chapter 3: PC based ECG acquisition system

Transcription

1 chapter 3: PC based ECG acquisition system This chapter describes development of a Data Acquisition System (DAS) for single lead ECG signal in a computer for storage and further processing. A microcontroller based standalone embedded system is used as DAS card for direct acquisition of ECG data from the source in a computer through the serial port. A MATLAB based application software collects the ECG data and processes them to extract the time plane features. A semi-skilled technician can acquire the ECG data to compute the wave durations and intervals using some GUI-based toolsets. The system is tested with synthetic ECG signal generated using Physionet data. 3.1 Block diagram The schematic diagram of the developed system is shown in Fig.3.1. The DAS card is a standalone embedded system consisting of 8051 microcontroller (MCU) as the main unit and instrumentation amplifier, level shifter, AD converter and MAX-232 level converter as peripheral components. The ECG signal is generated from an Arbitrary Waveform Generator (AWG) (Model Agilent 33220A) with the help of Agilent IntuiLink Waveform Editor Software loaded in another desktop PC. The signal generated by AWG is amplified by a low-offset instrumentation amplifier consisting of LF353 and OP07 in the range ±2.5V. The output of the amplifier is fed to the single channel AD converter 0804 through a dc offset +2.5V as the input range of this converter is 0-5V. A more detailed schematic of the TES module is shown is Fig.3.2. The AD converter output is sampled by the MCU at 1 khz frequency and each sample is converted into a RS-232 formatted data stream for serial delivery to the PC for storage.

2 Fig.3.1: Block diagram of PC-based ECG DAS Fig.3.2: Detailed Block schematic of the Data Acquisition System 3.2 Generation of synthetic ECG The developed system is tested with synthetic ECG signal generated using ptb-db records under Physionet For generation of synthetic ECG signal, a separate laptop computer is used. A ptb-db file is chosen and a precisely cut R-R interval from a particular single lead data is picked-up and stored in a separate text file as a single column format This file is required to be loaded with Agilent IntuiLink Waveform Editor for generation of the synthetic ECG signal. A screen layout of the Waveform Editor is shown in Fig.3.3. The frequency and peak amplitude setting of the generated signal can be set either from (i) the send arbitrary waveform menu of the Waveform Editor or, (ii) from the front panel soft keys of the AWG. The ECG samples from the linked text file (with Waveform Editor) are delivered through the USB link to the volatile memory of AWG, which re-generates the signal at die output by continuously repeating the R-R samples. In this way the ECG signal with required frequency and peak amplitude setting is obtained. The [ 51 ) :

3 reason of sending R-R interval is to avoid any discontinuity between successive cycles of the generated waveform, as may occur due to baseline modulation present within the raw data. Fig.3.3: Synthetic ECG generation using Agilent Waveform Editor: user front panel options 3.3 Operation of the DAS card The single channel AD converter 0804 is made to operate at free running mode at a speed of 0.60 MHz by use of an external timing (parallel RC combination) circuit. The output of the converter is sampled at a speed of 1 khz by the MCU. The UART of the PC is programmed in Mode 1 communication which converts each byte to RS-232 formatted data stream by automatic prefixing of start bit (logic 0 ) and suffixing stop bit (logic 1 ) with LSB sent first. Each 8 bit data sample is delivered to the PC using RS-232 serial protocol with a speed of 19.2 kbps. The related calculation for BAUD rate is done as follows: Baud Rate = bits/' sec

4 Bit width = 1/19200 sec Considering mode 1 communication using 10 bit/ frame (1 start bit, 8 data bits and 1 stop bit) total time to transmit one frame = 10/19200 sec = 520 ps. The time between two consecutive sampling is 1 ms. So, serial link remains idle for 480 ps between two successive transfers of samples to the PC. Figure 3.4 shows a time scale activity of the serial link between the DAS card and PC against sampling of the AD converter output Serial data transfer from MCU to PC At initial stages of testing, the DAS card is programmed to respond to the commands received from PC through the serial receive data line (RxD pin). Initiation and completion of acquisition by the DAS card are initiated by sending commands from the PC using separate commands, start and stop, issued from the GUI front panel push button switches. For start, the command code is a fixed byte 255h and for stop the same is 00^. When reliability of the data link is established, only the start of data acquisition is initiated using command. The DAS card acquires and transfers predetermined number of bytes, after which a stop command is automatically generated. This instructs the DAS card to stop acquisition of data as well as delivery to PC. The schematic flow-chart of the MCU firmware is shown in Fig.3.5.

