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Computers & Geosciences 33 (2007) 31–41

www.elsevier.com/locate/cageo

Mirone: A multi-purpose tool for exploring grid data$

J.F. Luis�

CIMA, Universidade do Algarve, Campus de Gambelas, 8000-117 Faro, Portugal

Received 15 October 2005; received in revised form 5 May 2006; accepted 26 May 2006

Abstract

Mirone is a Windows MATLAB-based framework tool developed by the author that allows the display and

manipulation of a large number of grid formats through its interface with the Geospatial Data Abstraction Library

(GDAL). Its main purpose is to provide users with an easy-to-use graphical interface to the more popular programs of the

Generic Mapping Tools (GMT) package. In addition it offers a range of tools dedicated to topics in the earth sciences,

including tools for multibeam mission planning, elastic deformation studies, tsunami propagation modeling, earth

magnetic field computations and magnetic Parker inversions, Euler rotations and poles computations, plate tectonic

reconstructions, and seismicity and focal mechanism plotting. The high-quality mapping and cartographic capabilities for

which GMT is renowned is guaranteed through Mirone’s ability to automatically generate GMT cshell scripts and dos

batch files. User-specific requirements that lie outside the current capabilities of Mirone can be met by simple programming

to provide the required functionality.

r 2006 Elsevier Ltd. All rights reserved.

Keywords: Mirone; GMT; Data conversion; Grids; Geomagnetism; Plate tectonics; Geophysics

1. Introduction

Mirone is an open source code written inMATLABs 6.5 by the author and has beendeveloped specifically for the purpose of visualizingand manipulating GMT netCDF grids. GMT(Wessel and Smith, 1991) is one of the most popularprograms within the scientific community onaccount of its mapping capabilities and high-qualitygraphics. However, most commercial softwarepackages ignore this format and products that areable to read GMT, and to display and manipulate

e front matter r 2006 Elsevier Ltd. All rights reserved

geo.2006.05.005

ilable from server at http://w3.ualg.pt/�jluis/

289 800938; fax: +351 289 818353.

ess: jluis@ualg.pt.

GMT grids, are rare. An additional problem thatusers face concerns data format. There are presentlytens of different formats for storing gridded dataand imagery data, and accessing data from dis-parate sources is a common problem. Mironeminimizes this obstacle through its interface withthe GDAL (www.gdal.org). GDAL is a unifying C/C++ API for accessing raster geospatial datareleased under the MIT Open Source license, whichaims to provide efficient access suitable for use inviewer applications, and which attempts to preservecoordinate systems and metadata.

MATLAB is a powerful tool for softwaredevelopment. The language is easy to learn andcontains a large collection of mathematical func-tions that facilitate the task of writing complicatedcode, including Graphical Users Interfaces (GUIs).

.

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However, it also has limitations including thoseof speed and memory consumption. In order tocircumvent these constraints, almost all substantialcomputations involving matrix data in Mirone havebeen made with the help of external code written inC and compiled as mex files. Because the mex filesuse scalar programming and employ single precisionor short integer variables in circumstances whereaccuracy is not compromised, their memory con-sumption is reduced to the minimum necessarywhilst the running speed is that of a compiled code.

This paper reports the general characteristics ofMirone, and describes and explains the program’smain capabilities and functions. The paper alsoprovides some example applications to topics in theearth sciences including elastic deformation, tsuna-mis, and plate tectonic motions. Aspects of thefuture refinement and development of Mirone arealso addressed, including an example of how it canbe extended by programming for particular needs.The source code and a stand-alone version, which isa version that does not require MATLAB, areavailable at w3.ualg.pt/�jluis/mirone.

2. The program design philosophy

Mirone was designed to address many of thespecific needs of those who regularly use griddeddata, but is particularly focused on the fields ofgeophysics and earth sciences. It provides compre-hensive data visualization and analysis in a user-friendly environment. One of Mirone’s advantagesis that the author is also a user. I have foundthat much graphically oriented software obligesthe user to follow a strict procedure that oftenrequires in-depth study of the accompanyingmanual in order to accomplish even simple displaytasks. In Mirone, the user merely loads the grid ofinterest (assuming that it belongs to one of therecognized formats) and views it. Particular atten-tion has been paid in the program to offer theuser the simpler and more often used options first,and to let the more specific options show up onlywhen they may be needed to solve a particularproblem.

