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PuffinPlot User Manual

1. File gt Save as allows you to save the current suite to a different filename or location File gt Close closes the current suite removing it from PuffinPlot s data display File gt Export data is a submenu allowing the export of various kinds of data to CSV files File gt Export data gt Export sample calculations saves a file containing all the data associ ated with individual samples Table 2 describes the fields which make up the file File gt Export data gt Export site calculations saves a file containing for suites with discrete samples all the data associated with sites Table 3 describes the fields which make up this file File gt Export data gt Export suite calculations saves a CSV file containing the Fisherian pa rameters for mean directions calculated across the entire suite see the documentation for the Calculate gt Suite means menu item section 4 1 3 for details File gt Export data gt Export multi suite calculations saves a CSV file containing the Fisherian parameters for mean directions calculated across all the currently open suites see the documentation for the Calculate gt Multi suite means menu item section 4 1 3 for details File gt Export data gt Export IRM data saves files containing IRM acquisition data It produces a folder of files one for each sample in the suite Each file is in tab delimited text format and each line within the file contains the IRM field stren
2. Identification of ferromagnetic minerals in a rock by coercivity and unblocking tem perature properties Geophysical Research Letters 17 2 159 162 Available from http dx doi org 10 1029 GL017i002p00159 Lurcock P C and Wilson G S 2012 Puffinplot A versatile user friendly program for paleomagnetic analysis Geochemistry Geophysics Geosystems 13 Q06Z45 Available from http dx doi org 10 1029 2012GC004098 McFadden P L and McElhinny M W 1988 The combined analysis of remagnetization circles and direct observations in palaeomagnetism Earth and Planetary Science Letters 87 161 172 Roberts A P 2006 High resolution magnetic analysis of sediment cores Strengths limitations and strate gies for maximizing the value of long core magnetic data Physics of the Earth and Planetary Interiors 156 3 4 162 178 Tauxe L Butler R E Banerjee S K and Van der Voo R 2010 Essentials of paleomagnetism University of California Press Berkeley Tauxe L Gee J S and Staudigel H 1998 Flow directions in dikes from anisotropy of magnetic susceptibility data the bootstrap way Journal of Geophysical Research 103 B8 17775 17790 32
3. Note that several other data plots are available but are not shown by default and that the layout may be freely rearranged by the user Data points above the 275 C demagnetization step have been hidden De select Select points amp Orientation Sample Magnetic all clear Menu bar correction orientation declination points calculations Zijderveld plot projections vertical and horizontal Formation PCA Perform Suite name orientation anchoring PCA Xx e Pu finPlot Exe Edit Zalculatioms Window mw ppl x Form corr Vvs E Y Nis up v Samp 852 0 38 0 Form 13 0 22 0 Daw 23 0 A c Sel ct all CA Clar mwbos27 2 Sample MWD1137 2 avertical shorizontal MWD0828 1 Units A m x1078 MWD0828 3 temp def inc int m s 23 3 57 29 7 25 264B 52 8 2 77e 05 3 0e 04 x 3 2 boss 50 249 58 0 2 29e 05 3 0e 04 g5 2 52 MWD0930 2 75 2544 47 8 2 18e 05 3 3e 04 Zz 2 I 100 244 48 4 1 32e 05 3 0e 04 T1 5 2 an MWD0931 2 125 2256 40 2 1 03e 05 3 0e 04 S 155 150 217 34 1 1 67e 05 3 0e 04 1 13 NU MWDO0932 1 175 2817 44 3 1 59e 05 3 1e04 38 Y 200 2958 34 7 8 14e 06 3 3e 04 205 0 53 25 MWD0932 2 225 106 44 2 8 95e 06 3 1e 04 Za D gt 250 214 32 2 5 98e 06 2 6e 04 gt 50 100 150 200 250 300 MWD1033 2 275 197 7 30 2 1 71e 05 2 6e 04 Temperature C 300 192 61 2 7 2 16e 05 2 9e 04 MWD1034 2 325 104 29 4 4 66e 05 5 9e 04 351 118 13 7 8 62e 05 8 0e 04 MW
4. topmost and this is the one which will be moved or resized Once the plots are arranged to your satisfaction click Edit layout on the Edit menu again to untick the menu item and resume normal operation The plot layout is saved with your other preferences and will be retained if PuffinPlot is closed and restarted You can restore the original layout using the Reset layout menu item Sometimes it can be useful to save and restore different plot layouts This can be done using the Export preferences and Import preferences menu items see section 4 1 1 4 4 The preferences window The preferences window is divided into three tabs with four action buttons at the bottom 4 4 1 The action buttons Clear clears all changed preferences resetting them to their default values Import sets your preferences from a file saved using Export preferences See the description of Export preferences for details Export saves your current preferences to a file In conjunction with the Import preferences fea ture this allows you to transfer your preferences from one computer to another It also allows you to keep multiple sets of preferences and switch between them as needed Probably the most useful application is to save different plot layouts for different sets of data Close closes the Preferences window 4 4 2 The 2G import tab This tab contains options connected with reading data from DAT files produced by the 2G Long Core
5. GC inc Inclination of great circle direction GC a95 Qos for great circle direction GC k k value for great circle direction GCN Number of great circles used in great circle fit GCM Number of PCA directions used in great circle fit GCR length of sum of direction vectors in great circle fit GC min points Tlmin Tlmax T2min T2max Lat Long VGP lat VGP long VGP dp VGP dm Note on T1min Tlmax T2min and T2max these four parameters give the ranges of demag netization steps used to fit the circles T1 denotes the first lowest demagnetization step in a circle path for an individual sample and T2 the last highest T1min is the minimum of the T1 values across all the circles for the site and T1max the maximum Similarly T2 denotes the last step used in a single circle and T2min T2max is the range of its values across all the samples at a site the smallest number of treatment steps used to define any of the great circles fitted at this site See note below See note below See note below See note below Site latitude Site longitude VGP latitude VGP longitude dp the first semi axis of the VGP confidence ellipse dm the second semi axis of the VGP confidence ellipse 11 File gt Import data gt Import site locations imports co ordinates latitude and longitude for sites in the suite These co ordinates are used to calculate virtual geomagnetic poles from site
6. as the current one 3 Use Copy point selection on the Edit menu or press Ctrl Shift C to select the corresponding points in all the selected samples 4 Select PCA from the Calculations menu or press Ctrl R This will immediately perform PCA on all 50 selected samples 4 3 Plots and other data displays 4 3 1 Available plot types This section lists and briefly describes the available plot types in PuffinPlot Some of them are not displayed by default but these may be activated via the preferences window see section 4 4 Note that the term plot is used rather loosely in this manual to refer to any movable element displaying data within the main window Thus the plots listed below include textual elements such as legends and tables Equal area sample is a Lambert azimuthal equal area projection showing the directions of the current sample s magnetization vectors Successive points are connected by great circle segments Points in the upper hemisphere are shown as unfilled white and connected by solid lines points in the lower hemisphere are filled black and con nected by dashed lines If a great circle fit has been calculated for the sample it is shown on this plot and the pole to the great circle is shown as a triangle 18 Zplot Demag is a Zijderveld plot overlaying an orthographic projection in the horizontal plane with an orthographic projection in a chosen vertical plane The vertical plane can be
7. axis of VGP confidence ellipse and dm second semi axis of VGP confidence ellipse VGPs can only be calculated for sites whose location has been set See Import site locations in Section 4 1 1 for details on reading site locations from a CSV file Suite table is a table showing suite level mean direction and VGP data See the entry on Site parameter table for explanations of the Fisher parameters associated with each mean direction The directions shown are Site dir the mean direction calculated from site mean directions Sample dir the mean direction calculated from sample mean direc tions Site VGP the mean of the VGPs of sites and Sample VGP the mean of the VGPs corresponding to individual sample directions As with most PuffinPlot operations the parameters shown are calculated using only the samples and sites selected at the time the calculation is done Zplot key is a legend for the Zijderveld plot showing the interpretations of the filled and unfilled points and giving the units in which the axes are calibrated NRM Histogram shows a histogram of NRM intensities across the whole suite AMS is a lower hemisphere equal area plot of AMS data if any has been imported Max imum intermediate and minimum anisotropy axes are shown as squares triangles and circles respectively If AMS statistics have been calculated see section 4 1 3 the mean directions and confidence ellipses are also shown Ternary d
8. component analysis for the selected points of all the selected samples Clear de selects all the points in all the selected samples and clears the results of any calcula tions done on them such as PCA or great circle analysis 4 Detailed usage This section gives a methodical account of PuffinPlot s features 4 1 Catalogue of functions This section lists all the items in PuffinPlot s menus giving a brief description of the functionality associated with each one 4 1 1 File menu This menu contains functions connected with opening closing and saving files File gt Open reads one or more files of demagnetization data into PuffinPlot as a new suite See section 4 2 1 for details of supported filetypes File gt Open folder reads a whole folder of data files into PuffinPlot This menu item only appears on OS X on other operating systems the Open menu item also allows selection of entire folders File gt Open recent file is a submenu which contains the names of the last eight files which have been opened in PuffinPlot allowing them to be opened again with a single click File gt Save saves the current suite as a PuffinPlot file If the suite was opened from a PuffinPlot file or if it has been previously saved as a PuffinPlot file it will immediately be saved to that file If no PuffinPlot file is associated with this suite yet a standard save file dialog box will prompt you for a file name and location
