surveys per year have varied from a low of 2 surveys and 21 stations to the current 7 surveys and 24 stations. Appendix A contains a table listing station numbers with respective geographic coordinates, average depth and general location descriptions. The positions of the stations should be entered as waypoints into the research vessel Alaskan Gyre’s chart plotter, GPS receiver (Rockwell PLGR+ Fed96) and/or the vessel’s on-board GIS system (PC interfaced directly with the GPS).

CTD Instrument Configurations

Oceanographic data are collected using one of two Sea-Bird SBE-19 Seacat profiling CTD’s (by Sea-Bird Electronics). Instrument #193353 - 436 (designated as CTD #1) and instrument #194652 - 0775 (designated CTD #2) are both configured exactly the same, as of December, 2000. Each has an SBE submersible pump (#2 has an SBE model 5-01 pump, #1 has the more recent model SBE 5T), an irradiance meter (PAR sensor, LI-COR model LI-192SA), a WetLabs WETstar fluorometer, and a D&A Instruments OBS-3 optical backscatterance (turbidity) sensor, in addition to the standard temperature probe, conductivity cell, and pressure port. Prior to August, 1999, CTD#2 did not have an OBS sensor and had a Sea-Tech fluorometer rather than a WETstar.

Instrument Maintenance

Instrument Calibration

Annually, send the entire instrument to Sea-Bird Electronics for calibration of the temperature, salinity, pressure, and irradiance sensors. The OBS sensor and the fluorometer should be re-calibrated every second calibration.

Shipping information:

SEA-BIRD ELECTRONICS, INC.

1808-136^th Place NE

Bellevue, WA 98005, USA

Phone: (425) 643-9866

Fax: (425) 643-9554

E-mail: Seabird@seabird.com

Contacts: Dave Armstrong, Andy Heard

Sea-Bird's website also has return information at: www.seabird.com

After Instrument Calibration

Before processing begins, a current configuration file (.con file) must exist in order to properly process each data (hex) file with updated calibration information. If the .con file has not been supplied with the instrument after calibration, a new one must be created using the SEACON software module (as of January, 1999, SEASAVE for WIN 95/NT V 1.07 is the current program). Run this program to enter the new calibration coefficients for the various sensors, which are printed on SeaBird's service report and included with the CTD upon return.

Refer to the SeaSoft manual (K:\eco_data\data\glba\ocean\protocol\information\seasave_win32_V1_00Word97.doc) for a full description of how to enter coefficients using the supplied calibration data sheets.

After running the SEACON software module, save the resulting .con file. This file will be used while processing raw data from the CTD using SeaSoft software modules. Name the file using the CTD number (436 for CTD #1 and 775 for CTD #2) and the date of the calibration. For example, 775_9908.con is the current file for CTD #2.

NOTE: since Seasoft software is, in part, DOS-based, be sure to limit the name of the .con file to eight characters.

Before Each Cruise

1. Rinse the entire instrument with fresh water.

2. For the WetLabs WETStar mini fluorometer, rinse thoroughly and air dry the instrument after each experiment (the flow tube must be rinsed after each cast).

3. Rinse the conductivity cell with distilled water.

4. Flush the conductivity cell with a pre-mixed 1% solution of Triton X-100, fill the tubing with the solution and let soak for 30 minutes. (Note…Triton X is a non-ionic biogenic detergent; be careful not to get the solution on your skin). Drain the cell and tubing.

5. Rinse the conductivity cell with warm (not hot) water.

6. Store the instrument with the tygon tubing submerging the conductivity cell in distilled water.

7. In freezing conditions, bring the CTD into the cabin between stations and during storage.

8. Check the battery status after uploading data; if the Vmain is less than 10V, replace the 9 D-cell batteries with fresh ones:

Loosen the top of the battery housing by unscrewing the plastic end cover off. Using a wrench of some sort for leverage is suggested.
Remove the Phillips head screws (3 of them) and lift out the retainer plate from inside.
Positive terminals align against the flat battery contacts, and negative terminals against the spring contacts.
Insert the batteries, reinstall the plate, and completely tighten the screws.
Replace the top of the battery housing tightly.

Before Each Cast

1. Turn the instrument off with magnetic switch.

2. Rinse the conductivity cell with distilled water.

3. Replace hoses on the conductivity cell with tygon tubing and fill with distilled water. If cell is allowed to dry out between usage, salt crystals may form on and in the platinized electrode surfaces.

4. Rinse the irradiance meter with distilled water, and replace the cover.

5. The miniature fluorometer should be flushed with fresh water.

6. Soapy water can be used to remove grease or oil.

7. Use a Q-tip to clean the flow tube (use care, as the quartz tube can be easily broken or scratched).

Field Operations

Before deployment of the CTD in the field, check the “status” of the instrument using the Seasoft software module TERM19. Connect the CTD to a personal computer using instructions outlined in the section Raw Data Upload: Connecting Hardware. In the TERM19 window, press F3. The display should read >10V Vmain for the 9 alkaline D-Cell batteries and cleared memory (nsamples = 0, memory = 0). If the batteries are low (near or less than 10V), replace the batteries (see Instrument Maintenance section for battery replacement instructions). Next, type ST in TERM19 and check that the time and date are current; change them if necessary.

Appendix B outlines equipment needed to complete oceanographic surveys. Use the CTD’s wooden box for transportation on bumpy roads in a car. Vibrations due to transportation have broken a connection on the CTD, causing sensor corrosion and failure. Please treat the instrument carefully (it is very expensive!). After the instrument is loaded onto the vessel, be sure to secure the end of the ground line to the CTD using 2 metal carabiners and the other end to the vessel.

The boat operator navigates to the waypoint of the station using the either the vessel's chartplotter, PLGR+ Fed96 GPS (Rockwell) with external antenna mounted to the top of the vessel, and/or PLGR GPS interfaced with the on-board computer navigation system (Pentium PC with ESRI ArcView 3.2 and Tracking Analyst loaded).

We are currently collecting data in decimal degrees with a NAD27 datum. We use this datum because all of the base layers for the Park are in NAD27. However, the default datum may change in the future since other collaborators collect data in WGS-84 (aka NAD83) and this is a slightly more accurate datum.

**NOTE: If you are using Tracking Analyst for navigation, remember that the PLGR can only output to Tracking Analyst in NAD83—so you will need a NAD83 View in ArcView to navigate correctly to stations. The oceanography latitudes and longitudes, however, need to be written in the field notebook in decimal degrees NAD27! You can set the PLGR to display in NAD27 to obtain the cast locations, and Tracking Analyst will still be working in NAD83. **

Upon arriving at a station, turn on the magnetic switch and hang the CTD from the block. Record the time “on” in the field notebook (see Appendix C for a sample data sheet). Attach a marker to the line with a gangion just above the instrument – an empty softdrink can works well. Next, lower the CTD into the water until just submerged to equilibrate for approximately one minute. This equilibration time will allow 45 seconds for the pump to turn on (45sec = the set delay interval for CTD#2) and will provide time for the instrument to adjust to ambient temperature and for the conductivity cells to flush.

At the beginning of the CTD cast, record in the field notebook the latitude and longitude of the cast location, using decimal degrees in NAD27 Alaska datum (called NAS-D on the PLGR GPS), or you can also mark a waypoint on the GPS and record the waypoint number in the logbook. Be sure to also record: the cast number (where the 1^st two digits refer to the CTD number – C1 for CTD #1 and C2 for CTD #2, the second four digits are the dump number, and the last two digits are the cast number within this dump, starting with “00”); date; time; and the station number and location.

Check the water depth on the vessel’s depth meter and record it on the data sheet (make sure to record depth in meters, as opposed to feet or fathoms). After equilibration, drop the CTD at a speed of one m/sec (meter per second) using a leaded ground line marked at 10-meter (and flagged at 100m) intervals. The instrument should be dropped no more than 90% of the depth at the station and never more than the maximum depth of 335m (for both CTD1 and CTD2).

Turn on the boat hydraulics and retrieve the CTD with a power block/davit or a long-line drum. Note that data are collected by the CTD on both the down- and up-casts; however, the up-cast data are not used for analysis (down-cast data are more accurate because the sensors are receiving and measuring a nearly-undisturbed water column on the way down) — so there is no need to go slowly on the way up. Be careful, however, as the instrument nears the surface, and be sure to control the power block. The marker (empty softdrink can) attached just above the instrument should alert you to its arrival at the surface.

Upon retrieval, immediately turn the instrument off, rinse the irradiance meter and cover it with its cap, rinse the conductivity cell with distilled water and secure the instrument for the run between stations. In freezing conditions, be sure to bring the CTD inside the cabin between stations and over-night. One $1500 conductivity cell has already been broken due to freezing on deck.

Record any irregularities about the cast on the data sheet. Include comments about such events as, e.g., the magnetic switch arriving at the surface in the “off” position, forcing a duplication of that station’s cast. Enter tide data (time to/since and heights of nearest low and high tides – see Term19 Setup Parameters section for details) onto the data sheet during the run between casts. If you marked a GPS waypoint for the cast’s location, enter the coordinates onto the data sheet now to prevent loss of the waypoint when others use the GPS later.

Uploading & Processing Raw Data

Various Seasoft software modules are required in order to successfully acquire, retrieve (upload), process, and display CTD data in the appropriate format. The primary programs include: TERM19, SEACON, and SEASAVE (Sea-Bird Electronics). As of January 1999, a new Windows module called SEASAVE for WIN 95/NT became available, which incorporates functions from the DOS versions of SEACON and SEASAVE.

Raw Data Upload

Upon completion of each survey, (or during the cruise, depending upon the status of the remaining memory on the CTD), download the instrument to a personal computer using the procedures described below.

Connecting Hardware

1. Check that the white magnetic switch at the bottom of the CTD is in the off position before starting.

2. Remove the bulkhead connector cover (unscrew the cap and pull it off) and inspect the pins for any signs of corrosion (green/black areas). If minor corrosion appears, it can be removed with alcohol/Q-tip.

3. With a lint-free cloth, clean in and around the connector AND inside the cable, making sure no dirt, dust, etc. remains.

4. After connector/cable is cleaned, put a small (<pea sized) dab of 100% silicon grease on your finger and apply around the black base of the connector (avoid getting grease onto the pins).

5. Connect the 4-pin port of the instrument to Com port 1 or 2 of a PC with >580 MB of low memory with the connector cable by aligning the cable end with the pins, and push into place (Do not twist). Next, (this is important!) run your hand down the length of the cable to pop out any trapped air. Screw on black cap to the connector.

Hardware Configuration Settings

The software module TERM19 is used to establish communications between the instrument and a personal computer. Information about the hardware configuration settings (communication, etc.) of the CTD and individual computer is stored in the TERM19.CFG file.

After the CTD has been properly connected to the computer, open the SeaSoft directory located in N:\apps\dos\ctd on the Bartlett Cove Network, select Sea4.246 (for CTD1, as of December, 2000) or Sea4.236 (for CTD2, as of August, 1999) and double-click on TERM19.exe. From the field laptop computer, navigate to C:\Apps\data\CTD\Sea4.236 or Sea4.032 and select term19.exe. Communication will automatically be detected. The screen should read "Communications established" when the computer detects the instrument. If communication is not detected automatically, press F6 (wake up) and communications should establish. If communication is still not detected, check the computer and CTD connections; you may have put the computer connection in the wrong port, or there may be another connection problem.

Before uploading a session (series of casts), the setup parameters must be checked using the TERM19 program (this file may need to be edited when switching between computers). Select F2 to view or edit the setup parameters stored in the TERM19.CFG file as described below.

TERM19.CFG Setup Parameters

· SBE 19 Firmware version = Less than 3.0

· Communication setup:

Serial Port = COM1 or COM2

Baud Rate = 9600

Data Upload Baud Rate = 9600

Data Bits = 7 Data Bits

Parity = Even Parity

· Data upload setup parameters:

Upload = Upload All Data Separated by Casts

Echo = Echo Data During Upload

Disk Drive to Write Uploaded HEX to [A-Z] = A on laptop, N on network

Upload File Name Choice = C1#### for CTD1, C2#### for CTD2 (The #### is the dump# on the logbook datasheet; the cast number will be added to the end during uploading).

Default Upload File Name = Use Default File Name

Upload Session Number = dump# (which should be determined by looking at archived CTD data and choosing the next sequential number depending upon which instrument is being used).

· Header = Prompt for Header Information

· Header Form = Check "Header" format and update the following cruise information: NEVER (ever) change these established header names or their order. New headers can be added at the end but the GIS processing won’t work if the old headers’ names are changed!

