algodif 1.0.0__tar.gz

algodif-1.0.0/LICENSE

@@ -0,0 +1,201 @@
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algodif-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: algodif
+Version: 1.0.0
+Summary: Data processing algorithms for diffraction-based X-ray techniques
+Author-email: Nghia Vo <nvo@bnl.gov>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/algodif/algodif
+Project-URL: Documentation, https://algodif.readthedocs.io
+Project-URL: Source, https://github.com/algodif/algodif
+Keywords: Energy-dispersive X-ray diffraction,EDX detector calibration,Energy calibration,q-calibration,Peak detection,Peak matching,Tomography
+Classifier: Programming Language :: Python :: 3
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Natural Language :: English
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: h5py
+Requires-Dist: pillow
+Requires-Dist: matplotlib
+Requires-Dist: joblib
+Requires-Dist: xraydb
+Provides-Extra: gui
+Requires-Dist: pyvista; extra == "gui"
+Requires-Dist: pyvistaqt; extra == "gui"
+Requires-Dist: pyside6; extra == "gui"
+Provides-Extra: docs
+Requires-Dist: sphinx>=2; extra == "docs"
+Requires-Dist: sphinx_rtd_theme; extra == "docs"
+Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
+Dynamic: license-file
+
+# Algodif
+### Data processing (**ALGO**)rithms for (**DIF**)fraction-based X-ray techniques 
+
+Methods and software for calibrating multi-element energy-dispersive X-ray (EDX) detectors,
+processing and visualizing energy-dispersive X-ray diffraction tomography (EDDT) data acquired 
+at a hard X-ray synchrotron beamline.
+
+A detailed description is provided in the paper under review: "Algorithms and software tools for 
+energy-dispersive X-ray diffraction tomography," Nghia T. Vo, Zhong Zhong, and Michael Drakopoulos. 
+
+The core of this work is to address a problem: 
+given a list of measured data points not knowing unit, how to map that into a list of reference points 
+knowing unit. The challenge is that the number of measured data points is not the same as the number of 
+reference points, so there are many local minima in the mapping transformation.
+For X-ray diffraction techniques, it addresses the problem of how to calibrate an instrument using 
+the diffraction pattern or fluorescence spectrum of a known calibrant in a robust and automated fashion.
+
+Although the work was initially aimed at calibrating the HEX beamline instrument (the GeRM detector), 
+the methods and software can be applied to other instruments given standard diffraction patterns or spectra. 
+The specific GeRM geometry is helpful for determining initial guesses of optimizing methods. 
+However, the algorithms in the software are not restricted to the GeRM detector.
+
+Features
+========
+- Methods for peak detection and sub-pixel location.
+- Methods for matching measured peaks to reference peaks.
+- Methods for energy calibration of an EDX detector.
+- Methods for q-calibration of an EDX detector and the GeRM detector.
+- GUIs/CLIs for processing and visualizing EDDT data from the GeRM detector. 
+
+Installation
+============
+
+Algodif can be installed using pip or conda:
+
+```commandline
+pip install algodif
+```
+
+```commandline
+conda install -c algotom -c conda-forge algodif
+```
+
+or from source:
+
+```commandline
+git clone https://github.com/algodif/algodif.git
+cd algodif
+pip install .
+```
+
+Documentation: https://algodif.readthedocs.io
+
+Introduction
+============
+
+The multi-strip germanium energy-dispersive X-ray detector, developed by the 
+detector group and combined with a pinhole geometry at the HEX beamline, NSLS-II, 
+enables both spatial cross-sectional imaging of samples and detailed mapping of their 
+crystal structures. This powerful technique has been routinely used at the beamline since 2023.
+
