Biospherical Instruments Inc MER-2040, MER-2041, MER-2050 Software User Manual

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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

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.

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Document: 003110UB.DOC

Edition: June, 1998

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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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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

: 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

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

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/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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<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

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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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is the checksum as calculated by the receiving program. If the data has been transmitted errorfree, 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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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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mode, choose Option <4>. You will see the file "DEMOPLOT.PLT" listed. Select this file and press <ENTER>. After making all necessary changes to the plotting parameters, press <ENTER> and you will be returned to the Selected Parameters window shown in Figure 2.1.

Figure 2.4. M24-PROF Present Plotting Parameters.

At this point, you should prepare to launch the instrument over the side. At the bottom of the screen is a menu by which you can control your instrument and data acquisition. Section 2.3 will describe each of the menu options. Data will not be recorded until the <F4> key is pressed. At this point, if you selected the Option for graphics display, data will be plotted as shown in Figure 2.5. Data will be recorded to disk, and will continue to be recorded until you stop data collection. It is recommended that you completely cover the MER sensor and record a series of dark readings before and after each profile. By analyzing these readings, you can estimate the noise in each channel of the instrument (see Section 3.2, Option E). If you are running the DEMO program, press <F4> to begin reading the example data file. The display will show a simulated vertical profile until the end of the DEMO data file is reached. At this point, the data parameters on the screen will stop changing and you may exit and end the program by using <F9>.

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Figure 2.5. M24-PROF Plot Example.

2.3 M24-PROF PROGRAM OPTIONS

The following are the options in the M24-PROF program which are listed at the bottom of the Selected Parameters screen (Figure 2.1) and Plotting screen (Figure 2.5). As each operation is initiated, it is annotated in the castcard file.

<F1> Switch the pump off and on. <F2> Switch the fluorometer off and on. <F3> Arm and fire the rosette. <F4> Start or end data recording. <F5> Denote the end of a downcast. <F6> Denote the end of an upcast. <F7> Abort the program. Choose <A> to verify that you wish to end the program and

discard all recorded data.

<F8> Toggle between the numerical and plotting displays. <F9> End the program. Press this key again to confirm that you wish to stop data

acquisition.

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3.0 M24-READ: DATA ANALYSIS PROGRAM

The data analysis program supplied by Biospherical Instruments is the program M24-READ. This program is used to read binary data files that have been previously recorded using the program M24-PROF. M24-READ will provide you with several options for plotting your data and creating ASCII files usable by other software. It will provide printed output as well.

M24-READ can display raw data as voltages or frequency, apply calibration constants for displays in optical or oceanographic units, calculate new channels based on transformations or combinations of other channels, and process the raw data to display one meter averages. A particularly useful feature is the calculation of the attenuation coefficient ("K").

3.1 M24-READ PROGRAM OPERATION

To read a data file that has been recorded in the primary directory MERPROG, move to that directory (<cd MERPROG>) and initiate the program by typing <M24-READ>. To read the DEMO data file, move to the DEMO directory (<cd DEMO>), make certain that it contains a copy of M24-READ, then initiate the program.

You will be presented with a listing of the data files (ending in ".BIN") that are found in the disk/path specified in the "DEFAULTS.CFG" file (i.e., C:\DEMO or C:\MERPROG). Choose the data file you wish to analyze. If the computer finds this file, the program will then display the master menu shown in Figure 3.1. The top section of this menu lists the program name and version number. The remainder of the screen is divided into four sections: Display Options, File and Plotting Options, Miscellaneous Options and Status. Each of the options will be discussed in Section 3.3. The Status section indicates the names of the calibration and data files being accessed and the current location in the data file (i.e., the current record number). This enables you to track the progress of the data analysis.

M24-READ is designed to read binary data files, accessing either one complete spectral data scan by record number or the numerical average of all records in a selected portion of the data file that correspond to each one meter depth interval. In a normal vertical profile, such as that recorded in the DEMO file, "DEMO.BIN", there are approximately 1850 complete scans, or record numbers. Note that the first and last several records in a data file are usually recorded when the instrument is covered (for dark readings), as the instrument enters or exits the water (yielding negative depth readings), or in the first few meters below the surface. These or other data may be eliminated from data analysis by redefining the beginning and ending data records using Option <E>, as described in the following section.

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Figure 3.1. M24-READ Master Menu.

3.2 M24-READ MISCELLANEOUS AND DISPLAY OPTIONS

The following are general functions that apply in almost any menu of the program:

<?>: QUICK HINTS

Offers a quick preview of all key assignments

<ESC>: RETURN TO MAIN MENU

Returns the user to the main menu (Figure 3.1) at any time during program operation.

<SPACE BAR>: TEMPORARILY HALT PROGRAM

Press the space bar to halt program operation, then press it again to restart the program.

<X>: EXIT THE SYSTEM

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<A>: DISPLAY ALL CHANNELS

This will initiate a display of all MER channels in calibrated units (see Figure 3.2). The display will indicate the calibration constants, as well as the format (position of the decimal point) and label (e.g., "Depth") that are specified in the calibration file. If frequency channels are available, the temperature and conductivity channels will be displayed followed by the salinity and density parameters.

The display will be updated as new records are read. To pause this display (and many others in this program), press the <space bar>. When you want to resume updating the screen with new readings, press the <space bar> again. Notice that the second line of the All Channels Display contains the current record number. When you reach the end of the data file, the file pointer will automatically be reset to the beginning record. You can return to the main program menu at any time by pressing <ESC>, or you will be returned to the main menu automatically when either the end of the file or a marked final record is reached.

This display, like all numerical (not graphics) displays in this program can be captured on paper by pressing the <PRTSCRN> key, provided you have a printer connected. Graphics displays may be captured with certain add-on programs.

Figure 3.2. M24-READ All Channels Display.

<E>: EXAMINE ONE CHANNEL AND CALCULATE STATISTICS

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A method for displaying one channel of data at a time is to select the <E> option. You will be presented with a list of available channels (Figure 3.3). Select the appropriate instrument number and channel numbers from the list that is presented. For instance, entering <1,4> will select channel 4 from instrument 1, the 507-nm downwelling irradiance channel. Notice that there are several options in addition to the ones that directly correspond to individual channels. For example, selection or <38> "% PAR" will read both the surface light PAR channel and the underwater PAR channel (if they are available), and automatically calculate the percentage of surface irradiance measured underwater. (NOTE: The selection of channels used in the calculation of %PAR is addressable with the program M24SETUP.)

