WebArAr Tutorial
Last updated: Feb 25, 2024
General procedure
Input data
Support to read the original mass spectrometer output file: See Import raw data.
Open arr files: arr is the format with which WebArAr saves Sample objects. See Arr files.
Open files of ArArCALC software, including age and xls files.
Create a new object: See Create new sample.
View, modify, and calculate for a open sample object
After the Sample object is successfully created and opened, the object page will display some tables and figures.
Any files that have been opened will no longer be associated with the user's local file, the Sample object is passed between the server and the client in the form of data streams, and will be not automatically saved, so unless the user downloads the arr file, all operations will be lost when the page is closed.
The actions that can be performed on the object page include::
Edit tables:
All tables are editable. After editing, click Save changes below the table to save your changes. See Tables and figures for content in each table or figure.
Edit parameters:
Note: The calculation will not be automatically called after the parameter is modified. See Recalculation.
Total Param include all parameters, editing this table and saving to set new parameters for the Sample.
Set parameters by three parameter sets, namely Irra Params, Calc Params, and Smp Params. This will change parameters of all sequences. See Setting parameters
Interaction with figures:
All figures are rendered by Echarts and therefore have Echarts features and attributes. Some commonly used properties are editable. See Change figure styles.
Select points used for regression in isochron plots
See Isochron scatter points selection.
WebArAr provides five isochrons, including normal and inverse isochrons and three chlorine related isochrons. All isochrons and age spectra will use the same sequence selection combination, supporting two combinations, namely Set1 and Set2.
Import raw data
The raw files usually include at least the following information: the zero-time, analysis time, and intensities of five isotopes of each cycle.
The raw files will be read based on given filters. Set raw-file filter provides instructions and examples for creating filters.
Mass Spec Raw Files
Multiple raw files can be opened together and filters need to be selected for each file
Extrapolating the intercepts at zero-time.
You can click to deselect some outliers, decide whether to cancel this scatter point for all isotopes of the current sequence, select the fitting method to be adopted, check whether to apply this fitting method to all isotopes, and set the current sequence as the background. It is possible to export the sequence for later use.
Assign blanks for each sample sequence.
In the case of example below, three sequences of 1-7-13 are defined as blank sequences. There are four strategies to couple sample and blank sequences. It is also possible to select blanks for each sample sequence in drop-down boxes. The blank sequences can be calculated in the right interface. See Calculate blank.
Four strategies:
- Pre-run: Each blank is used to correct the sample sequence performed after it until the next blank conducted, and if the first sequence is not blank, the first blank will also be used to deduct several sample sequence before it;
- Post-run: Each blank will be used to correct the sample stage performed before it, and if the last sequence is not the blank, the last blank will also be used to deduct the last several sample sequences;
- Adjacent: Each blank sequence will be used to correct the nearest several sample sequences.
- Interpolation: The fitting line between the time and blank intensities can be defined from the given several blank sequences, and blanks of sample sequences can be obtained by interpolation.
arr files
- The arr files are saved in binary format and in principle are JSON-serialized Sample object.
Create new sample
Creating an empty object supports manually entering data by users.
It is often convenient when only some parts of WebArAr's functionality is required, such as plotting age spectra.
Set raw-file filter
The entry of editing raw-file filters on the Run page.
Edit an existing filter (requires Pin-verification), or create a new one.
The filter is used to read isotope intensities and information correctly from the files. Text format files and Excel Multitable files (xls) are supported. For xls files, table, row, and column indexes are three-digit integers used to locate data. For text files, rows and columns are needed.
Note: all indexes are 1 based
Example 1: AHD files.
AHD files might have following contents. Download the AHD file.
Sample sample_name Experiment experiment_name Project Irradiation Standard Instrument Argus 1E-13 Time Stamp 21/06/2023 0:08:53 Analyst Temperature 0 Laser J-Value Fractionation Volume Correction 1 Counters 1 15 1 0 Time Intensity 37 38 39 40 Cycle # Peakreading # 96.124784 0.039713085 139.839784 0.017819889 96.124784 0.095037932 96.124784 8.217368387 96.124784 52.50271246 183.630784 0.039292885 227.343784 0.01599587 183.630784 0.088180873 183.630784 7.980598974 183.630784 53.55335785According to the contents above, we can find: head information count for 15 rows, sample name (0, 1, 2), experiment name (0, 2, 2), date of zero-time (0, 7, 2), time of zero-time (0, 7, 3), isotopic values are presented vertically in groups of five, so 36Ar is located at (1, 2), 37Ar (2, 2), 38Ar (3, 2), 39Ar (4, 2), 40Ar (5, 2), analysis time is 36Ar (1, 1), 37Ar (2, 1), 38Ar (3, 1), 39Ar (4, 1), 40Ar (5, 1). And note that date and time are in one string respectively.
