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+argo/argo_profiles_on_grid.zarr/grid_row/93 filter=lfs diff=lfs merge=lfs -text diff --git a/argo/argo_profiles_on_grid.zarr/.zmetadata b/argo/argo_profiles_on_grid.zarr/.zmetadata index 7856fa95c80414c5444c5f1fd163f9480a5bb9f7..61aabfba51a91ebec803550cff690d37e97954db 100644 --- a/argo/argo_profiles_on_grid.zarr/.zmetadata +++ b/argo/argo_profiles_on_grid.zarr/.zmetadata @@ -1 +1 @@ -{"metadata": {".zgroup": {"zarr_format": 2}, ".zattrs": {"created_by": "depth_recon.data.dataset_creation.export_dataset_geotiff.export_dataset_geotiff", "source_kind": "enriched", "temperature_units": "K", "temperature_stretch": {"name": "temperature_kelvin", "storage_dtype": "uint8", "minimum": 270.15, "maximum": 308.15, "units": "K", "nodata": 255, "valid_code_min": 0, "valid_code_max": 254, "valid_code_count": 255, "quantization_step": 0.14960629921259844, "max_abs_quantization_error": 0.07480314960629922, "decode": "minimum + code / 254 * (maximum - minimum)"}, "salinity_stretch": {"name": "salinity", "storage_dtype": "uint8", "minimum": 30.0, "maximum": 40.0, "units": "PSU", "nodata": 255, "valid_code_min": 0, "valid_code_max": 254, "valid_code_count": 255, "quantization_step": 0.03937007874015748, "max_abs_quantization_error": 0.01968503937007874, "decode": "minimum + code / 254 * (maximum - minimum)"}, "temporal_assignment": "nearest GLORYS target date inside centered 7-day window"}, "argo_psal_uint8/.zattrs": {"nodata": 255, "name": "salinity", "storage_dtype": "uint8", "minimum": 30.0, "maximum": 40.0, "units": "PSU", "valid_code_min": 0, "valid_code_max": 254, "valid_code_count": 255, "quantization_step": 0.03937007874015748, "max_abs_quantization_error": 0.01968503937007874, "decode": "minimum + code / 254 * (maximum - minimum)", "_ARRAY_DIMENSIONS": ["profile", "glorys_depth"]}, "argo_psal_uint8/.zarray": {"shape": [9451644, 50], "chunks": [50000, 50], "dtype": "|u1", "fill_value": null, "order": "C", "filters": null, "dimension_separator": ".", "compressor": {"id": "blosc", "cname": "lz4", "clevel": 5, "shuffle": 1, "blocksize": 0}, "zarr_format": 2}, "argo_psal_valid/.zattrs": {"dtype": "bool", "_ARRAY_DIMENSIONS": ["profile", "glorys_depth"]}, "argo_psal_valid/.zarray": {"shape": [9451644, 50], "chunks": [50000, 50], "dtype": "|i1", "fill_value": null, "order": "C", "filters": null, "dimension_separator": ".", "compressor": {"id": "blosc", "cname": "lz4", "clevel": 5, "shuffle": 1, "blocksize": 0}, "zarr_format": 2}, "argo_temp_kelvin_uint8/.zattrs": {"nodata": 255, "name": "temperature_kelvin", "storage_dtype": "uint8", "minimum": 270.15, "maximum": 308.15, "units": "K", "valid_code_min": 0, "valid_code_max": 254, "valid_code_count": 255, "quantization_step": 0.14960629921259844, "max_abs_quantization_error": 0.07480314960629922, "decode": "minimum + code / 254 * (maximum - minimum)", "_ARRAY_DIMENSIONS": ["profile", "glorys_depth"]}, "argo_temp_kelvin_uint8/.zarray": {"shape": [9451644, 50], "chunks": [50000, 50], "dtype": "|u1", "fill_value": null, "order": "C", "filters": null, "dimension_separator": ".", "compressor": {"id": "blosc", "cname": "lz4", "clevel": 5, "shuffle": 1, "blocksize": 0}, "zarr_format": 2}, "argo_temp_valid/.zattrs": {"dtype": "bool", "_ARRAY_DIMENSIONS": ["profile", "glorys_depth"]}, "argo_temp_valid/.zarray": {"shape": [9451644, 50], "chunks": [50000, 