xarpes 0.2.1__tar.gz → 0.2.3__tar.gz

{xarpes-0.2.1 → xarpes-0.2.3}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.1
 Name: xarpes
-Version: 0.2.1
+Version: 0.2.3
 Summary: Extraction from angle resolved photoemission spectra
 Author: xARPES Developers
-Requires-Python: >=3.5
+Requires-Python: >=3.7.0
 Description-Content-Type: text/markdown
-Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3
 Requires-Dist: igor2
 Requires-Dist: jupyterlab
@@ -14,6 +14,7 @@ Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: lmfit
+Requires-Dist: xarray
 Project-URL: Documentation, https://xarpes.github.io
 
 ![xARPES](https://xarpes.github.io/_images/xarpes.svg)
@@ -114,7 +115,7 @@ It is recommended to use JupyterLab to analyse data. JupyterLab is launched usin
 
 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 free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, 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-0.2.1 → xarpes-0.2.3}/README.md

@@ -96,6 +96,6 @@ It is recommended to use JupyterLab to analyse data. JupyterLab is launched usin
 
 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 free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, version 3, 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-0.2.1 → xarpes-0.2.3}/pyproject.toml

@@ -11,10 +11,10 @@ readme = "README.md"
 license = {file = "LICENSE"}
 urls = {Documentation = "https://xarpes.github.io"}
 classifiers = [
-    "License :: OSI Approved :: GNU General Public License v2 (GPLv2)",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
     "Programming Language :: Python :: 3",
 ]
-requires-python = ">=3.5"
+requires-python = ">=3.7.0"
 dependencies = [
     "igor2",
     "jupyterlab",
@@ -23,4 +23,5 @@ dependencies = [
     "numpy",
     "scipy",
     "lmfit",
+    "xarray",
 ]

xarpes-0.2.3/xarpes/.ipynb_checkpoints/__init__-checkpoint.py

@@ -0,0 +1,8 @@
+__version__ = '0.2.2'
+
+from . import plotting
+
+from .band_map import *
+from .distributions import *
+from .functions import *
+from .plotting import *

{xarpes-0.2.1 → xarpes-0.2.3}/xarpes/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.2.1'
+__version__ = '0.2.3'
 
 from . import plotting
 

{xarpes-0.2.1 → xarpes-0.2.3}/xarpes/band_map.py

@@ -12,9 +12,49 @@
 """The band map class and allowed operations on it."""
 
 import numpy as np
+
 from .plotting import get_ax_fig_plt, add_fig_kwargs
+from .functions import fit_leastsq
 from .distributions import fermi_dirac
 
+
+class MDCs():
+    r"""
+    """
+    def __init__(self, intensities, angles, ekin, angular_resolution):
+        self.intensities = intensities
+        self.angles = angles
+        self.ekin = ekin
+        self.angular_resolution = angular_resolution
+
+    # @add_fig_kwargs
+    # def fit(self):
+    #     r"""
+    #     """
+    #     return 0
+
+ 
+    # @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):
+    
+    
+    @add_fig_kwargs
+    def plot(self, ax=None, **kwargs):
+        r"""
+        """
+        ax, fig, plt = get_ax_fig_plt(ax=ax)
+
+        ax.scatter(self.angles, self.intensities)
+        
+        ax.set_xlabel("Angle ($\degree$)")
+        ax.set_ylabel('Counts (-)')
+        
+        return fig
+        
+
 class band_map():
     r"""Class for the band map from the ARPES experiment.
 
@@ -26,7 +66,9 @@ class band_map():
         1D array of angular values for the abscissa [degrees]
     ekin : ndarray
         1D array of kinetic energy values for the ordinate [eV]
-    energy_resolution : float
+    angular_resolution : float, None
+        Angular resolution of the detector [degrees]
+    energy_resolution : float, None
         Energy resolution of the detector [eV]
     temperature : float, None
         Temperature of the sample [K]
@@ -36,11 +78,13 @@ class band_map():
         Standard deviation of kinetic energy minus work function [eV]
     """
     def __init__(self, intensities, angles, ekin, energy_resolution=None,
-                 temperature=None, hnuminphi=None, hnuminphi_std=None):
+                 angular_resolution=None, temperature=None, hnuminphi=None,
+                 hnuminphi_std=None):
         self.intensities = intensities
         self.angles = angles
         self.ekin = ekin
         self.energy_resolution = energy_resolution
+        self.angular_resolution = angular_resolution
         self.temperature = temperature
         self.hnuminphi = hnuminphi
         self.hnuminphi_std = hnuminphi_std
@@ -106,13 +150,72 @@ class band_map():
         """
         self.angles = self.angles + shift
 
