dea-tools 0.3.5.dev21__tar.gz → 0.3.6.dev1__tar.gz

{dea_tools-0.3.5.dev21/dea_tools.egg-info → dea_tools-0.3.6.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dea-tools
-Version: 0.3.5.dev21
+Version: 0.3.6.dev1
 Summary: Functions and algorithms for analysing Digital Earth Australia data.
 Home-page: https://github.com/GeoscienceAustralia/dea-notebooks
 Author: Geoscience Australia
@@ -44,7 +44,7 @@ Requires-Dist: pyproj
 Requires-Dist: pystac-client
 Requires-Dist: planetary-computer
 Requires-Dist: python-dateutil
-Requires-Dist: pyTMD<2.1.5,>=2.0.0
+Requires-Dist: pyTMD<=2.1.6
 Requires-Dist: pytz
 Requires-Dist: rasterio
 Requires-Dist: rasterstats

{dea_tools-0.3.5.dev21 → dea_tools-0.3.6.dev1}/dea_tools/coastal.py

@@ -288,120 +288,243 @@ def _model_tides(
         lat.max() + buffer,
     ]
 
-    # Read tidal constants and interpolate to grid points
-    if pytmd_model.format in ("OTIS", "ATLAS", "TMD3"):
-        amp, ph, D, c = pyTMD.io.OTIS.extract_constants(
-            lon,
-            lat,
-            pytmd_model.grid_file,
-            pytmd_model.model_file,
-            pytmd_model.projection,
-            type=pytmd_model.type,
-            crop=crop,
-            bounds=bounds,
-            method=method,
-            extrapolate=extrapolate,
-            cutoff=cutoff,
-            grid=pytmd_model.format,
+    # TEMPORARY HACK to work on both old and new pyTMD
+    try:
+            
+        # Read tidal constants and interpolate to grid points
+        if pytmd_model.format in ("OTIS", "ATLAS", "TMD3"):
+            amp, ph, D, c = pyTMD.io.OTIS.extract_constants(
+                lon,
+                lat,
+                pytmd_model.grid_file,
+                pytmd_model.model_file,
+                pytmd_model.projection,
+                type=pytmd_model.type,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                grid=pytmd_model.format,
+            )
+    
+            # Use delta time at 2000.0 to match TMD outputs
+            deltat = np.zeros((len(timescale)), dtype=np.float64)
+    
+        elif pytmd_model.format == "netcdf":
+            amp, ph, D, c = pyTMD.io.ATLAS.extract_constants(
+                lon,
+                lat,
+                pytmd_model.grid_file,
+                pytmd_model.model_file,
+                type=pytmd_model.type,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                scale=pytmd_model.scale,
+                compressed=pytmd_model.compressed,
+            )
+    
+            # Use delta time at 2000.0 to match TMD outputs
+            deltat = np.zeros((len(timescale)), dtype=np.float64)
+    
+        elif pytmd_model.format == "GOT":
+            amp, ph, c = pyTMD.io.GOT.extract_constants(
+                lon,
+                lat,
+                pytmd_model.model_file,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                scale=pytmd_model.scale,
+                compressed=pytmd_model.compressed,
+            )
+    
+            # Delta time (TT - UT1)
+            deltat = timescale.tt_ut1
+    
+        elif pytmd_model.format == "FES":
+            amp, ph = pyTMD.io.FES.extract_constants(
+                lon,
