nxs-analysis-tools 0.0.34__tar.gz → 0.0.35__tar.gz

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2023 Steven J. Gomez Alvarado
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+MIT License
+
+Copyright (c) 2023 Steven J. Gomez Alvarado
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/MANIFEST.in

@@ -1,3 +1,3 @@
-# Exclude generated files
-prune */__pycache__
-global-exclude *.pyc *.pyo *.pyd *.swp *.bak *~ */magentropy.egg-info/*
+# Exclude generated files
+prune */__pycache__
+global-exclude *.pyc *.pyo *.pyd *.swp *.bak *~ */magentropy.egg-info/*

{nxs_analysis_tools-0.0.34/src/nxs_analysis_tools.egg-info → nxs_analysis_tools-0.0.35}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nxs-analysis-tools
-Version: 0.0.34
+Version: 0.0.35
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License: MIT License

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/README.md

@@ -1,19 +1,19 @@
-# nxs-analysis-tools
-
-## Overview
-
-nxs-analysis-tools provides a suite of tools for slicing (2D), cutting (1D), and transforming (e.g., symmetrizing, interpolating, deltaPDF) nexus format (.nxs) scattering data.
-
-View the documentation [here](https://nxs-analysis-tools.readthedocs.io/en/stable/).
-
-## Installation
-
-Install nxs-analysis-tools with ``pip``:
-
-```{code-block} console
-pip install nxs-analysis-tools
-```
-
-## License
-
-This project is licensed under the MIT License.
+# nxs-analysis-tools
+
+## Overview
+
+nxs-analysis-tools provides a suite of tools for slicing (2D), cutting (1D), and transforming (e.g., symmetrizing, interpolating, deltaPDF) nexus format (.nxs) scattering data.
+
+View the documentation [here](https://nxs-analysis-tools.readthedocs.io/en/stable/).
+
+## Installation
+
+Install nxs-analysis-tools with ``pip``:
+
+```{code-block} console
+pip install nxs-analysis-tools
+```
+
+## License
+
+This project is licensed under the MIT License.

