NOAA-OWP · CarsonPruitt-NOAA · Jun 16, 2022 · Jun 1, 2022 · Jun 2, 2022 · Jun 6, 2022
diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,7 @@
 .nfs*
 __pycache__/
 config/**
+!config/deny*.lst
 !config/*template*
 !config/*default*
 !config/symbology/

diff --git a/config/deny_gms_branch_zero.lst b/config/deny_gms_branch_zero.lst
@@ -0,0 +1,59 @@
+# List of files for gms branches to delete
+# Use comment to allow list the file
+# Use curly braces to denote branch_id
+agree_bufgrid.tif
+agree_bufgrid_allo.tif
+agree_bufgrid_dist.tif
+agree_smogrid.tif
+agree_smogrid_allo.tif
+agree_smogrid_dist.tif
+catch_list_{}.txt
+coordFile_{}.txt
+crosswalk_table_{}.csv
+demDerived_reaches_{}.dbf
+demDerived_reaches_{}.prj
+demDerived_reaches_{}.shp
+demDerived_reaches_{}.shx
+demDerived_reaches_split_{}.gpkg
+demDerived_reaches_split_filtered_{}.gpkg
+demDerived_reaches_split_filtered_addedAttributes_crosswalked_{}.gpkg
+demDerived_reaches_split_points_{}.gpkg
+demDerived_streamPixels_{}.tif
+demDerived_streamPixels_ids_{}.tif
+demDerived_streamPixels_ids_{}_allo.tif
+demDerived_streamPixels_ids_{}_dist.tif
+dem_burned_{}.tif
+dem_burned_filled_{}.tif
+dem_lateral_thalweg_adj_{}.tif
+#dem_meters_{}.tif
+dem_thalwegCond_{}.tif
+flowaccum_d8_burned_filled_{}.tif
+#flowdir_d8_burned_filled_{}.tif
+flowdir_d8_burned_filled_flows_{}.tif
+flows_grid_boolean_{}.tif
+flows_points_pixels_{}.gpkg
+gw_catchments_pixels_{}.tif
+gw_catchments_reaches_{}.gpkg
+gw_catchments_reaches_{}.tif
+#gw_catchments_reaches_filtered_addedAttributes_{}.gpkg
+#gw_catchments_reaches_filtered_addedAttributes_{}.tif
+gw_catchments_reaches_filtered_addedAttributes_crosswalked_{}.gpkg
+headwaters_{}.tif
+#hydroTable_{}.csv
+idFile_{}.txt
+nld_rasterized_elev_{}.tif
+nwm_catchments_proj_subset_levelPaths_{}.gpkg
+nwm_subset_streams_levelPaths_{}.gpkg
+nwm_subset_streams_levelPaths_dissolved_headwaters_{}.gpkg
+rem_{}.tif
+#rem_zeroed_masked_{}.tif
+slopes_d8_dem_meters_{}.tif
+slopes_d8_dem_meters_masked_{}.tif
+sn_catchments_reaches_{}.tif
+src_{}.json
+src_base_{}.csv
+#src_full_crosswalked_{}.csv
+stage_{}.txt
+streamOrder_{}.tif
+treeFile_{}.txt
+#usgs_elev_table.csv
diff --git a/config/deny_gms_unit_default.lst b/config/deny_gms_unit_default.lst
@@ -5,11 +5,11 @@ NHDPlusBurnLineEvent_subset.gpkg
 #branch_polygons.gpkg
 nhd_headwater_points_subset.gpkg
 #nld_subset_levees.gpkg
-nwm_catchments_proj_subset.gpkg
+#nwm_catchments_proj_subset.gpkg
 #nwm_catchments_proj_subset_levelPaths.gpkg
 nwm_headwaters.gpkg
 #nwm_lakes_proj_subset.gpkg
-nwm_subset_streams.gpkg
+#nwm_subset_streams.gpkg
 #nwm_subset_streams_levelPaths.gpkg
 #nwm_subset_streams_levelPaths_dissolved.gpkg
 #nwm_subset_streams_levelPaths_dissolved_headwaters.gpkg

diff --git a/config/params_template.env b/config/params_template.env
@@ -24,6 +24,7 @@ export min_stream_length=0.5
 export branch_id_attribute=levpa_id
 export branch_buffer_distance_meters=7000
 export branch_timeout=4000 # pass int or float. To make a percentage of median, pass a '%' at the end.
+export branch_zero_id="0"
 
