Merge pull request #113 from changliao1025/development

Development

docs/source/quickstart.rst

@@ -9,13 +9,14 @@ Users can run a PyFlowline simulation in the following steps:
     * `gdal`
     * `netCDF4`
     * `shapely`
-    * `cython` (optional)
+    * `cython` (optional, for performance)
     * `cartopy` (optional, for visualization)
     * `matplotlib` (optional, for visualization)
+
 2. Clone the latest PyFlowline repository from https://github.com/changliao1025/pyflowline. Or Install the PyFlowline through Conda for a released version.
 3. Download the additional large files (DEM and MPAS mesh) and move them under the `data/susquehanna/input` folder.
-4. Change the `sFilename_mesh_netcdf` and `sFilename_basins` to the actual paths,
+4. Change the `sFilename_mesh_netcdf`, `sFilename_basins`, and `sFilename_flowline_filter` to the actual paths,
 5. Open the preferred Python IDE and run the  `examples/susquehanna/run_simulation_mpas.py` Python script. Optionally, you can also run the `notebooks/pyflowline.ipynb` notebook.
 6. You should produce a list of model outputs in the `data/susquehanna/output` folder.
 
-If you encountered any issues, refer to the FAQ or submit a Github issue (https://github.com/changliao1025/pyflowline/issues).
+If you encounter any issues, refer to the FAQ or submit a GitHub issue (https://github.com/changliao1025/pyflowline/issues).

examples/susquehanna/pyflowline_susquehanna_basins.json

@@ -5,7 +5,7 @@
         "dAccumulation_threshold": 100000,
         "dThreshold_small_river": 10000,
         "iFlag_dam": 0,
-        "iFlag_debug":1,
+        "iFlag_debug":0,
         "iFlag_disconnected": 0,
         "lBasinID": 1,
         "sFilename_dam": "/qfs/people/liao313/data/hexwatershed/susquehanna/auxiliary/ICoM_dams.csv",

examples/susquehanna/run_simulation_hexagon.py

@@ -2,13 +2,16 @@
 from pathlib import Path
 from os.path import realpath
 
-from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
 
 
 #===================================
 #set up workspace path
 #===================================
 sPath_parent = str(Path(__file__).parents[2]) # data is located two dir's up
+import sys
+sys.path.append(sPath_parent)
+from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
+
 sPath_data = realpath( sPath_parent +  '/data/susquehanna' )
 sWorkspace_input =  str(Path(sPath_data)  /  'input')
 sWorkspace_output=  str(Path(sPath_data)  /  'output')
@@ -42,8 +45,6 @@
 oPyflowline.flowline_simplification()
 aCell = oPyflowline.mesh_generation()
 oPyflowline.reconstruct_topological_relationship(aCell)
-oPyflowline.analyze()
-oPyflowline.evaluate()
 oPyflowline.export()
 iCase_index= iCase_index+1
 

examples/susquehanna/run_simulation_latlon.py

@@ -2,13 +2,14 @@
 from pathlib import Path
 from os.path import realpath
 
-from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
-
-
 #===================================
 #set up workspace path
 #===================================
 sPath_parent = str(Path(__file__).parents[2]) # data is located two dir's up
+sPath_parent = str(Path(__file__).parents[2]) # data is located two dir's up
+import sys
+sys.path.append(sPath_parent)
+from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
 sPath_data = realpath( sPath_parent +  '/data/susquehanna' )
 sWorkspace_input =  str(Path(sPath_data)  /  'input')
 sWorkspace_output=  str(Path(sPath_data)  /  'output')
@@ -41,8 +42,6 @@
 oPyflowline.flowline_simplification()
 aCell = oPyflowline.mesh_generation()
 oPyflowline.reconstruct_topological_relationship(aCell)
-oPyflowline.analyze()
-oPyflowline.evaluate()
 oPyflowline.export()
 
 

examples/susquehanna/run_simulation_mpas.py

@@ -39,8 +39,6 @@
 oPyflowline.flowline_simplification()
 aCell = oPyflowline.mesh_generation()
 oPyflowline.reconstruct_topological_relationship(aCell)
-oPyflowline.analyze()
-oPyflowline.evaluate()
 oPyflowline.export()
 
 print('Finished')

examples/susquehanna/run_simulation_square.py

@@ -2,13 +2,15 @@
 from pathlib import Path
 from os.path import realpath
 
-from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
-
 
 #===================================
 #set up workspace path
 #===================================
 sPath_parent = str(Path(__file__).parents[2]) # data is located two dir's up
+sPath_parent = str(Path(__file__).parents[2]) # data is located two dir's up
+import sys
+sys.path.append(sPath_parent)
+from pyflowline.pyflowline_read_model_configuration_file import pyflowline_read_model_configuration_file
 sPath_data = realpath( sPath_parent +  '/data/susquehanna' )
 sWorkspace_input =  str(Path(sPath_data)  /  'input')
 sWorkspace_output=  str(Path(sPath_data)  /  'output')
@@ -41,8 +43,6 @@
 oPyflowline.flowline_simplification()
 aCell = oPyflowline.mesh_generation()
 oPyflowline.reconstruct_topological_relationship(aCell)
-oPyflowline.analyze()
-oPyflowline.evaluate()
 oPyflowline.export()
 
 

pyflowline/algorithms/auxiliary/find_index_in_list.py

@@ -149,7 +149,7 @@ def check_if_duplicates(aList_in):
     return iFlag_unique
 
 
-def add_unique_vertex(aVertex_in, pVertex_in):
+def add_unique_vertex(aVertex_in, pVertex_in, dThreshold_in = 1.0E-6):
     """[add a vertex to a list if it is not already included]
 
     Args:
@@ -162,7 +162,7 @@ def add_unique_vertex(aVertex_in, pVertex_in):
     iFlag_exist = 0
     nVertex = len(aVertex_in)     
 
-    iFlag_exist, dummy =  find_vertex_in_list(aVertex_in, pVertex_in)
+    iFlag_exist, dummy =  find_vertex_in_list(aVertex_in, pVertex_in, dThreshold_in)
 
     if iFlag_exist == 1:
         pass

pyflowline/algorithms/auxiliary/find_vertex_in_list.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-def find_vertex_in_list(aVertex_in, pVertex_in):
+def find_vertex_in_list(aVertex_in, pVertex_in, dThreshold_in=1.0E-6):
     """[find the index of a vertex in a list]
 
     Args:
@@ -18,7 +18,9 @@ def find_vertex_in_list(aVertex_in, pVertex_in):
     if nVertex > 0 :
         for i in np.arange( nVertex):
             pVertex = aVertex_in[i]
-            if pVertex == pVertex_in:
+            dDistance = pVertex.calculate_distance(pVertex_in)
+            #if pVertex == pVertex_in:
+            if dDistance < dThreshold_in:
                 iFlag_exist = 1      
                 lIndex = i 
                 break