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ODV4 - User's Guide - Ocean Data View

1. Action Object Response L Click Map Selects the closest station as current station Data Window Selects the closest sample as current sample and the parent station as current station Shft L Click Map Selects the closest station as current station Allows selection from list of mul tiple stations at the same location Data Window Selects the closest sample as current sample Allows selection from list of multiple samples at the same location L DbleClick Map Adds the closest station to the pick list and adds the data of this station to STATION data windows L Drag GObject Drags the graphics object if object allows dragging Canvas Map Data Window Drags the canvas if scroll bars are present Ctrl L Drag 1 Map Data Window Quick zooms into the map Quick zooms into the data window R Click 2 Canvas Map Data Window GObject Data List Windows Invokes element specific context menu Shft R Click 3 Map Data Window Invokes the Extras menu of the map or data window D On Mac OS X systems hold down the Apple key and click and drag the mouse 2 On Mac OS X systems with a single button mouse hold down the Alt key while clicking the mouse to simulate a right mouse button click 3 On Mac OS X systems with a single button mouse hold down the Alt and Shft keys while clicking the mouse to simulate a Shft right mouse button click 131 Version 4 5 0 Table 16
2. Spiciness Tt Flament Progr in Oceanogr 54 1 4 493 501 2002 Stability Ratio R TEOS 109 Thermal Expansion Coefficient 10 6 K 1 TEOS 100 Thermobaric Coefficient T 10 12 K 1 Pa 1 TEOS 100 Turner Angle Tu deg of rotation TEOS 109 Special Difference from Reference Data details Patches details Time Day of Month station date Decimal day of the Month derived from station date Day of Month time variable Decimal day of the Month derived from a time variable Day of Week station date Decimal day of the Week derived from station date Day of Week time variable Decimal day of the Week derived from a time variable Day of Year station date days Decimal day of the Year days derived from station date Day of Year time variable days Decimal day of the Year days derived from a time variable Day Time station time hours Decimal time of day hours derived from station time Day Time time variable hours Decimal time of day hours derived from a time variable Month of Year station date Decimal month of year derived from station date Month of Year time variable Decimal month of year derived from a time variable Time station date time yr Decimal time derived from station date and time 60 ODV User s Guide Time time variable yr Decimal time derived from a time
3. 317 Station Labet 0 99999099 Tree Botte cro xT Any Day Tene Station JO 1 100000000 Name Range Date Tene Doran Meta Data Numeric Meta Varables Mame Range Date Tee Doman Metadata Avatabity Requred Varables DEPTH METERS TEMPERATURE C 115 90 SALNTY PS5 78 E Bert selection Check this box to select al stations that do NOT satisfy the selection crtera 5 varable s selected Hep Figure 8 1 The station selection criteria pages You can modify the station selection criteria by using Station Selection Criteria from the Current Station Window popup menu or View gt Station Selection Criteria from the main menu Choose the category that you want to modify by clicking on the respective tab 73 Version 4 5 0 e g Name Range Date Time Domain Meta Data or Availability and modify the items of interest On the Name Range tab you can select stations by cruise label station label range sta tion type and range of internal station ID numbers For the cruise label selection you may select a specific cruise label from the list or you may specify one or more regular expressions wildcard patterns in the Cruise Label field In the latter case any cruise label that matches one of the regular expressions will be considered valid Example regular expressions that can be used for cruise labels are summarized in Table 8 1 If
4. ODV User s Guide stall gt coast if you are a normal user without administrator privileges please unpack into lt user gt coast Use Help gt About Ocean Data View on Mac odv4 gt About Ocean Data View to determine the Installation Path lt install gt or the User Directory lt user gt Resource Priorities If Automatic selection of map layers is switched on and more than one map resource is available on your system for the current map domain the one with the highest resolu tion is chosen by default Tiled resources are only considered if less than 9 tiles are needed to cover the map domain This default behavior can be changed by specifying the map resources priority on the Resource Priorities page Resources at the top of the list are preferred over ones further down Spreadsheet Import Specify position in degrees longitude or latitude and time in hours difference limits between lines Station breaks will always occur if these limits are exceeded even if sta tion labels are provided and remain the same on both lines If no station labels are pro vided in the import file station breaks will occur whenever position and or date and time change SDN Import Specify the output root directory for SeaDataNet data imports WOD Import Choose between short cruise labels such as WOD09_GR consisting only of the WOD identifier and a two character country code and long cruise labels which also contain the OCL cruise number
5. v ona UA U NBO Station Selection Criteria Sample Selection Criteria Manage Pick List Manage Section Extras a amp Rb RE Properties FS Ctrl 5 Ctrl F Alt 5 Shift 5 b Alt P Figure 2 3 The map popup menu 1 Redraw Plot FS 2 Save PlotAs Cirl S 3 Zoom 4 Z Zoom 5 Auto Zoom In 6 Auto Zoom Out 7 Full Range Ctrl F 8 Set Ranges 9 X Variable x 9 Variable hd 9 Z Variable Zz 10 Extras gt 11 Properties Figure 2 4 The data window popup menu The map popup menu offers the following op tions 1 Redraws the map and all data windows 2 Saves the map in gif png jpg or PostScript file 3 Manually zoom in or out the map domain 4 Zoom in to the point of the mouse right click 5 Automatically zoom out 6 Chooses domain of the currently valid stations 7 Chooses full domain of the collection 8 Chooses global map domain 9 10 Selects a new current station by name or in ternal number 11 Changes the station selection criteria 12 Changes the sample selection criteria 13 Lets manipulate the map s station pick list 14 Lets define a section and modify its properties 15 Access to the map s Extras menu 16 Allows modifying the properties of the map The data window popup menu offers the follow ing options 1 Redraws the data window 2 Saves the data window in gif png jpg or Post Script file 3 Manually zoom in or out the data window
6. In this case grid spacing along the X and Y directions varies according to data density High resolution small grid spacing is provided in regions with high data density whereas in areas of sparse sampling a coarser grid with reduced resolution is used For hydrographic sections this typically yields high spatial resolution in the upper water column and in boundary current regions where data coverage is good and a coarser resolution grid in open ocean regions and the deep sea where data typically are spars er After construction of the grid property estimates c Ya d a are calculated at every grid point using a simple weighted averaging scheme For efficiency reasons only data values di from a small neighborhood of the grid point are considered for summa tion see figure above The weights a decrease exponentially with increasing distance r between data and grid point e with r Ax L Ay L and separate aver aging length scales Lx and Ly in X and Y directions respectively Averaging length scales vary over the domain and are 144 ODV User s Guide Figure 16 2 Weighted averaging of data values red symbols at a grid node See text for details proportional to local grid spacing Thus small averaging length scales are used in areas with small grid spacing high grid resolution e g in the upper water column or in boundary current regions etc whereas in regions with large grid sp
7. The installation directory contains various subdirectories containing files needed for specific purposes Installation files that may be modified by the user such as macro files palette files or sample data collections are installed in subdirectory ODV under the user s document directory indicated as lt user gt below Following below is a list of directories used by ODV lt install gt bin_w32 on Windows platforms or lt install gt bin_macx on Mac OS X platforms or lt install gt bin_linux i386 on Linux i386 platforms or lt install gt bin_solaris sparc on SUN Solaris Sparc platforms or lt install gt bin_irix6 5_mips on SGI Irix platforms or lt install gt bin_aix powerpc on IBM AIX powerpc platforms ODV executable tools and PostScript preamble file lt install gt coast GlobHR High resolution coastline and topography files for the whole globe lt install gt doc4 ODV html help files pdf versions available from ODV web page lt install gt include Default directory for ODV include files e g GEBCO1 global topography Note that there are several sub directories containing other files of a given type lt install gt include atmhist Atmospheric concentration histories of various trace gases lt install gt samples Directory for ODV sample files Use these files as templates for data import or macro files lt user gt cmd_files ODV command files cmd lt user
8. for the different stations in the file In such cases the associated source variables are tested for data availability and the first value found is used You can specify default values for target variables for which no corresponding source variable is provided in the import file This is useful for instance if you import longitude latitude maps of some quantity Z from ASCII files containing three columns X Y Z but not containing data for the specific surface or depth lev el To set a default value for a target value first select a the variable in the Target Collection list then press the Use Default button and enter the desired default val ue for this target variable Note that target variables using default values are marked with a sign The specified value will be used for every sample of every station imported during this operation ODV User s Guide Source variables not associated with a target variable will not be imported into the collection If you merge data into the collection you should establish associa tions for the primary variable and those variables that should be added to the col lection Do not associate variables which already have data in the collection that should remain unchanged Note that the OK button of the Import Options dialog will remain disabled until the primary variable of the target collection is associat ed with one of the source variables Station and Sample Matching Criteria If the Che
9. GEBCO08 and IBCAO map data are organized in tiles These resources may be installed in two ways as 1 complete or 2 download on demand package In case 1 pressing the Install button will start the download and unpacking of the complete package This may take several minutes Afterwards all map data for the whole series domain are instantly available on your system and map drawing will proceed immedi ately In case 2 the installation is very quick However when drawing the station map ODV will have to download all required tile data for the current map domain not al ready on the system before any drawing can start Downloaded tiles are cached on your system and will not be downloaded a second time If disk space is not a limiting factor it is recommended to install the complete ETOPO1 or GEBCO08 6min and 2min packages Administrators of systems used by more than one ODV user should move the downloaded map data from the ODV user directory lt ODV user directory gt coast _ min to the ODV installation directory lt ODV installation directo ry gt coast _ min to make these map resources available to all ODV users on the system and to avoid multiple individual installations in the users ODV directories Regional packages should be installed if the package domain covers your region of in terest Again administrators of multi ODV user systems should move the resources from the ODV user s directory to the ODV installation directory The ET
10. Pressing the Delete Val ue s button removes the data values of all selected samples You should use this button with great care as the original data values will be lost permanently WARNING Please note that editing values of the primary variable e g Depth Pressure Time etc via the Change Value option is dangerous and can have unexpected side ef fects Specifically value changes of the primary variable may affect the order of the samples within the current station and the sample being edited may move up or down in the profile or time series causing its sample ID to change after editing Please be aware that if this happens the Current Sample Window after editing will no longer show the edited sample but the sample that takes the slot of the edited sample after re sorting Editing and deleting sample values should only be done when absolutely necessary Usually you should leave the actual data value unchanged and modify the data quality flags of the selected samples instead This is done by clicking the Change Quality Flag s button and selecting a new quality flag from the list of available flags Pressing OK saves the changes to disk pressing Cancel aborts the edit session and leaves the station data in their original form Note that you can filter data using their quality flag values Also note that edit opera tions are logged in the logfile of the collection This file can be viewed using the Collec tion gt Browse Log File o
11. The X Y Z data of a data window as well as the gridded values of that window if gridding is switched on are copied to the clipboard using the Extras gt Clipboard Copy option of the window s popup menu As a shortcut you may press Ctrl C while the mouse is over the par ticular window Once ODV has copied the data to the clipboard you may paste the clipboard contents into your favorite software for further processing Clipboard copy of the map win dow produces lists containing station positions and other metadata 55 Version 4 5 0 56 ODV User s Guide 6 Derived Variables In addition to the basic variables stored in the collection files ODV can calculate a large number of derived variables which once defined are available for analysis and use in the data plots in the same way as the basic variables There are three types of derived variables e built in derived variables including many commonly used parameters from physical and chemical oceanography e macro files of user defined expressions stored in files for use with arbitrary ODV collections e expressions defined by the user on the fly for the current collection only To define or delete derived variables choose the Derived Variables option from the Cur rent Sample Window popup menu or View gt Derived Variables from the menu bar To add a macro choose Macro File from the Choices list to add a user defined expression choose Expression To add a built in
12. axis respectively and a collection or isosurface variable as Z variable maps In section plots 1 there is a choice to use the section bathymetry polygon for domain separation or to not use domain separation and treat the entire X Y window range as a single domain see DIVA Settings page in Figure 10 4 146 ODV User s Guide Temperature C Depth m 100 Temperature C Depth m 100 Figure 16 3 Comparison of VG and DIVA gridding methods for a field with inhomogeneous data coverage Domain separation in maps is based on gridded bathymetric data and a threshold depth value All areas with water depths shallower than the specified threshold depth are considered barriers ODV allows selecting an appropriate bathymetry file containing elevation data on a regular grid as well as the threshold depth value see DIVA Settings page in Figure 10 5 By default ODV uses the 6 x6 subsampled global GEBCO bathyme try file GEBCO1 nc in the include directory which provides sufficient resolution for basin scale or global map domains Figures 16 3 and 16 4 For very small domains the 6 x6 resolution of the default bathymetry file is too coarse for reliable land mass barri er detection and custom bathymetry files must be provided by the user Files contain ing regional subsets of the new 0 5 resolution GEBCO_08 bathymetry can be delivered on request The custom bathymetry f
13. e g WOD09_US014887 Choosing long cruise labels may lead to a very large number of cruises when importing large amounts of data and is not rec ommended Printing Check the Show collection info box to include a time stamp as well as collection view and user information on printouts Adjust the position if necessary Program Locations Enter the full paths of your Web browser needed for ODV help and text viewer need ed for viewing text files On Mac OS X Linux and UNIX platforms the text viewer command can have zero or more arguments separated by spaces The path of the text viewer and of arguments may contain spaces which have to be escaped by backslashes Example Use emacs installation in usr local My editor path as text viewer and call the emacs client to reuse an already open emacs editor usr local My editor path emacsclient a usr local My editor path emacs Sidebar Folders The file open and file save dialogs of ODV provide quick access to a number of directo 19 Version 4 5 0 ries listed in the left sidebar of the dialog You may specify up to two often used directo ries of your choice to become part of the sidebar list not used on Mac OS X systems Identification Enter the user s login name and the computer s host name 20 ODV User s Guide 3 ODV Collections ODV uses a special data format that is designed to handle very large datasets efficiently This collection format
14. should not contain spaces All files must be located in the same directory collection directory File Format Comment Basic files Must be present lt col gt var ASCII Defines collection variables stores collection name and number of stations On Windows this file type is automatically associated with the ODV executable e g double clicking on the var file starts ODV and opens the respective collection lt col gt hob binary Stores the station meta data name position date etc lt col gt dob binary Stores the actual station data and quality flags Info File Optional lt col gt info ASCII Description of the collection in freeform text format ODV automati cally creates an info file containing information on dimensions and variables when opening a netCDF file Auxiliary Automatically created if not present Files 32 ODV User s Guide lt col gt inv ASCII Collection inventory listing by cruises lt col gt cid binary Cruise ID numbers lt col gt log ASCII Collection log file Keeps records of data changes lt col gt idv ASCII Lists IDs of key variables used as input for derived variables depth temperature oxygen etc lt col gt cfl ASCII Contains names of most recently used configuration file and output directory Table 3 10 Summary of ODVGENERIC view and section files File names lt name gt are arbitrar
15. starting depth Zo for the integral default 0 m For each sample of a given station ODV will calculate the integral A dz from Zo to the respective level The units of the integral are the units of the quantity A times the units of depth note that ODV4 uses m whereas previous ODV versions used km For variables with volumetric concentration units 63 Version 4 5 0 e g moles per cubic meter the calculated integral is equivalent to standing stock per square meters Note that by definition the value of the integral at zo is zero Example To obtain the salt content in the top 500 m of the water column select salinity as varia ble for the integral and use 0 as start value Then look up the value of the vertical inte gral at 500 m by interpolating between neighboring points or in SURFACE mode de fine the integral at depth 500 as an isosurface variable 6 2 Macros You can implement new derived variables not included in the list of built in derived quantities provided that the value of your new derived variable for a specific sample only depends on other variable values of the same sample In these cases you specify the input variables and the expression of the new derived quantity in a macro file Mac ro files must have the extension mac they must be located in the ODV macros directory lt documents gt ODV macros and their format must follow the specifications given be low You can use the ODV Macro Editor invoked by T
16. the style of the station dots as well as general properties such as graphics font size or the axis labeling color and style Figures 9 1 and 9 3 Map Properties Map Properties Map Properties General Dispiay Style Projection Layers Doman annot iP General Osplay Ste Preyection Layers Doman Annot 4 ib General Depiay Style Projection Layers Doman annot ib Defauk Settings Defauk Settings Defauk Settings Figure 9 1 The various pages of the Map Properties dialog part 1 of 3 General On the General page you can define the color palette used by the map the background color of the map window a base font size and font size factor and the color of the axis and axis annotations Grid lines can be switched on or off Display Style On the Display Style page you define the color and the size of the station marks in the map Choosing automatic for the color will cause different colors for the different cruises in the data collection Projection On the Projection page you choose the map projection and the longitude and latitude of the projection pole position of the viewer The following projections are currently available 1 Default Projection 2 Orthographic North Polar 3 Orthographic Equatorial 4 Orthographic South Polar 5 Orthographic Oblique and 6 Moll weide The default projection is linear in longitude and latitude directions The ortho graphic projections are hemisp
17. 0 0000 0 0200 Z v Station type W Cruise label l 1 Cruise Label Aliases f l V Add non matching samples as new samples Source file cruise label Target collection cruise label 1 A SC AA HLY 02 01 Associate 32H10201SBI1 y Default values Default values Help Cancel Help Cancel E Figure 4 4 The two pages of the Matching Criteria dialog If the cruise labels in the import file differ from the cruise labels of the same sta tions in the target collection you can establish cruise alias names by selecting a cruise in the Target collection cruise label combo box entering an alias name in the Source file cruise label field and pressing the Associate button Any alias cruise 49 Version 4 5 0 name found in the import file will be translated automatically to the correspond ing target cruise name before the station matching procedure is started This is useful when different versions of the cruise name are used in the import file and target collection e g ANT XV 4 versus SRO4_06AQANTXV_4 in Figure 4 4 Exact cruise name matches are required if no aliases are defined In addition to finding matching target stations in the collection ODV also needs to match the samples of import and target stations when performing Merge Data se lected variables and Update Data selected variables imports Sample matching is done by comparing the primary variable values of import and ta
18. 12 4 The Edit Sample Data dialog all variable values for a given sample W Change Value 4 IS dd i Quality Flag Values In addition to the methods described above you may also modify the quality flag values of the data of a given variable by right clicking on the variable in the Current Sample window and using one of the options of the Assign Quality Flags submenu 1 Current Sample 2 All Samples of Current Station 3 All Samples in Window n 4 All Samples of Valid Stations and 5 All Samples in Collection The set of samples to which the quality flag changes are applied depends on the option you choose and ranges from the current sample only option 1 to all samples of all sta tions in the collection 5 Option 3 lets you assign a new quality flag to the data of the 108 ODV User s Guide variable currently shown in data window n while options 4 and 5 apply the new QF value to all samples of all stations currently shown in the map valid stations or to all samples of all stations in the collection Options 3 to 5 modify a potentially very large set of samples and need to be confirmed by the user before any changes are made After choosing one of the submenu options ODV presents the Assign Quality Flags dia log Figure 12 5 On this dialog you select the new quality flag value to be assigned and you specify whether this flag should be assigned to all samples irrespective o
19. 2 Common key press actions Key Response Enter or Adds the current station to the pick list and adds the data of this station to the STATION data Return windows if any In window layout mode accepts the current layout and returns to normal mode Del or Deletes the graphics object pointed to by the mouse or if not over an graphics object removes Backspace the current station from the pick list and removes the data of this station from STATION data windows if any In window layout mode deletes the window containing the mouse Allows selection of a new current station by internal sequence numbers gt Selects the next station as current station Selects the previous station as current station HOME Selects the first sample as current sample l Selects the next sample as current sample t Selects the previous sample as current sample END Selects the last sample as current sample PgDn Steps down forward the current sample PgUp Steps up backward the current sample Ctrl 5 Mac F1 3 others Shows the ODV help document F4 Shows the data statistics of the window containing the mouse F5 Redraws the entire canvas or the window containing the mouse F8 3 Switches to full screen map layout F92 Switches to six STATION window layout F102 Switches to two SCATTER window layout F112 Switches to three SECTION window layout F122 Switches to o
20. 2 E Comments Estimation of anthropoganic CO2 using TrOCA Touratier F L Azouzi and C Goyet 2007 CFC 11 Delta 14C and 3H tracers as a means to assess anthropogenic CO2 concentrations in the ocean Tellus B 59 318 325 Input Variables Defined New 1 POTTEMP DEG C 2 OXYGEN UMOL KG 3 TCARBN UMOL KG 4 ALKALI UMOL KG Expression in Postfix Notation 2 1 279 3 4 0 5 7 511 0 01087 1 7 81e5 4 4 exp 1 279 Operands 1 9 0 9 t Time d Day of Year x Longitude y Latitude H Height Operators abs arccos arccot arcsin arcttan ceil cos cot exp floor int In min max sin sqrt tan 0 9 Figure 6 2 The macro editor dialog Input Variables List of input variables needed for the macro variable To add an input variable enter its label and units into the New field and press the lt lt button note that you can use format ting control sequences If you want to delete a defined input variable select it in the Defined list box and press the gt gt button The number of input variables is unlimited Expression In the Expression in Postfix Notation field you specify the algebraic operations to be per formed when the macro variable is evaluated The macro expression has to be in Postfix Notation also known as Reverse Polish notation with operands preceding operators The Tools gt Infix to Postfix Converter option allows input of m
21. 3000 Vapour Pressure hPa 4000 5000 i i 6000 1 30 wW 20 W 10 W 0 10 E 0 20 10 o 10 20 Temperature C e Figure 10 3 Example figures showing the use of logarithmic and stretched upper Y axis In case of Sized Dots the maximum size of the dots is taken as 10 times the specified Symbol size the fill color is given by the Symbol color the border color and border width are taken from the data mark color and Line width entries If you choose Arrows the Arrow Properties dialog Figure 10 4 will appear letting you select the variables providing x and y components of the arrows as well as an arrow scale line width and color for the arrows If you choose Color automatic the arrow color is determined by the value of the Z variable at the arrow location Make sure that a Z variable is defined if using automatic color To bring up the Arrow Properties dia log again and modify the arrow settings click on the Arrows entry under Original data Instead of showing colored dots at the sample positions you can also produce gridded property fields for any data window that has a Z variable property distributions along sections or on isosurfaces are examples by clicking on Gridded field Then choose one of the available gridding methods Quick Gridding VG Gridding and DIVA Gridding Then specify appropriate averaging length scales for the X and Y axis respectively Note that length scale values are in per mil
22. 5 After specifying the section spine ODV assigns a default width for the section band and selects distance from the starting point the first point entered as the default along section coordinate These and many other section properties may be modified on the Section Properties dialog Figure 9 7 that appears automatically after specifying the section spine The Section Properties dialog may be invoked at any time by choosing Manage Section gt Section Properties from the map popup menu Ocean Data View Figure 9 6 The GEOSECS western Atlantic section On the Section Properties dialog you may choose Distance Longitude or Latitude as along section coordinate you may set the width of the section band choose a color for the section bathymetry and specify a title for the section Every section may have a bathymetry polygon which can be defined in a number of ways 1 using the station s bottom depth metadata or 2 using global or regional gridded bathymetric datasets provided in specially structured netCDF files the GEBCO1 nc file available in the ODV installation include directory is an example of such 82 ODV User s Guide netCDF files or 3 using an ODV POLYGON graphics object from a gob file Figure 9 8 shows an example of a section using shipboard bathymetric data from a gob file as sec tion polygon i gt Section title WOCE A7 Section Coordinate Distance km 9 Longitude Latitude B
23. COPYING RENAMING AND DELETING COLLECTIONS cccseecccceseececceceececcececcceenees 103 12 2 SORTING AND GONDENSING 3 2 0 ses oedecco sec EIEE e edad do 103 L223 DELETING STATIONS 44 a ta as ee idad ete o ed 103 12 4 CHANGING COLLECTION PROPERTIES ssssccccsseececcessececceccececceccececcesecceccesecceeneners 103 12 5 KEY VARIABLE ASSOCIATIONS ccssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssaaaes 104 12 6 GOOD COVERAGE CRITERIA cccseececcccccccesessscscecccsccessssssscescessssuessusceccessseuenensgcsses 105 12 7 BROWSING COLLECTION INFORMATION ccccsseececcessececccseececcescececcseccecesseeceeeeners 105 12 8 PROPERTIES OF VARIABLES cccscccccccccccccsssssescecccsccssssscssceccessssuessescscccssseuuneasgssses 106 129 gt SEDITING DATA o e e dde e Aedes 106 13 WORKING WITH NETCDF FILES occococcoocccocccnncoonccnocococccnocccoocnns 111 13 1 NETO DF SUPPORT o iii 111 13 2 NETCDESETUE A e e id o a do a O 113 E PODES cid Se oD 117 1421 GEOSTROPHIC PLOWS Void 117 14 2 2DESTIMATION a ii 118 PATS gt SD ESTIMATION a a a E 118 1 4 4 BOX AVERAGING iii A tt se 119 14 5 FINDING OUTLIERS moonet entan aint ii it 120 14 6 FINDING DUPLICATE STATIONS scscccceseecccceseececcesseccccccteccccesescecceesecceeeececeeners 120 TE SOGEAN CALCULATOR discos 121 15 MISCELLANEA ua 123 5ST COLOR PALETTES Naiara rad 123 15 22 ANIMATION Sa IN ho
24. For windows with gridded fields ODV also exports the results of the gridding operation files win oao The format of the oao files is as follows 0 ignore ny Ny no of x and y grid points nx X grid values X grid positions ny Y grid values Y grid positions n n gridded values estimated field line by line starting at first Y grid value n n gridded values estimation quality line by line starting at first Y grid value 5 6 Exporting Reference Datasets You can save the original data of the current plot windows in separate ASCII files and use these data later as reference datasets by choosing Export gt X Y Z Window Data as Reference from ODV s menu bar Enter a descriptive text identifying the reference data in the ID String field and click OK ODV will create a sub directory in the user s ODV di rectory lt documents gt ODV reference lt ID String gt and writes all files to this directory If the directory already exists ODV asks for your permission to delete the current con tents before continuing Reference data are used by ODV for defining difference varia bles 5 7 Exporting Isosurface Data You can export the isosurface data of all stations currently shown in the map by select ing Export gt Isosurface Variables and choosing a target directory and output filename The output file includes the metadata of the stations and is ODV generic spreadsheet format compliant 5 8 Clipboard Copy
25. Note that iw and textAlign are integers x y and orientation are floats Note that the annotation text has to be enclosed in characters Example create_annotation 1 10 8 30 0 Some Text create_collection collection collection_type Create collection collection using the template set of collection variables collection_type collec tion_type may be one of the following ARGOPROFILES ARGOTRAJECTORIES GTSPP MEDATLASBOTTLE MEDATLASCTD MEDATLASTIMESERIES MEDATLASPROFILES MEDATLASSEDIMENTTRAP WORLDOCEANDATABASE Note If collection already exists the existing version is deleted before the new version is created Example create_collection c data ARGO_Atlantic odv ARGOPROFILES delete_collection collection Delete collection collection 126 ODV User s Guide Example delete_collection c data ARGO Atlantic odv export_data data_file Export the data of the current station set to file data_file using the generic ODV spreadsheet for mat Example export_data c output odv_data txt export_graphics iw graphics_file dpi Save graphics of window iw in file graphics_file using a resolution of dpi dots per inch Use graphics_file extensions eps gif png or jpg for PostScript GIF PNG or JPEG output respectively Although the dpi argument is not used for PostScript output it must still be provided Example export_graphics 1 c output odv_graph eps 300 import_data file_spec import_type
26. ODV shows the list of dimensions contained in the file Initially all these dimensions are selected except in cases of more than one X Y Z T coordinate system when only one of these systems is selected For a given selection of dimensions the set of netCDF variables defined on these dimensions is shown in the Corresponding netCDF variables list Other variables in the netCDF file that depend on dimensions not selected in the NetCDF dimensions list are not shown as Corresponding netCDF variables These variables will remain unavailable unless you select the corresponding dimensions Using extended selection techniques hold down the Ctrl or Shft keys while clicking the left mouse button select all the dimensions that should be used If multiple coordinates are provided for the common dimensions X Longitude Y Latitude Z Depth Height and T Time make sure to select only one for each direction To view the header information of the netCDF file similar to a ncdump h call press the View NetCDF Header button This should always be done if you are unfamiliar with the structure and contents of the file a NetCDF Setup Wizard Select Dimensions Step 1 of 4 NetCDF dimensions Corresponding netCDF variables lon 72 Latitude degrees_north var lat lat 36 Longitude degrees_east var lon time 1872 Time days since 1800 1 1 00 00 00 var time Monthly Anomalies of SST degC var sst All 3 dimensions selected
27. Weiss Deep Sea Res 32 1485 1497 1985 CFC 10 Saturation Bullister amp Wisegarver Deep Sea Res 45 1285 1302 1998 CFC 113 Saturation Bu amp Warner Deep Sea Res 42 1151 1161 1995 CH4 Saturation Wiesenburg amp Guinasso J Chem Eng Data 24 356 1979 Oxygen Saturation Weiss Deep Sea Res 17 721 735 1970 pCFC 11 pptv Warner amp Weiss Deep Sea Res 32 1485 1497 1985 pCFC 12 pptv Warner amp Weiss Deep Sea Res 32 1485 1497 1985 pCFC 10 pptv Bullister amp Wisegarver Deep Sea Res 45 1285 1302 1998 pCFC 113 pptv Bu amp Warner Deep Sea Res 42 1151 1161 1995 pCH4 ppbv Wiesenburg amp Guinasso J Chem Eng Data 24 356 1979 pSF6 pptv Bullister Wisegarver amp Menzia DSR I 49 1 175 187 2002 SF6 Saturation Bullister Wisegarver amp Menzia DSR I 49 1 175 187 2002 Metadata Cruise ID Unique ID per cruise Latitude Decimal latitude derived from station latitude Longitude Decimal longitude derived from station longitude Meta Variable Value Values of numeric meta variables Quality Flag Value Quality flag ASCII codes of any variable Station Number Number derived from Station label Physical Properties TEOS 10 Absolute Salinity Sa g kg TEOS 101 Absolute Salinity at Freezing Point g kg TEOS 101 Adiabatic Lapse Rate I mdegC dbar TEOS 101 Brunt V is l Freqency cycl h details Cabbeling Coefficient C 10 6 K 2 TEOS 101 Conservative Temperature O degC TEOS
28. a variety of spreadsheet type ASCII files If the for mat of the import file is ODV generic spreadsheet format compliant the data import will be fully automatic and no user interaction is required ODV generic spreadsheet files can be opened using File gt Open or they can be dropped on the ODV window or icon Other spreadsheet data files can also be read and imported by ODV however the im port of these files usually requires input by the user usually by identifying the particu lar columns in the import file that provide the data for meta and data variables in the collection e g longitude latitude date etc It is possible to import spreadsheet files with or without station metadata information and with or without column labels ODV spreadsheet files may contain comments and the column separation character may be TAB or semicolon Missing data may be indi cated by special numeric or text indicators or by empty data fields The spreadsheet files may contain data for many stations from one or more cruises Each station may contain an unlimited number of samples one line per sample The samples of a station must be in consecutive order but need not necessarily be sorted When reading a spreadsheet file ODV breaks the data into stations whenever one or more of the entries for Cruise Station and Type change from one line to the next A sta tion break also occurs if the date time longitude and or latitude change by more than some specif
29. be treated as an individual station using the meta variable and collec tion variable assignments from Table 3 4 Profile data in the atmosphere ice sheets or sediments can be organized in similar ways the only difference being in the choice of the primary variable e g height in the atmosphere or depth in the ice or sediment core Table 3 4 Recommended meta and collection variable assignments for profile data Meta Variables Values Cruise Cruise expedition or instrument name Station Unique station identifier Type B for bottle or C for CTD XBT or stations with gt 250 samples yyyy mm ddThh mm ss sss Date and time of station instrument at depth Longitude degrees_east Longitude of station instrument at depth Latitude degrees_north Latitude of station instrument at depth Bot Depth m Bottom depth of station 24 ODV User s Guide Unlimited number of other Text or numeric user defined text length or 1 to 8 byte integer meta variables or floating point numbers Collection Variables Comment Depth or pressure in water To be used as primary variable column ice core sediment core or soil elevation or height in the atmosphere etc Unlimited number of other Must be numeric 1 to 8 byte integer or floating point numbers measured or calculated var iables 3 2 2 Time Series Data This category covers observations at a given fixed
30. bottle WoceBtl Menu Bar Station ID 4742 Cruise AR 13_18HU93039_1 A Station 6 Current Station Position 45 63 42 26 Date 27 November 1993 Window Tene 17 39 00 000 Depth Range m 49 4672 Sample 18 20 Depth m Temperature C Tpot 0 C Salinity pss 78 Oxygen mol kg Phosphate umol kg Canvas Slate moles Nitrate mol ig Nitrite mol g CFC 11 pmolfrg CFC 12 pmol kg Data 3 CCL4 pmolkg Windows y i C113 pmolkg Tritum TU OELHES PERONT HELIUM NMOL KG Isosurface Values Projected Longitude Isosurface Data Projected Latitude Tene yr 1993 Window Map Current Sample Window Status Bar Status Information Current Mouse Position Current View Information Current Filter Settings Figure 2 1 Elements of the ODV application window Left clicking on station or data marks in the map or any of the data windows selects the respective station or sample Right clicking on most window elements brings up con text menus with different element specific options Resting the mouse over data listing items brings up popup windows with detailed data information The map displays stations that satisfy the current station selection criteria It maintains a pick station list and may have a section Data windows have one of the following scopes 1 STATION showing X Y data of the picked stations picked stations are marked in the map using the same marks as in the data windo
