pyTEMlib 0.2025.4.1__py3-none-any.whl → 0.2025.9.1__py3-none-any.whl

pyTEMlib/utilities.py

@@ -0,0 +1,314 @@
+"""
+# ###############################################################
+# Utility Functions for spectroscopy data in pyTEMlib
+# ################################################################
+"""
+import typing
+import numpy as np
+from numba import jit
+import scipy
+import sidpy
+
+from .xrpa_x_sections import x_sections
+
+ELECTRON_REST_ENERGY = 5.10998918e5  # electron rest energy in eV
+
+major_edges = ['K1', 'L3', 'M5', 'N5']
+
+all_edges = ['K1', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5',
+             'N1', 'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2',
+             'O3', 'O4', 'O5', 'O6', 'O7', 'P1', 'P2', 'P3']
+
+shell_occupancy = {'K1': 2, 'L1': 2, 'L2': 2, 'L3': 4, 'M1': 2, 'M2': 2, 'M3': 4, 'M4': 4, 'M5': 6,
+                   'N1': 2, 'N2': 2, 'N3': 4, 'N4': 4, 'N5': 6, 'N6': 6, 'N7': 8, 'O1': 2, 'O2': 2,
+                   'O3': 4, 'O4': 4, 'O5': 6, 'O6': 6, 'O7': 8, 'O8': 8, 'O9': 10}
+
+
+first_close_edges = ['K1', 'L3', 'M5', 'M3', 'N5', 'N3']
+
+elements = [' ', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na',
+            'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V',
+            'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br',
+            'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag',
+            'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr',
+            'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu',
+            'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi']
+
+def get_wave_length(e0: float) -> float:
+    """get deBroglie wavelength of electron accelerated by energy (in eV) e0"""
+    ev = scipy.constants.e * e0
+    m_e = scipy.constants.m_e
+    c = scipy.constants.c
+    h = scipy.constants.h
+    return h / np.sqrt(2 * m_e * ev * (1 + ev / (2 * m_e * c**2)))
+
+
+def effective_collection_angle(energy_scale: np.ndarray,
+                               alpha: float,
+                               beta: float,
+                               beam_ev: float) -> float:
+    """Calculates the effective collection angle in mrad:
+
+    Translate from original Fortran program
+    Calculates the effective collection angle in mrad:
+    Parameter
+    ---------
+    energy_scale: numpy array
+        first and last energy loss of spectrum in eV
+    alpha: float
+        convergence angle in mrad
+    beta: float
+        collection  angle in mrad
+    beamKV: float
+        acceleration voltage in V
+
+    Returns
+    -------
+    eff_beta: float
+        effective collection angle in mrad
+
+    # function y = effbeta(ene,  alpha, beta, beam_kv) Note Pierre uses keV
+    #
+    #       This program computes etha(alpha,beta), that is the collection
+    #       efficiency associated to the following geometry :
+    #
+    #       alpha = half angle of illumination  (0 -> pi/2)
+    #       beta  = half angle of collection    (0 -> pi/2)
+    #                                           (pi/2 = 1570.795 mrad)
+    #
+    #           A constant angular distribution of incident electrons is assumed
+    #       for any incident angle (-alpha,alpha). These electrons imping the
+    #       target and a single energy-loss event occurs, with a characteristic
+    #       angle theta-e (relativistic). The angular distribution of the
+    #       electrons after the target is analytically derived.
+    #           This program integrates this distribution from theta=0 up to
+    #       theta=beta with an adjustable angular step.
+    #           This program also computes beta* which is the theoretical
+    #       collection angle which would give the same value of etha(alpha,beta)
+    #       with a parallel incident beam.
+    #
+    #       subroutines and function subprograms required
+    #       ---------------------------------------------