9. dde woe a Soe 18 432 oi oy es fa ss ee es aw aE gohan Goa as tone Sen ve Se 21 44 The preferences Window ss 4 i402 564 Gadd eae eee ERR OE ed aa 21 4 41 Theaction DULONS gt seues e0e go Bade wes ee ee a 21 442 The 2G importitab 5 2 csc 00 cou a 0888 Re Ree Pas 21 AB The Plots tab ii oS ae baa OE ede ew 22 A A A E ey og ES eg teeter eRe es 22 4 5 ANNOAONS ceca A Ra SSMS OER es 25 4 6 EXPONE graphics so eseas maa clas a ee ee te I wee ee a 25 406 1 Introductions gs ee heh eA a eae ha A eda 25 4 62 Graphics EXPOLCOPUOAS os cde a eS eS 25 a av gg rE aoe Gio Gare we Ride we E ee Barbee ake BR ee A 26 5 Acknowledgements 27 6 Future development and bug reporting 28 A Citing PuffinPlot 29 B Release notes 30 C References 32 1 Introduction This manual gives a practical guide to the usage of the PuffinPlot palaeomagnetic data analysis program Note that it does not elucidate the principles of the analysis techniques themselves and a working knowledge of palaeomagnetic procedures is assumed For excellent introductions to palaeomagnetic analysis see Tauxe et al 2010 or Butler 1992 If you use PuffinPlot in the creation of published work please cite the PuffinPlot paper Lur cock and Wilson 2012 See Appendix A for further details PuffinPlot is free software distributed under the GNU General Public License Please see the LICENCE file in the PuffinPlot archive for details PuffinPlot is copyright 2012 201
10. depth rather than a list of sample names Above the main plot area is the toolbar which gives convenient access to some of the most frequently used facilities of the program From left to right these are choosers for the currently displayed data suite the orientation correction and the Zijderveld projection type displays of the sample and formation orientations and magnetic declination and buttons for three of the most commonly performed actions At the top of the window is the menu bar providing access to all the program s functions in a hierarchical manner On Mac OS the menu bar is at the top of the screen rather than the top of the window and includes an extra menu at the left entitled PuffinPlot 3 4 Data model Figure 2 PuffinPlot s hierarchical data model Each layer except the lowest contains multiple instances of the following layer Suit E Magnetic declination The complete set of all the data to be processed Sample r F Name Volume Orientation One physical rock specimen or one osition on a long core eee ssn The state of a Sample after a particular series of treatment steps PuffinPlot uses a hierarchical data structure with higher levels containing multiple instances of each lower level The structure is summarized in Figure 2 At the top is the suite which contains all the data to be analysed as part of a particular study For a discrete specimen study this will typically corres
11. shortcuts PuffinPlot provides a large number of keyboard shortcuts for its various capabilities most of them involve holding down the Ctrl key while pressing another key On Mac OS X these shortcuts use the command key rather than the Ctrl key in accordance with Apple user interface guidelines Throughout this manual keyboard shortcuts will be given as for example Ctrl A Users of Mac OS X should read these shortcuts as command A etc 3 2 Opening a file To open a file select Open from the File menu This will allow you to choose one or more files to open from a standard file selection window You may also select an entire folder in this case every file within the folder will be opened and combined into a single suite Note if you open multiple files or a whole folder they must have the same file type the same treatment type thermal alternating field etc and the same sample type discrete or continuous Opening for example a mixture of Caltech and IAPD files or a mixture of discrete and continuous files may result in errors during file reading 3 3 A tour of the main window Figure 1 shows an annotated screenshot of PuffinPlot s main window with a discrete sample data file open The bulk of the window is devoted to the data display itself and shows the four Figure 1 The main window of PuffinPlot with a discrete file loaded showing the default data plot layout Data plots information displays and controls are annotated
12. software Read magnetization from This setting controls whether PuffinPlot reads a sample s magnetic moment from the fields giving the Cartesian components of the magnetization vector X Y Z or whether it reads the polar represantation the declination inclination and intensity fields The Cartesian components are stored to higher precision in the file so using them is preferable when possible However if the Cartesian components are used when reading a long core file they must usually be corrected for the effective sensor lengths see below If the sensor lengths are unknown reading data from the polar fields can be a useful fallback When reading a file using the X Y Z setting PuffinPlot first looks for the X corr Y corr and Z corr fields to determine the magnetization vector If these are not present it falls back to X mean Y mean Z mean then to X intensity Y intensity Z intensity 21 SQUID sensor lengths As described above the Cartesian magnetization components in long core files are not corrected for effective sensor length which is determined by the response function of each SQUID and must be determined empirically when setting up the machine To produce a magnetization vector for long core files when using the X Y Z setting PuffinPlot corrects the SQUID readings for these configured sensor lengths when opening the file Protocol gives the measurement prot
13. to control a program using a scripting language in order to extend its capabilities integrate it conveniently with other programs or process large amounts of data without manual intervention The Java platform upon which PuffinPlot is built supports a number of scripting languages which can easily interface with PuffinPlot Perhaps most usefully an implementation of the Python programming language named Jython Juneau et al 2009 has been developed for the Java platform Since Python is widely used in scientific programming and scripting and familiar to a large number of scientists this should provide a convenient route for anyone wishing to integrate PuffinPlot with other data processing steps Using Jython PuffinPlot can be controlled either from a pre written script or interactively from a command shell which accepts and executes commands one at a time from the user PuffinPlot also includes a built in Jython interpreter allowing it to run Python scripts with no additional software Scripting allows you to extend the functionality of PuffinPlot without modifying the main program for example to perform extra processing on your data It also allows you to reuse parts of PuffinPlot as a convenient library for other programs There are three basic ways to control PuffinPlot with scripting 1 Save a Python script as a file and use Run Python script from the File menu to run it This will give your script access to any data wh
14. 5 by Pontus Lurcock 2 Installation This section describes the hardware and software requirements for running PuffinPlot and gives instructions for installing and running it 2 1 Requirements PuffinPlot runs on the Java platform version 7 or later which is preinstalled or freely available for a variety of operating systems including Windows Linux and Mac OS X Java is generally easy to install but detailed instructions for installing it are beyond the scope of this manual please consult the documentation for your operating system or visit http www java com for details If for any reason you are constrained to use an older version of Java on your system you may still be able to run an older version of PuffinPlot version 1 02 of PuffinPlot works on Java 6 and version 1 01 works on Java 5 2 2 Obtaining and installing PuffinPlot You may download the latest version of PuffinPlot from https bitbucket org pont puffinplot downloads PuffinPlot is distributed as a single zip archive file containing the program itself in two different variants as detailed below and documentation The documentation consists of this manual in both HTML and PDF format and a JavaDoc folder containing documentation for PuffinPlot s source code The JavaDoc is only of interest to users wishing to write scripts which interface directly with PuffinPlot s internal data structures see section 4 7 Table 1 lists the contents of the PuffinPlot archiv
15. D1035 2 375 48 8 2 5 81e 05 7 6e 04 400 103 5 1 7 85e 05 7 6e 04 MWD1036 1 425 123 37 2 1 38e 04 8 9e 04 450 107 21 2 1 64e 04 1 3e 03 MWD1036 2 475 137 49 0 9 74e 05 1 3e 03 500 110 32 5 8 07e 05 1 2e 03 625 129 34 3 1 10e 04 1 2e 03 550 112 52 1 1 74e 04 1 2e 03 MWD11B8 2 575 199 9 5 4 67e 04 6 5e 04 Woo Toe 15 S D Discrete Dash denotes Data Lower Equal area sample hidden table hemisphere projection chooser data point point Current Sample Demagnetization Upper Zijderveld selecte name intensity plot hemisphere plot sample point most popular data display methods for palaeomagnetic data a table a Zijderveld plot an equal area projection and a demagnetization intensity biplot which also shows an overlaid magnetic susceptibility plot The plots are interactive in that individual data points may be selected by clicking or by dragging a rectangle with the mouse The plot layout is configurable the sizes and positions of the plots can be changed and plots can be added to and removed from the display To the left of the main plot display area is the sample chooser which shows a complete list of the samples within the suite with the currently selected sample highlighted Multiple samples may be selected at once allowing functions such as PCA calculation to be performed en masse If a long core data file is loaded the sample chooser is shown as a vertical slider indicating
16. NRM was reduced to half in C or mT Y if magnetization intensity reached half the NRM intensity during demagnetization N otherwise Mean declination of treatment step directions Mean inclination of treatment step directions Qos of mean treatment step direction k value of mean treatment step direction number of directions used to calculate mean length of sum of directions used to calculate mean declination of major axis of AMS tensor inclination of major axis of AMS tensor declination of intermediate axis of AMS tensor inclination of intermediate axis of AMS tensor declination of minor axis of AMS tensor inclination of minor axis of AMS tensor Any user defined annotations are also exported as part of the sample export file See section 4 5 for details 10 Table 3 List of fields in exported site data file Field name Description Site Name of site Samples Number of samples at this site Fisher dec Mean declination of sample directions Fisher inc Mean inclination of sample directions Fisher a95 Qos of mean sample direction Fisher k k value of mean sample direction Fisher nDirs number of directions used to calculate site mean Fisher R length of sum of unit direction vectors GC valid Y if the great circle fit is valid N otherwise See section 4 4 4 for details on the validity test and how it may be customized GC dec Declination of great circle direction
