isaakiel / calibrator

Small command line tool for 14C calibration

calibrator

Calibrator is a small c++ command line tool to calibrate 14C dates. In can process inputs in csv, json or as cli parameters, and it outputs csv or json, that can be piped into a file.

Usage

Allowed arguments:
  -h [ --help ]               Produce this help message.
  -i [ --input-file ] arg     Specifies input file.
  -b [ --bp ] arg             The BP Value.
  -s [ --std ] arg            The standard deviation.
  -j [ --json-string ] arg    Input as as JSON string. Format: {"bp": xx, 
                              "std": xx}
  -r [ --ranges ]             calculate sigma ranges (only for json output).
  --sum                       calculate sum probability.
  -o [ --output ] arg (=json) csv for csv-output, json for json (default).

Examples

./calibrator -b 5000 -s 50
./calibrator -i input_test.txt
./calibrator -i input_test2.txt
./calibrator -i input_test3.csv

Documentation

See doxygen docu.

calibrator's Issues

Documentation of the input formats

Currently, the input formats are only documented via the example files. That is not desirable. Should write a more verbose explanation what the calibrator expects in terms of data structure.

Handle arbitrary calibration curves

Currently, at runtime, the calibration curve ../data/intcal13.14c is loaded. This cause an error when the bin is run outside of its directory. This is not a good behaviour.

1. Import the CalCurve at compile time (but than we loose the ability to use newer cal curves)?
2. Add a switch to specify a CalCurve at runtime, defaulting to the one shipped with the calibrator.

I would rather go for option 2.

Build issue

I just tried to make calibrator on Ubuntu 18.04.5 LTS x86_64, with GNU Make 4.1 and g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0 and get the following error:

$ make
 build/uncal_date_list.o build/main.o build/cal_date_list.o build/sigma_range.o build/uncal_date.o build/cal_curve.o build/cal_date.o
 g++ -O2 -g -Wall -std=c++11 -fmessage-length=0 -I ~/boost -c -o build/main.o src/main.cpp
In file included from src/../include/sigma_range.h:22:0,
                 from src/../include/cal_date.h:23,
                 from src/../include/uncal_date.h:23,
                 from src/main.cpp:13:
src/../include/json.hpp: In function ‘bool nlohmann::operator<(nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType>::const_reference, nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType>::const_reference)’:
src/../include/json.hpp:5539:62: error: wrong number of template arguments (1, should be 2)
                     return *lhs.m_value.array < *rhs.m_value.array;
                                                              ^~~~~
In file included from src/../include/json.hpp:33:0,
                 from src/../include/sigma_range.h:22,
                 from src/../include/cal_date.h:23,
                 from src/../include/uncal_date.h:23,
                 from src/main.cpp:13:
/usr/include/c++/7/array:94:12: note: provided for ‘template<class _Tp, long unsigned int _Nm> struct std::array’
     struct array
            ^~~~~
Makefile:23: recipe for target 'build/main.o' failed
make: *** [build/main.o] Error 1

It did work for me in the past on another system, so I assume it's some sort of dependency issue? Any ideas, @MartinHinz?

Location of the example files

Currently, the example datasets are stored in the bin-folder. That is probably not desirable. Might be necessary to find another location. Probably /examples or /test_data, or simply /data, where currently the calibration curve is living? I opt for the latter option.