pyTEMlib 0.2025.12.0__py3-none-any.whl

build/lib/pyTEMlib/eds_tools.py

@@ -0,0 +1,901 @@
+"""
+eds_tools
+Model based quantification of energy-dispersive X-ray spectroscopy data
+Copyright by Gerd Duscher
+
+The University of Tennessee, Knoxville
+Department of Materials Science & Engineering
+
+Sources:
+   
+Units:
+    everything is in SI units, except length is given in nm and angles in mrad.
+Usage:
+    See the notebooks for examples of these routines
+
+All the input and output is done through a dictionary which is to be found in the meta_data
+attribute of the sidpy.Dataset
+"""
+
+import os
+import csv
+import json
+import xml
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+import scipy
+import scipy.interpolate  # use interp1d,
+import scipy.optimize  # leastsq  # least square fitting routine fo scipy
+import sklearn  # .mixture import GaussianMixture
+
+import sidpy
+
+import pyTEMlib
+import pyTEMlib.file_reader
+from .utilities import elements as elements_list
+from .eds_xsections import quantify_cross_section, quantification_k_factors
+from .config_dir import config_path
+
+
+
+def detector_response(dataset):
+    """
+    Calculate the detector response for the given dataset based on its metadata.
+
+    Parameters:
+    - dataset: A sidpy.Dataset object containing the spectral data and metadata.
+
+    Returns:
+    - A numpy array representing the detector efficiency across the energy scale.
+    """
+    tags = dataset.metadata['EDS']
+
+    energy_scale = dataset.get_spectral_dims(return_axis=True)[0]
+    if 'start_channel' not in tags['detector']:
+        tags['detector']['start_channel'] = np.searchsorted(energy_scale, 100)
+
+    start = tags['detector']['start_channel']
+    detector_efficiency = np.zeros(len(dataset))
+    detector_efficiency[start:] += get_detector_response(tags, energy_scale[start:])
+    tags['detector']['detector_efficiency'] = detector_efficiency
+    return detector_efficiency
+
+def get_absorption(z, thickness, energy_scale):
+    """ Calculate absorption for material with atomic number z and thickness t in m"""
+    x_sections = pyTEMlib.eels_tools.get_x_sections()
+    photoabsorption = x_sections[str(z)]['dat']/1e10/x_sections[str(z)]['photoabs_to_sigma']
+    lin = scipy.interpolate.interp1d(x_sections[str(z)]['ene'], photoabsorption, kind='linear')
+    mu = lin(energy_scale) * x_sections[str(z)]['nominal_density']*100  #1/cm -> 1/m
+    return np.exp(-mu * thickness)
+
+
+def get_detector_response(detector_definition, energy_scale):
+    """
+    Calculates response of Si drift detector for EDS spectrum background based 
+    on detector parameters
+
+    Parameters:
+    ----------
+    detector_definition: dictionary
+        definition of detector
+    energy_scale: numpy array (1 dim)
+        energy scale of spectrum should start at about 100eV!!
+
+    Return:
+    -------
+    response: numpy array with length(energy_scale)
+        detector response
+
+    Example
+    -------
+
+    tags ={}
+    tags['acceleration_voltage'] = 200000
+
+    tags['detector'] ={}
+
+    ## layer thicknesses of common materials in EDS detectors in m
+    tags['detector']['layers'] = {13: {'thickness':= 0.05*1e-6, 'Z': 13, 'element': 'Al'},
+                                  6: {'thickness':= 0.15*1e-6, 'Z': 6, 'element': 'C'}
+                                  }
+    tags['detector']['SiDeadThickness'] = .13 *1e-6  # in m
+    tags['detector']['SiLiveThickness'] = 0.05  # in m
+    tags['detector']['detector_area'] = 30 * 1e-6 #in m2
+    tags['detector']['energy_resolution'] = 125  # in eV
+    tags['detector']['start_energy'] = 120  # in eV
+    tags['detector']['start_channel'] = np.searchsorted(spectrum.energy_scale.values,120)
+
+    energy_scale = np.linspace(.01, 20, 1199)*1000 # i eV
+    start = np.searchsorted(spectrum.energy, 100)
+    energy_scale = spectrum.energy[start:]
+    detector_Efficiency= pyTEMlib.eds_tools.detector_response(tags, spectrum.energy[start:])
+
+    p = np.array([1, 37, .3])/10000*3
+    E_0= 200000
+    background = np.zeros(len(spectrum))
+    bremsstrahlung =  p[0] + p[1]*(E_0-energy_scale)/energy_scale 
+    bremsstrahlung += p[2]*(E_0-energy_scale)**2/energy_scale
+    background[start:] = detector_Efficiency * bremsstrahlung
+
+    plt.figure()
+    plt.plot(spectrum.energy, spectrum, label = 'spec')
+    plt.plot(spectrum.energy, background, label = 'background')
+    plt.show()
+
+    """
+    response = np.ones(len(energy_scale))
+
+    for layer in detector_definition['detector']['layers'].values():
+        if layer['Z'] != 14:
+            response *= get_absorption(layer['Z'], layer['thickness'], energy_scale)
+    if 'SiDeadThickness' in  detector_definition['detector']:
+        response *= get_absorption(14, detector_definition['detector']['SiDeadThickness'],
+                                   energy_scale)
+    if 'SiLiveThickness' in  detector_definition['detector']:
+        response *= 1-get_absorption(14, detector_definition['detector']['SiLiveThickness'],
+                                     energy_scale)
+    return response
+
+
+def detect_peaks(dataset, minimum_number_of_peaks=30, prominence=10):
+    """
+    Detect peaks in the given spectral dataset.