17. PuffinPlot User Manual Pontus Lurcock Version 1 03 23 April 2015 Contents 1 Introduction 2 Installation 2 1 ROQUIFEMEM S cos dc a Sy a we ae e a 2 2 Obtaining and installing PutfinPlot ori aa 221 All Operaune systems etori A ee aes a a 222 MACOSX vaa dt a WER ce We ee Do 3 Basic usage 3 1 Anote On keyboard shortcuts ss aii face w es oe Sata da ee ee ee x 32 Opening a tile 2s 4 4 cod sae eee eS ee es RTS Oe SH eae eos 3 3 A tourof the main windOW s sas ser ea wa eee ae a ee e 34 Data model v oee ee a PA ew ee OR a a ee BARES oes 3 5 Main window features ooo oo et eee tenes 3 5 0 Plot area iw ose ai ORE Ra eee PES we Od 34 2 Sample Chooser swiss awl Saw wo ees A ae A Ee Doe 3 5 5 Woolbar ov cee eo 64a a ee ee ee BE ae 4 Detailed usage 8 4 1 Catalogue of functions eeoa di eee Soe eed Ge ee wR 9 ALLI Ple med cunda ee hae kG A owe eho ehh eee as 9 ALL EA TIO a a ae oe eS ee oe sd AA 12 Aia Calcula LOS METI a ee wh AA OR ats RRA AS e a 14 ALA Window Ment 2 05 A A AA Ra ee 16 Aco A a ae Bee ee bs ee oe oe ee ea 16 4 2 Features 42s cee ca aasa en cee as a a w 16 4 2 1 Supported file types s ace eee eee cee eee Ee ee 16 22 Importa o ii ai ee O 17 4 2 3 Selecta POMS iia e a ETS A me be G 18 4 2 4 Working with multiple samples 0 000000000 18 4 3 Plots and other data displays sice 2 eh ge ag SA Sea we os SE ee ees 18 4 3 1 Available plot types 2 20 4 4 td a Be are
18. an be labelled with the treatment level Added suite parameter table for mean directions and VGPs Site alpha 95s can be shown in the suite equal area plot Data import Selectable units for custom data import More variants of the AGICO AMS file can now be imported Direct import of sample directions IAPD file import Caltech file import Better guessing of measurement type in 2G files Site location data import for use with VGP calculation More palaeomagnetic data can now be appended to an existing suite Data export n and a95 are listed in sample parameter file Great circle strikes and dips are included in exported data Bug fixes Exporting FreeHEP SVG graphics no longer disables anti aliasing PuffinPlot no longer crashes if an incorrect 2G protocol is specified PuffinPlot will not save its own file over the original data file Cleared PCA directions no longer reappear Fixed potential crash during suite parameter export Measurement types now checked for consistency when opening a file 30 Documentation All new features are fully documented in the updated user manual Miscellaneous new features e Site calculations automatically update when sample calculations change e Site directions cleared automatically when all their sample directions are cleared e Warning when closing a file or quitting with unsaved data e Clearer error messages and warnings when reading corrupted files Treatmen
19. at for the display and editing of vector graphics data SVG files can be opened and edited by vector graphics programs such as Inkscape and Adobe Illustrator and can be incorporated into documents by a variety of programs The chief limitation of the SVG files exported by PuffinPlot is that they can only contain one page corresponding to the currently displayed data PDF Portable Document Format is a popular format for on screen display and printing of all kinds of documents PuffinPlot can produce multi page PDF documents with one page for each selected sample Many vector graphics programs can import PDF files but since PDF is a format designed primarily for display rather than editing the results may be inferior to those produced with SVG Both these formats are formally standardized however they are also large and complex and they are supported to varying extents by a huge number of programs For these reasons com patibility problems can sometimes occur It is difficult to produce a file which will be guaranteed to work well with any program on any operating system PuffinPlot attempts to mitigate this problem by offering a range of different graphics export options as detailed in the next section 4 6 2 Graphics export options All of these export functions may be found in the Export graphics submenu of the File menu except for the Print to PDF option 25 Export SVG Batik saves the current contents of the main data displ
20. ay as an SVG file using the Batik software library Export SVG FreeHEP saves the current contents of the main data display as an SVG file using the FreeHEP software library Export PDF iText produces PDF file using the iText software library The resulting PDF file will use the current graph layout and will contain one page for each of the selected samples Export PDF FreeHEP produces a PDF file using the FreeHEP software library The resulting PDF file will use the current graph layout and will contain one page for each of the selected samples Print to PDF is another way of producing a PDF file Select Print from the File menu and select PDF as the destination printer If the PDF option is not available you will first have to install a PDF printer driver please see your operating system documentation for details These options are to some extent redundant SVG files produced using the two menu items should appear practically identical as should the three varieties of PDF file However the internal structures of the files are different which is useful in improving compatibility with other pro grams If for example you find that another program has trouble reading the SVG file produced using the Batik option you may find that if FreeHEP option produces better results 4 7 Scripting PuffinPlot s graphical desktop interface is intended to be the primary way to interact with the program However it is often useful to be able
21. ce of PuffinPlot s windows and menus It has no effect on the functionality of the program Native gives an appearance intended to harmonize with other programs on the operating system on which PuffinPlot is running Metal and Nimbus are cross platform appearances which will look the same on any operat ing system Default will use the default appearance for Java programs on the current operating system in most cases this will be the same as Native for Mac OS X and Win dows and Metal for Linux Changes to this option will not take effect until PuffinPlot is restarted GC validity allows you to customize the conditions under which a site mean calculated by great circle intersection is considered valid The validity test is used in several ways e When site data is exported to a CSV file one of the exported columns gives the result of the validity test e Only valid site mean directions are shown on the suite equal area plot e Only valid site mean directions are used when calculating the overall mean direc tion for a suite The validity test takes the form of a logical expression in the syntax of the Python programming language involving the following variables M the number of stable endpoints PCA directions used in the fit N the number of great circles used in the fit a95 the do value semiangle of the 95 confidence region k the k value estimate for k The most useful components for contructing vailidity expressions are t
22. con trolled using the chooser on the toolbar see section 3 5 3 for details The horizontal projection is shown with filled points and the vertical projection with unfilled points If a PCA fit has been calculated for this sample the two projections of the PCA lines are overlaid on the plot in blue If the V vs H vertical projection is selected only the horizontal projection of the PCA line is shown since V vs H effectively uses a different vertical projection for each point The appearance of the PCA lines can be changed using the Preferences dialog see section 4 4 4 is a plot of demagnetization step in mT or C versus intensity of magnetization in A m shown as a line of filled points If magnetic susceptibility measurements have been taken they are overlaid on the same plot as unfilled points with the scale shown on the right of the graph If PuffinPlot cannot find any data describing the demagne tization treatment i e AF field strength or temperature the X axis will be labelled measurement number and the X values will correspond to the sequence of the data in the file Data table is a table in which each row represents one demagnetization step for the current sample The columns from left to right give the demagnetization step declination inclination intensity and magnetic susceptibility Selected points are denoted by an asterisk to their left hidden points are denoted by a dash to their left Sampl
23. d clears the results of any calculations done on them such as PCA or great circle analysis Calculations gt Clear sample PCAs clears any PCA calculations for the currently selected sam ples Calculations gt Clear sample GC fits clears any great circle fits on them for the currently selected samples Calculations gt Fit great circle calculates and displays a best fitting great circle for all the se lected points in all the selected samples Calculations gt Great circles calculates a best fitting direction for all the great circles fitted at the current site using the algorithm of McFadden and McElhinny 1988 The great circle fit is shown both in the Equal area site plot in the main window if the plot has been activated in the preferences and in a separate window which is opened automatically Calculations gt Clear site calculations clears the results of any calculations associated with the selected sites as opposed to samples at present this amounts to clearing the best fit great circle direction for each selected site Calculations gt Multi suite means calculates Fisherian means across all the samples in all the currently opened suites the results are not plotted but they are shown in a pop up window and can be saved using the File gt Export data gt Export multi suite calcula tions menu item AMS calculations PuffinPlot can show the results of statistical calculations on AMS tensors giving mean directio
24. directions The location file should be in CSV comma separated value for mat with no header line Column 1 contains the site name column 2 the latitude degrees north from equator negative for southern hemisphere and column 3 the longitude degrees east of Greenwich File gt Import data gt Import AMS imports AMS data from a file and adds it to the current suite The file must be in the ASC format produced by the Safyr and SUSAR programs distributed with AGICO kappabridges The AMS data is assigned to the appropriate samples within the suite by matching the sample names specified in the ASC file with the sample names for the demagnetization data If the AMS file contains data for sam ples not in the suite these samples will be created and added to the suite AMS data is not displayed by default the equal area plot of AMS data can be activated from the Preferences window AMS import has been tested with data from SAFYR versions 1 5 and 2 6 and SUSAR version 4 0 File gt Page Setup opens a window allowing you to change the paper size orientation and margins for printing File gt Print opens a window allowing you to print the selected samples Note that only the selected samples will be printed so if you wish to print the whole suite use Edit gt Select all first On most systems this will also allow you to print to a PDF file Windows users may need to install a virtual PDF printer such as CutePDF Writer or Bullzip PDF P
