Data Visualization

SORTIE runs produce output, which you can then use the SORTIE interface to view graphically. You can view both kinds of output files, summary files and detailed output files. SORTIE analyzes the contents of files that it is given and lets you know what it is capable of doing with that data. For more on output, including a guide on what to save, see the topic Output in SORTIE. In this document:


Loading an output file for data visualization
Displaying the data from a file
Viewing a chart's raw data
Viewing charts from a run as it progresses
Tips

For details on the chart types available, see Output Chart Types.

Loading an output file for data visualization

You can load a file by choosing the menu option "File->Open Run Output". Choose the file you want to view, either a summary output file with a ".out" extension, or a detailed output file with a ".gz.tar" extension. The file name will appear at the top of the main SORTIE window in the list that says "Open output files". You can have as many files open as you wish.

Displaying the data from a file

Choose a file in the list marked "Open output files" at the top of the main SORTIE window. SORTIE will analyze the contents of the file and show you what it can display in the list marked "Chart choices for this file". The chart choices are broken apart by type. There may not be a choice for every type of chart. Choose the chart you want to display and click the "Draw Chart" button. The chart will appear in the main SORTIE window. You can open as many charts as you wish. A legend also opens for each file that applies to all its chart windows.

The legends for detailed output files have an extra set of controls marked "Timestep" at the bottom. Use the arrows to step back and forth through the timesteps. As you step through and watch a chart, pay attention to axis ranges. The data visualizer is meant to analyze each dataset it charts and optimize the chart accordingly. It does not attempt to keep the view consistent.

Viewing a chart's raw data

You can save the raw data used to make any chart to a tab-delimited text file (suitable for viewing in spreadsheet programs). Use the File->Save menu option that appears on all charts, or press Ctrl-S. You can take this raw data to reproduce and adjust the chart in other graphing applications. If you have saved a summary outout file, be aware that this file already contains all its data in a tab-delimited text format; you can open this file directly if you wish.

Viewing charts from a run as it progresses

You can view the output from a run as it progresses. SORTIE will keep a set of open charts updated with the results of the latest timestep. Here's how to use this feature:

  1. Since SORTIE data visualization can only display the contents of output files, the first step in using this feature is to set up some output files to view. You can see more on individual chart types here, so you can save the appropriate data for the charts you're interested in seeing. For more on the output file types and how to set them up, see either the summary files or the detailed output files topics.
  2. Once you have completed a parameter file for your run and have set up your output, the next step is to create some output for SORTIE to analyze. A simple way to do this is to click the "Run one timestep" button (the one on the main window with two right-facing triangles). When SORTIE has completed the timestep, the message bar at the bottom of the window will display a message indicating that the run has paused. You can also run the model using "Model->Run" from the main menu or the Run button (with the single right-facing arrow); you can pause the run at any point to start viewing data.
  3. To view the output of the current run, it is recommended that you first pause the run. (This ensures that the model is not trying to write new output to the files at the same time as it is trying to open them to be read.) Then, click the "View run output" button. SORTIE will load the output files from the current run and analyze them to determine what charts you can view.
  4. Open the charts you wish to view (see Displaying the data from a file. If a chart you want is not listed for any output file, it means that the data it requires is not being saved. You must stop the run, change your output options, and start a new run.
  5. Start the model running again. As the model completes each timestep, it will update any open charts (while it does this, you may see a message that the model is paused at the bottom of the screen; this is normal). You can open new charts or close existing ones at any point in the run (again, pausing is recommended before opening new charts).

Note: While displaying a current run's output is a useful feature, it is not the most efficient way to do a run. If you do not actually need to keep tabs on a run's progress, or if you are satisfied with the way a current run is going, allow it to run without open charts. The run will execute much faster. If you currently have charts open for a run, you can use the menu command "File->Close run output file" to close each of the run's output files. Once all output files are closed, the run will switch back to the more efficient mode.

Tips

The data visualizer can only show you what you have saved from the run. If you do not save any data for a particular species in a detailed output file, for instance, that species won't show up in any charts you open, even if there were many individuals of that species in the run. If your data does not look the way you expect it to, start by carefully examining your output settings to make sure you actually saved everything you meant to.

Have patience when working with detailed output files. When you move through timesteps, change charts, and open new charts, the data visualizer often must go back and sift through the detailed output file for the data it needs. With large files and long runs this can be very time consuming. If you have an idea of the charts you want to work with, it will be faster if you only save the data needed to create those charts.


25-Jan-2005 01:05 PM