cubexpress 0.1.11__py3-none-any.whl → 0.1.12__py3-none-any.whl

cubexpress/__init__.py

@@ -1,6 +1,6 @@
 from cubexpress.conversion import lonlat2rt, geo2utm
 from cubexpress.geotyping import RasterTransform, Request, RequestSet, GeotransformDict
-from cubexpress.cloud_utils import s2_cloud_table
+from cubexpress.cloud_utils import s2_table
 from cubexpress.cube import get_cube
 from cubexpress.request import table_to_requestset
 
@@ -16,7 +16,7 @@ __all__ = [
     "RequestSet",
     "geo2utm",
     "get_cube",
-    "s2_cloud_table",
+    "s2_table",
     "table_to_requestset"
 ]
 

cubexpress/cloud_utils.py

@@ -15,9 +15,11 @@ from __future__ import annotations
 import datetime as dt
 import ee
 import pandas as pd
-
 from cubexpress.cache import _cache_key
+import datetime as dt
 from cubexpress.geospatial import _square_roi
+import warnings
+warnings.filterwarnings('ignore', category=DeprecationWarning)
 
 
 def _cloud_table_single_range(
@@ -55,61 +57,64 @@ def _cloud_table_single_range(
 
     center = ee.Geometry.Point([lon, lat])
     roi = _square_roi(lon, lat, edge_size, 10)
-
+    
     s2 = (
-        ee.ImageCollection("COPERNICUS/S2_HARMONIZED")
+        ee.ImageCollection("COPERNICUS/S2_SR_HARMONIZED")
         .filterBounds(roi)
         .filterDate(start, end)
     )
-
-    csp = ee.ImageCollection("GOOGLE/CLOUD_SCORE_PLUS/V1/S2_HARMONIZED")
-
     ic = (
         s2
-        .linkCollection(csp, ["cs_cdf"])
+        .linkCollection(
+            ee.ImageCollection("GOOGLE/CLOUD_SCORE_PLUS/V1/S2_HARMONIZED"), 
+            ["cs_cdf"]
+        )
         .select(["cs_cdf"])
     )
-
-    # image IDs for every expected date
-    ids = ic.aggregate_array("system:index").getInfo()
-    df_ids = pd.DataFrame({"id": ids})
-
-
-    region_scale = edge_size * 10 / 2
-
-
+    ids_inside = (
+        ic                              
+        .map(                           
+            lambda img: img.set(
+                'roi_inside_scene',
+                img.geometry().contains(roi, maxError=10)
+            )
+        )
+        .filter(ee.Filter.eq('roi_inside_scene', True))
+        .aggregate_array('system:index')               
+        .getInfo()
+    )
+    
     try:
-        raw = ic.getRegion(geometry=center, scale=region_scale).getInfo()
+        raw = ic.getRegion(
+            geometry=center,
+            scale=(edge_size) * 11
+        ).getInfo()
     except ee.ee_exception.EEException as e:
         if "No bands in collection" in str(e):
             return pd.DataFrame(
-                columns=["id", "cs_cdf", "date", "null_flag"]
+                columns=["id", "longitude", "latitude", "time", "cs_cdf", "inside"]
             )
-        raise 
-
-    df_raw = pd.DataFrame(raw[1:], columns=raw[0])
-
-
-    df = (
-        df_ids
-        .merge(df_raw, on="id", how="left")
+        raise e
+    
+    df_raw = (
+        pd.DataFrame(raw[1:], columns=raw[0])
+        .drop(columns=["longitude", "latitude"])
         .assign(
-            date=lambda d: pd.to_datetime(d["id"].str[:8], format="%Y%m%d").dt.strftime("%Y-%m-%d"),
-            null_flag=lambda d: d["cs_cdf"].isna().astype(int),
+            date=lambda d: pd.to_datetime(d["id"].str[:8], format="%Y%m%d").dt.strftime("%Y-%m-%d")
         )
-        .drop(columns=["longitude", "latitude", "time"])
     )
-
-    # fill missing scores with daily mean
-    df["lon"] = lon
-    df["lat"] = lat
-    df["cs_cdf"] = df["cs_cdf"].fillna(df.groupby("date")["cs_cdf"].transform("mean"))
-
-
-    return df
-
-
-def s2_cloud_table(
+    df_raw["inside"] = df_raw["id"].isin(set(ids_inside)).astype(int)
+    df_raw['cs_cdf'] = df_raw.groupby('date').apply(
+        lambda group: group['cs_cdf'].transform(
+            lambda _: group[group['inside'] == 1]['cs_cdf'].iloc[0] 
+            if (group['inside'] == 1).any() 
+            else group['cs_cdf'].mean()
+        )
+    ).reset_index(drop=True)
+    
+    return df_raw
+    
+def s2_table(
     lon: float,
     lat: float,
     edge_size: int,
@@ -117,8 +122,7 @@ def s2_cloud_table(
     end: str,
     max_cscore: float = 1.0,
     min_cscore: float = 0.0,
-    cache: bool = False,
-    verbose: bool = True,
+    cache: bool = False
 ) -> pd.DataFrame:
     """Build (and cache) a per-day cloud-table for the requested ROI.
 
