Development

docs/source/data/data.rst

@@ -80,6 +80,7 @@ An example parent JSON file is provided below:
         "iFlag_global": 0,
         "iFlag_multiple_outlet": 0,
         "iFlag_rotation": 0, 
+        "iFlag_mesh_boundary": 0,
         "iCase_index": 1,
         "iMesh_type": 1,    
         "dLongitude_left": -79,

examples/susquehanna/run_simulation_mpas.py

@@ -35,7 +35,22 @@
 oPyflowline = pyflowline_read_model_configuration_file(sFilename_configuration_in, 
     iCase_index_in=iCase_index, sDate_in=sDate)
 
+#take a look at the model parameters
 
+oPyflowline.print()
+
+#now we can change the following model parameters
+#there are two ways to change the model parameters
+#use a function or assign a value directly
+
+oPyflowline.change_model_parameter(sVariable_in='sWorkspace_output', sValue_in=sWorkspace_output)
+
+#if you need to change a parameter for a basin instead of the whole model domain, use the iFlag_basin_in option, this will change all the basins
+oPyflowline.change_model_parameter(sVariable_in='dLatitude_outlet_degree', sValue_in=39.462000, iFlag_basin_in=1)
+oPyflowline.change_model_parameter(sVariable_in='dLongitude_outlet_degree', sValue_in=-76.009300, iFlag_basin_in=1)
+
+
+#the second way is to assign a value directly
 oPyflowline.aBasin[0].dLatitude_outlet_degree=39.462000
 oPyflowline.aBasin[0].dLongitude_outlet_degree=-76.009300
 