Since Mirone offers a large number of operations,it has been designed in a modular fashion. Optionsthat require input parameters are run from inde-pendent windows which, whenever possible, offer‘‘clever’’ default values. A comprehensive set of‘‘tooltips’’ and ‘‘helps’’ has been attributed to thebuttons and boxes where data have to be entered, in

order to facilitate the comprehension of eachmodule’s operation, to the extent that manymodules should not require reference to the manual.The modular design can be explored further byusers with programming skills, and it is relativelyeasy to add new possibilities to the main program,as demonstrated in Section 7 below.

For the purposes of demonstration or teaching, anumber of datasets have been incorporated coveringtopics such as seismicity, active volcanoes, ODP/DSDP sites, plate boundaries, major cities, andmagnetic isochrons of the world’s oceans. Thesedatasets are not purely static but contain relevantinformation associated with various items. Forexample, right clicking on a plate boundary segmentinforms the user about neighboring plates as well asthe opening rate and direction.

3. Starting the program

Upon starting the user is presented with Mironein its basic form, which is a simple bar containingvarious menus. See Fig. 2 for an example of aMirone window with data already displayed.Activities are initiated by using these menus.Although Mirone has pre-defined defaults it is veryimportant that the user understand what thesedefaults mean and do. The first time the programis used the user is strongly advised to press thebutton with hammers icon. This icon opens thepreferences window (Fig. 1). The meanings of thosesettings are:

Use new GMT netCDF grid format . Starting withGMT version 4.1, a new type of COARS-compliantGMT net CDF grids was introduced. While thischange is transparent to users, the new grid formatwill not be recognized by previous GMT versions.

Grid coordinates . Select Geographic (default) ifworking with a grid whose coordinates are long-itude and latitude, otherwise select Cartesian. Thisis an important setting because some operations,such as measuring, depend on the grid coordinatesystem.

Grid Max size . In order to perform grid manip-ulations, Mirone stores the original grid in thecomputer’s memory (in single precision). This is themaximum size in Mb that a grid can occupy in thecomputer’s memory. This does not mean that largergrids/images cannot be processed, it means that ifthey exceed the size value they will be re-read fromdisk as required. The user must decide a reasonablevalue for this parameter based on the capabilities of

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Fig. 1. Parameter configuration window.

J.F. Luis / Computers & Geosciences 33 (2007) 31–41 33

the computer being used. Grid size is computed as:n_rows� n_columns� 4/(1024� 1024). (Note: Mir-one makes most of its heavy computation usingexternal mex files that use scalar single and doubleprecision arithmetic. However, some operationsmay be performed with MATLAB operators usingimply double precision, which takes twice as muchmemory. When image files are being used, however,this rule does not apply.)

Swath ratio . When performing a multibeamplanning, the swath width coverage as a functionof the water depth needs to be known. When thefirst track is started by the user, a question will bemade concerning whether the current value is to beused, or whether it should be changed.

Measure units . When computing distances, theresult is presented in the chosen unit. Availableoptions are nautical miles, kilometers, meters, anduser-defined.

Default ellipsoid . Mirone computes distances onan ellipsoidal Earth. The list of available ellipsoidsinclude the 63 GMT-supported ellipsoids plus onefor Mars, which is needed when working with

MOLA grids. Users that whish to set a customellipsoid will need to edit the mirone_prefs.m file.

Working directory . To reduce the cumbersometask of browsing through the directory tree everytime a file needs to be saved, the program uses adefault working directory. Either the full path maybe typed here, or the side button pressed to select adirectory within a new window.

New grids in new window . Many options involvethe computation of a new grid. This parametercontrols whether the newly computed grid isautomatically opened in a new Mirone window (ifthis option is checked) or saved on a disk file.

