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SCIMAP-Flood 2022 User Guide

Sim Reaney, Durham University 2022


SCIMAP-Flood is a spatial targeting tool for flow slowing natural flood risk management schemes. The tool considers the spatial structure of the landscape, rainfall patterns, the pattern of runoff generation and the communities at risk to highlight and guide the locations of NFM schemes. With this spatial targeting, SCIMAP-Flood aims to simultaneously ensure that projects are located in the most effective parts of the catchment for flood risk reduction and that unintended consequences are avoided, such as the synchronisation of tributaries. The details of the methods and scientific approach are given in the main SCIMAP-Flood journal paper (Reaney 2022). This document provides instructions on pre-processing the catchment data and running the SCIMAP-Flood tool.

Required data

Digital Elevation Model

SCIMAP-Flood requires a detailed digital elevation model used for the routing of the water through the catchment, the connectivity calculations, and the generation of runoff. Typical grid resolutions are 2m-5m, and the currently recommended data product is the NextMap 5m DTM. The approach is compatible with higher resolution datasets, such as the forthcoming national EA 1m LiDAR. Using this type of data will require more RAM and longer processing times. The NextMap 5m dataset or the new EA National Lidar Dataset are recommended.

Land Cover Map

The land cover partly determines the runoff generation at a location. Hence, SCIMAP-Flood uses information on the spatial pattern of the different land covers to calculate the flood risk generation. A land cover map can be sourced from several places:

  • Corine data is freely available across Europe but is limited in its spatial resolution.
  • CEH Land Cover Map has national (UK) coverage at a grid resolution of between 20 and 25m, depending on the year.  
  • A Landsat-8 or Sentinel-2 image can be classified into the required land cover classes. This approach gives an up-to-date land cover map at the expense of the processing time.

Communities at Risk

The floodwater generation pattern can affect multiple communities at risk, and slowing the flow for one community can negatively impact another. Therefore, SCIMAP-Flood works with multiple communities at risk or impact points, such as key infrastructure, in a catchment to give a balanced overview. The location of the communities at risk and impact points can be determined by catchment knowledge, such as the known locations at flood risk, from the EA communities at risk dataset or other flood risk mapping.


Not all rainfall causes flood events, and the high magnitude floods are often related to certain atmospheric circulation patterns. These rainfall patterns interact with the catchment topography, the pattern of land use, and the communities’ location at risk to give the flood risk. Therefore, SCIMAP-Flood considers a range of rainfall patterns. There are two key sources for spatial rainfall information:

  1. CEH GEAR is a collection of 1km daily rainfall maps for the UK
  2. TRMM or GPM datasets are available for tropical (60 degrees north and south of the equator).

For the UK, the CEH GEAR data set is recommended.

Pre-processing Part One – ArcMap

A set of grids must be prepared within a GIS system to use the SCIMAP-Flood tool. The grids need to be in the same metres-based map projection, such as the OS GB grid and have the same cell size and spatial extent. The instructions below are for a combination of ESRI ArcMap 10.x and SAGA-GIS.

Selection of rainfall patterns

SCIMAP-Flood uses 5 to 20 patterns that represent flood triggering rainfall events. The dates for these patterns can be selected by analysing the river discharge record for each point of impact, including the communities at risk, within the catchment for the key flood events and then selecting the rainfall pattern than triggered the flood. You need to consider the timing of the flood event within the day and the flood wave travel times within the catchment which may mean that the rainfall event was the day before the flood peak occurrence. If you are using the CEH GEAR dataset, then the data is supplied in NetCDF format. Within ArcMap, the ‘Make NetCDF Raster Layer tool‘ allows you to open the NetCDF file and select the required date. There is a detailed overview of this step here: From this dataset, export each of the flood triggering rainfall patterns to a set of national scale raster datasets. To export the data, right-click on the dataset in the table of contents and then select ‘export’. Put the dataset back into ArcMap after exporting.