50], "dtype": "|i1", "fill_value": null, "order": "C", "filters": null, "dimension_separator": ".", "compressor": {"id": "blosc", "cname": "lz4", "clevel": 5, "shuffle": 1, "blocksize": 0}, "zarr_format": 2}, "glorys_depth/.zattrs": {"_ARRAY_DIMENSIONS": ["glorys_depth"]}, "glorys_depth/.zarray": {"shape": [50], "chunks": [50], "dtype": " np.ndarray: @@ -185,15 +202,34 @@ class GeoTIFFRasterStore: return decoded.astype(np.float32, copy=False) +def _normalize_accepted_qc_flags(values: Sequence[int] | None) -> tuple[int, ...]: + """Return accepted ARGO QC flags as small integer codes.""" + if values is None: + return DEFAULT_ACCEPTED_ARGO_QC_FLAGS + flags = tuple(sorted({int(value) for value in values})) + if not flags: + raise ValueError("accepted_argo_qc_flags must contain at least one code.") + return flags + + class ArgoGeoTIFFProfileStore: """Profile-indexed ARGO zarr source exported with the GeoTIFF dataset.""" - def __init__(self, path: str | Path, *, include_salinity: bool = False) -> None: + def __init__( + self, + path: str | Path, + *, + include_salinity: bool = False, + filter_bad_quality: bool = True, + accepted_qc_flags: Sequence[int] | None = None, + ) -> None: """Open a compact ARGO profile zarr store.""" self.path = Path(path) if not self.path.exists(): raise FileNotFoundError(f"ARGO profile zarr does not exist: {self.path}") self.include_salinity = bool(include_salinity) + self.filter_bad_quality = bool(filter_bad_quality) + self.accepted_qc_flags = _normalize_accepted_qc_flags(accepted_qc_flags) self._pid = os.getpid() self.ds = self._open_dataset() self._zarr_pid = os.getpid() @@ -219,6 +255,8 @@ class ArgoGeoTIFFProfileStore: self.ds["glorys_depth"].values, dtype=np.float32 ).reshape(-1) temp_valid = np.asarray(self.ds["argo_temp_valid"].values, dtype=bool) + if self.filter_bad_quality: + temp_valid &= self._quality_mask_for_variable("temp") self._has_valid_temp = temp_valid.any(axis=1) ( self._valid_profile_indices_by_date, @@ -256,6 +294,61 @@ class ArgoGeoTIFFProfileStore: self._zarr_pid = pid return self._zarr_group + def _accepted_qc_mask(self, values: np.ndarray) -> np.ndarray: + """Return True where QC is missing or one of the accepted flags.""" + qc = np.asarray(values, dtype=np.int16) + missing = qc < 0 + accepted = np.isin(qc, np.asarray(self.accepted_qc_flags, dtype=np.int16)) + return missing | accepted + + def _profile_qc_names_for_variable(self, variable: str) -> tuple[str, ...]: + """Return profile-level QC variables relevant to one ARGO variable.""" + names = ["juld", "position", "profile_depth"] + if variable == "psal": + names.append("profile_psal") + return tuple(ARGO_PROFILE_QC_VARS[name] for name in names) + + def _level_qc_names_for_variable(self, variable: str) -> tuple[str, ...]: + """Return level-level QC variables relevant to one ARGO variable.""" + if variable == "psal": + return (ARGO_LEVEL_QC_VARS["depth"], ARGO_LEVEL_QC_VARS["psal"]) + return (ARGO_LEVEL_QC_VARS["depth"], ARGO_LEVEL_QC_VARS["temp"]) + + def _quality_mask_for_variable( + self, + variable: str, + *, + indices: np.ndarray | None = None, + ) -> np.ndarray: + """Return a profile-depth quality mask for one compact ARGO variable.""" + if indices is None: + profile_count = int(self.target_date.size) + mask = np.ones((profile_count, int(self.depth_axis_m.size)), dtype=bool) + indexer: Any = slice(None) + else: + selected = np.asarray(indices, dtype=np.int64).reshape(-1) + mask = np.ones( + (int(selected.size), int(self.depth_axis_m.size)), dtype=bool + ) + indexer = selected + ds = self._ensure_current_process() + compact_name = COMPACT_PROFILE_QC_VARS.get(variable) + if compact_name in ds: + qc = np.asarray(ds[compact_name].isel(profile=indexer).values).reshape(-1) + return mask & self._accepted_qc_mask(qc)[:, None] + for name in self._level_qc_names_for_variable(variable): + if name not in ds: + continue + qc = np.asarray(ds[name].isel(profile=indexer).values) + mask &= self._accepted_qc_mask(qc) + for name in self._profile_qc_names_for_variable(variable): + if name not in ds: + continue + qc = np.asarray(ds[name].isel(profile=indexer).values).reshape(-1) + # Bad profile-level QC rejects every depth for that profile. + mask &= self._accepted_qc_mask(qc)[:, None] + return mask + def _build_valid_profile_index( self, ) -> tuple[np.ndarray, dict[int, tuple[int, int]]]: @@ -352,6 +445,8 @@ class ArgoGeoTIFFProfileStore: group["argo_temp_valid"].get_orthogonal_selection((indices, slice(None))), dtype=bool, ) + if self.filter_bad_quality: + valid &= self._quality_mask_for_variable("temp", indices=indices) kelvin = _decode_stretched_uint8(encoded, self.temperature_stretch) kelvin[~valid] = np.nan return _kelvin_to_celsius(kelvin).astype(np.float32, copy=False) @@ -375,10 +470,22 @@ class ArgoGeoTIFFProfileStore: group["argo_psal_valid"].get_orthogonal_selection((indices, slice(None))), dtype=bool, ) + if self.filter_bad_quality: + valid &= self._quality_mask_for_variable("psal", indices=indices) salinity = _decode_stretched_uint8(encoded, self.salinity_stretch) salinity[~valid] = np.nan return salinity.astype(np.float32, copy=False) + def quality_cache_signature(self) -> str: + """Return the ARGO quality-filter settings that affect support counts.""" + marker_text = "markers-" + "-".join( + name for name in COMPACT_PROFILE_QC_VARS.values() if name in self.ds + ) + flags_text = "-".join(str(value) for value in self.accepted_qc_flags) + return _sanitize_cache_text( + f"filter{int(self.filter_bad_quality)}_flags{flags_text}_{marker_text}" + ) + def close(self) -> None: """Close the opened zarr dataset.""" self.ds.close() @@ -387,7 +494,7 @@ class ArgoGeoTIFFProfileStore: class GeoTIFFPatchIndex: """Build compact patch/date metadata rows for GeoTIFF training stores.""" - CACHE_VERSION = 1 + CACHE_VERSION = 3 def __init__( self, @@ -467,13 +574,18 @@ class GeoTIFFPatchIndex: if self.grid_params.val_year is not None else "patchsplit" ) + argo_quality_text = ( + "noargo" + if self.argo_store is None + else self.argo_store.quality_cache_signature() + ) name = ( f"argo_geotiff_gridded_v{self.CACHE_VERSION}_root{root_hash}_" f"dates{_date_signature(self.dates)}_" f"tile{int(self.grid_params.tile_size)}_res{res_text}_" f"stride{int(self.grid_params.effective_patch_stride)}_" f"grid{grid_source}_land{land_text}_mask{mask_hash}_" - f"force{force_hash}_{split_text}.csv" + f"force{force_hash}_{split_text}_argo{argo_quality_text}.csv" ) return self.cache_dir / name @@ -617,6 +729,8 @@ class ArgoGeoTIFFGriddedPatchDataset(Dataset): cache_size: int = 8, val_fraction: float = 0.2, val_year: int | None = None, + filter_bad_argo_quality: bool = True, + accepted_argo_qc_flags: Sequence[int] | None = None, ) -> None: """Initialize the GeoTIFF-backed patch dataset.""" self.split = str(split).strip().lower() @@ -677,6 +791,10 @@ class ArgoGeoTIFFGriddedPatchDataset(Dataset): self.require_argo_for_all = bool(require_argo_for_all) self.synthetic_mode = bool(synthetic_mode) self.synthetic_pixel_count = int(synthetic_pixel_count) + self.filter_bad_argo_quality = bool(filter_bad_argo_quality) + self.accepted_argo_qc_flags = _normalize_accepted_qc_flags( + accepted_argo_qc_flags + ) self.date_start = self._optional_int(date_start) self.date_end = self._optional_int(date_end) self.max_dates = None if max_dates is None else int(max_dates) @@ -828,6 +946,8 @@ class ArgoGeoTIFFGriddedPatchDataset(Dataset): return ArgoGeoTIFFProfileStore( _resolve_manifest_path(self.root_dir, raw_path), include_salinity=self.include_salinity, + filter_bad_quality=self.filter_bad_argo_quality, + accepted_qc_flags=self.accepted_argo_qc_flags, ) def _build_raster_stores( @@ -1071,6 +1191,20 @@ class ArgoGeoTIFFGriddedPatchDataset(Dataset): default=False, ) ), + filter_bad_argo_quality=bool( + cls._cfg_get( + ds_cfg, + "selection.filter_bad_argo_quality", + "filter_bad_argo_quality", + default=True, + ) + ), + accepted_argo_qc_flags=cls._cfg_get( + ds_cfg, + "selection.accepted_argo_qc_flags", + "accepted_argo_qc_flags", + default=None, + ), synthetic_mode=bool( cls._cfg_get( ds_cfg, "synthetic.enabled", "synthetic_enabled", default=False diff --git a/examples/torch_dataloader.py b/examples/torch_dataloader.py index 2037cf8e1186bc9612803eefb6c1fc1bf99daec0..62bf1448e98890f75fb69046625a278e99740e6f 100644 --- a/examples/torch_dataloader.py +++ b/examples/torch_dataloader.py @@ -1,5 +1,5 @@ # Example with all options: -# python examples/torch_dataloader.py --root . --split all --batch-size 2 --num-workers 0 --tile-size 128 --patch-stride 128 --max-land-fraction 0.30 --date-start 20000101 --date-end 20000101 --max-dates 1 --include-salinity --metadata-cache-dir /tmp/depthdif_cache --require-argo +# python examples/torch_dataloader.py --root . --split all --batch-size 2 --num-workers 0 --tile-size 128 --patch-stride 128 --max-land-fraction 0.30 --date-start 20000101 --date-end 20000101 --max-dates 1 --include-salinity --metadata-cache-dir /tmp/depthdif_cache --require-argo --accepted-argo-qc-flags 1 2 from __future__ import annotations @@ -45,6 +45,19 @@ def main() -> None: action="store_true", help="Filter rows to patches with ARGO profiles; this may scan the compact ARGO store on first use.", ) + parser.add_argument( + "--accepted-argo-qc-flags", + type=int, + nargs="+", + default=(1, 2), + help="Whole-profile ARGO QC codes accepted for compact temperature and salinity profiles.", + ) + parser.add_argument( + "--no-filter-bad-argo-quality", + action="store_false", + dest="filter_bad_argo_quality", + help="Disable filtering by compact ARGO profile QC markers.", + ) args = parser.parse_args() dataset = ArgoGeoTIFFGriddedPatchDataset( @@ -61,6 +74,8 @@ def main() -> None: require_argo_for_val=args.require_argo, require_argo_for_all=args.require_argo, count_argo_support=args.require_argo, + filter_bad_argo_quality=args.filter_bad_argo_quality, + accepted_argo_qc_flags=args.accepted_argo_qc_flags, metadata_cache_dir=args.metadata_cache_dir, ) loader = build_dataloader( @@ -73,6 +88,8 @@ def main() -> None: print(f"dataset rows: {len(dataset)}") print(f"depth levels: {len(dataset.depth_axis_m)}") + print(f"filter bad ARGO quality: {dataset.filter_bad_argo_quality}") + print(f"accepted ARGO QC flags: {dataset.accepted_argo_qc_flags}") print( f"date coverage in this run: {dataset.available_dates[0]}..{dataset.available_dates[-1]}" )