31. changing the object s properties Edit exporting copying deleting or changing the order in which the ob jects are drawn 11 1 Annotations You can add annotations by choosing Extras gt Add Graphics Object gt Annotation from the canvas map or data window popup menus A cross hair cursor will appear which you should move to the location where the annotation is to appear and then click the left mouse button Note that the window from which the creation was initiated will own the respective object When adding or editing annotations you may set the position orien tation degrees counter clockwise font size pt color and alignment parameter of the annotation text Annotations can have a frame and the annotation rectangle can be filled before drawing the text You can choose different colors for all these items In ODV annotations you can use various formatting control sequences as well as functions for auto text substitution Like all graphics objects you can drag an annotation to a different position by moving the mouse cursor over it pressing and holding down the left mouse button and moving the mouse You can edit an annotation by moving the mouse over it clicking the right mouse button and choosing Properties from the popup menu To delete an annotation 98 ODV User s Guide all annotations choose Delete Object Delete All Objects from its popup menu Note that the axis labels of the data plot windows are imp
32. define the collection variables choose Medatlas Bottle variables for Medatlas bottle data Medatlas CTD variables for Medatlas CTD XBT or MBT data Medatlas Sediment Trap variables for Medatlas sediment trap data or Medatlas Time Series variables for all other Medatlas time series data e g data from current meters thermistor chains sea level gauges or meteorology buoys To initiate the data import choose Import gt Medatlas Formats gt Profile Data for bottle CTD XBT or MBT data or Import gt Medatlas Formats gt Time Series Data for any kind of time series data Both import types allow selection of one or more Medatlas data files to be imported Alternatively you may also select a text file containing the list of file names to be processed This list file has to be prepared before starting the import It must contain one file entry per line and the file names must be either absolute path names or pathnames relative to the currently open collection The list file must have extension st You can generate file lists easily with the built in list file generator Note that Medatlas time series and sediment trap data collections created by ODV4 or later contain a meta variable Instrument Depth that contains the deployment depths of the respective instruments such as current meters thermistors sea level gauges mete orology buoys or sediment traps Multiple variables in Medatlas profile data files of the same type but in different units are
33. do main 4 Zoom into the window s color bar to modify the Z range 5 Zoom in to the point of the mouse right click 6 Automatically zoom out 7 Adjusts the axis ranges of this window to full scale 8 Sets axis ranges manually 9 Selects new variables on X Y or Z axis 10 Access to the data window s Extras menu 11 Allows modifying the properties of this data window 15 Version 4 5 0 You can also use keyboard keys to select new current stations the right arrow key will select the next station according to the station order in the collection while the left arrow key will select the previous one Choosing option Current Station by Name from the map popup menu lets you specific cruise label station label and station type making the matching station the current sta tion Choosing option Current Station by ID from the map popup menu or simply pressing the key while the mouse is over the map lets you select a new current station by en tering its internal ID number not to be confused with the station label One of the samples of the current station is the current sample The current sample is marked in the data windows by a red cross and its data values as well as its quality flags are shown in the Current Sample Window To select a new current sample and possibly new current station left click with the mouse on any data point in any of the data windows The down arrow key will select the next sam
34. entering more than one cruise label specification use two bars to separate the en tries Example OCE13 34 A16N SO5 Selects cruises OCE133 and OCE134 and cruise A16 and all cruises starting with S05 Table 8 1 Regular expression syntax for cruise labels Character Meaning Arbitrary character Any character represents itself apart from those mentioned below Example c matches the character c This matches any single character Example SAVE_LEG matches SAVE_LEG1 SAVE_LEG9 SAVE_LEGa etc sl This matches zero or more of any characters Examples 101_ matches any label that has 101_ at the beginning 06AQ matches any label that has 06AQ in the middle Sets of characters can be represented in square brackets Within the character class like outside backslash has no special meaning The dash is used to indicate a range of characters the caret negates the character set if it occurs as the first character i e immediately after the opening square bracket Examples IO5 EW matches IO5E and I05W LEG 0 2 matches LEGO LEG1 LEG2 SAVE_LEG 3 matches all SAVE_LEG cruises ex cept SAVE_LEG3 The Date Time tab lets you specify a valid time interval Period a valid calendar inter val Season and a valid day time range Day Time A station must satisfy all three cri teria to be considered valid The Season and Day Time ranges may span consecutive years or d
35. for the se lected variables and replaces the original station with the updated version If no matching station is found the user is notified Variable Association 48 Usually the number order and meaning of variables stored in the import file differ from the number order and meaning of variables stored in the collection There fore a source target association of variables must be established ODV automati cally associates variables with matching labels name and units and marks the associated variables with an asterisk You can click on such a variable in any of the two lists to identify its associated partner variable To establish an association between a source target variable pair click on the re spective target variable then click on the source variable to be associated with the target variable and either press the Associate or Convert buttons Use Associate if the data values in the import file should be imported without modification or Convert if transformations need to be performed during import When using Con vert you can choose between predefined commonly used transformations or al ternatively you can establish your own general linear transformation formula Note that you may associate more than one source variable with a given target variable This is useful if the data for a given target variable e g Oxygen are lo cated in different columns and possibly different units e g Oxygen umol kg and Oxygen ml l
36. given expedition following a given track Version 4 5 0 30 S 20 S Phosphate umol kg GIDE mle E ta pa 35 36 Salinity psu Oxygen umol kg c Ocean Data View 10 S EQ Phosphate pmol kg ann Toad Si pr Kee 3 Figure 1 5 Example window layout with two data windows of scope SECTION 1 and 2 and one SCATTER data window 3 Note that the SCATTER window 3 displays all data of all stations in the map while the SECTION windows 1 and 2 only show the data of the stations inside the section band Temperature C Depth m 300 Ocean Data View o Depth m Sigma 0 kg m 27 5 Ocean Data View Figure 1 6 Example window layout with two data windows of scope SURFACE showing property distribu tions on isosurfaces ODV User s Guide 1 6 4 SURFACE Scope In addition to meta variables and collection variables ODV defines a third set of varia bles isosurface variables Isosurface variables provide values of a given collection varia ble e g Temperature or Depth in Figure 1 6 on specific isosurfaces Isosurfaces are layers of constant values of another collection variable such as constant depth or den sity layers SURFACE scope windows show isosurface values of all stations in the map SURFACE windows support X Y and Z isosurface variables If Longitude and Latitude isosurface variables are assigned to the X and Y axis the window will beco
37. gt data Base directory for ODV data collections While ODV data collections may in principle reside anywhere on a read write hard disk memory stick etc or read only DVD CD ROM etc storage medium it is recommended to main tain all your collections under this directory Every collection should be stored in its own sub directory lt user gt diva DIVA working directory only present if DIVA has been used lt user gt export Base directory for datasets exported via Export gt X Y Z Window Data lt user gt gazetteers ODV gazetteer database files lt user gt macros ODV macro files mac lt user gt palettes ODV palette files pal 150 ODV User s Guide lt user gt reference Base directory for reference datasets exported via Export gt X Y Z Window Da ta as Reference 151
38. if necessary and perform the subsampling Presently ODV searches for the following Sea Bird parameter codes in the specified order 1 Pressure db prM prDM pr50M prSM prdM no conversion Pressure psi prE prDE pr50E prSE prdE multiplied by 0 0689476 Pressure FGP KPa fgp0 fgp7 multiplied by 0 001 Depth m depSM depFM dNMEA TEOS10 conversion Depth ft depSF depFF multiplied by 0 3048 TEOS10 conversion ae ee ES For each file containing pressure or depth data ODV will check whether the file con tains down and up casts and if this is the case break the two and store the data in two separate stations Up and down casts can be identified by the up and down suffix in the station label Sea Bird CNV file headers may differ considerably in the number and format of metada ta items provided ODV recognizes metadata items such as cruise name station name date and time longitude and latitude if the following rules are satisfied 1 The header lines must start with user metadata or NMEA GPS metada ta 2 The cruise name must be labeled as Cruise 3 The station name must be labeled as Station or at least contain the word Sta tion 4 Longitude and latitude must be labeled as Longitude and Latitude 5 Longitude and latitude must follow the format D DD MM mm O where D DD represents a two or three digit degrees value MM mm represents minutes an
39. if you want to see only samples that have values for one or more variables in specific value ranges For instance if you are stud ying the upper water column and only want to see samples between 0 and 500 m depth choose the depth variable and enter the desired range under Acceptable Range You can specify range filters for more than one variable at a time For text variables you can specify one or more wildcard expressions like this N Gerard This will select only samples for which the variable s text value starts with N or is equal to Gerard 75 Version 4 5 0 3 probably bad data that are potentially correctable Acceptable Range 4 bad data a AA 500 5 value changed 500 8 interpolated value 9 missing value Relax this qualty fiter Apply to all variables Relax this range fiter Relax all range filters 0 out of 27 variables range filtering 0 out of 27 variables range filtering 0 out of 27 variables quality filtering 0 out of 27 variables quality filtering Figure 8 2 The sample selection criteria pages 76 ODV User s Guide 9 Station Map 9 1 Map Properties The properties of the station map can be modified via the Properties option of the map s popup menu or via View gt Window Properties gt Map This includes changing the map do main and projection the appearance of ocean bathymetry coastlines and land topog raphy
40. in the sloping region Choosing a larger strength value would improve this further DIVA execution times are somewhat larger than for the other gridding methods never theless you should always consider using DIVA gridding for publication quality figures System requirements and troubleshooting For successful operation of the DIVA package you need a computer with at least 2GB of RAM If you run DIVA and the plot window remains white please try to free some memory by closing other applications and try again 148 ODV User s Guide a Sigma 0 kg m Oxygen umol kg o b f eo Sese 000 eoe s 20 gt A gt Depth m b Sigma 0 kg m Oxygen umol kg 0 Depth m 70 W B la a ig 20W 10 W Cc Sigma 0 kg m Oxygen umol kg o Depth m 70W 60w 50w 40 w 30 W 20 W 10 W Figure 16 5 The upper layer oxygen distribution across the Gulf Stream front in the subtropical North At lantic shown as a original data points b DIVA gridded field without direction constraint and c DIVA gridded field with direction constraint strength value 500 16 7 ODV Directory Structure The default installation directory for ODV is c Program Files Ocean Data View mp on Windows Applications ODV on Mac OS X and usr local odvmp for Linux and UNIX indicated as lt install gt below for Mac OS X Linux and UNIX replace by in the follow 149 Version 4 5 0 ing
41. lines 3 rectangles and squares 4 ellipses and circles 5 pol ylines straight line segments or Bezier smoothed 6 filled polygons straight line segments or Bezier smoothed 7 symbols 8 symbol sets 9 legends and 10 vari ous object types from files Detailed descriptions of these objects follow below A graphics object is owned by the canvas the map or a specific data window on which the object was created All graphics objects of the canvas the map or a data window are drawn whenever the respective parent window is drawn The coordinates of a graphics object are either specified in the coordinate system of the owner window or of the can vas Canvas coordinates are in cm from the lower left corner to the right or upwards The initial ownership and coordinate system of an object are derived from the window from which creation was initiated see below Like most other properties of a graphics object ownership and the coordinate system may be edited and modified at any time By default graphics objects are clipped to the parent window If you create objects out side the window s viewport make sure to uncheck the Clip to window box on the object s Properties dialog see below Graphics objects belong to the current view and are saved in view files Creation Except for legends which are created automatically you create and add any other graphics object by choosing Extras gt Add Graphics Object gt repres
42. location that are repeated over time Examples are measurements of currents and hydrographic parameters on moored oceanographic sensors sea level height measurements at coastal stations or meteoro logical observations on land stations In all these cases the entire time series of a given instrument or station should be treated as an individual station using a decimal time variable as primary collection variable and the other meta variable and collection vari able assignments from Table 3 5 Table 3 5 Recommended meta and collection variable assignments for time series data Meta Variables Values Cruise Cruise expedition or instrument name Station Unique station identifier Type B for bottle or C for CTD XBT or stations with gt 250 samples yyyy mm ddThh mm ss sss Deployment date and time of instrument Longitude degrees_east Deployment longitude of instrument Latitude degrees_north Deployment latitude of instrument Bot Depth m Bottom depth at station Unlimited number of other meta variables Text or numeric user defined text length or 1 to 8 describing the instrument and its deploy byte integer or floating point numbers ment depth Collection Variables Comment 25 Version 4 5 0 or umn label time_ISO8601 ISO8601 dates of the form 2003 02 17T13 57 12 3 in a single column with col Continuous decimal time variable To be used as primary variable calc
43. merged during import possibly involving unit conversions and or offset correc tions The following merging operations are performed Salinity psu 1 PSAL PRACTICAL SALINITY P S U 0 1 SSAL SALINITY PRE 1978 DEFN P S U 0 004 Oxygen m1 1 dl DOX1 DISSOLVED OXYGEN m1 1 0 0 02297 DOX2 DISSOLVED OXYGEN micromole kg 0 0 02241 DOXY DISSOLVED OXYGEN millimole m3 0 Silicate millimole m3 1 SLCA SILICATE Si04 Si CONTENT millimole m3 0 1 025 SLCW SILICATE Si04 Si CONTENT micromole kg 0 Nitrate Nitrite millimole m3 1 NTRZ NITRATE NITRITE CONTENT millimole m3 0 43 Version 4 5 0 1 025 NTZW NITRATE NITRITE CONTENT micromole kg Phosphate millimole m3 1 PHOS PHOSPHATE PO4 P CONTENT millimole m3 0 1 025 PHOW PHOSPHATE PO4 P CONTENT micromole kg 0 Alkalinity millimole m3 1 ALKY ALKALINITY millimole m3 0 1 025 ALKW ALKALINITY micromole kg 0 In each case the list of alias variables is traversed until a possibly converted value is found Note that the density p of the sample at laboratory conditions is needed for the conversion from volumetric units e g millimole m3 to per unit mass units e g mi cromole kg This information however is not included in the Medatlas files and an approximate conversion formula has to be applied Using a constant density value of p 1 025 kg l as above introduces errors smaller than 0 2 Th
44. most commonly however they are placed at the beginning of the file and con tain descriptions of the data information about the originator or definitions of the vari ables included in the file Comment lines are optional Comment lines may be used to carry structured information that may be exploited by ODV or other software Examples are the SDN_parameter_mapping block employed by the SeaDataNet project and containing references to variable definitions in official pa rameter dictionaries or the lt attribute_name gt lines defined by ODV containing values for given attribute names The currently defined attribute names are summarized in Table 16 6 Structured comment lines may only appear before the column labels line or the first data line 136 ODV User s Guide Table 16 6 Summary of comment line attributes names supported by ODV Attribute Name Possible Values File information Creator Free text specifying the creator of the file Example lt Creator gt rschlitz GSYSP168 lt Creator gt CreateTime Time of file creation in ISO 8601 extended format Example lt CreateTime gt 2008 05 16T09 53 45 2 lt CreateTime gt Software Software used to create the file Example lt Software gt Ocean Data View Version 4 0 0 lt Software gt Source Absolute path of source collection Example lt Source gt C eWOCE data whp bottle WoceBtl lt Source gt Source Last modified time of
45. on X Y and Z as well as various axis properties Normal axis orientation is to have increasing val ues from left to right for X bottom to top for Y and bottom to top in the color bar for Z You may reverse the orientation on one or more axes for instance to create depth in 87 Version 4 5 0 the ocean values decreasing upward by checking the respective Reverse range box To modify X Y and Z axis properties click on X Axis Settings Y Axis Settings or Color bar Settings The axis properties dialog Figure 10 2 will appear letting you specify the value range on the respective axis a linear logarithmic or stretched projection along the axis the spacing of labeled and unlabeled tic marks and the position of the labeled axis Choosing automatic for the tic mark spacing lets ODV determine the location and frequency of the marks automatically The Position entry allows a choice of axis position left or right bottom or top or lets you switch off the labeling of the respective axis altogether Note ODV applies special labeling strategies if detects a decimal time variable on an axis Label spacing may not be changed by the user in such cases 5 Axis Properties X Axis Temperature C Minimum 2 Maximum 30 Projection Logarithmic x Tic mark interval automatic Label interval automatic Position bottom Ga Figure 10 2 The Axis Properties dialog
46. output odv collection for a virtual pair station located at the mid point between the two stations in the pair The station label of the pair station contains the station labels of the original stations involved Note that geostrophic velocities are not calculated close to the Equator or for stations with sparse hydrographic observations Because results are very sensitive to data er rors it is essential to quality control the temperature and salinity data of the section carefully prior to invoking the Tools gt Geostrophic Flows option One way to proceed is to flag suspicious data as Questionable or Bad using the Edit Data option and to accept only Good and Unknown data by applying appropriate sample selection criteria Also by ap plying appropriate station selection criteria you should make sure that only stations for a given expedition are included in the calculations and that stations from other cruises crossing the section are excluded You should eliminate profiles covering only part of the water column and only use full top to bottom profiles 117 Version 4 5 0 14 2 2D Estimation For data windows that currently use the VG or DIVA gridding methods you can perform estimation of Z values at arbitrary user specified X Y points by choosing the Extras gt 2D Estimation option from the respective data window popup menu The estimated Z values at the user specified X Y positions are obtained by applying the window s cur rent grid
47. report the number of groups and duplicate stations found You may view the duplicate station list and inspect and edit the duplicate stations by checking the respec tive boxes If you choose to edit the duplicate stations the Duplicate Station Action dia log Figure 14 1 will appear for every duplicate station group You may either delete all but one of the stations in the group or merge the data of all stations in the group into the first station of the group Note that these operations change the contents of the col lection files and cannot be undone Duplicate Station Action Group 1 Station s 2 A Keep no 1 delete all others 9 Merge all stations in group Apply Apply to All een Cancel a Figure 14 1 The Duplicate Station Action dialog Ifyou want to apply the specified action to all remaining duplicate station groups click on Apply to All If you want to keep a group unchanged press Keep to abort the editing of duplicate stations press Cancel NOTE The computational load of the duplicate station scan scales with the square of the station number and may take hours for large collections with millions of stations In such cases the map domain should be divided into sub regions by zooming or manual ly setting the map domain and scans should be performed separately for every sub domain 14 7 Ocean Calculator ODV allows calculation of more than 40 commonly used parame
48. right Associated items are marked with an asterisk You can click on such items in any of the lists and ODV will show the associated item in the other list You may break the association by pressing Undo pressing Undo All will break all association and leave all key variables undefined You establish an association by selecting the relevant items in the two lists and pressing Associate Items in the key variable list that are not included in the list of collection vari ables may be marked as not available by pressing the Not Available button Such items are marked in the key variable list by a minus sign F gt Identify Key Variables Key variables Collection variables Pot Temperature C any ref a DEPTH METERS a Practical Salinity psu TEMPERATURE C ITS 90 Pressure in Water Column db SALNTY PSS 78 SF6 fmol kg CTD_SALNTY PSS 78 SF6 fmol OXYGEN UMOL KG Salinity psu NITRAT UMOL KG Seawater pH NITRIT UMOL KG Seawater pH Free Scale SILCAT UMOL KG Seawater pH SWS Scale iss PHSPHT UMOL KG Seawater pH Total Scale naza TCARBN UMOL KG Silicate umol ka ALKALI UMOL KG Silicate umol l Not Available pH sws25 TALK umol kg CFC 11 PMOL KG TALK mol l Undo CFC 12 PMOL KG TCARBN UMOL KG CFC113 PMOL KG T ERREA 4 PI rooz mol Lindo at Se omoun Temperature degC DELC14 MILLE Temperature C DELC13 MILLE Tota
49. source collection in ISO 8601 extended format LastModified Example lt SourceLastModified gt 2003 11 11T19 53 45 2 lt SourceLastModified gt Version Version of the file Example lt Version gt ODV Spreadsheet V4 0 lt Version gt MissingValue List of missing value indicators in the file Multiple entries are separated by Indicators spaces Example lt MissingValuelndicators gt 9 99 9 9999 lt MissingValuelndicators gt Data information DataField DataType Description of the field of data in the file Valid entries are GeneralField Ocean Atmosphere Land IceSheet Sealce Sediment Example lt DataField gt Ocean lt DataField gt Description of the type of data in the file Valid entries are GeneralType Pro files TimeSeries Trajectories Example lt DataType gt Profiles lt DataType gt 16 3 2 Column Labels There has to be exactly one line containing the labels of the columns This column labels line must always be present it must appear before any data line and it must be the first non comment line in the file ODV generic spreadsheet files must provide columns for all mandatory meta variables see Table 3 3 and the following labels must be used exactly as given as column labels 137 Version 4 5 0 Cruise Station Type one of the supported date time formats Longitude degrees_east Latitude degrees_north Bot Depth m The recommended date time format is ISO 86
50. tained in the file If the optional argument q is provided ODV is automatically closed after all commands have been processed cmd_file has to be an absolute pathname or a path relative to the current directory On some platforms ODV prompts for the following Quick Installation information when running for the first time 1 The full path name of the directory that contains the bin directory ODVMPHOME environment variable 2 The full path name ofa directory on your disk which will be used by ODV during runtime to write temporary files ODVMPTEMP environment variable Note that you must have write permission for this directory You can use the system tmp directory or you can create a special directory on a local disk e g odvtmp for this purpose The use of directories on network drives is not recommended because of potentially pour performance 3 The name of your computer 4 Your user or login name Press OK to finish the Quick Installation Then customize ODV font and external pro grams settings using the View gt Settings on Mac OS X odv4 gt Preferences dialog Once ODV is running you open a data collection netCDF file or any of the supported import data files using the File gt Open option A standard file open dialog will appear and you can choose the appropriate file type and file name to be opened If you open a sup ported import data file ODV will automatically create a new collection in the directory 10 OD
51. the VG gridding case Direction Constraint In section windows DIVA can apply special directional constraints that tend to align the field along isopycnals To enable this feature a potential density anomaly derived varia ble must have been defined and the Strength value on the DIVA Settings page in Figure 10 5 must be larger than 0 Typical values for Strength lie between 500 and 2000 The first potential density anomaly variable is used for the direction constraints if more than one such derived variable is defined The effect of the direction constraint is highlighted in Figure 16 5 showing the upper layer oxygen distribution across the Gulf Stream front As can be seen in the original data plot 16 5a there is an oxygen minimum layer on the western side of the section roughly following the o0 27 isopycnal This isopycnal lies at about 250 m depth near the coast but subducts to about 750 m just a few 100 kilometers offshore Maintaining the oxygen minimum as a continuous feature is a challenge for any gridding algorithm especially in the sloping region where O2 values east and west of the feature are much higher The influence of the neighboring high values leads to an erosion of the mini mum which can be seen in the DIVA gridding plot 16 5b Using DIVA gridding with the direction constraint switched on strength value 500 shows an enhanced alignment of the gridded field with the isopycnals and an improved representation of the oxygen field
52. the appropriate file type To print the graphics press Print EX Histogram i boe EE Histogram i x al A a mail 5 ha yr y Jg E 7 1 J i w i J ia 180 19 SOI OO i w ao 30 Time tyra Day of Year Save As Close Save As Cose E e J Figure 9 9 Example time and season histograms of stations in the map Pressing X Y Distribution on the Map Statistics dialog produces a plot showing the data density in the entire map domain via the number of stations within small tiles This dis tribution plot allows easy identification of areas of dense station coverage especially in cases with very large numbers of stations and many repeat stations plotting at the same location in the station map You may zoom into the map and repeat the above proce dures to obtain station density information with higher spatial resolution see Figure 9 10 84 ODV User s Guide 10 W 0 10 E 20 E 30 E 40 E 2500 1500 1000 Ocean Data View S 10 W 0 10 E 20 E 30 E 40 E 175 150 125 Ocean Data View Figure 9 10 Example station map and station distribution plots with different levels of spatial resolution 85 Version 4 5 0 86 ODV User s Guide 10 Data Windows 10 1 Data Window Properties The properties of data windows may be modified by right clicking on the respective window and choosing the Properties option Alternatively y
53. the display order in the data values list Popup windows containing the full variable label and quality flag text appear automati cally when resting the mouse over one of the list items 2 7 Graphics Canvas The canvas is the painting area of ODV and contains the station map and zero or more data windows You can adjust the size of the canvas via View gt Settings gt Canvas on Mac OS X odv4 gt Preferences gt Canvas 13 Version 4 5 0 2 8 Popup Menus Clicking the right mouse button on Mac OS X system with a single button mouse hold down the Alt key and click the mouse while over the canvas the map a data window a graphics object or a data list window invokes different popup menus providing element specific options Most of the ODV functionality is available via these popup menus po i eias ii F5 The canvas popup menu offers the following 2 Save Canvas As Ctrl 5 options 3 Print Canvas Ctrl P e 1 Redraws the entire canvas and all its windows 4 Full Range All Ctrl F e 2 Saves the entire canvas and all its windows in 5 Undo R gif png jpg or PostScript file e 3 Prints the entire canvas and all its windows 6 Add Graphics Object e 4 Adjusts the axis ranges of all windows to full 6 scale 7 Window Properties e 5 Allows undo of the most recent view changes e 6 Allows adding or managing the graphics objects 8 Window Layout Alt W 8 81mg grap J i of the canvas 8 Layout Templates ela e 7 Changes
54. the properties ofthe map and data 9 Save View As windows 9 Save View e 8 Changes the map and data window layout and 9 Load View Shift L implements window layout templates l e 9 Saves or loads a view to or from a file Figure 2 2 The canvas popup menu 2 9 Status Bar The ODV status bar displays help status and progress information The right most pane of the status bar indicates the number of currently shown stations in the map the total number of stations in the collection and the name of the current view file Resting the mouse over this pane brings up a popup window with more detailed information on the current state 2 10 Current Station and Sample ODV always points to a current station This station is marked in the map with a red cross and its metadata are listed in the Current Station Window You can select a new current station by clicking with the left mouse button on a station mark in the map If you suspect more than one station at the same location for instance because of repeat ed observations at the same site you can hold down the SHFT key while clicking on the station position If there are indeed multiple stations at the clicked position a list of these stations is shown and you can select the new current station from the list 14 ODV User s Guide Redraw Map Save Map As Zoom Auto Zoom In Auto Zoom Out Valid Domain Full Domain Global Map Current Station by Name Current Station by ID
55. the selection criteria on the different pages are combined using the logical AND operator e g a station is considered valid only if it satisfies all station selection criteria Press OK when you are done ODV will rebuild the station map using the new selection criteria 8 2 Sample Selection Criteria A given sample ofa valid station is considered valid only if it satisfies the current sam ple selection criteria Only valid samples are shown in the different data windows how ever all sample values valid or invalid are listed in the Current Sample Window You can modify the sample selection criteria via Sample Selection Criteria from the map s popup menu or View gt Sample Selection Criteria from the main menu Choose the category that you want to modify by clicking on the respective tab e g Quality or Range and modify the items of interest On the Quality tab select the variable for which you want to establish a data quality fil ter and then select the quality flags to be accepted Click on Apply to all variables to ap ply the same quality filter for all variables using the same quality flag schema as the se lected variable Click on Relax this quality filter if you want to accept all quality flags for the selected variable Then also click on Apply to all variables if you want to relax all quality filters of all variables using the same quality flag schema as the selected varia ble Use the selection criteria on the Range tab
56. then compiles the superset of variables occurring in these files and subsequently cre ates one ODV collection consisting of all variables in the compiled superset Data from all files in the group are finally imported into that particular collection While compiling the superset of variables of a given file group a new variable is created 37 Version 4 5 0 whenever a new variable label is found in the column header line of a file regardless of its SDN parameter code in the semantic header If for instance the two labels Tempera ture_sensor1 and Temperature_sensor2 both with semantic header entry SDN P011 TEMPPRO1 are found in a single file or in separate file of the group ODV will create separate variables Temperature_sensor1 and Temperature_sensor2 in the target collection Separate variables are also created if the same variable name but different units appear in different files Encountering for instance Phosphate umol l and Phosphate umol kg in two files will result in two separate variables Note that in any given file the variable names in the header line must be unique and using the same name repeat edly as in Phosphate umol l and Phosphate umol kg is not supported by ODV Two variants of a given variable may appear in a single file but the variable names must be different e g Phosphate_1 and Phosphate_2 The rules above for creating separate variables do not apply for variables listed in the sdn_import
57. time user User and host name collection Full path of current collection collectionName Name of current collection excluding extension view Full path of current view file section Full path of current section file 143 Version 4 5 0 16 6 Gridding Methods ODV lets the user project irregularly spaced original data onto equi or non equidistant rectangular grids for contouring and graphical display or output of gridded values using one of three available methods Quick Gridding VG Gridding and DIVA Gridding Quick Gridding is a weighted averaging algorithm optimized for speed that calculates estimates at all grid nodes requiring only one loop over the available data Quick Grid ding should only be used in cases when the other algorithms are too slow e g in cases with millions of data points VG Gridding uses a more sophisticated weighted averaging algorithm and yields good results in cases with good and homogeneous data coverage VG Gridding is the default gridding method DIVA Gridding is the most advanced grid ding method available in ODV It is computationally more expensive than the other methods but should always be used when preparing final graphs for publications or webpages 16 6 1 VG Gridding Algorithm In contrast to Quick Gridding for which an equidistant rectangular grid is used ODV constructs and uses a variable resolution rectangular grid if VG Gridding is requested
58. time in the NetCDF variables list and Year in the Meta variables list then press Convert ODV will try to establish a conversion automatically If not success ful ODV lets you choose an appropriate conversion algorithm manually Note that ODV assumes that the reference date is based on the Gregorian calendar ODV date values are Gregorian dates You can modify the default value of a meta variable e g Cruise etc by selecting it in the Meta variables list and pressing Set Default Note that the meta variables Cruise Station and Type are set automatically by ODV and need not be established manually If the netCDF file does not contain date and time in formation the Year Month Day Hour Minute and Second meta variables may remain unassociated Longitude and Latitude meta variables must be associated before you can advance to the next page of the wizard NetCDF Setup Wizard Associate Meta Variables Step 2 of 4 NetCDF variables Meta variables 1 Latitude degrees_north var lat Associate Cruise 2 Longitude degrees_east var lon Station 3 Time days since 1800 1 1 00 00 00 var time Convert Type 4 Monthly Anomalies of SST degC var sst Longitude degrees_east Set Default Latitude degrees_north Minute Second 3 of 4 variables used 8 of 11 variables associated Heb lt a Fish icancel Figure 13 2 The netCDF setup wizard step 2 of 4 Selecting the primary va
59. unchecking the Draw color bar box There are two ways of selecting a Series for use in the ODV station map automatic or manual Map Properties Map Properties Geneal Depiay Style Projection Layers Doman Anoor 4 iP General Depiay Style Projection Layers Doman annot dib Y Fi coins Layer Set Info Draw color bar Defauk Settings Draw color bar Defauk Settings Figure 9 2 The various pages of the Map Properties dialog part 2 of 3 Automatic Series Selection You switch automatic series selection on by checking the Automatic selection checkbox In this mode ODV will automatically determine the best available series for a given map domain and use this series for the station map Whenever the map domain is changed e g by zooming or using the Full Domain or Global Map options on the map popup 78 ODV User s Guide menu ODV will find and use the best installed series for the new domain ODV will also automatically select the ocean bathymetry and land topography layers suitable for the given domain You switch on or off the drawing of ocean bathymetry coastlines land topography lakes and rivers and national borders by checking or unchecking the re spective checkbox For automatic series selection to be useful you should install one or more of the high resolution bathymetry coastline topography series available from the ODV website For information on other available map resources and installation instructio
60. variable Year station date Integer year derived from station date Year time variable Integer year derived from a time variable 1 IOC SCOR and IAPSO 2010 The international thermodynamic equation of seawater 2010 Calculation and use of ther modynamic properties Intergovernmental Oceanographic Commission Manuals and Guides No 56 UNESCO English 196 pp 2 Note that in TEOS 10 specific volume anomaly is calculated using absolute salinity Sa 35 16504 g kg and conservative temperature 0 C as reference This differs from the traditional definition using a reference of practical salinity Sp 35 psu and in situ temperature t 0 C Relative differences of values can reach 25 in the deep ocean 3 Using TEOS 10 specific volume anomaly see 2 above Brunt V is l Freqency Brunt Vaisala Freqency is calculated as follows For a given profile ODV first establish es a sequence of standard depths and projects the observed pressures temperatures and salinities onto these standard depths Then Brunt V is l Freqency is calculated using vertical density gradients calculated from the new TEOS 10 equation of state 2010 for every standard depth interval and assigned to the interval mid point Finally the mid point Brunt Vaisala Freqency values are projected back to the original pressure or depth values of the profile Projection of values is done using linear least squares interpolation Parameters of the carbon dioxi