Figure 3.4 shows a sample output for Channel 4 of Instrument 1. Both individual channel readings and general statistics are displayed. The statistics (min, max, mean, and standard deviation) are calculated for all readings in the designated section of the data file, or until <ESC> is pressed. The standard deviation is particularly useful in examining the dark readings in a particular channel. Dark readings should be analyzed as voltages (see Option <V>). If a standard deviation is greater than several hundred microvolts, the channel may be excessively noisy or unstable; contact the factory for advice.

Option <E> can also be used to select a new end record (or “max record”). View the depth channel by selecting <33>. You will see the record numbers and depth readings quickly scrolling up the screen. To pause or restart the display, press the <space bar>. To choose an endpoint, press <F4>. Finally, press <ENTER> once or twice until you are returned to the main menu. You can now analyze the newly segmented data.

As an example of using this method to segment data, read the DEMO.BIN data file. Press <F4> at record number 1700 in the depth display. This will place a marker at the end of the downcast. Next, return to the main menu. Finally, choose <G> to plot the segmented downcast on the screen.

<H>: HARD COPY REPORT FORMAT

This is to provide you with a printer dump of selected scans. Usually, the MER scans more channels than can fit on a normal printer page, even with "compressed" print (which is automatically requested here). This option provides two methods of selecting which scans to print. The first method requires selection of the depth increment to print. If 5 meter increments are selected, the program will flag depths of 5, 10, 15, etc., meters for these depths and print them out. If you are scanning the upcast portion of a data file, the data will print out in order of deepest to the surface measurements. If a certain depth is missed on the downcast, and found on the upcast, it may be printed out of order.

The second method of selecting data to print is to choose all depths but limit the reading to a previously marked record range.

The DEFAULTS.CFG file contains the setup and "compressed" control code strings that are sent to the printer before any print job. Edit these settings to optimize the use of your printer’s capabilities.

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Figure 3.3. M24-READ Available Channels.

Figure 3.4. M24-READ Standard Deviation Analysis.

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: PRINT THE CASTCARD

The M24-PROF data acquisition program creates a "castcard" file to accompany each binary data file. Option will read the castcard files and print them. These files are ASCII files, so they can also be edited with most word processors and can be printed in DOS using the "PRINT" command (consult your DOS user’s manual).

<K>: ATTENUATION COEFFICIENT CALCULATION

Option <K> calculates and displays an Attenuation Coefficient, or "K", for a selected channel. You will be presented with four options for calculating and using the attenuation coefficient. First, you may calculate the coefficients and hold the values in memory. Second, you may print the attenuation coefficients to the printer (this takes one line per record, so a 2000 record data file will take 33 pages to print). Third, you can create one meter "binned" averages of the irradiance data and then calculate a "K" of these data. Finally, you can save the K’s to disk.

You will be presented with a list of channels for which to compute attenuation coefficients. Note that some of the channels are not useful. For instance, you could ask to compute the K of depth, which would be meaningless. Ignore these choices and choose only the channels you need.

Next, decide whether or not you want smoothing. This calculation uses a derivation of a method suggested by Ray Smith and Karen Baker (University of California Marine Bio-Optics Group). The algorithm reads each data value, calculates its natural log, calculates intermediate products and cross products, and computes sums until all points have been read. Next, a least squares fitting of a selected number of records before and after each data value is computed. (For example, a choice of eleven point smoothing involves five records before and after the selected data point.) The resulting multiplicative coefficient becomes the calculated attenuation coefficient. This attenuation coefficient is stored in memory for future display and manipulation.

After calculating the attenuation coefficient, you may wish to normalize the data to surface light. This option will again display the list of possible channels, and will prompt you for the desired surface channel. Again, some of the available channels will not be useful. DO NOT use this option for data recorded on a cloudless day. If you do, any variation in the surface light caused by shading of the ship’s antennae or by rocking of the ship will be transferred to this normalized ratio. This option is only helpful for cloudy days, though it will not be entirely successful in removing distortions in "K" caused by clouds. The reason for this is that the surface and underwater sensors are not both located at the same spot directly below the clouds. Therefore any cloud movement, particularly in low-lying clouds, will cause effects at slightly different times. In addition, breaks in the clouds will cause differences in above-surface radiance spatial distributions such that different portions of the total incident light will be transmitted through the air-water interface.

Finally, you may choose to exclude data close to the surface. Frequently, when data is collected in the open ocean, surface waves and ship motion make light readings in the top four meters very erratic. These data should probably be excluded from calculations of K.

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<R>: RAW DATA IN HEX

This option is helpful in "debugging" problems in data files, or in examining exactly how data is transmitted from the MER. The display shows, in hexadecimal, each byte that is recorded in the data file. A new line will begin for each new record. If you wish to use this option, refer to the programming and data decoding section of your MER hardware manual.

<V>: FORCE ALL READINGS TO VOLTS

Normally, M24-READ will display the various sensor readings in the engineering units specified in the calibration file. For example, the voltage output of the pressure sensor is translated to "meters" using the calibration information in the calibration file. If you preferred to display this measurement in "dBars", then the calibration constants and the units field must be appropriately changed in the calibration file (see Section 7.0). The <V> option will allow you to force the displays to volts or frequencies, which are useful in troubleshooting applications. Displays will continue in these units until the program ends or a calibration file is reloaded using Option <C>. Note that the <V> option cannot be used on one-meter binned data, but after this option is run, any binned data created will be in volts.

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

Option <Z> will clear the current start and stop record numbers so that you can access the entire data file. These reading stops are continuously displayed on the main menu. The default value for the final record number is 30000, which was selected with the assumption that no file would be that big and that this would cause the file to be read to the end.

3.3 M24-READ GRAPHICS AND PLOTTING OPTIONS

M24-READ supports both screen and pen plotter graphics. Most of the graphics options are organized so that you can first preview the plot on the CRT screen to optimize the scaling and parameter selection. When the screen plot is satisfactory, then the plotting conditions can be written to a data file, if desired, and a pen plotter dump can then be requested. The discussion will start with requesting a plot like that produced by the Profile program (Figure E).

