Update animations app (#534)

* Add dev dependency group

* Simplify dev conda env setup

* Update gitignore

* Rename environment file

* Update conda env setup

* Add date filtering for timeseries

* minor update

* Remove unused imports

* Move imports to top level

* Move imports to top level

* Minor changes

* Add error handling for coastlines overlay

* Bump version

Tools/.pre-commit-config.yaml

@@ -27,9 +27,8 @@ repos:
  - id: isort
  name: isort (python)
  args:
- - "--config"
- - "Tools/"
- - "--resolve-all-configs"
+ - "--settings-path"
+ - "Tools/pyproject.toml"
 - repo: https://github.com/pycqa/flake8
  rev: 7.0.0
  hooks:

Tools/deafrica_tools/__init__.py

@@ -1,6 +1,6 @@
 __locales__ = __path__[0] + "/locales"
 
-__version__ = "2.4.6"
+__version__ = "2.4.7"
 
 
 def set_lang(lang=None):

Tools/deafrica_tools/app/animations.py

@@ -1,62 +1,41 @@
 # -*- coding: utf-8 -*-
 """
-Satellite imagery animation widget, which can be used to interactively 
+Satellite imagery animation widget, which can be used to interactively
 produce animations for multiple DE Africa products.
 """
 
-# Import required packages
-
 # Force GeoPandas to use Shapely instead of PyGEOS
 # In a future release, GeoPandas will switch to using Shapely by default.
 import os
-os.environ['USE_PYGEOS'] = '0'
 
-import fiona
-import sys
-import datacube
-import warnings
-import matplotlib.pyplot as plt
-from datacube.utils.geometry import CRS
-from ipyleaflet import (
- WMSLayer,
- basemaps,
- basemap_to_tiles,
- Map,
- DrawControl,
- WidgetControl,
- LayerGroup,
- LayersControl,
- GeoData,
-)
-from traitlets import Unicode
-from ipywidgets import (
- GridspecLayout,
- Button,
- Layout,
- HBox,
- VBox,
- HTML,
- Output,
-)
-import json
+os.environ["USE_PYGEOS"] = "0"
+
+import datetime
 import itertools
-import numpy as np
-import geopandas as gpd
+import json
+import warnings
 from io import BytesIO
-import ipywidgets as widgets
-import datetime
-from skimage import exposure
-from skimage.filters import unsharp_mask
 
-from datacube.utils import masking
+import datacube
+import geopandas as gpd
+import ipywidgets as widgets
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
 from datacube.utils.geometry import Geometry
 from datacube.utils.masking import mask_invalid_data
+from ipyleaflet import LayerGroup, basemap_to_tiles, basemaps
+from ipywidgets import HTML, Button, GridspecLayout, HBox, Layout, Output, VBox
+from skimage.exposure import rescale_intensity
+from skimage.filters import unsharp_mask
+
 import deafrica_tools.app.widgetconstructors as deawidgets
+from deafrica_tools.coastal import get_coastlines
 from deafrica_tools.dask import create_local_dask_cluster
+from deafrica_tools.datahandling import load_ard
+from deafrica_tools.plotting import xr_animation
 from deafrica_tools.spatial import reverse_geocode
-from deafrica_tools.datahandling import pan_sharpen_brovey
-
-import warnings
 
 warnings.filterwarnings("ignore")
 
@@ -119,7 +98,7 @@ def update_map_layers(self):
  # Clear all layers and add basemap
  self.map_layers.clear_layers()
  self.map_layers.add_layer(self.basemap)
- 
+
 
 def extract_data(self):
 
@@ -135,7 +114,7 @@ def extract_data(self):
  # Create query.
  start_date = np.datetime64(self.start_date)
  end_date = np.datetime64(self.end_date)
- 
+
  self.query_params = {
  "time": (str(start_date), str(end_date)),
  "geopolygon": geopolygon,
@@ -164,7 +143,6 @@ def extract_data(self):
  }
 
  # Load data
- from deafrica_tools.datahandling import load_ard
 
  timeseries_ds = load_ard(
  dc=dc,
@@ -197,9 +175,7 @@ def plot_data(self, fname):
  # If rolling median specified
  if self.rolling_median:
  with self.status_info:
- print(
- f"\nApplying rolling median ({self.rolling_median_window} timesteps window)"
- )
+ print(f"\nApplying rolling median ({self.rolling_median_window} timesteps window)")
  to_plot = to_plot.rolling(
  time=int(self.rolling_median_window), center=True, min_periods=1
  ).median()
@@ -215,7 +191,7 @@ def plot_data(self, fname):
  if self.power < 1.0:
  with self.status_info:
  print(f"\nApplying power transformation ({self.power})")
- to_plot = to_plot ** self.power
+ to_plot = to_plot**self.power
 