5 Fig.3.5: Flowchart of DAS card MCU firmware 3.4 PC based application software The state of the art PC-based application software developed in MATLAB platform has two functions. First, serial acquisition of ECG samples from the DAS card for storage in a text file with time stamping. Second, processing of the pre-stored ECG data to compute ECG wave durations and intervals. The data

6 processing function is purely offline. These two operations are kept independent, i.e., the system can be used for quick collection of a multiple patients ECG or, multiple leads for a single patient Thereafter, these individual lead data can be analyzed one by one. The analysis function does not require the connection of the DAS to the PC. For achieving the two objectives, an application software is developed in MATALB. For easy Man- Machine-Interface (MMI), a GUI based front end is designed, which can be used by a technician or physician to collect ECG samples in the PC and process the data. For data analysis, the ECG samples are needed to be stored in a time-stamped text file in computer memory. The developed software performs the following tasks for data collection: (i) Reception of the serial ECG data delivered (by the DAS card) through its serial link and storage sequentially in a text file. (ii) Conversion of digital data with 8 bit resolution into the corresponding ECG samples calibrated in millivolt level. (iii) Generation of a graphical plot of the stored ECG samples on the front-panel of the GUI Implementing serial communication using MATLAB Basics of serial communication The RS-232 standard, recommended by EIA in 1961, defines the two devices connected with a serial cable as the Data Terminal Equipment (DTE) and Data Communication Equipment (DCE). This terminology reflects the RS-232 as a standard for communication between a computer terminal and an external device (CRO, modem, etc).the connection schematic between two devices conforming RS-232 standard is shown in Fig.3.6, where the two devices are connected by a serial cable. For implementing asynchronous serial transfer, primary communication is accomplished using three pins, viz., the Transmit Data pin, the Receive Data pin, and the Ground pin. A popular low pin version of RS-232 connector is shown in Fig.3.7, called 9- pin D connector.

7 Computer, a Male DB9 or DB25 Male DB9 or DB25 Telephone Interface Cable DTE Data Terminal Equipment Equipment Fig.3.6: Generalized connection diagram in RS-232 communication system t 0 0 o 4 o O 0 o Fig.3.7: 9-pin D-connector (male) Using the asynchronous protocol, each communication device uses its own internal clock, resulting in bytes that are transferred at arbitrary times. So, instead of using time as a way to synchronize the bits, a data format (called frame ) is used. A generalized data format for RS-232 protocol includes a low start bit, 8 data bits, a high stop bit and a parity bit (optional) as shown in Fig.3.8. j DO 01 D2 i i 1 Start 1! I Data bits 1 bit j...~1 ~ ~ D7 Parity bit Stop bits Fig.3.8: Data frame format in RS-232 protocol In asynchronous communication, the byte framing is performed by the Universal Synchronous Asynchronous Receiver Transmitter (USART) module associated with the COM port circuit of the PC. The signal level with RS-232 communication uses a different level than TTL logic level. A HIGH logic corresponds to -10 V and LOW corresponds to +10 V. So, a TTL level circuit interfaces with RS-232

8 logic through an interface, called level converter, which converts the TTL level logic (0-5V) into RS-232 level and vice versa for bidirectional data transfer. TABLE 3.1: SERIAL PORT PIN AND SIGNAL ASSIGNMENTS Pin Label Signal Name Signal Type 1 CD Carrier Detect Control 2 RD Receive Data Data 3 TD Transmit Data Data 4 DTR Data Terminal Ready Control 5 GND Signal Ground Control 6 DSR Data Set Ready Control 7 RTS Request to Send Control 8 CTS Clear to Send Control 9 RI Ring Indicator Control In synchronous communication, the transmitted bytes are synchronized to a common clock signal. The communicating devices initially synchronize themselves to each other, and continuously send characters to stay synchronized. Synchronous transfer allows faster data communication than asynchronous one due to lowering of communication overhead, since the additional characters like start, stop bits are not required. The synchronization is achieved using two lines Data Terminal Ready (DTR) and Data Set Ready (DSR) for updating the status of communication devices to each other. Normal microcontrollers don t support these pins directly. Other port pins with proper firmware support can be used for implementing synchronous communication Serial communication using MATLAB MATLAB supports direct data transfer between two devices TIA/ELA-232-C standard published by Telecommunications Industry Association. A generalized data flow (input) diagram involving the serial port in PC and the DAS card is shown in Fig.3.9. { 57 1

