From 1a00462220f970614e9e045af4a6b3198f47dc8b Mon Sep 17 00:00:00 2001
From: Mike <michael.j.shaw@erdc.dren.mil>
Date: Thu, 19 Nov 2020 14:47:50 -0500
Subject: [PATCH 01/13] ERA island effect weight changes

---
 RAPIDpy/gis/weight.py | 64 ++++++++++++++++++++++++++++++-------------
 1 file changed, 45 insertions(+), 19 deletions(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index f17c020..bc83836 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -80,7 +80,7 @@ def find_nearest(array, value):
     return (np.abs(array-value)).argmin()
 
 
-def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon,
+def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon, lsm_grid_mask,
                               in_catchment_shapefile, river_id,
                               in_rapid_connect, out_weight_table,
                               file_geodatabase=None, area_id=None):
@@ -103,7 +103,6 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon,
     else:
         ogr_catchment_shapefile = ogr.Open(in_catchment_shapefile)
         ogr_catchment_shapefile_lyr = ogr_catchment_shapefile.GetLayer()
-
     ogr_catchment_shapefile_lyr_proj = \
         ogr_catchment_shapefile_lyr.GetSpatialRef()
     original_catchment_proj = \
@@ -196,9 +195,11 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon,
                 connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
                 continue
 
+
             get_catchment_feature = \
                 ogr_catchment_shapefile_lyr.GetFeature(catchment_pos)
             feat_geom = get_catchment_feature.GetGeometryRef()
+
             # make sure coordinates are geographic
             if proj_transform:
                 feat_geom.Transform(proj_transform)
@@ -242,22 +243,40 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon,
                             lsm_grid_lon,
                             lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
                             lsm_grid_feature_list[sub_lsm_grid_pos]['lon'])
-                    intersect_grid_info_list.append({
-                        'rivid': rapid_connect_rivid,
-                        'area': poly_area,
-                        'lsm_grid_lat':
-                            lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
-                        'lsm_grid_lon':
-                            lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
-                        'index_lsm_grid_lon': index_lsm_grid_lon,
-                        'index_lsm_grid_lat': index_lsm_grid_lat
-                    })
+                    # If ocean/water point, ECMWF sets ro to very negative number.
+                    # This resulted at times in "island effect", i.e., large 
+                    # grid cell overlaying rivid and thus weird results.  So,
+                    # use land mask field to address these ECMWF points.
+                    # There are arguments for and against division by land fraction. E.g.,
+                    # it's arguable that division by mask might overemphasis some
+                    # pixels that contain fine grained islands with runoff.
+                    if lsm_grid_mask[int(index_lsm_grid_lat), int(index_lsm_grid_lon)] > 0:
+                        intersect_grid_info_list.append({
+                            'rivid': rapid_connect_rivid,
+                            'area': poly_area/lsm_grid_mask[int(index_lsm_grid_lat), int(index_lsm_grid_lon)],
+                            'lsm_grid_lat':
+                                lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
+                            'lsm_grid_lon':
+                                lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
+                            'index_lsm_grid_lon': index_lsm_grid_lon,
+                            'index_lsm_grid_lat': index_lsm_grid_lat
+                        })
+# Prior weight table write without addressing land mask.
+#                    intersect_grid_info_list.append({
+#                        'rivid': rapid_connect_rivid,
+#                        'area': poly_area,
+#                        'lsm_grid_lat':
+#                            lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
+#                        'lsm_grid_lon':
+#                            lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
+#                       'index_lsm_grid_lon': index_lsm_grid_lon,
+#                        'index_lsm_grid_lat': index_lsm_grid_lat
+#                    })
 
             npoints = len(intersect_grid_info_list)
             # If no intersection found, add dummy row
             if npoints <= 0:
                 connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
-
             for intersect_grid_info in intersect_grid_info_list:
                 connectwriter.writerow([
                     intersect_grid_info['rivid'],
@@ -268,7 +287,6 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon,
                     intersect_grid_info['lsm_grid_lon'],
                     intersect_grid_info['lsm_grid_lat']
                 ])
-
     time_end_all = datetime.utcnow()
     log(time_end_all - time_end_lsm_grid_rtree)
     log("TOTAL TIME: {0}".format(time_end_all - time_start_all))
@@ -332,15 +350,22 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
     in_ecmwf_lon_var = 'lon'
     if 'longitude' in variables_list:
         in_ecmwf_lon_var = 'longitude'
+    in_ecmwf_mask_var = 'mask'
+#    in_ecmwf_mask_var = 'LAND_P0_L1_GLL0'
+    if 'mask' in variables_list:
+        in_ecmwf_mask_var = 'mask'
+    if 'lsm' in variables_list:
+        in_ecmwf_mask_var = 'lsm'
 
     # convert [0, 360] to [-180, 180]
-    ecmwf_lon = \
-        (data_ecmwf_nc.variables[in_ecmwf_lon_var][:] + 180) % 360 - 180
+    ecmwf_lon = data_ecmwf_nc.variables[in_ecmwf_lon_var][:]
     # assume [-90, 90]
     ecmwf_lat = data_ecmwf_nc.variables[in_ecmwf_lat_var][:]
+    ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
+
     data_ecmwf_nc.close()
 
-    rtree_create_weight_table(ecmwf_lat, ecmwf_lon,
+    rtree_create_weight_table(ecmwf_lat, ecmwf_lon, ecmwf_mask, 
                               in_catchment_shapefile, river_id,
                               in_connectivity_file, out_weight_table,
                               file_geodatabase, area_id)
@@ -373,6 +398,8 @@ def CreateWeightTableLDAS(in_ldas_nc,
         The name of the field with the river ID (Ex. 'DrainLnID' or 'LINKNO').
     in_connectivity_file: str
         The path to the RAPID connectivity file.
+        is the name of the stream network feature class.
+        (WARNING: Not always stable with GDAL.)
     out_weight_table: str
         The path to the output weight table file.
     area_id: str, optional
@@ -383,7 +410,6 @@ def CreateWeightTableLDAS(in_ldas_nc,
         is the name of the stream network feature class.
         (WARNING: Not always stable with GDAL.)
 
-
     Example:
 
     .. code:: python
@@ -398,7 +424,7 @@ def CreateWeightTableLDAS(in_ldas_nc,
             river_id='LINKNO',
             in_connectivity_file='/path/to/rapid_connect.csv',
             out_weight_table='/path/to/ldas_weight.csv',
-        )
+            )
     """
     # extract LDAS GRID
     data_ldas_nc = Dataset(in_ldas_nc)

From 7bfd2d066014515b6fc8c0c4477e4819e2a3a7b3 Mon Sep 17 00:00:00 2001
From: mjshaw1 <22522597+mjshaw1@users.noreply.github.com>
Date: Thu, 19 Nov 2020 15:03:21 -0500
Subject: [PATCH 02/13] Update weight.py

Reverted to mask from 0-360 (so, shifting by 180 degrees).
---
 RAPIDpy/gis/weight.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index bc83836..3cd55c6 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -358,7 +358,8 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
         in_ecmwf_mask_var = 'lsm'
 
     # convert [0, 360] to [-180, 180]
-    ecmwf_lon = data_ecmwf_nc.variables[in_ecmwf_lon_var][:]
+    ecmwf_long = \
+        (data_ecmwf_nc.variables[in_ecmwf_lon_var][:] + 180) % 360 - 180
     # assume [-90, 90]
     ecmwf_lat = data_ecmwf_nc.variables[in_ecmwf_lat_var][:]
     ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]

From 6528184a422fcff4722db6b889dbcd3edefaad3f Mon Sep 17 00:00:00 2001
From: Matthew <mgeheran@gmail.com>
Date: Fri, 20 Nov 2020 06:50:21 -0600
Subject: [PATCH 03/13] Modifies island_effect code to allow weight table
 generation routines to be called without specifying a land-mask file.