@@ -147,9 +151,7 @@ def s2_cloud_table(
         Downstream path hint stored in ``result.attrs``; not used internally.
     cache
         Toggle parquet caching.
-    verbose
-        If *True* prints cache info/progress.
-
+    
     Returns
     -------
     pandas.DataFrame
@@ -161,10 +163,9 @@ def s2_cloud_table(
     scale = 10
     cache_file = _cache_key(lon, lat, edge_size, scale, collection)
 
-    # ─── 1. Load cached data if present ────────────────────────────────────
+    # Load cached data if present
     if cache and cache_file.exists():
-        if verbose:
-            print("📂  Loading cached metadata …")
+        print("📂  Loading cached metadata …")
         df_cached = pd.read_parquet(cache_file)
         have_idx = pd.to_datetime(df_cached["date"], errors="coerce").dropna()
 
@@ -175,8 +176,7 @@ def s2_cloud_table(
             dt.date.fromisoformat(start) >= cached_start
             and dt.date.fromisoformat(end) <= cached_end
         ):
-            if verbose:
-                print("✅  Served entirely from metadata.")
+            print("✅  Served entirely from metadata.")
             df_full = df_cached
         else:
             # Identify missing segments and fetch only those.
@@ -185,14 +185,22 @@ def s2_cloud_table(
                 a1, b1 = start, cached_start.isoformat()
                 df_new_parts.append(
                     _cloud_table_single_range(
-                        lon, lat, edge_size, a1, b1
+                        lon=lon, 
+                        lat=lat, 
+                        edge_size=edge_size, 
+                        start=a1, 
+                        end=b1
                     )
                 )
             if dt.date.fromisoformat(end) > cached_end:
                 a2, b2 = cached_end.isoformat(), end
                 df_new_parts.append(
                     _cloud_table_single_range(
-                        lon, lat, edge_size, a2, b2
+                        lon=lon, 
+                        lat=lat, 
+                        edge_size=edge_size, 
+                        start=a2, 
+                        end=b2
                     )
                 )
             df_new_parts = [df for df in df_new_parts if not df.empty]
@@ -207,21 +215,20 @@ def s2_cloud_table(
             else:
                 df_full = df_cached
     else:
-
-        if verbose:
-            msg = "Generating metadata (no cache found)…" if cache else "Generating metadata…"
-            print("⏳", msg)
+        print("⏳ Generating metadata…")
         df_full = _cloud_table_single_range(
-            lon, lat, edge_size, start, end
+            lon=lon, 
+            lat=lat, 
+            edge_size=edge_size, 
+            start=start, 
+            end=end
         )
-        
 
-    # ─── 2. Save cache ─────────────────────────────────────────────────────
+    # Save cache
     if cache:
         df_full.to_parquet(cache_file, compression="zstd")
 