9 Fig.3.9: Data flow diagram between the DAS card and PC serial port A portion of the computer memory is allocated as input and output buffer associated with the USART of the serial port of the PC. Ihe memory size allocated to this buffer can be changed through software instructions. As shown in Fig.3.9, the data exchange between DCE (here DAS card) and the PC takes place through the same buffer. The USART is programmed using commands from MATLAB platform. It serially transfers out the data from the output buffer memory to the external device or, receive data from external device through input buffer with the specified baud rate. The principle of event-driven-programming is used for transferring the bytes between the USART buffer and the PC memory. For a typical data input process, the following sequence of events take place: 1. Data from the external device (DCE) continuously fill up the input buffer of the USART using the RxD line; 2. When input buffer filling reaches predefined (user programmable) threshold value, then it generates an event, which triggers the corresponding MATLAB callback functions using bytes-available event ; 3. Data is picked-up from buffer using necessary command in MAT ALB For transferring data bytes to the outside world, an exact reverse sequence is executed, as stated below: i) From computer memory, data byes are sent to the output buffer of the USART by using commands in MATLAB; ii) The USART continuously transmits the data bytes to the external device using the TxD line; iii) An OutputEmpty event is generated when the output buffer goes empty, triggering fee corresponding event described by BytesAvailableFcn and OutputEmptyFcn, The calling function loads the next block of data to the USART for delivery to fee external device. The serial port communication in MATLAB is achieved defining a variable as serial port object, which corresponds to a physical port, setting its properties and using fee same for achieving real time communication.

10 Fig.3.10: Flowchart of serial data reception in MATLAB environment

11 A typical session for using serial port objects involves following steps to be initiated using software instructions: (i) Creating a serial port object using serial creation function. (ii) Opening the port. (ii) Setting the following properties related to the serial port functions: Baud Rate Parity Data bits Stop bits Input buffer size ReadAsyncMode which describes manual / automatic mode for reading the port for data availability BytesAvailableFcn describes the function which will be called every time an event described by BytesAvailableFcnMode property is generated BytesAvailableFcnCount describes the number of bytes which, when available in the input buffer will generate the callback event (iii) Picking up (or deliver) the data bytes available in the buffer in (or from) a data array. (iv) Closing the port. In the present work, the continuous data stream received to the PC through COM port is sequentially stored in a text file. The schematic flowchart of the algorithm is shown in Fig At first, the initialization functions like serial port settings and event related parameters are set Then the serial port is opened and a temporary text file is opened. With each overflow of the serial port input buffer by the incoming byte stream, the block of data is picked up and serially arranged (appended) in the same temporary file. This operation is repeated until either a predefined number of bytes are stored or, a manual stop command is initiated. This temporary data file stores digitized ECG samples in 8 bit resolution. The stored bytes in the temporary text file are converted into the corresponding ECG samples using the following formula: [Digital value (D) - digital equivalent of bias voltage] x 19.6 Analog (mv) value (V.)... (3.1) Total amplification achieved in Amplifiers

12 where, 19.6 mv corresponds to the resolution of the ADC. The digital value can have a range of The total amplification in the amplifier circuit is 569. A new text file is generated where the converted ECG samples are stored in time stamped two column arrays. The time array is generated by an arithmetic progression serial with an increment value of 1 ms, since the sampling frequency of the DAS card is 1 khz. This file is preserved for data archiving and further processing. The GUI based front end can be used to plot a graphical plot of the text file for visual examination of stored ECG data Processing of acquired ECG data The ECG analysis software extracts the durations and intervals of the constituent waves (P, QRS complex, T) and characteristic segments (RR, QRS, ST, QT etc) from the ECG data. Detail of the ECG feature extraction algorithm is given in Chapter 2, section 2.2 and section Testing and results The developed system is initially tested with known standard waveform at different frequencies. The test layout of the developed system is shown in Fig Fig.3.11: Layout of the test system

13 At this stage, the start and termination functions of the acquisition are controlled by using two push-button switches on the GUI front panel, as shown in Fig.3.12 and Fig The objective is to study the proper collection and reproduction of the acquired data in the PC. A detailed bandwidth study of the serial link is also performed. The test results of the system with ramp and sine wave at different frequencies are shown with corresponding CRO screenshot. (a) (b) Fig.3.12: Test results of the system with standard waveforms at 5 Hz (a) CRO screenshot of ramp wave generated; (b) Data plot of ramp wave in GUI; (c) Data plot of sine wave in GUI

14 KrtdlJ (a) (b) Fig.3.13: Test results of the system with sine wave (a) Using 50 Hz; (b) Using 100 Hz (a) (b) Fig.3.14; Test results of the system with ECG data (a) CRO screenshot; (b) Plot in GUI It is observed that the waveform is distorted for higher frequencies whereas, the test waveforms at lower frequencies are better reconstructed. The distortion is due to the time elapsed between the two successive pickups of input buffer data and calling function execution at the application software, it can be removed by increasing the input buffer size of the USART for higher frequencies.

