ICALEPCS2013 - List of Authors (Pasic, H.)

Paper

Title

Page

Implementation of an Overall Data Management at the Tomography Station at ANKA

558

D. Haas, W. Mexner, H. Pasic, T. Spangenberg
KIT, Eggenstein-Leopoldshafen, Germany

New technologies and research methods increase the complexity of data management at the beamlines of a synchrotron radiation facility. The diverse experimental data such as user and sample information, beamline status and parameters and experimental datasets, has to be interrelated, stored and provided to the user in a convenient way. The implementation of these requirements leads to challenges in fields of data life-cycle, storage, format and flow. At the tomography station at the ANKA a novel data management system has been introduced, representing a clearly structured and well organized data flow. The first step was to introduce the Experimental Coordination Service ECS, which reorganizes the measurement process and provides automatic linking of meta-, logging- and experimental-data. The huge amount of data, several TByte/week, is stored in NeXus files. These files are subsequently handled regarding storage location and life cycle by the WorkSpaceCreator development tool. In a further step ANKA will introduce the European single sign on system Umbrella and the experimental data catalogue ICAT as planned as the European standard solution in the PaNdata project.

Poster TUPPC005 [1.422 MB]

TUPPC008

A New Flexible Integration of NeXus Datasets to ANKA by Fuse File Systems

566

W. Mexner, E. Iurchenko, H. Pasic, D. Ressmann, T. Spangenberg
KIT, Eggenstein-Leopoldshafen, Germany

In the high data rate initiative (HDRI) german accelerator and neutron facilities of the Helmholtz Association agreed to use NeXus as a common data format. The synchrotron radiation source ANKA decided in 2012 to introduce NeXus as common data format for all beam lines. Nevertheless it is a challenging work to integrate a new data format in existing data processing work flows. Scientists rely on existing data evaluation kits which require specific data formats. To solve this obstacle, for linux a filesystem in userspace (FUSE) was developed, allowing to mount NeXus-Files as a filesystem. Easy in XML configurable filter rules allow a very flexible view to the data. Tomography data frames can be directly accessed as TIFF files by any standard picture viewer or scan data can be presented as a virtual ASCII file compatible to spec.

WECOBA01

Algebraic Reconstruction of Ultrafast Tomography Images at the Large Scale Data Facility

996

X. Yang, T. Jejkal, H. Pasic, R. Stotzka, A. Streit, T. dos Santos Rolo, T. van de Kamp
KIT, Eggenstein-Leopoldshafen, Germany

Funding: Kalsruhe Institute of Technology, Institute for Data Processing and Electronics; China Scholarship Council
The ultrafast tomography system built up at the ANKA Synchrotron Light Source at KIT makes possible the study of moving biological objects with high temporal and spatial resolution. The resulting amounts of data are challenging in terms of reconstruction algorithm, automatic processing software and computing. The standard operated reconstruction method yields limited quality of reconstruction images due to much fewer projections obtained from the ultrafast tomography. Thus an algebraic reconstruction technique based on a more precise forward transform model and compressive sampling theory is investigated. It results in high quality images, but is computationally very intensive. For near real–time reconstruction, an automatic workflow is started after data ingest, processing a full volume data in parallel using the Hadoop cluster at the Large Scale Data Facility (LSDF) to reduce the computing time greatly. It will not only provide better reconstruction results but also higher data analysis efficiency to users. This study contributes to the construction of the fast tomography system at ANKA and will enhance its application in the fields of chemistry, biology and new materials.

Slides WECOBA01 [1.595 MB]

Paper	Title	Page
TUPPC005	Implementation of an Overall Data Management at the Tomography Station at ANKA	558
	D. Haas, W. Mexner, H. Pasic, T. Spangenberg KIT, Eggenstein-Leopoldshafen, Germany
	New technologies and research methods increase the complexity of data management at the beamlines of a synchrotron radiation facility. The diverse experimental data such as user and sample information, beamline status and parameters and experimental datasets, has to be interrelated, stored and provided to the user in a convenient way. The implementation of these requirements leads to challenges in fields of data life-cycle, storage, format and flow. At the tomography station at the ANKA a novel data management system has been introduced, representing a clearly structured and well organized data flow. The first step was to introduce the Experimental Coordination Service ECS, which reorganizes the measurement process and provides automatic linking of meta-, logging- and experimental-data. The huge amount of data, several TByte/week, is stored in NeXus files. These files are subsequently handled regarding storage location and life cycle by the WorkSpaceCreator development tool. In a further step ANKA will introduce the European single sign on system Umbrella and the experimental data catalogue ICAT as planned as the European standard solution in the PaNdata project.
	Poster TUPPC005 [1.422 MB]

TUPPC008	A New Flexible Integration of NeXus Datasets to ANKA by Fuse File Systems	566
	W. Mexner, E. Iurchenko, H. Pasic, D. Ressmann, T. Spangenberg KIT, Eggenstein-Leopoldshafen, Germany
	In the high data rate initiative (HDRI) german accelerator and neutron facilities of the Helmholtz Association agreed to use NeXus as a common data format. The synchrotron radiation source ANKA decided in 2012 to introduce NeXus as common data format for all beam lines. Nevertheless it is a challenging work to integrate a new data format in existing data processing work flows. Scientists rely on existing data evaluation kits which require specific data formats. To solve this obstacle, for linux a filesystem in userspace (FUSE) was developed, allowing to mount NeXus-Files as a filesystem. Easy in XML configurable filter rules allow a very flexible view to the data. Tomography data frames can be directly accessed as TIFF files by any standard picture viewer or scan data can be presented as a virtual ASCII file compatible to spec.

WECOBA01	Algebraic Reconstruction of Ultrafast Tomography Images at the Large Scale Data Facility	996
	X. Yang, T. Jejkal, H. Pasic, R. Stotzka, A. Streit, T. dos Santos Rolo, T. van de Kamp KIT, Eggenstein-Leopoldshafen, Germany
	Funding: Kalsruhe Institute of Technology, Institute for Data Processing and Electronics; China Scholarship Council The ultrafast tomography system built up at the ANKA Synchrotron Light Source at KIT makes possible the study of moving biological objects with high temporal and spatial resolution. The resulting amounts of data are challenging in terms of reconstruction algorithm, automatic processing software and computing. The standard operated reconstruction method yields limited quality of reconstruction images due to much fewer projections obtained from the ultrafast tomography. Thus an algebraic reconstruction technique based on a more precise forward transform model and compressive sampling theory is investigated. It results in high quality images, but is computationally very intensive. For near real–time reconstruction, an automatic workflow is started after data ingest, processing a full volume data in parallel using the Hadoop cluster at the Large Scale Data Facility (LSDF) to reduce the computing time greatly. It will not only provide better reconstruction results but also higher data analysis efficiency to users. This study contributes to the construction of the fast tomography system at ANKA and will enhance its application in the fields of chemistry, biology and new materials.
	Slides WECOBA01 [1.595 MB]