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/pyproject.toml

@@ -1,66 +1,66 @@
-# keep consistent with _meta/__init__.py
-
-[build-system]
-requires = ['setuptools>=61.2.0', 'wheel']
-build-backend = 'setuptools.build_meta'
-
-[project]
-name = 'nxs-analysis-tools'
-version = '0.0.34'
-description = 'Reduce and transform nexus format (.nxs) scattering data.'
-readme = 'README.md'
-requires-python = '>=3.7'
-license = { file = 'LICENSE' }
-authors = [{ name = 'Steven J. Gomez Alvarado', email = 'stevenjgomez@ucsb.edu' }]
-
-keywords = [
-    'diffraction',
-    'xrd',
-    'nexusformat',
-    'nexus',
-    'nxs',
-    'scattering',
-]
-classifiers = [
-    'Development Status :: 1 - Planning',
-    'Intended Audience :: Science/Research',
-    'License :: OSI Approved :: MIT License',
-    'Programming Language :: Python',
-    'Programming Language :: Python :: 3',
-    'Programming Language :: Python :: 3.9',
-    'Programming Language :: Python :: 3.10',
-    'Topic :: Scientific/Engineering :: Image Processing',
-    'Topic :: Scientific/Engineering',
-]
-dependencies = [
-    'matplotlib>=3.7.1',
-    'numpy>=1.24.3',
-    'ipython>=1.0.0',
-    'pandas>=2.0.2',
-    'nexusformat>=1.0.1',
-    'lmfit>=1.2.1',
-    ]
-
-[project.optional-dependencies]
-dev = [
-    'build >= 0.8.0',
-    'furo >= 2022.6.21',
-    'ipykernel >= 6.9.1',
-    'myst-nb >= 0.16.0',
-    'myst-parser >= 0.18.0',
-    'numpydoc >= 1.4.0',
-    'pandoc >= 2.2',
-    'pylint >= 2.12.2',
-    'pytest >= 7.1.2',
-    'sphinx >= 5.0.2',
-    'sphinx-autobuild >= 2021.3.14',
-    'sphinx-copybutton >= 0.5.0',
-    'sphinxext-opengraph >= 0.6.3',
-    'twine >= 4.0.1',
-]
-
-[project.urls]
-'Download' = 'https://pypi.org/project/nxs-analysis-tools/'
-'Bug Tracker' = 'https://github.com/stevenjgomez/nxs_analysis_tools/issues'
-'Documentation' = 'https://nxs-analysis-tools.readthedocs.io/en/stable/'
-'Source Code' = 'https://github.com/stevenjgomez/nxs_analysis_tools'
+# keep consistent with _meta/__init__.py
+
+[build-system]
+requires = ['setuptools>=61.2.0', 'wheel']
+build-backend = 'setuptools.build_meta'
+
+[project]
+name = 'nxs-analysis-tools'
+version = '0.0.35'
+description = 'Reduce and transform nexus format (.nxs) scattering data.'
+readme = 'README.md'
+requires-python = '>=3.7'
+license = { file = 'LICENSE' }
+authors = [{ name = 'Steven J. Gomez Alvarado', email = 'stevenjgomez@ucsb.edu' }]
+
+keywords = [
+    'diffraction',
+    'xrd',
+    'nexusformat',
+    'nexus',
+    'nxs',
+    'scattering',
+]
+classifiers = [
+    'Development Status :: 1 - Planning',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: MIT License',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Topic :: Scientific/Engineering :: Image Processing',
+    'Topic :: Scientific/Engineering',
+]
+dependencies = [
+    'matplotlib>=3.7.1',
+    'numpy>=1.24.3',
+    'ipython>=1.0.0',
+    'pandas>=2.0.2',
+    'nexusformat>=1.0.1',
+    'lmfit>=1.2.1',
+    ]
+
+[project.optional-dependencies]
+dev = [
+    'build >= 0.8.0',
+    'furo >= 2022.6.21',
+    'ipykernel >= 6.9.1',
+    'myst-nb >= 0.16.0',
+    'myst-parser >= 0.18.0',
+    'numpydoc >= 1.4.0',
+    'pandoc >= 2.2',
+    'pylint >= 2.12.2',
+    'pytest >= 7.1.2',
+    'sphinx >= 5.0.2',
+    'sphinx-autobuild >= 2021.3.14',
+    'sphinx-copybutton >= 0.5.0',
+    'sphinxext-opengraph >= 0.6.3',
+    'twine >= 4.0.1',
+]
+
+[project.urls]
+'Download' = 'https://pypi.org/project/nxs-analysis-tools/'
+'Bug Tracker' = 'https://github.com/stevenjgomez/nxs_analysis_tools/issues'
+'Documentation' = 'https://nxs-analysis-tools.readthedocs.io/en/stable/'
+'Source Code' = 'https://github.com/stevenjgomez/nxs_analysis_tools'

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/setup.py

@@ -1,5 +1,5 @@
-'''This file is included as a workaround for a limitation in Setuptools support for PEP 660.'''
-
-from setuptools import setup
-
+'''This file is included as a workaround for a limitation in Setuptools support for PEP 660.'''
+
+from setuptools import setup
+
 setup()

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/src/_meta/__init__.py

@@ -1,10 +1,10 @@
-'''nxs-analysis-tools package metadata.'''
-
-# keep consistent with pyproject.toml
-__project__ = 'nxs-analysis-tools'
-__author__ = 'Steven J. Gomez Alvarado'
-__email__ = 'stevenjgomez@ucsb.edu'
-__copyright__ = f"2023, {__author__}"
-__license__ = 'MIT'
-__version__= '0.0.34'
-__repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'
+'''nxs-analysis-tools package metadata.'''
+
+# keep consistent with pyproject.toml
+__project__ = 'nxs-analysis-tools'
+__author__ = 'Steven J. Gomez Alvarado'
+__email__ = 'stevenjgomez@ucsb.edu'
+__copyright__ = f"2023, {__author__}"
+__license__ = 'MIT'
+__version__= '0.0.35'
+__repo_url__ = 'https://github.com/stevenjgomez/nxs_analysis_tools'

