refactor: switch from parameter files to argparse arguments (#36)

fix: degree spacing in spatial programs

Author: tsutterley

Dockerfile

@@ -1,12 +1,47 @@
-FROM python:3.7-alpine
-
-LABEL "com.github.actions.name"="gravity_toolkit"
-LABEL "com.github.actions.description"="Run pytest commands"
-LABEL "com.github.actions.icon"="upload-cloud"
-LABEL "com.github.actions.color"="yellow"
-
-RUN apk add --no-cache bash
-RUN pip install --upgrade pip
-RUN pip install pytest pytest-cov
-RUN pip install -r requirements.txt
-RUN python --version ; pip --version ; pytest --version
+FROM python:3.9-slim-buster
+
+LABEL Tyler Sutterley "[email protected]"
+
+ENV DEBIAN_FRONTEND="noninteractive" TZ="America/Los_Angeles"
+
+RUN useradd --create-home --shell /bin/bash gravity
+
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+        ca-certificates \
+        git \
+        libgeos-dev \
+        libhdf5-dev \
+        libnetcdf-dev \
+        libproj-dev \
+        libxml2-dev \
+        libxslt1-dev \
+        openssl \
+        proj-data \
+        proj-bin && \
+    apt-get clean
+
+WORKDIR /home/gravity
+
+RUN pip3 install --no-cache-dir --no-binary=cartopy \
+        cartopy \
+        future \
+        h5py \
+        lxml \
+        matplotlib \
+        netCDF4 \
+        numpy \
+        python-dateutil \
+        pyyaml \
+        scipy && \
+    pip3 install --no-cache-dir --no-deps git+https://github.com/tsutterley/read-GRACE-geocenter.git && \
+    pip3 install --no-cache-dir --no-deps git+https://github.com/tsutterley/geoid-toolkit.git
+
+COPY . .
+
+RUN --mount=source=.git,target=.git,type=bind \
+    pip install --no-cache-dir --no-deps .
+
+USER gravity
+
+CMD ["bash"]

doc/source/getting_started/Spatial-Maps.rst

@@ -119,149 +119,6 @@ as described in [Jekeli1981]_ [Swenson2002]_.
 GRACE/GRACE-FO coefficients are also impacted by correlated north/south "striping" errors,
 which can be spectrally filtered following [Swenson2006]_.
 
