ATS-GPU-OCT Programmer’s guide

License Agreement

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Introduction

ATS-GPU-OCT provides a framework to allow real-time OCT data processing from AlazarTech PCIe digitizers on a CUDA compatible GPU.

ATS-GPU-OCT internally calls ATS-CUDA-OCT, which is a low-level library that performs all the necessary operations to perform the Fourier Transform. ATS-CUDA-OCT is described in later in this guide in the section ATS-CUDA-OCT.

This document assumes that the reader is familiar with ATS-SDK, the standard interface for programming AlazarTech digitizers. Having a copy of the ATS-SDK manual available can be helpful, since many references to ATSApi functions are done here. The latest version of the ATS-SDK manual can be downloaded free of charge from AlazarTech’s website.

Prerequisites

System requirements

This software requires a PC with a CUDA-enabled GPU, and sufficient CPU resources to supply data to the GPU at the desired data acquisition rate. It also requires a working installation of the same version of ATS-GPU-BASE. It was tested with GeForce GTX Titan X (Maxwell), GeForce GTX980 and Quadro P5000. DDR4 memory and a modern chipset (X99, X299) will greatly improve transfer speed and overall performance.

Supported operating systems

Windows and Linux operating systems are supported. Please verify that your Linux distribution is supported by NVIDIA which supplies the CUDA toolkit required to use ATS-GPU.

Compiler support

CMake is required to build C/C++ code. CMake files are provided. On Linux, a C++11 compiler is required to build the library. On older Red Hat distributions, a devtoolset can be obtained to use a more recent version of gcc that supports C++11. NVCC is required to compile the example code, this compiler is included with CUDA toolkit.

CUDA driver requirements

In order to use ATS-GPU, you must install the appropriate driver for your CUDA-enabled GPU. Drivers can be downloaded at https://www.nvidia.com/Download/index.aspx.

Note

Under Windows operating systems, dynamic link libraries releated to ATS-GPU-OCT are installed by default in %WINDIR%System32. For applications to link approripately to them, %WINDIR%System32 must be added to the Windows PATH Environment Variable.

ATS-GPU-OCT

ATS-GPU-OCT leverages ATS-GPU-BASE to transfer data from an ATS PCIe digitizer to a GPU in a highly efficient manner. It then takes care of doing OCT processing on the data before sending it back to the host computer’s RAM.

Usage

ATS-GPU-OCT acquisitions are very similar to standard ATSApi acquisitions. Only the differences are listed here for brevity.

The central function of the ATS-GPU-OCT interface is ATS_GPU_OCT_Setup(). This function calls its ATS-GPU-BASE counterpart ATS_GPU_Setup() internally, which in turns calls AlazarBeforeAsyncRead(). It takes a few extra parameters:

  • OCTFlags: Used to define which data type, such as amplitude and phase, to obtain from the acquisition.

  • FFTLength: This is used to select the length of the Fourier transform done on the GPU. This value must be a power of two, and it also must be equal to or larger than the record length.

rc = ATS_GPU_OCT_Setup(
         boardHandle, channelMask, -(int) preTriggerSamples,
         samplesPerRecordPerChannel, recordsPerBuffer,
         buffersPerAcquisition * recordsPerBuffer, autoDMAFlags,
         OCTOptions, FFTLength, NULL, &fftBytesPerBuffer);

We then choose the window function applied to the acquired data before the FFT processing phase. The most common usage pattern is to first generate a window function using ATS_GPU_OCT_GenerateWindowFunction(), then to download it to the board using ATS_GPU_OCT_SetWindowFunction(). It is possible however to use entirely custom window functions instead of the ones generated by the API. It is also possible to use complex window functions by way of downloading two arrays of points: the first for the real part of the window and the other for the imaginary one.

rc = ATS_GPU_OCT_GenerateWindowFunction(
            FFT_WINDOW_HANNING, &window[0],
            samplesPerRecordPerChannel);
// Error handling

rc = ATS_GPU_OCT_SetWindowFunction(
            boardHandle, samplesPerRecordPerChannel,
            &window[0], NULL);
// Error handling