PACK A BINARY DATA FILE

This option creates one-meter averages for the data and, if desired, it stores the results in a ".PAC" data file on disk. The data will remain in this format for analysis until a new data file is selected using the <F> command.

<C> SELECT ANOTHER CALIBRATION FILE

To change the calibration file being used to decode the recorded data, select the <C> option and select among the available *.CFL files. This option automatically forces you to respecify a file.

WARNING: If you choose a calibration file for any instrument configuration (i.e. number of channels, etc.) other than the one that recorded the data, error may result.

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<F> OPEN A BINARY DATA FILE

To stop reading the data file currently in use, select the <F> option and enter the name of a new file. You will then be returned to the main menu with the file pointer positioned at the beginning of the file. This option is also useful if you wish to quickly reposition the file pointer to the beginning of the file. It will dump any binned or averaged data in memory and will reset the program to the binary file mode.

<G> GRAPHICS DISPLAY

This option will present you with the menu illustrated in Figure 3.5. The plotting parameters shown initially are those recorded in the DEFAULTS.CFG file. To alter any of the listed parameters, enter the number to the left of the selection. You will then be prompted accordingly. The format of these plots is depth versus up to four selected parameter(s). Depth is displayed on the vertical axis of the plot in ascending order, while the other parameters are displayed on the horizontal axis.

Figure 3.4. M24-READ Vertical Profile Plotting Parameters.

The following describe the selectable parameters in Figure 3.4:

<1> Minimum and Maximum Plotting Depths. The minimum depth displayed here means that all readings shallower than this depth will be rejected, but the plot axis will always start at zero. This is done because of the convention of starting plots at the surface while needing an easy method of filtering out erratic data recorded near the surface. The maximum depth in this option will be both the points where plotting stops and where the axis stops.

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<2> Graphics Device. Select the code for the graphics device that will be used. Permissible values are:

0 HPGL Pen Plotter. 2 200*640 medium resolution one color display (usable with the <PRNTSCRN> key for

printer dumps, or with monochrome displays, and no graphics card).

9 360*640 high (EGA) resolution 16 color display. (NOTE: <PRNTSCRN> will not work

in this mode!)

10 200*640 resolution monochrome plotting with an automatic screen dump to the printer.

This option is useful for batch processing as the computer does not pause at the end of the file and wait for you to take action, rather it automatically dumps the plot.

11 MCGA, useful on an IBM-PS2 Model 3, for example, supports very high resolution (two

color plotting on color and monochrome MCGA monitors). If you have selected MCGA, the background will automatically be set to 0 (black).

12 VGA higher resolution graphics adapter.

NOTE: IN ORDER FOR THE PLOT TO BE DUMPED TO THE PRINTER, YOU SHOULD HAVE EXECUTED THE DOS: "GRAPHICS" COMMAND Before RUNNING M24-READ. If you have not, you will simply dump the alphanumeric characters present, and not the graphics image.

<3> Number of Channels to Plot. Change the channels being plotted, and define which channels to plot by subsequently entering each channel number.

<4> Read a Set of Plotting Parameters. Option 4 will allow you to read a previously recorded plot description file. You will see a directory of the ".PLT" files present and be asked to select among them.

<5> Record This Set of Plotting Parameters. This saves the parameters specified for the plot including channel selections, depth and plotting limits. You will be offered a list of plot (*.PLT) description files already on the default disk/path, and will be prompted for a filename prefix to which the extension will be automatically appended.

NOTE: The object of Options 4 and 5 is to allow you to define several types of plots to be made and then easily recall these configurations either from the M24-PROF or M24-READ programs. When you start either of these programs, the file specified in the DEFAULTS.CFG file will be loaded. The plotting files will be recorded in the same directory as the defaults file.

<6> to <10> Channels to Plot. To change a channel plotting designation, enter the number to the left of the channel to be changed, and then select a new channel. You will also be prompted to choose between log and linear plots.

Finally, to proceed with plotting, simply press the <ENTER> key and, assuming you have not selected the pen plotter, the graphics screen will be drawn and plotting will start. Plotting may be paused at any time by pressing the <F10> key, or stopped by the <F9> key. Otherwise, plotting will continue until the end of the data file or until the previously marked final record is reached. At that point, the prompt at the upper left of the CRT screen will ask you to push <F9> to return to the main program menu.

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<L> LETTER A PEN PLOT

After you have plotted data using the pen plotter, you may wish to add text to the plot. This can be accomplished by selecting the <L> option from the main menu and following the instructions. This option will permit pen selection and changes in lettering height and direction.

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

Option <N> will allow you to select a section of a data file for display and analysis. It also allows you to toggle the printer control parameter and to select another averaging period if you have frequency output sensors (e.g., a Sea-Bird instrument). If you have marked "Events" in the data file by recording the record number, this option will allow you to key in the record numbers outlining these events directly.

PEN PLOTTING

There are two types of pen plots that can be generated with M24-READ. Option <0> creates a pen plotter interpretation of your CRT plot. Option , Pen Plotter Spectral Plot, will allow you to plot a range of channels where the Y-axis is log intensity and the X-axis is wavelength. This section will be described later, but first a description of the pen plotter translation of the CRT plots follows.

When you select Graphics Device <0> in the Vertical Profile Plotting Menu, you will see another menu specifically designed for Hewlett-Packard Pen Plotter output. This menu, shown in Figure 3.6, can be edited. For example, by selecting Entry <1> you can change the label height. Entry <3> allows pen speed adjustments if you are making transparencies. Entry <5> allows you to suppress axis generation for quick plots or multiple profiles plotted on one another. You can also edit the label fields, pen number, line type and select symbol plotting for the channels shown at the bottom of the screen. (NOTE: The label and number heights are in cm.) Editing of the last field (#11) allows plotting to a data file (spooling for later plots). If you enter the word "FILE:" followed by a filename, then the plot will be recorded on disk instead.

The selection of wavelength spectra plotting will allow you to plot a wavelength from the selected sensor array at selected depth intervals. Typically, you might choose to plot wavelength spectra from every 5 meters on the same plot. Figure 3.7 shows a list of the options available for the spectral plotting and the pen plot generated from the demo file follows this.

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Figure 3.6. M24-READ Pen Plotter Parameters.

Figure 3.7. Spectral Distribution vs. Depth Plot.