+                lat,
+                pytmd_model.model_file,
+                type=pytmd_model.type,
+                version=pytmd_model.version,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                scale=pytmd_model.scale,
+                compressed=pytmd_model.compressed,
+            )
+    
+            # Available model constituents
+            c = pytmd_model.constituents
+    
+            # Delta time (TT - UT1)
+            deltat = timescale.tt_ut1
+    
+        # Calculate complex phase in radians for Euler's
+        cph = -1j * ph * np.pi / 180.0
+    
+        # Calculate constituent oscillation
+        hc = amp * np.exp(cph)
+    
+        # Determine the number of points and times to process. If in
+        # "one-to-many" mode, these counts are used to repeat our extracted
+        # constituents and timesteps so we can extract tides for all
+        # combinations of our input times and tide modelling points.
+        # If in "one-to-one" mode, we avoid this step by setting counts to 1
+        # (e.g. "repeat 1 times")
+        points_repeat = len(x) if mode == "one-to-many" else 1
+        time_repeat = len(time) if mode == "one-to-many" else 1
+    
+        # If in "one-to-many" mode, repeat constituents to length of time
+        # and number of input coords before passing to `predict_tide_drift`
+        t, hc, deltat = (
+            np.tile(timescale.tide, points_repeat),
+            hc.repeat(time_repeat, axis=0),
+            np.tile(deltat, points_repeat),
         )
-
-        # Use delta time at 2000.0 to match TMD outputs
-        deltat = np.zeros((len(timescale)), dtype=np.float64)
-
-    elif pytmd_model.format == "netcdf":
-        amp, ph, D, c = pyTMD.io.ATLAS.extract_constants(
-            lon,
-            lat,
-            pytmd_model.grid_file,
-            pytmd_model.model_file,
-            type=pytmd_model.type,
-            crop=crop,
-            bounds=bounds,
-            method=method,
-            extrapolate=extrapolate,
-            cutoff=cutoff,
-            scale=pytmd_model.scale,
-            compressed=pytmd_model.compressed,
+    
+        # Predict tidal elevations at time and infer minor corrections
+        npts = len(t)
+        tide = np.ma.zeros((npts), fill_value=np.nan)
+        tide.mask = np.any(hc.mask, axis=1)
+    
+        # Predict tides
+        tide.data[:] = pyTMD.predict.drift(
+            t, hc, c, deltat=deltat, corrections=pytmd_model.format
         )
-
-        # Use delta time at 2000.0 to match TMD outputs
-        deltat = np.zeros((len(timescale)), dtype=np.float64)
-
-    elif pytmd_model.format == "GOT":
-        amp, ph, c = pyTMD.io.GOT.extract_constants(
-            lon,
-            lat,
-            pytmd_model.model_file,
-            crop=crop,
-            bounds=bounds,
-            method=method,
-            extrapolate=extrapolate,
-            cutoff=cutoff,
-            scale=pytmd_model.scale,
-            compressed=pytmd_model.compressed,
+        minor = pyTMD.predict.infer_minor(
+            t, hc, c, deltat=deltat, corrections=pytmd_model.format
         )
+        tide.data[:] += minor.data[:]
 