 #### bathy SRC estimation parameters ####
 export bathy_src_toggle=True # Toggle to run BARC routine (True=on; False=off)

diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -1,6 +1,39 @@
 All notable changes to this project will be documented in this file.
 We follow the [Semantic Versioning 2.0.0](http://semver.org/) format.
 
+## v4.0.5.0 - 2022-06-16 - [PR #611](https://github.com/NOAA-OWP/inundation-mapping/pull/611)
+
+'Branch zero' is a new branch that runs the HUCs full stream network to make up for stream orders 1 & 2 being skipped by the GMS solution and is similar to the FR extent in FIM v3. This new branch is created during `run_by_unit.sh` and the processed DEM is used by the other GMS branches during `run_by_branch.sh` to improve efficiency.
+
+## Additions
+
+- `src/gms/delineate_hydros_and_produce_HAND.sh`: Runs all of the modules associated with delineating stream lines and catchments and building the HAND relative elevation model. This file is called once during `gms_run_unit` to produce the branch zero files and is also run for every GMS branch in `gms_run_branch`.
+- `config/deny_gms_branch_zero.lst`: A list specifically for branch zero that helps with cleanup (removing unneeded files after processing).
+
+## Changes
+
+- `src/`
+    - `output_cleanup.py`: Fixed bug for viz flag.
+    - `gms/`
+        - `run_by_unit.sh`: Added creation of "branch zero", DEM pre-processing, and now calls.
+        -  `delineate_hydros_and_produce_HAND.sh` to produce HAND outputs for the entire stream network.
+        - `run_by_branch.sh`: Removed DEM processing steps (now done in `run_by_unit.sh`), moved stream network delineation and HAND generation to `delineate_hydros_and_produce_HAND.sh`.
+        - `generate_branch_list.py`: Added argument and parameter to sure that the branch zero entry was added to the branch list.
+- `config/`
+     - `params_template.env`: Added `zero_branch_id` variable.
+- `tools`
+     - `run_test_case.py`: Some styling / readability upgrades plus some enhanced outputs.  Also changed the _verbose_ flag to _gms_verbose_ being passed into Mosaic_inundation function.
+     - `synthesize_test_cases.py`: arguments being passed into the _alpha_test_args_ from being hardcoded from flags to verbose (effectively turning on verbose outputs when applicable. Note: Progress bar was not affected.
+     - `tools_shared_functions.py`: Some styling / readability upgrades.
+- `gms_run_unit.sh`: Added export of extent variable.
+- `gms_run_branch.sh`: Fixed bug when using overwrite flag saying branch errors folder already exists.
+
+## Removals
+
+- `tests/`: Redundant
+- `tools/shared_variables`: Redundant
+
+<br/><br/>
 
 ## v4.0.4.3 - 2022-05-26 - [PR #605](https://github.com/NOAA-OWP/inundation-mapping/pull/605)
 

diff --git a/gms_run_branch.sh b/gms_run_branch.sh
@@ -141,10 +141,9 @@ fi
 
 if [ ! -d "$outputRunDataDir/branch_errors" ]; then
     mkdir -p "$outputRunDataDir/branch_errors"
-else
-    if [ $overwrite -eq 1 ]; then
-        rm -rf $outputRunDataDir/branch_errors/
-    fi
+elif [ $overwrite -eq 1 ]; then
+    rm -rf $outputRunDataDir/branch_errors
+    mkdir -p $outputRunDataDir/branch_errors
 fi
 