  # Apply unsharp masking to enhance overall dynamic range,
  # and improve fine scale detail
@@ -225,7 +201,6 @@ def plot_data(self, fname):
  f"\nApplying unsharp masking with {self.unsharp_mask_radius} "
  f"radius and {self.unsharp_mask_amount} amount"
  )
- from skimage.exposure import rescale_intensity
 
  funcs_list = [
  rescale_intensity,
@@ -236,8 +211,6 @@ def plot_data(self, fname):
  else:
  funcs_list = None
 
- from deafrica_tools.plotting import xr_animation
-
  xr_animation(
  output_path=fname,
  ds=to_plot.dropna(dim="time", how="all"),
@@ -260,39 +233,32 @@ def plot_data(self, fname):
 
 
 def deacoastlines_overlay(ds):
-
- import geopandas as gpd
- import pandas as pd
- import matplotlib
- from shapely.geometry import box, Point
- from deafrica_tools.coastal import get_coastlines
-
  # Get bounding box of data
  xmin, ymin, xmax, ymax = ds.geobox.geographic_extent.boundingbox
- bounds = [xmin, ymin, xmax, ymax]
+ bounds = (xmin, ymin, xmax, ymax)
 
  # Load data
  deacl_gdf = get_coastlines(bbox=bounds)
 
  # Clip to extent of satellite data
  bbox = gpd.GeoDataFrame(geometry=[ds.geobox.extent.geom], crs=ds.geobox.crs)
  deacl_gdf = gpd.overlay(deacl_gdf, bbox.to_crs(deacl_gdf.crs))
- deacl_gdf = deacl_gdf.dissolve("year") # values("year", ascending=True)
-
- # Apply colours
- norm = matplotlib.colors.Normalize(vmin=0, vmax=len(deacl_gdf.index))
- cmap = matplotlib.cm.get_cmap("inferno")
- rgba = cmap(norm(deacl_gdf.reset_index().index))
- deacl_gdf["color"] = list(rgba)
- deacl_gdf["start_time"] = pd.to_datetime(deacl_gdf.index) + pd.DateOffset(months=0)
- deacl_gdf = deacl_gdf.sort_index()
 
  if len(deacl_gdf.index) > 0:
+ deacl_gdf = deacl_gdf.dissolve("year") # values("year", ascending=True)
+ # Apply colours
+ norm = matplotlib.colors.Normalize(vmin=0, vmax=len(deacl_gdf.index))
+ cmap = matplotlib.cm.get_cmap("inferno")
+ rgba = cmap(norm(deacl_gdf.reset_index().index))
+ deacl_gdf["color"] = list(rgba)
+ deacl_gdf["start_time"] = pd.to_datetime(deacl_gdf.index) + pd.DateOffset(months=0)
+ deacl_gdf = deacl_gdf.sort_index()
  return deacl_gdf
  else:
+ print(f"No annual shorelines data available for bounding box {bounds}")
  return None
 
- 
+
 class animation_app(HBox):
  def __init__(self):
  super().__init__()
@@ -366,9 +332,7 @@ def __init__(self):
  ##################
 
  # Create the Header widget
- header_title_text = (
- "<h3>Digital Earth Africa satellite imagery animations</h3>"
- )
+ header_title_text = "<h3>Digital Earth Africa satellite imagery animations</h3>"
  instruction_text = (
  "<p>Select the desired satellite data, imagery date range "
  "and image style, then zoom in and draw a rectangle to "
@@ -415,10 +379,7 @@ def update_geojson(target, action, geo_json):
  "<b>(Overriding maximum size limit; use with caution as may lead to memory issues)</b></span>"
  )
  self.header.value = (
- header_title_text
- + instruction_text
- + polyarea_text
- + confirmation_text
+ header_title_text + instruction_text + polyarea_text + confirmation_text
  )
  self.gdf_drawn = gdf
  elif area <= 50000:
@@ -428,10 +389,7 @@ def update_geojson(target, action, geo_json):
  "recommended 50000 ha limit)</b></span>"
  )
  self.header.value = (
- header_title_text
- + instruction_text
- + polyarea_text
- + confirmation_text
+ header_title_text + instruction_text + polyarea_text + confirmation_text
  )
  self.gdf_drawn = gdf
  else:
@@ -466,7 +424,7 @@ def update_geojson(target, action, geo_json):
  self.map_layers.name = "Map Overlays"
 
  # Create map widget
- self.m = deawidgets.create_map(map_center=(5.65,  26.17), zoom_level=13)
+ self.m = deawidgets.create_map(map_center=(5.65, 26.17), zoom_level=13)
  self.m.layout = make_box_layout()
 
  # Add tools to map widget
@@ -481,24 +439,16 @@ def update_geojson(target, action, geo_json):
  ############################
 