25. dit gt Paste step selection takes the selected treatment steps from the clipboard see Copy step selection and selects the corresponding treatment steps in all the selected samples Edit gt Rotate invert samples is a submenu allowing the demagnetization data from the selected samples to be rotated 180 around a selected axis Such functionality is rarely required but can be useful for example when it is found that a sample has been incorrectly oriented during measurement or when converting between different orientation con ventions Edit gt Rotate invert samples gt Flip samples around X axis rotates the magnetic moment val ues for all selected samples 180 around the X axis Edit gt Rotate invert samples gt Flip samples around Y axis rotates the magnetic moment val ues for all selected samples 180 around the Y axis Edit gt Rotate invert samples gt Flip samples around Z axis rotates the magnetic moment val ues for all selected samples 180 around the Z axis Edit gt Rotate invert samples gt Invert sample directions Inverts every magnetization vector in every selected sample Each of the x y and z co ordinates of each vector is negated this corresponds to a point reflection through the origin Edit gt Edit sites is a submenu allowing site names to be set for samples in various ways Edit gt Edit sites gt Set site name allows a single site name to be set for all the selected sam ples Edit gt E
26. dit sites gt Set sites from sample names sets site names for the selected samples by taking specified characters from the sample names The characters to use are specified by a list of comma separated numbers and number ranges for example entering 1 3 5 8 would give each selected sample a site name composed of the first third and fifth to eighth characters of the sample name so that a sample with the name FFQB0529 1 would get the site name FQ0529 The table below gives some further examples Sample name Character selection Resulting site name FFQB0529 1 1 3 5 8 FQ0529 FFQB0529 1 4 6 BOS CiLpA 10 53 1 2 5 7 8 CiA10 CiLpA 10 53 3 4 9 11 Lp 53 Edit gt Edit sites gt Set sites by depth sets site names in continuous suites using the depths of the individual samples PuffinPlot asks for a thickness value and groups the samples within the core into sites of that thickness effectively slicing the core into equally thick sites Each site is named after the shallowest depth within it Edit gt Hide steps hides all the selected treatment steps in all the selected samples This removes them from all the graphical plots which will be rescaled to avoid unnecessary blank space but not from the data table in the main plot window on the data table hidden treatment steps are marked with a dash symbol to their left Hidden steps can be restored using the Show all steps menu item 13 Edit gt Show all steps restores all h
27. e After downloading the archive move it to the folder where you would like PuffinPlot installed and extract its contents there 2 2 1 All operating systems The file PuffinPlot jar in the archive is the PuffinPlot program itself as a cross platform jar Java archive file This file is recommended for Linux Windows and other non Mac operating sys Table 1 The contents of the PuffinPlot archive file File Description README A text file briefly describing the archive PuffinPlot jar The PuffinPlot program suitable for all operating systems PuffinPlot app The PuffinPlot program tailored for Mac OS X Manual Folder containing this manual in PDF and HTML format JavaDoc Folder containing internal documentation for PuffinPlot Example files Folder containing example data files LICENCE The licence under which PuffinPlot is distributed tems it will also run on Mac OS X but the specific Mac OS X version described below is usually preferable The details of starting PuffinPlot vary between operating systems but double clicking on the file PuffinPlot jar is the most common method In some cases it may be necessary to right click on the file and select Open with Java runtime or some similar text from a menu PuffinPlot can also be started from a terminal prompt by setting the current folder to the one containing PuffinPlot and typing java jar PuffinPlot jar Note for Windows users Under Windows other programs may occasionally interfere
28. e Calculate gt Suite means function in section 4 1 3 Site parameters shows the site mean direction as calculated either by Fisher statistics or by the great circle technique of McFadden and McElhinny 1988 It gives the mean inclina tion and declination and the ag and k parameters If no site mean direction has been calculated for the current site this plot is invisible Equal area site shows all the great circles fitted at the current sample s site along with a best fit direction calculated by the method of McFadden and McElhinny 1988 On this plot the calculated site direction is shown as a circle Any sample PCA directions are shown as diamonds Demagnetization steps used for the great circle fits are shown as squares Poles to the great circles are shown as triangles Equal area suite shows all the site means for the suite and a Fisherian mean and 95 con fidence interval for them If two polarities are present in the suite two means are calculated and shown If no sites are defined individual sample PCA directions and their means are plotted instead Note that for site means calculated by great circle analysis only valid means are shown See section 4 4 4 for details on how validity is determined VGP table is a table showing virtual geomagnetic pole VGP data for each site in the current suite The columns are site name q site latitude A site longitude VGP p VGP latitude VGP A VGP longitude dp first semi
29. e column width Select this tick box to specify that the file format has fixed width columns In this case the column separator will be ignored and you must specify the widths of the columns see below If this box is not selected the column widths are ignored Column widths If your file format uses fixed width columns you must specify them here as a list of numbers separated by commas For example if you have six columns with the first being ten characters wide and the rest eight characters wide you would enter 10 8 8 8 8 8 in this box If your file format does not use fixed width columns this box is ignored Column definitions This part gives the column number for each item of measurement data to be read 17 Column no This is the number of the column to read columns are numbered from left to right starting at 1 Column contents This is the data to read from the specified column Note that not all data types need to be specified for a file format at minimum it is sufficient to specify the demagnetization step the three components of the magnetization vector either as X Y and Z moments or as declination inclination and magnetization 4 2 3 Selecting points For most of PuffinPlot s functions the data points of interest must be selected before anything can be done to them You can select data points simply by clicking on them if you click on a selected point it will be de selected Selected points are drawn in red to di
30. e parameters shows the results of PCA and or great circle fits for data in the current sample If neither of these calculations has been done this plot is invisible When vis ible it shows the inclination and declination of the first principal component which corresponds to a least squares linear fit It also shows the maximum angular deviation MAD values MAD1 and MAD3 which function as goodness of fit parameters smaller is better The MAD1 value gives an indication of how nearly the points lie in a single plane the MAD3 value gives an indication of how nearly they lie along a single line PCA analysis and MAD values are explained in Kirschvink 1980 and in section 9 7 of Tauxe et al 2010 The plot also show the Cartesian equation of the PCA best fit line For the great circle fit the plot gives the inclination and declination of one of the great circle s poles and the MAD1 value indicating the goodness of fit of the great circle Note that this may be different from the MAD1 for the PCA fit since different sets of points may be used for the two fits Sample parameter table shows a summary of parameters for each sample within the current site declination inclination and type of analysis PCAa and PCAw for anchored and unanchored PCA respectively and GC for great circle For PCA analysis the declina tion and inclination give the first principal component for great circle analysis they give the pole to the circ
31. emag is an experimental ternary plot designed to display data from triaxial IRM de magnetization experiments conducted according to the method of Lowrie 1990 The position of a point on the plot reflects the relative strengths of the three axes of magneti zation which in turn correspond to high medium and low coercivity components The path produced by points at successive demagnetization steps thus shows the relative effects of thermal unblocking and possibly thermal alteration on these components 20 4 3 2 Arranging the plots PuffinPlot allows the plots to be freely rearranged and resized within the display area they can also be switched on and off as required see section 4 4 To arrange the plots select Edit layout from the Edit menu This puts PuffinPlot temporarily into a special mode where plots become moveable A tick appears next to the menu item and the plots are overlaid by pale orange rectangles allowing you to manipulate them Each plot is also annotated with its name which helps to identify plots that are not currently displaying any data e g the PCA directions display if no PCA has been performed To resize a plot click and hold on an edge or corner of its rectangle then drag it to the desired size To move a plot click and hold in its central area and drag it to the desired location Plots may be overlapped freely When you click in an area where two or more plots overlap the smallest plot is treated as the
32. eneral it is appropriate to anchor the PCA if the analysed points are known to represent the final demagnetization component that is they are trending directly towards the origin and deviations from this path are known to be due to measurement noise rather than an offset in the true magnetization vectors Leaving PCA unanchored allows analysis of a non final component provided that it is sufficiently well separated from other components Calculations gt Fisher by site calculates a Fisherian mean direction for each selected site using the PCA directions of its samples Calculations gt Fisher on sample calculates a direction for each selected sample using the Fish erian mean of the directions for the selected treatment steps PCA is almost always preferable for establishing a reliable sample direction but this technique can some times be useful for determining a polarity from very noisy data Note that at present Fisherian sample directions are not saved as part of the PuffinPlot file although they can easily be recalculated if the selected demagnetization points are not changed The Fisherian mean and associated parameters are however included in exported sample data files see Table 2 Calculations gt Suite means calculates Fisherian means across all the selected samples Two sets of means are actually calculated one set is calculated from the PCA directions of in dividual samples and the other from the site mean directions i
