10.152. Write Avizo Uniform Coordinate

Group (Subgroup)

IO (Output)

Description

This filter writes an Image Geometry and its Cell FeatureIds array to a file that can be read by Avizo. Avizo is a commercial 3D visualization and analysis package. Its native data format is AmiraMesh, a header-plus-data file (commonly given an .am extension).

The filter requires two inputs: an Image Geometry, and an Int32 FeatureIds Cell Data Array that labels which Feature (for example, which grain) each cell belongs to. The FeatureIds values are produced earlier in the pipeline by a segmentation filter such as Segment Features (Scalar); this filter does not compute them. If no valid FeatureIds array is supplied, the filter will not execute.

The data is written in the uniform-coordinate form: the file records a single uniform spacing together with the grid’s bounding box (minimum and maximum X, Y, and Z), rather than listing per-axis coordinate values. This is the compact counterpart to the Write Avizo Rectilinear Coordinate filter, which writes explicit per-axis coordinate arrays. Use the uniform variant when the grid has uniform spacing (the usual case for an Image Geometry).

The Write Binary File parameter selects the on-disk encoding: false (the default) writes the data section as ASCII text, while true writes it in little-endian binary, producing smaller files.

Units caveat: the AmiraMesh header always records the coordinate units as microns, regardless of the actual units stored on the input Image Geometry. If the geometry uses different units, adjust them in Avizo after import.

Example AmiraMesh Header

# AmiraMesh BINARY-LITTLE-ENDIAN 2.1
# Dimensions in x-, y-, and z-direction
define Lattice
define Coordinates
Parameters {
    DREAM3DParams {
        Author "DREAM3D",
        DateTime "Mon Jun 1 10:01:14 2015"
    }
    Units {
        Coordinates "microns"
    }
    Content "int, uniform coordinates",
    # Bounding Box is xmin xmax ymin ymax zmin zmax
    BoundingBox 0 64 0 64 0 64,
    CoordType "uniform"
}
Lattice { int FeatureIds } = @1
# Data section follows

Required Input Sources

Image Geometry – the geometry whose dimensions and bounding box are written.
Cell Feature Ids – an Int32 per-cell label array, produced by a segmentation filter such as Segment Features (Scalar).

Input Parameter(s)

Parameter Name	Parameter Type	Parameter Notes	Description
Output File	FileSystemPath		Amira Mesh .am file created
Write Binary File	Bool		Whether or not to write the output file as binary
Image Geometry	Geometry Selection	Image	The path to the input image geometry
Cell Feature Ids	Array Selection	Allowed Types: int32 Comp. Shape: 1	Data Array that specifies to which Feature each Element belongs
Units	String		The units of the data

Example Pipelines

License & Copyright

Please see the description file distributed with this Plugin

DREAM3D-NX Help

If you need help, need to file a bug report or want to request a new feature, please head over to the DREAM3DNX-Issues GitHub site where the community of DREAM3D-NX users can help answer your questions.