PDF - BioMedSearch
Contents
1. Advanced software concepts for employing microcomputers in the laboratory Scott B Tilden and M Bonner Denton Department of Chemistry University of Arizona Tucson Arizona 85721 USA Introduction While a proliferation of commercial chemical instrument ation is appearing today employing microprocessors for a variety of control and data reduction applications the great potential of microprocessors has not been exploited extensively for individual custom applications The primary reason for this phenomenon is altogether too clear micro processor software is either difficult to develop or inefficient in memory requirements and speed This problem is even more important in situations requiring constant software Machine Code to Execute Commana B Machine Code to Execute Command C Machine Code to Execute Command D e etc Figure 1 The interpretative cycle of common types of languages such as BASIC After examining each command in the source file the interpreter searches for and branches to the corresponding block of machine code thus program execution always remains within the interpreter 128 Interpretative Machine Code bans v ie RSS YN are N S Machine Code 7 o5 to Execut a S Cormand A N modification Initially most instrument manufacturers utilized cross assemblers supported on large number cruncher computers to generate the required mach2. different in size and cost from one controlled by inflexible hardware In many ways chromatography is an ideal process for such automation Most instruments are given a high workload and although many applications may be routine and repetitive the versatility of the technique requires an instrument which can easily be used in a variety of modes In addition to improving the convenience to the user automation of a liquid chromatrograph should enhance the performance of the instrument Some aspects of high performance liquid chromatography HPLC which can benefit in this way are as follows 1 Accurate control of solvent flow rate will compensate for changes in pressure drop and lead to more reliable retention times 2 The composition of the mobile phase can be accurately controlled in either isocratic or gradient elution chrom atography using for example a proportioning valve on the low pressure side of the pump 3 Automatic sampling can be operated in a variety of modes to process a number of samples without super vision It is also more precise than manual injection Present address Pye Unicam Ltd York Street Cambridge CB1 2PX U K 134 4 A built in data handling facility can present the analyst with an easily read post run report of the analytical results with accurate peak area measurements even for peaks which are poorly resolved Although liquid chromatographs incorporating micro processors for control an
3. the more intelligent BASICS make very inefficient use of memory often requiring Figure 3 The threaded code approach used in CONVERS In threaded code programming modules for sub routines are used repetitively in a variety of combinations to allow implementation of an infinite number of functions Note that the flow of logic a minimum of 12 or 16 K bytes twelve or sixteen thousand threads its way in a very non linear fashion through these modules eight bit words Volume 1 No 3 April 1979 129 Tilden amp Denton Advanced software concepts Upper Memory Bound User s Application Dictionaries 4 5k Octal CONVERS Disk Operating System 3 7k Octal Standard High Level Dictionary 1 2k Octal Initial Machine Code Dictionary 199 Octal Figure 4 Memory map of the CONVERS dictionary The stack which is composed of data parameters etc acts as a constantly expanding or contracting memory buffer which allows one sub routine to communicate with another without either needing to know the other s location Type ACQUIRE ACQUIRE FORMATZ T PLOT EXECUTIVE Figure 5 If a previously defined program name ACQUIRE is entered when in EXECUTE mode a dictionary search takes place locating the ACQUIRE entry Once found this entry contains all the required machine code and or calls to addresses of other previously compiled machine code modules to completely execute the desired function 130 In
4. contrast to interpreters high level compilers such as FORTRAN offer a much faster run time execution speed This is accomplished through generation of the required machine code during a series of programming operations Compilers using FORTRAN which are designed to run on many minicomputers and some micros often first transform user symbolic source code into assembly code An assembler program subsequently transforms this into the required machine code This ready to run machine code is often loaded along with a run time package which executes in the manner shown in Figure 2 While this approach greatly improves execution speed the need for loading several different soft ware routines increases the hassle associated with editing and debugging Thus this makes some form of mass memory such as a disk or magnetic tape almost mandatory Additionally I O algorithms generally must be implemented in assembly level code One obvious question immediately arises why not incorporate the most desirable characteristics of both inter preters and compilers into a single language Additionally due to the unique requirements found in many applicat ions why not allow the programmer additional flexibility by providing him with the ability to actually develop his own individual modifications and additions to the language itself Other desirable features would include high memory efficiency high level I O programming ease of under