+    #       none
+    #
+    #       comments
+    #       --------
+    #
+    #       The following parameters are asked as input :
+    #        accelerating voltage (kV), energy loss range (eV) for the study,
+    #        energy loss step (eV) in this range, alpha (mrad), beta (mrad).
+    #       The program returns for each energy loss step :
+    #        alpha (mrad), beta (mrad), theta-e (relativistic) (mrad),
+    #        energy loss (eV), etha (#), beta * (mrad)
+    #
+    #       author :
+    #       --------
+    #       Pierre TREBBIA
+    #       US 41 : "Microscopie Electronique Analytique Quantitative"
+    #       Laboratoire de Physique des Solides, Bat. 510
+    #       Universite Paris-Sud, F91405 ORSAY Cedex
+    #       Phone : (33-1) 69 41 53 68
+    #
+    """
+    if beam_ev == 0:
+        beam_ev = 100.0 * 1e3
+
+    if alpha == 0:
+        return beta
+
+    if beta == 0:
+        return alpha
+
+    alpha = alpha * 0.001  # rad
+    beta = beta * 0.001  # rad
+    z7 = 500.0  # number of integration steps to be modified at will
+
+    #       main loop on energy loss
+    for zx in range(int(energy_scale[0]), int(energy_scale[-1]), 100):
+        # ! zx = current energy loss
+        eta = 0.0
+        # x0 = relativistic theta-e
+        x0 = float(zx) * (beam_ev + 511060.) / (beam_ev * (beam_ev + 1022120.))
+        dtheta = (beta - 0.1 * np.sqrt((x0**2 + alpha**2))) / 500  # integration steps
+    #
+    #        calculation of the analytical expression
+    #
+    for zi in range(1, int(z7)):
+        theta = 0.1 * np.sqrt((x0**2 + alpha**2)) + dtheta * float(zi)
+        x5 = theta**2
+        x6 = 4. * x5 * x0 * x0
+        x7 = (x0**2 + alpha**2) - x5
+        eta += 2. * theta * dtheta * np.log((np.sqrt(x7**2 + x6) + x7) / (2. * x0**2))
+    # addition of the central contribution
+    eta = eta + (x0**2 + alpha**2) / 100. * np.log(1. + alpha**2/x0**2)
+    # normalisation
+    eta = eta / alpha * alpha * np.log(1. + np.pi**2 / (4. * x0**2))
+    #
+    #        correction by geometrical factor (beta/alpha)**2
+    #
+    if beta < alpha:
+        x5 = alpha / beta
+        eta = eta * x5**2
+
+    #  etha2 = eta * 100.
+    #
+    #        calculation of beta *
+    #
+    x6 = np.power((1. + (1. + np.pi**2 / (4. * x0**2))), eta)
+    x7 = x0 * np.sqrt(x6 - 1.)
+    beta = x7 * 1000.  # in mrad
+
+    return beta
+
+def set_default_metadata(current_dataset: sidpy.Dataset) -> None:
+    """sets default metadata for the dataset"""
+
+    if 'experiment' not in current_dataset.metadata:
+        current_dataset.metadata['experiment'] = {}
+    if 'convergence_angle' not in current_dataset.metadata['experiment']:
+        current_dataset.metadata['experiment']['convergence_angle'] = 30
+    if 'collection_angle' not in current_dataset.metadata['experiment']:
+        current_dataset.metadata['experiment']['collection_angle'] = 50
+    if 'acceleration_voltage' not in current_dataset.metadata['experiment']:
+        current_dataset.metadata['experiment']['acceleration_voltage'] = 200000
+
+
+def lorentz(x, center, amplitude, width):
+    """ Lorentzian Function """
+    lorentz_peak = 0.5 * width / np.pi / ((x - center)**2 + (width / 2)**2)
+    return amplitude * lorentz_peak / lorentz_peak.max()
+
+@jit
+def gauss(x, p):  # p[0]==mean, p[1]= amplitude p[2]==fwhm,
+    """Gaussian Function
+
+        p[0]==mean, p[1]= amplitude p[2]==fwhm
+        area = np.sqrt(2* np.pi)* p[1] * np.abs(p[2] / 2.3548)
+        FWHM = 2 * np.sqrt(2 np.log(2)) * sigma = 2.3548 * sigma
+        sigma = FWHM/3548
+    """
+    if p[2] == 0:
+        return x * 0.
+    return p[1] * np.exp(-(x - p[0])**2 / (2.0 * (p[2] / 2.3548)**2))
+
+def get_atomic_number(z):
+    """Returns the atomic number independent of input as a string or number"""
+    return get_z(z)
+
+def get_z(z: typing.Union[int, str]) -> int:
