PSICAT.exe’ file.
This user guide, like PSICAT itself, is under active development. Some parts of PSICAT aren’t documented as completely as they need to be. Some of the content presented won’t be entirely clear or will assume that you know more about PSICAT than you do. If you find content that is clear or missing, please submit a bug or email me your suggestions.
PSICAT is drawing tool similar to Adobe Illustrator or CorelDRAW that is customized to the task of drawing core description and stratigraphic column diagrams. One key difference between PSICAT and these other drawing tools is that PSICAT works with data, not graphics. The focus on data was borne out of the realization that stratigraphic columns are great tools for conveying a large amount of data, but none of that data is directly accessible for analysis or search. When you draw an interval on your diagram, PSICAT analyzes what you’ve drawn and extracts the relevant data, e.g. top, base, grain size, lithology. This data is stored in your project and PSICAT uses it to generate a visual representation that closely matches what you’ve drawn.
What does this mean for you, the user? PSICAT can help you draw your core description or stratigraphic column diagram. Hopefully the process will be simpler than drawing the diagram by hand because PSICAT is working at the same semantic level as you—it knows about intervals and lithologies. If you’re interested in more than just a pretty diagram, all of the data PSICAT has captured is available for you to analyze. PSICAT can also help you generate diagrams from data captured externally in spreadsheets and databases. The rest of this section is devoted to instructions on installing PSICAT and an illustrated guide to creating your first project.
Installing PSICAT is as simple as downloading the most recent version for your specific platform from the right sidebar on the main PSICAT Development site.
The Windows version of PSICAT comes packaged as a zip file (.zip). Double-click the
downloaded file and choose ‘Extract all files’. This will create a ‘PSICAT’ folder
containing the application which you can launch by double-clicking the ‘PSICAT.exe’ file.
The Mac version of PSICAT comes packaged as a disk image (.dmg). Double-click
the downloaded file to mount the disk image. Drag the ‘PSICAT’ folder to your
Applications directory or another convenient location. You can launch PSICAT
by double-clicking on the ‘
PSICAT’ application in the PSICAT
folder.
The Linux version of PSICAT comes packaged as a tarball (.tar.gz). Untar the tarball to a convenient location. You can launch PSICAT by executing the ‘bin/PSICAT’ script in the PSICAT folder.
PSICAT requires Java 1.5/5 or higher. If you are having trouble running PSICAT, you likely need a newer version of Java. You can find the most recent version for your platform at the Java website.
In this chapter, we’ll get our feet wet by drawing a simple core description diagram in PSICAT. Along the way, we’ll will learn how to create a new project, create a new section, draw and describe an interval, and ultimately export our diagram as a PDF document. This chapter focuses on describing a core from the top down, but is equally applicable to describing an outcrop from the base up.
Launch PSICAT as described in Chapter 1. You should see a screen similar to the one below:
Before we can begin drawing, we must first create a project. A project is a directory on your computer that holds your PSICAT data and diagrams. Use the File > New Project... menu option to launch the New Project Wizard. The wizard will prompt you for the name, type, and a location of the project to create. Once created, you will see the name you entered for the project appear in the left sidebar.
Once we have a project, we must also create a section. Sections hold the data e.g., intervals and units, from the diagram and allow us to partition our project into logical units such as holes, cores, etc. Use the File > New Section... menu option to launch the New Section Wizard. The wizard will prompt you for the name and optionally a depth/height range and image for the section. Once created, you will see the section appear in the left sidebar. Double click the section to open a blank diagram.
Use your mouse to hover over the ’Lithology’ column. You should see a dark rectangle that tracks your mouse pointer. Click the left mouse button to create a new interval. You will see a black line appear under your mouse pointer and a set of property fields appear at the bottom of the application window:
Use the property fields to edit the Interval. Try typing ’1 ft’ or ’1 m’ into the ’Top’ field. The diagram should update accordingly. Also try typing ’Sand’ or selecting a lithology from the Lithology drop down list. Your interval should update with a color and pattern:
Use your mouse to hover in the ’Symbol’ column. You should see a dark rectangle that tracks your mouse pointer. Click and release the left mouse button to create a new symbol at a specific point, or click and drag to create a symbol over a range. A newly created symbol initially appears as box with an ’X’ in it. Use the property fields to select a symbol from the drop down list. The symbol box will update with the symbol you’ve chosen:
You can provide written descriptions for almost every object in a diagram. Enter some text into the Description field and it will show up in the Description column.