Force insitu transposition . This option helps withthe importation of large grids. Importing gridsinvolves a conversion that uses matrix transposi-tion, which requires twice the grid size in memorywhen a copy is made of the grid to speed importa-tion. The in situ transposition option uses onlythe grid size in memory and should be used wherethe computer has insufficient memory, although theimportation runs about 10 times more slowly than ifthe grid is copied.

When possible save as int16 . Some grids use shortints (2 bytes) to save disk space. Checking thisoption means that, if the grid is saved in the GMTformat, the 2 bytes original density will be retained(otherwise, it will be saved as floats of 4 bytes). Thisis useful, for example, to convert Shuttle RadarTopography Mission (SRTM) grids into GMTformat.

Default line thickness . This default value is usedfor drawing lines, circles or other graphical ele-ments.

Default line color . This default value is used fordrawing lines, circles or other graphical elements(such as text strings).

For a complete explanation of all options offeredby the program the reader is directed to the user’smanual.

4. General functionality

By default Mirone automatically detects andreads all types of netCDF GMT grids as well asSurfer 6 and 7 grids. Many of the formatsrecognized by GDAL may also be accessed throughthe File menu. Those include: GeoTIFF DEM,DTED, USGS DEM, USGS SDTS DEM, Gto-po30, SRTM DEM, Arc/Infos ascii/binary grids,ENVI, ERDAS. img, GeoTIFF, Grid ExchangeFile (GXF from Geosofts), Mars Orbiter Laser

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Fig. 2. Example case: base image was computing by shading

illumination of a GMT bathymetry grid. Dark dots represent

seismicity as imported from an ISC catalog. Triangles correspond

to active volcanoes. Also two logo images were inserted to

demonstrate this facility.

J.F. Luis / Computers & Geosciences 33 (2007) 31–4134

Altimeter (MOLA) grids, and the common imageformats. When the loaded grid is referenced ingeographical coordinates it is also possible to plotthe netCDF coastlines database (including riversand political divisions) provided by GMT. Theseinclude not only the coastlines themselves but alsothe rivers and political divisions (country frontiersand US states). The netCDF coastlines database isthe only currently available non-ASCII vectorformat. Other line and point data must be loadedfrom ASCII disk files containing x,y coordinates,one record per line. Multi-segment files, that is a filewhere segments are separated by a special record(the ‘4’ character), are also supported.

When a grid is loaded the Mirone windowexpands to accommodate the image derived fromthe grid. At the bottom of the window the currentmouse position is displayed in the grid’s coordi-nates. Clicking and dragging over the image showsthe distance in the selected user units. The generatedimage uses a default color map, but more than 100other color palettes are available by clicking on thepalette icon button to access the palette tool (notshown here). All palettes may be changed by adouble click over the color bar. This inserts colormarkers, which can be dragged to modify the colormap. A second double click deletes the marker. TheMin Z and Max Z fields may be used to impose afixed color map between those values. ExternalGMT color palettes may also be imported orexported via the File menu.

Another common operation is to show patternsand fine details in the grid image as revealed byapplying a shading illumination. Mirone offers fivedifferent algorithms for shading illuminations. Bydefault a mex version of the GMT grdgradient

program is used to do this, but the user can selectany of the five methods from within the controlwindow. Sun azimuth and elevation (when acceptedby the method) are controlled with the mouse.

The buttons with T, circle, line, rectangle, closedpolygon, and arrow icons permit the user to drawany of these graphical elements (Fig. 2). Thoseelements may be subsequently edited by double-clicking the selected target. Besides their use assimple drawings (which may be saved as ascii files)such elements (in particular the polylines, rectan-gles, and closed polygons) allow other possibilities.A polyline, for example, may be used to measure thedistance or azimuths of its individual segments, andit can be also used to extract and show a savablegrid profile in much the same way as the grdtrack