+![img](https://github.com/algodif/algodif/raw/main/figs/edxd_geometry.png)
+
+As illustrated, each detector element captures diffraction signals from a specific 
+region of the sample, known as the gauge volume. The multi-strip detector array 
+simultaneously records diffraction signals from different gauge volumes along 
+the X-ray beam, effectively providing 1D spatially resolved measurements without 
+tomographic reconstruction. By scanning the sample along the Y-axis, a 2D 
+cross-sectional map can be constructed. Importantly, each pixel in this map 
+contains a 1D diffraction pattern corresponding to a specific location within 
+the sample. This is why the technique is called energy-dispersive X-ray diffraction 
+tomography (EDDT): it enables direct tomographic imaging without the computation 
+required in conventional tomography. 
+
+![img](https://github.com/algodif/algodif/raw/main/figs/eddt_technique.png)
+
+Calibration
+===========
+
+The detector requires frequent calibration for different experimental conditions due to 
+variations in diffraction angles across gauge volumes and the complexity of the 
+detector and readout electronics. Under polychromatic X-ray illumination, the 
+detector can record both fluorescence and diffraction signals, depending on 
+the sample and detector angle. So, two types of calibration are required: 
+energy calibration and reciprocal-space (q) calibration.
+
+Energy calibration
+------------------
+
+For detector energy calibration, the key idea is to maximize the fluorescence 
+signal while minimizing the diffraction signal. We use a sample composed of thin foils 
+of Sn, Pb, and Au to cover a wide energy range from low to high. A small amount of U is 
+included to extend the calibration range beyond 110 keV. The results before and after energy 
+calibration are shown below.
+
+![img](https://github.com/algodif/algodif/raw/main/figs/energy_calib_before.png)
+![img](https://github.com/algodif/algodif/raw/main/figs/energy_calib_after.png)
+
+Q calibration
+-------------
+
+q-calibration, or reciprocal space calibration, is a major routine in the regular 
+use of this detector at the HEX beamline. The detector needs to be calibrated when 
+the theta angle changes or after a few days of use. In contrast to energy calibration, 
+q-calibration requires minimizing fluorescence and maximizing diffraction signals. 
+We tested several calibrants, including CeO2, Al2O3, Si, and LaB6, and found that Cr2O3 
+is the best choice for minimizing fluorescence. The tilt of the diffraction lines across 
+the detector strips reflects the variation in scattering angle across the detector.
+
+![img](https://github.com/algodif/algodif/raw/main/figs/q_calib_before.png)
+![img](https://github.com/algodif/algodif/raw/main/figs/q_calib_after.png)
+
+The robustness and reliability of this routine depend critically on the peak detection 
+and peak matching methods, which we have developed and refined over time. Details of these 
+methods are provided in the referenced paper and the source code.
+
+User interface software
+-----------------------
+
+We provide separate GUIs for different workflows and visualization tasks. Although combining 
+everything into a single GUI may seem appealing, we chose a modular approach to simplify 
+maintenance and accommodate the diverse needs of beamline operations. These tools (Python scripts) 
+can be organized and launched through the [script-runner GUI](https://pypi.org/project/scriptrunner-gui/). 
+
+![img](https://github.com/algodif/algodif/raw/main/figs/eddt_gui.png)
+
+![multi_lines_viewer](https://github.com/algodif/algodif/raw/main/GUIs_CLIs/figs/fig5_multi_lines_viewer.png)
+
+![4d_viewer](https://github.com/algodif/algodif/raw/main/GUIs_CLIs/figs/fig8_4d_rendering.png)
+
+Author
+------
+Nghia T. Vo - National Synchrotron Light Source II, Brookhaven National Lab, USA.
+

algodif-1.0.0/README.md

@@ -0,0 +1,134 @@
+# Algodif
+### Data processing (**ALGO**)rithms for (**DIF**)fraction-based X-ray techniques 
+
+Methods and software for calibrating multi-element energy-dispersive X-ray (EDX) detectors,
+processing and visualizing energy-dispersive X-ray diffraction tomography (EDDT) data acquired 
+at a hard X-ray synchrotron beamline.
+
+A detailed description is provided in the paper under review: "Algorithms and software tools for 
+energy-dispersive X-ray diffraction tomography," Nghia T. Vo, Zhong Zhong, and Michael Drakopoulos. 
+
+The core of this work is to address a problem: 
+given a list of measured data points not knowing unit, how to map that into a list of reference points 
+knowing unit. The challenge is that the number of measured data points is not the same as the number of 
+reference points, so there are many local minima in the mapping transformation.
+For X-ray diffraction techniques, it addresses the problem of how to calibrate an instrument using 
+the diffraction pattern or fluorescence spectrum of a known calibrant in a robust and automated fashion.
+
+Although the work was initially aimed at calibrating the HEX beamline instrument (the GeRM detector), 
+the methods and software can be applied to other instruments given standard diffraction patterns or spectra. 
+The specific GeRM geometry is helpful for determining initial guesses of optimizing methods. 
+However, the algorithms in the software are not restricted to the GeRM detector.
+
+Features
+========
+- Methods for peak detection and sub-pixel location.
+- Methods for matching measured peaks to reference peaks.
+- Methods for energy calibration of an EDX detector.
+- Methods for q-calibration of an EDX detector and the GeRM detector.
+- GUIs/CLIs for processing and visualizing EDDT data from the GeRM detector. 
+
+Installation
+============
+
+Algodif can be installed using pip or conda:
+
+```commandline
+pip install algodif
+```
+
+```commandline
+conda install -c algotom -c conda-forge algodif
+```
+
+or from source:
+
+```commandline
+git clone https://github.com/algodif/algodif.git
+cd algodif
+pip install .
+```
+
+Documentation: https://algodif.readthedocs.io
+
+Introduction
+============
+
+The multi-strip germanium energy-dispersive X-ray detector, developed by the 
+detector group and combined with a pinhole geometry at the HEX beamline, NSLS-II, 
+enables both spatial cross-sectional imaging of samples and detailed mapping of their 
+crystal structures. This powerful technique has been routinely used at the beamline since 2023.
+
+![img](https://github.com/algodif/algodif/raw/main/figs/edxd_geometry.png)
+
+As illustrated, each detector element captures diffraction signals from a specific 
+region of the sample, known as the gauge volume. The multi-strip detector array 
+simultaneously records diffraction signals from different gauge volumes along 
+the X-ray beam, effectively providing 1D spatially resolved measurements without 
+tomographic reconstruction. By scanning the sample along the Y-axis, a 2D 
+cross-sectional map can be constructed. Importantly, each pixel in this map 
+contains a 1D diffraction pattern corresponding to a specific location within 
+the sample. This is why the technique is called energy-dispersive X-ray diffraction 
+tomography (EDDT): it enables direct tomographic imaging without the computation 
+required in conventional tomography. 
+
+![img](https://github.com/algodif/algodif/raw/main/figs/eddt_technique.png)
+
+Calibration
+===========
+
+The detector requires frequent calibration for different experimental conditions due to 
+variations in diffraction angles across gauge volumes and the complexity of the 
+detector and readout electronics. Under polychromatic X-ray illumination, the 
+detector can record both fluorescence and diffraction signals, depending on 
+the sample and detector angle. So, two types of calibration are required: 
+energy calibration and reciprocal-space (q) calibration.
+
+Energy calibration
+------------------
+
+For detector energy calibration, the key idea is to maximize the fluorescence 
+signal while minimizing the diffraction signal. We use a sample composed of thin foils 
+of Sn, Pb, and Au to cover a wide energy range from low to high. A small amount of U is 
+included to extend the calibration range beyond 110 keV. The results before and after energy 
+calibration are shown below.
+
+![img](https://github.com/algodif/algodif/raw/main/figs/energy_calib_before.png)
+![img](https://github.com/algodif/algodif/raw/main/figs/energy_calib_after.png)
+
+Q calibration
+-------------
+
+q-calibration, or reciprocal space calibration, is a major routine in the regular 
+use of this detector at the HEX beamline. The detector needs to be calibrated when 
+the theta angle changes or after a few days of use. In contrast to energy calibration, 
+q-calibration requires minimizing fluorescence and maximizing diffraction signals. 
+We tested several calibrants, including CeO2, Al2O3, Si, and LaB6, and found that Cr2O3 
+is the best choice for minimizing fluorescence. The tilt of the diffraction lines across 
+the detector strips reflects the variation in scattering angle across the detector.
+
+![img](https://github.com/algodif/algodif/raw/main/figs/q_calib_before.png)
+![img](https://github.com/algodif/algodif/raw/main/figs/q_calib_after.png)
+
+The robustness and reliability of this routine depend critically on the peak detection 
+and peak matching methods, which we have developed and refined over time. Details of these 
+methods are provided in the referenced paper and the source code.
+
+User interface software
+-----------------------
+
+We provide separate GUIs for different workflows and visualization tasks. Although combining 
+everything into a single GUI may seem appealing, we chose a modular approach to simplify 
+maintenance and accommodate the diverse needs of beamline operations. These tools (Python scripts) 
+can be organized and launched through the [script-runner GUI](https://pypi.org/project/scriptrunner-gui/). 
+
+![img](https://github.com/algodif/algodif/raw/main/figs/eddt_gui.png)
+
+![multi_lines_viewer](https://github.com/algodif/algodif/raw/main/GUIs_CLIs/figs/fig5_multi_lines_viewer.png)
+
+![4d_viewer](https://github.com/algodif/algodif/raw/main/GUIs_CLIs/figs/fig8_4d_rendering.png)
+
+Author
+------
+Nghia T. Vo - National Synchrotron Light Source II, Brookhaven National Lab, USA.
+

algodif-1.0.0/algodif/__init__.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"