Merge branch 'master' into pre-commit-ci-update-config

data/shapefiles/Ethiopia_Tigray_2022_boundary/Ethiopia_Tigray_2022_boundary.cpg

@@ -0,0 +1 @@
+ISO-8859-1

data/shapefiles/Ethiopia_Tigray_2022_boundary/Ethiopia_Tigray_2022_boundary.prj

@@ -0,0 +1 @@
+GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]

maps/Sudan/area-sudan-22sept2024.csv

@@ -0,0 +1,3 @@
+Year,AlJazirah crop area,95% CI,AlJazirah Non-crop area,95% CI,AlQadarif crop area,95% CI,AlQadarif Non-crop area,95% CI,WestDarfur crop area,95% CI,WestDarfur Non-crop area,95% CI,CentralDarfur crop area,95% CI,CentralDarfur Non-crop area,95% CI,SouthDarfur crop area,95% CI,SouthDarfur Non-crop area,95% CI
+2022,1038357.67,211911.48,1405219.82,211911.48,3699444.03,327081.69,2728299.09,327081.69,365424.27,155661.61,1911921.47,155661.61,557058.29,185579.4,3165385.83,185579.4,1473342.87,287520.97,6349430.03,287520.97
+2023,1165285.74,209330.3,1278291.75,209330.3,3710186.82,337116.99,2717556.29,337116.99,351607.46,150545.59,1925738.28,150545.59,562417.16,178617.87,3160026.96,178617.87,1261626.04,291377.41,6561146.86,291377.41

maps/Sudan/config-area-sudan.yml

@@ -0,0 +1,63 @@
+rois:
+
+  - roi_name: AlJazirah
+    roi_boundary_path: '../data/shapefiles/aljazirah_boundary.zip'
+    samples_and_cropmap:
+      - year: 2022
+        set1_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_AlJazirah_2022_dw_may_march_cropmask-32637-cropped.tif'
+      - year: 2023
+        set1_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_AlJazirah_2023_dw_may_march_cropmask-32637-cropped.tif'
+
+  - roi_name: AlQadarif
+    roi_boundary_path: '../data/shapefiles/alqadarif_boundary.zip'
+    samples_and_cropmap:
+      - year: 2022
+        set1_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_AlQadarif_2022_dw_may_march_cropmask-32637-cropped.tif'
+      - year: 2023
+        set1_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_AlQadarif_2023_dw_may_march_cropmask-32637-cropped.tif'
+
+  - roi_name: WestDarfur
+    roi_boundary_path: '../data/shapefiles/westdarfur_boundary.zip'
+    samples_and_cropmap:
+      - year: 2022
+        set1_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_WestDarfur_2022_dw_may_march_cropmask-32635-cropped.tif'
+      - year: 2023
+        set1_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_WestDarfur_2023_dw_may_march_cropmask-32635-cropped.tif'
+
+  - roi_name: CentralDarfur
+    roi_boundary_path: '../data/shapefiles/centraldarfur_boundary.zip'
+    samples_and_cropmap:
+      - year: 2022
+        set1_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_CentralDarfur_2022_dw_may_march_cropmask-32635-cropped.tif'
+      - year: 2023
+        set1_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_CentralDarfur_2023_dw_may_march_cropmask-32635-cropped.tif'
+
+  - roi_name: SouthDarfur
+    roi_boundary_path: '../data/shapefiles/southdarfur_boundary.zip'
+    samples_and_cropmap:
+      - year: 2022
+        set1_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2022_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_SouthDarfur_2022_dw_may_march_cropmask-32635-cropped.tif'
+      - year: 2023
+        set1_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        set2_labels_path: '../maps/Sudan/sudan_2023_updated22sept2024.csv'
+        crop_mask_path: '../maps/Sudan/rasters/Sudan_dw_SouthDarfur_2023_dw_may_march_cropmask-32635-cropped.tif'
+
+output_path: '../maps/Sudan/area-sudan-22sept2024.csv'

src/area_utils.py

@@ -1,3 +1,4 @@
+import csv
 import json
 import os
 from typing import List, Optional, Tuple, Union
@@ -8,13 +9,55 @@
 import numpy as np
 import pandas as pd
 import rasterio as rio
+import seaborn as sns
+import yaml
 from osgeo import gdal
 from rasterio import transform
 from rasterio.mask import mask
 from shapely.geometry import box
 from sklearn.metrics import confusion_matrix
 