33. er sits at the leftmost edge of the main window and allows you to change the current sample the one for which data is plotted and the set of selected samples most of PuffinPlot s functions operate on the currently selected samples Often the set of selected samples will consist only of the current sample The sample chooser takes two forms depending on whether the current suite of data is for discrete samples or for a continuous long core measurement Using the discrete sample chooser The discrete sample chooser shows the names of the samples in the current suite The selected sample or samples are highlighted in a different colour The selected sample is the current sample and its data is displayed in the main plot area If more than one sample is selected the first of the selected samples is the current sample To select a single sample click on its name To select a contiguous range of samples click at one end of the range then hold down Shift while clicking at the other end of the range To select multiple non contiguous samples hold down Ctrl while clicking To select all samples press Ctrl A Using the continuous sample chooser The continuous sample chooser is a vertical grey bar representing the total length of the mea sured core striped with horizontal white lines representing the individual measurements at each depth If there are too many measurements for all the requisite white lines to be displayed they are omi
34. f any have been com puted Note that if there are site means computed by great circle intersection only those considered valid are used see section 4 4 4 for details of the validity test If a site has both a valid great circle direction and a Fisherian direction calculated from PCAs the great circle direction will be used Each set of means consists of an overall mean and individual means for the upper and lower hemisphere to cater for data sets containing reversals Corresponding VGPs are also calculated All these means can be exported as a CSV file using the File gt Export Data gt Export suite calculations menu item The overall means and VGPs but not the individual upper lower hemisphere means are also shown in the Suite table plot if it is active Note that like most PuffinPlot functions this feature operates on all the selected samples to calculate means for the entire suite you must first select all the samples 14 Calculations gt MDF calculates the Median Destructive Field or for thermal demagnetization the Median Destructive Temperature of the selected samples This is the field or tem perature at which the intensity of the sample s remanence has been reduced to half of its initial value Once calculated it is displayed on the demagnetization intensity plot and can be saved as part of the exported sample data Calculations gt Clear sample calculations de selects all the points in all the selected samples an
35. gth and the magnetization intensity of the sample after application of that field File gt Export graphics is a submenu with various options for exporting the plots for the current and selected samples See section 4 6 for full details File gt Import data is a submenu with functions to import additional data into the current suite File gt Import data gt Append more palaeomagnetic data reads a palaeomgnetic data file like the Open function in the main File menu The difference is that this function will append the data to the current suite rather than creating a new suite for it Table 2 List of fields in exported sample data file Note that in addition to the predefined fields any custom user annotations see section 4 5 will also be exported in this file Field name Description Suite Suite name Sample Sample name only present in discrete files Depth Depth in core only present in long core files NRM intensity A m MS jump temp C Steps PCA dec PCA inc PCA MAD1 PCA MAD3 PCA anchored PCA equation PCA start C or mT PCA end C or mT PCA contiguous GC dec GC inc GC strike GC dip GC MAD1 GC npoints MDF half intensity A m MDF demagnetization C or mT MDF midpoint reached Fisher dec Fisher inc Fisher a95 Fisher k Fisher nDirs Fisher R AMS decl AMS incl AMS dec2 AMS inc2 AMS dec3 AMS inc3 annotations NRM intensity in A m F
36. he comparison operators lt lt gt gt the logical operators and and or and parentheses A typical expression might be a95 lt 3 and k gt 5 and M gt 3 or N gt 5 which means that a great circle fit will be considered valid if it has an a9 below 3 ak above five and either at least three endpoints or at least five circles The default value of this setting is True which causes all great circle fits to be considered valid Zplot PCA display controls the manner in which PCA directions are shown on the Zijderveld plot see section 4 3 1 The available settings are Full PCA lines will extend right to the edges of the Zijderveld plot Long PCA lines will be shortened by 10 from the Full length Short PCA lines will only extend through the points used to calculate the PCA None No PCA lines will be shown Sample orientation controls how sample orientation is displayed at the top of the main win dow it can be shown either as azimuth and dip angle or as azimuth and hade the complement of the dip angle 24 Formation orientation controls how formation orientation is displayed at the top of the main window it can be shown either as dip azimuth and dip angle or as strike and dip angle 4 5 Annotations Annotations are a feature allowing short categorized notes to be added to each sample in a suite The categories can be freely chosen Annotations come in two varieties custom flags and custom notes Custom flags embod
37. heir default values Edit gt Sample parameters opens a window which allows you to change the sample volume sample orientation formation orientation and local magnetic declination for all the selected samples Each parameter type can be individually changed without affecting the values of the others For convenience sample orientation can be specified using either dip angle or hade it is possible but pointless to enter values for both of these parameters since one will overwrite the other Similarly formation orientation can be specified using either dip azimuth or strike 12 Edit gt Set treatment type opens a window which allows you to change the treatment type for the selected samples Normally the treatment type will be automatically determined on opening a data file If the file does not specify the treatment type PuffinPlot will attempt to guess it Set treatment type allows you to set the treatment type explicitly in cases where PuffinPlot guesses wrong or where the wrong treatment type is given in the data file Edit gt Copy step selection copies the selected treatment steps for the current sample to an in visible clipboard The selection can be pasted from the clipboard to other samples see Paste point selection selecting the same demagnetization steps in those samples This is useful for selecting the same treatment steps in a large number of samples without having to manually select them for each sample E
38. hysics Geosystems year 2012 month Jun day 26 publisher AGU volume 13 pages Q06Z45 issn 1525 2027 doi 10 1029 2012GC004098 url http dx doi org 10 1029 2012GC004098 RIS citation record TY Ti Al A1 Yi JO VL SP SN UR DO PB JOUR PuffinPlot A versatile user friendly program for paleomagnetic analysis Lurcock P C Wilson G S 2012 06 26 Geochemistry Geophysics Geosystems 13 Q06Z45 1525 2027 http dx doi org 10 1029 2012GC004098 10 1029 2012GC004098 AGU 29 B Release notes No release notes are available for PuffinPlot versions prior to 1 03 PuffinPlot 1 03 release notes Calculations Virtual geomagnetic pole calculation Fisher by site calculations can be done on continuous data sets Fisher analysis of demagnetization steps PCA and GC fits can be cleared individually R added to the available Fisher statistical parameters Data plotting Horizontal projection in Zplot supports west upward orientation Data points can be labelled with treatment step Equal area plots can be labelled to avoid confusion Site equal area plots now distinguish PCAs demag steps GC poles and site means Current site and sample are highlighted in the relevant data tables and plots Sample directions can be annotated with their names in the site equal area plot a95 added to site parameter table More compact default plot layout Treatment steps c
39. ich has already been loaded into PuffinPlot 2 Save a Python script as a file and run PuffinPlot from the command line specifying the name of the script as a parameter using the following syntax java jar PuffinPlot jar script MyScriptName py where MyScriptName py is the filename of the script you wish to run In this case the script will be run as soon as PuffinPlot starts 3 Use a scripting language interpreter separate from PuffinPlot In this case you must down load and install the language yourself This approach lets you use any language available for the Java platform not just Jython Additionally many languages including Jython provide an interactive console allowing you to control PuffinPlot by typing commands one at a time rather than executing a whole pre written file 26 Figure 3 A simple Python script to demonstrate the use of PuffinPlot from a scripting environ ment This script first opens a data file It then calculates the mean NRM of all the samples and displays it Then it calculates a PCA direction for each sample in the suite and saves the results to a CSV file Explanatory comments in the script are preceded by the character If Jython is installed and this script is saved as example py it may be executed with the command jython Dpython path PuffinPlot jar example py Import the required libraries from net talvi puffinplot data import Suite from net talvi puffinplot data import Correction from ja
40. ick inspection of suite data at a larger scale without editing the main plot layout 4 1 5 Help menu Help gt PuffinPlot website opens the PuffinPlot website using the default web browser Help gt Cite PuffinPlot opens a window containing information on the PuffinPlot paper Lur cock and Wilson 2012 and how to cite it Help gt About PuffinPlot displays some brief information about PuffinPlot including the version On Mac OS X this item is also present on the PuffinPlot menu 4 2 Features This section presents PuffinPlot s features in moderate detail 4 2 1 Supported file types PuffinPlot can read a number of commonly used palaeomagnetic data formats PuffinPlot filename suffix ppl PuffinPlot s own file format 2G filename suffix dat files produced by the Long Core program used with 2G Enterprises cryomagnetometers Caltech filename suffix sam with associated data files in same folder format used at the Caltech Paleomagnetics Laboratory and supported by the Paleomag program of Jones 2002 IAPD filename suffix dat format used by the IAPD program and its successors developed by T H Torsvik et al and used at the Geological Survey of Norway IAPD files contain an a95 value for each treatment step which gives an indication of the measurement s reliability PuffinPlot does not import these values but will show a warning if any of them has a value of 5 or greater Zplot filename suff
