IMPROVED SOFTWARE AND METHODS FOR DATA COLLECTION

改进的数据收集软件和方法

• 批准号: 8363412
• 负责人: ROBERT M SWEET
• 金额: $ 17.24万
• 依托单位: BROOKHAVEN SCIENCE ASSOC-BROOKHAVEN LAB
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363412
• 关键词: Advertisements; Architecture; Area; Chicago; Code; Collaborations; Computer software; Crystallography; Data Collection; Data Set; Development; Dose; Face; Funding; Grant; Height; Image Analysis; International; Java; Light; Location; Methods; Monitor; Names; National Center for Research Resources; Occupations; Online Systems; Positioning Attribute; Principal Investigator; Procedures; Process; Radiation; Reproducibility; Research; Research Infrastructure; Research Personnel; Resources; Running; Sampling; Scanning; Site; Skeleton; Source; Specimen; Spectrum Analysis; Students; Synchrotrons; System; Testing; United States National Institutes of Health; Work; Writing; X ray diffraction analysis; X-Ray Diffraction; absorption; analog; base; beamline; cost; detector; digital; experience; falls; flexibility; high school; improved; indexing; innovation; instrumentation; meetings; operation; posters; programs; research study; symposium; synchrotron radiation; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Objectives The objectives stated in the renewal proposal are these: We will develop a versatile web-based job-queuing system to allow asynchronous off-site control of the automated data-collection process, we'll develop and disseminate true remote operation of all of our beamline systems, we will continue in the international collaboration to produce the software named EDNA for autonomous and intelligent data collection, will incorporate the mini-kappa orienters on several of our diffractometers to provide automatic multi-pass data collection with complete data sets and true redundancy, and will work to extend the capabilities of our EPICS systems. Results  We have refined a grid-scanning procedure to locate crystals by searching for diffraction. It is fast and many users employ it. It has a very clean interface allowing the users to go to the grid location of best diffraction. Annie H¿roux presented this at the Chicago Synchrotron Radiation Instrumentation conference last fall. We made significant progress on asynchronous-remote "Q" data collection. The challenge is to be able to run through samples at an unattended beamline, review the results through a PXDB sweep query, then remount samples with enough reproducibility that the same position on the crystal, or a new user-chosen position, can be shot. Part of this requires a very reproducible centering and finding of the "flat face" of the loop. This has been improved by trading the C3D image-analysis program from Grenoble (ESRF) for the Hamburg(DESY)-written XREC in this step. We use XREC only to align the loop and find the flat face. We've integrated our grid scan into the procedure to find the crystal. EDNA is used to do preliminary analysis and indexing. At the end of the winter shutdown, this was all working and we ran through a full dewar worth of samples to test. We hope to push this further in the May shutdown. The Dectris Pilatus 6M arrived in March and we integrated it smoothly into CBASS at X25 with the EPICS area Detector module. The grid scan runs very much faster with this detector, thanks in part to software donated by Chris Nielsen of ADSC. Beamline X26-C's correlated X-ray diffraction and Absorption Spectroscopy work was pushed further through the summer of 2010 with the assistance of a high school summer student, Michael Skinner. He developed a Java program that continuously plots acquired spectra and allows for tracking of single light wavelengths during correlated runs. A version of this tool is available through the PXDB sweep query, allowing investigators to view results later. A Java-based interface to the Oxford Univ. program RADDOSE, which calculates the absorbed x-ray dose a specimen experiences, was also developed that lets one predict the radiation dose to samples, and preliminary work was done on putting RADDOSE results in spectra file headers. John Skinner gave a presentation on all of this at the 2010 ACA meeting in Chicago. Skinner adapted CBASS architecture for use at beamline X9 for SAXS/WAXS experiment control. He stripped CBASS down to just a skeleton of its architecture, then added what was needed to make it a SAXS/WAXS control program. This was not a lot of work, and the resulting GUI is in use and was a major component of two posters that the X9 staff has presented. One was at the ESRF and another at the SRI Chicago meeting. This relationship with X9 is a good case for our software having a place in NSLS-II. In a similar collaboration, John Skinner gave a presentation at IBM's Watson Research Center in Yorktown Heights NY to assist Beamline X20 staff with their software upgrade efforts, as they look ahead to NSLS-II. We added EPICS control of the beam-position monitor (at the monochromator) at X25. Using our grid-scan code and the general flexibility of CBASS to develop experiments on the fly, we assisted NSLS-II staff in their development of a White Beam Position Monitor, which is now in place and operational at X25. To further this effort, we built control of an Acromag IP 330 analog-to-digital converter module into our RTEMS kernel that runs on our VME crates. Again, this is a good advertisement for the suitability of our software at NSLS-II. Both BPMs now write to the HTML logs and can be viewed from PXDB sweep queries. Plans  We will continue to respond to opportunities and make firm contacts with NSLS-II software workers. Most of these projects, including Queue-driven data collection and super-fast grid scanning, continue vigorously. Significance  This group has thrived over the decades by being resolutely innovative in both software and flexibility in providing for the needs of experimenters.

