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Igor M. Yashayaev
Bedford Institute of Oceanography (BIO), Dartmouth, NS, Canada
till 1995, PPShirshov Institute of Oceanology (PPS), Moscow, Russia
YashayaevI@mar.dfo-mpo.gc.ca
Scientific coordinators:
R. Allyn Clarke (BIO) Sergei K. Gulev (PPS)
Acknowledgements:
Special thanks to
the scientific coordinators for encouraging the creation of the Atlas,
Sergei Grigoriev, PPS, for help in designing the user interface,
John Lazier, Anthony Isenor and other BIO scientists,
for testing the Atlas and commenting on this document.
The work on this project was supported by
the Ministry of Science and Technology (Russian Federation)
and the Department of Fisheries and Oceans (Canada).
Please note:
We will be happy to know that you have used this software in your
research
and referenced it if it helped you.
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1. Motivation and Origin
2. Data
3. Features and Functionality
4. Oceanographic Applications
4.1. Oceanographic Time Series Analysis
4.2. T-S Analysis
5. Installation
5.1. System Requirements
5.2. Installation Wizard (from a CD-ROM)
5.3. Manual Installation (from a CD-ROM)
5.4. Using the Files Downloaded from the CANWA Page
6. Quick Guide
6.1. Design
6.2. General Hints
6.2.1. General Query Hints
6.2.2. Map Hints
6.2.3. Setting the Contour Levels for the Property Maps and Sections
6.2.4. Quitting the Atlas and Saving the Settings and Parameters
6.3. Plotting
6.3.1. Data Coverage and Profiles
6.3.2. Sections
6.3.3. Fields
6.4. Applications
6.4.1. Time Series Analysis
6.4.2. T-S Analysis
6.5. Exporting
6.5.1. Sections
6.5.2. Fields
7. Some Q & A's:
In the 1980s and early 1990s research vessels of the former
Soviet Union, working under the SECTIONS program, made thousands of measurements
in the Newfoundland Basin. The SECTIONS (WOCE warm up) was generally
aimed to study and monitor water masses, currents, fronts, as well as atmospheric
processes in certain areas of the North Atlantic, named Energy Active Zones of
the Ocean (EAZO) by the program leaders. The Newfoundland Basin was
considered as one of these key regions, and assigned the highest priority in the
observational part of the program. Availability of the data, and importance of
oceanic and atmospheric processes in this area, inspired us to create a system,
capable of:
- storing and accessing large volumes of both historical and recent observations,
- data quality control,
- creating subsets of selected data types in any specified spatial and temporal
domain (including user-defined section and surface),
- performing various statistic and oceanographic analyses, gridding and visualizing
data and results.
These features were embedded in a computer product originally
named Computer Atlas of the Newfoundland Basin (CANB).
The choice of this region was motivated by:
- its importance in circulation and heat transport in the entire Atlantic,
- the presence of various water masses and sharp fronts,
- indications of temporal and spatial changes in the water mass properties,
- intense air-sea interaction,
- dense coverage with oceanographic data.
As the system developed, the spatial domain was extended
to include the regions of water mass formation. Although "canb" is a part
of the module names, the system is more correctly Computer Atlas of the
Northwest Atlantic.
The Atlas has been used in BIO for data
analysis, preparation of fields to initialize hydrodynamic models and various
comparisons of property distributions based on 'real' data and results of modeling.
The Atlas operates with different types of
oceanographic data: conductivity-temperature-depth (CTD), water bottle
(Bottle), bathythermograph (MBT, XBT), current meter, floats,
etc. The major data sets presently loaded into the Atlas were created
from historic and WOCE BIO archives; Russian data collected
in the "SECTIONS" program; data from NOAA National Oceanographic
Data Center "WOA94" (USA); Marine Environmental Data Service (Canada)
and Obninsk World Data Center (Russia).