+
+    Parameters:
+    -----------
+    - dataset: A sidpy.Dataset object containing the spectral data.
+    - minimum_number_of_peaks: The minimum number of peaks to detect.
+    - prominence: The prominence threshold for peak detection.
+
+    Returns:
+    --------
+    - An array of indices representing the positions of detected peaks in the spectrum.
+    """
+    if not isinstance(dataset, sidpy.Dataset):
+        raise TypeError('Needs an sidpy dataset')
+    if not dataset.data_type.name == 'SPECTRUM':
+        raise TypeError('Need a spectrum')
+
+    energy_scale = dataset.get_spectral_dims(return_axis=True)[0].values
+    if 'EDS' not in dataset.metadata:
+        dataset.metadata['EDS'] = {}
+    if 'detector' not in dataset.metadata['EDS']:
+        raise ValueError('No detector information found, add detector dictionary to metadata')
+
+    if 'energy_resolution' not in dataset.metadata['EDS']['detector']:
+        dataset.metadata['EDS']['detector']['energy_resolution'] = 138
+        print('Using energy resolution of 138 eV')
+    if 'start_channel' not in dataset.metadata['EDS']['detector']:
+        dataset.metadata['EDS']['detector']['start_channel'] =  np.searchsorted(energy_scale, 100)
+
+    resolution = dataset.metadata['EDS']['detector']['energy_resolution']
+    start = dataset.metadata['EDS']['detector']['start_channel']
+    ## we use half the width of the resolution for smearing
+    width = int(np.ceil(resolution/(energy_scale[1]-energy_scale[0])/2)+1)
+    new_spectrum =  scipy.signal.savgol_filter(np.array(dataset)[start:], width, 2)
+
+    minor_peaks, _  = scipy.signal.find_peaks(new_spectrum, prominence=prominence)
+
+    while len(minor_peaks) > minimum_number_of_peaks:
+        prominence+=10
+        minor_peaks, _  = scipy.signal.find_peaks(new_spectrum, prominence=prominence)
+    return np.array(minor_peaks)+start
+
+def peaks_element_correlation(spectrum, minor_peaks):
+    """
+    Identify elements present in the spectrum based on detected minor peaks.
+
+    Parameters:
+    - spectrum: A sidpy.Dataset object containing the spectral data.
+    - minor_peaks: An array of indices representing the positions of
+                   minor peaks in the spectrum.
+
+    Returns:
+    - A list of element symbols identified in the spectrum.
+    """
+    if not isinstance(spectrum, sidpy.Dataset):
+        raise TypeError(' Need a sidpy dataset')
+    energy_scale = spectrum.get_spectral_dims(return_axis=True)[0].values
+    element_list = set()
+    peaks = minor_peaks[np.argsort(spectrum[minor_peaks])]
+    accounted_peaks = set()
+    for i, peak in reversed(list(enumerate(peaks))):
+        for z in range(5, 82):
+            if i in accounted_peaks:
+                continue
+            edge_info  = pyTEMlib.eels_tools.get_x_sections(z)
+            # element = edge_info['name']
+            lines = edge_info.get('lines', {})
+            if abs(lines.get('K-L3', {}).get('position', 0) - energy_scale[peak]) <40:
+                element_list.add(edge_info['name'])
+                for key, line in lines.items():
+                    dist = np.abs(energy_scale[peaks]-line.get('position', 0))
+                    if key[0] == 'K' and np.min(dist)< 40:
+                        ind = np.argmin(dist)
+                        accounted_peaks.add(ind)
+            # This is a special case for boron and carbon
+            elif abs(lines.get('K-L2', {}).get('position', 0) - energy_scale[peak]) <30:
+                accounted_peaks.add(i)
+                element_list.add(edge_info['name'])
+
+            if abs(lines.get('L3-M5', {}).get('position', 0) - energy_scale[peak]) <50:
+                element_list.add(edge_info['name'])
+                for key, line in edge_info['lines'].items():
+                    dist = np.abs(energy_scale[peaks]-line.get('position', 0))
+                    if key[0] == 'L' and np.min(dist)< 40 and line['weight'] > 0.01:
+                        ind = np.argmin(dist)
+                        accounted_peaks.add(ind)
+    return list(element_list)
+
+
+def get_elements(spectrum, minimum_number_of_peaks=10, verbose=False):
+    """ Get the elments in a EDS spectrum 
+    Parameters:
+    -----------
+    minimum_number_of_peaks: int
+        approximate number of peaks in spectrum
+
+    Returns:
+    -------
+    elements: list
+        list of all elements found    
+    """
+    if not isinstance(spectrum, sidpy.Dataset):
+        raise TypeError(' Need a sidpy dataset')
+    if not isinstance(minimum_number_of_peaks, int):
+        raise TypeError(' Need an integer for minimum_number_of_peaks')
+
+    minor_peaks = detect_peaks(spectrum, minimum_number_of_peaks=minimum_number_of_peaks)
+
+    keys = list(spectrum.metadata['EDS'].keys())
+    for key in keys:
+        if len(key) < 3:
+            del spectrum.metadata['EDS'][key]
+
+    elements = peaks_element_correlation(spectrum, minor_peaks)
+    if verbose:
+        print(elements)
+    spectrum.metadata['EDS'].update(get_x_ray_lines(spectrum, elements))
+    return elements
+
+def get_x_ray_lines(spectrum, element_list):
+    """
+    Analyze the given spectrum to identify and characterize the X-ray emission lines
+    associated with the specified elements.
