Biospherical Instruments Inc MER-2040 User manual

MER-2040/2041/2050

Moorable Reflectance Radiometer

Software

User's Manual

Biospherical Instruments Inc.

5340 Riley Street

San Diego, CA 92110

(619) 686-1888

FAX (619) 686-1887

Version 003110UB.DOC

Date Printed: 04/18/00

MER-204X Software Instruction Manual 003110UB.DOC

BIOSPHERICAL INSTRUMENTS INC.ii

NOTICE

The information contained in this document is subject to change without notice. BIOSPHERICAL

INSTRUMENTS MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL,

INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MECHANTABILITY AND

FITNESS FOR A PARTICULAR PURPOSE. Biospherical Instruments shall not be liable for errors

contained herein or for incidental or consequential damages in connection with the furnishing,

performance, or use of this material.

This document contains proprietary information that is protected by copyright. All rights are reserved. No

part of this document may be photocopied, reproduced, or translated into another language without the

prior written consent of Biospherical Instruments Inc.

IBM® is a registered trademark of International Business Machines Corp.

IBM PC is a product of International Business Machines Corp.

MSDOS and Excel are products of Microsoft Corporation

Document: 003110UB.DOC

1st Edition: June, 1998

MER-204X Software Instruction Manual 003110UB.DOC

BIOSPHERICAL INSTRUMENTS INC.iii

BIOSPHERICAL INSTRUMENTS INC. warrants this instrument system or software (the Product) to be in

good working order for a period of one (1) year parts and good for a period of ninety (90) days labor from

the date of purchase. Should this Product fail to be in good working order at any time during the above

stated warranty period, Biospherical Instruments Inc. will, at its option, repair or replace this Product at no

additional charge except as set forth below. Repair parts and replacement Products will be furnished on

an exchange basis and will be either reconditioned or new. All replacement parts and Products become

the property of Biospherical Instruments Inc. This limited warranty does not include service to repair

damage to the Product resulting from accident, disaster, misuse, abuse, or non-Biospherical Instruments

Inc. modification of the Product.

Limited warranty service may be obtained by delivering the Product during the warranty period to

Biospherical Instruments Inc. at its San Diego, California, Service Center, showing proof of purchase. If

this Product is delivered by mail, you agree to insure the Product or assume risk for loss or damage in

transit; to prepay shipping charges to the San Diego, California, Service Center; to use the original

shipping container or equivalent; and to pay for return shipping charges.

ALL EXPRESS AND IMPLIED WARRANTIES FOR THIS PRODUCT INCLUDING THE WARRANTIES

OR MERCHATABILITY AND FITNESS FOR A PARTICULAR PURPOSE, ARE LIMITED IN DURATION

TO THE ABOVE WARRRANTY PERIOD, AND NO WARRANTIES, WHETHER EXPRESSED OR

IMPLIED, WILL APPLY AFTER THIS PERIOD. SOME STATES DO NOT ALLOW LIMITATIONS ON

HOW LONG AN IMPLIED WARRANTY LASTS, SO THE ABOVE LIMITATIONS MAY NOT APPLY TO

YOU.

IF THIS PRODUCT IS NOT IN GOOD WORKING ORDER AS WARRANTED ABOVE, YOUR SOLE

REMEDY SHALL BE REPAIR OR REPLACEMENT AS PROVIDED ABOVE. IN NO EVENT WILL

BIOSPHERICAL INSTRUMENTS INC. BE LIABLE TO YOU FOR ANY DAMAGES, INCLUDING ANY

LOST PROFITS, LOST SAVINGS OR OTHER INCIDENTAL OR CONSEQUENTIAL DAMAGES

ARISING OUT OF THE USE OR INABILITY TO USE SUCH PRODUCT, EVEN IF BIOSPHERICAL

INSTRUMENTS INC. HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. NOR WILL

BIOSPHERICAL INSTRUMENTS INC. BE LIABLE FOR ANY CLAIM BY ANY OTHER PARTY.

SOME STATES DO NOT ALLOW FOR THE EXCLUSION OR LIMITATION OF INCIDENTAL OR

CONSEQUENTIAL DAMAGES FOR CONSUMER PRODUCTS, SO THE ABOVE LIMITATIONS OR

EXCLUSIONS MAY NOT APPLY TO YOU.

THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS, AND YOU MAY ALSO HAVE OTHER

RIGHTS WHICH MAY VARY FROM STATE TO STATE.