-    # ─── 3. Filter by cloud cover and requested date window ────────────────
-    
+    # Filter by cloud cover and requested date window 
     result = (
         df_full.query("@start <= date <= @end")
         .query("@min_cscore <= cs_cdf <= @max_cscore")

cubexpress/cube.py

@@ -14,9 +14,10 @@ The core download/split logic lives in *cubexpress.downloader* and
 from __future__ import annotations
 
 import pathlib
-import concurrent.futures
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from typing import Dict, Any
 import ee
+from tqdm import tqdm
 
 
 from cubexpress.downloader import download_manifest, download_manifests
@@ -29,9 +30,7 @@ from cubexpress.geotyping import RequestSet
 def get_geotiff(
     manifest: Dict[str, Any],
     full_outname: pathlib.Path | str,
-    join: bool = True,
-    nworks: int = 4,
-    verbose: bool = True,
+    nworks: int = 4
 ) -> None:
     """Download *manifest* to *full_outname*, retrying with tiled requests.
 
@@ -44,34 +43,27 @@ def get_geotiff(
     nworks
         Maximum worker threads when the image must be split; default **4**.
     """
-    full_outname = pathlib.Path(full_outname)
+    
     try:
-        download_manifest(manifest, full_outname)
+        download_manifest(
+            ulist=manifest, 
+            full_outname=full_outname
+        )
     except ee.ee_exception.EEException as err:
-
-        size = manifest["grid"]["dimensions"]["width"]  # square images assumed
+        size = manifest["grid"]["dimensions"]["width"]
         cell_w, cell_h, power = calculate_cell_size(str(err), size)
         tiled = quadsplit_manifest(manifest, cell_w, cell_h, power)
+        
         download_manifests(
-            manifests = tiled, 
-            full_outname = full_outname, 
-            join = join, 
-            max_workers = nworks
+            manifests=tiled,
+            full_outname=full_outname,
+            max_workers=nworks
         )
 
-    if verbose:
-        print(f"Downloaded {full_outname}")
-
-
 def get_cube(
-    # table: pd.DataFrame,
     requests: pd.DataFrame | RequestSet,
     outfolder: pathlib.Path | str,
-    mosaic: bool = True,
-    join: bool = True,
-    nworks: int = 4,
-    verbose: bool = True,
-    cache: bool = True
+    nworks: int = 4
 ) -> None:
     """Download every request in *requests* to *outfolder* using a thread pool.
 
@@ -87,46 +79,22 @@ def get_cube(
     nworks
         Pool size for concurrent downloads; default **4**.
     """
-
-    # requests = table_to_requestset(
-    #     table=table, 
-    #     mosaic=mosaic
-    # )
     
     outfolder = pathlib.Path(outfolder).expanduser().resolve()
-
-    with concurrent.futures.ThreadPoolExecutor(max_workers=nworks) as pool:
-        futures = []
-        for _, row in requests._dataframe.iterrows():
-            outname = pathlib.Path(outfolder) / f"{row.id}.tif"
-            if outname.exists() and cache:
-                continue
-            outname.parent.mkdir(parents=True, exist_ok=True)
-            futures.append(
-                pool.submit(
-                    get_geotiff, 
-                    row.manifest, # manifest = row.manifest
-                    outname, # full_outname = outname
-                    join, # join = join
-                    nworks, # nworks = nworks
-                    verbose # verbose = verbose
-                )
-            )
-
-        for fut in concurrent.futures.as_completed(futures):
+    outfolder.mkdir(parents=True, exist_ok=True)
+    dataframe = requests._dataframe if isinstance(requests, RequestSet) else requests
+    
+    with ThreadPoolExecutor(max_workers=nworks) as executor:
+        futures = {
+            executor.submit(
+                get_geotiff,
+                manifest=row.manifest,
+                full_outname=pathlib.Path(outfolder) / f"{row.id}.tif",
+                nworks=nworks
+            ): row.id for _, row in dataframe.iterrows()
+        }
+        for future in tqdm(as_completed(futures), total=len(futures)):
             try:
-                fut.result()
-            except Exception as exc:  # noqa: BLE001 – log and keep going
-                print(f"Download error: {exc}")
-
-    # download_df = requests._dataframe[["outname", "cs_cdf", "date"]].copy()
-    # download_df["outname"] = outfolder / requests._dataframe["outname"]
-    # download_df.rename(columns={"outname": "full_outname"}, inplace=True)
-
-    return 
-
-# manifest = row.manifest
-# full_outname = outname
-# join: bool = True,
-# nworks: int = 4,
-# verbose: bool = True,
+                future.result()
+            except Exception as exc:
+                print(f"Download error for {futures[future]}: {exc}")