-Parameter Files
-###############
-
-The ``grace_spatial_maps.py`` program works by accepting parameter file system arguments
-(``sys.argv``) listed after the program.
-These parameter files can be ran individually or in a series.
-
-.. code-block:: bash
-
-     python grace_spatial_maps.py inp1 inp2 inp3
-     python grace_spatial_maps.py --np 2 inp1 inp2 inp3
-     python grace_spatial_maps.py -P 2 inp1 inp2 inp3
-
-
-The program can be run in series (default) or in parallel with the python
-multiprocessing package using options ``--np`` and ``-P``.
-The number after the ``--np`` and ``-P`` options declares the number of processes to run in parallel.
-
-The parameter files are read line by line to fill a python dictionary variable
-mapping specific parameter names with their values.
-The parameter names are the first column in the file and the parameter values are the second column.
-For parameters consisting of lists (e.g. GRACE/GRACE-FO missing months),
-the parameter values are separated by commas.
-
-- Column 1: parameter name (such as ``LMAX``)
-- Column 2: parameter value (e.g. ``60``)
-- Column 3: comments (which are discarded)
-
-Dataset Parameters
-##################
-
-- ``PROC``: GRACE Processing Center (CSR, GFZ, JPL, CNES)
-- ``DREL``: GRACE data release for given processing center
-- ``DSET``: GRACE data product (see `GRACE Data File Formats <./GRACE-Data-File-Formats.html>`_)
-- ``LMIN``: minimum spherical harmonic degree (lower bound of truncation)
-- ``LMAX``: maximum spherical harmonic degree (upper bound of truncation)
-- ``MMAX``: maximum spherical harmonic order (None if ``LMAX``)
-- ``START``: first month to be analyzed
-- ``END``: last month to be analyzed
-- ``MISSING``: GRACE/GRACE-FO months that are not be analyzed (see available GRACE/GRACE-FO months)
-- ``RAD``: Gaussian smoothing radius in km [Jekeli1981]_
-- ``DESTRIPE``: filter coefficients using destriping procedure [Swenson2006]_
-- ``SLR_C20``: replace *C*\ :sub:`20` coefficients with values from Satellite Laser Ranging (SLR)
-
-     * `None`: use original values
-     * ``'CSR'``: use values from CSR (TN-07, TN-09, TN-11)
-     * ``'GFZ'``: use values from GFZ
-     * ``'GSFC'``: use values from GSFC (TN-14)
-
-- ``SLR_21``: replace *C*\ :sub:`21` and *S*\ :sub:`21` coefficients with values from Satellite Laser Ranging (SLR)
-
-     * `None`: use original values
-     * ``'CSR'``: use values from CSR
-     * ``'GFZ'``: use values from GFZ GravIS
-
-- ``SLR_22``: replace *C*\ :sub:`22` and *S*\ :sub:`22` coefficients with values from Satellite Laser Ranging (SLR)
-
-     * `None`: use original values
-     * ``'CSR'``: use values from CSR
-
-- ``SLR_C30``: replace *C*\ :sub:`30` coefficients with values from Satellite Laser Ranging (SLR)
-
-     * `None`: use original values
-     * ``'CSR'``: use values from CSR (5x5 with 6,1)
-     * ``'GFZ'``: use values from GFZ GravIS
-     * ``'GSFC'``: use values from GSFC (TN-14)
-     * ``'LARES'``: use filtered values from CSR
-
-- ``SLR_C50``: replace *C*\ :sub:`50` coefficients with values from Satellite Laser Ranging (SLR)
-
-     * `None`: use original values
-     * ``'CSR'``: use values from CSR (5x5 with 6,1)
-     * ``'GSFC'``: use values from GSFC
-     * ``'LARES'``: use filtered values from CSR
-
-- ``DEG1``: account for variations in geocenter with specified values
-
-     * `None`
-     * ``'Tellus'``: GRACE/GRACE-FO TN-13 coefficients from PO.DAAC
-     * ``'SLR'``: satellite laser ranging coefficients from CSR
-     * ``'SLF'``: Sutterley and Velicogna coefficients, Remote Sensing (2019)
-     * ``'Swenson'``: GRACE-derived coefficients from Sean Swenson
-     * ``'GFZ'``: GRACE/SLR derived coefficients from GFZ GravIS
-
-- ``MODEL_DEG1``: use a least-squares regression model to predict geocenter values where unavailable
-- ``GIA``: GIA model type
-
-     * `None`
-     * ``'IJ05-R2'``: `Ivins R2 GIA Models <https://doi.org/10.1002/jgrb.50208>`_
-     * ``'W12a'``: `Whitehouse GIA Models <https://doi.org/10.1111/j.1365-246X.2012.05557.x>`_
-     * ``'SM09'``: `Simpson/Milne GIA Models <https://doi.org/10.1029/2010JB007776>`_
-     * ``'ICE6G'``: `ICE-6G GIA Models <https://doi.org/10.1002/2014JB011176>`_
-     * ``'Wu10'``: `Wu (2010) GIA Correction <https://doi.org/10.1038/ngeo938>`_
-     * ``'AW13-ICE6G'``: `Geruo A ICE-6G GIA Models <https://doi.org/10.1093/gji/ggs030>`_
-     * ``'Caron'``: `Caron JPL GIA Assimilation <https://doi.org/10.1002/2017GL076644>`_
-     * ``'ICE6G-D'``: `ICE-6G Version-D GIA Models <https://doi.org/10.1002/2016JB013844>`_
-     * ``'netCDF4'``: reformatted GIA in netCDF4 format
-     * ``'HDF5'``: reformatted GIA in HDF5 format
-
-- ``GIA_FILE``: path to specific GIA file to be read
-- ``DATAFORM``: input data format and output data format
-
-     * ``'ascii'``
-     * ``'netCDF4'``
-     * ``'HDF5'``
-
-- ``MEAN``: Remove a mean field to isolate the time-variable gravity field
-- ``MEAN_FILE``: use a file to remove as static field (default: mean of imported month)
-- ``MEANFORM``: Data format for input ``MEAN_FILE``
-
-     * ``'ascii'``
-     * ``'netCDF4'``
-     * ``'HDF5'``
-     * ``'gfc'``
-
-- ``DIRECTORY``: Directory to output data
-- ``REMOVE_FILE``: Remove sets of spherical harmonics (can be multiple files)
-- ``REMOVEFORM``: Data format for input ``REMOVE_FILE`` (can be a single value for a uniform type or values for each file)
-
-     * ``'ascii'``
-     * ``'netCDF4'``
-     * ``'HDF5'``
-     * ``'index'``: index file containing monthly files in ``DATAFORM``
-
-- ``REDISTRIBUTE_REMOVED``: Redistribute total mass of removed harmonics over the ocean
-- ``POLE_TIDE``: correct GSM *C*\ :sub:`21` and *S*\ :sub:`21` for pole tide [Wahr2015]_
-- ``ATM``: correct Atmosphere with ECMWF "jump" corrections [Fagiolini2015]_
-- ``UNITS``: Output units of the spatial fields
-
-     * ``1``: Equivalent Water Thickness (cm)
-     * ``2``: Geoid Height (mm)
-     * ``3``: Elastic Crustal Uplift (mm)
-     * ``4``: Gravitational Undulation (\ |mu|\ Gal)
-     * ``5``: Equivalent surface pressure (millibar)
-
-- ``DDEG``: spatial longitude and latitude degree spacing
-- ``INTERVAL``: determines the spatial field degree interval
-
-     * ``1``: (90:-90,0:360)
-     * ``2``: (degree interval/2)
-
-- ``FILENAME``: Start of the output filename
-
 References
 ##########
 