+
+    Parameters:
+    - spectrum: A sidpy.Dataset object containing the spectral data.
+    - elements: A list of element symbols (e.g., ['Fe', 'Cu']) to look for in the spectrum.
+
+    Returns:
+    - A dictionary where each key is an element symbol and each value is another dictionary
+      containing information about the X-ray lines detected for that element.
+    
+    alpha_k = 1e6
+    alpha_l = 6.5e7
+    alpha_m = 8*1e8  # 2.2e10
+    # My Fit
+    alpha_K = .9e6
+    alpha_l = 6.e7
+    alpha_m = 6*1e8 #  2.2e10
+    # omega_K = Z**4/(alpha_K+Z**4)
+    # omega_L = Z**4/(alpha_l+Z**4)
+    # omega_M = Z**4/(alpha_m+Z**4)
+    """
+
+    out_tags = {}
+    x_sections = pyTEMlib.xrpa_x_sections.x_sections
+    energy_scale = spectrum.get_spectral_dims(return_axis=True)[0].values
+    for element in element_list:
+        atomic_number = pyTEMlib.eds_tools.elements_list.index(element)
+        out_tags[element] ={'Z': atomic_number}
+        lines = pyTEMlib.xrpa_x_sections.x_sections.get(str(atomic_number), {}).get('lines', {})
+        if not lines:
+            break
+        line_dict = {'K': {'lines': [],
+                           'main': None,
+                           'weight': 0}, 
+                     'L': {'lines': [],
+                           'main': None,
+                           'weight': 0}, 
+                     'M': {'lines': [],
+                           'main': None,
+                           'weight': 0}}
+
+        for key, line in lines.items():
+            if key[0] in line_dict:
+                if line['position'] < energy_scale[-1]:
+                    line_dict[key[0]]['lines'].append(key)
+                    if line['weight'] > line_dict[key[0]]['weight']:
+                        line_dict[key[0]]['weight'] = line['weight']
+                        line_dict[key[0]]['main'] = key
+
+        for key, family in line_dict.items():
+            if family['weight'] > 0:
+                out_tags[element].setdefault(f'{key}-family', {}).update(family)
+                position = x_sections[str(atomic_number)]['lines'][family['main']]['position']
+                height = spectrum[np.searchsorted(energy_scale, position)].compute()
+                out_tags[element][f'{key}-family']['height'] = height/family['weight']
+                z = str(atomic_number)
+                for key in family['lines']:
+                    out_tags[element][f'{key[0]}-family'][key] = x_sections[z]['lines'][key]
+        spectrum.metadata.setdefault('EDS', {}).update(out_tags)
+    return out_tags
+
+
+def get_fwhm(energy: float, energy_ref: float, fwhm_ref: float) -> float:
+    """ Calculate FWHM of Gaussians"""
+    return np.sqrt(2.5*(energy-energy_ref)+fwhm_ref**2)
+
+
+def gaussian(energy_scale: np.ndarray, mu: float, fwhm: float) -> np.ndarray:
+    """ Gaussian function"""
+    sig = fwhm/2/np.sqrt(2*np.log(2))
+    return np.exp(-np.power(np.array(energy_scale) - mu, 2.) / (2 * np.power(sig, 2.)))
+
+
+def get_peak(energy: float, energy_scale: np.ndarray,
+             energy_ref: float = 5895.0, fwhm_ref: float = 136) -> np.ndarray:
+    """ Generate a normalized Gaussian peak for a given energy."""
