16.19. dem_mosaic

The program dem_mosaic takes as input a list of DEM files and creates a mosaic. By default, it seamlessly blends the DEMs where they overlap. It can also combine the inputs in other ways.

See many examples in Section 16.19.2.

16.19.1. Overview

The output mosaic is written as non-overlapping tiles with desired tile size, with the size set either in pixels or in georeferenced (projected) units. The default tile size is large enough that normally the entire mosaic is saved as one tile, named as:

output_file_prefix-tile-0.tif

Alternatively, one can pass to the -o option an output file, such as output.tif. Then the mosaic will be written with this exact name. (This will fail if the tool decides there is a need for more than one tile.)

Individual tiles can be saved via the --tile-index option (the tool displays the total number of tiles when it is being run). As such, separate processes can be invoked for individual tiles for increased robustness and perhaps speed.

By the default, the output mosaicked DEM will use the same grid size and projection as the first input DEM. These can be changed via the --tr and --t_srs options. Also note the --tap option.

The default behavior is to blend the DEMs everywhere. If the option --priority-blending-length integer is invoked, the blending behavior will be different. At any location, the pixel value of the DEM earliest in the list present at this location will be kept, unless closer to the boundary of that DEM than this blending length (measured in input DEM pixels), only in the latter case blending will happen. This mode is useful when blending several high-resolution “foreground” DEMs covering small regions with larger “background” DEMs covering a larger extent. Then, the pixels from the high-resolution DEMs are more desirable, yet at their boundary these DEMs should blend into the background.

To obtain smoother blending when the input DEMs are quite different at the boundary, one can increase --weights-blur-sigma and --weights-exponent. The latter will result in weights growing slower at each DEM boundary faster inwards. Some experimentation may be necessary, helped for example by examining the weights used in blending; they can be written out with --save-dem-weight integer.

Instead of blending, dem_mosaic can compute the image of first, last, minimum, maximum, mean, standard deviation, median, and count of all encountered valid DEM heights at output grid points. For the “first” and “last” operations, the order in which DEMs were passed in is used. With any of these options, the tile names will be adjusted accordingly. It is important to note that with these options blending will not happen, since it is explicitly requested that particular values of the input DEMs be used.

If the number of input DEMs is very large, the tool can fail as the operating system may refuse to load all DEMs. In that case, it is suggested to use the parameter --tile-size to break up the output DEM into several large tiles, and to invoke the tool for each of the output tiles with the option --tile-index. Later, dem_mosaic can be invoked again to merge these tiles into a single DEM.

If the DEMs have reasonably regular boundaries and no holes, smoother blending may be obtained by using --use-centerline-weights.

This tool can also apply hole-filling, smoothing, and pixel erosion at boundary.

16.19.2. Examples

16.19.2.1. Blend DEMs

This creates a seamless DEM:

dem_mosaic dem1.tif dem2.tif -o blended.tif

16.19.2.2. Priority blending

Read the DEMs from a list, and apply priority blending. The first DEM in the list is given priority, with the others used as a background with this transition length.

echo dem1.tif dem2.tif > image_list.txt
dem_mosaic -l image_list.txt --priority-blending-length 14 \
  -o priority_blended

Since an extension for the output was not specified, it will be saved as priority_blended/tile-0.tif (there may be more than one tile if the --tile-size parameter is set).

16.19.2.3. Mean height DEM

dem_mosaic -l image_list.txt --mean -o mosaic

This uses no blending. Also supported are the options --first, --last, --min, --max, --stddev, --median, --nmad, and --count.

16.19.2.4. Regridding

Enforce that the grid is at integer multiples of grid size (like the GDAL gdalwarp tool, Section 16.23):

dem_mosaic --tr 0.10 --tap input.tif -o output.tif

If the bounds of the output DEM from above are examined with gdalinfo (Section 16.23), they will be multiples of 0.05, because each grid point is centered at an integer multiple of 0.10, and extends for half a grid vertically and horizontally.

(Note that point2dem (Section 16.54) and mapproject (Section 16.39) create their outputs by default that way, and if dem_mosaic is invoked on such datasets, it will respect the input grid even without --tap being explicitly set.)

16.19.2.5. Apply a blur

dem_mosaic --dem-blur-sigma 1 input.tif -o output.tif

This option will also extend the DEM somewhat and fill some holes, especially with a larger sigma.

16.19.2.6. Erosion

Erode 3 pixels at the boundary:

dem_mosaic --erode-length 3 input.tif -o output.tif

16.19.2.7. Fill small holes

dem_mosaic --hole-fill-length 50 input.tif -o output.tif

16.19.2.8. Grow a DEM

dem_mosaic                  \
    --fill-search-radius 25 \
    --fill-power 8          \
    --fill-percent 10       \
    --fill-num-passes 3     \
    input.tif -o filled.tif

Unlike the earlier example, in this mode the tool will not try to fill small holes of a given diameter that are fully surrounded by valid data. Instead, for any pixel that is invalid (lacks data), dem_mosaic will search for valid pixels within the specified search radius. If the percentage of valid to total number of found pixels is no less than the specified value, the invalid pixel will be filled with the weighted average of the valid pixel values, with the weight given as:

\[\frac{1}{d^p + 1}\]

where \(d\) is the distance from the invalid to the valid pixel to borrow the value from, and \(p\) is given by --fill-power.

This process will be repeated the specified number of times, with the valid portion of the DEM growing each time.

This method will also grow the DEM outwards, not just within a hole.

This command will become very slow for large --fill-search-radius. It is suggested to increase --fill-num-passes instead.

