Getting to know SoilFluxPro

SoilFluxPro Software v5.3 is designed to view and analyze soil gas flux data recorded by the LI-8250 Multiplexer, 8200-01S Smart Chamber, 6800-09 Soil CO₂ Flux Chamber for the LI-6800, LI-8100A Automated Soil CO₂ Flux System, and LI-8150 Multiplexer.

This section provides an overview of the SoilFluxPro interface and capabilities.

Interface tour

SoilFluxPro Software opens to a main screen made up of four subsections shown in Figure 1‑1.

File management menu

The File Management bar is where you can open, save, export, and create .kml files to view your data in the Google Earth™ mapping service. This bar also contains the cut, copy, paste, and delete buttons for observations.

• Open opens .82z, .81x, and .json observation files to be viewed and worked with in SoilFluxPro Software. Each file includes raw time series data and metadata that provides observation context.
• Save saves either the observations you have selected or all observations to a chosen location as a new set of .82z files.
• Export takes summary data from the files loaded in SoilFluxPro Software and exports it as one combined .csv file.
• Import lets you import time series data from stand-alone LI-78xx Trace Gas Analyzers and third-party gas analyzers (when used with a LI-COR soil gas flux system) for use in SoilFluxPro.
• Map uses GPS location data to export a .kml file which can be viewed in the Google Earth™ mapping service.

The following tools will allow you to combine or remove observations within a File Group.

• Cut cuts the selected observations to the clipboard.
• Copy copies the selected observations to the clipboard.
• Paste pastes observations from the clipboard to the Summary view.
• Remove Observation removes the selected observations from the Summary view.

Data interaction menu

The Data Interaction bar contains the primary tools you will use to interact with and revise data from your observations. This is also where you can load different .82z file groups that you have opened in SoilFluxPro Software.

• File Group is where observations from opened files are organized. This pane displays the name of the file and the range of start and end times for the observations in that file.
• Recompute lets you adjust parameters used in the flux calculation, such as start and stop time. Any adjustments automatically recompute the flux in real time and chart the raw times series data for an observation. Guidance can be used to optimize your settings using analysis tools.
• Transform allows you to apply a mathematical function to a variable in the dataset or to compute something new using one or more variables. This will then create a new column or replace an existing one with the transformed data.
• Repair lets you replace a bad chamber temperature reading on a port with one from another port. This may be necessary if there is a bad temperature sensor or if the sensor has become damaged.
• Remove allows you to remove data from a data file that may not be relevant or to reduce the file size. This will not overwrite the data in the existing .82z file.
• Statistics provides statistics for a single observation or a range of observations.
• Display allows you to choose what variables are displayed for the observations in the Summary view.

Summary table

An observation includes the entire time that a port is selected and active, including purge times and measurements. The Summary shows all the observations you have loaded from a particular file group. This view shows the Measured, Metadata, and Flux variables you have selected from the Display pane. It includes a header made up of 3 lines.

• Device: The device that is the source of the measurement (e.g., LI-8250)
• Label and Type: A label that defines the variable name (e.g., Pressure) and the type (e.g., Mean)
• Units: The units for the variable (e.g., kPa)

Table 1‑1 shows the different devices you may encounter in SoilFluxPro. For a complete list of the variables and units seen in SoilFluxPro, see the Data dictionary and Supported units and data dictionary.

Table 1‑1. SoilFluxPro device labels and their corresponding devices.

Device Label in SoilFluxPro	Corresponding Device
LI-8250	LI-8250 Multiplexer
8250-01	8250-01 Extension Manifold
LI-8200	Smart Chamber
LI-8100A	LI-8100A Automated Soil CO2 Flux System
LI-8150	LI-8150 Multiplexer
LI-6800	LI-6800 Portable Photosynthesis System
CHAMBER	See Table 1‑2
LI-870	LI-870 CO2/H2O Analyzer
LI-7810	LI-7810 CH4/CO2/H2O Trace Gas Analyzer
LI-7815	LI-7815 CO2/H2O Trace Gas Analyzer
LI-7820	LI-7820 N2O/H2O Trace Gas Analyzer
User-Defined Device Name	Imported third-party or standalone gas analyzer
TRANSFORMED	Created when using the Transform tool

Table 1‑2. SoilFluxPro device labels and their possible associated chambers.

Device Label in SoilFluxPro	Possible Associated Chambers
LI-8250	8200-104 Opaque Long-Term Chamber, 8200-104C Clear Long-Term Chamber, or digital custom chamber
LI-8200	Smart Chamber
LI-8100A and LI-8150	8100-104 Opaque Long-Term Chamber, 8100-104C Clear Long-Term Chamber, 8100-102 10 cm Survey Chamber, 8100-103 20 cm Survey Chamber, flasks, or custom chamber
LI-6800	6800-09 Soil CO2 Flux Chamber

Log, Chart, and Details

The bar at the lower left provides a variety of tools to show details and chart data from observations or to view a log of activity in SoilFluxPro Software.

• Log opens a pane that shows a running log of the operations you have performed since opening SoilFluxPro. The log will also record any errors you receive.
• Chart lets you make charts for all observations or selected observations using the x and y axis parameters you specify. You can save chart configurations for easy access later and all charts can be saved as an image.
• Details provides the raw time series data for a selected observation.

See Log, chart, and details for more information.

Menu

The Menu bar is found in the upper left-hand corner of SoilFluxPro Software and includes three sections: File, Sample File, and Help.

File

File includes an option called Open Directory. For details on using this feature, see Opening files in a directory.

Sample File

Sample File provides some sample datasets to familiarize yourself with the features and capabilities of SoilFluxPro Software.

Help

Help provides you with the resources you need to get the most out of SoilFluxPro.

• About tells you which version of SoilFluxPro you have installed.
• View SoilFluxPro Guide provides you with a direct link to this manual for future reference.
• Support for SoilFluxPro will take you directly to the LI-COR SoilFluxPro support resources, for the latest videos, instructions, and tips.
• Credits lists open source and other software used to build SoilFluxPro.
• Check for Updates will see if there is a newer version of SoilFluxPro available for you to install.
• Quit closes the application.

Opening a file

Before exploring how to analyze and visualize your data, you will first need to open a data file. SoilFluxPro Software can open files individually or from an entire .zip archive.

You can drag and drop files into the summary view to open them. Or you can use the menu:

1. From the main screen click Open.

2. 

2. Navigate to the location of your .zip archive or individual file.
3. Select the file and click Open.
4. SoilFluxPro will extract the observations and open them in the Summary view.

Note: The name of the File Group defaults to the filename of either the .zip archive, the file, or the first file selected in a series.

Opening multiple files

You can select multiple files and .zip archives from the dialog box (or drag and drop multiple files) by using Ctrl + click to select each. This will open all files into a single file group in the Summary view.

Opening files in a directory

Under File is an option called Open Directory. Open Directory will open a window where you can navigate to a directory and have SoilFluxPro search for and open any .82z, .81x, or .json files within that directory. Files can be opened in a new File Group (using the directory name as the File Group name) or in an existing one.