 ## RUN GMS BY BRANCH ##

diff --git a/gms_run_unit.sh b/gms_run_unit.sh
@@ -65,9 +65,9 @@ in
         shift
         deny_gms_unit_list=$1
         ;;
-	 -s|--dropLowStreamOrders)
-		  dropLowStreamOrders=1
-		  ;;
+    -s|--dropLowStreamOrders)
+        dropLowStreamOrders=1
+        ;;
     *) ;;
     esac
     shift
@@ -129,6 +129,7 @@ export input_nhd_flowlines=$inputDataDir/nhdplus_vectors_aggregate/agg_nhd_strea
 export input_nhd_headwaters=$inputDataDir/nhdplus_vectors_aggregate/agg_nhd_headwaters_adj.gpkg
 export input_GL_boundaries=$inputDataDir/landsea/gl_water_polygons.gpkg
 export deny_gms_unit_list=$deny_gms_unit_list
+export extent=GMS
 
 ## Input handling ##
 $srcDir/check_huc_inputs.py -u "$hucList"

diff --git a/src/gms/delineate_hydros_and_produce_HAND.sh b/src/gms/delineate_hydros_and_produce_HAND.sh
@@ -0,0 +1,178 @@
+#!/bin/bash -e
+
+## Level is equal to the parent script: 'unit' or 'branch'
+level=$1
+
+## INITIALIZE TOTAL TIME TIMER ##
+T_total_start
+
+## D8 FLOW ACCUMULATIONS ##
+echo -e $startDiv"D8 Flow Accumulations $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$taudemDir/aread8 -p $outputCurrentBranchDataDir/flowdir_d8_burned_filled_$current_branch_id.tif -ad8 $outputCurrentBranchDataDir/flowaccum_d8_burned_filled_$current_branch_id.tif -wg $outputCurrentBranchDataDir/headwaters_$current_branch_id.tif -nc
+Tcount
+
+# THRESHOLD ACCUMULATIONS ##
+echo -e $startDiv"Threshold Accumulations $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$taudemDir/threshold -ssa $outputCurrentBranchDataDir/flowaccum_d8_burned_filled_$current_branch_id.tif -src $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif -thresh 1
+Tcount
+
+## PREPROCESSING FOR LATERAL THALWEG ADJUSTMENT ###
+echo -e $startDiv"Preprocessing for lateral thalweg adjustment $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+python3 -m memory_profiler $srcDir/unique_pixel_and_allocation.py -s $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif -o $outputCurrentBranchDataDir/demDerived_streamPixels_ids_$current_branch_id.tif -g $outputCurrentBranchDataDir/temp_grass
+Tcount
+
+## ADJUST THALWEG MINIMUM USING LATERAL ZONAL MINIMUM ##
+echo -e $startDiv"Performing lateral thalweg adjustment $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+python3 -m memory_profiler $srcDir/adjust_thalweg_lateral.py -e $outputCurrentBranchDataDir/dem_meters_$current_branch_id.tif -s $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif -a $outputCurrentBranchDataDir/demDerived_streamPixels_ids_"$current_branch_id"_allo.tif -d $outputCurrentBranchDataDir/demDerived_streamPixels_ids_"$current_branch_id"_dist.tif -t 50 -o $outputCurrentBranchDataDir/dem_lateral_thalweg_adj_$current_branch_id.tif -th $thalweg_lateral_elev_threshold
+Tcount
+
+## MASK BURNED DEM FOR STREAMS ONLY ###
+echo -e $startDiv"Mask Burned DEM for Thalweg Only $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+gdal_calc.py --quiet --type=Int32 --overwrite --co "COMPRESS=LZW" --co "BIGTIFF=YES" --co "TILED=YES" -A $outputCurrentBranchDataDir/flowdir_d8_burned_filled_$current_branch_id.tif -B $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif --calc="A/B" --outfile="$outputCurrentBranchDataDir/flowdir_d8_burned_filled_flows_$current_branch_id.tif" --NoDataValue=0
+Tcount
+
+## FLOW CONDITION STREAMS ##
