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Rychlá rekonstrukce fotoakustických obrazů
Kukliš, Filip ; Dvořák, Václav (oponent) ; Jaroš, Jiří (vedoucí práce)
Schopnost rekonstrukce fotoakustických obrazů je důležitým předpokladem pro studium měkkých tkaniv, nebo vaskulárního a lymfatického systému v malém prostoru a ve vysokém rozlišení. V současné době řešení vyžaduje enormní výpočetní výkon a je znatelně časově náročný. V této studii by jsme rádi představili nové řešení, které by bylo mnohem rýchlejší a jednodušší na použití. Moje řešení je až 20x rychlejší a potřebuje o čtyřicet procent méně paměti. Toto řešení může být lepší alternativou pro vědce, kteří studují měkké tkáně pomocí fotoakustického zobrazování.
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Acceleration of Axisymetric Ultrasound Simulations
Kukliš, Filip ; Vaverka, Filip (oponent) ; Jaroš, Jiří (vedoucí práce)
The simulation of ultrasound propagation through soft biological tissue has a wide range of practical applications. These include the design of transducers for diagnostic and therapeutic ultrasound, the development of new signal processing and imaging techniques, studying the aberration of ultrasound beams in heterogeneous media, ultrasonic tissue classification, training ultrasonographers to use ultrasound equipment and interpret ultrasound images, model-based medical image registration, and treatment planning and dosimetry for high-intensity focused ultrasound. However, ultrasound simulation presents a computationally difficult problem, as simulation domains are very large compared with the acoustic wavelengths of interest. But if the problem is axisymmetric, the governing equations can also be solved in 2D. This allows running simulations with larger grid size, with less computational resources and in a shorter time. This paper model and implements an acceleration of the Full-wave Nonlinear Ultrasound Simulation in an Axisymmetric Coordinate System implemented in Matlab using Mex Files for FFTW DST and DCT transformations. The axisymmetric simulation was implemented in C++ as an extension to the open source K-WAVE toolbox. The codes were optimized to run using one node of Salomon supercomputer cluster (IT4Innovations, Ostrava, Czechia) with two twelve-core Intel Xeon E5-2680v3 processors. To maximize computational efficiency, several stages of code optimization were performed. First, the FFTs were computed using the real-to-complex FFT from the FFTW library. Compared to the complex-to-complex FFT, this reduced the compute time and memory associated with the FFT by nearly 50%. Also, real-to-real DCTs and DSTs were computed using FFTW library, which ones in Matlab version, had to be invoked from dynamically loaded MEX Files. Second, to save memory bandwidth, all operations were computed in single precision. Third, element-wise operations were parallelized using OpenMP and then optimized using streaming SIMD extensions (SSE). The overall computation of the C++ k-space model is up to 34-times faster and uses less than one-third of the memory than Matlab version. The simulation which would take nearly two days by Matlab implementation can be now computed in one and half hour. This all allows running the simulation on the computational grid with 16384 × 8192 grid points within a reasonable time.
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Acceleration of Axisymetric Ultrasound Simulations
Kukliš, Filip ; Vaverka, Filip (oponent) ; Jaroš, Jiří (vedoucí práce)
The simulation of ultrasound propagation through soft biological tissue has a wide range of practical applications. These include the design of transducers for diagnostic and therapeutic ultrasound, the development of new signal processing and imaging techniques, studying the aberration of ultrasound beams in heterogeneous media, ultrasonic tissue classification, training ultrasonographers to use ultrasound equipment and interpret ultrasound images, model-based medical image registration, and treatment planning and dosimetry for high-intensity focused ultrasound. However, ultrasound simulation presents a computationally difficult problem, as simulation domains are very large compared with the acoustic wavelengths of interest. But if the problem is axisymmetric, the governing equations can also be solved in 2D. This allows running simulations with larger grid size, with less computational resources and in a shorter time. This paper model and implements an acceleration of the Full-wave Nonlinear Ultrasound Simulation in an Axisymmetric Coordinate System implemented in Matlab using Mex Files for FFTW DST and DCT transformations. The axisymmetric simulation was implemented in C++ as an extension to the open source K-WAVE toolbox. The codes were optimized to run using one node of Salomon supercomputer cluster (IT4Innovations, Ostrava, Czechia) with two twelve-core Intel Xeon E5-2680v3 processors. To maximize computational efficiency, several stages of code optimization were performed. First, the FFTs were computed using the real-to-complex FFT from the FFTW library. Compared to the complex-to-complex FFT, this reduced the compute time and memory associated with the FFT by nearly 50%. Also, real-to-real DCTs and DSTs were computed using FFTW library, which ones in Matlab version, had to be invoked from dynamically loaded MEX Files. Second, to save memory bandwidth, all operations were computed in single precision. Third, element-wise operations were parallelized using OpenMP and then optimized using streaming SIMD extensions (SSE). The overall computation of the C++ k-space model is up to 34-times faster and uses less than one-third of the memory than Matlab version. The simulation which would take nearly two days by Matlab implementation can be now computed in one and half hour. This all allows running the simulation on the computational grid with 16384 × 8192 grid points within a reasonable time.
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Rychlá rekonstrukce fotoakustických obrazů
Kukliš, Filip ; Dvořák, Václav (oponent) ; Jaroš, Jiří (vedoucí práce)
Schopnost rekonstrukce fotoakustických obrazů je důležitým předpokladem pro studium měkkých tkaniv, nebo vaskulárního a lymfatického systému v malém prostoru a ve vysokém rozlišení. V současné době řešení vyžaduje enormní výpočetní výkon a je znatelně časově náročný. V této studii by jsme rádi představili nové řešení, které by bylo mnohem rýchlejší a jednodušší na použití. Moje řešení je až 20x rychlejší a potřebuje o čtyřicet procent méně paměti. Toto řešení může být lepší alternativou pro vědce, kteří studují měkké tkáně pomocí fotoakustického zobrazování.
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