5. AY LOCATION STOP gt IF messages When the new program has been completed it is entered in a program library or dictionary which is constant ly building up from low memory see Figure 4 If the operator now wants to execute this program he can request it from his terminal A dictionary search will begin at the last entry and progress until the requested program is located Once located the requested program will run in its entirety without need for any additional dictionary searches For example let us assume an algorithm called ACQUIRE has been programmed to take data from some hypothetical experimental system When ACQUIRE is requested from the terminal a dictionary search is initiated The program names ACQUIRE see Figure 5 once located contains the starting addresses of a series of previously defined modules which implement the various steps necessary to perform the desired experiment For example the module SCAN which might be intended to scan a monochromator s wavelength in some desired manner has been previously defined and tested This ability to easily test each module separately and then efficiently combine a series of modules to perform a more complex function test this function and then employ it in a vastly more complex function etc i e testing each step as the threaded code is made increasingly complex is a major factor contributing to the speed with which software can be developed using CONVERS Use o
6. E AY A ND value STOP the two are compared to gt to see if the incremented value at LOCATION is larger then the STOP value if it is the program ends if not it repeats the process starting at BEGIN HERE It should be noted that whilst many variables have been pushed on the stack only the data will remain since each time a value is used it is popped removed from the stack If a different spectra region is to be scanned i e from 3000 to 6500 with 10 increments the variables need only be changed thus 3000 START 6500 STOP 10 INCREMENT and type SCAN system will now scan from 3000 to 6500 taking data every 10 steps While the code might look a little strange at first it quickly becomes very easy to work with The SCAN program of Figure 6 could be combined with other modules as shown in Figure 5 to perform some more complex experimental function Each module of the program can be easily tried out to ensure that it is operational before proceeding with the next Presently CONVERS is being used in the authors laboratories for a variety of spectrochemical investigations including laser excited optoacoustic spectroscopy Figure 7 and inductively coupled plasma optical emission spectro scopy Figure 8 Rather complex interactive control and data acquisition programs have been easily implemented Memory requirements and operating speed have been found to be far superior to conventional approaches Additionally
7. I O is normally accomplished using the stack in conjunction with the INDEVICE or OUTDEVICE commands For example to take data from a device located at I O port 7 the number seven is pushed onto the stack 7 goes to this I O port takes in a number and pushes the number on the stack OUTDEVICE functions in a similar manner requiring the number to be sent to the desired device to be pushed onto the stack followed by the device s I O port address Hence to send the number 131 to device 11 the number 131 is pushed on the stack followed by 11 and then OUTDEVICE This pops the top number 11 from the stack uses it as the output port and then sends the number 131 to that location Applications of CONVERS To appreciate the ease with which real programs can be written a few examples will be considered A trivial program called SOUND which rings the terminal bell three times might be written 132 INTEL 8080 based MICROCOMPUTER 24K RAM PIEZOELECTRIC OPTOACOUSTIC TRANSLATOR CELL gt X OUTPUT POWER MIRROR CHOPPER DETECTOR K TRANSLATOR DRIVER LOCK IN ADC AMP LOCK IN lt TERMINAL SOUND BELL BELL BELL The colon denotes changing from EXECUTE to COMPILE mode After typing the name of the new routine in this case to be called SOUND typing the name of the earlier defined routine BELL a previously defined simple program to ring the terminal bell initiates a diction