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<W> WRITE A CSV DATA FILE

This option of M24-READ is designed to translate a binary data file to an ASCII data file in which the readings for each channel will appear in engineering units. This translation process uses the formats specified in the calibration file, and separates each reading using the delimiter specified in the DEFAULTS.CFG file. This delimiter is usually a comma, and the file created is thus known as a CSV file (comma-separated value). Each data record begins on a new line.

This extraction process prompts you to enter the beginning and final records to be translated. To read the entire file, just press <ENTER> in response to each question.

The resulting data file has the same name as the original data file except that the file extension is ".CSV". When file translation is completed, the program returns to the master menu with the file pointer positioned at the beginning of the file.

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4.0 M24-TEST

M24-TEST is a program that is designed to test your MER to confirm that it is operational. This module has the ability to perform real-time data acquisition and storage in addition to reading binary data files that have been previously stored using the "M24-PROF" or this program, M24TEST.

4.1 M24-TEST PROGRAM OPERATION

To start the program, move to the MERPROG directory and enter the command <M24-TEST>. The program will begin by searching for the file labeled "DEFAULTS.CFG". This file contains the instructions directing the program's execution. If this program is not found, an error will occur and program execution will stop. You will then have to make sure that this file is found on the default drive/path (i.e., in the MERPROG directory).

M24-TEST will next display the communications port address (COM1 or COM2) specifying where the MER is connected to your computer, and then will prompt you to select between the available calibration files. Next, you will be shown a table of operational parameters from the calibration file. Its primary purpose is to allow you to review the number of active channels in the instruments and the serial number of the instrument and choose another calibration file if necessary.

After calibration file selection, you will be presented the M24-TEST menu shown in Figure 4.1. To proceed further, you must have your MER connected to the appropriate com port and powered on. The following section details the options available in the M24-TEST menu.

4.2 M24-TEST PROGRAM OPTIONS

<A> ALL CHANNELS IN UNITS

This option will display calibrated data in units such as meters, degrees, microwatts, cm², etc. The data is calibrated, formatted (position of the decimal point) and labeled (e.g., "Depth") using specifications in the calibration file. If frequency channels are available with your instrument, salinity and density will be displayed as well as temperature and conductivity parameters. This display, like all numerical (not graphics) displays in this program, can be captured on paper by pressing the <PRTSCRN> key, assuming you have a printer connected.

The All Channels in Units display will be updated continuously as new records are read/acquired and displayed. Notice that the second line of the all channels display contains the Record Number. To pause the display (and many others in this program), just press the <space bar>. When you want to resume updating the screen with new readings, press the <space bar> again. To return to the master menu, press the <ESC> key at any time. Note that if you are in the TEST MODE, the record counter will point to the last data record read and NOT AT THE START OF THE DATA FILE!.

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Figure 4.1. M24-TEST Main Menu.

<C> SELECT ANOTHER CALIBRATION FILE

If you wish to change the calibration file being used to decode the recorded data, select the <C> option. Here you will have a chance to select among the available data files.

WARNING: If you change to a calibration file containing a configuration for any instrument other than the one that recorded the data, error may result.

<E> EXAMINE ONE CHANNEL WITH STATISTICS

This option first prompts you to choose between units and volts and then asks for the instrument and channel to display. The program extracts the desired parameter from the data stream, applies the calibration constants, and, when you press the <ESC> key on the keyboard, it displays the mean, standard deviation, minimum and maximum of all of the readings that have been accessed. Press any key to return to the main menu.

<ESC>: RETURN TO MAIN MENU

Returns the user to the main menu (Figure 4.1) at any time during program operation.

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<H> HARD COPY DUMP

This option will print selected parameters in engineering units on your printer. The selected channels are those specified in the DEFAULTS.CFG file. Other printed dumps of all channels can be obtained using the <PRTSCRN> key function during the desired CRT display.

I/O CONTROL

This option allows you to program the MER to set various parameters including turning the pump on and off, turning the fluorometer on and off, arming and firing the rosette, and changing the number of averages, samples and delay in the instrument.

<L> LOG A CALIBRATION RUN

This option calculates the average, standard deviation, minimum, maximum and raw voltages of a range of channels on the instrument. After the instrument, channels to be sampled and number of samples to be taken have been chosen, the program calculates the values and displays them. It then offers the choice to write the values to disk, normalize them, repeat the calibration run, repeat test without change to normalization, or exit to the main menu.

<O> VIEW ONE CHANNEL ONLY

The <O> option presents you with a list of the available channels. This list will include both the "real" and the computed or derived pseudo channels. For example, salinity is a derived channel since the salinity measure is derived from conductivity, temperature, and depth. The channel display shows the instrument number, the channel number, the channel label, the raw units (volts or frequency), the computed parameter, calibration data applied, and the units of measure.

<R> DISPLAY RAW DATA IN HEX

This option is helpful in "debugging" problems in data files or in the data scan transmitted from the MER. Each byte is displayed in hexadecimal. A new line will be begin for each new record/scan.

<S> STATUS BYTE DISPLAY

This option will quickly read the recorded data and display the contents of the "status byte" that is transmitted by the MER with each data scan. Reviewing this will allow you to see if the recorded data has transmission errors or power dropouts, which will block power-ups (see the programming and data recording section of your MER hardware manual).

<T> TEST THE DATA TRANSMISSION

This option is provided to quickly scan the data from the instrument looking for transmission errors as detected by either a checksum or header error, and to measure the instrument cycle rates. The display will show the buffer pointer, which is the number of data characters in the

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host computer buffer that have not yet been collected for display. This is meaningful when operating in the non-handshake mode where the MER is freely transmitting data. If the host computer is fast enough to capture data, calculate values, and check the checksum, the buffer pointer should stay low (less than 150). If, however, you are using a slow computer, like an IBM XT, and the MER is programmed for little or no analog averaging, then this value will grow until it approaches 3000, at which point the software will discard the awaiting data and reset the buffer. This mode can be useful in optimizing the sampling rates in non-handshake applications. Remember, however, that the M24-PROF program has a higher overhead of processing for display and storage so a slower sampling rate may be imposed. The <T> option will also compute the number of complete scans per second being achieved.