+    def slice(self, angle_min, angle_max, energy_value):
+        r"""
+        Parameters
+        ----------
+        angle_min : float
+            Minimum angle of integration interval [degrees]
+        angle_max : float
+            Maximum angle of integration interval [degrees]
+            
+
+        Returns
+        -------
+        angle_range : ndarray
+            Array of size n containing the angular values
+        energy_range : ndarray
+            Array of size m containing the energy values
+        mdcs : 
+            Array of size nxm containing the MDC intensities
+        """
+        
+        energy_index = np.abs(self.ekin-energy_value).argmin()
+        angle_min_index = np.abs(self.angles-angle_min).argmin() 
+        angle_max_index = np.abs(self.angles-angle_max).argmin()
+        
+        angle_range = self.angles[angle_min_index:angle_max_index+1]
+        energy_range = self.ekin[energy_index]
+        mdcs = self.intensities[energy_index, angle_min_index:angle_max_index+1]
+
+        return mdcs, angle_range, energy_range, self.angular_resolution
+
+    
+    @add_fig_kwargs
+    def plot_band_map(self, ax=None, **kwargs):
+        r"""Plots the band map.
+        
+        Parameters
+        ----------
+
+        Other parameters
+        ----------------
+        **kwargs : dict, optional
+            Additional arguments passed on to add_fig_kwargs. See the keyword
+            table below.      
+
+        Returns
+        -------
+        fig : Matplotlib-Figure
+            Figure containing the Fermi edge fit
+        """        
+        ax, fig, plt = get_ax_fig_plt(ax=ax)
+
+        Angl, Ekin = np.meshgrid(self.angles, self.ekin)
+        mesh = ax.pcolormesh(Angl, Ekin, self.intensities, shading="auto", cmap=plt.get_cmap("bone").reversed())
+        cbar = plt.colorbar(mesh, ax=ax)
+        
+        ax.set_xlabel("Angle ($\degree$)")
+        ax.set_ylabel("$E_{\mathrm{kin}}$ (eV)")
+        
+        return fig
+    
     @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.
+        r"""Fits the Fermi edge of the band map and plots the result.
         Also sets hnuminphi, the kinetic energy minus the work function in eV.
         The fitting includes an energy convolution with an abscissa range
         expanded by 5 times the energy resolution standard deviation.
@@ -148,8 +251,6 @@ class band_map():
         fig : Matplotlib-Figure
             Figure containing the Fermi edge fit
         """
-        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))

{xarpes-0.2.1 → xarpes-0.2.3}/xarpes/distributions.py

@@ -3,6 +3,8 @@
 
 """The distributions used throughout the code."""
 
+import numpy as np
+
 class distribution:
     r"""Parent class for distributions. The class cannot be used on its own,
     but is used to instantiate unique and non-unique distributions.
@@ -27,6 +29,7 @@ class distribution:
         """
         return self._name
 
+        
 class unique_distribution(distribution):
     r"""Parent class for unique distributions, to be used one at a time, e.g.,
     during the background of an MDC fit or the Fermi-Dirac distribution.
@@ -53,6 +56,7 @@ class unique_distribution(distribution):
         """
         return self._label
 
+
 class constant(unique_distribution):
     r"""Child class for constant distributions, used e.g., during MDC fitting.
     The constant class is unique, only one instance should be used per task.
@@ -62,8 +66,8 @@ class constant(unique_distribution):
     offset : float
         The value of the distribution for the abscissa equal to 0.
     """
-    def __init__(self, offset):
-        super().__init__(name='constant')
+    def __init__(self, offset, name='constant'):
+        super().__init__(name)
         self._offset = offset
 
     @property
@@ -88,65 +92,6 @@ class constant(unique_distribution):
         """
         self._offset = x
 