15 PC based ECG acquisition system chapter 3 The test results with ECG data with corresponding CRO screenshot is shown in Fig The data file containing digital samples and reconverted ECG samples is shown in Fig S81 D Microsoft I «ccl - ccf 3initizcd Samples r" 'ir -a 1 f B: Chart Area v Look CN»t at,vtow Hefc Adofet W 1 JPlot on GUI J laj ] : Reconstructed Sample Fig.3.15: Stored file screenshots and plot of ECG after final acquisition The reliability of the acquired data in the PC is ensured by comparing a suitably cut R-R samples of a captured lead data in the PC with the corresponding one computed from the raw samples generated by the AWG. The raw signal generated by the AWG is directly collected in a PC, bypassing the DAS card, by using a DSO (Model Tektronix TDS1001B) in conjunction with Tektronix Open Choice Desktop software. This software provides a facility to capture the raw data samples directly from the AWG in a time stamped data file. The sampling of this direct acquisition is kept as 1 khz to match the sampling of ADC bv the DAS card MCU. After the data reliability is ensured, the data processing algorithm is tested. For this, the starting and termination of data acquisition function by the DAS card is first converted into an automatic mode. By this, a fixed number of bytes (equal to 7168) are picked up every time from the ECG source. The following time plane features are computed from the acquired data. (i) QRS interval; (ii) ST interval; (iii) QT interval; (iv) corrected Qt interval or (QT)C ; and (v) R-R interval.

16 Figure 3.16 represents R-peak detection from the acquired data from the DAS card, re-calibrated to the millivolt level. The sensitivity figure for different captured data using the DAS card is given in Table 32. An accuracy of 99.62% is obtained over 120 data leads such tested. The extracted features are compared with corresponding actual values. Table 3.3 and Table 3.4 show the comparison of some of the computed values with actual ones. tlme(a»o) Fig.3.16: R-peak determination from ECG data acquired by DAS card TABLE 32: SENSITIVITY FIGURE FOR R-PEAK DETECTION Patient file ID Lead I Leadll Lead vl P237/ s0465 (N)

17 P252/s0487(N) P241/ s0470 (N) P267/ s0504(n) P266/ s0502 (N) P275/s P238/ s0466 (N) P240/ S0468 (N) P279/ 0533 (N) TABLE 3.3: QRS WIDTH CALCULATION (IN MILLISECOND) Patient file ED LeadI Lead II Lead vl algorithm actual algorithm actual algorithm actual P236/s0463(N) P236/s0464(N) P237/s0465(N) P238/s0466(N) P240/s0468(N) P241/s0470(N) P248/s0481(N) P264/s0500 (N) P266/s0502(N) TABLE 3.4: QT-INTERVAL CALCULATION (IN MILLISECOND) Patient file ID LeadI Lead II Lead vl algorithm actual algorithm actual algorithm actual P236/S0463 (N) P236/s0464(N) P238/s0466(N)

18 P240/ s0468 (N) P241 / s0470 (N) P248/s0481 (N) P264/ s0500 (N) P266/s0502(N) Finally the PC based application software is embedded in the application software developed. A screenshot of the digital data plot, reconstructed samples plot, R-R plot and different computed wave intervals is shown in Fig The GUI also provides a provision to store the R-R interval data instead of all cardiac cycles for optimum memory usage. Fig.3.17: ECG plot with extracted time plane features on the GUI

19 3.6 Conclusion A method of acquiring EGG samples from a local source into a PC for computerized processing is described in this chapter. A standalone DAS card along with an application software is used for collection of ECG samples in a PC through serial port for sequential storage in a time-stamped text file. Then the different wave durations and intervals are computed by analysis of the pre-stored data. The GUI-based toolsets provide an offline method to assist a cardiologist to assess the patient scardiac condition based on visual analysis and extracted time-plane features from the captured ECG data. The system need to be slightly customized for connection with an ECG lead system and amplifier assembly to collect and analyze the data collected from a live patient. The present capacity of single dead acquisition can be extended to multi-lead acquisition by replacing the single channel ADC with a multi-channel one. In the next chapter a modular system of ECG transmission is described, where the ECG samples are collected near the source and transmitted using a bi-phase modulation technique to a remote end computer for automatic acquisition.