Python implementation

.circleci/config.yml

@@ -62,3 +62,5 @@ jobs:
             # run tests
             python ${PYSOLID_HOME}/tests/point.py
             python ${PYSOLID_HOME}/tests/grid.py
+            python ${PYSOLID_HOME}/tests/point_pyimpl.py
+            python ${PYSOLID_HOME}/tests/grid_pyimpl.py

src/pysolid/__init__.py

@@ -11,16 +11,17 @@
 
 
 # top-level functions
-from pysolid.grid import (
+from .grid import (
     calc_solid_earth_tides_grid,
     plot_solid_earth_tides_grid,
 )
-from pysolid.point import (
+from .point import (
     TIDES,
     calc_solid_earth_tides_point,
     plot_solid_earth_tides_point,
     plot_power_spectral_density4tides,
 )
+from . import py_solid
 
 __all__ = [
     '__version__',
@@ -30,4 +31,5 @@
     'calc_solid_earth_tides_point',
     'plot_solid_earth_tides_point',
     'plot_power_spectral_density4tides',
+    'py_solid',
 ]

src/pysolid/py_solid/__init__.py

@@ -0,0 +1,20 @@
+from .grid import (
+    calc_solid_earth_tides_grid,
+    plot_solid_earth_tides_grid,
+)
+
+from .point import (
+    TIDES,
+    calc_solid_earth_tides_point,
+    plot_solid_earth_tides_point,
+    plot_power_spectral_density4tides,
+)
+
+__all__ = [
+    'TIDES',
+    'calc_solid_earth_tides_grid',
+    'plot_solid_earth_tides_grid',
+    'calc_solid_earth_tides_point',
+    'plot_solid_earth_tides_point',
+    'plot_power_spectral_density4tides',
+]