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/src/nxs_analysis_tools/__init__.py

@@ -1,12 +1,12 @@
-'''
-Reduce and transform nexus format (.nxs) scattering data.
-'''
-
-import numpy as np
-from _meta import __author__, __copyright__, __license__, __version__
-from .datareduction import load_data, load_transform, plot_slice, reciprocal_lattice_params, Scissors, rotate_data
-from .chess import TempDependence
-
-# What to import when running "from nxs_analysis_tools import *"
-__all__ = ['load_data', 'load_transform', 'plot_slice', 'Scissors', 'TempDependence',
-           'reciprocal_lattice_params', 'rotate_data']
+'''
+Reduce and transform nexus format (.nxs) scattering data.
+'''
+
+import numpy as np
+from _meta import __author__, __copyright__, __license__, __version__
+from .datareduction import load_data, load_transform, plot_slice, reciprocal_lattice_params, Scissors, rotate_data
+from .chess import TempDependence
+
+# What to import when running "from nxs_analysis_tools import *"
+__all__ = ['load_data', 'load_transform', 'plot_slice', 'Scissors', 'TempDependence',
+           'reciprocal_lattice_params', 'rotate_data']

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/src/nxs_analysis_tools/chess.py

@@ -75,6 +75,11 @@ class TempDependence:
                     # Initialize linecutmodel object at each temperature
                     self.linecutmodels[temperature] = LinecutModel()
 
+        # Convert to int temporarily to sort temperatures list
+        self.temperatures = [int(t) for t in self.temperatures]
+        self.temperatures.sort()
+        self.temperatures = [str(t) for t in self.temperatures]
+
     def load_datasets(self, file_ending='hkli.nxs', temperatures_list=None):
         """
         Load scattering datasets from the specified folder.

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35/src/nxs_analysis_tools.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nxs-analysis-tools
-Version: 0.0.34
+Version: 0.0.35
 Summary: Reduce and transform nexus format (.nxs) scattering data.
 Author-email: "Steven J. Gomez Alvarado" <stevenjgomez@ucsb.edu>
 License: MIT License

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/tests/test_chess.py

@@ -1,16 +1,16 @@
-import matplotlib.pyplot as plt
-from nxs_analysis_tools import TempDependence
-
-sample = TempDependence()
-
-sample.load_datasets(folder='../docs/source/examples/example_data/sample_name')
-
-print(sample.datasets)
-
-print(sample.datasets['15'])
-
-sample.datasets['15'][:,:,0.0].plot()
-
-sample.cut_data(center=(0,0,0), window=(0.1,1,0.1))
-
+import matplotlib.pyplot as plt
+from nxs_analysis_tools import TempDependence
+
+sample = TempDependence()
+
+sample.load_datasets(folder='../docs/source/examples/example_data/sample_name')
+
+print(sample.datasets)
+
+print(sample.datasets['15'])
+
+sample.datasets['15'][:,:,0.0].plot()
+
+sample.cut_data(center=(0,0,0), window=(0.1,1,0.1))
+
 sample.plot_linecuts()

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/tests/test_chess_fitting.py