+echo -e $startDiv"Flow Condition Thalweg $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$taudemDir/flowdircond -p $outputCurrentBranchDataDir/flowdir_d8_burned_filled_flows_$current_branch_id.tif -z $outputCurrentBranchDataDir/dem_lateral_thalweg_adj_$current_branch_id.tif -zfdc $outputCurrentBranchDataDir/dem_thalwegCond_$current_branch_id.tif
+Tcount
+
+## D8 SLOPES ##
+echo -e $startDiv"D8 Slopes from DEM $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+mpiexec -n $ncores_fd $taudemDir2/d8flowdir -fel $outputCurrentBranchDataDir/dem_lateral_thalweg_adj_$current_branch_id.tif -sd8 $outputCurrentBranchDataDir/slopes_d8_dem_meters_$current_branch_id.tif
+Tcount
+
+# STREAMNET FOR REACHES ##
+echo -e $startDiv"Stream Net for Reaches $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$taudemDir/streamnet -p $outputCurrentBranchDataDir/flowdir_d8_burned_filled_$current_branch_id.tif -fel $outputCurrentBranchDataDir/dem_thalwegCond_$current_branch_id.tif -ad8 $outputCurrentBranchDataDir/flowaccum_d8_burned_filled_$current_branch_id.tif -src $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif -ord $outputCurrentBranchDataDir/streamOrder_$current_branch_id.tif -tree $outputCurrentBranchDataDir/treeFile_$current_branch_id.txt -coord $outputCurrentBranchDataDir/coordFile_$current_branch_id.txt -w $outputCurrentBranchDataDir/sn_catchments_reaches_$current_branch_id.tif -net $outputCurrentBranchDataDir/demDerived_reaches_$current_branch_id.shp
+Tcount
+
+## SPLIT DERIVED REACHES ##
+echo -e $startDiv"Split Derived Reaches $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$srcDir/split_flows.py -f $outputCurrentBranchDataDir/demDerived_reaches_$current_branch_id.shp -d $outputCurrentBranchDataDir/dem_thalwegCond_$current_branch_id.tif -s $outputCurrentBranchDataDir/demDerived_reaches_split_$current_branch_id.gpkg -p $outputCurrentBranchDataDir/demDerived_reaches_split_points_$current_branch_id.gpkg -w $outputHucDataDir/wbd8_clp.gpkg -l $outputHucDataDir/nwm_lakes_proj_subset.gpkg -ds $dropLowStreamOrders
+Tcount
+
+## GAGE WATERSHED FOR REACHES ##
+echo -e $startDiv"Gage Watershed for Reaches $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+mpiexec -n $ncores_gw $taudemDir/gagewatershed -p $outputCurrentBranchDataDir/flowdir_d8_burned_filled_$current_branch_id.tif -gw $outputCurrentBranchDataDir/gw_catchments_reaches_$current_branch_id.tif -o $outputCurrentBranchDataDir/demDerived_reaches_split_points_$current_branch_id.gpkg -id $outputCurrentBranchDataDir/idFile_$current_branch_id.txt
+Tcount
+
+## VECTORIZE FEATURE ID CENTROIDS ##
+echo -e $startDiv"Vectorize Pixel Centroids $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$srcDir/reachID_grid_to_vector_points.py -r $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif -i featureID -p $outputCurrentBranchDataDir/flows_points_pixels_$current_branch_id.gpkg
+Tcount
+
+## GAGE WATERSHED FOR PIXELS ##
+echo -e $startDiv"Gage Watershed for Pixels $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+mpiexec -n $ncores_gw $taudemDir/gagewatershed -p $outputCurrentBranchDataDir/flowdir_d8_burned_filled_"$current_branch_id".tif -gw $outputCurrentBranchDataDir/gw_catchments_pixels_$current_branch_id.tif -o $outputCurrentBranchDataDir/flows_points_pixels_$current_branch_id.gpkg -id $outputCurrentBranchDataDir/idFile_$current_branch_id.txt
+Tcount
+
+# D8 REM ##
