**-m**- Interpret distance as map units, not number of cells
**-p**- Preserve original cell values
- By default original values are smoothed
**-w**- Just print the spatial weights matrix
**-u**- Just print estimated memory usage
**-s**- Single precision floating point output
**--overwrite**- Allow output files to overwrite existing files
**--help**- Print usage summary
**--verbose**- Verbose module output
**--quiet**- Quiet module output
**--ui**- Force launching GUI dialog

**input**=*name***[required]**- Raster map with data gaps to fill
**output**=*name***[required]**- Name of result output map
**uncertainty**=*name*- Name of uncertainty output map
**distance**=*value***[required]**- Distance threshold (default: in cells) for interpolation
- Default:
*3* **mode**=*name***[required]**- Statistic for interpolated cell values
- Options:
*wmean, mean, median, mode* - Default:
*wmean* **minimum**=*value*- Minimum input data value to include in interpolation
**maximum**=*value*- Maximum input data value to include in interpolation
**power**=*value***[required]**- Power coefficient for IDW interpolation
- Default:
*2.0* **cells**=*value***[required]**- Minimum number of data cells within search radius
- Default:
*8*

The *r.fill.gaps* module is capable of quickly filling small
data gaps in large and high-resolution raster maps. It's primary purpose
is to improve high-resolution, rasterized sensor data (such as Lidar
data). As a rule of thumb, there
should be at least as many data cells as there are "no data" (NULL) cells in
the input raster map. Several interpolation modes are available. By
default, all values of the input raster map will be replaced with
locally interpolated values in the output raster map. This is the
equivalent of running a low-pass smoothing filter on the interpolated
data and is often desirable, owing to noisy nature of high-resolution
sensor data. With dense data and small gaps, this should result in only slight
deviations from the original data and produce smooth output. Alternatively,
setting the **-p** flag will disable the low-pass filter and preserve
the original cell values.

Available gap filling modes:

- spatially weighted mean (default)
- simple mean
- simple median
- simple mode

The spatially weighted mean is equivalent to an Inverse Distance
Weighting (IDW;
see also *r.surf.idw*)
interpolation. The simple mean is equivalent to a simple low-pass filter.
Median and mode replacements can also be achieved using
*r.neighbors*.

Note that *r.fill.gaps* is highly optimized for fast processing
of large raster datasets with a small interpolation distance threshold
(i.e. closing small gaps). As a trade-off for speed and a small memory
foot print, some spatial accuracy is lost due to the rounding of the
distance threshold to the closest approximation in input raster cells
and the use of a matrix of precomputed weights at cell resolution (see
further down for details). Note also that processing time will increase
exponentially with higher distance settings. Cells outside the distance
threshold will not be interpolated, preserving the edges of the original data
extent.

This module is not well suited for interpolating sparse input data and
closing large gaps. For such purposes more appropriate
methods are available, such as
*v.surf.idw* or
*v.surf.rst*.

Applications where the properties of *r.fill.gaps* are
advantageous include the processing of high resolution, close range
scanning and remote sensing datasets. Such datasets commonly feature
densely spaced measurements that have some gaps after rasterization,
due to blind spots, instrument failures, and misalignments between the
GIS' raster cell grids and the original measurement locations. In these
cases, *r.fill.gaps* should typically be run using the "weighted
mean" (default) method and with a small distance setting (the default
is to use a search radius of just three cells).

The images below show a gradiometer dataset with gaps and its
interpolated equivalent, produced using the spatially weighted mean
operator (`mode="wmean"`).

In addition, *r.fill.gaps* can be useful for raster map
generalization. Often, this involves removing small clumps of
categorized cells and then filling the resulting data gaps without
"inventing" any new values. In such cases, the "mode" or "median"
interpolators should be used.

Note that proper handling of geodetic coordinates (lat/lon) and
distances is currently not implemented. For lat/lon data, the distance
should therefore be specified in cells and usage of
*r.fill.gaps* should be restricted to small areas to avoid large
inaccuracies that may arise from the different extents of cells along
the latitudinal and longitudinal axes.

Distances specified in map units (**-m** flag) will be approximated
as accurately as the current region's cell resolution settings allow.
The program will warn if the distance cannot be expressed as whole
cells at the current region's resolution. In such case, the number of
cells in the search window will be rounded up. Due to the rounding
effect introduced by using cells as spatial units, the actual maximum
distance considered by the interpolation may be up to half a cell
diagonal larger than the one specified by the user.

The interpolator type "wmean" uses a precomputed matrix of spatial
weights to speed up computation. This matrix can be examined (printed
to the screen) before running the interpolation, by setting the
**-w** flag. In mode "wmean", the **power** option has the usual
meaning in IDW: higher values mean that cell values in the neighborhood
lose their influence on the cell to be interpolated more rapidly with
increasing distance from the latter. Another way of explaining this
effect is to state that larger "power" settings result in more
localized interpolation, smaller ones in more globalized interpolation.
The default setting is `power=2.0`.

The interpolators "mean", "median" and "mode" are calculated from all cell values within the search radius. No spatial weighting is applied for these methods. The "mode" of the input data may not always be unique. In such case, the mode will be the smallest value with the highest frequency.

Often, input data will contain spurious extreme measurements (spikes,
outliers, noise) caused by the limits of device sensitivity, hardware
defects, environmental influences, etc. If the normal, valid range of
input data is known beforehand, then the **minimum** and
**maximum** options can be used to exclude those input cells that
have values below or above that range, respectively. This will prevent
the influence of spikes and outliers from spreading through the
interpolation.