cubexpress/downloader.py

@@ -13,16 +13,14 @@ from __future__ import annotations
 
 import json
 import pathlib
-import concurrent.futures
+from concurrent.futures import ThreadPoolExecutor, as_completed
 from copy import deepcopy
-from typing import Any, Dict, List
+from typing import Any, Dict
 
 import ee
 import rasterio as rio
 from rasterio.io import MemoryFile
 import logging
-from rasterio.merge import merge
-from rasterio.enums import Resampling
 import os
 import shutil
 import tempfile
@@ -31,7 +29,10 @@ from cubexpress.geospatial import merge_tifs
 os.environ['CPL_LOG_ERRORS'] = 'OFF'
 logging.getLogger('rasterio._env').setLevel(logging.ERROR)
 
-def download_manifest(ulist: Dict[str, Any], full_outname: pathlib.Path) -> None:
+def download_manifest(
+    ulist: Dict[str, Any], 
+    full_outname: pathlib.Path
+) -> None:
     """Download *ulist* and save it as *full_outname*.
 
     The manifest must include either an ``assetId`` or an ``expression``
@@ -45,36 +46,38 @@ def download_manifest(ulist: Dict[str, Any], full_outname: pathlib.Path) -> None
         ulist_deep = deepcopy(ulist)
         ulist_deep["expression"] = ee_image
         images_bytes = ee.data.computePixels(ulist_deep)
-    else:  # pragma: no cover
+    else:
         raise ValueError("Manifest does not contain 'assetId' or 'expression'")
-
-    with MemoryFile(images_bytes) as memfile:
-        with memfile.open() as src:
-            profile = src.profile
-            profile.update(
-                driver="GTiff", 
-                tiled=True,
-                interleave="band",
-                blockxsize=256,
-                blockysize=256,
-                compress="ZSTD",
-                zstd_level=13,
-                predictor=2,
-                num_threads=20,
-                nodata=65535,
-                dtype="uint16",
-                count=12,
-                photometric="MINISBLACK"
-            )
-
-            with rio.open(full_outname, "w", **profile) as dst:
-                dst.write(src.read())
+    
+    with open(full_outname, "wb") as src:
+        src.write(images_bytes)
+
+    # with MemoryFile(images_bytes) as memfile:
+    #     with memfile.open() as src:
+    #         profile = src.profile
+    #         profile.update(
+    #             driver="GTiff", 
+    #             tiled=True,
+    #             interleave="band",
+    #             blockxsize=256,
+    #             blockysize=256,
+    #             compress="ZSTD",
+    #             zstd_level=13,
+    #             predictor=2,
+    #             num_threads=20,
+    #             nodata=65535,
+    #             dtype="uint16",
+    #             count=12,
+    #             photometric="MINISBLACK"
+    #         )
+
+    #         with rio.open(full_outname, "w", **profile) as dst:
+    #             dst.write(src.read())
 
 def download_manifests(
     manifests: list[Dict[str, Any]],
     full_outname: pathlib.Path,
-    join: bool = True,
-    max_workers: int = 4,
+    max_workers: int,
 ) -> None:
     """Download every manifest in *manifests* concurrently.
 
