pySPM is a python library (python3, but should be compatible with python2) in order to read, handle and plot Scanning Probe Microscopy (SPM) images as well as ToF-SIMS data.

For now it support the following formats:

• Nanoscan .xml file format
• Bruker
• Iontof ToF-SIMS fileformats:
  • ITA
  • ITM
  • ITS
• Nanonis SXM file

This library is offered as it is and is still in development. Please note that reading the raw data was done by reverse engineering and guessing and not with a manual as the file format is proprietary. It seems to work well with the data used by the developper of this library, but there is NO GUARANTY that this library will work correctly with your own specific data.

If you find bugs and issues, please report them to the developpe: https://github.com/scholi/pySPM/issues

A setup.py is prestent in order to install the package easily. => in order to use the library do pip install -e .

it now supports Field of View correction as well as the dead-time correction. So now both ITA spectra and the reconstructed ones fit perfectly:

import matplotlib.pyplot as plt
import pySPM
import numpy as np

A = pySPM.ITA(filename_ita)
I = pySPM.ITM(filename_itm)
m, S = A.getSpectrum()
m_raw, S_raw = I.getRawSpectrum()
plt.plot(m, S)
plt.plot(pySPM.utils.binning(m_raw,ufunc=np.mean), pySPM.utils.binning(S_raw))
plt.show()

This library requires the following packages

• mendatory
  • numpy
  • scipy
  • matplotlib
• for PCA
  • scikit-learn
  • pandas
• for GUI
  • pyQT5
• displaying progressbar (while passing the prog=True parameter to functions)
  • tqdm

python setup.py install

If you wish to adjust the library to your need, the best is to install it in editable mode as follow from the root pySPM directory:

pip install -e .

The documentation is still in its early stage read the documentation

If you use this library for your work, please think about citing it.