-        # Delta time (TT - UT1)
-        deltat = timescale.tt_ut1
-
-    elif pytmd_model.format == "FES":
-        amp, ph = pyTMD.io.FES.extract_constants(
-            lon,
-            lat,
-            pytmd_model.model_file,
-            type=pytmd_model.type,
-            version=pytmd_model.version,
-            crop=crop,
-            bounds=bounds,
-            method=method,
-            extrapolate=extrapolate,
-            cutoff=cutoff,
-            scale=pytmd_model.scale,
-            compressed=pytmd_model.compressed,
+    except:
+        # Read tidal constants and interpolate to grid points
+        if pytmd_model.format in ("OTIS", "ATLAS-compact", "TMD3"):
+            amp, ph, D, c = pyTMD.io.OTIS.extract_constants(
+                lon,
+                lat,
+                pytmd_model.grid_file,
+                pytmd_model.model_file,
+                pytmd_model.projection,
+                type=pytmd_model.type,
+                grid=pytmd_model.file_format,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+            )
+    
+            # Use delta time at 2000.0 to match TMD outputs
+            deltat = np.zeros((len(timescale)), dtype=np.float64)
+    
+        elif pytmd_model.format in ("ATLAS-netcdf",):
+            amp, ph, D, c = pyTMD.io.ATLAS.extract_constants(
+                lon,
+                lat,
+                pytmd_model.grid_file,
+                pytmd_model.model_file,
+                type=pytmd_model.type,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                scale=pytmd_model.scale,
+                compressed=pytmd_model.compressed,
+            )
+    
+            # Use delta time at 2000.0 to match TMD outputs
+            deltat = np.zeros((len(timescale)), dtype=np.float64)
+    
+        elif pytmd_model.format in ("GOT-ascii", "GOT-netcdf"):
+            amp, ph, c = pyTMD.io.GOT.extract_constants(
+                lon,
+                lat,
+                pytmd_model.model_file,
+                grid=pytmd_model.type,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                scale=pytmd_model.scale,
+                compressed=pytmd_model.compressed,
+            )
+    
+            # Delta time (TT - UT1)
+            deltat = timescale.tt_ut1
+    
+        elif pytmd_model.format in ("FES-ascii", "FES-netcdf"):
+            amp, ph = pyTMD.io.FES.extract_constants(
+                lon,
+                lat,
+                pytmd_model.model_file,
+                type=pytmd_model.type,
+                version=pytmd_model.version,
+                crop=crop,
+                bounds=bounds,
+                method=method,
+                extrapolate=extrapolate,
+                cutoff=cutoff,
+                scale=pytmd_model.scale,
+                compressed=pytmd_model.compressed,
+            )
+    
+            # Available model constituents
+            c = pytmd_model.constituents
+    
+            # Delta time (TT - UT1)
+            deltat = timescale.tt_ut1
+    
+        # Calculate complex phase in radians for Euler's
+        cph = -1j * ph * np.pi / 180.0
+    
+        # Calculate constituent oscillation
+        hc = amp * np.exp(cph)
+    
+        # Determine the number of points and times to process. If in
+        # "one-to-many" mode, these counts are used to repeat our extracted
+        # constituents and timesteps so we can extract tides for all
+        # combinations of our input times and tide modelling points.
+        # If in "one-to-one" mode, we avoid this step by setting counts to 1
+        # (e.g. "repeat 1 times")
+        points_repeat = len(x) if mode == "one-to-many" else 1
+        time_repeat = len(time) if mode == "one-to-many" else 1
+    
+        # If in "one-to-many" mode, repeat constituents to length of time
+        # and number of input coords before passing to `predict_tide_drift`
+        t, hc, deltat = (
+            np.tile(timescale.tide, points_repeat),
+            hc.repeat(time_repeat, axis=0),
+            np.tile(deltat, points_repeat),
         )
-
-        # Available model constituents
-        c = pytmd_model.constituents
-
-        # Delta time (TT - UT1)
-        deltat = timescale.tt_ut1
-
-    # Calculate complex phase in radians for Euler's
-    cph = -1j * ph * np.pi / 180.0
-
-    # Calculate constituent oscillation
-    hc = amp * np.exp(cph)
-
-    # Determine the number of points and times to process. If in
-    # "one-to-many" mode, these counts are used to repeat our extracted
-    # constituents and timesteps so we can extract tides for all
-    # combinations of our input times and tide modelling points.
-    # If in "one-to-one" mode, we avoid this step by setting counts to 1
-    # (e.g. "repeat 1 times")
-    points_repeat = len(x) if mode == "one-to-many" else 1
-    time_repeat = len(time) if mode == "one-to-many" else 1
-
-    # If in "one-to-many" mode, repeat constituents to length of time
-    # and number of input coords before passing to `predict_tide_drift`
-    t, hc, deltat = (
-        np.tile(timescale.tide, points_repeat),
-        hc.repeat(time_repeat, axis=0),
-        np.tile(deltat, points_repeat),
-    )
-
-    # Predict tidal elevations at time and infer minor corrections
-    npts = len(t)
-    tide = np.ma.zeros((npts), fill_value=np.nan)
-    tide.mask = np.any(hc.mask, axis=1)
-
-    # Predict tides
-    tide.data[:] = pyTMD.predict.drift(
-        t, hc, c, deltat=deltat, corrections=pytmd_model.format
-    )
-    minor = pyTMD.predict.infer_minor(
-        t, hc, c, deltat=deltat, corrections=pytmd_model.format
-    )
-    tide.data[:] += minor.data[:]
+    
+        # Predict tidal elevations at time and infer minor corrections
+        npts = len(t)
+        tide = np.ma.zeros((npts), fill_value=np.nan)
+        tide.mask = np.any(hc.mask, axis=1)
+    
+        # Predict tides
+        tide.data[:] = pyTMD.predict.drift(t, hc, c, deltat=deltat, corrections=pytmd_model.corrections)
+        minor = pyTMD.predict.infer_minor(
+            t,
+            hc,
+            c,
+            deltat=deltat,
+            corrections=pytmd_model.corrections,
+            minor=pytmd_model.minor,
+        )
+        tide.data[:] += minor.data[:]
 