Ship: (e.g., R/V Alaskan Gyre)

Cruise: (e.g., Glacier Bay Oceanography Survey, June 2000)

Station #, Location: (number, description)

Lat: (at Glacier Bay use decimal degrees, NAD27)

Long: (at Glacier Bay use decimal degrees, NAD27)

Bottom depth: <no units! Always meters!>

CTD dropped to: <no units! Always meters!>

Time Since/to Low: < no units! Always meters! “-” is OK, but do not use “+” >

Time Since/to Hi: < no units! Always meters! “-” is OK, but do not use “+” >

HiHight: < no units! Always meters! “-” is OK, but do not use “+” >

LowHight: < no units! Always meters! “-” is OK, but do not use “+” >

Comments: (for information such as PLGR+ accuracy, visible surface features, line angle, rate of drop, and any type of irregularity that occurred during the cast)

NOTE: To calculate the time since/to the low and high, the Tides and Currents program can be used. Pick the high and low tide closest to the time of every cast, and calculate the number of minutes to or from the cast to the high and low tides. If the cast is before the low tide, for example, the number of minutes to/since low tide should be a negative number. Conversely, if the cast is after the low tide, time to/since low tide should be a positive number. ONLY a minus sign “-“ can be included when entering these data during data upload from the CTD -- do not use the plus sign “+”. Calculating these numbers and entering them onto the data sheet between casts during the cruise is much easier and will save time during data upload.

Once the setup parameters are checked, the next step is to display and check the instrument status by selecting F3. Instrument status provides information such as software version, instrument serial number, time/date, battery voltage remaining, number of stored and free samples in memory, etc. Check the following settings:

· Time and date should be current.

· Sample rate = 1 scan every 0.5 seconds

· Ncasts = should match the number of data sheet entries (number of actual casts done)

· Samples = Note that the instrument's memory capacity is 256K, or 43336 (free) samples.

· Vmain = main battery level should be > 10 volts; if not, batteries must be replaced (see Instrument Maintenance section for instructions on changing the batteries).

Uploading CTD Data (aka “dumping” the CTD)

1. Select F9 to begin uploading data.

2. For each cast, check the top of the screen to make sure that time and cast # on the computer correspond to time and cast # on the data sheet, then enter data sheet information into headers prompted for each cast.

3. After all the header information has been entered, press the escape key.

4. Either a series of dots (………….) will appear or the data will appear indicating that the cast is uploading to the computer.

5. Repeat for each cast #, making sure for each one that time and cast # on the data sheet correspond to time and cast # on the instrument

6. Exit TERM19 by pressing F10

7. Check that all the hex files are in the directory n:\apps\dos\ctd\sea4.246 or sea4.236 (or in designated drive letter) and that they contain data. They can be viewed in a text editor (e.g., Textpad) and should display header info and rows of hexidecimal digits.

8. Files that do not contain data will interrupt batch processing of data files. Looking at file size can indicate if any files do not contain data. Very small files can be viewed for raw data as ASCII characters below the header. If they do not contain any ASCII characters, delete the files.

9. Make a copy of all new files to disk, as well as to the Network. See the later section Data Management: Raw Data for the appropriate directories in which to store the raw .hex data files.

10. When ready to initialize the machine for data logging, run TERM19 again and select F8 (Init Log). This will permanently clear the CTD memory. The memory must be cleared before the next cruise; however, it can be done either right after data upload or (if you’re concerned about the raw data) immediately before the next cruise.

11. When finished, log the CTD data upload in the “dump” logbook on the network (CTD_Dump_Log.xls) and note the battery status, etc. (see Appendix D for a sample page from this file). If you do not have a network computer available, then log the cast dump into the white CTD notebook and transfer this information to the network later.

Processing Raw Data

SeaSoft software versions

Various SeaSoft software versions (and corresponding manuals) have been supplied on floppy disk and/or CD-ROM with the CTD upon return from calibration at SeaBird. The following software versions have been used for processing data files from .hex to .cnv format: SeaSoft version 4.032; SeaSoft version 4.203; and SeaSoft version 4.236. As of December, 2000, SeaSoft version 4.236 is being utilized to process all CTD#2 hex files.

Processing hex files with SeaSoft software

This section describes the procedure for processing hex files from CTD#2 using SeaSoft version 4.236 software. From the directory n:\apps\dos\ctd\sea4.236\, double click on the batch file _sea.bat. This file has been set up to properly process all files in the directory at one time. Note that data files must (temporarily) reside and be written to the Sea4.236 root directory only! SeaSoft does not recognize (read/write) to any other directory. Raw data files should be copied (not moved) into this folder (the Sea4.236 root directory) for processing, and then the converted (.cnv) files can be moved out of this folder to another directory after processing is complete. Delete the copied .hex files from this directory once processing is finished, and, after they have been copied to their final locations, delete the converted (.cnv) files from this directory. Leave the original raw data (.hex) files in the raw data folders to ensure that original raw data are never lost!

A batch file called _sea.bat is currently set up to process an entire group of files in the directory through the set of modules listed below, rather than having to process a file at a time. The batch file contains 6 DOS statements. The “-a” argument instructs each module to process all the files in the current directory:

datcnv -a

filter -a
alignctd -a
loopedit -a
derive -a
binavg -a

There are six software modules in the batch processing that perform various different processing functions sequentially on the data; all of these modules should be correctly set up for data processing. In case they are not correct, the setup screens for each of the software modules should be checked before standard data processing; exceptions to the standard data processing are noted later in the Data Processing Troubleshooting Section.

Press F10 to begin batch processing of data files and to check the setup screen variables.

DATCNV

This first module uses instrument calibration coefficients and configuration to convert raw data (.hex or .dat files) to engineering units (ASCII or binary format with .cnv extension). Ensure that the settings are as follows:

· Configuration file: 775_9908.con (or most recent *.con file see section After Instrument Calibration)

· Input file path: n:\apps\dos\ctd\sea4.236\

· Output Data File Path: n:\apps\dos\ctd\sea4.236\

· DATCNV Format = ASCII

· DATCNV Variables (by column). To alter or check these variables, use the ¯ arrows to select this field, then press <Enter>. Once in the next window, again use the ¯ arrows to select a variable and press <Enter> to modify it:

o Conversion units: Metric

o Scan Number

o Pressure [db]

o Temperature IPTS-68 [deg C]

o Conductivity [S/m]

o Irradiance (PAR)

o WETlabs, WETStar chlorophyll concentration [μg/l]

o Backscatterance

o Time [Seconds - s]

· Output Cast Select = Down Cast Only

· Number of Scans to Skip Over = 0

· Output Water Bottle Data: No

· Water Bottle Data Set Up: Do not bother modifying these parameters because we do not do water bottle sampling.

Press F10 to move on to the next module.

FILTER

This step forces conductivity to have the same response as temperature. Make sure the settings are as follows:

· Input data file: should automatically show the first .cnv data file that you will be filtering. Only the first file is shown here, but all of the files in the root directory will be processed.

· Input file path: n:\apps\dos\ctd\sea4.236

· Output file path: n:\apps\dos\ctd\sea4.236

· Low pass Filter A, Time Constant: 0.5

· Low Pass Filter B, Time Constant: 2.0

· Variables to Filter – To alter or check these variables, use the ¯ arrows to select this row, then press <Enter>. Once in the next window, use the ¯ arrows to select a variable if it needs to be modified:

o Low Pass filter A: Conductivity

o Low Pass filter B: Pressure

o All other variables should be: None

Press F10 to move on to the next module.

ALIGNCTD

This step aligns temperature, conductivity and oxygen measurements in time relative to pressure, ensuring that calculations are made from the same parcel of water. When measurements are properly aligned, salinity spiking errors are minimized, and plots agree between down and up profiles. Check the following settings:

· Input data file: should automatically show the first .cnv data file that you will be aligning. Only the first file is shown here, but all of the files in the root directory will be processed.

· Input file path: n:\apps\dos\ctd\sea4.236\

· Output file path: n:\apps\dos\ctd\sea4.236\

· # Seconds to advance primary conductivity relative to pressure: 0.62 (This value was obtained by adding the seconds to advance temperature - 0.5 - to the seconds to advance pressure - 0.12)

· # Seconds to advance primary temperature relative to pressure = 0.5

· Do not enter anything (defaults to 0.0) for secondary conductivity and secondary temperature. Also do not enter anything for oxygen because we do not have an O₂ sensor.

Press F10 to move on to the next module.

LOOPEDIT

This software module marks scans with “badflag” if the scan fails pressure reversal, slowdowns or minimum velocity tests. Check the flowing settings:

· Input data file: should automatically show the first .cnv data file that you will be loopediting. Only the first file is shown here, but all of the files in the root directory will be processed.

· Input file path: n:\apps\dos\ctd\sea4.236\

· Output file path: n:\apps\dos\ctd\sea4.236\

· Minimum velocity selection: Fixed Minimum Velocity

· Minimum CTD velocity: 0.25 m/s

· Exclude scans marked bad: YES

Press F10 to move on to the next module.

DERIVE

Derive reads in .cnv files and calculates derived variables (including salinity, density, depth, and sound velocity). Check the following settings:

· Input data file: should automatically show the first .cnv data file that you will be deriving. Only the first file is shown here, but all of the files in the root directory will be processed.

· Input file path: n:\apps\dos\ctd\sea4.236\

· Output file path: n:\apps\dos\ctd\sea4.236\

· Input variables: While batching files, this module should automatically pick up the list of variables initially entered into the DATCNV module, as follows. To alter or check these parameters, use the ¯ arrows to select this row, then press <Enter>. Once in the next window, use the ¯ arrows to select a parameter if it needs to be modified:

o Scan Number

o Pressure [decibars]

o Temperature IPTS-68 [deg. Celsius]

o Conductivity [S/m]

o Irradiance (PAR)

o WETlabs, WETStar chlorophyll concentration (μg/l)

o Backscatterance

o Time [seconds]

· Variables to be Derived – To alter or check these variables, use the ¯ arrows to select this row, then press <Enter>. Once in the next window, use the ¯ arrows to select a variable if it needs to be modified:

o Depth, salt water [m] –Latitude is requested when you press <Enter>; it should be 58.4 as an average for Glacier Bay.

o Salinity, PSS78 [PSU]

o Density, sigma-t [kg/m³]

o Sound Velocity [m/s] (methods to be determined, but chen millero selected in the interim)

o Average Sound Velocity [m/s] (methods and parameters to be determined, but chen millero and the below parameters selected in the interim.

§ Minimum pressure (decibars): 0

§ Minimum salinity (psu): 0

§ Pressure window size (decibars): 1

§ Time window size (seconds): 300.00

· Variable Coefficients – these do not need to be set for our current configuration, because we do not have an oxygen meter and we are binaveraging by depth, not using descent rate

o Time window size for doc/dt: 0.0. We believe “doc/dt” refers to the rate of change of dissolved oxygen content, which we do not measure.

o Time Window size for descent rate: 0.0. We use depth bins for averaging, so descent rate is not important. (or, if this time window size is used in the doc/dt calculation, again we don’t measure oxygen so this parameter does not apply to our calculations).

Press F10 to move on to the next module.

BINAVG

BINAVG averages data in converted data (.cnv) files into pressure or depth bins. Input data file: should automatically show the first .cnv data file that you will be binaveraging. Only the first file is shown here, but all of the files in the root directory will be processed. Check that the settings are as follows:

· Input file path: n:\apps\dos\ctd\sea4.236\

· Output file path: n:\apps\dos\ctd\sea4.236\

· Bin type: Depth Bins

· Bin Size: 1.0

· Include # Scans/bin: YES

· Exclude scans marked bad: YES

· Number of scans to skip over: 0

· Surface bin setup parameters – To alter or check these parameters, use the ¯ arrows to select this row, then press <Enter>. Once in the next window, use the ¯ arrows to select a parameter if it needs to be modified:

o Include surface bin: Yes

o Surface bin minimum value: 0.2

o Surface bin maximum value: 0.5

o Value for surface bin: 0.00

F10 must be pressed a total of 6 times, to continue running through each of the different modules: DATCNV, FILTER, ALIGNCTD, LOOPEDIT, DERIVE, and BINAVG.

Once files are processed, move all .cnv (converted) files to the following folder: k:\eco_data\data\glba\ocean\data\processed\<2000>\<200005oceanography> (note that <2000> and <200005> are examples of the year and month of the cruise – create an appropriate folder if one does not already exist). The raw data (.hex) files should be deleted from the program folder after conversion. The original raw data files should still be in the oceanography project file, where they initially were stored and where they should remain.

Immediately after converting the .hex files to .cnv files, open at least one of the .cnv files with a text editor. Examine the dates, header information and briefly check the data. It is very important to correct any header name, spelling and prefix problems prior to doing any GIS processing. If the headers differ in any way, ArcView will be unable to locate them during GIS processing. Be sure to check for the correct date in the “start_time” field! As of December, 2000, the SeaSoft software (v. 4.236) appears to have a bug causing year in the “start_date” field to be “0100” in the .cnv files even though the year is correctly entered on the CTD itself and appears correct in the .hex files. It is important that the date is correct in this field since it will be used by Oceanographic Analyst Extension the during GIS processing to obtain the date of the cast. Finally, quickly scan the data to ensure that they are as expected; make sure there are no missing values, or no zero values or that all the values are not the same.

After all files have been processed, open the CTD_Process_Log.xls (located on the network: k:\eco_data\data\glba\ocean\data\processed\) and record files processing.

Plotting

After processing the raw CTD data we move the data into ArcView to complete the GIS processing. If, however, you need to create and print a classic cast profile, the seaplot.exe software should be used and this is the procedure to follow:

1. From DOS or Windows, run SeaPlot

2. For each profile, the maximum depth (50, 100, 150 or 200m) should be specified and Station#, description, and date entered.