41. idden treatment steps in all the selected samples Edit gt Edit custom flags allows you to add or remove user defined flags for the suite see section 4 5 for details Edit gt Edit custom notes allows you to add or remove user defined note categories for the suite see section 4 5 for details Edit gt Rescale mag sus scales all the magnetic susceptibility values for the suite by a spec ified factor This is useful since magnetic susceptibility meters typically do not report values in standard S I units Note that unlike many PuffinPlot operations the scaling is applied to the entire suite not just the selected samples 4 1 3 Calculations menu The calculations menu provides facilities for calculating magnetic parameters and directions Note that most calculations operate on all the selected samples not just the current sample Calculations gt Calculate PCA calculates a best fitting line to all the selected points in all the selected samples using principal component analysis Kirschvink 1980 The PCA di rection is projected onto the Zijderveld plot If the PCA anchored menu item below is ticked the resulting PCA fit line will be anchored to the origin if PCA anchored is not ticked the PCA fit will be unanchored Calculations gt PCA anchored is a menu item which may be toggled on or off When it is on a tick mark appears next to it and PCA analyses are constrained to pass through the origin In g
42. irection the chooser controls the x axis which may correspond to North V vs N or East V vs E The third option V vs H projects each data point separately in the plane containing itself and the origin this is sometimes referred to as a modified Zijderveld plot Zijderveld horizontal projection N is up W is up This chooser controls the horizontal projection used in the Zijderveld plot The upward direction on the plot can correspond to either north or west Sample orientation Samp The first number is the azimuth of the sample orientation the second is its either its dip angle or its hade depending on the current setting in the user preferences see section 4 4 4 By default PuffinPlot uses dip angle rather than hade For a long core the azimuth and dip will usually be 0 and 90 respectively throughout the core Formation orientation Form The first number is either the azimuth of the dip for the bed ding or its strike the second is the dip angle By default PuffinPlot uses the dip az imuth rather than the strike but this can be changed in the preferences window see section 4 4 4 Magnetic declination Dev This is the angle between magnetic north and true north at the sampling site It is abbreviated Dev for deviation to avoid any possible confusion with the declinations of sample magnetizations Select all selects all the treatment steps in the current sample PCA performs principal
43. ix txt format used by the Zplot program developed by Steve Hurst at Woods Hole 16 Sample directions filename suffix txt a file of sample level directional data This lets you use PuffinPlot to analyse directions even when no demagnetization data is available or when the data is not palaeomagnetic in origin Input files must contain three fields per line with no header lines sample name or depth declination in degrees and inclination in degrees Fields are separated by commas tabs or space characters Custom formats This option imports data from a file format freely defined by the user within certain limits Custom formats allow PuffinPlot to read a large variety of textual tabular data formats See section 4 2 2 for details Note that there are different ways to read 2G data files users are encouraged to read section 4 4 2 and ensure that the preferences are correctly set for their needs In particular magnetization vectors may be read incorrectly from 2G long core files if the wrong import settings are used so it is important to check the settings before importing data In general support for other file formats is straighforward to add and most tabular textual file formats can be opened using the File gt Import data function 4 2 2 Importing data When File gt Import data is selected PuffinPlot shows a window allowing you to describe a text based tabular file format once you have specified a format yo
44. le Clicking on a line within this table will show the correspond ing sample s data in effect it works as an extra sample chooser Site parameter table shows a summary of parameters for each site within the current suite The columns are Site the name or identifier of the site n the number of samples at the site PCA the number of PCA analyses for samples at the site GC the number of great circles fitted for samples at the site dec the declination of the site mean direction inc the inclination of the site mean direction a95 the aos value of the site mean direction R the total length of the sum of the direction unit vectors type the type of analysis used Fshr for Fisher 1953 analysis on PCA directions GC for great circle analysis McFadden and McElhinny 1988 GC is suffixed with either v for valid or i for invalid See section 4 4 4 for details on the validity test and how it may be customized 19 If both a valid great circle direction and a Fisherian direction exist for a site only the great circle direction will be shown Clicking on a line within the site parameter table will jump to the first sample of the corresponding site Title shows the name of the current sample and the current site for a discrete suite For a continuous long core suite it shows the current depth This plot also shows suite level Fisher statistics calculated over samples and over sites if these are available see th
45. n 4 3 1 4 4 4 The Misc tab Label equal area plots If this box is ticked the equal area plots sample site suite and AMS will be shown with text labels at the bottom right making them easier to distinguish from one another Label treatment steps If this box is ticked each point on the demagnetization plots Zijderveld and equal area will be labelled with the appropriate treatment step AF intensity or temperature Label samples in site plots If this box is ticked sample directions PCA or Fisher will be labelled with the sample s name or depth in the site equal area plot Label points in suite plots If this box is ticked sample and site directions will be labelled with the appropriate name or depth in the suite equal area plot Highlight current sample site If this box is ticked the current sample and site data will be shown in red on the site and suite equal area plots and on the sample and site parameter tables This feature makes it easier to pick out the current sample and site in the context of larger scale analyses and is useful for exploring data particularly in conjunction with the ability to jump to a sample or site by clicking on its line in a parameter table Show site a95s on suite plot If this box is ticked any site direction shown on the suite equal area plot will be plotted along with a projected small circle denoting the ag interval The site ao circles are plotted in blue to distinguish them from the sui
46. ns and confidence ellipses for the principal axes by one of three methods at present however these calculations cannot be performed by PuffinPlot itself Instead it makes use of two Python scripts from the PmagPy suite Tauxe et al 2010 bootams py and s_hext py In order to calculate AMS statistics these scripts must first be installed on the computer running PuffinPlot and the folder containing them must be specified in the Preferences window The PmagPy programs may be obtained from http earthref org PMagPy All AMS calculations operate on the currently selected samples Tauxe et al 1998 and chapter 13 of Tauxe et al 2010 give more details of tensor statistics particularly with regard to the application of bootstrap methods Calculations gt Calculate bootstrap AMS calculates bootstrap statistics using the bootams py program producing Kent error ellipses which are shown on the AMS plot in the main window Calculations gt Parametric bootstrap AMS calculates bootstrap statistics using the bootams py program producing Kent error ellipses which are shown on the AMS plot It differs from the previous function in employing a parametric bootstrap which can provide more realistic confidence intervals for small numbers of samples on the often reason able assumption that measurement uncertainties are normally distributed across the selected samples Calculations gt Calculate Hext on AMS calculates Hext 1963 statistics using
47. ocol used in taking the readings A protocol is a particular sequence of empty tray measurements and sample measurements in defined orienta tions undertaken for each set of measured samples The tray and sample measure ments are combined by PuffinPlot as it reads the file providing a more accurate cor rected moment measurement for each sample Magnetic susceptibility measurements if present are also automatically associated with the preceding magnetic moment mea surement or measurements Table 4 describes the available protocols Warning incorrectly set sensor lengths can produce erroneous data The sensor lengths are not written to the 2G file so they must be correctly set in PuffinPlot s preferences before importing 2G long core data from the X Y Z vector components When importing discrete data or reading from the polar fields in the 2G file sensor lengths are not required If the sensor lengths are not known use the Dec Inc Intensity setting in the 2G import tab Failing to correct for sensor length is particularly dangerous because the deviations from the correct vectors are often small enough not to be immediately obvious See Section 3 of Roberts 2006 for a fuller discussion of sensor response functions 4 4 3 The Plots tab This tab shows a list of plots which PuffinPlot can display You can control which plots are shown by ticking and unticking the boxes next to the plot names The plot types are detailed in sec tio
48. or thermal demagnetization the temperature step at which the first jump in magnetic susceptibility occurs A jump is de fined as a susceptibility of at least 2 5 times the previous value Number of treatment steps for this sample Declination of PCA direction Inclination of PCA direction The Maximum Angle of Deviation for the planar PCA fit the smaller the value the more coplanar the points See sec tion 4 3 1 for more details The Maximum Angle of Deviation for the linear PCA fit the smaller the value the more collinear the points See sec tion 4 3 1 for more details Y if the PCA fit was anchored N if not The Cartesian equation of the PCA best fit line Field in mT or temperature in C of first demagnetization step used for PCA analysis Field in mT or temperature in C of last demagnetization step used for PCA analysis Y if all steps between the first and last were selected for PCA N if any were omitted the declination of the pole to the fitted great circle if any the inclination of the pole to the fitted great circle if any the strike of the plane of the fitted great circle if any the dip of the plane of the fitted great circle if any the MAD1 value for the great circle fit indicating goodness of fit smaller is better See section 4 3 1 for more details the number of points used for the great circle fit half of the NRM in A m the demagnetization treatment level at which the