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BIOSPHERICAL INSTRUMENTS INC.iv

TABLE OF CONTENTS

1.0 INTRODUCTION ...........................................................................................6

1.1 SOFTWARE DESIGN ......................................................................................6

1.2 SOFTWARE REQUIREMENTS .......................................................................7

2.0 M24-PROF: DATA ACQUISITION PROGRAM.............................................8

2.1 M24-PROF PROGRAM OPERATION..............................................................8

2.3 M24-PROF PROGRAM OPTIONS.................................................................12

3.0 M24-READ: DATA ANALYSIS PROGRAM.................................................13

3.1 M24-READ PROGRAM OPERATION............................................................13

3.2 M24-READ MISCELLANEOUS AND DISPLAY OPTIONS............................14

<?>: QUICK HINTS .................................................................................14

<ESC>: RETURN TO MAIN MENU ........................................................14

<SPACE BAR>: TEMPORARILY HALT PROGRAM ..............................14

<X>: EXIT THE SYSTEM ........................................................................14

<A>: DISPLAY ALL CHANNELS.............................................................15

<E>: EXAMINE ONE CHANNEL AND CALCULATE STATISTICS ........15

<H>: HARD COPY REPORT FORMAT ..................................................16

<I>: PRINT THE CASTCARD .................................................................18

<K>: ATTENUATION COEFFICIENT CALCULATION ...........................18

<R>: RAW DATA IN HEX........................................................................19

<V>: FORCE ALL READINGS TO VOLTS .............................................19

<Z>: CLEAR THE MIN AND MAX R(ECORD) LIMITS ...........................19

3.3 M24-READ GRAPHICS AND PLOTTING OPTIONS.....................................19

<B> PACK A BINARY DATA FILE ..........................................................19

<C> SELECT ANOTHER CALIBRATION FILE ......................................19

<F> OPEN A BINARY DATA FILE ..........................................................20

<G> GRAPHICS DISPLAY......................................................................20

<L> LETTER A PEN PLOT .....................................................................22

<N> CLEAR THE MIN AND MAX R(ECORD) LIMITS............................22

<P> PEN PLOTTING...............................................................................22

<W> WRITE A CSV DATA FILE.............................................................24

4.0 M24-TEST ...................................................................................................25

4.1 M24-TEST PROGRAM OPERATION ............................................................25

4.2 M24-TEST PROGRAM OPTIONS .................................................................25

<A> ALL CHANNELS IN UNITS..............................................................25

<C> SELECT ANOTHER CALIBRATION FILE ......................................26

<E> EXAMINE ONE CHANNEL WITH STATISTICS .............................26

<ESC>: RETURN TO MAIN MENU ........................................................26

<H> HARD COPY DUMP........................................................................27

<I> I/O CONTROL...................................................................................27

<L> LOG A CALIBRATION RUN.............................................................27

<O> VIEW ONE CHANNEL ONLY .........................................................27

<R> DISPLAY RAW DATA IN HEX ........................................................27

<S> STATUS BYTE DISPLAY ................................................................27

<T> TEST THE DATA TRANSMISSION.................................................27

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BIOSPHERICAL INSTRUMENTS INC. v

<V> ALL CHANNELS IN VOLTS.............................................................28

<W> WRITE A BINARY FILE..................................................................28

<X>: EXIT SYSTEM ...............................................................................28

<Z>: WRITE A COMMA SEPARATED FILE..........................................28

5.0 M24SETUP: AN EDITOR FOR DEFAULTS.CFG .......................................29

5.1 MENU 1: CALIBRATION FILE EDITING.......................................................29

5.2 MENU 2: SETUP OPTIONS..........................................................................29

5.3 MENU 3: ADDITIONAL SETUP OPTIONS ...................................................32

5.4 PRINTER CONTROL CODE SEQUENCES ..................................................33

6.0 CALIBRATION FILES..................................................................................34

APPENDIX A: GLOSSARY OF TERMS USED..................................................36

APPENDIX B: RS-232 CABLE AND CONNECTOR ..........................................38

B.1 RS-232 CABLE CONSTRUCTION ................................................................38

B.2 RS-232 CONNECTOR CONFIGURATION ...................................................39

APPENDIX C: SOFTWARE INSTALLATION ....................................................41

APPENDIX D: PROGRAMMERS' NOTES.........................................................42

D.1 GRAPHICS SUPPORT..................................................................................42

D.2 PEN PLOTTER ..............................................................................................42

SOFTWARE END USER LICENSE AGREEMENT ...........................................45

BIOSPHERICAL INSTRUMENTS INC. 6

1.0 INTRODUCTION

This manual provides instructions for Version 3.1 of Biospherical Instruments’ MER-2040 data

acquisition and analysis software. This software is compatible with the MER-2040, MER-2041,

and MER-2050 Spectroradiometers. It is easy to use and is designed to run on IBM-PC and

equivalent computers ("clones").

There are two principal and two secondary programs that comprise this software package:

•"M24-PROF" is used for recording data during a vertical profile. It supports graphic and

numerical displays, annotated rosette firing, and castcard recording.