Please note
that the data set distributed with the current version of the Atlas is not
final. Since the data quality control is not completed, some bad profiles and
individual measurements recently fixed or calibrated appear in the Atlas
in original form. Nevertheless, all the data passed the intial control, including
the check if the station is located off the coast and its depth stands in agreement
with the bottom topography. We plan to present the cleaned Northwest Atlantic
hydrographic data set (including the WOCE data) in the next release of the Atlas.
The Atlas locates data from a simple query, produces
plots (field, section, volume, scatter, etc.), and runs different statistical
and oceanographic applications. Data sets, regions and procedures can be easily
added, replaced or changed. Scale-independence is one of its features, allowing
users to work on different spatial and temporal scales, and adjust the working
environment for their own needs and requirements.
The current version includes two major tools to analyze
the data confined in any temporal and spatial domain: i) time series
analysis and ii) generation of composite picture of water mass properties.
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4.1.
Oceanographic Time Series Analysis
A comparison of unevenly distributed space-time observations
is a task usually requiring a large effort. The Computer Atlas solves this problem,
by creating time series at any arbitrary point, section, area (by the means of
search, selection and interpolation on defined levels), for a given time interval
or using all available data, and performing decomposition of the series onto the
seasonal component, interannual and mesoscale variability. To minimize the influence
of bad data on parameters of the seasonal cycle and to obtain robust estimates, the
Atlas (optionally) repeats the computations excluding, after each iteration, suspicious
data that produce anomalies greater than a given tolerance. The ability to produce
an accurate estimate of the seasonal cycle, fractions of seasonal, short and long
term components in the total variability helped us with the detection of climatic
variability from the hydrographic data (WOCE & historic) collected in different seasons.
4.2.
T-S Analysis
The Atlas computes various scatter and statistical
(area, volume) diagrams allowing one to examine spatial and temporal changes
in water mass properties.
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5.1. System Requirements
- ability to run MS-DOS programs,
- free conventional MS-DOS memory of at least 490K,
- free disc space: full installation requires 95M and partial 3M-24M of
free disc space.
5.2. Installation Wizard (from a CD-ROM)
Install.exe performs automatic installation of the
Atlas. Please follow the instructions appearing on your screen.
5.3. Manual Installation (from a CD-ROM)
Complete installation (with data sets):
Xcopy directory CANWA from CD-ROM to your hard drive or just
drag and drop the directory icon.
Partial installation (saves disc space,
but the Atlas works slower): Copy the contents of CANWA
excluding the files *.r, *.hd and *.bin from
CANWA/DATA to your hard drive. To make the files visible to the Atlas,
edit file fnames in directory WORK. Substitute lines 1-3 in
fnames with the lines following the comment and change the drive letter
(e.g. - f:) to the letter specifying your CD-ROM. The partially installed
Atlas will be looking for the data sets in the current CD-ROM directory.
So, before starting the Atlas, please change the CD-ROM's current
directory to CANWA/DATA. Then switch back to the Atlas on your
hard drive. Type canb.exe to start.
5.4.
Using the Files Downloaded from the
CANWA Page
Copy or move canwa.exe (complete Bottle and
CTD data sets, partial XBT data set) or canwa_li.exe (all data sets are
partial) to a location where you plan to expand the Atlas. Enter
canwa.exe or canwa_li.exe. Change your current directory to
CANWA. Type canb.exe to start.
You can also update the data files: download them
(bottle.zip, ctd.zip, xbt.zip) from our website, unzip and move the
*.r, *.hd and *.bin files to CANWA/DATA. The extracted
files may replace the partial version. It won't cause a problem, for
bottle.zip, ctd.zip, xbt.zip contain the most complete and updated data.
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6.1.
Design
The major Atlas components are:
- independent utilities (modules with extension ovl)
performing various operations on data,
- user interface (canb.exe) starting up the modules and
passing the user instructions, and
- data sets.
The modules read and store the instructions in a
text file canb.sts, located in directory WORK. Each module can be
run from the command line, assuming the extension *.ovl is changed
to *.exe. A diagram below reflects the general concept of the Atlas
modules.
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Click to see larger image
The utilities are grouped in two sections,
Plotting and Applications.