GMT program. Rectangles may be used to limit therange of one operation to the area delimited by therectangle. The Crop Image operation is quitecommon in many programs that display image typefiles. In Mirone I have extended that concept toother operations. It is thus possible to extract a sub-region of a grid, compute histograms and powerspectrums, determine autocorrelation, apply medianfilters, smooth by spline interpolation, fill gaps(holes) in the grid, set all grid nodes to a constantvalue, and utilize a separate tool, also included inthe package, to perform Region Of Interest (ROI)image processing type manipulations. Furthermore,the rectangle’s limits may be used to register animage into another coordinate system. The rectan-gle corner coordinates are used to compute an affinetransformation that registers the image to therectangle’s coordinate system. The closed polygonsalso offer the possibility of measuring areas,cropping grids, and performing ROI manipulations.The polygonal cropping differs from the rectangularone in that the grid nodes external to the polygonare set to not a number (NaN).

Mirone contains a large collection of bothgeneral-purpose operations and discipline specificmodules. Among the first group, generally orga-nized inside the Grid Tools menu, the user may findinteractive tools to drive a selection of GMTprograms, namely:

Grdfilter—filters grids in the time domain usingone of the selected convolution or non-convolutionfilters.

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Fig. 3. SRTM mosaic tool showing four successful tile selections

and error message displayed when intend SRTM tile could not be

found in indicated directory.

J.F. Luis / Computers & Geosciences 33 (2007) 31–41 35

Grdgradient—computes the directional deri-vative in a given direction, or the direction (andthe magnitude) of the vector gradient of thedata.

Grdproject—transforms a gridded data set froma rectangular coordinate system into a geographicalsystem (or vice-versa) by resampling the surface atthe new nodes.

Grdsample—reinterpolates and creates a newgrid with either a different registration or a newgrid-spacing or number of nodes, and perhaps also anew sub-region. Interpolation is bicubic or bilinearand uses boundary conditions.

Grdtrend —fits a low-order polynomial trend tothe grid of interest using (optionally weighted) least-squares.

Surface and nearneighbor—interpolates random-ly space triplets (x,y,z) into a regular matrix (thatcan later be saved as a GMT grid).

Other options involve computing histograms,clipping a grid above and/or below selected planes,writing a mask grid where non-NaN values arereplaced by the number 1, computing spectra andautocorrelations, smoothing grids by spline inter-polation, computing slope, aspect, and directionalderivatives, and computing a Second Derivative inthe direction of Gradient (SDG). The SDG is thealgorithm recommended by the United NationsConvention for the Law Of Sea (UNCLOS) to beused in the determination of the Foot Of continentalSlope (FOS).

The SRTM has obtained elevation data overmost of the globe to generate the most completehigh-resolution digital topographic database of theplanet. It is distributed as 11 DTM tiles of 1 arcsecfor the US territories and 3 arcsecs for the rest of theworld between 561S and 601N. In areas of highrelief, areas covered by water (e.g., rivers, dams, andnatural lakes), and at land-ocean transitions, theSRTM models commonly display zones of no-data(grid holes). Although strategies to fill these holesusing coarser data (e.g., from the elevation datamodel GTOPO30) could potentially be used, thecoarser resolution may not depict such areas withsufficient accuracy. Therefore, the Mirone solutionis simply to offer the user the possibility to fill theholes, which are automatically detected in Mirone,by either minimum curvature or bilinear interpola-tion. The resulting processed file may be saved in theSRTM format.

Given the limited coverage (11� 11) of eachindividual SRTM tile, it is often desirable to be

able to create mosaics. Mirone has a dedicated andeasy-to-use tool to accomplish this task (Fig. 3).With the SRTM mosaic tool the user first draws arectangle to define the ROI. By right clicking on therectangle and choosing mesh , yellow quadranglescorresponding to possible SRTM tiles can bedrawn. A mouse-click on each individual quad-rangle searches the previously selected workingdirectory for existing SRTM files. The square turnsred if the matching file exists, if it does not exist awarning message is displayed and the square returnsto yellow.

