NAME
i.segment.gsoc - Outputs a single segmented map (raster) based on input values in an image group.
KEYWORDS
imagery,
segmentation
SYNOPSIS
i.segment.gsoc
i.segment.gsoc --help
i.segment.gsoc [-tdwfl] group=name output=name threshold=float method=string similarity=string minsize=integer radioweight=float smoothweight=float [seeds=name] [bounds=name] [endt=integer] [final_mean=name] [--overwrite] [--help] [--verbose] [--quiet] [--ui]
Flags:
- -t
- Estimate a threshold based on input image group and exit.
- -d
- Use 8 neighbors (3x3 neighborhood) instead of the default 4 neighbors for each pixel.
- -w
- Weighted input, don't perform the default scaling of input maps.
- -f
- Final forced merge only (skip the growing portion of the algorithm.
- -l
- segments are limited to be included in only one merge per pass
- --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
Parameters:
- group=name [required]
- Name of input imagery group
- output=name [required]
- Name for output raster map
- threshold=float [required]
- Similarity threshold.
- method=string [required]
- Segmentation method.
- Options: region_growing
- Default: region_growing
- similarity=string [required]
- Similarity calculation method.
- Options: euclidean, manhattan
- Default: euclidean
- minsize=integer [required]
- Minimum number of cells in a segment.
- The final iteration will ignore the threshold for any segments with fewer pixels.
- Options: 1-100000
- Default: 1
- radioweight=float [required]
- Importance of radiometric (input raseters) values relative to shape
- Options: 0-1
- Default: 0.9
- smoothweight=float [required]
- Importance of smoothness relative to compactness
- Options: 0-1
- Default: 0.5
- seeds=name
- Optional raster map with starting seeds.
- Pixel values with positive integers are used as starting seeds.
- bounds=name
- Optional bounding/constraining raster map
- Pixels with the same integer value will be segmented independent of the others.
- endt=integer
- Maximum number of passes (time steps) to complete.
- Default: 1000
- final_mean=name
- Save the final mean values for the first band in the imagery group.
Image segmentation is the process of grouping similar pixels into
unique segments. Boundary and region based algorithms are described
in the literature, currently a region growing and merging algorithm
is implemented. Each grouping (usually refered to as objects or
segments) found during the segmentation process is given a unique ID
and is a collection of contiguous pixels meeting some criteria.
(Note the contrast with image classification, where continuity and
spatial characteristics are not important, but rather only the
spectral similarity.) The results can be useful on their own, or
used as a preprocessing step for image classification. The
segmentation preprocessing step can reduce noise and speed up the
classification.
NOTES
This segmentation algorithm sequentially examines all current
segments in the map. The similarity between the current segment and
each of its neighbors is calculated according to the given distance
formula. Segments will be merged if they meet a number of criteria,
including: 1. The pair is mutually most similar to each other (the
similarity distance will be smaller then all other neighbors), and
2. The similarity must be lower then the input threshold. All
segments are checked once per pass. The process is repeated until
no merges are made during a complete pass.
The similarity between segments and unmerged pixels is used to
determine which are merged. The Euclidean version uses the
radiometric distance between the two segments and also the shape
characteristics. The Manhatten calculations currently only uses only
the radiometric distance between the two segments, but eventually
shape characteristics will be included as well. NOTE:
Closer/smaller distances mean a lower value for the similarity
indicates a closer match, with a similarity score of zero for
identical pixels.
During normal processing, merges are only allowed when the
similarity between two segments is lower then the calculated
threshold value. During the final pass, however, if a minimum
segment size of 2 or larger is given with the minsize
parameter, segments with a smaller pixel count will be merged with
their most similar neighbor even if the similarity is greater then
the threshold.
Unless the -w flag for weighted data is used, the threshold
should be set by the user between 0 and 1.0. A threshold of 0 would
allow only identical valued pixels to be merged, while a threshold
of 1 would allow everything to be merged.
The threshold will be multiplied by the number of rasters included
in the image group. This will allow the same threshold to achieve
similar segmentation results when the number of rasters in the image
group varies.
The -t flag will estimate the threshold, it is calculated at 3% of
the range of data in the imagery group. Initial empirical tests
indicate threshold values of 1% to 5% are reasonable places to start.
Calculation Formulas
Both Euclidean and Manhattan distances use the normal definition,
considering each raster in the image group as a dimension.
Furthermore, the Euclidean calculation also takes into account the
shape characteristics of the segments. The normal distances are
multiplied by the input radiometric weight. Next an additional
contribution is added: (1-radioweight) * {smoothness * smoothness
weight + compactness * (1-smoothness weight)}, where compactness =
the Perimeter Length / sqrt( Area ) and smoothness = Perimeter
Length / the Bounding Box. The perimeter length is estimated as the
number of pixel sides the segment has.
