writematrix – Data file writing methods

Module with data writing function definitions

This module includes several functions used in writing data to files in a well defined way. While you are free to write data to a file in any way you want, it is preferable to try to keep a lab wide standard by using these methods.

The module was written early on and could probably do with some cleanup… Specifically old style format strings as well as redundant methods no longer required.

stlabutils.writematrix.params_to_str(params, f='%.10e', delim=', ')

Converts fit parameter values to a single line string

Takes a lmfit.Parameters object and converts its parameter values to a single line string.

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• params (lmfit.Parameters) – Parameters object input from fit

• delim (str, optional) – Field delimiter (separation character)

Returns

Joined string will all parameters

Return type

str

stlabutils.writematrix.savedict(myfile, mydict, f='%.10e', delim=', ', blocksep='\n')

Write a data dictionary to a file as a matrix block

Writes a given dictionary where each element is a list of numbers, i.e., each element in the dict is though of as a column. Expects all columns to be the same length. Also, if the file is empty (no writes have been yet performed on it), it will use the dictionary keys to write the title line.

Internally this function converts the dict to a matrix and uses stlab.utils.writematrix.savetxt() to save to the file.

The main stlab import renames this function to stlab.savedict

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• mydict (dict) – Dict containing the data. Each element should be a data column.

• f (str, optional) – Format specifier for the data (old style).

• delim (str, optional) – Field delimiter (separation character)

• blocksep (str, optional) – Characters to write at the end of the matrix. This is generally a single newline to separate blocks of data.

stlabutils.writematrix.savedictarray(myfile, mydictarray, f='%.10e', delim=', ', blocksep='\n')

Writes an array of data dictionaries to a file

Intended for writing a list of dictionaries containing the data columns as elements to a file. Essentially just repeats savedict on every element of the list making sure to include the title line (derived from the first dictionarly key values) if the file is new.

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• mydictarray (list of dict) – List containing the Dicts to be written.

• f (str, optional) – Format specifier for the data (old style).

• delim (str, optional) – Field delimiter (separation character)

• blocksep (str, optional) – Characters to write at the end of the matrix. This is generally a single newline to separate blocks of data.

stlabutils.writematrix.saveframe(myfile, myframe, f='%.10e', delim=', ', blocksep='\n')

Write a pandas Dataframe to a file as a matrix block

Writes a given pandas.DataFrame to a file. Is analogous to savedict Also, if the file is empty (no writes have been yet performed on it), it will use the dataframe column indexes to write the title line.

Internally this function converts just writes the matrix using stlab.utils.writematrix.savetxt()

The main stlab import renames this function to stlab.saveframe

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• mydict (dict) – Dict containing the data. Each element should be a data column.

• f (str, optional) – Format specifier for the data (old style).

• delim (str, optional) – Field delimiter (separation character)

• blocksep (str, optional) – Characters to write at the end of the matrix. This is generally a single newline to separate blocks of data.

stlabutils.writematrix.saveframearray(myfile, myframearray, f='%.10e', delim=', ', blocksep='\n')

Writes an array of pandas DataFrame to a file

Analogous to savedictarray but using pd.Dataframe instead of dicts. Expects a list of pd.DataFrames to be written to the file. Also handles writing the title line if the file is new.

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• mydictarray (list of dict) – List containing the Dicts to be written.

• f (str, optional) – Format specifier for the data (old style).

• delim (str, optional) – Field delimiter (separation character)

• blocksep (str, optional) – Characters to write at the end of the matrix. This is generally a single newline to separate blocks of data.

stlabutils.writematrix.savetxt(myfile, mat, f='%.10e', delim=', ', blocksep='\n')

Write a matrix to a given file

Writes a matrix to a file with a given format specifier and a delimiter. Adds a block separator at the end. This is very similar to np.savetxt. However, since python3 np.savetxt requires the file to be open in binary write mode.

This function is used internally by both savedict and saveframe

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• mat (list or np.array) – List containing the lines of data to be written as lists (a matrix or list of lists).

• f (str, optional) – Format specifier for the data (old style).

• delim (str, optional) – Field delimiter (separation character)

• blocksep (str, optional) – Characters to write at the end of the matrix. This is generally a single newline to separate blocks of data.

stlabutils.writematrix.writeline(myfile, line, f='.10e', delim=', ')

Writes a list of numbers as a single line to a file

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• line (list of float) – List containing the numbers to be written

• f (str, optional) – Format specifier for the data (new style).

• delim (str, optional) – Field delimiter (separation character)

stlabutils.writematrix.writeparams(myfile, params, f='%.10e', delim=', ')

Writes fit parameter values to file

Intended for writing fit parameter values given a lmfit.Parameters object to a file.

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• params (lmfit.Parameters) – Parameters object input from fit

• delim (str, optional) – Field delimiter (separation character)

stlabutils.writematrix.writeparnames(myfile, params, delim=', ')

Writes fit parameter names to file

Intended for writing fit parameter names given a lmfit.Parameters object to a file.

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• params (lmfit.Parameters) – Parameters object input from fit

• delim (str, optional) – Field delimiter (separation character)

stlabutils.writematrix.writetitle(myfile, vv, delim)

Given a list of strings writes the file title line

Does not do anything if the file already has contents. Includes a ‘#’ as first character for gnuplot. Is used by savedict and saveframe.

Parameters

• myfile (_io.TextIOWrapper) – Open file handle for writing

• vv (list of str) – List of column titles

• delim (str, optional) – Field delimiter (separation character)