The size of raster datasets grows very quickly.For example, the General Bathymetric Chart of theOceans (GEBCO) 1min resolution grid contains445Mb of data, but the global mosaic of the SRTMtiles amounts to 1.9Gb in GeoTIFF DEM format.This means that the majority of computers ownedby typical users will probably not be able to processthose files at their full resolutions. One way tocircumvent this problem, as used by some soft-ware packages, is to use complicated algorithmsthat split the entire dataset (if the data formatallows them to) in layers of variable resolution.Mirone approaches the problem of loading datafrom very large grids somewhat differently. Withthe File�4open overview tool the user mayinspect the contents of a very large grid withoutloading it. What this tool actually does is to read n-other rows and columns in order to obtain anoverview grid that is as close as possible to200� 200 rows and columns, and builds a pre-view image. The user can then draw a rectangu-lar area in order to extract the data at its fullresolution.

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Fig. 4. Example of parameter settings used to characterize

movement along a fault and to compute elastic deformation

produced by that movement.

J.F. Luis / Computers & Geosciences 33 (2007) 31–4136

5. Discipline-specific tools

Mirone contains a range of specific tools forapplication to topics in geophysics and earthsciences. The list of applications cover multi-beammission planning, elastic deformation, tsunamimodeling; including travel time estimation, platetectonic reconstructions, Euler rotations and Eulerpoles computations, magnetic field computationsand magnetic inversions, and seismicity and focalmechanism plotting. A selection of these tools isdiscussed below.

5.1. Elastic deformations

The elastic deformation tools are accessible viathe Geophysics�4Elastic deformation menu.Here, a line or polyline can be imported or drawnover the image grid. The line is interpreted as thesurface trace of a fault. Right clicking on the lineallows the user options to open new windows inwhich can be specified the fault parameters (width,depth, dip) as well as the movement/deformation tobe simulated.

The two available deformation options are calledOkada and Mansinha (Okada, 1985). The Okada

tool is more general and can be used to simulate co-seismic displacement (that can be compared withGPS measurements) for an initial condition ofthe far field tsunami modeling (see below) or tocompute synthetic interferograms. The Okada

window provides help in the form of tooltips whenthe mouse rests over individual entry boxes. For acomplete reference to the use of the Okada windowthe user should read the RNGCHN program paper(Feigl and Dupre, 1999). In that original paper, theRNGCHN code is provided both as a stand-aloneFORTRAN code and as a MATLAB FOR-TRAN77 mex file. The stand-alone code dependson some C code to deal with input/output but it issystem dependent (it runs only on Sun and HPUNIX systems). The mex file, because it is written inF77, has the limitation of not supporting dynamicmemory allocation. Mirone uses a C version inwhich coordinate conversion routines were added.

The Mansinha option computes only the verticalcomponent of the deformation produced by anearthquake. The two codes should produce equalresults and trials show this to be the case. In bothOkada and Mansinha , all distances are computedby projecting the geographical coordinates toTransverse Mercator with the origin being the

fault’s first point. Fig. 4 presents an example ofusing Okada .

5.2. Tsunami modeling

Mirone has two codes to perform tsunamimodeling of propagation and inundation. TheSWAN code (Madder, 2004, rMader ConsultingCo) and the TUNAMI-N2 code (Imamura, 1997).Both of these codes were converted from FOR-TRAN to C to allow dynamic memory allocation.The example presented here uses the SWAN code.To use this program, the user needs to have twogrids that are exactly compatible (i.e. they mustcover the same region and have the same number ofrows and columns). One of the grids represents thebathymetry (z positive up) in meters and the othercontains the initial deformation as produced bythe Mansinha or Okada deformation module.A required parameter file ‘‘swan.par’’ can be foundin the data directory of the root Mirone installation,which can be used as an example for other cases.

The user must choose between computing thesimulation on specific points, termed ‘‘maregraphs’’here, and/or on the whole grid region. If the firstoption is desired, the stations can be plottedgraphically (using the Plot Stations option), or themaregraphs’ locations can be imported in an x,y file.If the simulation is to be performed over the wholeregion, then the Compute option is used. A newwindow called swan_options will popup where thefinal selections are made. See the user’s manual forfurther details on using this tool.