+    """Returns the atomic number independent of input as a string or number
+
+    Parameter
+    ---------
+    z: int, str
+        atomic number of chemical symbol (0 if not valid)
+    Return:
+    ------
+    z_out: int
+        atomic number
+    """
+    z_out = 0
+    if str(z).isdigit():
+        z_out = int(z)
+    elif isinstance(z, str):
+        z_out = elements.index(z)
+    else:
+        raise TypeError('A valid element string or number is required')
+    return z_out
+
+
+def get_x_sections(z: int=0) -> dict:
+    """Reads X-ray fluorescent cross-sections from a dictionary.
+
+    Parameters
+    ----------
+    z: int
+        atomic number if zero all cross-sections will be returned
+
+    Returns
+    -------
+    dictionary
+        cross-section of an element or of all elements if z = 0
+    """
+    if z < 1:
+        return x_sections
+    z = str(z)
+    if z in x_sections:
+        return x_sections[z]
+    return {}
+
+
+def get_spectrum(dataset, x=0, y=0, bin_x=1, bin_y=1):
+    """
+    Extracts a spectrum from a sidpy.Dataset object
+    Parameter
+    ---------
+    dataset: sidpy.Dataset object
+        contains spectrum or spectrum image
+    x: int default = 0
+        x position of spectrum image
+    y: int default = 0
+        y position of spectrum
+    bin_x: int default = 1
+        binning of spectrum image in x-direction
+    bin_y: int default = 1
+        binning of spectrum image in y-direction
+
+    Returns:
+    --------
+    spectrum: sidpy.Dataset object
+
+    """
+    if dataset.data_type.name == 'SPECTRUM':
+        spectrum = dataset.copy()
+    else:
+        image_dims = dataset.get_image_dims()
+        x = min(x, dataset.shape[image_dims[0]] - bin_x)
+        y = min(y, dataset.shape[image_dims[1]] - bin_y)
+        selection = []
+        dimensions = dataset.get_dimension_types()
+        for dim, dimension_type in enumerate(dimensions):
+            # print(dim, axis.dimension_type)
+            if dimension_type == 'SPATIAL':
+                if dim == image_dims[0]:
+                    selection.append(slice(x, x + bin_x))
+                else:
+                    selection.append(slice(y, y + bin_y))
+            elif dimension_type == 'SPECTRAL':
+                selection.append(slice(None))
+            elif dimension_type == 'CHANNEL':
+                selection.append(slice(None))
+            else:
+                selection.append(slice(0, 1))
+        spectrum = dataset[tuple(selection)].mean(axis=tuple(image_dims))
+        spectrum.squeeze().compute()
+        spectrum.data_type = 'Spectrum'
+    return spectrum
+
+def second_derivative(dataset: sidpy.Dataset) -> None:
+    """Calculates second derivative of a sidpy.dataset"""
+    energy_scale = dataset.get_spectral_dims(return_axis=True)[0]
+    if dataset.data_type.name == 'SPECTRAL_IMAGE':
+        spectrum = dataset.view.get_spectrum()
+    else:
+        spectrum = np.array(dataset)
+    spec = scipy.ndimage.gaussian_filter(spectrum, 3)
+    dispersion = energy_scale.slope
+    second_dif = np.roll(spec, -3) - 2 * spec + np.roll(spec, +3)
+    second_dif[:3] = 0
+    second_dif[-3:] = 0
+
+    # find if there is a strong edge at high energy_scale
+    noise_level = 2. * np.std(second_dif[3:50])
+    [indices, _] = scipy.signal.find_peaks(second_dif, noise_level)
+    width = max(50 / dispersion, 50)
+    start_end_noise = int(len(energy_scale) - width)
+    for index in indices[::-1]:
+        if index > start_end_noise:
+            start_end_noise = index - 70
+
+    # noise_level_start = sensitivity * np.std(second_dif[3:50])
+    # noise_level_end = sensitivity * np.std(second_dif[start_end_noise: start_end_noise + 50])
+    # slope = (noise_level_end - noise_level_start) / (len(energy_scale) - 400)
+    # noise_level = noise_level_start #+ np.arange(len(energy_scale)) * slope
+    return second_dif , noise_level

