Tip of the Month

Following on from the last newsletter's 'Tip of the Month', where Dr. Mark Bailes introduced the concept of batch running ISIS simulations, this month we take this further to show batch post-processing of ISIS simulations.

Batch processing simply enables you to extract the same information (e.g. Peak Water Level at Cross Section 1) from a whole series of ISIS Results Files (.ZZN). Typically you might be interested in Peak Water Level for the 2, 5 and 10 year fluvial flow.

Two approaches to batch processing ISIS simulations are presented below. It is a matter of personal preference which you choose. Approach 1 is slightly more complex to set up - but is more flexible. Approach 2 is easy to set up - but less flexible.

Approach 1 - Running ISIS models and then processing the results afterwards

• Launch Tabular CSV from the Tools Menu and browse to an ISIS Results file (.ZZN)
• Set up Tabular CSV to extract the Information you want e.g. Peak Stage at Cross Section 1
• Then rather than clicking on the run button instead select 'Save Settings' from the File Menu. This will create a Tabular CSV Script File (.TCS). This informs ISIS of the results that you wish to extract.
• In a text editor (e.g. TextPad) create something similar to what is shown below:

Please note that you will need to specify the location of your .ZZN files and the .TCS file created earlier. You can add as many lines as you wish and will need one line for each .ZZN file.

Once complete Save the File as .BAT (rather than .TXT).

In Windows Explorer double click the .BAT file and it will execute. Tabular CSV will then create a .CSV file from each .ZZN file based on the settings you specified in the .TCS file.

Tip: Advanced users might want to set up a whole series of .TCS files (e.g. one to extract peak level and one to extract peak flow). These can then be referenced in the .BAT file as needed.

Approach 2 - Running ISIS models and processing the results at the same time

• Launch Tabular CSV from the Tools Menu and browse to an ISIS Results file (.ZZN)
• Set up Tabular CSV to extract the Information you want e.g. Peak Stage at Cross Section 1
• Next, rather than clicking on the run button instead select 'Save Settings' from the File Menu. This will create a Tabular CSV Script File (.TCS). This informs ISIS of the results that you wish to extract.
• In the ISIS Run Scheduler Form, you need to specify both the .IEF files you wish to use and select 'Auto Postprocess' tick box. You also need to specify the file path of the .TCS file you wish to use to post process the results.
• Once you start the Run, ISIS will write the hydraulic results to the .ZZN file and post process those results to create a .CSV file.

See Figure below:



Tip: It is only possible to specify one .TCS file using Approach 2 - so you can only extract one set of results (e.g. Peak Stage). If you wish to extract a series of variables, Approach 1 is likely to be more appropriate.

Many of you will be familiar with the concept of running a batch of models one after another. This is done using the Batch Simulation option on the Run menu. A series of ISIS Control Files (.IEF) are loading into the ISIS Run Scheduler Form and when instructed ISIS will then run one after another. In this month's Tip of the Month Halcrow's Mark Bailes introduces the concept of ISIS Event Files (.IED) which can assist running the same model with different boundary conditions.  This is typically used when running the same model with lots of different return periods.

The Problem

If you construct a hydraulic model (e.g. Model1.DAT) representing your site and you wish to run various return period flows through that model (e.g. 2 year, 5 year, 10 year etc) you could set up a series of .DAT files, each with the different return period flows e.g. Model1_2year.DAT, Model1_5year.DAT, Model1_10year.DAT etc) You then need to run each one of these models with the corresponding ISIS Control File (.IEF) e.g. Model1_2year.IEF, Model1_5year.IEF, Model1_10year.IEF.

A complete set of files would therefore look like:

• Model1_2year.IEF which would reference Model1_2year.DAT
• Model1_5year.IEF which would reference Model1_5year.DAT
• Model1_10year.IEF which would reference Model1_10year.DAT

Whilst it is perfectly acceptable to adopt this approach, problems arise if you wish to change the hydraulic model. You have to make the same change to a whole series of hydraulic models. Not only is this inconvenient and time consuming, it also increases the likelihood of inconsistencies and errors. The recommended approach is presented below:

The Solution

A single hydraulic model is created (including dummy boundary conditions) and saved as a ISIS.dat file in the usual way.

