dea-tools 0.3.3.dev21__tar.gz → 0.3.4.dev41__tar.gz

{dea_tools-0.3.3.dev21/dea_tools.egg-info → dea_tools-0.3.4.dev41}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dea-tools
-Version: 0.3.3.dev21
+Version: 0.3.4.dev41
 Summary: Functions and algorithms for analysing Digital Earth Australia data.
 Home-page: https://github.com/GeoscienceAustralia/dea-notebooks
 Author: Geoscience Australia

dea_tools-0.3.4.dev41/dea_tools/app/geomedian.py

@@ -0,0 +1,126 @@
+"""
+Geomedian widget: generates an interactive visualisation of
+the geomedian summary statistic. 
+"""
+
+# Load modules 
+import ipywidgets as widgets
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+import xarray as xr
+from odc.algo import xr_geomedian
+
+def run_app():
+    
+    """
+    An interactive app that allows users to visualise the difference between the median and geomedian time-series summary statistics. By modifying the red-green-blue values of three timesteps for a given pixel, the user changes the output summary statistics. 
+    
+    This allows a visual representation of the difference through the output values, RGB colour, as well as showing values plotted as a vector on a 3-dimensional  space.
+    
+    Last modified: December 2021
+    """
+    
+    # Define the red-green-blue sliders for timestep 1
+    p1r = widgets.IntSlider(description='Red', max=255, value=58)
+    p1g = widgets.IntSlider(description='Green', max=255, value=153)
+    p1b = widgets.IntSlider(description='Blue', max=255, value=68)
+
+    # Define the red-green-blue sliders for timestep 2
+    p2r = widgets.IntSlider(description='Red', max=255, value=208)
+    p2g = widgets.IntSlider(description='Green', max=255, value=221)
+    p2b = widgets.IntSlider(description='Blue', max=255, value=203)
+
+    # Define the red-green-blue sliders for timestep 3
+    p3r = widgets.IntSlider(description='Red', max=255, value=202)
+    p3g = widgets.IntSlider(description='Green', max=255, value=82)
+    p3b = widgets.IntSlider(description='Blue', max=255, value=33)
+
+    # Define the median calculation for the timesteps
+    def f(p1r, p1g, p1b, p2r, p2g, p2b, p3r, p3g, p3b):
+        print('Red Median = {}'.format(np.median([p1r, p2r, p3r])))
+        print('Green Median = {}'.format(np.median([p1g, p2g, p3g])))
+        print('Blue Median = {}'.format(np.median([p1b, p2b, p3b])))
+
+    # Define the geomedian calculation for the timesteps
+    def g(p1r, p1g, p1b, p2r, p2g, p2b, p3r, p3g, p3b):
+        print('Red Geomedian = {:.2f}'.format(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).red.values.ravel()[0]))    
+        print('Green Geomedian = {:.2f}'.format(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).green.values.ravel()[0]))    
+        print('Blue Geomedian = {:.2f}'.format(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).blue.values.ravel()[0]))    
+
+    # Define the Timestep 1 box colour
+    def h(p1r, p1g, p1b):
+        fig1, axes1 = plt.subplots(figsize=(2,2))
+        fig1 = plt.imshow([[(p1r, p1g, p1b)]])
+        axes1.set_title('Timestep 1')
+        axes1.axis('off')
+        plt.show(fig1)
+
+    # Define the Timestep 2 box colour
+    def hh(p2r, p2g, p2b):    
+        fig2, axes2 = plt.subplots(figsize=(2,2))
+        fig2 = plt.imshow([[(p2r, p2g, p2b)]])
+        axes2.set_title('Timestep 2')
+        axes2.axis('off')
+        plt.show(fig2)
+
+    # Define the Timestep 3 box colour
+    def hhh(p3r, p3g, p3b):    
+        fig3, axes3 = plt.subplots(figsize=(2,2))
+        fig3 = plt.imshow([[(p3r, p3g, p3b)]])
+        axes3.set_title('Timestep 3')
+        axes3.axis('off')
+        plt.show(fig3)
+
