fix: create mask for output gridded variables (#79)

refactor: set plot tick formatter to not use offsets

gravity_toolkit/utilities.py

@@ -1,14 +1,15 @@
 #!/usr/bin/env python
 u"""
 utilities.py
-Written by Tyler Sutterley (05/2022)
+Written by Tyler Sutterley (07/2022)
 Download and management utilities for syncing time and auxiliary files
 
 PYTHON DEPENDENCIES:
     lxml: processing XML and HTML in Python
         https://pypi.python.org/pypi/lxml
 
 UPDATE HISTORY:
+    Updated 07/2022: add s3 endpoints and buckets for Earthdata Cumulus
     Updated 05/2022: function for extracting bucket name from presigned url
     Updated 04/2022: updated docstrings to numpy documentation format
         update CMR queries to prepare for version 1 of RL06
@@ -759,8 +760,29 @@ def build_opener(username, password, context=ssl.SSLContext(),
     #-- HTTPPasswordMgrWithDefaultRealm will be confused.
     return opener
 
+# NASA Cumulus AWS S3 credential endpoints
+_s3_endpoints = {
+    'gesdisc': 'https://data.gesdisc.earthdata.nasa.gov/s3credentials',
+    'ghrcdaac': 'https://data.ghrc.earthdata.nasa.gov/s3credentials',
+    'lpdaac': 'https://data.lpdaac.earthdatacloud.nasa.gov/s3credentials',
+    'nsidc': 'https://data.nsidc.earthdatacloud.nasa.gov/s3credentials',
+    'ornldaac': 'https://data.ornldaac.earthdata.nasa.gov/s3credentials',
+    'podaac': 'https://archive.podaac.earthdata.nasa.gov/s3credentials'
+}
+
+# NASA Cumulus AWS S3 buckets
+_s3_buckets = {
+    'gesdisc': 'gesdisc-cumulus-prod-protected',
+    'ghrcdaac': 'ghrc-cumulus-dev',
+    'lpdaac': 'lp-prod-protected',
+    'nsidc': 'nsidc-cumulus-prod-protected',
+    'ornldaac': 'ornl-cumulus-prod-protected',
+    'podaac': 'podaac-ops-cumulus-protected'
+}
+
 #-- PURPOSE: get AWS s3 client for PO.DAAC Cumulus
-def s3_client(HOST=None, timeout=None, region_name='us-west-2'):
+def s3_client(HOST=_s3_endpoints['podaac'], timeout=None,
+    region_name='us-west-2'):
     """
     Get AWS s3 client for PO.DAAC Cumulus
 

notebooks/GRACE-Spatial-Error.ipynb

@@ -391,7 +391,8 @@
     "    d_sin[:,k] = np.sum(PLM2[:,:,k]*YLM2.slm, axis=0)\n",
     "\n",
     "# Multiplying by c/s(phi#m) to get spatial maps (lon,lat)\n",
-    "grid.data = np.sqrt(np.dot(ccos.T,d_cos) + np.dot(ssin.T,d_sin)).T"
+    "grid.data = np.sqrt(np.dot(ccos.T,d_cos) + np.dot(ssin.T,d_sin)).T\n",
+    "grid.mask = np.zeros_like(grid.data, dtype=bool)"
    ]
   },
   {

notebooks/GRACE-Spatial-Maps.ipynb

@@ -526,6 +526,7 @@
     "# combining harmonics to calculate output spatial fields\n",
     "# output spatial grid\n",
     "grid.data = np.zeros((nlat,nlon,nt))\n",
+    "grid.mask = np.zeros((nlat,nlon,nt), dtype=bool)\n",
     "for i,grace_month in enumerate(GRACE_Ylms.month):\n",
     "    # GRACE/GRACE-FO harmonics for time t\n",
     "    # and monthly files to be removed\n",
@@ -843,7 +844,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.9.9 64-bit",
+   "display_name": "Python 3.8.10 64-bit",
    "language": "python",
    "name": "python3"
   },
@@ -857,11 +858,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.9"
+   "version": "3.8.10"
   },
   "vscode": {
    "interpreter": {
-    "hash": "0a543bbca308973fff805d6c95eaeb86a663fe83f433025aa1f3fc59463e3b6f"
+    "hash": "31f2aee4e71d21fbe5cf8b01ff0e069b9275f58929596ceb00d14d90e3e16cd6"
    }
   }
  },

scripts/calc_degree_one.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 calc_degree_one.py
-Written by Tyler Sutterley (05/2022)
+Written by Tyler Sutterley (07/2022)
 