Getting all the data into the same project and extent

Import catchment outline polygon into ArcMap. Go to the ‘Geoprocessing’ menu and select ‘Environments’. In the dialogue box that appears, select ‘Extents’ and then set the extent to be the same as the catchment shapefile. ArcMap will now only process data within this spatial extent.

For each rainfall map, resample the grids to the same resolution as the DEM. If you are using NextMap, this will be 5m. The resample tool uses the bilinear or cubic interpolation method to avoid sharp lines in the final map.

Landcover based runoff generation

SCIMAP-Flood uses a map of the land cover, converted to relative runoff generation risk units ranging from zero, for the least amount of runoff generation potential, to one, for the most. Typical values are given in the table below. You can use the reclassify tool in ArcMap to do this conversion.

IdLand CoverWeightNotes
1Woodland0.05Woodland has been given a lower risk weight due to the high infiltration rates and lower saturation deficits within the soil
2Arable0.8Arable has been assigned a high-risk weight due to the widespread use of soil drainage that rapidly transfers water to the river channels.
3Improved Grassland0.3Improved grassland has been given a high weighting than unimproved grasslands due to the likely compaction of the soils by livestock, which results in lower infiltration rates.
4Unimproved Grassland0.15Unimproved grassland has been given a risk weight above woodland
5Urban1.0Urban has been assigned a high-risk weight due to the impervious surfaces and effective drainage that rapidly transfers water to the river channels. Although not tackled directly with NFM, SuDS and elements of NFM could be applied.
6Moorland0.1Moorland has been given a lower weighting than unimproved grasslands to reflect the more natural soil structure and low potential compaction.
7Water and inland rock0.0Although lakes, rivers and inland rock will convert all of the rainfall water to runoff, it is not possible to modify this behaviour with NFM measures, and hence water has been given a low value

Clip the DEM

Import the DEM into ArcMap and then use Raster Calculator to clip the dataset to the processing extent. In Raster Calculator, put in just the DEM in the equation and click OK. Clipping the DEM to the catchment boundary at this stage is best to simplify later processing.

Export from ArcMap

Export the DEM, reclassified land cover and the rainfall patterns from ArcMap using the Raster to ASCII tool.

Pre-processing Part Two – SAGA-GIS

The next preprocessing step uses the SAGA-GIS with the included SCIMAP module, available at: This tool is used for the calculation of the connectivity mapping and the travel times to points of impact. Using the ‘Import ESRI Arc/Info Grid’ tool in the ‘Import/Export – Grids’ section of the Modules list, select your DEM that you exported from ArcMap and click ‘Okay’.


To calculate the hydrological connectivity potential within the catchment, you will use the SCIMAP tools. Since we are not running a sediment risk map calculation, we can set the rainfall pattern and land cover risks to be constant. To do this, create a constant grid with a value of one using the ‘Constant Grid’ tool in the ‘Grid – Tools’ section of the modules list.

Select the SCIMAP Risk Maps module and then ‘Fine Sediment Risk’. Select the grid system at the top of the model, put the DEM grid into the ‘Digital Elevation Model’ selection and the constant grid into the ‘Erodibility’ and ‘Rainfall pattern’ selections.

Click ‘Okay’ to run the tool.

When it has finished processing, you can close the grids other than ‘DEM’, ‘Channel network’ and ‘Connectivity’.

Travel times to points of impact

To calculate the travel times to the points of impact and communities at risk, you will use the ‘Overland Flow Distance to Channel’ tool within the ‘Terrain Analysis – Channels’ section of the modules list.

For each of your points of impact, note down the grid reference. It may be simpler to do this in ArcMap. You may want to have between one and ten points of impact.

For each point of impact:

  1. Use the ‘change grid values – interactive’ tool to change the raster value in a cell on the river channel at your point of interest to a value greater than the current maximum value of the grid.
  2. Reclassify the grid so that all values below the value assigned to the point of interest are No Data, normally ‘-99999’ in SAGA-GIS. This processing will leave you with a grid that is all no data except for a cell in the river channel at the point of impact.
  3. Use the ‘Overland Flow Distance to Channel’ tool within the ‘Terrain Analysis – Channels’ section of the modules list with the DEM and the raster you just created to calculate the overland flow distances to the point of impact.

