Removed post-processing function form Layers class and moved into tes…

…ting code

city_metrix/layers/layer.py

@@ -37,15 +37,6 @@ def get_data(self, bbox: Tuple[float]) -> Union[xr.DataArray, gpd.GeoDataFrame]:
         """
         ...
 
-    @abstractmethod
-    def prepare_for_map_rendering(self, data, **kwargs) -> Union[xr.DataArray, gpd.GeoDataFrame]:
-        """
-        Applies the standard post-processing adjustment used for rendering of the layer
-        :param are specific to the layer
-        :return: A rioxarray-format DataArray or a GeoPandas DataFrame
-        """
-        return data
-
     def mask(self, *layers):
         """
         Apply layers as masks
@@ -83,15 +74,13 @@ def write(self, bbox, output_path, tile_degrees=None, **kwargs):
             file_names = []
             for tile in tiles["geometry"]:
                 data = self.aggregate.get_data(tile.bounds)
-                data = self.prepare_for_map_rendering(data, **kwargs)
 
                 file_name = f"{output_path}/{uuid4()}.tif"
                 file_names.append(file_name)
 
                 write_layer(file_name, data)
         else:
             data = self.aggregate.get_data(bbox)
-            data = self.prepare_for_map_rendering(data, **kwargs)
             write_layer(output_path, data)
 
 

city_metrix/layers/ndvi_sentinel2_gee.py

@@ -1,5 +1,4 @@
 import ee
-from tools.xarray_tools import convert_ratio_to_percentage
 from .layer import Layer, get_image_collection
 
 class NdviSentinel2(Layer):
@@ -45,21 +44,3 @@ def calculate_ndvi(image):
         xdata = ndvi_data.to_dataarray()
 
         return xdata
-
-    def prepare_for_map_rendering(self, data, ndvi_threshold=0.4, convert_to_percentage=True, **kwargs):
-        """
-        Applies the standard post-processing adjustment used for rendering of NDVI including masking
-        to a threshold and conversion to percentage values.
-        :param ndvi_threshold: (float) minimum threshold for keeping values
-        :param convert_to_percentage: (bool) controls whether NDVI values are converted to a percentage
-        :return: A rioxarray-format DataArray
-        """
-        # Remove values less than the specified threshold
-        if ndvi_threshold is not None:
-            data = data.where(data >= ndvi_threshold)
-
-        # Convert to percentage in byte data_type
-        if convert_to_percentage is True:
-            data = convert_ratio_to_percentage(data)
-
-        return data

tests/resources/layer_dumps_for_br_lauro_de_freitas/test_write_layers_to_geotiff.py → tests/resources/layer_dumps_for_br_lauro_de_freitas/test_write_layers_to_qgis_files.py

@@ -1,8 +1,6 @@
 # This code is mostly intended for manual execution
 # Execution configuration is specified in the conftest file
-
 import pytest
-import os
 
 from city_metrix.layers import (
     Albedo,
@@ -23,7 +21,7 @@
     TreeCanopyHeight,
     TreeCover,
     UrbanLandUse,
-    WorldPop
+    WorldPop, Layer
 )
 from .conftest import RUN_DUMPS, prep_output_path, verify_file_is_populated
 
@@ -86,8 +84,7 @@ def test_write_natural_areas(target_folder, bbox_info):
 @pytest.mark.skipif(RUN_DUMPS == False, reason='Skipping since RUN_DUMPS set to False')
 def test_write_ndvi_sentinel2_gee(target_folder, bbox_info):
     file_path = prep_output_path(target_folder, 'ndvi_sentinel2_gee.tif')
-    (NdviSentinel2(year=2023)
-     .write(bbox_info.bounds, file_path, tile_degrees=None, ndvi_threshold=0.4, convert_to_percentage=True))
+    NdviSentinel2(year=2023).write(bbox_info.bounds, file_path, tile_degrees=None)
     assert verify_file_is_populated(file_path)
 
 @pytest.mark.skipif(RUN_DUMPS == False, reason='Skipping since RUN_DUMPS set to False')

tests/test_layer_dimensions.py

@@ -0,0 +1,21 @@
+from city_metrix.layers import NdviSentinel2
+from tests.resources.bbox_constants import BBOX_BRA_LAURO_DE_FREITAS_1
+from tests.tools import post_process_layer
+
+COUNTRY_CODE_FOR_BBOX = 'BRA'
+BBOX = BBOX_BRA_LAURO_DE_FREITAS_1
+
+def test_ndvi_dimensions():
+    data = NdviSentinel2(year=2023).get_data(BBOX)
+    data_for_map = post_process_layer(data, value_threshold=0.4, convert_to_percentage=True)
+
+    expected_size = 37213
+    actual_size = data_for_map.size
+    expected_min = 0
+    actual_min = data_for_map.values.min()
+    expected_max = 85
+    actual_max = data_for_map.values.max()
+
+    assert actual_size == expected_size
+    assert actual_min == expected_min
+    assert actual_max == expected_max

tests/tools.py

@@ -0,0 +1,35 @@
+import numpy as np
+
+def post_process_layer(data, value_threshold=0.4, convert_to_percentage=True):
+    """
+    Applies the standard post-processing adjustment used for rendering of NDVI including masking
+    to a threshold and conversion to percentage values.
+    :param value_threshold: (float) minimum threshold for keeping values
+    :param convert_to_percentage: (bool) controls whether NDVI values are converted to a percentage
+    :return: A rioxarray-format DataArray
+    """
+    # Remove values less than the specified threshold
+    if value_threshold is not None:
+        data = data.where(data >= value_threshold)
+
+    # Convert to percentage in byte data_type
+    if convert_to_percentage is True:
+        data = convert_ratio_to_percentage(data)
+
+    return data
+
+def convert_ratio_to_percentage(data):
+    """
+    Converts xarray variable from a ratio to a percentage
+    :param data: (xarray) xarray to be converted
+    :return: A rioxarray-format DataArray
+    """
+
+    # convert to percentage and to bytes for efficient storage
+    values_as_percent = np.round(data * 100).astype(np.uint8)
+
+    # reset CRS
+    source_crs = data.rio.crs
+    values_as_percent.rio.write_crs(source_crs, inplace=True)
+
+    return values_as_percent