61. you do not want quality flag values of meta and or collec tion variables to be exported uncheck the Export metadata quality flags and or Export data quality flags boxes i Spreadsheet File Properties Missing value string CESSA Longitude range 0 360 E y Metadata date format yyyy mm dd Thh mm ss sss y Data date format Data fitter Export all data v W Use compact output format Export data quality flags __ Export metadata quality flags oe 4 Figure 5 1 Spreadsheet File Properties dialog Note that exported ODV spreadsheet files can be re imported into ODV using the Im port gt ODV Spreadsheet option or by simply dropping the file onto the ODV icon Note that output filenames may not contain any of the following characters Export data filenames should not contain spaces ODV generic spreadsheet files are column oriented ASCII files See chapter 17 3 for a detailed format description 51 Version 4 5 0 5 2 ODV Collection You can export the data of the currently selected stations into a new ODV collection by choosing Export gt 0DV Collection Then select the variables to be included in the new collection default all variables and specify destination directory and file name using the standard file select dialog box 5 3 NetCDF Files You can export the data of the currently selected stations into a single NetCDF file by choosing Expo
62. you should create a custom template and place the template in the tem plates collections subdirectory of the ODV user directory User collection template files have the odv extension and follow the format of odv collection files As last step in the definition of new collections ODV presents the Collection Properties 29 Version 4 5 0 dialog Figure 3 5 on which you can specify the field and type of data to be stored in the collection You also select the primary variable which is used to sort the data FT r Meta Variables E F Collection Variables Cruise Top Station Type Longitude degrees east Latitude degrees_north Year Month Day Hour Minute Bot Depth m PrimaryVarMin primaryVarttax ea Edt Delete Delete Up Down Down Bottom Bottom 14 variables defined 3 variables defined 1 variables selected 0 variables selected o J one eme Figure 3 4 Dialogs for the definition of meta and collection variables ODV then creates the collection and draws a global map on the canvas Note that at this stage the collection is still empty and does not contain any station data You must im port data into the collection using options from the Import menu on the menu bar Note that all dialogs that appear during collection creation contain meaningful initial set tings If you don t have special requirements you can simply press OK on all these dia lo
63. 01 which combines date and time as yyyy mm ddThh mm ss sss in a single column The labels Lon E and Lat N for longitude and latitude are still supported for back wards compatibility Metadata column labels Metadata labels may have qualifiers of the form METAVAR lt valueType gt lt valueBytes gt to indicate that the column represents a meta variable of a given value type and byte length valueType may be one of the following BYTE SHORT INTEGER FLOAT DOUBLE or TEXT valueBytes represents the number of bytes per value and only needs to be specified for valueType TEXT This value represents the maximum number of characters to be stored in the text field default length 21bytes Note that one of the characters is used for string termination and is not available for actual metadata text e g a TEXT field of 21 bytes can store a maximum of 20 characters of metadata text Examples Longitude degrees_east METAVAR DOUBLE Citation METAVAR TEXT 81 DOT METAVAR TEXT 81 Note The qualifiers are only used when the spreadsheet file is used as a tem plate for collection creation e g when dropping the file onto ODV open ing the file via File gt Open or choosing the file as template when creating a new collection via File gt New They have no effect if you import the file into an existing collection Data column labels Data variable labels should include unit specifications enclosed in brackets e g Depth m Variables w
64. 0508 64 9835 1 TENOR FLAG W 7 32H10201SBI1 HL0201 0 1 10 10 2 20020508 64 9835 1 DINER FLAG 8 32H10201SBI1 HL0201 0 1 9 9 2 20020508 64 9835 16 PTF 9 32H10201SBI1 HLO201 0 1 8 8 2 20020508 64 9835 16 Suero 10 32H10201SBI1 HLO201 0 1 7 7 2 20020508 64 9835 1 PN 11 32H10201SBI1 HLO201 0 1 6 6 2 20020508 64 9835 1 PEP TR l 12 32H10201SBI1 HLO201 0 1 5 5 2 20020508 64 9835 1 CTOPRe FLAG w E 13 32H10201SBI1 HLO201 0 1 3 3 2 20020508 64 9835 1 Cor FLAG 14 32H10201SBI1 HLO201 0 1 4 4 2 20020508 64 9835 1 CTOTMP FLAG W 15 32H10201SBI1 HLO201 0 1 2 2 2 20020508 64 9835 1 Coen T 16 32H10201SB11 HL0201 0 2 6 6 2 20020508 65 0132 1 Cea FLAG_W SALNTY j E z J Figure 4 1 The spreadsheet file properties dialog If the labels for the metadata columns differ from the recommended labels defined in the ODV generic spreadsheet format see below a Meta Variable Association dialog box appears This dialog lets you associate input columns with the collection meta variables or it lets you set defaults for those meta variables not provided in the input file Already associated variables are marked by asterisks See chapter Meta Variable Association Dialog for more details 36 ODV User s Guide 4 2 SDN Spreadsheet Files The EU SeaDataNet SDN project allows retrieval of oceanographic data f
65. 101 Depth from Pressure m TEOS 101 Dynamic Enthalpy kJ kg TEOS 101 Dynamic Height dyn m TEOS 1013 any reference pressure Freezing Temperature Of degC TEOS 101 In Situ Density Anomaly o kg m3 TEOS 109 using in situ pressure and temperature In Situ Temperature from Conservative Tempera TEOS 109 using in situ pressure and conservative temperature ture degC Isentropic Compressibility 10 1 Pa 1 TEOS 101 Latent Heat of Evaporation kJ kg TEOS 101 39 Version 4 5 0 Latent Heat of Melting kJ kg TEOS 109 Neutral Density y kg m Jackett 8 McDougall J Phys Ocean 237 263 1997 more Potential Density Anomaly o kg m3 TEOS 1009 any reference pressure Potential Temperature 6 degC TEOS 1009 any reference pressure Potential Vorticity Q 10 12 m t s1 Potential vorticity derived from Brunt Vaissala Frequency Q f g N Practical Salinity from Absolute Salinity TEOS 101 Practical Salinity from Conductivity TEOS 101 Preformed Salinity S g kg TEOS 101 Pressure from Depth dbar TEOS 101 Reference Salinity Sr g kg TEOS 101 Saline Contraction Coefficient B 103 kg g TEOS 101 Sound Speed m s TEOS 101 Specific Enthalpy h kJ kg TEOS 101 Specific Entropy n J kg K TEOS 101 Specific Heat Capacity Cp J kg degC TEOS 101 Specific Internal Energy u kJ kg TEOS 101 Specific Volume Anomaly mm3 g TEOS 1012
66. 11 ODV User s Guide Contents 1 GENERALOVERVTE Wisin did 1 Ved EASEOER USE ea ie acade eae Eas Dae 1 1 22 DENSE DATA FORMA Titi add 1 1 37 EXTENSIBI Ti iiad id Dia iia iaa wesiaa Re 2 1 4 DERIVED VARIABLES Ao NTA 2 E PLOT ye e e e e E EA 2 1 6 WINDOW SCOPES otan nnna aiii liado Sedads eliana bestias 4 1 7 GRAPHICS OUTPUT ide 7 1 8 DATA STATISTICS e os a a e e A EMS E BE 7 1 9 ESTIMATION AND AVERAGING s cfs3s cveiseesidehea ei ea clases sana bhencg av de bedaus E shasta rastas 7 1 10 NETCDE SUPPORT lt a S 8 2 FIRST STEPS 00 donadas 9 2A INSTALEING OCEAN DATA VIE Weiss dad 9 2 2 RUNNING OCEAN DATA VIEW desnot ainan diia 9 Zed GETTING HELP aora arrasar 11 2 4 APPLICATION MIN O oo oben 11 2 5 MENU BAR dsd laos 12 2 6 METADATA AND DATA WINDOWG cccseesessccececccecsessnsecececccecsesessaaecececcesenesensaaeceseeeens 13 2 7 GRAPHICS CANVAS naaa di 13 2 87 POPUP MENUS vidas is 14 ZO ESTATUS BAR ontario orita encoder aU EE 14 2 10 CURRENT STATION AND SAMPLE ococcccconcncncnnnnnnnnnnonononnnonnnnnnnnnnnononononononanonanenininaninenes 14 2 11 MAP AND DATA WINDOW DRAWING sss ccccccccceceesensececesececeesessseeececcesesessnssaeceseeeens 16 2ili2 SETTINGS taa iia 16 3 ODV COLEECTION Sucursal 21 Belt DATA MODEL sosa it tail 21 3 2 EXAMPLE COLLECTION TYPES 1d ds 24 3 3 EREATING COLLECTIONS ata I a E A E AI a 27 BAe COLLECTION FILES esaa a T EE A SEA te aus UATE 30 3 5 PL
67. ATFORM INDEPENDENCE cccccccsccsccssssssssssscssccccscssssssesssscescssssssusessssceseseesssauesssesens 33 4 IMPORTING DATA essseesosseecessssoesossscoososseecossesocsosseeossssocsssseeosssssoesssso 35 4 1 gt 0ODV SPREADSHEETEIES 0 E E E e A EEA 35 4 2 SDN SPREADSHEET FILES ecc aid a 37 4 3 WORLD OCEAN DATABASE DATA niinn a e E A A a Aa 38 AVA ARGOELOAT DATA o OR 39 4 5 GTSPP GLOBAL TEMPERATURE SALINITY PROFILE PROGRAM cccccccnnononnncncnnnnnnnns 41 4 6 WOCE HYDROGRAPHIC DATA ccccccccccecessesscecesececeesesssseceseccesenessasaececcesesenessaaeeeseeeens 41 4 7 MEDATEAS EORMATDATA 0 A A EE 42 AB SEA BIRD CNV FILES cs focusses de a EA EA AE As 44 4 9 ASSOCIATE META VARIABLES DIALOG occcccccccncnnnononononononononononononononononononononononinonaneneness 46 111 Version 4 5 0 4 10 IMPORT OPTIONS DIALOG ccecccceseececcecseccccecssccccsseccccecsecccceeccecceeeseceeeeeeceeners 46 AVL GENERATING FILE LISTS co cc eebicte ficeshedsiocgesesueds tab bet iendiaeccnletalcceeseavecsaabisbisu devon lend 50 5 EXPORTING DATA s sssssssosssesssssossossssssssssssosssssssososssssossssossssosessossoso 51 51 SPREADSHEET FILES beaded A lob hes 51 5 2 ODV COLLECTIONS 8 cars ieee reo entero Saket ne becas de ole de e be eed Me et 52 53 INETEDE FILES anen di ia iha 52 5 4 WHP EXCHANGE FORMAT EXPORT c ccccssescccccsseccccectececcetececceeececceeececeeseececeeners 53 5 5 EXPORTING X Y
68. DV opening the file via File gt Open or choosing the file as template when creating a new collection via File gt New They have no effect if you import the file into an existing collection Quality flag column labels Quality flag column labels must comply with the following naming conventions to ena ble automatic identification of the meta or collection variable they belong to as well as of the particular quality flag scheme used ODV generic spreadsheet quality flag labels may be specified in one of the following forms e QV lt Text gt lt SchemalD gt lt columnLabel gt e QV lt Text gt lt SchemalD gt STATION e QV lt Text gt lt SchemalD gt SAMPLE e QF lt Text gt is an arbitrary and optional string lt SchemalD gt is one of the supported quality flag schema identifier see Table 16 5 and lt columnLabel gt is the column label of the variable to which the quality flag column belongs The lt Text gt lt SchemalD gt and lt columnLabel gt parts of the quality flag label are optional If the lt SchemalD gt item is missing it is assumed that the quality flag values are ODV generic quality flags If the lt columnLabel gt part is missing it is assumed that the quality flags belong to the variable preceding the quality flag column Note that if the lt Text gt item is present it may not contain the separation character Also note that lt Text gt is not evaluated or used by ODV This item is only included to all
69. DV icon On most systems you can also drag and drop ODV collection odv and var files netCDF files or any supported data import file onto the ODV icon Version 4 5 0 ODV can also be started from DOS boxes or terminal windows by entering the path name of the executable and optional arguments On some systems a script file run_odv is available to start ODV from the command line If you start ODV from the command line the following arguments are supported Note that file and path names including spaces Cd must be enclosed within quotation marks There are two ways of starting ODV from the command line odv4 file view view file or odv4 x cmd_file q The first case opens an ODV collection odv or var collection files or netCDF nc or cdf file file and loads the view from view file view_file The view view_file argument is op tional If it is not provided a default view or the most recently used view is used initially If the ODV binary directory is not in your PATH you have to specify the full pathname of the ODV executable e g c Program Files Ocean Data View mp bin_w32 odv4 on Windows or Applications ODV bin_macx odv4 on Mac OS X systems file has to be an absolute pathname or a path relative to the current directory view_file has to be an absolute pathname or a path relative to the directory containing file The second case opens the ODV command file cmd_file and executes the commands con
70. DV will visit all identified outliers and allows you to delete the respective value or to modify the quality flag associated with the value If you press Apply to All ODV applies the selected operation to all outliers otherwise the user is prompted for an action for each individual outlier Note that the currently edited outlier is marked in the data plots 14 6 Finding Duplicate Stations You can scan the currently valid station set the stations shown in the map for stations with identical or nearly identical positions and times of occupation duplicate stations by choosing Tools gt Find Duplicate Stations Information about the detected groups of duplicate stations is written to a file Specify the maximum allowed differences in time of occupation and geographical position for two stations to be considered duplicates press OK and then select the file that will receive the output of the duplicates search ODV will perform the duplicates search and will write information about detected du plicate station groups to the selected output file The following information is provided for each station 1 station ID 2 cruise label 3 station label 4 station type 5 date and time 6 longitude 7 latitude 8 number of samples 9 deepest sample 120 ODV User s Guide 10 availability indicators for basic variables 2 to nVar e g 7 indicates between 70 and 79 of the samples contain data for a given variable ODV will
71. ESC or right click the mouse to abort the zoom operation Exploring the netCDF file Once all four steps of the netCDF setup wizard are completed ODV draws a station map and lets you explore the data in the netCDF file in the same way as if you were using a native ODV data collection Note that ODV treats netCDF files as read only datasets and never writes to these files Therefore all options requiring data write access are disa bled This also includes all data import options the editing of metadata and data op tions and most collection manipulation options ODV stores netCDF setup settings in view files and uses these settings the next time you open the netCDF file If you want to establish a new setup for an already open netCDF file open the netCDF file again using the File gt Recent Files option Remote netCDF access When working with remote netCDF files data access speed depends on the bandwidth of your Internet connection as well as on the particular type of data request issued Fetching the data of individual stations triggered for instance by clicking on the map can take quite long if the length of the primary variable see above is large This hap pens for instance if the netCDF file contains profile data for thousands of pressure or depth values e g CTD data or time series data with thousands of recorded times e g current meter data In such cases try to avoid clicking on the station map unintention ally to not tri
72. Import the data from all files satisfying file_spec using import route import_type import_type may be one of the following ARGOPROFILES ARGOTRAJECTORIES GTSPP MEDATLASPROFILES MEDATLASTIMESERIES MEDATLASSEDIMENTTRAP WORLDOCEANDATABASE file_spec may be the pathname of a single import file or a wildcard file specification or the pathname of a lst list file containing the pathnames of the files to import file_spec must be an absolute pathname or relative to the base directory specified in a previous set_base_directory command Entries in lst list files must be absolute pathnames Example import_data c data nc ARGOPROFILES load_view view_file Load view file view_file View_file can be a xview or cfg file load_view is equivalent to load_cfg which is still supported for backwards compatibility Example load_view c cfg_files abc xview open_collection collection view_file Open collection collection and load the view view_file The view_file argument is optional Example open_collection c ewoce WoceBtl odv quit Terminate and exit ODV Example quit save_view view_file Save the current view to file view_file View_file must have the xview extension Example save_view c cfg_files abc xview set_annotation_style ptSize textColor bckgrdColor frameColor frameWidth Set the style of text annotations subsequently created with create_annotation ptSize is the font size in points textColor is the color of the text bckg
73. ODV can be used to identify undersea features like seamounts ridges fracture zones troughs basins etc To invoke the gazetteer option choose Extras gt Gazetteer from the map popup menu The gazetteer dialog box is shown which lets you select a specific database lets you specify feature selection criteria as well as size and color of the gazet teer marks drawn by ODV When you press the Switch On button or Update if you have modified the gazetteer settings the information from the selected gazetteer database is loaded and the feature positions are marked in the map Moving the mouse close to a feature point invokes a popup window displaying the name of the feature To switch off the gazetteer marks invoke the gazetteer dialog box again and press the Switch Off but ton A number of gazetteer files are provided with the ODV distribution These include 1 GazetteerGEBCO gzt from the International Hydrographic Bureau IHB 2 Gazet teerBGN gzt from the US Defense Mapping Agency and 3 WHP_Sections gzt which is a compilation of the sections occupied during the WOCE Hydrographic Programme You can select feature subsets by specifying a feature type and or feature name sub string using the gazetteer dialog box Note that the name and type selections are case insensitive Use the gazetteer feature selection if you know the name of a feature or part of the name and want to identify its location note that you might have to open the map to
74. ODV supports the following projections of the X and Y axis 1 Linear the default 2 Logarithmic 3 Stretched Left Upper Part 4 Stretched Left Upper Part strong 5 Stretched Middle Part 6 Stretched Middle Part strong 7 Stretched Right Top Part 8 7 Stretched Right Top Part strong Following below are example figures showing the use of logarithmic and stretched upper Y axis Note the increased resolution in the upper water column in the section plot Display Style On the Display Style page you can switch between the two fundamental plot types of ODV Original data and Gridded field by clicking on the respective item For Original data you may select display types Colored Dots Sized Dots Numbers or Ar rows to obtain colored dots sized dots numerical values or arrows at the measurement locations Specify the size and color of the dots or the font size and color for the numeri cal values in the two fields under Symbol size Note that the selected color is only hon ored in SECTION SCATTER and SURFACE data windows without a Z variable In data windows with Z variable the color or size of the dots is determined by the Z values In STATION windows the different picked stations use different colors These colors are assigned automatically but may be modified by the user at any time The Line width entry is only honored in STATION data windows 88 ODV User s Guide 1000 2000 Depth m
75. OPO1 and GEBCO08 2min packages replace many of the previously existing re gional optional packages and provide equal or even better quality If you only need high resolution map support for a specific small domain it is recom mended to install the ETOPO1 or GEBCO08_2min download on demand packages in stead of the complete packages to reduce download time and storage space Obviously you need a working Internet connection to perform any of the map layer series installations Information on how to use map resources in automatic or manual mode can be found in chapter 9 1 If you have a slow Internet connection and encounter the ODV download time out error please download the package of interest manually using the respective URL below http odv awi de fileadmin user_upload odv coast Baltic zip http odv awi de fileadmin user_upload odv coast ETOPO1_2min_complete zip http odv awi de fileadmin user_upload odv coast ETOPO1_6min_complete zip http odv awi de fileadmin user_upload odv coast GEBCO08_2min_complete zip http odv awi de fileadmin user_upload odv coast GEBCO08_6min_complete zip http odv awi de fileadmin user_upload odv coast IBCAO_2008_complete zip http odv awi de fileadmin user_upload odv coast Kerguelen zip http odv awi de fileadmin user_upload odv coast MeditHR zip http odv awi de fileadmin user_upload odv coast NorthSea zip If you have administrator privileges please unpack the downloaded zip file into lt in 18
76. Ocean Data View User s Guide Version 4 5 0 May 15 2012 Version 4 5 0 Acknowledgements Many users have provided comments suggestions and bug reports and thereby helped to make ODV a stable and useful product Jean Marie Beckers from the University of Liege has assisted in integrating the gridding software DIVA into ODV Stephan Heckendorff and Michael Menzel have contributed significantly to the ODV4 code This includes porting the import routines to ODV4 implementing the SDN file aggregation tool creating the xview functionality as well as adding support for ESRI shapefiles Financial support from the European Commission under FP7 projects SeaDataNet2 EPOCA and CarboChange is gratefully acknowledged 11 ODV User s Guide License Agreement By downloading or using this Software you agree to be bound by the following legal agreement between you and the Alfred Wegener Institute for Polar and Marine Research AWI If you do not agree to the terms of this Agreement do not download or use the Software 1 SCIENTIFIC USE AND TEACHING Ocean Data View can be used free of charge for non commercial non military research and teaching purposes If you use the software for your scientific work please cite Ocean Data View in your publications as follows Schlitzer R Ocean Data View http odv awi de 2012 2 COMMERCIAL AND MILITARY USE For the use of Ocean Data View or any of its components for commercial or milit
77. Overlay Window some properties required for over lay windows will be set automatically and the new window will be properly aligned with the existing one You modify the properties of an existing or new window by right clicking on this window and choosing option Properties To select new variables on X Y and Z axis of the window select the Data page of the Properties dialog and choose appropriate variables in the combo boxes of the different axes Note that by default var iable values increase to the right and upwards If you want to reverse the direction e g depth in depth profiles check the respective Reverse range box Press OK to accept the new properties Note that the properties of the map or any data window may also be changed any time after leaving Window Layout mode see above In addition to manual arrangement of map and data windows you may also implement a predefined window layout by choosing from a wide range of layout templates choose Layout Templates from the View menu or the canvas or window layout popup menus and select one of the templates Right click the mouse and choose Accept to leave Window Layout mode and accept the new window layout Choose Cancel if you want to discard the modification and keep the original window layout 10 5 Graphics Output Printing Choose Print Canvas from the File or canvas popup menus to print the contents of the entire canvas PostScript Files To produce Encapsulated PostScrip
78. Sete a RN A EVO eo 123 15 3 DRAG AND DROP icono daria tddi aint N 125 15 4 ODV COMMAND FILES vous 126 15 5 GAZETTEER OF UNDERSEA FEATURES ccsssssececcceccccesseesceccccccccsasesecccccceecaaeaseces 128 16 APPENDIX did ii 131 16 1 MOUSE AND KEYBOARD ACTIONS ooococcccccnononnninacinncnnononenanenocicnnnnonenanacncconccnonanananinos 131 16 27 QUALITY FLAG SCHEMES crecen a A dada 134 16 3 GENERIC ODV SPREADSHEET FORMAT cccceseececceseccccecteccccsescccceecceccsseseceneners 136 16 4 SUPPORTED DATE AND TIME FORMATS IN ODV SPREADSHEET FILES 00eeceeeeeeee 141 16 5 CONTROL SEQUENCES AND FUNCTIONS IN ANNOTATIONS cococonononononononononononononononononos 143 16 6 GRIDDING METHODS ccc cece cece cesssesecccccccceeesescscecccscsssssscsceccessssususasscsccssssaueneasecsses 144 16 7 ODV DIRECTORY STRUCTURE cccscccccssseccccessececcessececcssseccccscesceceesececeeeeeeeeneners 149 Version 4 5 0 vi ODV User s Guide 1 General Overview Ocean Data View ODV is a computer program for the interactive exploration and graphical display of oceanographic and other geo referenced profile trajectory or time series data The software is available for Windows Mac OS X Linux and UNIX systems ODV data collection and view files are platform independent and can be exchanged be tween all supported systems ODV lets you maintain and analyze large sets of station data on inexpensive and portable ha
79. Temperature C Potential Density Anomaly 00 UM 27s Oxygen mol kg Potential Density Anomaly o0 kg m3 27 4 Delete Edit V Sync Jl S Sync Figure 7 1 The isosurface variables dialog box If an isosurface variable is selected in the Already Defined box you can synchronize all 71 Version 4 5 0 other variables to use the same surface by clicking on the S Sync button surface syn chronization You can synchronize all other variables to use the same display variable by clicking on the V Sync button variable synchronization Calculation of isosurface variables with numeric surface value e g Salinity psu Depth m 500 is performed as follows 1 the samples of the given station are scanned and if one of the samples is found to be close to the isosurface e g Depth m 500 the Salinity value of this samples is used 2 if no matching sample is found during step 1 the available sample Salinity values are used to obtain an interpolated value on the isosurface Before performing the interpolation however the data cover age for the display variable Salinity is evaluated and if gaps between the data are found to be too large no interpolation will be attempted and no isosurface value will be calculated for this station The good coverage criteria that are used to evaluate the sig nificance of gaps may be inspected and modified using option Collection
80. V User s Guide of the selected file import the data from the file and open the newly created data col lection Note that after opening a collection ODV loads the most recent view settings of the col lection These view settings may include station and sample selection filters and as a consequence only a subset of the stations and data values in the collection may be shown in the map and data windows Use View gt Station Selection Criteria or View gt Sample Selection Criteria to reset or modify the selection criteria You may load other previously saved view files using View gt Load View you may change the window layout with View gt Window Layout load one of the pre defined layout tem plates with View gt Layout Templates gt or change the various settings interactively us ing the View menu options or the popup menus that appear when right clicking the mouse while over the canvas area the map or one of the data windows 2 3 Getting Help Pressing F1 or using option Help gt User s Guide opens the ODV User s Guide this docu ment Note that a pdf version of the User s Guide is available on the ODV website Con text sensitive help is provided by pressing the Help button on many ODV dialogs This will invoke the web browser specified under View gt Settings gt Program Locations on Mac OS X odv4 gt Preferences gt Program Locations and the browser will jump to a particular chapter in the User s Guide On Windows context sens
81. View NetCDF Header Help Back Finist Cancel Figure 13 1 The netCDF setup wizard step 1 of 4 Specifying metadata information On the second page of the setup wizard Figure 13 2 you must identify the netCDF var iables that provide metadata such as longitude latitude as well as date and time of the data In many cases ODV can identify and associate the respective variables automati cally Such automatically associated meta variables are marked with an asterisk In some cases it is necessary to modify the automatic settings and establish associations between variables from the netCDF file NetCDF variables list and ODV meta variables 113 Version 4 5 0 Meta variables list manually To establish a 1 to 1 association between a netCDF variable and a meta variable se lect the netCDF variable in the NetCDF variables list and the meta variable in the Meta variables list and press Associate To establish a conversion between a netCDF and ODV meta variable usually needed for netCDF time variables select the two variables as above and then press Convert Choose one of the available conversion options from the combo box and press OK For the General Linear Transformation provide a scale factor and an offset Many netCDF files use relative times given as days or hours since a specific start date You can exploit this information to obtain date and time meta information To do so select the relative
82. Z WINDOW DATA cccccessesececcceccccsssssececececcccssetsceceecceccaaeaesesceeeceeea 54 5 6 EXPORTING REFERENCE DATASETS cccccessesececececcccesessscecececcccsceseseeccesccccaaeaeseecececeeea 55 5 7 EXPORTING ISOSURFACE DATA ceccccccccessssececcceccccssessseececcccccssessececeecceccuaeeseseeeeceeea 55 5 87 CLIPBOARD COPY otitis 55 6 DERIVED VARIABLES ccccccsccccccccccccccccccccccccccccccccccsccccccsccccecees 57 6 1 BUILT IN DERIVED VARIABLES sscccccseececcccsecccccscceccntsecccatssceceuseseceeansesecaaeseeeeens 57 Gila E OE PRE iras 64 6 3 EXPRESION Sisi dl des 66 6 4 DIFFERENCE VARIABLEG s sececccssececcccescecenssccccassscecensesecccatsecccateseceeausscsceaaeeeeeeees 68 6 01 PATCHES Sa a e Aah ection teat ae de duct Rien ido dates Bile da 68 7 ISOSURFACE VARIABLES cccccccccccccccccccccccccccccccccccccscccccsccccceees 71 7 1 DRAWING ISOSURFACE VARIABLES ccccccesceccccesceccccscececcscecccsescecccsseeccesesecceaneneeees 72 8 SELECTION CRITERIA leia 73 S 1 STATION SELECTION CRITERIA da taco ad doo 73 8 2 SAMPLE SELECTION CRITERIA csceccccccsececcccsecececsscceccnsesecccensceccasesecceausecccaaeseseeees 75 9 STATION MAP 0 cion asa 77 or MAP PROPERTIES a onto nec en ena le cado e al O BS 77 IZ UPIGRED STATION Siecoes td dit os cane dai so dada 81 TS SECTIONS edson acid eto 81 9 4 STATION DISTRIBUTIONS ccccsseec
83. _ Variable Association Source file variables SECT_ID CASTNO SAMPNO BTLNBR BTLNBR_FLAG_W DEPTH METERS CTDPRS DBARS CTDPRS_FLAG_W CTDTMP ITS 90 CTDTMP_FLAG_W CTDSAL CTDSAL_FLAG_W SALNTY SALNTY_FLAG_W CTDOXY UMOL KG CTDOXY_FLAG_W 13 out of 56 variables used x v Check for existing stations CCL4 PMOL KG CFC113 PMOL KG Target collection variables DEPTH M a CTDTMP degrees C SALNTY PSS 78 OXYGEN UMOL KG PHSPHT UMOL KG SILCAT UMOL KG NITRAT UMOL KG NITRIT UMOL KG CFC 11 PMOL KG CFC 12 PMOL KG SF6 FMOL KG TRITUM TU DELHE3 PERCNT HELIUM NMOL KG X 13 of 53 variables associated Figure 4 3 The Import Options dialog Add Replace Station Data Choose this option if you want to add data from the im port file to the collection If the Check for existing stations box is checked ODV searches the collection for stations with the same name date and position and if found asks for permission to replace the existing station in the collection with the new version from the import file see Station and Sample Matching Criteria below for a description of the station search procedure Merge Data selected variables Choose this option if you want to add data for one or more variables merge variables and leave existing data for other variables unchanged A merged value of a merge variable at a g
84. abine C L Christian J R 2007 Guide to best practices for ocean CO2 measurements PICES Special Publication 3 1 191 Lavigne H A Proye J P Gattuso 2008 SeaCarb Calculates parameters of the seawater carbonate sys tem R package version 2 1 http www obs vlfr fr gattuso seacarb php Version June 10 2009 Lewis E and D W R Wallace 1998 Program Developed for CO2 System Calculations ORNL CDIAC 105 Carbon Dioxide Information Analysis Center Oak Ridge National Laboratory U S Department of Energy Oak Ridge Tennessee http cdiac ornl gov oceans co2rprt html Vertical Derivative Select the variable for which the vertical derivative is to be calculated designated A in the following any basic or already defined derived variable can be used The calcula tions proceed in three steps 1 the observed values of A are interpolated onto a set of densely spaced standard depths 2 vertical derivatives are calculated at the standard depth mid values 3 the vertical derivatives values are interpolated back to the origi nal sample depths Note that before starting the calculations ODV verifies that the sta tion contains sufficient data by checking the Good Coverage Criteria and excludes sta tions with large data gaps Vertical Integral Select the variable for which the vertical integral is to be calculated designated A in the following any basic or already defined derived variable can be used and specify the
85. acing large aver aging length scales are applied automatically This approach of spatially varying length scales allows resolving small scale features in areas of dense data coverage and at the same time provides smooth and stable fields in other regions with sparse data coverage The user provided length scales Lxo and Lyo on the Display Options dialog are measured in per mille of the respective axis range and are representative for the area of poorest data coverage coarsest grid The ODV implementation of the weighted averag ing algorithm is highly optimized for speed to allow field estimations within a few se conds even for fields with thousands of data points Once estimates have been obtained for all grid points the field is passed to shading and contouring routines for display on the screen or a printer 16 6 2 DIVA Gridding Integration DIVA is a gridding software developed at the University of Liege http modb oce ulg ac be projects 1 diva that offers a number of advantages over the weighted averaging methods built into ODV DIVA allows analyzing and interpolat ing data in an optimal way comparable to optimal interpolation OI Unlike OI DIVA also takes into account coastlines and bathymetry features to structure and subdivide the domain on which estimation is performed Calculations are optimized and per formed on a finite element mesh adapted to the specific gridding domains The DIVA tools to generate the finite element mes
86. ack Operands and operators must be separated by one or more spaces You may continue the definition of the macro expression on following lines if necessary The evaluation of macro formulas is implemented using a simple stack based scheme 1 operands constants or variable values e g 1 2 etc 0 1 etc H Mt d x and y are added at the top of the stack as they appear 2 operators In etc take their operands from the top of the stack and push the result of the operation back at the top of the stack At the end of a successful calculation the only element remaining on the stack is the fi nal result Table 6 2 Example expressions Postfix Expression Meaning 135 1 2 PO 135 POs O2 with PO as 1 and O2 as 2 t 80 17 6 exp 1 e esos tritium decay correction to 1980 cas 1 1 In In 1 natural logarithm 1 In 0 43429 log 1 base 10 logarithm 0 1 max max 0 1 maximum value 6 3 Expressions Expression derived variables are similar to macros They can be defined and edited with the ODV macro editor and they use the same syntax and operator set To set up an 66 ODV User s Guide expression select Derived Variables from the current sample window popup menu choose Expression from the Choices list and press Add ODV will show a dialog similar to the macro editor dialog You should enter the label of the new variable and the corr
87. aging ODV can be used to estimate values of any basic or derived variable at arbitrary longi tude latitude depth points 3D point estimation 3D point estimation is implemented as a fast weighted averaging procedure and uses the currently valid station and sample set together with user specified longitude latitude and depth averaging length scales The coordinates at which estimation is requested are provided in ASCII files The points can be irregularly spaced or may form a uniform or non uniform rectangular or curvi linear grid You invoke 3D point estimation from the main menu through Tools gt 3D Es timation For data windows with a Z variable another method 2D point estimation can be used to estimate Z values at arbitrary X Y points As for 3D estimation the X Y coordinates are provided in ASCII files The points can be irregularly spaced or may be on a uniform Version 4 5 0 or non uniform rectangular or curvilinear grid Choose Extras gt 2D Estimation from the respective data window popup menu to invoke 2D point estimation A third estimation method 1D Estimation is available for data plots that have the pri mary variable on their X or Y axis For every station contained in the plot this option allows estimation of the other variable at user specified values for the primary variable These user specified coordinates have to be provided in ASCII files one coordinate per line The results of the estimation one requested s
88. alinity Any pressure values in GTSPP files are converted to depth during import GTSPP collections have an additional metavariable called Data Type This variable holds information about the instrument type or type of IGOSS radio message used You need ODV version 4 4 2 or higher to access this information Previous versions do not display these values GTSPP data quality flags in the netCDF file are recognized and converted to the quality flag schemes of the target variables during import If the target collection is a GTSPP collection recommended created by ODV4 or later no quality flag conversion occurs and the original GTSPP quality flag values are stored in the collection For details of the quality flag mapping see the file ODV4_QualityFlagSets pdf Once imported you may filter the data and exclude bad data from the analysis by set ting appropriate quality flag selection criteria via the View gt Sample Selection Criteria option 4 6 WOCE Hydrographic Data You can use ODV to import original hydrographic data in WHP exchange format into existing or new data collections WHP exchange format data files can be found at the WHP DAC http whpo ucsd edu or on the final WOCE data release on DVD ROM To import the data into an existing collection open the collection To import into anew collection create the collection and make sure you choose either WOCE WHP Bottle var iables or WOCE WHP CTD variables when defining the variables to be sto
89. ame locale country however non ASCII characters likely display incorrectly on different platforms or in different countries ASCII only text should always be used for the sake of platform independence of data collections The maximum number of bytes that can be stored per value of a text data variable byte length is fixed and must be specified at collection creation time The actual requested byte length must include one extra byte for text termination If for instance a text vari able must be able to store 40 characters of text the requested byte length must be 41 The byte length of a text variable cannot be smaller than 2 and is otherwise arbitrary Choosing large byte lengths such as 5001 accommodates long texts but also leads to large collection files because all individual text values occupy the specified number of bytes If a given text value represents a DOI or a URL of a website ODV will allow click ing on the value and will open the DOI or URL in a web browser Using URLs or DOIs should be considered as alternative to using large amounts of text directly 16 4 Supported Date and Time Formats in ODV Spreadsheet Files ODV supports the single column ISO 8601 date time format This is the recommended date time format for ODV import and export files In addition ODV also supports a wide range of other date and time formats to allow easy import of data provided in one of the many custom file formats commonly used in the scientific
90. ange of the sample selection criteria range and quality filters Ctrl 0 Opens the general settings dialog Mac only ESC Aborts the current operation if supported by operation In window layout mode cancels all layout changes made and returns to normal mode Ctrl Q Mac Alt F4 others Exit ODV 1 On MacOSX systems hold down the Apple key while pressing the other key 2 On MacOSX systems hold down the fn key while pressing the function keys The fn key is not necessary if you check the Use all F1 F2 etc keys as standard function keys box in the keyboard tab of the Mac system preferences 133 Version 4 5 0 Table 16 3 Mouse and key press actions in Zoom or Z Zoom modes Action Object Response L Drag L DbleClick or Boundaries and corners of zoom rectangle Resizes the zoom rectangle anywhere Accepts current settings and terminates zooming ENTER R Click or ESC anywhere Discards changes and aborts zooming 1 On Mac OS X systems with a single button mouse hold down the Alt key while clicking the mouse to simulate a right mouse button click Table 16 4 Mouse and key press actions in GetPoints modes Action Object Response L Click Canvas Map Data Win Add current point to list dow R Click Canvas Map Data Win Remove closest point from list dow ENTER anywhere Accept current settings and terminate GetPoints ESC an