     # Replace invalid values with fill value
     tide.data[tide.mask] = tide.fill_value
@@ -615,6 +738,10 @@ def model_tides(
     **ensemble_kwargs,
 ):
     """
+    DEPRECATED: This function has been moved to the `eo-tides` Python package,
+    and will be retired in a future release. Please migrate your code to use
+    `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/
+
     Compute tides at multiple points and times using tidal harmonics.
 
     This function supports all tidal models supported by `pyTMD`,
@@ -764,6 +891,14 @@ def model_tides(
     combination of time and point coordinates.
 
     """
+    warnings.warn(
+        "This function has been moved to the `eo-tides` Python package, "
+        "and will be retired in a future release. Please migrate your code "
+        "to use `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+
     # Set tide modelling files directory. If no custom path is provided,
     # first try global environmental var, then "/var/share/tide_models"
     if directory is None:
@@ -1046,6 +1181,10 @@ def pixel_tides(
     **model_tides_kwargs,
 ):
     """
+    DEPRECATED: This function has been moved to the `eo-tides` Python package,
+    and will be retired in a future release. Please migrate your code to use
+    `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/
+
     Obtain tide heights for each pixel in a dataset by modelling
     tides into a low-resolution grid surrounding the dataset,
     then (optionally) spatially resample this low-res data back
@@ -1148,6 +1287,14 @@ def pixel_tides(
     import odc.geo.xr
     from odc.geo.geobox import GeoBox
 
+    warnings.warn(
+        "This function has been moved to the `eo-tides` Python package, "
+        "and will be retired in a future release. Please migrate your code "
+        "to use `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+
     # First test if no time dimension and nothing passed to `times`
     if ("time" not in ds.dims) & (times is None):
         raise ValueError(
@@ -1326,6 +1473,10 @@ def tidal_tag(
     **model_tides_kwargs,
 ):
     """
+    DEPRECATED: This function has been moved to the `eo-tides` Python package,
+    and will be retired in a future release. Please migrate your code to use
+    `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/
+
     Takes an xarray.Dataset and returns the same dataset with a new
     `tide_m` variable giving the height of the tide at the exact
     moment of each satellite acquisition.
@@ -1378,6 +1529,14 @@ def tidal_tag(
 
     import odc.geo.xr
 
+    warnings.warn(
+        "This function has been moved to the `eo-tides` Python package, "
+        "and will be retired in a future release. Please migrate your code "
+        "to use `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+
     # If custom tide modelling locations are not provided, use the
     # dataset centroid
     if not tidepost_lat or not tidepost_lon:
@@ -1470,6 +1629,10 @@ def tidal_stats(
     **model_tides_kwargs,
 ):
     """
+    DEPRECATED: This function has been moved to the `eo-tides` Python package,
+    and will be retired in a future release. Please migrate your code to use
+    `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/
+
     Takes an xarray.Dataset and statistically compares the tides
     modelled for each satellite observation against the full modelled
     tidal range. This comparison can be used to evaluate whether the
@@ -1556,6 +1719,13 @@ def tidal_stats(
                   all available tide heights and time
 
     """
+    warnings.warn(
+        "This function has been moved to the `eo-tides` Python package, "
+        "and will be retired in a future release. Please migrate your code "
+        "to use `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/",
+        DeprecationWarning,
+        stacklevel=2,
+    )
 
     # Model tides for each observation in the supplied xarray object
     ds_tides, tidepost_lon, tidepost_lat = tidal_tag(
@@ -1738,6 +1908,10 @@ def tidal_tag_otps(
     return_tideposts=False,
 ):
     """
+    DEPRECATED: This function has been moved to the `eo-tides` Python package,
+    and will be retired in a future release. Please migrate your code to use
+    `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/
+
     Takes an xarray.Dataset and returns the same dataset with a new
     `tide_m` variable giving the height of the tide at the exact
     moment of each satellite acquisition.
@@ -1781,6 +1955,13 @@ def tidal_tag_otps(
     location used in the analysis).
 