Plotting addresses property-property
profiles, property sections and distributions on iso-surfaces. Any parameter
can be used as a vertical coordinate for a section and iso-surface.
Applications perform statistical and
oceanographic analyses of the data and visualize the results.
6.2.
General Hints
Originally the Atlas was written for MS-DOS.
This makes the system usable in MS-DOS, Windows 3.1 or Windows 95/NT
environment. If you are using Windows to start the Atlas either
click an icon associated with canb.exe, run canb.exe from a
command line or MS-DOS prompt. If in Windows the CANB
appears in a window, occupying only a part of a screen, you might want to change
it to the full screen by pressing Alt-Enter (it helps to have better
control over the mouse).
The system is intuitive and simple in use. The
Atlas modules generate four basic types of screens:
- Query Window or user interface, providing a list
with major options and parameters,
- Map, with positions of stations, XBT drops etc. in
specified time domain(s), allowing the user to select key points of
local areas, sections, domains,
- Search and Selection,
- Results.
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6.2.1. General Query Hints
All fields in a query window are prompted at
the bottom of the screen. To switch between the fields you can use one
of the following: Tab / Alt + highlighted hot key / a
mouse (locate the pointer and press the left button). Though the applications
have a different number of key parameters, most of the query windows
have a similar structure.
Parameter sets a name of the property to
analyze. Parameter is often followed by the name of a vertical variable
(Section) or iso-surface (Field). Some applications also prompt
for the vertical axis range Top-Bottom (in the axis units) or the
iso-surface value. This prompt is usually located to the right of the
Parameter or verical variable name.
Users also select (indicated with 'X') the
Data Types to be used in analysis (file work\fnames
contains filenames associated with the list of data types in the query
window). Although more than four data sets can be linked to the system,
for the sake of simplicity the present release is limited to four.
Time Selection provides four different
scenarios for filtering the data stream regarding when (day, month and year)
an observation was taken:
- unchecked Date Interval and Season (no 'X'
in [ ]) admit all data of selected Data Types,
- checked ([X]) Date Interval with unchecked ([ ])
Season prompts for a
continuous time period
From - To (day-month-year
) when the measurements were taken; e.g.,
From 14-07-66 To 2-10-98 selects all the data between 14 July,
1966 and 2 October, 1998 (inclusive),
- checked Season with unchecked Date Interval
performs a search for the data from
all years, falling in a certain
day-of-month to day-of-month
range; e.g., From 11.12 To
21.03 selects all the data between 11 December and
21 March (inclusive)
regardless of year,
- both Date Interval and Season are checked
(combined search), locates data in a certain
day-of-month to day-of-month
range within a selected time interval, covering any number of years; e.g.,
From 14-07-66 To 2-10-98 (in the
Data Interval line) and From 11.12
To 21.03 (in the Season line) selects all the data
falling in between 11 December and 21 March (inclusive)
starting 14 July, 1966 and ending 2 October, 1998 (inclusive).
Depending on the task, the set of parameters for
spatial selection varies. Commonly the user specifies pair(s) of
coordinates (Latitude and Longitude,
degrees.minutes) and Width or Radius (kilometers) of a
searchable area. The 'Use Map' tool ('Ok' in 'Data and
Profiles') provides the most convenient and easy way for entering
coordinates, avoiding typing and allowing to view the actual data coverage
(for a given Time Selection) and make a proper choice
of locations.
6.2.2.
Map Hints
Map window is activated any time you press
the OK button in the Data Distribution window or press
Use Map in any Plotting or Application. To select
the key points in the map window please follow the instructions
in the lower right part of the screen, to exit the map window
with no action just press 2 or the right mouse button. To change
the location and size of the region please edit the file
work\region.ini or execute config.bat from the main
Atlas directory.
6.2.3.
Setting the Contour
Levels for the Property Maps and Sections
Checking the Manual and/or
Additional Contours (indicated with 'X') in the
Options window instructs the Atlas to use the
contour levels from the Set Manual and/or Additional
Contours lists. Otherwise the Atlas generates the major
(solid white) or/and additional
(dashed
blue) sets of levels automatically. The levels,
entered in one of the Contours lists are stored on the
disk and appear next time the list is visited. The levels are stored
individually for each parameter and procedure. They can be edited or
deleted (Ctrl-U).
