SBPLOT: oceanographic data presentation				navigation
Datafiles	Data manipulation	Plotstyle

SBPLOT: Oceanographic data presentation

This is a small matlab toolbox to make different graphical representations of oceanographic data using a graphical user interface. The data is supposed to be in Seabird CNV format (ascii or binary) or in netcdf Format (essentially one profile per netcdf file). It should be easy to include other formats.

Sbplot has been developped for Matlab 6 on Linux operating systems, but do also work on Matlab 6 for Windows. It definitely does not work under Matlab 4. For using sbplot it is required to include the CSIRO Seawater Toolbox in the matlab search path as well as the sbplot directory itselves. Working with netcdf files the netcdf toolbox is necessary.

Calling sbplot, a GUI opens (show picture). This GUI is divided into three parts:

Datafiles, where the input data is defined
• Data manipulation, where some simple data processing can be choosen.
• Plotstyle, where the the kind of graphics can be choosen.

Datafiles

PATH

This option is intended for single cruise data, which is stored within one directory, with filenames that just differ by the profile/ station number (e.g. CTD001.cnv, CTD002.cnv,...). The following mask has to be filled out:

• In the box Verzeichnissangabe (directoryname), the complete path of the directory containing the desired datafiles is demanded.
• In the box 1 Namensteil (first part of name), the first letters of the filename has to be given. Usually those letters are representing the short name of a cruise.
• In the box Dateinummern (file numbers), the second part of the filename is asked for; the numerical identity of a station. The input should follow the Matlab notation. Therefore input of [1 2 3 4 5] could be done like [1:5] in a shorter way.
• The extension is the third part of the filenames, in general the extension. If this does not includes a point, one is added. Including a point it is possible to adress also files, where the extension doesn't follow right after the file number (e.g. CTD001new.cnv). To supress the automatic inclusion of a point use "*" as the first character of the extension.

LIST

Within this option individual file names can be given manually, respective browsed for. The input is a text mask which can be edited and shows the choosen filenames:

It is also possible to include several files, using a comma separated format as given below:

• DISK,NAME,NR1,NR2,EXT
  similar as in the optiion PATH above, this selects all files from station number NR1 to station number NR2. (If NR1 is larger the NR2 is just means NR1:-1:NR2).
• **,filelist
  The filenames will be read from the file FILELIST, one filename per line.
• *LABEL,filelist
  The file FILELIST will be read, till a line beginning with *LABEL is found. All following lines are then taken as names of datafiles, until a line beginning with a * is found.

Another detail the user should notice is, following the interaktive selection by , the option filelist is allways active. A change to option now, causes sbplot to take the path and the filename of the interactive selection (usually the last line of the list) as settings for the input mask of option path. If the structure of the filename is not a simple common one, the settings must be corrected manually.

Data manipulations

Some basic data processing can be choosen here. These are exluding the up-profile or data near the surface and average to regular pressure steps.

In the box of Werte entfernen mit Druck kleiner als (db) one can choose to exclude values with pressure less then the given value. This is useful, if the values on deck or when the pump was still not working have not been removed yet.
Checking Hievteile entfernen it can be determined to leave out upcast data.
If the value at Mitteln auf db is larger then zero, values are averaged onto fixed pressure steps each given db. This is necessary for cross-sectional pictures. The value of Druckfenster beim mitteln determines the size of pressure window used in the averaging. A value 5 for the pressure step and 10 for window size means, average values are calculated for every 5 dbar. Further, the calculation of the average for the depth of 25 dbar is based on values between 15 and 35 dbar. In this case, the graph is smoothend strongly.
If no input happened, the plot will be made by default settings.