Separately each set of boundary conditions is then saved as an ISIS Event File (.IED), i.e. one for each return period. So you would have a 2year.IED file, a 5year.IED file and a 10year.IED file. Event files are created in the same way as an ISIS Model is created the only difference being when you come to save the file you "Save As" .IED rather than .DAT. It is important to note that the Event file should only contain boundary conditions and the ISIS nodes in the Event file must have the same name as the dummy ISIS nodes representing the boundary conditions in the hydraulic model. This is so ISIS knows to replace those in the ISIS.DAT file with those in the ISIS.IED File.



Having set up your ISIS.IED files the next step is to set up a series of .IEF files in the usual way. The only differences are that on the Files Tab you not only need to specify the ISIS.DAT file you wish to use, you also need to specify the Boundary Conditions you wish to use and a different results file name to which the model results are saved. You do the former by referencing the IED file in the Event Box at the bottom of the ISIS Run Form, and the latter in the "Results File" box.

A complete set of files would therefore look like:

• Model1_2year.IEF which would reference both Model1.DAT and 2year.IED
• Model1_5year.IEF which would reference both Model1.DAT and 5year.IED
• Model1_10year.IEF which would reference both Model1.DAT and 10year.IED

With this approach there is only one hydraulic model to update should you need to make any changes.

Tip: Advanced users might want to store the Fluvial flows in one event file (.IED) and Tidal Boundaries in another event file (.IED). This gives you complete flexibility when combining events together e.g. You may wish to use the 2 year Fluvial flow with the 100 year Tidal Boundary. Having set up your IED Files as before, you simply add both .IED files to the Event Data window (as described above).

ISIS Mapper v3.3 can be used to georeference non-georeferenced cross sections. A fully geo-referenced cross-section is essential to produce a flood map since this is required to create the TIN, from which the flood map is derived.

You can fully georeference cross-sections which are either already partially georeferenced, or those without georeferencing, although the latter also requires a node location shapefile to be available.

Georeferencing non-georeferenced cross sections

Non-georeferenced cross sections are those which do not have the easting and northing coordinates specified for all the points of all or some of the cross sections in the ISIS model file. Please note that a gxy node locations point shapefile should be available for this model in order to use this functionality.


An example of a non-georeferenced cross section shown in the
River Section data entry form in ISIS

Step-by-step guide for georeferencing non-georeferenced cross sections

Step 1 - Import non-georeferenced ISIS data file. Go to Layer > ISIS Data Import > ISIS Model as Shapefile.

Step 2 - Import a GXY node locations file. Go to Layer > ISIS Data Import > ISIS Model as Shapefile. The GXY node locations file should be for the non–georeferenced ISIS data file loaded in Step 1.

Step 3 - Start editing the layer with the cross sections shapefile created at Step 1. Right-click on the name of the cross sections shapefile file in the Table of Contents. Select the menu item Start Edit. 

Step 4 - Click on the menu item 'Georeference Cross Sections from Node Locations'. Go to the shapes details drop-down menu (see screenshot below), then 'Cross Section Operations', then 'Geo-reference Cross Sections From Node Locations'.  The points of each cross section will be placed on a line perpendicular to the river centreline (averaged if the centreline is kinked at this node).



Notes:

• If no match between the node name in the GXY node locations file and a node label in the cross sections file was found, then this particular cross section will not be geo-referenced.
• If there are at least two geo-referenced points in a cross section, then the GXY file node location for this section will not be taken into account (if available) and the georeferencing of this section will be done as for the case of partially georeferenced cross sections (see next section).

Step 5 - Save the shapefile or convert it into a file in ISIS format. In order to save the shapefile, click on the 'Save Shapefile' button (second button from the left) on the 'Shapefile Editor Toolbar'. In order to convert the shapefile into a file in ISIS format (.dat file), go to the 'Shapes Details' drop-down menu, then 'Cross Section Operations', then 'Save as ISIS File'.  After saving the file in one of the formats mentioned above, you can exit the editing mode of the shapefile by clicking on the 'Stop Editing Shapefile' button on the 'Shapefile Editor'.

Georeferencing partially georeferenced cross sections

Partially georeferenced cross-sections are those cross sections which have easting and northing coordinates specified for only some of the points (for all or some of the cross sections in the ISIS model file).


An example of a partially georeferenced cross section shown in the
River Section data entry form in ISIS

In order to georeference partially georeferenced cross sections, the user has to import an ISIS Model file into a shapefile (by selecting the menu items 'Layer > ISIS Data Import > ISIS Model as Shapefile'), enter the 'Edit' mode for this file (right-click on the file in the table of contents and select the menu item 'Start Edit'), and then select the menu item 'Geo-reference Partially Geo-referenced Cross Sections' from the 'Shapes Details' dropdown menu.