doc/source/getting_started/Time-Series-Analysis.rst

@@ -34,141 +34,6 @@ The ``calc_mascon.py`` program will output a text file of the time series for ea
 estimated monthly mass anomaly [Gt], estimated monthly error [Gt],
 mascon area [km\ :sup:`2`]).
 
-Parameter Files
-###############
-
-The ``calc_mascon.py`` program works by accepting parameter file system arguments
-(``sys.argv``) listed after the program.
-These parameter files can be ran individually or in a series.
-
-.. code-block:: bash
-
-	python calc_mascon.py inp1 inp2 inp3
-	python calc_mascon.py --np=2 inp1 inp2 inp3
-	python calc_mascon.py -P 2 inp1 inp2 inp3
-
-The program can be run in series (default) or in parallel with the python
-multiprocessing package using options ``--np`` and ``-P``.
-The number after the ``--np`` and ``-P`` options declares the number of processes to run in parallel.
-
-The parameter files are read line by line to fill a python dictionary variable
-mapping specific parameter names with their values.
-The parameter names are the first column in the file and the parameter values are the second column.
-For parameters consisting of lists (e.g. GRACE/GRACE-FO missing months),
-the parameter values are separated by commas.
-
-- Column 1: parameter name (such as ``LMAX``)
-- Column 2: parameter value (e.g. ``60``)
-- Column 3: comments (which are discarded)
-
-Dataset Parameters
-##################
-
-- ``PROC``: GRACE Processing Center (CSR, GFZ, JPL, CNES)
-- ``DREL``: GRACE data release for given processing center
-- ``DSET``: GRACE data product (see `GRACE Data File Formats <./GRACE-Data-File-Formats.html>`_)
-- ``LMIN``: minimum spherical harmonic degree (lower bound of truncation)
-- ``LMAX``: maximum spherical harmonic degree (upper bound of truncation)
-- ``MMAX``: maximum spherical harmonic order (None if ``LMAX``)
-- ``START``: first month to be analyzed
-- ``END``: last month to be analyzed
-- ``MISSING``: GRACE/GRACE-FO months that are not be analyzed (see available GRACE/GRACE-FO months)
-- ``RAD``: Gaussian smoothing radius in km [Jekeli1981]_
-- ``DESTRIPE``: filter coefficients using destriping procedure [Swenson2006]_
-- ``SLR_C20``: replace *C*\ :sub:`20` coefficients with values from Satellite Laser Ranging (SLR)
-
-	* `None`: use original values
-	* ``'CSR'``: use values from CSR (TN-07, TN-09, TN-11)
-	* ``'GFZ'``: use values from GFZ
-	* ``'GSFC'``: use values from GSFC (TN-14)
-
-- ``SLR_21``: replace *C*\ :sub:`21` and *S*\ :sub:`21` coefficients with values from Satellite Laser Ranging (SLR)
-
-	* `None`: use original values
-	* ``'CSR'``: use values from CSR
-    * ``'GFZ'``: use values from GFZ GravIS
-
-- ``SLR_22``: replace *C*\ :sub:`22` and *S*\ :sub:`22` coefficients with values from Satellite Laser Ranging (SLR)
-
-	* `None`: use original values
-	* ``'CSR'``: use values from CSR
-
-- ``SLR_C30``: replace *C*\ :sub:`30` coefficients with values from Satellite Laser Ranging (SLR)
-
-	* `None`: use original values
-	* ``'CSR'``: use values from CSR (5x5 with 6,1)
-	* ``'GFZ'``: use values from GFZ GravIS
-	* ``'GSFC'``: use values from GSFC (TN-14)
-	* ``'LARES'``: use filtered values from CSR
-
-- ``SLR_C50``: replace *C*\ :sub:`50` coefficients with values from Satellite Laser Ranging (SLR)
-
-	* `None`: use original values
-	* ``'CSR'``: use values from CSR (5x5 with 6,1)
-	* ``'GSFC'``: use values from GSFC
-	* ``'LARES'``: use filtered values from CSR
-
