Segmentation - Segmentation

Performs segmentation of an image, and output either a raster or a vector file. In vector mode, large input datasets are supported.

Detailed description

This application allows one to perform various segmentation algorithms on a multispectral image.Available segmentation algorithms are two different versions of Mean-Shift segmentation algorithm (one being multi-threaded), simple pixel based connected components according to a user-defined criterion, and watershed from the gradient of the intensity (norm of spectral bands vector). The application has two different modes that affects the nature of its output.

In raster mode, the output of the application is a classical image of unique labels identifying the segmented regions. The labeled output can be passed to the ColorMapping application to render regions with contrasted colours. Please note that this mode loads the whole input image into memory, and as such can not handle large images.

To segment large data, one can use the vector mode. In this case, the output of the application is a vector file or database. The input image is split into tiles (whose size can be set using the tilesize parameter), and each tile is loaded, segmented with the chosen algorithm, vectorized, and written into the output file or database. This piece-wise behavior ensure that memory will never get overloaded, and that images of any size can be processed. There are few more options in the vector mode. The simplify option allows simplifying the geometry (i.e. remove nodes in polygons) according to a user-defined tolerance. The stitch option tries to stitch together the polygons corresponding to segmented region that may have been split by the tiling scheme.

Parameters

This section describes in details the parameters available for this application. Table [1] presents a summary of these parameters and the parameters keys to be used in command-line and programming languages. Application key is Segmentation .

[1]Table: Parameters table for Segmentation.
Parameter Key Parameter Name Parameter Type
in Input Image Input image
filter Segmentation algorithm Choices
filter meanshift Choice Mean-Shift
filter cc Choice Connected components
filter watershed Choice Watershed
filter mprofiles Choice Morphological profiles based segmentation
filter.meanshift.spatialr Spatial radius Int
filter.meanshift.ranger Range radius Float
filter.meanshift.thres Mode convergence threshold Float
filter.meanshift.maxiter Maximum number of iterations Int
filter.meanshift.minsize Minimum region size Int
filter.cc.expr Condition String
filter.watershed.threshold Depth Threshold Float
filter.watershed.level Flood Level Float
filter.mprofiles.size Profile Size Int
filter.mprofiles.start Initial radius Int
filter.mprofiles.step Radius step. Int
filter.mprofiles.sigma Threshold of the final decision rule Float
mode Processing mode Choices
mode vector Choice Tile-based large-scale segmentation with vector output
mode raster Choice Standard segmentation with labeled raster output
mode.vector.out Output vector file Output File name
mode.vector.outmode Writing mode for the output vector file Choices
mode.vector.outmode ulco Choice Update output vector file, only allow creating new layers
mode.vector.outmode ovw Choice Overwrite output vector file if existing.
mode.vector.outmode ulovw Choice Update output vector file, overwrite existing layer
mode.vector.outmode ulu Choice Update output vector file, update existing layer
mode.vector.inmask Mask Image Input image
mode.vector.neighbor 8-neighbor connectivity Boolean
mode.vector.stitch Stitch polygons Boolean
mode.vector.minsize Minimum object size Int
mode.vector.simplify Simplify polygons Float
mode.vector.layername Layer name String
mode.vector.fieldname Geometry index field name String
mode.vector.tilesize Tiles size Int
mode.vector.startlabel Starting geometry index Int
mode.vector.ogroptions OGR options for layer creation String list
mode.raster.out Output labeled image Output image
inxml Load otb application from xml file XML input parameters file
outxml Save otb application to xml file XML output parameters file

Input Image: The input image to segment.

Segmentation algorithm: Choice of segmentation algorithm (mean-shift by default). Available choices are:

  • Mean-Shift: OTB implementation of the Mean-Shift algorithm (multi-threaded).
  • Spatial radius: Spatial radius of the neighborhood.
  • Range radius: Range radius defining the radius (expressed in radiometry unit) in the multispectral space.
  • Mode convergence threshold: Algorithm iterative scheme will stop if mean-shift vector is below this threshold or if iteration number reached maximum number of iterations.
  • Maximum number of iterations: Algorithm iterative scheme will stop if convergence hasn’t been reached after the maximum number of iterations.
  • Minimum region size: Minimum size of a region (in pixel unit) in segmentation. Smaller clusters will be merged to the neighboring cluster with the closest radiometry. If set to 0 no pruning is done.
  • Connected components: Simple pixel-based connected-components algorithm with a user-defined connection condition.
  • Condition: User defined connection condition, written as a mathematical expression. Available variables are p(i)b(i), intensity_p(i) and distance (example of expression : distance < 10 ).
  • Watershed: The traditional watershed algorithm. The height function is the gradient magnitude of the amplitude (square root of the sum of squared bands).
  • Depth Threshold: Depth threshold Units in percentage of the maximum depth in the image.
  • Flood Level: flood level for generating the merge tree from the initial segmentation (between 0 and 1).
  • Morphological profiles based segmentation: Segmentation based on morphological profiles, as described in Martino Pesaresi and Jon Alti Benediktsson, Member, IEEE: A new approach for the morphological segmentation of high resolution satellite imagery. IEEE Transactions on geoscience and remote sensing, vol. 39, NO. 2, February 2001, p. 309-320.
  • Profile Size: Size of the profiles.
  • Initial radius: Initial radius of the structuring element (in pixels).
  • Radius step.: Radius step along the profile (in pixels).
  • Threshold of the final decision rule: Profiles values under the threshold will be ignored.