Once you are done drawing on your diagram, use the File > Export > Diagram menu option to export your diagram as a PDF. When prompted, choose your export options. You can either export the whole diagram as a single page or specify a particular depth/height range and page size to export a multiple page PDF.
Hopefully this short introduction has piqued your interest. The next part of this guide describes how to perform specific tasks in PSICAT.
This part of the user guide focuses on describing specific tasks you may want to perform in the PSICAT software.
This chapter describes tasks related to editing data and diagrams.
Use the File > New Project... menu options to create a new project. A project is simply a directory on your computer which holds all of your data and diagrams. PSICAT currently supports two types of projects: Well or Outcrop. A well project defines the origin at the top of the diagram with depths increasing downwards. An outcrop project defines the origin at the bottom of the diagram with heights increasing upwards.
To begin drawing, you must first create a section. Sections hold the data e.g., intervals and units, for diagrams and allow us to partition our project into logical units such as holes, cores, etc. Use the File > New Section... menu option to create a new section.
Drawing in PSICAT is much like drawing in any graphics program, only slightly more structured. Below are a few common drawing interactions you are likely to encounter.
Some columns work with continuous types of data, such as intervals, which stretch unbroken from the origin. To draw these types, click beyond (either below for well projects or above for outcrop projects) the last item in the column. As you hover your mouse over the column, you will see a feedback rectangle:
Some columns work with discrete types of data, such as symbols, which can exist at a specific depth/height or over a depth/height range and may overlap. To draw these types, either click and release or click and drag in the column. As you hover and/ or drag your mouse, you will see a feedback rectangle:
Drawing is not always precise when it comes to capturing data. PSICAT mitigates this by rounding drawn values to increments half of the smallest hash marks on the ruler. So if the ruler has hash marks every 1 meter, PSICAT will round drawn values to the nearest 0.5 meter. If you need better resolution, you can either zoom in or enter an exact value for a specific property on the drawn item.
Lithologies and symbols in PSICAT are organized into schemes of entries. Each entry has a name, a code, an image or pattern, and optionally other parameters. By default, PSICAT ships with a lithology and symbol set that is based on the USGS standards. However, these schemes are easily customized with SchemeEditor tool in the PSICAT/tools/ folder. Launch the SchemeEditor application and you will be presented with a screen similar to the one below:
You can customize the existing schemes by using the File > Open... menu option to open the PSICAT/resources/lithologies.jar file or the PSICAT/resources/symbols.jar file. Once opened, you will be able to select a specific entry in the Entries list. From there you will be able to update the details of the entry. If an entry is not needed, you can use the Remove button to remove it from the scheme.
Instead of customizing the existing schemes, you may create your own scheme from scratch using the File > New menu option. Every scheme requires an id, name, type, and one or more entries. New entries can be added with the Add button. Each entry requires a name and a code. The name is what is displayed to the user, and the code is something to identify the entry, such as a unique id or a comma-separated list of keywords. Each entry can also have an image and a color associated with it via the Set Image and Set Color buttons:
When you are done creating your scheme use the File > Save menu option to save it to the PSICAT/resources/ folder. All scheme packs in this folder are automatically added to the lithology and symbol lists. If you wish to use your scheme exclusively, remove the existing lithologies.jar and symbols.jar files.
Customizing the diagram, such as changing the changing the type and order of columns, is possible but is currently a manual process. There is currently an open issue for graphical diagram editor. This section will be updated when the issue is resolved.
The chapter describes tasks related to importing and exporting data and diagrams.