+    # Define the Median RGB colour box
+    def i(p1r, p1g, p1b, p2r, p2g, p2b, p3r, p3g, p3b):
+        fig4, axes4 = plt.subplots(figsize=(3,3))
+        fig4 = plt.imshow([[(int(np.median([p1r, p2r, p3r])), int(np.median([p1g, p2g, p3g])), int(np.median([p1b, p2b, p3b])))]])
+        axes4.set_title('Median RGB - All timesteps')
+        axes4.axis('off')
+        plt.show(fig4)
+
+    # Define the Geomedian RGB colour box
+    def ii(p1r, p1g, p1b, p2r, p2g, p2b, p3r, p3g, p3b):
+        fig5, axes5 = plt.subplots(figsize=(3,3))
+        fig5 = plt.imshow([[(int(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).red.values.ravel()[0]), int(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).green.values.ravel()[0]), int(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).blue.values.ravel()[0]))]])
+        axes5.set_title('Geomedian RGB - All timesteps')
+        axes5.axis('off')
+        plt.show(fig5)
+
+    # Define 3-D axis to display vectors on 
+    def j(p1r, p1g, p1b, p2r, p2g, p2b, p3r, p3g, p3b):
+        fig6 = plt.figure()
+        axes6 = fig6.add_subplot(111, projection='3d')
+        x = [p1r, p2r, p3r, int(np.median([p1r, p2r, p3r])), int(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).red.values.ravel()[0])]
+        y = [p1g, p2g, p3g, int(np.median([p1g, p2g, p3g])), int(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).green.values.ravel()[0])]
+        z = [p1b, p2b, p3b, int(np.median([p1b, p2b, p3b])), int(xr_geomedian(xr.Dataset({"red": (("x", "y", "time"), [[[np.float32(p1r), np.float32(p2r), np.float32(p3r)]]]), "green": (("x", "y", "time"), [[[np.float32(p1g), np.float32(p2g), np.float32(p3g)]]]),  "blue": (("x", "y", "time"), [[[np.float32(p1b), np.float32(p2b), np.float32(p3b)]]])})).blue.values.ravel()[0])]
+        labels = [' 1', ' 2', ' 3', ' median', ' geomedian']
+        axes6.scatter(x, y, z, c=['black','black','black','r', 'blue'], marker='o')
+        axes6.set_xlabel('Red')
+        axes6.set_ylabel('Green')
+        axes6.set_zlabel('Blue')
+        axes6.set_xlim3d(0, 255)
+        axes6.set_ylim3d(0, 255)
+        axes6.set_zlim3d(0, 255)
+        for ax, ay, az, label in zip(x, y, z, labels):
+            axes6.text(ax, ay, az, label)
+        plt.title('Each band represents a dimension.')
+        plt.show()
+
+    # Define outputs
+    outf = widgets.interactive_output(f, {'p1r': p1r, 'p2r': p2r,'p3r': p3r, 'p1g': p1g, 'p2g': p2g,'p3g': p3g, 'p1b': p1b, 'p2b': p2b,'p3b': p3b})
+    outg = widgets.interactive_output(g, {'p1r': p1r, 'p2r': p2r,'p3r': p3r, 'p1g': p1g, 'p2g': p2g,'p3g': p3g, 'p1b': p1b, 'p2b': p2b,'p3b': p3b})
+
+    outh = widgets.interactive_output(h, {'p1r': p1r, 'p1g': p1g, 'p1b': p1b})
+    outhh = widgets.interactive_output(hh, {'p2r': p2r, 'p2g': p2g, 'p2b': p2b})
+    outhhh = widgets.interactive_output(hhh, {'p3r': p3r, 'p3g': p3g, 'p3b': p3b})
+
+    outi = widgets.interactive_output(i, {'p1r': p1r, 'p2r': p2r,'p3r': p3r, 'p1g': p1g, 'p2g': p2g,'p3g': p3g, 'p1b': p1b, 'p2b': p2b,'p3b': p3b})
+    outii = widgets.interactive_output(ii, {'p1r': p1r, 'p2r': p2r,'p3r': p3r, 'p1g': p1g, 'p2g': p2g,'p3g': p3g, 'p1b': p1b, 'p2b': p2b,'p3b': p3b})
+
+    outj = widgets.interactive_output(j, {'p1r': p1r, 'p2r': p2r,'p3r': p3r, 'p1g': p1g, 'p2g': p2g,'p3g': p3g, 'p1b': p1b, 'p2b': p2b,'p3b': p3b})
+
+    app_output = widgets.HBox([widgets.VBox([widgets.HBox([outh, widgets.VBox([ p1r, p1g, p1b])]), widgets.HBox([outhh, widgets.VBox([p2r, p2g, p2b])]), widgets.HBox([outhhh, widgets.VBox([ p3r, p3g, p3b])])]), widgets.VBox([widgets.HBox([widgets.VBox([outf, outi]), widgets.VBox([outg, outii])]), outj])])
+    
+    return app_output