 Calculates degree 1 variations using GRACE coefficients of degree 2 and greater,
     and ocean bottom pressure variations from ECCO and OMCT/MPIOM
@@ -153,6 +153,7 @@
         https://doi.org/10.1029/2007JB005338
 
 UPDATE HISTORY:
+    Updated 07/2022: set plot tick formatter to not use offsets
     Updated 05/2022: use argparse descriptions within documentation
         use GIA reference and citation output from GIA read program
         use command line option to set degree 1 gravitational love number
@@ -235,7 +236,7 @@
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
 from matplotlib.offsetbox import AnchoredText
-from matplotlib.ticker import MultipleLocator, FormatStrFormatter
+from matplotlib.ticker import MultipleLocator
 import gravity_toolkit.utilities as utilities
 from gravity_toolkit.grace_input_months import grace_input_months, \
     read_ecmwf_corrections
@@ -918,7 +919,7 @@ def calc_degree_one(base_dir, PROC, DREL, MODEL, LMAX, RAD,
         ax[2].xaxis.set_ticks(np.arange(2003,2008,1))
         ax[2].xaxis.set_minor_locator(MultipleLocator(0.25))
         ax[2].yaxis.set_ticks(np.arange(-6,8,2))
-        ax[2].xaxis.set_major_formatter(FormatStrFormatter('%0.0f'))
+        ax[2].xaxis.get_major_formatter().set_useOffset(False)
         #-- add axis labels and adjust font sizes for axis ticks
         fig_labels = ['C10','C11','S11']
         for i in range(3):
@@ -969,7 +970,7 @@ def calc_degree_one(base_dir, PROC, DREL, MODEL, LMAX, RAD,
         xmax = np.ceil(GSM_Ylms.month[-1]/10.)*10.
         ax[2].set_xlim(xmin,xmax)
         ax[2].xaxis.set_minor_locator(MultipleLocator(5))
-        ax[2].xaxis.set_major_formatter(FormatStrFormatter('%0.0f'))
+        ax[2].xaxis.get_major_formatter().set_useOffset(False)
         #-- add axis labels and adjust font sizes for axis ticks
         fig_labels = ['C10','C11','S11']
         for i in range(3):

scripts/calc_sensitivity_kernel.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 calc_sensitivity_kernel.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (07/2022)
 
 Calculates spatial sensitivity kernels through a least-squares mascon procedure
 
@@ -75,6 +75,7 @@
         https://doi.org/10.1029/2009GL039401
 
 UPDATE HISTORY:
+    Updated 07/2022: create mask for output gridded variables
     Updated 04/2022: use wrapper function for reading load Love numbers
         include utf-8 encoding in reads to be windows compliant
         use argparse descriptions within sphinx documentation
@@ -385,6 +386,7 @@ def calc_sensitivity_kernel(LMAX, RAD,
         #-- convert spherical harmonics to output spatial grid
         grid.data = harmonic_summation(kern_Ylms.clm, kern_Ylms.slm,
             grid.lon, grid.lat, LMAX=LMAX, MMAX=MMAX, PLM=PLM).T
+        grid.mask = np.zeros_like(grid.data, dtype=bool)
         grid.time = total_area[k]
 
         #-- output names for sensitivity kernel Ylm and spatial files

scripts/combine_harmonics.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 combine_harmonics.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (07/2022)
 Converts a file from the spherical harmonic domain into the spatial domain
 
 CALLING SEQUENCE:
@@ -68,6 +68,7 @@
     utilities.py: download and management utilities for files
 
 UPDATE HISTORY:
+    Updated 07/2022: create mask for output gridded variables
     Updated 04/2022: use wrapper function for reading load Love numbers
         use argparse descriptions within sphinx documentation
     Updated 12/2021: can use variable loglevels for verbose output
@@ -230,6 +231,7 @@ def combine_harmonics(INPUT_FILE, OUTPUT_FILE,
         nlat = len(grid.lat)
     #-- output spatial grid
     grid.data = np.zeros((nlat,nlon,nt))
+    grid.mask = np.zeros((nlat,nlon,nt), dtype=bool)
     #-- update attributes
     grid.update_spacing()
     grid.update_extents()

scripts/geocenter_compare_tellus.py

@@ -30,8 +30,7 @@
 import matplotlib
 import matplotlib.font_manager
 import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator, FormatStrFormatter
-from matplotlib.offsetbox import AnchoredText,AnchoredOffsetbox,TextArea,VPacker
+from matplotlib.offsetbox import AnchoredText
 from gravity_toolkit.time import convert_calendar_decimal
 import gravity_toolkit.geocenter as geocenter
 