---
 RAPIDpy/gis/weight.py | 85 ++++++++++++++++++++-----------------------
 1 file changed, 40 insertions(+), 45 deletions(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index 3cd55c6..9e87b13 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -80,10 +80,11 @@ def find_nearest(array, value):
     return (np.abs(array-value)).argmin()
 
 
-def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon, lsm_grid_mask,
+def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon,
                               in_catchment_shapefile, river_id,
                               in_rapid_connect, out_weight_table,
-                              file_geodatabase=None, area_id=None):
+                              file_geodatabase=None, area_id=None,
+                              lsm_grid_mask=None):
     """
     Create Weight Table for Land Surface Model Grids
     """
@@ -103,6 +104,7 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon, lsm_grid_mask,
     else:
         ogr_catchment_shapefile = ogr.Open(in_catchment_shapefile)
         ogr_catchment_shapefile_lyr = ogr_catchment_shapefile.GetLayer()
+
     ogr_catchment_shapefile_lyr_proj = \
         ogr_catchment_shapefile_lyr.GetSpatialRef()
     original_catchment_proj = \
@@ -195,11 +197,9 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon, lsm_grid_mask,
                 connectwriter.writerow([rapid_connect_rivid] + dummy_row_end)
                 continue
 
-
             get_catchment_feature = \
                 ogr_catchment_shapefile_lyr.GetFeature(catchment_pos)
             feat_geom = get_catchment_feature.GetGeometryRef()
-
             # make sure coordinates are geographic
             if proj_transform:
                 feat_geom.Transform(proj_transform)
@@ -243,35 +243,21 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon, lsm_grid_mask,
                             lsm_grid_lon,
                             lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
                             lsm_grid_feature_list[sub_lsm_grid_pos]['lon'])
-                    # If ocean/water point, ECMWF sets ro to very negative number.
-                    # This resulted at times in "island effect", i.e., large 
-                    # grid cell overlaying rivid and thus weird results.  So,
-                    # use land mask field to address these ECMWF points.
-                    # There are arguments for and against division by land fraction. E.g.,
-                    # it's arguable that division by mask might overemphasis some
-                    # pixels that contain fine grained islands with runoff.
-                    if lsm_grid_mask[int(index_lsm_grid_lat), int(index_lsm_grid_lon)] > 0:
-                        intersect_grid_info_list.append({
-                            'rivid': rapid_connect_rivid,
-                            'area': poly_area/lsm_grid_mask[int(index_lsm_grid_lat), int(index_lsm_grid_lon)],
-                            'lsm_grid_lat':
-                                lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
-                            'lsm_grid_lon':
-                                lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
-                            'index_lsm_grid_lon': index_lsm_grid_lon,
-                            'index_lsm_grid_lat': index_lsm_grid_lat
-                        })
-# Prior weight table write without addressing land mask.
-#                    intersect_grid_info_list.append({
-#                        'rivid': rapid_connect_rivid,
-#                        'area': poly_area,
-#                        'lsm_grid_lat':
-#                            lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
-#                        'lsm_grid_lon':
-#                            lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
-#                       'index_lsm_grid_lon': index_lsm_grid_lon,
-#                        'index_lsm_grid_lat': index_lsm_grid_lat
-#                    })
+
+                    if lsm_grid_mask is not None:
+                        if lsm_grid_mask[int(index_lsm_grid_lat), int(index_lsm_grid_lon)] > 0:
+                            poly_area /= lsm_grid_mask[int(index_lsm_grid_lat), int(index_lsm_grid_lon)]
+                            
+                    intersect_grid_info_list.append({
+                        'rivid': rapid_connect_rivid,
+                        'area': poly_area,
+                        'lsm_grid_lat':
+                            lsm_grid_feature_list[sub_lsm_grid_pos]['lat'],
+                        'lsm_grid_lon':
+                            lsm_grid_feature_list[sub_lsm_grid_pos]['lon'],
+                        'index_lsm_grid_lon': index_lsm_grid_lon,
+                        'index_lsm_grid_lat': index_lsm_grid_lat
+                    })
 
             npoints = len(intersect_grid_info_list)
             # If no intersection found, add dummy row
@@ -287,6 +273,7 @@ def rtree_create_weight_table(lsm_grid_lat, lsm_grid_lon, lsm_grid_mask,
                     intersect_grid_info['lsm_grid_lon'],
                     intersect_grid_info['lsm_grid_lat']
                 ])
+
     time_end_all = datetime.utcnow()
     log(time_end_all - time_end_lsm_grid_rtree)
     log("TOTAL TIME: {0}".format(time_end_all - time_start_all))
@@ -350,26 +337,34 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
     in_ecmwf_lon_var = 'lon'
     if 'longitude' in variables_list:
         in_ecmwf_lon_var = 'longitude'
-    in_ecmwf_mask_var = 'mask'
-#    in_ecmwf_mask_var = 'LAND_P0_L1_GLL0'
-    if 'mask' in variables_list:
-        in_ecmwf_mask_var = 'mask'
-    if 'lsm' in variables_list:
-        in_ecmwf_mask_var = 'lsm'
-
+        
     # convert [0, 360] to [-180, 180]
-    ecmwf_long = \
+    ecmwf_lon = \
         (data_ecmwf_nc.variables[in_ecmwf_lon_var][:] + 180) % 360 - 180
     # assume [-90, 90]
     ecmwf_lat = data_ecmwf_nc.variables[in_ecmwf_lat_var][:]
-    ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
 
+    mask_var_names = ['mask', 'lsm']
+    mask_var_intersect_variable_list = (
+        set(variables_list) & set(mask_var_names))
+
+    try:
+        in_ecmwf_mask_var = mask_var_intersect_variable_list.pop()
+    except KeyError:
+        in_ecmwf_mask_var = None
+
+    if in_ecmwf_mask_var is None:
+        ecmwf_mask = None
+    else:
+        ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
+        
     data_ecmwf_nc.close()
 
-    rtree_create_weight_table(ecmwf_lat, ecmwf_lon, ecmwf_mask, 
+    rtree_create_weight_table(ecmwf_lat, ecmwf_lon,
                               in_catchment_shapefile, river_id,
                               in_connectivity_file, out_weight_table,
-                              file_geodatabase, area_id)
+                              file_geodatabase, area_id,
+                              lsm_grid_mask=ecmwf_mask)
 
 
 def CreateWeightTableLDAS(in_ldas_nc,
@@ -425,7 +420,7 @@ def CreateWeightTableLDAS(in_ldas_nc,
             river_id='LINKNO',
             in_connectivity_file='/path/to/rapid_connect.csv',
             out_weight_table='/path/to/ldas_weight.csv',
-            )
+        )
     """
     # extract LDAS GRID
     data_ldas_nc = Dataset(in_ldas_nc)

From 799fdf9c679af9c3b1d0fefffdcb7bdd32d18f60 Mon Sep 17 00:00:00 2001
From: Matthew <mgeheran@gmail.com>
Date: Mon, 23 Nov 2020 13:08:31 -0600
Subject: [PATCH 04/13] Simplifies handling of land mask variable.