@@ -1,21 +1,21 @@
-import sys
-sys.path.append('../src/nxs_analysis_tools/')
-from datareduction import load_data, Scissors
-from chess import *
-from fitting import *
-
-from lmfit.models import GaussianModel, LinearModel, LorentzianModel
-
-sample = TempDependence()
-sample.load_datasets(folder=r'K:\pokharel-3470-a\PrCd3P3\BRO7')
-sample.cut_data(center=(0.5,-3,0), window=(0.1,0.3,0.1))
-
-sample.set_model_components([GaussianModel(prefix='peak'), LorentzianModel(prefix='diffuse'), LinearModel(prefix='background')])
-sample.set_param_hint('peakcenter', min=-0.1, max=0.1)
-sample.make_params()
-sample.guess()
-sample.print_initial_params()
-sample.plot_initial_guess()
-sample.fit()
-sample.plot_fit()
+import sys
+sys.path.append('../src/nxs_analysis_tools/')
+from datareduction import load_data, Scissors
+from chess import *
+from fitting import *
+
+from lmfit.models import GaussianModel, LinearModel, LorentzianModel
+
+sample = TempDependence()
+sample.load_datasets(folder=r'K:\pokharel-3470-a\PrCd3P3\BRO7')
+sample.cut_data(center=(0.5,-3,0), window=(0.1,0.3,0.1))
+
+sample.set_model_components([GaussianModel(prefix='peak'), LorentzianModel(prefix='diffuse'), LinearModel(prefix='background')])
+sample.set_param_hint('peakcenter', min=-0.1, max=0.1)
+sample.make_params()
+sample.guess()
+sample.print_initial_params()
+sample.plot_initial_guess()
+sample.fit()
+sample.plot_fit()
 sample.print_fit_report()

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/tests/test_datareduction.py

@@ -1,19 +1,19 @@
-import sys
-sys.path.append('../src/nxs_analysis_tools/')
-from datareduction import load_data, Scissors, rotate_data, plot_slice
-
-data = load_data('../docs/source/examples/example_data/sample_name/15/example_hkli.nxs')
-# scissors = Scissors(data, center=(0,0,0), window=(0.1,2,0.3))
-# scissors.cut_data()
-# print(scissors.integration_window)
-# scissors.plot_integration_window()
-# scissors.linecut.plot()
-# scissors.highlight_integration_window()
-
-import matplotlib.pyplot as plt
-
-plot_slice(data[:, :, 0.0])
-plt.show()
-rotated_data = rotate_data(data=data, lattice_angle=90, rotation_angle=45, rotation_axis=2, printout=True)
-plot_slice(rotated_data[:, :, 0.0])
-plt.show()
+import sys
+sys.path.append('../src/nxs_analysis_tools/')
+from datareduction import load_data, Scissors, rotate_data, plot_slice
+
+data = load_data('../docs/source/examples/example_data/sample_name/15/example_hkli.nxs')
+# scissors = Scissors(data, center=(0,0,0), window=(0.1,2,0.3))
+# scissors.cut_data()
+# print(scissors.integration_window)
+# scissors.plot_integration_window()
+# scissors.linecut.plot()
+# scissors.highlight_integration_window()
+
+import matplotlib.pyplot as plt
+
+plot_slice(data[:, :, 0.0])
+plt.show()
+rotated_data = rotate_data(data=data, lattice_angle=90, rotation_angle=45, rotation_axis=2, printout=True)
+plot_slice(rotated_data[:, :, 0.0])
+plt.show()

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/tests/test_fitting.py

@@ -1,28 +1,28 @@
-import sys
-sys.path.append('../src/nxs_analysis_tools/')
-from fitting import LinecutModel
-
-from nxs_analysis_tools.datareduction import load_data, Scissors
-from lmfit.models import GaussianModel, LinearModel
-
-data = load_data('../docs/source/examples/example_data/sample_name/15/example_hkli.nxs')
-
-s = Scissors(data=data)
-
-linecut = s.cut_data(center=(0,0,0), window=(0.1,0.5,0.1))
-
-lm = LinecutModel(data=linecut)
-
-lm.set_model_components([GaussianModel(prefix='peak'), LinearModel(prefix='background')])
-
-lm.set_param_hint('peakcenter', min=-0.1, max=0.1)
-
-lm.make_params()
-
-lm.guess()
-
-lm.print_initial_params()
-
-lm.params
-
+import sys
+sys.path.append('../src/nxs_analysis_tools/')
+from fitting import LinecutModel
+
+from nxs_analysis_tools.datareduction import load_data, Scissors
+from lmfit.models import GaussianModel, LinearModel
+
+data = load_data('../docs/source/examples/example_data/sample_name/15/example_hkli.nxs')
+
+s = Scissors(data=data)
+
+linecut = s.cut_data(center=(0,0,0), window=(0.1,0.5,0.1))
+
+lm = LinecutModel(data=linecut)
+
+lm.set_model_components([GaussianModel(prefix='peak'), LinearModel(prefix='background')])
+
+lm.set_param_hint('peakcenter', min=-0.1, max=0.1)
+
+lm.make_params()
+
+lm.guess()
+
+lm.print_initial_params()
+
+lm.params
+
 lm.plot_initial_guess()

