SonarMapper Manual

Getting started

SonarMapper creates a depth map of a water body from echo sounder recordings, calculates water surface and volume and combines side-scan recordings into an image of the bottom. Results can be exported as a PDF report, as images, for GIS programs and for Google Earth. The program runs completely without internet.

Installation and license

The setup guides you through the installation. At the first start, SonarMapper asks for the license key from your order.

• With internet: enter the key, check the box for the license terms, click “Activate online”.
• Without internet: check the box for the license terms, click “Show & copy request code”, send the code by e-mail to lizenz@sonarmapper.com and redeem the activation code you receive.

The license is bound to the computer. To change computers, choose Menu › License “Release on this computer” and activate again on the new computer.

Term: The license is valid for two years from purchase, all updates included, after that you renew for one year at a time. Menu › License shows until when it is valid and which modules are included. Four weeks before it expires, SonarMapper reminds you at startup; “Renew …” opens the shop. After purchasing, choose “Update online”, without internet “Redeem code …” (request code by e-mail). After expiry the program keeps running for two more weeks, after that only with a renewal. Projects and exports are kept.

Side scan add-on module: mosaic, tracks and sonar viewer are an add-on module. Without it, the side scan tab shows “Add module …”. After purchasing, SonarMapper activates it on its own at startup on every computer with internet (it checks with the license server at most once a week); “Update online” activates it right away.

Language

SonarMapper is available in English and German. At the first start the program uses the language chosen in the installer, otherwise the Windows language. To switch, choose Menu › Sprache / Language; the change takes effect after a restart (“Restart now” restarts immediately and asks to save first).

Numbers and dates follow the language (English: 1,234.5 and 8 Oct 2026). Exports do as well: the CSV of the volume curve uses commas and decimal points. Contour lines for GIS and CAD have the attribute depth_m in both languages, so templates always fit. Projects can be opened in either language.

The workflow in four steps

Below the header bar, four tabs guide you through the work:

The header bar at the top contains Menu, Import, Export, Undo/Redo, the tabs Map, 2D, 3D, Measure, Side scan and “New map”. On the far right, Help leads to this manual and to the online help (sonarmapper.com/support), Feedback opens an e-mail for suggestions and bug reports. Once the map is calculated, the steps disappear; changes are then made in the Map tab.

1 Import data

Drag files onto the window or click “Import data”. Several files can be loaded at once, for example several runs on different days. All checked datasets go into the map together.

Step 1 with a survey of Lake Lippesee (764,872 points). On the right, the point cloud colored by depth.

Supported formats

Sonar logs

For echo sounder recordings a short dialog appears:

• Transducer offset: how deep the transducer sits below the water surface. The value is added to the measured depth.
• Water level above reference: only needed if several survey days with different water levels should fit together.
• Merge pings per GPS position and Remove false echoes: leave both switched on. The echo sounder measures much more often than the GPS delivers a new position; merged, the map becomes calmer and more accurate.

Text files

For text files, a preview shows the first lines. SonarMapper usually detects separator, columns and coordinate system by itself, including UTM with the zone in the easting. The green line at the bottom shows the first point in degrees: if it is at the right place, the assignment is correct. Frequently used settings can be saved as a template.

Data check

After the import, SonarMapper checks every dataset. The result is shown in the Check column:

If a dataset lies several kilometers away from the others, it usually belongs to a different water body and should be unchecked or processed in a separate project.

Outliers

An outlier is a depth that differs clearly from its neighbors. For this, SonarMapper divides the area into squares of 5 × 5 m and compares each point with the typical depth in the square. A deviation of more than 1 m and more than 30 % of the depth, which is also clearly larger than the usual scatter at this spot, counts as an outlier. Typical causes are fish, plants, air bubbles or false echoes.

When a dataset is selected in the list, its outliers are marked as red crosses on the map. This lets you judge whether they are disturbances or something real: a single object on the bottom can also appear as an outlier. That is why SonarMapper does not remove them by itself.

“Remove outliers” takes the marked points out of the project. The original file stays unchanged, and the PDF report states for the dataset how many points were removed. Ctrl+Z undoes it.

2 Define the area

The area determines where the map is calculated. Without a choice, SonarMapper uses the surveyed area. There are four ways to use a different area:

The wide tile below, Surveyed area (default), applies as long as nothing else is chosen: the map covers exactly the area that was driven and ends at the outermost survey points. This fits in most cases, especially when only part of a water body was surveyed, such as a harbor basin or a search area. A click on the tile discards a different area again.