---
 RAPIDpy/gis/weight.py | 20 ++++++--------------
 1 file changed, 6 insertions(+), 14 deletions(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index 9e87b13..44bd126 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -285,7 +285,8 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
                            in_connectivity_file,
                            out_weight_table,
                            area_id=None,
-                           file_geodatabase=None):
+                           file_geodatabase=None,
+                           in_ecmwf_mask_var=None):
     """
     Create Weight Table for ECMWF Grids
 
@@ -344,20 +345,11 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
     # assume [-90, 90]
     ecmwf_lat = data_ecmwf_nc.variables[in_ecmwf_lat_var][:]
 
-    mask_var_names = ['mask', 'lsm']
-    mask_var_intersect_variable_list = (
-        set(variables_list) & set(mask_var_names))
-
-    try:
-        in_ecmwf_mask_var = mask_var_intersect_variable_list.pop()
-    except KeyError:
-        in_ecmwf_mask_var = None
-
-    if in_ecmwf_mask_var is None:
-        ecmwf_mask = None
-    else:
+    if in_ecmwf_mask_var is not None and mask_var in variables_list:
         ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
-        
+    else:
+	ecmwf_mask = None
+
     data_ecmwf_nc.close()
 
     rtree_create_weight_table(ecmwf_lat, ecmwf_lon,

From bb2c69d6f3722b1fa1a2239d63e113db5639f6f4 Mon Sep 17 00:00:00 2001
From: Matthew <mpg56@drexel.edu>
Date: Mon, 23 Nov 2020 18:40:41 -0600
Subject: [PATCH 05/13] Adds statement to notify user if specified land-mask
 variable is not found in input LSM file.

---
 RAPIDpy/gis/weight.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index 44bd126..5f664ba 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -345,10 +345,14 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
     # assume [-90, 90]
     ecmwf_lat = data_ecmwf_nc.variables[in_ecmwf_lat_var][:]
 
-    if in_ecmwf_mask_var is not None and mask_var in variables_list:
-        ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
-    else:
-	ecmwf_mask = None
+    if in_ecmwf_mask_var is not None:
+        if mask_var in variables_list:
+            ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
+        else:
+            print('Variable {} not found in {}.'.format(in_ecmwf_mask_var,
+                                                        in_ecmwf_nc))
+            print('Continuing with no land mask.')
+            ecmwf_mask = None
 
     data_ecmwf_nc.close()
 

From 5f0c0ec3c66494c655e8dec7ace670df7eaf9885 Mon Sep 17 00:00:00 2001
From: Matthew <mpg56@drexel.edu>
Date: Mon, 23 Nov 2020 19:22:35 -0600
Subject: [PATCH 06/13] Adds ECMWF land-mask file test.

---
 tests/test_gis.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/tests/test_gis.py b/tests/test_gis.py
index cbe7285..9ae3d54 100644
--- a/tests/test_gis.py
+++ b/tests/test_gis.py
@@ -765,3 +765,34 @@ def test_weight_table_with_area_id():
                                   generated_weight_table_file_solution))
 
     remove_files(generated_weight_table_file)
+
+def test_gen_weight_table_era5_land_mask():
+    """
+    Checks generating weight table for ERA5 grid with land mask.
+    """
+    print("TEST 18: TEST GENERATE WEIGHT TABLE FOR ERA5 GRID WITH LAND MASK.")
+    generated_weight_table_file = os.path.join(
+        OUTPUT_DATA_PATH, "mendocino_nhdplus_catchment",
+        "weight_mendocino_sample_era5.csv")
+
+    #rapid_connect
+    rapid_connect_file = os.path.join(COMPARE_DATA_PATH,
+                                      "mendocino_nhdplus_catchment",
+                                      "rapid_connectivity_mendocino_sample.csv")
+
+    lsm_grid = os.path.join(LSM_INPUT_DATA_PATH, "era5", "era5_land-sea_mask_mendocino_subset.nc")
+
+    CreateWeightTableECMWF(in_ecmwf_nc=lsm_grid,
+                           in_catchment_shapefile=os.path.join(GIS_INPUT_DATA_PATH, 'mendocino_nhdplus_catchment', 'NHDCat_mendocino_watershed_hopland_sample.shp'),
+                           river_id="FEATUREID",
+                           in_connectivity_file=rapid_connect_file,
+                           out_weight_table=generated_weight_table_file)
+
+    generated_weight_table_file_solution = os.path.join(
+        COMPARE_DATA_PATH, 'mendocino_nhdplus_catchment',
+        'weight_mendocino_sample_era5.csv')
+    
+    assert (compare_csv_decimal_files(generated_weight_table_file,
+                                      generated_weight_table_file_solution))
+
+    remove_files(generated_weight_table_file)

From 682d1ba9d2d16b03159a93fbb8b5370c54c042d5 Mon Sep 17 00:00:00 2001
From: Matthew <mgeheran@gmail.com>
Date: Mon, 23 Nov 2020 14:34:55 -0600
Subject: [PATCH 07/13] Corrects path names in land-mask test.

---
 tests/test_gis.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_gis.py b/tests/test_gis.py
index 9ae3d54..41e7cb8 100644
--- a/tests/test_gis.py
+++ b/tests/test_gis.py
@@ -772,8 +772,7 @@ def test_gen_weight_table_era5_land_mask():
     """
     print("TEST 18: TEST GENERATE WEIGHT TABLE FOR ERA5 GRID WITH LAND MASK.")
     generated_weight_table_file = os.path.join(
-        OUTPUT_DATA_PATH, "mendocino_nhdplus_catchment",
-        "weight_mendocino_sample_era5.csv")
+        OUTPUT_DATA_PATH, "weight_mendocino_era5_land_mask.csv")
 
     #rapid_connect
     rapid_connect_file = os.path.join(COMPARE_DATA_PATH,
@@ -786,11 +785,12 @@ def test_gen_weight_table_era5_land_mask():
                            in_catchment_shapefile=os.path.join(GIS_INPUT_DATA_PATH, 'mendocino_nhdplus_catchment', 'NHDCat_mendocino_watershed_hopland_sample.shp'),
                            river_id="FEATUREID",
                            in_connectivity_file=rapid_connect_file,
-                           out_weight_table=generated_weight_table_file)
+                           out_weight_table=generated_weight_table_file,
+                           in_ecmwf_mask_var='lsm')
 
     generated_weight_table_file_solution = os.path.join(
         COMPARE_DATA_PATH, 'mendocino_nhdplus_catchment',
-        'weight_mendocino_sample_era5.csv')
+        'weight_mendocino_era5_land_mask.csv')
     
     assert (compare_csv_decimal_files(generated_weight_table_file,
                                       generated_weight_table_file_solution))

From d98caacfed9f8770ff885f3b3f3754c561cd65b0 Mon Sep 17 00:00:00 2001
From: Matthew <mgeheran@gmail.com>
Date: Mon, 23 Nov 2020 14:36:11 -0600
Subject: [PATCH 08/13] Corrects variable name in CreateWeightTableECMWF.

