xarpes 0.1.0__tar.gz

xarpes-0.1.0/LICENSE

@@ -0,0 +1,339 @@
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xarpes-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: xarpes
+Version: 0.1.0
+Summary: Extraction from angle resolved photoemission spectra
+Author: xARPES Developers
+Requires-Python: >=3.5
+Description-Content-Type: text/markdown
+Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
+Classifier: Programming Language :: Python :: 3
+Requires-Dist: igor2
+Requires-Dist: jupyterlab
+Requires-Dist: jupytext
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: scipy
+Project-URL: Documentation, https://xarpes.github.io
+
+![xARPES](https://xarpes.github.io/_images/xarpes.svg)
+
+Repository for the code xARPES – extraction from angle resolved photoemission spectra.
+
+This preliminary release can only be used to fit a Fermi edge. The complete functionality will be made available soon.
+
+# Installation
+
+xARPES can be installed with `pip`:
+
+	python3 -m pip install xarpes
+
+Or with `conda`:
+
+	conda install conda-forge::xarpes
+
+More detailed instructions for installing the development version, tested for recent Ubuntu and Debian GNU/Linux, are provided below.
+
+## pip
+
+It is highly recommended to set up a pristine Python virtual environment. First, the `venv` module might have to be installed:
+
+	sudo apt install python3-venv
+
+Afterwards, one can activate a virtual environment named `<my_venv>` using:
+
+	python3 -m venv <my_venv>
+
+It has to be activated whenever installing/running xARPES:
+
+	source <my_venv>/bin/activate
+
+It is recommended to upgrade `pip` to the latest version:
+
+	python3 -m pip install --upgrade pip
+
+Finally, the installation can be performed:
+
+	git clone git@github.com:xARPES/xARPES.git
+	cd xARPES
+	python3 -m pip install -e .
+
+## conda
+
+The user is assumed to be in a pristine virtual environment provided by conda. First, download the required version for your operating system from <https://docs.anaconda.com/free/miniconda/>. For example:
+
+	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+
+Start the installation:
+
+	bash Miniconda3-latest-Linux-x86_64.sh
+
+Then scroll down the license agreement and answer `yes` to the following question:
+
+	Do you accept the license terms? [yes|no]
+
+Also specify your installation location.
+
+It is convenient to also answer `yes` to the following, which will append new lines to your `~/.bashrc`:
+
+	You can undo this by running `conda init --reverse $SHELL`? [yes|no]
+
+A conda base environment is then activated with `source ~/.bashrc` or by starting a new terminal session.
+
+Alternatively, you can answer `no` to the above question and activate conda whenever you need it:
+
+	eval "$(<your_path>/miniconda3/bin/conda shell.<your_shell> hook)"
+
+Next, we install `conda-build` for developing xARPES (answer `y` to questions):
+
+	conda install conda-build
+
+Finally, the following steps are executed for the installation &ndash; the `<my_env>` environment will have to be launched whenever running xARPES:
+
+	git clone git@github.com:xARPES/xARPES.git
+	cd xARPES
+	conda create -n <my_env> -c defaults -c conda-forge --file requirements.txt
+	conda activate <my_env>
+	conda develop .
+
+Answer `y` to questions.
+
+# Execution
+
+It is recommended to use JupyterLab to analyse data. JupyterLab is launched using:
+
+	jupyter lab
+
+# License
+
+Copyright (C) 2024 xARPES Developers
+
+This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2, as published by the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+

