Python package to facilitate use of the streamflow-routing (SFR) package in MODFLOW. Currently, SFRmaker consists of three primary modules:

####sfr_classes.py Intersects linework with model grid and develops routed segments and reaches from information in NHDPlus. Produces two tables, Mat1 and Mat2, which contain SFR package information by reach and by segment, respectively. Also produces a shapefile of linework broken by the grid, which contains the stream geometries represented by the SFR reaches.

####postproc.py Postproc operates on Mat1 and Mat2 as pandas dataframe attributes, to produce and visualize an SFR package. Includes methods to:

• sample streambed top elevations from a DEM, and smooth them so they decrease monotonically downstream
• incorporate field measurements of streambed elevation
• visualize routing by outlet
• visualize stream profiles (sequences of SFR segments) from headwaters to outlet
• adjust SFR streambed conductance so that only one reach per cell has conductance
• adjust the MODFLOW discretization file so that the geometry of layer 1 is consistent with the SFR elevations
• read in SFR results from a MODFLOW run, allowing for interactive plotting of SFR stages and mass balance components.
• write shapefiles of the SFR package input and results
• write an SFR package file and updated versions of Mat1 and Mat2

####diagnostics.py Contains methods to check for common SFR problems such as

• continuity in segment/reach numbering
• circular routing, spatial gaps in routing, breaks in routing (outlets in the interior of the model)
• multiple SFR conductances in a single cell (can lead to circular routing of water between SFR reaches)
• elevations that rise in the downstream direction (either within a segment, or segment ends that rise)
• slope values below the a user-defined minimum (can lead to artifically high stages)

SFRmaker runs in Python 2.7. The Anaconda Scientific Python Distribution (https://store.continuum.io/cshop/anaconda/) is available for free, and provides an easy way for managing python packages through its package manager conda. Additional dependencies are listed by module below:

####sfr_classes

• ESRI Arcpy, which must be added to the path of your main python distribution. See instructions below.
• flopy, available via pip, or at https://github.com/modflowpy/flopy

####postproc

• fiona
• shapely (fiona and shapely are available via conda or pip; instructions on installing pip and these packages are available here: https://github.com/aleaf/LinesinkMaker/blob/master/README.md, under "Installing the required Python packages"")
• rasterstats (also available via pip, see https://github.com/perrygeo/python-raster-stats for more info)
• flopy
• GIS_utils (see https://github.com/aleaf/GIS_utils)

####Adding Arcpy to the python path:

1. Make a file called: Desktop10.pth, with the following lines:

C:\ArcGIS\Desktop10.1\arcpy  
C:\ArcGIS\Desktop10.1\bin64  
C:\ArcGIS\Desktop10.1\ArcToolbox\Script

Notes:
The second line may be "bin" for 32 bit or "bin64" for 64 bit.
If you are using ArcMap 10.0 or 10.2, "Desktop10.1" in the above path needs to be modified accordingly.

2. Place this file in your python path where all your site-packages are installed. For example, for users of the Enthought Canopy Distribution, the file would need to be placed at: C:\Users\<username>\AppData\Local\Enthought\Canopy\User\Lib\site-packages\

#####1) NHDPlus v2 hydrography datasets

• Available at http://www.horizon-systems.com/NHDPlus/NHDPlusV2_data.php
• Archives needed/relevant files:
  • NHDPlusV21_XX_YY_NHDSnapshot_.7z**
    • NHDFcode.dbf
    • NHDFlowline.dbf, .prj, .shp, .shx
  • NHDPlusV21_XX_YY_NHDPlusAttributes_.7z**
    • elevslope.dbf
    • PlusFlow.dbf
    • PlusFlowlineVAA.dbf
  • If model domain contains a major divide (i.e. multiple HUC2 hydrologic regions), need to merge relevant NHD datasets (e.g. 04 and 07) prior to running this script

Notes:

• XX is Drainage Area ID (e.g., GL for Great Lakes) and YY is the Vector Processing Unit (VPU; e.g. 04) in the above (see NHDPlus website for details).
• If model domain encompases multiple Drainage Areas, need to merge NHD datasets prior to running this script (e.g. in ArcMap, using the Merge tool under ArcToolbox>Data Management>General>Merge)
• The NHDFlowline shapefile should be reprojected into the same coordinate system of the model, if necessary. In ArcMap this can be done under ArcToolbox>Data Management>Projections and Transformations.
• Edit the NHD datasets at your own risk!! Editing may corrupt routing or other information, greatly complicating automated setup of an SFR package. NHD elevation units should be left as is (cm).

#####2) DEM and/or topographic contours for area of model domain

• Available from the National Map Viewer and Download Platform: http://viewer.nationalmap.gov/viewer/
  • In "Overlays" tab, select "Elevation Availability" to view available DEM resolutions
  • click "Download Data" link in upper right to download DEM(s)
  • select "elevation" and/or "contours" to download
• Internal WIWSC source for DEMs in Wisconsin:
  \\igsarmewfsapa\GISData\BaseData\Wisconsin\Statewide\Elevation\NED_2013_10m\NED_10m_DEM_WI_UP.gdb

Notes:

• If model domain area has multiple DEMs or elevation contour shapefiles, they need to be merged prior to setting up SFR. The merged DEM should be in the same coordinate system as the model.

#####3) Model grid information

• polygon shapefile export of model grid (in same coordinate system as Flowlines and DEM)
• row and column information must be supplied as attributes to the shapefile, named "row" and "column" respectively
• polygon shapefile of model domain (can be created by dissolving the grid shapefile using Geoprocessing>dissolve in the ArcToolbox). Note: this polygon (it must be a shapefile polygon, not a line) defines the area where streams are represented by SFR within the model. If SFR in only a subset (i.e. nearfield) area of the model is desired, then this polygon is not the same as the model boundary.
• discretization file for model

• SFR package file
• Mat1 (Text file table with reach information (r,c,l,elevation, width, slope, etc.))
• Mat2 (Text file table with segment/routing data (e.g. icalc, outseg, iupseg, etc.) )

####Run sfr_classes

1. Setup XML input file (see EXAMPLE.XML in <InputFiles> section) to point to the above input datasets

• check settings in <GlobalSettings> section; make sure that <preproc> is set to True
• select an elevation method under <elevflag

2. Make sure that the "infile" variable in SFR_main.py (see SFR_main_EXAMPLE.py) points to the XML input file. Also make sure that the calls to classes are entered correctly.

3. Run SFR_main.py by typing python SFR_main.py at the command prompt

4. If a "manual intervention" message is encountered in screen output,

• **check the following files: **
  • fix_com_IDs.txt: Lists stream segments that have multiple ends and starts; usually these are streams that are broken into mulitple parts by the grid boundary.
  • boundary_manual_fix_issues.txt: Lists stream segments that don't have any connections to other segments.
• edit the offending segments (COMIDs) in the shapefile specified under <IntermediateFiles><intersect> in the XML input file (usually this means deleting the parts of multi-part COMIDs that are isolated by the grid boundary, and possibly deleting any unconnected segments).

5. set <preproc> in the XML input file to False (meaning the existing <intersect> shapefile will be read in lieu of the preprocessing operations). Then rerun SFR_main.py. ####Run postproc and diagnostics
6. Once the reach and segment information tables have been written, the methods in postproc.py can be run to address all of the issues listed under the postproc and diagnostics modules above. An example workflow for postproc is given here:

http://nbviewer.ipython.org/github/aleaf/SFRmaker/blob/master/Examples/Example_postproc_workflow.ipynb

#####Obtaining SFR output
Prior to running your model, make sure that variable ISTCB2 in the SFR package file (see SFR manual) is set to a positive unit number, which is also listed in the MODFLOW NAM file, in association with an ouput text file name. The text file generated by this setting has information on streamflow and steam/aquifer exchange which is needed for the visualization tools below.

#####Plotting streambed profiles An example of reading in SFR results from the output text file is given here: http://nbviewer.ipython.org/github/aleaf/SFRmaker/blob/master/Examples/SFR_results_visualization_example.ipynb The example includes:

• using SFRmaker to read the SFR output, and write it to a shapefile
• plotting profiles of streamflow, stream-aquifer interactions, and stage for a selected segment
• reading in the MODFLOW dis file using flopy, and comparing grid cell elevations to profiles of stage
• using flopy to read SFR information from the MODFLOW cell-by-cell budget (cbb) file

#####Visualizing routing Routing can be visualized in a shapefile, as produced in the first (postproc workflow) example above. SFR reaches in the shapefile are attributed by segment, reach, outseg, and outlet.

#####Visualizing streamflow and aquifer interactions
The shapefile of SFR output (including streamflow, stream-aquifer interactions, etc.) can be visualized in Arcmap with the symbology contained in the layer files below (available in the Symbology folder).

To view in Arc, after importing the shapefile, under Properties>Symbology, click Import and choose:

• SFR_flow_symbology.lyr to plot flow by line thickness
• SFR_interactions_symbology.lyr to plot gaining, loosing, and dry segments by color
• SFR_interactions_graduated_symbology.lyr to plot stream/aquifer interactions as graduated colors (i.e. dark blue for largest gains, gray for dry, red for largest losses)