Presentations can be used to show the height field in another way than as a false color map of the heights, for instance with shading or with highlighted edges. It is also possible to superimpose an arbitrary data field over another one as the presentation.
Note the superimposed presentation is really only a presentation, it is never used for calculations. In all data processing functions or tools the results are always computed from the original underlying data. Since presentations can be computationaly intensive to calculate, they are not automatically updated when the underlying data change. The various presentations available are described in section Presentations.
The presence of presentation over the data is indicated by flag P in the data browser and also by the empty false color map ruler on the right side of the data window that does not display any ticks nor the minimum and maximum value.
Masks are used for special areal selections, e.g. grains, defects or factes with certain orientation. Masks can have any shape and within the data window and they are visualized by a color overlayed over the data. The mask color and opacity can be changed in the right-click context menu of the data window.
Since grain marking is the most common use of masks, several functions that operate on marked areas are called “grain” functions, e.g. Grain Statistics. Also, a contignuous part of mask is sometimes called grain in this guide. However, since a mask does not bear any information how it was created all mask functions can be used with masks of any origin.
Visualization of masks and presentations. If you look from above they can be imagined to be stacked as in the picture.
Both masks and presentations can be removed from the data by functions in the right-click menu of the data window, or with keyboard shortcuts.
Data in default false color representation (left), with superimposed mask visualized with a red color (centre) and with shading presentation (right).
The mask-related functions can be divided into three main groups:
Masks are created by various types of marking functions, namely grain marking functions (Mark by Threshold, Mark by Watershed), defect marking functions (Mask of Outliers, Mark Scars) and feature marking functions (Mask by Correlation, Facet Analysis, Certainty Map). In addition, some general mask editting functions provide means to create masks from scratch.
Masks are also used to mark invalid pixels in files imported from formats that distinguish between valid and invalid pixels since Gwyddion does not have a concept of invalid pixels.
In general, the mask-covered area is considered to be the area of interest, i.e. the area to operate on. This applies namely to statistical functions such as the Statstical Quantities tool. Function Remove Data Under Mask replaces the data under mask, while the Remove Grains tool can perform such replacement for individual grains. There are several functions for the examination of grain properties, see section Grain Statstics.
Some functions ask whether to consider the area under mask included or excluded (or ignore the mask), namely leveling functions. Such choice is offered only if a mask is present on the data.
A few basic mask operations, such as inversion or complete removal, are available in Remove Grains tool and Remove by Threshold that provide different means to remove parts of the mask, as well as Mask Editor tool and Mark With focused on general mask editting.
→ menu. More advanced functions include the grain-orientedThe Mask Editor is the basic mask modification tool. It provides two groups of functions: editing of the mask by drawing shapes directly in the data window and global operations with the mask such as inversion or growing and shrinking. The drawing operations are controlled by the buttons in the Editor group.
Buttons in the Mode row select how the shape drawn in the data window will modify the mask:
The mask is set to the drawn shape, discarding any mask already present.
The mask is extended by the drawn shape (if there is no mask yet a mask is created).
The drawn shape is cut out from the mask This function has no effect if there is no mask.
The mask is set to the intersection of the drawn shape and the already present mask. This function has no effect if there is no mask.
Buttons in the Shape row control which shape is drawn on the mask. The choices include rectangles, ellipses and thin lines.
The basic global operation with masks, i.e. inversion, removal and filling the entire data field area with a mask are available in the Actions row. Additional operations include:
Extends the mask by Amount pixels on each side. More precisely, the mask is extended by one pixel on each side and this is repeated Amount times.
Normally, growing does not distinguish between individual parts of the mask. Parts that grow so much that they touch therefore merge. This can be prevented by Prevent grain merging by growing which makes individual parts of the mask stop growing once there is only one-pixel space between them.
Reduces the mask by Amount pixels from each side. More precisely, the mask is reduced by one pixel from each side and this is repeated Amount times.
The reduction may or may not occur from the data field borders. This is controlled by the Shrink from border check box.
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Mark With can create or modify masks using another mask or data of the same dimensions. The operations that can be applied to the current mask are the same as in the Mask Editor tool: creation, union, subtraction and intersection. The source of the other mask can be one of the following:
This is the simplest case, a mask can be combined with another mask using the specified logical operations.
In the Data mode, another height field is used as the other mask source. The mask consists of pixels within a range of heights, specified as relative values within the total range. To use pixels outside a certain range for the masking, set the upper bound to a smaller value than the lower bound.
The Presentation mode differs from Data mode only in that a presentation is used instead of the data.
This is an exception to the rule stating that presentations are never used for further processing. Sometimes it can be useful to mark, for instance, edges found on the data even though the corresponding presentation visualizes a quantity weird from the physical point of view.