Analysis

docs/docs/tutorials/analysis.ipynb

@@ -0,0 +1,352 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "8643b10c",
+   "metadata": {},
+   "source": [
+    "# Analysis\n",
+    "It is time to analyse some data. We here show how to set up an Analysis object and use it to first fit an artificial vanadium measurement. Next, we use the fitted resolution to fit an artificial measurement of a model with diffusion and some elastic scattering. \n",
+    "\n",
+    "We extract and plot the relevant parameters. Finally, we show how to fit directly to the diffusion model.\n",
+    "\n",
+    "In the near future, it will be possible to fit the width and area of the Lorentzian to the diffusion model as well."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bca91d3c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Imports\n",
+    "from easydynamics.analysis.analysis import Analysis\n",
+    "from easydynamics.experiment import Experiment\n",
+    "from easydynamics.sample_model import BrownianTranslationalDiffusion\n",
+    "from easydynamics.sample_model import ComponentCollection\n",
+    "from easydynamics.sample_model import DeltaFunction\n",
+    "from easydynamics.sample_model import Gaussian\n",
+    "from easydynamics.sample_model import Lorentzian\n",
+    "from easydynamics.sample_model import Polynomial\n",
+    "from easydynamics.sample_model.background_model import BackgroundModel\n",
+    "from easydynamics.sample_model.instrument_model import InstrumentModel\n",
+    "from easydynamics.sample_model.resolution_model import ResolutionModel\n",
+    "from easydynamics.sample_model.sample_model import SampleModel\n",
+    "\n",
+    "%matplotlib widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8deca9b6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Load the vanadium data\n",
+    "vanadium_experiment = Experiment('Vanadium')\n",
+    "vanadium_experiment.load_hdf5(filename='vanadium_data_example.h5')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6762faba",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Example of Analysis with a simple sample model and instrument model\n",
+    "# The scattering from vanadium is purely elastic, so we model it with a\n",
+    "# delta function\n",
+    "delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
+    "sample_model = SampleModel(\n",
+    "    components=delta_function,\n",
+    ")\n",
+    "\n",
+    "# The resolution is in this case modeled as a Gaussian. However, we can\n",
+    "# add as many components as we like to the resolution model\n",
+    "res_gauss = Gaussian(width=0.1)\n",
+    "res_gauss.area.fixed = True\n",
+    "resolution_components = ComponentCollection()\n",
+    "resolution_components.append_component(res_gauss)\n",
+    "resolution_model = ResolutionModel(components=resolution_components)\n",
+    "\n",
+    "# The background model is created in the same way. In this case, we use\n",
+    "# a flat background\n",
+    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "\n",
+    "# We combine the resolution abd background model into an instrument\n",
+    "# model. This model also contains a small energy offset to account for\n",
+    "# instrument misalignment.\n",
+    "\n",
+    "instrument_model = InstrumentModel(\n",
+    "    resolution_model=resolution_model,\n",
+    "    background_model=background_model,\n",
+    ")\n",
+    "\n",
+    "# Collect everything into an analysis object.\n",
+    "vanadium_analysis = Analysis(\n",
+    "    display_name='Vanadium Full Analysis',\n",
+    "    experiment=vanadium_experiment,\n",
+    "    sample_model=sample_model,\n",
+    "    instrument_model=instrument_model,\n",
+    ")\n",
+    "\n",
+    "# Let us first fit a single Q index and plot the data and model to see\n",
+    "# how it looks\n",
+    "fit_result_independent_single_Q = vanadium_analysis.fit(fit_method='independent', Q_index=5)\n",
+    "vanadium_analysis.plot_data_and_model(Q_index=5)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e98e3d65",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# It looks good, so let us fit all Q indices independently and plot the\n",
+    "# results\n",
+    "fit_result_independent_all_Q = vanadium_analysis.fit(fit_method='independent')\n",
+    "vanadium_analysis.plot_data_and_model()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "133e682e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Inspect the Parameters as a scipp Dataset\n",
+    "vanadium_analysis.parameters_to_dataset()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "dfacdf24",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot some of fitted parameters as a function of Q\n",
+    "vanadium_analysis.plot_parameters(names=['DeltaFunction area'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b6f9f316",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vanadium_analysis.plot_parameters(names=['Gaussian width'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "572664a0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vanadium_analysis.plot_parameters(names=['energy_offset'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3609e6c1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Now it's time to look at the data we want to fit. We first load the\n",