+    # all energies in eV
+    fwhm  = get_fwhm(energy, energy_ref, fwhm_ref)
+    gauss = gaussian(energy_scale, energy, fwhm)
+
+    return gauss /(gauss.sum()+1e-12)
+
+
+def initial_model_parameter(spectrum):
+    """ Initialize model parameters based on the spectrum's metadata.""" 
+    tags = spectrum.metadata['EDS']
+    energy_scale = spectrum.get_spectral_dims(return_axis=True)[0]
+    p = []
+    peaks = []
+    keys = []
+    for element, lines in tags.items():
+        if 'K-family' in lines:
+            model = np.zeros(len(energy_scale))
+            for line, info in lines['K-family'].items():
+                if line[0] == 'K':
+                    model += get_peak(info['position'], energy_scale)*info['weight']
+            lines['K-family']['peaks'] = model  /model.sum()  # *lines['K-family']['probability']
+
+            p.append(lines['K-family']['height'] / lines['K-family']['peaks'].max())
+            peaks.append(lines['K-family']['peaks'])
+            keys.append(element+':K-family')
+        if 'L-family' in lines:
+            model = np.zeros(len(energy_scale))
+            for line, info in lines['L-family'].items():
+                if line[0] == 'L':
+                    model += get_peak(info['position'], energy_scale)*info['weight']
+            lines['L-family']['peaks'] = model  /model.sum() # *lines['L-family']['probability']
+            p.append(lines['L-family']['height'] / lines['L-family']['peaks'].max())
+            peaks.append(lines['L-family']['peaks'])
+            keys.append(element+':L-family')
+        if 'M-family' in lines:
+            model = np.zeros(len(energy_scale))
+            for line, info in lines['M-family'].items():
+                if line[0] == 'M':
+                    model += get_peak(info['position'], energy_scale)*info['weight']
+            peaks_max = lines['M-family'].get('peaks', np.zeros(3)).max()
+            model_normalized = model / model.sum()*lines['M-family'].get('probability', 0.0)
+            lines['M-family']['peaks'] = model_normalized
+            if peaks_max >0:
+                p.append(lines['M-family']['height'] / peaks_max)
+            else:
+                p.append(0)
+            peaks.append(lines['M-family']['peaks'])
+            keys.append(element+':M-family')
+
+    p.extend([1e7, 1e-3, 1500, 20])
+    return np.array(peaks), np.array(p), keys
+
+def get_model(spectrum):
+    """
+    Construct the model spectrum from the metadata in the given spectrum object.
+
+    Parameters:
+    - spectrum: The spectrum object containing metadata and spectral data.
+
+    Returns:
+    - model: The constructed model spectrum as a numpy array.
+    """
+    model = np.zeros(len(np.array(spectrum)))
+    for key in spectrum.metadata['EDS']:
+        if isinstance(spectrum.metadata['EDS'][key], dict) and key in elements_list:
+            for family in spectrum.metadata['EDS'][key]:
+                if '-family' in family:
+                    intensity  = spectrum.metadata['EDS'][key][family].get('areal_density', 0)
+                    peaks = spectrum.metadata['EDS'][key][family].get('peaks', np.zeros(len(model)))
+                    if peaks.sum() <0.1:
+                        print('no intensity',key, family)
+                    model += peaks * intensity
+
+    if 'detector_efficiency' in spectrum.metadata['EDS']['detector'].keys():
+        detector_efficiency = spectrum.metadata['EDS']['detector']['detector_efficiency']
+    else:
+        detector_efficiency = None
+    e_0 = spectrum.metadata['experiment']['acceleration_voltage']
+    pp = spectrum.metadata['EDS']['bremsstrahlung']
+    energy_scale = spectrum.get_spectral_dims(return_axis=True)[0].values
+
+    if detector_efficiency is not None:
+        bremsstrahlung = (pp[-3] + pp[-2] * (e_0 - energy_scale) / energy_scale +
+                          pp[-1] * (e_0 - energy_scale) ** 2 / energy_scale)
+        model += bremsstrahlung
+        model *= detector_efficiency
+    return model
+
+def fit_model(spectrum, use_detector_efficiency=False):
+    """
+    Fit the EDS spectrum using a model composed of elemental peaks and bremsstrahlung background.
+
+    Parameters:
+    - spectrum: The EDS spectrum to fit.
+    - elements: List of elements to consider in the fit.
+    - use_detector_efficiency: Whether to include detector efficiency in the model.
+
+    Returns:
+    - peaks: The fitted peak shapes.
+    - p: The fitted parameters.
+    """
+    peaks, pin, _ = initial_model_parameter(spectrum)
+
+    energy_scale = spectrum.get_spectral_dims(return_axis=True)[0].values
+
+    if 'detector' in spectrum.metadata['EDS'].keys():
+        start = spectrum.metadata['EDS'].get('detector', {}).get('start_channel', 120)
+        spectrum.metadata['EDS']['detector']['start_channel'] = np.searchsorted(energy_scale, start)
+        if use_detector_efficiency:
+            efficiency = spectrum.metadata['EDS']['detector'].get('detector_efficiency', [])
+            if not isinstance(efficiency, (list, np.ndarray)):
+                if len(efficiency) != len(spectrum):
+                    efficiency = detector_response(spectrum)
+        else:
+            use_detector_efficiency = False
+    else:
+        print('need detector information to fit spectrum')
+        return None, None
+
+    e_0 = spectrum.metadata.get('experiment', {}).get('acceleration_voltage', 0.)