Export to ASCII

Use the ‘Export ESRI Arc/Info Grid’ tool in the ‘Import/Export – Grids’ section of the Modules list to export the connectivity map and each travel times map.

Running the SCIMAP-Flood Tool

SCIMAP-Flood combines all the input maps to calculate a map of the locations suitable for flow slowing NFM. The tool is called ‘SCIMAP-Flood.exe’ and is available as an x64 Windows, compatible with Windows 7, 8, 10 and 11 or as a macOS 12 for both Intel and Arm (M1) Apple hardware. SCIMAP-Flood is a command-line application that reads in a parameter file with the details of the input data.

Setting up the parameter file

The parameter file is a text file with a ‘tag and value’ format. Each line is a separate parameter and has a tag that defines what the map is and a value which is the filename. The tags are detailed in the table below, and an example file is shown below and is included with the fileset. You can edit and create this file in Notepad on Windows, Text Edit on macOS or Atom and save it as a text document, ‘.txt’.

An Example SCIMAP-Flood parameter file.

rainfallPattern Rainfall_patterns/170709.txt
rainfallPattern Rainfall_patterns/070105.txt
rainfallPattern Rainfall_patterns/190804.txt
rainfallPattern Rainfall_patterns/280612.txt
ofDistance Points_of_impact/pointOne.asc
ofDistance Points_of_impact/pointTwo.asc
ofDistance Points_of_impact/pointThree.asc
connectivity connectivity.asc
runoffGen landCoverPatterns/runoffGen01.asc
runoffGen landCoverPatterns/runoffGen02.asc
runoffGen landCoverPatterns/runoffGen03.asc
  • ‘SCIMAP-Flood’ is the header to define the parameter file format
  • ‘rainfallPattern’ is the tag for the different rainfall patterns. One is required. Multiple uses of the tag are allowed. No maximum number but limited by RAM.
  • ‘ofDistance’ is the tag for the different overland flow travel distance maps for each point of impact. Multiple uses of the tag are allowed. No maximum number but limited by RAM.
  • ‘connectivity’ is the tag for the connectivity map. One is required and with a maximum of one being used. If the tag is used multiple times, the last one in the file will be used.
  • ‘runoffGen’ is the tag for the runoff generation potential map based on land cover. One is required. Multiple uses of the tag are allowed. No maximum number but limited by RAM.

Running the calculations

Open the command prompt on windows.

  • Windows 7:
    • Right-click on the folder with your data and the SCIMAP-Flood.exe file and select ‘Open Command window here’
    • At the command prompt, you need to type ‘SCIMAP-Flood params.txt’ where ‘params.txt’ is your text parameter file created in the previous step.
  • Windows 10 and 11:
    • Right-click on the folder with your data and the SCIMAP-Flood.exe file and select ‘Open PowerShell window here’
    • At the command prompt, you need to type ‘./SCIMAP-Flood params.txt’ where ‘params.txt’ is your text parameter file created in the previous step.
  • macOS
    • Open the terminal (cmd+space and search for terminal)
    • Change folder into where your data and the SCIMAP-Flood program is
    • At the terminal prompt, you need to type: ‘./SCIMAP-Flood params.txt’ where ‘params.txt’ is your text parameter file created in the previous step.

SCIMAP will process the data and produce two output files called ‘floodRiskScoresMean.asc’ and ‘floodRiskScoresCoV.asc’. The first dataset is the mean of the complete set of flood hazard factors (travel times, connectivity, rainfall and land cover), and the second set is the Coefficient of Variation of the distribution score.

Output dataset

The output dataset contains the flood risk scores for each location and identifies critical areas of the catchment to implement works. The output file can be generalised with either a per sub-catchment based approach with zonal statistics in ArcMap or through the production of an intervention heat map using a tool such as

Cited Reference

Reaney, Sim M. (2022) ‘Spatial targeting of nature‐based solutions for flood risk management within river catchments‘. Journal of Flood Risk Management e12803