     """
+    warnings.warn(
+        "This function has been moved to the `eo-tides` Python package, "
+        "and will be retired in a future release. Please migrate your code "
+        "to use `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/",
+        DeprecationWarning,
+        stacklevel=2,
+    )
 
     # Load tide modelling functions from either OTPS for pyfes
     try:
@@ -1879,6 +2060,10 @@ def tidal_stats_otps(
     round_stats=3,
 ):
     """
+    DEPRECATED: This function has been moved to the `eo-tides` Python package,
+    and will be retired in a future release. Please migrate your code to use
+    `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/
+
     Takes an xarray.Dataset and statistically compares the tides
     modelled for each satellite observation against the full modelled
     tidal range. This comparison can be used to evaluate whether the
@@ -1959,6 +2144,13 @@ def tidal_stats_otps(
                   all available tide heights and time
 
     """
+    warnings.warn(
+        "This function has been moved to the `eo-tides` Python package, "
+        "and will be retired in a future release. Please migrate your code "
+        "to use `eo-tides` instead: https://geoscienceaustralia.github.io/eo-tides/migration/",
+        DeprecationWarning,
+        stacklevel=2,
+    )
 
     # Load tide modelling functions from either OTPS for pyfes
     try:

{dea_tools-0.3.5.dev21 → dea_tools-0.3.6.dev1}/dea_tools/datahandling.py

@@ -1090,7 +1090,6 @@ def _esri_pansharpen(ds, pan_band, band_weights=None):
     ds_pansharpened : xarray.Dataset
         Pansharpened dataset with the same dimensions as the input dataset.
     """
-
     # Create new dataarrays with and without pan band
     da_nopan = ds.drop(pan_band).to_array()
     da_pan = ds[pan_band]
@@ -1157,6 +1156,8 @@ def _hsv_timestep_pansharpen(ds_i, pan_band):
     ds_pansharpened : xarray.Dataset
         Pansharpened dataset with the same dimensions as the input dataset.
     """
+    # Squeeze out any single dimensions
+    ds_i = ds_i.squeeze()
 
     # Convert to an xr.DataArray and move "variable" to end
     da_i = ds_i.to_array().transpose(..., "variable")
@@ -1209,6 +1210,8 @@ def _pca_timestep_pansharpen(ds_i, pan_band, pca_rescaling="histogram"):
     ds_pansharpened : xarray.Dataset
         Pansharpened dataset with the same dimensions as the input dataset.
     """
+    # Squeeze out any single dimensions
+    ds_i = ds_i.squeeze()
 
     # Reshape to 2D by stacking x and y dimensions to prepare it
     # as an input to PCA. Drop NA rows as these are not supported

{dea_tools-0.3.5.dev21 → dea_tools-0.3.6.dev1}/dea_tools/spatial.py

@@ -535,7 +535,7 @@ def subpixel_contours(
 
         contour_arrays = {
             _time_format(i, time_format): _contours_to_multiline(
-                da_i, z_values[0], min_vertices
+                da_i.squeeze(), z_values[0], min_vertices
             )
             for i, da_i in da.groupby(dim)
         }

{dea_tools-0.3.5.dev21 → dea_tools-0.3.6.dev1/dea_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dea-tools
-Version: 0.3.5.dev21
+Version: 0.3.6.dev1
 Summary: Functions and algorithms for analysing Digital Earth Australia data.
 Home-page: https://github.com/GeoscienceAustralia/dea-notebooks
 Author: Geoscience Australia
@@ -44,7 +44,7 @@ Requires-Dist: pyproj
 Requires-Dist: pystac-client
 Requires-Dist: planetary-computer
 Requires-Dist: python-dateutil
-Requires-Dist: pyTMD<2.1.5,>=2.0.0
+Requires-Dist: pyTMD<=2.1.6
 Requires-Dist: pytz
 Requires-Dist: rasterio
 Requires-Dist: rasterstats

{dea_tools-0.3.5.dev21 → dea_tools-0.3.6.dev1}/dea_tools.egg-info/requires.txt

@@ -26,7 +26,7 @@ pyproj
 pystac-client
 planetary-computer
 python-dateutil
-pyTMD<2.1.5,>=2.0.0
+pyTMD<=2.1.6
 pytz
 rasterio
 rasterstats

{dea_tools-0.3.5.dev21 → dea_tools-0.3.6.dev1}/setup.py

@@ -56,7 +56,7 @@ REQUIRED = [
     'pystac-client',
     'planetary-computer',
     'python-dateutil',
-    'pyTMD>=2.0.0,<2.1.5',    
+    'pyTMD<=2.1.6',    
     'pytz',
     'rasterio',
     'rasterstats',