xarpes-0.1.0/README.md

@@ -0,0 +1,95 @@
+![xARPES](https://xarpes.github.io/_images/xarpes.svg)
+
+Repository for the code xARPES – extraction from angle resolved photoemission spectra.
+
+This preliminary release can only be used to fit a Fermi edge. The complete functionality will be made available soon.
+
+# Installation
+
+xARPES can be installed with `pip`:
+
+	python3 -m pip install xarpes
+
+Or with `conda`:
+
+	conda install conda-forge::xarpes
+
+More detailed instructions for installing the development version, tested for recent Ubuntu and Debian GNU/Linux, are provided below.
+
+## pip
+
+It is highly recommended to set up a pristine Python virtual environment. First, the `venv` module might have to be installed:
+
+	sudo apt install python3-venv
+
+Afterwards, one can activate a virtual environment named `<my_venv>` using:
+
+	python3 -m venv <my_venv>
+
+It has to be activated whenever installing/running xARPES:
+
+	source <my_venv>/bin/activate
+
+It is recommended to upgrade `pip` to the latest version:
+
+	python3 -m pip install --upgrade pip
+
+Finally, the installation can be performed:
+
+	git clone git@github.com:xARPES/xARPES.git
+	cd xARPES
+	python3 -m pip install -e .
+
+## conda
+
+The user is assumed to be in a pristine virtual environment provided by conda. First, download the required version for your operating system from <https://docs.anaconda.com/free/miniconda/>. For example:
+
+	wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+
+Start the installation:
+
+	bash Miniconda3-latest-Linux-x86_64.sh
+
+Then scroll down the license agreement and answer `yes` to the following question:
+
+	Do you accept the license terms? [yes|no]
+
+Also specify your installation location.
+
+It is convenient to also answer `yes` to the following, which will append new lines to your `~/.bashrc`:
+
+	You can undo this by running `conda init --reverse $SHELL`? [yes|no]
+
+A conda base environment is then activated with `source ~/.bashrc` or by starting a new terminal session.
+
+Alternatively, you can answer `no` to the above question and activate conda whenever you need it:
+
+	eval "$(<your_path>/miniconda3/bin/conda shell.<your_shell> hook)"
+
+Next, we install `conda-build` for developing xARPES (answer `y` to questions):
+
+	conda install conda-build
+
+Finally, the following steps are executed for the installation &ndash; the `<my_env>` environment will have to be launched whenever running xARPES:
+
+	git clone git@github.com:xARPES/xARPES.git
+	cd xARPES
+	conda create -n <my_env> -c defaults -c conda-forge --file requirements.txt
+	conda activate <my_env>
+	conda develop .
+
+Answer `y` to questions.
+
+# Execution
+
+It is recommended to use JupyterLab to analyse data. JupyterLab is launched using:
+
+	jupyter lab
+
+# License
+
+Copyright (C) 2024 xARPES Developers
+
+This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 2, as published by the Free Software Foundation.
+
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

xarpes-0.1.0/pyproject.toml

@@ -0,0 +1,25 @@
+[build-system]
+requires = ["flit_core>=3.4"]
+build-backend = "flit_core.buildapi"
+
+[project]
+name = "xarpes"
+dynamic = ["version"]
+authors = [{name = "xARPES Developers"}]
+description = "Extraction from angle resolved photoemission spectra"
+readme = "README.md"
+license = {file = "LICENSE"}
+urls = {Documentation = "https://xarpes.github.io"}
+classifiers = [
+    "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
+    "Programming Language :: Python :: 3",
+]
+requires-python = ">=3.5"
+dependencies = [
+    "igor2",
+    "jupyterlab",
+    "jupytext",
+    "matplotlib",
+    "numpy",
+    "scipy",
+]

xarpes-0.1.0/xarpes/__init__.py

@@ -0,0 +1,8 @@
+__version__ = '0.1.0'
+
+from . import plotting
+
+from .band_map import *
+from .distributions import *
+from .functions import *
+from .plotting import *

