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.
| | Spot | Map | Comment | |:---------------------|-------:|---------:|:---------------------------------| | Acceralating Voltage | 15 kV | 15 kV | Must be same in spot and map | | Probe diameter | 3 μm | 20 μm | Must be smaller in spot than map | | Probe current | 10 nA | 100 nA | | | Peak dwell | 10 sec | 120 msec | | | Background dwell | 5 sec | NA | No need to analyze in map |
.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.
library(qntmap)
qntmap()
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 .
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