---
 RAPIDpy/gis/weight.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index 5f664ba..db64f43 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -346,13 +346,15 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
     ecmwf_lat = data_ecmwf_nc.variables[in_ecmwf_lat_var][:]
 
     if in_ecmwf_mask_var is not None:
-        if mask_var in variables_list:
+        if in_ecmwf_mask_var in variables_list:
             ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
         else:
-            print('Variable {} not found in {}.'.format(in_ecmwf_mask_var,
+            print('Variable "{}" not found in {}.'.format(in_ecmwf_mask_var,
                                                         in_ecmwf_nc))
             print('Continuing with no land mask.')
             ecmwf_mask = None
+    else:
+        ecmwf_mask = None
 
     data_ecmwf_nc.close()
 

From 9ccd0a915127c429f82ef7f736e8db5dfabf3325 Mon Sep 17 00:00:00 2001
From: Matthew <mgeheran@gmail.com>
Date: Mon, 23 Nov 2020 14:46:14 -0600
Subject: [PATCH 09/13] Adds Mendocino land-mask test data files.

---
 .../rapid_connectivity_mendocino_sample.csv     |   6 ++++++
 .../weight_mendocino_era5_land_mask.csv         |   9 +++++++++
 ...HDCat_mendocino_watershed_hopland_sample.cpg |   1 +
 ...HDCat_mendocino_watershed_hopland_sample.dbf | Bin 0 -> 2382 bytes
 ...HDCat_mendocino_watershed_hopland_sample.prj |   1 +
 ...HDCat_mendocino_watershed_hopland_sample.sbn | Bin 0 -> 188 bytes
 ...HDCat_mendocino_watershed_hopland_sample.sbx | Bin 0 -> 124 bytes
 ...HDCat_mendocino_watershed_hopland_sample.shp | Bin 0 -> 14852 bytes
 ...HDCat_mendocino_watershed_hopland_sample.shx | Bin 0 -> 148 bytes
 .../era5/era5_land-sea_mask_mendocino_subset.nc | Bin 0 -> 2976 bytes
 10 files changed, 17 insertions(+)
 create mode 100755 tests/compare/gis/mendocino_nhdplus_catchment/rapid_connectivity_mendocino_sample.csv
 create mode 100644 tests/compare/gis/mendocino_nhdplus_catchment/weight_mendocino_era5_land_mask.csv
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.cpg
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.dbf
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.prj
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.sbn
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.sbx
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.shp
 create mode 100755 tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.shx
 create mode 100755 tests/data/lsm_grids/era5/era5_land-sea_mask_mendocino_subset.nc

diff --git a/tests/compare/gis/mendocino_nhdplus_catchment/rapid_connectivity_mendocino_sample.csv b/tests/compare/gis/mendocino_nhdplus_catchment/rapid_connectivity_mendocino_sample.csv
new file mode 100755
index 0000000..26d9523
--- /dev/null
+++ b/tests/compare/gis/mendocino_nhdplus_catchment/rapid_connectivity_mendocino_sample.csv
@@ -0,0 +1,6 @@
+8267669,8267695,0,0,0,0,0
+8267671,8267695,0,0,0,0,0
+8267697,8267725,0,0,0,0,0
+8267723,8267745,0,0,0,0,0
+8267695,8267725,2,8267669,8267671,0,0
+8267725,8267745,2,8267695,8267697,0,0
diff --git a/tests/compare/gis/mendocino_nhdplus_catchment/weight_mendocino_era5_land_mask.csv b/tests/compare/gis/mendocino_nhdplus_catchment/weight_mendocino_era5_land_mask.csv
new file mode 100644
index 0000000..f453973
--- /dev/null
+++ b/tests/compare/gis/mendocino_nhdplus_catchment/weight_mendocino_era5_land_mask.csv
@@ -0,0 +1,9 @@
+rivid,area_sqm,lon_index,lat_index,npoints,lsm_grid_lon,lsm_grid_lat
+8267669,1022424.4461225494,7,2,1,-123.25,39.5
+8267671,678361.3599336375,7,2,2,-123.25,39.5
+8267671,313143.12121458724,7,3,2,-123.25,39.25
+8267697,887055.8385729626,7,3,1,-123.25,39.25
+8267723,1539436.066144096,7,3,1,-123.25,39.25
+8267695,710034.1467391531,7,2,2,-123.25,39.5
+8267695,4245512.985625456,7,3,2,-123.25,39.25
+8267725,2136545.1570262704,7,3,1,-123.25,39.25
diff --git a/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.cpg b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.cpg
new file mode 100755
index 0000000..3ad133c
--- /dev/null
+++ b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.cpg
@@ -0,0 +1 @@
+UTF-8
\ No newline at end of file
diff --git a/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.dbf b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.dbf
new file mode 100755
index 0000000000000000000000000000000000000000..bda85fac9f9c39aefdaaab387769695d7181d102
GIT binary patch
literal 2382
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literal 0
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diff --git a/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.prj b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.prj
new file mode 100755
index 0000000..5ded4bc
--- /dev/null
+++ b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.prj
@@ -0,0 +1 @@
+GEOGCS["GCS_North_American_1983",DATUM["D_North_American_1983",SPHEROID["GRS_1980",6378137.0,298.257222101]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]]
\ No newline at end of file
diff --git a/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.sbn b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.sbn
new file mode 100755
index 0000000000000000000000000000000000000000..f4794b4125bc3e45449dbe694968dcf82976a450
GIT binary patch
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literal 0
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diff --git a/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.sbx b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.sbx
new file mode 100755
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literal 0
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diff --git a/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.shx b/tests/data/gis/mendocino_nhdplus_catchment/NHDCat_mendocino_watershed_hopland_sample.shx
new file mode 100755
index 0000000000000000000000000000000000000000..c7aed03dc5747e77d67c1acf73bb7888f20c9ae0
GIT binary patch
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diff --git a/tests/data/lsm_grids/era5/era5_land-sea_mask_mendocino_subset.nc b/tests/data/lsm_grids/era5/era5_land-sea_mask_mendocino_subset.nc
new file mode 100755
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From 4b22a726fbcdd9c9ffc98faf6124bfe3ca27e2f4 Mon Sep 17 00:00:00 2001
From: Matthew <mpg56@drexel.edu>
Date: Mon, 23 Nov 2020 20:15:04 -0600
Subject: [PATCH 10/13] Fixes typesetting.