+
+    def residuals(pp, yy):
+        """ residuals for fit"""
+        model = np.zeros(len(yy))
+        for i in range(len(pp)-4):
+            model += peaks[i]*pp[i]
+        if use_detector_efficiency:
+            bremsstrahlung = (pp[-3] + pp[-2] * (e_0 - energy_scale) / energy_scale +
+                              pp[-1] * (e_0 - energy_scale)**2 / energy_scale)
+            model += bremsstrahlung
+            model *= efficiency
+        err = np.abs(yy - model)  # /np.sqrt(np.abs(yy[start:])+1e-12)
+        return err
+
+    y = np.array(spectrum)  # .compute()
+    [p, _] = scipy.optimize.leastsq(residuals, pin, args=(y,), maxfev=10000)
+
+    update_fit_values(spectrum.metadata['EDS'], peaks, p)
+    return np.array(peaks), np.array(p)
+
+
+def update_fit_values(out_tags, peaks, p):
+    """
+    Update the out_tags dictionary with the fitted peak shapes and parameters.
+
+    Parameters:
+    - out_tags: Dictionary containing the initial tags for each element and line family.
+    - peaks: Array of fitted peak shapes.
+    - p: Array of fitted parameters.
+    """
+    index = 0
+    for lines in out_tags.values():
+        if 'K-family' in lines:
+            lines['K-family']['areal_density'] = p[index]
+            lines['K-family']['peaks'] = peaks[index]
+            index += 1
+        if 'L-family' in lines:
+            lines['L-family']['areal_density'] = p[index]
+            lines['L-family']['peaks'] = peaks[index]
+            index += 1
+        if 'M-family' in lines:
+            lines['M-family']['areal_density'] =p[index]
+            lines['M-family']['peaks'] = peaks[index]
+            index += 1
+    out_tags['bremsstrahlung'] = p[-4:]
+
+
+def get_phases(dataset, mode='kmeans', number_of_phases=4):
+    """
+    Perform phase segmentation on the dataset using the specified clustering mode.
+
+    Parameters:
+    - dataset: The dataset to be segmented.
+    - mode: The clustering mode to use ('kmeans' or other).
+    - number_of_phases: The number of phases (clusters) to identify.
+
+    Returns:
+    None. The results are stored in the dataset's metadata.
+    """
+    x_vec = np.array(dataset).reshape(dataset.shape[0]*dataset.shape[1], dataset.shape[2])
+    x_vec = np.divide(x_vec.T, x_vec.sum(axis=1)).T
+    if mode != 'kmeans':
+        #choose number of components
+        gmm = sklearn.mixture.GaussianMixture(n_components=number_of_phases, covariance_type="full")
+
+        gmm_results = gmm.fit(np.array(x_vec)) #we can intelligently fold the data and perform GM
+        gmm_labels = gmm_results.fit_predict(x_vec)
+
+        dataset.metadata['gaussian_mixing_model'] = {'map': gmm_labels.reshape(dataset.shape[0],
+                                                                               dataset.shape[1]),
+                                                    'covariances': gmm.covariances_,
+                                                    'weights': gmm.weights_,
+                                                    'means':  gmm_results.means_}
+    else:
+        km = sklearn.cluster.KMeans(number_of_phases, n_init =10) #choose number of clusters
+        km_results = km.fit(np.array(x_vec)) #we can intelligently fold the data and perform Kmeans
+        dataset.metadata['kmeans'] = {'map': km_results.labels_.reshape(dataset.shape[0],
+                                                                        dataset.shape[1]),
+                                      'means': km_results.cluster_centers_}
+
+def plot_phases(dataset, image=None, survey_image=None):
+    """
+    Plot the phase maps and corresponding spectra from the dataset.
+
+    Parameters:
+    - dataset: The dataset containing phase information.
+    - image: Optional. The image to overlay the phase map on.
+    - survey_image: Optional. A survey image to display alongside the phase maps.