-class linear(unique_distribution):
-    r"""Child cass for for linear distributions, used e.g., during MDC fitting.
-    The constant class is unique, only one instance should be used per task.
-
-    Parameters
-    ----------
-    offset : float
-        The value of the distribution for the abscissa equal to 0.
-    slope : float
-        The linear slope of the distribution w.r.t. the abscissa.
-    """
-    def __init__(self, slope, offset):
-        super().__init__(name='linear')
-        self._offset = offset
-        self._slope = slope
-
-    @property
-    def offset(self):
-        r"""Returns the offset of the linear distribution.
-
-        Returns
-        -------
-        offset : float
-            The value of the distribution for the abscissa equal to 0.
-        """
-        return self._offset
-
-    @offset.setter
-    def set_offset(self, x):
-        r"""Sets the offset of the linear distribution.
-
-        Parameters
-        ----------
-        offset : float
-            The value of the distribution for the abscissa equal to 0.
-        """
-        self._offset = x
-
-    @property
-    def slope(self):
-        r"""Returns the slope of the linear distribution.
-
-        Returns
-        -------
-        slope : float
-            The linear slope of the distribution w.r.t. the abscissa.
-        """
-        return self._slope
-
-    @slope.setter
-    def set_slope(self, x):
-        r"""Sets the slope of the linear distribution.
-
-        Parameters
-        ----------
-        slope : float
-            The linear slope of the distribution w.r.t. the abscissa.
-        """
-        self._slope = x
 
 class linear(unique_distribution):
     r"""Child cass for for linear distributions, used e.g., during MDC fitting.
@@ -159,9 +104,8 @@ class linear(unique_distribution):
     slope : float
         The linear slope of the distribution w.r.t. the abscissa.
     """
-    def __init__(self, slope, offset):
-
-        super().__init__(name='linear')
+    def __init__(self, slope, offset, name='linear'):
+        super().__init__(name)
         self._offset = offset
         self._slope = slope
 
@@ -209,6 +153,7 @@ class linear(unique_distribution):
         """
         self._slope = x
 
+
 class fermi_dirac(unique_distribution):
     r"""Child class for Fermi-Dirac (FD) distributions, used e.g., during Fermi
     edge fitting. The FD class is unique, only one instance should be used
@@ -357,7 +302,7 @@ class fermi_dirac(unique_distribution):
             1D array of the energy-convolved FD distribution [counts]
         """
         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))
@@ -387,8 +332,7 @@ class fermi_dirac(unique_distribution):
         -------
         evalf : ndarray
             1D array of the evaluated FD distribution [counts]
-        """
-        import numpy as np
+        """        
         k_B = 8.617e-5 # Boltzmann constant [eV/K]
         k_BT = self.temperature * k_B
         evalf = (self.integrated_weight
@@ -414,8 +358,8 @@ class fermi_dirac(unique_distribution):
         evalf : ndarray
             1D array of the energy-convolved FD distribution [counts]
         """
-        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))
@@ -427,4 +371,135 @@ class fermi_dirac(unique_distribution):
                              len(energy_range) + 2 * enumb)
         evalf = gaussian_filter(self.evaluate(extend),
                                 sigma=estep)[enumb:-enumb]
-        return evalf
+        return evalf
+
+
+class non_unique_distribution(distribution):
+    r"""Parent class for unique distributions, to be used one at a time, e.g.,
+    during the background of an MDC fit or the Fermi-Dirac distribution.
+
+    Parameters
+    ----------
+    label : str
+        Unique label for instances, identical to the name for unique
+        distributions. Not to be modified after instantiation.
+    """
+    def __init__(self, name, index):
+        super().__init__(name)
+        self._label = name + index
+
+    @property
+    def label(self):
+        r"""Returns the unique class label.
+
+        Returns
+        -------
+        label : str
+            Unique label for instances, identical to the name for unique
+            distributions. Not to be modified after instantiation.
+        """
+        return self._label
+
+
+class dispersion(distribution):
+    r"""Dispersions are assumed to be unique, so they need an index.
+    """
+    def __init__(self, amplitude, center, broadening, name, index):
+        super().__init__(name)
+        self._amplitude = amplitude
+        self._center = center
+        self._broadening = broadening
+        self._label = name + index
+
+    @property
+    def label(self):
+        r"""
+        """
+        return self._label
+
+    @property
+    def amplitude(self):
+        r"""
+        """
+        return self._amplitude
+
+    @amplitude.setter
+    def set_amplitude(self, x):
+        r"""
+        """
+        self._amplitude = x
+
+    @property
+    def center(self):
+        r"""
+        """
+        return self._center
+
+    @amplitude.setter
+    def set_center(self, x):
+        r"""
+        """
+        self._center = x
+
+    @property
+    def broadening(self):
+        r"""
+        """
+        return self._broadening
+
+    @broadening.setter
+    def set_broadening(self, x):
+        r"""
+        """
+        self._broadening = x
+
+
+# class spectral_linear(dispersion):
+#     r"""Class for the linear dispersion spectral function"""
+#     def __init__(self, amplitude, center, broadening, name, index):
+#         super().__init__(amplitude=amplitude, center=center,
+#                          broadening=broadening, name=name, index=index)
+    
+#     def result(self, x):
+#         r"""
+#         """
+#         dtor = np.pi/180
+#         evalf = self.amplitude / np.pi * self.broadening / ((np.sin(x*dtor)
+#               - np.sin(self.center*dtor))**2 + self.broadening**2)
+#         return evalf
+
+
+# class spectral_linear(dispersion):
+#     r"""Class for the linear dispersion spectral function"""
+#     def __init__(self, amplitude, center, broadening, bottom, side, name, 
+#                  index):
+#         super()__init__(amplitude=amplitude, center=center,
+#                          broadening=broadening, name=name, index=index)
+#         self._bottom = bottom
+#         self._side = side
+
+#     @property
+#     def bottom(self):
+#         r"""
+#         """
+#         return self._bottom
+
+#     @bottom.setter
+#     def set_bottom(self, x):
+#         r"""
+#         """
+#         self._bottom = x
+
+#     @property
+#     def side(self):
+#         r"""
+#         """
+#         return self._side
+    
+#     def result(self, x):
+#         r"""
+#         """
+#         dtor = np.pi/180
+#         evalf = self.amplitude / np.pi * self.broadening / (((np.sin(x*dtor)
+#               - np.sin(self.bottom*dtor))**2 - np.sin(self.center*dtor)**2)**2
+#               + self.broadening**2)    

