Squid

Squid3 development is hosted on GitHub.com and is iterative and community-driven.

Please visit wiki.

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We encourage you to download
and evaluate the latest release, the “.jar” file found here.
Squid3 requires Oracle’s Java 1.8. Java 1.9 and 1.10 are no longer supported and Java 1.11 through 1.17 involve major architectural changes that we have elected to avoid until 2024-2025. You can read here about the community’s plans for Java.

UPDATE JAN 2021
Liberica OpenJDK 8 also works: be sure to download the “full jre” or “full jdk”.

To contribute issues and feedback, please join GitHub here. While using Squid3,
the help menu provides a link that
initializes a new GitHub issue for you – please use freely.

The current versions – Squid3-1.6.n.jar – provide full workflow
support for processing and interpreting Shrimp data outputs in the form of
Prawn xml files and ‘OP’ files including project, data, task, expressions, visualizations, reports, and parameters management. Squid3 provides for creating and saving Squid3 Project files that have an
extension of “.squid” and are intended to save the current state of work on a project. The workflow is mapped left to right
in the menus, as described below.

The Project menu provides for creating new GEOCHRON and RATIO projects. The functionality for RATIO projects is still under development – please feel free to contribute ideas. A new GEOCHRON project can be created from a single Prawn XML file, from a single Prawn XML file zipped, from merging two Prawn XML files, or from an ‘OP’ file. A special demonstration Squid3 project is available from this menu, thanks to @NicoleRayner. The project manager allows for naming the project,
naming the analyst, and reviewing statistics about the loaded data as well as keeping notes about the project.

    All data-processing parameters are specified on the Project Manager page: whether or not to normalize counts for SBM; ratio calculation method; preferred index isotope, constraints on weighted means of reference materials; the common lead model for reference materials; and the physical constants model to be used in the project. Note on parameter models: See below for how to manage these models from the Parameters menu item. Changing these model selections updates all the dependent calculations within the Squid3 task. The currently-used names and values from these models are listed in the Expressions Manager left-hand panel and display as read-only expressions. The ‘notes’ window in the Expressions manager provides additional info about each model value. Models selected for a task are saved with the Squid3 Project (.squid) file so if anyone opens a .squid file, the included models will be added to the local store of models available to Squid3, if not already present.

The Data menu – 1) Manage Sample Names,
2) Manage Spots and Reference Materials, and 3) Audit Raw Data for all data files. For Prawn data files, it also provides for saving and swapping out data files. ‘Manage Sample Names’ automates with overrides the naming of samples based on delimeters or leading character counts. ‘Manage Spots and Reference Materials’ supports editing spot names,
filtering spots by name, and setting both the project’s reference material spots and
concentration reference material spots by using the same
filtering feature. The reference material models are selected here as well.
The context menu on the left-side list is accessed by a
right-mouse click and has items for removing a spot and
splitting the data file into two files. Any modifications to the data file can be saved
to a new file if needed. Note that saving the project preserves the changes to the
data within the project file but without changing the source data file. ‘Audit masses’ provides
time-based views of masses and is configuable to show mass diferences as well.

The Task menu – 1) ‘View Current Task’ provides for the user to configure the metadata about a task including choosing directives for daughter/parent ratios. Additional editing of the task is available via the ‘Edit Current Task’ button at the bottom of the view task page. The task editor provides for editing the masses, the index of the background mass, the ratios using these masses, the directives, and the four special expressions: Uncor_206Pb238U_CalibConst, Uncor_208Pb232Th_CalibConst, 232Th238U_RM, and ParentElement_ConcenConst. Please note that Squid3 in GEOCHRON Mode requires mass labels 204, 206, 207, 208 and ratios 204/206, 207/206, and 208/206 as they inhabit the built-in expressions engine. In order to use this task with the current data file, the count of masses must match and Squid3 will alert the user if they do not.

    The ‘Directives’ allow switching between using the primary ages of 206/Pb/238U or 208Pb/232Th and whether to directly calculate 208Pb/232Th – these are the pair of choices that Squid2.5 also makes available. These choices interact with the list of preferred index isotopes shown – ‘208Pb’ is only available when the primary age is 206Pb/238U and the calculation of 208Pb/232Th is indirect. Also, if ‘208Pb’ is selected, the directives cannot be changed.

    2) ‘New Task from …’ a) current task without custom expressions, b) current task including custom expressions, c) empty task – will each open the task editor. 3) ‘Browse, load, or edit task files …’ a) from Squid3 Built-In Tasks Library, b) Squid3 Custom Tasks Folder, c) Squid2.5 Custom Tasks Folder – each provide access to a list of tasks with their details, which can then be edited or used directly in the current task, provided the mass counts align.

The Isotopes menu: 1) ‘Map Isotopes from Data to Task’ provides for mapping the isotope or mass labels provided by the data file for each mass staton to the task’s isotope or mass labels. Tasks generally refer to masses using integers such as ‘204’ or simple decimals such as ‘195.8’, whereas the labels for the mass stations recorded in the data file usually have several significant digits of atomic mass, such as ‘195.75123’. The background mass can be specified here or in the task editor. After clicking the orange button at the bottom to copy the labels, the columns D (Data Isotope Label) and T (Task Isotope Label) will contain the same values.