---
 RAPIDpy/gis/weight.py |  9 ++++-----
 tests/test_gis.py     | 11 +++++++----
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/RAPIDpy/gis/weight.py b/RAPIDpy/gis/weight.py
index db64f43..f2eee8d 100644
--- a/RAPIDpy/gis/weight.py
+++ b/RAPIDpy/gis/weight.py
@@ -338,7 +338,7 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
     in_ecmwf_lon_var = 'lon'
     if 'longitude' in variables_list:
         in_ecmwf_lon_var = 'longitude'
-        
+
     # convert [0, 360] to [-180, 180]
     ecmwf_lon = \
         (data_ecmwf_nc.variables[in_ecmwf_lon_var][:] + 180) % 360 - 180
@@ -349,8 +349,8 @@ def CreateWeightTableECMWF(in_ecmwf_nc,
         if in_ecmwf_mask_var in variables_list:
             ecmwf_mask = data_ecmwf_nc.variables[in_ecmwf_mask_var][0,:,:]
         else:
-            print('Variable "{}" not found in {}.'.format(in_ecmwf_mask_var,
-                                                        in_ecmwf_nc))
+            print('Variable "{}" not found in {}.'.format(
+                in_ecmwf_mask_var, in_ecmwf_nc))
             print('Continuing with no land mask.')
             ecmwf_mask = None
     else:
@@ -392,8 +392,6 @@ def CreateWeightTableLDAS(in_ldas_nc,
         The name of the field with the river ID (Ex. 'DrainLnID' or 'LINKNO').
     in_connectivity_file: str
         The path to the RAPID connectivity file.
-        is the name of the stream network feature class.
-        (WARNING: Not always stable with GDAL.)
     out_weight_table: str
         The path to the output weight table file.
     area_id: str, optional
@@ -404,6 +402,7 @@ def CreateWeightTableLDAS(in_ldas_nc,
         is the name of the stream network feature class.
         (WARNING: Not always stable with GDAL.)
 
+
     Example:
 
     .. code:: python
diff --git a/tests/test_gis.py b/tests/test_gis.py
index 41e7cb8..933bff7 100644
--- a/tests/test_gis.py
+++ b/tests/test_gis.py
@@ -775,14 +775,17 @@ def test_gen_weight_table_era5_land_mask():
         OUTPUT_DATA_PATH, "weight_mendocino_era5_land_mask.csv")
 
     #rapid_connect
-    rapid_connect_file = os.path.join(COMPARE_DATA_PATH,
-                                      "mendocino_nhdplus_catchment",
-                                      "rapid_connectivity_mendocino_sample.csv")
+    rapid_connect_file = os.path.join(
+        COMPARE_DATA_PATH, "mendocino_nhdplus_catchment",
+        "rapid_connectivity_mendocino_sample.csv")
 
     lsm_grid = os.path.join(LSM_INPUT_DATA_PATH, "era5", "era5_land-sea_mask_mendocino_subset.nc")
 
     CreateWeightTableECMWF(in_ecmwf_nc=lsm_grid,
-                           in_catchment_shapefile=os.path.join(GIS_INPUT_DATA_PATH, 'mendocino_nhdplus_catchment', 'NHDCat_mendocino_watershed_hopland_sample.shp'),
+                           in_catchment_shapefile=os.path.join(
+                               GIS_INPUT_DATA_PATH,
+                               'mendocino_nhdplus_catchment',
+                               'NHDCat_mendocino_watershed_hopland_sample.shp'),
                            river_id="FEATUREID",
                            in_connectivity_file=rapid_connect_file,
                            out_weight_table=generated_weight_table_file,

From 7573313677650ef6670cc98efb6811ec248f3e4a Mon Sep 17 00:00:00 2001
From: Mike <michael.j.shaw@erdc.dren.mil>
Date: Wed, 25 Nov 2020 11:41:43 -0500
Subject: [PATCH 11/13] ERA5 and ERA Interim t1279 changes for inflow
 processing.

---
 .../inflow/CreateInflowFileFromERARunoff.py   | 88 ++++++++++++++++++
 .../CreateInflowFileFromGriddedRunoff.py      | 20 ++++
 RAPIDpy/inflow/lsm_rapid_process.py           | 93 ++++++++++++++-----
 3 files changed, 179 insertions(+), 22 deletions(-)
 create mode 100644 RAPIDpy/inflow/CreateInflowFileFromERARunoff.py

diff --git a/RAPIDpy/inflow/CreateInflowFileFromERARunoff.py b/RAPIDpy/inflow/CreateInflowFileFromERARunoff.py
new file mode 100644
index 0000000..50a2e8b
--- /dev/null
+++ b/RAPIDpy/inflow/CreateInflowFileFromERARunoff.py
@@ -0,0 +1,88 @@
+# -*- coding: utf-8 -*-
+"""
+   CreateInflowFileFromERARunoff.py
+   RAPIDpy
+
+   Created by Alan D. Snow, 2015
+   Adapted from CreateInflowFileFromECMWFRunoff.py.
+   License: BSD-3-Clause
+"""
+from netCDF4 import Dataset
+
+from .CreateInflowFileFromGriddedRunoff import \
+    CreateInflowFileFromGriddedRunoff
+
+
+class CreateInflowFileFromERARunoff(CreateInflowFileFromGriddedRunoff):
+    """Create Inflow File From ERA Runoff
+
+    Creates RAPID NetCDF input of water inflow based on
+    ERA runoff and previously created weight table.
+    """
+    land_surface_model_name = "ERA"
+    header_wt = ['rivid', 'area_sqm', 'lon_index', 'lat_index', 'npoints']
+    dims_oi = [['lon', 'lat', 'time'],
+               ['longitude', 'latitude', 'time'],
+               ['time','lon','lat'],
+               ['time','longitude','latitude'],
+               ['latitude','longitude','time'],
+               ['time','latitude','longitude']]
+    vars_oi = [['lon', 'lat', 'time', 'RO'],['lon','lat','time','ro'],
+               ['time','lon','lat','RO'],['time','lon','lat','ro'],
+               ['time','longitude','latitude','RO'],['time','longitude','latitude','ro'],
+               ['longitude', 'latitude', 'time', 'RO'],['longitude', 'latitude', 'time', 'ro'],
+               ['latitude','longitude','time','RO'],['latitude','longitude','time','ro'],
+               ['latitude','longitude','RO','time'],['latitude','longitude','ro','time'],
+               ['time','latitude','longitude','RO'],['time','latitude','longitude','ro']]
+    length_time = {"Daily": 1, "3-Hourly": 8, "1-Hourly":24}
+
+    def __init__(self):
+        """Define the attributes to look for"""
+        self.runoff_vars = ['ro']
+        super(CreateInflowFileFromERARunoff, self).__init__()
+
+    def data_validation(self, in_nc):
+        """Check the necessary dimensions and variables in the input
+        netcdf data"""
+        data_nc = Dataset(in_nc)
+
+        dims = list(data_nc.dimensions)
+
+        if dims not in self.dims_oi:
+            data_nc.close()
+            raise Exception("{0} {1}".format(self.error_messages[1], dims))
+
+        nc_vars = list(data_nc.variables)
+
+        if nc_vars == self.vars_oi[0]:
+            self.runoff_vars = [self.vars_oi[0][-1]]
+        elif nc_vars == self.vars_oi[1]:
+            self.runoff_vars = [self.vars_oi[1][-1]]
+        elif nc_vars == self.vars_oi[2]:
+            self.runoff_vars = [self.vars_oi[2][-1]]
+        elif nc_vars == self.vars_oi[3]:
+            self.runoff_vars = [self.vars_oi[3][-1]]
+        elif nc_vars == self.vars_oi[4]:
+            self.runoff_vars = [self.vars_oi[4][-1]]
+        elif nc_vars == self.vars_oi[5]:
+            self.runoff_vars = [self.vars_oi[5][-1]]
+        elif nc_vars == self.vars_oi[6]:
+            self.runoff_vars = [self.vars_oi[6][-1]]
+        elif nc_vars == self.vars_oi[7]:
+            self.runoff_vars = [self.vars_oi[7][-1]]
+        elif nc_vars == self.vars_oi[8]:
+            self.runoff_vars = [self.vars_oi[8][-1]]
+        elif nc_vars == self.vars_oi[9]:
+            self.runoff_vars = [self.vars_oi[9][-1]]
+        elif nc_vars == self.vars_oi[10]:
+            self.runoff_vars = [self.vars_oi[10][-2]]
+        elif nc_vars == self.vars_oi[11]:
+            self.runoff_vars = [self.vars_oi[11][-2]]
+        elif nc_vars == self.vars_oi[12]:
+            self.runoff_vars = [self.vars_oi[12][-1]]
+        elif nc_vars == self.vars_oi[13]:
+            self.runoff_vars = [self.vars_oi[13][-1]]
+        else:
+            data_nc.close()
+            raise Exception("{0} {1}".format(self.error_messages[2], nc_vars))
+        data_nc.close()
diff --git a/RAPIDpy/inflow/CreateInflowFileFromGriddedRunoff.py b/RAPIDpy/inflow/CreateInflowFileFromGriddedRunoff.py
index b299ab7..4b62011 100644
--- a/RAPIDpy/inflow/CreateInflowFileFromGriddedRunoff.py
+++ b/RAPIDpy/inflow/CreateInflowFileFromGriddedRunoff.py
@@ -481,6 +481,26 @@ def execute(self, nc_file_list, index_list, in_weight_table,
                             np.concatenate([ro_first_half, ro_second_half]),
                             area_sqm_npoints)
 