Boundary from a KMZ file (dashed). The gaps in the survey points are islands: this KMZ contains none, they are drawn as described below.

Drawing islands

Islands are not part of the water surface and must not go into the map or the volume. “Detect lake” and KMZ files often bring islands along. If one is missing, it is drawn by hand:

1. Click “Draw island”.
2. Click points around the island. The mouse wheel zooms, so you can work precisely.
3. To close, click the first point (blue circle). Right-click discards.

While drawing: the circle marks the start point for closing.

The finished island is left out. Below the button you can see how many islands apply.

Any number of islands can be drawn. “Remove islands” deletes all islands drawn by hand.

Shoreline as 0 m

An echo sounder does not measure up to the shore: the boat does not go into the shallows, and the last meters are missing. Without further information, the map therefore ends at the outermost survey points.

If an area with a real shoreline is defined (detect lake, draw shoreline, KMZ), the check box Use shoreline as 0 m can be set. SonarMapper then includes the shoreline with a depth of 0 m and fills the strip between the shore and the last survey points.

Without shoreline: the map ends at the survey points.

With shoreline as 0 m: the map fills the area up to the shore and runs out to 0 m there. The bay at the top right was not driven; the depth there is only estimated and almost 0 m. Such spots are shown by the quality figure “distance to the nearest survey point”.

3 Calculate the map

• Detail level (grid resolution): size of a grid cell. The recommended value fits in most cases. Finer shows more detail but takes longer; the expected duration is shown below.
• Smoothing: fills gaps between the survey lines and removes measurement noise. “None” shows the measured values as unchanged as possible.
• Water level at the time of the survey: the official water level on the survey day. The depths stay unchanged; the value is the reference for later water levels.

“Generate map” starts the calculation in the background; it can be cancelled. With “New map” in the header bar, further maps with other settings are created from the same data.

Result

The finished map with contour lines. On the right, the key figures.

Changing a map later

The Map tab shows the settings of the selected map: area, detail level (cell size), smoothing and shoreline as 0 m. When a value is changed, the difference is shown next to it and “Recalculate” becomes active. The map is then replaced, name and water levels are kept. “As new map” keeps the previous one, for example to compare two smoothings side by side.

Smoothing changed: “Recalculate” is active.

“Change area …” leads to step 2, “‹ Data” to step 1, for example to add more files. From there, “Result” takes you back.

Volume and area

On the right, the selected map shows volume, water surface, surveyed area, maximum and mean depth and the number of survey points. Under Maps you choose which map applies; the check box shows or hides a map, a double-click renames it. The depth at the mouse position is shown at the bottom right.

Quality figures

Below the key figures, gray text shows how reliable the map is:

• Measured: share of the map area where a survey point actually lies. The rest is interpolated between the survey points.
• Distance to the nearest survey point: 95 % of the area is at most this far from a survey point. Large values mean large gaps between the survey lines.
• Cross-check: SonarMapper leaves out random blocks of 5 × 5 m, recalculates the map and compares there with the real measurements. The mean deviation shows how well the map estimates between the survey points.

Water level

Under Water level, further water levels with a date can be entered (“New water level …”). SonarMapper recalculates area and volume for the selected water level without measuring again and shows the change compared with the survey day. A double-click edits an entry.

2D, 3D, colors

The 2D tab contains color scheme, custom color ranges (“Color ranges …”: set depths and colors yourself, save as a scheme or delete a saved scheme), contour interval, basemap, hillshade, point cloud, area and scale bar. 3D shows the water body in three dimensions; the vertical exaggeration can be set (x1 = true to scale).

The mouse wheel zooms, dragging with the mouse button held down moves the map.

Measuring

• Profile: click start and end point, the depth profile appears on the right, “Show profile large” enlarges it.
• Distance: click two points.
• Area: click points, a click on the start point closes the area.

Measurements are listed on the right; they can be renamed, deleted and exported individually and are saved with the project. Right-click resets a running measurement.