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5.3. IGRF calculator

The International Geomagnetic GeoreferenceField (IGRF) calculator (Fig. 5) is a tool thatcomputes the value of the total magnetic field (or itscomponents) for given points. A single point can beselected either by a mouse click on the world map orby entering its exact coordinates. Alternatively, afile can be read and imported that contains themagnetic data along with longitude and latitudepositions. The user has the option of choosing tocompute the magnetic anomaly (measured totalfield minus the IGRF magnitude). Computing themagnetic anomaly requires knowing the date ofdata acquisition, in which case the file readingfunction has the ability to decode many dateformats, including text formats. The IGRF modelused is the 10th generation IGRF as agreed in

Fig. 5. Illustration of IGRF calculator. Points for which

geomagnetic field is to be computed can be selected by clicking

on image. ‘‘Griding Line Geometry’’ configures grid parameters

necessary to compute a grid, e.g., of total field or magnetic

declination.

December 2004 by IAGA Working Group V-MOD.It is valid for dates 1900.0 to 2010.0 inclusive.

The IGRF routine (a C mex file) is also usedwithin the Parker Directand Parker Inversion

tools. The first allows the computation of themagnetic anomaly given a magnetization andbathymetry map using Parker’s (1972) Fourierseries summation approach. The second performsthe inverse operation, which is the computation ofthe magnetization from magnetic field and bathy-metry (Parker and Huestis, 1974). This inversionprocedure eliminates the dependency on the shapeand amplitude of the magnetic anomalies with thedistance between the survey altitude and theseafloor.

5.4. Geographic calculator

This tool is an interface to both the mapproject

and grdproject programs in GMT. It uses a mexversion of these programs and its use is fairlystraightforward. GMT version 4 introduced datumconversions in mapproject (but not in grdproject )and shifts that allow conversion between the manyprojection systems in use. Currently, only thePortuguese systems are coded in Mirone. Overall,this tool frees GMT users from the need to providea correct –R for the transformation (potentiallyparticular hard to know in advance in inversetransformations), a problem, which has preventedmany users from being able to use grdproject .

5.5. Plate reconstructions

This tool lies somewhere between a plate recon-struction demonstration and an application that canbe used to do advanced plate motion work. Thereare some dedicated software packages available onthe web that perform plate reconstructions (see forexample www.geodynamics.no/gmap/ngu@gmap/Geodynamics.htm and links therein). However, theMirone plate reconstructions tool is easy to use andhas good functionality. Options can be obtained byright clicking over the plates. New menus pop up(see Fig. 6) from which the user can control how theplates move. By default the program associates a‘‘movement history’’ to three plates: Iberia, Eurasia,and Africa. The movement is defined by the poles asdisplayed in the window’s bottom left corner. Inaddition to the default files, the user can load his/herown data, including poles files and plates files.

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Fig. 6. Pate reconstruction tool. Reconstructions for particular

times are performed using time slider. Example shows position of

Iberia, Eurasia, and Africa relative to a fixed North America at

90Ma ago.

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The poles used in this program are stage poles(not finite rotation poles). They have a particularformat as described in the ‘‘rotconverter’’ GMTprogram, but example files can be found in Mirone’s‘‘continents’’ directory. To create new stage polesfiles from finite rotations poles, Make stage poles isclicked and the ensuing instructions followed.

The plates files are simple ascii files with twocolumns ‘‘longitude’’ and ‘‘latitude’’. The files maybe multisegments, with the character ‘‘4’’ servingas the separator. The individual segments may beclosed, in which case the contour is filled; otherwisethey are drawn as lines. The first line in a file musttake the form ‘‘]Name’’, where ‘‘Name’’ is theplate’s name. This allows the program to associate aplate and its companion lines with a stage pole. Italso allows other elements (e.g., the 3000m bathy-metric contour) to be added.

