Dealing with age data

Dealing with age data#

Tc1D supports the option to both read in measured ages from a data file and write summary age output to a file.

Reading age data from a file#

The age data file format and how to read in a data file are described below.

Age data file format#

Tc1D expects the age data file you use to have the following format:

  • It should be a plain text file with commas separating the values in the file

  • It should contain 3–6 columns:

    1. The age types (AHe, AFT, ZHe, or ZFT)

    2. The ages in Ma

    3. The age uncertainties (standard deviations) in Myrs

    4. (optional) The eU concentration in parts per million

    5. (optional) The effective spherical grain radius in micrometers

    6. (optional) A sample ID

  • The text file should include a header as the first line

An example of the file format can be found in the file sample_data.csv in the Tc1D GitHub repository. The contents of that file are also shown below, for convenience.

Age type, Age (Ma), Standard deviation (Ma), eU concentration (ppm), Grain radius (um), Sample ID
AHe, 9.0, 0.5, 40.0, 60.0, 2025-DW001
AFT, 18.0, 1.5, , , 2025-DW001
ZHe, 28.0, 1.5, 900.0, 60.0, 2025-DW001
ahe, 12.0, 1.0, 120.0, 90.0, 2025-DW002
ZHe, 33.0, 1.5, 2000.0, 80.0, 2025-DW002
ZHe, 35.0, 1.5, 3200.0, 55.0, 2025-DW003
ZFT, 45.0, 2.5

Notes about the age file#

  • The eU and grain radius values are currently only supported for AHe and ZHe ages.

  • Any He age lacking either an eU or radius value will use the defaults for those values.

  • The sample ID is not required.

  • If a sample ID is listed for a fission-track sample, it should be preceded by three commas, as the expectation is that the sample ID is in column 6 of the comma-separated values data file. Line 3 in the data file example above shows the required format.

How to use your own data file#

To use your own text file you should ensure a copy of it is in the directory where you are running Tc1D (or you give the complete path to the file). You can enable reading of your age data file using the obs_age_file parameter if using the init_params() function or using the --obs-age-file command-line flag. Examples of both can be found below.

Reading an age data file using the init_params() function#

init_params(obs_age_file="sample_data.csv")

Reading an age data file from the command line#

./tc1d_cli.py --obs-age-file sample_data.csv

Writing summary age data to a file#

A summary of measured and predicted ages can be written to a file if either (1) age data are read from a file or (2) observed ages are passed to Tc1D from the command line or in the init_params() function. The output file will contain all of the information passed to Tc1D (observed ages, uncertainties, eU/radius, sample ID) as well as the predicted age(s) and eU/radius values used for age prediction ((U-Th)/He ages only). This can be handy to have in case you want to tweak plotting of the age data or further explore your results. The file will be written to csv/age_summary.csv.

An example of the output that is written to the age data file can be found below:

Age type, Observed age (Ma), Observed age stdev (Ma), Observed age eU (ppm), Observed age grain radius (um), Sample ID, Predicted age (Ma), Predicted age eU (ppm), Predicted age grain radius (um)
AHe,9.0,0.5,40.0,60.0,2025-DW001,7.45,40.0,60.0
AHe,12.0,1.0,120.0,90.0,2025-DW001,8.49,120.0,90.0
AFT,18.0,1.5,,,2025-DW001,13.03,,
ZHe,28.0,1.5,900.0,60.0,2025-DW002,22.0,900.0,60.0
ZHe,33.0,1.5,2000.0,80.0,2025-DW002,24.4,2000.0,80.0
ZHe,35.0,1.5,3200.0,55.0,2025-DW003,24.24,3200.0,55.0
ZFT,45.0,2.5,,,,43.95,,

Note: The ZFT age on the last line was missing a sample ID when the model was run. This is not a typo, this is the expected behavior.

Nicer looking output#

It is perhaps easier to read the output in table format, as it might look in pandas or a spreadsheet program. An example is shown below:

Age type

Observed age (Ma)

Observed age stdev (Ma)

Observed age eU (ppm)

Observed age grain radius (µm)

Sample ID

Predicted age (Ma)

Predicted age eU (ppm)

Predicted age grain radius (µm)

AHe

9.0

0.5

40.0

60.0

2025-DW001

7.45

40.0

60.0

AHe

12.0

1.0

120.0

90.0

2025-DW001

8.49

120.0

90.0

AFT

18.0

1.5

2025-DW001

13.03

ZHe

28.0

1.5

900.0

60.0

2025-DW002

22.0

900.0

60.0

ZHe

33.0

1.5

2000.0

80.0

2025-DW002

24.4

2000.0

80.0

ZHe

35.0

1.5

3200.0

55.0

2025-DW003

24.24

3200.0

55.0

ZFT

45.0

2.5

43.95

How to enable output of the summary age data file#

Writing summary age output using the init_params() function#

init_params(write_age_output=True)

Writing summary age output from the command line#

./tc1d_cli.py --write-age-output