OOF2: The Manual

Every Microstructure has two sizes: a physical size and a pixel size. The physical size is the size of the real microstructure that the Microstructure represents, 100μ×100μ, for example. (See Section 2.1.1.) The pixel size of a Microstructure is the number of pixels along its x and y dimensions. Note that pixels need not be square: a 100μ×100μ Microstructure might be divided into 100×160 pixels.

The fact that Microstructures have two sizes means that they have two coordinate systems. We can talk about a physical point (x,y) in the Microstructure, where x and y are given in physical units, (that is, in whatever units were used to specify the physical size) and the origin is at the lower left corner of the Microstructure. We can also talk about the position (i,j) of a pixel, where i and j are integers specifying the column and row of the pixel. Row 0 is the bottom row, and column 0 is the leftmost column.

	Note
	Most image processing programs label the pixels as if they were matrix elements -- pixel (i,j) is in the ith row from the top and the jth column from the left. OOF2 does not do this, choosing instead to use the same origin and axes for both the physical and pixel coordinate systems.

A third coordinate system, one that is rarely relevant in OOF2, is the screen pixel coordinate system. Microstructures and Images can be displayed on the computer screen at different resolutions. This doesn't change the number of pixels in the Microstructure, it only changes the number of screen pixels used to draw one Microstructure pixel. A few parameters to some of the display methods are in units of the screen pixel size, though.

Many operations on Microstructures work on sets of pixels. Each Microstructure keeps track of a set of currently selected pixels. There are tools to select pixels and to modify the selected set. Each Microstructure has its own set of selected pixels.

Commands for selecting pixels are in OOF.PixelSelection. The GUI tools for the same operations are described in Section 3.4 and Section 4.7.3.

The set of selected pixels is used in many other commands. For example, it is possible to assign a Material to the currently selected pixels, or to put the pixels into a pixel group.

Pixel Groups are a way of storing and retrieving named sets of pixels. The Microstructure maintains a list of Pixel Groups and keeps track of which pixels belong to which groups. Many operations that apply to the Pixel Selection also apply to Pixel Groups. Pixel Groups can also be used to distinguish pixels from one another when creating Skeletons, if the group is marked meshable.

Commands for manipulating Pixel Groups are discussed in OOF.PixelGroup.

Microstructures are usually created from Images. An Image in OOF2 is a digitized micrograph or other digital image. Images live inside their Microstructures -- that is, each Image is associated with one and only one Microstructure, and the size of the Image, in pixels, must be exactly the same as the size of its Microstructure^[4]. One Microstructure, however, may contain more than one Image or more than one version of the same image. This can be useful when different processing techniques are needed to bring out different features of a micrograph.

When pixels are selected in an Image, they are actually being selected in the Microstructure containing the image. This means that all of the Images in a Microstructure share the same pixel selection.

Commands for manipulating Images are in OOF.Image. The corresponding GUI is described in Section 3.3. Creating a Microstructure directly from an image file is discussed in Section 3.2 and OOF.Microstructure.Create_From_ImageFile.

It is often convenient to restrict the scope of OOF2 operations to a portion of a Microstructure, called the Active Area. Pixel selections, pixel group operations, and Skeleton modifications are all restricted to the current Active Area. Image and Mesh operations, however, are not.

By default, the Active Area is the whole Microstructure. Commands to manipulate the Active Area are described in Section 3.5 and OOF.ActiveArea.

Orientation Maps assign an Orientation to every pixel in a Microstructure. They are usually obtained via electron backscatter diffraction (EBSD). A Microstructure can contain at most one Orientation Map, which must have a pixel size and physical size that match the Microstructure's size. (The easiest way to ensure this is to create the Microstructure from the Orientation Map, using the OOF.Microstructure.Create_From_OrientationMap_File command.)

Commands for manipulating Orientation Maps are found in the OOF.OrientationMap menu in the main OOF2 menu bar.

The crystal orientations in an Orientation Map are not automatically used by Materials. They are only used if the Material contains an explicit OrientationMap Property.