•"M24-READ" is the data analysis program. It supports the decoding of the recorded binary

data to CRT Graphics, pen plotter graphics, line printer dumps, ASCII file generation,

attenuation coefficient calculations, and many other features. M24-READ works with either

raw or packed data.

•"M24-TEST" facilitates testing of the MER instrument.

•“M24SETUP” is an editor for the configuration file (DEFAULTS.CFG).

In addition to these programs, the software contains two ASCII files: DEFAULTS.CFG and a

calibration file (*.CFL). These files allow you to support two instruments from one program and

make it possible for you to collect data from one type of computer and analyze it on another.

"DEFAULTS.CFG" holds system information, accessory device information, and default

suggestions as to which channels to plot and which to print in reports. The program

“M24SETUP” has been provided to facilitate customization of this file. All data covering the

exact configuration of an instrument and its calibration constants are contained in a second

ASCII file called the calibration file, which ends in the suffix ".CFL". You may change both of

these files to suit your purposes, but you must be very careful not to change the order of

parameters in either file. An example alteration would be to change the display of depth from

"Meters" to "dBars" by changing the label in the calibration file and adjusting the scale factor

appropriately. To make changes in software that require more than editing of the

DEFAULT.CFG and calibration files, you can either contact Biospherical Instruments at (619)

686-1888 and inquire about custom software or make the changes yourself using a Microsoft

compiler for Professional Basic Version 7.1.

This manual offers instructions for editing the ASCII files and for operating the four MER-2040

programs. For your convenience, we have included a sample data file so that you can practice

using M24-PROF and M24-READ before attempting to connect your MER system. It is

imperative that you read both this manual and your MER instrument manual carefully so that

you can fully understand the capabilities of your system and achieve the highest quality of data.

1.1 SOFTWARE DESIGN

Raw data is recorded in a packed binary (8 bit) format that follows the format of the data

transmitted by the MER instrument. Located at the end of the data stream from the MER

instrument is the data from the surface sensors (if any). The last character in the data stream

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BIOSPHERICAL INSTRUMENTS INC. 77

is the checksum as calculated by the receiving program. If the data has been transmitted error-

free, then this checksum should match the checksum transmitted from the MER.

The MER-2040 programs are written in Professional Basic Version 7.1. The source codes for

the programs are provided for two reasons: (1) to help you understand exactly what goes on in

the data analysis, and (2) to enable you to modify the programs to better suit your purposes.

We work hard to make sure the original factory supplied code is as error-free as possible, and

we correct errors that you discover to the limits of our time and ability. However, if you find it

necessary to modify these programs, please be warned that you must provide your own support

for the changes.

Before using or altering the software, we strongly recommend that you make several

copies of the original disks so that you can always go back to the original software if

you suspect a problem with the instrument or the data files. If you continue to have a

problem with unmodified software, please contact the factory.

Please note that the MER software is written to support several versions of MER instruments.

Therefore, some parameters in the software may not be applicable to your specific system. For

example, there are options dealing with "frequency" channels. These options only apply to the

larger MER instruments, and should be ignored if you are using a smaller (i.e., fewer channels)

MER.

1.2 SOFTWARE REQUIREMENTS

Minimum Required Hardware: IBM PC/AT, or "100% compatible clone"; 640 Kbytes RAM

memory; 10 Mbytes hard drive; "CGA" (Color Graphics Adapter), with a color monitor if CRT

graphics are to be used; and one RS-232 serial port.

Strongly Recommended Hardware: Enhanced Graphic Adapter (EGA or VGA); printer for data

dumps; pen plotter for high quality plots (Hewlett-Packard 7470, 7475 or Color Pro with RS-232

interface or 100% compatible plotter accepting "HP-GL" graphics language serial inputs); and

second serial port for plotter connection (plotter may also use first serial port if only one is

available, but you have to switch between ports for operation of the MER).

Required Files:

M24SETUP EXE - Configures the software using DEFAULTS.CFG

M24-READ EXE - Reads and analyzes recorded data

M24-PROF EXE - Acquires data from your instrument

M24-TEST EXE - Tests instrument operation

DEFAULTS CFG - Contains the normal operation conditions

DEFAULT PLT - A plot which will automatically appear

####.CFL - The specific calibration file for your instrument

NOTE: We have not tested all possible combinations of computers, MERs, printers, and

plotters. Therefore, before going on a deployment, we urge you to fully connect the exact

instruments, cables, and data acquisition system you intend to use and test all software

thoroughly. If there are any problems, please contact the factory.

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2.0 M24-PROF: DATA ACQUISITION PROGRAM

The program titled "M24-PROF" is provides acquisition of data during a vertical profile. This

program is designed to execute rapidly and it documents the conditions of the profile by

recording a "castcard". It records data in a packed binary format that follows exactly the format

of the data transmitted from the MER and optional deck sensors. For a full explanation of the

format of this data, consult the MER hardware manual. The only alteration to the data stream is

the addition of a comparison checksum at the end.