Processing mode: Choice of processing mode, either raster or large-scale. Available choices are:

  • Tile-based large-scale segmentation with vector output: In this mode, the application will output a vector file or database, and process the input image piecewise. This allows performing segmentation of very large images.
  • Output vector file: The output vector file or database (name can be anything understood by OGR).
  • Writing mode for the output vector file: This allows one to set the writing behaviour for the output vector file. Please note that the actual behaviour depends on the file format. Available choices are:
  • Update output vector file, only allow creating new layers: The output vector file is opened in update mode if existing. If the output layer already exists, the application stops, leaving it untouched.
  • Overwrite output vector file if existing.: If the output vector file already exists, it is completely destroyed (including all its layers) and recreated from scratch.
  • Update output vector file, overwrite existing layer: The output vector file is opened in update mode if existing. If the output layer already exists, it si completely destroyed and recreated from scratch.
  • Update output vector file, update existing layer: The output vector file is opened in update mode if existing. If the output layer already exists, the new geometries are appended to the layer.
  • Mask Image: Only pixels whose mask value is strictly positive will be segmented.
  • 8-neighbor connectivity: Activate 8-Neighborhood connectivity (default is 4).
  • Stitch polygons: Scan polygons on each side of tiles and stitch polygons which connect by more than one pixel.
  • Minimum object size: Objects whose size is below the minimum object size (area in pixels) will be ignored during vectorization.
  • Simplify polygons: Simplify polygons according to a given tolerance (in pixel). This option allows reducing the size of the output file or database.
  • Layer name: Name of the layer in the vector file or database (default is Layer).
  • Geometry index field name: Name of the field holding the geometry index in the output vector file or database.
  • Tiles size: User defined tiles size for tile-based segmentation. Optimal tile size is selected according to available RAM if null.
  • Starting geometry index: Starting value of the geometry index field.
  • OGR options for layer creation: A list of layer creation options in the form KEY=VALUE that will be passed directly to OGR without any validity checking. Options may depend on the file format, and can be found in OGR documentation.
  • Standard segmentation with labeled raster output: In this mode, the application will output a standard labeled raster. This mode can not handle large data.
  • Output labeled image: The output labeled image.

Load otb application from xml file: Load otb application from xml file.

Save otb application to xml file: Save otb application to xml file.

Examples

Example 1:

Example of use with vector mode and watershed segmentationTo run this example in command-line, use the following:

otbcli_Segmentation -in QB_Toulouse_Ortho_PAN.tif -mode vector -mode.vector.out SegmentationVector.sqlite -filter watershed

To run this example from Python, use the following code snippet:

#!/usr/bin/python

# Import the otb applications package
import otbApplication

# The following line creates an instance of the Segmentation application
Segmentation = otbApplication.Registry.CreateApplication("Segmentation")

# The following lines set all the application parameters:
Segmentation.SetParameterString("in", "QB_Toulouse_Ortho_PAN.tif")

Segmentation.SetParameterString("mode","vector")

Segmentation.SetParameterString("mode.vector.out", "SegmentationVector.sqlite")

Segmentation.SetParameterString("filter","watershed")

# The following line execute the application
Segmentation.ExecuteAndWriteOutput()
Example 2:

Example of use with raster mode and mean-shift segmentationTo run this example in command-line, use the following:

otbcli_Segmentation -in QB_Toulouse_Ortho_PAN.tif -mode raster -mode.raster.out SegmentationRaster.tif uint16 -filter meanshift

To run this example from Python, use the following code snippet:

#!/usr/bin/python

# Import the otb applications package
import otbApplication

# The following line creates an instance of the Segmentation application
Segmentation = otbApplication.Registry.CreateApplication("Segmentation")

# The following lines set all the application parameters:
Segmentation.SetParameterString("in", "QB_Toulouse_Ortho_PAN.tif")

Segmentation.SetParameterString("mode","raster")

Segmentation.SetParameterString("mode.raster.out", "SegmentationRaster.tif")
Segmentation.SetParameterOutputImagePixelType("mode.raster.out", 3)

Segmentation.SetParameterString("filter","meanshift")

# The following line execute the application
Segmentation.ExecuteAndWriteOutput()

Limitations

In raster mode, the application can not handle large input images. Stitching step of vector mode might become slow with very large input images. MeanShift filter results depends on the number of threads used. Watershed and multiscale geodesic morphology segmentation will be performed on the amplitude of the input image.

Authors

This application has been written by OTB-Team.

See Also

These additional resources can be useful for further information:

MeanShiftSegmentation