FLIIMP - FARLAB liquid water isotope measurements processor

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Installation

Get the current code from the FLIIMP git repository

(optional) copy the script FLIIMP.sh to your computer to start FLIIMP with a double click. Path settings need to be adjusted to your computer.

Running interactively

A. run the script

FLIIMP.m 

with matlab

-or-

B. double-click the script

FLIIMP.sh

Running in batch mode

edit the file

batch_FLIIMP_example.m 

to process a set of files. The example is using calls to the routine FLIIMP_batch.m

For further details, see the comments within the files.

Detailed user instructions:

Watch the video walk-through here

USING FLIIMP:

FLIIMP has 3 windows, that have to be completed in a fixed sequence.

1. Path settings, instrument and time  FLIIMP reads in the injection files from an instrument for a particular time, time range, or day. The Input file path for all injection files is specified in the first entry field.

FLIIMP creates a report on the calibrated data in HTML format within a new subfolder. The base output file path where the new output folder will be created is specified in the second entry field.

The instrument on which the liquid samples were measured is chosen from the pulldown list "Instrument".

Next, either a time range or specific files are selected. If choosing time range, only a date in format YYYYMMDD_HHMMSS needs to be given. If a range is given, all files that fall within the time period will be loaded. If only one date is given, either all files from that day (YYYYMMDD) or if a specific date with HHMMSS is given, that specific time will be looked for. The search path for files is combined from the input file path, the instrument, and the time range, for example

HKDS2038/IsotopeData/HKDS2038_IsoWater_20180912_120312.csv

At any point, the settings can be saved to a .mat file, or loaded from a previous run. The settings are saved and loaded across all three steps of the calibration, not for each step separately.

The button "Next >" advances to the second step. After clicking, please check the matlab command window for error messages or warnings.

Path settings are saved automatically to the file "FLIIMP_settings.mat" in your home directory ($HOME on linux/mac systems).

![FLiiMP_1](uploads/965cac19a14e7a9464ca2682c80fc74c/FLiiMP_1.png)

2. Sample screening and selection

In the second step, the data files for the selected period are loaded, and displayed for screening and selection. The table shows each identified sample by its "Identifier 1" value, them mean H2O concentration (in ppmv), and the standard deviation based on all samples.

The figure panels to the right show box-and-whisker plots of H2O vs. Injection number (top) and a selected isotope parameter from the Parameter drop-down below vs. Injection nr.

Clicking on a list item will display the injections of a sample. Using the checkmark "Exclude sample from processing" it is possible to disregard the currently selected sample from analysis. When the tickbox is checked, a "X" will appear in the list in front of an excluded sample.

Using the buttons "Exclude all" and "Include all", it is possible to set all samples in the list as excluded/included.

In the Injections line below, it is possible to exclude specific injections from the processing. If no sample is to be excluded, a value "-1" is displayed in the text entry box. To exclude injections 3 and 4 of the current sample, enter 3 and 4 separated by a space character in the input box. After choosing a different sample in the list, and combing back to the sample with excluded injections, these will be marked in red in the graphic display panels.

Manually excluded samples and injections are listed in the FLIIMP report in the section "Pre-processing".

![FLIIMP_2](uploads/0e50e2fd3cdb0e030f09cdf006fa2739/FLIIMP_2.png)

3. Run parameters and calibration settings

In the third step, the run parameters and calibration settings are entered. Each FARLAB project has a unique id that is entered in the first input field. The accounting can either be internal, collaborator, or external, which will influence the analysis cost (not considered in the report at present).

The report date defaults to the current date (format YYYYMMDD), but can be set to any other date. This date will be appended to the output directory name. The checkbox "Detailed report" determines whether additional analysis information is included in the report. For normal customers that are not part of FARLAB, the checkbox "Detailed report" should not be checked, as FARLAB-internal information about the instruments and processing are included in the detailed report.

Often, a project contains several runs/batches. The serial number or identifier of a run is entered in the field "Run ID" (for example "run01" and so on).

The next two lines should contain a name and email of the customer, and of the operator at FARLAB who can be contacted by the customer in case of questions.

Processing at FARLAB is based on local laboratory standards, that were calibrated on the VSMOW2-SLAP2 scale at several instances. The most current instance (run 3) is the default setting, for comparison purposes an older calibration run of the lab standards may be chosen. The delta values of the calibration standards are included in the report.

The calibration type can be either 1-point or 2-point linear. The third option, 3-point is not yet implemented. Using 1-point will use an average of the standard measurements in the beginning and end of a run. Using 2-point linear will linearly interpolate between the standard measurements in the beginning and end of a run. The option 2-point linear is recommended.

The input field "Calibration standards" should contain the chosen pair of calibration standards for slope and offset calibration. The first standard will be the offset correction, the first and second will be used in the slope correction. Standard names should appear as they are listed in the table visible in step 2. If more than 2 standards were measured, that are not used in the calibration, these names should be listed after the first two standards. If not included here, additional standard measurements will be treated as samples.

The field "Drift standard" contains the name of a standard that was repeatedly measured during the run but not used in calibration. It is displayed in a separate section in the report. The fields "Calibration standards" and "Drift standard" must not be empty. If no drift standard was in included in a run, use one of the calibration standards here.

The field "Averaging injections" sets how many of the last injections will be used in the averaging step. A number of 3 or 4 is currently recommended (without memory correction). The checkbox "include 17-O excess" needs to be checked for runs that are intended for 17-O excess analysis.

Pressing the button "Calibrate" that will start to produce the output report in HTML format. Watch the matlab command line window for progress, error messages and warnings.

Remember, settings across all three steps can be saved and loaded at any time using the buttons "Save" and "Load".  ![FLIIMP_3](uploads/68266f681b7e2f2f21789771bcee76bc/FLIIMP_3.png)

Detailed description of calibration procedure

1. Identification of standards

- Calibration standards

- Drift standards

2. Calibration

- Using IAEA procedures

3. Instrument characteristics

- Cavity temperature, cavity pressure, warm-box temperature, DAS temperature

4. Quality flags

- Humidity variation

- Isotope variation

- Temperature variation

- Quality flags

5. Sample report

Reference

IAEA, 20xx