这个子项目是利用资源的许多研究子项目之一。 由NIH/NCRR资助的中心拨款提供。对子项目的主要支持 子项目的首席调查员可能是由其他来源提供的， 包括美国国立卫生研究院的其他来源。为子项目列出的总成本可能 表示该子项目使用的中心基础设施的估计数量， 不是由NCRR赠款提供给次级项目或次级项目工作人员的直接资金。 目标：我们将开发一个多功能的基于网络的作业排队系统，以实现对自动数据收集过程的异地异步控制；我们将开发和传播我们所有光束线系统的真正远程操作；我们将继续与国际合作生产用于自主和智能数据收集的名为EDNA的软件；将在我们的几台衍射仪上安装迷你卡帕定向器，以提供具有完整数据集和真正冗余的自动多通道数据收集；并将努力扩展我们的EPICS系统的能力。 结果我们改进了一种通过搜索衍射来定位晶体的网格扫描方法。它速度很快，很多用户都在使用它。它有一个非常干净的界面，让用户可以去最佳的衍射网格位置。安妮·H？鲁在去年秋天的芝加哥同步辐射仪器会议上提出了这一点。 我们在异步-远程“Q”数据收集方面取得了重大进展。挑战是能够在无人值守的光束线上运行样品，通过PXDB扫描查询查看结果，然后以足够的重复性重新安装样品，从而可以拍摄晶体上的相同位置或用户选择的新位置。这其中的一部分需要一个非常可重复性的对中，并找到环路的“平面”。在这一步中，通过用格勒诺布尔(ESRF)的C3D图像分析程序交换汉堡(DESY)编写的XREC，这一点得到了改进。我们使用XREC只是为了对齐环路并找到平面。我们已经将栅格扫描整合到寻找水晶的程序中。使用EDNA进行初步分析和索引。在冬季停工结束时，这一切都起作用了，我们运行了整整相当于杜瓦尔的样本进行测试。我们希望在5月份的停摆中进一步推动这一点。 Dectris Pilatus 6M在3月份到达，我们在X25上顺利地将其与EPICS区域探测器模块集成到CBass中。有了这个探测器，网格扫描的速度要快得多，这在一定程度上要归功于ADSC的克里斯·尼尔森捐赠的软件。 在高中暑期学生迈克尔·斯金纳的帮助下，Beamline X26-C的相关X射线衍射和吸收光谱工作在2010年夏天进一步推进。他开发了一个Java程序，可以连续绘制获取的光谱，并允许在相关运行期间跟踪单个光波长。该工具的一个版本可以通过PXDB Sweep查询获得，允许调查人员稍后查看结果。牛津大学的一个基于Java的接口。还开发了计算样品经历的吸收X射线剂量的程序RADDOSE，使用户可以预测样品的辐射剂量，并在光谱文件标题中进行了初步工作。约翰·斯金纳在2010年芝加哥ACA会议上就这一切发表了演讲。 斯金纳将CBass体系结构应用于波束线X9，用于SAXS/WAXS实验控制。他将CBass简化为其体系结构的骨架，然后添加了使其成为SAXS/WAXS控制程序所需的东西。这并不是大量的工作，生成的图形用户界面正在使用中，并且是X9工作人员展示的两个海报的主要组成部分。一次是在ESRF，另一次是在SRI芝加哥会议上。与X9的这种关系是我们的软件在NSLS-II中占有一席之地的一个很好的例子。 在类似的合作中，John Skinner在纽约州约克敦高地的IBM沃森研究中心做了一次演讲，帮助Beamline X20员工在展望NSLS-II时进行软件升级。 我们在X25增加了对束流位置监测器(在单色仪)的EPICS控制。使用我们的栅格扫描代码和CBass的一般灵活性来开发飞行实验，我们帮助NSLS-II工作人员开发了白色光束位置监视器，现在已经到位并在X25上运行。为了进一步推进这一工作，我们在VME机箱上运行的RTEMS内核中构建了对Acromag IP 330模数转换器模块的控制。再一次，这是我们的软件在NSLS-II上适用性的一个很好的广告。这两个BPM现在都写入到HTML日志中，并且可以从PXDB Sweep查询中查看。 计划我们将继续抓住机遇，与NSLS-II软件工作者建立牢固的联系。这些项目中的大多数，包括队列驱动的数据收集和超快网格扫描，都在大力继续。 意义这一群体几十年来凭借在软件方面的坚定创新和在满足实验者需求方面的灵活性而蓬勃发展。