+echo -e $startDiv"D8 REM $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$srcDir/gms/rem.py -d $outputCurrentBranchDataDir/dem_thalwegCond_"$current_branch_id".tif -w $outputCurrentBranchDataDir/gw_catchments_pixels_$current_branch_id.tif -o $outputCurrentBranchDataDir/rem_$current_branch_id.tif -t $outputCurrentBranchDataDir/demDerived_streamPixels_$current_branch_id.tif
+Tcount
+
+## BRING DISTANCE DOWN TO ZERO & MASK TO CATCHMENTS##
+echo -e $startDiv"Bring negative values in REM to zero and mask to catchments $hucNumber $current_branch_id"$stopDiv
+date -u
+gdal_calc.py --quiet --type=Float32 --overwrite --co "COMPRESS=LZW" --co "BIGTIFF=YES" --co "TILED=YES" -A $outputCurrentBranchDataDir/rem_$current_branch_id.tif -B $outputCurrentBranchDataDir/gw_catchments_reaches_$current_branch_id.tif --calc="(A*(A>=0)*(B>0))" --NoDataValue=$ndv --outfile=$outputCurrentBranchDataDir/"rem_zeroed_masked_$current_branch_id.tif"
+Tcount
+
+## RASTERIZE LANDSEA (OCEAN AREA) POLYGON (IF APPLICABLE) ##
+if [ -f $outputHucDataDir/LandSea_subset.gpkg ]; then
+    echo -e $startDiv"Rasterize filtered/dissolved ocean/Glake polygon $hucNumber $current_branch_id"$stopDiv
+    date -u
+    Tstart
+
+    gdal_rasterize -ot Int32 -burn $ndv -a_nodata $ndv -init 1 -co "COMPRESS=LZW" -co "BIGTIFF=YES" -co "TILED=YES" -te $xmin $ymin $xmax $ymax -ts $ncols $nrows $outputHucDataDir/LandSea_subset.gpkg $outputCurrentBranchDataDir/LandSea_subset_$current_branch_id.tif
+    Tcount
+fi
+
+## POLYGONIZE REACH WATERSHEDS ##
+echo -e $startDiv"Polygonize Reach Watersheds $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+gdal_polygonize.py -8 -f GPKG $outputCurrentBranchDataDir/gw_catchments_reaches_$current_branch_id.tif $outputCurrentBranchDataDir/gw_catchments_reaches_$current_branch_id.gpkg catchments HydroID
+Tcount
+
+## PROCESS CATCHMENTS AND MODEL STREAMS STEP 1 ##
+echo -e $startDiv"Process catchments and model streams $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+python3 -m memory_profiler $srcDir/filter_catchments_and_add_attributes.py -i $outputCurrentBranchDataDir/gw_catchments_reaches_$current_branch_id.gpkg -f $outputCurrentBranchDataDir/demDerived_reaches_split_$current_branch_id.gpkg -c $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.gpkg -o $outputCurrentBranchDataDir/demDerived_reaches_split_filtered_$current_branch_id.gpkg -w $outputHucDataDir/wbd8_clp.gpkg -u $hucNumber -s $dropLowStreamOrders
+Tcount
+
+## RASTERIZE NEW CATCHMENTS AGAIN ##
+echo -e $startDiv"Rasterize filtered catchments $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+gdal_rasterize -ot Int32 -a HydroID -a_nodata 0 -init 0 -co "COMPRESS=LZW" -co "BIGTIFF=YES" -co "TILED=YES" -te $xmin $ymin $xmax $ymax -ts $ncols $nrows $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.gpkg $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.tif
+Tcount
+
+## MASK SLOPE TO CATCHMENTS ##
+echo -e $startDiv"Mask to slopes to catchments $hucNumber $current_branch_id"$stopDiv
+date -u
+gdal_calc.py --quiet --type=Float32 --overwrite --co "COMPRESS=LZW" --co "BIGTIFF=YES" --co "TILED=YES" -A $outputCurrentBranchDataDir/slopes_d8_dem_meters_$current_branch_id.tif -B $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.tif --calc="A*(B>0)" --NoDataValue=$ndv --outfile=$outputCurrentBranchDataDir/slopes_d8_dem_meters_masked_$current_branch_id.tif