notebooks/mpas_example.ipynb

@@ -39,7 +39,49 @@
     "import os\n",
     "import sys\n",
     "from pathlib import Path\n",
-    "from os.path import realpath"
+    "from os.path import realpath\n",
+    "import importlib\n",
+    "import requests"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bf81807a",
+   "metadata": {},
+   "source": [
+    "Then we will check whether some additional packages are installed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a75e5100",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "#check pyflowline\n",
+    "iFlag_pyflowline = importlib.util.find_spec(\"pyflowline\") \n",
+    "if iFlag_pyflowline is not None:\n",
+    "    pass\n",
+    "else:\n",
+    "    print('The pyflowline package is not installed. Please install it following the quickstart document.')\n",
+    "\n",
+    "#check optional packages    \n",
+    "iFlag_cython = importlib.util.find_spec(\"cython\") \n",
+    "iFlag_cartopy = importlib.util.find_spec(\"cartopy\") \n",
+    "iFlag_geopandas = importlib.util.find_spec(\"geopandas\") \n",
+    "if iFlag_cartopy is not None:\n",
+    "    iFlag_cartopy = 1\n",
+    "    pass\n",
+    "else:\n",
+    "    #if cartopy is not avaialble, we will use the geopanda for visualization\n",
+    "    if iFlag_geopandas is not None:\n",
+    "        pass\n",
+    "    else:\n",
+    "        print('We will install the geopandas package for visualization.')\n",
+    "        !conda install --yes --prefix {sys.prefix} gepandas\n",
+    "        iFlag_geopandas = 1\n",
+    "        pass\n"
    ]
   },
   {
@@ -105,6 +147,43 @@
     "sys.path.append(sPath_parent)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "9f2f1520",
+   "metadata": {},
+   "source": [
+    "We need to download an additional NetCDF file for this example.\n",
+    "This file is stored on the Github release:\n",
+    "https://github.com/changliao1025/pyflowline/releases/tag/0.2.0\n",
+    "https://github.com/changliao1025/pyflowline/releases/download/0.2.0/lnd_cull_mesh.nc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c52960d0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "sFilename_mpas = 'https://github.com/changliao1025/pyflowline/releases/download/0.2.0/lnd_cull_mesh.nc'\n",
+    "\n",
+    "#combind folder with filename to get the full path\n",
+    "sFilename_download = os.path.join(sPath_parent, 'mpas_mesh.nc')\n",
+    "\n",
+    "# Send an HTTP GET request to the URL\n",
+    "response = requests.get(sFilename_mpas)\n",
+    "\n",
+    "# Check if the request was successful\n",
+    "if response.status_code == 200:\n",
+    "    # Save the content of the response to the local file\n",
+    "    with open(sFilename_download, 'wb') as file:\n",
+    "        file.write(response.content)\n",
+    "    print(f\"File '{sFilename_download}' downloaded successfully.\")\n",
+    "else:\n",
+    "    print(f\"Failed to download file from '{sFilename_mpas}'.\")"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "25edfaeb",
@@ -274,6 +353,16 @@
     "                                                    sMesh_type_in= sMesh_type, sDate_in=sDate)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "17e011b8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "oPyflowline.change_model_parameter('sFilename_mesh_netcdf', sFilename_download)"
+   ]
+  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -419,25 +508,26 @@
     }
    ],
    "source": [
-    "iVisualization_method = 1\n",
-    "if iVisualization_method == 1: # you need to install the geopanda package and matplotlib package using conda or pip\n",
-    "    import geopandas as gpd\n",
-    "    import matplotlib.pyplot as plt\n",
-    "    #use the geopanda package\n",
-    "    #the raw/original geojson file \n",
-    "    sFilename_geojson = oPyflowline.aBasin[0].sFilename_flowline_filter_geojson\n",
-    "    gdf = gpd.read_file(sFilename_geojson)\n",
-    "    gdf.plot()\n",
-    "    plt.show()\n",
-    "\n",
-    "    pass\n",
-    "\n",
-    "else: #use the default visualization method, only experimental\n",
     "\n",
+    "if iFlag_cartopy == 1: # you need to install the geopanda package and matplotlib package using conda or pip\n",
     "    oPyflowline.plot(sVariable_in = 'flowline_filter' )\n",
     "    #if you provide a filename, a png file will be saved\n",
     "    oPyflowline.plot(sVariable_in = 'flowline_filter', sFilename_in = 'filter_flowline.png' )\n",
-    "    pass"
+    "    pass\n",
+    "else: #use the default visualization method, only experimental\n",
+    "    if iFlag_geopandas = 1:\n",
+    "        import geopandas as gpd\n",
+    "        import matplotlib.pyplot as plt\n",
+    "        #use the geopanda package\n",
+    "        #the raw/original geojson file \n",
+    "        sFilename_geojson = oPyflowline.aBasin[0].sFilename_flowline_filter_geojson\n",
+    "        gdf = gpd.read_file(sFilename_geojson)\n",
+    "        gdf.plot()\n",
+    "        plt.show()\n",
+    "    else:\n",
+    "        print('The visulization packages are not installed.')\n",
+    "    pass\n",
+    "    "
    ]
   },
   {
@@ -491,7 +581,7 @@
    "source": [
     "\n",
     "#the default visualization method has an option to set the extent you want to plot\n",
-    "if iVisualization_method ==2:\n",
+    "if iFlag_cartopy ==1:\n",
     "    #aExtent_full = [-78.5,-75.5, 39.2,42.5]\n",
     "    aExtent_meander = [-76.5,-76.2, 41.6,41.9] \n",
     "    oPyflowline.plot( sVariable_in = 'flowline_filter', aExtent_in = aExtent_meander  )"
@@ -515,7 +605,7 @@
     }
    ],
    "source": [
-    "if iVisualization_method ==2:\n",
+    "if iFlag_cartopy ==1:\n",
     "    aExtent_braided = [-77.3,-76.5, 40.2,41.0]  \n",
     "    oPyflowline.plot( sVariable_in='flowline_filter' , aExtent_in =aExtent_braided ) "
    ]
@@ -604,7 +694,11 @@
    ],
    "source": [
     "\n",
-    "if iVisualization_method == 1: # you need to install the geopanda package and matplotlib package using conda or pip\n",
+    "if iFlag_cartopy == 1: # use the default visualization method, only experimental\n",
+    "    oPyflowline.plot( sVariable_in='flowline_simplified' ) \n",
+    "\n",
+    "else: \n",
+    "      \n",
     "    import geopandas as gpd\n",
     "    import matplotlib.pyplot as plt\n",
     "    #use the geopanda package\n",
@@ -614,10 +708,7 @@
     "    gdf.plot()\n",
     "    plt.show()\n",
     "\n",
-    "    pass\n",
-    "\n",
-    "else: #use the default visualization method, only experimental\n",
-    "    oPyflowline.plot( sVariable_in='flowline_simplified' )   "
+    "    pass"
    ]
   },
   {
@@ -751,7 +842,11 @@
     }
    ],
    "source": [
-    "if iVisualization_method == 1: # you need to install the geopanda package and matplotlib package using conda or pip\n",
+    "if iFlag_cartopy == 1: # you need to install the geopanda package and matplotlib package using conda or pip\n",
+    "    oPyflowline.plot( sVariable_in='mesh' ) \n",
+    "\n",
+    "else:\n",
+    "    \n",
     "    import geopandas as gpd\n",
     "    import matplotlib.pyplot as plt\n",
     "    #use the geopanda package\n",
@@ -761,10 +856,7 @@
     "    gdf.plot()\n",
     "    plt.show()\n",
     "\n",
-    "    pass\n",
-    "\n",
-    "else:\n",
-    "    oPyflowline.plot( sVariable_in='mesh' ) "
+    "    pass"
    ]
   },
   {
@@ -879,7 +971,11 @@
    ],
    "source": [
     "\n",
-    "if iVisualization_method == 1: \n",
+    "if iFlag_cartopy == 1: \n",
+    "    oPyflowline.plot( sVariable_in='overlap') \n",
+    "    pass\n",
+    "else:\n",
+    "    \n",
     "    #\n",
     "    file1_path = oPyflowline.aBasin[0].sFilename_mesh_geojson\n",
     "    file2_path = oPyflowline.aBasin[0].sFilename_flowline_conceptual_geojson\n",
@@ -889,9 +985,6 @@
     "    gdf1.plot(ax=ax, color='blue')\n",
     "    gdf2.plot(ax=ax, color='red')\n",
     "    plt.show()\n",
-    "    pass\n",
-    "else:\n",
-    "    oPyflowline.plot( sVariable_in='overlap') \n",
     "    pass"
    ]
   },