pyTEMlib/version.py

@@ -1,6 +1,5 @@
 """
 version
 """
-_version = '0.2025.04.1'
-__version__ = _version
-_time = '2025-05-25 19:58:26'
+__version__ = '0.2025.09.1'
+__time__ = '2025-09-03 19:58:26'

pyTEMlib/xrpa_x_sections.py

@@ -1,6 +1,7 @@
 """  X-ray photo-absorption cross-sections for inelastic scattering from NIST
 The cross sections are given in atoms/nm^3 not barns!!
 See xsec_xrpa function in eels_tools for usage.
+https://physics.nist.gov/PhysRefData/FFast/html/form.html
 
 for pyTEMLib by Gerd
 
@@ -21,6 +22,7 @@ Z = 1 -100
 page 25
 by: S. T. Perkins, D. E. CuUen, M. H. Chen, J. H. Hubbell, J. Rathkopf, J. Scofield
 https://www.osti.gov/servlets/purl/10121422
+
 """
 
 import numpy as np
@@ -403,15 +405,15 @@ x_sections = {'1': {'name': 'H',
         7.638578e+04, 8.165640e+04, 8.729069e+04, 9.331374e+04,
         9.975239e+04]),
                     'dat': np.array([0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.73384709E+17, 
-       1.68319106E+17, 4.17741709E+16, 3.70675760E+16, 3.27899957E+16, 
-       2.89145043E+16, 2.83239362E+16, 2.75089880E+16, 2.72971733E+16, 
+       1.68319106E+17, 4.17741709E+16, 3.70675760E+16, 3.27899957E+16,
+       2.89145043E+16, 2.83239362E+16, 2.75089880E+16, 2.72971733E+16,
        3.39872874E+16, 3.34739059E+16, 3.29533443E+16, 3.11062482E+16,
        2.96127749E+16, 2.82646998E+16, 2.69920165E+16, 2.57318984E+16,
        2.44484448E+16, 2.31237053E+16, 2.17576798E+16, 2.03593437E+16,
        1.89430571E+16, 1.75265911E+16, 1.61291524E+16, 1.47677941E+16,
        1.34574149E+16, 1.22096826E+16, 1.10330339E+16, 9.93339235E+15,
-       8.91327112E+15, 7.97374718E+15, 7.11320501E+15, 6.32841352E+15, 
-       5.61416710E+15, 4.96741419E+15, 4.38492371E+15, 3.86202856E+15, 
+       8.91327112E+15, 7.97374718E+15, 7.11320501E+15, 6.32841352E+15,
+       5.61416710E+15, 4.96741419E+15, 4.38492371E+15, 3.86202856E+15,
        3.39477965E+15, 2.97833037E+15, 2.60639808E+15, 2.27431568E+15,
        1.98172416E+15, 1.72436928E+15, 1.49846349E+15, 1.30052443E+15,
        1.12741077E+15, 9.76268405E+14, 8.44476568E+14, 7.29737611E+14,
@@ -421,7 +423,7 @@ x_sections = {'1': {'name': 'H',
        6.08787816E+15, 5.17851090E+15, 4.39156536E+15, 3.71447627E+15,
        3.13431934E+15, 2.63924731E+15, 2.21813093E+15, 1.86091797E+15,
        1.55881274E+15, 1.30384525E+15, 1.08906872E+15, 9.08505645E+14,
-       7.56932467E+14, 6.29897486E+14, 5.23595218E+14, 4.34740738E+14, 
+       7.56932467E+14, 6.29897486E+14, 5.23595218E+14, 4.34740738E+14,
        3.60515834E+14, 2.98658755E+14, 2.47194958E+14, 2.04490957E+14,
        1.67685457E+14, 1.37494679E+14, 1.12742872E+14, 9.24481501E+13,
        7.58135144E+13, 6.21730054E+13, 5.09917013E+13, 4.18226370E+13,
@@ -437,9 +439,9 @@ x_sections = {'1': {'name': 'H',
        5.30236866E+10, 4.90476730E+10, 4.57681349E+10, 4.30468542E+10,
        4.07797187E+10, 3.88626160E+10, 3.72434899E+10, 3.58648992E+10,
        3.46819678E+10, 3.36534099E+10, 3.27487098E+10, 3.19445318E+10,
-       3.12157456E+10, 3.05515808E+10, 2.99358821E+10, 2.93578792E+10, 
-       2.88103920E+10, 2.82844453E+10, 2.77764490E+10, 2.72810179E+10, 
-       2.67963571E+10, 2.63170814E+10, 2.58449859E+10, 2.53746854E+10, 
+       3.12157456E+10, 3.05515808E+10, 2.99358821E+10, 2.93578792E+10,
+       2.88103920E+10, 2.82844453E+10, 2.77764490E+10, 2.72810179E+10,
+       2.67963571E+10, 2.63170814E+10, 2.58449859E+10, 2.53746854E+10,
        2.49061800E+10,])},
               '6': {'name': 'C',
                     'barns': 199447000000.0,
@@ -1017,7 +1019,7 @@ x_sections = {'1': {'name': 'H',
 		       'lines': {'K-L3': {'weight': 1.0, 'position': 1253.6},
 			          'K-L2': {'weight': 0.507, 'position': 1253.6},
 			         },
-                    'fluorescent_yield': {'K': 0.027775},
+                    'fluorescent_yield': {'K': 0.02333},
                     'total_fluorescent_yield': {'K': 0.027692},
                      'L3': {'filename': 'Mg.L3', 'excl before': 5, 'excl after': 50, 'onset': 51.4, 'factor': 1.0,
                             'twin': 'L2', 'shape': 'hydrogenic'},
@@ -4863,6 +4865,8 @@ x_sections = {'1': {'name': 'H',
         3.97919316e+12, 3.28605194e+12, 2.69759840e+12, 2.21449596e+12,
         1.81803617e+12, 1.49269500e+12, 1.22431507e+12, 1.00189688e+12,
         8.19920778e+11, 6.71022793e+11]), },
+        
+        
               '36': {'name': 'Kr',
                      'barns': 1391530000000.0,
                      'NumEdges': 9,
@@ -6435,7 +6439,7 @@ x_sections = {'1': {'name': 'H',
 			          'M4-N2': {'weight': 0.01, 'position': 263.8},
 			          'M5-N3': {'weight': 0.1, 'position': 259.1},
 			         },
-                     'fluorescent_yield':{'K': 0.81257, 'L': 0.04641, 'M': 0.000961},
+                     'fluorescent_yield':{'K': 0.81257, 'L': 0.04641, 'M': 0.000836},
                      'total_fluorescent_yield':{'K': 0.808090, 'L1': 0.049941, 'L2': 0.054357, 'L3': 0.048963, 'M1': 0.001151, 'M2': 0.001219, 'M3': 0.001128, 'M4': 0.000349, 'M5': 0.000309},
                      'N5': {'filename': 'None', 'excl before': 5, 'excl after': 50, 'onset': 2.5, 'factor': 1.0,
                             'twin': 'N4'},