+Tcount
+
+## MAKE CATCHMENT AND STAGE FILES ##
+echo -e $startDiv"Generate Catchment List and Stage List Files $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$srcDir/make_stages_and_catchlist.py -f $outputCurrentBranchDataDir/demDerived_reaches_split_filtered_$current_branch_id.gpkg -c $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.gpkg -s $outputCurrentBranchDataDir/stage_$current_branch_id.txt -a $outputCurrentBranchDataDir/catch_list_$current_branch_id.txt -m $stage_min_meters -i $stage_interval_meters -t $stage_max_meters
+Tcount
+
+## MASK REM RASTER TO REMOVE OCEAN AREAS ##
+echo -e $startDiv"Additional masking to REM raster to remove ocean/Glake areas $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+[ -f $outputCurrentBranchDataDir/LandSea_subset.tif ] && \
+gdal_calc.py --quiet --type=Float32 --overwrite --co "COMPRESS=LZW" --co "BIGTIFF=YES" --co "TILED=YES" -A $outputCurrentBranchDataDir/rem_zeroed_masked_$current_branch_id.tif -B $outputCurrentBranchDataDir/LandSea_subset_$current_node_id.tif --calc="(A*B)" --NoDataValue=$ndv --outfile=$outputCurrentBranchDataDir/"rem_zeroed_masked_$current_branch_id.tif"
+Tcount
+
+## HYDRAULIC PROPERTIES ##
+echo -e $startDiv"Sample reach averaged parameters $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+$taudemDir/catchhydrogeo -hand $outputCurrentBranchDataDir/rem_zeroed_masked_$current_branch_id.tif -catch $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.tif -catchlist $outputCurrentBranchDataDir/catch_list_$current_branch_id.txt -slp $outputCurrentBranchDataDir/slopes_d8_dem_meters_masked_$current_branch_id.tif -h $outputCurrentBranchDataDir/stage_$current_branch_id.txt -table $outputCurrentBranchDataDir/src_base_$current_branch_id.csv
+Tcount
+
+## FINALIZE CATCHMENTS AND MODEL STREAMS ##
+echo -e $startDiv"Finalize catchments and model streams $hucNumber $current_branch_id"$stopDiv
+date -u
+Tstart
+if [ "$level" = "branch" ]; then
+    b_arg=$outputCurrentBranchDataDir/nwm_subset_streams_levelPaths_$current_branch_id.gpkg
+    z_arg=$outputCurrentBranchDataDir/nwm_catchments_proj_subset_levelPaths_$current_branch_id.gpkg
+elif [ "$level" = "unit" ]; then
+    # Branch zero has a different source for -b and -z arguments
+    b_arg=$outputHucDataDir/nwm_subset_streams.gpkg
+    z_arg=$outputHucDataDir/nwm_catchments_proj_subset.gpkg
+fi
+python3 -m memory_profiler $srcDir/add_crosswalk.py -d $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_$current_branch_id.gpkg -a $outputCurrentBranchDataDir/demDerived_reaches_split_filtered_$current_branch_id.gpkg -s $outputCurrentBranchDataDir/src_base_$current_branch_id.csv -l $outputCurrentBranchDataDir/gw_catchments_reaches_filtered_addedAttributes_crosswalked_$current_branch_id.gpkg -f $outputCurrentBranchDataDir/demDerived_reaches_split_filtered_addedAttributes_crosswalked_$current_branch_id.gpkg -r $outputCurrentBranchDataDir/src_full_crosswalked_$current_branch_id.csv -j $outputCurrentBranchDataDir/src_$current_branch_id.json -x $outputCurrentBranchDataDir/crosswalk_table_$current_branch_id.csv -t $outputCurrentBranchDataDir/hydroTable_$current_branch_id.csv -w $outputHucDataDir/wbd8_clp.gpkg -b $b_arg -y $outputCurrentBranchDataDir/nwm_catchments_proj_subset.tif -m $manning_n -z $z_arg -p $extent -k $outputCurrentBranchDataDir/small_segments_$current_branch_id.csv
+Tcount