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Added index then blend.

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This commit is contained in:
Felix Delattre 2026-04-11 17:39:19 +02:00
parent 8e7fb1de18
commit 55d6facc4d
8 changed files with 661 additions and 68 deletions
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221
metrics_indices.py
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@ -1,4 +1,5 @@
"""Index generation: NDVI and GCC from S2/S3/fusion GeoTIFFs."""
import json
import numpy as np
import rasterio
@ -67,7 +68,9 @@ def _get_ndvi_value(ndvi_file, site_position):
return None
def _create_timeseries_for_dir(input_dir, output_dir, site_position, source_name, pattern="*.geotiff"):
def _create_timeseries_for_dir(
input_dir, output_dir, site_position, source_name, pattern="*.geotiff"
):
print(f"[NDVI-{source_name}] Creating timeseries.json...")
timeseries = []
@ -196,13 +199,23 @@ def create_ndvi_timeseries_post_process(season, site_position, site_name):
processed_dir = f"processed_{strategy}_sigma{sigma}"
for source in ["s2", "s3"]:
input_dir = Path(f"data/{site_name}/{season}/{processed_dir}/{source}/")
output_dir = Path(f"data/{site_name}/{season}/{processed_dir}/ndvi/{source}/")
output_dir = Path(
f"data/{site_name}/{season}/{processed_dir}/ndvi/{source}/"
)
_create_timeseries_for_dir(
input_dir, output_dir, site_position, f"POST-PROCESS-{source.upper()}-{strategy}-σ{sigma}"
input_dir,
output_dir,
site_position,
f"POST-PROCESS-{source.upper()}-{strategy}-σ{sigma}",
)
input_dir = Path(f"data/{site_name}/{season}/{processed_dir}/fusion/")
output_dir = Path(f"data/{site_name}/{season}/{processed_dir}/ndvi/fusion/")
_create_timeseries_for_dir(input_dir, output_dir, site_position, f"POST-PROCESS-FUSION-{strategy}-σ{sigma}")
_create_timeseries_for_dir(
input_dir,
output_dir,
site_position,
f"POST-PROCESS-FUSION-{strategy}-σ{sigma}",
)
def _calculate_and_write_gcc(input_file, output_file):
@ -261,6 +274,25 @@ def _get_gcc_from_original(input_file, site_position):
"""Calculate GCC directly from original file without creating GeoTIFF."""
try:
with rasterio.open(input_file) as src:
if src.count == 1:
g = src.read(1).astype(np.float32)
lon, lat = site_position[1], site_position[0]
x, y = transform_coords("EPSG:4326", src.crs, [lon], [lat])
if not (
src.bounds.left <= x[0] <= src.bounds.right
and src.bounds.bottom <= y[0] <= src.bounds.top
):
return None
row, col = src.index(x[0], y[0])
if row < 0 or row >= src.height or col < 0 or col >= src.width:
return None
r0, r1 = max(0, row - 1), min(src.height, row + 2)
c0, c1 = max(0, col - 1), min(src.width, col + 2)
win = g[r0:r1, c0:c1]
mask = np.isfinite(win) & (win > 0)
if not np.any(mask):
return None
return float(np.mean(win[mask]))
if src.count < 3:
return None
@ -290,11 +322,21 @@ def _get_gcc_from_original(input_file, site_position):
# Calculate GCC for each pixel in window
total = red_window + green_window + blue_window
mask = (total > 0) & ~np.isnan(total) & (blue_window >= 0) & (green_window >= 0) & (red_window >= 0)
mask = (
(total > 0)
& ~np.isnan(total)
& (blue_window >= 0)
& (green_window >= 0)
& (red_window >= 0)
)
if not np.any(mask):
negative_pixels = np.sum((blue_window < 0) | (green_window < 0) | (red_window < 0))
negative_pixels = np.sum(
(blue_window < 0) | (green_window < 0) | (red_window < 0)
)
if negative_pixels > 0:
print(f"Warning: {input_file.name} excluded - all pixels have negative band values ({negative_pixels} negative pixels in window)")
print(
f"Warning: {input_file.name} excluded - all pixels have negative band values ({negative_pixels} negative pixels in window)"
)
return None
gcc_window = np.zeros_like(green_window, dtype=np.float32)
@ -303,11 +345,13 @@ def _get_gcc_from_original(input_file, site_position):
# Return mean of valid GCC values
valid_gcc = gcc_window[mask]
return float(np.mean(valid_gcc)) if len(valid_gcc) > 0 else None
except Exception as e:
except Exception:
return None
def _create_gcc_timeseries_for_dir(input_dir, output_dir, site_position, source_name, pattern="*.geotiff"):
def _create_gcc_timeseries_for_dir(
input_dir, output_dir, site_position, source_name, pattern="*.geotiff"
):
print(f"[GCC-{source_name}] Creating timeseries.json...")
