xarpes 0.2.3__tar.gz → 0.2.4__tar.gz

{xarpes-0.2.3 → xarpes-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: xarpes
-Version: 0.2.3
+Version: 0.2.4
 Summary: Extraction from angle resolved photoemission spectra
 Author: xARPES Developers
 Requires-Python: >=3.7.0
@@ -15,6 +15,7 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: lmfit
 Requires-Dist: xarray
+Requires-Dist: pyqt5
 Project-URL: Documentation, https://xarpes.github.io
 
 ![xARPES](https://xarpes.github.io/_images/xarpes.svg)

{xarpes-0.2.3 → xarpes-0.2.4}/pyproject.toml

@@ -24,4 +24,5 @@ dependencies = [
     "scipy",
     "lmfit",
     "xarray",
+    "pyqt5",
 ]

{xarpes-0.2.3 → xarpes-0.2.4}/xarpes/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.2.3'
+__version__ = '0.2.4'
 
 from . import plotting
 

{xarpes-0.2.3 → xarpes-0.2.4}/xarpes/band_map.py

@@ -17,7 +17,6 @@ from .plotting import get_ax_fig_plt, add_fig_kwargs
 from .functions import fit_leastsq
 from .distributions import fermi_dirac
 
-
 class MDCs():
     r"""
     """
@@ -33,14 +32,12 @@ class MDCs():
     #     """
     #     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):
-    
-    
+    #                    integrated_weight_guess=1.0, angle_min=-np.inf,
+    #                    angle_max=np.inf, ekin_min=-np.inf,
+    #                    ekin_max=np.inf, ax=None, **kwargs):
+
     @add_fig_kwargs
     def plot(self, ax=None, **kwargs):
         r"""
@@ -48,12 +45,11 @@ class MDCs():
         ax, fig, plt = get_ax_fig_plt(ax=ax)
 
         ax.scatter(self.angles, self.intensities)
-        
-        ax.set_xlabel("Angle ($\degree$)")
+
+        ax.set_xlabel('Angle ($\degree$)')
         ax.set_ylabel('Counts (-)')
-        
+
         return fig
-        
 
 class band_map():
     r"""Class for the band map from the ARPES experiment.
@@ -158,7 +154,6 @@ class band_map():
             Minimum angle of integration interval [degrees]
         angle_max : float
             Maximum angle of integration interval [degrees]
-            
 
         Returns
         -------
@@ -166,25 +161,25 @@ class band_map():
             Array of size n containing the angular values
         energy_range : ndarray
             Array of size m containing the energy values
-        mdcs : 
+        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_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]
+        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
         ----------
 
@@ -192,29 +187,30 @@ class band_map():
         ----------------
         **kwargs : dict, optional
             Additional arguments passed on to add_fig_kwargs. See the keyword
-            table below.      
+            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())
+        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)")
-        
+
+        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):
+                       integrated_weight_guess=1.0, angle_min=-np.inf,
+                       angle_max=np.inf, ekin_min=-np.inf,
+                       ekin_max=np.inf, ax=None, **kwargs):
         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
@@ -303,4 +299,4 @@ class band_map():
 
         ax.legend()
 
-        return fig
+        return fig

{xarpes-0.2.3 → xarpes-0.2.4}/xarpes/distributions.py

@@ -29,7 +29,6 @@ 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.
@@ -56,7 +55,6 @@ 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.
@@ -92,7 +90,6 @@ 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.
@@ -153,7 +150,6 @@ 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
@@ -302,7 +298,7 @@ class fermi_dirac(unique_distribution):
             1D array of the energy-convolved FD distribution [counts]
         """
         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))
@@ -332,7 +328,7 @@ class fermi_dirac(unique_distribution):
         -------
         evalf : ndarray
             1D array of the evaluated FD distribution [counts]
-        """        
+        """
         k_B = 8.617e-5 # Boltzmann constant [eV/K]
         k_BT = self.temperature * k_B
         evalf = (self.integrated_weight
@@ -359,7 +355,7 @@ class fermi_dirac(unique_distribution):
             1D array of the energy-convolved FD distribution [counts]
         """
         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))
@@ -373,7 +369,6 @@ class fermi_dirac(unique_distribution):
                                 sigma=estep)[enumb:-enumb]
         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.
@@ -400,7 +395,6 @@ class non_unique_distribution(distribution):
         """
         return self._label
 
-
 class dispersion(distribution):
     r"""Dispersions are assumed to be unique, so they need an index.
     """
@@ -453,13 +447,12 @@ class dispersion(distribution):
         """
         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"""
 #         """
@@ -468,10 +461,9 @@ class dispersion(distribution):
 #               - 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, 
+#     def __init__(self, amplitude, center, broadening, bottom, side, name,
 #                  index):
 #         super()__init__(amplitude=amplitude, center=center,
 #                          broadening=broadening, name=name, index=index)
@@ -495,11 +487,11 @@ class dispersion(distribution):
 #         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)    
+#               + self.broadening**2)

{xarpes-0.2.3 → xarpes-0.2.4}/xarpes/functions.py

@@ -29,7 +29,6 @@ def error_function(p, xdata, ydata, function, extra_args):
     residual = function(xdata, *p, extra_args) - ydata
     return residual
 
-
 def fit_leastsq(p0, xdata, ydata, function, extra_args):
     r"""Wrapper arround scipy.optimize.leastsq.
 
@@ -54,7 +53,7 @@ def fit_leastsq(p0, xdata, ydata, function, extra_args):
         Covariance matrix of the optimized parameters
     """
     from scipy.optimize import leastsq
-    
+
     pfit, pcov, infodict, errmsg, success = leastsq(
         error_function, p0, args=(xdata, ydata, function, extra_args),
         full_output=1)
@@ -76,12 +75,11 @@ def fit_leastsq(p0, xdata, ydata, function, extra_args):
     perr_leastsq = np.array(error)
 
     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
@@ -92,22 +90,23 @@ def download_examples():
     import os
     import shutil
     import io
-    
+
     repo_url = 'https://github.com/xARPES/xARPES_examples'
-    output_dir = '.'  # Directory from which the function is called
-    
+    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.")
+        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"
+    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}")
+    print(f'Downloading {zip_url}')
     response = requests.get(zip_url)
     if response.status_code == 200:
         zip_file_bytes = io.BytesIO(response.content)
@@ -116,10 +115,12 @@ def download_examples():
             zip_ref.extractall(output_dir)
 
         # Path to the extracted main folder
-        main_folder_path = os.path.join(output_dir, repo_parts.split('/')[-1] + '-main')
+        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
+        # Move the 'examples' directory to the target location
         if os.path.exists(examples_path):
             shutil.move(examples_path, final_examples_path)
             print(f"'examples' subdirectory moved to {final_examples_path}")
@@ -128,8 +129,9 @@ def download_examples():
 
         # Remove the rest of the extracted content
         shutil.rmtree(main_folder_path)
-        print(f"Cleaned up temporary files in {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
+        print(f'Failed to download the repository. Status code: \
+                {response.status_code}')
+        return 1

{xarpes-0.2.3 → xarpes-0.2.4}/xarpes/plotting.py

@@ -26,7 +26,6 @@ def plot_settings(name='default'):
     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`