Inherit parameters from previously quantified maps
YASUMOTO Atsushi
2021-04-05
Source:vignettes/parameterize.Rmd
parameterize.RmdIntroduction
This document introduces a way to quantify X-ray maps without quantitatively analyzed spots by inheriting parameters from a previously quantified X-ray map (See figure below).
Requirements
-
qntmap 0.3.2or later - Referencial quantified maps from a single area.
- The maps must be constructed by
quantify(saving = TRUE)underqntmap 0.3.2or later. - To construct a referencial maps, read “Get started”.
- The maps must be constructed by
- X-ray maps to be quantified.
- The new maps must be analyzed under the same conditions to the reference maps.
- The new maps must comprise mineral assemblage which is a subset of the reference maps.
Instructions
Read X-ray mapping data to be quantified
xmap <- read_xmap(".map/2 for example")Cluster analysis
Initialize cluster centers
Suppose available quantified maps are constructed by following “Get started”, centers_initial0.csv is available as well. Read the csv file by following codes.
centers <- read.csv("example/centers_initial0.csv")
centers| phase | Si | Mg |
|---|---|---|
| Ol | 4263.8 | 5722.45 |
| Qtz | 10002.0 | 0.00 |
The above is a example format of initial centers given by sample data introduced in “Get started”. Edit the csv file manually if initial centers require modifications, or if there are any phase abscent in new maps to be quantified.
Run cluster analysis
cluster <- cluster_xmap(xmap, centers)Quantification
When available quantified mapes are compsoed by quantify() function, parameters.csv is saved in the qntmap directory within the directory storing X-ray mapping data. Specify a file path of parameters.csv as fix parameter of quantify() function.
quantify(xmap = xmap, qnt = NULL, cluster = cluster, fix = "example/qntmap/parameters.csv")Note that qnt paramter is ignored when fix parameter is specified.