3. No other settings should need changing but check to be sure. The correct setup screen follows:

Input file path: K:\eco_data\data\glba\ocean\ctd
Plot parameters file: seaplot.plt
Plot format: Overlaid X-Y plots
Variables to plot: Depth (minimum = 0, maximum = the nearest multiple of 50 to profile maximum)
Temperature (minimum = 0, maximum = 12, major units = 3, minor units = 4)
Salinity (minimum = 10, maximum = 35, major units = 5, minor units = 5)
Irradiance (minimum = .001, maximum = 1000, major units = 6, minor units = 10)
Fluorescence (minimum = .1, maximum = 10, major units = 2, minor units = 10)
Plot label: Type in the Station #, location, and date of profile from CTD data sheets

4. Press F10 to display the profile

5. Press Ctrl F9 to print the profile

6. Printed profiles are archived in the USGS data archive files

GIS Data Processing

** WARNING: As of December, 2000, only the operating systems Windows 2000 Professional and Windows NT have been successful at fully GIS processing CTD data. During tests on a Windows 98 operating system it appears that there is a bug during the “Contouring Profile Slices” step. All other functions apparently function properly in Win98. Testing has not yet been extensive, however.**

Once the raw data have been initially processed with the standard protocols by the SeaSoft software, which converts the raw .hex data files into converted (.cnv) files, the next step is to convert the .cnv files into a database format and plot the data in ArcView.

The ArcView extension called Oceanographic Analyst Extension (Hooge and Hooge, 2000a) is used in order to automate the conversion of the .cnv files to .dbf tables and to bring the oceanography data into the geo-referenced GIS environment. This extension will also be used to create three-dimensional views and contour plots of the cast data.

Set Up

To begin, go to the following pathway: Science(K:)\eco_data\data\glba\ocean\GIS\ and open: ocean_template.apr This template has been created as a basic outline for GIS processed oceanographic data. If the template were to be lost, the configuration of this particular template file is as follows.

The ocean_template project has three extensions loaded: Spatial Analyst, 3D Analyst, and Oceanographic Analyst. To check or load extensions, go to the File Menu and select Extensions… Be sure to check the boxes on the left rather than merely clicking on the extensions’ names.

There are three views in the ocean_template.apr. The first view is the Oceanography Main View DD_NAD27, which should be used when processing and projecting location data collected in decimal degrees (NAD 27). This view is projected in UTM (Zone 8) and the following themes should be present:

Ocean_stations.shp
Oceanog_line.shp
Noaa_cst.shp
Glb_bath
Bath100
Gl17318_nad27

The second view is Oceanography Main View UTM_NAD27 (not projected) and should be used when processing and projecting location data collected in UTM (NAD 27). As of December, 2000, all of the processed oceanography data are in UTM Nad27. The following themes should be present in this view:

Ocean_stations_utm.shp
Oceanog_line_utm.shp
Noaa_cst_utm.shp
Glb_bath
Bath100
Gl17318_nad27

The third view is called Oceanography Main View DD_Nad83 and should be used when processing and projecting data collected in decimal degrees (NAD83). This view is projected in UTM (Zone 8) and the following themes should be present:

· Ocean_stations_wgs84.shp

· Oceanog_line_nad83.shp

· Noaa_cst_nad83.shp

· Glb_bath83

· 17318_nad83

All the themes for the three views can be found either in Science(K:)\eco_data\data\glba\OCEAN\GIS\ or in: ocean\gis depending on which system you are working on (Bartlett Cove computer network or CD-ROM).

There are also three 3-D scenes in the project. If these are not present, you can created them by double-clicking on the 3-D icon in the project window. A 3-D window should come up, and you can change the name of the window by going to the 3D Scene Menu à Properties, or by selecting Rename 3-D Scene under the Project Menu, from the Project Window.

The first 3-D scene is called Oceanography 3D DD_nad27. This 3D view has a 2D projection in UTM (Zone 8) and should include the following themes:

Ocean_stations.shp
Noaa_cst.shp

The second 3-D view is called Oceanography 3D DD_nad83. This 3D view has a 2D projection in UTM (Zone 8) and should include the following themes:

Noaa_cst_nad83.shp
Ocean_stations_wgs84.shp

The third 3-D view is called Oceanography 3D UTM_Nad27 (Not Projected). This 3D view should include the following themes:

Ocean_stations_utm.shp
Noaa_cst_utm.shp

To update the Oceanographic Analyst, navigate to: K:\eco_data\data\glba\OCEAN\GIS\

OceanographicAnalyst_extension\ then copy and paste the ocean.avx document into the following pathway: C:\ESRI\AV_GIS30\Arcview\EXT32 (or wherever your ArcView EXT32 folder is located). Also make sure, especially in ArcView versions prior to v3.2, that in the C:\ESRI\AV_GIS30\Arcview\EXT32 folder there is an avdlog.dll document (avdlog.dll is a dynamic link library document).

Once the template is set up, select the file menu and Save As (be sure to Save As, since this will create a new project using the template as the base without overwriting the template, so that the template can be used again to create other projects). Name the new project with the following format: <yearmonth>ocean.apr (e.g., 200001ocean.apr) and save it in the following location: Science(K:)\eco_data\data\glba\ocean\DATA\Processed\<2000>\<200001>oceanography\<200001>ocean.apr (create folders for the year and month if necessary).

The final step before beginning the GIS data processing steps is to set the newly created project’s working directory. With a View Window selected, go to the File Menu. Select Set Working Directory. Set the working directory as: K:\eco_data\data\glba\ocean\data\processed\ <2000>\<200001>oceanography

Processing Converted (.cnv) Files

Creating .dbf Files

1. In the new project: Highlight/activate the project window (<200001>oceanography.apr)

2. Click on CTD Menu, then select Process CTD files.

3. A dialog box will appear labeled: Process Seabird Files: Get Prefixes. This part of the program identifies the header information in the particular .cnv files you are processing. If you have changed these headers in any way, this is where you would incorporate those changes into the processing program. The first field is Station Prefix, and the default is Station #, Location. The next two fields are X field prefix and Y field prefix, with defaults of Lat: and Long: respectively.

At this point in the dialog box you have the option to select a check-box labeled: Capture Tide Values. If tidal information has been entered into the .cnv header information, check this box and confirm or alter the four header prefixes. Note that it is alright to select this box even if the data do not exist in the .cnv files; fields will be created in the resulting .dbf table, with bad data flags (“-99999”) as the values.

4. Click on Run.

5. Select all of the “.cnv” data files you wish to process (double check the whole list to make sure none are missing), click OK.

6. The prompt will then ask What is the CTD master file? Press Cancel – unless CTDmaster existed previously… This choice is available to allow the user to append single files onto an already-created CTDmaster file (for instance, if a file was initially overlooked), or to permit the creation of large combined CTDmaster files.

7. A prompt will ask for The New CTD master file Make sure that the pathway is correct: (…/ocean/data/processed/<date>/<trip>), then name the new file: ctdmaster<200001> (where <2000> is the year, and <01> is the month of the desired data that you are processing).

8. A prompt will ask: What is the Profile master file? Press Cancel – unless Profilemaster existed previously… This choice is available to allow the user to append single files onto an already-created Profilemaster file (for instance, if a file was initially overlooked), or to permit the creation of large combined Profilemaster files.

9. The next dialog box will then ask for The New Profile Master file Check for the same pathway given in step #7 for the CTD master, and name the new file: profilemaster<200001>.

10. Processing should now occur and you should see many .dbf files appearing in the project window while processing is under way. After processing, all the new individual files will be automatically deleted from the project window and the new ctdmaster and profilemaster files will be in the project window. The individual processed files do still exist in the “processed” file on the network, where you can later access them if desired at the previously specified pathway.

Georeferencing the dbf Files

1. Activate the Oceanography Main View DD_NAD27 (or whichever view you are using to process and project your data, depending on the projection and datum of your coordinates).

2. Go to the View menu, then select Add Event Theme

3. The Add Event Theme dialog box will appear; make sure that the following is entered in the appropriate boxes:

· Table: ctdmaster<200005>.dbf (once again, 200005 is just an example of a year and month, make sure you input the correct name of the CTD master file that you are processing)

· Xfield: Xaxis

· Yfield: Yaxis

4. Click OK. The ctdmaster will now be added (as a point event theme) to the list of themes at the left side of the view window

5. Go to the ctdmaster point event theme that you just created and click on the check box so that the theme is displayed.

6. Visually check that the points are in the correct location on the bay (i.e. that the coordinates in the file are correct). One good way to double check this is to highlight/activate this theme, then click on the Zoom to Active Theme button in the toolbar. If any points are “off in space” you will now see them. Also, count up the points you see on-screen and compare that with the number of casts you processed. Investigate any discrepancies.

7. Repeat the same steps again, except you will next add the Profilemaster as an event theme. Go to the View menu, select Add Event Theme

8. Make sure that the following are correct:

Table: profilemaster<200001>.dbf
X: X-axis
Y: Y-axis

9. Click on OK. The Profilemaster will now be added (as a point event theme) to the list of themes at the left side of the View Window.

10. Go to the Profilemaster point event theme that you just created and click on the check box so that the theme is displayed.

11. Again, visually check that the points are in the correct location on the bay, and that the number of points equals the number of CTD casts taken. Investigate any discrepancies.

12.

Open both the CTDmaster and ProfileMaster dbf attribute tables. To do this, either, go to Theme Menu → Table or click on the attribute table icon:

In the tables, examine the headers and all the data, both the cast information and the sensor values, to find gross errors or problems.

NOTE: If, despite all precautions, an error is discovered in the headers or data values of the CTDmaster and/or ProfileMaster, now is definitely the time to fix the problem – before shape files are created from these tables and further analysis proceeds. One can either fix the raw .hex and converted .cnv files and then re-create the CTDmaster and ProfileMaster tables, or one can simply edit the two .dbf tables. However, the policy at Glacier Bay is to fix both the .hex and .cnv files and then reprocess them, in order to avoid future problems if the .cnv files were ever reprocessed at a later date.

How to Edit dbf tables

If an error was not caught at the .cnv stage (for example: because of a bug in the SeaSoft v4.236 software, as described in section on Processing .hex files with SeaSoft software, the year is not correct), the following is the procedure to correct year problems in the .dbf tables:

1. Select the dbf theme and go to the attribute table

2. Go to Table Menu ® Start editing

3. In the table, select (click on) the header of the Date field

4. Go to Field Menu ® Calculate

5. The Field Calculator dialog box will appear saying: [Date] =

Type: ([Date].SetFormat(“yyyyMMdd”).AsString.AsNumber + 19000000).AsDate

6. Click OK

7. Go to Table menu ® Stop editing.

8. Save edits? Yes

Creating 3-D Shapefiles

At this point, the CTD casts have been brought into ArcView and exist as point event themes made from .dbf tables; now these tables need to be converted to 3-D shapefiles.

1. Go to the profilemaster .dbf file that you created (which was added to the list of themes on the left side of the view window) and “activate the theme” by clicking on it – it should appear highlighted or embossed.

2. Go to the Theme menu, select Convert to 3D shape file

3. It will ask you about Getting Z values: select Attribute in the dialog box.

4. A dialog box will appear that says: Convert profilemaster<200001>.dbf and asks you to Choose the field that will provide the Z-values. Make sure you select deps (which is the depth field). Click OK.

5. The next dialog box is called: Output Shape file name. Check that the file is being saved in the following directory: \eco_data\data\glba\ocean\data\processed\<2000>\… Name the file <200001>ocean.shp Note once again that the <2000> represents the desired year, and <01> the month that you are currently processing, and is only used here as an example. (Note in the past some of these files have been named <200001>oceanography.shp)

6. Then add theme to view, and click OK. You should now see the 200001ocean.shp theme in the View Window.

7. Click on profilemaster200001.dbf and delete that theme from the view window by selecting the desired theme and going to the Edit Menu and selecting Delete Theme. Do not delete the profilemaster200001.dbf file from the list of Tables; simply delete it from the View.

Summarizing Cast Data

During the next series of steps you will be performing some recalculations and summaries of the 3-dimensional cast data. These summaries will then be added into the CTDmaster file.

OBS Recalculation

The raw OBS sensor data values are reported as microvolts. These raw data need to be converted from voltages to sediment densities. The following procedure describes this process.

Check OBS calibration parameters

Go to the attribute table of the Ocean_stations file you will be using. Check that all stations have the three correct numbers (in three separate fields) that constitute the variables in the 2^nd-order polynomial for OBS calibration. These variables are:

1. Obs_V02: the coefficient of the 2^nd order term (determines the “curviness” of the hyperbola)

2. Obs_V0: the coefficient of the 1^st order term (which can be thought of as the slope of the main regression line)

3. Obs_const: a constant (the Y-intercept of the curve)

The particular values for each variable at each station can be found on the OBS sensor calibration sheets. Calibration is performed by the D&A Instrument Company (the OBS sensor manufacturer), and measures the response of our particular sensor to sediments from the different locations that we sample.

NOTE: As of December, 2000, OBS calibration of the OBS sensor on CTD2 has been done using sediment samples collected at the very heads of Tarr Inlet and Muir Inlet. These samples, however, are not appropriate for calibration since sediments farther from the glacier faces may vary in nature/constituents and concentration. We expect to collect several new calibration samples throughout the Bay and to have all CTD instruments calibrated to those samples sometime in 2001.