The test mode will tabulate which kind of error is occurring. If you continually get "checksum error" but not "header error", the match between your MER and the specified calibration file is probably incorrect. An example would be if you selected the demo calibration file "DEMO1" yet were connected to a MER-1010. Since the calibration file specifies many more characters of data, the checksums will be improperly located, causing errors. If you received "UART errors", your instrument may be operating at the wrong baud rate (controlled by switches inside the MER), you may have a defective com port inside your computer, or there may be poor connections in your cable.

<V> ALL CHANNELS IN VOLTS

This option will present a display of all of the channels in the MER System, including any surface light or frequency channels. All of the parameters will be shown in low level units, either volts or frequency.

<W> WRITE A BINARY FILE

This option will prompt you to enter a filename in which to store data and the number of scans to write to disk. You will then be returned to the main menu and any subsequent data displayed in the above modes will be combined and written to disk. This file can later be read by M24READ.

<X>: EXIT SYSTEM

This option stops the program and re-enters DOS.

<Z>: WRITE A COMMA SEPARATED FILE

This option opens a ".CSV" file in which to record data. It then reads from the instrument(s) and stores the data in ASCII format. The <ESC> key will stop the option and return you to the main menu.

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5.0 M24SETUP: AN EDITOR FOR DEFAULTS.CFG

The MER software is designed to support Biospherical Instruments' Series 204X and 2050 Spectroradiometers. It is also designed to work with several types of display devices. To avoid having an extensive dialogue about system configuration each time a program is run, we have created a file called "DEFAULTS.CFG" that contains the default, or most likely, parameters for your data acquisition system. These parameters include the names of the calibration files, display types, printer control codes, channels of most interest and location of the communications port. M24SETUP facilitates editing of this defaults file.

To start the program, from the MERPROG directory prompt type <M24SETUP>. The first screen will prompt you to confirm that you wish to truly edit the DEFAULTS.CFG file and that you are not working on the original system disks. Enter <Y> to acknowledge this.

5.1 MENU 1: CALIBRATION FILE EDITING

The next screen will present the choices of calibration files to include in the defaults file, followed by the option to choose a preferred file for automatic selection (see Figure 5.1). To confirm your choices, press <Y>.

Figure 5.1. M24SETUP Calibration Filename Editing Screen.

5.2 MENU 2: SETUP OPTIONS

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The next screen (Figure 5.2) lists all setup parameters. Line 1 contains a flag noting whether or not you normally have a printer connected. If this is set to 1, then the program M24-PROF will automatically dump to the printer at various stages in its operation. If no printer is available, set this entry to 0, and most places in the software requiring a printer will be skipped.

Figure 5.2. M24SETUP Setup Options Menu 2.

Line 2 contains the COM (communications port or RS-232 serial port) address that will be used by the MER. This address can be either 1 or 2 for COM1 or COM2. The port will automatically be set to 9600 baud for data transmission.

Line 3 contains the disk designation and path for data storage. Valid examples are <A:\DATA\>, <C:>, and <\DATA\.>.

Line 4 contains the disk designation and path for overflow data storage that might be used during a vertical profile if the primary data storage section becomes full. This could be a floppy disk, for instance.

Line 5 contains the disk designator for the location of the calibration files. Leave it blank (" ") if the calibration files are in the same location (directory or subdirectory) as the programs.

NOTE: The DEFAULTS.CFG file is always searched for on the currently logged drive/path.

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Line 6 contains the code for the CRT graphics device that will be used. Permissible values are:

0 No device, no graphics displays. 2 200*640 medium resolution one color display (usable with the <PRTSCRN> key

for printer dumps, or with monochrome displays). Printer dumps first require executing “Graphics" from DOS.

9 360*640 high (EGA) resolution 16 color display. (NOTE: <PRTSCRN> will not

work in this or higher modes!)

11 MCGA. This option, useful on our IBM-PS2 Model 30, for example, supports

very high resolution (two color plotting on color and monochrome MCGA monitors). If you have selected MCGA, the background will automatically be set to 0 (black).

12 VGA higher resolution color display.

Line 7 contains a line of text that will be added to all castcard files by the program M24-PROF. Set this once at the beginning of a cruise and it will be used until you change it.

Line 8 contains the test flag for checking the programs. If this is set to 1, the data file found on the next line will be read instead of reading the instrument when you run M24-PROF. Normally, this must be set to 0, but if you want to try out the programs in the lab, this can be helpful.

Line 9 contains the name of the data file referred to in Line 8. The data file listed here is a profile with a MER-1048 to 65 meters in coastal water with clear skies. The demo data file C870919E.BIN requires the calibration file "CALYPS87.CFL". In normal operation this will not matter.

Line 10 will record local time or GMT in the castcard file before recording data in the M24PROF program. This is simply an annotation in the printouts and depends on your computer's clock agreeing.

Line 11 specifies the normal maximum wavelength to be used in plotting intensity versus wavelength in the M24-READ program.

Line 12 specifies the normal maximum plotting depth in depth units (meters or dBars). The M24-PROF program will use this value in plotting the profile, and the M24-READ program will use it for CRT plots. Both the M24-PROF and M24-READ programs will allow you to alter this value during the run of the particular program.

Line 13 is used during data plotting on a multi-pen plotter and specifies which pen will be used first for data. The value can be changed during program execution.

Lines 14 and 15 refer to the calculation of percent light during a vertical profile. The channel named in line 14 will be used to normalize data to surface light (assuming the MER system is equipped to measure surface light during a vertical profile). Line 15 names the channel for underwater light (this would normally be the channel of a PAR sensor). If your unit is not equipped with a PAR channel, you may wish to specify a channel in the blue-green range. If

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you have a four-channel deck sensor, then pair the channels at the same wavelength. In selecting these channel numbers, DO NOT simply use channel numbers from the examples in this manual!

Line 16 states the type of plotter.

Line 17 contains the plotter initialization string that is used by the operating system (DOS) to initialize the serial port for communications. You may set the baud rate and port address by changing this. See your DOS manual "MODE" section for a discussion of what this means. By using "FILE:M24-PROF.PLT" instead of that shown, the plotter output will be written to the file "PLOTFILE.PLT".

Line 18 contains the character to be used as the delimiter in generating ASCII extracted data files. Normally this is a comma.

5.3 MENU 3: ADDITIONAL SETUP OPTIONS

Figure 5.3 presents the next menu seen in M24SETUP. Line 1 contains the name of the plot description file to be used in normal graphics displays in M24-PROF and M24-READ. This selection can be overridden in each of these programs.