We then allocate memory on the GPU and CPU for data to be transferred to, and we post those buffers to the board. For this purpose, we use ATS_GPU_OCT_AllocBuffer(). This function allocates buffers on the GPU, and sets up all the intermediary state necessary for ATS-GPU-OCT to successfully transfer data. It also allocates data on the CPU to receive the processed OCT data.

for (int i = 0; i < numberOfBuffers; i++)
{
    buffers[i] = (float*) ATS_GPU_OCT_AllocBuffer(
        boardHandle, bytesPerResultBuffer, NULL);

    rc = ATS_GPU_OCT_PostBuffer(
        boardHandle, buffers[i], bytesPerResultBuffer);
    // Error handling
}

We can then start the acquisition with ATS_GP_OCT_StartCapture(). Once acquisition is started, ATS_GPU_OCT_GetBuffer() must be called as often as possible to retrieve a buffer containing processed data on the CPU. The data can then be used by the calling application. When no longer needed, the buffer needs to be posted back.

for (size_t i; i < buffers_per_acquisition; i++)
{
    rc = ATS_GPU_OCT_GetBuffer(
        boardHandle, buffers[bufferIndex],timeout_ms);
    // Error handling

    // TODO: Process sample data in this buffer.

    rc = ATS_GPU_OCT_PostBuffer(
        boardHandle, buffers[bufferIndex], bytesPerResultBuffer);
    // Error handling
}

When acquisition is complete, ATS_GPU_OCT_AbortCapture() must be called. Buffers allocated with ATS_GPU_OCT_AllocBuffer() should then be freed with ATS_GPU_OCT_FreeBuffer().

ATS_GPU_OCT_AbortCapture(boardHandle);

if (gpuFile != NULL)
    fclose(gpuFile);

// Free buffers
for (int i = 0; i < numberOfBuffers; i++) {
    ATS_GPU_OCT_FreeBuffer(boardHandle, buffers[i]);
}

LabVIEW Programming

LabVIEW applications must use the managed interface which allows the API to allocate and manage a list of buffers available to be filled by the board. These applications should call ATS_GPU_OCT_Setup() with the AMDA_ALLOC_BUFFERS option selected in the “autoDMAFlags” parameter. This option will cause the API to allocate and manage a list of buffers available to be filled by the board. It is therefore not necessary for the application to call ATS_GPU_OCT_AllocBuffer() or ATS_GPU_OCT_FreeBuffer(). The application must call ATS_GPU_OCT_ManageGetBuffer() to wait for a buffer to be filled. When the board receives sufficient trigger events to fill a buffer, the API will copy the data from the internal buffer to the user-supplied buffer. ATS_GPU_OCT_ManageGetBuffer() internally calls ATS_GPU_OCT_GetBuffer() and ATS_GPU_OCT_PostBuffer() so applcation should not use these API calls when using the managed interface.

LabVIEW users might find it convenient to edit the VI search paths to locate the appropriate subVIs for the different ATS-GPU packages and ATS-SDK. The VI Search Path can be set in the “Tools” menu under “Options”, in the “Path” category. Then select the “VI Search Path” from the drop down list. By unselecting “Use default” custom VI search paths can be added.

API Reference

Note

Errors from ATS-GPU-OCT will be logged in ATS_GPU.log. Relevant information about the error will be logged here and can be useful for debugging. For Windows users log file is located in %TEMP%. For Linux users log file is located in /tmp/.

enum ATS_GPU_OCT_OPTIONS

Types of data output that are generated by the acquisition. This is used in ATS_GPU_OCT_Setup()