8. aS e R AAS EoSPESS SP EE DSS 5 NOISE a number five is pushed onto the stack NOISE pushes its address on the stack and goes to the address indicated by the top number on the stack and deposits the next number Now sound would ring the terminal bell five times A much less trivial program which could be written to scan and take data from a monochromator equipped with a DENCO SM2A stepper motor controller 2 the SM2A takes a parallel number as an address sends one of two stepper motors to this location and outputs an arrival flag when the address is reached is given in Figure 6 Assume that the experimental system is configured so the SM2A is at I O port 5 and an analog to digital converter to acquire data is at I O port 7 Let us assume that initially a scan is designed from a starting stepper motor location of 2000 to a final location of 5000 taking data every 20 steps The program illustrated in figure 6 acts in the following manner Line 1 defines a variable called START to be 2000 which is the starting location of the scan The end of the scan is defined as 5000 in the next line Line 3 defines the increment between data points A variable called LOCATION where the next address is stored is defined in line 4 Colon in line 5 puts the system in the compile mode A D7 will be the name of the module which when called will cause a 7 to be pushed onto the stack INDEVICE will pop it back off and use it as a device addr
9. ary search to locate this routine s starting address which subsequentially is entered three times The resulting SOUND routine contains machine code calls to the BELL routine which itself is composed of machine code Of course SOUND could also have been defined using a DO LOOP i e SOUND 3 1 DO BELL LOOP where the numbers three and one set the upper and lower indices If it were desirable to change the actual number of bell rings from some other program this value could be defined asa VARIABLE let s call it NOISE 3 VARIABLE NOISE In this case the number three is first pushed on the stack VARIABLE transfers the top number on the stack the three to a dictionary location named NOISE If SOUND were now defined as SOUND NOISE 1 DO BELL LOOP j the bell would again ring three times In this case when the word NOISE is encountered its address is pushed on the stack the is a simple program which goes to the address indicated on the top of the stack that of NOISE and replaces it with the actual value located at that address the number three At any future time the value of a VARIABLE can be changed by pushing the new value onto the stack followed by the address of the variable to be changed generated by its name and an exclamation mark To change NOISE to 5 The Journal of Automatic Chemistry Tilden amp Denton Advanced software concepts cee REA S DSRS PTS PSS A a AES TS 7c SARA OPE PASSES a
10. d data handling purposes are commercially available these instruments are so far relatively inflexible This paper describes in detail the automation of a liquid chromatograph using an inexpensive general purpose microcomputer which has previously been applied in atomic absorption spectrophotometry 1 and for column switching in HPLC 2 Figure 1 illustrates the interconnection of the chromato graph and the microcomputer which controls the mobile phase flow rate operates an automatic sampler and analyses data from the detector The control and data handling functions are integrated in a program which enables the user to communicate with the instrument in plain English via a visual display unit VDU or teletypewriter keyboard A variety of operational modes is offered giving the analyst an opportunity to establish the best conditions for a partic ular separation before leaving the instrument to perform its given tasks without further interaction The microcomputer Hardware The computer is a general purpose instrument constructed using a set of ready made circuit cards Philips Science and The Journal of Automatic Chemistry
11. ess to go and take a data point and push the data onto the stack Line 6 defines a module INITIALIZE START puts its address on the stack replaces the address with the value at that address LOCAT ION puts its address on the stack P goes to the address specified by the number on the stack and deposits the second number and the net result value at START is put into LOCATION Line 7 defines STEP to take values from 10 KW LINEAR AMPLIFIER DAC PREAMP ORIVER 2712 MHz X TAL OSC MICRODISK 90K byte Figure 8 A schematic of the inductively coupled plasma emission spectrometer in which the microcomputer is used to control radio frequency power and flame positioning as well as to monitor light intensity Volume 1 No 3 April 1979 LOCATION and INCREMENT adds them together and puts the result into LOCATION i e LOCATION puts its address on the stack replaces the top value on the stack with the number stored at the address INCREMENT gets the value at INCREMENT and puts it in to the stack and adds the top two stack numbers and pushes the result on the stack LOCATION puts its address on the stack and goes to the address specified by the top number on the stack and deposits the second number The module defined in line 8 takes a number from the stepper motor controller assume device numbered 5 pushes on the stack and pushes the value 10 on the stack and does a logical AND to see if the controllers flag is