2.1 M24-PROF PROGRAM OPERATION

Before beginning to explore the software, remember to make one or more copies of all

software using the DISKCOPY command (consult your DOS manual). Consult Appendix C for

instructions on installing the software. In normal operation, you may start the program by move

to the MERPROG directory (<cd MERPROG>) of your hard drive and typing <M24-PROF>.

However, to allow you to get a feel of the program before connecting the instrument, we have

provided a sample data file in the DEMO subdirectory. To run the demo software, make certain

that there is a copy of M24-PROF in the DEMO subdirectory, move to that subdirectory (<cd

DEMO>), then initiate the program by typing <M24-PROF>.

NOTE: All commands to be entered by the user are enclosed in brackets: < >. DO NOT

include the brackets as you enter the command.

After the program has been initiated, it will start executing a search for the file labeled

"DEFAULTS.CFG". This file contains conditions directing the program's execution. If this file is

not found, an error will occur and program execution will stop. You will then have to make sure

that this file is found in the directory from which you are operating.

The DEFAULTS.CFG file causes the program to load the appropriate calibration file. If there

are two or more valid calibration files present, you are prompted to select the desired file. An

example of when there might be more than one calibration file would be when an instrument is

used in water and in air and, thus, has one file for "WET" (in water) calibration constants and

one for "DRY' (in air) use. It is important to note that the selection of a calibration file will only

affect the way that data are displayed; data are recorded in raw (uncalibrated) volts in binary

files. If, at a later time, you wish to modify the calibration file (see Chapter 6.0), subsequent

replaying of the binary files will reflect these changes.

If you are operating in the DEMO subdirectory, the DEFAULTS.CFG file there will tell the

program that this is a test run, and there is not a MER connected. The DEFAULTS.CFG will

load calibration files called "DEMO1.CFL" and "DEMO2.CFL", which specify that a VGA is

connected, and that the computer has a display and no printer. In addition, the program will be

instructed that the data file titled "DEMO.BIN" is to be substituted for the operating instrument to

allow you to simulate a vertical profile. This file contains depth and data values which simulate

a full vertical profile. To change the DEFAULTS.CFG file, see Chapter 5.0.

After loading all default parameters, the program will display an initial information screen and

ask "Press ENTER to continue...". After <ENTER> is pressed, the program will send

instructions to turn the pump and fluorometer off and then display several parameters on the

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BIOSPHERICAL INSTRUMENTS INC. 99

screen, as shown in Figure 2.1. The parameters to be displayed in are designated in the

DEFAULTS.CFG file.

Figure 2.1. M24-PROF Selected Parameters Screen.

The next step is to set up the castcard file by pressing the <F4> key. As shown in Figure 2.2,

the M24-PROF program will automatically assign a filename by which to record data. This

filename will start with the letter "P" followed by the current date in the format YYMMDD,

followed by a series letter ranging from A to Z. The software will assign the series letter after

looking for the last file recorded with the same date. If you have been very busy, and have

recorded files through letter Z, you will be prompted to enter your own choices for filename.

Finally, the suffix on the filename name will be ".BIN" to indicate that it is a binary file. You may

override the automatic filename by choosing <N> and then selecting your own filename.

NOTE: NEVER edit the binary file for two reasons: (1) it is original data, and (2) it is in binary

format and consequently cannot be edited by a text editor. If you do edit the binary file, the

MER-READ program may not be able to read it afterwards, and checksum errors may be

found.

After entering the file name, you will be prompted to enter answers to a series of questions that

are used to create the "castcard" (see Figure 2.3). The castcard is an ASCII data file that

contains information that documents the conditions under which the original data was recorded.

Automatically added to the file will be the date and time of both the start and stop of the profile;

the times you signaled a rosette firing, turned the pump on or off, or turned the fluorometer on

or off; how many records were recorded; and other parameters. You may later print out this

file, but recorded to be kept with the binary data file.

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Figure 2.2 M24-PROF Data File Opening Section .

Figure 2.3. M24-Prof Cast Card Parameters.

At the end of the castcard dialogue, you will be asked to approve its contents <Y> and will be

prompted to choose between a graphics display <G> and a numerical display. The graphics

option can be used only if you have a graphics monitor. If you enter <G>, and you do not have

a graphics monitor, or if you have specified the wrong graphics adapter, the program will crash.

If you selected a numerical display you will be returned to the Selected Parameters screen

shown in Figure 2.1. If you have selected a graphics display, you will see a menu of the default

graphics display conditions, which are specified in the DEFAULTS.CFG file (see Figure 2.4).

These conditions will include the maximum depth, and other parameters. If you are in DEMO

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