Join Point-Z File to Ocean Stations

Next, join the tables for the Ocean_stations and Point-Z files through a Spatial Join:

1. Load the GeoProcessing Wizard extension, if it is not already loaded (File Menu ® Extensions).

2. With your View active, start the GeoProcessing Wizard (View Menu ® GeoProcessing Wizard).

3. Select Assign Data by Location (Spatial Join) à Next

4. In the dialog box:

· Select the theme to assign data to: this is your Point-Z file <200001>ocean.shp

· Select the theme to assign data from: this is the Ocean_stations shape file, the one that is in your View and that you checked for the OBS calibration variables. Be sure you aren’t selecting an Ocean_stations file with the wrong projection or datum (i.e., UTM vs. Lat/Long, NAD27 vs. NAD83).

5. Press Finish. The Spatial Join will now assign data based on nearest (nearest is the only option because both themes are point themes).

6. Check that the spatial join was done correctly. A quick way to do so is to query one point per cast. For example: Query the Point-Z file (Table Menu ® Query) where: [Deps] = -20 then click New Set. Now, label the theme in the View (View Menu ® Auto Label) by the Label Field: Stn, which is one of the newly joined fields. Check if each cast is properly labeled with the number of the intended station. Delete all graphics when done.

The Point-Z table now displays the three OBS variable fields (at the end of the table), but the join is temporary. The next step is to perform the final OBS recalculation:

7. Unload the GeoProcessing Wizard

8. Save the Project

9. Now, Query the Point-Z table (go to the Attribute table, then Table Menu ® Query) and select the fields where [OBS] > 0. This query removes from consideration spurious OBS sensor readings, indicated by negative numbers or 0.0. The records selected are those on which the recalculation will be performed; other records (in this case those with bad data) will have no value at all (a blank) in the recalculated field.

10. Start editing the Point-Z table (Table Menu ® Start Editing)

11. Add a new field (Edit Menu ® Add Field)

Name: OBS_mg --for sediment in mg/liter
Type: Number
Width: 6 digits overall, 0 decimal places.

12. Select (click on) the new OBS_mg field (it should already be selected, having just been created)

13. Go to the Field Menu ® Calculate and enter the calibration formula. This formula is found on the OBS sensor calibration sheets and is also saved in a text file at …ocean/gis/ArcView_CalculateFormulas/obs_mg_formula.txt. The formula can be copied and pasted from this text file if entering the formula is confusing. The calibration formula is a second-order polynomial that utilizes the raw OBS sensor values plus the three numeric variables indicated by the appropriate calibration for each cast, which previously have been entered in the Ocean_Stations file. The formula is as follows:

([Obs_vo2] * ( [Obs] * [Obs]) )+( [Obs_vo] * [Obs] ) + [Obs_const]

14. Stop editing and save the edits (Table Menu ® Stop Editing ® Yes, save edits)

15. Remove all joins (Table Menu ® Remove All Joins)

16. Save the Project.

Obtaining Min/Max Values by Cast (3-D to 2-D)

Summarizing Data by Casts

1. Open the Point-Z attribute table for <200001>Ocean.shp (Theme Menu ® Table)

2. Select (click on) the Cast field (this is the aggregating field).

3. Go to: Field Menu ® Summarize.

The Summary Table Definition dialog box will appear. Click on Save As and check that the file path is correct, then name the new table: MaxMinValues.dbf

4. Back in the Summary Table Definition dialog box, Add all of the following field summarizations:

· Deps by both Min and Max (first choose Summarized by Min, click Add, then do the same for Summarized by Max).

· PAR by Max only

· T068 by both Min and Max

· Wetstar (Fls prior to August, 1999) by Min, Max, and Sum

· OBS_mg by Min, Max, and Sum

· Sal00 by both Min and Max

· Sigma_t00 by both Min and Max

5. Click OK

The new table is now created and opened (appears on-screen). The fields of this new table are named automatically and refer to the contributing fields and to how each was summarized (Max, Min, or Sum).

Joining Min/Max Results to CTDmaster

This step will perform a “one-to-one” Join of the table of results to your CTDmaster file (OR, if your naming scheme is different, to your “parent” file that contains only a single record per CTD cast).

1. Open the attribute tables for both CTDmaster and MaxMinValues.dbf.

2. Select (click on) the Cast field of the MaxMinValues.dbf table.

3. Bring forward (click on) the CTDmaster table and select (click on) the Cast field.

4. Go to: Table Menu ® Join

At this point, the MaxMinValues.dbf table disappears (closes) and your CTDmaster table should now have the results, which are, however, only temporarily joined.

Making the Join Permanent

1. Go to: CTD Menu ® Permanent Table Join

2. Select the fields to join: select the field Count plus all of the summarized variables (15 of them) you created in the MaxMinValues.dbf table.

3. Choose Auto join all selected fields as the Method of Join. This will rename the fields by adding an underscore _ to the end (and possibly by shortening the name if it is over 10 characters).

4. Press OK

5. Save the edits. The temporary join is removed and the table is closed to editing.

Photic Zone Calculation

This step will perform an initial “one-to-many” join in order to calculate the depths to which usable light penetrates the water column. This calculation will then be moved back to the CTDmaster (or “parent”) file.

Calculating PAR as a Proportion of the Surface Value

1. Open the attribute tables for both CTDmaster.dbf and the Point-Z table (<200001>ocean.shp)

2. Select Cast field in both tables

3. Bring Point-Z (<200001>ocean.shp) table forward.

4. Go to: Table Menu ® Join This is a temporary Join only! This brings the data from the CTDmaster into the Point-Z table.

5. Start editing the Point-Z table (Table Menu ® Start editing)

6. Add a new field to the table (Edit Menu ® Add field)

· Field Name: Prop_PAR

· Type: Number

· Width: 5 digits overall, with 3 decimal places

7. Add another new field

Field Name: MaxDepth
Type: Number
Width: 6 digits overall, with 0 decimal places

8. Select (click on) the Prop_PAR field header, then calculate it (Field Menu ® Calculate) as: [Prop_PAR] = [PAR] / [Max_PAR_]

9. Click OK

10. Select the MaxDepth field, and calculate it as: [MaxDepth] = [Min_Deps_]

NOTE: depths are negative from the 0 surface level, so the maximum depth is the minimum value of Deps

11. Click OK

12. Stop editing the table and save it (Table Menu ® Stop editing ® Yes, save edits). Do not yet remove Joins.

13. Save the Project.

Transferring 1% Photic Zone Depth to the 2-D File

1. In the Point-Z table (<200001>ocean.shp), Query the table (Table Menu ® Query) for the depths at which light reaches 1% of its surface value (the 1% photic zone). Type: ([Prop_PAR >= 0.01) and ([Max_PAR] >= 10.0)

Then click on New Set

NOTE: The second part of this query removes any casts that were taken at night or under very dim ambient light conditions (as sometimes happens during winter surveys). Proportional PAR is not meaningful at night, and very dim light appears to result in an artificially shallow depth for the 1% light level. This lower limit of 10.0 micro-Einsteins per second per m² is somewhat arbitrary; it is based on an initial examination of the casts made during March of 2000, which included a wide variety of surface light levels.

2. Select (click on) the Cast field. Then go to: Field Menu ® Summarize. The Summary Table Definition dialog box will appear. Click on Save As and check that the path of the file is correct, then name the new table: PhoticDepth.dbf

3. Back in the Summary Table Definition dialog box, Add the following field summarization:

· Deps, summarized by: Minimum

4. Click OK and the new table PhoticDepth.dbf is created and opened.

5. Remove all Joins from the Point-Z table (Table Menu ® Remove All Joins)

6. Unselect all the records in the Point-Z table (<200001>ocean.shp) and close the table.

7. Select (click on) the Cast field in the PhoticDepth.dbf table

8. Open the CTDmaster attribute table (or your “parent” one-record-per-cast file), select the Cast field and leave this table forward

9. Join the two tables (Table Menu ® Join). This is a temporary Join only! You will see blank values in the CTDmaster for any casts for which Max_PAR was less than 10.0. The PhoticDepth.dbf table disappeared (was closed by the Join).

10. Now make the Join permanent: CTD Menu ® Permanent Table Join

11. Select only one field to join: Select the field Min_Deps

12. Choose Enter New Field Name for Each as the Method of Join

13. Press OK, then name the new field PhoticDep1 (for depth of the 1% photic zone)

14. Press OK, and Save the edits. The temporary join is removed and the table is closed to editing

15. Save Project

Calculating Depth-Integrated Chlorophyll-a

Now we can calculate the standing crop of chlorophyll-a over depth increments, such as within the 1% photic zone, or within designated depths such as the surface 10m or 35m.

1. In the CTDmaster attribute table, click on (select) the Cast field.

2. Open the Point-Z attribute table (<200001>ocean.shp), select the Cast field, and leave this table forward.

3. Join the two tables (Table Menu ® Join). This is a temporary Join only! The CTDmaster table will be closed.

4. Query the Point-Z table for depths at and above the 1% photic zone depth (Table Menu ® Query). Type: [Deps] >= [PhoticDep1] and [Wetstar] > 0.05 (or: [Fls] > 0.05 prior to August of 1999)

NOTE: The second part of this query removes from the analysis any casts with spurious fluorescence values, as evidenced by negative numbers or extremely small positive numbers.

5. Click New Set

6. Select (click on) the Cast field and Summarize it: Field Menu ® Summarize. The Summary Table Definition dialog box will appear. Click on Save As , check the file path and name the file: DIC_Photic1.dbf (for depth-integrated chlorophyll over the 1% photic zone).

7. Back in the Summary Table Definition dialog box, Add the following field summarization:

Wetstar (or Fls prior to August, 1999) summarized by: Sum

8. Click OK

9. The new dbf table is created and opened.

We now will repeat these steps twice more to calculate depth-integrated chlorophyll for the surface 15m and 35m :

10. Return to the Point-Z table, unselect all records, and Query the table for: [Deps] >= -15 and [Wetstar] > 0.05 (or: [Fls] > 0.05 prior to August of 1999) as a New Set

11. Select (click on) the Cast field and go to: Field Menu ® Summarize. The Summary Table Definition dialog box will appear. Click on Save As, check the path and name the file: DIC_15m.dbf (for depth-integrated chlorophyll over the surface 15m).

12. Then, Add the following field summarization:

· Wetstar (or Fls prior to August, 1999) summarized by: Sum

13. Click OK (second new dbf table opens up).

14. Return to the Point-Z table, unselect all records, and Query the table for: [Deps] >= -35 and

[Wetstar] > 0.05 (or: [Fls] > 0.05 prior to August of 1999) as a New Set.

15. Select (click on) the Cast field and go to: Field Menu ® Summarize. Click on Save As, check the path and then name the file: DIC_35m.dbf (for depth-integrated chlorophyll over the surface 35m)

16. Next, Add the following field summarization:

Wetstar (or Fls prior to August, 1999) summarized by: Sum

17. Click OK (third new dbf table opens up)

18. Return to the Point-Z table, remove all Joins (Table Menu ® Remove All Joins), unselect all records, and close the table.

19. In DIC_Photic1.dbf, select (click on) the Cast field

20. Open the CTDmaster table, select the Cast field, and then Join these two tables (Table Menu ® Join). The DIC_Photic1.dbf table is closed after this temporary Join.

21. Perform a Permanent Table Join (CTD Menu ® Permanent Table Join) for only the Sum_Wetstar field (or Sum_Fls field prior to August, 1999). Name the new field DIC_Photic1 (for depth-integrated chlorophyll over the 1% photic depth). (For Permanent Table Join instructions, see page 22.)

22. Repeat steps 19-21 for both of the other depth-integrated-chlorophyll tables (DIC_15m.dbf and DIC_35m.dbf), naming the permanently joined fields DIC_15m and DIC_35m, respectively.

23. Save Project.

Calculating Depth-Integrated Sediment

Repeat all the steps in the previous section (steps 1-22), this time summing OBS_mg rather than Wetstar, to obtain depth-integrated sediment values for the 1% photic zone and for the top 15m and 35m of the water column. Name the resulting three new permanently joined fields in CTDmaster:

DI_Obs_Pho
DI_Obs_15m
DI_Obs_35m

Now the initial summarization of an oceanographic survey’s data is complete (congratulations!) These data, summarized by cast, can now be manipulated in ArcView to create both contour slices (or plots) and 3-D scenes of the data, where features will appear vertically as if through the water column. The cast summaries can also be exported to Excel and printed.

Exporting Cast Summaries for Printing

For examination and to file in the notebooks of oceanographic print-outs:

1. In the CTDmaster (or “parent” ) table, select all records

2. From the CTD Menu, choose Export Selected Record to Excel

3. The first time this function is run on a computer, it will ask for the location of Microsoft Excel on that computer. Navigate to the executable file for Excel and select it (double-click it or OK)

4. The Excel program will be opened, a new Excel worksheet will be created, and a dialog box will ask which fields to export.

5. Select all of the fields, and click OK

6. The values are exported, and the active window returns to ArcView. Excel remains in the background.

7. Print the Excel worksheet. Saving the table is probably not necessary, because it is very quick to re-create, and may change if more values are summarized for that survey.

