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Add examples to all docstrings and update notebooks (#214)
* Standardize repr strings * pixi run fix * Add examples to model components and diffusion models * Add examples to all docstrings and update notebook examples
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Lines changed: 1021 additions & 376 deletions

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‎docs/docs/tutorials/analysis.ipynb‎

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@@ -23,18 +23,8 @@
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"# Imports\n",
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"import pooch\n",
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"\n",
26-
"from easydynamics.analysis.analysis import Analysis\n",
27-
"from easydynamics.experiment import Experiment\n",
28-
"from easydynamics.sample_model import BrownianTranslationalDiffusion\n",
29-
"from easydynamics.sample_model import ComponentCollection\n",
30-
"from easydynamics.sample_model import DeltaFunction\n",
31-
"from easydynamics.sample_model import Gaussian\n",
32-
"from easydynamics.sample_model import Lorentzian\n",
33-
"from easydynamics.sample_model import Polynomial\n",
34-
"from easydynamics.sample_model.background_model import BackgroundModel\n",
35-
"from easydynamics.sample_model.instrument_model import InstrumentModel\n",
36-
"from easydynamics.sample_model.resolution_model import ResolutionModel\n",
37-
"from easydynamics.sample_model.sample_model import SampleModel\n",
26+
"import easydynamics as edyn\n",
27+
"import easydynamics.sample_model as sm\n",
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"\n",
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"%matplotlib widget"
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]
@@ -47,7 +37,7 @@
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"outputs": [],
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"source": [
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"# Load the vanadium data\n",
50-
"vanadium_experiment = Experiment('Vanadium')\n",
40+
"vanadium_experiment = edyn.Experiment('Vanadium')\n",
5141
"file_path = pooch.retrieve(\n",
5242
" url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
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" known_hash='16cc1b327c303feeb88fb9dda5390dc4880b62396b1793f98c6fef0b27c7b873',\n",
@@ -66,34 +56,34 @@
6656
"# Example of Analysis with a simple sample model and instrument model\n",
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"# The scattering from vanadium is purely elastic, so we model it with a\n",
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"# delta function\n",
69-
"delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
70-
"sample_model = SampleModel(\n",
59+
"delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=1)\n",
60+
"sample_model = sm.SampleModel(\n",
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" components=delta_function,\n",
7262
")\n",
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"\n",
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"# The resolution is in this case modeled as a Gaussian. However, we can\n",
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"# add as many components as we like to the resolution model\n",
76-
"res_gauss = Gaussian(width=0.1)\n",
66+
"res_gauss = sm.Gaussian(width=0.1)\n",
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"res_gauss.area.fixed = True\n",
78-
"resolution_components = ComponentCollection()\n",
68+
"resolution_components = sm.ComponentCollection()\n",
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"resolution_components.append_component(res_gauss)\n",
80-
"resolution_model = ResolutionModel(components=resolution_components)\n",
70+
"resolution_model = sm.ResolutionModel(components=resolution_components)\n",
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"\n",
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"# The background model is created in the same way. In this case, we use\n",
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"# a flat background\n",
84-
"background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
74+
"background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
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"\n",
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"# We combine the resolution abd background model into an instrument\n",
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"# model. This model also contains a small energy offset to account for\n",
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"# instrument misalignment.\n",
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"\n",
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"instrument_model = InstrumentModel(\n",
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"instrument_model = sm.InstrumentModel(\n",
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" resolution_model=resolution_model,\n",
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" background_model=background_model,\n",
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")\n",
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"\n",