49. pond to a section in the field for a long core study it will correspond to a core A suite is initially created by opening one or more data files from a magnetometer it is saved as a file in PuffinPlot s own format A suite can contain multiple sites A site corresponds to a Sites are not required If none Al samples rom one location o sono a saree ae aa are defined the samples directly set of samples taken from one spot in a section or from a particular range of depths A site s associated data can include such things as bedding attitude and stratigraphic height as well as calculated parameters such as the mean palaeomagnetic direction for all the samples at the site Sites are not required if no sites have been defined samples are contained directly within the suite Each site or if no sites are defined the suite contains multiple samples A sample corre sponds to a small physical volume of rock For a discrete study this will usually be a typical palaeomagnetic 25mm cylinder or IODP cube sample For long cores it is the portion of the core at a particular depth The data associated with a sample consists of information specific to this physical unit which does not change with the application of demagnetization techniques for example a sample code or name or for long cores a depth the field orientation of the sample and its volume For discrete samples this data can also include a tensor representing anisotro
50. py of magnetic susceptibility which is imported separately from an Agico kappabridge datafile and collated with the magnetization data by matching the sample names The sample can also contain calculated parameters such as a direction fitted by principal component analysis or a best fitting great circle Each sample contains multiple demagnetization steps A step represents a sample at a particu lar point during the treatment protocol Its associated data thus includes details of the treatment the type thermal AF IRM etc and parameters temperature field strength etc The data also includes the state of the sample itself most importantly the measured magnetization vector For thermal studies the magnetic susceptibility is usually also recorded after every heating cycle and is also stored as part of the step 3 5 Main window features This section describes the parts and functions of the main PuffinPlot window as shown in figure 1 3 5 1 Plot area The plot area is the largest part of the window and plots the data for the current sample using various plots By default four plots are shown a demagnetization intensity biplot a Zijderveld plot an equal area projection and a table of demagnetization steps The plots can be moved and resized see section 4 3 2 Other plots are also available and the preferences window can be used to control which plots are displayed see section 4 4 3 5 2 Sample chooser The sample choos
51. rements This is the simplest tray correction the tray is measured once at the start and all subseuent measurements are sample mea surements PuffinPlot corrects each sample measurement us ing the initial tray measurement This option reads a file measured using the TRAY NORMAL protocol but like TRAY FIRST makes all sample corrections using the initial tray measurement and ignores all subsequent tray measurements The main intended use for this option is to allow direct comparison between the TRAY FIRST and TRAY NORMAL protocols to avoid the extra work of using the TRAY NORMAL protocol on sample suites for which it is unnecessary 23 magnetic north if it is relative to geographic north a magnetic declination of zero can be specified Demag y axis label allows to you customize the text which labels the y axis of the demagnetization intensity plot PmagPy folder sets the location of the PmagPy programs If you wish to do calculations of AMS statistics within PuffinPlot it is necessary to have the PmagPy programs bootams py and s_hext py installed see section 4 1 3 for details This box allows you to specify to PuffinPlot the folder in which the programs are installed Font allows you to change the font used in the plots enter a font family name into the box PuffinPlot must be restarted for the change to take effect If the specified font cannot be found a default fallback font is used Look and feel controls the appearan
52. rinter in order to produce PDF files File gt Print suite EA window prints the contents of a separate window showing an equal are plot of sample site directions through the suite see section 4 1 4 for more details File gt Print site EA window prints the contents of a separate window showing an equal area plot of directions at the current site see section 4 1 4 for more details File gt Run Python script runs a user specified external script written in the Python program ming language See section 4 7 for details File gt Preferences opens the preferences window See section 4 4 for details On Mac OS X this item is found on the PuffinPlot menu to the left of the File menu rather than on the File menu File gt Quit terminates PuffinPlot On Mac OS X this item is found on the PuffinPlot menu to the left of the File menu rather than on the File menu 4 1 2 Edit menu The Edit menu provides various basic functions mainly to do with manipulation of data points Edit gt Select all steps selects all the treatment steps in all the selected samples excluding treat ment steps which have been hidden see Hide steps below Edit gt Clear step selection de selects all the treatment steps in all the selected samples Edit gt Edit layout allows you to reposition and resize the plots in the main display area See section 4 3 2 for details Edit gt Reset layout resets the sizes and positions of all the plots to t
53. so be run directly from within PuffinPlot The script opens a data file calculates the mean NRM and produces a file containing a PCA direction for each sample Note that virtually all of PuffinPlot s data and functionality is available to the Python script so far more complex examples are possible Internal documentation for PuffinPlot To write scripts interacting with PuffinPlot some knowledge of its internals is of course necessary PuffinPlot comes with complete documentation JavaDoc for all its accessible data structures If more detail is required the source code is also freely available 5 Acknowledgements Libraries PuffinPlot makes use of several software libraries generously released under liberal terms e Jama a basic linear algebra package for Java for matrix calculations 27 Figure 4 A Python script intended to be run from PuffinPlot s File gt Run Python script menu item to act on the currently loaded data Note that in this case it is not necessary to create a Puffin application since the current Puffin application is supplied to the script in the puffin_app variable This script goes through all the data in the current suite For any datum that doesn t have a magnetic susceptibility measurement it sets the magnetic susceptibility to zero suite puffin_app getSuite find the current suite for sample in puffin_app getSamples For every sample in the suite for datum in sample ge
54. stinguish them from the black unselected points Note that the notional data point itself is the thing being selected not the visual representation that you click on Thus if you click on a point in one plot the corresponding point in all the visible plots will also turn red since they are visual representations of the same datum Since data points are relatively small clicking accurately on them can be inconvenient Puffin Plot offers two alternative selection methods to alleviate this problem Firstly by holding down the Shift key you can select a point simply by left clicking near it holding Shift and right clicking will de select nearby points instead Secondly you can left click hold the button and drag the pointer across the graph creating a rectangle Every point within the rectangle will be selected Dragging a rectangle with the right button will instead de select every point within the rectangle 4 2 4 Working with multiple samples Since most PuffinPlot operations are automatically applied to all the selected samples repeti tive analysis work can often be done automatically using the Copy point selection feature For example if you wish to apply a PCA to the 100 250 C demagnetization range of a series of 50 samples it can be done in four quick steps 1 For the first sample select the points corresponding to the 100 250 C demagnetization range 2 Select the 50 samples using the sample chooser keeping the first sample
55. t type can be set manually e Site definitions can be cleared Treatment steps can be deselected by dragging a box e PuffinPlot will ask for confirmation before overwriting files e Native file open dialog is now used on Mac OS X e Added invert sample moment feature e Open file dialogs now remember the last used folder Sample volume can be edited Other notes e PuffinPlot now requires Java 7 or higher PuffinPlot is now hosted on BitBucket due to the imminent demise of Google Code 31 C References Butler R E 1992 Paleomagnetism Magnetic Domains to Geologic Terranes Blackwell Scientific Oxford Fisher R 1953 Dispersion on a sphere Proceedings of the Royal Society of London Series A Mathematical and Physical Sciences 217 295 305 Hext G R 1963 The estimation of second order tensors with related tests and designs Biometrika 50 3 4 353 373 Available from http biomet oxfordjournals org content 50 3 4 353 abstract Jones C H 2002 User driven integrated software lives Paleomag paleomagnetics analysis on the Macintosh Computers amp Geosciences 28 1145 1151 Juneau J Baker J Munoz L S Wierzbicki F and Ng V 2009 The Definitive Guide to Jython Apress New York Kirschvink J L 1980 The least squares line and plane and the analysis of palaeomagnetic data Geo physical Journal of the Royal Astronomical Society 62 3 699 718 Lowrie W 1990
56. tData and for every datum in the sample if not datum hasMagSus if it doesn t have a mag sus value datum setMagSus 0 set the mag sus to 0 e Apache batik for SVG export e iText for PDF export FreeHEP for graphics export e Jython for scripting Other software PuffinPlot was created with the assistance of a cornucopia of free and open source software among the more significant tools are the Java language and platform NetBeans Ant Emacs ETFX plus many BIEX packages TeX4ht the Gimp and the Ubuntu operating system I thank all who contributed to these projects People PuffinPlot was initially developed at the Otago Palaeomagnetic Research Facility at the University of Otago Dunedin New Zealand Several colleagues provided valuable testing and feedback during PuffinPlot s early development in particular I thank Christian Ohneiser Faye Nelson Claudio Tapia and Bethany Fox for their time and effort Further improvements were made during revision of the PuffinPlot paper in response to thoughtful suggestions from Gary Acton and an anonymous reviewer Since its initial release PuffinPlot has benefited from bug reports and suggestions from Bill Phillips Jonathan M Glen Fabio Florindo Eric Horsman Terence Day Yoichi Usui Adrian Muxworthy Russ Burmester and Andrei Kosterov Icon PuffinPlot s icon and the frontispiece for this manual are from an illustration by the Finnish artist Wilhelm