91. ariable as well as sample data values may be missing Schematic summaries of station metadata and data arrays maintained by ODV are shown in Tables 3 1 and 3 2 Table 3 1 Station metadata values v and quality flags q maintained by ODV Meta variable values may be either text or numeric The total number of meta variables m is unlimited Metavar Metavar2 Metavarm Station QF V1 q1 V2 q2 Vin qm q Table 3 2 Station data values and quality flags maintained by ODV Values of collection variables must be numeric text entries are ignored The minimum number of collection variables is two the total number n is unlimited The number of samples k is unlimited One of the collection variables is defined as primary varia ble Samples are sorted in ascending order of primary variable values Sample Var Varz cor Varn ar Smpl V11 q11 V12 q12 Vin din q1 Smpl V21 q21 Vaz q22 Van q2n q2 Smplx Vk1 041 Vk2 qk2 Vin dkn qk 22 ODV User s Guide 3 1 1 Meta Variables ODV requires availability of some types of metadata for its basic operation The geo graphic location of a station for instance must be known to be able to plot the station in the station map Date and time of observation or the names of the station and cruise or expedition it belongs to are needed to fully identify the station and to be able to apply station selection filters that only allow stati
92. ary applications and products a special written software license is needed Please contact the address below for further information 3 REDISTRIBUTION Redistribution of the Ocean Data View software on CD ROM DVD or other electronic media or the Internet is not permitted without the prior written consent of the AWI Please contact the address below for further information 4 WARRANTY DISCLAIMER THE ODV SOFTWARE IS PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU SHOULD THE SOFTWARE PROVE DEFECTIVE YOU ASSUME THE COST OF ALL NECESSARY SERVICING REPAIR OR CORRECTION IN NO EVENT WILL AWI ITS CONTRIBUTORS OR ANY ODV COPYRIGHT HOLDER BE LIABLE TO YOU FOR DAMAGES INCLUDING ANY DIRECT INDIRECT GENERAL SPECIAL EXEMPLARY INCIDENTAL OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE OR BUSINESS INTERRUPTION 1990 2012 Reiner Schlitzer Alfred Wegener Institute Columbusstrasse 27568 Bremerhaven Germany E mail Reiner Schlitzer awi de Version 4 5 0
93. athematical expressions in normal infix notation and conversion to postfix for use in ODV expressions and macros You can use the operators for the basic arithmetic operations sqrt for the square root min and max for minimum and maximum of two operands In and exp for the natural logarithm and exponential sin cos tan and cot for sine cosine tangents 65 Version 4 5 0 and cotangents arguments in radians arcsin arccos arctan and arccot for the in verse sine cosine tangents and cotangents result in radians abs for the absolute val ue and int floor ceil for integer parts of the argument respectively You use terms of the form 1 2 etc to reference the values of the respective input variable Use the term H for the elevation at the station position given in meters above sea level positive for land and negative for ocean t for the time of observa tion in years since 1900 calculated from station date and time metadata e g t 84 4877 for June 27 1984 d for the day of the year also calculated from station date metadata x for the east longitude and y for the north latitude respec tively You can store intermediate results of the calculations in internal variables 0 1 etc using the operators 0 1 etc Stored values can be used later in the calculation by typing 0 1 etc Note that the n operators consume their operands e g the re spective value is taken off the st
94. athymetry No bathymetry Station bottom depth 9 File A7_bathymetry gob Mean Width Bathymetry Color 200 00 km Mio y Figure 9 7 The Section Properties dialog You can save the current section in a file by choosing the Manage Section gt Save Section As option You can load saved sections later by choosing Manage Section gt Load Section Select Manage Section gt Remove Section to remove a section Note that all stations inside the section band marked in the map belong to the section The data of all these stations are plotted in SECTION data windows CFC 11 pmol kg 1000 2000 3000 4000 5000 Ocean Data View Data C Andrie LODC Paris 6000 30W 20 W 10 W 0 10 E Figure 9 8 Section using shipboard bathymetric data for the section bathymetry polygon 83 Version 4 5 0 9 4 Station Distributions You can produce plots of the spatial and temporal distributions of the stations in the map by choosing Extras gt Statistics from the map popup menu or by pressing F4 while the mouse is over the map The Map Statistics dialog will appear that lets you view the distributions of the currently selected stations in the map versus time or season press buttons Time Histogram or Season Histogram respectively The histograms are shown in separate dialog windows see Figure 9 9 You may save the graphics in GIF PNG JPG or Encapsulated PostScript files by pressing Save As and choosing
95. average curves You may choose one of these curve types from the top combo box of the Fitted Curves group Then choose an orientation for the fit in the example of Figure 10 7 we want oxygen as a function of depth e g X Y For curve types 2 and 3 you may also specify the number of points at which the curve will be evaluated default 30 choose a larger value for smoother curves For moving average curves type 3 you may specify an averag ing length scale in per mille of the axis range of the variable between parenthesis e g Y Depth in Figure 10 7 Large averaging length scales will result in smooth small val ues will preserve more of the structure in the data Press Construct Curve to have the curve calculated and the results displayed in the box to the right These results may be copied to the clipboard by pressing Clipboard Copy and then pasted into other docu ments or applications for external use You may also add the constructed curve to the data window by pressing Show Curve Note that the curve is added as a polyline graphics objects which means that you can edit or delete the object at any time using the normal graphics object s procedures 2000 1500 7 3 S Count 1000 Depth m s S s 500 4 s S 300 100 200 100 200 Oxygen umol kg Oxygen umol kg Figure 10 8 The data distribution histogram for oxygen left a
96. ays e g Oct 20 Feb 03 or 21 09 04 15 are acceptable season and day time ranges In the Domain category you can define a rectangular sub domain of the map by specify ing respective longitude latitude values or you can press the Zoom button to define a rectangle by zooming You can define a polygon as the valid domain by pressing the Pol ygon button and then entering the vertices of the polygon with the mouse Note that the 74 ODV User s Guide polygon is closed automatically On the Meta Data tab you may specify ranges for numeric meta variables and wildcard patterns for text meta variables To enter a specification first click on the combo boxes containing the lists of variables choose your variable of interest and then specify the acceptable value range or the wildcard pattern See Table 8 1 for asummary of possible wildcard patterns In the Availability category you can mark one or more variables for which data must be available for a station to be considered valid On the Invert tab you can invert the station selection e g all stations that do NOT satis fy the criteria will be selected if the Invert Selection box is checked Pages containing active station selection criteria have an asterisk appended to their page name and are easily identified To remove the selection criteria of a given page click on the respective page title and press the Relax Criteria Map Domain or None Re quired buttons Note that
97. be either nc or cdf by dropping the file on the ODV icon or window or by choosing File gt Open and selecting the file in the standard file selection dialog Once a netCDF file has been opened before you can also use the File gt Recent Files option to access the file Additionally you can start ODV from the command line and specify a netCDF file name as a command line argu ment You open a netCDF file on a remote OPeNDAP server by using option File gt Open Remote and entering the URL to the netCDF file example http motherlode ucar edu 8080 thredds dodsC testdods coads_climatology nc URLs to public climate data resources in netCDF format can be found on the Internet for in stance at http www esrl noaa gov psd thredds catalog ODV opens the netCDF file and retrieves information about dimensions and variables contained in the file ODV will also retrieve all global attributes and all attributes of the variables and will write this information to an ASCII file in a format similar to what ncdump h lt file gt produces This file can be viewed by clicking the View NetCDF Header button on the first page of the setup wizard see below or at any time using the Collec tion gt Browse Info File option 112 ODV User s Guide 13 2 NetCDF Setup Once the netCDF file has been analyzed ODV presents a four page wizard to gather nec essary information Selecting netCDF dimensions On the first page of the setup wizard Figure 13 1
98. by means of the PalEdt exe program in the ODV binaries directory PalEdt exe can be invoked from ODV by choosing Tools gt Palette Editor 15 2 Animations ODV lets you produce animated GIF files of the map or any data window by right clicking on the respective window and choosing Extras gt Animation and one of the sub options Metadata Time Metadata Time of Year Validate Variable or Ex tras gt Animation gt Isosurface Then follow the instructions below 1 Metadata Time Specify a start date to the interval step dt in days the number of frames n to be pro duced and the interval type ODV will then construct n time intervals and use the re spective start and end dates for the Date Time gt Period station selection criteria Depending on the selected interval type the start and end dates of interval i i 0 n 1 are defined as follows 123 Version 4 5 0 Interval Type Start of Interval i End of Interval i Zero Width t t i dt i dt Fixed Width t i dt t i 1 dt Fixed Start fy by i 1 dt Fixed End i dt lo n dt For each such time interval the map will be re build including only those stations with metadata dates in the respective time window If the animation is for a data window this data window will also be redrawn using data from the currently selected station set only The current map or data window will then be added to the animation file 2 Metadata Time o
99. ced ODV then shows the list of basic and derived variables and lets you choose one or more variables for the averaging procedure The box definition file has to be pre pared prior to invoking the Box Averaging option The format of the box definition file is as follows e plain ASCII one box definition per line 6 numbers separated by one or more spaces e meaning of numbers see figure lon lat dep box center Aion Arat Adep box sizes Lon gitudes and latitudes are in decimal degrees and depth is in meters Once you have specified a box definition file ODV will start working Note that while averaging ODV will check for data outliers and will use only data within 3 standard de viations of the mean The output will be written to the directory of the box definition file The output file names consist of the box definition file name the label of the varia ble that is processed and the extension est The format of the est output file is as follows e plain ASCII one line of output per line in the box definition file 10 values sepa rated by TABS e meaning of values lon lat dep same as in box definition file Jon lat dep val nu nr lon lat dep val are average longitude latitude depth and variable values of the data 119 Version 4 5 0 used o is the standard deviation of the variable values ny is the number of data points used and n is the number of data points rejected Note that the error of the
100. chosen variable 124 ODV User s Guide Depending on the selected interval type the start and end values of interval i 0 n 1 are defined as follows Interval Type Start of Interval i End of Interval i Zero Width Vo i dv Vo i dv Fixed Width Vy ti dv Y i 1 dv Fixed Start Vy Vo i 1 dv Fixed End Vy i dy y tne dy For each such interval the data window will be redrawn including only those data from the respective variable value interval The current data window snapshot will then be added to the animation file 4 Isosurface This option is available for isosurface data windows only Select a start value so the in terval step ds and the number of frames n to be produced ODV will then construct n isosurface values and will re build the data window for each such value The current data window snapshot will then be added to the animation file For all animations ODV will draw an animation bar indicating the current animation interval The animation bar is centered below the respective window 15 3 Drag and Drop On most supported platforms you can drag and drop ODV supported files on the ODV window or icon Depending on the extension of the dropped file ODV will perform the following actions odv or var close current collection or netCDF file and open the dropped collection nc or cdf close current collection or netCDF file and open dropped netCDF file txt ODV
101. ck for existing stations box is checked you may click on the Edit Matching Criteria button to customize the tests that are performed to determine whether a station from the import file matches one of the existing stations in the target col lection Station Matching page see Figure 4 4 You will also be able to modify the criteria for matching the samples of the import and target stations Sample Match ing page Sample matching is performed during Merge Data selected variables and Update Data selected variables imports only On the Station Matching page you can switch on or off various tests that compare position date time and names of import and target stations The two stations are considered to match if all requested tests succeed For Longitude Latitude and Time a match is obtained if import and target values agree within the specified tolerances a na A Matching Criteria O N Matching Criteria Station Matching Station Matching Sample Matching Matching of an import sample at a DEPTH M value Z is done by finding the target Checks Tolerances station sample closest to Z This closest target sample is accepted if the Z difference is Y Longitud 0 1000 2 smaller than tol Z Non matching import samples are added to the target station if the ongktude d Y Add non matching samples as new samples box is checked y Latitude 0 1000 Y Time 1 0000 days v Station label i tol Z max 10 0000
102. collections and the ex ported datasets may easily be re imported into the same or a different collection possi bly after editing and modifying the data in the file Exporting data from the open collec tion into a generic spreadsheet file is done via the Export gt ODV Spreadsheet option ODV generic spreadsheet files use the ASCII encoding and the preferred file extension is txt Station metadata and data are provided in separate columns where metadata and data columns can be in arbitrary order Every metadata and data column may have an optional quality flag column A quality flag column may appear anywhere after the metadata or data column it belongs to Quality flag values may be in any one of the sup ported quality flag schemes see Table 16 5 The total number of columns in the file is unlimited All non comment lines see below in the file must have the same number of columns Individual columns are separated by TAB or semicolon Typically ODV spreadsheet files hold the data of many stations from many cruises The number of lines in a file as well as the length of individual lines is unlimited There are three types of lines in ODV generic spreadsheet files 1 comment lines 2 the column labels line and 3 data lines 16 3 1 Comment Lines Comment lines start with two slashes as first two characters of the line and may con tain arbitrary text in free format Comment lines may in principle appear anywhere in the file
103. community This includes many date and time specifications that differ in the order of the day month year values and cases with day month year hour and minute data in individual columns Use of the column labels in Table 16 8 is strongly recommended lower upper or mixed case as this allows automatic date time identification by ODV The default date time format in ODV spreadsheet output files is ISO 8601 141 Version 4 5 0 Table 16 8 Supported date formats column labels may be upper lower or mixed case Column label Comment yyyy mm dd hh mm or yyyy mm ddThh mm or yyyy mm ddThh mm ss sss ISO 8601 Recommended ODV date time format Com bines date and time in a single column Examples 2006 02 23 10 23 or 2006 02 23T10 23 for Feb 23 2006 10 23h Time xxx since yyyy mm dd Date and time as a decimal value in units of xxx days or years since the specified reference date yyyy mm dd Example Time days since 2012 01 01 1 5 for Jan 02 2012 12h d tonya yE Date in one column Time provided separately g Example 02 23 2006 for Feb 23 2006 mm dd yyyy dd Date in one column Time provided separately mm yyy Example 23 02 2006 for Feb 23 2006 T Date in one column Time provided separately yyyy mm Example 2006 02 23 for Feb 23 2006 Date in one column Time provided separately mmddyyyy Example 02232006 for Feb 23 2006 Date in one column Time provided sepa
104. created list file As before you then specify import op tions and press OK to start the data import ODV will read all the files listed in the list file and will import all stations into the currently open collection Please note that WOD data have been quality controlled and often contain significant amounts of data that have been flagged by data originators or by the U S NODC as being of poor or questionable quality ODV imports and maintains the data quality infor mation in the WOD files and automatically maps WOD quality flags to the quality flag scheme used in the target data collection If the target collection was created using World Ocean Database variables the collection variables use the WOD quality flag scheme and the original WOD quality flags in the import files will be maintained in the ODV collection When viewing the data you should consider applying data quality fil ters via option View gt Sample Selection Criteria to exclude questionable and bad data from the analysis 4 4 ARGO Float Data You can use ODV to import float profile and trajectory data from single or multiple ARGO netCDF version 2 2 or 2 1 format files into ODV float profile or trajectory data 39 Version 4 5 0 collections ARGO files can be downloaded from the Coriolis and GODAE data centers at http www coriolis eu org cdc argo htm and http www usgodae org argo argo html ARGO profile or trajectory data should be imported into data collection
105. ction information prj file is written all geographic coordinates are assumed WGS84 c except for symbol sets no attribute dbf file is written for symbol sets the legend string is written to at tribute Name d all objects are written to the first and only layer multiple layers are not supported 102 ODV User s Guide 12 Working with Collections 12 1 Copying Renaming and Deleting Collections You can create a copy of the currently open collection using Collection gt Copy you re name and possibly move the currently open collection using Collection gt Move Rename and you delete the currently open collection using Collection gt Delete Note that view and section files associated with a deleted collection may have to be deleted manually 12 2 Sorting and Condensing The station search and selection algorithms of ODV work most efficiently if the stations in a collection are ordered by cruises Therefore it is recommended that you sort and condense your collections after importing replacing merging or deleting large numbers of stations You invoke the sort and condense procedure by choosing Collection gt Sort and Condense 12 3 Deleting Stations You can delete the currently selected stations from the collection by choosing Collec tion gt Delete Station Subset from ODV s main menu To delete the current station only choose Collection gt Delete Current Station Note that the data space of the deleted sta tions in
106. ctions and cfg configuration files created with previous versions of ODV When creating new collec tions however ODV4 will use the new ODVCF5 format providing all the new features and allowing for more flexibility in the definition of meta and collection variables 3 1 Data Model ODV can handle a very wide range of data types such as profile data ocean atmos phere lakes marine and lacustrine sediments ice sheets etc or time series data from fixed or drifting stations in the ocean on ice floats or on land The fundamental data entity handled by ODV is the station representing a 2D table of data obtained for a specific sampling event at a given geographical location and date and time ODV collates the data of a potentially very large number of stations in ODV data collections Users typically open a data collection and work with the station data in this collection Collections are expandable and new data can be appended at any time Stations are described by a number of metadata items meta variables such as cruise and station names or space and time coordinates An unlimited number of additional descriptive meta variables may also be included Meta variables may store numeric val ues or text In addition to the metadata each station also contains a 2D table of data consisting of one or more lines and two or more columns Table 3 2 Every line holds the data of one sample and every column represents one of the collection var
107. d O represents the orientation N S E or W 6 Date and Time must be labeled as UTC Time 7 Date and Time must follow the format MMM dd yyyy hh mm ss where MMM represents the month abbreviation in English e g May Please note that if longitude or latitude could not be detected in a Sea Bird CNV file the data of that file will not be imported If the cruise and or station name could not be found ODV assigns unknown and the file s name respectively 45 Version 4 5 0 4 9 Associate Meta Variables Dialog When importing data ODV will try to automatically detect the sources in the import file for mandatory metadata such as cruise and station names date of observation and ge ographical location Ifthis automatic association of meta variables is not successful the Associate Meta Variables dialog appears see Figure 4 2 asking the user to identify the sources of metadata manually To define a new association select items in the Source Variables and Meta Variables lists and press Associate To invoke a conversion during import press Convert and choose one of the available conversion algorithms To delete an existing association select the respective variables and press Undo If the import file does not contain information for a given meta variable you can specify a default value as follows 1 select the respective meta variable 2 press Set Default and 3 enter the default value Note tha
108. d isosurface varia bles To delete one or more existing isosurface variables select them in the Already De fined list and press Delete To add a new isosurface variable first construct the new vari able inside the New box and then press Add Constructing an isosurface variable re quires specification of 1 the variable to be displayed on a given surface display varia ble 2 the variable that defines the surface surface variable and 3 the value of the surface variable on the surface Instead of a numeric value defining the surface you may also enter the keywords first or last entering the first characters for is sufficient In these cases the first or last non miss value of the display variable is used as isosurface value first or last according to the sort order of the primary variable values If derived variables such as potential density or pressure are used as display or surface variable of an isosurface variable they must be defined first before invoking the Isosur face Variables dialog The number of isosurface variables is unlimited Isosurface varia ble values for the current station are shown in the Isosurface Data Window r Isosurface Variables New Oxygen umol kg y Potential Density Anomaly 00 ka m3 27 v Add Already Defined Temperature C Depth m 500 a Salinity pss 78 Depth m 500 Oxygen ymol kg Depth m 3000 Phosphate ymol kg Depth m 3000 h 00
109. de bles default 20 characters The use of numbers for station labels will enable enhanced internal sorting and selection functionality and is recommended Station Type is a single character string You should use B for stations with less than about 250 samples e g bottle data and C for stations with more than about 250 sam ples e g CTD XBT etc Specifying for Type lets ODV make the choice If Bot Depth values are not available you should leave this field empty The station metadata must be provided on the first line of a given station The metadata fields on the remaining lines of the station may remain empty to reduce file size com pact spreadsheet format An ODV generic spreadsheet file usually stores the data of many stations from many cruises The metadata and data of the first sample of the next station follow immediately after the last sample of the previous station There are no separator lines between stations Numeric values may have periods or commas to indicate decimals e g 2 57 or 2 57 are both valid entries If entries are enclosed in double quotes these are automatical ly removed before processing Data variables of type TEXT use a one byte per character encoding ODV collections re main platform and country independent if the text values are strictly confined to the ASCII character set codes 0 126 Usage of non ASCII characters will work fine on the same platform and within the s
110. de system in sea water The following parameters of the carbon dioxide system in sea water are provided as derived variables 1 Alkalinity Dissolved Inorganic Carbon DIC Fugacity and partial pressure of CO fC02 and pCOz Concentrations of CO 2 CO32 and HCOy pH on Total SWS or Free scale Revelle or homogeneous buffer factor Solubility ratios C0O32 Ca2 Ksp for calcite and aragonite Omegac and Ome gaa A O All these quantities can be calculated using one of the following carbon input data pairs ALK DIC ALK pH ALK fCO2 ALK pCO2 DIC pH DIC fCO2 DIC pCO2 fCO2 pH pCO2 pH SN AAA ee 61 Version 4 5 0 You define one of these carbon parameters by choosing the respective entry in the Choices list of the Derived Variables dialog and pressing Add The carbon parameter set tings dialog in Figure 6 1 appears which lets you define various settings for the requested variable The Equilibrium constants combo box allows choosing among different equilibrium con stants from the literature to be used in the calculations the Input box allows specifying the data input pair as well as the conditions at which the input data were measured and the Out put box allows specifying output conditions at which the requested variable is to be calculat ed Depending on the type of variable requested and depending on the chosen Input varia bles some of the entries are not relevant and are hidden If
111. derived variable choose any other item in the Choices list 6 1 Built in Derived Variables Algorithms for many physical oceanographic parameters such as potential tempera ture potential density relative to arbitrary reference pressures neutral density Brunt Vaisala Freqency and dynamic height are built into the ODV software In addi tion various parameters of the carbon dioxide system in seawater the saturation con centrations and partial pressures of many gases and many other variables from chemi cal oceanography are also available as easily selectable derived variables Some useful mathematical expressions such as the ratio of two arbitrary variables as well as vertical integrals and derivatives are also available The Physical Properties TEOS 10 derived variables group new in version 4 4 2 re places previous EOS 80 based variables and adds more than 20 new variables Refer ences to previous EOS 80 based variables in cfg and xview files are automatically mapped to the new TEOS 10 replacements Complete lists of available built in derived variables are shown below All these varia bles can be requested by the user ODV will calculate values for all requested derived variables when station data are loaded into memory Requested derived variables can be used and visualized in the same way as the basic variables stored in the collection files To define or delete built in derived variables choose the Derived Variables option
112. ding method using the same parameter settings that are also used for generat ing the window s gridded field shown on the screen As for the gridded field the results at the user specified X Y positions depend on the magnitudes of the gridding averaging length scales large length scales result in smooth fields whereas small scales allow maintaining small scale features in the data Also note that the length scales are specified in per mille of the current X and Y ranges Changing the axis ranges by zooming in or out may lead to changes of the averaging length scale values which will also affect the 2D Estimation results Use the data plots Properties dia log to adjust the length scales until you are satisfied with the distribution displayed in the data window Then invoke the Extras gt 2D Estimation option ODV will prompt you for a file called input file in the following with the X Y coordi nates of the points for which estimation is requested This file has to be prepared prior to invoking the 2D Estimation option It has to be in plain ASCII format with one X Y co ordinate pair per line and the X and Y values must be separated by one or more spaces or TABs The number of points or lines is unlimited For each point in the input file ODV will estimate a Z value and will write the estimated values together with the re spective X and Y coordinate to an output file Name and location of the output file may be specified by the user The defau
113. display modes ODV allows the export of window data and gridded fields to ASCII files or the clipboard for subsequent use out side ODV Depth m Sigma 0 kg m 27 2 Depth m Sigma 0 kg m 27 2 400 40 S z 3 3 E z Ocean Data View 60 S Z0 5 60 W 40W 20 W 0 20 E 60 W 40 W 20 W 0 20 E Figure 1 1 Data displayed as a colored dots and b gridded field In addition to scalar property fields ODV also supports the display of vector fields for datasets providing the X and Y vector components as distinct variables see Figure 1 2 FSU Psuedostress January 1978 4 Lis fue seer he ARERR ARRE EELEE Harris CTEM RE RT TT SUIS SITET TREE f f OMB OEE Eh Figure 1 2 Arrow plot of historical wind field Version 4 5 0 1 6 Window Scopes The ODV application window always displays a map of available stations In addition the user may define an unlimited number of other windows for the display of the actual data Each of these data windows can have one of the following scopes STATION SCATTER SECTION or SURFACE Each window has its own scope and the scopes of the different data windows may be different 1 6 1 STATION Scope A STATION scope window see Figure 1 3 provides a X Y plots showing only the data of stations in the map s pick list You can add the current station to the pick list by pressing ENTER or you can remove it by pressing the Delet
114. diterranean and Black Sea database of tempera ture salinity and bio chemical parameters Climatological Atlas IFREMER Edition 4 CDs The Medatlas format is also used for various types of time series data ranging from current meters thermistor chains sea level gauges meteorology buoys to sedi ment traps ODV lets you import all these diverse data types Because variable sets for the different data types differ greatly it is essential to ensure that the receiving data collection uses a matching set of variables There are predefined variable sets for Medatlas bottle and CTD profile data as well as two variable sets for time series data one for sediment trap data and one for all other time series data When creating new collections for Medatlas 42 ODV User s Guide data the user should choose the appropriate variable set see below Medatlas formatted data can be imported into arbitrary ODV data collections however manual associations of Medatlas import variables with the collection target variables are usually required Note that Time in Medatlas time series collections is always pro vided as years since 1900 01 01 00 00 It is not possible to use other units e g days or use a different reference date To facilitate data import and avoid manual variable asso ciations you should create target collections using the appropriate Medatlas variables sets To create such collections use the File gt New option When prompted to
115. e sponding units in the Label and Units fields Then select the input variables required by the new variable e g select a variable in the Choices list and press lt lt Finally specify the expression to be evaluated for the new quantity See the paragraph Expression un der Macro Editor for a description of supported operators and general syntax guide lines Press OK to finish the setup of the new expression You can edit ODV macros and expressions by using the Derived Variables option from the current sample window popup menu Then select the respective variable in the Al ready Defined list box and press Edit You can save an expression in an ODV macro file by pressing Save As on the Edit Expression dialog la s E a le A Label Units Digits NO m mol kg 3 E Input Variables Defined Choices 1 Nitrate umol kg Depth m a 2 Oxygen umol kg Temperature C p Salinity pss 78 l Oxygen umol kg Phosphate mol kg Silicate umol kg Nitrate umol kg Nitrite umol kg CFC 11 pmol kg CFC 12 pmol kg Pot a toii Expression in Postfix Notation 9 1 2 4 Operands 1 9 0 9 t Time d Day of Year x Longitude y Latitude H Height Operators abs arccos arccot arcsin arcttan ceil cos cot exp floor int In min max sin sqrt tan 0 9 Help Save As Figure 6 3 The edit expression dialog 67 Version 4 5 0 6 4 Differ
116. e SDN P011 PSALCC01 value Salinity gt The sdn_import_settings xml file also contains the lt PrimaryVarAttributes gt tag specifying target collection names collection field one of the following GeneralField Ocean Atmosphere Land IceSheet Sealce Sediment and collection data types one of the fol lowing GeneralType Profiles Trajectories TimeSeries for known primary variables You may specify additional entries in your user sdn_import_settings xml file 4 3 World Ocean Database Data You can use ODV to import original hydrographic data from the US NODC World Ocean Database WOD into existing or new data collections ODV currently supports WOD 38 ODV User s Guide versions 2009 2005 2001 and 1998 and you can use data files either from the WOD CD ROMs or downloaded from the WOD web site To import WOD data into an existing collection open the collection To import into a new collection create the collection and make sure you choose World Ocean Database variables when defining the collection variables To manually select one or more WOD data files for import into the currently open collection choose Import gt U S NODC Formats gt World Ocean Database Use the standard file open dialog to select one or more WOD gz data files to be imported Choose file type All Files if you want to select WOD files that are already unzipped Then specify import options and press OK to start the data import ODV will read th
117. e selected WOD data files and import all stations that satisfy the station selection criteria The cruise labels of the imported stations consist of the WOD identifier WOD09 WODO5 WOD01 or WOD98 followed by the two characters NODC country code and the unique OCL cruise number Individual entries are separated by underscores _ Note To create simplified cruise labels without the OCL cruise number modify the WOD Im port settings via the View gt Settings option and check the Short WOD cruise labels box The unique OCL profile number is used by ODV as station number ODV recognizes and uses the NODC data quality flags found in the import files see below Quality flags pro vided by the data originators are ignored As an alternative to manual selection of import files using the file open dialog you can prepare an ASCII file containing the names of all the files that you want to import and then select the list file on the file open dialog This is useful if you want to import many files from more than one directory or simply if you plan to repeat the import and don t want to manually select a large number of files again The filenames in the list file must be absolute pathnames one filename per line Default extension of ODV list files is st You can generate file lists easily with the built in list file generator Once the list file is created you choose Import gt U S NODC Formats gt World Ocean Data base and select the previously
118. e GTSPP quality flags in Medatlas data files are recognized and converted to the qual ity flag schemes of the target variables during import If the target collection is a Medat las profile time series or sediment trap collection created by ODV4 or later no quality flag conversion occurs and the original GTSPP quality flag values are stored in the col lection For details of the quality flag mapping see the file ODV4_QualityFlagSets pdf 4 8 Sea Bird CNV Files You can use ODV to import data from Sea Bird CNV files into an existing ODV data col lection or an automatically created new collection based on the contents of the import files Sea Bird CNV files are created from raw Sea Bird files using Sea Bird s SBE Data Processing software When importing such files ODV can split down and up casts into separate stations and subsample the data using a user specified interval To import data from Sea Bird CNV files into an existing ODV data collection first open the receiving collection in ODV Then drag and drop one or more Sea Bird CNV files on to the ODV application window Alternatively select Import gt Sea Bird CNV from the main menu and select one or more Sea Bird CNV files You may also select an ASCII file containing the list of file names to be processed This list file has to be prepared before you start the import It must contain one file path entry per line and the file paths must be either absolute pathnames or pathnames relative
119. e a single CSV text file that ends with _hy1 csv When exporting as CTD the resulting file will be a ZIP Package with suffix _ct1 zip containing one CSV file for every exported station Export to WHP exchange files is only possible or meaningful for ODV collections having pressure or depth as primary variable profiles Depth values in the collection are con verted to pressure before writing to the WHP parameter CTDPRS ODV cruise names are exported under WHP parameter EXPOCODE station names un der STNNBR and the station s time and date information under DATE and TIME Miss ing time and date information is indicated by zeros in the output file so if the time is unknown its value will be 0000 Positions are stored in the range of 90 90 for lati tude and 180 180 for longitude Bottom Depth if present in the ODV collection is mapped to WHP parameter DEPTH If the ODV collection contains a meta variable SECT_ID its values are exported under WHP parameter SECT_ID When exporting to WOCE WHP Bottle files the collection is scanned for variables CASTNO SAMPNO und BTLNBR If CASTNO cast number is missing in the collection 1 is used as default value If SAMPLNO sample number is missing ODV assigns 1 based sequential sample numbers If BTLNBR bottle number is missing in the collection no such column will appear in the output file All other variables are exported using the names in the collection Variables that do not contain a
120. e button You can edit the station pick list using the Manage Pick List gt Edit Pick List option of the map popup menu Among other things this lets you adjust the graphics style for each individual picked station As for all other data window types STATION windows allow you to assign arbi trary collection variables basic or derived on the X and Y axis For easy identification picked stations are marked in the map using the same symbol and color as in the data windows If the map has station annotation switched on the picked stations positions are also labeled with the station label ef 0 5 10 15 20 25 30 Temperature C 3 8 Depth m Depth m por gt a das aie ae Ocean Data View 50 100 150 200 250 300 0 0 5 1 1 5 2 25 Oxygen ymol kg Phosphate mol kg 34 5 35 35 5 36 36 5 Tpot 0 C Ocean Dats View 0 50 100 150 345 35 355 36 365 Silicate umol kg Salinity psu Figure 1 3 Example window layout with an orthographic map and six data windows using STATION scope The pick list stations are marked in the map for easy identification ODV User s Guide 1 6 2 SCATTER Scope SCATTER scope windows see Figure 1 4 display the data of all stations currently shown in the map thereby providing overviews over potentially very large data sets SCATTER windows are particularly useful for data quality con