6.2.4.
Quitting the Atlas and
Saving the Settings and Parameters
The Quit button is located in the
About menu. The option Save Status and Quit allows the
Atlas to "remember" the last actions of each module.
(Each module has unique settings and parameters.)
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6.3.
Plotting
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6.3.1.
Data Coverage and Profiles
This component generates a map, showing
coverage with original data and draws vertical and property-property
profiles in a specified location. The data distribution maps can be
presented in one of two forms: scatter diagram (Location of
Stations) or two dimensional histogram (Number of Stations).
On the Map a click of the left mouse button will highlight a site
where the user wants to display the data profiles. The center of the
site and its radius can be also entered in the Profile Site
section of the Data Distribution window.
To display the profiles matching the specified
criteria press Profile. The profile browser was the first
module developed for the Atlas, and it was aimed to perform a quick
check of availability and quality of the data. Since a drawing of
property vs depth or property vs property profiles is a simple task
that is nicely solved by a numerous packages, it was decided to keep
just a basic but fast profile browser, and focus on more challenging
tasks of data analysis.
6.3.2.
Sections
This component generates a section plot using
the data matching the specified spatial and temporal criteria. The
First and Last points of the section can be entered
from the Map (Use Map) or typed in the Section part of
the query window. The Atlas searches for the data locating
within the Width of the Belt from the section line. The vertical
coordinate for the section can be selected from the Y-axis list.
To change the Parameter or Y-axis activate one of the
lists by using the Tab key, arrow keys and Enter or typing
the red letter from the list name ('t' or 'y') or a mouse
(locate the pointer and press the left button) and choose the variable
name. The Horizontal Smoothing Scale stands for the effective
scale of the low-passing cosine filter, applied to the gridded data.
Changing the scale one can achieve desired resolution and presentation
on the section plot.
6.3.3.
Fields
This component generates a property map on a
selected iso-surface. The Latitude and Longitude Ranges
of the Region for the map is either set on the Map (Use
Map) or typed (edited) in the query window. The variable and
iso-surface names can be chosen from the lists by either the
Tab (or 'd') key, arrow keys and Enter or a
mouse (locate the pointer and press the left button). The Horizontal
Smoothing Scale is the effective scale of the low-passing
bi-cosine filter, applied to the gridded data. Changing the scale one
can achieve desired resolution and presentation on the map.
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6.4.
Applications
The basic queries in the application windows are
similar to those in Plotting (6.3). The data entering the analyses
are confined to satisfy the temporal and spatial criteria.
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6.4.1.
Time Series Analysis
This component generates time series at different
depths within a local area or along a section, estimates the seasonal
cycle and reveals the long term component of variability (anomalies).
The number of harmonics used in the analysis (only the annual amplitudes
and phases are displayed) depends on the number of observations in the
time series and a fraction of the harmonics in total and seasonal
variability. Note that the time series of anomalies are not shown in
the Section of Time Series. The reason for that is a lack
of MS-DOS resources to display three dimensional fields
(distance-depth-time).
6.4.2. T-S Analysis
This component creates scatter and statistical
Potential Temperature - Salinity diagrams. To change the diagram
settings or the reference pressure for the density computation, please
edit the file work\ts.ini or execute config.bat from the
Atlas main directory.
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6.5.
Exporting
To convert the data matching the specified spatial
and temporal criteria to a variety of file forms type export.exe or
start this program from Windows. All component in the export utility
are similar to those in Plotting (6.3), except they create
ASCII or text files with station positions, original and interpolated (gridded)
data, bottom masks. All these products can be found in the working directory.
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6.5.1.
Sections
The output data files created by this component
have a simple structure and can be easily used by other applications.
The file export.dat has all the data required to regenerate a
section plot, station.dat lists station positions. There are also
files generated by this component presenting the data in various formats.
