PSICAT User Manual

Welcome to the PSICAT User's Manual. This document is divided into two parts. The first part provides an overview of PSICAT. The second part provides step by step instructions on how to perform various tasks in PSICAT.

Part 0: Quickstart

PSICAT.mov (36.76 MB)

For the impatient readers out there, this section is aimed at quickly getting you up and running with the current version of PSICAT. It is not intended to be a comprehensive guide to using PSICAT.

Step 1: Download PSICAT

Download the appropriate PSICAT package for your platform from the Downloads section. PSICAT currently comes packaged as a zip archive, so you will need to unzip and extract the files from the archive. It should create a 'PSICAT' folder.

Step 2: Launch PSICAT

Open the 'PSICAT' folder and launch the 'PSICAT' executable. On Windows, it will be named 'PSICAT.exe'. You should see a small splash screen as PSICAT loads. If you get errors or PSICAT doesn't launch, you likely need a more recent version of Java. PSICAT requires the Java Runtime Environment (JRE) version 1.5/5 or higher to run. The JRE is freely available here.

Step 3: Creating a Project

To get started using PSICAT, you will first need to create a Project. To do this, use the 'File->New..' menu option. Select the Project option from the list. You will need to provide a name for the project.

Step 4: Creating a Diagram

Once you have created a Project, it should show up in the workspace list on the right side of the program. Double-click the Project to begin drawing. The first time you double-click a Project, a small wizard will pop up and ask you to create a Diagram. A Diagram just specifies which columns should be shown, and what order they should be shown in. If it is your first time using PSICAT, I suggest enabling the columns in the following order: Depth Ruler Column, Core Box Column, Unit Column, Interval Column, Symbols Column, and Bioturbation Index Column. This will allow you to experiment with most of the functionality PSICAT currently has.

Step 5: Using the Tools

The drawing tools are in the Palette area on the far right of the diagram. To use the drawing tools, select a tool from the palette and mouse over the diagram. If the tool works in a particular column, you should see some feedback such as a gray box appearing with the current depth displayed near your mouse cursor.

Step 6: Drawing an Interval

The Interval Column is currently the most interesting column to work with. It allows you to draw stratigraphic intervals and beds, and associate lithologies and contacts with them. To draw a new interval, click the Interval tool in the Palette. When you mouse over the middle column of the diagram, you should see a gray box appear. This is the outline of your interval. If you click and release, the interval will be the size of the gray box. Alternatively, you can click and drag to create an interval of a different size and shape. Once you release the mouse button, you should see a blank box. This indicates that the interval has been drawn but no lithology has been associated with it. You can choose one or more lithologies from the Properties pane at the bottom of the application. The rest of the tools in the palette work similarly, and you should be able to manipulate objects with your mouse or via the Properties pane at the bottom of the application.

Part 1: Introduction

This section provides an overview of PSICAT, the terminology that will be used through out the rest of this document, and the layout of the PSICAT application. After reading this part, you should be familiar with the PSICAT concepts and the application layout.

Overview

PSICAT, CHRONOS's Paleontological Stratigraphic Interval Construction and Analysis Tool, is a stand-alone Java based graphical editing tool for creating and viewing stratigraphic column diagrams from drill cores and outcrops. It is customized to the task of working with stratigraphic columns and captures data digitally as you draw and edit the diagram.

Simplified to the task at hand

One of the unique features that sets PSICAT apart from other drawing tools, such as Photoshop and CorelDRAW, is that it is customized to the task of drawing stratigraphic columns. To draw a new interval in CorelDRAW, you would have to draw a rectangle and perhaps freehand the right side if you wanted to represent grain size changes. Then you choose the pattern that represents the lithology of the interval and fill your rectangle with it. All this is necessary because these other programs have no idea what an interval is.

PSICAT works at a higher level; it knows what an interval is. So instead of drawing a box, you simply draw an interval. Instead of filling in the interval with a pattern to denote the lithology, you simply select a lithology from a drop down list and PSICAT fills in the interval for you. And since drawing with a mouse is far from exact, PSICAT will let you specify the exact depths and extents via the keyboard.

It's about the data, not the image

In addition to simplifying the task of drawing the stratigraphic columns, PSICAT also captures data, such as depths, grain sizes, lithologies, intervals, etc., about the diagram. CorelDRAW will give you a nice image of the column. PSICAT will give you the same nice image but will also give you data that can be uploaded into a database and searched. And the data can be used to recreate the diagram, possibly at different scales or perspectives.