Mirone contains several other tools to manageplate movements. For example, under the Draw

menu the Draw circle�4circle about an Euler pole

opens a window where the user can draw an arccircle about Euler poles representing the plate’spresent-day movement. Both relative and absoluteplate movement options are available. These arccircles also let the user compute the velocity vector(magnitude and direction) at any point along thecircle. This is a useful tool for discovering how oneplate is moving relative to another at a certainpoint.

The rotation of magnetic isochrons and thecreation of flow lines are accomplished using thetool in Geophysics�4euler rotations . Any line

element, either drawn or imported from an ascii fileor point symbol, may be rotated by using either astage pole file as described above or a finite rotationpole. When performing rotations with stage poles,an age file that controls the ages for which therotation is computed is required. For each entry ofthat age file (displayed in the window’s listbox) anew rotated line is plotted in the Mirone mainwindow. The Magnetic Bar Code button providesan easy way to select an age sequence using thegeomagnetic polarity scale as reference. If a singlepoint is selected (using the Pick line from figure

button) instead of a line/polyline, then a single flowline is plotted. In the Add poles tab the user maycompute the pole that results from a combination oftwo finite rotations.

Users who desire to compute their ownEuler poles can do this with theGeophysics�4compute Euler pole tool. To use thistool, two lines in the main window are mouse-selected by depressing the Pick line from figure

button, and an initial estimate of the Euler pole isentered. The results of the search algorithm aregraphically displayed every time a better-fitting poleis found. The process may be rerun using alternativeinitial estimates of the Euler pole if satisfactoryresults are not obtained with the initial estimate.

6. 3D view and printing

Because Mirone does not use the 3D MATLABfunctions, the program does not offer any built-inway of displaying graphics in 3D perspective.Although MATLAB can display in 3D by usingits surface primitive, this consumes a lot of memoryand has poor interactive response. As an alternative,Mirone uses the IVS Fledermaus free iView3Dviewer (www.ivs.unb.ca/products/iview3d). Fleder-maus is a fast, powerful 3D visualization toolcapable of viewing large amounts of data (Fig. 7).Translations, rotations, and scaling are accom-plished by simple mouse controls. For launchingthe 3D view all is need is to hit the button with theeye icon. By launching the 3D view via the ‘‘eye’’icon (Fig. 2), a temporary fledermaus object(sd. file) is created and used as an argument forthe iView3D call. As an alternative, the usermay choose to save the fledermaus object inFile�4Save As Fledermaus Objects and later im-port that object directly from the viewer.

Saving the Mirone display can be achievedin three ways. The first is through

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Fig. 7. 3D view of a bathymetry grid using Fledermaus free iView3D viewer. Light gray cubes represent seismic events. There are more

epicenters represented but they are hidden behind current figure display. Changing viewpoint with mouse controls will show them. White

line represents coastlines extracted from GMT coastlines database.

Fig. 8. Example of settings used to generate a GMT shell script

to plot contents of a Mirone window. Rectangle, which represents

map’s size, can be dragged over page or have its limits altered.

Any of GMT map projections may be selected.

J.F. Luis / Computers & Geosciences 33 (2007) 31–41 39

File�4Save Image As . . . which saves the currentdisplay image into one of the common imageformats but without including any graphic elements(e.g., lines, symbols). The second way, throughFile�4Export saves both the image and allelements that may have been added to it in ascreen capture. A third possibility involves generat-ing a GMT cshell script or dos batch file. TheFile�4Save GMT script opens a window (Fig. 8)in which it is possible to fine tune map details suchas size, position on the page, and projection systemused. This tool searches all elements in the displayand decides the best way to reproduce thedisplay using only GMT commands. For example,if the image displayed is derived from a GMTgrid illuminated with a shading method fromgrdgradient , the script lines will generate anillumination grid from the original GMT grid anduse ‘‘grdimage’’ with the –I option. If that is not thecase then a screen capture is executed and the imagesaved as three R, G, and B grids. The three grids arethen utilized by ‘‘grdimage’’ to rebuild a colorimage. Line elements are written on disk and usedby ‘‘psxy’’. However, coastlines, national borders,

rivers, and contour lines are not saved. Instead,appropriate calls to ‘‘pscoast’’ or ‘‘grdcontour’’ areinserted into the script.

