https://github.com/advancedphotonsource/xrf-maps
XRF-Maps is a C++ open source software package that implements these functions to provide a tool set for the analysis of XRF data sets
https://github.com/advancedphotonsource/xrf-maps
Last synced: about 2 months ago
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XRF-Maps is a C++ open source software package that implements these functions to provide a tool set for the analysis of XRF data sets
- Host: GitHub
- URL: https://github.com/advancedphotonsource/xrf-maps
- Owner: AdvancedPhotonSource
- License: other
- Created: 2016-09-08T20:23:21.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2026-05-01T13:58:12.000Z (about 2 months ago)
- Last Synced: 2026-05-01T15:32:11.879Z (about 2 months ago)
- Language: C++
- Homepage:
- Size: 5.61 MB
- Stars: 13
- Watchers: 6
- Forks: 14
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# XRF-Maps
X-ray fluorescence (XRF) imaging typically involves the creation and analysis of 3D data sets, where at each scan position a full energy dispersive x-ray spectrum is recorded. This allows one to later process the data in a variety of different approaches, e.g., by spectral region of interest (ROI) summation with or without background subtraction, principal component analysis, or fitting. XRF-Maps is a C++ open source software package that implements these functions to provide a tool set for the analysis of XRF data sets. It is based on the MAPS software http://www.aps.anl.gov/Xray_Science_Division/Xray_Microscopy_and_Imaging/Software_and_Tools/maps.html
# Compiling
## Requires
Visual Studio 2015 or greater (Windows build)
GCC 6.0 or greater (Linux build)
Cmake 3.5 or greater
## Libraries
HDF5 : https://www.hdfgroup.org/downloads/
NetCDF : http://www.unidata.ucar.edu/downloads/netcdf/index.jsp (Download http://www.unidata.ucar.edu/software/netcdf/docs/winbin.html)
Eigen : http://eigen.tuxfamily.org/index.php?title=Main_Page (submodule in src/support)
## Optional Libraries
QT : https://www.qt.io/download
ZeroMQ : http://zeromq.org/area:download
## Compile Default
1) git clone --recurse-submodules https://github.com/AdvancedPhotonSource/XRF-Maps.git
2) cd XRF-Maps
3) mkdir build
4) cd vcpkg
5) vcpkg set Linux
1) ./bootstrap-vcpkg.sh
2) ./vcpkg install hdf5 netcdf-c yaml-cpp cppzmq nlopt jsoncpp
6) vcpkg setup windows
1) .\bootstrap-vcpkg.bat
2) .\vcpkg install hdf5 netcdf-c yaml-cpp cppzmq nlopt jsoncpp --triplet x64-windows
7) cd ../build
8) cmake `-DCMAKE_TOOLCHAIN_FILE=../vcpkg/scripts/buildsystems/vcpkg.cmake -DBUILD_WITH_ZMQ=ON ..`
9) make
## Building optional features
### QT support
-DBUILD_WITH_QT=ON
### Streaming support with ZeroMQ
-DBUILD_WITH_ZMQ=ON
### Python bindings (NOTE: this may interfere with QT options if QT lib version is different than python qt lib version as with anaconda python)
-DBUILD_WITH_PYBIND11=ON
-DPYTHON_EXECUTABLE={path to python.exe if not found}
# Data Analysis
## General
Run from bin directory. The software looks for references one directory up ( ../references ).
```bash
Help:
Usage: xrf_maps [Options] --dir [dataset directory]
Options:
--nthreads : number of threads to use (default is all system threads)
--quantify-with : File to use as quantification standard
--detectors : Detectors to process, Defaults to 0,1,2,3 for 4 detector
--generate-avg-h5 : Generate .h5 file which is the average of all detectors .h50 - h.53 or range specified.
--add-v9layout : Generate .h5 file which has v9 layout able to open in IDL MAPS software.
--add-exchange : Add exchange group into hdf5 file with normalized data.
--export-csv : Export Integrated spec, fitted, background to csv file.
--update-theta : Update the theta dataset value using theta_pv_string as new pv string ref.
--update-amps ,: Updates upstream and downstream amps if they changed inbetween scans.
--update-quant-amps ,: Updates upstream and downstream amps for quantification if they changed inbetween scans.
--quick-and-dirty : Integrate the detector range into 1 spectra.
--optimize-fit-override-params : Integrate the 8 largest mda datasets and fit with multiple params.
1 = matrix batch fit
2 = batch fit without tails
3 = batch fit with tails
4 = batch fit with free E, everything else fixed
--optimizer : Choose which optimizer to use for --optimize-fit-override-params or matrix fit routine
Fitting Routines:
--fit comma seperated
roi : element energy region of interest
roi_plus : SVD method
nnls : Non-Negative Least Squares
tails : Fit with multiple parameters
matrix : Fit with locked parameters
Dataset:
--dir : Dataset directory
--files : Dataset files: comma (',') separated if multiple
Network:
--streamin [source ip] : Accept a ZMQ stream of spectra to process. Source ip defaults to localhost (must compile with -DBUILD_WITH_ZMQ option)
--streamout : Streams the analysis counts over a ZMQ stream (must compile with -DBUILD_WITH_ZMQ option)
Examples:
Perform roi and matrix analysis on the directory /data/dataset1
xrf_maps --fit roi,matrix --dir /data/dataset1
Perform roi and matrix analysis on the directory /data/dataset1 but only process scan1 and scan2
xrf_maps --fit roi,matrix --dir /data/dataset1 --files scan1.mda,scan2.mda
Perform roi, matrix, and nnls analysis on the directory /data/dataset1, use maps_standard.txt information for quantification
xrf_maps --fit roi,matrix,nnls --quantify-with maps_standard.txt --dir /data/dataset1
```