This focus on the data makes doing some things in PSICAT more difficult than in a traditional drawing applications. The user can't go in and freehand something directly on the diagram in PSICAT like they would be able to if they were working with a regular image. However, because the data and the drawing are separated, PSICAT can be made to draw the same data in multiple different ways. Imagine trying to update a lithology pattern for 1000m of core in CorelDRAW. For PSICAT, it's just a matter of changing the drawing settings a bit.

An open, extensible platform

PSICAT has been designed from the beginning to be an open, extensible platform. It is built on the Eclipse Rich Client Platform and follows the same philosophy. PSICAT is composed of many collaborating plug-ins; each contributing new functionality and features. This makes it easy to add a new feature--just write a new plug-in and add it to the PSICAT application. It also makes it easy to customize PSICAT to different tasks--simply pick and choose the plug-ins that provide the functionality that you need and only include them. And best of all, plug-ins can build on each other so a problem only has to be solved once and other plug-ins can leverage that solution. This greatly simplifies adding new features that are similar to existing features.

Concepts

There are three main concepts that the user should be familiar with: Models, Diagrams, and Plug-ins.

Models

Because PSICAT is focused on capturing data, it introduces the concept of a 'model'. Models define what data is captured for a particular object. Models can also define and enforce constraints, such as not allowing any child models or requiring that a specific property be a number. Almost everything the user interacts with in PSICAT is a model.

Diagrams

In PSICAT there is a distinct separation between the data and the visual representation of that data. As explained in the previous point, the data is managed via models. To manage the display the data, PSICAT introduces the concepts of 'diagrams' and 'columns'. Columns display the visual representation of the model and provide the drawing and editing tools used to interact with the models. Diagrams simply define a list of columns and the order they should be displayed in. If no column included in the diagram knows how to display a particular model, that model will not be displayed. This allows the user to define exactly what type of data gets displayed, and (to a lesser extent) how that data gets displayed. Users can define multiple diagrams that are suited for different tasks, e.g. one diagram that has a limited number of columns for entering a specific type of data and one diagram that includes all of the available columns so that all of the collected data can be displayed.

Plug-ins

PSICAT is built around the idea of plug-ins. Plug-ins are small, self-contained software modules that provide new functionality and features to a larger software system. All of the functionality in PSICAT, including every data type and column, is contributed via plug-ins.

Application Layout

Below is a screenshot of the PSICAT application. Various areas on the image are highlighted. Each of these areas has a specific name and function which will be detailed below.

Workspace

The workspace area contains the projects that you've been working on in PSICAT. Each project is a hierarchical tree of models. You can double-click on any model in the workspace to open it in an editor.

Properties

The properties area contains various property tabs for viewing and editing the properties of the currently selected model. When you select models in either the workspace or in the editor, the properties area will update to show you the properties of the selected model.

Viewer/Editor

The viewer/editor area displays any diagrams you are currently viewing or editing. When you double click on a model in the workspace, it will open a new editor in the viewer/editor area. You may have multiple editors open at the same time. Each will show up as a separate tab and you may arrange them so you can view two editors side by side.

Palette

The palette is highlighted in yellow in the screenshot above. It is only available when an editor is open and is associated with a specific editor. The palette contains all of the tools that are available for working with the diagram open in the editor. The available tools will depend on whether the diagram is in view-only mode and on what columns are included in the diagram.

Customizing the Layout

The PSICAT application layout can easily be customized to suit the user's preference. In general, each of the areas above can be resized and moved to different places in the application. For example, the workspace area can be dragged to the bottom of the application next to the properties area, the palette can be moved to the left side of the application, etc. If you would like to restore the original layout, use the Tools->Reset View menu option.

Part 2: Tasks

This section provides step by step instructions for performing various tasks in PSICAT. The tasks are organized into three groups:

General Tasks: These are basic tasks that deal with getting started using PSICAT.
Editing Tasks: These are editing-specific tasks. Most deal with using tools from the palette to draw specific models.
Advanced Tasks: These tasks deal with the more advanced features of PSICAT.

Conventions

Each task is broken into one or more steps that must be performed to complete the task. If a particular step is not required, then it will be marked with an Optional indicator. If a particular step may or may not be required, depending on your particular set up or previous tasks completed, it will be marked with a Conditional indicator. Steps that involve interacting with a button or menu option will include the name of the button or menu item in bold. The results of a step, such as a window opening or a folder being created, will be listed in italics. Where appropriate, a series of screenshots or a short video will accompany the task description.

General Tasks

This section provides instructions for performing basic tasks that deal with getting started using PSICAT. Below is an index of the tasks in this section:

Editing Tasks

Tasks in this section deal with drawing and editing core description diagrams in PSICAT. Below is an index of the tasks in this section:

Advanced Tasks

This section covers advanced of PSICAT, including exporting the core description data in multiple formats, creating summary diagrams, and connecting to a central server.