{pytemlib-0.2025.4.1.dist-info → pytemlib-0.2025.9.1.dist-info}/METADATA

@@ -1,11 +1,12 @@
 Metadata-Version: 2.4
 Name: pyTEMlib
-Version: 0.2025.4.1
+Version: 0.2025.9.1
 Summary: pyTEM: TEM Data Quantification library through a model-based approach
-Home-page: https://pycroscopy.github.io/pyTEMlib/about.html
-Author: Gerd Duscher
-Author-email: gduscher@utk.edu
-License: MIT
+Author-email: Gerd Duscher <gduscher@utk.edu>
+License-Expression: MIT
+Project-URL: Homepage, https://pycroscopy.github.io/pyTEMlib/about.html
+Project-URL: Repository, https://github.com/pycroscopy/pyTEMlib
+Project-URL: Documentation, https://pycroscopy.github.io/pyTEMlib/
 Keywords: imaging,spectra,transmission,electron,microscopy,scientific,scanning,eels,visualization,processing,storage,hdf5,diffraction
 Platform: Linux
 Platform: Mac OSX
@@ -13,7 +14,6 @@ Platform: Windows 11/10
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Cython
@@ -24,6 +24,8 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Python: >=3.9
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: scipy
 Requires-Dist: numpy
@@ -36,22 +38,17 @@ Requires-Dist: requests
 Requires-Dist: lxml
 Requires-Dist: ipympl
 Requires-Dist: spglib
+Requires-Dist: simpleitk
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: pyNSID>=0.0.7
 Requires-Dist: sidpy>=0.12.7
 Requires-Dist: SciFiReaders>=0.0.8
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: home-page
-Dynamic: keywords
-Dynamic: license
+Requires-Dist: xraylib
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-runner; extra == "test"
 Dynamic: license-file
-Dynamic: platform
-Dynamic: requires-dist
-Dynamic: summary
 
 pyTEMlib
 ========

pytemlib-0.2025.9.1.dist-info/RECORD

@@ -0,0 +1,86 @@
+build/lib/pyTEMlib/__init__.py,sha256=qZ09_LrmgKUMyhC317QYiK4EFT-HITbQzJbYThqYFb0,1132
+build/lib/pyTEMlib/animation.py,sha256=PY_vI7K25CHNZYQHC9h0bosxcTsrI3nSNnakimqupE8,25632
+build/lib/pyTEMlib/atom_tools.py,sha256=d7FfRFT8kLXtvjr9Nklpgum4vi9kRpNdVPmC-ByTtcE,7167
+build/lib/pyTEMlib/config_dir.py,sha256=Gj3ySjA5gfHUp5jL4E4GJnM8UeWebaHg_dQ1qg6q23I,1234
+build/lib/pyTEMlib/crystal_tools.py,sha256=JWi_wHywR6ufNck_TFf2HV5_7xrULCVzIJ-8iF-npn0,61388
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{pytemlib-0.2025.4.1.dist-info → pytemlib-0.2025.9.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pytemlib-0.2025.9.1.dist-info/top_level.txt

@@ -0,0 +1,6 @@
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+data
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+example_data
+notebooks
+pyTEMlib