  # Create parameter widgets
- dropdown_basemap = deawidgets.create_dropdown(
- self.basemap_list, self.basemap_list[0][1]
- )
- dropdown_dealayer = deawidgets.create_dropdown(
- self.dealayer_list, self.dealayer_list[0][1]
- )
- dropdown_output = deawidgets.create_dropdown(
- self.output_list, self.output_list[0][1]
- )
+ dropdown_basemap = deawidgets.create_dropdown(self.basemap_list, self.basemap_list[0][1])
+ dropdown_dealayer = deawidgets.create_dropdown(self.dealayer_list, self.dealayer_list[0][1])
+ dropdown_output = deawidgets.create_dropdown(self.output_list, self.output_list[0][1])
  date_picker_start = deawidgets.create_datepicker(
  value=start_date,
  )
  date_picker_end = deawidgets.create_datepicker(
  value=end_date,
  )
- dropdown_styles = deawidgets.create_dropdown(
- self.styles_list, self.styles_list[0]
- )
+ dropdown_styles = deawidgets.create_dropdown(self.styles_list, self.styles_list[0])
  slider_percentile = widgets.FloatRangeSlider(
  value=[0.01, 0.99],
  min=0,
@@ -520,14 +470,13 @@ def update_geojson(target, action, geo_json):
 
  checkbox_rolling_median = deawidgets.create_checkbox(
  self.rolling_median,
- "Apply rolling median<br>to produce smooth, <br> cloud-free animations",
- layout={"width": "90%",
- "height": "4em"},
+ "Apply rolling median to produce smooth, cloud-free animations",
+ layout={"width": "90%", "height": "4em"},
  )
  text_rolling_median_window = widgets.IntText(
  value=20,
  step=1,
- description="</br>Rolling window (timesteps)",
+ description="Rolling window (timesteps)",
  layout={
  "width": "85%",
  "margin": "0px",
@@ -537,25 +486,23 @@ def update_geojson(target, action, geo_json):
  )
 
  # Expandable advanced section
- text_interval = widgets.IntText(
- value=100, description="", step=50, layout={"width": "95%"}
- )
+ text_interval = widgets.IntText(value=100, description="", step=50, layout={"width": "95%"})
  text_resolution = widgets.FloatText(
  value=30,
  description="",
  layout={"width": "95%", "margin": "0px", "padding": "0px"},
  )
- text_width = widgets.IntText(
- value=900, description="", step=50, layout={"width": "95%"}
- )
+ text_width = widgets.IntText(value=900, description="", step=50, layout={"width": "95%"})
  dropdown_resampling = deawidgets.create_dropdown(
  self.resample_list,
  self.resample_freq,
  description="",
  layout={"width": "95%"},
  )
  checkbox_cloud_mask = deawidgets.create_checkbox(
- self.cloud_mask, "Mask out cloudy <br> pixels", layout={"width": "95%", "height": "auto"}
+ self.cloud_mask,
+ "Mask out cloudy pixels",
+ layout={"width": "95%", "height": "auto"},
  )
  slider_power = widgets.FloatSlider(
  value=1.0,
@@ -646,13 +593,9 @@ def update_geojson(target, action, geo_json):
  dropdown_styles.observe(self.update_styles, "value")
 
  slider_percentile.observe(self.update_slider_percentile, "value")
- floatslider_max_cloud_cover.observe(
- self.update_floatslider_max_cloud_cover, "value"
- )
+ floatslider_max_cloud_cover.observe(self.update_floatslider_max_cloud_cover, "value")
  checkbox_rolling_median.observe(self.update_checkbox_rolling_median, "value")
- text_rolling_median_window.observe(
- self.update_text_rolling_median_window, "value"
- )
+ text_rolling_median_window.observe(self.update_text_rolling_median_window, "value")
  dropdown_output.observe(self.update_output, "value")
  run_button.on_click(self.run_app)
  draw_control.on_draw(update_geojson)
@@ -824,7 +767,7 @@ def update_checkbox_max_size(self, change):
  # Add DE Africa Coastlines overlay
  def update_deacoastlines(self, change):
  self.deacoastlines = change.new
- 
+
  # Apply cloud mask in load_ard
  def update_checkbox_cloud_mask(self, change):
  self.cloud_mask = change.new
@@ -911,14 +854,10 @@ def run_app(self, change):
  fname = (
  f"{self.dealayer}_{site}_{self.start_date}_"
  f"{self.end_date}_{self.style}_{self.resolution:.0f}m."
- f"{self.output_format}".replace(" ", "")
- .replace(",", "")
- .lower()
+ f"{self.output_format}".replace(" ", "").replace(",", "").lower()
  )
 
- print(
- f"\nExporting animation for {site}.\nThis may take several minutes..."
- )
+ print(f"\nExporting animation for {site}.\nThis may take several minutes...")
 
  ############
  # Plotting #
@@ -937,6 +876,4 @@ def run_app(self, change):
 
  else:
  with self.status_info:
- print(
- 'Please draw a valid rectangle on the map, then press "Generate animation".'
- )
+ print('Please draw a valid rectangle on the map, then press "Generate animation".')

Tools/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "deafrica-tools"
 # reflect version changes in deafrica_tools/__init__.py
-version = "2.4.6"
+version = "2.4.7"
 description = "Functions and algorithms for analysing Digital Earth Africa data."
 authors = [{name = "Digital Earth Africa", email = "[email protected]"}]
 maintainers = [{name = "Digital Earth Africa", email = "[email protected]"}]