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Commit 8d72a548 authored by Eva Börgens's avatar Eva Börgens
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remove typos from docstring and export Docstrings as documentation

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<section>
<h2 class="section-title" id="header-submodules">Sub-modules</h2>
<dl>
<dt><code class="name"><a title="src.covariance" href="covariance.html">src.covariance</a></code></dt>
<dd>
<div class="desc"><p>Module handling the computation of the covariances and uncertainties</p></div>
</dd>
<dt><code class="name"><a title="src.input_arguments" href="input_arguments.html">src.input_arguments</a></code></dt>
<dd>
<div class="desc"><p>Module checking the input parameter</p></div>
</dd>
<dt><code class="name"><a title="src.io" href="io.html">src.io</a></code></dt>
<dd>
<div class="desc"><p>Module handling input and output</p></div>
</dd>
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<li><code><a title="src.covariance" href="covariance.html">src.covariance</a></code></li>
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<header>
<h1 class="title">Module <code>src.input_arguments</code></h1>
</header>
<section id="section-intro">
<p>Module checking the input parameter</p>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">&#34;&#34;&#34;
Module checking the input parameter
&#34;&#34;&#34;
from argparse import ArgumentParser, FileType, RawTextHelpFormatter
from .io import test_coordiantes
def arg_parser():
&#34;&#34;&#34;
Argument parser of input line
Returns:
ArgumentParser.arguments
&#34;&#34;&#34;
parser = ArgumentParser(
prog=&#34;tws_covariances.sh&#34;,
description=&#34;Programm to compute the covariances of given region and return the &#34;
&#34;standard deviation of the mean TWS of this region and/or the full &#34;
&#34;covariance matrix&#34;,
formatter_class=RawTextHelpFormatter,
)
parser.add_argument(
&#34;-f&#34;,
&#34;--filename&#34;,
required=True,
type=FileType(),
help=&#34;Filename of the netcdf TWS input file, as downloaded from gravis.gfz-potsdam.de&#34;
)
parser.add_argument(
&#34;-r&#34;,
&#34;--region&#34;,
required=True,
type=FileType(),
help=&#34;Filename of the ascii file defining the requested region. List of coordinates &#34;
&#34;lon, lat, each line one coordinate.&#34;
&#34;Coordinates have to be on an even spaced grid. Comment lines have to start with &#39;#&#39;. &#34;
)
parser.add_argument(
&#34;-o&#34;,
&#34;--output&#34;,
required=True,
type=str,
help=&#34;Filename of the netcdf output file&#34;
)
parser.add_argument(
&#34;-m&#34;,
&#34;--matrix&#34;,
action=&#34;store_true&#34;,
help=&#34;Return full covariance matrix&#34;
)
parser.add_argument(
&#34;-u&#34;,
&#34;--uncertainty&#34;,
action=&#34;store_true&#34;,
help=&#34;Return time series of standard deviations for mean TWS time series&#34;
)
parser.add_argument(
&#34;-t&#34;,
&#34;--timeseries&#34;,
action=&#34;store_true&#34;,
help=&#34;Return mean TWS time series&#34;
)
args = parser.parse_args()
if not args.matrix and not args.uncertainty and not args.timeseries:
raise RuntimeError(&#34;Either covariance matrix (-m) or uncertainties (-u) or timeseries (-t) &#34;
&#34;have to be set for the output!&#34;)
test_coordiantes(args.region.name)
return args</code></pre>
</details>
</section>
<section>
</section>
<section>
</section>
<section>
<h2 class="section-title" id="header-functions">Functions</h2>
<dl>
<dt id="src.input_arguments.arg_parser"><code class="name flex">
<span>def <span class="ident">arg_parser</span></span>(<span>)</span>
</code></dt>
<dd>
<div class="desc"><p>Argument parser of input line</p>
<h2 id="returns">Returns</h2>
<p>ArgumentParser.arguments</p></div>
<details class="source">
<summary>
<span>Expand source code</span>
</summary>
<pre><code class="python">def arg_parser():
&#34;&#34;&#34;
Argument parser of input line
Returns:
ArgumentParser.arguments
&#34;&#34;&#34;
parser = ArgumentParser(
prog=&#34;tws_covariances.sh&#34;,
description=&#34;Programm to compute the covariances of given region and return the &#34;
&#34;standard deviation of the mean TWS of this region and/or the full &#34;
&#34;covariance matrix&#34;,
formatter_class=RawTextHelpFormatter,
)
parser.add_argument(
&#34;-f&#34;,
&#34;--filename&#34;,
required=True,
type=FileType(),
help=&#34;Filename of the netcdf TWS input file, as downloaded from gravis.gfz-potsdam.de&#34;
)
parser.add_argument(
&#34;-r&#34;,
&#34;--region&#34;,
required=True,
type=FileType(),
help=&#34;Filename of the ascii file defining the requested region. List of coordinates &#34;
&#34;lon, lat, each line one coordinate.&#34;
&#34;Coordinates have to be on an even spaced grid. Comment lines have to start with &#39;#&#39;. &#34;
)
parser.add_argument(
&#34;-o&#34;,
&#34;--output&#34;,
required=True,
type=str,
help=&#34;Filename of the netcdf output file&#34;
)
parser.add_argument(
&#34;-m&#34;,
&#34;--matrix&#34;,
action=&#34;store_true&#34;,
help=&#34;Return full covariance matrix&#34;
)
parser.add_argument(
&#34;-u&#34;,
&#34;--uncertainty&#34;,
action=&#34;store_true&#34;,
help=&#34;Return time series of standard deviations for mean TWS time series&#34;
)
parser.add_argument(
&#34;-t&#34;,
&#34;--timeseries&#34;,
action=&#34;store_true&#34;,
help=&#34;Return mean TWS time series&#34;
)
args = parser.parse_args()
if not args.matrix and not args.uncertainty and not args.timeseries:
raise RuntimeError(&#34;Either covariance matrix (-m) or uncertainties (-u) or timeseries (-t) &#34;
&#34;have to be set for the output!&#34;)
test_coordiantes(args.region.name)
return args</code></pre>
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</dd>
</dl>
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<section>
</section>
</article>
<nav id="sidebar">
<h1>Index</h1>
<div class="toc">
<ul></ul>
</div>
<ul id="index">
<li><h3>Super-module</h3>
<ul>
<li><code><a title="src" href="index.html">src</a></code></li>
</ul>
</li>
<li><h3><a href="#header-functions">Functions</a></h3>
<ul class="">
<li><code><a title="src.input_arguments.arg_parser" href="#src.input_arguments.arg_parser">arg_parser</a></code></li>
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This diff is collapsed.