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/tests/test_lmfit.py

@@ -1,95 +1,95 @@
-import sys
-
-sys.path.append('../src/nxs_analysis_tools/')
-from datareduction import load_data, Scissors
-# from fitting import *
-
-
-from test_lmfit.models import GaussianModel
-from test_lmfit.models import PseudoVoigtModel
-from test_lmfit.models import LorentzianModel
-from test_lmfit.models import LinearModel
-from test_lmfit.model import CompositeModel
-import operator
-import matplotlib.pyplot as plt
-import numpy as np
-
-data = load_data('../docs/source/examples/example_data/sample_name/15/example_hkli.nxs')
-s = Scissors(data=data, center=(0, 0, 0), window=(0.1, 0.1, 0.5))
-s.cut_data()
-
-x = s.linecut[s.linecut.axes[0]].nxdata
-y = s.linecut[s.linecut.signal].nxdata
-
-# Create model components
-model_components = [
-    GaussianModel(prefix='peak'),
-    LinearModel(prefix='background')
-]
-
-# Create composite model (in function)
-model = CompositeModel(*model_components, operator.add)
-
-# Intialize empty parameters (in function)
-params = model.make_params()
-fwhm_params = {key:value for key,value in params.items() if 'fwhm' in key}
-for key,value in fwhm_params.items():
-    pi_str = str(np.pi)
-    params.add(key.replace('fwhm','corrlength'), expr='(2 * ' + pi_str + ') / ' + key)
-
-# Perform initial guesses for each model component (in function)
-for model_component in model_components:
-    params.update(model_component.guess(y, x=x))
-
-# Show initial guesses (in function)
-for param, hint in model.param_hints.items():
-    print(f'{param}')
-    for key, value in hint.items():
-        print(f'\t{key}: {value}')
-
-# Plot initial guess (in function)
-y_init_fit = model.eval(params=params, x=x)
-plt.plot(x, y_init_fit, '--', label='guess')
-plt.plot(x, y, 'o', label='data')
-plt.legend()
-plt.show()
-
-# Perform fit (in function)
-model_result = model.fit(y, params, x=x)
-# # Determine correlation lengths after fitting
-# fwhm_params = {key:value for key,value in model_result.params.items() if 'fwhm' in key}
-# for key,value in fwhm_params.items():
-#     corrlength = correlation_length = (2 * np.pi) / value
-#     new_key = key.replace('fwhm','corrlength')
-#     model_result.params.add(new_key, value=corrlength)
-
-x_fit = x
-# x_fit = np.linspace(x.min(), x.max(), num_points)
-y_fit = model_result.eval(x=x_fit)
-y_fit_components = model_result.eval_components(x=x_fit)
-
-# Plot fit with **kwargs (in function)
-model_result.plot(show_init=True)
-plt.show()
-
-# Show fit report
-print(model_result.fit_report())
-
-# # Calculate correlation length (can be done from expr in lmfit)
-# fwhm_entries = {key: value for key, value in model_result.values.items() if 'fwhm' in key}
-# correlation_lengths = {}
-# for key, fwhm in fwhm_entries.items():
-#     correlation_length = (2 * np.pi) / fwhm
-#     new_key = key.replace('fwhm', 'correlationlength')
-#     correlation_lengths[new_key] = correlation_length
-#
-# fwhm_errors = {key: param.stderr for key, param in model_result.params.items() if 'fwhm' in key}
-# correlation_length_errors = {}
-# for key, error in fwhm_errors.items():
-#     new_key = key.replace('fwhm', 'correlationlength')
-#     correlation_length_errors[new_key] = ((2 * np.pi) / fwhm_entries[key] ** 2) * error if error is not None else None
-#
-# print('[[Correlation Lengths]]')
-# for key in correlation_lengths.keys():
-#     print(f'\t{key}: {correlation_lengths[key]} +/- {correlation_length_errors[key]} ' +
