Refactored a bit.
This commit is contained in:
Felix Delattre
parent
290c8f8c57
commit
6bbaa4b3eb
8 changed files with 323 additions and 331 deletions
168
ndvi.py
168
ndvi.py
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@ -5,12 +5,14 @@ from rasterio.warp import transform as transform_coords
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from pathlib import Path
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from datetime import datetime
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RED_BAND = 3
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NIR_BAND = 4
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def _calculate_and_write_ndvi(input_file, output_file):
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"""Calculate NDVI from red and NIR bands and write to output file."""
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with rasterio.open(input_file) as src:
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red = src.read(3).astype(np.float32)
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nir = src.read(4).astype(np.float32)
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red = src.read(RED_BAND).astype(np.float32)
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nir = src.read(NIR_BAND).astype(np.float32)
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mask = (red > 0) & (nir > 0)
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ndvi = np.zeros_like(red, dtype=np.float32)
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@ -31,13 +33,26 @@ def _calculate_and_write_ndvi(input_file, output_file):
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dst.set_band_description(1, "NDVI")
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def _get_ndvi_value(ndvi_file, site_position):
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try:
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with rasterio.open(ndvi_file) as src:
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lon, lat = site_position[1], site_position[0]
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x, y = transform_coords("EPSG:4326", src.crs, [lon], [lat])
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samples = list(src.sample([(x[0], y[0])]))
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if samples:
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value = float(samples[0][0])
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if value != 0 and not np.isnan(value):
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return value
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except Exception:
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pass
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return None
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def _create_timeseries_for_dir(output_dir, site_position, source_name):
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"""Create timeseries.json for NDVI files in the given directory."""
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print(f"[NDVI-{source_name}] Creating timeseries.json...")
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timeseries = []
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ndvi_files = sorted(output_dir.glob("*.geotiff"))
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for ndvi_file in ndvi_files:
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for ndvi_file in sorted(output_dir.glob("*.geotiff")):
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filename = ndvi_file.name
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date_str = filename.split("_")[0]
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try:
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@ -45,18 +60,9 @@ def _create_timeseries_for_dir(output_dir, site_position, source_name):
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except ValueError:
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date = date_str
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ndvi_value = None
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try:
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with rasterio.open(ndvi_file) as src:
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lon, lat = site_position[1], site_position[0]
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x, y = transform_coords("EPSG:4326", src.crs, [lon], [lat])
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samples = list(src.sample([(x[0], y[0])]))
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if samples:
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value = float(samples[0][0])
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if value != 0 and not np.isnan(value):
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ndvi_value = value
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except Exception as e:
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print(f"[NDVI-{source_name}] Warning: Could not sample {filename}: {e}")
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ndvi_value = _get_ndvi_value(ndvi_file, site_position)
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if ndvi_value is None:
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print(f"[NDVI-{source_name}] Warning: Could not sample {filename}")
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timeseries.append({"date": date, "filename": filename, "ndvi": ndvi_value})
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@ -68,30 +74,35 @@ def _create_timeseries_for_dir(output_dir, site_position, source_name):
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print(f"[NDVI-{source_name}] Saved: {timeseries_file} ({len(timeseries)} entries)")
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def _process_ndvi_files(
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input_dir, output_dir, source_name, pattern="*.geotiff", output_namer=None
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):
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output_dir.mkdir(parents=True, exist_ok=True)
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print(f"[NDVI-{source_name}] Processing {input_dir}...")
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geotiff_files = sorted(input_dir.glob(pattern))
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if not geotiff_files:
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print(f"[NDVI-{source_name}] No files found")
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return
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for geotiff_file in geotiff_files:
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output_file = output_dir / (
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output_namer(geotiff_file) if output_namer else geotiff_file.name
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)
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if output_file.exists():
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print(f"[NDVI-{source_name}] Skipping {geotiff_file.name} (exists)")
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continue
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_calculate_and_write_ndvi(geotiff_file, output_file)
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print(f"[NDVI-{source_name}] Saved: {output_file}")
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def generate_ndvi_raw(season, site_position, site_name):
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for source in ["s2", "s3"]:
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input_dir = Path(f"data/{site_name}/{season}/raw/{source}/")
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output_dir = Path(f"data/{site_name}/{season}/raw/ndvi/{source}/")
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output_dir.mkdir(parents=True, exist_ok=True)
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print(f"[NDVI-{source.upper()}] Processing {input_dir}...")
