added surface buffer arg

cshelph/cshelph.py

@@ -162,14 +162,14 @@ def bin_data(dataset, lat_res, height_res):
 
     return dataset1
 
-def get_sea_height(binned_data):
+def get_sea_height(binned_data, surface_buffer):
     '''Calculate mean sea height for easier calculation of depth and cleaner figures'''
 
     # Create sea height list
     sea_height = []
 
     # Group data by latitude
-    binned_data_sea = binned_data[(binned_data['photon_height'] > -0.5)] # Filter out subsurface data
+    binned_data_sea = binned_data[(binned_data['photon_height'] > surface_buffer)] # Filter out subsurface data
     grouped_data = binned_data_sea.groupby(['lat_bins'], group_keys=True)
     data_groups = dict(list(grouped_data))
 

cshelph/run_bathy_extraction.py

@@ -57,6 +57,7 @@ def main():
     parser.add_argument("-elat", "--end_lat", type=float, required = False, help="Specify the stop latitude")
     parser.add_argument("-minb", "--min_buffer", type=float, default = -40, required = False, help="Specify the stop latitude")
     parser.add_argument("-maxb", "--max_buffer", type=float, default=5, required = False, help="Specify the stop latitude")
+    parser.add_argument("-sb", "--surface_buffer", type=float, default=-0.5, required = False, help="Specify the point at which sea surface points are excluded")
 
     args = parser.parse_args()
 
@@ -116,15 +117,15 @@ def main():
     # Filter data that should not be analyzed
     # Filter for quality flags
     print('filter quality flags')
-    if args.minb == -40:
-        pass
+    if args.min_buffer == -40:
+        min_buffer = -40
     else:
-        min_buffer = args.minb
+        min_buffer = args.min_buffer
 
-    if args.maxb == 5:
-        pass
+    if args.max_buffer == 5:
+        max_buffer = 5
     else:
-        max_buffer = args.maxb
+        max_buffer = args.max_buffer
 
 
     dataset_sea1 = dataset_sea[(dataset_sea.confidence != 0)  & (dataset_sea.confidence != 1)]
@@ -142,7 +143,11 @@ def main():
     binned_data_sea = cshelph.bin_data(dataset_sea1, args.lat_res, args.h_res)
 
     # Find mean sea height
-    sea_height = cshelph.get_sea_height(binned_data_sea)
+    if args.surface_buffer==-0.5:
+        surface_buffer = -0.5
+    else:
+        surface_buffer = args.surface_buffer
+    sea_height = cshelph.get_sea_height(binned_data_sea, surface_buffer)
 
     # Set sea height
     med_water_surface_h = np.nanmedian(sea_height)
@@ -154,7 +159,7 @@ def main():
         try:
             water_temp = cshelph.get_water_temp(args.input, latitude, longitude)
         except Exception as e:
-            print('NO SST pROVIDED OR RETRIEVED: 20 degrees C assigned')
+            print('NO SST PROVIDED OR RETRIEVED: 20 degrees C assigned')
             water_temp = 20
 
     print("water temp:", water_temp)
@@ -179,12 +184,14 @@ def main():
     # Bin dataset again for bathymetry
     binned_data = cshelph.bin_data(dataset_bath, args.lat_res, args.h_res)
 
+    print("Locating bathymetric photons...")
     if isinstance(args.thresh, int) == True:
         # Find bathymetry
         bath_height, geo_df = cshelph.get_bath_height(binned_data, args.thresh, med_water_surface_h, args.h_res)
 
         # Create figure
         plt.close()
+        print('Creating figa nd writing to GPKG')
         cshelph.produce_figures(binned_data, bath_height, sea_height, 10, -20, args.thresh, file, geo_df, ref_y, ref_z, args.laser, epsg_num)
     elif isinstance(args.threshlist, list)==True:
         for thresh in args.threshlist:
@@ -193,6 +200,7 @@ def main():
 
             # Create figure
             plt.close()
+            print('Creating figa nd writing to GPKG')
             cshelph.produce_figures(binned_data, bath_height, sea_height, 10, -20, str(thresh), file, geo_df, ref_y, ref_z, args.laser, epsg_num)
 
 

cshelph/run_bathymetry_extraction.ipynb

@@ -143,7 +143,8 @@
     "- start_lat: The latitude at which you want the analysis to start\n",
     "- end_lat: The latitude at which you want the analysis to end\n",
     "- surface_buffer_min: When searching for the water surface this is the max value for the search window, default is 5m\n",
-    "- surface_buffer_max: When searching for the water surface this is the min value for the search window, default is -40m"
+    "- surface_buffer_max: When searching for the water surface this is the min value for the search window, default is -40m\n",
+    "- surface_buffer: When finding the water surface, photons below -0.5m are excluded. This parameter allows that threshold to be changed where the water surface is not at 0m (e.g., some raised bathymetry that causes a swell effect)"
    ]
   },
   {