In this case georeferencing is based on the coordinates of the two furthest available geo-referenced points in the cross section.  A line is drawn between these points and other points of the cross section are placed along this line taking into account the information from the model file about this cross section.   

For more details about this process please refer to the page 'How do I georeference non-georeferenced cross sections' in the web version of the ISIS Mapper manual.

This tool will find the optimal storm duration (OSD) for one or more FEH or ReFH boundaries, i.e. that storm duration which will give you a maximum stage (or flow) at a particular node in your model. All other parameters in the boundary will not change.

Where can I find it?

On the Run menu in the main ISIS interface.

What do I need?

A valid ISIS model containing FEH and/or ReFH boundaries and an ISIS Event (run parameter) file (*.ief).

How do I use it?

After loading the data file into ISIS and selecting the OSD option, you will be presented with the OSD form.

• On the left, select the FEH/ReFH boundary(s) for which you require the storm duration to be optimised. (Use shift-click to select multiple boundaries).
• From the next table, select the [single] node at which you require the optimal value to be found.
• At the top, select whether to optimise Flow or Stage (default) at this node, and to find the maximum (default) or minimum of this value.
• For Optimising method, "Brent" performs an intelligent search; "Exhaustive" tries each possible duration in turn.
• Select the bounds for the storm duration within which the optimal duration should lie; it is also advised to select an Initial duration - one can select the "Use current" box to read the initial storm duration from the data file.
• By default, the simulation duration used will be that in the ief file; one can change this to be relative to the storm duration, but ticking the "Set simulation period as a multiple of storm duration" box. This guards against setting a simulation duration that is too short for a long storm duration. A suggested value for this is 1.2, but should be greater if the point of interest is a long way downstream of the inflow(s).
• Enter the name of the ief file in the "Base ISIS event file" box. All parameters within this will be used, excepting the simulation time (if the above box is checked). 
• Hit the "Optimise" button to run.

Output

When the optimal duration is found, the results (optimised variable against duration) are displayed in graphical and tabular form, on separate tabs of the OSD form.



More details

The process involves running simulations of varying storm durations until the optimum duration is found. Hence, it could be time-consuming if the model run-time is long. To this end, the Brent method is employed (if selected), which converges to a solution within few simulations. Simulations containing ISIS event data files (*.ied) are permitted.

Constraints

• The storm durations used are discrete, and must be valid storm durations (i.e. odd integer multiple of the data interval).
• User input rainfall profiles can not be used.

What is this?

This is a readable text file which contains settings for your ISIS interface, such as: position and size of windows; recently used file lists; user interface options, etc.

Where can I find this file?

This file (formsed.ini) is located in your [My Documents] folder. Thus it is personal to you, should you be using a shared machine.

Why do I need to know about this?

Occasionally windows "disappear" off the screen, giving the illusion that they are not opening properly. This typically happens if one has previously used two screens, and then reverted to one. The window may be being "displayed" on the second screen, which is no longer connected. Also, the splitter bar, separating the model data from the initial conditions in the main window, may have been dragged so far down that it can't be moved up again by dragging it.

Can I edit it myself?

Yes. Just take care to put sensible values in (screen positions and sizes are measured in pixels, measured from top-left). Also remember to shut down ISIS applications before editing, since this file is usually overwritten on exiting ISIS.

How do I know which settings to change?

These should be self-explanatory; for instance, each screen position has a header associated with it, e.g. [UnitFormLayout] for the Unit Forms (e.g. RIVER, QTBDY, etc.), followed by the screen position and size (Top, Left, Height, Width) in pixels. The splitter bar position for the main window is named "Splitter" in the [Layout] section and is measured in pixels from the top of the window - this should be significantly less than the FormHeight value.

For example, the following settings indicate that the cross section plots will be placed with the top-left corner at (43,212) of size 921 x 611 pixels.

[CrossSectionFormLayout]
Left=43
Top=212
Height=611
Width=921

Why do I need to do this?

If the conveyance does not monotonically increase with depth within a cross section, this can lead to model instabilities,

What causes such irregularities?

Usually this is caused by a relatively large increase in wetted perimeter, compared with the increase in wetted area for a small increase in water level. Typically this will be as the water goes out-of-bank. Incorrect section data can also cause problems.

How can I tell before running a simulation?

With the new conveyance plotting facility in ISIS v3.1, one can overlay the conveyance curve on a cross section plot - this gives an instant relationship between the cross section and conveyance. Any irregularities in conveyance can be matched to a section elevation point.