 
+def plot_confusion_matrix(cm, labels, datatype="d") -> None:
+    """Pretty prints confusion matrix.
+
+    Expects row 'Reference' and column 'Prediction/Map' ordered confusion matrix.
+
+    Args:
+        cm:
+            Confusion matrix of reference and map samples expressed in terms of
+            sample counts, n[i,j]. Row-column ordered reference-row, map-column.
+        labels:
+            List-like containing labels in same order as confusion matrix. For
+            example:
+
+            ["Stable NP", "PGain", "PLoss", "Stable P"]
+
+            ["Non-Crop", "Crop"]
+
+    """
+
+    _, ax = plt.subplots(nrows=1, ncols=1)
+    sns.heatmap(
+        cm,
+        cmap="crest",
+        annot=True,
+        fmt=datatype,
+        cbar=False,
+        square=True,
+        ax=ax,
+        annot_kws={"size": 20},
+    )
+    ax.xaxis.tick_top()
+    ax.xaxis.set_label_coords(0.50, 1.125)
+    ax.yaxis.set_label_coords(-0.125, 0.50)
+    ax.set_xticklabels(labels=labels, fontsize=16)
+    ax.set_yticklabels(labels=labels, fontsize=16)
+    ax.set_xlabel("Map", fontsize=20)
+    ax.set_ylabel("Reference", fontsize=20)
+    plt.tight_layout()
+
+
 def gdal_reproject(target_crs: str, source_crs: str, source_fn: str, dest_fn: str) -> None:
     cmd = (
         f"gdalwarp -t_srs {target_crs} -s_srs {source_crs} -tr 10 10 "
@@ -175,7 +218,7 @@ def cal_map_area_class(
         crop_area = crop_px[0].shape[0] * (px_size * px_size) / 10000
         noncrop_area = noncrop_px[0].shape[0] * (px_size * px_size) / 10000
         print(
-            f"Crop area: {crop_area:.2f} ha, Non-crop area: {noncrop_area:.2f} ha \n \
+            f"[Pixel counting] Crop area: {crop_area:.2f} ha, Non-crop area: {noncrop_area:.2f} ha \n \
              Total area: {crop_area + noncrop_area:.2f} ha"
         )
 
@@ -190,7 +233,7 @@ def cal_map_area_class(
     elif unit == "fraction":
         crop_area = int(crop_px[0].shape[0]) / total
         noncrop_area = int(noncrop_px[0].shape[0]) / total
-        print(f"Crop area: {crop_area:.2f} fraction, Non-crop area: {noncrop_area:.2f} fraction")
+        print(f"[Fraction] Crop area: {crop_area:.2f}, Non-crop area: {noncrop_area:.2f}")
         assert crop_area + noncrop_area == 1
 
     else:
@@ -316,7 +359,9 @@ def reference_sample_agree(
         px, py = transform.rowcol(meta["transform"], lat, lon)
 
         try:
-            ceo_agree_geom.loc[r, "Mapped class"] = int(binary_map[px, py])
+
+            ceo_agree_geom.loc[r, "Mapped class"] = int(binary_map[int(px), int(py)])
+
             if (
                 row[label_question].lower() == "cropland"
                 or row[label_question].lower() == "crop"
@@ -741,3 +786,185 @@ def plot_area(summary: pd.DataFrame) -> None:
 