{xarpes-0.2.1 → xarpes-0.2.3}/xarpes/functions.py

@@ -3,62 +3,7 @@
 
 """Separate functions mostly used in conjunction with various classes."""
 
-def download_examples():
-    """Downloads the examples folder from the xARPES code only if it does not
-    already exist. Prints executed steps and a final cleanup/failure message.
-    
-    Returns
-    -------
-    0, 1 : int
-        Returns 0 if the execution succeeds, 1 if it fails.
-    """
-    import requests
-    import zipfile
-    import os
-    import shutil
-    import io
-    
-    repo_url = 'https://github.com/xARPES/xARPES_examples'
-    output_dir = '.'  # Directory from which the function is called
-    
-    # Check if 'examples' directory already exists
-    final_examples_path = os.path.join(output_dir, 'examples')
-    if os.path.exists(final_examples_path):
-        print("Warning: 'examples' folder already exists. No download will be performed.")
-        return 1 # Exit the function if 'examples' directory exists
-
-    # Proceed with download if 'examples' directory does not exist
-    repo_parts = repo_url.replace("https://github.com/", "").rstrip('/')
-    zip_url = f"https://github.com/{repo_parts}/archive/refs/heads/main.zip"
-
-    # Make the HTTP request to download the zip file
-    print(f"Downloading {zip_url}")
-    response = requests.get(zip_url)
-    if response.status_code == 200:
-        zip_file_bytes = io.BytesIO(response.content)
-
-        with zipfile.ZipFile(zip_file_bytes, 'r') as zip_ref:
-            zip_ref.extractall(output_dir)
-
-        # Path to the extracted main folder
-        main_folder_path = os.path.join(output_dir, repo_parts.split('/')[-1] + '-main')
-        examples_path = os.path.join(main_folder_path, 'examples')
-
-        # Move the 'examples' directory to the target location if it was extracted
-        if os.path.exists(examples_path):
-            shutil.move(examples_path, final_examples_path)
-            print(f"'examples' subdirectory moved to {final_examples_path}")
-        else:
-            print("'examples' subdirectory not found in the repository.")
-
-        # Remove the rest of the extracted content
-        shutil.rmtree(main_folder_path)
-        print(f"Cleaned up temporary files in {main_folder_path}")
-        return 0
-    else:
-        print(f"Failed to download the repository. Status code: {response.status_code}")
-        return 1
-
+import numpy as np
 