Example 2: xls files exported from NGX software.
Contents of the file are partly shown as the following figure. Download NGX_Exported_XLS for reference.
For this file, the filter Settings are as follows:
Calculate blank
Click the blank name to add the blank into Input input-box. Click again to delete the blank.
Choose to calculating average or fitting the interpolation.
As shown in the figure below, three blank sequences give a regression constraining blanks of ten sample sequences.
After calculating the average or interpolation, a new blank name will appear in the Output text-box, click the Add button to add it as a blank, after which you can select it in the drop-down boxes on the left.
Tables and figures
Tables
- Information: Sample information, such as number, mineral material, laboratory, etc
- Unknown: Isotopic values for each sample sequence. Errors are in 1σ.
- Blank: Used blank values of each sample sequence.
- Corrected: The isotopic values of each sample sequence after necessary corrections, including blank correction, mass discrimination correction, and decay correction.
- Degas Pattern: The value of each isotope after distinguishing their sources.
- Publish: In most cases, it is used to publish Ar-Ar data in a paper, including stage name, stage conditions, 36Ara, 37ArCa, 38ArCl, 39ArK, 40Arr, apparent age, age error, proportion of 40Arr in each sequence, ratio of 39ArK released in each sequence to the total amount, and Ca/K value.
- Age Spectra: 40Arr/39ArK and apparent ages.
- Isochrons: Data of normal, inverse, and Cl-related isochrons and the 3D plot.
- Total Params: All parameters involved in calculation.
Figures
- Age Spectra: Age spectra.
- Nor. Isochron: Normal isochron plot.
- Inv. Isochron: Inverse isochron plot.
- K-Cl-Ar 1: Cl correlation plot 1 in two dimensions. Note the difference in axes between three Cl plots.
- K-Cl-Ar 2: Cl correlation plot 2 in two dimensions.
- K-Cl-Ar 3: Cl correlation plot 3 in two dimensions.
- 3D Correlation: Correction plot in three dimensions.
- Degas Pattern: Shows the proportion of different isotope contributions released at each sequence.
- Ages Distribution: Shows the distribution of apparent ages, including bar charts and KDE curves.
Set parameters
The parameter setting is divided into three categories: Irradiation Params, Calculation Params (calculation constants), and Sample Params.
Add or edit parameter sets in Run page for later use.
It is also possible to modify parameters arbitrarily in the Total Params table, which allows you to set different parameters for each sequence.
Irradiation Params
Calculation Params
Sample Params
Recalculation
Recalculation will be not called after setting new parameters.
The options that can be used:
- Reset Arr Attributes: Check the structure of Arr files, which can be used to fix old files that are missing some attributes due to program updates.
Recalculate Correction and Degas:
For correct recalculation, specific procedures and subsequent calculations need to be selected. For example, if you modify some blank values, you need to select all the options from blank correction to age calculation, otherwise the new parameters will not really affect the final result; If you just modify the J-value, you only need to select recalculation of apparent age, the previous stage is not affected by the J-value, and you should also Reset Plot Data to recalculate plateau and isochron ages wiht the new J value
Reset Plot Style: reset styles of figures
Isochron scatter points selection
The isochron supports two sets of point selection (Set1 and Set2), and the corresponding age plateau will be drawn in the age spectrum (the age plateau will be deducted for the air argon by the specified initial value according to the setting). The normal and inverse isochrons and plateau ages of the two point groups are displayed on the right.
Clicking a scatter allows you to select or deselect a point for regression. Regression and age are automatically recalculated with each click, and response speed is related to network speed and number of stages.
In order to improve the operation, you can hold down the Ctrl and then click on multiple data points. It will not automatically recalculate, and then need to trigger recalculation, or release the Ctrl and click a scatter point. In this case only one recalcualtion is conducted.
Change figure styles
Click the Style button at the bottom to set styles of the currently displayed figure, such as axes range, line width, color, size, etc.
When the Style dialog is open, click on elements, such as lines, points, or texts, to set styles of the corresponding elements.
For example, after opening Style, click a Scatter to open scatter style Settings, as shown in the following figure.
Set the point size to 20:
Air-corrected plateaus
Set initial values for Set1 and Set2 in the Sample Parameter.
Air-corrected using the initial value of inverse isochron lines:
Air-corrected using the specific initial values. In the following case a value same to the blank age spectra was used, so the red/blue lines and black lines overlap:
Age distribution figure
Age profiles are often used for single-grain Ar-Ar age analysis. Data are derived from apparent ages in the Age Spectra table. The figure includes KDE curves, bar charts, and age boxes.
After opening Style, click on the red KDE curve to set the properties and KDE parameters: Normal probability density function is often used. Scott and Silverman are two methods to calculate bandwidth automatically. Or setting Auto Width to none and entering bandwidth.