timeseries = []
@ -342,7 +386,9 @@ def _create_gcc_timeseries_for_dir(input_dir, output_dir, site_position, source_
f"[GCC-{source_name}] Warning: Could not sample {filename} (outside bounds or nodata)"
)
timeseries.append({"date": date, "filename": filename, "greenness_index": gcc_value})
timeseries.append(
{"date": date, "filename": filename, "greenness_index": gcc_value}
)
timeseries.sort(key=lambda x: x["date"])
output_dir.mkdir(parents=True, exist_ok=True)
@ -400,13 +446,41 @@ def create_gcc_timeseries_post_process(season, site_position, site_name):
processed_dir = f"processed_{strategy}_sigma{sigma}"
for source in ["s2", "s3"]:
input_dir = Path(f"data/{site_name}/{season}/{processed_dir}/{source}/")
output_dir = Path(f"data/{site_name}/{season}/{processed_dir}/gcc/{source}/")
output_dir = Path(
f"data/{site_name}/{season}/{processed_dir}/gcc/{source}/"
)
_create_gcc_timeseries_for_dir(
input_dir, output_dir, site_position, f"POST-PROCESS-{source.upper()}-{strategy}-σ{sigma}"
input_dir,
output_dir,
site_position,
f"POST-PROCESS-{source.upper()}-{strategy}-σ{sigma}",
)
input_dir = Path(f"data/{site_name}/{season}/{processed_dir}/fusion/")
output_dir = Path(f"data/{site_name}/{season}/{processed_dir}/gcc/fusion/")
_create_gcc_timeseries_for_dir(input_dir, output_dir, site_position, f"POST-PROCESS-FUSION-{strategy}-σ{sigma}")
_create_gcc_timeseries_for_dir(
input_dir,
output_dir,
site_position,
f"POST-PROCESS-FUSION-{strategy}-σ{sigma}",
)
itb_dir = f"processed_{strategy}_itb_sigma{sigma}"
base_itb = Path(f"data/{site_name}/{season}/{itb_dir}")
if not base_itb.exists():
continue
for source in ["s2", "s3"]:
inp, out = base_itb / source, base_itb / "gcc" / source
_create_gcc_timeseries_for_dir(
inp,
out,
site_position,
f"POST-ITB-{source.upper()}-{strategy}-σ{sigma}",
)
_create_gcc_timeseries_for_dir(
base_itb / "fusion",
base_itb / "gcc" / "fusion",
site_position,
f"POST-ITB-FUSION-{strategy}-σ{sigma}",
)
def _get_bands_from_original(input_file, site_position):
@ -425,7 +499,10 @@ def _get_bands_from_original(input_file, site_position):
row, col = src.index(x[0], y[0])
r0, r1 = max(0, row - 1), min(src.height, row + 2)
c0, c1 = max(0, col - 1), min(src.width, col + 2)
bands = [src.read(i + 1, window=((r0, r1), (c0, c1))).astype(np.float32) for i in range(4)]
bands = [
src.read(i + 1, window=((r0, r1), (c0, c1))).astype(np.float32)
for i in range(4)
]
mask = ~np.any([np.isnan(b) for b in bands], axis=0)
mask &= np.all([b > 0 for b in bands], axis=0)
if not np.any(mask):
@ -440,7 +517,9 @@ def _get_bands_from_original(input_file, site_position):
return None
def _create_bands_timeseries_for_dir(input_dir, output_dir, site_position, source_name, pattern="*.geotiff"):
def _create_bands_timeseries_for_dir(
input_dir, output_dir, site_position, source_name, pattern="*.geotiff"
):
print(f"[BANDS-{source_name}] Creating timeseries.json...")
timeseries = []
for f in sorted(input_dir.glob(pattern)):
@ -456,11 +535,14 @@ def _create_bands_timeseries_for_dir(input_dir, output_dir, site_position, sourc
timeseries.sort(key=lambda x: x["date"])
output_dir.mkdir(parents=True, exist_ok=True)
(output_dir / "timeseries.json").write_text(json.dumps(timeseries, indent=2))
print(f"[BANDS-{source_name}] Saved: {output_dir / 'timeseries.json'} ({len(timeseries)} entries)")
print(
f"[BANDS-{source_name}] Saved: {output_dir / 'timeseries.json'} ({len(timeseries)} entries)"
)
def _write_export(ndvi_dir, gcc_dir, bands_dir, export_dir):
"""Merge ndvi, gcc, bands into combined timeseries.json and timeseries.csv."""