12. f a software stack also contributes toward improved memory efficiency and simpli fied programming The stack is an area of memory set aside to handle parameters data numbers etc One of the primary advantages of the stack is that entries can leave temporary parameters on the stack without having to assign specific 131 Tilden amp Denton Advanced software concepts DUAL REGULATED POWER SUPPLY IOKV 100 ma GRATING STEPPER MOTOR CONTROLLER MICROFLOPPY DISK Figure 7 The optoacoustic experiment in which a microcomputer is used to control laser wavelength and to monitor laser power and optoacoustic signal memory locations to store them This not only can save considerable memory but also allows programs to be easily relocatable since one algorithm need only know that a previous routine left so many words of data etc on the stack It need not know where the previous routine is nor even where the stack is located A series of stack handling routines which should appear quite familiar to many small calculator users provide an array of capabilities including the ability to PUSH a number on the stack POP it off duplicate it SWAP the top two numbers locate a number some distance into the stack and copy it on top of the stack etc Additionally a variety of logic functions familiar to the minicomputer user are provided including OR AND shift left shift right greater than less than etc Input output
13. ine code binary program More recently the trend has been toward the use of a developmental system at a cost comparable to a moderate minicomputer the authors use the term mini in contrast to micro reluctantly because of the ever increasing overlap in computing capability to write and debug assembly level porgrams which are subsequently con verted to binary and incorporated into an instrument in the form of read only memory ROM While this approach Source Code File Various commands making up users source program The Journal of Automatic Chemisty Tilden amp Denton Advanced software concepts Users Source File Command A p The Compiler J y Machine Code to Execute etc Command A Machine Code to Execute Onma nd B Machine Code to Execute Command C Machine Code to Execute amem sew 20 Command B Command C Command D a Figure 2 Note that the compiler transforms each source command into executable machine code This code will sub sequently be loaded and executed independently of the compiler has proven cost effective for high volume mass produced applications it possesses serious limitations for system up dates and custom applications Additionally the ability to program efficiently at the assembly level is a talent requiring a significant expenditure of time to develop During the past several years a virtual del
14. many of the desirable features found in both interpreters and compilers by separating the compile and execute states as a compiler does while maintaining a resident user interactive and conversational executive which oversees system operation The ability to realise such advanced software capabilities in a very modest amount of memory less than 4 K bytes on an 8080 based micro is the direct result of exploiting threaded code programming techniques see Figure 3 The approach involves highly efficient use of simple macro instructions to build more complex subroutines which are recombined with additional macroinstructions to form super subroutines This process of combining previously defined modules to form ever increasingly sophisticated routines for performing the task at hand is the essence of threaded code programming When initially loaded and running CONVERS acts much like an interpreter i e it is conversat ional ready to either execute a previously programmed algorithm or accept a new one However in contrast to BASIC when a new program is being entered under CONVERS it is immediately transformed into binary machine code or to the binary starting addresses of other previously entered and compiled machine code programs During this process the operator is kept informed of the status of the program by a series of error and diagnostic Volume 1 No 3 April 1979 18 AND e LOCATION IF A D7 ELSE BEGIN THEN STEP DEL
