This package generates mass concentration maps and phase distribution maps based on X-ray mapping data and spot analysis data from EPMA.
See “How to” for a usage and Yasumoto et al. (2018) for implementations.
Current version supports data from JEOL-style EPMA.
Copy & paste a following command to R.
source("https://install-github.me/atusy/qntmap")
Details below.
Conversion is performed by utilizing spot analysis data as internal standards. Thus, spot analysis must be done prior to mapping.
.map/1
)..map
directory and .qnt
directoryThe exported data are stored in a directory named by .qnt
in most environments. If using JXA-8230, a directory’s name is {PROJECT}_{#}_QNT
where {PROJECT}
is name of a project’s name defined by user or “PROJECT” if undefined, and{#}
is a variable integer (e.g., PROJECT_0001_QNT
).
File name | Descriptions |
---|---|
.cnd/elemw.cnd or Pos_001/data001.qnt | Metadata including dwell time for peak and background, and relative positions of backgrounds. In some case, .cnd/elemw.qnt is incomplete or missing, and needs to be prepared manually (e.g., https://gist.github.com/atusy/f1577b67b8874c9e915941c0725d0e22). JXA-8230 lacks .cnd/elemw.cnd , but provides Pos_001/data/qnt . |
bgm.qnt | Minus-side background intensity |
bgp.qnt | Plus-side background intensity |
elem.qnt | Element names specified for matrix corrections (e.g., oxide or metal in ZAF) |
elint.qnt | Element names as is. |
mes.qnt | Probe current |
net.qnt | Net intensity |
peak.qnt | Peak intensity. This file is optional. If missing, peak intensity is calculated from net and background intensities. |
stg.qnt | Coordinates and comments |
wt.qnt | Mass concentrations wt |
The exported data are stored in a directory .map/{#}
where {#}
is a variable integer in most environments (e.g., .map/1
). If using JXA-8230, a directory name is {PROJECT}_{#1}_MAP_{#2}_csv
where {PROJECT}
is name of a project’s name defined by user or “PROJECT” if undefined, and{#1}
and {#2}
are variable integers (e.g., PROJECT_0001_MAP_0001_csv
).
File name | Descriptions |
---|---|
*_map.txt or data*.csv | ASCII converted mapping data (e.g., 1_map.txt, 2_map.txt,… or data001.csv, data002.csv, …) |
*.cnd | Analytical conditions: element name, dwell time, probe current, step size, pixel size, and coordinates. File names must corresponds to mapping data (e.g, 1_map.cnd, data001.cnd) |
*
indicates wild cards.
For data processing.
Follow instructions shown by running the following code.
As a result, phase identification result is saved in “clustering
” directory and mass concentration data as csv files in “qntmap
” directory both under the directory contaning mapping data.
Note that interactive mode has limited functions. Use manual mode for full functionality.
A work-flow is available with an example dataset at https://qntmap.atusy.net/articles/qntmap.html .