Figure 5.3. M24SETUP Setup Options Menu 3.

Line 2 will display a numerical list of the channels displayed in "report format" in M24-PROF and M24-READ printed reports. To edit this list, you will need the numbers associated with the channels in the Channel Selection menus of these programs.

Lines 3 to 6 can be used to predefine up to 4 ratios to be displayed.

Line 7 will define the transmissometer path length for calculation of "K" if a transmissometer is connected.

Line 8 will allow definition of the background color in EGA and VGA graphics modes. This, normally, is set to 8 (gray) but can be set to 0 (black) or any other number.

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5.4 PRINTER CONTROL CODE SEQUENCES

Figure 5.4 shows you the final menu in M24SETUP. This will allow you to define printer control code sequences used during most printer outputs.

Figure 5.4. M24SETUP Printer Control Code Sequences.

Following this menu you will be asked to confirm that you want the changes recorded. Enter <Y> to do this and exit the program.

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6.0 CALIBRATION FILES

A complete instrument description is found in the calibration file. This file must end in ".CFL" and it must match the format specified here. You may have more than one calibration file present on the operating disk (such as one for each cruise or each instrument calibration), but only one can be active. The source code that reads the calibration files is found in the subprogram "CALCON" of MIBINARY.BAS.

Line 1 contains a description enclosed in quotes. This should include the date and must include the model number (e.g. 2040, 2041or 2050), followed by the number of averages, delay in ms, and number of samples. Next are the filename., serial number, and tag number of the instrument.

Line 2 contains the format description of the following calibration lines for the instrument.

Line 3 lists a number in enclosed by quotation marks. This is the number of channels to be read.

Lines 4 through 30 have the following format:

1,1,"Ed410",.006919,.001519,.0001,5,"dnwell irr uW/cm2/nm","###.####",1,25.5

These parameters are as follows:

1 Channel type where:

1= underwater downwelling irradiance analog channel 2= underwater physical parameter analog channel (e.g., depth) 3= upwelling radiance channel 4= upwelling irradiance channel 5= frequency channel for temperature 6= frequency channel for conductivity 7= surface light channel 9= DAS channel (not normally used)

1 Channel number.

Ed410 Channel label. This must be exactly five characters long. It is displayed

frequently in the software. The labels "DEPTH" and "TRANS" should not be altered as they allow special functions.

0.006919 Scale factor (volts/units).

0.001519 Offset volts. These calibration factors are used by the routines found in the MER-SUBS.LIB section of the code such that

Final Units = (Volts - offset) / scale

0.0001 Default minimum voltage. Any voltage below this value is considered to be in the noise range of the instrument and will be set to 0 when calibrated.

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5 Default maximum voltage. "dnwell irr uW/cm²/nm" The units label for the calibrated data. Keep this line brief,

or only part of it will be printed or displayed by a program.

"###.####" The numeric format that will be used in the displays. Do not change the

length of this, or the formatted displays will not be pretty. This format may be made exponential if desired by using the ^^^^ notation (e.g. #.##^^^^). Consult any BASIC manual under "PRINT USING ..." for more information.

1 The gain setting for the individual channels. 0 is for autoranging, 1 is for a gain

of 1, 2 is for a gain of 16, and 3 is for a gain of 256. For a more complete description, please consult the command of your MER instrument manual.

25.5 The PAR weighting value that can be used in calculating PAR based on the

downwelling irradiance channels. This weighting value is multiplied by the calculated value for that channel and all downwelling channels are likewise treated. The software then sums these values to calculate PAR in the same units as the downwelling irradiances (microwatts or quanta or microEinsteins).

NOTES:

A line starting with “5” specifies that the channel is a frequency (as opposed to analog) channel for temperature. Following the label are five numbers representing the Sea-Bird Electronics calibration factors for the frequency output temperature probe. These numbers are used to calculate temperature in degrees C from the output frequency using an equation suggested by Sea Bird. This is found in the source code file "MER-FREQ.LIB". The next entries on the line are the channel units ("degrees C(#642)"), the default display format, the frequency choice (1, 2, or 3) and the available frequencies.

A line starting with "6" specifies that the channel is for a Conductivity sensor. The label "Cond" will be used in printouts, and the following numbers are the Sea-Bird Electronics calibration factors for use in calculating conductivity from one of their sensors. The entry similar to "mmho (#237)" is the units line for the displays with 237 referring to the sensor's serial number and "##.####" specifying the display format. The last entries are the frequency choice (1, 2, or 3) and the available frequencies.

A line beginning with 7, as follows, describes a surface light channel (from the deck sensor, if supplied) and is treated in the same way as the underwater analog channels.

7,1,"S.Lit",-1.6157,.00046,0,1,"E17 q/cm²/sec","#.##### ",0,0

A line such as ["Clock",2457830,21] contains the frequency channel reference crystal measured in hertz (meaningful only if your instrument has frequency channels, but always necessary) and the version of the software in the MER EPROM.

A line starting with "NOTES:" contains notes that will not be read by the programs, but are present only for purposes of documentation.

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APPENDIX A: GLOSSARY OF TERMS USED

ASCII - American Standard Code for Information Interchange. Such files can be examined using an editor or a word processor in the non-document mode or other method.

BAUD RATE - The number of signal level changes per second in a serial Transmission. Data Rate (e.g.9600, 1200, 300 baud).

BINARY - The most concise form of representing data. Unreadable when displayed with a text editor.

BINS - Number of divisions. Used in one meter averaging as one meter "bins".

CHANNELS - MER input channels, normally on per sensor is required.

CHANNEL UNITS - Assigned to channels (e.g. microwatts, engineering units).

CHECKSUM - When the MER transmits data, an arithmetic sum of the binary values of all characters is computed and transmitted as the final character. The host computer software will recompute this and compare the total as an indicator that data was correctly transmitted.

CONSOLE - The keyboard or other interactive device.

CRT - The Cathode Ray Tube or display monitor.

CTD CABLE - Cable commonly found on oceanographic ships and normally consists of an outer coaxial conductor with outer steel armor that is capable of supporting the weight of a heavy instrument. Normally several thousand meters long.

DISPLAY FORMAT - The number of digit and format (exponential or decimal) of numerical displays.