121. e position and size of the station map as well as the number position and size of zero or more data windows can easily be modified using View gt Window Layout from the main menu the Window Layout option of the canvas popup menu or by pressing the shortcut key Alt W ODV will outline the current layout and lets you move resize delete or create windows To perform one of these operations on a window move the mouse over this window click the right mouse button and select the appropriate option 92 ODV User s Guide If you choose Move Resize a red zoom frame appears around the respective window You move and or resize this zoom frame by moving the mouse over a corner edge or the interior press and hold down the left mouse button and move the mouse To accept the new size and position for the window double click the left mouse button or press ENTER To abort the Move Resize operation leaving the window position unchanged press ESC Note that overlay windows see below cannot be moved or resized You create new windows by moving the mouse over one of the existing windows right clicking and choosing option Create New Window or Create Overlay Window In both cases the initial properties of the new window are derived from the existing one If you use Create New Window the new window will be placed in the middle of the ODV graphics canvas and you have to position and resize it using the Move Resize option described above If you use Create
122. e series data ODV maintains quality flags for all individual data values These quali ty flags may be used for data quality filtering to exclude for instance bad or questiona ble data from the analysis Numerical values and quality flags may be edited and modi fied All modifications are logged in the collection s log file allowing unintentional changes to be reversed if necessary 1 3 Extensibility ODV allows easy import of new data into collections and also allows easy export of data from a collection Oceanographic data in the following widely used formats can directly be read into the ODV system e ASCII spreadsheet data e Argo profile and trajectory data e World Ocean Database data e WOCE and CLIVAR data in WHP exchange format e SeaDataNet data 1 4 Derived Variables In addition to the basic measured variables stored in the data files ODV can calculate and display a large number of derived variables Algorithms for these derived variables are either coded in the ODV software potential temperature potential density dynam ic height all referenced to arbitrary levels neutral density Brunt Vaisala Frequency sound speed oxygen saturation etc or are defined in user provided macro files or ex pressions The macro language is easy and general enough to allow a large number of applications Use of expressions and macro files for new derived quantities broadens the scope of ODV considerably and allows easy experimentat
123. e way the user looks at the data in a collection View settings include items such as map domain station and sample selec tion criteria window layout and many other parameters To copy or move a ODVCE5 collection you must copy or move the odv file and the lt col gt Data directory including all its subdirectories ODV collection files should not be edited manually Table 3 7 Summary of ODVCF5 collection files Collection names lt col gt may not contain or and should not contain spaces for platform independence File Format Comment Collection files lt col gt odv ASCII Defines meta and collection variables collection field and type On Windows this file type is associated with the ODV executable e g double clicking on the odv file will start ODV and open the collection Subdirectory lt col gt Data metadata binary Stores the station metadata name position date etc data binary Stores the station data and quality flags info ASCII Description of the collection free form text format file is optional inventory binary Collection s inventory listing by cruises logfile ASCII Collection s log file Keeps records of data changes settings ASCII Contains settings such as key variable identifications name of most recently used view file or recent import and export directories 31 Version 4 5 0 Table 3 8 Summary of ODVCF5 view a
124. eccecseccccecsececcastscccccssecccceseecscceaeccecceecceceeseeceeeeners 84 10 DATAWINDOW Sissi iii 87 10 1 DATA WINDOW PROPERTIES ccccceccccccccccssssscecccccsccssesssesccccsssseueusesececessssssensnsseescs 87 10 2 ZOOMING AND AUTOMATIC SCALING ccceeeccccssceccccesceccccsseececceeececcsseeseceeseeceeneners 91 LOIS JZ2ZOOMING 40 eet Eh Se Ses tek Ries Malan ile ih AIRES e i a e T 92 10 4 CHANGING WINDOW LAYOUT 0 ccccccccccccccesesescsccccccceesessscsceccsssssusssuscecesessuuenenssescs 92 10 5 GRAPHICS QUTPUT is 93 TO 6 DATA STATISTICS o BRI ER EES de e Bed EE ME a T 94 TOZ ISOPYENAL Scsi dat nt al 96 11 GRAPHICS OBJECTS ninia nina Ras 97 Tal ANNOTATION Storia nadal adas 98 11 2 LINES AND POLYGONS 000 cccceeeeeccccescececceccececccsceccccsccececcesecccecsseeceeceseececeeseeceeeeners 99 iv ODV User s Guide 11 3 RECTANGLES AND ELLIPSES ococcnononocncnnncnnononananacinnnnnononnnanarocncnnononenananacicnncnonenanninoss 99 TAA SYMBOLS cra davis 99 11 5 SYMBOL SETS AND LEGENDS csssceccccccccessesececececcacessseseeccecccaceasseseeccccceecuaeassesces 100 11 6 GRAPHICS OBJECTS FROM FILES cccccccccccccssesescecccccecessesscececssessssasscsccccsssseneaeeeeees 101 11 7 MANAGING GRAPHICS OBJECTS ccccccccccccssesesssceccccccssssssssceccessssssseuscsccessssueneuseesses 101 12 WORKING WITH COLLECTIONS 2 ccccccccsccccccccccccccccccsccccses 103 12 1
125. ect your template file ODV will then present the Collection Variables dialog Figure 3 2 that allows modifying the meta and collections vari ables in many different ways r Collection Variables Spreadsheet Column Labels Cruise Station Type yyyy mm dd Thh mm ss sss Longitude degrees East Latitude degrees North Bot Depth m Depth m Temperature C Salinity pss 78 Oxygen umol kg Phosphate ymol kg Silicate ymol kg Nitrate umol kg Nitrite umol kg CFC 11 pmol kg CFC 12 pmol kg CCL4 pmol kg CFC113 pmol kg Tritum TU DELHE3 PERCNT HELIUM NMOL KG NEON NMOL KG Alkalinity umol kg TCarbon mol kg PCO2TMP DEG C PCO2 UATM PHTEMP DEG C PH Une cia P M 1 El Help Ml Meta Variables lt lt Collection Variables Cruise New Station Type Longitude degrees_east a EL Latitude degrees_north 3 Year Month Day Hour Minute Second ne Depth m A EF Temperature C Salinity pss 78 Oxygen mol kg Phosphate umol kg Silicate ymol kg Nitrate ymol kg Nitrite umol kg CFC 11 pmol kg CFC 12 pmol kg CCL4 pmol kg CFC113 pmol kg Tritum TU DELHE3 PERCNT HELIUM NMOL KG Wi Figure 3 2 The Collection Variables dialog Note that the first eleven meta variables up to and including Second are mandatory You may change properties of mandatory meta variab
126. ed Note that edit operations are logged in the logfile of the collection This file can be viewed using the Collection gt Browse Log File option r Edit Station Metadata male F Cruise 585C19980520 Poe ais Type B Longitude degrees_east 162 400 Latitude degrees_north 29 730 Year 1998 Month 5 Day 23 Hour 17 Minute 47 Second Cruise Name SK27E Bot Depth m 5981 DOI doi 10 1594 PANGAEA 145352 Is Averaged Y Hep one Figure 12 2 The Edit Station Metadata dialog 106 ODV User s Guide Station Data To modify the data of a given variable of the current station right click on the particular variable in the current sample list window and select Edit Data The Edit Data dialog appears showing the data value and quality flags of the variable for all samples of the current station You may change data values and quality flags for the current sample initial selection or for a user defined sample subset You define a sample subset in the data list by pressing the standard extended selection keys Ctrl and Shft while left clicking the mouse Click on Select All to select all samples or press Invert Selection to invert the current selection If you have selected a single data item you can change its value by clicking on the Change Value and entering a new numerical value If you have selected more than one sample in the data list the Change Value button is deactivated
127. ed to consider the data of a given variable sufficient These criteria are applied to any variable required for a specific operation If one or more required variables fail the test the respective opera tion is not performed Obs Number of required observations per station Fraction gt Percentage of samples that must contain data for a given variable gap Z Specifies the depth dependent tolerable gap between data points 12 7 Browsing Collection Information Collection Info Every collection may have a free text description of the data in the collection This in formation is stored in the collection s info file You may view or edit the info file of the currently open collection by choosing Collection gt Browse Info File Cruise Inventory You can view the cruise inventory table of the currently open collection by choosing Collection gt Browse Cruise Inventory The following information is provided for every cruise cruise ID number of stations number of samples station IDs longitude and lati tude ranges time period and data availability indicators for each of the basic variables Data availability indicators are single digit numbers with for instance 9 indicating that more than 90 of the samples containing data for the particular variable Collection Logfile All actions that modify the contents of a collection creation import of data station de letions editing of metadata or data etc are logged in the collect
128. ence Variables You can compare property distributions of the currently selected stations with previ ously saved reference data and produce difference fields by defining property differ ences as derived variables Choose View gt Derived Variables or press Alt D and select Difference from Reference Then choose the ExportID txt file of the reference dataset that you want to use in one of the subdirectories of reference data directory tree ODV will show a list of available reference data files from that directory Select an oal file that has the variable for which you want to produce the difference field as Z variable and appropriate X and Y variables e g for producing longitude vs depth sections make sure the reference data file has longitude as X and depth as Y variable Then identify the Z X and Y variables in the current collection if longitude or latitude are required define them as derived variables prior to invoking the Difference from Reference option to complete the definition of the difference variable Note that the name of the new var iable is composed of the name of the Z variable and the identification string of the refer ence data set Once defined you can use the difference variable in any data plot 6 5 Patches You can define water mass patches by specifying polygons in the X Y space of any data plot currently displayed on the screen To do so move the mouse over the data plot that you want to use for definition e g t
129. enting the fractional day The reference date is chosen as January 1 of the year containing the oldest sta tion e NetCDF variables of name META_VAR_i where i represents an integer value be tween 1 and N_ META _VARS store the data values of ODV meta variables These netCDF variables as well as Longitude Latitude and Date_Time only depend on the dimension N_STATIONS 52 ODV User s Guide NetCDF variables with names of the form VAR_i 1 lt i lt N_VARS store data val ues of ODV data variables They depend on the dimensions N_STATIONS and N_SAMPLES If requested the quality flag values of meta and or data variables are stored in netCDF variables with names of the form QF VAR i Attributes mostly standard NetCDF attributes As aminimum all netCDF data variables except quality flag variables contain the attributes long_name and _FillValue long_name stores the name of the variable as used in ODV _ FillValue stores the miss value used Some variables also con tain the attributes units C_format FORTRAN_format valid_min valid_max and or comment NetCDF quality flag variables have the attributes gf convention and comment that describe the quality flag scheme used A number of global attributes are used to document the source of the data and the soft ware that produced the file see table 16 6 5 4 WHP Exchange Format Export You can export the data of the currently selected stations into a WHP Exchange Format fi
130. ents the desired object type from the map or data window popup menus or by choosing Add Graphics Object gt from the canvas popup menu After initial creation dialog boxes appear that let you define various properties of the object These properties may later be changed again at any time see Edit below A graphics object is owned by the window or can vas from which the creation was initiated and the coordinates of the graphics object are in the respective window coordinate system As a consequence all objects of a win dow follow automatically when the respective window is moved or resized Graphics objects can also be created as copies of existing objects via the Copy Object option of the graphics object context menu or the Copy button of the graphics objects management dialog see below You may also import graphics objects from ODV gob files previously created by exporting existing graphics objects Other window objects such as bathymetry polygons in section plots contour lines in data windows showing gridded field colored data dots in data windows showing original data or the station selection polygons in the station map may also be exported to gob files All these ex ported objects may later be imported and added as graphics objects to the canvas the map or any data window 97 Version 4 5 0 Edit and Delete The properties of a given object can be modified by moving the mouse over it for sym bol sets move the m
131. es based on visible data Q a a Moving average x Moving average E Orientation x Y y Depth m Oxygen umol kg 9 09495e 13 188 423 a 123 113 164 895 Number of gridpoints 30 1253435 135 544 x xj 391 667 111 766 Averaging length scale permille 80 538 553 91 5066 694 853 75 2132 Construct Curve Show Curve 861 294 65 6926 3 _ 1038 51 622113 i 5 y 0 100 300 200 Oxygen mol kg Figure 10 7 The statistics dialog box right for a SCATTER data window showing oxygen data from the 94 ODV User s Guide northeast Pacific versus depth left You obtain distribution histograms of the X Y and if present Z data by pressing on the respective Histogram button An example histogram is shown below Note that the his togram is based on the currently visible data only You obtain plots of the data distribu tion in X Y space by pressing the X Y Distribution button All histogram and distribution plots may be send to the printer or they may be saved in GIF PNG JPG or Encapsulated PostScript files The Gridding Misfits button will be enabled if the parent data window currently uses VG or DIVA gridding Pressing this button will produce a plot showing the estimate data differences of the current gridding procedure see Figure 10 9 ODV will also allow you to fit three types of curves through the data 1 least squares lines 2 piece wise least squares lines and 3 moving
132. es are con sidered missing data You can also specify the first data line and the lines containing the column labels and units The latter two line numbers should only be different if labels and units are on separate lines ODV provides reasonable defaults for all items and only a few changes should be necessary in most cases For the Column separator choose the character that will give a vertical list of labels in the Column labels box Press OK when all spreadsheet file properties are set or press Cancel to abort the import r Spreadsheet File Properties Please adjust the entries under General such that you see a proper list of column labels under Column labels If there is no line containing column labels use the first data line If missing values are indicated by special numeric values enter these values under Missing value indicator s Multiple entries are separated by spaces General Column separator n Column labels line 2 Untts line 3 E Missing value indicator s 999 99 First data line 4 E Contents Info Tot More Column labels 1 BOTTLE 20020801STSSIOKMS A Pe 2 2 EXPOCODE SECT_ID STNNBR CASTNO SAMPNO BTLNBR BTLNBI gt r 3 son METERS DBARS 1TS 90 UMOL KG UMOL KG MU L L E STENER 2 4 32H10201SBI1 HLO201 0 1 1 1 2 20020508 64 9835 16 SAS TNO 3 5 32H1020158I1 HLO201 0 1 11 11 2 20020508 64 9835 1 non 6 32H10201SBI1 HL0201 0 1 12 12 2 2002
133. etween the schemes see file ODV4_QualityFlagSets pdf r Properties Longitude Label Longitude Units degrees_east Comment Error Variable Significant Digits 2 QF Schema ODV y Data Type DOUBLE y Byte Length 8 _ Heb cancel A Figure 3 3 Properties dialog for meta and collection variables Once the set of meta variables is defined you may work on the collection variables by adding deleting reordering and modifying their properties When entering a label or units for the variable you may use formatting control sequences to create subscripts superscripts and special symbols Labels and units may not contain any of the following characters TAB For a description of the supported quality flag schemes and the mappings between the schemes see file ODV4_QualityFlagSets pdf 3 3 2 Manual Entry Ifyou choose manual entry of variables option 2 in Figure 3 1 you will be prompted with separate Meta Variables and Collection Variables Figure 3 4 dialogs that allow modifications of meta and collection variables in ways similar to the ones described in section 3 3 1 above 3 3 3 Using a Pre defined Template If you choose one of the standard or user supplied collection templates ODV loads the lists of meta and collection variables from the template Changes of the properties of the variables by the user are not supported Ifyou want to adapt standard variable tem plates
134. f Year Specify a start month and day to the interval step dt in days the number of frames n to be produced and the interval type ODV will then construct n time intervals and use the respective start and end dates for the Date Time gt Season station selection criteria Depending on the selected interval type the start and end dates of interval i 0 n 1 are defined as follows Interval Type Start of Interval i End of Interval i Zero Width ty i dt i dt Fixed Width t i dt t i 1 dt Fixed Start fy ty 1 1 dt Fixed End ta i d to n dt For each such time interval the map will be re build including only those stations with metadata months and days in the respective time window Note that data from more than one year may be used if the data collection contains stations from multiyear peri od If the animation is for a data window this data window will also be redrawn using data from the currently selected station set only The current map or data window will then be added to the animation file 3 Validate Variable This option is available for data windows only Select a validate variable and specify a start value vo the interval step dv the number of frames n to be produced and the inter val type ODV will then construct n intervals for the validate variable and use the re spective start and end values for the Sample Selection Criteria gt Range selection criteria of the
135. f their cur rent value or to samples equal or not equal to a specific QF value only Note that this operation is logged in the collection s log file You can browse the log file using option Collection gt Browse Log File r Assign Quality Flags Select new quality flag 0 no QC was performed 1 good data 2 probably good data 3 probably bad data that are potentially correctable 4 bad data 5 value changed 8 interpolated value 9 missing value Assign to samples with QF value equal eave ot enol C anca E A Figure 12 5 The Assign Quality Flags dialog 109 Version 4 5 0 110 ODV User s Guide 13 Working with NetCDF Files NetCDF is a set of software libraries and self describing machine independent data formats that support the creation access and sharing of array oriented scientific data NetCDF is widely used in climate research and other fields of geo sciences and many important datasets and model output files are distributed in netCDF format NetCDF files have the following properties e Self Describing A netCDF file includes information about the data it contains e Architecture independent A netCDF file is represented in a form that can be ac cessed by computers with different ways of storing integers characters and floating point numbers e Direct access A small subset of a large dataset may be accessed efficiently wi
136. from the Current Sample Window popup menu ODV will show lists of available and already defined derived variables The available derived variables are organized in thematic groups and are shown in the Choices list The most recently used thematic group is ex panded initially Other groups may be expanded by clicking on their name 57 Version 4 5 0 To add a particular derived variable select this entry in the Choices list you may need to expand the group the variable belongs to first and press Add If a derived variable re quires additional information such as the reference pressure for potential temperature or potential density ODV will automatically prompt for this information Many derived variables also require identification of the input variable s needed for the calculation of the derived variable Note that this identification of key variables has to be done only once and that the associations are remembered by ODV Use option Collection gt Identify Key Variables to verify and modify key variable associations if necessary Note that the calculated values of derived variables may be wrong if key variable associations are not correct To delete a derived variable select this variable in the Already Defined list box and press Delete or simply double click on the item to be deleted Note that when deleting a varia ble that is required as input by other derived variables these child variables are deleted as well To edit the parame
137. gger unwanted data retrievals Loading the data of ODV SECTION windows is very time consuming when working with remote netCDF files Therefore the options for defining and managing sections are dis abled in such cases You can still view distributions along zonal or meridional sections by subsetting the latitude longitude dimension on page 4 of the NetCDF Setup wizard and choosing just a single value You can enter the setup wizard at any time via Collec tion gt Properties gt NetCDF Setup Then proceed by defining the derived variable Metada ta gt Longitude Metadata gt Latitude and establish a SCATTER window with the derived longitude latitude variable on X the vertical coordinate on Y and the variable to dis play as Z 116 ODV User s Guide 14 Tools 14 1 Geostrophic Flows If a section is currently defined you may calculate and visualize geostrophic flows across the section using the Tools gt Geostrophic Flows option Specify the name of the odv output collection that receives the results and define a reference layer by choosing a depth horizon isopycnal or any other iso surface Note that by default the output is written to subdirectory GeoVel of the parent collection directory This subdirectory is created automatically if not already present ODV will start the calculations and export the station pair results and geostrophic velocities to the odv collection specified above Once completed ODV allows you to view t
138. global extent in order to see the feature mark Gazetteer settings are not saved in configuration files Whenever you open a collection the gazetteer option is switched 128 ODV User s Guide off initially Gazetteer files can be edited and extended You can also create your own new gazetteer databases In order to use a private gazetteer with ODV the file must have the extension gzt it must be located in the ODV gazetteer directory lt home gt odv_local gazetteers where lt home gt represents your home directory and its format must satisfy the specifi cations below The first line of the file must start with GZTO1 followed by the name of the file Then there are 7 lines starting with and containing arbitrary comments The next line must be Feature Type No East Longitude North Latitude there has to be one blank line following The rest of the file contains the actual item definitions Each feature is listed ona separate line The name of the feature its type the number of longitude latitude points and the longi tude latitude entries are separated by semicolons Longitude is specified in degrees East 0 360 The number of longitude latitude points can be up to 1500 and the length of a line may be up to 200 000 characters 129 Version 4 5 0 130 ODV User s Guide 16 Appendix 16 1 Mouse and Keyboard Actions Table 16 1 Mouse actions in ODV s Ready status
139. gs to generate perfectly valid collections Collection Properties Data Field Ocean x Data Type Profiles 57 Primary Variable Depth m Z Figure 3 5 Dialog for the definition of collection properties 3 4 Collection Files This section provides an overview over the directory structure and the various files that make up an ODVCE5 or ODVGENERIC collection respectively The information is pro vided for expert users and may be useful in case of problems or unexpected behavior Normally a user need not be concerned with the collection file structure 30 ODV User s Guide 3 4 1 ODVCF5 The information about meta and collection variables is stored in file lt col gt odv This is the definition file of collection lt col gt and this file has to be selected when opening a col lection On Windows the odv file type is associated with the ODV executable e g double clicking on a odv file will start ODV and open the collection The directory containing the odv file is the collection s root directory All other files of the collection are con tained in a subdirectory of the collection s root directory named lt col gt Data collection base directory The collection base directory contains the collection s metadata and data files as well as other subdirectories for specific file types such as views and sections or graphics ob jects xview files store view settings that define th
140. gt Good Coverage Criteria Note that isosurface variables specified with the keywords first and last return the first or last non miss value of the display variable and not necessarily the value of the first or last sample Station meta information such as decimal time day of the year as well as longitude and latitude of a station are provided as automatic isosurface values 7 1 Drawing Isosurface Variables Once you have defined isosurface variables you can use these variables on the Y Y and Z axes of data windows with SURFACE scope If plotting gridded fields on depth levels the closest isobath will be used automatically as an overlay layer If original data points are plotted a gray shaded ocean bathymetry is used as background 72 ODV User s Guide 8 Selection Criteria 8 1 Station Selection Criteria While drawing the station map ODV checks all stations in the currently open collection and determines whether the current station selection criteria are satisfied Only sta tions that pass this test are considered valid Only these stations are marked in the map and only this station subset is available for subsequent browsing and plotting Oste Ime Qoman Meta Data avatsbiey inyot Mama fango Date Tme Doman mata Data ambiy Jo rwoe Pernod From 330w 01 1900 To oec a an 20b a Cruise Labet OCE13134 I A168 11 505 Season From Jan gt 025 To Dec
141. gt About odv4 on Mac OS X systems Complementary high resolution coastline and topography packages that previously had to be downloaded and installed as optional packages are now installed using ODV s View gt Settings ODV4 gt Preferences on Mac OS X option See section 2 12 below for fur ther information 2 2 Running Ocean Data View Once ODV is installed on your system you can start the program in a number of ways On Windows the installation procedure will create an ODV icon on your desktop and will automatically associate odv and var collection files with the ODV application To launch ODV you can double click odv or var files or the ODV desktop icon Any ODV supported file can be dragged onto the ODV icon This will start ODV and open the dragged file in a single operation When ODV is running you can drag an ODV sup ported file onto the ODV window to open this file Supported file types include ODV col lections odv and var netCDF files nc cdf ODV spreadsheet files txt and others On Mac OS X Linux and UNIX systems you can create aliases or icons for the ODV exe cutable odv4 or the ODV startup script file run_odv using methods specific to your oper ating system The ODV executable odv4 is located in the bin_ directory of your ODV installation e g bin_macx on MacOS X bin_linux i386 on Linux systems etc Once a desktop or taskbar dock icon is created you start ODV by double or single clicking on the O
142. h optimize the parameters of the analysis and calculate the gridded field are part of the basic ODV installation A third gridding option DIVA Gridding is available on the Properties gt Display Style dialog of data windows with a Z variable You activate DIVA gridding by choosing this option and specifying appropriate X and Y correlation length scales ODV creates all necessary files for the operation of DIVA automatically in directory lt user gt diva work where lt user gt represents your ODV user directory runs the DIVA mesh generation and field estima tion steps and reads the DIVA output for graphical display of the field by ODV As for 145 Version 4 5 0 the other gridding algorithms the smoothness of the estimated field is controlled by adjusting the X and Y length scales on the Display Style page of the data window s Properties dialog Note that the scale length values are in per mille of the respective axis range and that large values result in smooth fields Other DIVA parameters such as the data signal to noise ratio and the method for setting up the gridding domain see Do main Separation below may be accessed on the DIVA Settings page of the data win dow s Properties dialog DIVA experts may adjust additional DIVA parameters by editing the DIVA settings file lt user gt diva diva settings Non negativity Constraint Weighted averaging methods such as Quick Gridding or VG Gridding always generate estimates s
143. haded by ODV if Do color shading is checked The positions of the actual data points are marked in the plot if Draw marks is checked and appropriate size and color are specified for the dots Contouring see below and color shading of the property fields are supported for all gridding modes Properties Window 1 Properties Window 1 Properties Window 1 General Data Depiay Stye tozs Color Mapping DIVA Setungs General Data Depay Style Contours slor Maporg DIVA Settings General Data Depay Stye Contours Color mappng Rm He x Gance Hep Ox Cancel neo os Cancel Figure 10 5 The various pages of the Data Window Properties dialog part 2 of 2 Contours The Contours page of the data window properties page allows you to define contour lines for the plot This page is only enabled if Gridded field is choosen as display style see above To add sets of contour lines specify Start Increment and End Z values in the New group Choose appropriate line and label properties and press the lt lt button to add the set of contour lines to the Already Defined list If necessary repeat this proce dure with different Start Increment and End values and possibly different line and label properties You can modify the properties of an existing contour line by selecting it in the Already Defined list modifying the properties in the New group and pressing the lt lt 90 ODV User s Guide button to implement the cha
144. he log file of the calculations and to invoke a new ODV session on the newly calculated section pair and velocity data Once the out put collection is open you should define an appropriate map domain by zooming into the map you should switch to a SECTION layout by pressing F11 and define Geostr Vel cm s Geostr Vel north comp cm s and or Geostr Vel east comp cm s as Z variable of one or more plot windows The station label of a given station pair A gt B alpha consists of the original station numbers A and B of the stations used in the pair and the direction alpha of positive Geostr Vel flow values alpha 0 eastward al pha 90 northward etc The meta variable Distance contains the distance between the two stations in km Geostrophic velocities are derived from dynamic height differences between two hy drographic stations Calculations proceed in two steps 1 First the data of the two sta tions are mapped to a set of standard depths by piecewise linear least squares 2 Then dynamic heights at the standard depths are calculated for both stations and the geo strophic velocities for the station pair at the standard depths are obtained from the dy namic height differences ODV also calculates average values for all variables in the col lection pair averages Both the pair averages and the geostrophic velocities are rep resentative for the mid point between the two stations involved and ODV writes those values to the
145. he user s document directory Create directory cmd_files if it is not already present and place your command files in this directory The following commands are currently supported in ODV command files Note that a slash should be used as path separation character in all filenames appearing in ODV command files to ensure platform independence Once a base directory is defined using the set_base_directory command all subsequent relative filenames are considered relative to base directory If no base directory is defined and a collection or netCDF file has been opened relative filenames are considered relative to the collection or netCDF directory Multiple arguments must be separated by commas The window index parameter iw used in some commands may have the following values 1 for the graphics canvas 0 for the map and positive integer values for data windows Lines in ODV command files may not exceed 255 characters in length Lines with as first character are treated as com ments and are not executed create_annotation iw x y orientation textAlign text Create a text annotation text for window iw at position x y window iw coordinates oriented along orientation degrees measured counter clockwise from positive x axis textAlign determines the alignment of the text relative to x y center_center 0 center_top 1 center_bottom 2 right_top 3 right_bottom 4 left_top 5 left_bottom 6 right_center 7 left_center 8
146. heric while the default and Mollweide projections are 77 Version 4 5 0 global in extent All projections allow zooming in with the mouse or the definition of sub regions using the Domain page of the map Properties dialog see below For the Orthographic Oblique projection you can specify an arbitrary longitude latitude eye position pole from which the globe is then viewed For the other projections the pole latitude is fixed and the user may only vary the pole longitude Note that for projections 2 to 6 the definition of sub domains by zooming can be tricky If you need accurate results either use the Domain page of the map Properties dialog see below or switch to default projection temporarily then zoom thereby de fining the sub region and finally switch back to the desired map projection Layers ODV comes with a large number of map resource packages called Series containing medium or high resolution bathymetric and topographic contours as well as coastline lake river and border data The medium resolution global GlobHR series is automati cally installed with the ODV software For information on other available map resources and installation instructions see the Map Layer Series section in chapter 2 12 On the Layers page you select the bathymetry coastline topography Series and specify the layers within the different Layer Set categories You switch on or off the drawing of the map s color bar by checking or
147. heta S plot and click the right mouse button From the popup menu choose Extras gt Define Patch note that the cursor changes to a cross hair and define the nodes of the patch polygon by clicking the left mouse button at the node positions You may delete points by moving the mouse close to the respective point and clicking the right button Terminate definition of the polygon by pressing En ter or double clicking the left mouse button Note that the polygon is automatically closed by ODV ODV then prompts you for a patch name no extension and writes the patch definition to a file in the collection directory Once you have defined one or more water mass patches for a collection you can use them to compose and activate the derived variable Patches Choose View gt Derived Vari ables and select Patches from the Choices list You can compose the Patches variable by selecting one or more of the available water mass patches defined previously as de scribed above into it Press OK when you are done To evaluate the Patches variable for a given sample ODV determines whether the sample is inside one of the patch polygons selected into the variable and if found assigns the number of the respective patch as Patches value Ifthe sample is outside all the selected patches its value is set to the missing data value Like all other variables basic or derived you can use the Patches variable on any axis of any data window Use it for instance as Z va
148. iables stored in the collec tion The number and meaning of the variables may be different in different collections 21 Version 4 5 0 One of the collection variables the primary variable is special and serves as ordering variable for the samples of a station Usually but not necessarily this is the first collec tion variable The sets of meta and collection variables are defined when the collection is created but may be modified at any time later For each station ODV maintains data values for all meta variables and also for all collec tion variables and all samples In addition ODV also maintains quality flag values asso ciated with every individual metadata and data value There are additional quality flags describing the overall quality of a station station quality flag and of each individual sample sample quality flags Quality flag values reflect the degree of confidence in the data and constitute an extremely valuable part of the data set ODV supports all widely used quality flag schemes in the oceanographic community ODV also defines its own simple quality flag scheme that is applicable for oceanographic and most other kinds of environmental data ODV can use data quality flag information for data filtering Data quality flag values of collection variables can directly be worked with by means of quality flag derived variables Individual meta and collection variables may use different quality flag schemes Meta v
149. ide 4 5 GTSPP Global Temperature Salinity Profile Program You can use ODV to import data from GTSPP netCDF version 3 8 and 4 0 format files into ODV data collections GTSPP files can be downloaded from the US National Oceano graphic Data Center at http www nodc noaa gov GTSPP GTSPP data should be imported into data collections using the GTSPP variables If you don t already have such a collection open create one using the File gt New option When prompted to define the collection variables choose GTSPP Global Temperature Salinity Profile Program To initiate the data import choose Import gt U S NODC Formats gt GTSPP ODV then presents a standard file open dialog and lets you select one or more zipped GTSPP package files tgz or zip or GTSPP netCDF data files nc in a given directory Alternatively you may select an ASCII file containing the list of file names to be pro cessed This list file has to be prepared before you start the import It must contain one file path entry per line and the file paths must be either absolute pathnames or path names relative to the currently open collection The list file must have extension Ist You can generate file lists easily with the built in list file generator ODV then displays the import options dialog If you import into a collection created for GTSPP data see above you may simply press OK to start the data import The variables in GTSPP collections are depth temperature and s
150. ied tolerances even if Cruise Station and Type remain unchanged The de fault tolerance values are one day one hour and one degree longitude or latitude but you may specify your own tolerances by modifying the Spreadsheet Import settings via the View gt Settings option If Station information is not provided in the data file the Date Time Longitude and Lati tude values are checked and a station break occurs whenever one or more of these val ues change All metadata of a station such as date time longitude and latitude are tak en from the first sample line of the station in the import file Imported data from the file are added to the currently open data collection or if no col lection is currently open are added to a newly created collection To import data from a spreadsheet file into the currently open collection choose Im port gt ODV Spreadsheet and use the standard file select dialog to identify the data file Specify import options and press OK to start the data import Spreadsheet files can also 35 Version 4 5 0 be dragged and dropped onto the ODV icon or an open ODV window If the file is not a generic ODV spreadsheet file a Spreadsheet File Properties dialog box appears and lets you specify the column separation character and one or more missing data values Note that multiple missing data values must be separated by one or more spaces Fields in the import file that are empty or contain one of these valu
