Value-reading and basic geometrical operations represent the core of any data processing program. Gwyddion offers a wide set of functions for data scaling, rotation, resampling or profile extraction. This section describes these simple but essential functions.
Within basic modules it is possible to perform the following operations with 2D data field:
Tool Read Value offers more value reading possibilities: it displays coordinates and values of the last point of the data window the mouse button was pressed. It can average the value from a circular neighbourhood around the selected point, this is controlled by option Averaging radius. When the radius is 1, the value of a single pixel is displayed (as the simplest method does). Button shifts the surface to make the current z the new zero level.
Read Value can also display the inclination of the local facet. Averaging radius again determines the radius of the area to use for the plane fit.
In all Gwyddion tools, facet and plane inclinations are displayed as the spherical angles (ϑ, φ) of the plane normal vector.
Angle ϑ is the angle between the upward direction and the normal, this means that ϑ = 0 for horizontal facets and it increases with the slope. It is always positive.
Angle φ is the counter-clockwise measured angle between axis x and the projection of the normal to the xy plane, as displayed on the following figure. For facets it means φ corresponds to the downward direction of the facet.
Distances and differences can be measured with the Distance tool. It displays the horizontal (Δx), vertical (Δy) and total planar (R) distances; the azimuth φ (measured identically to inclination φ ) and the endpoint value difference Δz for a set of lines selected on the data.
The distances can be copied to the clipboard or saved to a text file using the buttons below the list.
The profile extraction tool can be accessed from the toolbox. You can use mouse to draw several profiles in the image and they can be further moved and adjusted. The dialog includes a live profile graph preview. Profiles can be of different “thickness” which means that more neighbour data perpendicular to profile direction are used for evaluation of one profile point for thicker profiles. This can be very useful for noise suppression while measuring regular objects.
After profiles are chosen, they can be extracted to graphs (separate or grouped in one Graph window) that can be further analysed using Graph functions.
The profile curve is constructed from data sampled at regular intervals along the selected line. Values in points that do not lie exactly at pixel centres (which normally occurs for oblique lines) are interpolated using the chosen interpolation mode. Unless an explicit number of samples to take is set using the Fix res. option, the number of samples corresponds to the line length in pixels. This means that for purely horizontal or purely vertical lines no interpolation occurs.
It is also possible to extract radial profiles, i.e. angularly averaged shapes of symmetrical surface features, by selecting the Radial profiles check box. In this case the abscissa of the extracted graph is the distance from the centre instead of the distance along the line. The origin is in the centre of the selected line.
Although the line can be adjusted manually, finding the best centre for the radial profile manually may be difficult. Therefore, the tool can perform the precise location of the best centre itself. You only need to select the line approximately and then pressto adjust the currently edited line or to adjust all lines. The lines will be shifted slightly to minimise the differences between line profiles taken in different directions from the centre.
Function → → creates volume data from an image. The height field is interpreted as the surface of a solid object, as usual in AFM. Voxels below the surface (inside the material) are filled with 1s while voxels above the surface (outside) are filled with 0s. The z-coordinate of the volume data therefore corresponds to the image values, while the volume data values are unitless.
Function → → creates volume data from a sequence of images. All images in the file must have the same dimensions. They are then treated as planes in the volume data that are created by stacking the images. The z-coordinate of the volume data therefore corresponds to the stack index (and can be specified in the dialogue), while the volume data values have the same units as the image data.
Function → → creates XYZ data from an image. Each image pixel corresponds to one point in the created XYZ data. Therefore, the xy coordinates thus form a regular grid and all units are the same as for the image.