Unless the **-p** (preserve) flag is given, data cells of the input
map will be replaced with interpolated values instead of preserving
them in the output. In modes "wmean" and "mean", this results in a
smoothing effect that includes the original data (see below)!

Besides the result of the interpolation/gap filling, a second output
map can be specified via the **uncertainty** option. The cell values
in this map represent a simple measure of how much uncertainty was
involved in interpolating each cell value of the primary output map,
with "0" being the lowest and "1" being the theoretic highest
uncertainty. Uncertainty is measured by summing up all cells in the
neighborhood (defined by the search radius **distance**) that
contain a value in the **input** map, multiplied by their weights,
and dividing the result by the sum of all weights in the neighborhood.
For `mode=wmean`, this means that interpolated output cells that
were computed from many nearby input cells have very low uncertainty
and vice versa. For all other modes, all weights in the neighborhood
are constant "1" and the uncertainty measure is a simple measure of how
many input data cells were present in the search window.

*
Effect of smoothing the original data: The top row shows a gap-filled surface computed from a rasterized Lidar point
cloud (using mode=wmean and power=2), and the derived slope, aspect,
and profile curvature maps. The smoothing effect is clearly visible.
The bottom row shows the effect of setting the -p flag: Preserving the original
cell values in the interpolated output produces and unsmoothed, noisy surface, and likewise
noisy derivative maps.
*

(Note that the effects of noisy data can also be avoided by using modules
that are not restricted to minimal kernel sizes. For example, aspect and other morphometric parameters can be computed
using the *r.param.scale* module
which operates with variable-size cell neighborhoods.)

The illustration below shows the precomputed weights matrix for a search distance of four cells from the center cell:

000.00 000.01 000.04 000.07 000.09 000.07 000.04 000.01 000.00 000.01 000.06 000.13 000.19 000.22 000.19 000.13 000.06 000.01 000.04 000.13 000.25 000.37 000.42 000.37 000.25 000.13 000.04 000.07 000.19 000.37 000.56 000.68 000.56 000.37 000.19 000.07 000.09 000.22 000.42 000.68 001.00 000.68 000.42 000.22 000.09 000.07 000.19 000.37 000.56 000.68 000.56 000.37 000.19 000.07 000.04 000.13 000.25 000.37 000.42 000.37 000.25 000.13 000.04 000.01 000.06 000.13 000.19 000.22 000.19 000.13 000.06 000.01 000.00 000.01 000.04 000.07 000.09 000.07 000.04 000.01 000.00Note that the weights in such a small window drop rapidly for the default setting of

If the distance is given in map units (flag `-m`), then the
search window can be modeled more accurately as a circle. The
illustration below shows the precomputed weights for a distance in map
units that is approximately equivalent to four cells from the center
cell:

...... ...... ...... 000.00 000.00 000.00 ...... ...... ...... ...... 000.00 000.02 000.06 000.09 000.06 000.02 000.00 ...... ...... 000.02 000.11 000.22 000.28 000.22 000.11 000.02 ...... 000.00 000.07 000.22 000.44 000.58 000.44 000.22 000.07 000.00 000.00 000.09 000.28 000.58 001.00 000.58 000.28 000.09 000.00 000.00 000.07 000.22 000.44 000.58 000.44 000.22 000.07 000.00 ...... 000.02 000.11 000.22 000.28 000.22 000.11 000.02 ...... ...... 000.00 000.02 000.06 000.09 000.06 000.02 000.00 ...... ...... ...... ...... 000.00 000.00 000.00 ...... ...... ......

When using a small search radius, **cells** must also be set to a
small value. Otherwise, there may not be enough cells with data within
the search radius to support interpolation.

If the distance is set to a relatively large value, processing time
will quickly approach and eventually exceed that of point-based
interpolation modules such as
*v.surf.rst*.

This module can handle cells with different X and Y resolutions. However, note that the weight matrix will be skewed in such cases, with higher weights occurring close to the center and along the axis with the higher resolution. This is because weights on the lower resolution axis are less accurately calculated. The skewing effect will be stronger if the difference between the X and Y axis resolution is greater and a larger "power" setting is chosen. This property of the weights matrix directly reflects the higher information density along the higher resolution axis.

Note on printing the weights matrix (using the **-w** flag): the
matrix cannot be printed if it is too large.

The memory estimate provided by the **-u** flag is a lower limit on
the amount of RAM that will be needed.

If the **-s** flag is set, floating point type output will be
saved as a "single precision" raster map, saving ~50% disk space
compared to the default "double precision" output.

r.fill.gaps input=measurements output=result dist=3.0 -m mode=wmean uncertainty=uncert_map

r.fill.gaps input=measurements output=result dist=10 mode=mean

r.fill.gaps input=categories output=result dist=100 -m mode=mode -p

r.in.lidar -e input=points.las output=density method=n resolution=5 class_filter=2

g.region -pa raster=density res=1

r.in.lidar input=points.las output=ground_raw method=mean class_filter=2

r.univar map=ground_raw

total null and non-null cells: 2340900 total null cells: 639184 ...Fill in the NULL cells using the default 3-cell search radius:

r.fill.gaps input=ground output=ground_filled uncertainty=uncertainty distance=3 mode=wmean power=2.0 cells=8

*
Binning of Lidar and resulting ground surface with filled gaps.
Note the remaining NULL cells (white) in the resulting ground surface.
These are areas with a lack of cells with values in close proximity.
*

Inverse Distance Weighting in Wikipedia

*Last changed: $Date$*

Available at: r.fill.gaps source code (history)

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