xarpes-0.1.0/xarpes/band_map.py

@@ -0,0 +1,168 @@
+# Copyright (C) 2024 xARPES Developers
+# This program is free software under the terms of the GNU GPLv2 license.
+
+# get_ax_fig_plt and add_fig_kwargs originate from pymatgen/util/plotting.py.
+# Copyright (C) 2011-2024 Shyue Ping Ong and the pymatgen Development Team
+# Pymatgen is released under the MIT License.
+
+# See also abipy/tools/plotting.py.
+# Copyright (C) 2021 Matteo Giantomassi and the AbiPy Group
+# AbiPy is free software under the terms of the GNU GPLv2 license.
+
+"""The band map class and allowed operations on it."""
+
+import numpy as np
+from .plotting import get_ax_fig_plt, add_fig_kwargs
+from .distributions import fermi_dirac
+
+class band_map():
+    r"""Class for the band map from the ARPES experiment.
+
+    Parameters
+    ----------
+    intensities : ndarray
+        2D array of counts for given (E,k) or (E,angle) pairs [counts]
+    angles : ndarray
+        1D array of angular values for the abscissa [degrees]
+    ekin : ndarray
+        1D array of kinetic energy values for the ordinate [eV]
+    energy_resolution : float
+        Energy resolution of the detector [eV]
+    temperature : float
+        Temperature of the sample [K]
+    hnuminphi : float
+        Kinetic energy minus the work function [eV]
+    """
+    def __init__(self, intensities, angles, ekin, energy_resolution=None,
+                 temperature=None, hnuminphi=None):
+
+        self.intensities = intensities
+        self.angles = angles
+        self.ekin = ekin
+        self.energy_resolution = energy_resolution
+        self.temperature = temperature
+        self.hnuminphi = hnuminphi
+
+    @property
+    def hnuminphi(self):
+        r"""Returns the photon energy minus the work function in eV.
+
+        Returns
+        -------
+        hnuminphi : float
+            Kinetic energy minus the work function [eV]
+        """
+        return self._hnuminphi
+
+    @hnuminphi.setter
+    def hnuminphi(self, hnuminphi):
+        r"""Manually sets the photon energy minus the work function in eV.
+
+        Parameters
+        ----------
+        hnuminphi : float
+            Kinetic energy minus the work function [eV]
+        """
+        self._hnuminphi = hnuminphi
+
+    def shift_angles(self, shift):
+        r"""
+        Shifts the angles by the specified amount in degrees. Used to shift
+        from the detector angle to the material angle.
+
+        Parameters
+        ----------
+        shift : float
+            Angular shift [degrees]
+        """
+        self.angles = self.angles + shift
+
+    @add_fig_kwargs
+    def fit_fermi_edge(self, hnuminphi_guess, background_guess=0.0,
+                       integrated_weight_guess=1.0, angle_min=-np.infty,
+                       angle_max=np.infty, ekin_min=-np.infty,
+                       ekin_max=np.infty, ax=None, **kwargs):
+        r"""
+        Fits the Fermi edge of the band map and plots the result.
+
+        Parameters
+        ----------
+        hnuminphi_guess : float
+            Initial guess for kinetic energy minus the work function [eV]
+        background_guess : float
+            Initial guess for background intensity [counts]
+        integrated_weight_guess : float
+            Initial guess for integrated spectral intensity [counts]
+        angle_min : float
+            Minimum angle of integration interval [degrees]
+        angle_max : float
+            Maximum angle of integration interval [degrees]
+        ekin_min : float
+            Minimum kinetic energy of integration interval [eV]
+        ekin_max : float
+            Maximum kinetic energy of integration interval [eV]
+        ax : Matplotlib-Axes / NoneType
+            Axis for plotting the Fermi edge on. Created if not provided by
+            the user.
+        **kwargs : dict, optional
+            Additional arguments passed on to add_fig_kwargs. See the keyword
+            table below.
+
+        Returns
+        -------
+        Matplotlib-Figure
+        """
+        from xarpes.functions import fit_leastsq
+
+        ax, fig, plt = get_ax_fig_plt(ax=ax)
+
+        min_angle_index = np.argmin(np.abs(self.angles - angle_min))
+        max_angle_index = np.argmin(np.abs(self.angles - angle_max))
+
+        min_ekin_index = np.argmin(np.abs(self.ekin - ekin_min))
+        max_ekin_index = np.argmin(np.abs(self.ekin - ekin_max))
+
+        energy_range = self.ekin[min_ekin_index:max_ekin_index]
+
+        integrated_intensity = np.trapz(
+            self.intensities[min_ekin_index:max_ekin_index,
+                min_angle_index:max_angle_index], axis=1)
+
+        fdir_initial = fermi_dirac(temperature=self.temperature,
+                                   hnuminphi=hnuminphi_guess,
+                                   background=background_guess,
+                                   integrated_weight=integrated_weight_guess,
+                                   name='Initial guess')
+
+        parameters = np.array(
+            [hnuminphi_guess, background_guess, integrated_weight_guess])
+
+        extra_args = (self.energy_resolution)
+
+        popt, pcov = fit_leastsq(parameters, energy_range, integrated_intensity,
+                                 fdir_initial, extra_args)
+
+        fdir_final = fermi_dirac(temperature=self.temperature,
+                                 hnuminphi=popt[0], background=popt[1],
+                                 integrated_weight=popt[2],
+                                 name='Fitted result')
+
+        self.hnuminphi = popt[0]
+
+        ax.set_xlabel(r'$E_{\mathrm{kin}}$ (-)')
+        ax.set_ylabel('Counts (-)')
+        ax.set_xlim([ekin_min, ekin_max])
+
+        ax.plot(energy_range, integrated_intensity, label='Data')
+
+        ax.plot(energy_range, fdir_initial.convolve(energy_range,
+                energy_resolution=self.energy_resolution),
+                label=fdir_initial.name)
+
+        ax.plot(energy_range, fdir_final.convolve(energy_range,
+                energy_resolution=self.energy_resolution),
+                label=fdir_final.name)
+
+        ax.legend()
+
+        return fig

