SAM-class: Sam Prediction

In uFTIR: Process and Analyze Agilent Cary 620 FTIR Microscope Images

Description

The class holds the resuls of the Spectral Angle Mapping algorithm and it originates by a call to tile_sam or to mosaic_compose. It has three slots with congruent cubes. Each cube has its first two dimensions equal to the FPA size of the uFTIR Microscope image processed and the third dimension equal to the number of substances in the SpectralReference passed when calling tile_sam or mosaic_sam. This class have methods to plot, summarize, and extract the readings of pixel matching a given SpectralReference substance. You can use the generics plot, summary, and get_profile but beware, you might have to provide extra arguments! (so, please don't see only the generic but the method for this class, see the section see also)

The sam object can be postprocessed by calling smooth_sam and/or clipped to a given extent by calling clipper (currently only circular extents are supported).

Value

An S4 object of class SAM

Slots

raw_sam

a cube -array-. The numeric score for each SpectralReference substance passed by the call (slices), for each pixel of the FPA array of the Tile (rows and cols).

substances

a cube -array-. The slices of the cube hold the substances (as number) of the SpectralReference object passed when calling tile_sam or mosaic_sam. The substance number are sorted in a decreacing order. In this way, the first slide is the best match, the second the second-best, and so on according to the Spectral Angle Mapping algorithm.

clusters

a cube -array-. Equivalent to the cube in the substances slot but instead of a substance number it has per ech slice the cluster number that corresponds to the clusterlist slot of the SpectralReference object.

See Also

plot_tile summary_sam get_profile_tile get_profile_sinfo

Examples

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uFTIR documentation built on Oct. 25, 2021, 9:08 a.m.