pyflowline/algorithms/intersect/intersect_flowline_with_mesh.py

@@ -48,8 +48,8 @@ def intersect_flowline_with_mesh(iMesh_type_in, sFilename_mesh_in, sFilename_flo
     pLayerOut = pDataset_out.CreateLayer('flowline', pSpatial_reference_flowline, ogr.wkbMultiLineString)
     # Add one attribute
     pLayerOut.CreateField(ogr.FieldDefn('lineid', ogr.OFTInteger64)) #long type for high resolution
-    pLayerOut.CreateField(ogr.FieldDefn('segment', ogr.OFTInteger)) #long type for high resolution
-    pLayerOut.CreateField(ogr.FieldDefn('order', ogr.OFTInteger)) #long type for high resolution
+    pLayerOut.CreateField(ogr.FieldDefn('stream_segment', ogr.OFTInteger)) #long type for high resolution
+    pLayerOut.CreateField(ogr.FieldDefn('stream_order', ogr.OFTInteger)) #long type for high resolution
     pLayerDefn = pLayerOut.GetLayerDefn()
     pFeatureOut = ogr.Feature(pLayerDefn)       
     lID_flowline = 0          
@@ -84,8 +84,8 @@ def intersect_flowline_with_mesh(iMesh_type_in, sFilename_mesh_in, sFilename_flo
             for j in range (nfeature_flowline):
                 pFeature_flowline = pLayer_flowline.GetFeature(j)
                 pGeometry_flowline = pFeature_flowline.GetGeometryRef()
-                iStream_segment = pFeature_flowline.GetField("segment")
-                iStream_order = pFeature_flowline.GetField("order")
+                iStream_segment = pFeature_flowline.GetField("stream_segment")
+                iStream_order = pFeature_flowline.GetField("stream_order")
                 if (pGeometry_flowline.IsValid()):
                     pass
                 else:
@@ -99,8 +99,8 @@ def intersect_flowline_with_mesh(iMesh_type_in, sFilename_mesh_in, sFilename_flo
                     if pGeometrytype_intersect == 'LINESTRING':
                         pFeatureOut.SetGeometry(pGeometry_intersect)
                         pFeatureOut.SetField("lineid", lID_flowline)         
-                        pFeatureOut.SetField("segment", iStream_segment)    
-                        pFeatureOut.SetField("order", iStream_order)           
+                        pFeatureOut.SetField("stream_segment", iStream_segment)    
+                        pFeatureOut.SetField("stream_order", iStream_order)           
                         pLayerOut.CreateFeature(pFeatureOut)    
 
                         aCoords = list()
@@ -125,8 +125,8 @@ def intersect_flowline_with_mesh(iMesh_type_in, sFilename_mesh_in, sFilename_flo
                                 Line = pGeometry_intersect.GetGeometryRef(i) 
                                 pFeatureOut.SetGeometry(Line)
                                 pFeatureOut.SetField("lineid", lID_flowline)         
-                                pFeatureOut.SetField("segment", iStream_segment)    
-                                pFeatureOut.SetField("order", iStream_order)           
+                                pFeatureOut.SetField("stream_segment", iStream_segment)    
+                                pFeatureOut.SetField("stream_order", iStream_order)           
                                 pLayerOut.CreateFeature(pFeatureOut)    
                                 aCoords = list()
                                 for i in range(0, Line.GetPointCount()): 

pyflowline/algorithms/merge/merge_flowline.py

@@ -11,10 +11,10 @@
 
 lID = 0
 
-def merge_flowline(aFlowline_in, aVertex_in, \
-    pVertex_outlet_in, \
-        aIndex_headwater_in,\
-            aIndex_middle_in, \
+def merge_flowline(aFlowline_in, aVertex_in, 
+    pVertex_outlet_in, 
+        aIndex_headwater_in,
+            aIndex_middle_in, 
                 aIndex_confluence_in ):
 
     nVertex=len(aVertex_in)

pyflowline/classes/_visual.py

@@ -125,7 +125,7 @@ def _plot_mesh_with_flowline(self,
         sFilename_json = os.path.join(pBasin.sWorkspace_output_basin, dummy)
         aFilename_in.append(sFilename_json)
         aFlag_color.append(1)
-        aVariable_in.append('segment')
+        aVariable_in.append('stream_segment')
 
     map_multiple_vector_data(aFiletype_in,
                              aFilename_in,