{dea_tools-0.3.3.dev21 → dea_tools-0.3.4.dev41}/dea_tools/app/widgetconstructors.py

@@ -274,7 +274,7 @@ def create_dea_wms_layer(product, date, **params):
     ----------
     product : string
         The Digital Earth Australia product to load
-        (e.g. 'ga_ls8c_nbart_gm_cyear_3')
+        (e.g. 'ga_ls8cls9c_gm_cyear_3')
     date : string (yyyy-mm-dd format)
         The date to load the product for
         

{dea_tools-0.3.3.dev21 → dea_tools-0.3.4.dev41}/dea_tools/spatial.py

@@ -16,7 +16,7 @@ here: https://gis.stackexchange.com/questions/tagged/open-data-cube).
 If you would like to report an issue with this script, file one on 
 GitHub: https://github.com/GeoscienceAustralia/dea-notebooks/issues/new
 
-Last modified: June 2024
+Last modified: July 2024
 
 """
 
@@ -33,8 +33,6 @@ import geopandas as gpd
 import rasterio.features
 import scipy.interpolate
 import multiprocessing as mp
-from odc.geo.geom import Geometry
-from odc.geo.crs import CRS
 from scipy import ndimage as nd
 from scipy.spatial import cKDTree as KDTree
 from skimage.measure import label
@@ -42,9 +40,74 @@ from rasterstats import zonal_stats
 from skimage.measure import find_contours
 from geopy.geocoders import Nominatim
 from geopy.exc import GeocoderUnavailable, GeocoderServiceError
+from shapely.geometry import (
+    MultiPoint,
+    MultiLineString,
+    LineString,
+    Polygon,
+    MultiPolygon,
+    Point,
+    shape,
+    mapping,
+)
 
 from datacube.utils.cog import write_cog
-from shapely.geometry import LineString, MultiLineString, shape, mapping
+from odc.geo.geom import Geometry
+from odc.geo.crs import CRS
+
+
+def _geom_to_multipoint(geom):
+    """
+    Convert a LineString, MultiLineString, Polygon, MultiPolygon or
+    Point to a MultiPoint geometry.
+    """
+    if isinstance(geom, LineString):
+        points = list(geom.coords)
+    elif isinstance(geom, MultiLineString):
+        points = [point for line in geom.geoms for point in line.coords]
+    elif isinstance(geom, Polygon):
+        points = list(geom.boundary.coords)
+    elif isinstance(geom, MultiPolygon):
+        points = [point for poly in geom.boundary.geoms for point in poly.coords]
+    elif isinstance(geom, Point):
+        points = [geom]
+    elif isinstance(geom, MultiPoint):
+        points = [point for point in geom.geoms]
+
+    return MultiPoint(points)
+
+
+def extract_vertices(gdf, explode=True, ignore_index=True):
+    """
+    Extract vertices from any GeoDataFrame features, returning Point or
+    MultiPoint geometries.
+
+    Parameters
+    ----------
+    gdf : geopandas.GeoDataFrame
+        Input GeoDataFrame containing geometries to be converted.
+    explode : bool, optional
+        By default, MultiPoint geometries will be exploded into individual
+        Points. If False, geometries will be returned as MultiPoints.
+    ignore_index : bool, optional
+        If True and explode=True, the resulting GeoDataFrame will have a
+        new index.
+
+    Returns
+    -------
+    geopandas.GeoDataFrame
+        Updated GeoDataFrame with geometries converted to Points or
+        MultiPoints.
+    """
+
+    # Convert all input features to MultiPoints
+    gdf["geometry"] = gdf["geometry"].apply(_geom_to_multipoint)
+
+    # Optionally break MultiPoints into individual Points
+    if explode:
+        gdf = gdf.explode(ignore_index=ignore_index)
+
+    return gdf
 
 
 def points_on_line(gdf, index, distance=30):
@@ -850,7 +913,7 @@ def xr_interpolate(
 
     # Run interpolation on values from each numeric column,
     for col, z_values in numeric_gdf.items():
-        
+
         # Apply scipy.interpolate.griddata interpolation methods
         if method in ("linear", "nearest", "cubic"):
             # Interpolate x, y and z values
@@ -1047,6 +1110,13 @@ def contours_to_arrays(gdf, col):
     of each vertex in the input GeoDataFrame.
 
     """
+    
+    warnings.warn(
+        "This function is deprecated and will be retired in a future "
+        "release. Please use `extract_vertices` instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
 
     coords_zvals = []
 

{dea_tools-0.3.3.dev21 → dea_tools-0.3.4.dev41}/dea_tools/wetlands.py

@@ -274,7 +274,7 @@ def display_wit_stack_with_df(
         ["open water", "wet", "green veg", "dry veg", "bare soil"][::-1],
         loc="lower left",
     )
-    handles = legend.legendHandles
+    handles = legend.legend_handles
 
     for i, handle in enumerate(handles):
         handle.set_facecolor(pal[::-1][i])

{dea_tools-0.3.3.dev21 → dea_tools-0.3.4.dev41/dea_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dea-tools
-Version: 0.3.3.dev21
+Version: 0.3.4.dev41
 Summary: Functions and algorithms for analysing Digital Earth Australia data.
 Home-page: https://github.com/GeoscienceAustralia/dea-notebooks
 Author: Geoscience Australia

{dea_tools-0.3.3.dev21 → dea_tools-0.3.4.dev41}/dea_tools.egg-info/SOURCES.txt

@@ -34,6 +34,7 @@ dea_tools/app/animations.py
 dea_tools/app/changefilmstrips.py
 dea_tools/app/crophealth.py
 dea_tools/app/deacoastlines.py
+dea_tools/app/geomedian.py
 dea_tools/app/imageexport.py
 dea_tools/app/miningrehab.py
 dea_tools/app/widgetconstructors.py