Converter Utilites

One goal for this project is to allow users to use serpentTools as a pipeline for taking SERPENT data to other programs. The first demonstration of this is creating binary .mat files that can be read into MATLAB, when a large text file would cause issues, done with the MatlabConverter.

Classes intending do first look for specific methods for gathering data on each object. These are obscured from the public API as they don’t serve a direct purpose besides a simple method by which to translate data from one place to the next. This collection is called inside the primary convert method, which is reponsible for gathering and writing the data into the new form.

Keeping with the MatlabConverter as an example, it looks for _gather_matlab method. This method simply places data into a dictionary, but do to the layout of each object, must be reimplemented as a unique method. Due to the simplicity of scipy.io.savemat(), the main writing function, serpentTools.io.base.MatlabConverter.convert(), is rather light. However, some data forms may require more depth to ensure fidelity in the converted data.

There may be some cases where a conversion does not make sense for all data types. Detector objects are the few pieces of data that can have a spatial grid attached, yet this grid varies across detectors. It may be advantageous to implement converters directly as instance methods. The decision will be up to the developer and the review process in that case.

Converters should also make sure, prior to potentially expensive collection steps are taken, that the user is in the best position to execute this operation. As of this writing and 0.6.1, scipy is not a requirement for this package, yet it is required for MATLAB conversion. Therefore, the MatlabConverter implements a check for scipy in checkImports(). The other check method, checkContainerReq(), is responsible for checking the container has the required data gathering routines, e.g. _gather_matlab. These checks are called at creation of the converter object.

class serpentTools.io.base.MatlabConverter(container, output)

Class for assisting in writing container data to MATLAB

Parameters

  • obj (serpentTools container) – Parser or container to be written to file

  • fileP (str or file-like object) – Name of the file to write

See also

  • serpentTools.io.toMatlab() - high level function for writing to MATLAB that uses this class

checkContainerReq(container)

Ensure that data from the container can be collected.

checkImports()

Ensure that scipy >= 1.0 is installed.

convert(reconvert, append=True, format='5', longNames=True, compress=True, oned='row')

Save contents of object to .mat file

Parameters

  • fileP (str or file-like object) – Name of the file to write

  • reconvert (bool) – If this evaluates to true, convert values back into their original form as they appear in the output file, e.g. MAT_TOTAL_ING_TOX. Otherwise, maintain the mixedCase style, total_ingTox.

  • append (bool) – If true and a file exists under output, append to that file. Otherwise the file will be overwritten

  • format ({'5', '4'}) – Format of file to write. '5' for MATLAB 5 to 7.2, '4' for MATLAB 4

  • longNames (bool) – If true, allow variable names to reach 63 characters, which works with MATLAB 7.6+. Otherwise, maximum length is 31 characters

  • compress (bool) – If true, compress matrices on write

  • oned ({'row', 'col'}:) – Write one-dimensional arrays as row vectors if oned=='row' (default), or column vectors

See also

scipy.io.savemat()