Importing data from previous versions of PSICAT is accomplished via the File > Import > Data > Legacy PSICAT Data menu option. Data may be imported into a new or an existing project. The legacy import is somewhat limited, currently only supporting the import of interval data, but there is an open issue to expand its capabilities. This section will be updated when the issue is resolved.
Note: this menu option is only enabled when a diagram is open.
Importing data from Excel is accomplished via the File > Import > Data > Excel menu option. This option requires an Excel workbook saved in the older 97/2000/XP file format (.xls) rather than the new .xslx format. Each sheet in the Excel workbook named after a specific data type with the columns in each sheet corresponding a specific property of the data type. The first row of the sheet is expected to contain the data type property names, and the second row should be left blank. Each additional row is interpreted as data to import. Data may be imported into a new or an existing project.
Note: this menu option is only enabled when a diagram is open.
Importing images into your diagram is not currently available but will be supported in the next release (issue). This section will be updated when the issue is resolved.
Importing data from other formats should be easy to support. Check out Chapter 8 for more details orsubmit a bug with a description of the format and an example data file if possible.
Exporting a diagram to JPEG, PNG, or BMP is accomplished via the File > Export > Graphical > JPEG/PNG/BMP menu option. When prompted, choose your export options. You can either export the whole diagram as a single page or specify a particular depth/height range and page size to export multiple pages. Each page will be a separate image file.
Exporting a diagram to PDF is accomplished via the File > Export > Graphical > PDF menu option. When prompted, choose your export options. You can either export the whole diagram as a single page or specify a particular depth/height range and page size to export a multiple page PDF.
Exporting a diagram to SVG is accomplished via the File > Export > Graphical > SVG menu option. When prompted, choose your export options. You can either export the whole diagram as a single page or specify a particular depth/height range and page size to export multiple pages. Each page will be a separate SVG file.
You can generate blank documents for logging by hand using the instructions above. Simply specify the depth/height and page size you expect to log, even if they don’t currently exist on your diagram, and PSICAT will generate blank diagrams for you to print.
Exporting data to Excel is accomplished via the File > Export > Data > Excel menu option. Each type of data will be exported as a separate sheet in a 97/2000/XP formatted Excel workbook (.xls). The columns in each sheet correspond to the data type properties as described in Chapter 6.
Exporting data and diagrams to other formats should be easy to support. Check out Chapter 8 for more details orsubmit a bug with a description of the format and an example file if possible.
This chapter describes tasks related to changing how PSICAT displays diagrams.
Diagrams can be displayed either vertically or horizontally. Use the View > Horizontal/Vertical menu option to change the orientation.
Note: this menu option is only enabled when a diagram is open.
Diagrams can be displayed at arbitrary zoom levels to facilitate editing and viewing at whatever level of detail makes sense to the user. Use the View > Zoom * menu options to change the zoom level.
Note: this menu option is only enabled when a diagram is open.
Diagrams can be displayed using various length measurement units even if the data was originally logged in a different unit. Use the View > Units menu options to change the display units.
The final part of this guide covers advanced topics such as adding new data and column types.
Data types are a core concept in PSICAT. A data type defines what individual pieces of data are captured when you draw an object on a diagram. Below is the current list of data types in the main distribution of PSICAT:
| Name | Description |
| top | The top of the image in terms of a value with units, e.g. ’1 m’ |
| base | The base of the image in terms of a value with units, e.g. ’2 m’ |
| path | The URL to the image file |
| Name | Description |
| top | The top of the interval in terms of a value with units, e.g. ’1 m’ |
| base | The base of the interval in terms of a value with units, e.g. ’2 m’ |
| lithology | A reference to an entry in a lithology Scheme |
| description | A written description of the interval |
| Name | Description |
| top | The top of the interval in terms of a value with units, e.g. ’1 m’ |
| base | The base of the occurrence in terms of a value with units, e.g. ’2 m’ |
| type | The type of the occurrence |
| symbol | A reference to an entry in an occurrence Scheme |
| description | A written description of the occurrence |
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