The seeds map can be used to provide either seed pixels (random or
selected points from which to start the segmentation process) or
seed segments (results of previous segmentations or
classifications). The different approaches are automatically
detected by the program: any pixels that have identical seed values
and are contiguous will be lumped into a single segment ID.
It is expected that the minsize will be set to 1 if a seed
map is used, but the program will allow other values to be used. If
both options are used, the final iteration that ignores the
threshold also will ignore the seed map and force merges for all
pixels (not just segments that have grown/merged from the seeds).
For the region growing algorithm without starting seeds, each pixel
is sequentially numbered. The current limit with CELL storage is 2
billion starting segment ID's. If the initial map has a larger
number of non-null pixels, there are two workarounds:
1. Use starting seed pixels. (Maximum 2 billion pixels can be
labeled with positive integers.)
2. Use starting seed segments. (By initial classification or other
methods.)
Boundary constraints limit the adjacency of pixels and segments.
Each unique value present in the
bounds raster are
considered as a MASK. Thus no segments in the final segmentated map
will cross a boundary, even if their spectral data is very similar.
To reduce the salt and pepper affect, a
minsize greater
than 1 will add one additional pass to the processing. During the
final pass, the threshold is ignored for any segments smaller then
the set size, thus forcing very small segments to merge with their
most similar neighbor.
This example uses the ortho photograph included in the NC Sample
Dataset. Set up an imagery group:
i.group group=ortho_group input=ortho_2001_t792_1m@PERMANENT
Because the segmentation process is computationally expensive,
start with a small processing area to confirm if the segmentation
results meet your requirements. Some manual adjustment of the
threshold may be required.
g.region raster=ortho_2001_t792_1m@PERMANENT n=220400 s=220200 e=639000 w=638800
Try out a first threshold and check the results.
i.segment -w -l group=ortho_group output=ortho_segs threshold=4 \
method=region_growing
From a visual inspection, it seems this results in oversegmentation.
Increasing the threshold:
i.segment -w -l --overwrite group=ortho_group output=ortho_segs \
threshold=10 method=region_growing
This looks better. There is some noise in the image, lets next force
all segments smaller then 5 pixels to be merged into their most similar
neighbor (even if they are less similar then required by our
threshold):
i.segment -w -l --overwrite group=ortho_group output=ortho_segs \
threshold=10 method=region_growing minsize=5
Each of these segmentation steps took less then 1 minute on a decent
machine. Now that we are satisfied with the settings, we'll process
the entire image:
g.region raster=ortho_2001_t792_1m@PERMANENT
i.segment -w -l --overwrite group=ortho_group output=ortho_segs \
threshold=10 method=region_growing minsize=5 endt=5000
Processing the entire ortho image (over 9 million pixels) took about
a day.
- Further testing of the shape characteristics (smoothness,
compactness), if it looks good it should be added to the Manhatten
option.
in progress
- Malahanobis distance for the similarity calculation.
- Improve the optional output from this module, or better yet, add a
module for i.segment.metrics.
- Providing updates to i.maxlik to ensure the segmentation output can
be used as input for the existing classification functionality.
- Integration/workflow for r.fuzzy.
- User input for how much RAM can be used.
- Check input map type(s), currently storing in DCELL sized SEG file,
could reduce this dynamically depending on input map time. (Could only
reduce to FCELL, since will be storing mean we can't use CELL. Might
not be worth the added code complexity.)
If the seeds map is used to give starting seed segments, the segments
are renumbered starting from 1. There is a chance a segment could be
renumbered to a seed value that has not yet been processed. If they
happen to be adjacent, they would be merged. (Possible fixes: a. use
a processing flag to make sure the pixels hasn't been previously used,
or b. use negative segment ID's as a placeholder and negate all values
after the seed map has been processed.)
REFERENCES
This project was first developed during GSoC 2012. Project
documentation, Image Segmentation references, and other information
is at the
project wiki.
Information about classification in
GRASS GIS is also available on the wiki.
i.group,
i.maxlik,
r.fuzzy,
i.smap,
r.seg (Addon)
Eric Momsen - North Dakota State University
GSoC mentor: Markus Metz
SOURCE CODE
Available at:
i.segment.gsoc source code
(history)
Latest change: Thursday Aug 15 15:27:16 2024 in commit: a0e37beaf0ce8a4cc6ec615b6d3d40e39f9d725f
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GRASS Development Team,
GRASS GIS 8.4.1dev Reference Manual