Values:

enumerator ATS_GPU_OCT_LOG_OUTPUT
enumerator ATS_GPU_OCT_AMPLITUDE_OUTPUT
enumerator ATS_GPU_OCT_PHASE_OUTPUT
enumerator ATS_GPU_OCT_REAL_OUTPUT
enumerator ATS_GPU_OCT_IMAG_OUTPUT
enumerator ATS_GPU_OCT_SQRT_OUTPUT
enumerator ATS_GPU_OCT_RAWDATA_OUTPUT
enum ATS_GPU_OCT_WINDOWS

Window functions that can be generated by ATS_GPU_OCT_GenerateWindowFunction()

Values:

enumerator FFT_WINDOW_NONE
enumerator FFT_WINDOW_HANNING
enumerator FFT_WINDOW_HAMMING
enumerator FFT_WINDOW_BLACKMAN
enumerator FFT_WINDOW_BLACKMAN_HARRIS
enumerator FFT_WINDOW_BARTLETT
enumerator NUM_FFT_WINDOW_ITEMS
RETURN_CODE ATS_GPU_OCT_AbortCapture(HANDLE boardHandle)

Stops the acquisition.

Aborts an acquisition, stops data processing, and releases allocated resources.

Parameters

boardHandle – Handle to the board

Returns

ApiSuccess

void *ATS_GPU_OCT_AllocBuffer(HANDLE boardHandle, U32 bytesPerBuffer, void *reserved)

Allocates page-aligned pinned memory for ATS and GPU boards.

This function must be called after ATS_GPU_OCT_Setup() to perform the necessary memory allocations. This function returns a CPU result buffer pointer.

Parameters

  • boardHandle – Handle to the board

  • bytesPerBuffer – Total number of bytes to allocate per buffer

  • reserved – Pass NULL.

RETURN_CODE ATS_GPU_OCT_EnableVerificationMode(BOOL enable, U32 boardType)

Enable verification mode to supply already acquired data.

Parameters

  • enable – Pass 1 to enable

  • boardType – Board identifier used to perform the acquisition.

RETURN_CODE ATS_GPU_OCT_FreeBuffer(HANDLE boardHandle, void *buffer)

Free buffers allocated with ATS_GPU_OCT_AllocBuffer();.

Parameters
RETURN_CODE ATS_GPU_OCT_GenerateWindowFunction(U32 windowType, float *window, U32 windowLength_samples)

Generate a window function for FFT.

Parameters

  • windowType – A member of the ATS_GPU_OCT_WINDOWS enum

  • window – A pointer to a preallocated array where the window will be written.

  • windowLength_samples – Number of points in the window

RETURN_CODE ATS_GPU_OCT_GetBuffer(HANDLE boardHandle, void *buffer, U32 timeout_ms)

Get processed buffer.

This function must be called at average rate that is equal to or greater than the rate at which DMA buffers complete. This function returns the GPU-processed buffer.

Parameters

  • boardHandle – Handle to the board

  • buffer – Pointer to the buffer

  • timeout_ms – Time the board will wait for a trigger before throwing an error.

Returns

ApiSuccess (512) if the board received sufficient triggers to fill a DMA buffer.

Returns

ApiNotInitialized if ATS_GPU_OCT_StartCapture() was not called before calling this function, or it was called and failed.

Returns

ApiInvalidHandle if the boardHandle parameter is not valid.

Returns

ApiBufferOverflow if the board filled all the available DMA buffers and its on-board memory. This may happen if the acquisition rate exceeds the bus bandwidth or the GPU processing bandwidth.

Returns

ApiWaitTimeout if the timeout interval expired before the board received a sufficient number of triggers to fill a buffer.

Returns

ApiFailed if a system of internal error occurred.

RETURN_CODE ATS_GPU_OCT_GetVersion(U8 *major, U8 *minor, U8 *revision)

Get ATS-GPU-OCT version number.

Parameters

  • major – ATS-GPU-OCT major version number.

  • minor – ATS-GPU-OCT minor version number.

  • revision – ATS-GPU-OCT revision number.