57. te a95s plotted in black Bedding is vs magnetic north If this box is ticked the bedding azimuth for formation orienta tion correction is assumed to be relative to magnetic north and a correction is applied for local magnetic deviation The sample azimuth is always assumed to be relative to 22 Table 4 Measurement protocols for 2G data files Protocol Description NORMAL TRAY_NORMAL NORMAL TRAY TRAY NORMAL _YFLIP TRAY FIRST TRAY NORMAL IGNORE No extra tray or sample measurements are made Each mea surement run consists simply of measuring the samples once in their normal orientation Before each sample measurement run an empty tray mea surement run is made The input file thus consists alternately of empty tray lines and sample measurement lines Each tray measurement is used to correct the subsequent sample mea surement As TRAY_NORMAL but the tray measurement is made after the sample measurement rather than before it As TRAY_NORMAL but adding an extra sample measurement as a third step In the extra measurement the sample is ro tated 180 around its y axis so that the x and z measurements are inverted Combining these readings improves not only the precision but also the accuracy of the magnetic moments mea sured on the x and z axes since any systematic bias should be cancelled out by the inversion For the y axis accuracy is not affected but precision is improved by averaging the two mea su
58. the s_hext py pro gram and displays the mean directions and error ellipses on the AMS plot Calculations gt Clear AMS calculations Clears any previously done bootstrap and Hext calcula tions 15 4 1 4 Window menu This menu allows you to open or close auxiliary windows Window gt Data table opens or closes a window showing all the demagnetization data for the current sample as a table This table is far more extensive than the brief table displayed in the main window and allows data to be selected and copied to the clipboard so that it can be pasted into a spreadsheet or text editor Window gt Site equal area plot opens or closes a window containing an equal area plot for the current site the plot is created by selecting the Calculations gt Fisher by site or Calculations gt Great circles menu items and may be printed using the File gt Print site EA window menu item Note that the main display area provides a similar plot this window can be useful for a quick inspection of site data at a larger scale without editing the main plot layout Window gt Suite equal area plot opens or closes a window containing an equal area plot of sample or site directions across the whole suite the plot is created by selecting the Calculations gt Suite means menu item and may be printed using the File gt Print suite EA window menu item Note that the main display area provides a similar plot this window can be useful for a qu
59. tted A black triangle and line show the current depth this is the depth for which the data is displayed in the main window If there are selected samples they are highlighted in red on the sample chooser To select a single depth click on the appropriate part of the sample chooser To scroll rapidly through a range of samples click and drag the mouse along the sample chooser To select a range of samples hold down Shift then click drag and release the mouse on the chooser Keyboard shortcuts for sample selection Use Ctrl B and Ctrl N to change the current sample Use Ctrl A to select all the samples in the current suite You can also use the up and down arrow keys to change the sample 3 5 3 Toolbar The toolbar displays various data and provides several controls From left to right these are Suite chooser This shows the name of the current suite of data If more than one suite of data has been opened the suite chooser allows you to switch between them Orientation correction chooser This chooser allows you to choose whether data is displayed in laboratory co ordinates uncorrectea in field co ordinates corrected for sample ori entation samp corr or in tectonic co ordinates corrected for both sample orientation and bedding orientation form corr Zijderveld vertical projection V vs This chooser controls the vertical projection used in the Zijderveld plot The y axis always corresponds to the vertical d
60. u can choose one or more files in that format which PuffinPlot will then open The file is assumed to contain one magnetic measurement per line The file format specification consists of two parts General settings and Column definitions General settings This part describes parameters relating to the file as a whole rather than individual columns Number of header lines to skip Data files may include extra data header lines at the start of the file most often a line containing textual descriptions of the columns This field lets you specify how many lines PuffinPlot should ignore at the start of the file letting it skip over them Measurement type This specifies whether the files contain discrete or long core measurements Treatment type This specifies the type of treatment applied to the samples thermal AE IRM etc Column separator For files which do not use fixed width columns for example CSV files this drop down lets you select the character used to separate the columns If Use fixed width columns is selected the column separator is not used Use fixed width columns Tabular text files usually use one of two conventions for separating columns either the columns have widths which differ from line to line and are separated with a special character such as a comma or tab or the columns have the same width in every line and are padded out to this width with space characters when the contents are shorter than th
61. va io import File Create a Suite and read a data file into it input_file File example ppl Specify an input file suite Suite Example script create a new Suite suite readFiles input_file Read the data into a Suite object samples suite getSamples Get a list of the Samples in the Suite Calculate and display the mean NRM total nrm sum sample getNrm for sample in samples print total nrm suite getNumSamples Perform a PCA calculation for each sample for sample in samples do this for each sample sample selectAll select all points in the sample sample useSelectionForPca and mark them for use in PCA suite doSampleCalculations Correction NONE perform PCA for each sample HH Save the results of the PCA calculation output file File example results csv suite saveCalcsSample output file For the first two techniques when the script is run by PuffinPlot itself a variable called puffin_app is created which represents the currently running instance of PuffinPlot This variable can be used for example to gain access to any data already loaded into PuffinPlot If an external scripting language interpreter is used the script must start the PuffinPlot application before doing anything else this is demonstrated in the examples below Figure 3 shows a simple script demonstrating the use of PuffinPlot from within an external Jython interpreter although it can al
62. von Wright 1810 1887 published in Svenska faglar efter naturen och p sten ritade 2nd ed 1929 6 Future development and bug reporting PuffinPlot continues to be developed albeit slowly and sporadically now that its main function ality is stable and fairly complete Bugs in existing functionality are fixed as quickly as possible when they are reported and new features are added when time permits The PuffinPlot project including downloadable packages of all released versions and the complete source code is hosted at https bitbucket org pont puffinplot downloads Bug reports feature suggestions and feed back of all kinds are always very welcome Please send them to puffinplot gmail com 28 A Citing PuffinPlot PuffinPlot was introduced and described in a 2012 paper published in Geochemistry Geophysics Geosystems If you make use of PuffinPlot in published work please include the following citation Lurcock P C and G S Wilson 2012 PuffinPlot A versatile user friendly pro gram for paleomagnetic analysis Geochemistry Geophysics Geosystems 13 Q06Z45 doi 10 1029 2012GC004098 For convenience citation data is provided below in two formats commonly used by bibliography management software BibTeX citation record article lurcock2012puffinplot author Lurcock P C and Wilson G S title PuffinPlot A versatile user friendly program for paleomagnetic analysis journal Geochemistry Geop
63. with the Java platform if you have the Java platform installed on Windows but are still unable to run jar files such as PuffinPlot jar the situation can usually be fixed by running the jarfix program At the time of writing jarfix may be downloaded from http johann loefflmann net en software jarfix 2 2 2 Mac OS X The PuffinPlot archive also contains a special variant of the program for Mac OS X This variant is packaged as a standard OS X application and conforms more nearly to OS X user interface standards than the cross platform version described in the previous section It is named Puffin Plot app although the extension app is usually hidden by Mac OS X In the extracted archive contents the PuffinPlot application is shown as an icon representing a puffin specifically the Atlantic Puffin Fratercula arctica This application may be dragged into the Applications folder or any other convenient place PuffinPlot is started by double clicking on its application icon Recent versions of Mac OS X include a security feature called Gatekeeper which may prevent PuffinPlot from running The Apple support note at http support apple com en gb HT202491 gives instructions for config uring Gatekeeper to allow the execution of an unidentified application such as PuffinPlot 3 Basic usage This section gives a brief introduction to the PuffinPlot data model and to the features of its main window 3 1 A note on keyboard
64. y a true false value and are intended to record whether a sample fulfils some criterion for example messy low temperature alteration or multiple components Custom notes are intended for adding short items of information which are not automatically inferred by PuffinPlot for example number of components or behaviour type Adding annotation categories Annotations categories defined by selecting the Edit custom flags or Edit custom notes item from the Edit menu This will show a window allowing you to add rearrange or remove the annotation categories If an annotation category is removed all annotations made within that category will be lost Using annotations When custom flags or notes have been defined an extra panel appears at the right hand side of the main window For each custom note category there is a text box into which text may be typed For each custom flag category there is a tick box which may be selected or de selected Annotations are saved with the rest of the data in the PuffinPlot file they are also exported in the sample data CSV file produced by the File gt Export data gt Export sample calculations menu item 4 6 Exporting graphics 4 6 1 Introduction PuffinPlot can export the displayed plots in several ways for printing incorporation into docu ments and editing by other programs Two formats are supported SVG Scalable Vector Graphics is a widely supported form

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