15. new system users have encountered a difficulty in utilising previously developed custom software for a particular experiment even when documentation was vague Discusston The authors hope that this short introduction to only a few of the concepts employed in CONVERS will generate interest in its capabilities A much more complete discussion is available in the form of a user s manual 3 available from the authors ACKNOWLEDGEMENTS The development of the CONVERS system was partially supported by the Office of Naval Research and a Alfred P Cloan Foundation Research Fellowship to M Bonner Denton REFERENCES 1 C Moore Astronomical Astrophysics Supplemental 15 1974 497 2 M B Denton J D Mack M W Routh and D B Swartz American Laboratory 8 69 1976 3 CONVERS An Interpretive Compiler developed by Scott B Tilden and M Bonner Denton Department of Chemistry University of Arizona Tucson Arizona 85721 USA eased The use of a microcomputer for flexible automation of a liquid chromatograph A D Mills 1 Mackenzie and R J Dolphin Philips Research Laboratories Redhill Surrey RH1 5HA U K Introduction Microprocessors are being used to add inexpensive automatic control and data handling facilities to a variety of chemical instruments With a microcomputer it is now possible to realise the flexibility formerly available only with a relatively large and expensive minicomputer in an instrument little
16. set if this is true the A D7 module will be called to input data if the flag is not set the program is returned to BEGIN HERE Therefore the DELAY module is a loop waiting for the stepper motor to arrive at its new location followed by a call to A D7 data acquisition module MOVE defined in line 9 gets the value stored at LOCATION pushes the device code onto the stack performs an outdevice which uses the top stack number as a 1 0 port address to send the next value to call the STEP module ie the value at LOCATION this increments LOCATION by the INCRE MENT value and finally calls DELAY and waits for a flag from the stepper motor controller to signal its arrival at the desired address and then takes a data point The final line shown in the example called SCAN itself calls the INITIAL IZE module which sets LOCATION to the START location for the Scan it also calls MOVE which sends this value to the motor LOCATION controller increments the value stored in LOCATION by INCREMENT and calls DELAY which waits for the motor to arrive and then takes a data point Next the incremented value from LOCATION is placed on the stack LOCATION followed by the STOP tei SCANNING Pi MONOCHRMATOR p A STEPPER MOTOR CONTROLLER ll MULTIPLEXER INTEL 8080 based MICROCOMPUTER TERMINAL 16K RAM 133 Tilden amp Denton Advanced software concepts oa A A A SS a Sa eS RA AA PS SS SS SSS SSS SS SSS YS SPE SPF T
17. standing the language s inter working and the ability to be trans ferred from one CPU to another with minimum effort of characters Q SCAN CALC T SS DISPLAY lt RETURN The Journal of Automatic Chemistry Tilden amp Denton Advanced software concepts a a a RS ST ty PSS 7S fa PS SS St SE SS CEE LL A ES EET 2008 VARIABLE START 58898 VARIABLE STOP 28 VARIABLE INCREMENT VARIABLE LOCATION A D7 7 INDEVICE INITIALIZE START LOCATION STEP LOCATION INCREMENT DELAY BEGIN HERE 5 INDEVICE MOVE LOCATION 5 OUTDEVICE SCAN INITIALIZE BEGIN HERE MOVE END ELSE BEGIN THEN 3000 START 6500 START 1 INCREMENT SCAN Figure 6 Ten lines of typical CONVERS code to scan wavelengths between two easily changed limits and acquire data By reference to notes in the text it can be easily understood NOTE a number or name pushes the number of address occupied by the name on the stack The symbol pips the top number from the stack uses it as the address from which to obtain a number and pushes that number on the stack Development of CONVERS During the past two years a different approach to soft ware has been taking place at the University of Arizona referred to as an Interpretive Compiler called CONVERS This package which is conceptually similar to the FORTH language currently being used in several minicomputer astronomical applications 1 is able to provide
18. uge of sophist icated flexible high performance computer hardware has been introduced primarily aimed at a rapidly growing hobbyist market Manufacturers quickly realilsed that to sell the public hardware some form of reasonably high level software must be made available A variety of BASIC inter preters ranging from rather dumb to quite intelligent have since evolved The more intelligent BASIC interpreters have several highly attractive attributes for hobbyist applications The language is both easy to master and con versational Error and caution messages are provided as aids during programming Why not apply the hobbyist technology toward the implementation of custom laboratory systems Many invest igators have and no doubt many more will take this approach However BASIC interpreters possess serious limitations in terms of system speed flexibility and input output I O capabilities In BASIC each command must first be interpreted and then executed see Figure 1 In many cases the interpretation process takes much more time than the actual execution This problem is compounded by the fact that commands interpreted in the past must be re interpreted each time they are used causing iterative programs to be very slow While speed is often not a serious limitation in playing computer games laboratory applicat ion requiring high speed data acquisition and or data manipulation are common Additionally
Download Pdf Manuals
Related Search