6.5.2.
Fields
In addition to its Plotting analogue
this component generates a file with a property values on a selected
iso-surface (exp_hdt.dat for the temperature output,
exp_hds.dat for the salinity output, exp_hdd.dat for the
density output and exp_hdp.dat for pressure output) and mask
file (mask.dat with 0 flag for no data, 2000 for the point where
the gridded value was generated).
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Questions |
Answers |
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Why is there no Windows
95/NT version available? |
Back in 1993 in Russia, when the work on the Atlas began, the only promising
operating system for the Atlas was MS-DOS. In the past 5 years, while
the Atlas has been developed, technology changed a lot. To make the whole
system object-oriented and adopt it to Windows NT/95 or even
UNIX wouldn't be difficult, but time-consuming.
If the Atlas meets positive responses, the system will be updated (e.g. moved
to the internet).
(Please note that the existing PC version can be successfully run in
a MS-DOS window in either Windows NT or 95). |
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Is this a final version of the Atlas? |
No. We stopped at this point to make a decision, if there is a need for
such a system and in what form oceanographers would like to use it.
Some modules have been excluded from this release, but they can be requested.
We didn't want to overload the demo release, but if you find the Atlas useful,
please contact us and
upgrade CANWA to CANWA-PRO or more advanced CANWA-PRO++ with computation of
spectra included in time series analysis (Both are beta or test). Any
feedback will be highly appreciated.
The documentation is raw, but the system is intuitive and well-prompted. I
also haven't included all utilities for exporting and importing the data from
a simple spreadsheet, which will be happily provided if requested. My interest
in holding some pieces back is to get an idea how often the system is used
and what's the number of potential users of an atlas like this. It will also
help to improve and enhance the software as well as enrich the data sets and
documentation of the next release of the Atlas. |
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Can the Atlas create color fills
instead of contour plots? |
No. Contouring is still the most common way to visualize property fields.
We don't try to achieve publication quality at this stage, but perform
accurate interpolation, gridding and contouring. After you created fields
or results, which you would like to see in your paper, you can export the
data and results of gridding or analyses in the form of a simple ASCII
spreadsheet and use your favorite graphics package to achieve the best
appearance. |
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Why are the CTD and
Bottle stations covered with a cloud of XBTs in the station map? |
Historically the number of BTs greatly exceeds the number of
CTD and Bottle stations. I ranked the data regarding its importance
in the climate studies: I - Bottle, II - CTD,
III -M/XBT. Since the number of BTs is prevailing, they
mask the other data types. You can easily change the order swapping the first
and third line in the file work/fnames.
All BTs were loaded just for the sake of completeness of the data.
If having a vast BT data set ("BThive") causes a problem or
inconvenience, just check off the MBT and XBT from the
Data Type list or make the third line in
work/fnames blank.
If you want to use a data set, which you converted to the atlas format,
move the set to data directory and type the name in
work/fnames (e.g. instead of XBT). Please contact
Igor Yashayaev for
any information regarding the Atlas. |
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Are the observations used in
the Atlas quality controlled? |
Only partially. Though we cleaned up most of the data we had, we decided
to leave parts based on well known and commonly used data sets (WOA94)
as they are, but excluding some flagged profiles and measurements. There
are few reasons why we didn't provide our version of quality controlled data
with the Atlas:
- a design of criteria for quality control depends on particular
tasks to be solved using the data, in other words: what's acceptable
for us is not necessarily acceptable for other researchers,
- data analysts and modelers are widely using WOA94 gridded
climatology, and if there was a problem in WOA94 observed data
it usually appears in the climatology. So, a researcher can use the
Atlas to check if a "permanent" eddy or meander in the WOA94
climatology was produced by a poor measurement,
- one can edit and control the data sets building up his own criteria.
The only data sets that we provided in the advanced
quality controlled state, were those BIO and Russian SECTIONS data.
Nevertheless, all the stations included in the Atlas passed the
intial control and check of the position and depth in respect to the
coastline and bottom topography (there are many stations over the land
in WOA94). |
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