DRIVE - Storage media. Either a floppy or hard disk, or "RAM" disk.

FILENAME - The name of a file. You see the name when you list the directory or use it to access a file. The general form for a filename is: NAME.TXT. For a further definition see your DOS manual.

HANDSHAKING - Two directional data communication where the host computer asks for data from the MER as opposed to when the MER is sending data without being asked each time (in the FSK mode, for example). Requires 4 cable connectors.

HEADER - The first character of all MER data transmissions. Normally the "S" character (53H in ASCII code).

INPUT CHANNEL - See CHANNEL.

MENU - A list of information or options.

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PATH - Searches specified directories for commands or batch files that were not found by a search of the current directory.

PLOTTER - An external graphic device. For the MER programs, it must use the HewlettPackard Graphics Language ("HPGL") and must be a plotter for one of the DOS recognized serial data ports.

UNPACK - Conversion of data from ("packed") binary to ASCII.

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APPENDIX B: RS-232 CABLE AND CONNECTOR

B.1 RS-232 CABLE CONSTRUCTION

WARNING: Dangerous voltages, capable of causing death, are present in this instrument. Use caution when handling, testing, and adjusting.

Table B.1. Cables for IBM-PC type computers with 25 PIN CONNECTOR (DB-25).

MER DECK BOX

"MALE" RS-232

DB-25-P FUNCTION

N/A shield (FG) Pin 1 N/A Pin 2 from computer (TD) Pin 2 Pin 3 Pin 3 to computer (RD) Pin 3 Pin 2

N/A clear to send (CTS) Pin 5* Pin 8*

N/A data set ready (DSR) Pin 6* Pin 6* Pin 7 signal ground (SG) Pin 7 Pin 5

N/A data terminal ready (DTR) Pin 20* Pin 4*

*** NOTES ***

COMPUTER

"FEMALE" RS-232

DB-25-S

COMPUTER

"FEMALE" RS-232

DB - 9

* Pins 5,6,20 on DB-25-S or 4,6,8 on DB-9 are tied together at the computer end.

Shield SHOULD NOT be connected at MER DECK BOX end.

WARNING: THIS CABLE WILL PROBABLY NOT WORK WITH YOUR X-Y

PLOTTER. Consult the manual for your plotter to obtain the proper cable for its

operation. Plotter will need to be connected to the same input as the MER Deck

Box which will mean that you will need to switch devices and cables using

COM1.

SELECTION OF DTE OR DCE CONNECTOR CONFIGURATION: There are two yellow jumpers near the RS-232 connector (J1) to select if the MER Deck Box is to be DCE (Data Communication Equipment) or DTE (Data Terminal Equipment). This reverses pins 2 and 3 of the RS-232 connector. The unit is shipped as a DCE device. The jumpers are installed in a fore/aft position. Installing the jumpers in a side to side position makes the unit a DTE device. Pin 1 is Frame and AC power ground. No other signals are connected to J1. Pins 4, 5, 6, 8, and 20 are not connected. Three unused receivers with their input grounded are available. The outputs are connected to pads. Likewise three unused drivers with their input grounded are available. The outputs are connected to pads. Signal ground is connected to pin 7.

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B.2 RS-232 CONNECTOR CONFIGURATION

Table B.2. Pins and Pin Functions.

Pin Function 1 Protective Ground 2 Output data (DTE) or Input data (DCE) 3 Input data (DTE) or Output data (DCE) 4 not connected * 5 not connected * 6 not connected * 7 Signal Ground 8 not connected * 20 not connected * * See above paragraph

HEWLETT PACKARD PLOTTER (HP7470A - option 01) CONNECTION: The XY pen plotter is connected to the IBM-PC through the "Serial Printer Output". It is VERY IMPORTANT to use the DOS "MODE" command to set the baud rate before running either the PREAD or M24READ programs with the XY plotter. These programs will program the baud rate, but you will sometimes get incomplete plots unless you first execute the following:

MODE COM1: 9600,n,8,1,P

(see the DOS manual, "MODE" command definition for a complete explanation of what this does).

The cable is made up as follows:

Table B.3. Plotter cable connection.

PLOTTER(male RS-

232)

Description IBM-PC (female RS-

232) DB-25-P DB-25-S 3 data from

IBM 2 data to IBM 3 7 common 7 20 clear to send 5

- shield 1

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Table B.4. DB25 versus DB9 connectors.

PLOTTER (male RS-

232)

IBM-PC

(female) DB-25-P DB-9-S FG 1-| |-9 RI TD 2 2 RD RD 3 3TD RTS 4 8 CTS CTS 5 7 RTS DSR 6; DCD 8 4 DTR SG 7 5 SG DTR 20 6 DSR; 1 DCD

The plotter settings for the RS-232c/CCITT V.24 interface are :

S2 0 S1 0 Y 0 US 1 B4 1 B3 0 B2 0 B1 0

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APPENDIX C: SOFTWARE INSTALLATION

1. Make at least one copy of all of the software using the DISKCOPY command (consult your DOS manual for instructions).

2. Create a directory for the MER software called "MERPROG" by typing <md MERPROG>.

3. Move to that directory by typing <cd MERPROG>.

4. Copy all of the contents of the root directories (do not copy subdirectories) of the original diskettes to the MERPROG directory using <copy A:\*.* C:/V> (i.e., copy with verify).

5. Make a subdirectory called DEMO: <md DEMO>.

6. Copy the subdirectory DEMO on disk 2 to this subdirectory: <copy A:\demo\*.* C:\demo>.

7. If you plan to edit the source codes, make a subdirectory called SOURCE: <md SOURCE>.

8. Copy the subdirectory SOURCE on disk 2 to this subdirectory: <copy A:\source\*.* C:\source>.

9. To run demonstrations of M24-PROF and M24-READ, copy each of these programs to the DEMO subdirectory: <copy M24-PROF.* c:\demo>, <copy M24-READ.* c:\demo>.

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APPENDIX D: PROGRAMMERS' NOTES

This section is for the use of computer programmers who wish to understand the structure of the programs comprising Biospherical Instruments software MER software package. The programs are written in a variant of MICROSOFT BASIC called "Professional Basic". We have chosen this compiler because it is fast, relatively structured (no line numbers required, etc.) for a Basic, and mainline in that it is derived from IBM Basic. This software is currently Version 7.1 of Professional Basic and supports the 8087 and similar math co-processors.