+    """
+    if survey_image is not None:
+        ncols = 3
+    else:
+        ncols = 2
+    axis_index = 0
+    fig, axes = plt.subplots(nrows=1, ncols=ncols, figsize = (10,3))
+    if survey_image is not None:
+        im = axes[0].imshow(survey_image.T)
+        axis_index += 1
+
+    if 'kmeans' not in dataset.metadata:
+        raise ValueError('No phase information found, run get_phases first')
+    phase_spectra = dataset.metadata['kmeans']['means']
+    map_data = dataset.metadata['kmeans']['map']
+
+    cmap = plt.get_cmap('jet', len(phase_spectra))
+    im = axes[axis_index].imshow(image.T,cmap='gray')
+    im = axes[axis_index].imshow(map_data.T, cmap=cmap,vmin=np.min(map_data) - 0.5,
+                          vmax=np.max(map_data) + 0.5,alpha=0.2)
+
+    cbar = fig.colorbar(im, ax=axes[axis_index])
+    cbar.ax.set_yticks(np.arange(0, len(phase_spectra) ))
+    cbar.ax.set_ylabel("GMM Phase", fontsize = 14)
+    axis_index += 1
+    for index, spectrum in enumerate(phase_spectra):
+        axes[axis_index].plot(dataset.energy/1000, spectrum, color = cmap(index), label=str(index))
+        axes[axis_index].set_xlabel('energy (keV)')
+    plt.legend()
+    plt.tight_layout()
+    plt.show()
+    return fig
+
+
+def plot_lines(eds_quantification: dict, axis: plt.Axes):
+    """
+    Plot EDS line strengths on the given matplotlib axis.
+
+    Parameters:
+    - eds_quantification: A dictionary containing EDS line data.
+    - axis: A matplotlib Axes object where the lines will be plotted.
+    """
+    colors = plt.get_cmap('Dark2').colors # jet(np.linspace(0, 1, 10))
+
+    index = 0
+    for key, lines in eds_quantification.items():
+        color = colors[index % len(colors)]
+        if 'K-family' in lines:
+            intensity = lines['K-family']['height']
+            for line in lines['K-family']:
+                if line[0] == 'K':
+                    pos = lines['K-family'][line]['position']
+                    axis.plot([pos,pos], [0, intensity*lines['K-family'][line]['weight']],
+                              color=color)
+                    if line == lines['K-family']['main']:
+                        axis.text(pos,0, key+'\n'+line, verticalalignment='top', color=color)
+
+        if 'L-family' in lines:
+            intensity = lines['L-family']['height']
+            for line in lines['L-family']:
+                if line[0] == 'L':
+                    pos = lines['L-family'][line]['position']
+                    axis.plot([pos,pos], [0, intensity*lines['L-family'][line]['weight']],
+                              color=color)
+                    if line in [lines['L-family']['main'], 'L3-M5', 'L3-N5', 'L1-M3']:
+                        axis.text(pos,0, key+'\n'+line, verticalalignment='top', color=color)
+
+        if 'M-family' in lines:
+            intensity = lines['M-family']['height']
+            for line in lines['M-family']:
+                if line[0] == 'M':
+                    pos = lines['M-family'][line]['position']
+                    axis.plot([pos,pos],
+                              [0, intensity*lines['M-family'][line]['weight']],
+                              color=color)
+                    if line in [lines['M-family']['main'], 'M5-N7', 'M4-N6']:
+                        axis.text(pos,0, key+'\n'+line, verticalalignment='top', color=color)
+
+        index +=1
+        index = index % 10
+
+
+def get_eds_xsection(x_section, energy_scale, start_bgd, end_bgd):
+    """
+    Calculate the EDS cross-section by subtracting the background and zeroing out
+    values outside the specified energy range.
+    The processed cross-section data with background removed 
+    and values outside the energy range set to zero.
+
+    Parameters:
+    - x_section: The raw cross-section data.
+    - energy_scale: The energy scale corresponding to the cross-section data.
+    - start_bgd: The start energy for background calculation.
+    - end_bgd: The end energy for background calculation.
+
+    Returns:
+    - cross_section_core: np.array
+    """
+    background = pyTEMlib.eels_tools.power_law_background(x_section, energy_scale,
+                                                          [start_bgd, end_bgd], verbose=False)
+    cross_section_core = x_section- background[0]
+    cross_section_core[cross_section_core < 0] = 0.0
+    cross_section_core[energy_scale < end_bgd] = 0.0
+    return cross_section_core
+
+
+def add_k_factors(element_dict, element, k_factors):
+    """Add k-factors to element dictionary."""
+    family = element_dict.get('K-family', {})
+    line = k_factors.get(element, {}).get('Ka1', False)
+    if not line:
+        line = k_factors.get(element, {}).get('Ka2', False)
+    if not line:
+        family = element_dict.get('L-family', {})
+        line = k_factors.get(element, {}).get('La1', False)
+        family['k_factor'] = float(line)
+        print('using L k-factor for', element)
+    if not line:
+        family = element_dict.get('M-family', False)
+        line = k_factors.get(element, {}).get('Ma1', False)
+        if line:
+            print('using M k-factor for', element)
+    family['k_factor'] = float(line)
+
+
+def quantify_eds(spectrum, quantification_dict=None, mask=None ):
+    """Calculate quantification for EDS spectrum with either k-factors or cross sections."""