+import sys
+
+sys.path.append('../src/nxs_analysis_tools/')
+from datareduction import load_data, Scissors
+# from fitting import *
+
+
+from test_lmfit.models import GaussianModel
+from test_lmfit.models import PseudoVoigtModel
+from test_lmfit.models import LorentzianModel
+from test_lmfit.models import LinearModel
+from test_lmfit.model import CompositeModel
+import operator
+import matplotlib.pyplot as plt
+import numpy as np
+
+data = load_data('../docs/source/examples/example_data/sample_name/15/example_hkli.nxs')
+s = Scissors(data=data, center=(0, 0, 0), window=(0.1, 0.1, 0.5))
+s.cut_data()
+
+x = s.linecut[s.linecut.axes[0]].nxdata
+y = s.linecut[s.linecut.signal].nxdata
+
+# Create model components
+model_components = [
+    GaussianModel(prefix='peak'),
+    LinearModel(prefix='background')
+]
+
+# Create composite model (in function)
+model = CompositeModel(*model_components, operator.add)
+
+# Intialize empty parameters (in function)
+params = model.make_params()
+fwhm_params = {key:value for key,value in params.items() if 'fwhm' in key}
+for key,value in fwhm_params.items():
+    pi_str = str(np.pi)
+    params.add(key.replace('fwhm','corrlength'), expr='(2 * ' + pi_str + ') / ' + key)
+
+# Perform initial guesses for each model component (in function)
+for model_component in model_components:
+    params.update(model_component.guess(y, x=x))
+
+# Show initial guesses (in function)
+for param, hint in model.param_hints.items():
+    print(f'{param}')
+    for key, value in hint.items():
+        print(f'\t{key}: {value}')
+
+# Plot initial guess (in function)
+y_init_fit = model.eval(params=params, x=x)
+plt.plot(x, y_init_fit, '--', label='guess')
+plt.plot(x, y, 'o', label='data')
+plt.legend()
+plt.show()
+
+# Perform fit (in function)
+model_result = model.fit(y, params, x=x)
+# # Determine correlation lengths after fitting
+# fwhm_params = {key:value for key,value in model_result.params.items() if 'fwhm' in key}
+# for key,value in fwhm_params.items():
+#     corrlength = correlation_length = (2 * np.pi) / value
+#     new_key = key.replace('fwhm','corrlength')
+#     model_result.params.add(new_key, value=corrlength)
+
+x_fit = x
+# x_fit = np.linspace(x.min(), x.max(), num_points)
+y_fit = model_result.eval(x=x_fit)
+y_fit_components = model_result.eval_components(x=x_fit)
+
+# Plot fit with **kwargs (in function)
+model_result.plot(show_init=True)
+plt.show()
+
+# Show fit report
+print(model_result.fit_report())
+
+# # Calculate correlation length (can be done from expr in lmfit)
+# fwhm_entries = {key: value for key, value in model_result.values.items() if 'fwhm' in key}
+# correlation_lengths = {}
+# for key, fwhm in fwhm_entries.items():
+#     correlation_length = (2 * np.pi) / fwhm
+#     new_key = key.replace('fwhm', 'correlationlength')
+#     correlation_lengths[new_key] = correlation_length
+#
+# fwhm_errors = {key: param.stderr for key, param in model_result.params.items() if 'fwhm' in key}
+# correlation_length_errors = {}
+# for key, error in fwhm_errors.items():
+#     new_key = key.replace('fwhm', 'correlationlength')
+#     correlation_length_errors[new_key] = ((2 * np.pi) / fwhm_entries[key] ** 2) * error if error is not None else None
+#
+# print('[[Correlation Lengths]]')
+# for key in correlation_lengths.keys():
+#     print(f'\t{key}: {correlation_lengths[key]} +/- {correlation_length_errors[key]} ' +
 #           f'({correlation_length_errors[key] / correlation_lengths[key] * 100:.2f}%)')