+    "# data\n",
+    "diffusion_experiment = Experiment('Diffusion')\n",
+    "diffusion_experiment.load_hdf5(filename='diffusion_data_example.h5')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e685909a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Now we set up the model, similarly to how we set up the model for the\n",
+    "# vanadium data.\n",
+    "delta_function = DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
+    "lorentzian = Lorentzian(display_name='Lorentzian', area=0.5, width=0.3)\n",
+    "component_collection = ComponentCollection(\n",
+    "    components=[delta_function, lorentzian],\n",
+    ")\n",
+    "\n",
+    "sample_model = SampleModel(\n",
+    "    components=component_collection,\n",
+    ")\n",
+    "\n",
+    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "\n",
+    "instrument_model = InstrumentModel(\n",
+    "    background_model=background_model,\n",
+    ")\n",
+    "\n",
+    "diffusion_analysis = Analysis(\n",
+    "    display_name='Diffusion Full Analysis',\n",
+    "    experiment=diffusion_experiment,\n",
+    "    sample_model=sample_model,\n",
+    "    instrument_model=instrument_model,\n",
+    ")\n",
+    "\n",
+    "# We need to hack in the resolution model from the vanadium analysis,\n",
+    "# since the setters and getters overwrite the model. This will be fixed\n",
+    "# asap.\n",
+    "diffusion_analysis.instrument_model._resolution_model = (\n",
+    "    vanadium_analysis.instrument_model.resolution_model\n",
+    ")\n",
+    "\n",
+    "# We fix all parameters of the resolution model.\n",
+    "diffusion_analysis.instrument_model.resolution_model.fix_all_parameters()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c66828eb",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Let us see how good the starting parameters are\n",
+    "diffusion_analysis.plot_data_and_model()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2a4b7572",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Now we fit the data and plot the result. Looks good!\n",
+    "diffusion_analysis.fit(fit_method='independent')\n",
+    "diffusion_analysis.plot_data_and_model()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "df14b5c4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Let us look at the most interesting fit parameters\n",
+    "diffusion_analysis.plot_parameters(names=['Lorentzian width', 'Lorentzian area'])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "eb226c8f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# It will be possible to fit this to a DiffusionModel, but that will\n",
+    "# come later."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4c6d7808",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Let us now fit directly to a diffusion model. We replace the\n",
+    "# Lorentzian with a Brownian translational diffusion model and keep the\n",
+    "# other parameters the same.\n",
+    "delta_function = DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
+    "component_collection = ComponentCollection(\n",
+    "    components=[delta_function],\n",
+    ")\n",
+    "diffusion_model = BrownianTranslationalDiffusion(\n",
+    "    display_name='Brownian Translational Diffusion', diffusion_coefficient=2.4e-9, scale=0.5\n",
+    ")\n",
+    "\n",
+    "sample_model = SampleModel(\n",
+    "    components=component_collection,\n",
+    "    diffusion_models=diffusion_model,\n",
+    ")\n",
+    "\n",
+    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "\n",
+    "instrument_model = InstrumentModel(\n",
+    "    background_model=background_model,\n",
+    ")\n",
+    "\n",
+    "diffusion_model_analysis = Analysis(\n",
+    "    display_name='Diffusion Full Analysis',\n",
+    "    experiment=diffusion_experiment,\n",
+    "    sample_model=sample_model,\n",
+    "    instrument_model=instrument_model,\n",
+    ")\n",
+    "\n",
+    "# We again need to hack in the resolution model from the vanadium\n",
+    "# analysis, since the setters and getters overwrite the model. This will\n",
+    "# be fixed asap.\n",
+    "diffusion_model_analysis.instrument_model._resolution_model = (\n",
+    "    vanadium_analysis.instrument_model.resolution_model\n",
+    ")\n",
+    "diffusion_model_analysis.instrument_model.resolution_model.fix_all_parameters()\n",
+    "\n",
+    "# Let us see how good the starting parameters are\n",
+    "diffusion_model_analysis.plot_data_and_model()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fd04d359",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# We now fit all the data simultaneously to the diffusion model, then\n",
+    "# plot the result. Looks good.\n",
+    "diffusion_model_analysis.fit(fit_method='simultaneous')\n",
+    "diffusion_model_analysis.plot_data_and_model()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "842c1f01",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Let us look at the fitted diffusion coefficient\n",
+    "diffusion_model.get_all_parameters()"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "easydynamics_newbase",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.12"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}