3-D Scene Creation

Next you will create 3-dimensional scenes of your data in order to visualize the CTD casts down through the water column in Glacier Bay:

1. Open the 3-D Scene that is appropriate for your data (e.g., decimal degrees, NAD27). The 3-D Scene is empty except for the two themes ocean_stations and Noaa_coast. To open a 3-D Scene, in the Project Window: click ONCE (if you double-click then a new 3D Scene is created) on “3D Scenes” from the vertical icon list on the left (the bottom icon), then double-click on the file which now shows up in the Project Window.

2. Unlike a normal View Window, a 3-D Scene has 2 separate windows. One window is the list of themes and the other window is the 3-D map. When open, the 3-D map window ALWAYS floats on top of all other windows. Although you can select other windows or items in other windows, the 3-D map window will still be on top. To fully see the windows beneath, you must close the 3-D Scene. To close a 3-D Scene you need to close the 3-D Scene’s theme list window (click once on the “x” in the upper right corner); both of the 3-D Scene windows will then close.

3. Copy the Point-Z shape file (<200001>ocean.shp) from the View Window to the 3-D Scene. To do this, activate the Main Oceanography view and highlight the <200001>ocean.shp 3-D file that was created from the profile master previously. Go to the Edit Menu and select Copy Theme. Then activate the 3-D view: go to the Edit Menu and select Paste. This should place the 3-D shape file in the 3-D scene.

4. For this 3-D scene, you need to alter the Theme Properties of the <200001>ocean.shp so that features will be displayed 3-dimensionally on the map (i.e. the features will appear vertically as if through the water column). To do this, activate (click once) on <200001>ocean.shp and go to the Theme Menu → 3D Properties.

5. In the dialog box that opens up, the first portion of the box, Assign base heights by, should be set to “Existing 3D Shapes” (select this option if it is not already selected).

6. The Z factor should be set to 100.0 (type 100 in the box).

7. In the next part of the dialog box, called Offset heights by value or expression, do not enter anything (the default in the box should be 0).

8. In the third portion of the dialog box regarding the extrusion of features, Extrude features by value or expression should be set to 100 (type 100 in the box). Extrude by should be set to Adding to base height (select this option from the pull-down list).

9. Do not alter any of the “Advanced…” settings.

10. At the bottom, click Apply, and then once it has processed that action click OK, which will close the dialog box.

11. Now make 5 more copies of this 3-D theme in the 3-D Scene, so there will be a total of 6 identical 3-D themes (or, one for each type of CTD data). To do this, activate the theme that you wish to copy and go to the Edit Menu select Copy Theme and then Paste. You can now continue to paste until you get 6 total 3-D themes. The 5 new 3-D themes should now (already) have their 3D Theme Properties set in the exact same way as the first one (that is why we set the 3D Theme Properties before copying and pasting the themes).

12. Rename all 6 of the 3-D themes so that each one reflects one parameter measured by the CTD (i.e. temperature, salinity, density anomaly, photosynthetically active radiation, fluorescence, and turbidity). The correct 3-D theme names should be, respectively:

· T068_<200001>

· SAL_<200001>

· SigmaT_<200001>

· Prop_PAR_<200001>

· FLS_<200001>

· OBS_mg_<200001>

To rename a 3-D theme select the theme that you wish to rename, go to Theme Menu → Properties (not 3-D properties). In the properties dialog box, the first box is the Theme Name-- this is where you can change the name. Recall that in the above example, T068_<200001>, <2000> represents the year, while <01> represents the month of the project that you are creating.

For each 3-D theme the values of the features now need to be displayed on the map. To do this, the legend for each theme will need to be set to display the values for the appropriate parameter in graduated colors.

13. Activate one 3-D theme, go to the Theme Menu → Edit Legend (or you can double click the desired 3-D theme, and the Legend will come up).

14. The Legend Editor dialog box opens:

15. For Legend Type choose Graduated Color.

16. The Classification Field should be the parameter that this theme has been named (e.g. select T068 from the drop-down box if this is the 3-D theme named T068_200001).

17. Then click on the Classify button, and in the dialog box that appears select Natural Breaks as the type, and enter 24 for the number of classes. Click OK.

18.

For Color Ramps select the following colors for the various parameters so that all the projects are visually similar:

T068: Blues to Oranges Dichromatic
Sal00: Blues to Oranges Dichromatic
SigmaT: Blues to Oranges Dichromatic

ALL THREE of these should be ramped so that Blue represents low numerical values and Orange represents high numerical values (i.e. Blue would be low salinity, low temperature, and low density anomaly).

Prop_PAR: Yellow to Green to Dark Blue (Blue should represent low and Yellow high)
Wetstar (or Fls before August,1999): Purples to Greens Dichromatic (Purple should represent low and green high)
OBS_mg: Gray Monochromatic (Pale Gray should represent low numerical values and dark gray high)

To reverse the direction of the color ramping (i.e. to alter whether one end of the color scale represents high or low numerical values), click the button in the row of buttons beneath the legend values that has a figure of two arrows pointing in opposite directions around a graduated bar. Clicking this button once will reverse the color ramping. Clicking again returns the ramp to the original setting. For example, reversing the direction of the color ramping must be done when setting the Prop_PAR parameters.

19. Unselect all the themes, selecting only one at a time so only that one displays. For each parameter, look at the map and move it around and make sure that the values being displayed seem to make sense (i.e., for temperature, blue ought to generally be on the bottom, except at the surface near the tidewater glaciers or on the surface during winter. For Prop_PAR the yellow ought to be at the surface, and for density anomaly (SigmaT) orange should ALWAYS be at the bottom, etc.).

20. Visually check for consistency with expected (or normal) data patterns for that time of year for all six parameters. This step is where we found 1998’s odd temperature inversion, with warm temps (oranges) at the bottom of the basins. This step is also where we should catch some obvious errors.

Three-dimensional view of temperature data.

21. When done with 3-D Scene creation, save and close the 3-D Scene so that it is not floating on top of all the other windows any more.

Contouring Profile Slices (i.e., “Plotting”)

1. In the Oceanography Main View window (whichever one you are using for your data), open the attribute table for the Oceanog_line theme. (To do this: click once on the Oceanog_line theme, then Theme Menu → Table).

2. Make sure none of the polylines are selected, and then select only the Main Bay-West Arm polyline, which should become highlighted in yellow both in the attribute table and on the map in the View window.

You can select the polyline on the map in the View window, but having the attribute table open makes it clear and obvious that only one polyline is selected, and which one it is. We will now contour profile slices for all six CTD-measured parameters along this one particular polyline before selecting another polyline to contour. You cannot contour along multiple polylines at once.

3. Now select the 3-D shape file <200001>ocean.shp

4. On the map in the View window, select ONLY THOSE POINTS of this theme that should be profiled along the already-selected polyline.

To do this, click on the Select Feature Tool, which is in the upper left hand corner on the screen; it is a button on the bottom tool bar, left side, with an open square icon. After selecting this tool, you can select the points that you want with the mouse. To select multiple points, hold down the shift key while you are selecting. These points will now appear highlighted in yellow on the map in the View window. In the first instance, for the Main Bay-West Arm polyline, you should select only the 14 stations that lie along this polyline (stations 00 through 12 plus station 21). There are a few stations at the mouth of the bay that are duplicated at different stages of the tide cycle. If you include both casts for each of the duplicated stations, the contouring will be confused and inaccurate. For the Main Bay contour, select those casts that were taken at the slack portion of the tide. These casts, along with the others needed for this contour, can be selected using a Query. Selection via Query should also be done when selecting the stations for the two Lower Bay contours. One Lower Bay contour should be made with the casts taken during the slack tide, and another with the casts taken during the peak current portion of the tide (flood).

With the survey polyline and the 3-D shape (Point Z) files properly set up, the processing can now begin.

5. With the 3-D shape file <200001>ocean.shp still selected in the View window, go to the CTD Menu → Create a profile graph….

6. The Contour CTD Profiles dialog box will appear. First, select the parameters (= the fields) to be contoured. You can contour either one field or multiple fields at a time, but it saves time to process more than one field at once. The fields T068, Sal00, and SigmaT can be contoured together because they all can be processed with the same contour interval. However, Prop_PAR, Wetstar (Fls before August, 1999), and OBS_mg should each be processed individually. The first time through, select TO68, Sal00, and SigmaT (to select multiple fields press the Shift button while clicking on the fields in the drop-down box).

7. Next, select the Depth Field, which is normally deps, but if your data structure is different than our standard one you can select a different field from the drop-down box.

8. Select a method of calculating distance, which is the distance plotted along the x-axis in the final contour graph. Because we are using a polyline from the polyline theme Oceanog_line, select Use a polyline theme from the drop-down box.

NOTE: Although not done for the standard Glacier Bay oceanography project, there are two other alternatives possible here. You could have drawn a graphic (line) onto the map in the View window and selected it prior to initiating this contouring process; in this case you would select Use a selected line graphic and the final contour graph would run along that line graphic. The other alternative is to allow the program to Use actual distance, in which a straight line is drawn between each cast or data point. Intervening bathymetric features such as islands or trenches/mounts are reasons not to choose this option; we do not use this option in the standard oceanographic project because we are creating a longitudinal profile down Glacier Bay and its arms, which is not necessarily represented by straight lines drawn directly between the survey stations.

9.
Put a check mark in the box next to: Do want to use a bathymetric grid as a bottom mask?

10. Select Glb_bath as the mask from the drop-down box.

11. Do NOT select “Use mask extent for interpolation,” so that the interpolation does not extend beyond the edges of the sampled regions.

12. For the interpolation method, select Trend from the drop-down box.

13. The Polynomial Order should be 5.

NOTE: This method of interpolation has been selected for the standard oceanographic projects based not on theoretical considerations but based on numerous empirical trials in which the 5^th order polynomial trend produced the smoothest, most accurate, and most consistent trend surface Grids between casts.

14. The interval between contours should be:

· 0.25 for T068, Sal00, and SigmaT. This is why these three parameters can be processed together.

· For Prop_PAR use a contour interval of 0.1

· For Wetstar (Fls prior to August, 1999), the interval should be 5 for surveys during March through October and 0.5 during the winter (contour intervals may need to be increased if the contour lines are too close together).

· For OBS_mg use a contour interval of 5 or 10.

These intervals have been selected based on the appearance of the resulting contour graphs, so that enough information is presented but not so much that the graph is unreadable. The contour intervals may be adjusted (i.e. a parameter may need to be re-contoured with a different interval) by the user once the final graph is produced and examined.

15. The base contour should be 0.

16. The labels of the x and y axis can be changed, but the defaults are fine as: Distance (m) and Depth (m).

17. Click on Run to initiate the processing.

18. A dialog box will prompt you for which line theme to use for the distance calculation. Select Oceanog_line.shp from the drop-down box and then click OK.

19. If this is the second time (or later) you have contoured profiles from the 3-D shape file (<200001>oceanography.shp) you will next see a dialog box asking Field Sucs_Dist already exists. Overwrite existing values? This is fine, so click Yes. You will not encounter this question the first time you contour the shape file. If a second dialog box with a similar question appears immediately afterwards, click Yes again to completely overwrite the existing fields. …Some processing will now occur...

20. The next dialog box asks for the name of the Output Bathymetry Mask. Renaming the masks is time-consuming and isn’t really necessary, so permit the automatic numbering scheme to name the mask. Usually the first mask run is named Mask<###>.shp and successive masks will iterate the number so that the second mask will be Mask<###+1>.shp, etc.

**MAKE SURE that this file will be written to the correct folder (in the processed data folder, in the month you are working on). If it is not pointed to the right location, click on Cancel now and change the project’s working directory; this is done by setting the working directory, which is explained above in the GIS Data Processing section. Click on OK if the file name and destination are correct.

21.

The next dialog box asks for the name and destination of the output transposed point theme. Again, permit the automatic numbering scheme to name this file; the name will include the name of the parameter being contoured (such as t068), an underscore, then maybe a “p” to indicate this is a point theme (there will be no “p” for parameters with longer names, such as sal00 and sigmaT), then a number, which is incremented up when later contours of this same parameter are created. Again check that the destination folder is correct. Click on OK. …Some more processing will occur…

22. The next dialog box will ask you for output grid specifications. Make the output grid the same extent as the main oceanography 3-D shape file by choosing the output grid extent from the drop-down box to be: Same as t068_Pt_<200001>ocean.shp (the parameter shown will change depending on which field is currently being contoured). Do not bother with the other input options in this dialog box (Output grid cell size, Number of Rows, Number of Columns). Click OK. …More processing will occur...

23. The next dialog box asks for the name and destination of the output contour file. Once again permit the automatic numbering scheme to name this file, which will be named similarly to the output transposed point theme except it will have a “c” instead of a “p” to indicate that it is a contour file (except, again, the parameters with longer names will not have a “c” in the file name).

24. If you are contouring multiple parameters at once, you will see a dialog box requesting the file name and destination of the next parameter’s output transposed point theme, then its grid specifications, and finally its contour file name and destination. Only a single mask will be used by all the parameters that are contoured in one batch.

25. When all parameters have been contoured (i.e., when processing is complete), a new View Window will open up for each parameter To aid viewing and printing, change the bathymetry mask’s default black color to an opaque stippled pattern, and place it on top of the contour lines.