scripts/geocenter_monte_carlo.py

@@ -28,9 +28,7 @@
 import matplotlib.font_manager
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
-import matplotlib.colors as colors
-from matplotlib.ticker import MultipleLocator, FormatStrFormatter
-from matplotlib.offsetbox import AnchoredText,AnchoredOffsetbox,TextArea,VPacker
+from matplotlib.offsetbox import AnchoredText
 from gravity_toolkit.time import convert_calendar_decimal
 import gravity_toolkit.geocenter as geocenter
 

scripts/geocenter_ocean_models.py

@@ -39,8 +39,7 @@
 matplotlib.rcParams['font.family'] = 'sans-serif'
 matplotlib.rcParams['font.sans-serif'] = ['Helvetica']
 matplotlib.rcParams['mathtext.default'] = 'regular'
-from matplotlib.ticker import MultipleLocator, FormatStrFormatter
-from matplotlib.offsetbox import AnchoredText,AnchoredOffsetbox,TextArea,VPacker
+from matplotlib.offsetbox import AnchoredText
 import gravity_toolkit.geocenter as geocenter
 
 #-- PURPOSE: plots the GRACE/GRACE-FO geocenter time series

scripts/geocenter_processing_centers.py

@@ -38,8 +38,7 @@
 import matplotlib
 import matplotlib.font_manager
 import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator, FormatStrFormatter
-from matplotlib.offsetbox import AnchoredText,AnchoredOffsetbox,TextArea,VPacker
+from matplotlib.offsetbox import AnchoredText
 from gravity_toolkit.time import convert_calendar_decimal
 from gravity_toolkit.geocenter import geocenter
 

scripts/grace_spatial_maps.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 grace_spatial_maps.py
-Written by Tyler Sutterley (04/2022)
+Written by Tyler Sutterley (07/2022)
 
 Reads in GRACE/GRACE-FO spherical harmonic coefficients and exports
     monthly spatial fields
@@ -144,6 +144,7 @@
     utilities.py: download and management utilities for files
 
 UPDATE HISTORY:
+    Updated 07/2022: create mask for output gridded variables
     Updated 04/2022: use wrapper function for reading load Love numbers
         use argparse descriptions within sphinx documentation
     Updated 12/2021: can use variable loglevels for verbose output
@@ -437,6 +438,7 @@ def grace_spatial_maps(base_dir, PROC, DREL, DSET, LMAX, RAD,
         grid.data = harmonic_summation(Ylms.clm, Ylms.slm,
             grid.lon, grid.lat, LMIN=LMIN, LMAX=LMAX,
             MMAX=MMAX, PLM=PLM).T
+        grid.mask = np.zeros_like(grid.data, dtype=bool)
         #-- copy time variables for month
         grid.time = np.copy(Ylms.time)
         grid.month = np.copy(Ylms.month)

scripts/monte_carlo_degree_one.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 u"""
 monte_carlo_degree_one.py
-Written by Tyler Sutterley (05/2022)
+Written by Tyler Sutterley (07/2022)
 
 Calculates degree 1 errors using GRACE coefficients of degree 2 and greater,
     and ocean bottom pressure variations from OMCT/MPIOM in a Monte Carlo scheme
@@ -143,6 +143,7 @@
         https://doi.org/10.1029/2005GL025305
 
 UPDATE HISTORY:
+    Updated 07/2022: set plot tick formatter to not use offsets
     Updated 05/2022: use argparse descriptions within documentation
         use GIA reference and citation output from GIA read program
         use command line option to set degree 1 gravitational love number
@@ -192,7 +193,7 @@
 import matplotlib.pyplot as plt
 import matplotlib.cm as cm
 from matplotlib.offsetbox import AnchoredText
-from matplotlib.ticker import MultipleLocator, FormatStrFormatter
+from matplotlib.ticker import MultipleLocator
 import gravity_toolkit.utilities as utilities
 from gravity_toolkit.grace_input_months import grace_input_months, \
     read_ecmwf_corrections
@@ -803,7 +804,7 @@ def monte_carlo_degree_one(base_dir, PROC, DREL, LMAX, RAD,
         ax[2].set_xlabel('Grace Month', fontsize=14)
         ax[2].set_xlim(np.floor(months[0]/10.)*10.,np.ceil(months[-1]/10.)*10.)
         ax[2].xaxis.set_minor_locator(MultipleLocator(5))
-        ax[2].xaxis.set_major_formatter(FormatStrFormatter('%0.0f'))
+        ax[2].xaxis.get_major_formatter().set_useOffset(False)
         #-- add axis labels and adjust font sizes for axis ticks
         for i,lbl in enumerate(['C10','C11','S11']):
             #-- axis label