.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/plot_postprocessing_isoscan.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_plot_postprocessing_isoscan.py: Postprocessing on isoscan ==================================== Example of isoscan postprocessing procedures. The data are a deflector scan on graphene as simulated from a third nearest neighbor tight binding model. The same workflow can be applied to any tilt-, polar-, deflector- or hv-scan. .. GENERATED FROM PYTHON SOURCE LINES 13-14 Import the "fundamental" python libraries for a generic data analysis: .. GENERATED FROM PYTHON SOURCE LINES 14-17 .. code-block:: default import numpy as np .. GENERATED FROM PYTHON SOURCE LINES 18-19 Instead of loading the file as for example: .. GENERATED FROM PYTHON SOURCE LINES 19-24 .. code-block:: default # from navarp.utils import navfile # file_name = r"nxarpes_simulated_cone.nxs" # entry = navfile.load(file_name) .. GENERATED FROM PYTHON SOURCE LINES 25-27 Here we build the simulated graphene signal with a dedicated function defined just for this purpose: .. GENERATED FROM PYTHON SOURCE LINES 27-39 .. code-block:: default from navarp.extras.simulation import get_tbgraphene_deflector entry = get_tbgraphene_deflector( scans=np.linspace(-0.1, 0.1, 3), angles=np.linspace(-25, 6, 400), ebins=np.linspace(-13, 0.4, 700), tht_an=-18, phi_an=0, hv=120, gamma=0.05 ) .. GENERATED FROM PYTHON SOURCE LINES 40-42 Fermi level autoset ^^^^^^^^^^^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 42-49 .. code-block:: default entry.autoset_efermi(scan_range=[-2, 2], energy_range=[115.2, 115.8]) print("Energy of the Fermi level = {:.0f} eV".format(entry.efermi)) print("Energy resolution = {:.0f} meV".format(entry.efermi_fwhm*1000)) entry.plt_efermi_fit() .. image-sg:: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_001.png :alt: plot postprocessing isoscan :srcset: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none Fermi level at 115.4066 eV Energy resolution = 142.5 meV (i.e. FWHM of the Gaussian shape which, convoluted with a step function, fits the Fermi edge) Photon energy is now set to 120.0066 eV (instead of 120.0000 eV) Energy of the Fermi level = 115 eV Energy resolution = 143 meV .. GENERATED FROM PYTHON SOURCE LINES 50-52 Set the k-space for the transformation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. GENERATED FROM PYTHON SOURCE LINES 52-61 .. code-block:: default entry.set_kspace( tht_p=0.1, k_along_slit_p=1.7, scan_p=0, ks_p=0, e_kin_p=114.3, ) .. rst-class:: sphx-glr-script-out .. code-block:: none tht_an = -17.979 scan_type = deflector inn_pot = 14.000 scans_0 = 0.000 phi_an = 0.000 kspace transformation ready .. GENERATED FROM PYTHON SOURCE LINES 62-65 Post processing on the isoscan: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ First of all let's show it: .. GENERATED FROM PYTHON SOURCE LINES 65-68 .. code-block:: default entry.isoscan(0).show() .. image-sg:: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_002.png :alt: plot postprocessing isoscan :srcset: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 69-75 The second derivative can be obtained using sigma in the definition, which define the extension in points of the Gaussian filter used to then get the second derivative. In this case the sigma is different from zero only on the second element, meaning that the derivative will be performed only along the energy axis: sphinx_gallery_thumbnail_number = 3 .. GENERATED FROM PYTHON SOURCE LINES 75-78 .. code-block:: default entry.isoscan(0, sigma=[3, 5]).show() .. image-sg:: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_003.png :alt: plot postprocessing isoscan :srcset: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 79-82 Only the Gaussian filtered image can be obtained using again sigma but also specifying the order=0, which by default is equal to 2 giving the second derivative as before.: .. GENERATED FROM PYTHON SOURCE LINES 82-85 .. code-block:: default entry.isoscan(0, sigma=[10, 10], order=0).show() .. image-sg:: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_004.png :alt: plot postprocessing isoscan :srcset: /auto_examples/images/sphx_glr_plot_postprocessing_isoscan_004.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 86-87 To export it as NXdata class of the nexus format uncomment this line: .. GENERATED FROM PYTHON SOURCE LINES 87-90 .. code-block:: default # entry.isoscan(0, 0, sigma=[3, 5], order=0).export_as_nxs('fermimap.nxs') .. GENERATED FROM PYTHON SOURCE LINES 91-92 To export it as igor-pro text file (itx) uncomment this line: .. GENERATED FROM PYTHON SOURCE LINES 92-94 .. code-block:: default # entry.isoscan(0, 0, sigma=[3, 5], order=0).export_as_itx('fermimap.itx') .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 1.039 seconds) .. _sphx_glr_download_auto_examples_plot_postprocessing_isoscan.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_postprocessing_isoscan.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_postprocessing_isoscan.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_