+                elif grid_type == 't1279':
+                    # A) ERA Interim Low Res (T1279) - data is cumulative
+                    # from time 6/12
+                    # 0 1 2 3 4
+                    # (time zero not included, so assumed to be zero)
+                    ro_first_half = \
+                        np.concatenate([data_goal[0:1, ],
+                                        np.subtract(data_goal[1:2, ],
+                                                    data_goal[0:1, ])])
+                    # from time 15/18/21/24
+                    # (time restarts at time 12, assumed to be zero)
+                    ro_second_half = \
+                        np.concatenate([data_goal[2:3, ],
+                                        np.subtract(data_goal[3:, ],
+                                                    data_goal[2:3, ])])
+                    ro_stream = \
+                        np.multiply(
+                            np.concatenate([ro_first_half, ro_second_half]),
+                            area_sqm_npoints)
+
                 else:
                     ro_stream = data_goal * area_sqm_npoints * \
                                 conversion_factor
diff --git a/RAPIDpy/inflow/lsm_rapid_process.py b/RAPIDpy/inflow/lsm_rapid_process.py
index 6088f7a..6ef861d 100644
--- a/RAPIDpy/inflow/lsm_rapid_process.py
+++ b/RAPIDpy/inflow/lsm_rapid_process.py
@@ -20,8 +20,8 @@
 
 # local imports
 from ..rapid import RAPID
-from .CreateInflowFileFromERAInterimRunoff import \
-    CreateInflowFileFromERAInterimRunoff
+from .CreateInflowFileFromERARunoff import \
+    CreateInflowFileFromERARunoff
 from .CreateInflowFileFromLDASRunoff import CreateInflowFileFromLDASRunoff
 from .CreateInflowFileFromWRFHydroRunoff import \
     CreateInflowFileFromWRFHydroRunoff
@@ -31,9 +31,6 @@
                          get_valid_directory_list,
                          partition)
 
-from ..pangaea.read import open_mfdataset
-
-
 
 # -----------------------------------------------------------------------------
 # MULTIPROCESSING FUNCTION
@@ -66,12 +63,10 @@ def generate_inflows_from_runoff(args):
         index_string = "Index: {0}".format(file_index_list[0])
         if len(file_index_list) > 1:
             index_string += " to {0}".format(file_index_list[-1])
-        print(index_string)
         runoff_string = "File(s): {0}".format(runoff_file_list[0])
         if len(runoff_file_list) > 1:
             runoff_string += " to {0}".format(runoff_file_list[-1])
-        print(runoff_string)
-        print("Converting inflow ...")
+        print("Converting inflow in generate inflow from runoff...")
         try:
             rapid_inflow_tool.execute(nc_file_list=runoff_file_list,
                                       index_list=file_index_list,
@@ -94,6 +89,14 @@ def generate_inflows_from_runoff(args):
 # UTILITY FUNCTIONS
 # -----------------------------------------------------------------------------
 DEFAULT_LSM_INPUTS = {
+    'llera5': {
+        'file_datetime_re_pattern': r'\d{8}',
+        'file_datetime_pattern': "%Y%m%d",
+    },
+    't1279': {
+        'file_datetime_re_pattern': r'\d{8}',
+        'file_datetime_pattern': "%Y%m%d",
+    },
     't255': {
         'file_datetime_re_pattern': r'\d{8}',
         'file_datetime_pattern': "%Y%m%d",
@@ -232,7 +235,6 @@ def identify_lsm_grid(lsm_grid_path):
     elif 'X' in var_list:
         # FLDAS
         longitude_var = 'X'
-
     time_var = None
     if 'time' in var_list:
         time_var = 'time'
@@ -280,6 +282,9 @@ def identify_lsm_grid(lsm_grid_path):
         elif var.lower() == "ro":
             # ERA Interim
             total_runoff_var = var
+        elif var.lower() == "RO":
+            # ERA5
+            total_runoff_var = var
         elif var == "total runoff":
             # CMIP5 data
             total_runoff_var = var
@@ -312,9 +317,11 @@ def identify_lsm_grid(lsm_grid_path):
 
     runoff_vars = [surface_runoff_var, subsurface_runoff_var]
 
