Refactored efast.py to leverage efast package functions.

README.md

@@ -57,6 +57,17 @@ data/
       clouds.json    # Cloud detection results
 ```
 
+### File Formats
+
+**Sentinel-2 (raw/s2/)**: Multi-band GeoTIFF
+- Bands: B02 (blue), B03 (green), B04 (red), B8A (nir)
+- Metadata: `VIEWING_ZENITH_ANGLE` tag (degrees)
+- Filename: `{YYYYMMDD}_{increment}.geotiff`
+
+**Sentinel-3 (raw/s3/)**: Multi-band GeoTIFF
+- Bands: SDR_Oa04 (blue), SDR_Oa06 (green), SDR_Oa08 (red), SDR_Oa17 (nir)
+- Filename: `{YYYYMMDD}_{increment}.geotiff`
+
 ## Web Viewer
 
 Run a local HTTP server to view the web interface:

efast.py

@@ -1,36 +1,24 @@
 import json
 import shutil
-import importlib.util
 from pathlib import Path
 from datetime import datetime, timedelta
+from collections import defaultdict
 import numpy as np
 import rasterio
 from rasterio.warp import Resampling
 from rasterio.vrt import WarpedVRT
 from rasterio import shutil as rio_shutil
-from scipy import ndimage
-
-RESOLUTION_RATIO = 21
 
 try:
-    import efast as efast_fusion
+    import efast
+    from efast.s2_processing import distance_to_clouds
+    from efast.s3_processing import reproject_and_crop_s3
 except ImportError:
-    import site
+    raise ImportError(
+        "efast package not found. Install with: pip install git+https://github.com/DHI-GRAS/efast.git"
+    )
 
-    efast_fusion = None
-    for site_pkg in site.getsitepackages():
-        candidate = Path(site_pkg) / "efast" / "efast.py"
-        if candidate.exists():
-            spec = importlib.util.spec_from_file_location(
-                "efast_fusion_module", candidate
-            )
-            efast_fusion = importlib.util.module_from_spec(spec)
-            spec.loader.exec_module(efast_fusion)
-            break
-    if efast_fusion is None:
-        raise ImportError(
-            "efast package not found. Install with: pip install git+https://github.com/DHI-GRAS/efast.git"
-        )
+RESOLUTION_RATIO = 21
 
 
 def _load_clouds(clouds_file):
@@ -42,27 +30,24 @@ def _load_clouds(clouds_file):
     return clouds
 
 
-def _reproject_to_target(
-    data, src_transform, src_crs, target_bounds, target_crs, width, height, resampling
-):
+def _reproject_raster_to_target(src_path, dst_path, target_bounds, target_crs, width, height, resampling=Resampling.cubic):
     dst_transform = rasterio.transform.from_bounds(
-        target_bounds.left,
-        target_bounds.bottom,
-        target_bounds.right,
-        target_bounds.top,
-        width,
-        height,
+        target_bounds.left, target_bounds.bottom,
+        target_bounds.right, target_bounds.top,
+        width, height
     )
-    reprojected, _ = rasterio.warp.reproject(
-        source=data,
-        destination=np.zeros((data.shape[0], height, width), dtype=data.dtype),
-        src_transform=src_transform,
-        src_crs=src_crs,
-        dst_transform=dst_transform,
-        dst_crs=target_crs,
-        resampling=resampling,
-    )
-    return reprojected, dst_transform
+    with rasterio.open(src_path) as src:
+        vrt_options = {
+            "transform": dst_transform,
+            "height": height,
+            "width": width,
+            "crs": target_crs,
+            "resampling": resampling,
+        }
+        with WarpedVRT(src, **vrt_options) as vrt:
+            profile = vrt.profile.copy()
+            profile.update({"dtype": "float32", "nodata": 0})
+            rio_shutil.copy(vrt, dst_path, driver="GTiff", **profile)
 
 
 def prepare_s2(season, site_position, site_name, date_range=None):
@@ -72,7 +57,6 @@ def prepare_s2(season, site_position, site_name, date_range=None):
     clouds_file = Path(f"data/{site_name}/{season}/clouds.json")
 
     clouds = _load_clouds(clouds_file)
-
     s2_output_dir.mkdir(parents=True, exist_ok=True)
 
     s3_files = [f for f in s3_dir.glob("*.geotiff") if f.name not in clouds["s3"]]
@@ -82,77 +66,29 @@ def prepare_s2(season, site_position, site_name, date_range=None):
     with rasterio.open(s3_files[0]) as s3_ref:
         target_bounds = s3_ref.bounds