xarpes-0.1.0/xarpes/distributions.py

@@ -0,0 +1,104 @@
+# Copyright (C) 2024 xARPES Developers
+# This program is free software under the terms of the GNU GPLv2 license.
+
+"""The distributions used throughout the code."""
+
+class distribution:
+    def __init__(self, name):
+        self.name = name
+
+    def dist(self):
+        return self._dist
+
+
+class unique_distribution(distribution):
+    def __init__(self, name):
+        super().__init__(name)
+        self._label = name
+
+    def label(self):
+        return self._label
+
+
+class fermi_dirac(unique_distribution):
+    def __init__(self, temperature, hnuminphi, background=0,
+                 integrated_weight=1, name='fermi_dirac'):
+
+        super().__init__(name)
+        self.temperature = temperature
+        self.hnuminphi = hnuminphi
+        self.background = background
+        self.integrated_weight = integrated_weight
+        self.name = name
+
+    def __call__(self, energy_range, hnuminphi, background, integrated_weight,
+                 energy_resolution):
+        from scipy.ndimage import gaussian_filter
+        import numpy as np
+        sigma_extend = 5 # Extend data range by "5 sigma"
+        # Conversion from FWHM to standard deviation [-]
+        fwhm_to_std = np.sqrt(8 * np.log(2))
+        k_B = 8.617e-5 # Boltzmann constant [eV/K]
+        k_BT = self.temperature * k_B
+        step_size = np.abs(energy_range[1] - energy_range[0])
+        estep = energy_resolution / (step_size * fwhm_to_std)
+        enumb = int(sigma_extend * estep)
+        extend = np.linspace(energy_range[0] - enumb * step_size,
+                             energy_range[-1] + enumb * step_size,
+                             len(energy_range) + 2 * enumb)
+        result = (integrated_weight / (1 + np.exp((extend - hnuminphi) / k_BT))
+            + background)
+        return gaussian_filter(result, sigma=estep)[enumb:-enumb]
+
+    def evaluate(self, energy_range):
+        import numpy as np
+        k_B = 8.617e-5 # Boltzmann constant [eV/K]
+        k_BT = self.temperature * k_B
+        return (self.integrated_weight
+            / (1 + np.exp((energy_range - self.hnuminphi) / k_BT))
+            + self.background)
+
+    def convolve(self, energy_range, energy_resolution):
+        import numpy as np
+        from scipy.ndimage import gaussian_filter
+        sigma_extend = 5 # Extend data range by "5 sigma"
+        # Conversion from FWHM to standard deviation [-]
+        fwhm_to_std = np.sqrt(8 * np.log(2))
+        step_size = np.abs(energy_range[1] - energy_range[0])
+        estep = energy_resolution / (step_size * fwhm_to_std)
+        enumb = int(sigma_extend * estep)
+        extend = np.linspace(energy_range[0] - enumb * step_size,
+                             energy_range[-1] + enumb * step_size,
+                             len(energy_range) + 2 * enumb)
+        return gaussian_filter(self.evaluate(extend), sigma=estep)[enumb:-enumb]
+
+
+class constant(unique_distribution):
+    def __init__(self, offset):
+        super().__init__(name='constant')
+        self._offset = offset
+
+    def offset(self):
+        return self._offset
+
+    def set_offset(self, x):
+        self._offset = x
+
+
+class linear(unique_distribution):
+    def __init__(self, slope, offset):
+        super().__init__(name='linear')
+        self._offset = offset
+        self._slope = slope
+
+    def offset(self):
+        return self._offset
+
+    def set_offset(self, x):
+        self._offset = x
+
+    def slope(self):
+        return self._slope
+
+    def set_slope(self, x):
+        self._slope = x