+
+    for key in spectrum.metadata['EDS']:
+        element = 0
+        if isinstance(spectrum.metadata['EDS'][key], dict) and key in elements_list:
+            element = spectrum.metadata['EDS'][key].get('Z', 0)
+        if element < 1:
+            continue
+        if quantification_dict is None:
+            quantification_dict = {}
+
+        edge_info = pyTEMlib.eels_tools.get_x_sections(element)
+        spectrum.metadata['EDS'][key]['atomic_weight'] = edge_info['atomic_weight']
+        spectrum.metadata['EDS'][key]['nominal_density'] = edge_info['nominal_density']
+
+        for family, item in edge_info['fluorescent_yield'].items():
+            if spectrum.metadata['EDS'][key].get(f"{family}-family", {}):
+                spectrum.metadata['EDS'][key][f"{family}-family"]['fluorescent_yield'] = item
+        if quantification_dict.get('metadata', {}).get('type', '') == 'k_factor':
+            k_factors = quantification_dict.get('table', {})
+            add_k_factors(spectrum.metadata['EDS'][key], key, k_factors)
+    if quantification_dict is None:
+        print('using cross sections for quantification')
+        quantify_cross_section(spectrum, mask=mask)
+    elif not isinstance(quantification_dict, dict):
+        pass
+    elif quantification_dict.get('metadata', {}).get('type', '') == 'k_factor':
+        print('using k-factors for quantification')
+        quantification_k_factors(spectrum, mask=mask)  # , quantification_dict['table'],
+    elif quantification_dict.get('metadata', {}).get('type', '') == 'cross_section':
+        print('using cross sections for quantification')
+        quantify_cross_section(spectrum, quantification_dict['table'], mask)
+    else:
+        print('using cross sections for quantification')
+        quantify_cross_section(spectrum, mask=mask)
+
+
+def read_esl_k_factors(filename, reduced=False):
+    """ Read k-factors from esl file."""
+    k_factors = {}
+    if not os.path.isfile(filename):
+        print('k-factor file not found', filename)
+        return None, 'k_factors_Bruker_15keV.json'
+    tree = xml.etree.ElementTree.parse(filename)
+    root = tree.getroot()
+    k_dict = pyTEMlib.file_reader.etree_to_dict(root)
+    k_dict = k_dict.get('TRTStandardLibrary', {})
+    k_factor_dict = (k_dict.get('ClassInstance', {}).get('CliffLorimerFactors', {}))
+    for index, item in enumerate(k_factor_dict.get('K_Factors', '').split(',')):
+        if index < 84:
+            if item.strip() != '0':
+                k_factors[elements_list[index]] = {'Ka1': float(item)}
+            else:
+                k_factors[elements_list[index]] = {}
+    for index, item in enumerate(k_factor_dict.get('L_Factors', '').split(',')):
+        if index < 84:
+            if item.strip() != '0':
+                k_factors[elements_list[index]]['La1'] =  float(item)
+    for index, item in enumerate(k_factor_dict.get('M_Factors', '').split(',')):
+        if index < 84:
+            if item.strip() != '0':
+                k_factors[elements_list[index]]['Ma1'] =  float(item)
+    primary = int(float(k_dict.get('ClassInstance', {}).get('Header', {}).get('PrimaryEnergy', 0)))
+    name = f'k_factors_Bruker_{primary}keV.json'
+    metadata = {'origin': 'pyTEMlib',
+                'source_file': filename,
+                'reduced': reduced,
+                'version': pyTEMlib.__version__,
+                'type': 'k-factors',
+                'spectroscopy': 'EDS',
+                'acceleration_voltage': primary,
+                'microscope': 'Bruker',
+                'name': name}
+    return k_factors, metadata
+
+
+def get_absorption_correction(spectrum, thickness=50):
+    """
+    Calculate absorption correction for all elements in the spectrum based on thickness t in nm
+    Updates the element in spectrum.metadata['EDS']['GUI'] dictionary
+    Parameters:
+    - spectrum: A sidpy.Dataset object containing the spectral data and metadata.
+    - t: Thickness in nm
+    Returns:
+        None
+    """
+    start_channel = np.searchsorted(spectrum.energy_scale.values, 120)
+    absorption = spectrum.energy_scale.values[start_channel:]*0.
+    take_off_angle = spectrum.metadata['EDS']['detector'].get('ElevationAngle', 0)
+    path_length = thickness *2 / np.cos(take_off_angle) * 1e-9 # /2?    in m
+    count = 1
+    for element, lines in spectrum.metadata['EDS']['GUI'].items():
+        if element in elements_list:
+            part = lines['atom%']/100
+            if part > 0.01:
+                count += 1
+                absorption += get_absorption(pyTEMlib.utilities.get_atomic_number(element),
+                                            path_length*part,
+                                            spectrum.energy_scale[start_channel:])
+
+    for element, lines in spectrum.metadata['EDS']['GUI'].items():
+        symmetry =  lines['symmetry']
+        peaks = []
+        if symmetry in spectrum.metadata['EDS'][element]:
+            peaks = spectrum.metadata['EDS'][element][symmetry].get('peaks', [])
+        if len(peaks) > 0:
+            peaks = peaks[start_channel:]
+            lines['absorption'] = (peaks * absorption / count).sum()
+            lines['thickness'] = thickness
+        else:
+            lines['absorption'] = 1.0
+            lines['thickness'] = 0.0
+
+
+def apply_absorption_correction(spectrum, thickness):
+    """ 
+    Apply Absorption Correction to Quantification
+    Updates the element in spectrum.metadata['EDS']['GUI'] dictionary
+    Parameters:
+    - spectrum: A sidpy.Dataset object containing the spectral data and metadata.