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geotiff_files = sorted(input_dir.glob("*.geotiff"))
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if not geotiff_files:
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print(f"[NDVI-{source.upper()}] No files found")
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continue
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for geotiff_file in geotiff_files:
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output_file = output_dir / geotiff_file.name
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if output_file.exists():
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print(f"[NDVI-{source.upper()}] Skipping {geotiff_file.name} (exists)")
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continue
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_calculate_and_write_ndvi(geotiff_file, output_file)
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print(f"[NDVI-{source.upper()}] Saved: {output_file}")
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print(f"[NDVI-{source.upper()}] Completed")
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_process_ndvi_files(input_dir, output_dir, source.upper())
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def create_ndvi_timeseries_raw(season, site_position, site_name):
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@ -100,67 +111,50 @@ def create_ndvi_timeseries_raw(season, site_position, site_name):
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_create_timeseries_for_dir(output_dir, site_position, source.upper())
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def _get_output_name_prepared(geotiff_file):
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if geotiff_file.suffix == ".tif":
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if "REFL" in geotiff_file.stem:
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date_str = geotiff_file.stem.split("_")[1]
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return f"{date_str}_ndvi.geotiff"
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return geotiff_file.name.replace(".tif", ".geotiff")
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return geotiff_file.name
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def _fusion_namer(f):
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date_str = f.stem.split("_")[1]
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return f"{date_str}_ndvi.geotiff"
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def generate_ndvi_prepared(season, site_position, site_name):
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for source in ["s2", "s3"]:
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input_dir = Path(f"data/{site_name}/{season}/prepared/{source}/")
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output_dir = Path(f"data/{site_name}/{season}/prepared/ndvi/{source}/")
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output_dir.mkdir(parents=True, exist_ok=True)
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print(f"[NDVI-PREPARED-{source.upper()}] Processing {input_dir}...")
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geotiff_files = sorted(input_dir.glob("*.geotiff")) + sorted(input_dir.glob("*.tif"))
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if not geotiff_files:
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print(f"[NDVI-PREPARED-{source.upper()}] No files found")
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continue
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for geotiff_file in geotiff_files:
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if geotiff_file.suffix == ".tif":
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if "REFL" in geotiff_file.stem:
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date_str = geotiff_file.stem.split("_")[1]
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output_file = output_dir / f"{date_str}_ndvi.geotiff"
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else:
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output_file = output_dir / geotiff_file.name.replace(".tif", ".geotiff")
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else:
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output_file = output_dir / geotiff_file.name
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if output_file.exists():
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print(f"[NDVI-PREPARED-{source.upper()}] Skipping {geotiff_file.name} (exists)")
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continue
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_calculate_and_write_ndvi(geotiff_file, output_file)
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print(f"[NDVI-PREPARED-{source.upper()}] Saved: {output_file}")
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print(f"[NDVI-PREPARED-{source.upper()}] Completed")
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for pattern in ["*.geotiff", "*.tif"]:
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_process_ndvi_files(
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input_dir,
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output_dir,
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f"PREPARED-{source.upper()}",
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pattern=pattern,
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output_namer=_get_output_name_prepared,
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)
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input_dir = Path(f"data/{site_name}/{season}/prepared/fusion/")
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output_dir = Path(f"data/{site_name}/{season}/prepared/ndvi/fusion/")
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output_dir.mkdir(parents=True, exist_ok=True)
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print(f"[NDVI-FUSION] Processing {input_dir}...")
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geotiff_files = sorted(input_dir.glob("REFL_*.tif"))
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if not geotiff_files:
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print(f"[NDVI-FUSION] No files found")
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return
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for geotiff_file in geotiff_files:
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date_str = geotiff_file.stem.split("_")[1]
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output_file = output_dir / f"{date_str}_ndvi.geotiff"
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if output_file.exists():
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print(f"[NDVI-FUSION] Skipping {geotiff_file.name} (exists)")
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continue
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_calculate_and_write_ndvi(geotiff_file, output_file)
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print(f"[NDVI-FUSION] Saved: {output_file}")
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print(f"[NDVI-FUSION] Completed")
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_process_ndvi_files(
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input_dir,
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output_dir,
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"FUSION",
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pattern="REFL_*.tif",
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output_namer=_fusion_namer,
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)
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def create_ndvi_timeseries_prepared(season, site_position, site_name):
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for source in ["s2", "s3"]:
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output_dir = Path(f"data/{site_name}/{season}/prepared/ndvi/{source}/")
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_create_timeseries_for_dir(output_dir, site_position, f"PREPARED-{source.upper()}")
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_create_timeseries_for_dir(
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output_dir, site_position, f"PREPARED-{source.upper()}"
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)
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output_dir = Path(f"data/{site_name}/{season}/prepared/ndvi/fusion/")
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_create_timeseries_for_dir(output_dir, site_position, "FUSION")
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