Example contour view, showing June, 1998’s intrusion of hot saline water into the deep basin of Glacier Bay.

Editing of Contour Files

Some contour profiles are very large when they are created, with numerous extraneous contours that are unrelated to the actual data. The usual cause is that the procedure mathematically extrapolates into areas with no data. Each contour profile created should be checked for extra contour lines. These extraneous contour lines should be edited out, so that the project size, and the time it takes it to load it, are kept to a minimum. To begin editing, the contour file that you want to edit must be selected (highlighted or “embossed” in the View Window), then go to Theme Menu, and select Start Editing. Use the tools (buttons) on the tool bar to select and visualize what to delete. Delete any extra contour lines, spurious “cells” (circles) of contours, etc. When done editing, return to Theme Menu, select Stop Editing, and Save Edits. Delete all contour labels (numbers) corresponding to the deleted contours. Save the project.

Joining all Oceanographic Data

The “master” ArcView oceanography databases, named All_CTDmasters.dbf and All_Profilemasters.dbf, reside at the top level (root directory) of the Processed Data folder, with the following file paths:

Science(K:)\eco_data\data\glba\ocean\data\processed\All_CTDmasters.dbf.

Science(K:)\eco_data\data\glba\ocean\data\processed\All_Profilemasters.dbf.

These “master” files contain ALL of the CTD casts ever uploaded by the Glacier Bay Field Station, from any CTD at any Glacier Bay location and during any project. Because these are the “master” files and are very large, correcting them is difficult and time consuming, and subjects the files to potential errors. Therefore, do not add a new batch of CTD profiles to the All_Profilemasters.dbf or All_CTDmasters.dbf files until these new profiles have previously been checked by careful visual examination of the printed-out depth profiles.

To confirm that data files are “good” and therefore are ready for inclusion in these two “master” files, they must have been run through the ArcView processing and contouring steps and saved to a database file specific to the particular cruise or project. Only good data should be added to the Master database file, so make sure that you have done good error-checking during the GIS Processing steps. Data are added to the All_CTDmasters and All_ProfileMasters tables by utilizing the Merge Command in the CTD Menu, accessed from the View Window. Select the themes you wish to merge from the pull-down list. The first theme in the selected list determines the fields that are used in the merge. Due to variation between surveys (in the instruments used and in other variable fields), care must be taken to insure that fields are labeled exactly the same or that a blank field with the alternative field name exists in the first file.

Data Management

This section is an overview of where various types of oceanography-related files and data are stored.

A directory called Ocean, located on the Glacier Bay National Park computer network (K:\eco_data\data\glba\ocean) contains all oceanographic data and information files related to the oceanographic project, including raw/converted data, logistics, protocol, datasheets, base GIS layers, and analyses.

Raw Data

Raw CTD data are acquired in the field, initially uploaded to a portable computer while on board the field vessel, and/or uploaded directly to the Glacier Bay National Park computer network in a .hex (ASCII) file format.

One file is made and uploaded for every cast, and is labeled with the CTD number, dump number, and individual sequential cast number. Raw data in .hex format should be stored in the following raw data directories, which are organized first by CTD #, then by year, and finally by cruise date (or project name):

For CTD 1

Science\eco_data\data\glba\ocean\data\Ctd1_raw\<1998>\<199810>oceanography\c1003302.hex

For CTD 2

Science\eco_data\data\glba\ocean\data\Ctd2_raw\<1998>\<199810>oceanography\c2003706.hex

Once raw .hex files are stored in these directories, they should never be moved! These are the permanent raw data files. Any data processing should be performed on copies of these files if moving the files is required.

Processed Data

Once the raw data have been initially processed by the SeaSoft software, the resulting files have the “.cnv” extension. These converted files from both CTD 1 and CTD 2 should be stored in processed data directories, which are organized first by year (not by CTD number) and then by cruise date (month) and project name. An example is:

Science(K:)\eco_data\data\glba\ocean\data\processed\<1998>\<199810>oceanography\c2003706.cnv

Analyzed Data

Data analyzed using GIS Arcview applications should also be stored in the processed data files. During processing, you can set the working directory to automatically deposit these files in the correct processed file according to year and month. For both CTD1 and CTD2, the processed dbf files, and the apr project with all corresponding files should be stored in the same folder. An example is:

Science\eco_data\data\glba\ocean\data\processed\<1998>\<199810>oceanography\ <199810>ocean.apr

Documentation & Protocols

This manual (Microsoft Word 2000 file) resides in:

Science\eco_data\data\glba\ocean\protocol\oceanography_handbook.doc

In addition, an Adobe Acrobat (.pdf) version of this handbook resides in the same directory, and is available over the Internet at: http://www.absc.usgs.gov/glba/index.htm

Archiving Written Data

All original data sheets from the oceanography survey project are stored in several notebooks in the data cabinet in the USGS office, where all Glacier Bay Field Station research project data are stored.

Archiving Digital Data

Save the raw data (.hex files) onto floppy disks and place them in the USGS data cabinet. Copy the entire Ocean folder (contains all raw and processed data, protocols, etc.) to CD-ROM’s and archive them off-site at least once per year.

Reference List

Hooge, P.N. and E.R. Hooge. 2000a. The Oceanographic Analyst Extension to ArcView GIS. USGS Alaska Biological Science Center. http://www.absc.usgs.gov/glba/gistools/

Hooge, P.N. and E.R. Hooge. 2000b. Fjord Oceanographic Processes in Glacier Bay, Alaska. Report to the National Park Service. USGS Alaska Biological Science Center.

Appendices

Appendix A: Oceanographic Station Locations

Location and average depths of oceanographic stations in Glacier Bay National Park, Alaska

Station Number	Latitude (Nad27)	Longitude (Nad27)	Description	Average Depth (m)
STN00	58.327077	-135.873287	Icy Strait, Mouth of Glacier Bay	53
STN01	58.412910	-135.993279	Mouth Glacier Bay	62
STN02	58.490410	-136.049941	Sitakaday	93
STN03	58.572075	-136.063270	SE of Willoughby Island	112
STN04	58.651241	-136.113264	N of Drake I and N of Marble I.	288
STN05	58.704575	-136.231592	Between N Drake and SW Tlingit PT	366
STN06	58.759576	-136.349919	E of Hugh Miller Inlet	288
STN07	58.812076	-136.471580	N of Blue Mouse, W of Tidal Inlet	435
STN08	58.865410	-136.591574	S of Rendu Inlet	426
STN09	58.897912	-136.734902	S of Russell Island	377
STN10	58.899580	-136.838232	E of Russell Island	361
STN11	58.972079	-136.914893	Tarr Inlet	338
STN12	59.033746	-137.016554	Head of Tarr Inlet	288
STN13	58.732906	-136.111594	SE of Tlingit PT, NW of Sturgess	146
STN14	58.792072	-136.106591	Muir sill	81
STN15	58.815405	-136.103256	W of Muir PT	116
STN16	58.896236	-136.091586	E of Hunter Cove	313
STN17	58.975402	-136.134914	E of Westdahl Pt	212
STN18	59.050401	-136.183242	S of Riggs, NW of McBride	214
STN19	59.072069	-136.334904	Muir Inlet	225
STN20	59.086403	-136.369069	Head of Muir Inlet	179
STN21	59.048100	-137.055850	Marjorie/Grand Pacific	195
STN22	58.658067	-136.363600	Entrance to Geikie	155
STN23	58.598500	-136.504633	Head of Geikie	66

Appendix B: Oceanographic Survey Equipment List

Equipment Needed for Monthly Oceanographic Surveys

RESEARCH VESSEL & SUPPORT EQUIPMENT

RV Tamnik, 50feet; 60,000lbs
Longline Drum
Power Block/Davit
Hydraulics

CTD SAMPLING EQUIPMENT

SEACAT SBE 19-03 Conductivity, Temperature, Depth Recorder (Sea-Bird Electronics)
Ground line (marked every 10m) and plastic tub
Smart Block (if not using marked line)
9 spare D-cell batteries
2 Locking carabiners and soda can/gangion
Distilled Water (1gallon)
Triton-X* detergent (+2 squirt bottles)
Small tube of Silicon Grease (Dow Corning 4 Electrical Insulating Compound)
Rubbing alcohol
Lint-free cloth
Data Cable including RS232 to DB9 connector
Portable Computer and formatted computer discs
Office Box (containing general office equipment)
2 PLGR+ Fed 96 GPS units (Rockwell)
Extra PLGR GPS battery, power/antenna cables and external antennas

* Triton X-100 is non-ionic detergent, which is used as a 1% percent solution in distilled water. One source is VWR Scientific Products in Seattle, WA at 800-932-5000, or http://www.vwrsp.com.

MANUALS & DOCUMENTATION

Seacat SBE 19-03 and Seasoft 4.236 operating manuals
PLGR+Fed 96 operating manual
Last CTD cast number (recorded in CTD log)
Waterproof field notebook with Rite-in-the-rain or Duracopy paper
Oceanography notebook (contains protocol, station locations, maintenance info, etc.)
CTD datasheets Xeroxed on waterproof paper (approx.10 sheets, 3 stations per page)

GENERAL FIELD GEAR

Rite-in-the-Rain waterproof paper
Several black Ultra Fine Point Sharpie pens and/or pencils.
Personal Flotation Devices
Immersion (survival) suits
Handheld (waterproof) radio with ParkNet frequencies
Groceries
Rain gear
Waterproof gloves (insulated ideal)
Waterproof boots
Binoculars

CTD DATA ACQUISITION SOFTWARE

SEASOFT Version 4.236/4.023

28 April 1994

Sea-Bird Electronics, Inc.

Intended for use on an IBM-PC 386/386 or higher compatible computer

Software includes 3 modules: TERM19, SEACON, and SEASAVE
1/99 Upgraded Windows Module: SEASAVE for WIN 95/NT V 1.07

GENERAL COMPUTER EQUIPMENT & SOFTWARE

On-board Pentium PC with Windows NT
ESRI ArcView 3.2
ESRI Tracking Analyst (with TCP/IP enabled on system, com port configured)
MPS (Mission Planning Software)
TextPad, NotePad, or other Text Editor Software

Appendix C: CTD Data Sheet

OCEANOGRAPHY SURVEY

Glacier Bay National Park & Preserve, Alaska

Name:______________________ Logbook Page: _____________

Appendix D: CTD “Dump” Log

(also known as: the Upload Log)

Appendix E: FGDC Metadata

For ProfileMaster and CTDMaster ArcView shape files (including database field definitions)

A. ProfileMaster File

IDENTIFICATION_INFORMATION

Citation:

Citation_Information:

Originator: Philip N. Hooge

Originator: Elizabeth Ross Hooge

Publication_Date: 20001201

Title: Oceanographic CTD 3d Profiles from Seabird Instruments

Edition: 1

Geospatial_Data_Presentation_Form: Map

Publication_Information:

Publication_Place: Glacierr Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Other_Citation_Details:

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Larger_Work_Citation:

Citation_Information:

Originator: P. Hooge

Publication_Date: 20001201

Title: Fjord Oceanography of Glacier Bay

Publication_Information:

Publication_Place: Glacier Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Description:

Abstract:

The Bay is a recently (300 years ago) deglaciated fjord

located within Glacier Bay National Park in Southeast

Alaska. Glacier Bay is a fjord estuarine system that has

multiple sills. These sills are often associated with

contractions and are backed by very deep basins with

tidewater glaciers and many streams. Glacier Bay

experiences a large amount of runoff, high sedimentation,

and large tidal variations. Melting occurs year-round,

which fuels the estuarine circulation even through the

winter. This runoff, and the presence of the tidewater

glaciers makes the bay extremely cold. There are many

small- and large-scale mixing and upwelling zones at sills,

glacial faces, and streams. The complex topography and

strong currents lead to highly variable salinity,

temperature, sediment, productivity, light penetration, and

current patterns within a small area. This complexity

defies simple characterization or modeling based on other

areas in Southeast Alaska. While several oceanographic

studies have been conducted in Glacier Bay, these studies

are contradictory and were of short duration and limited

coverage, missing much of the spatial, seasonal and annual

variation. In addition, some assumptions based on past

studies have been contradicted by recent results (Hooge, et

al. 2000) . The constantly changing nature of the Bay may

contribute to contradictions among past studies and between

recent and historical results.

Purpose:

The Glacier Bay oceanographic project was designed for the

acquisition, analysis, and modeling of fjord-estuarine

oceanographic data in Glacier Bay, Alaska. Located along

the glacial chronosequence in the Bay, 24 stations are

profiled multiple times each year in order to acquire

measurements of temperature, salinity, productivity

(phytoplankton biomass through chlorophyll-a), sediment

load, and light penetration throughout the water column at

1-meter depth intervals from the surface to near the sea

floor. Duplicate samples are taken at slack and peak

current flow in those areas where water column

characteristics are strongly affected by tidal stage. Each

survey data set is integrated into a Geographic Information

System environment utilizing the Oceanographic Analyst

Extension (OAE), which allows viewing and manipulation of

3- and 4-D oceanographic datasets within ESRI's ArcView GIS.