     plt.tight_layout()
     plt.show()
+
+
+def area_estimate_pipeline(
+    aoi_path: str, map_path: str, ceo_set_1: str, ceo_set_2: str, visual_outputs: bool
+) -> dict:
+    """Returns area estimate for a particular region of interest (ROI) using cropland raster and labels.
+
+    Args:
+        aoi_path (str): The file path to the Area of Interest (AOI) ShapeFile/GeoJSON file, which defines the region for which the area estimates are computed.
+        map_path (str): The file path to the cropland raster file (.tif) that contains the land cover map of the area of interest.
+        ceo_set_1 (str): The file path to the first CEO (Collect Earth Online) set, which includes ground truth labels.
+        ceo_set_2 (str): The file path to the second CEO set, which includes additional ground truth labels for further validation or comparison.
+        visual_outputs (bool): A boolean flag indicating whether to generate visual outputs (plots, maps, etc.) to visualize the results.
+
+    Returns:
+        dict: A dictionary containing area estimates and accuracy metrics for each class in the confusion matrix.
+
+        The dictionary has the following keys:
+            - 'user_accuracy': A list of user's accuracy values for each class.
+            - 'producer_accuracy': A list of producer's accuracy values for each class.
+            - 'area_estimates': A nested dictionary containing area estimates and 95% confidence intervals in different units:
+                - 'pr': Proportional area estimates and confidence intervals.
+                - 'px': Area estimates and confidence intervals in pixels.
+                - 'ha': Area estimates and confidence intervals in hectares.
+            - 'confidence_interval': The 95% confidence interval for each class.
+
+    """
+    aoi = gpd.read_file(aoi_path)
+    roi = aoi.dissolve()
+
+    map_array, map_meta = load_raster(map_path, roi)
+
+    if map_array.data.dtype == "uint8":
+        binary_map = map_array
+    else:
+        binary_map = binarize(map_array, map_meta)
+
+    crop_area_px, noncrop_area_px = cal_map_area_class(binary_map, unit="pixels")
+    crop_area_ha, noncrop_area_ha = cal_map_area_class(binary_map, unit="ha")
+    crop_area_frac, noncrop_area_frac = cal_map_area_class(binary_map, unit="fraction")
+
+    ceo_geom = reference_sample_agree(binary_map, map_meta, ceo_set_1, ceo_set_2)
+    ceo_geom = ceo_geom[ceo_geom["Mapped class"] != 255]
+
+    cm = compute_confusion_matrix(ceo_geom)
+
+    a_j = np.array([noncrop_area_px, crop_area_px], dtype=np.int64)
+    total_px = a_j.sum()
+    w_j = a_j / total_px
+    am = compute_area_error_matrix(cm, w_j)
+
+    px_size = map_meta["transform"][0]
+
+    estimates = compute_area_estimate(cm, a_j, px_size)
+
+    if visual_outputs:
+        plt.imshow(binary_map, cmap="YlGn", vmin=0, vmax=1)
+        plt.show()
+        plot_confusion_matrix(cm, ["Non-crop", "Crop"])
+        plot_confusion_matrix(am, ["Non-crop", "Crop"], datatype="0.2f")
+        a_ha, err_ha = estimates["area"]["ha"]
+        u_j, err_u_j = estimates["user"]
+        p_i, err_p_i = estimates["producer"]
+        summary = create_area_estimate_summary(
+            a_ha, err_ha, u_j, err_u_j, p_i, err_p_i, columns=["Non-Crop", "Crop"]
+        )
+        print(summary)
+
+    return estimates
+
+
+def write_area_estimate_results_to_csv(data: dict, output_file: str) -> bool:
+    """
+    Writes area estimate results to a CSV file in an easy-to-interpret format.
+
+    Args:
+        data (dict): A nested dictionary containing the area estimates and their respective confidence intervals
+                     for different regions of interest (ROIs) and years. The dictionary structure is expected to be:
+                     {
+                        'ROI_name_1': {
+                            'year': [list of years],
+                            'crop area': [list of crop area estimates],
+                            '95%CI crop': [list of 95% confidence intervals for crop area],
+                            'Non-crop area': [list of non-crop area estimates],
+                            '95%CI noncrop': [list of 95% confidence intervals for non-crop area]
+                        },
+                        'ROI_name_2': {...},
+                        ...
+                     }
+        output_file (str): The file path where the output CSV will be saved.
+
+    Returns:
+        bool: Returns True when the CSV file is successfully written.
+
+    """
+
+    # The header based on the RoI results names(keys)
+    header = ["Year"]
+    for roi in data.keys():
+        header.extend([f"{roi} crop area", "95% CI", f"{roi} Non-crop area", "95% CI"])
+
+    with open(output_file, "w", newline="") as file:
+
+        writer = csv.writer(file)
+        writer.writerow(header)
+
+        years = data[list(data.keys())[0]]["year"]
+
+        for i, year in enumerate(years):
+            row = [year]
+            for roi in data.keys():
+                row.append(data[roi]["crop area"][i])
+                row.append(data[roi]["95%CI crop"][i])
+                row.append(data[roi]["Non-crop area"][i])
+                row.append(data[roi]["95%CI noncrop"][i])
+            writer.writerow(row)
+
+    return True
+
+
+def run_area_estimates_config(config: dict, show_output_charts: bool = False) -> dict:
+    """
+    Runs area estimates for multiple regions of interest (ROIs) and compiles the results.
+
+    Args:
+        config (dict): A dictionary containing configuration information for the ROIs and their associated data.
+                       It includes details such as the names of the ROIs, paths to boundary files, crop mask files,
+                       CEO datasets, and the output path for saving the CSV file.
+        show_output_charts (bool): A boolean flag indicating whether to display visual output charts during processing.
+
+    Returns:
+        dict: A dictionary containing area estimates and confidence intervals for each ROI and year.
+
+    Raises:
+        Exception: If there is an error writing the results to the CSV file.
+
+    """
+
+    all_results = {}
+    for roi in config["rois"]:
+        all_results[roi["roi_name"]] = {
+            "year": [],
+            "crop area": [],
+            "95%CI crop": [],
+            "Non-crop area": [],
+            "95%CI noncrop": [],
+        }
+        roi_results = all_results[roi["roi_name"]]
+
+        for yearly_data in roi["samples_and_cropmap"]:
+
+            print("\n" * 3 + f"_____ Running for {roi['roi_name']}, {yearly_data['year']} _____")
+
+            # Call the function for yearly estimate
+            estimates = area_estimate_pipeline(
+                aoi_path=roi["roi_boundary_path"],
+                map_path=yearly_data["crop_mask_path"],
+                ceo_set_1=yearly_data["set1_labels_path"],
+                ceo_set_2=yearly_data["set2_labels_path"],
+                visual_outputs=show_output_charts,
+            )
+
+            a_ha, err_ha = estimates["area"]["ha"]
+            a_ha, err_ha = a_ha.round(2), err_ha.round(2)
+
+            non_crop_area = a_ha[0]
+            crop_area = a_ha[1]
+            non_crop_area_err = err_ha[0]
+            crop_area_err = err_ha[1]
+
+            # Keep yearly results
+            roi_results["year"].append(yearly_data["year"])
+            roi_results["crop area"].append(crop_area)
+            roi_results["95%CI crop"].append(crop_area_err)
+            roi_results["Non-crop area"].append(non_crop_area)
+            roi_results["95%CI noncrop"].append(non_crop_area_err)
+
+    if write_area_estimate_results_to_csv(all_results, config["output_path"]):
+        return all_results
+
+    else:
+        raise Exception("Error Writing Estimates to CSV")