         target_crs = s3_ref.crs
-        s3_width = s3_ref.width
-        s3_height = s3_ref.height
-        s2_width = s3_width * RESOLUTION_RATIO
-        s2_height = s3_height * RESOLUTION_RATIO
+        s2_width = s3_ref.width * RESOLUTION_RATIO
+        s2_height = s3_ref.height * RESOLUTION_RATIO
 
     for s2_file in s2_dir.glob("*.geotiff"):
         if s2_file.name in clouds["s2"]:
             continue
         date_str = s2_file.name.split("_")[0]
-
         refl_dst = s2_output_dir / f"S2A_MSIL2A_{date_str}_REFL.tif"
-        if not refl_dst.exists():
-            with rasterio.open(s2_file) as src:
-                data = src.read().astype("float32") / 10000.0
-                reprojected_data, dst_transform = _reproject_to_target(
-                    data,
-                    src.transform,
-                    src.crs,
-                    target_bounds,
-                    target_crs,
-                    s2_width,
-                    s2_height,
-                    Resampling.cubic,
-                )
-                profile = src.profile.copy()
-                profile.update(
-                    {
-                        "dtype": "float32",
-                        "nodata": 0,
-                        "width": s2_width,
-                        "height": s2_height,
-                        "transform": dst_transform,
-                        "crs": target_crs,
-                    }
-                )
-                with rasterio.open(refl_dst, "w", **profile) as dst_file:
-                    dst_file.write(reprojected_data)
+        if refl_dst.exists():
+            continue
 
-        dist_cloud_dst = s2_output_dir / f"S2A_MSIL2A_{date_str}_DIST_CLOUD.tif"
-        if not dist_cloud_dst.exists():
-            with rasterio.open(refl_dst) as src:
-                s2_hr = src.read(1)
-                mask = s2_hr == 0
-                distance_to_cloud_hr = np.clip(
-                    ndimage.distance_transform_edt(~mask), 0, 255
-                ).astype("float32")
+        temp_normalized = s2_output_dir / f"temp_{s2_file.name}"
+        with rasterio.open(s2_file) as src:
+            data = src.read().astype("float32") / 10000.0
+            profile = src.profile.copy()
+            profile.update({"dtype": "float32", "nodata": 0})
+            with rasterio.open(temp_normalized, "w", **profile) as dst:
+                dst.write(data)
 
-                distance_to_cloud_lr, lr_transform = _reproject_to_target(
-                    distance_to_cloud_hr[np.newaxis, :, :],
-                    src.transform,
-                    src.crs,
-                    target_bounds,
-                    target_crs,
-                    s3_width,
-                    s3_height,
-                    Resampling.average,
-                )
-                distance_to_cloud_lr = distance_to_cloud_lr[0]
+        _reproject_raster_to_target(temp_normalized, refl_dst, target_bounds, target_crs, s2_width, s2_height)
+        temp_normalized.unlink()
 
-                profile = src.profile.copy()
-                profile.update(
-                    {
-                        "count": 1,
-                        "dtype": "float32",
-                        "width": s3_width,
-                        "height": s3_height,
-                        "transform": lr_transform,
-                    }
-                )
-                with rasterio.open(dist_cloud_dst, "w", **profile) as dst:
-                    dst.write(distance_to_cloud_lr, 1)
+    distance_to_clouds(s2_output_dir, ratio=RESOLUTION_RATIO)
 
 
 def prepare_s3(season, site_position, site_name, date_range=None):
@@ -164,72 +100,37 @@ def prepare_s3(season, site_position, site_name, date_range=None):
     clouds = _load_clouds(clouds_file)
     s3_preprocessed_dir.mkdir(parents=True, exist_ok=True)
 
-    # Get reference profile from S2 DIST_CLOUD file
-    dist_cloud_files = list(s2_prepared_dir.glob("*DIST_CLOUD.tif"))
-    if not dist_cloud_files:
-        raise ValueError("No S2 DIST_CLOUD files found. Run prepare_s2 first.")