+    print('Checking grid type.',total_runoff_var.lower(),institution)
     if institution == "European Centre for Medium-Range Weather Forecasts" \
-            or total_runoff_var.lower() == "ro":
+            or total_runoff_var.lower() == "ro" or total_runoff_var.lower() == "RO":
         # these are the ECMWF models
+        print('This is an ECMWF model')
         if lat_dim_size == 361 and lon_dim_size == 720:
             print("Runoff file identified as ERA Interim Low Res (T255) GRID")
             # A) ERA Interim Low Res (T255)
@@ -343,17 +350,53 @@ def identify_lsm_grid(lsm_grid_path):
             # Downloaded as 1.125 degree grid
             #  dimensions:
             #   longitude = 320 ;
+            # Downloaded as 1.125 degree grid
+            #  dimensions:
+            #   longitude = 320 ;
+            lsm_file_data["grid_type"] = 't511'
+        elif lat_dim_size == 161 and lon_dim_size == 320:
+            print("Runoff file identified as ERA 20CM (T159) GRID")
+            # C) ERA 20CM (T159) - 3hr - 10 ensembles
+            # Downloaded as 1.125 degree grid
+            #  dimensions:
+            #   longitude = 320 ;
+            # C) ERA 20CM (T159) - 3hr - 10 ensembles
+            # Downloaded as 1.125 degree grid
+            #  dimensions:
+            #   longitude = 320 ;
             #   latitude = 161 ;
             lsm_file_data["description"] = "ERA 20CM (T159 Grid)"
             lsm_file_data["weight_file_name"] = r'weight_era_t159\.csv'
             lsm_file_data["model_name"] = "era_20cm"
             lsm_file_data["grid_type"] = 't159'
+        elif lat_dim_size == 721 and lon_dim_size == 1440:
+            print("Runoff file identified as ERA5 lat lon .25 degree GRID")
+            # C) ERA 20CM (lat lon quarter degree) - 1hr
+            # Downloaded as .25 degree grid
+            #  dimensions:
+            #   longitude = 1440 ;
+            #   latitude = 721 ;
+            lsm_file_data["description"] = "ERA5 (LL Grid)"
+            lsm_file_data["weight_file_name"] = r'weight_era5_ll\.csv'
+            lsm_file_data["model_name"] = "era5"
+            lsm_file_data["grid_type"] = 'llera5'
+        elif lat_dim_size == 1280 and lon_dim_size == 2576:
+            print("Runoff file identified as ERAI Gaussian GRID")
+            # C) ERA INTERIM (Gaussian) - Daily
+            # Downloaded as Gaussian grid
+            #  dimensions:
+            #   longitude = 2576 ;
+            #   latitude = 1280 ;
+            lsm_file_data["description"] = "ERAI (Gaussian Grid)"
+            lsm_file_data["weight_file_name"] = r'weight_erai_1279\.csv'
+            lsm_file_data["model_name"] = "erai_1279"
+            lsm_file_data["grid_type"] = 't1279'
         else:
             lsm_example_file.close()
             raise Exception("Unsupported ECMWF grid.")
 
         lsm_file_data["rapid_inflow_tool"] = \
-            CreateInflowFileFromERAInterimRunoff()
+            CreateInflowFileFromERARunoff()
 
     elif institution == "NASA GSFC":
         if title == "GLDAS2.0 LIS land surface model output":
@@ -530,7 +573,8 @@ def determine_start_end_timestep(lsm_file_list,
                               file_datetime_pattern) \
             + timedelta(seconds=(file_size_time-1) * time_step)
     else:
-        with open_mfdataset(lsm_file_list, #pangaea.open_mfdataset
+#        with pangaea.open_mfdataset(lsm_file_list,
+        with open_mfdataset(lsm_file_list,
                                     lat_var=lsm_grid_info['latitude_var'],
                                     lon_var=lsm_grid_info['longitude_var'],
                                     time_var=lsm_grid_info['time_var'],
@@ -592,7 +636,13 @@ def run_lsm_rapid_process(rapid_executable_location,
                           modeling_institution="US Army Engineer Research "
                                                "and Development Center",
                           convert_one_hour_to_three=False,
-                          expected_time_step=None):
+                          expected_time_step=None,
+                          BS_opt_dam='',
+                          IS_dam_tot=0,
+                          IS_dam_use=0,
+                          dam_tot_id_file='',
+                          dam_use_id_file='',
+                          dam_file=''):
     # pylint: disable=anomalous-backslash-in-string
     """
     This is the main process to generate inflow for RAPID and to run RAPID.
@@ -802,7 +852,6 @@ def run_lsm_rapid_process(rapid_executable_location,
                     lsm_file_list.append(
                         os.path.join(walkdir_info[0], lsm_file))
         lsm_file_list = sorted(lsm_file_list)
-
         # IDENTIFY THE GRID
         lsm_file_data = identify_lsm_grid(lsm_file_list[0])
 
@@ -815,7 +864,6 @@ def run_lsm_rapid_process(rapid_executable_location,
                 DEFAULT_LSM_INPUTS[lsm_file_data['grid_type']][
                     'file_datetime_pattern']
         file_re_match = re.compile(file_datetime_re_pattern)
-
         # get subset based on time bounds
         if simulation_start_datetime is not None:
             print("Filtering files by datetime ...")
@@ -828,9 +876,7 @@ def run_lsm_rapid_process(rapid_executable_location,
                     break
                 if file_date >= simulation_start_datetime:
                     lsm_file_list_subset.append(lsm_file)
-
             lsm_file_list = sorted(lsm_file_list_subset)
-
         print("Running from {0} to {1}".format(lsm_file_list[0],
                                                lsm_file_list[-1]))
 
@@ -843,7 +889,6 @@ def run_lsm_rapid_process(rapid_executable_location,
                 file_datetime_pattern=file_datetime_pattern,
                 expected_time_step=expected_time_step,
                 lsm_grid_info=lsm_file_data)
-
         # VALIDATING INPUT IF DIVIDING BY 3
         if (lsm_file_data['grid_type'] in ('nldas', 'lis', 'joules')) \
                 and convert_one_hour_to_three:
@@ -863,7 +908,6 @@ def run_lsm_rapid_process(rapid_executable_location,
                     actual_simulation_start_datetime,
                     actual_simulation_end_datetime,
                     ensemble_file_ending)
-
         # run LSM processes
         for master_watershed_input_directory, \
                 master_watershed_output_directory in rapid_directories:
@@ -939,7 +983,7 @@ def run_lsm_rapid_process(rapid_executable_location,
 #                   generate_inflows_from_runoff((
 #                       cpu_grouped_file_list,
 #                       partition_index_list[loop_index],
-#                       lsm_file_data['weight_table_file'],
+#                       weight_table_file, #m_file_data['weight_table_file'],
 #                       lsm_file_data['grid_type'],
 #                       master_rapid_runoff_file,
 #                       lsm_file_data['rapid_inflow_tool'],
@@ -959,7 +1003,13 @@ def run_lsm_rapid_process(rapid_executable_location,
                 ZS_TauR=time_step,
                 ZS_dtR=15 * 60,
                 ZS_TauM=total_num_time_steps * time_step,
-                ZS_dtM=time_step)
+                ZS_dtM=time_step,
+                BS_opt_dam=BS_opt_dam,
+                IS_dam_tot=IS_dam_tot,
+                IS_dam_use=IS_dam_use,
+                dam_tot_id_file=dam_tot_id_file,
+                dam_use_id_file=dam_use_id_file,
+                dam_file=dam_file)
 
             if initial_flows_file and os.path.exists(initial_flows_file):
                 rapid_manager.update_parameters(
@@ -1027,7 +1077,6 @@ def run_lsm_rapid_process(rapid_executable_location,
                         num_cpus=num_cpus,
                         storm_duration_days=storm_length_days,
                         method=return_period_method)
-
                 # generate seasonal averages file
                 if generate_seasonal_averages_file and \
                         os.path.exists(lsm_rapid_output_file) and \

From e0ddff54cc592367c012e41fbe3373c27073459c Mon Sep 17 00:00:00 2001
From: Chase Hamilton <chase.o.hamilton@erdc.dren.mil>
Date: Thu, 11 Aug 2022 13:41:23 -0500
Subject: [PATCH 12/13] 'all references to "erdc-cm" changed to "erdc"'

---
 README.md                   | 6 +++---
 docs/gis_stream_network.rst | 2 +-
 docs/index.rst              | 4 ++--
 docs/installation.rst       | 6 +++---
 setup.py                    | 6 +++---
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index effd289..e4cd38f 100644
--- a/README.md
+++ b/README.md
@@ -7,9 +7,9 @@ More information about installation and the input parameters for RAPID can be fo
 
 The source code for RAPID is located at https://github.com/c-h-david/rapid/.
 