+    - thickness: Thickness in nm
+    Returns:
+        None
+    """
+    get_absorption_correction(spectrum, thickness)
+
+    atom_sum = 0.
+    weight_sum = 0.
+    for lines in spectrum.metadata['EDS']['GUI'].values():
+        atom_sum += lines.get('atom%', 0) / lines.get('absorption', 1)
+        weight_sum += lines.get('weight%', 0) / lines.get('absorption', 1)
+    for lines in spectrum.metadata['EDS']['GUI'].values():
+        absorb = lines.get('absorption', 1)
+        lines['corrected-atom%'] = lines.get('atom%', 0) / absorb / atom_sum * 100
+        lines['corrected-weight%'] = lines.get('weight%', 0) / absorb / weight_sum * 100
+
+
+def read_csv_k_factors(filename, reduced=True):
+    """ Read k-factors from csv file of ThermoFisher TEMs."""
+    k_factors = {}
+    with open(filename, newline='', encoding='utf-8') as csvfile:
+        reader = csv.reader(csvfile, delimiter=',', quotechar='|')
+        start = True
+        for row in reader:
+            if start:
+                k_column = row.index('K-factor')
+                start = False
+            else:
+                element, line = row[0].split('-')
+                if element not in k_factors:
+                    k_factors[element] = {}
+                if reduced:
+                    if line[-1:] == '1':
+                        k_factors[element][line] = row[k_column]
+                else:
+                    k_factors[element][line] = row[k_column]
+    metadata = {'origin': 'pyTEMlib',
+                'source_file': filename,
+                'reduced': reduced,
+                'microscope': 'ThermoFisher', 
+                'acceleration_voltage': 200000,
+                'version': pyTEMlib.__version__,
+                'type': 'k-factors',
+                'spectroscopy': 'EDS',
+                'name': 'k_factors_Thermo_200keV.json'}
+    return k_factors, metadata
+
+
+def convert_k_factor_file(file_name, reduced=True, new_name=None):
+    """ Convert k-factor file to a dictionary."""
+    if not os.path.isfile(file_name):
+        print('k-factor file not found', file_name)
+        return None
+    _, filename = os.path.split(file_name)
+    _, extension = os.path.splitext(filename)
+    if extension == '.csv':
+        k_factors, metadata = read_csv_k_factors(file_name, reduced=reduced)
+    elif extension == '.esl':
+        k_factors, metadata = read_esl_k_factors(file_name)
+    else:
+        print('unknown k-factor file format', extension)
+        return None
+    if new_name is None:
+        new_name = metadata['name']
+    write_k_factors(k_factors, metadata, file_name=new_name)
+    return k_factors, metadata
+
+
+def get_k_factor_files():
+    """ Get list of k-factor files in the .pyTEMlib folder."""
+    k_factor_files = []
+    for file_name in os.listdir(config_path):
+        if 'k_factors' in file_name:
+            k_factor_files.append(file_name)
+    return k_factor_files
+
+
+def write_k_factors(k_factors, metadata, file_name='k_factors.json'):
+    """ Write k-factors to a json file."""
+    file_name = os.path.join(config_path, file_name)
+    save_dict = {"table" : k_factors, "metadata" : metadata}
+    with open(file_name, "w", encoding='utf-8') as json_file:
+        json.dump(save_dict, json_file, indent=4, encoding='utf-8')
+
+
+def read_k_factors(file_name='k_factors.json'):
+    """ Read k-factors from a json file."""
+    if not os.path.isfile(os.path.join(config_path, file_name)):
+        print('k-factor file not found', file_name)
+        return None
+    with open(os.path.join(config_path, file_name), 'r', encoding='utf-8') as json_file:
+        table, metadata = json.load(json_file)
+    return table, metadata
+
+
+def load_k_factors(reduced=True):
+    """ Load k-factors from csv files in the .pyTEMlib folder."""
+    k_factors = {}
+    metadata = {}
+    data_path = os.path.join(os.path.expanduser('~'), '.pyTEMlib')
+    for file_name in os.listdir(data_path):
+        if 'k-factors' in file_name:
+            path = os.path.join(data_path, file_name)
+            k_factors, metadata = read_csv_k_factors(path, reduced=reduced)
+            metadata['type'] = 'k_factor'
+    return {'table': k_factors, 'metadata': metadata}