About files and folders

Data files are always logged as tab-delimited text files, and if selected, Microsoft® Excel® files. Text files can be opened in any text editor or imported into a spreadsheet application (you may need to change the file extension to .txt before importing). Text files, in contrast with the Excel files, do not have any mechanism to embed equations.

Naming convention

File names on the LI-6800 can be as long as you want to make them, and can consist of any combination of numbers, letters, spaces, and punctuation, except the forward slash character(/). File names can be upper and lower case, so the following could be distinct files:

Dots (full stops) can be used as well:

Directories

Directories provide a mechanism for grouping files logically (or illogically, if you prefer). Directories can be named in any way described previously. Directories that are used for measurements are named logs and flrevents.

Navigating directories

Tap a folder to open that folder. Tap New Folder to create a new one under the selected folder, and New File to create a new file in the selected directory. There is a home button that takes you to the top level.

Sorting folders and files

In any of the file views, you can sort the contents of a folder by name, size, and date by tapping the corresponding sort filter. If you tap the filter again, you can sort by descending order, tap again and return to ascending order.

Folders

All files and folders in the file system that you need to be concerned with are contained in the folder /home/licor. This is the home folder for the user named licor (that’s you). The home folder in turn contains folders holding your log files, configuration files, and so on.

This section gives a brief description your home folder’s contents. Not described here are the hidden folders—their names start with a dot—that you can (and should) safely ignore.

/home/licor/apps

/home/licor/apps contains background programs (BPs, described in Section 12), grouped into a number of subfolders. When you are loading or launching a BP (Programs > BP Builder > Open/New), you are selecting files from /home/licor/apps.

You can add and delete folders and files as you wish in /home/licor/apps, with a couple of restrictions: 1) You will not be allowed to delete or modify factory supplied files in this section, and 2) the expected subfolders shown below will be automatically replaced on startup if they are missing.

When you backup data (Backup and restore), the /home/licor/apps folder (and all of its content) is included as part of the Configuration option.

Note: The “factory supplied” files are not included in backups. This allows backup/restore to be used across software versions without conflict.

Folders in /home/licor/apps/	Description
basic/	Basic data collection BPs.
dynamic/	BPs for fast A-Ci curves.
examples/	Example BPs used in the BP documentation (Using Background Programs).
system/	Support BPs launched by the system. (Ignore everything in here.)
tech/	BP utilities for techs. Ignore unless a LI-COR tech directs you here.
utilities/	Potentially useful example BPs.

/home/licor/autoprogs

The “original style” Auto Programs (launched from the Programs > Programs) screen are found in /home/licor/autoprogs. There is also a data/ folder, within which is a folder for each of the Auto Programs, that contains settings files.

Unlike BPs, this style of program is not designed to be user editable, so you can safely ignore everything in this directory. However, you may wish to save the settings files in the data/ folder, and/or share them between consoles, and they are included in backups (Backup and restore), as part of the Configuration option.

/home/licor/configs

When you save or load configurations (Start Up > Configuration screen) you are dealing with files and folders in the /home/licor/configs folder. How you might choose to arrange the content in subfolders is entirely up to you. There are no factory or default files or folders here.

When you backup data (Backup and restore), the /home/licor/configs folder (and all of its content) is included as part of the Configuration option.

/home/licor/diagnostics

The /home/licor/diagnostics folder contains operational diagnostics which can be of interest when troubleshooting. It contains four main folders, described below.

Folders in /home/licor/diagnostics/	Description
scriptslogs/	Scripts logs text files, one for each date of operation.
matchlogs/	Matching log files, one for each date of operation.
rangedata/	Copy of range match data generated by the acquire utility.
snapshots/	System snapshot data files.
systests/	Most recent results for each of the warmup tests.

Most of the diagnostics files are generated automatically. The snapshots, however, are generated only when you ask for them (Save Snapshot button in Start Up > System Settings > General). The diagnostic files are not large, but they accumulate over time, so every so often you might want to move everything older than a certain date to the trash (see Moving files to the trash). Nothing in /home/licor/diagnostics is needed for normal operation—you can freely get rid of anything you like.

When you backup data (Backup and restore), the /home/licor/diagnostics folder (and all of its content) is included as the Diagnostics option.

/home/licor/logs

The /home/licor/logs folder is where your logged data is found. You can create subfolders here to organize your data however you wish. However, there are three “standard” subfolders that the system will generate as needed:

Folders in /home/licor/logs/	Description
dynamic/	Contains dynamic tuning files, grouped by chamber.
flrevents/	Contains fluorescence events files, grouped by date.
soil/	Contains soil respiration data files, grouped by date.

When you backup data (Backup and restore), the /home/licor/logs folder (and all of its content) is included as the UserData option.

As you might expect, the /home/licor/logs is where most of the space on the file system is consumed as you operate the system, so when clearing space, this is a good place to start (refer to What's using the space?)

Nothing in /home/licor/logs is needed for operation, with the following possible exceptions:

• Fluorescence “DarkAdapted” files are saved in the appropriate date folder under the flrevents/ folder. If you wish to load a Fluorescence constants from such a file (The Load button in the Fluorometry > Constants screen), the system brings you here to pick the file.
• When doing dynamic tuning (e.g. CO2 Test Current in Constants > Dynamic > Utilities/Tests, the raw data is saved under dynamic/, and the processed data becomes a point in the user table (user tables are saved elsewhere). The only time you would ever need the raw data again (unless you are simply curious about it later) is if you delete that user table entry, and then wish to reload it (CO2 Reload or H2O Reload). To reload and rebuild a user table entry, the system looks for “unused” raw data files in the appropriate chamber folder under dynamic/.

/home/licor/resources

The /home/licor/resources folder contains resources used by background programs (BPs) and the BP Builder environment.

Folders in /home/licor/resources/	Description
defines/	Python files used as built-in DEFINEs.
groups/	Python files defining built-in BP GROUPs.
libs/	Python files used as libraries (EXEC, file option) for BPs.

Most of the files here are “factory supplied”, so you cannot overwrite them. But you certainly can modify and rename, or add your own resource files, and these would be included in backups (Backup and restore) as part of the Configuration option.

Note: The “factory supplied” files are not included in backups.

/home/licor/trash

The LI-6800 uses a trash system for deleting files. Also, if you choose to overwrite a log file, the original is actually moved to the trash, just in case you later regret your decision.

There is usually no need to directly access the trash; utilities for viewing, emptying, moving to, and removing from the trash are provided in Tools > Trash, discussed in Trash.

As items are moved to the trash, they maintain their original folder structure location. For example, if you delete

It will move to

This allows trashed items to be easily located in the trash (you know where to look), and to be restored to their original location, should you choose to do so.

The trash folder is never included in a backup. But if you want to be very cautious, you can easily move the trash folder to a USB stick, before emptying the trash on the console. Note that you can selective empty the trash—it doesn’t have to be all or nothing. Once an item is emptied (erased) from the trash, however, it is irretrievable. If you share the instrument with other people or labs, be aware that your haphazard labmates might be storing the only copy of precious data on the instrument. So, use discretion when deleting unknown files. Once you delete a file from the trash, it is gone. For good. Like last year. You can't get it back. So be careful and backup your files regularly.