Save and export
Click Export to open the Export dialog.
To download the arr file, click sample_name.arr or right-click to save it.
Choose another format to export::
- Excel: Contains all data and charts (except 3D plot);
- PDF: Export 2D figures to PDF, which can be opened and edited with Illustrator and CorelDRAW.
- SVG: Export 2D figures to SVG.
Example 1: Open files
Example 1-1: Open arr、age、xls files
Nonte: herein xls files refer to files exported from ArArCALC, usually with similar file names such as xxxx.full.xls
arr files
age files
xls files
Example 1-2: Open raw data files
Example 2: Enter data manually for calculation and making figures
Example 2-1: Make age spectra
For the following data, including a series of apparent ages, corresponding errors, and released 39ArK at each sequence, an age spectrum would be made.
ages sages 39ArK
---------------------------------------------
310.2176 6.751487 0.609066
247.3470 5.148231 0.827120
181.8897 3.651214 1.114444
78.62951 1.499786 1.164400
46.35105 0.777316 2.393310
25.54040 0.332920 4.833698
17.78667 0.158893 8.091584
14.99925 0.096756 11.02284
13.37219 0.062124 12.43698
12.88552 0.052385 12.25010
12.82013 0.052100 10.68799
12.92644 0.057349 8.552752
13.14080 0.066860 6.502910
13.50955 0.094057 4.772416
13.86147 0.108181 3.397764
14.32179 0.136590 2.627816
15.01300 0.191949 2.019118
15.84402 0.240927 1.453867
15.86743 0.272241 1.095365
16.73648 0.286714 0.879736
17.61575 0.396227 0.709635
17.85348 0.394215 0.579252
18.15503 0.400108 0.491160
18.06496 0.418386 0.423491
17.94611 0.449840 0.397428
18.49410 0.547799 0.351599
18.04896 0.498315 0.314126
Example 2-2: Make isochron diagrams
Here is an example of the normal isochron, the following data is required:
39ArK/36Ara s 40Ar*/36Ara s r
----------------------------------------------------------------------------
2.2751877337 0.0048052876 1025.80432325 2.0780870475 0.9583594665
3.2975019175 0.0069230743 1106.38664780 2.2460834483 0.9652901189
6.0105856008 0.0125928899 1129.37582601 2.2957337825 0.9681744730
11.011886341 0.0230813208 1031.99720845 2.1002662774 0.9691720209
21.166235256 0.0445848717 1032.99035293 2.1147591021 0.9694927363
38.319930905 0.0802844606 1161.70364073 2.3634476617 0.9683575059
73.534352138 0.1541520678 1424.54372436 2.9001681727 0.9680880478
123.79413109 0.2600566737 1853.22212767 3.7827521310 0.9679013050
153.88009163 0.3267535355 2014.19098315 4.1574887414 0.9680163127
169.26290975 0.3585793106 2082.32698095 4.2899067708 0.9675027883
176.63909925 0.3841523273 2118.74942736 4.4886093793 0.9702703124
173.34246119 0.3715170066 2053.75380022 4.2846436868 0.9697460420
155.86396720 0.3301618618 1890.74520283 3.8947628293 0.9694010629
140.36930466 0.3062175333 1764.29506449 3.7505862656 0.9717015933
111.89720737 0.2417092178 1485.86613648 3.1244156563 0.9716471684
89.596934208 0.1943473730 1289.37540024 2.7214060085 0.9709019830
74.759825437 0.1629035766 1176.13040758 2.4954842282 0.9700300082
54.783766008 0.1209899702 992.623614989 2.1345085268 0.9711071450
49.944918143 0.1124668310 958.882771121 2.1001119929 0.9688506856
41.885267737 0.0966704784 878.915538075 1.9638220829 0.9645186720
36.117315422 0.0846212613 817.979157915 1.7920764969 0.9317125525
35.339155787 0.0910717060 829.231298578 2.1075521253 0.9643027965
33.032540877 0.0827595535 797.007327462 1.9386916525 0.9667530193
33.887955355 0.1034956784 822.155008652 2.4563990293 0.9746915090
31.516055387 0.0875097358 782.986056641 2.1059773490 0.9647646486
30.867564655 0.1875046762 767.179621092 4.1062809401 0.8801480023
31.690337436 0.1828130406 786.765990745 4.0486556249 0.8198342732
Example 3: Datapoint selection in isochron figures
Example 4: Change styles of figures
Example 4-1: Change styles of isochrons
Example 4-2: Change styles of text elements
Example 4-3: Change scale of axes
Example 5: Export and save
Example 5-1: Save arr
Example 5-2: Export to DPF
Example 5-3: Export to EXCEL
Example 6: Edit parameter sets
Example 6-1: Create a parameter set
Example 6-2: Update a parameter set
Example 6-3: Delete a parameter set
