[1pt] PR: Updating bathymetry-preprocessing script

data/bathymetry/preprocess_bathymetry.py

@@ -52,6 +52,7 @@ def preprocessing_ehydro(tif, bathy_bounds, survey_gdb, output, min_depth_thresh
         bathy_affine = bathy_ft.transform
         bathy_ft = bathy_ft.read(1)
         bathy_ft[np.where(bathy_ft == -9999.0)] = np.nan
+        bathy_ft[np.where(bathy_ft <= 0.0)] = 0.000001
     survey_min_depth = np.nanmin(bathy_ft)
 
     assert survey_min_depth < min_depth_threshold, (
@@ -81,6 +82,10 @@ def preprocessing_ehydro(tif, bathy_bounds, survey_gdb, output, min_depth_thresh
     zs_area = zs_area.set_crs(nwm_streams.crs)
     zs_area = zs_area.rename(columns={"sum": "missing_volume_m3"})
 
+    # print("------------------------------")
+    # print(zs_area.ID)
+    # print("------------------------------")
+
     # Derive slope tif
     output_slope_tif = os.path.join(os.path.dirname(tif), 'bathy_slope.tif')
     slope_tif = gdal.DEMProcessing(output_slope_tif, bathy_gdal, 'slope', format='GTiff')
@@ -115,14 +120,22 @@ def preprocessing_ehydro(tif, bathy_bounds, survey_gdb, output, min_depth_thresh
     )
 
     # Add survey meta data
-    bathy_nwm_streams['SurveyDateStamp'] = bathy_bounds.loc[0, 'SurveyDateStamp']
+    time_stamp = bathy_bounds.loc[0, 'SurveyDateStamp']
+    time_stamp_obj = str(time_stamp)
+
+    bathy_nwm_streams['SurveyDateStamp'] = time_stamp_obj  # bathy_bounds.loc[0, 'SurveyDateStamp']
     bathy_nwm_streams['SurveyId'] = bathy_bounds.loc[0, 'SurveyId']
     bathy_nwm_streams['Sheet_Name'] = bathy_bounds.loc[0, 'Sheet_Name']
     bathy_nwm_streams["Bathymetry_source"] = 'USACE eHydro'
 
     # Export geopackage with bathymetry
     num_streams = len(bathy_nwm_streams)
     bathy_nwm_streams = bathy_nwm_streams.to_crs(epsg=5070)
+
+    # schema = gpd.io.file.infer_schema(bathy_nwm_streams)
+    # print(schema)
+    # print("---------------------------")
+
     if os.path.exists(output):
         print(f"{output} already exists. Concatinating now...")
         existing_bathy_file = gpd.read_file(output, engine="pyogrio", use_arrow=True)

docs/CHANGELOG.md

@@ -1,11 +1,20 @@
 All notable changes to this project will be documented in this file.
 We follow the [Semantic Versioning 2.0.0](http://semver.org/) format.
 
+## v4.5.4.2 - 2024-08-02 - [PR#1125](https://github.com/NOAA-OWP/inundation-mapping/pull/1125)
+
+This PR focuses on updating the preprocess_bathymetry.py for 3 issues: 1) the capability of preprocessing SurveyJobs that have negative depth values, 2) changing the SurveyDateStamp format, and 3) the capability of including multiple SurveyJobs for one NWM feature-id if needed.
+
+### Changes
+`data/bathymetry/preprocess_bathymetry.py`: Addressing 3 issues including, the capability of preprocessing SurveyJobs that have negative depth values, changing the SurveyDateStamp format, and the capability of including multiple SurveyJobs for one NWM feature-id.
+
+
+<br/><br/>
+
 ## v4.5.4.1 - 2024-08-02 - [PR#1185](https://github.com/NOAA-OWP/inundation-mapping/pull/1185)
 
 This PR brings back the `preprocess_ahps_nws.py` code to FIM4 and generates new AHPS benchmark datasets for sites SXRA2 and SKLA2 in Alaska.  The new AHPS benchmark datasets are available on dev1 here: "/dev_fim_share/foss_fim/outputs/ali_ahps_alaska/AHPS_Results_Alaska/19020302/"
 
-This PR closes issue #1130. 
 
 To process a new station, follow these steps: