lumispy.utils.io module

File input/output utility functions.

lumispy.utils.io.savetxt(S, filename, fmt='%.5f', delimiter='\t', axes=True, transpose=False, **kwargs)

Write signal object to simple text file.

Writes single spectra to a two-column data file with signal axis as X and data as Y. Writes linescan data to file with signal axis as first row and navigation axis as first column (flipped if transpose=True).

Write image to file with the navigation axes as first column and first row. Write 2D data (e.g. map of a fit parameter value) to file with the signal axes as first column and first row.

Parameters:

  • filename (string)

  • fmt (str or sequence of strs, optional) – A single or sequence of format strings. Default is ‘%.5f’.

  • delimiter (str, optional) – String or character separating columns. Default is ‘,’

  • axes (bool, optional) – If True (default), include axes in saved file. If False, save the data array only.

  • transpose (bool, optional) – If True, transpose data array and exchange axes. Default is false. Ignored for single spectra.

  • **kwargs – Takes any additional arguments of numpy.loadtxt, e.g. newline header, footer, comments, or encoding.

See also

numpy.savetxt

Examples

>>> import lumispy as lum
>>> import numpy as np
...
>>> # Spectrum:
>>> S = lum.signals.LumiSpectrum(np.arange(5))
>>> lum.savetxt(S, 'spectrum.txt')
0.00000 0.00000
1.00000 1.00000
2.00000 2.00000
3.00000 3.00000
4.00000 4.00000
...
>>> # Linescan:
>>> L = lum.signals.LumiSpectrum(np.arange(25).reshape((5,5)))
>>> lum.savetxt(L, 'linescan.txt')
0.00000 0.00000 1.00000 2.00000 3.00000 4.00000
0.00000 0.00000 5.00000 10.00000        15.00000        20.00000
1.00000 1.00000 6.00000 11.00000        16.00000        21.00000
2.00000 2.00000 7.00000 12.00000        17.00000        22.00000
3.00000 3.00000 8.00000 13.00000        18.00000        23.00000
4.00000 4.00000 9.00000 14.00000        19.00000        24.00000
lumispy.utils.io.to_array(S, axes=True, transpose=False)

Return signal object as numpy array (optionally including the axes).

Returns single spectra as two-column array. Returns linescan data as array with signal axis as first row and navigation axis as first column (flipped if transpose=True).

Return image as array with the navigation axes as first column and first row. Return 2D data (e.g. map of a fit parameter value) as array with the signal axes as first column and first row.

Parameters:

  • axes (bool, optional) – If True (default), include axes in array. If False, return the data array only.

  • transpose (bool, optional) – If True, transpose data array and exchange axes. Default is false. Ignored for single spectra.

  • **kwargs – Takes any additional arguments of numpy.loadtxt, e.g. newline header, footer, comments, or encoding.

Notes

The output of this function can be used to convert a signal object to a pandas dataframe, e.g. using df = pd.Dataframe(lum.to_array(S)).

Examples

>>> import lumispy as lum
>>> import numpy as np
...
>>> # Spectrum:
>>> S = lum.signals.LumiSpectrum(np.arange(5))
>>> lum.to_array(S)
array([[0., 0.],
      [1., 1.],
      [2., 2.],
      [3., 3.],
      [4., 4.]])
...
>>> # Linescan:
>>> L = lum.signals.LumiSpectrum(np.arange(25).reshape((5,5)))
>>> lum.to_array(L)
array([[ 0.,  0.,  1.,  2.,  3.,  4.],
      [ 0.,  0.,  1.,  2.,  3.,  4.],
      [ 1.,  5.,  6.,  7.,  8.,  9.],
      [ 2., 10., 11., 12., 13., 14.],
      [ 3., 15., 16., 17., 18., 19.],
      [ 4., 20., 21., 22., 23., 24.]])