 def error_function(p, xdata, ydata, function, extra_args):
     r"""The error function used inside the fit_leastsq function.
@@ -108,8 +53,8 @@ def fit_leastsq(p0, xdata, ydata, function, extra_args):
     perr_leastsq : ndarray
         Covariance matrix of the optimized parameters
     """
-    import numpy as np
     from scipy.optimize import leastsq
+    
     pfit, pcov, infodict, errmsg, success = leastsq(
         error_function, p0, args=(xdata, ydata, function, extra_args),
         full_output=1)
@@ -130,4 +75,61 @@ def fit_leastsq(p0, xdata, ydata, function, extra_args):
     pfit_leastsq = pfit
     perr_leastsq = np.array(error)
 
-    return pfit_leastsq, perr_leastsq
+    return pfit_leastsq, perr_leastsq
+    
+
+def download_examples():
+    """Downloads the examples folder from the xARPES code only if it does not
+    already exist. Prints executed steps and a final cleanup/failure message.
+    
+    Returns
+    -------
+    0, 1 : int
+        Returns 0 if the execution succeeds, 1 if it fails.
+    """
+    import requests
+    import zipfile
+    import os
+    import shutil
+    import io
+    
+    repo_url = 'https://github.com/xARPES/xARPES_examples'
+    output_dir = '.'  # Directory from which the function is called
+    
+    # Check if 'examples' directory already exists
+    final_examples_path = os.path.join(output_dir, 'examples')
+    if os.path.exists(final_examples_path):
+        print("Warning: 'examples' folder already exists. No download will be performed.")
+        return 1 # Exit the function if 'examples' directory exists
+
+    # Proceed with download if 'examples' directory does not exist
+    repo_parts = repo_url.replace("https://github.com/", "").rstrip('/')
+    zip_url = f"https://github.com/{repo_parts}/archive/refs/heads/main.zip"
+
+    # Make the HTTP request to download the zip file
+    print(f"Downloading {zip_url}")
+    response = requests.get(zip_url)
+    if response.status_code == 200:
+        zip_file_bytes = io.BytesIO(response.content)
+
+        with zipfile.ZipFile(zip_file_bytes, 'r') as zip_ref:
+            zip_ref.extractall(output_dir)
+
+        # Path to the extracted main folder
+        main_folder_path = os.path.join(output_dir, repo_parts.split('/')[-1] + '-main')
+        examples_path = os.path.join(main_folder_path, 'examples')
+
+        # Move the 'examples' directory to the target location if it was extracted
+        if os.path.exists(examples_path):
+            shutil.move(examples_path, final_examples_path)
+            print(f"'examples' subdirectory moved to {final_examples_path}")
+        else:
+            print("'examples' subdirectory not found in the repository.")
+
+        # Remove the rest of the extracted content
+        shutil.rmtree(main_folder_path)
+        print(f"Cleaned up temporary files in {main_folder_path}")
+        return 0
+    else:
+        print(f"Failed to download the repository. Status code: {response.status_code}")
+        return 1

{xarpes-0.2.1 → xarpes-0.2.3}/xarpes/plotting.py

@@ -25,6 +25,8 @@ def plot_settings(name='default'):
     mpl.rcParams['xtick.minor.size'] = 2
     mpl.rcParams['xtick.major.width'] = 0.8
     mpl.rcParams.update({'font.size': 16})
+    mpl.use('Qt5Agg') # Backend for showing plots in terminal
+    
 
 def get_ax_fig_plt(ax=None, **kwargs):
     r"""Helper function used in plot functions supporting an optional `Axes`

xarpes-0.2.1/xarpes/.ipynb_checkpoints/__init__-checkpoint.py

@@ -1,13 +0,0 @@
-__version__ = '0.1.0'
-
-from . import plotting
-
-from .band_map import *
-from .distributions import *
-from .functions import *
-from .plotting import *
-
-# from . import plotting
-# from xarpes.plotting import *
-# from xarpes.distributions import *
-# from xarpes.distributions import fermi_dirac