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Plotstyle

Cross-sectional plots/"Gitter"

When all settings are done, the window will be closed by . After the data have been read, a new window opens, displaying the geographic position and waterdepth of each station (show picture). If necessary, the values can be corrected now. Otherwise, the window is closed by . If after having done some corrections, these are not readable (for example letters or a comma instead of a decimal point) the mask will be shown again with the unreadable fields marked in red. These fields must then be corrected.
After this step, two another windows opens. On the right handed side a preview of the plot, on the left handed side a GUI (show picture) to modify isolines and colors. Now, different settings for colors, lines and ranges may be tested. Selecting colors manually, it is important to know, that white color means transparency. This is made, to allow to plot a isoline, without changing the background color. By pressing , the plot is redrawn in regard to the current settings. If the user is content with the presentation, the menue isolines might be closed by . Now, in the remaining window (showing the plot), the positions of the inscriptions of the isolines have to be given by a mouse-klick. This work is finished by a mouse-klick in the gray shaded area around the plot or a [Enter] in the matlab command window. Afterwards, in case of a cross-section plot, the bottom contour will be drawn, before, in any case, a colorbar is added and the plot is finished.
If the presentation is not representing your expectations, it might be caused by several frequently mistakes or you have to modify the presentation afterwards (adding labels etc.).

XY-Plots

XYZ-Plots

select a variable [back to cross-sections] [back to XY-Plots]

Modify isolines and colors [back]

frequently mistakes [back]

• Datafiles can't be found in path-mode because the directoryname does not end with a slash! In this case, sbplot looks for /dataSB001.dat instead of /data/SB001.dat.
• Drawing a cross-section, the plot is completely or partially painted black. As a matter of principle, this is correct, because the bottom topography should be plotted. This is done by reading the waterdepth out of the header files. For this reason, it is important that the informations of the header file do correspond to the maximum pressure of a station. If the header files provide wrong values, it is possible to correct them in the window. Another posibility is to go without bottom topograpy. To do this, you have to choose "gitter" and take pressure as y-axis.
• It is suspicious, if the colored area is smaller than the space given by the axes. This may point to wrong values for position or even the information for position is badly analysed. This may be caused by missing or wrong signs, values set to zero or missing or wrong interpreted nautical minutes because of using a comma instead of a decimal point. For this reason again, it is important to fill out the header carefully.
• Non colored areas in a colored cross-section indicate missing data. In this case you should examine, if the data have been recorded down to the bottom.
• Sometimes, the presentation of isolines on strong inclined topography is wrong. This is caused by a faulty extrapolation of data to this area. On the other hand, this extrapolation is needed, to avoid unsightly non-colored areas next to the topography. If you are interested in displaying especially layers next to the bottom, it might be better to use "gitter" for your presentation, with variable Pmax-P for the y-axis.

Modify the presentation afterwards [back]

The most used features to improve a presentation and how they are used is described here.

• As long as variable "P" has not been cleared or changed, you may do several plots of this data without reading them again and again. This can be done entering mk4ins(P) in the matlab command window.
• To draw aditional non-colored isolinies over a colored cross-section, enter mk4ins(P,[0.005 0.015],2,[],1) in the matlab command. In this synthax, the second parameter gives the values for the desired isoline(s). The third has to be set to "2" meaning "no-colored". The fourth is empty and must be set in the way "[]". The fifth parameter must be set to "1" to care for plotting the isolines over an existing plot. (further information on mk4ins is given by help mk4ins in the matlab command).
• Inscriptions: whith title('TEXT'), xlabel('TEXT') and ylabel('TEXT') the text of title and labels may be changed.
• To show smaller parts of the plot, you can change the maximum and minimum values of the axes with the command axis([440 580 0 2000]). Another possibility is to do an interactive selection either with the command zoom on or with the button in the menubar.
• With command axis you can switch between y-axis in ascending order (axis('xy')) or descending order (axis('ij')).
• Manipulations of single graphical elements of the plot may also be done by the editing-tool in the figures menubar.
• A mark for the positions of the stations you get with the command plot(P.X,27.7,'rh','markersize',15). In this case, along y=27.7, the positions of the stations are marked with a bigger red hexagon.

Subroutinen [top of the page]