-    
-    with rasterio.open(dist_cloud_files[0]) as src:
-        target_profile = src.profile
-
-    # Group S3 files by date
-    s3_by_date = {}
+    s3_by_date = defaultdict(list)
     for s3_file in s3_dir.glob("*.geotiff"):
-        if s3_file.name in clouds["s3"]:
-            continue
-        date_str = s3_file.name.split("_")[0]
-        if date_str not in s3_by_date:
-            s3_by_date[date_str] = []
-        s3_by_date[date_str].append(s3_file)
+        if s3_file.name not in clouds["s3"]:
+            s3_by_date[s3_file.name.split("_")[0]].append(s3_file)
+
+    temp_composite_dir = s3_preprocessed_dir / "temp_composites"
+    if temp_composite_dir.exists():
+        shutil.rmtree(temp_composite_dir)
+    temp_composite_dir.mkdir()
 
-    # Process each date
     for date_str, s3_files in s3_by_date.items():
-        output_path = s3_preprocessed_dir / f"composite_{date_str}.tif"
-        if output_path.exists():
-            continue
-
+        composite_path = temp_composite_dir / f"composite_{date_str}.tif"
         if len(s3_files) == 1:
-            # Single file: reproject directly
-            with rasterio.open(s3_files[0]) as src:
-                vrt_options = {
-                    "transform": target_profile["transform"],
-                    "height": target_profile["height"],
-                    "width": target_profile["width"],
-                    "crs": target_profile["crs"],
-                    "resampling": Resampling.cubic,
-                }
-                with WarpedVRT(src, **vrt_options) as vrt:
-                    rio_shutil.copy(vrt, output_path, driver="GTiff")
+            shutil.copy(s3_files[0], composite_path)
         else:
-            # Multiple files: create weighted composite
             s3_stack = []
             for s3_file in s3_files:
                 with rasterio.open(s3_file) as src:
-                    vrt_options = {
-                        "transform": target_profile["transform"],
-                        "height": target_profile["height"],
-                        "width": target_profile["width"],
-                        "crs": target_profile["crs"],
-                        "resampling": Resampling.cubic,
-                    }
-                    with WarpedVRT(src, **vrt_options) as vrt:
-                        data = vrt.read()
-                        # Remove abnormally high values (pixel-wise mean across bands)
-                        pixel_means = np.abs(np.nanmean(data, axis=0))
-                        mask = pixel_means >= 5
-                        data[:, mask] = np.nan
-                        s3_stack.append(data)
-            
-            s3_stack = np.array(s3_stack)
-            # Simple mean composite (can be enhanced with temporal weighting)
-            composite = np.nanmean(s3_stack, axis=0)
-            composite = composite.astype("float32")
-            
-            profile = target_profile.copy()
-            profile.update({"count": composite.shape[0], "dtype": "float32"})
-            with rasterio.open(output_path, "w", **profile) as dst:
+                    data = src.read()
+                    data[:, np.abs(np.nanmean(data, axis=0)) >= 5] = np.nan
+                    s3_stack.append(data)
+            composite = np.nanmean(np.array(s3_stack), axis=0).astype("float32")
+            with rasterio.open(s3_files[0]) as src:
+                profile = src.profile.copy()
+                profile.update({"count": composite.shape[0], "dtype": "float32"})
+            with rasterio.open(composite_path, "w", **profile) as dst:
                 dst.write(composite)
 
+    reproject_and_crop_s3(temp_composite_dir, s2_prepared_dir, s3_preprocessed_dir)
+    shutil.rmtree(temp_composite_dir)
+
 
 def run_efast(season, site_position, site_name, date_range=None):
     lat, lon = site_position
@@ -241,7 +142,6 @@ def run_efast(season, site_position, site_name, date_range=None):
     fusion_output_dir = efast_base_dir / "fusion"
 
     fusion_output_dir.mkdir(parents=True, exist_ok=True)
-
     print(f"[EFAST] Starting fusion: {site_name} ({lat:.6f}, {lon:.6f}), {season}")
 
     start_str, end_str = datetime_range.split("/")
@@ -251,32 +151,19 @@ def run_efast(season, site_position, site_name, date_range=None):
     current_date = start_date
     while current_date <= end_date:
         date_str = current_date.strftime("%Y%m%d")
-
         output_file = fusion_output_dir / f"REFL_{date_str}.tif"
         if output_file.exists():
             print(f"[EFAST] Skipping {date_str} (exists)")
-            current_date += timedelta(days=1)
-            continue
-
-        try:
-            efast_fusion.fusion(
-                current_date,
-                s3_output_dir,
-                s2_output_dir,
-                fusion_output_dir,
-                product="REFL",
-                max_days=30,
-                date_position=2,
-                minimum_acquisition_importance=0.0,
-                ratio=RESOLUTION_RATIO,
-            )
-            if output_file.exists():
-                print(f"[EFAST] Saved: {output_file}")
-            else:
-                print(f"[EFAST] No output for {date_str} (insufficient nearby data)")
-        except Exception as e:
-            print(f"[EFAST] Error processing {date_str}: {e}")
-
+        else:
+            try:
+                efast.fusion(
+                    current_date, s3_output_dir, s2_output_dir, fusion_output_dir,
+                    product="REFL", max_days=30, date_position=2,
+                    minimum_acquisition_importance=0.0, ratio=RESOLUTION_RATIO,
+                )
+                print(f"[EFAST] Saved: {output_file}" if output_file.exists() else f"[EFAST] No output for {date_str} (insufficient nearby data)")
+            except Exception as e:
+                print(f"[EFAST] Error processing {date_str}: {e}")
         current_date += timedelta(days=1)
 
     print("[EFAST] Completed")

webapp/cloudy.html

@@ -20,6 +20,7 @@
         .map-label { font-size: 12px; margin-bottom: 5px; color: #666; }
         .map { height: 500px; border: 1px solid #ccc; }
         .leaflet-image-layer { image-rendering: pixelated; }
+        .leaflet-control-attribution { display: none; }
     </style>
 </head>
 <body>