To display this, first plot a RIVER cross section. Then right click and select "Edit Series" (or use the Ctrl-D shortcut). Tick the Conveyance check box to display the conveyance curve on the cross section.



Note: You can also display the conveyance curve for the section immediately upstream and/or downstream on the same plot (if such sections exist).

Alternatively, you can select the "Tabulate Cross-Section Properties" option from the Tools menu to display Conveyance and other cross section properties in tabular or graphical form for one or any number of selected cross sections.



What can I do to prevent decreasing conveyance?

By inserting panel markers at the bank top, this compartmentalises the conveyance. The conveyance for each panel, delimited by panel markers, will be calculated separately, and then added together to give a total conveyance for the section. By separating out any sudden changes in geometry from the main channel section, this minimises the chances of decreasing conveyance occurring.

One can use ISIS Mapper to create a flood map from ISIS 1-D model results, with little effort, providing the user has the following available:

• ISIS model results in the form of binary files (.zzn/.zzl files) or Tabular CSV files (.csv)
• a ground grid (e.g. DEM) for the area of interest
• a shapefile of model data (cross-section polylines or flood cell reservoir polygons) or geo-referenced ISIS model files. Creating these can also be performed in ISIS Mapper.

Step 1

Launch ISIS Mapper by clicking the ISIS Mapper icon or selecting > Tools > ISIS Mapper from the main menu of ISIS.

Step 2

Import river sections of your ISIS Model either by loading the shapefile of your model (if you have it) or by clicking on the model import icon. ISIS Mapper will then convert the sections into separate polylines within a new shapefile.

Step 3

Create a TIN (Triangulated Irregular Network) for displaying 1D model results as a water surface. From the ISIS Mapper main menu select > Modelling > 1D Flood Map > Triangulate shapefiles. When prompted select the cross section shapefile and a filename for your TIN. The TIN Creator tool will then open with your cross section shapefile pre-loaded. Create a TIN by clicking the triangulate icon . Use editing tools in TIN Creator to remove triangles linking non-adjacent points (if present). Click the ISIS Mapper icon to close TIN Creator and automatically load your TIN into the ISIS Mapper viewport.

Step 4

Add the ISIS results to a TIN. These results (binary or csv format) can be added to the TIN by selecting Modelling > 1D Flood Map> Add Binary ISIS Results to TIN or Add Tabular CSV Results to TIN respectively. Please ensure that the Tabular CSV results have been created in ISIS using the output format ’One Column per Timestep’.

Step 5

Load the ground data into ISIS Mapper by clicking Open Raster Data icon .

The user can now see the flood extent in ISIS Mapper. This can also be saved in the form of a flood depth grid or a flood extent shapefile by using the 1D Flood Calculator (select Modelling > 1D Flood Map > Generate Flood Map).

For more information about 1D Flood Calculator and other functions of ISIS Mapper, including those described above, see the ISIS Mapper manual either by selecting > Help > Open Help in ISIS Mapper.

ISIS can produce outputs in a number of graphical and tabular formats. For the long section plot, the horizontal axis displays the node labels by default. To display the chainages as well:

• From the standard ISIS Long Section graph, right-click and select Edit Chart.
• Select the following tabs: Chart -> Axis -> Scales -> Options.
• Highlight "Top Axis" from the list on the left-hand side and select the "Visible" check box. The chainage will then appear on the Top axis.
• If you wish to switch between displaying either chainage or node label, select the tabs Chart -> Axis -> -> Labels -> Style; a Style of "Value" displays the chainage; a Style of "Text" displays the node label.

...and how to export the data to a spreadsheet

For further analysis or reporting, e.g. to create cross-referencing of the node labels, chainages and results, the user may wish to export these graph data to Excel or a similar package. The trick here is to use the ISIS Graph output.

• Again, on the Long Section plot window, right-click and select Export -> ISIS Graph file (*.adp) and save the file.
• Edit the saved file in a text editor - the plot data is arranged in a series of blocks separated by header lines.
• The final block (beneath the header line "LINE SIZE 1 COLTAB 0.00 0.00 1.00 UNBROKEN !DRAWLABEL LABEL") contains the chainage (1st column) and node label (3rd column); the second column is the value of the default output variable (e.g. bed elevation).
• This block can be cut and pasted into e.g. Excel (using the "Text to Columns" tool to separate the columns).
• The other blocks can similarly be cut and pasted side by side to display the remaining output data.