Supplemental_Information:

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1993

Ending_Date: Present

Currentness_Reference: Current

Status:

Progress: Complete

Maintenance_and_Update_Frequency: Annually

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -137.0492

East_Bounding_Coordinate: -135.8733

North_Bounding_Coordinate: 59.0591

South_Bounding_Coordinate: 58.3144

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: Oceanography

Theme_Keyword: CTD

Theme_Keyword: Glacier Bay

Theme_Keyword: Fjord

Theme_Keyword: Estuarine

Theme_Keyword: Estuary

Theme_Keyword: Tidewater Glacier

Theme_Keyword: Sill

Theme_Keyword: Contraction

Theme_Keyword: Hydraulic Control

Theme_Keyword: Marine Ecosystem

Theme_Keyword: Temperature

Theme_Keyword: Salinity

Theme_Keyword: Density

Theme_Keyword: Sigma-T

Theme_Keyword: OBS

Theme_Keyword: PAR

Theme_Keyword: Chlorophyll-a

Theme_Keyword: Photosynthetically Active Radiation

Theme_Keyword: Backscatterance

Theme_Keyword: Sedimentation

Theme_Keyword: Flocculation

Theme_Keyword: Primary Productivity

Theme_Keyword: Primary Production

Theme_Keyword: Photic Depth

Theme_Keyword: Photic Zone

Theme_Keyword: Halocline

Theme_Keyword: Thermocline

Theme_Keyword: Pycnocline

Theme_Keyword: Mixed Layer

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Glacier Bay

Place_Keyword: Alaska

Place_Keyword: Gustavus

Place_Keyword: Southeast Alaska

Place_Keyword: Norther Lattitude

Place_Keyword: High Lattitude

Place_Keyword: Sub-Arctic

Place_Keyword: Cross Sound

Place_Keyword: Icy Strait

Place_Keyword: Inside Passage

Place_Keyword: Gulf of Alaska

Place_Keyword: North Pacific

Access_Constraints:

Use_Constraints:

Please contact before publication use

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: mailing and physical address

Address: P.O. Box 292, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

Native_Data_Set_Environment:

ArcView version 3.2 shapefile format

k:\eco_data\data\glba\ocean\data\processed\2000\200003oceanography\200003oceanography.shp

DATA_QUALITY_INFORMATION

Attribute_Accuracy:

Attribute_Accuracy_Report:

Accuracy varies with the different oceanographic variables

locations, and years. However the insturments were

calibrated each year, values checked for errors, and all

observationally deviant data removed. See the oceanographic

protocol manual and report at

www.absc.usgs.gov/glba/oceanography/index.htm for details

on the way values were recorded and accuracy issues.

Logical_Consistency_Report:

Completeness_Report:

This data is updated after each survey which occurs

approximately five times a year.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report:

4 meters absolute accuracy using military crypto code

receivers. Approximately 100 meter aquisition of repeated

station position.

Vertical_Positional_Accuracy:

Vertical_Positional_Accuracy_Report:

None

Lineage:

Source_Information:

Source_Citation:

Citation_Information:

Originator: Philip N. Hooge

Publication_Date: Varies

Title: Seabird Instruments CNV files which are Georeferenced

Edition: Varies with software and insturment

Geospatial_Data_Presentation_Form: map

Publication_Information:

Publication_Place: Glacierr Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Other_Citation_Details:

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Larger_Work_Citation:

Citation_Information:

Originator: P. Hooge

Publication_Date: Varies

Title: Fjord Oceanography of Glacier Bay

Publication_Information:

Publication_Place: Glacier Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Source_Scale_Denominator:

Type_of_Source_Media: Digital

Source_Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1993

Ending_Date: Present

Source_Currentness_Reference: Current

Source_Citation_Abbreviation:

Source_Contribution:

The Seabird Instrument files are the primary part of the

georeferenced CTD profiles. Locational and tide information

is added as well as some locationally dependent calibration coeficients.

Process_Step:

Process_Description:

Processing steps of this data are highly detailed and

involved. These processing steps involve both detailed

manipulation of the instrument derived variables as well as

extensive parsing, databasing, georeferencing, creation of

2, 3 and 4-D spatial datasets, and then spatial and

database joining and aggregation. These processes are

described in detail in the Fjord Oceanographic Monitoring

Handbook available in pdf form at www.absc.usgs.gov/glba/oceanography/index.htm

Source_Used_Citation_Abbreviation:

Process_Date: 1993 to current: each survey processed as obtained

Source_Produced_Citation_Abbreviation:

Process_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: mailing and physical address

Address: P.O. Box 292, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

SPATIAL_DATA_ORGANIZATION_INFORMATION

Direct_Spatial_Reference_Method: Vector

Point_and_Vector_Object_Information:

SDTS_Terms_Description:

SDTS_Point_and_Vector_Object_Type:

Point_and_Vector_Object_Count: 4378

SPATIAL_REFERENCE_INFORMATION

Horizontal_Coordinate_System_Definition:

Planar:

Map_Projection:

Map_Projection_Name: Transverse Mercator

Transverse_Mercator:

Scale_Factor_at_Central_Meridian: 0.999600

Longitude_of_Central_Meridian: -135.000000

Latitude_of_Projection_Origin: 0.000000

False_Easting: 500000.000000

False_Northing: 0.000000

Planar_Coordinate_Information:

Planar_Coordinate_Encoding_Method: Coordinate pair

Coordinate_Representation:

Abscissa_Resolution:

Ordinate_Resolution:

Planar_Distance_Units: Meters

Geodetic_Model:

Horizontal_Datum_Name: North American Datum of 1927

Ellipsoid_Name: Clarke 1866

Semi-major_Axis: 6378206.4000000

Denominator_of_Flattening_Ratio: 294.98

ENTITY_AND_ATTRIBUTE_INFORMATION

Detailed_Description:

Entity_Type:

Entity_Type_Label: 200003oceanography.dbf

Entity_Type_Definition: Shapefile Attribute Table

Entity_Type_Definition_Source: None

Attribute:

Attribute_Label: Cast

Attribute_Definition: The Oceanographic Instrument Cast Number

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Character Field

Attribute:

Attribute_Label: Date

Attribute_Definition: The Date of the Cast

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Date Field

Attribute:

Attribute_Label: Time

Attribute_Definition: The time the cast was made

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Character Field

Attribute:

Attribute_Label: Utmx

Attribute_Definition: The X coordinate Nad 27 Zone 8

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Utmy

Attribute_Definition: The Y coordinate Nad 27 Zone 8

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Scan

Attribute_Definition: Instrument Scan Number

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Pr

Attribute_Definition: Pressure

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: T068

Attribute_Definition: Temperature Celsius

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: C0s_m

Attribute_Definition: Conductivity

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Par

Attribute_Definition: Photosynthetically Active Radiation

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Wetstar

Attribute_Definition: Chlorophyl-a concentration mg/m3

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Obs

Attribute_Definition: Optical Backscatter in mv

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Times

Attribute_Definition: Time of the instrument reading

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Deps

Attribute_Definition: Depth in seawater -derived from pressure

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Sal00

Attribute_Definition: Salinity ppt, derived from conductivity

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Sigma_t00

Attribute_Definition: Density, derived from conductivity and temperature

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Svc

Attribute_Definition: Sound Velocity derived from density

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Avgsvc

Attribute_Definition: Average Sound Velocity

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Flag

Attribute_Definition: Bad Value Flag

Attribute_Definition_Source:

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0.000

Enumerated_Domain_Value_Definition: Good Value

Enumerated_Domain_Value_Definition_Source:

Attribute:

Attribute_Label: Nbin

Attribute_Definition: Number of measurments average in a depth bin

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Sucs_Dist

Attribute_Definition: Distance between casts, a recalculated value dependent on

chosen contouring profiles

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Attribute:

Attribute_Label: Prop_par

Attribute_Definition: Proportional Par of highest value in cast

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 1

Attribute:

Attribute_Label: Maxdepth

Attribute_Definition: The maximum depth of the cast

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Numeric Field

Overview_Description:

Entity_and_Attribute_Overview:

Entity_and_Attribute_Detail_Citation:

DISTRIBUTION_INFORMATION

Distributor:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: mailing and physical address

Address: P.O. Box 292, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

Resource_Description:

Profile Master Data For Glacier Bay, Alaska

Distribution_Liability:

None

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name:ArcView Shape Files PointZ

Digital_Transfer_Option:

Offline_Option:

Offline_Media: CD Rom

Recording_Format: Juliet

Compatibility_Information:

Can be used with any vector GIS capable system able to use

or import ArcView Shape Files. The information can also be

accessed from the dbf files containing the attribute

information since the XY coordinates are in the table.

Fees: None

Ordering_Instructions:

Contact Philip N. Hooge Ph.D. at

philip_hooge@usgs.gov see

www.absc.usgs.gov/glba/oceanography/index.htm for current

ordering or downloading methods.

METADATA_REFERENCE_INFORMATION

Metadata_Date: 11/22/2000

Metadata_Review_Date: 11/22/2000

Metadata_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: Mailing and physical address

Address: P.O. Box 292, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

Metadata_Standard_Name: FGDC CSDGM

Metadata_Standard_Version: FGDC-STD-001-1998

A. CTDMaster File

IDENTIFICATION_INFORMATION

Citation:

Citation_Information:

Originator: Philip N. Hooge

Originator: Elizabeth Ross Hooge

Publication_Date: 20001201

Title: Oceanographic CTD 2d Profiles from Seabird Instruments

Edition: 1

Geospatial_Data_Presentation_Form: Map

Publication_Information:

Publication_Place: Glacier Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Other_Citation_Details:

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Larger_Work_Citation:

Citation_Information:

Originator: P. Hooge

Publication_Date: 20001201

Title: Fjord Oceanography of Glacier Bay

Publication_Information:

Publication_Place: Glacier Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Description:

Abstract:

Oceanography describes one of the most fundamental physical

aspects of a marine ecosystem. Most of the resource and

research issues in Glacier Bay are marine in whole or part.

Glacier Bay exhibits a highly complex oceanographic regime

within a small area. An understanding of many of the

resource and research issues in Glacier Bay will not be

possible without an understanding of the underlying

oceanographic processes causing the large spatial and

annual variation.

The Bay is a recently (300 years ago) deglaciated fjord

located within Glacier Bay National Park in Southeast

Alaska. Glacier Bay is a fjord estuarine system that has

multiple sills. These sills are often associated with

contractions and are backed by very deep basins with

tidewater glaciers and many streams. Glacier Bay

experiences a large amount of runoff, high sedimentation,

and large tidal variations. Melting occurs year-round,

which fuels the estuarine circulation even through the

winter. This runoff, and the presence of the tidewater

glaciers makes the bay extremely cold. There are many

small- and large-scale mixing and upwelling zones at sills,

glacial faces, and streams. The complex topography and

strong currents lead to highly variable salinity,

temperature, sediment, productivity, light penetration, and

current patterns within a small area. This complexity

defies simple characterization or modeling based on other

areas in Southeast Alaska. While several oceanographic

studies have been conducted in Glacier Bay, these studies

are contradictory and were of short duration and limited

coverage, missing much of the spatial, seasonal and annual

variation. In addition, some assumptions based on past

studies have been contradicted by recent results (Hooge, et

al. 2000) . The constantly changing nature of the Bay may

contribute to contradictions among past studies and between

recent and historical results.

Because of the importance of oceanography to understanding

critical resource and research problems, the complexity of

the Bay's oceanographic system, as well as the limited and

contradictory prior work, it is imperative that a

sustained, rigorous, and complete monitoring program be

developed and implemented.

Purpose:

The Glacier Bay oceanographic project was designed for the

acquisition, analysis, and modeling of fjord-estuarine

oceanographic data in Glacier Bay, Alaska. Located along

the glacial chronosequence in the Bay, 24 stations are

profiled multiple times each year in order to acquire

measurements of temperature, salinity, productivity

(phytoplankton biomass through chlorophyll-a), sediment

load, and light penetration throughout the water column at

1-meter depth intervals from the surface to near the sea

floor. Duplicate samples are taken at slack and peak

current flow in those areas where water column

characteristics are strongly affected by tidal stage. Each

survey data set is integrated into a Geographic Information

System environment utilizing the Oceanographic Analyst

Extension (OAE), which allows viewing and manipulation of

3- and 4-D oceanographic datasets within ESRI's ArcView GIS.

