OOF2: The Manual
Microstructure is the fundamental object in OOF2, just like a
document is the fundamental object in a word processor. A
Microstructure (with a capital M) is the
computer's representation of a physical microstructure (with a
small m). Before doing anything else in
OOF2 you must create a
Microstructure. Because OOF2 is designed to
work on images, and images are usually rectangular,
must be rectangular.
Just as photographs, when digitized, are divided into pixels, a
Microstructure is also divided into pixels. A pixel is the smallest
component of a
Microstructure that can be manipulated by OOF2. The
Microstructure contains arrays of data describing each pixel, such as
Material has been assigned to it, and what Pixel
Groups it belongs to.
Microstructure has two sizes: a physical size and a pixel size.
The physical size is the size of the real
microstructure that the
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
Microstructure might be divided into
The fact that
Microstructures have two sizes means that they have two
coordinate systems. We can talk about a physical point (x,y)
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.
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.
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
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
has its own set of selected pixels.
Pixel Groups are a way of storing and retrieving named sets of
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
Skeletons, if the group is marked
Commands for manipulating Pixel Groups are discussed in OOF.PixelGroup.
Microstructures are usually created from
OOF2 is a digitized micrograph or other digital image.
Images live inside their
Microstructures -- that is, each
is associated with one and only one
Microstructure, and the size of
Image, in pixels, must be exactly the same as the size
Microstructure, however, may contain more than one
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
Image, they are actually being selected in the
containing the image. This means that all of the
Microstructure share the same pixel selection.
Commands for manipulating
Images are in OOF.Image. The corresponding GUI is
described in Section 3.3. Creating
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.
however, are not.
Orientation Maps assign an
to every pixel in a
Microstructure. They are usually obtained via
electron backscatter diffraction (EBSD). A
Microstructure can contain at most
Orientation Map, which must have a
pixel size and physical size that match the
(The easiest way to ensure this is to create the
Orientation Map, using the OOF.Microstructure.Create_From_OrientationMap_File
Commands for manipulating
Maps are found in the OOF.OrientationMap menu in the main
OOF2 menu bar.