src/pysolid/py_solid/grid.py

@@ -0,0 +1,141 @@
+#!/usr/bin/env python3
+#######################################################################
+# A Python wrapper for solid Earth tides calculation using solid.for.
+#   Fortran code is originally written by Dennis Milbert, 2018-06-01.
+#   Available at: http://geodesyworld.github.io/SOFTS/solid.htm.
+# Author: Zhang Yunjun, Simran Sangha, Sep 2020
+# Copyright 2020, by the California Institute of Technology.
+#######################################################################
+# Recommend usage:
+#   import pysolid
+#   pysolid.calc_solid_earth_tides_grid()
+
+
+import os
+
+import numpy as np
+from scipy import ndimage
+
+
+##################################  Earth tides - grid mode  ###################################
+def calc_solid_earth_tides_grid(dt_obj, atr, step_size=1e3, display=False, verbose=True):
+    """Calculate SET in east/north/up direction for a spatial grid at a given date/time.
+
+    Note that we use step_size to speedup >30 times, by feeding the Fortran code (SET calc and
+    text file writing) the coarse grid, then resize the output to the same shape as the original
+    input size. This uses the fact that SET varies slowly in space. Comparison w and w/o step_size
+    shows a difference in tide_u with max of 5e-8 m, thus negligible.
+
+    Parameters: dt_obj    - datetime.datetime object (with precision up to the second)
+                atr       - dict, metadata including the following keys:
+                                LENGTH/WIDTTH
+                                X/Y_FIRST
+                                X/Y_STEP
+                step_size - float, grid step feeded into the fortran code in meters
+                                to speedup the calculation
+                display   - bool, plot the calculated SET
+                verbose   - bool, print verbose message
+    Returns:    tide_e    - 2D np.ndarray, SET in east  direction in meters
+                tide_n    - 2D np.ndarray, SET in north direction in meters
+                tide_u    - 2D np.ndarray, SET in up    direction in meters
+    Examples:   atr = readfile.read_attribute('geo_velocity.h5')
+                tide_e, tide_n, tide_u = calc_solid_earth_tides_grid('20180219', atr)
+    """
+    try:
+        from .solid import solid_grid
+    except ImportError:
+        msg = "Cannot import name 'solid' from 'pysolid'!"
+        msg += '\n    Maybe solid.for is NOT compiled yet.'
+        msg += '\n    Check instruction at: https://github.com/insarlab/PySolid.'
+        raise ImportError(msg)
+
+    vprint = print if verbose else lambda *args, **kwargs: None
+
+    # location
+    lat0 = float(atr['Y_FIRST'])
+    lon0 = float(atr['X_FIRST'])
+    lat1 = lat0 + float(atr['Y_STEP']) * int(atr['LENGTH'])
+    lon1 = lon0 + float(atr['X_STEP']) * int(atr['WIDTH'])
+
+    vprint('PYSOLID: ----------------------------------------')
+    vprint('PYSOLID: datetime: {}'.format(dt_obj.isoformat()))
+    vprint('PYSOLID: SNWE: {}'.format((lat1, lat0, lon0, lon1)))
+
+    # step size
+    num_step = int(step_size / 108e3 / abs(float(atr['Y_STEP'])))
+    num_step = max(1, num_step)
+    length = np.rint(int(atr['LENGTH']) / num_step - 1e-4).astype(int)
+    width = np.rint(int(atr['WIDTH']) / num_step - 1e-4).astype(int)
+    lat_step = float(atr['Y_STEP']) * num_step
+    lon_step = float(atr['X_STEP']) * num_step
+    vprint('SOLID  : calculate solid Earth tides in east/north/up direction')
+    vprint('SOLID  : shape: {s}, step size: {la:.4f} by {lo:.4f} deg'.format(
+        s=(length, width), la=lat_step, lo=lon_step))
+
+    lats = lat0 + np.arange(length) * lat_step
+    lons = lon0 + np.arange(width) * lon_step
+
+    # calc solid Earth tides
+    tides = solid_grid(dt_obj, lats, lons)
+    tide_e = tides[0]
+    tide_n = tides[1]
+    tide_u = tides[2]
+
+    # resample to the input size
+    # via scipy.ndimage.zoom or skimage.transform.resize
+    if num_step > 1:
+        in_shape = tide_e.shape
+        out_shape = (int(atr['LENGTH']), int(atr['WIDTH']))
+        vprint(
+            f'PYSOLID: resize data to the shape of {out_shape} '
+            'using order-1 spline interpolation')
+
+        enu = np.stack([tide_e, tide_n, tide_u])
+        zoom_factors = [1, *np.divide(out_shape, in_shape)]
+        kwargs = dict(order=1, mode="nearest", grid_mode=True)
+        tide_e, tide_n, tide_u = ndimage.zoom(enu, zoom_factors, **kwargs)
+
+    # plot
+    if display:
+        plot_solid_earth_tides_grid(tide_e, tide_n, tide_u, dt_obj)
+
+    return tide_e, tide_n, tide_u
+
+
+#########################################  Plot  ###############################################
+def plot_solid_earth_tides_grid(tide_e, tide_n, tide_u, dt_obj=None,
+                                out_fig=None, save=False, display=True):
+    """Plot the solid Earth tides in ENU direction."""
+    from matplotlib import pyplot as plt, ticker
+
+    # plot
+    fig, axs = plt.subplots(nrows=1, ncols=3, figsize=[6, 3], sharex=True, sharey=True)
+    for ax, data, label in zip(axs.flatten(),
+                               [tide_e, tide_n, tide_u],
+                               ['East', 'North', 'Up']):
+        im = ax.imshow(data*100, cmap='RdBu')
+        ax.tick_params(which='both', direction='in', bottom=True, top=True, left=True, right=True)
+        fig.colorbar(im, ax=ax, orientation='horizontal', label=label+' [cm]', pad=0.1, ticks=ticker.MaxNLocator(3))
+    fig.tight_layout()
+
+    # super title
+    if dt_obj is not None:
+        axs[1].set_title('solid Earth tides at {}'.format(dt_obj.isoformat()), fontsize=12)
+
+    # output
+    if out_fig:
+        save = True
+
+    if save:
+        if not out_fig:
+            out_fig = os.path.abspath('SET_grid.png')
+        print('save figure to {}'.format(out_fig))
+        fig.savefig(out_fig, bbox_inches='tight', transparent=True, dpi=300)
+
+    if display:
+        print('showing...')
+        plt.show()
+    else:
+        plt.close()
+
+    return