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"# Collect everything into an analysis object.\n",
96-
"vanadium_analysis = Analysis(\n",
86+
"vanadium_analysis = edyn.Analysis(\n",
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" display_name='Vanadium Full Analysis',\n",
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" experiment=vanadium_experiment,\n",
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" sample_model=sample_model,\n",
@@ -180,7 +170,7 @@
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"source": [
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"# Now it's time to look at the data we want to fit. We first load the\n",
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"# data\n",
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"diffusion_experiment = Experiment('Diffusion')\n",
173+
"diffusion_experiment = edyn.Experiment('Diffusion')\n",
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"\n",
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"file_path = pooch.retrieve(\n",
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" url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/diffusion_data_example.h5',\n",
@@ -200,23 +190,23 @@
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"# Now we set up the model, similarly to how we set up the model for the\n",
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"# vanadium data.\n",
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"\n",
203-
"delta_function = DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
204-
"lorentzian = Lorentzian(display_name='Lorentzian', area=0.5, width=0.3)\n",
205-
"component_collection = ComponentCollection(\n",
193+
"delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
194+
"lorentzian = sm.Lorentzian(display_name='Lorentzian', area=0.5, width=0.3)\n",
195+
"component_collection = sm.ComponentCollection(\n",
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" components=[delta_function, lorentzian],\n",
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")\n",
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"\n",
209-
"sample_model = SampleModel(\n",
199+
"sample_model = sm.SampleModel(\n",
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" components=component_collection,\n",
211201
")\n",
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"\n",
213-
"background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
203+
"background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
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"\n",
215-
"instrument_model = InstrumentModel(\n",
205+
"instrument_model = sm.InstrumentModel(\n",
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" background_model=background_model,\n",
217207
")\n",
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"\n",
219-
"diffusion_analysis = Analysis(\n",
209+
"diffusion_analysis = edyn.Analysis(\n",
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" display_name='Diffusion Full Analysis',\n",
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" experiment=diffusion_experiment,\n",
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" sample_model=sample_model,\n",
@@ -286,26 +276,26 @@
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"# Let us now fit directly to a diffusion model. We replace the\n",
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"# Lorentzian with a Brownian translational diffusion model and keep the\n",
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"# other parameters the same.\n",
289-
"delta_function = DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
290-
"component_collection = ComponentCollection(\n",
279+
"delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
280+
"component_collection = sm.ComponentCollection(\n",
291281
" components=[delta_function],\n",
292282
")\n",
293-
"diffusion_model = BrownianTranslationalDiffusion(\n",
283+
"diffusion_model = sm.BrownianTranslationalDiffusion(\n",
294284
" display_name='Brownian Translational Diffusion', diffusion_coefficient=2.4e-9, scale=0.5\n",
295285
")\n",
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"\n",
297-
"sample_model = SampleModel(\n",
287+
"sample_model = sm.SampleModel(\n",
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" components=component_collection,\n",
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" diffusion_models=diffusion_model,\n",
300290
")\n",
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"\n",
302-
"background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
292+
"background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
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"\n",
304-
"instrument_model = InstrumentModel(\n",
294+
"instrument_model = sm.InstrumentModel(\n",
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" background_model=background_model,\n",
306296
")\n",
307297
"\n",
308-
"diffusion_model_analysis = Analysis(\n",
298+
"diffusion_model_analysis = edyn.Analysis(\n",
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" display_name='Diffusion Full Analysis',\n",
310300
" experiment=diffusion_experiment,\n",
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" sample_model=sample_model,\n",
@@ -367,4 +357,4 @@
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}