-[![DOI](https://zenodo.org/badge/19918/erdc-cm/RAPIDpy.svg)](https://zenodo.org/badge/latestdoi/19918/erdc-cm/RAPIDpy)
+[![DOI](https://zenodo.org/badge/19918/erdc/RAPIDpy.svg)](https://zenodo.org/badge/latestdoi/19918/erdc-cm/RAPIDpy)
 
-[![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-yellow.svg)](https://github.com/erdc-cm/RAPIDpy/blob/master/LICENSE)
+[![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-yellow.svg)](https://github.com/erdc/RAPIDpy/blob/master/LICENSE)
 
 [![PyPI version](https://badge.fury.io/py/RAPIDpy.svg)](https://badge.fury.io/py/RAPIDpy)
 
@@ -60,5 +60,5 @@ Ahmad A Tavakoly. (2017). RAPID input files corresponding to the Mississippi Riv
 ## Other tools to prepare input for RAPID
 
 - For ESRI users: https://github.com/Esri/python-toolbox-for-rapid
-- Modified version of the ESRI RAPID Toolbox: https://github.com/erdc-cm/python-toolbox-for-rapid
+- Modified version of the ESRI RAPID Toolbox: https://github.com/erdc/python-toolbox-for-rapid
 - For the NHDPlus dataset: https://github.com/c-h-david/RRR
diff --git a/docs/gis_stream_network.rst b/docs/gis_stream_network.rst
index 45857ef..0d5b9b4 100644
--- a/docs/gis_stream_network.rst
+++ b/docs/gis_stream_network.rst
@@ -7,7 +7,7 @@ Using ArcHydro to Generate Stream Network
 See: 
 
 - https://github.com/Esri/python-toolbox-for-rapid
-- https://github.com/erdc-cm/python-toolbox-for-rapid
+- https://github.com/erdc/python-toolbox-for-rapid
 
 Using TauDEM to Generate Stream Network
 ---------------------------------------
diff --git a/docs/index.rst b/docs/index.rst
index 782a2e3..5aa9c4d 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -26,7 +26,7 @@ https://github.com/c-h-david/rapid.
 .. |Coverage Status| image:: https://coveralls.io/repos/github/erdc/RAPIDpy/badge.svg?branch=master
    :target: https://coveralls.io/github/erdc/RAPIDpy
 .. |License (3-Clause BSD)| image:: https://img.shields.io/badge/license-BSD%203--Clause-yellow.svg
-   :target: https://github.com/erdc-cm/RAPIDpy/blob/master/LICENSE
+   :target: https://github.com/erdc/RAPIDpy/blob/master/LICENSE
 
 Contents:
 
@@ -90,7 +90,7 @@ Other tools to prepare input for RAPID
 ---------------------------------------
 
 - For ESRI users: https://github.com/Esri/python-toolbox-for-rapid
-- Modified version of the ESRI RAPID Toolbox: https://github.com/erdc-cm/python-toolbox-for-rapid
+- Modified version of the ESRI RAPID Toolbox: https://github.com/erdc/python-toolbox-for-rapid
 - For the NHDPlus dataset: https://github.com/c-h-david/RRR
 
 
diff --git a/docs/installation.rst b/docs/installation.rst
index 563cfa6..364ff74 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -79,11 +79,11 @@ or from https://conda.io/miniconda.html.
 
 This is how you get the most up-to-date version of the code.
 
-.. note:: If you don't have git, you can download the code from https://github.com/erdc-cm/RAPIDpy
+.. note:: If you don't have git, you can download the code from https://github.com/erdc/RAPIDpy
 
 ::
 
-    $ git clone https://github.com/erdc-cm/RAPIDpy.git
+    $ git clone https://github.com/erdc/RAPIDpy.git
     $ cd RAPIDpy
     $ conda env create -f rapidpy_env.yml
     $ conda activate rapidpy_env
@@ -93,7 +93,7 @@ To develop on the latest version:
 
 ::
 
-    $ git clone https://github.com/erdc-cm/RAPIDpy.git
+    $ git clone https://github.com/erdc/RAPIDpy.git
     $ cd RAPIDpy
     $ conda env create -f rapidpy_env.yml
     $ conda activate rapidpy_env
diff --git a/setup.py b/setup.py
index 3bff51f..ef0b48f 100644
--- a/setup.py
+++ b/setup.py
@@ -11,12 +11,12 @@
          'parameters for RAPID can be found at http://rapid-hub.org.'
          ' The source code for RAPID is located at '
          'https://github.com/c-h-david/rapid/. \n\n'
-         '.. image:: https://zenodo.org/badge/19918/erdc-cm/RAPIDpy.svg \n'
-         '   :target: https://zenodo.org/badge/latestdoi/19918/erdc-cm/RAPIDpy',
+         '.. image:: https://zenodo.org/badge/19918/erdc/RAPIDpy.svg \n'
+         '   :target: https://zenodo.org/badge/latestdoi/19918/erdc/RAPIDpy',
     keywords='RAPID',
     author='Alan Dee Snow',
     author_email='alan.d.snow@usace.army.mil',
-    url='https://github.com/erdc-cm/RAPIDpy',
+    url='https://github.com/erdc/RAPIDpy',
     license='BSD 3-Clause',
     packages=find_packages(),
     package_data={'': ['gis/lsm_grids/*.nc']},

From ca4d593c8c48e856d4aa30d3ce5ecbbc0cf5c0be Mon Sep 17 00:00:00 2001
From: Chase Hamilton <chase.o.hamilton@erdc.dren.mil>
Date: Thu, 11 Aug 2022 14:36:54 -0500
Subject: [PATCH 13/13] 'all references to "erdc-cm" changed to "erdc"'

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index e4cd38f..30f2eff 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@ More information about installation and the input parameters for RAPID can be fo
 
 The source code for RAPID is located at https://github.com/c-h-david/rapid/.
 
-[![DOI](https://zenodo.org/badge/19918/erdc/RAPIDpy.svg)](https://zenodo.org/badge/latestdoi/19918/erdc-cm/RAPIDpy)
+[![DOI](https://zenodo.org/badge/19918/erdc/RAPIDpy.svg)](https://zenodo.org/badge/latestdoi/19918/erdc/RAPIDpy)
 
 [![License (3-Clause BSD)](https://img.shields.io/badge/license-BSD%203--Clause-yellow.svg)](https://github.com/erdc/RAPIDpy/blob/master/LICENSE)