RETURN_CODE ATS_GPU_OCT_ManageGetBuffer(HANDLE boardHandle, void *buffer, U32 bytesToCopy, U32 timeout_ms)

Query a buffer through the managed DMA buffer API. For LabVIEW programmers view LabVIEW Programming section.

Parameters

  • boardHandle – Handle to the board

  • buffer – Pointer to a user-allocated buffer to receive data

  • bytesToCopy – Number of bytes to copy to the user buffer

  • timeout_ms – Maximum time to wait for data to be ready to be copied to buffer before returning ApiWaitTimeout.

RETURN_CODE ATS_GPU_OCT_PostBuffer(HANDLE boardHandle, void *buffer, U32 bytesPerBuffer)

Signal the library a particular buffer can be used for data transfer.

This function is the equivalent of AlazarPostAsyncBuffer for ATS-GPU-OCT. Buffers posted must have previously been allocated with ATS_GPU_OCT_AllocBuffer().

Parameters

  • boardHandle – Handle to the board

  • buffer – Pointer to a previously allocated buffer

  • bytesPerBuffer – Size in bytes of the buffer, must be the same size as setup for the acquisition.

RETURN_CODE ATS_GPU_OCT_SetBuffer(void *dataInputBuffer, void *CPUResultBuffer, U32 samplesPerBuffer)

Supply a buffer for verification mode.

Parameters

  • dataInputBuffer – Pointer to data buffer to be processed

  • CPUResultBuffer – Pointer to data buffer to contain result data

  • samplesPerBuffer – Size in samples of the buffer

RETURN_CODE ATS_GPU_OCT_SetWindowFunction(HANDLE boardHandle, U32 samplesPerRecord, float *realWindowArray, float *imagWindowArray)

Set window function used in FFT calculation.

Parameters

  • boardHandle – Handle to the board

  • samplesPerRecord – Length of the window, equal to the number of samples per FFT.

  • realWindowArray – Pointer to array of size samplesPerRecord that contains the real part of the window. Passing null is equivalent to passing an array filled with ones.

  • imagWindowArray – Pointer to array of size samplesPerRecord that contains the imaginary part of the window. Passing null is equivalent to passing an array filled with zeros.

RETURN_CODE ATS_GPU_OCT_Setup(HANDLE boardHandle, U32 channelSelect, long transferOffset, U32 samplesPerFFT, U32 FFTsPerBuffer, U32 FFTsPerAcquisition, U32 autoDMAFlags, U32 OCTFlags, U32 FFTLength, void *reserved, U32 *bytesPerResultBuffer)

Prepares the ATS board and GPU for acquisition.

This function calls ATS_GPU_Setup() internally and most parameters are passed directly to it. In addition, it sets up the GPU for DMA transfers and receives options specific to OCT processing.

Parameters

  • boardHandle – Handle to the board. Set to NULL for data validation mode.

  • channelSelect – Channel mask with each channel identifier OR’d

  • transferOffset – Pass a negative integer for pretrigger samples

  • samplesPerFFT – Number of samples in a record or transfer

  • FFTsPerBuffer – Number of records in a buffer, 1 for triggered streaming and continuous streaming modes.

  • FFTsPerAcquisition – In this version of the library, it is required to pass 0x7FFFFFFF to this parameter, which stands for an infinite acquisition. It is possible to interrupt the acquisition at any time using ATS_GPU_OCT_AbortCapture()

  • autoDMAFlags – ATSApi flags for AlazarBeforeAsyncRead

  • OCTFlags – Defines the types of data outputs to be obtained from the OCT acquisition. This parameter can receive one or more elements of ATS_GPU_OCT_OPTIONS and ATS_GPU_PSOCT_OPTIONS, OR’d with the binary OR operator.

  • FFTLength – Length of FFT, should be a power of 2.

  • reserved – Pass NULL

  • bytesPerResultBuffer – Returns the size of a result buffer

RETURN_CODE ATS_GPU_OCT_StartCapture(HANDLE boardHandle)

Start the acquisition.

