xarpes 0.3.3__tar.gz → 0.3.4__tar.gz

{xarpes-0.3.3 → xarpes-0.3.4}/PKG-INFO

@@ -1,12 +1,13 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: xarpes
-Version: 0.3.3
+Version: 0.3.4
 Summary: Extraction from angle resolved photoemission spectra
 Author: xARPES Developers
 Requires-Python: >=3.7.0
 Description-Content-Type: text/markdown
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Programming Language :: Python :: 3
+License-File: LICENSE
 Requires-Dist: igor2>=0.5.8
 Requires-Dist: jupyterlab
 Requires-Dist: jupytext
@@ -15,7 +16,8 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: lmfit
 Requires-Dist: pyqt5
-Requires-Dist: ipympl
+Requires-Dist: ipympl>=0.9.3
+Requires-Dist: ipywidgets>=8.1.5
 Requires-Dist: ipykernel<6.32.0
 Project-URL: Documentation, https://xarpes.github.io
 
@@ -31,7 +33,7 @@ This project is currently undergoing **beta testing**. Some of the functionaliti
 
 # Contributing
 
-Contributions to the code are most welcome. xARPES is intended to co-develop alongside the increasing complexity of experimental ARPES data sets. Contributions can be made by forking the code and creating a pull request. Importing of file formats from different beamlines is particularly encouraged.
+Contributions to the code are most welcome. xARPES is intended to co-develop alongside the increasing complexity of experimental ARPES data sets. Contributions can be made by forking the code and creating a pull request. Importing of file formats from different beamlines is particularly encouraged. Files useful for developers can be found in `/dev_tools`, such as the `Rmd2py.py` script for the development of examples.
 
 # Installation
 
@@ -40,6 +42,8 @@ xARPES installation can be divided into graphical package manager instructions,
 - via conda-forge, out-of-the-box or editable installation, sourcing the [conda-forge package](https://anaconda.org/conda-forge/xarpes).  
 - via Pip, out-of-the-box or editable installation, sourcing the [PyPI package](https://pypi.org/project/xarpes).
 
+We strongly recommend installing xARPES in a (conda/pip) virtual environment, and to activate the environment each time before activating xARPES.
+
 ## Graphical package manager installation
 
 Most IDEs and scientific Python distributions include a GUI-based package manager.  
@@ -82,11 +86,13 @@ Example for Linux:
     wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh  
     bash Miniconda3-latest-Linux-x86_64.sh
 
-Create and activate an environment:
+Answer `y` to questions. Create and activate a new environment:
 
     conda create -n <my_env> -c defaults -c conda-forge  
     conda activate <my_env>
 
+Where `<my_env>` must be replaced by your desired name.
+
 ### Installing xARPES
 
 #### Option A — Out-of-the-box installation (from conda-forge)
@@ -116,8 +122,8 @@ Install venv if necessary:
 
 Create and activate a virtual environment:
 
-    python3 -m venv <my_venv>  
-    source <my_venv>/bin/activate
+    python3 -m venv <my_env>  
+    source <my_env>/bin/activate
 
 Upgrade pip:
 
@@ -146,6 +152,8 @@ After installation of xARPES, the `examples/` folder can be downloaded to the cu
 
     python -c "import xarpes; xarpes.download_examples()"
 
+This attempts to download the examples from the version corresponding encountered in `__init__.py`. If no corresponding tagged version can be downloaded, the code attempts to download the latest examples instead.
+
 # Execution
 
 It is recommended to use JupyterLab to analyse data. JupyterLab is launched using:

{xarpes-0.3.3 → xarpes-0.3.4}/README.md

@@ -10,7 +10,7 @@ This project is currently undergoing **beta testing**. Some of the functionaliti
 
 # Contributing
 
-Contributions to the code are most welcome. xARPES is intended to co-develop alongside the increasing complexity of experimental ARPES data sets. Contributions can be made by forking the code and creating a pull request. Importing of file formats from different beamlines is particularly encouraged.
+Contributions to the code are most welcome. xARPES is intended to co-develop alongside the increasing complexity of experimental ARPES data sets. Contributions can be made by forking the code and creating a pull request. Importing of file formats from different beamlines is particularly encouraged. Files useful for developers can be found in `/dev_tools`, such as the `Rmd2py.py` script for the development of examples.
 
 # Installation
 
@@ -19,6 +19,8 @@ xARPES installation can be divided into graphical package manager instructions,
 - via conda-forge, out-of-the-box or editable installation, sourcing the [conda-forge package](https://anaconda.org/conda-forge/xarpes).  
 - via Pip, out-of-the-box or editable installation, sourcing the [PyPI package](https://pypi.org/project/xarpes).
 
+We strongly recommend installing xARPES in a (conda/pip) virtual environment, and to activate the environment each time before activating xARPES.
+
 ## Graphical package manager installation
 
 Most IDEs and scientific Python distributions include a GUI-based package manager.  
@@ -61,11 +63,13 @@ Example for Linux:
     wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh  
     bash Miniconda3-latest-Linux-x86_64.sh
 
-Create and activate an environment:
+Answer `y` to questions. Create and activate a new environment:
 
     conda create -n <my_env> -c defaults -c conda-forge  
     conda activate <my_env>
 
+Where `<my_env>` must be replaced by your desired name.
+
 ### Installing xARPES
 
 #### Option A — Out-of-the-box installation (from conda-forge)
@@ -95,8 +99,8 @@ Install venv if necessary:
 
 Create and activate a virtual environment:
 
-    python3 -m venv <my_venv>  
-    source <my_venv>/bin/activate
+    python3 -m venv <my_env>  
+    source <my_env>/bin/activate
 
 Upgrade pip:
 
@@ -125,6 +129,8 @@ After installation of xARPES, the `examples/` folder can be downloaded to the cu
 
     python -c "import xarpes; xarpes.download_examples()"
 
+This attempts to download the examples from the version corresponding encountered in `__init__.py`. If no corresponding tagged version can be downloaded, the code attempts to download the latest examples instead.
+
 # Execution
 
 It is recommended to use JupyterLab to analyse data. JupyterLab is launched using:

{xarpes-0.3.3 → xarpes-0.3.4}/examples/graphene/graphene.Rmd

@@ -48,8 +48,7 @@ data_file_path = os.path.join(script_dir, dfld, flnm + extn)
 ```{python}
 # %matplotlib inline
 
-fig = plt.figure(figsize=(8, 5))
-ax = fig.gca()
+fig = plt.figure(figsize=(8, 5)); ax = fig.gca()
 
 bmap = xarpes.BandMap(data_file_path, energy_resolution=0.01,
                       angle_resolution=0.1, temperature=50)
@@ -124,9 +123,8 @@ fig = mdcs.visualize_guess(distributions=guess_dists, energy_value=energy_value,
 ```
 
 #### Note on interactive figures
-- Operability of the interactive figure is sensitive to configuration of the plotting backend.
-- With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
-- As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+- The interactive figure might not work inside the Jupyter notebooks, despite our best efforts to ensure stability.
+- As a fallback, the user may switch from "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
 
 ```{python}
 # %matplotlib widget
@@ -180,7 +178,7 @@ from xarpes.constants import stdv
 
 ax.errorbar(self_energy.enel_range, self_energy.imag, 
             yerr=stdv * self_energy.imag_sigma, label =r"$-\Sigma''(E)$")
-ax.errorbar(self_energy.enel_range, self_energy.real, 
+ax.errorbar(self_energy.enel_range, self_energy.real,
             yerr=stdv * self_energy.real_sigma, label =r"$\Sigma'(E)$")
 ax.set_xlabel(r'$E-\mu$ (eV)'); ax.set_ylabel(r"$\Sigma'(E), -\Sigma''(E)$ (eV)")
 
@@ -202,8 +200,7 @@ xarpes.SpectralLinear(amplitude=450, peak=-7.25, broadening=0.01,
                       name='Linear_left', index='1'),
 ])
 
-fig = plt.figure(figsize=(8, 6))
-ax = fig.gca()
+fig = plt.figure(figsize=(8, 6)); ax = fig.gca()
 
 fig = mdc2.visualize_guess(distributions=guess_dists2, energy_value=0, ax=ax)
 ```
@@ -213,11 +210,71 @@ fig = mdc2.visualize_guess(distributions=guess_dists2, energy_value=0, ax=ax)
 
 fig = mdc2.fit_selection(distributions=guess_dists2, show=False, fig_close=True)
 
-self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_1'))
+self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_1',
+fermi_velocity=-2.67, fermi_wavevector=-0.354))
+```
+
+```{python}
+import numpy as np
+
+from xarpes.constants import dtor, pref
+
+Angl, Ekin = np.meshgrid(bmap.angles, bmap.ekin)
+Mome = np.sqrt(Ekin / pref) * np.sin(Angl * dtor)
+
+kmin, kmax = np.min(Mome), np.max(Mome)
+
+kspc = np.linspace(kmin, kmax, len(bmap.angles))
+
+dis1 = self_energy.fermi_velocity * (kspc - self_energy.fermi_wavevector)
+
+dis2 = self_left.fermi_velocity *(kspc - self_left.fermi_wavevector)
+```
+
+```{python}
+# ax.set_xlim([np.min(Mome), np.max(Mome)])
+# ax.set_ylim([np.min(Ekin - bmap.hnuminphi), np.max(Ekin - bmap.hnuminphi)])
+
+from importlib import reload
+import xarpes
+reload(xarpes)
+
+# %matplotlib inline
+
+fig = plt.figure(figsize=(8, 5))
+ax = fig.gca()
+
+self_energies= xarpes.CreateSelfEnergies([
+    self_energy, 
+    self_left
+    ])
+
+fig = bmap.plot(abscissa='momentum', ordinate='electron_energy',
+                self_energies=self_energies,  ax=ax, markersize=1.0)
 ```
 
 ```{python}
+# %matplotlib inline
+
+fig = plt.figure(figsize=(8, 5))
+ax = fig.gca()
+
+from xarpes.constants import stdv
+
+ax.errorbar(self_left.mdc_maxima, self_left.enel_range, 
+            xerr=stdv * self_left.peak_positions_sigma,
+           markersize=2, color='tab:red', label=self_left.label)
+
+ax.errorbar(self_energy.mdc_maxima, self_energy.enel_range, 
+            xerr=stdv * self_energy.peak_positions_sigma,
+           markersize=2, color='tab:blue', label=self_energy.label)
 
+ax.plot(kspc, dis1, linestyle='--'); ax.plot(kspc, dis2, linestyle='--')
+
+ax.set_xlim([np.min(Mome), np.max(Mome)])
+ax.set_ylim([np.min(Ekin - bmap.hnuminphi), np.max(Ekin - bmap.hnuminphi)])
+
+fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 ```
 
 ```{python}
@@ -413,4 +470,6 @@ self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_
 # ax = fig.gca()
 
 # fig = mdcs.plot(distributions=guess_dists, ax=ax, energy_value=-0.003)
+
+
 ```

{xarpes-0.3.3 → xarpes-0.3.4}/examples/graphene/graphene.py

@@ -28,8 +28,7 @@ extn = '.ibw'         # Extension of the file
 data_file_path = os.path.join(script_dir, dfld, flnm + extn)
 
 
-fig = plt.figure(figsize=(8, 5))
-ax = fig.gca()
+fig = plt.figure(figsize=(8, 5)); ax = fig.gca()
 
 bmap = xarpes.BandMap(data_file_path, energy_resolution=0.01,
                       angle_resolution=0.1, temperature=50)
@@ -94,9 +93,8 @@ ax = fig.gca()
 fig = mdcs.visualize_guess(distributions=guess_dists, energy_value=energy_value, ax=ax)
 
 # #### Note on interactive figures
-# - Operability of the interactive figure is sensitive to configuration of the plotting backend.
-# - With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
-# - As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+# - The interactive figure might not work inside the Jupyter notebooks, despite our best efforts to ensure stability.
+# - As a fallback, the user may switch from "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
 
 
 fig = plt.figure(figsize=(7, 5))
@@ -136,7 +134,7 @@ from xarpes.constants import stdv
 
 ax.errorbar(self_energy.enel_range, self_energy.imag, 
             yerr=stdv * self_energy.imag_sigma, label =r"$-\Sigma''(E)$")
-ax.errorbar(self_energy.enel_range, self_energy.real, 
+ax.errorbar(self_energy.enel_range, self_energy.real,
             yerr=stdv * self_energy.real_sigma, label =r"$\Sigma'(E)$")
 ax.set_xlabel(r'$E-\mu$ (eV)'); ax.set_ylabel(r"$\Sigma'(E), -\Sigma''(E)$ (eV)")
 
@@ -155,8 +153,7 @@ xarpes.SpectralLinear(amplitude=450, peak=-7.25, broadening=0.01,
                       name='Linear_left', index='1'),
 ])
 
-fig = plt.figure(figsize=(8, 6))
-ax = fig.gca()
+fig = plt.figure(figsize=(8, 6)); ax = fig.gca()
 
 fig = mdc2.visualize_guess(distributions=guess_dists2, energy_value=0, ax=ax)
 
@@ -164,10 +161,64 @@ fig = mdc2.visualize_guess(distributions=guess_dists2, energy_value=0, ax=ax)
 
 fig = mdc2.fit_selection(distributions=guess_dists2, show=False, fig_close=True)
 
-self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_1'))
+self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_1',
+fermi_velocity=-2.67, fermi_wavevector=-0.354))
+
+import numpy as np
+
+from xarpes.constants import dtor, pref
+
+Angl, Ekin = np.meshgrid(bmap.angles, bmap.ekin)
+Mome = np.sqrt(Ekin / pref) * np.sin(Angl * dtor)
+
+kmin, kmax = np.min(Mome), np.max(Mome)
+
+kspc = np.linspace(kmin, kmax, len(bmap.angles))
+
+dis1 = self_energy.fermi_velocity * (kspc - self_energy.fermi_wavevector)
+
+dis2 = self_left.fermi_velocity *(kspc - self_left.fermi_wavevector)
+
+# ax.set_xlim([np.min(Mome), np.max(Mome)])
+# ax.set_ylim([np.min(Ekin - bmap.hnuminphi), np.max(Ekin - bmap.hnuminphi)])
+
+from importlib import reload
+import xarpes
+reload(xarpes)
+
+
+fig = plt.figure(figsize=(8, 5))
+ax = fig.gca()
+
+self_energies= xarpes.CreateSelfEnergies([
+    self_energy, 
+    self_left
+    ])
 
+fig = bmap.plot(abscissa='momentum', ordinate='electron_energy',
+                self_energies=self_energies,  ax=ax, markersize=1.0)
 
 
+fig = plt.figure(figsize=(8, 5))
+ax = fig.gca()
+
+from xarpes.constants import stdv
+
+ax.errorbar(self_left.mdc_maxima, self_left.enel_range, 
+            xerr=stdv * self_left.peak_positions_sigma,
+           markersize=2, color='tab:red', label=self_left.label)
+
+ax.errorbar(self_energy.mdc_maxima, self_energy.enel_range, 
+            xerr=stdv * self_energy.peak_positions_sigma,
+           markersize=2, color='tab:blue', label=self_energy.label)
+
+ax.plot(kspc, dis1, linestyle='--'); ax.plot(kspc, dis2, linestyle='--')
+
+ax.set_xlim([np.min(Mome), np.max(Mome)])
+ax.set_ylim([np.min(Ekin - bmap.hnuminphi), np.max(Ekin - bmap.hnuminphi)])
+
+fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
+
 
 
 
@@ -329,3 +380,5 @@ self_left = xarpes.SelfEnergy(*mdc2.expose_parameters(select_label='Linear_left_
 # ax = fig.gca()
 
 # fig = mdcs.plot(distributions=guess_dists, ax=ax, energy_value=-0.003)
+
+

{xarpes-0.3.3 → xarpes-0.3.4}/examples/srtio3/srtio3.Rmd

@@ -29,7 +29,7 @@ import os
 xarpes.plot_settings('default')
 
 # If needed, close figures before running other cells, if figures show up in the wrong places.
-get_ipython().events.register('pre_run_cell', lambda info: plt.close('all'))
+# get_ipython().events.register('pre_run_cell', lambda info: plt.close('all'))
 ```
 
 ```{python}
@@ -71,9 +71,7 @@ print('The optimised h nu - Phi = ' + f'{bmap.hnuminphi:.4f}' + ' +/- '
 ```{python}
 # %matplotlib inline
 
-from xarpes.constants import dtor
-
-k_0 = -0.0014
+k_0 = -0.0014 # 0.02
 theta_0 = 0
 
 guess_dists = xarpes.CreateDistributions([
@@ -86,7 +84,7 @@ xarpes.SpectralQuadratic(amplitude=1800, peak=-3.6, broadening=0.0004,
 
 import numpy as np
 
-mat_el = lambda x: np.sin((x - theta_0) * dtor) ** 2
+mat_el = lambda x: np.sin((x - theta_0) * xarpes.dtor) ** 2
 
 mat_args = {}
 
@@ -104,9 +102,8 @@ fig = mdcs.visualize_guess(distributions=guess_dists, matrix_element=mat_el,
 ```
 
 #### Note on interactive figures
-- Operability of the interactive figure is sensitive to configuration of the plotting backend.
-- With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
-- As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+- The interactive figure might not work inside the Jupyter notebooks, despite our best efforts to ensure stability.
+- As a fallback, the user may switch from "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
 
 ```{python}
 # %matplotlib widget
@@ -128,8 +125,10 @@ fig = mdcs.fit_selection(distributions=guess_dists, matrix_element=mat_el,
 - Instead, the user is advised to carefully check correspondence of peak maxima with MDC fitting results.
 
 ```{python}
+fermi_one = 0.142
+
 self_energy = xarpes.SelfEnergy(*mdcs.expose_parameters(select_label='Inner_band_1', 
-                                bare_mass=0.6, fermi_wavevector=0.142, side='right'))
+                                bare_mass=0.6, fermi_wavevector=fermi_one, side='right'))
 
 self_two = xarpes.SelfEnergy(*mdcs.expose_parameters(select_label='Outer_band_2',
                                 bare_mass=0.6, fermi_wavevector=0.207))
@@ -171,28 +170,46 @@ ax.set_ylim([0, 0.06])
 plt.legend(); plt.show()
 ```
 
+```{python}
+import numpy as np
+
+Angl, Ekin = np.meshgrid(bmap.angles, bmap.ekin)
+Mome = np.sqrt(Ekin / xarpes.pref) * np.sin(Angl * xarpes.dtor)
+
+kmin, kmax = np.min(Mome), np.max(Mome)
+
+kspc = np.linspace(kmin, kmax, len(bmap.angles))
+
+dis1 = xarpes.pref * (((kspc - self_energy.center_wavevector)**2 - self_energy.fermi_wavevector**2)) \
+    / self_energy.bare_mass
+
+# dis1 = self_energy.fermi_velocity * (kspc - self_energy.fermi_wavevector)
+
+# dis2 = self_left.fermi_velocity *(kspc - self_left.fermi_wavevector)
+```
+
 ```{python}
 # %matplotlib inline
 
 fig = plt.figure(figsize=(10, 7))
 ax = fig.gca()
 
-from xarpes.constants import stdv
+self_energies = xarpes.CreateSelfEnergies([self_energy, self_two])
 
-ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
-            xerr=stdv * self_energy.peak_positions_sigma,
-           markersize=2, color='tab:blue', label=self_energy.label)
-ax.errorbar(self_two.peak_positions, self_two.enel_range, 
-            xerr=stdv * self_two.peak_positions_sigma,
-           markersize=2, color='tab:purple', label=self_two.label)
+# ax.errorbar(self_energy.mdc_maxima, self_energy.enel_range, 
+#             xerr=stdv * self_energy.peak_positions_sigma,
+#            markersize=2, color='tab:blue', label=self_energy.label)
+# ax.errorbar(self_two.mdc_maxima, self_two.enel_range, 
+#             xerr=stdv * self_two.peak_positions_sigma,
+#            markersize=2, color='tab:purple', label=self_two.label)
+
+ax.plot(kspc, dis1, linestyle='--')
 
 ax.set_xlim([-0.25, 0.25]); ax.set_ylim([-0.3, 0.1])
 
 plt.legend()
 
 fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
-
-plt.show()
 ```
 
 ```{python}
@@ -245,16 +262,16 @@ ax = fig.gca()
 
 from xarpes.constants import stdv
 
-ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
+ax.errorbar(self_energy.mdc_maxima, self_energy.enel_range, 
             xerr=stdv * self_energy.peak_positions_sigma,
            markersize=2, color='tab:blue', label=self_energy.label)
-ax.errorbar(self_two.peak_positions, self_two.enel_range, 
+ax.errorbar(self_two.mdc_maxima, self_two.enel_range, 
             xerr=stdv * self_two.peak_positions_sigma,
            markersize=2, color='tab:purple', label=self_two.label)
-ax.errorbar(self_three.peak_positions, self_three.enel_range, 
+ax.errorbar(self_three.mdc_maxima, self_three.enel_range, 
             xerr=stdv * self_three.peak_positions_sigma,
             markersize=2, color='tab:brown', label=self_three.label)
-ax.errorbar(self_four.peak_positions, self_four.enel_range, 
+ax.errorbar(self_four.mdc_maxima, self_four.enel_range, 
             xerr=stdv * self_four.peak_positions_sigma, 
             markersize=2, color='palevioletred', label=self_four.label)
 
@@ -262,14 +279,10 @@ ax.set_xlim([0, 0.25]); ax.set_ylim([-0.15, 0.05])
 
 plt.legend()
 
-# Put <1 zorder such that scatters aren't overrridden
-bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax, zorder=0.5)
 
-plt.show()
-```
-
-```{python}
+bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
+plt.show()
 ```
 
 ```{python}
@@ -581,8 +594,7 @@ plt.show()
 
 # plt.legend()
 
-# # Put <1 zorder such that scatters aren't overrridden
-# bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax, zorder=0.5)
+# bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
 # plt.show()
 ```

{xarpes-0.3.3 → xarpes-0.3.4}/examples/srtio3/srtio3.py

@@ -46,9 +46,7 @@ print('The optimised h nu - Phi = ' + f'{bmap.hnuminphi:.4f}' + ' +/- '
       + f'{bmap.hnuminphi_std:.4f}' + ' eV.')
 
 
-from xarpes.constants import dtor
-
-k_0 = -0.0014
+k_0 = -0.0014 # 0.02
 theta_0 = 0
 
 guess_dists = xarpes.CreateDistributions([
@@ -61,7 +59,7 @@ xarpes.SpectralQuadratic(amplitude=1800, peak=-3.6, broadening=0.0004,
 
 import numpy as np
 
-mat_el = lambda x: np.sin((x - theta_0) * dtor) ** 2
+mat_el = lambda x: np.sin((x - theta_0) * xarpes.dtor) ** 2
 
 mat_args = {}
 
@@ -78,9 +76,8 @@ fig = mdcs.visualize_guess(distributions=guess_dists, matrix_element=mat_el,
                            matrix_args=mat_args, energy_value=-0.000, ax=ax)
 
 # #### Note on interactive figures
-# - Operability of the interactive figure is sensitive to configuration of the plotting backend.
-# - With Python V>=3.13 in a conda environment, the figure may fail to show up more than once. In that case, the user could try to run "conda env config vars unset MPLBACKEND" inside the conda environment; in Python, this command can be preceded with an exclamation mark ("!conda env ...") such that the command is executed in the terminal. The reset should work after restarting the conda environment.
-# - As a fallback, the user may switch "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
+# - The interactive figure might not work inside the Jupyter notebooks, despite our best efforts to ensure stability.
+# - As a fallback, the user may switch from "%matplotlib widget" to "%matplotlib qt", after which the figure should pop up in an external window.
 
 
 fig = plt.figure(figsize=(7, 5))
@@ -98,8 +95,10 @@ fig = mdcs.fit_selection(distributions=guess_dists, matrix_element=mat_el,
 # - However, this would also require setting boundaries for the fitting range.  
 # - Instead, the user is advised to carefully check correspondence of peak maxima with MDC fitting results.
 
+fermi_one = 0.142
+
 self_energy = xarpes.SelfEnergy(*mdcs.expose_parameters(select_label='Inner_band_1', 
-                                bare_mass=0.6, fermi_wavevector=0.142, side='right'))
+                                bare_mass=0.6, fermi_wavevector=fermi_one, side='right'))
 
 self_two = xarpes.SelfEnergy(*mdcs.expose_parameters(select_label='Outer_band_2',
                                 bare_mass=0.6, fermi_wavevector=0.207))
@@ -133,18 +132,36 @@ ax.set_ylim([0, 0.06])
 
 plt.legend(); plt.show()
 
+import numpy as np
+
+Angl, Ekin = np.meshgrid(bmap.angles, bmap.ekin)
+Mome = np.sqrt(Ekin / xarpes.pref) * np.sin(Angl * xarpes.dtor)
+
+kmin, kmax = np.min(Mome), np.max(Mome)
+
+kspc = np.linspace(kmin, kmax, len(bmap.angles))
+
+dis1 = xarpes.pref * (((kspc - self_energy.center_wavevector)**2 - self_energy.fermi_wavevector**2)) \
+    / self_energy.bare_mass
+
+# dis1 = self_energy.fermi_velocity * (kspc - self_energy.fermi_wavevector)
+
+# dis2 = self_left.fermi_velocity *(kspc - self_left.fermi_wavevector)
+
 
 fig = plt.figure(figsize=(10, 7))
 ax = fig.gca()
 
-from xarpes.constants import stdv
+self_energies = xarpes.CreateSelfEnergies([self_energy, self_two])
 
-ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
-            xerr=stdv * self_energy.peak_positions_sigma,
-           markersize=2, color='tab:blue', label=self_energy.label)
-ax.errorbar(self_two.peak_positions, self_two.enel_range, 
-            xerr=stdv * self_two.peak_positions_sigma,
-           markersize=2, color='tab:purple', label=self_two.label)
+# ax.errorbar(self_energy.mdc_maxima, self_energy.enel_range, 
+#             xerr=stdv * self_energy.peak_positions_sigma,
+#            markersize=2, color='tab:blue', label=self_energy.label)
+# ax.errorbar(self_two.mdc_maxima, self_two.enel_range, 
+#             xerr=stdv * self_two.peak_positions_sigma,
+#            markersize=2, color='tab:purple', label=self_two.label)
+
+ax.plot(kspc, dis1, linestyle='--')
 
 ax.set_xlim([-0.25, 0.25]); ax.set_ylim([-0.3, 0.1])
 
@@ -152,8 +169,6 @@ plt.legend()
 
 fig = bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
-plt.show()
-
 
 guess_dists = xarpes.CreateDistributions([
 xarpes.Constant(offset=600),
@@ -194,16 +209,16 @@ ax = fig.gca()
 
 from xarpes.constants import stdv
 
-ax.errorbar(self_energy.peak_positions, self_energy.enel_range, 
+ax.errorbar(self_energy.mdc_maxima, self_energy.enel_range, 
             xerr=stdv * self_energy.peak_positions_sigma,
            markersize=2, color='tab:blue', label=self_energy.label)
-ax.errorbar(self_two.peak_positions, self_two.enel_range, 
+ax.errorbar(self_two.mdc_maxima, self_two.enel_range, 
             xerr=stdv * self_two.peak_positions_sigma,
            markersize=2, color='tab:purple', label=self_two.label)
-ax.errorbar(self_three.peak_positions, self_three.enel_range, 
+ax.errorbar(self_three.mdc_maxima, self_three.enel_range, 
             xerr=stdv * self_three.peak_positions_sigma,
             markersize=2, color='tab:brown', label=self_three.label)
-ax.errorbar(self_four.peak_positions, self_four.enel_range, 
+ax.errorbar(self_four.mdc_maxima, self_four.enel_range, 
             xerr=stdv * self_four.peak_positions_sigma, 
             markersize=2, color='palevioletred', label=self_four.label)
 
@@ -211,12 +226,10 @@ ax.set_xlim([0, 0.25]); ax.set_ylim([-0.15, 0.05])
 
 plt.legend()
 
-# Put <1 zorder such that scatters aren't overrridden
-bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax, zorder=0.5)
-
-plt.show()
 
+bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
+plt.show()
 
 
 # fig = plt.figure(figsize=(7, 5))
@@ -476,8 +489,7 @@ plt.show()
 
 # plt.legend()
 
-# # Put <1 zorder such that scatters aren't overrridden
-# bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax, zorder=0.5)
+# bmap.plot(abscissa='momentum', ordinate='electron_energy', ax=ax)
 
 # plt.show()
 

{xarpes-0.3.3 → xarpes-0.3.4}/pyproject.toml

@@ -24,8 +24,9 @@ dependencies = [
     "scipy",
     "lmfit",
     "pyqt5",
-    "ipympl",
-    "ipykernel<6.32.0"
+    "ipympl>=0.9.3",
+    "ipywidgets>=8.1.5",
+    "ipykernel<6.32.0"    
 ]
 
 [project.scripts]