-- ``DEG1``: account for variations in geocenter with specified values
-
-	* `None`
-	* ``'Tellus'``: GRACE/GRACE-FO TN-13 coefficients from PO.DAAC
-	* ``'SLR'``: satellite laser ranging coefficients from CSR
-	* ``'SLF'``: Sutterley and Velicogna coefficients, Remote Sensing (2019)
-	* ``'Swenson'``: GRACE-derived coefficients from Sean Swenson
-	* ``'GFZ'``: GRACE/SLR derived coefficients from GFZ GravIS
-
-- ``GIA``: GIA model type
-
-     * `None`
-     * ``'IJ05-R2'``: `Ivins R2 GIA Models <https://doi.org/10.1002/jgrb.50208>`_
-     * ``'W12a'``: `Whitehouse GIA Models <https://doi.org/10.1111/j.1365-246X.2012.05557.x>`_
-     * ``'SM09'``: `Simpson/Milne GIA Models <https://doi.org/10.1029/2010JB007776>`_
-     * ``'ICE6G'``: `ICE-6G GIA Models <https://doi.org/10.1002/2014JB011176>`_
-     * ``'Wu10'``: `Wu (2010) GIA Correction <https://doi.org/10.1038/ngeo938>`_
-     * ``'AW13-ICE6G'``: `Geruo A ICE-6G GIA Models <https://doi.org/10.1093/gji/ggs030>`_
-     * ``'Caron'``: `Caron JPL GIA Assimilation <https://doi.org/10.1002/2017GL076644>`_
-     * ``'ICE6G-D'``: `ICE-6G Version-D GIA Models <https://doi.org/10.1002/2016JB013844>`_
-     * ``'netCDF4'``: reformatted GIA in netCDF4 format
-     * ``'HDF5'``: reformatted GIA in HDF5 format
-
-- ``GIA_FILE``: path to specific GIA file to be read
-
-- ``DATAFORM``: input data format for mascon files and files to be removed from the GRACE/GRACE-FO data
-
-	* ``'ascii'``
-	* ``'netCDF4'``
-	* ``'HDF5'``
-
-- ``DIRECTORY``: Directory to output data (will create directory if non-existent)
-- ``MASCON_INDEX``: file index listing the full path to each mascon file to fit to the GRACE data
-- ``FIT_METHOD``: method of fitting mascons coefficients
-
-	* ``1``: convert coefficients to mass
-	* ``2``: keep coefficients as normalized geoid
-
-- ``MEAN``: Remove a mean field to isolate the time-variable gravity field
-- ``MEAN_FILE``: use a file to remove as static field (default: mean of imported month)
-- ``MEANFORM``: Data format for input ``MEAN_FILE``
-
-	* ``'ascii'``
-	* ``'netCDF4'``
-	* ``'HDF5'``
-	* ``'gfc'``
-
-- ``REMOVE_FILE``: Remove sets of spherical harmonics (can be multiple files)
-- ``REMOVEFORM``: Data format for input ``REMOVE_FILE`` (can be a single value for a uniform type or values for each file)
-
-	* ``'ascii'``
-	* ``'netCDF4'``
-	* ``'HDF5'``
-	* ``'index'``: index file containing monthly files in ``DATAFORM``
-
-- ``REDISTRIBUTE_REMOVED``: Redistribute total mass of removed harmonics over the ocean
-- ``MASCON_OCEAN``: remove uniformly distributed mascon mass over ocean
-- ``RECONSTRUCT``: remove the reconstructed time series for a region to get the statistical leakage
-- ``POLE_TIDE``: correct GSM *C*\ :sub:`21` and *S*\ :sub:`21` for pole tide [Wahr2015]_
-- ``ATM``: correct Atmosphere with ECMWF "jump" corrections [Fagiolini2015]_
-
 References
 ##########
 

doc/source/index.rst

@@ -102,10 +102,10 @@ missions
     user_guide/calc_sensitivity_kernel.rst
     user_guide/combine_harmonics.rst
     user_guide/convert_harmonics.rst
-    user_guide/grace_mean_harmonics.md
+    user_guide/grace_mean_harmonics.rst
     user_guide/grace_spatial_error.rst
     user_guide/grace_spatial_maps.rst
-    user_guide/mascon_reconstruct.md
-    user_guide/regress_grace_maps.md
+    user_guide/mascon_reconstruct.rst
+    user_guide/regress_grace_maps.rst
     user_guide/run_grace_date.md
     user_guide/scale_grace_maps.rst