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Refactor using tqdm and pathlib #206

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7523c76
Update predict_on_data(), project_to_geojson(), stitch_crowns() with …
CiSong10 Sep 4, 2025
76cd62b
Rewrite functions with pathlib
CiSong10 Sep 24, 2025
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123 changes: 61 additions & 62 deletions detectree2/models/evaluation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,27 +191,24 @@ def tree_height(self):
# Regular functions now
def get_tile_width(file):
"""Split up the file name to get width and buffer then adding to get overall width."""
filename = file.replace(".geojson", "")
filename_split = filename.split("_")

tile_width = (2 * int(filename_split[-2]) + int(filename_split[-3]))

file = Path(file)
filename_split = file.stem.split("_")
tile_width = 2 * int(filename_split[-2]) + int(filename_split[-3])
return tile_width


def get_epsg(file):
"""Splitting up the file name to get EPSG"""
filename = file.replace(".geojson", "")
filename_split = filename.split("_")

file = Path(file)
filename_split = file.stem.split("_")
epsg = filename_split[-1]
return epsg


def get_tile_origin(file):
"""Splitting up the file name to get tile origin"""
filename = file.replace(".geojson", "")
filename_split = filename.split("_")
file = Path(file)
filename_split = file.stem.split("_")

buffer = int(filename_split[-2])
# center = int(filename_split[-3])
Expand Down Expand Up @@ -343,7 +340,7 @@ def initialise_feats(

def initialise_feats2(
directory,
file,
filename,
lidar_img,
area_threshold,
conf_threshold,
Expand All @@ -353,21 +350,21 @@ def initialise_feats2(
epsg
):
"""Creates a list of all the features as objects of the class."""
with open(directory + "/" + file) as feat_file:
feat_path = Path(directory) / filename
with feat_path.open() as feat_file:
feat_json = json.load(feat_file)
feats = feat_json["features"]

feats = feat_json["features"]
all_feats = []
count = 0

for feat in feats:
feat_obj = GeoFeature(file, directory, count, feat, lidar_img, epsg)
feat_obj = GeoFeature(filename, directory, count, feat, lidar_img, epsg)

if feat_threshold_tests2(feat_obj, conf_threshold, area_threshold,
border_filter, tile_width, tile_origin):
all_feats.append(feat_obj)
count += 1
else:
continue

return all_feats

Expand Down Expand Up @@ -634,10 +631,10 @@ def site_f1_score2(
area of the corresponding polygons.

Args:
tile_directory: path to the folder containing all of the tiles
test_directory: path to the folder containing just the test files
pred_directory: path to the folder containing the predictions and the reprojections
lidar_img: path to the lidar image of an entire region
tile_directory (str | Path): path to the folder containing all of the tiles
test_directory (str | Path): path to the folder containing just the test files
pred_directory (str | Path): path to the folder containing the predictions and the reprojections
lidar_img (str | Path): path to the lidar image of an entire region
IoU_threshold: minimum value of IoU such that the intersection can be considered a true positive
min_height: minimum height of the features to be considered
max_height: minimum height of the features to be considered
Expand All @@ -649,69 +646,71 @@ def site_f1_score2(
save: bool to tell program whether the filtered crowns should be saved
"""

test_entries = os.listdir(test_directory)
total_tps = 0
total_fps = 0
total_fns = 0
tile_directory = Path(tile_directory)
test_directory = Path(test_directory)
pred_directory = Path(pred_directory)

total_tps = total_fps = total_fns = 0
heights = []
# total_tests = 0

for file in test_entries:
if ".geojson" in file:
print(file)
for file in test_directory.iterdir():
if file.suffix != ".geojson":
continue

# work out the area threshold to ignore these crowns in the tiles
# tile_width = get_tile_width(file) * scaling[0]
# area_threshold = ((tile_width)**2) * area_fraction_limit
print(file.name)

tile_width = get_tile_width(file)
tile_origin = get_tile_origin(file)
epsg = get_epsg(file)
# work out the area threshold to ignore these crowns in the tiles
# tile_width = get_tile_width(file) * scaling[0]
# area_threshold = ((tile_width)**2) * area_fraction_limit

test_file = file #.replace(".geojson", "_geo.geojson")
all_test_feats = initialise_feats2(tile_directory, test_file,
lidar_img, area_threshold,
conf_threshold, border_filter,
tile_width, tile_origin, epsg)
tile_width = get_tile_width(file)
tile_origin = get_tile_origin(file)
epsg = get_epsg(file)

new_heights = get_heights(all_test_feats, min_height, max_height)
heights.extend(new_heights)
all_test_feats = initialise_feats2(tile_directory, file.name,
lidar_img, area_threshold,
conf_threshold, border_filter,
tile_width, tile_origin, epsg)

pred_file = "Prediction_" + file.replace(".geojson", "_eval.geojson")
all_pred_feats = initialise_feats2(pred_directory, pred_file,
lidar_img, area_threshold,
conf_threshold, border_filter,
tile_width, tile_origin, epsg)
new_heights = get_heights(all_test_feats, min_height, max_height)
heights.extend(new_heights)

if save:
save_feats(tile_directory, all_test_feats)
save_feats(tile_directory, all_pred_feats)
pred_file = "Prediction_" + file.stem + "_eval.geojson"
all_pred_feats = initialise_feats2(pred_directory, pred_file,
lidar_img, area_threshold,
conf_threshold, border_filter,
tile_width, tile_origin, epsg)

find_intersections(all_test_feats, all_pred_feats)
tps, fps, fns = positives_test(all_test_feats, all_pred_feats,
IoU_threshold, min_height, max_height)
if save:
save_feats(tile_directory, all_test_feats)
save_feats(tile_directory, all_pred_feats)

print("tps:", tps)
print("fps:", fps)
print("fns:", fns)
print("")
find_intersections(all_test_feats, all_pred_feats)
tps, fps, fns = positives_test(all_test_feats, all_pred_feats,
IoU_threshold, min_height, max_height)

total_tps += tps
total_fps += fps
total_fns += fns
print(f"tps: {tps}")
print(f"fps: {fps}")
print(f"fns: {fns}\n")

total_tps += tps
total_fps += fps
total_fns += fns

try:
prec, rec = prec_recall(total_tps, total_fps, total_fns)
# not used!
f1_score = f1_cal(prec, rec) # noqa: F841
med_height = median(heights)
print("Precision ", "Recall ", "F1")
print(prec, rec, f1_score)
print(" ")
print("Total_trees=", len(heights))
print("med_height=", med_height)
print(prec, rec, f1_score, "\n")
print(f"Total_trees = {len(heights)}")
print(f"med_height = {med_height}")

except ZeroDivisionError:
print("ZeroDivisionError: Height threshold is too large.")

return prec, rec, f1_score


Expand Down
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