Use this function in replacement of AlazarStartCapture(). It starts the acquisition. The application must be ready to call ATS_GPU_OCT_GetBuffer() to prevent data overflows

Parameters

boardHandle – Handle to the board

ATS-CUDA-OCT

ATS-CUDA-OCT provides a framework to allow OCT data processing on a CUDA-enabled GPU. ATS-CUDA-OCT should be used with ATS-CUDA for buffer and stream manipulation. ATS-CUDA-OCT requires an AlazarTech board on the system in order to be used.

API Reference

Note

Errors from ATS-CUDA-OCT will be logged in ATS_GPU.log. Relevant information about the error will be logged here and can be useful for debugging. For Windows users log file is located in %TEMP%. For Linux users log file is located in /tmp/.

cudaFFTPlan *ATS_CUDA_OCT_CreateFFTPlan(U32 FFTLength, U32 recordsPerBuffer, U32 channelCount, cudaStream_t stream)

Creates an FFT plan and associates it with a CUDA stream. Requires an AlazarTech board on the system in order to succeed.

This function is used to configure a GPU kernel to perform FFT processing. It also associates the newly created FFT plan with a CUDA stream. All kernel executed with this plan are to be run on this stream.

Parameters

  • FFTLength – Length of the data on which to perform an FFT

  • recordsPerBuffer – Number of FFTs to perform per active channel.

  • channelCount – Number of input signals.

  • stream – The CUDA stream to run the FFT plan with.

Returns

This function returns a pointer to the created FFT plan.

RETURN_CODE ATS_CUDA_OCT_DestroyFFTPlan(cudaFFTPlan *FFTPlan)

Destroy an FFT plan.

Frees all GPU resources associated with an FFT plan.

Parameters

FFTPlan – Pointer to the FFT plan to be destroyed.

void *ATS_CUDA_OCT_GenerateGPUWindowFunction(U32 samplesPerRecordPerChannel, float *realWindowArray, float *imagWindowArray)

Generates a window function on the GPU for FFT processing.

Parameters

  • samplesPerRecordPerChannel – Length of the window, equal to the number of samples per record per channel.

  • realWindowArray – Pointer to array of size samplesPerRecord that contains the real part of the window. Passing null is equivalent to passing an array filled with ones.

  • imagWindowArray – Pointer to array of size samplesPerRecord that contains the imaginary part of the window. Passing null is equivalent to passing an array filled with zeros.

Returns

Pointer to an array of complex floating point elements that contains the window generated on the GPU.

RETURN_CODE ATS_CUDA_OCT_FFT(cudaFFTPlan *FFTPlan, void *GPUFFTIn, void *GPUFFTOut)

Launches on the GPU a kernel to perform the Fast Fourier Transform.

Parameters

  • FFTPlan – Pointer to a FFT plan created with ATS_CUDA_OCT_CreateFFTPlan().

  • GPUFFTIn – Pointer to a GPU buffer on which FFT is to be performed. Input buffer has complex float32 precision.

  • GPUFFTOut – Pointer to a GPU FFT result buffer. Output buffer has complex float32 precision.

RETURN_CODE ATS_CUDA_OCT_GetVersion(U8 *major, U8 *minor, U8 *revision)

Get ATS-CUDA-OCT version number.

Parameters

  • major – ATS-CUDA-OCT major version number.

  • minor – ATS-CUDA-OCT minor version number.

  • revision – ATS-CUDA-OCT revision number.

RETURN_CODE ATS_CUDA_OCT_PostFFT(void *GPUFFTOutput, void *GPUResultBuffer, cudaStream_t stream, U32 FFTLength, U32 recordsPerBuffer, U32 channelCount, U32 OCTFlags)

Launches on the GPU a kernel to extract relevant output information from the FFT.

Parameters

  • GPUFFTOutput – Pointer to a GPU buffer in Fourier domain from which outputs are to de extracted. This buffer has complex float32 precision.