xarpes-0.1.0/xarpes/functions.py

@@ -0,0 +1,38 @@
+# Copyright (C) 2024 xARPES Developers
+# This program is free software under the terms of the GNU GPLv2 license.
+
+"""Separate functions used in conjunction with various classes."""
+
+import numpy as np
+from scipy.optimize import leastsq
+
+def error_function(p, x, y, function, extra_args):
+    r"""The error function used inside the fit_leastsq function.
+    """
+    return function(x, *p, extra_args) - y
+
+
+def fit_leastsq(p0, xdata, ydata, function, extra_args):
+    r"""Wrapper arround scipy.optimize.leastsq.
+    """
+    pfit, pcov, infodict, errmsg, success = leastsq(
+        error_function, p0, args=(xdata, ydata, function, extra_args),
+        full_output=1)
+
+    if (len(ydata) > len(p0)) and pcov is not None:
+        s_sq = (error_function(pfit, xdata, ydata, function,
+                               extra_args) ** 2).sum() / (len(ydata) - len(p0))
+        pcov = pcov * s_sq
+    else:
+        pcov = np.inf
+
+    error = []
+    for i in range(len(pfit)):
+        try:
+          error.append(np.absolute(pcov[i][i]) ** 0.5)
+        except:
+          error.append(0.00)
+    pfit_leastsq = pfit
+    perr_leastsq = np.array(error)
+
+    return pfit_leastsq, perr_leastsq