Waypoints

The Waypoints tab brings everything together:

• Set waypoint: every click on the map sets a waypoint with depth. Click the button again to stop.
• Symbol and color: apply to the waypoint selected in the list on the right and to all new ones. “Custom color …” opens the color picker, “Apply to all” changes all waypoints at once.
• Import … (GPX, KML, KMZ) and As GPX … for echo sounder or GPS. Garmin devices take over circle, diamond, square and triangle with color (the nearest of red, green or blue), other devices show their default symbol.
• Show waypoints shows or hides all of them on the map.

The list on the right shows name and depth. Waypoints can be renamed and deleted there; the check box in front hides a waypoint on the map and in the report. Symbol, color and everything else are saved with the project.

Volume and area curve

The button below the key figures shows how water surface and volume decrease as the water level falls, as a chart and table, with export as CSV.

Side scan

Lowrance, Humminbird and Garmin recordings (SideVü) often contain a side-scan image in addition to the depth: an acoustic image of the bottom to the left and right of the boat. Side scan is an add-on module (see Installation and license).

Mosaic

In the Side scan tab, “Create mosaic” combines all runs into one image on the map. If there is no depth map, “Side-scan mosaic only” in step 1 leads there directly.

• Mode: “Best data (sharp)” takes the best recording for each spot, “Average (soft)” blends overlapping runs, “Order” lets the upper track in the list win.
• Tracks …: switch individual runs on and off, set order and section per run, with preview.
• Cell size, range, brightness, contrast, opacity and palette adjust the image.

Side-scan mosaic of Lake Hägenichsee in “Average (soft)” mode.

Sonar viewer

“Sonar viewer” shows a strip below the map with one run as a continuous image. The run goes to the right, port is at the top, starboard at the bottom, the middle is below the boat. The height of the strip can be changed at the divider between map and strip, “×” closes it.

• Click on the map: the strip jumps to the run that covered this spot best. An arrow above the strip and a circle show the spot, an orange X appears on the map.
• Scroll through the run with the mouse wheel or the scroll bar. A boat symbol moves along on the map, the yellow line shows the swath width. If the boat leaves the map section, the map follows.
• Mouse over the strip: a yellow circle on the map shows where this spot lies.
• Zoom 1:1 to 1:16 (also Ctrl + mouse wheel), brightness, contrast and palette in the bar above the strip.
• Remove water column (default: off) converts to the distance on the bottom, as in the mosaic. Off shows the raw image with the water column; there you can also see whether something floats in the water.
• A click in the strip marks the spot with an orange X on the map. “Set waypoint” turns it into a waypoint.

Export and report

For the report, you are asked for title, author and a remark, and which parts it should contain. The first page shows the map with the key figures. Measurements are on separate pages: first an overview with all measurements on the map, then each measurement individually with a map section and, for profiles, the depth profile.

After each export, SonarMapper reports where the file is. “Open folder” shows it in Explorer, “Open file” opens it directly.

Projects, undo

A project (.smap) contains survey data, area, maps, water levels, measurements, waypoints and side-scan settings. For depth maps, the original files are no longer needed afterwards. SonarMapper still reads side-scan images from the sonar logs, though, so do not move or delete them.

Basemaps and offline use

basemap.de (Germany) and OpenStreetMap are available as background. Outside Germany, SonarMapper automatically uses OpenStreetMap. Without internet, the offline map karte.mbtiles in the program folder is used if available; otherwise the background stays empty. All other functions work without internet.

Accuracy

A depth map is always as good as the survey. Values between the survey points are interpolated and smoothed for a better display. Important influences:

Updates

SonarMapper checks once a day at startup whether there is a new version. Without internet, nothing happens. If there is one, a green Update button appears at the top right. It shows what is new and whether the license covers the update (all updates during the license term).

1. “Download”: the setup is saved in the download folder and checked for completeness.
2. “Install now”: SonarMapper asks to save, closes and starts the installation. Administrator rights are often required for the installation.

Projects, settings and license are kept during an update. Manual check: Help › “Check for updates …”. Where IT does not want outgoing connections, the check can be switched off under Help › “Check for updates automatically”.

Tips and problems

• The map looks frayed: increase the smoothing or define an area.
• Huge area or strange triangles: a dataset lies far away (Check column), uncheck it.
• Calculation takes long: choose a coarser detail level.
• Sonar log without points: the device did not detect the bottom or had no GPS; the message during import names the reason.
• Reporting errors: the log file helps with the search. Its path is shown under Menu › About SonarMapper.