Supplemental_Information:

This database supplments the 3-D ProfileMaster shapefile

and provides 2-D summary information in order to integrate

the cast profile data with other 2-D data sets.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1992

Ending_Date: present

Currentness_Reference: Current

Status:

Progress: Complete

Maintenance_and_Update_Frequency: Annually

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -136.9230

East_Bounding_Coordinate: -135.8750

North_Bounding_Coordinate: 59.0920

South_Bounding_Coordinate: 58.3177

Keywords:

Theme:

Theme_Keyword_Thesaurus: None

Theme_Keyword: Backscatterance

Theme_Keyword: Chlorophyll-a

Theme_Keyword: Contraction

Theme_Keyword: CTD

Theme_Keyword: Density

Theme_Keyword: Estuarine

Theme_Keyword: Estuary

Theme_Keyword: Fjord

Theme_Keyword: Flocculation

Theme_Keyword: Glacier Bay

Theme_Keyword: Halocline

Theme_Keyword: Hydraulic Control

Theme_Keyword: Marine Ecosystem

Theme_Keyword: Mixed Layer

Theme_Keyword: OBS

Theme_Keyword: Oceanography

Theme_Keyword: PAR

Theme_Keyword: Photic Depth

Theme_Keyword: Photic Zone

Theme_Keyword: Photosynthetically Active Radiation

Theme_Keyword: Primary Production

Theme_Keyword: Primary Productivity

Theme_Keyword: Pycnocline

Theme_Keyword: Salinity

Theme_Keyword: Sedimentation

Theme_Keyword: Sigma-T

Theme_Keyword: Sill

Theme_Keyword: Temperature

Theme_Keyword: Thermocline

Theme_Keyword: Tidewater Glacier

Place:

Place_Keyword_Thesaurus: None

Place_Keyword: Alaska

Place_Keyword: Cross Sound

Place_Keyword: Glacier Bay

Place_Keyword: Gulf of Alaska

Place_Keyword: Gustavus

Place_Keyword: High Lattitude

Place_Keyword: Icy Strait

Place_Keyword: Inside Passage

Place_Keyword: North Pacific

Place_Keyword: Norther Lattitude

Place_Keyword: Southeast Alaska

Place_Keyword: Sub-Arctic

Access_Constraints:

Use_Constraints:

Please contact before publication and cite P.N. Hooge and

E.R. Hooge. 2000. Glacier Bay Fjord Oceanography Dataset.

USGS, Alaska Biological Science Center.

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: mailing and physical address

Address: P.O. Box 140, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

Native_Data_Set_Environment:

ArcView version 3.2 shapefile format

k:\eco_data\data\glba\ocean\data\processed\2000\200005oceanography\ctdmaster.shp

DATA_QUALITY_INFORMATION

Attribute_Accuracy:

Attribute_Accuracy_Report:

Accuracy varies with the different oceanographic variables

locations, and years. However the insturments were calibrated each year, values checked for errors, and all

observationally deviant data removed. See the oceanographic protocol manual and report at

www.absc.usgs.gov/glba/oceanography/index.htm for details on the way values were recorded and accuracy issues.

Logical_Consistency_Report:

This data is logically consistent.

Completeness_Report:

These data are updated after each survey which is occurs

appromately five times of a year.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report:

4 meters absolute accuracy using military crypto code

receivers. Approximately 100 meter aquisition of repeated

station position.

Vertical_Positional_Accuracy:

Vertical_Positional_Accuracy_Report:

All positions are at sea level and these data do not have a

vertical component.

Lineage:

Source_Information:

Source_Citation:

Citation_Information:

Originator: Philip N. Hooge

Publication_Date: Varies

Title: Seabird Instruments CNV files which are Georeferenced

Edition: Varies with software and insturment

Geospatial_Data_Presentation_Form: map

Publication_Information:

Publication_Place: Glacier Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Other_Citation_Details:

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Larger_Work_Citation:

Citation_Information:

Originator: P. Hooge

Publication_Date: Varies

Title: Fjord Oceanography of Glacier Bay

Publication_Information:

Publication_Place: Glacier Bay National Park, Gustavus, Alaska

Publisher: USGS Alaska Biological Science Center, Glacier Bay National Park

Online_Linkage: www.absc.usgs.gov/glba/oceanography/index.htm

Source_Scale_Denominator:

Type_of_Source_Media: Digital

Source_Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 1992

Ending_Date: present

Source_Currentness_Reference: Current

Source_Citation_Abbreviation:

Source_Contribution:

The Seabird Instrument files are the primary part of the georeferenced CTD profiles. Locational and tide information is added as well as some locationally dependent calibration coeficients.

Process_Step:

Process_Description:

Processing steps of this data are highly detailed and involved. These processing steps involve both detailed manipulation of the instrument derived variables as well as

extensive parsing, databasing, georeferencing, creation of 2, 3 and 4-D spatial datasets, and then spatial and

database joining and aggregation. These processes are described in detail in the Fjord Oceanographic Monitoring

Handbook available in pdf form at wwww.absc.usgs.gov/glba/oceanography/index.htm

Source_Used_Citation_Abbreviation:

Process_Date: 1992 to current; each survey processed as obtained

Source_Produced_Citation_Abbreviation:

Process_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: mailing and physical address

Address: P.O. Box 140, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

SPATIAL_DATA_ORGANIZATION_INFORMATION

Direct_Spatial_Reference_Method: Point

Point_and_Vector_Object_Information:

SDTS_Terms_Description:

SDTS_Point_and_Vector_Object_Type: Point

Point_and_Vector_Object_Count: 25

SPATIAL_REFERENCE_INFORMATION

Horizontal_Coordinate_System_Definition:

Planar:

Grid_Coordinate_System:

Grid_Coordinate_System_Name: Universal Transverse Mercator

Universal_Transverse_Mercator:

UTM_Zone_Number: 8

Transverse_Mercator:

Scale_Factor_at_Central_Meridian: 0.999600

Longitude_of_Central_Meridian: -135.000000

Latitude_of_Projection_Origin: 0.000000

False_Easting: 500000.000000

False_Northing: 0.000000

Planar_Coordinate_Information:

Planar_Coordinate_Encoding_Method: Coordinate pair

Coordinate_Representation:

Abscissa_Resolution: 1 meter

Ordinate_Resolution: 1 meter

Planar_Distance_Units: Meters

Geodetic_Model:

Horizontal_Datum_Name: North American Datum of 1927

Ellipsoid_Name: Clarke 1866

Semi-major_Axis: 6378206.4000000

Denominator_of_Flattening_Ratio: 294.98

ENTITY_AND_ATTRIBUTE_INFORMATION

Detailed_Description:

Entity_Type:

Entity_Type_Label: ctdmaster.dbf

Entity_Type_Definition: Shapefile Attribute Table

Entity_Type_Definition_Source: None

Attribute:

Attribute_Label: Cast

Attribute_Definition: Cast Name as a composite of instrument id, dump number and cast number

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Character Field

Attribute:

Attribute_Label: Location

Attribute_Definition: Oceanographic Station

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Character Field

Attribute:

Attribute_Label: Date

Attribute_Definition: The day the cast was taken

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Date Field

Attribute:

Attribute_Label: Time

Attribute_Definition: The specific time the instument was lowered

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Character Field

Attribute:

Attribute_Label: Header

Attribute_Definition: All the Seabird header information as a comment

Attribute_Definition_Source:

Attribute_Domain_Values:

Unrepresentable_Domain: Character Field

Attribute:

Attribute_Label: Xaxis

Attribute_Definition: The X coordinate in Nad27

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 389783

Range_Domain_Maximum: 448751

Attribute:

Attribute_Label: Yaxis

Attribute_Definition: The Y coodinate in Nad27

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 6.46541e+006

Range_Domain_Maximum: 6.55043e+006

Attribute:

Attribute_Label: Timetolow

Attribute_Definition: Time to low tide (in minutes)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -99999

Range_Domain_Maximum: 400

Attribute:

Attribute_Label: Timetohi

Attribute_Definition: The number of minutes to high tide (as a positive or negative number)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -99999

Range_Domain_Maximum: 4000

Attribute:

Attribute_Label: Hiheight

Attribute_Definition: The height of the high tide (in meters)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -99999

Range_Domain_Maximum: 8

Attribute:

Attribute_Label: Lowheight

Attribute_Definition: The height of the nearest low tide (in meters)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -99999

Range_Domain_Maximum: 0.2

Attribute:

Attribute_Label: Count_

Attribute_Definition: Number of depth bins used in statistics

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 47

Range_Domain_Maximum: 303

Attribute:

Attribute_Label: Min_Deps_

Attribute_Definition: Minimum Depth of the cast

Attribute_Definition_Source: The deepest depth reach on a cast

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -302

Range_Domain_Maximum: -47

Attribute:

Attribute_Label: Max_Deps_

Attribute_Definition: The shallowest depth bin used in summary statistics

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -3

Range_Domain_Maximum: 0

Attribute:

Attribute_Label: Max_Par_

Attribute_Definition: The Maximum values of photosenthetically active radiation

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 2000

Attribute:

Attribute_Label: Min_T068_

Attribute_Definition: The minimum temperature found on a cast

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 15

Attribute:

Attribute_Label: Max_T068_

Attribute_Definition: The maximum temperature found on a cast

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 15

Attribute:

Attribute_Label: Min_Wetsta

Attribute_Definition: The minimum values of chlorophyll-a in ug/l

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 100

Attribute:

Attribute_Label: Max_Wetsta

Attribute_Definition: THe maximum value of chlorophyll-a found on a cast (in ug/l)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 100

Attribute:

Attribute_Label: Min_OBS_mg

Attribute_Definition: Minimum value of sediment found on a cast (in mg/l)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 1000

Attribute:

Attribute_Label: Max_OBS_mg

Attribute_Definition: The maximum value of sediment found on a cast (in mg/l)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 1000

Attribute:

Attribute_Label: Sum_OBS_mg

Attribute_Definition: The integrated amount of sediment found throughout the cast (in g/meter2)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 100000

Attribute:

Attribute_Label: Min_Sal00_

Attribute_Definition: The minimum value of salinity found in the cast (in ppt)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 35

Attribute:

Attribute_Label: Max_Sal00_

Attribute_Definition: The maximum value of salinity found in the cast (in ppt)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 35

Attribute:

Attribute_Label: Min_Sigma_

Attribute_Definition: Minumim density values found in the cast (in sigma-t values)

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 30

Attribute:

Attribute_Label: Max_Sigma_

Attribute_Definition: The maximum sigma-t values found in the cast

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 0

Range_Domain_Maximum: 30

Attribute:

Attribute_Label: Photicdep1

Attribute_Definition: The depth to which only 1 percent of the surface of light penetrates

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -100

Range_Domain_Maximum: 0

Attribute:

Attribute_Label: Zsum_wetst

Attribute_Definition: The integrated amount of chlorophyll-a throughout the cast in mg/meter2

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -9999

Range_Domain_Maximum: 5000

Attribute:

Attribute_Label: Dic_photic

Attribute_Definition: The integrated amount of chlorophyll-a throughout the photic depth portion of the cast in mg/meter2

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -9999

Range_Domain_Maximum: 5000

Attribute:

Attribute_Label: Dic_15m

Attribute_Definition: The integrated amount of chlorophyll-a throughout the photic the upper 15 m portion of the cast in mg/meter2

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -9999

Range_Domain_Maximum: 5000

Attribute:

Attribute_Label: Dic_35m

Attribute_Definition: The integrated amount of chlorophyll-a throughout the upper 35 meter portion of the cast in mg/meter2

Attribute_Definition_Source:

Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -9999

Range_Domain_Maximum: 5000

DISTRIBUTION_INFORMATION

Distributor:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: mailing and physical address

Address: P.O. Box 140, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

Resource_Description:

CTDMaster Data for Glacier Bay, Alaska

Distribution_Liability:

User must assume to determine the appropriate use of these data.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name:ArcView Point Shape File

Digital_Transfer_Option:

Offline_Option:

Offline_Media: CD ROM in Juliet format

Recording_Format:

Compatibility_Information:

Can be used in any vector GIS capable system able to use or import ArcView Shape Files. The information can also be accesed from dbf files containing the attribute information since the XY coordiates are in the table

Fees: None

Ordering_Instructions:

Contact: Philip N. Hooge PhD at philip_hooge@usgs.gov or

see www.absc.usgs.gov/glba/oceanography/index.htm for current ordering or downloading methods.

METADATA_REFERENCE_INFORMATION

Metadata_Date: 12/6/2000

Metadata_Review_Date: 12/7/2000

Metadata_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: USGS Alaska Biological Science Center

Contact_Person: Philip N. Hooge

Contact_Position: Research Population Ecologist

Contact_Address:

Address_Type: Mailing and physical address

Address: P.O. Box 140, Glacier Bay National Park

City: Gustavus

State_or_Province: AK

Postal_Code: 99826

Country: USA

Contact_Voice_Telephone: 907-697-2637

Contact_Facsimile_Telephone: 907-697-2654

Contact_Electronic_Mail_Address: philip_hooge@usgs.gov

Hours_of_Service: 10:00-18:00 Alaska Time

Metadata_Standard_Name: FGDC CSDGM

Metadata_Standard_Version: FGDC-STD-001-1998

Jennifer Mondragon

CTD Instrument Configurations

Raw Data Upload

TERM19.CFG Setup Parameters

Uploading CTD Data (aka “dumping” the CTD)

SeaSoft software versions

Processing hex files with SeaSoft software

DATCNV

FILTER

ALIGNCTD

LOOPEDIT

DERIVE

BINAVG

GIS Data Processing

Processing Converted (.cnv) Files

Georeferencing the dbf Files

Join Point-Z File to Ocean Stations

Making the Join Permanent

Photic Zone Calculation

Calculating PAR as a Proportion of the Surface Value

Transferring 1% Photic Zone Depth to the 2-D File

Calculating Depth-Integrated Chlorophyll-a

Calculating Depth-Integrated Sediment

Exporting Cast Summaries for Printing

Contouring Profile Slices (i.e., “Plotting”)

Editing of Contour Files

Appendix C: CTD Data Sheet

Appendix D: CTD “Dump” Log