@@ -82,38 +85,27 @@ def download_manifests(
     ``full_outname.parent/full_outname.stem`` with names ``000000.tif``,
     ``000001.tif`` … according to the list order.
     """
-    # full_outname = pathlib.Path("/home/contreras/Documents/GitHub/cubexpress/cubexpress_test/2017-08-19_6mfrw_18LVN.tif")
-
-    if join:
-        tmp_dir = pathlib.Path(tempfile.mkdtemp(prefix="s2tmp_"))
-        full_outname_temp = tmp_dir / full_outname.name
-
-    with concurrent.futures.ThreadPoolExecutor(max_workers=max_workers) as executor:
-        futures = []
-
-        for index, umanifest in enumerate(manifests):
-            folder = full_outname_temp.parent / full_outname_temp.stem
-            folder.mkdir(parents=True, exist_ok=True)
-            outname = folder / f"{index:06d}.tif"
-            futures.append(
-                executor.submit(
-                    download_manifest, 
-                    umanifest, # ulist = umanifest
-                    outname # full_outname = outname
-                )
-         )
-
-        for fut in concurrent.futures.as_completed(futures):
+    tmp_dir = pathlib.Path(tempfile.mkdtemp(prefix="cubexpress_"))
+    full_outname_temp = tmp_dir / full_outname.stem
+    full_outname_temp.mkdir(parents=True, exist_ok=True)
+
+    with ThreadPoolExecutor(max_workers=max_workers) as exe: # -
+        futures = {
+            exe.submit(
+                download_manifest, 
+                ulist=umanifest, 
+                full_outname=full_outname_temp / f"{index:06d}.tif" 
+            ): umanifest for index, umanifest in enumerate(manifests)               
+        }
+        for future in as_completed(futures):
             try:
-                fut.result()
-            except Exception as exc:  # noqa: BLE001
-                print(f"Error en una de las descargas: {exc}")  # noqa: T201
-
-
-    dir_path = full_outname_temp.parent / full_outname_temp.stem
-    if dir_path.exists():
-        input_files = sorted(dir_path.glob("*.tif"))
+                future.result()
+            except Exception as exc:
+                print(f"Error in one of the downloads: {exc}")
+        
+    if full_outname_temp.exists():
+        input_files = sorted(full_outname_temp.glob("*.tif"))
         merge_tifs(input_files, full_outname)
-        shutil.rmtree(dir_path) 
+        shutil.rmtree(full_outname_temp) 
     else:
         raise ValueError(f"Error in {full_outname}")

cubexpress/geospatial.py

@@ -57,8 +57,6 @@ def _square_roi(lon: float, lat: float, edge_size: int, scale: int) -> ee.Geomet
     point = ee.Geometry.Point([lon, lat])
     return point.buffer(half).bounds()
 
-
-
 def merge_tifs(
     input_files: list[pathlib.Path],
     output_path: pathlib.Path,

cubexpress/geotyping.py

@@ -259,13 +259,8 @@ class RequestSet(BaseModel):
     def create_manifests(self) -> pd.DataFrame:
         """
         Exports the raster metadata to a pandas DataFrame.
-
         Returns:
             pd.DataFrame: A DataFrame containing the metadata for all entries.
-
-        Example:
-            >>> df = raster_transform_set.export_df()
-            >>> print(df)
         """
         # Use ProcessPoolExecutor for CPU-bound tasks to convert raster transforms to lon/lat
         with ProcessPoolExecutor(max_workers=None) as executor:

cubexpress/request.py

@@ -11,9 +11,9 @@ from cubexpress.conversion import lonlat2rt
 
 
 def table_to_requestset(
-        table: pd.DataFrame, 
-        mosaic: bool = True
-    ) -> RequestSet:
+    table: pd.DataFrame, 
+    mosaic: bool = True
+) -> RequestSet:
     """Return a :class:`RequestSet` built from *df* (cloud_table result).
 
     Parameters
@@ -35,7 +35,7 @@ def table_to_requestset(
     df = table.copy()
 
     if df.empty:
-        raise ValueError("cloud_table returned no rows; nothing to request.")
+        raise ValueError("There are no images in the requested period. Please check your dates or your ubication.")
 
     rt = lonlat2rt(
         lon=df.attrs["lon"],
@@ -43,11 +43,11 @@ def table_to_requestset(
         edge_size=df.attrs["edge_size"],
         scale=df.attrs["scale"],
     )
+    
     centre_hash = pgh.encode(df.attrs["lat"], df.attrs["lon"], precision=5)
-    reqs: list[Request] = []
+    reqs = []
 
     if mosaic:
-
         grouped = (
             df.groupby('date')
             .agg(
@@ -66,8 +66,7 @@ def table_to_requestset(
         )
 
         for day, row in grouped.iterrows():
-            
-            
+
             img_ids   = row["id_list"]
             cdf  = row["cs_cdf_mean"]
             
@@ -100,16 +99,16 @@ def table_to_requestset(
     else:
         for _, row in df.iterrows():
             img_id = row["id"]
-            # tile = img_id.split("_")[-1][1:]
+            tile = img_id.split("_")[-1][1:]
             day = row["date"]
             cdf = int(round(row["cs_cdf"], 2) * 100)
             reqs.append(
                 Request(
-                    id=f"{day}_{centre_hash}_{cdf}",
+                    id=f"{day}_{tile}_{cdf}",
                     raster_transform=rt,
                     image=f"{df.attrs['collection']}/{img_id}",
                     bands=df.attrs["bands"],
                 )
             )
 
-    return RequestSet(requestset=reqs)
+    return RequestSet(requestset=reqs)

{cubexpress-0.1.11.dist-info → cubexpress-0.1.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: cubexpress
-Version: 0.1.11
+Version: 0.1.12
 Summary: Efficient processing of cubic Earth-observation (EO) data.
 Home-page: https://github.com/andesdatacube/cubexpress
 Keywords: earth-engine,sentinel-2,geospatial,eo,cube
@@ -31,7 +31,7 @@ Description-Content-Type: text/markdown
 <h1></h1>
 
 <p align="center">
-  <img src="./docs/logo_cubexpress.png" width="39%">
+  <img src="https://raw.githubusercontent.com/andesdatacube/cubexpress/refs/heads/main/docs/logo_cubexpress.png" width="39%">
 </p>
 
 <p align="center">

cubexpress-0.1.12.dist-info/RECORD

@@ -0,0 +1,13 @@
+cubexpress/__init__.py,sha256=G_9FKWrdFh44oYjD78jtH9gXqrdARIFFM0MaSl6WttY,606
+cubexpress/cache.py,sha256=EZiR2AJfplaLpqMIVFb5piCAgFqHKF1vgLIrutfz8tA,1425
+cubexpress/cloud_utils.py,sha256=EhLqHrefia7AUp75HZXKrQSPKQb6BSYFKD3hjI_sj1M,7681
+cubexpress/conversion.py,sha256=JSaMnswY-2n5E4H2zxb-oEOTJ8UPzXfMeSVCremtvTw,2520
+cubexpress/cube.py,sha256=lqJJyf1EmNYszIztx62OCrdo0HGtIveOmw-pFGI2nuI,3230
+cubexpress/downloader.py,sha256=rnk-oX51_YFWz1iZuBWEYTDSTV48F780o1aujTsKCwE,3725
+cubexpress/geospatial.py,sha256=jldZ-aFqUEvp1SF8ZJEa-pDHSAs3akzqk43dHai0TKM,3820
+cubexpress/geotyping.py,sha256=uTaoZnaegGUShAHy-t0og22vpBbSrnJhCxp_4UoO9TM,16597
+cubexpress/request.py,sha256=gLY8eBkMVal0uF6auGIfqmOhUPWFHwJzBxXOXU4aRuA,3370
+cubexpress-0.1.12.dist-info/LICENSE,sha256=XjoS-d76b7Cl-VgCWhQk83tNf2dNldKBN8SrImwGc2Q,1072
+cubexpress-0.1.12.dist-info/METADATA,sha256=u1EpUC4n5Jdpewvjv67l2IWp9ULCqRzshPqNTY85Tcs,9724
+cubexpress-0.1.12.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+cubexpress-0.1.12.dist-info/RECORD,,

cubexpress-0.1.11.dist-info/RECORD

@@ -1,13 +0,0 @@
-cubexpress/__init__.py,sha256=sKXcYQQPREFhVCHP81lL_5hAurUTm8MX1xVOEOMF-nA,618
-cubexpress/cache.py,sha256=EZiR2AJfplaLpqMIVFb5piCAgFqHKF1vgLIrutfz8tA,1425
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