{nxs_analysis_tools-0.0.34 → nxs_analysis_tools-0.0.35}/tests/test_pairdistribution.py

@@ -1,40 +1,40 @@
-from nxs_analysis_tools.datareduction import load_data
-from nxs_analysis_tools.pairdistribution import *
-import matplotlib.pyplot as plt
-
-data = load_data('../docs/source/examples/example_data/pairdistribution_data/test_hkli.nxs')
-# s = Symmetrizer3D(data)
-
-# s.plane1symmetrizer.set_parameters(theta_min=0, theta_max=90, mirror=True)
-# s.plane1symmetrizer.test(data[:,:,len(data.L)//2])
-#
-# s.plane2symmetrizer.set_parameters(theta_min=45, theta_max=90, mirror=True)
-# s.plane2symmetrizer.test(data[:,len(data.K)//2,:])
-#
-# s.plane3symmetrizer.set_parameters(theta_min=0, theta_max=90, mirror=False)
-# s.plane3symmetrizer.test(data[len(data.H)//2,:,:])
-#
-# s.symmetrize()
-
-p = Puncher()
-p.set_data(data)
-p.set_lattice_params((1,1,1,90,90,90))
-bm = p.generate_bragg_mask(punch_radius=0.25)
-p.add_mask(bm)
-p.punch()
-plot_slice(p.punched[:,:,0.0])
-plt.show()
-
-m = p.generate_mask_at_coord(coordinate=(0.33, 0.33, 0.0), punch_radius=0.25)
-p.add_mask(m)
-p.punch()
-plot_slice(p.punched[:,:,0.0])
-plt.show()
-
-m = p.generate_mask_at_coord(coordinate=(-0.1, -0.1, 0.0), punch_radius=0.2)
-p.subtract_mask(m)
-p.punch()
-plot_slice(p.punched[:,:,0.0])
-plt.show()
-
+from nxs_analysis_tools.datareduction import load_data
+from nxs_analysis_tools.pairdistribution import *
+import matplotlib.pyplot as plt
+
+data = load_data('../docs/source/examples/example_data/pairdistribution_data/test_hkli.nxs')
+# s = Symmetrizer3D(data)
+
+# s.plane1symmetrizer.set_parameters(theta_min=0, theta_max=90, mirror=True)
+# s.plane1symmetrizer.test(data[:,:,len(data.L)//2])
+#
+# s.plane2symmetrizer.set_parameters(theta_min=45, theta_max=90, mirror=True)
+# s.plane2symmetrizer.test(data[:,len(data.K)//2,:])
+#
+# s.plane3symmetrizer.set_parameters(theta_min=0, theta_max=90, mirror=False)
+# s.plane3symmetrizer.test(data[len(data.H)//2,:,:])
+#
+# s.symmetrize()
+
+p = Puncher()
+p.set_data(data)
+p.set_lattice_params((1,1,1,90,90,90))
+bm = p.generate_bragg_mask(punch_radius=0.25)
+p.add_mask(bm)
+p.punch()
+plot_slice(p.punched[:,:,0.0])
+plt.show()
+
+m = p.generate_mask_at_coord(coordinate=(0.33, 0.33, 0.0), punch_radius=0.25)
+p.add_mask(m)
+p.punch()
+plot_slice(p.punched[:,:,0.0])
+plt.show()
+
+m = p.generate_mask_at_coord(coordinate=(-0.1, -0.1, 0.0), punch_radius=0.2)
+p.subtract_mask(m)
+p.punch()
+plot_slice(p.punched[:,:,0.0])
+plt.show()
+
 # SUCCESS