syris: a flexible and efficient framework for X-ray imaging
experiments simulation

J 2017

syris: a flexible and efficient framework for X-ray imaging experiments simulation

FARAGÓ, Tomáš, Petr MIKULÍK, A. ERSHOV, M. VOGELGESANG, D. HANSCHKE et. al.

Basic information

Original name

syris: a flexible and efficient framework for X-ray imaging experiments simulation

Authors

FARAGÓ, Tomáš (703 Slovakia), Petr MIKULÍK (203 Czech Republic, guarantor, belonging to the institution), A. ERSHOV (643 Russian Federation), M. VOGELGESANG (276 Germany), D. HANSCHKE (276 Germany) and T. BAUMBACH (276 Germany)

Edition

Journal of Synchrotron Radiation, CHESTER, INT UNION CRYSTALLOGRAPHY, 2017, 1600-5775

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10302 Condensed matter physics

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.232

RIV identification code

RIV/00216224:14310/17:00098888

Organization unit

Faculty of Science

DOI

http://dx.doi.org/10.1107/S1600577517012255

UT WoS

000414172900018

Keywords (in Czech)

simulace; zobrazování; radiografie; CT; fázový kontrast; synchrotronové záření

Keywords in English

simulation; high-speed imaging; parallelization; free-space propagation; coherence; X-ray imaging; synchrotron radiation

Abstract

V originále

An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.

Citovat

FARAGÓ, Tomáš, Petr MIKULÍK, A. ERSHOV, M. VOGELGESANG, D. HANSCHKE and T. BAUMBACH. syris: a flexible and efficient framework for X-ray imaging experiments simulation. Journal of Synchrotron Radiation. CHESTER: INT UNION CRYSTALLOGRAPHY, 2017, vol. 24, November, p. 1283-1295. ISSN 1600-5775. Available from: https://dx.doi.org/10.1107/S1600577517012255.

@article{1400059,
   author = {Faragó, Tomáš and Mikulík, Petr and Ershov, A. and Vogelgesang, M. and Hanschke, D. and Baumbach, T.},
   article_location = {CHESTER},
   article_number = {November},
   doi = {http://dx.doi.org/10.1107/S1600577517012255},
   keywords = {simulation; high-speed imaging; parallelization; free-space propagation; coherence; X-ray imaging; synchrotron radiation},
   language = {eng},
   issn = {1600-5775},
   journal = {Journal of Synchrotron Radiation},
   title = {syris: a flexible and efficient framework for X-ray imaging experiments simulation},
   url = {http://onlinelibrary.wiley.com/doi/10.1107/S1600577517012255/abstract},
   volume = {24},
   year = {2017}
}

TY  - JOUR
ID  - 1400059
AU  - Faragó, Tomáš - Mikulík, Petr - Ershov, A. - Vogelgesang, M. - Hanschke, D. - Baumbach, T.
PY  - 2017
TI  - syris: a flexible and efficient framework for X-ray imaging experiments simulation
JF  - Journal of Synchrotron Radiation
VL  - 24
IS  - November
SP  - 1283-1295
EP  - 1283-1295
PB  - INT UNION CRYSTALLOGRAPHY
SN  - 16005775
KW  - simulation
KW  - high-speed imaging
KW  - parallelization
KW  - free-space propagation
KW  - coherence
KW  - X-ray imaging
KW  - synchrotron radiation
UR  - http://onlinelibrary.wiley.com/doi/10.1107/S1600577517012255/abstract
L2  - http://onlinelibrary.wiley.com/doi/10.1107/S1600577517012255/abstract
N2  - An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.
ER  -

FARAGÓ, Tomáš, Petr MIKULÍK, A. ERSHOV, M. VOGELGESANG, D. HANSCHKE and T. BAUMBACH. syris: a flexible and efficient framework for X-ray imaging experiments simulation. \textit{Journal of Synchrotron Radiation}. CHESTER: INT UNION CRYSTALLOGRAPHY, 2017, vol.~24, November, p.~1283-1295. ISSN~1600-5775. Available from: https://dx.doi.org/10.1107/S1600577517012255.

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