Fix issue with count data type

digitalearthpacific · Feb 2, 2024 · 008773a · 008773a
1 parent 79c124f
commit 008773a
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Showing 3 changed files with 61 additions and 15 deletions.
diff --git a/Load_S1_Mosaic.ipynb b/Load_S1_Mosaic.ipynb
@@ -7,7 +7,9 @@
    "outputs": [],
    "source": [
     "from pystac_client import Client\n",
-    "from odc.stac import load"
+    "from odc.stac import load\n",
+    "\n",
+    "import numpy as np"
    ]
   },
   {
@@ -29,7 +31,7 @@
     "fiji_bbox = [177.2, -18.4, 178.9, -17.2]\n",
     "datetime = \"2023\"\n",
     "\n",
-    "items = list(client.search(collections=[\"dep_s1_mosaic\"], bbox=fiji_bbox, datetime=datetime).items())\n",
+    "items = list(client.search(collections=[\"dep_s1_mosaic\"], bbox=fiji_bbox).items())\n",
     "\n",
     "print(f\"Found {len(items)} items\")"
    ]
@@ -40,7 +42,20 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = load(items, bbox=fiji_bbox, resolution=100, chunks={}).squeeze()\n",
+    "cfg = {\n",
+    "    \"dep_s1_mosaic\": {\n",
+    "        \"assets\": {\n",
+    "            \"*\": {\n",
+    "                \"data_type\": \"float32\",\n",
+    "            },\n",
+    "            \"count\": {\n",
+    "                \"data_type\": \"int64\",\n",
+    "            },\n",
+    "        }\n",
+    "    }\n",
+    "}\n",
+    "\n",
+    "data = load(items, bbox=fiji_bbox, resolution=100, chunks={}, stac_cfg=cfg)\n",
     "data"
    ]
   },
@@ -50,15 +65,35 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data.median_vv_vh.plot.imshow(size=10, robust=True)"
+    "data.mean_vv.plot.imshow(col=\"time\", size=10, robust=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "log_10_vv = (10 * np.log10(data.mean_vv)).compute()"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "log_10_vv.plot.imshow(col=\"time\", col_wrap=2, size=10, robust=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data[\"count\"].plot.imshow(col=\"time\", col_wrap=2, size=10, robust=True)"
+   ]
   }
  ],
  "metadata": {

diff --git a/Test_S1_Mosaic.ipynb b/Test_S1_Mosaic.ipynb
@@ -194,7 +194,7 @@
     "    convert_to_int16=False\n",
     ")\n",
     "print(f\"Writing to: {dep_path._folder(item_id)}\")\n",
-    "out_files = writer.write(loaded, item_id)"
+    "out_files = writer.write(output_data, item_id)"
    ]
   },
   {
@@ -216,10 +216,22 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "d = load([item])\n",
-    "\n",
-    "d.median_vv_vh.plot.imshow(size=8, robust=True)"
+    "d = load([item])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "d[\"count\"].plot()"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

diff --git a/src/run_task.py b/src/run_task.py
@@ -63,10 +63,6 @@ def _get_items(self, area):
             area, collections=["sentinel-1-rtc"], datetime=self.datetime, query=query
         )
 
-        # Fix a few issues with STAC items
-        # fix_bad_epsgs(item_collection)
-        # item_collection = remove_bad_items(item_collection)
-
         if len(item_collection) == 0:
             raise EmptyCollectionError()
 
@@ -99,14 +95,17 @@ def process(self, input_data: DataArray) -> Dataset:
             arrays.append(input_data[band].std("time").rename(f"std_{band}"))
 
         # Add count
-        arrays.append(input_data["vv"].count("time").rename("count"))
+        arrays.append(input_data["vv"].count("time").rename("count").astype("int16"))
 
         # Merge the arrays together into a Dataset with the names we want
         data = merge(arrays, compat="override")
 
         # Set nodata on all the outputs
         for band in data.data_vars:
-            data[band].attrs["nodata"] = -32768
+            if band == "count":
+                data[band].attrs["nodata"] = 0
+            else:
+                data[band].attrs["nodata"] = -32768
 
         output = set_stac_properties(input_data, data)