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7. Evolution of Mirone

Mirone is a powerful tool for displaying andanalyzing grid and vector data loaded in a variety offormats. The Mirone code comprises more than90,000 lines of MATLAB code and about 30,000 ofC mex code. Due to its modular design, carefulprogramming, and interface to GMT and GDALlibraries, the program is able to read large amountsof data that would otherwise prove impossible ifonly MATLAB primitives had been used. Currently,however, the GDAL and GMT links are weaklydeveloped. For example, at the moment it is notpossible to load any of the satellite image formatsrecognized by GDAL or to import ECW or MrSid(wavelet-based image compression technologies de-veloped, respectively, by ERMappers and Lizard-Techs) compressed images. Adding options to dothese tasks is not technically difficult to program,but great care will need to be taken owing to thepotentially huge size of these types of image files.

GMT itself continues to evolve. The developingversion 5 will be significantly different fromprevious versions (although backward compatible).It will be reborn as a true code library thatprogrammers will be able to use with littlewrapping code in order to access its full capabilities(P. Wessel, pers. commun., April 15, 2005).A MATLAB compatibility layer is also planned,at which stage Mirone will be able to more fullyexplore GMT’s capacities. A full range of mapprojections will also be added.

In the meantime adding new options is arelatively straightforward task. I give a simpleexample on how Mirone can be extended to performanother operation, in this case to add a menu entrythat allows a grid to be flipped upside-down. Thefirst step is to decide where the new entry will beadded: in the GridTools menu after the Write mask

option is appropriate. The menus are declaredin the mirone_uis.m file. Searching this file forWrite mask reveals lines that read:

uimenuð‘Parent’; h278; . . .

‘Callback’; ‘mironeð‘‘GridToolsGridMask_Callback’’; gcbo; ½�; guidataðgcboÞÞ’; . . .

‘Label’; ‘Write Mask’; ‘Tag’; ‘GridToolsGridMask’Þ;

A new uimenu call and a new callback name function are declared, here denoted ‘‘GridToolsFlipUD_Call-back’’

uimenuð‘Parent’; h278; . . .

‘Callback’; ‘mironeð‘‘GridToolsFlipUD_Callback’’; gcbo; ½�; guidataðgcboÞÞ’; . . .

‘Label’; ‘Flip Up; Down’; Tag’; ‘GridToolsFlipUD’Þ;

Now a new callback function is added to the mirone.m file, and programmed. It would look something like(without error checking):

function ‘GridToolsFlipUD_CallbackðhObject; eventdata; handlesÞ

% retrieve the arrays stored in figure’s appdata

½X;Y;Z;head� ¼ load_grdðhandlesÞ;

% Flip the grid array Up Down

Z ¼ flipudðZÞ;

% Save back the flipped array for future use

setappdataðhandles:figure1; ‘dem_z’; ZÞ;

% Get the image handle

h_img ¼ findobjðhandles:figure1; ‘Type’; ‘image’Þ;

% Flip also the displayed image

setðh_img; ‘CData’; flipdimðgetðh_img; ‘CData’Þ; 1ÞÞ

ARTICLE IN PRESSJ.F. Luis / Computers & Geosciences 33 (2007) 31–41 41

A final aspect of Mirone’s evolution regards itsportability to other operating systems. In its currentform, despite the fact that it is written in MATLAB,Mirone runs only in Windows. This is a conse-quence of using many compiled C mex files that areeither self-contained or make calls to the GDALand GMT libraries. To port Mirone to Unix/Linuxor Mac Os X, all that must be done, in principle, isto recompile all such mex files under the specific OS.

Acknowledgements

Maurice Tivey for giving permission to use hisParker inversion routines. MATLAB contributorsto file exchange from which many ideas were taken.This paper and many improvements to the codewere written during the author’s sabbatical year.This work was supported by the STRIPAREA—POCI/CTE-GIN/59653/2004 project.

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