Expressions menu – 1) ‘Manage Expressions’ has a left panel organized by expression type that provides for sorting the expressions within each list by Name, Execution order, or Target spot set – reference material, concentration reference material, and unknowns – denoted by left-hand superscripts of R or C, and U. All of the built-in expressions have been named in a consistent fashion per issue #164 discussions and have explanatory text in their ‘notes’ panel provided by @sbodorkos . Of particular note (idea thanks to @NicoleRayner ) is that the expressions targeting reference materials only are suffixed by “_RM”. The tab for ‘Unhealthy Expressions / Mismatched Targets’ will appear in red if any are present. Squid3 supports the assignment of a sample – a group of unknowns – as the target of custom expressions – see the drop down box populated with the sample names to the right of the unknown samples checkbox. The drop down only appears if unknowns is checked and reference material is not checked.

    Squid3 operates under the hood with units of annum and 1-sigma absolute uncertainties as defaults. Squid3 provides a context for SHRIMP geochronology in the peek window of the expressions manager that displays ages and their absolute uncertainties in Ma as well as concentrations in ppm, and displays both absolute and percent uncertainties. Expression grammar has been simplified so that the only times that the surrounding '["..."]' brackets and quotes are needed is for isotopes, as in TotalCPS(["206"]), for ratios, as in ["204/206"], for expression names that use other that any combination of letters,digits, and the underscore, and finally for all expressions where you seek the absolute (±) or percent (%) uncertainty, as in [±"204/206"]. The expression audit includes an audit of the target spots for compatibility – it checks and reports whether the target choice of Reference Material and / or Unknowns matches at every level of an expression. Thanks to @sbodorkos for the suggestion.

Common Pb menu – 1) ‘Unknowns: 204 Count Corrections & Assign Common Pb Ratios’ provides for customizing how Squid3 handles common Pb for Unknowns.

Interpretations menu – 1) ‘Reference Materials’ and 2) ‘Unknowns’ provide Wetherill and Tera-Wasserburg Concordia diagrams produced by Topsoil, customizable weighted means with plots, and a generic plotting function for any two expressions using reference materials.

Reports menu – 1) ‘Custom Report Builder’ provides built-in reports for Reference Materials, Unknowns, and Weighted Means. The report builder supports custom categories with drag and drop columns from the left-side list of available expressions and drag and drop ordering of categories and columns. Reports can be viewed or saved as ‘.csv’ files into the project’s Squid3ProjectReports folder that is created in the same folder in which the current Squid3 project is saved. 2) ‘Summary Expressions and Values’ creates reports for Reference Materials and Unknowns detailing the summary expressions defined for each. 3) ‘Project Audit’ and 4) ‘Task Audit’ produce meta-data reports for each. 5) ‘Generate all Reports’ produces all reports into the project’s Squid3ProjectReports folder mentioned above. 6) ‘Miscellaneous Reports’ provides a variety of reports of interest.

Archiving menu is not yet active. We seek input from the community as to how archiving might be implemented.

Parameters menu – 1) ‘Reference Material Models’, 2) ‘Common Pb Models’, and 3) ‘Physical Constants Models’ each open the Parameters Manager to the appropriate tab. Squid3 provides several documented default models in each category. Models can be created, imported from ‘xml’ files, and exported as ‘xml’ files. Parameter models used in a Squid3 project remain with the ‘.squid’ project file so that opening that file provides access to the contained models. Note that reference material models can be based on TIMS-generated ratios with calculated apparent ages or using a simplified approach to support the transition from Squid2.5 that provides the requisite “Reference Dates”, inspired by input from @NicoleRayner.

About menu – 1) ‘About Squid3’ summarizes Squid3’s purpose and identifies collaborators and financial supporters. 2) ‘How to cite Squid3’ provides a link to our latest publication. 3) ‘Squid3 Github Repository’ provides a link to this repository. 4) ‘Squid3 Development Notes’ links to a wiki documenting the porting of Squid2.5 to Squid3. 5) ‘CIRDLES.org” links here, the home of the College of Charleston development team. 6) ‘Topsoil Github Repository’ links to Topsoil, used to provide Concordia diagrams in Squid3.

Help menu – 1) ‘Introduction and Guide to Menu’ opens this document. 2) ‘Video Tutorials’ features YouTube videos produced by @NicoleRayner and found here. 3) ‘Contribute an Issue on Github’ is a shortcut to creating a new issue with key metadata automatically supplied.

Thank you in advance for any suggestions you contribute. We are available for walk-throughs, etc.
if needed to help convince you to participate and contribute.

Additional features will appear over time and may not be documented here concurrently.
Please be patient and contribute your ideas via the issues tracker.

Please volunteer to help with documentation, how-to videos, coding, etc.

Updated 20 November 2020.