xarpes-0.1.0/xarpes/plotting.py

@@ -0,0 +1,145 @@
+# Copyright (C) 2024 xARPES Developers
+# This program is free software under the terms of the GNU GPLv2 license.
+
+# get_ax_fig_plt and add_fig_kwargs originate from pymatgen/util/plotting.py.
+# Copyright (C) 2011-2024 Shyue Ping Ong and the pymatgen Development Team
+# pymatgen is released under the MIT License.
+
+# See also abipy/tools/plotting.py.
+# Copyright (C) 2021 Matteo Giantomassi and the AbiPy Group
+# AbiPy is free software under the terms of the GNU GPLv2 license.
+
+"""Functions related to plotting."""
+
+from functools import wraps
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+
+def my_plot_settings(name='default'):
+    mpl.rc('xtick', labelsize=10, direction='in')
+    mpl.rc('ytick', labelsize=10, direction='in')
+    lw = dict(default=2.0, large=4.0)[name]
+    mpl.rcParams['lines.linewidth'] = lw
+    mpl.rcParams['lines.markersize'] = 3
+    mpl.rcParams['xtick.major.size'] = 4
+    mpl.rcParams['xtick.minor.size'] = 2
+    mpl.rcParams['xtick.major.width'] = 0.8
+    mpl.rcParams.update({'font.size': 16})
+
+
+def get_ax_fig_plt(ax=None, **kwargs):
+    r"""Helper function used in plot functions supporting an optional Axes
+    argument. If ax is None, we build the `matplotlib` figure and create the
+    Axes else. We return the current active figure.
+
+    Args:
+        ax (Axes, optional): Axes object. Defaults to None.
+        kwargs: keyword arguments are passed to plt.figure if ax is not None.
+
+      Returns:
+        ax: :class:`Axes` object
+        figure: matplotlib figure
+        plt: matplotlib pyplot module.
+    """
+    if ax is None:
+        fig = plt.figure(**kwargs)
+        ax = fig.gca()
+    else:
+        fig = plt.gcf()
+
+    return ax, fig, plt
+
+
+def add_fig_kwargs(func):
+    """Decorator that adds keyword arguments for functions returning matplotlib
+    figures.
+
+    The function should return either a matplotlib figure or None to signal
+    some sort of error/unexpected event.
+    """
+    @wraps(func)
+    def wrapper(*args, **kwargs):
+        # pop the kwds used by the decorator.
+        title = kwargs.pop('title', None)
+        size_kwargs = kwargs.pop('size_kwargs', None)
+        show = kwargs.pop('show', True)
+        savefig = kwargs.pop('savefig', None)
+        tight_layout = kwargs.pop('tight_layout', False)
+        ax_grid = kwargs.pop('ax_grid', None)
+        ax_annotate = kwargs.pop('ax_annotate', None)
+        fig_close = kwargs.pop('fig_close', False)
+
+        # Call func and return immediately if None is returned.
+        fig = func(*args, **kwargs)
+        if fig is None:
+            return fig
+
+        # Operate on matplotlib figure.
+        if title is not None:
+            fig.suptitle(title)
+
+        if size_kwargs is not None:
+            fig.set_size_inches(size_kwargs.pop('w'), size_kwargs.pop('h'),
+                                **size_kwargs)
+
+        if ax_grid is not None:
+            for ax in fig.axes:
+                ax.grid(bool(ax_grid))
+
+        if ax_annotate:
+            tags = ascii_letters
+            if len(fig.axes) > len(tags):
+                tags = (1 + len(ascii_letters) // len(fig.axes)) * ascii_letters
+            for ax, tag in zip(fig.axes, tags):
+                ax.annotate(f'({tag})', xy=(0.05, 0.95),
+                            xycoords='axes fraction')
+
+        if tight_layout:
+            try:
+                fig.tight_layout()
+            except Exception as exc:
+                # For some unknown reason, this problem shows up only on travis.
+                # https://stackoverflow.com/questions/22708888/valueerror-when-using-matplotlib-tight-layout
+                print('Ignoring Exception raised by fig.tight_layout\n',
+                      str(exc))
+
+        if savefig:
+            fig.savefig(savefig)
+
+        if show:
+            plt.show()
+        if fig_close:
+            plt.close(fig=fig)
+
+        return fig
+
+    # Add docstring to the decorated method.
+    doc_str = """\n\n
+        Keyword arguments controlling the display of the figure:
+
+        ================  ====================================================
+        kwargs            Meaning
+        ================  ====================================================
+        title             Title of the plot (Default: None).
+        show              True to show the figure (default: True).
+        savefig           "abc.png" or "abc.eps" to save the figure to a file.
+        size_kwargs       Dictionary with options passed to fig.set_size_inches
+                          e.g. size_kwargs=dict(w=3, h=4)
+        tight_layout      True to call fig.tight_layout (default: False)
+        ax_grid           True (False) to add (remove) grid from all axes in fig.
+                          Default: None i.e. fig is left unchanged.
+        ax_annotate       Add labels to  subplots e.g. (a), (b).
+                          Default: False
+        fig_close         Close figure. Default: False.
+        ================  ====================================================
+
+"""
+
+    if wrapper.__doc__ is not None:
+        # Add s at the end of the docstring.
+        wrapper.__doc__ += f'\n{doc_str}'
+    else:
+        # Use s
+        wrapper.__doc__ = doc_str
+
+    return wrapper