src/__main__.py
View file @ 8d72a548
""""
"""
This is the main file to invoke the regional tws uncertainty routines.
"""
from io import read_netcdf, read_ascii, save_results
from covariance import get_timeseries, compute_covariance
from input_arguments import arg_parser
from .io import read_netcdf, read_ascii, save_results
from .covariance import get_timeseries, compute_covariance
from .input_arguments import arg_parser
parsed_command_line_input = arg_parser()
......
src/covariance.py
View file @ 8d72a548
""""
"""
Module handling the computation of the covariances and uncertainties
"""
......@@ -12,7 +12,7 @@ rho = np.pi/180
R = 6367.4447
def get_grid_area(lon : np.ndarray, lat : np.ndarray) -> np.ndarray:
""""
"""
Function getting the area weights of a coordinate list
Args:
......@@ -35,7 +35,7 @@ def get_grid_area(lon : np.ndarray, lat : np.ndarray) -> np.ndarray:
return area
def get_area(lon_ll: float, lat_ll: float, lon_ur: float,lat_ur: float) -> float:
""""
"""
returns area of rectangular on sphere, defined by corner points lower left ll and upper right ur
Args:
......@@ -63,7 +63,7 @@ def cov_function_lat(lat1: float, lat2: float,
a_0: float, k_a_0_2: float, k_a_0_4: float, k_a_0_6: float, k_a_0_8: float,
a_1: float, k_a_1_2: float, k_a_1_4: float, k_a_1_6: float, k_a_1_8: float,
c_0: float, k_2: float, k_4: float, k_6: float, k_8: float) -> float:
""""
"""
Function to compute covariance function between two points according to
publication Boergens et al. 2020
......
src/input_arguments.py
View file @ 8d72a548
""""
"""
Module checking the input parameter
"""
from argparse import ArgumentParser, FileType, RawTextHelpFormatter
from io import test_coordiantes
from .io import test_coordiantes
def arg_parser():
"""
......
src/io.py
View file @ 8d72a548
""""
"""
Module handling input and output
"""
......@@ -9,10 +9,9 @@ from typing import Dict
import netCDF4
import numpy as np
import numpy.typing as npt
def read_netcdf(filename: str) -> Dict[str, np.ndarray]:
""""
"""
Reads a TWS netcdf file as provided from GravIS
Args:
......@@ -37,7 +36,7 @@ def read_netcdf(filename: str) -> Dict[str, np.ndarray]:
return grid, grid_std, lon, lat, time
def read_ascii(filename: str) -> np.ndarray:
""""
"""
Reads an Ascii file with coordinates
Args:
......@@ -61,7 +60,7 @@ def read_ascii(filename: str) -> np.ndarray:
return coords
def test_coordiantes(filename: str):
""""
"""
Tests if more than 2 coordinates are given in the file
Args:
......@@ -83,8 +82,8 @@ def test_coordiantes(filename: str):
raise RuntimeError("Latitudes of region not evenly spaced")
def same_dist_elems(arr: npt.ArrayLike) -> bool:
""""
def same_dist_elems(arr: np.ndarray) -> bool:
"""
Tests if coordinates are evenly spaced
Args:
......@@ -98,13 +97,13 @@ def same_dist_elems(arr: npt.ArrayLike) -> bool:
def save_results(outname: str,
inname: str,
results: Dict[str, npt.ArrayLike],
region_coords: npt.ArrayLike,
timeseries: npt.ArrayLike,
results: Dict[str, np.ndarray],
region_coords: np.ndarray,
timeseries: np.ndarray,
flag_uncertainty: bool,
flag_matrix: bool,
flag_timeseries: bool):
""""
"""
Saving the results of the regional tws uncerty tools to a NetCDF file
Args:
......
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