‎docs/docs/tutorials/analysis1d.ipynb‎

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@@ -18,15 +18,9 @@
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"source": [
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"import pooch\n",
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"\n",
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"import easydynamics as edyn\n",
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"import easydynamics.sample_model as sm\n",
2123
"from easydynamics.analysis.analysis1d import Analysis1d\n",
22-
"from easydynamics.experiment import Experiment\n",
23-
"from easydynamics.sample_model import DeltaFunction\n",
24-
"from easydynamics.sample_model import Gaussian\n",
25-
"from easydynamics.sample_model import Polynomial\n",
26-
"from easydynamics.sample_model.background_model import BackgroundModel\n",
27-
"from easydynamics.sample_model.instrument_model import InstrumentModel\n",
28-
"from easydynamics.sample_model.resolution_model import ResolutionModel\n",
29-
"from easydynamics.sample_model.sample_model import SampleModel\n",
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"\n",
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"%matplotlib widget"
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]
@@ -38,7 +32,7 @@
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"metadata": {},
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"outputs": [],
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"source": [
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"vanadium_experiment = Experiment('Vanadium')\n",
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"vanadium_experiment = edyn.Experiment('Vanadium')\n",
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"\n",
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"file_path = pooch.retrieve(\n",
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" url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
@@ -56,18 +50,18 @@
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"outputs": [],
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"source": [
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"# Example of Analysis1d with a simple sample model and instrument model\n",
59-
"delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
60-
"sample_model = SampleModel(\n",
53+
"delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=1)\n",
54+
"sample_model = sm.SampleModel(\n",
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" components=delta_function,\n",
6256
")\n",
6357
"\n",
64-
"res_gauss = Gaussian(width=0.1)\n",
65-
"resolution_model = ResolutionModel(components=res_gauss)\n",
58+
"res_gauss = sm.Gaussian(width=0.1)\n",
59+
"resolution_model = sm.ResolutionModel(components=res_gauss)\n",
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"\n",
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"\n",
68-
"background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
62+
"background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
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"\n",
70-
"instrument_model = InstrumentModel(\n",
64+
"instrument_model = sm.InstrumentModel(\n",
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" resolution_model=resolution_model,\n",
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" background_model=background_model,\n",
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")\n",
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}

‎docs/docs/tutorials/component_collection.ipynb‎

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@@ -20,11 +20,7 @@
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"import matplotlib.pyplot as plt\n",
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"import numpy as np\n",
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"\n",
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"from easydynamics.sample_model import ComponentCollection\n",
24-
"from easydynamics.sample_model import DampedHarmonicOscillator\n",
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"from easydynamics.sample_model import Gaussian\n",
26-
"from easydynamics.sample_model import Lorentzian\n",
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"from easydynamics.sample_model import Polynomial\n",
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"import easydynamics.sample_model as sm\n",
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"\n",
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"%matplotlib widget"
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]
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"metadata": {},
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"outputs": [],
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"source": [
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"component_collection = ComponentCollection()\n",
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"component_collection = sm.ComponentCollection()\n",
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"\n",
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"# Creating components\n",
42-
"gaussian = Gaussian(display_name='Gaussian', width=0.5, area=1)\n",
43-
"dho = DampedHarmonicOscillator(display_name='DHO', center=1.0, width=0.3, area=2.0)\n",
44-
"lorentzian = Lorentzian(display_name='Lorentzian', center=-1.0, width=0.2, area=1.0)\n",
45-
"polynomial = Polynomial(display_name='Polynomial', coefficients=[0.1, 0, 0.5]) # y=0.1+0.5*x^2\n",
38+
"gaussian = sm.Gaussian(display_name='Gaussian', width=0.5, area=1)\n",
39+
"dho = sm.DampedHarmonicOscillator(display_name='DHO', center=1.0, width=0.3, area=2.0)\n",
40+
"lorentzian = sm.Lorentzian(display_name='Lorentzian', center=-1.0, width=0.2, area=1.0)\n",
41+
"polynomial = sm.Polynomial(display_name='Polynomial', coefficients=[0.1, 0, 0.5]) # y=0.1+0.5*x^2\n",
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"\n",
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"# Adding components to the component collection\n",
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"component_collection.append_component(gaussian)\n",
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}

