CHANGES.adoc

PuffinPlot release notes

Next release

• Don’t show the sensor length warning for discrete data.

• Show a warning if a 2G file has few or no valid headers.

• Demagnetization plot: include a tick and label at 0 on the x axis. If there is no magnetic susceptibility data to plot, include a tick and label at 0 on the y axis too.

• Show a warning if using default area or volume when loading a 2G file.

• Convert build process from Ant to Maven.

• Convert manual from LaTeX to AsciiDoc.

• Update ‘how to cite’ information in the program and documentation with the 2019 paper.

• Update the Jython version to 2.7.2 and update the location from which Jython is downloaded (closes #330 and #403).

• Switch from Bugs Everywhere to GitHub for issue tracking.

• Update documentation.

• Various internal improvements in error handling, data validity checking, and code formatting.

• Bug fix: PuffinPlot no longer crashes if the y axis label is set to an empty string.

• Data table window now allows treatment steps to be selected and deselected.

• Add ‘Treatment step ranges…’ dialog to allow operations on treatment steps specified by treatment level range (closes #52).

• Allow size of main graph display to be configured in preferences

PuffinPlot 1.4.1 release notes

This is a minor release which fixes some bugs in version 1.4 and adds two new plot types.

Data manipulation

• Declination realignment can now align to a mean declination as well as to a top declination.

Graphing and data display

• Added a VGP map plot.

• Added an RPI/depth plot.

Calculations

• PuffinPlot no longer calculates an MDF values for samples which never reach half-intensity, since the MDF is undefined in this case.

Data import

• Added support for more PMD file format variants.

Bug fixes

• Fixed a bug which prevented the Mac OS X app from starting.

• Re-enabled section numbering in the manual (accidentally disabled in version 1.4).

• Deleting the current sample previously caused an error; now fixed.

PuffinPlot 1.4 release notes

The release numbering scheme changed with the 1.4 release: 1.4 is the immediate successor of 1.03.

Installation requirements

• PuffinPlot now requires Java 8 or higher.

Data manipulation

• ‘Discrete to continuous’ feature implemented, allowing conversion of discrete suites to continuous suites using a supplementary CSV file containing a sample-to-depth map.

• Automatic realignment of declination data, allowing reconstruction of a continuous declination record for continuous suites in which the core sections are not azimuthally oriented with respected to each other.

• Allow user to remove samples outside a specified depth range.

• Allow user to remove samples with a specified treatment type.

Calculations

• RPI calculation implemented, using normalization to ARM, IRM, or magnetic susceptibility.

• Arason-Levi inclination-only statistics implemented, but currently only accessible via the API, not the GUI.

Scripting

• The Jython package is no longer bundled as part of PuffinPlot, dramatically reducing the download size. PuffinPlot still retains Python support: Jython is downloaded and installed automatically if and when it is required.

• PuffinPlot now supports scripting in JavaScript as well as Python.

• The user-defined great circle validity check now uses Javascript rather than Python. In practice, this only means a slight change in syntax.

• Some classes and methods in the PuffinPlot API have been renamed to be clearer and more descriptive. This has no effect on users who only use the graphical interface, but scripts written for older PuffinPlot versions may have to be updated to work with the new API.

User interface

• Files can now be opened by dragging them to the main window.

• Current suite name and ‘unsaved’ indicator added to the title bar.

• When saving files, PuffinPlot now defaults to the last-used folder.

• Status bar added to main window. When the mouse pointer is over a data point representing a demagnetization step, the status bar shows details of this step.

• The ‘Edit’ menu has been divided into more submenus to more conveniently accommodate the newly added functions.

Graphing and data display

• Per-sample Fisher statistics are now shown in the sample parameters legend.

• R parameter now shown to 4 decimal places in site and suite parameter tables.

Data import

• PuffinPlot can now import the text-based PMD format developed by R. Enkin and supported by several palaeomagnetic programs including PMGSC, Paleomac, and Remasoft.

• PuffinPlot can now import the JR6 format developed by AGICO and supported by programs including REMA6W, Remasoft, and Paleomac.

• When importing from a custom file format, PuffinPlot now sets default values for the sample and formation corrections if these are not specified in the file.

• When importing AMS data from an Agico ASC file, PuffinPlot can now read a formation correction from the file. All possible orientation conventions are now supported on ASC file import; if necessary, orientations are converted to PuffinPlot’s conventions using the orientation parameters stored in the file. Optionally, existing sample and formation corrections can be overwritten with values read from the ASC file.

• Import from Caltech (CIT) files has been improved: demagnetization levels for thermal treatment are now read correctly, as is the ‘NRM’ treatment code.

Data export

• Degree signs in exported data replaced with ‘deg’, to accommodate software that has trouble with non-ASCII character sets.

• Precision of exported parameters increased to four decimal places.

• PuffinPlot can now export a bundle containing both data and a processing script, allowing analyses to be reproduced automatically.

• In exported site data, field strengths for minimum and maximum great-circle steps are written in millitesla rather than tesla.

Miscellaneous bug fixes

• Custom flags and notes are now included in exported sample data.

• PDF export no longer produces an extra page.

• Display is now updated automatically when sites are edited.

• Formatting of PCA equations in exported CSV files is now locale-independent, so will always use ‘.’ rather than ‘,’ as the decimal separator.

• Custom file import used to ignore the sample volume field; it now makes use of it if present, and defaults to a volume of 1 cm³ if it is not present.

• In demagnetization / intensity plots with AF treatment type, data points for magnetic susceptibility measurements (if present) could sometimes be plotted with an incorrect x position. This has now been corrected.

Developer notes

• The build process now uses the Ivy dependency manager to download required libraries automatically.

• Several hundred unit tests have been added, mainly for the data and calculation classes. This helps to verify the correctness of PuffinPlot’s data processing, and to avoid the introduction of bugs during future development.

• PuffinPlot’s version control has been migrated from Mercurcial to Git, and the main repository from Bitbucket to GitHub. (The Bitbucket repository has been retained as a mirror.)

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 can 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.

Documentation

• All new features are fully documented in the updated user manual.

Miscellaneous new features

• Site calculations automatically update when sample calculations change.

• Site directions cleared automatically when all their sample directions are cleared.

• Warning when closing a file or quitting with unsaved data.

• Clearer error messages and warnings when reading corrupted files.

• Treatment type can be set manually.

• Site definitions can be cleared.

• Treatment steps can be deselected by dragging a box.

• PuffinPlot will ask for confirmation before overwriting files.

• Native file open dialog is now used on Mac OS X.

• Added ‘invert sample moment’ feature.

• ‘Open file’ dialogs now remember the last used folder.

• Sample volume can be edited.

Other notes

• PuffinPlot now requires Java 7 or higher.

• PuffinPlot is now hosted on BitBucket, due to the imminent demise of Google Code.