151. ies are applied to all objects in the shapefile but can be changed later using the Manage Graphic Objects option see below If the shapefile has an accompanying prj projection file ODV will use the projection information and convert geographical coordinates to WGS84 if necessary If the prj projection file is missing ODV assumes that all geographic coordinates are WGS84 and are within the 180 to 360 and 90 to 90 degree ranges ODV currently supports shapefile points multi points lines multi lines polygons and multi polygons For poly gons only the outer ring is drawn Note that the drawing of very large shapefiles may be slow 11 7 Managing Graphics Objects You can obtain full lists of all graphics objects of the canvas the map or any data win dow by right clicking on the respective area and choosing Manage Graphics Objects or Extras gt Manage Graphics Objects Window 1 Graphics Objects Edit Type Value a 2 auto Annotation Patches 1 AABW 2 AAIW 3 LNP 4 NADW Export w auto Annotation Depth m Copy auto Annotation Salinity psu F Delete 1 35 2522 5765 43 2 35 8418 2026 47 6 Annotation Test Foreground 7 Symbol Set SAVE_LG5 244 B dot Up 8 Symbol Set SAVE_LG3 112 B dot La Dahiman 1 26 5855 202 N 10 26 5855 202 N E 1 out of 10 graphics objects selected Background Select All Select All Non Auto Inve
152. ile the main challenges for ODV users are to correctly identify the space and time dimensions to detect situations with multiple coordinate systems and to choose a proper primary variable Choosing for instance Z as the primary varia ble will turn the netCDF file into a vertical profile database with nr stations at every X Y position The total number of stations in this case is nr ny nx where nx is the length of dimension K If alternatively Tis chosen as primary variable the data in the netCDF file are interpreted as time series In this case there will be one station time series at every X Y Z point and the total number of stations is nz ny nx To provide a maximum level of user control ODV presents a netCDF setup wizard when a netCDF file is opened for the first time The various controls on this four page dialog are initialized with automatically determined settings and in many cases the us er only needs to confirm the settings by pressing OK on each page These settings are remembered by ODV and the setup wizard will not appear when the file is opened again You can force ODV to show the setup wizard in the following ways 1 open the netCDF file for instance via the File gt Open option and open the same netCDF file again for instance via the File gt Recent Files option or 2 use Collection gt Properties gt NetCDF Setup while the netCDF file is open You open a netCDF file on the local file system extension must
153. iles must be in netCDF format they must have the same logical structure as lt install gt include GEBCO1 nc and they must be located in lt install gt include where lt install gt represents your ODV installation directory To use a custom bathym etry file for DIVA select the file under Domain Selection gt Map on the DIVA Settings page of the window s Properties dialog Note that ODV switches domain separation off automatically if the selected bathymetry file provides insufficient resolution for the given domain For the threshold depth you may enter a specific depth value or the keyword automat ic If automatic is used and the Z variable is an isosurface variable defined on a Depth or Pressure surface the depth or pressure of the surface is used as threshold depth In these cases ODV needs to be able to identify your Depth or Pressure variable Please use option Collection gt Identify Key Variables and ensure that the key variable Depth in Water Column m or Pressure in Water Column db is associated with your Depth or Pressure variable If the isosurface variable is defined using the keyword first e g XXX Depth m first an automatic threshold depth of 1m is used 147 Version 4 5 0 Salinity psu Depth m 1000 Salinity psu Depth m 1000 Figure 16 4 Comparison of VG and DIVA gridding methods for separated ocean basins Note the influence of Pacific values in the Caribbean in
154. ing col QV or QF amni QV SEADATANET SeaDataNet quality flags for the variable in the preceding col umn QV ARGO Nitrate umol kg ARGO quality flags for Nitrate umol kg QV ODV Nitrate umol kg or ODV generic quality flags for Nitrate umol kg QV Nitrate umol kg QV WOCESAMPLE SAMPLE WOCESAMPLE sampler quality flags QV WODSTATION STATION WODSTATION entire station quality flags QV STATION ODV generic quality flags for entire station IMPORTANT NOTE Column labels must not contain the column separation character used in the spreadsheet file 16 3 3 Data Lines Every non comment line following the column labels line is considered a data line All data lines must have the same number of columns as the column labels line Each data line contains metadata and data for one sample All samples of a given station must be in consecutive order but need not be sorted Missing values may be indicated by an empty field the value 1 e10 or by a text indicator such as na not available or NaN not a number If special numeric values such as 9 or 9999 are used as missing value indicators in the file the special values must be specified in an attribute line of the form lt MissingValuelndicators gt 9 9999 lt MissingValuelndicators gt near the top of the file before any data line Cruise and station labels are limited to the length of the Cruise and Station meta varia 140 ODV User s Gui
155. into current collection supported formats include various spreadsheet formats ARGO MedAtlas World Ocean Database and WOCE Export Export data of currently selected stations to ASCII file ODV collection or netCDF file export window X Y Z data to ASCII files export window X Y Z data as reference dataset export of isosurface values to ASCII file Tools Calculation of geostrophic flows 3D estimation calculation of box average values outlier and duplicate station identification macro editor color palette ed itor Windows only list file generator Ocean Calculator Help Invoke ODV help system visit the ODV web page send bug reports show ODV version and installation details 2 6 Metadata and Data Windows The Current Station Window contains the metadata values and associated quality flags of the current station marked in the map with a red cross the Current Sample Window contains the data values and associated quality flags of the current sample marked in data windows with a red cross and the Isosurface Data Window contains the isosurface values of the current station Different colors are used to display metadata and data values to instantly reveal the quality of individual values Right clicking the mouse button on a list window brings up window specific popup menus letting you edit the metadata or data or allowing modifications of variable prop erties This includes changing the variable labels the numeric format and
156. ion s logfile You can view the contents of the logfile by choosing Collection gt Browse Log File 105 Version 4 5 0 12 8 Properties of Variables You may modify properties of meta and collection variables by right clicking on the current station or current sample list windows and choosing the Properties option From the list of variables choose the one you want to modify and press Edit On the properties dialog of the selected variable you may edit the strings for variable label units and comment You may also modify the number of digits used to show values in the current station or sample windows 12 9 Editing Data You can edit the metadata and data values of the current station as well as their associ ated quality flags and save the modified values in the collection data files on disk Station Metadata To modify the metadata of the current station right click on the current station list window and choose Edit gt Metadata The Edit Station Metadata dialog appears showing the metadata of the current station You can edit an individual entry by double clicking into the respective value field You modify a particular quality flag by clicking on its field and then clicking the Change Quality Flag button and selecting the new quality flag Press OK on the Edit Station Metadata dialog to write the new metadata to the collection files Press Cancel to discard your modifications and leave the metadata of the current station unchang
157. ion with new quantities not yet established in the scientific community ODV provides a built in macro editor that facilitates creation and modification of ODV macros Any basic or derived variable may be displayed in one or more data windows In addi tion any variable can be used to define isosurfaces such as depth horizons isopycnals isothermals or isohalines Property minimum or maximum layers like for instance the intermediate water salinity minimum layer can be selected as isosurface by finding zero values of the vertical derivative variable of these variables 1 5 Plot Types ODV displays data in two basic ways 1 either by showing the original data at the data locations as colored dots of user defined size see Figure 1 1a numeric values or ar rows see Figure 1 2 or 2 by projecting the original data onto equidistant or variable resolution rectangular grids and then displaying the gridded fields see Figure 1 1b Method 1 produces the most elementary and honest views of the data instantly reveal 2 ODV User s Guide ing occasional bad data values and regions of poor sampling In contrast method 2 pro duces nicer plots and avoids the overlapping of the colored dots that occurs with meth od 1 especially for large dot sizes It has to be noted however that the gridded fields of method 2 are data products and that small scale or extreme features in the data may be lost due to the gridding procedure For both
158. is optimized for irregularly spaced variable length data and pro vides dense storage and fast data access The data model is general and accommodates profile trajectory and time series data from various fields of environmental sciences including oceanography meteorology glaciology or geology In addition to observed data ODV can also be used to analyze and visualize gridded data or numerical model output Such data may be provided in one of ODV s import formats as ODV collection or as netCDF datasets ODV4 defines a new collection data format ODVCF5 that is more general than its pre decessor format ODVGENERIC used by previous versions of ODV ODVCF5 overcomes many limitations of ODVGENERIC In particular there is now support for an unlimited set of metadata variables an unlimited number of collection variables and a virtually unlimited number of samples per station For the first time ODVCF5 now supports data quality flags for meta variables and for meta and collection variables alike the user may now choose custom quality flag schemes from a set of the 14 most popular schemes used in the oceanographic community Collections with more than 50 varia bles and custom data types ranging from double precision 8 bytes to single byte inte gers are now possible with ODVCF5 Meta variables may be numeric 1 to 8 bytes per value or of type TEXT with user specified text length ODV4 is backwards compatible and fully supports ODVGENERIC colle
159. ithout units do not contain the units part Data variable labels may have qualifiers of the form PRIMARYVAR lt valueType gt lt valueBytes gt lt SchemalD gt where valueType may be one of the following BYTE SHORT INTEGER FLOAT DOUBLE or TEXT valueBytes represents the number of bytes per value and only needs to be specified for valueType TEXT or if the SchemalD entry is present In case of TEXT the valueBytes value represents the maximum number of characters to be stored in the text field default length 21Bytes Note that one of the characters is used for string termi nation and is not available for actual data text e g a TEXT field of 21 bytes can store a maximum of 20 characters of data text SchemalD may be one of the following ARGO BODC ESEAS GTSPP OCEANSITES ODV QARTOD PANGAEA SEADATANET SMHI WOCEBOTTLE WOCECTD WOCESAMPLE WOD or WODSTATION Note that if the variable has an associated quality flag column 138 ODV User s Guide see below the SchemalD of the quality flag column will prevail Only one column label may have the PRIMARYVAR qualifier to indicate that this column is the primary variable Examples Depth m PRIMARYVAR DOUBLE Sample Number SHORT Salinity psu Phosphate m mol kg FLOAT 4 WOCEBOTTLE Sediment Type TEXT 41 SEADATANET Note The qualifiers are only used when the spreadsheet file is used as a template for collection creation e g when dropping the file onto O
160. itive help works best with the Firefox browser When using Internet Explorer it may be necessary to click into address field and to press ENTER On Mac OS X and some Linux systems a running web browser may have to be closed before ODV context sensitive help will be displayed 2 4 Application Window The ODV4 application window consists of the following elements see Figure 2 1 Menu Bar The menu bar provides access to main menus Canvas The graphics canvas contains a map always present and an unlimited number of data windows The canvas the map and the data windows may contain an un limited number of graphics objects such as text annotations symbols or user defined shapes Status Bar Three panes providing 1 status information 2 coordinates at current mouse position or a progress bar and 3 the number of currently selected sta tions the total number of stations in the collection and the name of the current view Current Station Window Metadata values and quality flags of the current station marked in the map with a red cross Current Sample Window Data values and quality flags of the current sample marked in data windows with a red cross Only data satisfying the current sample selection criteria are shown 11 Version 4 5 0 Isosurface Data Window Isosurface values of the current station Current Station Current Section Current Sample List Windows E Ocean Data View X rschlit data eWOCE data whp
161. iven sample depends on ex isting and new variable values according table 4 1 Note that the Check for existing stations box cannot be unchecked for this mode Before adding data ODV searches the collection for matching stations see Station and Sample Matching Criteria be low for a description of the station search procedure and if found reads the orig inal station from the collection adds the data for the selected variables and re places the original station with the updated version If no matching station is found the user is notified Table 4 1 Results of merging existing and imported values Existing value New value Merged value yes yes Average of existing and new values yes no Existing value no yes New value 47 Version 4 5 0 no no Missing value Update Data selected variables Choose this option if you want to update data for one or more variables update variables and leave existing data for other varia bles unchanged An updated value of an update variable at a given sample only de pends on the new variable values and existing values are discarded Note that the Check for Existing Stations box cannot be unchecked for this mode Before updat ing data ODV searches the collection for matching stations see Station and Sam ple Matching Criteria below for a description of the station search procedure and if found reads the original station from the collection updates the data
162. l Alkalinity umol kg TRITUM TU Total Alkalinity umol 1 DELHE3 PERCNT Total Dissolved Inorganic Carbon umol kg HELIUM NMOL KG Total Dissolved Inorganic Carbon pmol DELC14 Error MILLE Variable with fCO2 oCO2 or DH input pressure vali TRITUM Error TU pe u DELHE3 Error PERCNT Heb E Gene Figure 12 1 The Identify Key Variables dialog 104 ODV User s Guide Important Note Errors made in the key variable associations can lead to wrong and meaningless values of affected derived variables For instance imagine the key variable Salinity psu was erroneously associated to collection variable Oxygen umol kg This would cause all derived variables requiring Salinity psu as input variable e g poten tial temperature potential density etc to return wrong values Verifying the validity of key variable associations using option Collection gt Identify Key Variables should be the first check whenever you receive doubtful derived variable values 12 6 Good Coverage Criteria Some ODV operations such as the interpolation to standard depths or the calculation of various derived variables require that there are sufficient input data available Calcula tion of dynamic height for instance requires full profiles of temperature and salinity data and gaps between the data points should not be too large Using Collection gt Good Coverage Criteria you may specify the criteria that must be satisfi
163. lags Reference ODV User s Guide http odv awi de en documentation QARTOD Qartod quality flags Reference http dmac ocean us dacsc docs apr2005_post_mtg QARTODL II ppt PANGAEA PANGAEA generic quality flags Reference http wiki pangaea de wiki Quality_flag SEADATANET SeaDataNet quality codes Reference http vocab ndg nerc ac uk term L201 1 SMHI Swedish Meteorological and Hydrographic Institute quality codes WOCEBOTTLE WOCE bottle value quality codes Reference http odf ucsd edu joa userguide docs woceigossqualitycodes html WOCECTD WOCE CTD value quality codes Reference http odf ucsd edu joa userguide docs woceigossqualitycodes html WOCESAMPLE WOCE WHP quality flags for the water bottle itself Reference http odf ucsd edu joa userguide docs woceigossqualitycodes html WOD World Ocean Database individual observed level quality codes Reference ftp ftp nodc noaa gov pub WOD05 DOC wod05_tutorial pdf WODSTATION World Ocean Database entire station quality flags Reference ftp ftp nodc noaa gov pub WOD05 DOC wod05_tutorial pdf 135 Version 4 5 0 16 3 Generic ODV Spreadsheet Format The ODV generic spreadsheet format is the recommended format for exchange of data between data producers and data users The generic spreadsheet format allows auto matic import of data into ODV collections not requiring any user interaction ODV also uses the generic spreadsheet format when exporting data from
164. lates includes templates for ARGO profile and trajectory data World Ocean Data base data published by the U S NODC and various data types from the World Ocean Cir culation Experiment WOCE as well as the Medatlas project r M pe Creating collection Definition of collection variables Use txt ody var or other file as template User specifies variables manually standard templates ARGO Profile ARGO Trajectory GTSPP Global Temperature Salinity Profile Program Medatlas Bottle Medatlas CTD Medatlas Sediment Trap Medatlas Time Series NODC SD2 WOCE ADCP WOCE Current Meter WOCE Sea Level WOCE Subsurface Float WOCE Surface Velocity WOCE WHP Bottle WOCE WHP CTD World Ocean Database user templates ARGO_Profile_with_CNES_Extensions World_Ocean_Database_with_GTSPP QF Y Customized collection creation Cancel Figure 3 1 Collection template selection dialog In addition to the pre defined standard templates the user may prepare custom collec tion templates and store these templates in the templates collections subdirectory of the ODV user directory User collection template files have the odv extension and follow the format of odv collection files 27 Version 4 5 0 3 3 1 Using a File as Template If you are using a txt odv var or other file as template first option in Figure 3 1 a file open dialog will appear that lets you sel
165. le by choosing Export gt WHP Exchange File ODV supports both Bottle and CTD output files as specified in Description of WHP Exchange Format for CTD Hydrographic Data James H Swift amp Stephen C Diggs September 2001 updated May 2006 April 2008 http cchdo ucsd edu formats exchange index html To perform WHP Bottle or CTD exports please proceed as follows 1 2 If necessary select the set of stations you want to export by adjusting the map s domain and or apply special station selection criteria Select Export gt WHP Exchange File gt Bottle or Export gt WHP Exchange File gt CTD from ODV s main menu In case ODV cannot automatically identify critical variables you are prompted to identify these variables a WHP Bottle export Key variable Pressure in Water Column db or alter natively Depth in Water Column m must be identified b WHP CTD export When exporting as CTD the variables Temperature C and either Pressure in Water Column db or Depth in Water Column m are required In addition you may be asked to identify Salinity psu and Oxygen in umol kg or ml l Specify output directory and filename 53 Version 4 5 0 5 Specify information required for the WOCE file header first line of file and ad ditional comments you want to be part of the output file Once the export is finished a file will be written to the location specified in step 3 When exporting Bottle data the output file will b
166. le of the full axis range and that large values result in smooth fields You should experiment using different length scale values until an ac ceptable compromise between preservation of structure in the data and smoothness is achieved If you check the Automatic scale lengths checkbox ODV will analyze the data distribution and choose the gridding length scales automatically Note that gridded fields may be poor representations of the data if performed improp erly All ODV gridding methods assign for every estimate at a given grid point x y a dimen sionless quality value Quality values are based on the distances from the estimation point measured in units of respective averaging scale lengths of all data points used for the estimate Quality values larger than about 3 should normally be considered as problematic indicating that the nearest measurement is more than two length scales away from the estimation point You can choose to hide bad estimates with large quali ty values by checking the Hide bad estimate box and specifying an appropriate Quality limit value 89 Version 4 5 0 i Arrow Properties Window 1 X Y Components x Zonal Surface Current cm s Depth m first d Y Meridional Surface Current cm s Depth m first v Scale 50 per cm Line width very thin x Color l E 0 nf Cora E E d Figure 10 4 The Arrow Properties dialog The gridded field is color s
167. lected Available Backgrd nn A 1000m 2 Line 6500m 100m 6000m 1250m very thin v 5500m 1500m soid y 5000m 2000m 4500m 2500m E none y 4000m i 250m se 3500m 3000m 3000m gt gt 3500m 2500m ____ 4000m 2000m 4500m 1500m 5000m Fill 1250m 500m A 1000m 50m automatic v sr 5500m ya ee Default Settings lati canca Figure 9 3 The map s layer definition dialog 79 Version 4 5 0 If you pressed the Compose button the layer definition dialog Figure 9 3 appears You add layers by selecting them in the Available list and pressing the lt lt button Layers can be removed by selecting them in the Selected list and pressing the gt gt button Depending on the properties in the Line and Fill boxes a given layer may be filled and or its outline may be stroked The default color settings are automatic in which case an appropriate color will be chosen automatically recommended You may override these settings and choose specific colors by clicking into the respective combo box Choose none if you don t want filling and or stroking Note that you may change the properties of a given layer in the Selected list by clicking on it then modifying the settings under Line and Fill and finally clicking lt lt to implement the changes Domain On the Domain page of the map s property dialog you may specify the map domain by providing east and west longitudes and south and north latit
168. lemented as automatic anno tations They are created automatically when the plot window is drawn and they are deleted when the respective data plot window is deleted You may not edit or delete automatic axis titles If you want to change an axis label permanently you should switch off automatic axis titles see General page of the window s Properties dialog and create an annotation manually by choosing Extras gt Add Graphics Object gt Annotation from the canvas popup menu 11 2 Lines and Polygons You add straight lines polylines and polygons to the map data windows or the canvas by choosing Extras gt Add Graphics Object gt Line gt Polyline or gt Polygon from the map data window or canvas popup menus In all three cases the cursor changes to a cross hair and you should proceed by specifying the nodes of the object For a Line graphics object you must define starting and endpoint move the cross hair to the start of the line and click the left mouse button then move to the end point and click the left button again For Polyline or Polygon graphics objects you may define up 1000 nodes Note that polygons are closed automatically by ODV If you want to delete a point move the cross hair close to it and click the right mouse button You end the definition of polygon or polyline points by pressing ENTER Once you have specified the nodes of the line polyline or polygon ODV presents a dia log box that lets you define color width a
169. les select the variable and press Edit but you may not delete or reorder them Other meta variables may be reordered deleted or their properties may be edited To add a not already used spreadsheet col umn label as meta variable select this label in the Spreadsheet Column Labels list and press the Meta Variables gt gt button To add an additional meta variable press New and define the properties of the new meta variable see Properties dialog below The total number of meta variables is unlimited To inspect or modify the properties of a meta variable select the variable and press Edit A Properties dialog Figure 3 3 appears that lets you specify label and units of the vari able the number of significant digits used to display values in the current station win dow if numeric the quality flag scheme to be used for this variable and the data type and byte length if text 28 ODV User s Guide When entering a label or units for the meta variable you may use formatting control sequences to create subscripts superscripts and special symbols Labels and units may not contain or TAB characters If you need better than about 100 m precision for station positions make sure to use datatype DOUBLE for the longitude and latitude meta variables Also make sure not to use datatype TEXT for longitude latitude or any of the time meta variables For a description of the supported quality flag schemes and the mappings b
170. lt name is the input file name appended with est and the default location is in the same directory as the input file Each line contains the X Y and Z values of one estimation point A Z value of 1 e10 indicates that the particular X Y point is far from any data point and that no reliable estimation could be performed Z values at points outside the window domain or in regions exceeding the window s qual ity limit white areas in the plot are set to 1 e10 14 3 3D Estimation You can estimate values for a basic or derived variable at arbitrary geographical loca tions by choosing Tools gt 3D Estimation ODV will prompt you for an ASCII file that con tains the longitude latitude and depth values of the points for which Z variable esti mates are to be obtained This 3D point definition file has to be prepared prior to invok ing the Tools gt 3D Estimation option When creating the point definition file specify one point per line and provide decimal longitude latitude and depth values in this order with one or more spaces separating the individual values ODV will let you choose the variable for which the estimation should be performed and it lets you specify x y z av eraging length scales used for the estimation Note that the length scale units for longi tude and latitude are in per mille of the current map ranges whereas the unit of the depth length scale is in meters Choosing large values for the averaging length scales will resul
171. m the import procedure will be written to this subdirectory The name of the subdirectory consists of the current date and time and will be unique for all SDN imports that you perform ODV will then automatically unzip all selected SDN zip archive files and will analyze the contents of all individual spreadsheet files This includes analyzing the SDN semantic header lines and the column header lines of the input files testing for SDN spreadsheet format compliance non compliant files are excluded gathering information about available variables and grouping of files according to the primary variables encountered in the files ODV will create separate data collections for every data type encountered and will im port the data of the matching files into the particular collection Once the SDN import process has finished you can open the newly created collections via File gt Recent Files option Use Collection gt Move Rename if you want to move the collections to a different directory and or give them names of your choice Following below is a detailed description of the strategies applied by ODV for the crea tion of target collections and the composition of variable sets in each of them As first step ODV parses the column header lines of all SDN import files detects the primary variable first variable after the meta variables used in any given file and groups the import files according to their primary variable For every file group ODV
172. me a map displaying the selected Z variable see Figure 1 6 Such map data windows use the projection and lay ers settings of the station map It is also possible to assign other isosurface variables to the X and Y axis of the SURFACE data window resulting in general isosurface variable correlation plots possibly colored using another isosurface variable as Z variable 1 7 Graphics Output Printouts of the ODV graphics canvas can easily be obtained using the File gt Print Canvas option As an alternative you can also write the entire graphics canvas individual data windows or the map to gif png jpg tiff or PostScript files These files can subsequently be included in electronic documents and web pages The resolution of the image files can be specified by the user and is not limited by the graphics resolution of the screen 1 8 Data Statistics Statistics information for the X Y Z data of a data window or the position and date time metadata of the stations in the map can easily be obtained by pressing F4 while the mouse is over the respective data window or the map A dialog will appear showing mean standard deviation number of data points as well as minimal and maximal values for X Y and Z variables separately In addition histograms of X Y and Z data as well as X Y data distribution plots can be obtained by simple button clicks For the map you can also obtain station coverage histograms over time or season 1 9 Estimation and Aver
173. me way as if the data were stored in an ODV data collection ODV will produce a clickable station map and supports most types of graphics output as for collections Options requiring write permission are not available and are grayed out ODV treats netCDF files as read only and will never modify these files Note that netCDF files are platform independent and the same file can be used on all supported platforms The data of a given variable S in a netCDF file are stored as single or multi dimensional array The set of dimensions of a space and time varying variable include the three space coordinates X Y and Z as well as a time coordinate T Itis a convention to order these dimensions as S T Z Y X e g Xis the fastest and T the slowest changing dimen 111 Version 4 5 0 sion For geo scientific data X and Y represent longitude and latitude while Z is a verti cal coordinate such as depth or pressure in the ocean height in the atmosphere or depth in a sediment or ice core It is possible that a netCDF file contains more than one X Y Z T coordinate system For instance it is quite common for model output netCDF files to contain data defined at the centers of the model grid e g tracer concentrations as well as the velocity data defined on the grid interfaces ODV can handle only one X Y Z T coordinate system at a time and the corresponding dimensions must be selected during netCDF setup see below When opening a netCDF f
174. mean val can be calculated as Om O If no data point is found within a box val is set to 1 e10 if only one data point is found o is set to 1 e10 Also note that all individual data values used for given boxes are exported to ASCII files with names of the form lt box number gt _ lt var name gt dat where lt box number gt repre sents the respective box number e g line number in the box definition file and lt var name gt represents the variable name for which the average is calculated In the dat files the meaning of values is as follows sample ID longitude latitude depth decimal year day of year value weight used rejected flag Note that the dat files are overwritten by subsequent box averaging requests No dat files are written if the total number of re quested averages exceeds 5000 14 5 Finding Outliers You can scan the currently selected stations for samples with data values inside or out side a user specified value range by choosing Tools gt Find Outliers Range Check Select the variable to be scanned from the list of variables and enter the range values under Range Under Action choose whether you want to find values inside or outside the speci fied range Press OK to start the scan ODV will report the number of outliers found and lets you view the list of outliers ODV also lets you inspect and modify the data values and or quality flags of the outlier samples If you check Inspect and Edit Outliers O
175. n the variable label and 3 the adjustment errors third group suffix adj error in the variable label Note that in real time data files there are no data for groups 2 and 3 ARGO data quality flags in the netCDF file are recognized and converted to the quality flag schemes of the target variables during import If the target collection is an ARGO profile or trajectory collection created by ODV4 or later no quality flag conversion oc curs and the original ARGO quality flag values are stored in the collection For details of the quality flag mapping see the file ODV4_QualityFlagSets pdf Any Depth values in ARGO profile files are converted to pressure during import For ARGO profile data the ODV station name consists of cycle number profile direction if available A ascending D descending the data mode R real time data D delayed mode data A real time data with adjusted values and the project name if available The ARGO platform number is used for Cruise When importing ARGO trajectory files ODV averages pressure temperature salinity and oxygen values for given float cycles pressure gt 100 dbar required and uses these average values in the collections Only records with valid geographical position are im ported Once imported you may filter the data and exclude bad data from the analysis by set ting appropriate quality flag selection criteria via the View gt Sample Selection Criteria option 40 ODV User s Gu
176. nd section files File names lt name gt are arbitrary Default location of xview and sec files is directory lt col gt Data views but these files may also be stored in any other directory Extension Format Comment lt name gt xview ASCII View files storing layout value ranges derived and isosurface variable selections and many other settings The name of the collection that owns a configuration is recorded inside the xview file Certain re strictions apply if a different collection uses the xview file lt name gt sec Stores section outlines and characteristics 3 4 2 ODVGENERIC The information about collection variables station metadata and actual station data are stored in separate files var hob and dob respectively cfg files store view settings that define the way the user looks at the data in a collection View settings include items such as map domain station selection criteria window layout and many other parameters The required var hob and dob files of a collection must all be located in the same directory collection directory cfg files may be stored anywhere on the disk ODVGENERIC collections are supported by ODV4 for reasons of backwards compatibil ity All new collections created by ODV4 are ODVCE5 collections ODV collection files should not be edited manually Table 3 9 Summary of ODVGENERIC collection files Collection names lt col gt may not contain or and
177. nd the oxygen depth data distribution right for the data from Figure 10 7 95 Version 4 5 0 Estimate Data Misfits mean 0 0399973 rms 1 83696 Silicate umol kg Pi 10 5 s s eos 0 0 gt Q R 5 APO so ARE 10 5 15 Section Latitude Figure 10 9 Example plot showing the estimate data differences at the data locations 10 7 Isopycnals You may add isopycnals to T S data plots that have the derived variable Absolute Salini ty on the X axis and the derived variable Conservative Temperature on the Y axis or Practical Salinity on X and Potential Temperature on Y by choosing the Ex tras gt Isopycnals option of the data plot s popup menu On the Isopycnal Properties dialog specify the reference pressure of the isopycnals as well as their graphical properties Press the Switch On button to enable isopycnals To switch off the isopycnals choose Extras gt Isopycnals and press Switch Off The Extras gt Isopycnals option is disabled if the X variable of the window is not absolute salinity or the Y variable is not conservative temperature 96 ODV User s Guide 11 Graphics Objects You can add text annotations symbols lines and other geometric objects to the canvas the map or any data window Geographic feature data provided in ESRI shapefiles may be added to the station map The following graphics objects are supported 1 text an notations 2 straight
178. nd type of the poly line and the fill color of the polygon ignored for Line and Polyline choose none as fill color to avoid filling of the polygon Also note that lines wider than 1 pixel are always solid on many screen and printer devices However the requested line type is always honored in ODV Post Script files Polylines and polygons may be smoothed by checking the Bezier smoothing box 11 3 Rectangles and Ellipses You add rectangles squares and ellipses circles to the map data windows or the canvas by choosing Extras gt Add Graphics Object gt Rectangle or gt Ellipse from the map data window or canvas popup menus A red zoom rectangle will appear that represents the bounding box of the new rectangle or ellipse The zoom rectangle can be moved and resized then press ENTER to accept a setting or ESC to abort creation of the object A dialog box appears that lets you define properties of the rectangle or ellipse for details see Lines and Polygons 11 4 Symbols You add symbols dots squares diamonds triangles inverted triangles stars crosses pluses to the map data windows or the canvas by choosing Extras gt Add Graphics Ob ject gt Symbol from the map data window or canvas popup menus A cross hair cursor will appear and you should move it to the location where the symbol should appear Then click the left mouse button The Symbol Properties dialog box appears and lets you 99 Version 4 5 0 set vari
179. ne SURFACE window layout Ctrl Plus or Ctrl Wheel Zoom in at mouse position Ctrl Minus or Ctrl Wheel Zoom out at mouse position Ctrl A D Adds an annotation to the window containing the mouse Ctrl C 5 Copies the data or gridded field of the window containing the mouse to the clipboard or if the mouse is over a graphics object creates a copy of that object Ctrl F Adjusts the X Y Z ranges of the window containing the mouse or of all data windows to full 132 ODV User s Guide range CtrI N 4 Creates a new ODV collection Ctrl O 5 Opens an ODV collection netCDF file or supported ASCII data file Ctrl P Prints the entire graphics canvas Ctrl R D Move or resize the window containing the mouse window layout mode only Ctrl S 0 Saves the window containing the mouse or the entire canvas to an image file gif png jpg or PostScript Ctrl W or Closes the current collection or netCDF file Ctrl F4 Ctrl Z Undoes the last change Alt D Allows definition of derived variables Alt P Allows property changes of the window or graphics object containing the mouse Alt S Allows change of the station selection criteria Alt W Allows change of the window layout Alt Z Undoes all changes Shft E Edits the meta or sample data Shft L Loads view settings from a file Shft P Shows print preview of entire graphics canvas Shft S Allows ch