def load(p):
p = Path(p)
if not p.exists():
@ -469,6 +551,7 @@ def _write_export(ndvi_dir, gcc_dir, bands_dir, export_dir):
return json.loads((p / "timeseries.json").read_text())
except Exception:
return []
ndvi = {str(t.get("date", ""))[:10]: t for t in load(ndvi_dir)}
gcc = {str(t.get("date", ""))[:10]: t for t in load(gcc_dir)}
bands = {str(t.get("date", ""))[:10]: t for t in load(bands_dir)}
@ -482,12 +565,16 @@ def _write_export(ndvi_dir, gcc_dir, bands_dir, export_dir):
export_dir.mkdir(parents=True, exist_ok=True)
(export_dir / "timeseries.json").write_text(json.dumps(merged, indent=2))
cols = ["date", "filename", "ndvi", "greenness_index", "b02", "b03", "b04", "b8a"]
def esc(v):
s = str(v) if v is not None else ""
return f'"{s}"' if "," in s or '"' in s else s
rows = [cols] + [[esc(r.get(c)) for c in cols] for r in merged]
(export_dir / "timeseries.csv").write_text("\n".join(",".join(x) for x in rows))
print(f"[EXPORT] Saved {export_dir / 'timeseries.json'} and timeseries.csv ({len(merged)} entries)")
print(
f"[EXPORT] Saved {export_dir / 'timeseries.json'} and timeseries.csv ({len(merged)} entries)"
)
def create_prepared_fusion_timeseries(season, site_position, site_name):
@ -497,17 +584,86 @@ def create_prepared_fusion_timeseries(season, site_position, site_name):
for source in ["s2", "s3"]:
inp = base / source
if inp.exists():
_create_timeseries_for_dir(inp, base / "ndvi" / source, site_position, f"PREPARED-{source.upper()}-{strategy}", "*.tif")
_create_gcc_timeseries_for_dir(inp, base / "gcc" / source, site_position, f"PREPARED-{source.upper()}-{strategy}", "*.tif")
_create_bands_timeseries_for_dir(inp, base / "bands" / source, site_position, f"PREPARED-{source.upper()}-{strategy}", "*.tif")
_write_export(base / "ndvi" / source, base / "gcc" / source, base / "bands" / source, base / "export" / source)
_create_timeseries_for_dir(
inp,
base / "ndvi" / source,
site_position,
f"PREPARED-{source.upper()}-{strategy}",
"*.tif",
)
_create_gcc_timeseries_for_dir(
inp,
base / "gcc" / source,
site_position,
f"PREPARED-{source.upper()}-{strategy}",
"*.tif",
)
_create_bands_timeseries_for_dir(
inp,
base / "bands" / source,
site_position,
f"PREPARED-{source.upper()}-{strategy}",
"*.tif",
)
_write_export(
base / "ndvi" / source,
base / "gcc" / source,
base / "bands" / source,
base / "export" / source,
)
for sig, fusion_sub in [(None, "fusion"), (30, "fusion_sigma30")]:
inp = base / fusion_sub
if inp.exists():
_create_timeseries_for_dir(inp, base / "ndvi" / fusion_sub, site_position, f"FUSION-{strategy}-σ{sig or 20}", "*.tif")
_create_gcc_timeseries_for_dir(inp, base / "gcc" / fusion_sub, site_position, f"FUSION-{strategy}-σ{sig or 20}", "*.tif")
_create_bands_timeseries_for_dir(inp, base / "bands" / fusion_sub, site_position, f"FUSION-{strategy}-σ{sig or 20}", "*.tif")
_write_export(base / "ndvi" / fusion_sub, base / "gcc" / fusion_sub, base / "bands" / fusion_sub, base / "export" / fusion_sub)
_create_timeseries_for_dir(
inp,
base / "ndvi" / fusion_sub,
site_position,
f"FUSION-{strategy}-σ{sig or 20}",
"*.tif",
)
_create_gcc_timeseries_for_dir(
inp,
base / "gcc" / fusion_sub,
site_position,
f"FUSION-{strategy}-σ{sig or 20}",
"*.tif",
)
_create_bands_timeseries_for_dir(
inp,
base / "bands" / fusion_sub,
site_position,
f"FUSION-{strategy}-σ{sig or 20}",
"*.tif",
)
_write_export(
base / "ndvi" / fusion_sub,
base / "gcc" / fusion_sub,
base / "bands" / fusion_sub,
base / "export" / fusion_sub,
)
itb = Path(f"data/{site_name}/{season}/prepared_{strategy}_itb")
if not itb.exists():
continue
for source in ["s2", "s3"]:
inp = itb / source
if inp.exists():
_create_gcc_timeseries_for_dir(
inp,
itb / "gcc" / source,
site_position,
f"PREPARED-ITB-{source.upper()}-{strategy}",
"*.tif",
)
for sig, fusion_sub in [(None, "fusion"), (30, "fusion_sigma30")]:
inp = itb / fusion_sub
if inp.exists():
_create_gcc_timeseries_for_dir(
inp,
itb / "gcc" / fusion_sub,
site_position,
f"FUSION-ITB-{strategy}-σ{sig or 20}",
"*.tif",
)
def create_bands_timeseries_post_process(season, site_position, site_name):
@ -518,5 +674,16 @@ def create_bands_timeseries_post_process(season, site_position, site_name):
for source in ["s2", "s3", "fusion"]:
inp, out = base / source, base / "bands" / source
if inp.exists():
_create_bands_timeseries_for_dir(inp, out, site_position, f"POST-{source.upper()}-{strategy}-σ{sigma}", "*.geotiff")
_write_export(base / "ndvi" / source, base / "gcc" / source, base / "bands" / source, base / "export" / source)
_create_bands_timeseries_for_dir(
inp,
out,
site_position,
f"POST-{source.upper()}-{strategy}-σ{sigma}",
"*.geotiff",
)
_write_export(
base / "ndvi" / source,
base / "gcc" / source,
base / "bands" / source,
base / "export" / source,
)