ENH: Allow index inputs for read_timeseries (#139)

src/spectral_recovery/_config.py

@@ -8,6 +8,9 @@
 
 REQ_DIMS = ["band", "time", "y", "x"]
 
+# Index configurations
 STANDARD_BANDS = list(spx.bands)
+SUPPORTED_DOMAINS = ["vegetation", "burn"]
+SUPPORTED_INDICES = [ix for ix in list(spx.indices) if spx.indices[ix].application_domain in SUPPORTED_DOMAINS] + ["GCI", "TCW", "TCG"]
 
 VALID_YEAR = re.compile(r"^\d{4}$")

src/spectral_recovery/indices.py

@@ -19,11 +19,11 @@
 from typing import List, Dict
 
 from spectral_recovery._utils import maintain_rio_attrs
+from spectral_recovery._config import SUPPORTED_DOMAINS
 
 # Set up global index configurations:
 #    1. Only support vegetation and burn indices
 #    2. Init index-specific constant defaults
-SUPPORTED_DOMAINS = ["vegetation", "burn"]
 with pkg_resources.open_text(
     "spectral_recovery.resources", "constant_defaults.json"
 ) as f:

src/spectral_recovery/io/raster.py

@@ -14,6 +14,7 @@
 import xarray as xr
 
 from spectral_recovery._utils import bands_pretty_table, common_and_long_to_short
+from spectral_recovery._config import SUPPORTED_INDICES
 from rasterio._err import CPLE_AppDefinedError
 
 from spectral_recovery._config import (
@@ -227,16 +228,17 @@ def _to_standard_band_names(in_names: List[str]) -> Tuple[List[str], List[str]]:
             converted = True
             standard_names.append(COMMON_LONG_SHORT_DICT[given_name])
             attr_names.append(given_name)
-
         elif given_name in STANDARD_BANDS:
             converted = True
             standard_names.append(given_name)
+        elif given_name in SUPPORTED_INDICES:
+            converted = True
+            standard_names.append(given_name)
 
         if not converted:
             raise ValueError(
-                "Band must be named standard, common, or long name. Could not find"
-                f" '{given_name}' in catalogue. See table below for accepted names:"
-                f" \n\n {BANDS_TABLE} \n\n"
+                "Band must be named standard, common, or long name for a spectral band, or a spectral index. Could not find"
+                f" '{given_name}' in supported bands or indices."
             ).with_traceback(None) from None
 
     return (standard_names, attr_names)
@@ -249,40 +251,4 @@ def _mask_stack(stack: xr.DataArray, mask: xr.DataArray, fill=np.nan) -> xr.Data
             f"Only 2D masks are supported. {len(mask.dims)}D mask provided."
         )
     masked_stack = stack.where(mask, fill)
-    return masked_stack
-
-
-def _metrics_to_tifs(
-    metric: xr.DataArray,
-    out_dir: str,
-) -> None:
-    """
-    Write a DataArray of metrics to TIFs.
-
-    Parameters
-    ----------
-    metric : xr.DataArray
-        The metric to write to TIFs. Must have dimensions: 'metric', 'band', 'y', and 'x'.
-    out_dir : str
-        Path to directory to write TIFs.
-
-    """
-    # NOTE: out_raster MUST be all null otherwise merging of rasters will fail
-    out_raster = xr.full_like(metric[0, 0, :, :], np.nan)
-    for m in metric["metric"].values:
-        xa_dataset = xr.Dataset()
-        for band in metric["band"].values:
-            out_metric = metric.sel(metric=m, band=band)
-
-            merged = out_metric.combine_first(out_raster)
-            xa_dataset[str(band)] = merged
-            try:
-                filename = f"{out_dir}/{str(m)}.tif"
-                xa_dataset.rio.to_raster(raster_path=filename)
-            # TODO: Probably shouldn't except on an error hidden from API users...
-            except CPLE_AppDefinedError:
-                raise PermissionError(
-                    f"Permission denied to overwrite {filename}. Is the existing TIF"
-                    " open in an application (e.g QGIS)? If so, try closing it before"
-                    " your next run to avoid this error."
-                ) from None
+    return masked_stack

src/tests/unit/test_io.py

@@ -473,7 +473,31 @@ def test_no_band_desc_or_band_names_throws_value_err(
                 path_to_tifs="a/dir",
                 array_type="numpy",
             )
+
+    @patch(
+        "rioxarray.open_rasterio",
+    )
+    @patch("spectral_recovery.io.raster._get_tifs_from_dir")
+    def test_index_band_names_accepted(
+        self, mocked_get_tifs, mocked_rasterio_open, filenames
+    ):
+        expected_bands = ["GCI", "NBR", "NDVI"]
+        rasterio_return = xr.DataArray(
+            [[[[0]]], [[[0]]], [[[0]]]],
+            dims=["band", "time", "y", "x"],
+            coords={"band": [1, 2, 3]},
+        )
+        mocked_get_tifs.return_value = filenames
+        mocked_rasterio_open.return_value = rasterio_return
 
+        stacked_tifs = read_timeseries(
+            path_to_tifs="a/dir",
+            band_names={1: "GCI", 2: "NBR", 3: "NDVI"},
+            array_type="numpy",
+        )
+        # assert
+        print(stacked_tifs["band"].data, expected_bands)
+        assert_array_equal(stacked_tifs["band"].data, expected_bands)
 
 class TestReadTimeseriesDictInput: