Collaborative Proposal: ATREX - integrated open source data analysis software for mineral and environmental sciences

同步辐射用户设施是关键资源，使国家的最先进的研究和培训，矿物学，矿物物理学和环境科学。进入这些设施是非常有竞争力的，分配给实验的时间是有限的。最受欢迎和最基本的实验类型是X射线衍射，它产生有关矿物和其他晶体固体的晶体结构，对称性，化学键，成分和密度的信息。现代的基于同步加速器的衍射实验通常使用面探测器进行，在这种情况下，数据被记录为数字衍射图像。同步加速器实验中使用的技术迅速发展，提高了数据收集的速度，产生了大量的实验数据，对数据分析提出了新的严峻挑战。实验通常是决策驱动的，并且需要至少部分的真实的时间数据解释来指导实验者。提供这种真实的时间分析能力的软件目前不可用。这一项目的重点是在地球和环境科学中基于衍射的同步加速器研究的新工具的组合，包括：（IM 1）确定天然和合成样品中未知相结构和识别已知相的新能力;（IM 2）为固态动态过程研究中的真实的时间分析开辟新的可能性;（IM 3）对异常值、不确定性和缺失数据进行稳健的贝叶斯分析;（IM 4）为在同步加速器研究中利用现有的矿物学数据库创造新的免费先进工具。利用现有的，经过良好测试和广泛使用的软件组件的组合开发的交互式数据语言，Python，该项目创建了一个新的集成多平台，开源Python软件包ATREX（用于极端X射线照相研究的高级工具），具有处理各种形式样品衍射图像数据的独特能力，包括玻璃和熔体、散装粉末，尽管是粗多晶粒，到单晶，这将支持新的超快X射线成像探测器产生的新的数据类型，提供广泛的自动化串行处理能力，为大量的数据集，并将允许真实的时间数据分析的时间限制的决策驱动的同步加速器实验。ATREX将包括利用免费的美国矿物学家晶体结构数据库的数据库访问能力。

Synchrotron radiation user facilities are critical resourcces which enable state-of-the-art research and training in mineralogy, mineral physics and environmental science. Access to these facilties is very competitive and time allocated for experiments is constrained. The most popular and fundamental type of experiment is X-ray diffraction, which produces information on crystal structure, symmetry, chemical bonding, composition and density of minerals and other crystalline solids. Modern synchrotron-based diffraction experiments are typically conducted with the use of area detectors, in which case the data is recorded as digital diffraction images. Technology used in synchrotron experiments evolves rapidly increasing the speed of the data collection and producing massive volumes of experimental data, posing new serious challenges for data analysis. The experiments are often decision-driven, and require at least partial real time data interpretation to guide the experimenter. Software offering such real time analysis capabilities is currently not available. This proposal is a collaborative effort to provide this scientific community with easily accessible tools and training opportunities for using these codes.This project focuses on a combination of novel tools for diffraction-based synchrotron research in Earth and environmental sciences including: (IM1) New capabilities for structure determination of unknown phases and identification of known phases in natural and synthetic samples; (IM2) Opening new possibilities for real time analysis in studies of solid state dynamic processes; (IM3) Robust Bayesian analysis of outliers, uncertainties and missing data; and (IM4) Creation of new free advanced tools for utilizing the available mineralogical database in synchrotron research. Utilizing a combination of existing, well-tested and widely used software components developed in the Interactive Data Language , Python, the project creates a new integrated multiplatform, open-source Python software package ATREX (Advanced Tools for Research in Extreme Xtallography), with unique capabilities to process diffraction image data from samples in all forms from glasses and melts, bulk powders, though coarse multi grains, to single crystals, which will support new data types produced by novel ultrafast X-ray imaging detectors, offer extensive automated serial processing capabilities for massive data sets and will allow real time data analysis for time-constrained decision-driven synchrotron experiments. ATREX will include database access capabilities utilizing the free American Mineralogist Crystal Structure Database.