It is suggested to blur a little the obtained DEM, such as:

dem_mosaic --dem-blur-sigma 2 filled.tif -o blurred.tif

To preserve as much as possible the input DEM values in the produced DEM, except a small transition area at the boundary, run:

dem_mosaic --priority-blending-length 20 \
  input.tif blurred.tif -o output.tif

16.19.3. Usage

dem_mosaic [options] <dem files> -o output_file_prefix

or:

dem_mosaic [options] -l dem_files_list.txt -o output_file_prefix

16.19.4. Command-line options

-l, --dem-list-file <string>

Text file listing the DEM files to mosaic, one per line.

-o, --output-prefix <string>

Specify the output prefix. One or more tiles will be written with this prefix. Alternatively, an exact output file can be specified, with a .tif extension.

--tile-size <integer (default: 1000000)>

The maximum size of output DEM tile files to write, in pixels.

--tile-index <integer>

The index of the tile to save (starting from zero). When this program is invoked, it will print out how many tiles are there. Default: save all tiles.

--tile-list <string>

List of tile indices (in quotes) to save. A tile index starts from 0.

--priority-blending-length <integer (default: 0)>

If positive, keep unmodified values from the earliest available DEM except a band this wide measured in pixels inward of its boundary where blending with subsequent DEMs will happen.

--tr <double>

Output grid size, that is, the DEM resolution in target georeferenced units per pixel. Default: use the same resolution as the first DEM to be mosaicked.

--t_srs <string>

Specify the output projection as a GDAL projection string (WKT, GeoJSON, or PROJ.4). If not provided, use the one from the first DEM to be mosaicked.

--t_projwin <double double double double>

Limit the mosaic to this region, with the corners given in georeferenced coordinates (xmin ymin xmax ymax). Max is exclusive. See the --tap option if desired to apply addition adjustments to this extent.

--tap

Let the output grid be at integer multiples of the grid size (like the default behavior of point2dem and mapproject, and gdalwarp when invoked with -tap, though the latter does not have the half-a-pixel extra extent this tool has). If this option is not set, the input grids determine the output grid.

--first

Keep the first encountered DEM value (in the input order).

--last

Keep the last encountered DEM value (in the input order).

--min

Keep the smallest encountered DEM value.

--max

Keep the largest encountered DEM value.

--mean

Find the mean DEM value.

--stddev

Find the standard deviation of DEM values.

--median

Find the median DEM value (this can be memory-intensive, fewer threads are suggested).

--nmad

Find the normalized median absolute deviation DEM value (this can be memory-intensive, fewer threads are suggested).

--count

Each pixel is set to the number of valid DEM heights at that pixel.

--hole-fill-length <integer (default: 0)>

Maximum dimensions of a hole in the DEM to fill, in pixels. See also --fill-search-radius.

--fill-search-radius <double (default: 0.0)>

Fill an invalid pixel with a weighted average of pixel values within this radius in pixels. The weight is \(1/(d^p + 1)\), where the distance is measured in pixels. See an example in Section 16.19.2. See also --fill-power, --fill-percent and --fill-num-passes.

--fill-power <double (default: 8.0)>

Power exponent to use when filling nodata values with --fill-search-radius.

--fill-percent <double (default: 10.0)>

Fill an invalid pixel using weighted values of neighbors only if the percentage of valid pixels within the radius given by --fill-search-radius is at least this.

--fill-num-passes <integer (default: 0)>

Fill invalid values using --fill-search-radius this many times.

--erode-length <integer (default: 0)>

Erode the DEM by this many pixels at boundary.

--georef-tile-size <double>

Set the tile size in georeferenced (projected) units (e.g., degrees or meters).

--output-nodata-value <double>

No-data value to use on output. Default: use the one from the first DEM to be mosaicked.

--ot <string (default: Float32)>

Output data type. Supported types: Byte, UInt16, Int16, UInt32, Int32, Float32. If the output type is a kind of integer, values are rounded and then clamped to the limits of that type.

--weights-blur-sigma <double (default: 5.0)>

The standard deviation of the Gaussian used to blur the weights. Higher value results in smoother weights and blending. Set to 0 to not use blurring.

--weights-exponent <float (default: 2.0)>

The weights used to blend the DEMs should increase away from the boundary as a power with this exponent. Higher values will result in smoother but faster-growing weights.

--use-centerline-weights

Compute weights based on a DEM centerline algorithm. Produces smoother weights if the input DEMs don’t have holes or complicated boundary.

--dem-blur-sigma <double (default: 0.0)>

Blur the DEM using a Gaussian with this value of sigma. A larger value will blur more. Default: No blur.

--extra-crop-length <integer (default: 200)>

Crop the DEMs this far from the current tile (measured in pixels) before blending them (a small value may result in artifacts).

--nodata-threshold <float>

Values no larger than this number will be interpreted as no-data.

--force-projwin

Make the output mosaic fill precisely the specified projwin, by padding it if necessary and aligning the output grid to the region.

--save-dem-weight <integer>

Save the weight image that tracks how much the input DEM with given index contributed to the output mosaic at each pixel (smallest index is 0).

--save-index-map

For each output pixel, save the index of the input DEM it came from (applicable only for --first, --last, --min, --max, --median, and --nmad). A text file with the index assigned to each input DEM is saved as well.

--threads <integer (default: 0)>

Select the number of threads to use for each process. If 0, use the value in ~/.vwrc.

--tif-tile-size <integer (default: 256 256)>

The dimensions of each block in the output image.

--cache-size-mb <integer (default = 1024)>

Set the system cache size, in MB.

--no-bigtiff

Tell GDAL to not create bigtiffs.

--tif-compress <None|LZW|Deflate|Packbits (default: LZW)>

TIFF compression method.

-v, --version

Display the version of software.

-h, --help

Display this help message.