180. ne of the following pH fCOz or pCOz you must spec 62 ODV User s Guide ify output pressure and temperature conditions at which these variables are to be cal culated If the requested derived variable is pH you must also specify the output pH scale The recommended choice of equilibrium constants Best Practices Handbook 2007 fol lows Dickson et al 2007 except for Kr K and Kz are from Luecker et al 2007 Ko is from Weiss 1974 Kg is from Dickson 1990 Ks is from Dickson 1990 Kris from Dickson and Riley 1979 Kwis from Millero 1995 Kip K2zp K3p and Ks are from Mil lero 1995 and the solubility products Ksp of calcite and aragonite are from Mucci 1983 The pressure dependence of the equilibrium constants is from Millero 1995 Typographical errors in various publications as summarized in Lewis and Wallace 1998 are considered If phosphate and or silicate data are not available concentration values of zero are as sumed ODV uses the alkalinity definition of Dickson 1981 and treats all terms except HS S and NH3 pH is calculated using an iterative Newton method The SeaCarb version 2 1 2 software of Lavigne et al 2008 and the Matlab version of CO2SYS v1 01 Lewis and Wallace 1998 ported to Matlab by Denis Pierrot University of Miami has been run on the same sample data and excellent agreement of results has been found for all parameters of the carbon system offered by ODV Dickson A G S
181. ng the Validate or Clear buttons Individual entries may be deleted or edited directly in the list 50 ODV User s Guide 5 Exporting Data 5 1 Spreadsheet Files You can export the data of the currently selected stations into a single ODV generic spreadsheet file by choosing Export gt ODV Spreadsheet Then choose a target directory and filename select the variables to be included in the export file default all basic var iables and finally specify properties of the export file to be written On the Spreadsheet File Properties dialog see Figure 5 1 you may specify a missing value string default empty string the range used for longitude values 0 to 360 E or 180 to 180 E the metadata date format ISO08601 yyyy mm ddThh mm ss sss or mon day year the date time format used for time series date time values ISO8601 yyyy mm ddThh mm ss sss or Chronological Julian Days or Decimal Time in years Note that the Data date format entry is only enabled for time series data You may also specify whether all data should be exported or only those that satisfy the current quality and or range filters Checking the Use compact format box causes sta tion metadata to be exported for the first sample only while metadata fields for all oth er samples remain empty Using this option leads to significant reductions in export file size especially for data with many samples per station such as CTD XBT and many kinds of time series data If
182. nges In addition to stroking the contour line associated with a given Z value z you can also ask ODV to fill the region defined by Z values larger than z using an automatic or user specified color by choosing the color under Fill Figure 10 6b was produced by using automatic under Fill for all contour lines Depth m Sigma 0 kg m 27 2 Depth m Sigma 0 kg m 27 2 EQ 20 S 40 S 60 S 60 W 40 w 20W 0 20 E 60 W 40 w 20W 0 20 E Figure 10 6 Comparison of a continuously shaded and b contour shaded fields Color Mapping The Color Mapping page lets you manipulate the mapping between Z variable values and associated color This page is only enabled for data window with a Z variable e g color sections or color distributions on isosurfaces Press the Auto Adjust button to es tablish a possibly non linear mapping automatically constructed on the basis of the distribution of Z values Pressing the Linear Mapping button will restore the default linear color mapping You may establish customized color mappings by moving the Me dian trackbar to the Z value to receive the highest color resolution and increase the non linearity using the Nonlinearity trackbar DIVA Settings The DIVA Settings page lets you manipulate parameters that control the DIVA gridding algorithm For details see the description of the DIVA gridding method Note that this page is disabled if the data window does not use DIVA g
183. ns see the Map Layer Series section in chapter 2 12 If you have created your own custom coastline bathymetry series and want to have it included in the automatic series search you must create a settings file containing in formation on the domain and spatial resolution of the series See chapter Preparing Cus tom Coastline and Bathymetry Files for more information Manual Series Selection Unchecking the Automatic selection checkbox lets you select the bathymetry coastline topography series manually and also allows composing individual layer sets and speci fying their graphical appearance This mode gives you widest possible control over the design of the station map You may select any of the installed series by clicking into the Series combo box Please note that some series are regional and that you may have to manually adjust the map domain to the respective series domain Once a series is chosen you may define the lay ers in the various Layer Set categories see below When the map is drawn the layer sets and the layers within the sets are drawn in the given order To obtain information on a selected layer set e g Ocean Bathymetry click on the Layer Set Info button To define the layers of a selected layer set click on the Compose button Note that default layers are defined for all categories if the resulting map display suits your needs you don t have modify any layer set fi Ocean bathymetry Layer Set Se
184. nt Text or numeric user defined text length or 1 to 8 byte integer or floating point numbers Collection Variables Comment Continuous decimal time variable Unlimited number of other measured or calculated var iables To be used as primary variable Must be numeric 1 to 8 byte integer or floating point numbers 26 ODV User s Guide 3 3 Creating Collections New ODV collections can be created in a number of ways 1 Using the File gt New option 2 opening a spreadsheet data file with File gt Open or 3 by dropping spreadsheet data files onto the ODV icon Windows only or the ODV application window when no collec tion is open When using the File gt New option a file open dialog appears and you specify a collection name and directory in which the collection will be created The following characters are not allowed in collection names Y lt gt SPACE ODV then lets you define the meta and collection variables that will be stored in the col lection Meta and collection variables can be specified in a number of ways You may use variable names taken from a supported template file txt odv var or an ASCII spread sheet file with arbitrary extension you may enter the variable labels manually or you may use pre defined sets of variables standard and user supplied templates suitable for various published oceanographic datasets see Figure 3 1 The list of standard temp
185. ny data values for the set of sta tions being exported are excluded from the output file Note that ODV derived variables are not exported Quality flags are preserved if the collection already uses WOCE quality flags Otherwise the quality flags in the collection are mapped to WOCE schemas before exporting see ODV4_QualityFlagSets pdf for mapping details In case of WHP CTD export the output quality flags are either WOCECTD or GTSPP same as IGOSS In case of WHP Bottle ex port the output quality flags are either WOCEBOTTLE or GTSPP except for the CTDSAL or CTDOXY variables which use WOCECTD or GTSPP and the BTLNBR variable which uses WOCESAMPLE or GTSPP 5 5 Exporting X Y Z Window Data You can export the data values displayed in ODV plot windows to separate ASCII files by choosing Export gt X Y Z Window Data from the ODV menu bar Enter a descriptive text identifying the data of this export in the ID String field and click OK ODV will create a sub directory in the user s ODV directory lt documents gt ODV export lt ID String gt All exported files will be written to this directory If it already exists ODV asks for permis sion to delete all files from the directory before continuing Note that the names of the exported files start with win where represents the respective window number The 54 ODV User s Guide actual X Y Z data are found in files win oai one data point per line fourth column al ways 1
186. of Use ODV is designed to be flexible and easy to use Users need not know the details of the internal data storage format nor are they required to have programming experience ODV always displays a map of available stations on the screen and facilitates navigating through the data by letting the user select stations samples sections and isosurfaces with the mouse The screen layout and various other view settings can be modified easi ly and favorite settings can be stored in view files for later use ODV can create and manage very large data collections containing millions of stations on relatively inexpen sive and portable hardware Existing data collections can be extended easily if new data become available With its wide range of plot types and flexible interactive controls ODV greatly facilitates data quality control and is useful for training and teaching 1 2 Dense Data Format The ODV data format is optimized for variable length irregularly spaced profile trajec tory and time series data It provides dense storage and allows instant access to the data of arbitrary stations even in very large data collections The data format is flexible and accepts data for an unlimited number of variables The metadata and collection var 1 Version 4 5 0 iables are defined by the user at collection create time and different ODV collection may be created to store the values of different data types such as profiles trajectories or tim
187. one of the following variables pH fCOz or pCOz is among the selected input variables you must specify pressure and temperature at which these variables have been meas ured If pH is one of the input variables you must also specify the pH scale on which the pH values are reported Possible choices for the input pressure are 1 In situ pressure 2 Select pressure variable and 3 Enter your pressure value here You choose 1 if the input values are at in situ pressure you choose 2 if one of the collection variables con tains the input pressure values the respective variable will be identified later and you choose 3 if the measurements were done at fixed pressure e g laboratory conditions To enter the value select the Enter your pressure value here text and replace with the numeric value There are four possible choices for the input temperature 1 In situ temperature 2 Potential temperature 3 Select temperature variable and 4 Enter your temperature value here Choices and procedures are as for pressure above Fr Settings pH any C input pair Equilibrium constants Best Practices Handbook 2007 54 j Input Input Variables ALK fCO2 x Pressure dBar 0 v Temperature deg C 25 v Output Pressure dBar In situ pressure v Temperature deg C In situ temperature v pH Scale Total y Figure 6 1 The carbon parameter settings dialog If the requested derived variable is o
188. ons of given name patterns are from specific time periods Because of this fundamental importance ODV defines a set of mandatory meta variables providing name location and timing information of a given station see Table 3 3 Other suggested meta variables are optional and still others may be added by the user as necessary Meta variable values can be either text or numeric and the respective byte lengths can be set by the user The value type text or numeric of the mandatory meta variables may not be changed while the byte length may As an example the data type of the longitude and latitude meta variables may be set as 8 bytes double precision to accommodate better than cm scale precision of station location Meta variables with values in the ranges 0 to 255 or 32 768 to 32 767 may be represented by 1 or 2 byte integers respectively to conserve storage space Table 3 3 Mandatory and optional ODV meta variables Meta Variable Recommended Label Mandatory Cruise label text Cruise Station label text Station Station type text Type Date and time of observation numeric year month day hour yyyy mm ddThh mm ss sss minute and seconds Longitude numeric Longitude degrees_east Latitude numeric Latitude degrees_north Optional SeaDataNet station identifier text LOCAL_CDLID SeaDataNet institution identifier numeric EDMO_code Bottom depth at station or instrument dep
189. ools gt Invoke Macro Editor to facil itate macro definition Use the example macro files distributed with ODV as sample files for your own definitions You activate a macro derived variable by selecting Derived Variables from the current sample window popup menu and choosing Macro File from the list of available quanti ties Then select one of the macro files found in the ODV macros directory lt docu ments gt ODV macros and identify the variables needed to calculate the new quantity If one of the required variables is not available press Not Available to abort setup of the macro file 6 2 1 Macro Editor You can create and edit Ocean Data View macro files using the Tools gt Macro Editor op tion Select an existing macro file or choose a new macro name and define the macro following the instructions below When done press Save As and specify a name for the macro Macro Variable Label Enter the label of the macro variable Use formatting control sequences for Greek symbols exponents or indices Units Enter the units of the macro variable Use formatting control sequences for Greek symbols exponents or indices Digits Enter the number of significant digits for the display of values in the cur rent sample window Comments Enter one or more comments lines describing the macro variable 64 ODV User s Guide la Macro Editor Cant TrOCA_Tellus07 mac Label Units Digits C A N T TrOCA Telus07 umol kg
190. or Sec tion Distance depending on your choice of the Section Coordinate If you want to pro duce property distributions along the section put the section coordinate on the X axis of the plot 2 12 Settings You can customize general ODV settings such as the graphics and text fonts the size of the canvas or the browser and text file viewing commands using option View gt Settings on Mac OS X odv4 gt Preferences 16 ODV User s Guide Canvas Size Adjust the width and height of the ODV graphics canvas e g the white area onto which the map and data windows are drawn Click on Fit to screen to establish optimal settings for the current screen Note that it may be necessary to adjust the Graphics Font Size on the Font tab after large changes of the canvas size Fonts Choose a font family and various font properties and set a global font scaling factor Size Increase the Size value if you want larger graphics text and axis annotations or de crease it otherwise Note that some fonts may not be supported in ODV s PostScript output Also note that Graphics Font Size adjustments may be necessary after large changes of the canvas size see below The Text Font Size entry determines the font size used for menus dialogs and the cur rent station and sample list windows Highlighting Choose the color to be used for highlighting the position of the current station in the map and the current sample and data of the current sta
191. ou may also use View gt Window Properties gt Window x where x is the number of the window Some of the window settings such as value ranges or variables on the X Y and Z axis of the window may also be modified using the Set Ranges and X Y and Z Variable options of the data window popup menu Properties Window 1 Properties Window 1 Properties Window 1 Data Dapy Stye Contours Color Mapong ONA Settings General D a Depay Style Contows Coormappng OMA Settings General Data Duoi stve Comtows Coir Mappng ONA Setengs ope SECTIONE Duta of al stators nade the section Sand Section Leaghude YA Settings Defaut saung Aoo af window Heo x Gance nep Lo Gance Heo os Cancel Figure 10 1 The various pages of the Data Window Properties dialog part 1 of 2 The data window Properties dialog consists of six separate pages see Figures 10 1 and 10 5 General On the General page you can define the color palette used by the data window the background color of the data window the highlighting style of the current station a base font size and font size factor and the color of the axis and axis annotations Grid lines as well as the automatic variable labels on the axes can be switched on or off You may customize the text on the axes by switching off the automatic axis titles and creat ing your own annotation graphics objects Data On the Data page you can define the scope of the data window the variables
192. ous symbol properties 11 5 Symbol Sets and Legends You can highlight a subset of the data points in a data window or a subset of stations in the map by assigning a symbol to the selected data points symbol set To create a symbol set for a data window or the map move the mouse over this window and choose Extras gt Add Graphics Object gt Symbol Set The Symbol Set Selection dialog appears and lets you select the subset of data points select one or more cruises in the Cruises list stations in the Stations list and or individual samples in the Samples list Then press the lt lt button to add the selected data points to the Selected list Press OK once all desired points are selected The Symbol Set Properties dialog appears which lets you define the symbol and line characteristics A symbol set can have a descriptive text leg end which will automatically be added to the legends of the respective window check the Add to legends box Unlike other graphics objects symbol sets cannot be dragged because of their association with the selected data points You can change all symbol set properties at any time by moving the mouse over any one of its symbols clicking the right mouse button and choosing Properties Silicate Limol kg 150 25 125 204 100 157 10 Tpot 0 C O SAVE_LG6 361 Ocean Data View 34 35 36 37 Salinity psu Figure 11 1 Sample SCATTER plot
193. ouse over one of the symbols clicking the right mouse button and choosing Properties from the popup menu Some graphics objects such as axis labels unit arrow boxes or legends are created and deleted automatically automatic graphics objects These objects may not be edited or deleted manually automatic axis titles are switched on off on the General page of the window s Properties dialog Dialog boxes different for the different objects appear and let you change properties easily and quickly Graphics objects may be clipped to their parent window check the Clip to window box and they may be drawn before the data of the window are drawn check the Pre data plot box You delete an object by moving the mouse over it clicking the right mouse button and choosing Delete Object Dragging If the attribute Allow dragging of a graphics object is set the object can be re positioned by simply dragging it to a different location To drag an object move the mouse over it click and hold down the left mouse button and move the mouse By default dragging is switched on initially for all graphics objects except symbol sets which are linked to ac tual data values You can change the Allow dragging attribute at any time using the ob ject s Properties dialog see above Managing Graphics Objects You can manage the graphics objects of the canvas map or any data window using the respective Extras gt Manage Graphics Objects option This includes
194. ow unique column labels for applications that re quire this feature e g QV1 QV2 etc lt SchemalD gt may be one of the following ARGO BODC ESEAS GTSPP OCEANSITES ODV QARTOD PANGAEA SEADATANET SMHI WOCEBOTTLE WOCECTD WOCESAMPLE WOD or WODSTATION See Table 16 5 for more information on quality flag schemas In addition to quality flag values for individual data values ODV also supports entire station quality flags describing general quality aspects of the entire station single flag for a given station e g WOCE entire station flags as well as sample quality flags that 139 Version 4 5 0 may be used to indicate problems with the sampling device possibly affecting the quali ty of all measurements made on that sample one flag for every sample Entire station and sample quality flags are indicated with the words STATION or SAMPLE in the lt columnLabel gt part of the column label Note that the QV syntax of quality flag labels is not recognized by ODV versions 3 or earlier If ODV generic spreadsheets file needs to be compatible with these earlier soft ware versions you must use QF as the label of quality flag columns In such cases it is assumed that the quality flag values are ODV generic flags and that they belong to the variable preceding the quality flag column Table 16 7 Example quality flag column labels Quality Flag Label Comment ODV generic quality flags for the variable in the preced
195. ple in ascending order of primary variable values while the up arrow key will select the previous one Pressing the PgUp or PgDn keys will move the current sample forward or backward in larger steps Pressing Pos 1 or End will move to the first or last sample of the station 2 11 Map and Data Window Drawing The map and data windows automatically draw or redraw themselves at program start or whenever a view is loaded or one of the many layout or display properties is modi fied Data windows of scope STATION or SECTION remain empty if the list of picked sta tions is empty and no section is currently defined To adda station to the pick list either double click on the particular station mark in the map or click on the mark to make the station the current station and then press ENTER Repeat this procedure for other stations that you want to add to the pick list The pick list can hold an unlimited number of stations You delete a station from the pick list by making it the current station e g click on one of its data points in a STATION window and pressing the Delete button You can edit the properties of pick list entries via the Manage Pick List gt Edit Pick List option of the map popup menu To define a section or change section properties use options from the Manage Section menu of the map popup menu Once a section is defined the along section coordinate is available as a derived variable This can be Section Longitude Section Latitude
196. ption To modify the data of a given sample of the current station right click on the current sample list window and select Edit Sample Data The Edit Sample Data dialog appears showing the data values and quality flags of all collection variables for the current sam ple You change the data value or quality flag of a particular variable by clicking on that variable and then on the Change Value Delete Value or Change Quality Flag buttons You may delete the current sample including all data values for all collection variables by right clicking on the sample list window and choosing option Delete Current Sample Alternatively you may add a new sample by right clicking on the sample list window and choosing option Add New Sample Enter the primary variable value of the new sam ple and press OK 107 Version 4 5 0 Edit Data Salinity pss 78 ll Data Depth m Salinity pss 78 OF js 20 2957 34 928 4 21 2958 34 923 0 zo o 23 3348 34 91 o E 24 3545 34 902 0 Delete value s 25 3741 34 897 o O Change Quality Flag s 26 3838 34 893 0 27 3935 34 888 o E 1 out of 32 samples selected Select All Invert Selection Data gt Variable 1 Depth m 2 Temperature C 3 Salinity pss 78 PA Oxygen mol kg 5 Phosphate umol kg 6 Silicate umol kg 7 Nitrate umol kg 8 Nitrite umol kg 9 CFC 11 pmol kg 10 CFC 12 pmol kg 11 CCL4 pmol kg L12 CEC113 fonmal kal Figure
197. rately ddmmyyyy Example 23022006 for Feb 23 2006 Date in one column Time provided separately yyyymmdd Example 20060223 10 23 for Feb 23 2006 10 23h year Date information in individual columns any order Time month provided separately day Example 2006 2 23 for Feb 23 2006 Table 16 9 Supported time formats column labels may be upper lower or mixed case Column label Comment hh mm Time in one column Date provided separately Example 10 23 for 10 23h hhmm Time in one column Date provided separately Example 1023 for 10 23h 142 ODV User s Guide hour Time information in individual columns any order Date provided sepa minute rately Example 10 23 for 10 23h 16 5 Control Sequences and Functions in Annotations Table 16 10 Formatting control sequences in ODV annotations Control Sequence Action Switches to Symbol font Greek symbols Switches to normal text font Produces per mille character o A Next character drawn as superscript Next character drawn as subscript Example S CO _2 m mol kg will produce CO2 umol kg ABXAE OTHISKAMNOTI PLTYcQER PZ ABCDEFGHIJKLMNOPQRSTUVWXYZ aByoebynipKALVvoTOpotU aM oye abcdefghijklmnopqrstuvwxyz Figure 16 1 Greek symbols and Latin equivalents Table 16 11 Available auto functions in ODV annotations Function Substituted Text date Current date time Current
198. rd step 3 of 4 Subsetting dimensions When working with large netCDF datasets it is convenient to restrict data access to the domain and depth or time ranges of interest By default ODV adjusts the increment val ues stride of the longitude and latitude dimensions such that the total number of sta tions does not exceed 300 000 E NetCDF Setup Wizard Subset Dimensions Step 4 of 4 2592 stations You can reduce the number of stations by subsetting one or more dimensions or by zooming into the map NetCDF dimensions lon 72 use 0 1 71 lat 36 use 0 1 35 time 1872 use 0 1 1871 Heb J lt Back Next gt cancel Figure 13 4 The netCDF setup wizard step 4 of 4 115 Version 4 5 0 You can manually subset any of the coordinate variables or narrow down the domain by zooming into the map To subset a particular dimension select the corresponding item in the NetCDF dimensions list and press the Subset Dimension button ODV shows a list of the respective coordinate values and lets you specify a start index increment and end index for this coordinate Press OK to accept the new index set Repeat this proce dure for all dimensions that you want to subset To define a sub region of interest press the Zoom into Map button then resize and or move the red zoom box to the desired domain and press the Enter button or double click the left mouse to accept your choice Press
199. rdColor is the background color of the text bounding box frameColor is the frame color of the text bounding box and frameWidth is the width of the frame around the text bounding box All colors are specified as index values into the current color palette Specify 1 for bckgrdColor and or frameColor to avoid drawing of a background box or frame Note that all arguments to set_annotation_style are integers Default values are 16 0 1 1 0 which will produce 16pt black text without box or frame 127 Version 4 5 0 Example set_annotation_style 24 8 7 0 1 set_base_directory base_directory Define a base directory All subsequent file names are assumed to be absolute pathnames or names relative to base_directory Example set_base_directory c ewoce data Following below is an example ODV command file that opens a collection loads a view adds an annotation writes two image files of the entire canvas and of data window 1 respectively exports the data of the currently selected stations to an ODV spreadsheet file and finally shuts down ODV set_base directory c data eWOCE data whp bottle set_annotation_style 18 0 7 0 1 open_collection WoceBtl var load_view cfgAtlanticSections A15_OXYGEN xview create_annotation 1 13 18 65 83 0 6 Test export_graphics 1 c atmp A15_OXYGEN png 100 export_graphics 1 c atmp A15_OXYGEN_1 png 200 export_data c atmp A15_OXYGEN txt quit 15 5 Gazetteer of Undersea Features
200. rdware You can produce high quality station maps general property property plots of one or more stations scatter plots of selected stations section plots along arbitrary cruise tracks and property distributions on gen eral isosurfaces ODV supports display of original scalar and vector data by colored dots numerical data values or arrows In addition there is choice between three differ ent gridding algorithms providing estimates on automatically generated grids and al lowing color shading and contouring of fields along sections and on isosurfaces A large number of derived quantities can be calculated on the fly These variables may be dis played and analyzed in the same way as the basic variables stored on disk This version ODV4 is based on a new object oriented software code and overcomes many limitations of previous ODV versions To ensure backwards compatibility ODV4 supports existing collections and configuration files now called views created under previous ODV versions All newly created collections however now use a new and more general data model and internal storage format As before ODV4 data collections maintain platform independence and may be moved between all supported systems Among the novel features of the new data model are more flexible metadata schemes support for an unlimited number of collection variables user specified data types and custom quality flag schemes for meta and collection variables 1 1 Ease
201. recording the new entries in the collection s settings or variables files Adding or deleting variables changing the collection s primary variable or altering the data type or quality flag schema of a variable are severe changes that require a com plete re writing of the metadata and data files of a collection You should make a backup 103 Version 4 5 0 copy of the entire collection for instance by using the Collection gt Copy option before applying severe collection changes Please note that if collection re writing occurs the new version will always use the new ODVCF5 collection format odv collection even if the original collection was ODVGENERIC var collection The new ODVCF5 collection cannot be opened with the previous ODV3 12 5 Key Variable Associations Many derived variables require identification of the input variable s needed for the calculation of the derived variable This identification of key variables is done during the first definition of the derived variable and the selected variables are remembered in the collection s settings file If the derived variable is requested again at a later time the stored key variable information is used and the user is not prompted again You can inspect and modify the current key variable associations using Collec tion gt Identify Key Variables The Identify Key Variables dialog will appear showing lists of key variables on the left and collection variables on the
202. red in the col lection To import WHP exchange format bottle data into the currently open collection choose Import gt WOCE formats gt WHP Bottle exchange format from ODV s main menu Use the standard file selection dialog to select the WHP data set The default suffix of WHP bot 41 Version 4 5 0 tle exchange files is_hy1 csv If your data file has a different extension choose file type All Files in the file selection dialog The next step is to identify the variables Depth in Water Column In situ Temperature and Salinity in the receiving collection because these variables are required for successfully importing the data files The identification needs to be done only once for a given collection and the choices are remembered See chap ter 12 5 for further information on variable identification Then specify import options and press OK to start the data import ODV will read and import all stations in the data file ODV identifies and imports the WOCE data quality flags in addition to the actual data values These quality flags can later be used to filter the data by excluding for instance bad or questionable data from the analysis You can modify the data quality filter by choosing selection criteria from the map popup menu choose the Sample Selection tab To import CTD data into the currently open collection choose Import gt WOCE for mats gt WHP CTD exchange format from ODV s main menu and select the _ct1 zip file tha
203. rget samples and finding the closest matches On the Sample Matching page you may specify pa rameters that determine how close import and target samples have to be in order to be considered a match Non matching samples will be added to the target sta tion as new samples if the Add non matching samples as new samples box is checked Otherwise non matching samples are ignored and a warning message is written to the import log file 4 11 Generating File Lists ODV has a built in list file generator which can be used to create lst files for multi file data imports These list files are useful if you want to import large numbers of ARGO SDN WOD or WOCE data files into ODV in one step To invoke the list file generator you use option Tools gt List File Generator The generation of these files is done by simply dragging and dropping files or entire directories of interest onto the dialog When dropping a directory all files in this direc tory or any of the sub directories are added to the list If you apply filters specifying the beginning or end of the filenames only those files satisfying the filter are added to the list These filters must be applied before dropping the files This allows creating lists of files with different start and or suffix Note that you can activate case sensitive filtering by checking the Case sensitive check box Once a file list is created duplicates can be re moved or the current selection can be cleared by pressi
204. riable On the third page of the setup wizard Figure 13 3 you select the primary variable This variable plays the role of the primary collection variable and determines whether the data are interpreted as vertical profiles or time series If for instance Depth or oth er vertical dimensions are used as primary variable the stations will represent vertical 114 ODV User s Guide profiles if you use a Time variable the stations will represent sequences in time If the Year meta variable was defined on page 2 of the wizard the Use decimal date time item is enabled and you can use a decimal time variable units YEARS derived from the sta tion header as primary variable note that for time series the date time meta infor mation refers to the start of the time series and is a constant value Quite often netCDF files contain data values on a horizontal grid e g fluxes across the air sea interface or concentrations at given depth layers without providing a variable specifying the exact value of the layer e g depth 0 m or depth 1000 m In such cases you should choose the Use dummy variable item a gt NetCDF Setup Wizard Select Primary Variable Step 3 of 4 Available netCDF dimensions Time days since 1800 1 1 00 00 00 9 Use selected variable Use decimal date time header Use dummy variable Hep l lt Back Finish Cancel E Figure 13 3 The netCDF setup wiza
205. riable along sections or for isosurface variables in order to display the spatial extent of specific water masses see Figure 6 4 68 ODV User s Guide Patches DEPTH M amp S 40 S 20 S EQ SALINITY PSS78 Patches 20 p g 5 E 3 Ele E o 405 205 EQ 20N N 60N 34 35 A SALINITY PSS78 San borer Figure 6 4 Using patches to identify the extent of water masses 69 Version 4 5 0 70 ODV User s Guide 7 Isosurface Variables Often there is a scientific need to calculate and display the distribution of a variable on a specific 3 dimensional surface defined by some constant value of another variable isosurface The concept of isosurfaces is quite general In oceanography for example isosurfaces may be defined as constant depth pressure or potential density surfaces isopycnals For sediment core data with known down core age estimates isosurfaces could be defined as constant sediment age surfaces thereby producing distributions of others variables on the constant age surfaces easily time slicing Isosurface variables are defined in ODV using View gt Isosurface Variables or by right clicking on the Isosurface Data Window and choosing Isosurface Variables ODV will show the Isosurface Variables dialog Figure 7 1 that lets you define new isosurface variables modify existing ones or delete some of the currently define
206. ridding 10 2 Zooming and Automatic Scaling You can change the variable ranges of any data plot by moving the mouse over this window clicking the right mouse button to invoke the data window popup menu and choosing either Full Range or Zoom For Full Range the X and Y Ranges of the current window are adjusted to accommodate all plotted data values in this window If you use Full Range All on the canvas popup menu you can auto scale all data plots on the 91 Version 4 5 0 screen in one operation If you select Zoom a red zoom frame appears around the current window To manipu late this zoom frame move the mouse over its edges corners or interior press the left mouse button and drag the edges corners or the entire frame to the desired locations Note that the x y coordinates of the lower left and upper right corners are indicated in the middle part of the status bar To accept the current setting of the zoom frame and adjust the variable ranges accordingly double click the left mouse button or press ENTER If you want to abort the zoom operation and keep the original variable ranges press ESC or click the right mouse button In addition to the normal zoom procedure described in the previous paragraph there is an additional zoom method quick zoom that may be even easier and quicker to use in many situations While the mouse is over a data window or the map press and hold down the Ctrl key on Macintosh systems use the Apple ke
207. rmore note that for picked stations whose station type dif fers from B no symbols are assigned initially and just the line between the station s samples is highlighted Once you define a symbol type manually it will be used perma nently introduced in ODV version 4 2 0 9 3 Sections You must define a section in the station map before SECTION data windows can be plot ted To define a new section or use a previously defined section right click on the map to invoke the map popup menu Choose Manage Section gt Define Section if you want to 81 Version 4 5 0 define a new section or Manage Section gt Load Section if you want to load a previously defined one In the latter case simply select a section file from the file open dialog e g by double clicking on it If you create a new section ODV temporarily switches to a full page map for easier definition of the section spine Note that the mouse cursor changes to a cross hair indicating that the user is expected to enter a sequence of points defining the centerline of the section You enter a point by moving the cross hair to the desired location and clicking the left mouse button To remove a point move the mouse close to it and click the right mouse button To accept the set of points press ENTER or specify the last point with a double click of the left mouse button Note that you may construct rather complicated sections following arbitrary cruise tracks as shown in Figure 9
208. rom a net work of European data centers http www seadatanet org As the result of a data query SDN delivers a number of zip files one from every data center responding to the query These zip files contain a potentially large number of individual data files each one holding the data of a single profile time series or trajectory The individual data files are in ODV spreadsheet format and could in principle be im ported into ODV directly However direct spreadsheet imports would be tedious be cause of the large number of files and the fact that only one file can be dealt with at a time A further complication is that the type of data profiles time series and trajecto ries and the set of variables in the individual data files may differ greatly thereby pre cluding import into a single ODV data collection The Import gt SDN Spreadsheet option addresses these problems All selected individual import files will be processed in one step and separate ODV data collection will be cre ated and filled for every data type found in the SDN import package Once you have downloaded the SDN data zip files invoke Import gt SDN Spreadsheet Then navigate to the directory containing the downloaded data and select the files that you want to import and specify a parent directory to receive the results of the SDN im port Note that every time you initiate a SDN import a subdirectory will be created in the SDN parent directory and the output fro