  • GPUResultBuffer – Pointer to a GPU buffer where data is to be output. Output buffer has float32 precision.

  • stream – Stream identifier on which processing is to take place.

  • FFTLength – length of the FFT to perform. Equal to the sum of samplesPerRecordPerChannel and the length of zero padding.

  • recordsPerBuffer – records per buffer per channel.

  • channelCount – number of input signals.

  • OCTFlags – Defines the types of data outputs to be obtained. This parameter can receive one or more elements of ATS_GPU_OCT_OPTIONS, OR’d with the binary OR operator.

RETURN_CODE ATS_CUDA_OCT_PreFFT(void *GPUBuffer, void *GPUFFTIn, cudaStream_t stream, void *GPUWindow, U32 samplesPerRecordPerChannel, U32 FFTLength, U32 recordsPerBuffer, U32 channelCount, U32 inputDataType)

Launches on the GPU a kernel to perform preliminary windowing of the data and zero padding (if required) before doing the FFT.

Parameters

  • GPUBuffer – Pointer to a GPU buffer to on which to apply PreFFT kernel. This buffer should have 8 bits or 16 bits data packing and remain interleaved if multiple channels were acquired with an AlazarTech digitizer.

  • GPUFFTIn – Pointer to a GPU buffer where data is to be output. Output buffer has complex float32 precision.

  • stream – Stream identifier on which processing is to take place

  • GPUWindow – Pointer to a GPU window buffer allocated with ATS_CUDA_OCT_GenerateGPUWindowFunction()

  • samplesPerRecordPerChannel – Samples per record per channel

  • FFTLength – length of the FFT to perform. Equal to the sum of samplesPerRecordPerChannel and the length of zero padding.

  • recordsPerBuffer – records per buffer per channel.

  • channelCount – number of input signals.

  • inputDataType. – Data type of the input data. This parameter must receive one element of ATS_CUDA_Input_DataType.

ATS-CUDA-PSOCT

ATS-CUDA-PSOCT is an add-on library to ATS-GPU-OCT that allows to output the signals of interest in polarization sensitive OCT. Using ATS-CUDA-PSOCT requires a seperate license.

API Reference

enum ATS_GPU_PSOCT_OPTIONS

Types of data output that are generated by the acquisition. This is used in ATS_GPU_OCT_Setup() or ATS_GPU_NUFFT_Setup()

Values:

enumerator ATS_GPU_PSOCT_REFLECTIVITY_OUTPUT
enumerator ATS_GPU_PSOCT_LOG_OUTPUT
enumerator ATS_GPU_PSOCT_RETARDATION_OUTPUT
enumerator ATS_GPU_PSOCT_AXIS_ORIENTATION_OUTPUT
RETURN_CODE ATS_CUDA_PSOCT_PostFFT(void *GPUVerticalFFTOutput, void *GPUHoriozontalFFTOutput, void *GPUResultBuffer, cudaStream_t stream, U32 FFTLength, U32 recordsPerBuffer, U32 OCTFlags)

Launches on the GPU a kernel to extract relevant output information from the FFT.

Parameters

  • GPUVerticalFFTOutput – Pointer to a GPU buffer of the vertical polarization state in Fourier domain from which outputs are to be extracted. This buffer has complex float32 precision.

  • GPUHoriozontalFFTOutput – Pointer to a GPU buffer of the horizontal polarization state in Fourier domain from which outputs are to be extracted. This buffer has complex float32 precision.

  • GPUResultBuffer – Pointer to a GPU buffer where data is to be output. Output buffer has float32 precision.

  • stream – Stream identifier on which processing is to take place.

  • FFTLength – length of the FFT to perform. Equal to the sum of samplesPerRecordPerChannel and the length of zero padding.

  • recordsPerBuffer – records per buffer per channel.

  • OCTFlags – Defines the types of data outputs to be obtained. This parameter can receive one or more elements of ATS_GPU_PSOCT_OPTIONS, OR’d with the binary OR operator.