‎docs/docs/tutorials/components.ipynb‎

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"import numpy as np\n",
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"import scipp as sc\n",
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"\n",
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"from easydynamics.sample_model import DampedHarmonicOscillator\n",
27-
"from easydynamics.sample_model import DeltaFunction\n",
28-
"from easydynamics.sample_model import Exponential\n",
29-
"from easydynamics.sample_model import ExpressionComponent\n",
30-
"from easydynamics.sample_model import Gaussian\n",
31-
"from easydynamics.sample_model import Lorentzian\n",
32-
"from easydynamics.sample_model import Polynomial\n",
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"import easydynamics.sample_model as sm\n",
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"\n",
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"%matplotlib widget"
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]
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"outputs": [],
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"source": [
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"# Creating a component\n",
45-
"gaussian = Gaussian(display_name='Gaussian', width=0.5, area=1)\n",
46-
"dho = DampedHarmonicOscillator(display_name='DHO', center=1.0, width=0.3, area=2.0)\n",
47-
"lorentzian = Lorentzian(display_name='Lorentzian', center=-1.0, width=0.2, area=1.0)\n",
48-
"polynomial = Polynomial(display_name='Polynomial', coefficients=[0.1, 0, 0.5]) # y=0.1+0.5*x^2\n",
49-
"exponential = Exponential(display_name='Exponential', amplitude=1.0, rate=-0.5)\n",
39+
"gaussian = sm.Gaussian(display_name='Gaussian', width=0.5, area=1)\n",
40+
"dho = sm.DampedHarmonicOscillator(display_name='DHO', center=1.0, width=0.3, area=2.0)\n",
41+
"lorentzian = sm.Lorentzian(display_name='Lorentzian', center=-1.0, width=0.2, area=1.0)\n",
42+
"polynomial = sm.Polynomial(display_name='Polynomial', coefficients=[0.1, 0, 0.5]) # y=0.1+0.5*x^2\n",
43+
"exponential = sm.Exponential(display_name='Exponential', amplitude=1.0, rate=-0.5)\n",
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"\n",
5145
"x = np.linspace(-2, 2, 100)\n",
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"\n",
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"metadata": {},
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"outputs": [],
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"source": [
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"delta = DeltaFunction(display_name='Delta', center=0.0, area=1.0)\n",
83+
"delta = sm.DeltaFunction(display_name='Delta', center=0.0, area=1.0)\n",
9084
"x1 = np.linspace(-2, 2, 100)\n",
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"y = delta.evaluate(x1)\n",
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"x2 = np.linspace(-2, 2, 51)\n",
@@ -114,7 +108,7 @@
114108
"x1 = sc.linspace(dim='x', start=-2.0, stop=2.0, num=100, unit='meV')\n",
115109
"x2 = sc.linspace(dim='x', start=-2.0 * 1e3, stop=2.0 * 1e3, num=101, unit='microeV')\n",
116110
"\n",
117-
"polynomial = Polynomial(display_name='Polynomial', coefficients=[0.1, 0, 0.5]) # y=0.1+0.5*x^2\n",
111+
"polynomial = sm.Polynomial(display_name='Polynomial', coefficients=[0.1, 0, 0.5]) # y=0.1+0.5*x^2\n",
118112
"y1 = polynomial.evaluate(x1)\n",
119113
"y2 = polynomial.evaluate(x2)\n",
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"\n",
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"metadata": {},
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"outputs": [],
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"source": [
135-
"expr = ExpressionComponent(\n",
129+
"expr = sm.ExpressionComponent(\n",
136130
" 'A * exp(-(x - x0)**2 / (2*sigma**2)) +B*sin(2*pi*x/period)',\n",
137131
" parameters={'A': 10, 'x0': 0, 'sigma': 1},\n",
138132
")\n",
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158152
"metadata": {},
159153
"outputs": [],
160154
"source": [
161-
"expr = ExpressionComponent(\n",
155+
"expr = sm.ExpressionComponent(\n",
162156
" 'A*erf(B*x)',\n",
163157
")\n",
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"\n",
@@ -197,4 +191,4 @@
197191
},
198192
"nbformat": 4,
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"nbformat_minor": 5
200-
}
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}

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