209. rt Selection Figure 11 2 The Graphics Objects dialog The Graphics Objects dialog Figure 11 2 appears letting you select individual objects 101 Version 4 5 0 sub groups of objects or the entire list of objects If you have selected one or more ob jects you may delete all selected objects by pressing Delete or you may export all select ed objects to a gob or shp file for subsequent re use by pressing Export If you have se lected just one object you may also copy the object by pressing Copy or change the properties of the object by pressing Edit You may also change the drawing order and bring the object closer to the foreground Foreground or Up or background Back ground or Down If you are exporting multiple objects into a shapefile please note that ODV will create individual files for every object type in the selected set For all created shapefiles except the first one ODV will automatically append to the filename strings describing the ob ject type e g _points _polygons or _lines Note that if at least one of the exported ob jects is a symbol set all symbols and symbol sets are written to a shapefile with mul tipoint geometry If at least one of the exported objects is a polygon all lines and poly gons are written to the shapefile as polygons The current shapefile export implementation has some limitations a CDT file objects and annotations cannot be exported to shapefiles yet b no proje
210. rt gt NetCDF File Then choose a target directory and filename select the variables to be included in the export file default all basic variables and finally specify properties of the export file to be written On the NetCDF File Properties dialog you may specify the range used for longitude values 0 to 360 E or 180 to 180 E and whether all data samples should be exported or only those that satisfy the current quality and or range filters If you do not want quality flag values of meta and or collection variables to be exported uncheck the Export metadata quality flags and or Export data quality flags boxes Structure of the exported netCDF file Dimensions e N STATIONS contains the number of stations contained in the file e N SAMPLES contains the maximum number of samples per station e N META VARS and N_VARS contain the numbers of meta and data variables in the netCDF file The names of meta and data variables typically start with META_VAR_ and VAR see variables section below for further details e In addition there may be one or more dimensions of the form N_STRING 1 where represents an integer value These dimensions are used for string meta variables and indicate the maximum string length Variables e The netCDF variables Longitude and Latitude store the stations positions e Date_Time contains the decimal time in Gregorian Days of the stations relative to a certain reference date with the decimal part repres
211. s using the ARGO profile or trajectory variables If you don t already have such a collection open create one using the File gt New option When prompted to define the collection variables choose ARGO profile variables or ARGO trajectory variables depending on the type of data that you want to import To initiate the data import choose Import gt ARGO For mats gt Float Profiles netCDF v2 2 or v2 1 or Import gt ARGO Formats gt Float Trajectories netCDF v2 2 or v2 1 ODV then presents a standard file open dialog and lets you select one or more ARGO netCDF data files in a given directory Alternatively you may select an ASCII file containing the list of file names to be processed This list file has to be pre pared before you start the import It must contain one filepath entry per line and the file paths must be either absolute pathnames or pathnames relative to the currently open collection The list file must have extension st You can generate file lists easily with the built in list file generator ODV then displays the import options dialog If you import into a collection created for ARGO float profile or trajectory data see above you may simply press OK to start the data import The variables in ARGO profile or trajectory collections include pressure temperature salinity and oxygen These variables come in three versions 1 the real time or raw data first group 2 the delayed mode or adjusted data second group suffix adj i
212. settings xml file located in the lt install gt include import directory The user may create an additional sdn_import_settings xml file in the lt user gt import directory containing additional user specific settings User settings prevail in case of conflicts Whenever a variable included in the sdn_import_settings xml file is encountered in a SDN import file the variable label specified in the settings file is used rather than the label in the SDN import file For instance variables with codes SDN P011 PRESPRO1 SDN P011 PRESPS01 and SDN P011 PRESPSO2 are all assigned the label Pressure and only one collection variable Pressure is created During import data from all three im port variables will be assigned to the single Pressure target variable If you want to ensure that data for two or more SDN parameter codes are merged into a single collection variable you should create a user settings file lt user gt import sdn_import_settings xml and add entries for the particular codes For instance if you know that different codes SDN P011 0DSDM021 SDN P011 PPSUCSO1 SDN P011 PSALCC01 etc are used for Salinity in different SDN import files and you want to merge all these data into a single variable Salinity you should add the following lines to the lt Labels gt tag of you user sdn_import_settings xml file lt Entry code SDN P011 ODSDM021 value Salinity gt lt Entry code SDN P011 PPSUCS01 value Salinity gt lt Entry cod
213. spreadsheet files 04x ODV list files On all platforms ODV supported file names can also be used as command line argu ments Start ODV from any terminal window by typing odv4 file name extension Note that for file name you either use absolute pathnames or pathnames relative to the directory from which you start ODV If you use a relative pathname and are not allowed You can use command line arguments to 1 start ODV and open an existing collection use the collection name for file name If you omit an extension the default odv is used 2 create anew collection and import data use the name of the data file must be 125 Version 4 5 0 one of ODV s import types e g 04x txt to be imported for file name In this case you must provide the extension ODV will create a new collection in the di rectory of the import file and will import the data from the file The collection variables are determined from information in the data file 15 4 ODV Command Files You can store commands for frequently used operations such as opening a collection loading specific view files and creating graphics or data output files in ODV command files ODV command files can be executed at any time batch mode using the File gt Execute Command File option or using the x cmd_file command line option The default extension of ODV command files is cmd The default location is the directory ODV cmd files in t
214. t eps files for the entire screen or any individual data window or the map right click on the canvas or the respective data window or map and choose Save Canvas As Save Plot As or Save Map As alternatively you can also press Ctrl S while the mouse is over the canvas data window or map choose PostScript eps for the file type and specify the name and destination of the output file ODV then presents the PostScript Settings dialog that lets you specify the orientation and size of the PostScript output The resulting Encapsulated PostScript files can be printed by 93 Version 4 5 0 sending it to a PostScript printer or it can be imported into LaTex or Word documents or may be opened with external graphics software such as Adobe Illustrator or Corel Draw for editing and processing If you intend to include the ODV eps output files in other documents make sure to uncheck the Show Collection Info box on the PostScript Settings dialog GIF PNG JPG and Tiff Files You can save the entire canvas individual data windows or the map in gif png jpg or tiff files by choosing Save Canvas As from the canvas popup menu Save Plot As or Save Map As from a data window or map popup menu and selecting the respective file type These options can also be invoked by shortcut key strokes 1 pressing Ctrl S while the mouse is over the canvas area saves the ODV graphics canvas while 2 pressing Ctrl S with the mouse over the map or a data windo
215. t contains the CTD data to be imported The next step is to identify the variables Pressure or if not available Depth in Water Column In situ Temperature Salinity and Oxygen umol kg or if not available Oxygen ml l in your collection After setting the import options ODV will then unpack the zipped file and import all CTD stations into the currently open collection Import files with different extensions can be selected by switching the file type filter to either _ct1 csv for single CTD profiles or All Files You can import data from multiple WHP Bottle or CTD exchange files in a single import operation One way to do so is to prepare an ASCII file with default extension st that contains the names of the files to be imported Use full pathnames and specify one file name per line Then choose either WOCE formats gt WHP Bottle exchange format or WOCE formats gt WHP CTD exchange format change the file type filter to st select your list file specify import options and press OK to start the data import Another way of multi file data import is to simply select multiple WHP bottle or CTD exchange files on the file open dialog When selecting multiple st list files only the first one will be rec ognized for data import 4 7 Medatlas Format Data The Medatlas format was used to create the MEDAR Medatlas 2002 data compilation containing water column data for the Mediterranean and Black Sea MEDAR Group 2002 MEDATLAS 2002 database Me
216. t in smooth estimates For the 3D Estimation all original data points from all stations currently shown in the map will be used The weight with which a given data point influences the estimate at a specific target location is inversely proportional to the 118 ODV User s Guide distance between data and target points The output file contains one line of results for every longitude latitude and depth point specified in the input file Each line contains six numbers x y z v d n with the following meaning XY Z longitude latitude depth as specified in the input file v estimated value d normalized distance of averaged data x y z positions from estimation point in units of averaging length scales n number of data points used 14 4 Box Averaging You can use ODV to calculate averages and standard deviations for basic or derived var iables in given longitude latitude depth boxes Only stations currently shown in the map are considered and only stations and data points inside the requested box are ac tually used for the mean and standard deviation You can specify appropriate station selection criteria prior to invoking the Box Averaging option to obtain averages for dif ferent station subsets years months or seasons To invoke box averaging choose Tools gt Box Averaging from the main menu ODV prompts for the ASCII box definition file containing the geometry information of the boxes for which output is to be pro du
217. t the speci fied default settings are used for all data lines in the file Press OK when done or Cancel to abort the import procedure Note that the Longitude and Latitude meta variables have to be associated ODV cannot handle stations without given geographical posi tion and that the OK button will remain disabled otherwise Note that associations or conversions of composite source variables such as the ISO 8601 date and time specification YYYY MM DDTHH MM SS SSS will automatically con nect with multiple target meta variables e g Year Month Day etc Meta Variable Association Source Variables Meta Variables 1 EXPOCODE a Cruise 2 SECT_ID E Station 3 STNNBR E NAR A ES 4 CASTNO Longitude degrees_east 5 SAMPNO Latitude degrees_north 6 BTLNBR sebBe ai year 7 BTLNBR_FLAG_W F Month 8 DATE Undo Day 9 LATITUDE Hour 10 LONGITUDE Minute 11 DEPTH METERS Second 12 CTDPRS DBARS Bot Depth m 13 CTDPRS FLAG W ad 5 out of 61 variables used 5 out of 12 variables associated Heo a ene Figure 4 2 The Associate Meta Variables dialog 4 10 Import Options Dialog When importing data ODV will present an Import Options dialog that lets you control the actions taken during data import see Figure 4 3 46 ODV User s Guide Import Mode rc Import Options Import Mode Add Replace Station Data
218. tation after the other are written to ODV spreadsheet format files e g these files themselves can be imported easily and visualized with ODV You can use the 1D Estimation option to obtain for instance standard depth pressure profiles of a variable stored in your collection Choose Ex tras gt 1D Estimation from the respective data plot popup menu to invoke 1D Estimation In addition to the various point estimation methods described above ODV can also be used to calculate averages and standard deviations for user specified longi tude latitude depth boxes All currently valid samples inside a given box are used for the averaging Box averaging differs from point estimation whereas all point estima tion methods always yield a value potentially of poor quality ifno data are found nearby the box averaging procedure only returns results if data values are actually found inside the box 1 10 NetCDF Support In addition to native data collections ODV can also access and visualize data in local or remote netCDF files widely used for platform independent storage of original data as well as model output ODV requests help from the user for the identification of key co ordinates and variables in the netCDF file by means of an easy to use netCDF emulation wizard The content of the netCDF file is then presented to the user as if the netCDF file was a native ODV collection All ODV analysis and visualization options are available for the explora
219. ters in physical and chemi cal oceanography by invoking the Tools gt Ocean Calculator option On the Ocean Calculator dialog Figure 14 2 you first select in the Available functions list the function that you want to be calculated you then enter values for the input variables under Input values and finally press the Evaluate button to receive the desired function value in the Result field You change the calculator settings by pressing the Settings button On the Calculator Settings dialog Figure 14 3 you may specify the vertical coordinate in the water column Pressure dbar or Depth m the set of equilibrium constants the carbon data input pair and the pH scales input and output used for the calculation of carbon parameters in seawater ODV remembers your settings and the last input values between Ocean Calculator invocations Note that you can continue using ODV while the Ocean Calculator is open 121 Version 4 5 0 Note that some functions require practical salinity as input while others use absolute salinity 122 Pressure dbar Temperature degC Practical Salinity psu Phosphate umol kg Silicate umol kg ALK umol kg DIC umol kg Result 4 20750302 Latent Heat of Evaporation kJ kg Latent Heat of Melting kJ kg Neutral Density yn kg m Omega_A ALK DIC Omega_C ALK DIC Oxygen Saturation Oxygen Saturation umol kg pCO2 ALK DIC uatm pH ALK DIC Potential Densi
220. ters of a derived variable or the expressions of ODV macros and expressions for more information on these special derived variables see below select the respective variable in the Already Defined list box and press Edit Table 6 1 List of built in derived variables Variable Comment Carbon Alkalinity any C input pair umol kg details CO 2 any C input pair umol kg details CO32 any C input pair umol kg details DIC any C input pair umol kg details fCO2 any C input pair Atm details HCO any C input pair umol kg details Omegaa any C input pair details Omegac any C input pair details pCO 2 any C input pair uAtm details pH any C input pair details Revelle Factor any C input pair d fCO2 d TCO gt fCO2 TCO gt details Expressions Derivatives Integrals Expression User defined expressions Macro File User defined expressions from macro files Ratio Any two variables Vertical Derivative Any variable details Second Vertical Derivative Any variable Vertical Integral Any variable details 58 ODV User s Guide Gases AOU umol kg Apparent oxygen utilization CFC 11 Saturation Warner amp Weiss Deep Sea Res 32 1485 1497 1985 CFC 12 Saturation Warner amp
221. th out first reading through all the preceding data e Appendable Data can be appended to a netCDF dataset along one dimension without copying the dataset or redefining its structure The structure of a netCDF dataset can be changed though this sometimes causes the dataset to be copied e Sharable One writer and multiple readers may simultaneously access the same netCDF file The netCDF data model is very general and the structure and contents of netCDF files can vary considerably In order to facilitate and promote the interchange and sharing of netCDF datasets a number of conventions have been defined Two of these conventions CF and COARDS see http www unidata ucar edu packages netcdf conventions html for detailed specifications are widely used by climate researchers and modelers and many datasets are available as CF COARDS compliant netCDF files Examples of such datasets can be downloaded from http www cdc noaa gov PublicData http ferret wrc noaa gov http ingrid ldeo columbia edu or http www epic noaa gov epic ewb For more information on netCDF see the netCDF web page http www unidata ucar edu packages netcdf 13 1 NetCDF Support ODV can open a wide range of netCDF files including but not limited to CF COARDS compliant files These files may reside on the local file system or on a remote OPeNDAP server Once a netCDF file has been successfully opened ODV presents the data in the file to the user in the sa
222. th numeric Bot Depth m Additional user defined meta variables text or numeric 23 Version 4 5 0 3 1 2 Collection Variables The collection variables represent the parameters for which data have been obtained on the samples of the stations The total number n of collection variables Var see Table 3 2 and their particular meaning are arbitrary All collection variables must have nu meric values text values are currently not supported One of the collection variables the primary variable is special and is used for sorting the samples in ascending order of primary variable values Usually the first collection variable Var serves as primary variable but any other variable can be chosen for this purpose The primary variable is defined when the collection is created 3 2 Example Collection Types The ODV data model described above is flexible enough to support a wide range of dif ferent data types from various fields of geosciences and environmental research The following examples cover some of the main applications Other more exotic cases not listed here may also be within the scope ofthe ODV data model 3 2 1 Profile Data This category covers a wide range of observations including for example oceano graphic profiles made at fixed positions or along steered or passive current following tracks by moored or drifting instruments or from ships In all these cases each individ ual profile should
223. the collection disk files is not freed until you sort and condense the collection 12 4 Changing Collection Properties The properties of the open collection may be modified using the Collection gt Proper ties gt options There are three sub options General Meta Variables and Collection Var iables With the General option you may define the field of the data GeneralField Ocean Atmosphere Land IceSheet Sealce Sediment the type of the data General Type Profiles Trajectories TimeSeries and the primary variable used to sort the data The data field and type entries are not used presently Future ODV versions however may offer different sets of derived variables depending on the data field or may apply different default plotting styles depending on the data type The Meta Variables and Collection Variables options allow modifications of the meta and collection variable sets This includes adding new variables deleting existing ones or changing the properties of the variables The properties of a variable that may be modified are the data type byte length as well as the quality flag schema used for the variable s quality flags Note that the first eleven meta variables are mandatory and that they may not be deleted or re ordered Some modifications such as changes of the collection s data field data type or the la bels units and number of significant digits of variables are simple changes that can be dealt with by
224. tion in the data windows Axis Synchronization Switch on or off the range synchronization between different data windows If range synchronization is on and the axis range of a variable is changed in one window the range of this variable in other windows will be changed accordingly Other windows remain unchanged if range synchronization is switched off Map Resources Install or uninstall optional high resolution coastline and topography resources for the whole world or specific regions The following map resources are available for download and installation 1 the ETOPO1 global relief data of Amante and Eakins 2009 in 2 x2 and 6 x6 resolution 2 the GEBCO08 global elevation data version 2010 09 27 http www gebco net in 2 x2 and 6 x6 resolution 3 the JBCAO bathymetric data http www ngdc noaa gov mgg bathymetry arctic for the region north of 60N in 1 x1 resolution taken from the ETOPO1 2009 resource 4 regional series for the Baltic North Sea Mediterranean and Kerguelen area Figure 2 5 Example maps of the Fram Strait region using a GlobHR b ETOPO1_6min and c ETOPOI_2min 17 Version 4 5 0 These extra series can be installed or uninstalled at any time from within ODV using the View gt Settings gt Map gt Resources ODV4 gt Preferences gt Map gt Resources on Mac OS X option Manual download and installation of optional packages is no longer needed The ETOPO1
225. tion of the data in the netCDF file NetCDF files are platform independent and can be used on all ODV supported systems ODV User s Guide 2 First Steps 2 1 Installing Ocean Data View You must install ODV on your computer before you can use the software The latest ODV installation files for Windows Mac OS X Linux and UNIX systems can be downloaded from http odv awi de en software download Note that you have to register and use your personal login data to get access to the download pages Detailed installation instructions are provided in INSTALL txt files Please see the License Agreement for ODV usage rules SUPPORTED PLATFORMS This ODV release runs on the following platforms Windows NT 98 2000 XP Vista and Windows 7 Mac OS 10 3 9 or higher Linux distributions released since June 2006 running kernel version 2 6 15 or higher The Linux version was tested under Fedora 9 Ubuntu 6 0 6 OpenSUSE 10 2 and Debian 4 1 IMPORTANT NOTE The ODV user directory has been moved from odv_local in the us er s home directory in ODV3 to sub directory ODV in the user s document directory Private palette macro gazetteer command or graphics objects files created by the user have to be manually copied to the new user directory to make them available to ODV4 The same applies to reference datasets saved with previous ODV versions The full user directory path as well as other ODV settings can be obtained via Help gt About ODV or odv4
226. to the currently open collection The list file must have extension st You can generate file lists easily with the built in list file generator ODV then displays the import options dialog As a final step you are prompted to enter a pressure subsampling value If you do not want data subsampling keep the zero value ODV will then import all selected files If no collection is open when you drop Sea Bird CNV files onto the ODV window or you 1 Gordon L I J Joe C Jennings A A Ross and J M Krest 1993 A Suggested Protocol for Continuous Flow Automated Analysis of Seawater Nutrients Phosphate Nitrate Nitrite and Silicic Acid in the WOCE Hydrographic Program and the Joint Global Ocean Fluxes StudyWHPO 91 1 55 pp see page 48f 44 ODV User s Guide select Sea Bird CNV files via the Import gt Sea Bird CNV option ODV will analyze the con tents of the Sea Bird files and will automatically create a collection with all the variables contained in the import files and this collection will receive the data from the files ODV will display a standard file save dialog and you may specify name and path of the newly created data collection ODV can subsample the Sea Bird data using a user specified pressure interval Subsam pling will occur if the specified subsampling pressure value is greater than zero and the files contain pressure or depth values For each file ODV will search for such a parame ter convert data to pressure
227. trictly lying in the interval between smallest and largest data values and these estimates never exceed the observed value range DIVA gridding is different in this respect and occasionally produces gridded field values beyond the data range As a special case you may encounter negative gridded values in some regions of the X Y domain even if all data values are positive or zero and you are expecting a non negative field If you are gridding a variable that is guaranteed to be non negative for instance the concentration of a chemical tracer and DIVA generates areas with nega tive concentrations please check the Prevent negative gridded values checkbox on the DIVA Settings page to prevent such unrealistic values Domain Separation DIVA gridding generally produces better results than Quick Gridding or VG Gridding in cases of sparse and heterogeneous data coverage see Figure 16 3 and in cases where sub regions with quite different property values are separated by land masses ridges or other bathymetric barriers see Figure 16 4 Whereas the weighted averaging schemes used for Quick Gridding or VG Gridding wrongly transmit information across the barriers this does not happen with DIVA gridding The DIVA domain separation feature is activated for two types of data windows 1 section plots that have Depth or Pressure on the Y axis and have section bathymetry shown in the plot and 2 data windows with longitude and latitude on the X and Y
228. trol Like for all subse quent scopes SCATTER windows support a Z variable in addition to variables on X and Y Values of the Z variable determine the colors drawn at given X Y data locations Plots with Z variables for SECTION and SURFACE modes as well can be displayed in two ways 1 by placing colored dots or the actual data value at the X Y locations default or 2 as continuous gridded fields estimated on the basis of the observed data Gridded fields can be color shaded and or contoured Oxygen mol kg Depth m 350 r Boo pa A 25 ey 2o 5000 15 10 Ss 4000 SAVE_LG1 19 8 2 5 o 0 6 a 3000 34 35 36 37 S Salinity psu D 2000 Y 1000 e SAVE_LG1 19 B l js 12 a 0 0 5 1 1 5 2 2 5 Phosphate mol kg Figure 1 4 Example window layout with two data windows using SCATTER scope The data of one station are highlighted using symbolset graphics objects 1 6 3 SECTION Scope SECTION scope windows see Figure 1 5 display the data of all stations belonging to the section currently defined in the map e g all stations inside the red section band Sections are defined or modified using the Manage Section options of the map popup menu SECTION windows also support Z variables and the display of original data or gridded fields SECTION windows are most useful to display along track property dis tributions or property property plots for the stations of a
229. ty Anomaly o kg m Potential Temperature 8 degC Drartical Salinity fram Conductivity neu Function description Hee senos _ Figure 14 3 The Calculator Settings dialog Figure 14 2 The Ocean Calculator tool Calcite solubility ratio for seawater at given Pressure Depth Temperature Salinity Total Alkalinity Dissolved Inorganic Carbon Phospate and Silicate Vertical coordinate Pressure dbars v Equilibrium constants Best Practices Handbook 2007 Carbon input pair ALK DIC Zi pH Scale Input Total pH Scale Output Total ODV User s Guide 15 Miscellanea 15 1 Color Palettes ODV style color palettes define 177 colors see Figure 15 1 e 0 15 basic colors 16 31 gray scale 32 144 main palette used for color shading 145 160 colors used for map bathymetry and continents 161 176 colors used for map land topography o 15 M Te ee ee 16 31 SEP ot PE yy 145 160 FRR eee ee 161 176 PPR Figure 15 1 The ODV default color palette You can change the color palette of the map or any data window by right clicking on the window choosing the Properties option and selecting one of the available palette files from the Palette combo box on the General page ODV will redraw the map or data win dow using the new palette On Windows you can create new color palettes or modify existing palettes
230. udes You may also choose the domain spanned by the stations in the collection native domain by clicking on Full Domain or a global domain by clicking on Global Map Map Properties Map Properties General Depay Style Projection Layers Dornan annot 4 ih i Deplay Style Projection Layers Doman Annotations 4 Map Domain Staton Annotahons Ful Doman Gioba Map Defauk Settings l Figure 9 4 The various pages of the Map Properties dialog part 3 of 3 Annotations On the Annotations page you may specify whether you want the picked stations see below annotated in the map or not Choose Station labels if you want the station labels of the picked stations drawn next to the station positions choose Cruise and station la bels if the annotations should also include the cruise label or choose No annotations if you don t want annotations Note that you can change the position of the annotation relative to the station position using the Pick List Editor see below 80 ODV User s Guide 9 2 Picked Stations The station map maintains a list of picked stations The data of the picked stations are drawn in STATION data windows and the picked stations are also marked in the map using the same color and symbol as in the data windows You can add a station to the pick list by making it the current station for instance by left clicking on that station and pressing ENTER Double clicking a station with the left mouse button
231. ulated variables Unlimited number of other measured or Must be numeric 1 to 8 byte integer or floating point numbers 3 2 3 Trajectory Data This category covers observations made from a moving platform e g ship drifter float glider airplane etc that are repeated over time Examples are underway meas urements of hydrographic parameters at a given depth made during a ship expedition and from actively moving or passively drifting Lagrangean instruments In all these cases each individual measurement made at a given location and time should be treated as an individual station using the depth or elevation of the measurement as primary collection variable and the other meta variable and collection variable assignments from Table 3 6 Trajectory data of this form have exactly one sample per station The number of stations equals the number of observation along the trajectory which is usu ally large Table 3 6 Recommended meta and collection variable assignments for trajectory data yyyy mm ddThh mm ss sss Meta Variables Values Cruise Cruise expedition or instrument name Station Unique station identifier Type B Date and time of the measurement Longitude degrees_east Longitude of the measurement Latitude degrees_north Latitude of the measurement Bot Depth m Bottom depth or elevation at station Unlimited number of other meta variables describing the individual measureme
232. using symbol sets and legends to highlight the data of a particular station If a data window or the map contains symbol sets and the Add to legends option is switched on a legend box containing the symbol and legend text of all symbol sets for this window appears automatically Legend sets can be dragged to different locations and their properties the size of the legend box is modified by changing the font size for the legend text can be modified at any time move mouse over legend set click right mouse button and choose Properties 100 ODV User s Guide 11 6 Graphics Objects from Files ODV supports the import of bathymetry coastline or topography contours from cdt files graphics objects from gob files and of geographical features from ESRI shp shape files You add graphics objects from these files to the map data windows or canvas by choosing Extras gt Add Graphics Object from File gt type from the map data window or canvas popup menus ODV currently supports the following types 1 Graphics Object File gob 2 CDT File cdt and 3 Shapefile shp In all cases a file open dialog will appear that lets you choose a file from which the graphics object s will be loaded cdt and shp files can only be added to maps When opening a shapefile the user is informed about the kind and number of objects in the file ODV then allows specification of graphics properties such as color line type or width These propert
233. w will save the respective data plot ODV will present a file save dialog that lets you choose the appropriate output file type GIF gif PNG png JPG jpg or TIFF tif Note that the default output filename is derived from the current view name If required you can choose any other name or destination ODV then lets you define the resolution of the output image Note that the maximum achievable resolution is limited by the available memory on your system 10 6 Data Statistics You can obtain statistics information for the data shown in a given data window by right clicking on the window and choosing Extras gt Statistics or by pressing F4 while the mouse is over the window The window s statistics page will appear see Figure 10 7 and show mean standard deviation number of data points as well as minimum and maximum values for the X Y and if present Z variables of the respective window Note that mean standard deviation and number of data points are based on the cur rently visible data only while minimum and maximum are using all available data Window 1 Statistics Summary Visible data All data Mean Stand Dev Points Minimum Maximum Oxygen umol kg 121 8 73 3 93599 0 355 1 Depth m i 1498 4 1537 1 93599 Lo 7280 Distributions E X Histogram Y Histogram Z Histograr Gridding Misfits X Y Distribution AOE OT Le AAN Q Fitted Curv
234. will also add the station to the pick list Note that the data of the newly added pick station are added to all STATION data windows and that it is also marked in map To delete a station from the pick list make it the current station for instance by clicking on one of its data points in one of the STATION data windows and press the Del button You may edit the entire pick list using option Manage Pick List gt Edit Pick List from the map popup menu The Pick List Editor dialog will appear letting you edit the properties and graphical appearance of every station in the pick list You may also change the or der in the list or delete individual stations from the list or empty the list altogether a gt Pick List Editor Symbol Station ID Cruise Station 1 0 134 SAVE_LG3 144 B 2 E 145 SAVE_LG3 155 B 3 26 SAVE_LG1 36 B Edit 4 A 11 SAVE_LG1 21 B Remove Bole lo A 6 109 SAVE_LG3 119 B Remove All sal X 286 SAVE_LGS 296 B ag 175 SAVE_LG4 185 B I Foreground 9 188 SAVE_LG4 198 B 10 DO 69 SAVE_LG2 79 B Up 11 226 SAVE_LGS 236 B aa Background Heo Lo cance Figure 9 5 The Pick List Editor dialog Note that if your current view contains picked stations but no STATION data window is displayed the picked stations are simply highlighted in the map by a black cycle around the station symbols As soon as a STATION data window is created the chosen symbols are displayed again Furthe
235. ws 2 SCATTER show ing X Y Z data of all selected stations shown in the map 3 SECTION showing X Y Z data of all stations inside the section band and 4 SURFACE showing isosurface X Y Z data of all selected stations shown in the map The current window layout and parame ter settings are collectively called a view Views can be stored in files for later use Some of the ODV window elements and popup menus are described in more detail be low 2 5 Menu Bar The main menu provides basic functionality 12 ODV User s Guide File Open or create a collection open netCDF file open a ODV supported data file execute ODV commands in batch mode print the current ODV graphics canvas produce gif png jpg tiff or PostScript files of current ODV graphics canvas exit ODV 1 Collection Copy rename delete collection sort and condense data collection delete current station or valid station subset view collection info inventory and log files add a comment to the collection log file identify key variables define good coverage criteria view or edit the collection properties and vari ables 2 View Change station and sample selection criteria define derived variables define isosurface variables change map and data window layout change var iable labels numeric format and display order in listing windows undo re cent changes load and save configuration settings define general ODV set tings Import Import data
236. y then press and hold down the left mouse button and move the mouse to open a zoom box Releasing the left mouse button applies the zoom box settings to the window from which the quick zoom was initiated The changes are applied to the window that was zoomed into If range synchronization is on see the View gt Settings gt Windows dialog page on Mac OS X odv4 gt Preferences gt Windows the new ranges are also applied to other windows using one of the modified variables 10 3 Z Zooming All data windows with a color bar allow modifications of the Z variable range by zoom ing into the color bar Z zooming To invoke Z zooming move the mouse over such a data window and click the right mouse button to bring up the data window popup menu Selecting Z Zoom will draw a red zoom frame around the color bar of the respec tive window Manipulate and drag this zoom frame as described above To accept the current setting of the zoom frame and adjust the Z variable range accordingly double click the left mouse button or press ENTER If you want to abort the zoom operation and keep the original Z variable range press ESC or click the right mouse button The changes are applied to the window that was zoomed into If range synchronization is on see the View gt Settings gt Windows dialog page on Mac OS X odv4 gt Preferences gt Windows the new ranges are also applied to other windows using one of the modified variables 10 4 Changing Window Layout Th
237. y cfg and sec files may be located in any directory Extension Format Comment lt name gt cfg Configuration files storing layout value ranges derived and isosurface variable selections and many other settings The name of the collec tion that owns a configuration is recorded inside the cfg file Certain restrictions apply if a different collection uses the cfg file lt name gt sec_ ASCII Stores section outlines and characteristics 3 5 Platform Independence Data collections and view files produced with ODV are platform independent and can be used on all supported systems Windows Mac OS X Linux and UNIX without modifica tion 33 Version 4 5 0 34 ODV User s Guide 4 Importing Data ODV can import new data and append the imported data to existing collections or add the data to newly created collections Support is provided for a large variety of file for mats including many of the important oceanographic data formats as well as a wide range of column oriented spreadsheet files Data imports can be done one file at a time or alternatively by handling a potentially large number of import files in one import procedure The import files may be selected manually via file selection dialogs or by providing a list of file names in a separate file You can generate file lists easily with the built in list file generator 4 1 ODV Spreadsheet Files ODV can read and import data from
238. ywhere Abort GetPoints 1 On Mac OS X systems with a single button mouse hold down the Alt key while clicking the mouse to simulate a right mouse button click 16 2 Quality Flag Schemes ODV supports most quality flag schemes widely used in the oceanographic community Any of these schemes can be used to encode the quality flags of a given meta or collec tion variable See Table 16 5 and file ODV4_QualityFlagSets pdf for summaries of sup ported schemes lists of quality flag codes and their meaning as well as code mappings between the schemes 134 ODV User s Guide Table 16 5 Quality flag schemes supported by ODV For full lists of quality flag values and value mappings between the different schemes see file ODV4_QualityFlagSets pdf SchemalD Comment ARGO ARGO quality codes Reference Argo data management User s manual Version 2 1 http www usgodae org argo argo dm user manual pdf BODC BODC quality codes Reference http www bodc ac uk data codes_and_formats request format ESEAS European Sea Level Service quality codes Reference www eseas org eseas ri deliverables d1 2 ESEAS_QC_29032005 doc GTSPP GTSPP quality codes Reference http www meds sdmm dfo mpo gc ca meds Databases OCEAN GTSPPcodes_e htm OCEANSITES OceanSITES quality flags Reference http www oceansites org docs oceansites_user_manual_version1 2 doc ODV ODV generic quality f

ODV4 - User's Guide - Ocean Data View

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