs_laptop(fp, ship, ship_function=None, progressbar=True):
                 dat = _dgs_laptop_general(path)
             elif ship == 'Thompson':
                 dat = _dgs_laptop_Thompson(path)
+            elif ship == 'Sikuliaq':
+                dat = _dgs_laptop_Sikuliaq(path)
             else:
                 print('R/V %s not supported for dgs laptop file read' % ship)
                 return -999
@@ -581,6 +593,17 @@ def _dgs_laptop_general(path):
     return dat
 
 
+def _dgs_laptop_Sikuliaq(path):
+    """Read single laptop file for Sikuliaq, has more of a header than the others
+    """
+    dat = pd.read_csv(path,skiprows=19,names=['rgrav','long_a','crss_a','status','ve','vcc',
+                                              'al','ax','lat','lon','year','month','day',
+                                              'hour','minute','second'],
+                      usecols=(1,2,3,6,10,11,12,13,14,15,19,20,21,22,23,24))
+    dat['date_time'] = pd.to_datetime(dat[['year','month','day','hour','minute','second']],utc=True)
+    return dat
+
+
 def _dgs_laptop_Thompson(path):
     """Read single laptop file for Thompson, which does things its own way.
     """