We have attempted to write this software in such a way that most modifications can be made by editing the DEFAULTS.CFG file. Of course we cannot anticipate all necessary modifications-which is why we provide the source code for these programs.

D.1 GRAPHICS SUPPORT

These programs support the standard IBM style screen graphics devices: The CGA in the 200*640 modes (graphics device=2) and the EGA (graphics device=9). The VGA is highly recommended barring one aspect; it does not support screen dumps to the printer. We have decided to overlook this and live with it in most cases, and we recommend the EGA despite this one drawback. Color is not required, but once you have it on an EGA it's hard to give up. Color on a lower resolution is not much to be excited about, and we prefer to use the single color higher resolution version at 200*640 resolution, which does not use colors on a color monitor.

For hard copy, use the print screen option after first running the DOS utility "GRAPHICS" and choose either option 10 in the Graphics device menu (200*640 one color) for automatic dump (note: this calls an assembly language routine to emulate the pressing of the <PRTSCRN> key) under the M24-READ Program, or option 2 for graphics device and push the print screen key yourself. For screen dumps you must first execute the DOS "GRAPHICS" program (see your DOS Manual for more information).

This latest section of the software also supports the VGA displays when graphics device number 12 is chosen. Users have reported success using add-on graphics programs to capture screen images and send them to a printer. We have also heard it is possible to send color images to the HP Color Jet printer. We, however, have not had first-hand experience with this.

D.2 PEN PLOTTER

An alternative to the printscreen printer dump is to use the pen plotter support. This code is written in to use function definitions callable from basic to create commands in under the "HPGL" format. This stands for "Hewlett-Packard Graphics Language" and is the language that most Hewlett-Packard (and some other makes) pen plotters will use. Provisions are made in the DEFAULTS.CFG file to support various baud rate and output drivers for these plotters. We have only tested this software on the 7470, 7475 and ColorPro Versions. The plotter output can be redirected to a file for later plotting (see defaults file section).

The main variables used in these programs are defined as follows:

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1. U$(Inst%, CHAN%): The string carrying the description of the units for a particular channel on an instrument (e.g., "uW/cm²/nm" or "degrees")

2. C(Inst%, CHAN%) is the calibration constant for that channel. This is defined in the calibration file.

3. MIN(Inst%, CHAN%) is the minimum usable value in volts for a channel. If this value is > 0 then the data will be tested to see if it is bigger than this value before decoding it into engineering units. This is defined in the calibration file.

4. MAX(Inst%, CHAN%) is the maximum allowable value for a channel. It is defined in the calibration file. It has little use in the programs.

5. DESC$(Inst%, CHAN%) contains the channel identifying string and is found in most sections of the code. It is defined in the calibration file, read in CALCON. The length of this should always be 5 characters.

6. OFFSET(Inst%, CHAN%) is used with C (Inst%, CHAN%) to calculate the individual channel values in engineering units. This is also defined and read in the calibration file section.

7. DISPFMT$(Inst%, CHAN%) contains the formatting string for the display of the various channels. Don't change this string length from that in the calibration file or messy displays will result. This will allow you to switch between exponential format and various digits in relation to the decimal point. See the definitions of the PRINT USING command in IBM Basic, GW BASIC, QuickBasic, or Professional Basic for further details.

8. WEIGHT(Inst%, CHAN%) is used to describe how the channel should be weighted for the calculation of PAR from the MER downwelling irradiance in whatever units that downwelling irradiance is defined in. This represents a wavelength summing weighting factor for integration between 400 and 700 nanometers (or whatever you choose it to be).

9. Gain%(Inst%, CHAN%) is the gain setting for any particular channel used in programming the MER.

10. CALFILE$(20) contains a list of the calibration files that are currently active for this set of programs.

11. REPORT.CHANNEL%(16) define the parameters that are normally displayed in an abbreviated display or printer dump of data. These are defined in the DEFAULTS.CFG file and are discussed in the section dealing with that file.

12. DIM Z!(DDD%),Y!(DDD%),ZZ!(DDD%),YY!(DDD%),ZY!(DDD%),K!(DDD%): Various parameters used in the display of the attenuation coefficient (K!). These are normally dimensioned to fit available memory.

13. BIN%(230): This parameter defines bins for averaging. 250 for 230 meters.

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14. DELIMITER$: A character defined in the DEFAULTS.CFG file to delimit individual values in an ASCII data file that is being written to disk. The most frequent value here is a comma, which will create a comma separated value (.CSV) file.

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SOFTWARE END USER LICENSE AGREEMENT

1. We have tested this software as best we can. However, we have found combinations of

computer hardware that are different from what we have available and that can result in unpredictable results. Therefore, test this software with the computer BEFORE GOING TO SEA. We make no guarantees that this software is bug free or that it will work with your specific combination of hardware/software. As bugs are reported, we make every effort to rectify any problems that are discovered. If you find a bug, please contact the factory as soon as possible. Bugs we try to fix immediately; suggestions we include in future releases.

2. The software is included with the instrument at no additional charge.

3. You may make as many copies of it as you need.

4. We formally hold the copyright for this software, so we prohibit you from ripping off this code

for other purposes.

5. If you want to receive software updates, send in the following registration form.

This is the entire agreement between the parties, and any modification hereto must be in writing and signed by an officer of Biospherical Instruments Inc. California law shall govern this license, except as to copyright matters that are covered by Federal laws, and is deemed entered into at San Diego, San Diego County, CA, by both parties.

PLEASE SIGN THIS LICENSE BELOW, FILL IN THE REQUIRED INFORMATION, AND RETURN TO BIOSPHERICAL INSTRUMENTS INC. A FULLY EXECUTED COPY WILL BE RETURNED TO YOU.

CUSTOMER LICENSED COMPUTER

SIGNATURE:_______________________MAKE/MODEL:_____________________

NAME:_______________________SERIAL NUMBER:__________________

ADDRESS :_______________________DATE:___________________________

CITY:_______________________

STATE/ZIP:_______________________

BIOSPHERICAL INSTRUMENTS INC.

BY:______________________________ DATE:____________________________

IOSPHERICAL INSTRUMENTS INC.45

Biospherical Instruments Inc MER-2040, MER-2041, MER-2050 Software User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual