doc added; reading of isochronal bds

doc/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= /autohome/dominik/miniconda3/bin/sphinx-build
+SOURCEDIR     = /autohome/dominik/nmreval/docs/source
+BUILDDIR      = /autohome/dominik/nmreval/docs/build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

doc/examples/README.rst

@@ -0,0 +1,9 @@
+.. examples-index:
+
+.. _gallery:
+
+========
+Examples
+========
+
+This page contains example plots. Click on any image to see the full image and source code.

doc/examples/distribution/README.rst

@@ -0,0 +1,6 @@
+ .. _distribution_examples:
+
+.. _distribution-examples-index:
+
+Distribution of correlation times
+=================================

doc/examples/distribution/plot_ColeCole.py

@@ -0,0 +1,50 @@
+"""
+=========
+Cole-Cole
+=========
+
+Example for Cole-Cole distributions
+"""
+import matplotlib.pyplot as plt
+import numpy as np
+
+from nmreval.distributions import ColeCole
+
+x = np.logspace(-5, 5, num=101)
+
+cc = ColeCole
+
+alpha_CC = [0.3, 0.5, 0.7]
+
+fig, axes = plt.subplots(2, 3, constrained_layout=True)
+
+lines = []
+for a in alpha_CC:
+    axes[0, 0].plot(np.log10(x), cc.correlation(x, 1, a))
+    axes[1, 0].plot(np.log10(x), np.log10(cc.specdens(x, 1, a)))
+    axes[0, 1].plot(np.log10(x), np.log10(cc.susceptibility(x, 1, a).real))
+    axes[1, 1].plot(np.log10(x), np.log10(cc.susceptibility(x, 1, a).imag))
+    l, = axes[0, 2].plot(np.log10(x), cc.distribution(x, 1, a),
+                         label=rf'$\alpha={a}$')
+    lines.append(l)
+
+fig_titles = ('Correlation function', 'Susceptibility (real)', 'Distribution',
+              'Spectral density', 'Susceptibility (imag)')
+fig_xlabel = (r'$\log(t/\tau_\mathrm{HN})$', r'$\log(\omega\tau_\mathrm{HN})$',
+              r'$\log(\tau/\tau_\mathrm{HN})$', r'$\log(\omega\tau_\mathrm{HN})$',
+              r'$\log(\omega\tau_\mathrm{HN})$')
+fig_ylabel = (r'$C(t)$', r"$\log(\chi'(\omega))$", r'$G(\ln\tau)$',
+              r'$\log(J(\omega))$', r"$\log(\chi''(\omega))$")
+
+for title, xlabel, ylabel, ax in zip(fig_titles, fig_xlabel, fig_ylabel, axes.ravel()):
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+
+labels = [l.get_label() for l in lines]
+leg = fig.legend(lines, labels, loc='center left', bbox_to_anchor=(1.05, 0.50),
+                 bbox_transform=axes[1, 1].transAxes)
+
+fig.delaxes(axes[1, 2])
+
+plt.show()

doc/examples/distribution/plot_ColeDavidson.py

@@ -0,0 +1,50 @@
+"""
+=============
+Cole-Davidson
+=============
+
+Example for Cole-Davidson distributions
+"""
+import matplotlib.pyplot as plt
+import numpy as np
+
+from nmreval.distributions import ColeDavidson
+
+x = np.logspace(-5, 5, num=101)
+
+cd = ColeDavidson
+
+gamma_CD = [0.3, 0.5, 0.7]
+
+fig, axes = plt.subplots(2, 3, constrained_layout=True)
+
+lines = []
+for g in gamma_CD:
+    axes[0, 0].plot(np.log10(x), cd.correlation(x, 1, g))
+    axes[1, 0].plot(np.log10(x), np.log10(cd.specdens(x, 1, g)))
+    axes[0, 1].plot(np.log10(x), np.log10(cd.susceptibility(x, 1, g).real))
+    axes[1, 1].plot(np.log10(x), np.log10(cd.susceptibility(x, 1, g).imag))
+    l, = axes[0, 2].plot(np.log10(x), cd.distribution(x, 1, g),
+                         label=rf'$\gamma={g}$')
+    lines.append(l)
+
+fig_titles = ('Correlation function', 'Susceptibility (real)', 'Distribution',
+              'Spectral density', 'Susceptibility (imag)')
+fig_xlabel = (r'$\log(t/\tau_\mathrm{CD})$', r'$\log(\omega\tau_\mathrm{CD})$',
+              r'$\log(\tau/\tau_\mathrm{CD})$', r'$\log(\omega\tau_\mathrm{CD})$',
+              r'$\log(\omega\tau_\mathrm{CD})$')
+fig_ylabel = (r'$C(t)$', r"$\log(\chi'(\omega))$", r'$G(\ln\tau)$',
+              r'$\log(J(\omega))$', r"$\log(\chi''(\omega))$")
+
+for title, xlabel, ylabel, ax in zip(fig_titles, fig_xlabel, fig_ylabel, axes.ravel()):
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+
+labels = [l.get_label() for l in lines]
+leg = fig.legend(lines, labels, loc='center left', bbox_to_anchor=(1.05, 0.50),
+                 bbox_transform=axes[1, 1].transAxes)
+
+fig.delaxes(axes[1, 2])
+
+plt.show()

doc/examples/distribution/plot_HavriliakNegami.py

@@ -0,0 +1,53 @@
+"""
+================
+Havriliak-Negami
+================
+
+Example for Havriliak-Negami distributions
+"""
+from itertools import product
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from nmreval.distributions import HavriliakNegami
+
+x = np.logspace(-5, 5, num=101)
+
+hn = HavriliakNegami
+
+alpha_CC = [0.4, 0.8]
+gamma_CD = [0.3, 0.7]
+
+fig, axes = plt.subplots(2, 3, constrained_layout=True)
+
+lines = []
+for a, g in product(alpha_CC, gamma_CD):
+    axes[0, 0].plot(np.log10(x), hn.correlation(x, 1, a, g))
+    axes[1, 0].plot(np.log10(x), np.log10(hn.specdens(x, 1, a, g)))
+    axes[0, 1].plot(np.log10(x), np.log10(hn.susceptibility(x, 1, a, g).real))
+    axes[1, 1].plot(np.log10(x), np.log10(hn.susceptibility(x, 1, a, g).imag))
+    l, = axes[0, 2].plot(np.log10(x), hn.distribution(x, 1, a, g),
+                         label=rf'$\alpha={a}, \gamma={g}$')
+    lines.append(l)
+
+fig_titles = ('Correlation function', 'Susceptibility (real)', 'Distribution',
+              'Spectral density', 'Susceptibility (imag)')
+fig_xlabel = (r'$\log(t/\tau_\mathrm{HN})$', r'$\log(\omega\tau_\mathrm{HN})$',
+              r'$\log(\tau/\tau_\mathrm{HN})$', r'$\log(\omega\tau_\mathrm{HN})$',
+              r'$\log(\omega\tau_\mathrm{HN})$')
+fig_ylabel = (r'$C(t)$', r"$\log(\chi'(\omega))$", r'$G(\ln\tau)$',
+              r'$\log(J(\omega))$', r"$\log(\chi''(\omega))$")
+
+for title, xlabel, ylabel, ax in zip(fig_titles, fig_xlabel, fig_ylabel, axes.ravel()):
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+
+labels = [l.get_label() for l in lines]
+leg = fig.legend(lines, labels, loc='center left', bbox_to_anchor=(1.05, 0.50),
+                 bbox_transform=axes[1, 1].transAxes)
+
+fig.delaxes(axes[1, 2])
+
+plt.show()

doc/examples/distribution/plot_KWW.py

@@ -0,0 +1,50 @@
+"""
+=========================
+Kohlrausch-Williams-Watts
+=========================
+
+Example for KWW distributions
+"""
+import matplotlib.pyplot as plt
+import numpy as np
+
+from nmreval.distributions import KWW
+
+x = np.logspace(-5, 5, num=101)
+
+kww = KWW
+
+beta_KWW = [0.3, 0.5, 0.7]
+
+fig, axes = plt.subplots(2, 3, constrained_layout=True)
+
+lines = []
+for b in beta_KWW:
+    axes[0, 0].plot(np.log10(x), kww.correlation(x, 1, b))
+    axes[1, 0].plot(np.log10(x), np.log10(kww.specdens(x, 1, b)))
+    axes[0, 1].plot(np.log10(x), np.log10(kww.susceptibility(x, 1, b).real))
+    axes[1, 1].plot(np.log10(x), np.log10(kww.susceptibility(x, 1, b).imag))
+    l, = axes[0, 2].plot(np.log10(x), kww.distribution(x, 1, b),
+                         label=rf'$\beta={b}$')
+    lines.append(l)
+
+fig_titles = ('Correlation function', 'Susceptibility (real)', 'Distribution',
+              'Spectral density', 'Susceptibility (imag)')
+fig_xlabel = (r'$\log(t/\tau_\mathrm{KWW})$', r'$\log(\omega\tau_\mathrm{KWW})$',
+              r'$\log(\tau/\tau_\mathrm{KWW})$', r'$\log(\omega\tau_\mathrm{KWW})$',
+              r'$\log(\omega\tau_\mathrm{KWW})$')
+fig_ylabel = (r'$C(t)$', r"$\log(\chi'(\omega))$", r'$G(\ln\tau)$',
+              r'$\log(J(\omega))$', r"$\log(\chi''(\omega))$")
+
+for title, xlabel, ylabel, ax in zip(fig_titles, fig_xlabel, fig_ylabel, axes.ravel()):
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+
+labels = [l.get_label() for l in lines]
+leg = fig.legend(lines, labels, loc='center left', bbox_to_anchor=(1.05, 0.50),
+                 bbox_transform=axes[1, 1].transAxes)
+
+fig.delaxes(axes[1, 2])
+
+plt.show()

doc/examples/distribution/plot_LogGaussian.py

@@ -0,0 +1,50 @@
+"""
+============
+Log-Gaussian
+============
+
+Example for Log-Gaussian distributions
+"""
+import matplotlib.pyplot as plt
+import numpy as np
+
+from nmreval.distributions import LogGaussian
+
+x = np.logspace(-5, 5, num=101)
+
+lg = LogGaussian
+
+sigma_lg = [1, 3, 5]
+
+fig, axes = plt.subplots(2, 3, constrained_layout=True)
+
+lines = []
+for s in sigma_lg:
+    axes[0, 0].plot(np.log10(x), lg.correlation(x, 1, s))
+    axes[1, 0].plot(np.log10(x), np.log10(lg.specdens(x, 1, s)))
+    axes[0, 1].plot(np.log10(x), np.log10(lg.susceptibility(x, 1, s).real))
+    axes[1, 1].plot(np.log10(x), np.log10(lg.susceptibility(x, 1, s).imag))
+    l, = axes[0, 2].plot(np.log10(x), lg.distribution(x, 1, s),
+                         label=rf'$\sigma={s}$')
+    lines.append(l)
+
+fig_titles = ('Correlation function', 'Susceptibility (real)', 'Distribution',
+              'Spectral density', 'Susceptibility (imag)')
+fig_xlabel = (r'$\log(t/\tau_\mathrm{LG})$', r'$\log(\omega\tau_\mathrm{LG})$',
+              r'$\log(\tau/\tau_\mathrm{LG})$', r'$\log(\omega\tau_\mathrm{LG})$',
+              r'$\log(\omega\tau_\mathrm{LG})$')
+fig_ylabel = (r'$C(t)$', r"$\log(\chi'(\omega))$", r'$G(\ln\tau)$',
+              r'$\log(J(\omega))$', r"$\log(\chi''(\omega))$")
+
+for title, xlabel, ylabel, ax in zip(fig_titles, fig_xlabel, fig_ylabel, axes.ravel()):
+    ax.set_title(title)
+    ax.set_xlabel(xlabel)
+    ax.set_ylabel(ylabel)
+
+labels = [l.get_label() for l in lines]
+leg = fig.legend(lines, labels, loc='center left', bbox_to_anchor=(1.05, 0.50),
+                 bbox_transform=axes[1, 1].transAxes)
+
+fig.delaxes(axes[1, 2])
+
+plt.show()

doc/examples/nmr/README.rst

@@ -0,0 +1,6 @@
+.. _nmr_examples:
+
+.. _nmr-examples-index:
+
+NMR specifics
+=============

doc/examples/nmr/plot_RelaxationEvaluation.py

@@ -0,0 +1,67 @@
+"""
+=======================
+Spin-lattice relaxation
+=======================
+
+Example for
+"""
+import numpy as np
+from matplotlib import pyplot as plt
+
+from nmreval.distributions import ColeDavidson
+from nmreval.nmr import Relaxation, RelaxationEvaluation
+from nmreval.nmr.coupling import Quadrupolar
+from nmreval.utils.constants import kB
+
+# Define temperature range
+inv_temp = np.linspace(3, 9, num=30)
+temperature = 1000/inv_temp
+
+# spectral density parameter
+ea = 0.45
+tau = 1e-21 * np.exp(ea / kB / temperature)
+gamma_cd = 0.1
+
+# interaction parameter
+omega = 2*np.pi*46e6
+delta = 120e3
+eta = 0
+
+r = Relaxation()
+r.set_distribution(ColeDavidson)  # the only parameter that has to be set beforehand
+
+t1_values = r.t1(omega, tau, gamma_cd, mode='bpp',
+                 prefactor=Quadrupolar.relax(delta, eta))
+# add noise
+rng = np.random.default_rng(123456789)
+noisy = (rng.random(t1_values.size)-0.5) * 0.5 * t1_values + t1_values
+
+# set parameter and data
+r_eval = RelaxationEvaluation()
+r_eval.set_distribution(ColeDavidson)
+r_eval.set_coupling(Quadrupolar, (delta, eta))
+r_eval.data(temperature, noisy)
+r_eval.omega = omega
+
+t1_min_data, _ = r_eval.calculate_t1_min()  # second argument is None
+t1_min_inter, line = r_eval.calculate_t1_min(interpolate=1, trange=(160, 195), use_log=True)
+
+fig, ax = plt.subplots()
+ax.semilogy(1000/t1_min_data[0], t1_min_data[1], 'rx', label='Data minimum')
+ax.semilogy(1000/t1_min_inter[0], t1_min_inter[1], 'r+', label='Parabola')
+ax.semilogy(1000/line[0], line[1])
+
+found_gamma, found_height = r_eval.get_increase(t1_min_inter[1], idx=0, mode='distribution')
+print(found_gamma)
+
+plt.axhline(found_height)
+plt.show()
+
+#%%
+# Now we found temperature and height of the minimum we can calculate the correlation time
+
+plt.semilogy(1000/temperature, tau)
+tau_from_t1, opts = r_eval.correlation_from_t1()
+print(opts)
+plt.semilogy(1000/tau_from_t1[:, 0], tau_from_t1[:, 1], 'o')
+plt.show()

doc/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

doc/source/_templates/autosummary/class.rst

@@ -0,0 +1,14 @@
+:mod:`{{ module | escape }}`.{{ objname }}
+{{ underline }}==================
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+    :members:
+    :inherited-members:
+
+.. include:: {{ fullname }}.examples
+
+.. raw:: html
+
+    <div class="clearer"></div>

doc/source/api/data.rst

@@ -0,0 +1,5 @@
+.. automodule:: nmreval.data
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
+

doc/source/api/distributions.rst

@@ -0,0 +1,4 @@
+.. automodule:: nmreval.distributions
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:

doc/source/api/distributions2/index.rst

@@ -0,0 +1,29 @@
+*********************************
+Distribution of correlation times
+*********************************
+
+List of all implemented distributions and the associated correlation functions, spectral densities, susceptibilies
+
+.. contents:: Table of Contents
+   :depth: 3
+   :local:
+   :backlinks: entry
+
+Cole-Cole
+---------
+
+.. automodule:: nmreval.distributions.colecole
+   :members:
+
+
+Cole-Davidson
+-------------
+
+.. automodule:: nmreval.distributions.coledavidson
+   :members:
+
+Havriliak-Negami
+----------------
+
+.. automodule:: nmreval.distributions.havriliaknegami
+   :members:

doc/source/api/index.rst

@@ -0,0 +1,13 @@
+=========
+Reference
+=========
+
+.. toctree::
+   :caption: Table of contents
+   :maxdepth: 1
+   :glob:
+
+   data
+   models
+   distributions
+   nmr

doc/source/api/models.rst

@@ -0,0 +1,4 @@
+.. automodule:: nmreval.models
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:

doc/source/api/models2/basic.rst

@@ -0,0 +1,6 @@
+************************
+``nmreval.models.basic``
+************************
+
+.. automodule:: nmreval.models.basic
+   :members:

doc/source/api/models2/index.rst

@@ -0,0 +1,31 @@
+**************
+Model function
+**************
+
+List of all implemented functions
+
+.. contents:: Table of Contents
+   :depth: 3
+   :local:
+   :backlinks: entry
+
+Basic functions
+---------------
+
+.. currentmodule:: nmreval
+
+.. autosummary::
+   :toctree:
+
+   nmreval.models.basic
+
+
+
+
+NMR relaxation functions
+------------------------
+
+.. automodule:: nmreval.models.relaxation
+   :members:
+
+

doc/source/api/models2/nmreval.models.basic.rst

@@ -0,0 +1,37 @@
+nmreval.models.basic
+====================
+
+.. automodule:: nmreval.models.basic
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      Constant
+      ExpFunc
+      Linear
+      Log
+      MittagLeffler
+      Parabola
+      PowerLaw
+      PowerLawCross
+      Sine
+   
+   
+
+   
+   
+   
+
+
+

doc/source/api/nmr.rst

@@ -0,0 +1,4 @@
+.. automodule:: nmreval.nmr
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:

doc/source/conf.py

@@ -0,0 +1,422 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+import sphinx_bootstrap_theme
+sys.path.append('/autohome/dominik/nmreval')
+import nmreval
+
+
+# -- Project information -----------------------------------------------------
+project = 'NMREval'
+author = 'Dominik Demuth'
+copyright = '2022, Dominik Demuth'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version
+release = nmreval.__version__
+# The full version, including alpha/beta/rc tags.
+version = release
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.intersphinx',
+    'sphinx_gallery.gen_gallery',
+]
+
+# configuration for intersphinx
+intersphinx_mapping = {
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'python': ('https://docs.python.org/3/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
+    'PyQt': ('https://www.riverbankcomputing.com/static/Docs/PyQt5/', None),
+    'matplotlib': ('https://matplotlib.org/stable', None),
+}
+
+# autodoc options
+autodoc_typehints = 'none'
+autodoc_class_signature = 'separated'
+autoclass_content = 'class'
+autodoc_member_order = 'groupwise'
+# autodoc_default_options = {'members': False, 'inherited-members': False}
+
+# autosummay options
+autosummary_generate = True
+
+# spinx-gallery
+sphinx_gallery_conf = {
+    'examples_dirs': '../examples',   # path to your example scripts
+    'gallery_dirs': ['gallery'],  # path to where to save gallery generated output
+    'backreferences_dir': os.path.join('api', 'generated'),  # directory where function/class granular galleries are stored
+    'doc_module': 'nmreval',  # Modules for which function/class level galleries are created.
+    'reference_url': {
+        'nmreval': None,  # The module you locally document uses None
+    },
+    'download_all_examples': False,
+    'plot_gallery': True,
+    'inspect_global_variables': False,
+    'remove_config_comments': True,
+    'min_reported_time': 10000000000,
+    'show_memory': False,
+    'show_signature': False,
+}
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#
+# today = ''
+#
+# Else, today_fmt is used as the format for a strftime call.
+#
+# today_fmt = '%B %d, %Y'
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#
+# default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#
+add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#
+add_module_names = False
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#
+# show_authors = False
+
+# A list of ignored prefixes for module index sorting.
+# modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+# keep_warnings = False
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'pydata_sphinx_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+html_theme_options = {
+    'collapse_navigation': False,
+    'show_prev_next': False,
+    'navbar_end': ['navbar-icon-links.html', 'search-field.html'],
+}
+
+# Add any paths that contain custom themes here, relative to this directory.
+# html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+
+# The name for this set of Sphinx documents.
+# "<project> v<release> documentation" by default.
+#
+# html_title = u'NMREval v0.0.1'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+# html_short_title = None
+
+# (Optional) Logo. Should be small enough to fit the navbar (ideally 24x24).
+# Path should be relative to the ``_static`` files directory.
+html_logo = '_static/logo.png'
+
+# Custom sidebar templates, maps document names to template names.
+html_sidebars = {'**': ['sidebar-nav-bs.html']}
+# html_sidebars = {
+#     '**': ['localtoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'],
+# }
+
+# If true, links to the reST sources are added to the pages.
+html_show_sourcelink = False
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+# html_favicon = None
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+html_last_updated_fmt = ''
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+html_additional_pages = {}
+
+# If false, no module index is generated.
+html_domain_indices = False
+
+# If false, no index is generated.
+html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+html_split_index = False
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+# html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+# html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+# html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+html_file_suffix = None
+
+# Output file base name for HTML help builder.
+# htmlhelp_basename = 'pydoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'NMREval.tex', u'NMREval Documentation',
+     u'Dominik Demuth', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#
+# latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#
+# latex_use_parts = False
+
+# If true, show page references after internal links.
+#
+# latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#
+# latex_appendices = []
+
+# It false, will not define \strong, \code, 	itleref, \crossref ... but only
+# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
+# packages.
+#
+# latex_keep_old_macro_names = True
+
+# If false, no module index is generated.
+#
+# latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'nmreval', u'NMREval Documentation',
+     [author], 1)
+]
+
+# If true, show URL addresses after external links.
+#
+# man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'NMREval', u'NMREval Documentation',
+     author, 'NMREval', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+#
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#
+# texinfo_no_detailmenu = False
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = project
+epub_author = author
+epub_publisher = author
+epub_copyright = copyright
+
+# The basename for the epub file. It defaults to the project name.
+# epub_basename = project
+
+# The HTML theme for the epub output. Since the default themes are not
+# optimized for small screen space, using the same theme for HTML and epub
+# output is usually not wise. This defaults to 'epub', a theme designed to save
+# visual space.
+#
+# epub_theme = 'epub'
+
+# The language of the text. It defaults to the language option
+# or 'en' if the language is not set.
+#
+# epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+# epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#
+# epub_identifier = ''
+
+# A unique identification for the text.
+#
+# epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#
+# epub_cover = ()
+
+# A sequence of (type, uri, title) tuples for the guide element of content.opf.
+#
+# epub_guide = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#
+# epub_pre_files = []
+
+# HTML files that should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#
+# epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+# The depth of the table of contents in toc.ncx.
+#
+# epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#
+# epub_tocdup = True
+
+# Choose between 'default' and 'includehidden'.
+#
+# epub_tocscope = 'default'
+
+# Fix unsupported image types using the Pillow.
+#
+# epub_fix_images = False
+
+# Scale large images.
+#
+# epub_max_image_width = 0
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#
+# epub_show_urls = 'inline'
+
+# If false, no index is generated.
+#
+# epub_use_index = True

doc/source/gallery/index.rst

@@ -0,0 +1,179 @@
+:orphan:
+
+
+
+.. _sphx_glr_gallery:
+
+.. examples-index:
+
+.. _gallery:
+
+========
+Examples
+========
+
+This page contains example plots. Click on any image to see the full image and source code.
+
+
+.. raw:: html
+
+    <div class="sphx-glr-clear"></div>
+
+
+
+.. _sphx_glr_gallery_distribution:
+
+ .. _distribution_examples:
+
+.. _distribution-examples-index:
+
+Distribution of correlation times
+=================================
+
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Example for KWW distributions">
+
+.. only:: html
+
+ .. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_KWW_thumb.png
+     :alt: Kohlrausch-Williams-Watts
+
+     :ref:`sphx_glr_gallery_distribution_plot_KWW.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /gallery/distribution/plot_KWW
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Example for Cole-Cole distributions">
+
+.. only:: html
+
+ .. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_ColeCole_thumb.png
+     :alt: Cole-Cole
+
+     :ref:`sphx_glr_gallery_distribution_plot_ColeCole.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /gallery/distribution/plot_ColeCole
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Example for Log-Gaussian distributions">
+
+.. only:: html
+
+ .. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_LogGaussian_thumb.png
+     :alt: Log-Gaussian
+
+     :ref:`sphx_glr_gallery_distribution_plot_LogGaussian.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /gallery/distribution/plot_LogGaussian
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Example for Cole-Davidson distributions">
+
+.. only:: html
+
+ .. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_ColeDavidson_thumb.png
+     :alt: Cole-Davidson
+
+     :ref:`sphx_glr_gallery_distribution_plot_ColeDavidson.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /gallery/distribution/plot_ColeDavidson
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Example for Havriliak-Negami distributions">
+
+.. only:: html
+
+ .. figure:: /gallery/distribution/images/thumb/sphx_glr_plot_HavriliakNegami_thumb.png
+     :alt: Havriliak-Negami
+
+     :ref:`sphx_glr_gallery_distribution_plot_HavriliakNegami.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /gallery/distribution/plot_HavriliakNegami
+.. raw:: html
+
+    <div class="sphx-glr-clear"></div>
+
+
+
+.. _sphx_glr_gallery_nmr:
+
+.. _nmr_examples:
+
+.. _nmr-examples-index:
+
+NMR specifics
+=============
+
+
+
+.. raw:: html
+
+    <div class="sphx-glr-thumbcontainer" tooltip="Example for">
+
+.. only:: html
+
+ .. figure:: /gallery/nmr/images/thumb/sphx_glr_plot_RelaxationEvaluation_thumb.png
+     :alt: Spin-lattice relaxation
+
+     :ref:`sphx_glr_gallery_nmr_plot_RelaxationEvaluation.py`
+
+.. raw:: html
+
+    </div>
+
+
+.. toctree::
+   :hidden:
+
+   /gallery/nmr/plot_RelaxationEvaluation
+.. raw:: html
+
+    <div class="sphx-glr-clear"></div>
+

doc/source/gallery/searchindex.bak

@@ -0,0 +1,3 @@
+'/autohome/dominik/nmreval/doc/_build/html/index.html', (0, 6969)
+'/autohome/dominik/nmreval/doc/_build/html/_static/documentation_options.js', (7168, 364)
+'/autohome/dominik/nmreval/doc/_build/html/searchindex.js', (7680, 29280)

doc/source/gallery/searchindex.dir

@@ -0,0 +1,3 @@
+'/autohome/dominik/nmreval/doc/_build/html/index.html', (0, 6969)
+'/autohome/dominik/nmreval/doc/_build/html/_static/documentation_options.js', (7168, 364)
+'/autohome/dominik/nmreval/doc/_build/html/searchindex.js', (7680, 29280)

doc/source/index.rst

@@ -0,0 +1,24 @@
+.. NMREval documentation master file, created by
+   sphinx-quickstart on Sun Feb 20 17:26:03 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+#####################
+NMREval documentation
+#####################
+
+.. toctree::
+   :maxdepth: 1
+
+   user_guide/index
+   gallery/index
+   api/index
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

doc/source/nmr/index.rst

@@ -0,0 +1,8 @@
+=============
+NMR specifics
+=============
+
+.. toctree::
+   :maxdepth: 2
+
+   pake

doc/source/nmr/pake.rst

@@ -0,0 +1,43 @@
+.. _nmr.pake:
+
+Wideline spectra
+^^^^^^^^^^^^^^^^
+
+Calculation of spectra
+----------------------
+
+In general, time signals are calculated by integration of all orientations (see also :ref:`list.orienations`):
+
+.. math::
+   g(t) = \int f[\omega_\text{int}(\theta, \phi)t]\sin\theta\,\mathrm{d}\theta\,\mathrm{d}\phi
+
+with :math:`f(\theta, \phi, t) = \cos[\omega_\text{int}(\theta, \phi) t]` or :math:`\exp[i\omega_\text{int}(\theta) t]` and fourier transform for a spectrum.
+However, summation over :math:`\theta`, :math:`\phi`, and calculating :math:`f(\theta, \phi, t)` for each orientation is time consuming.
+
+Alternatively, if the orientations are equidistant in :math:`\cos\theta`, one can get to the spectrum directly by creating a histogram of :math:`\omega_\text{int}(\theta, \phi)`, thus circumventing a lot of calculations.
+
+
+De-Paked spectra
+----------------
+
+A superposition of different Pake spectra complicates the evaluation of relaxation times or similar.
+The idea is to deconvolute these broad spectra into one line corresponding to relative orientation :math:`\theta = 0` [mccabe97]_.
+
+For :math:`\omega_\text{int}(\theta) \propto (3\cos^2\theta -1)/2 = P_2(\cos\theta)`, the property :math:`\omega_\text{int}(\theta) = \omega_\text{int}(0) \omega_\text{int}(\theta)` is used to write
+
+.. math::
+   g(t) = \int_0^{1} f[0, \omega_\text{int}(\theta)t]\,\mathrm{d}\cos\theta.
+
+This way, the integration is not over orientations at one time :math:`t`, but over times at one orientation 0.
+After some integrations, rearrangenments, and substitutions, a spectrum can be calculated by
+
+.. math::
+  F(-2\omega) = \sqrt{\frac{3|\omega |}{2\pi}}(1\pm i) \text{FT}[g(t)\sqrt{t}]
+
+with :math:`1+i` for :math:`\omega > 0` and :math:`1-i` for :math:`\omega > 0`.
+
+.. figure:: depake.png
+   :scale: 50 %
+
+
+.. [mccabe97] M.A. McCabe, S.R. Wassail: Rapid deconvolution of NMR powder spectra by weighted fast Fourier transformation, Solid State Nuclear Magnetic Resonance (1997). https://doi.org/10.1016/S0926-2040(97)00024-6

doc/source/user_guide/fit.rst

@@ -0,0 +1,43 @@
+.. _user_guide.fit:
+
+============
+Fitting data
+============
+
+.. image:: ../_static/fit_dialog.png
+    :scale: 80%
+    :align: center
+
+The picture gives an example of dialog to setup and start fits.
+First, there is the possibiity to fit different functions, called models to differentiate from the functions inside each
+model, to different data simultaneously.
+In the given example, two models were would be used during fit:
+test1 and test3 use the default model, in this case model a,
+while test2 uses model b.
+
+In the middle column, the functions of model a are currently given in a tree structure:
+It is comprised of three functions: a constant, a sine curve, which is a child of the constant, and free diffusion.
+Functions can be dragged by mouse to each position, including a child position, and it is possible to switch between the
+four basic arithmetic operations (+, -, \*, /) by striking the corresponding key.
+Function at the same level, e.g., constant and free diffusion, are evaluated in the given order.
+Children of a function take precedence over the following functions.
+This means for the given example, that model a is something like
+
+.. math::
+    f(x) = [\text{constant} / \text{sine}] + \text{diffusion}
+
+It is possible to skip functions by de-selecting it.
+This choice alse affects children, even if they are selected.
+
+The right column gives access to the parameter of selected function, in this case of the free diffusion function.
+Here, the parameter :math:`M_0` is linked to the parameter :math:`C` of another constant function of model b
+(identifiable by the number behind the name).
+Linkage links not only parameter between function but all settings, e.g., if :math:`C` is fixed, :math:`M_0` is fixed.
+Some parameters like gradient :math:`g` are predefined as fixed parameters and are lacking any options besides their value.
+Upper and lower bounds may be given.
+If one or two of the bounds are not given, this parameter is unbounded on the respective side.
+
+If a parameter has one entry, this value is initial parameter for all data sets.
+If the number of entries is greater than the number of data sets, the first :math:`n` values are used.
+Here, test1 uses 1 as parameter for :math:`t_{ev}` and test3 uses 3.
+If the number of entries is less than the number of data sets, the last value will be used for each additional set.

doc/source/user_guide/index.rst

@@ -0,0 +1,11 @@
+==========
+User Guide
+==========
+
+
+.. toctree::
+   :maxdepth: 2
+
+   read
+   fit
+   shift_scale

doc/source/user_guide/read.rst

@@ -0,0 +1,19 @@
+.. _user_guide.read:
+
+*************
+Reading files
+*************
+
+Supported filetypes are
+
+   * Text files,
+   * DAMARIS HDF5 files,
+   * Grace images.
+   * HP alpha-analyzer EPS files
+   * NTNMR .tnt files
+
+DAMARIS HDF files
+=================
+
+After scanning the selected file the program shows a list of the available data.
+

doc/source/user_guide/shift_scale.rst

@@ -0,0 +1,16 @@
+.. _usage.shift_scale:
+
+Moving and scaling
+^^^^^^^^^^^^^^^^^^
+
+Values are always used and displayed in scientific notation *x.yyyyez* where x is a signed single digit larger than 0.
+The relative stepsize (by default 0.0001) increases or decreases is always of the same magnitude as the current value, e.g.,
+1.2345e0 changes by 0.0001, but 1.2345e20 changes by 0.0001e20.
+If the step results in a new order of magnitude the value will be adjusted accordingly, i.e., a step from 9.9999e1 to 10.0000e1 will become 1.0000e2.
+
+.. note::
+    This behaviour leads almost always to values different from zero when using the arrow buttons. Please enter it directly to get a value of zero.
+
+Boxes :guilabel:`log x` and :guilabel:`log y` change the respective axis from a linear to logarithmic scaling and vice versa.
+
+Every selected set will be recalculated according to :math:`new = scale \cdot old + offset`.