Analysis

docs/docs/tutorials/analysis.ipynb

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+{
+ "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 measurements, and next an artificial measurement of a model with diffusion and some elastic scattering.\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 as fitting the diffusion model directly to the data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bca91d3c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "from easydynamics.analysis.analysis import Analysis\n",
+    "from easydynamics.experiment import Experiment\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": [
+    "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",
+    "delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
+    "sample_model = SampleModel(\n",
+    "    components=delta_function,\n",
+    ")\n",
+    "\n",
+    "res_gauss = Gaussian(width=0.1)\n",
+    "res_gauss.area.fixed = True\n",
+    "resolution_model = ResolutionModel(components=res_gauss)\n",
+    "\n",
+    "\n",
+    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "\n",
+    "instrument_model = InstrumentModel(\n",
+    "    resolution_model=resolution_model,\n",
+    "    background_model=background_model,\n",
+    ")\n",
+    "\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",
+    "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": [
+    "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": "af13afce",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fit_result_simultaneous = vanadium_analysis.fit(fit_method='simultaneous')\n",
+    "fit_result_simultaneous\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": [
+    "# Set up the diffusion analysis with the same resolution model as the\n",
+    "# vanadium analysis\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": [
+    "# We set up the model first.\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",
+    "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",
+    "diffusion_analysis.instrument_model.resolution_model.fix_all_parameters()\n",
+    "diffusion_analysis.plot_parameters(names=['Gaussian width'])"
+   ]
+  },
+  {
+   "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": "197b44c5",
+   "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."
+   ]
+  }
+ ],
+ "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
+}

docs/docs/tutorials/analysis1d.ipynb

@@ -0,0 +1,109 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "8643b10c",
+   "metadata": {},
+   "source": [
+    "# Analysis1d\n",
+    "Sometimes, you will only be interested in a particular Q, not the full dataset. For this, use the Analysis1d object. We here show how to set it up to fit an artificial vanadium measurement."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bca91d3c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from easydynamics.analysis.analysis1d import Analysis1d\n",
+    "from easydynamics.experiment import Experiment\n",
+    "from easydynamics.sample_model import DeltaFunction\n",
+    "from easydynamics.sample_model import Gaussian\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": [
+    "vanadium_experiment = Experiment('Vanadium')\n",
+    "vanadium_experiment.load_hdf5(filename='vanadium_data_example.h5')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "41f842f0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Example of Analysis1d with a simple sample model and instrument model\n",
+    "delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
+    "sample_model = SampleModel(\n",
+    "    components=delta_function,\n",
+    ")\n",
+    "\n",
+    "res_gauss = Gaussian(width=0.1)\n",
+    "resolution_model = ResolutionModel(components=res_gauss)\n",
+    "\n",
+    "\n",
+    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "\n",
+    "instrument_model = InstrumentModel(\n",
+    "    resolution_model=resolution_model,\n",
+    "    background_model=background_model,\n",
+    ")\n",
+    "\n",
+    "my_analysis = Analysis1d(\n",
+    "    display_name='Vanadium Analysis',\n",
+    "    experiment=vanadium_experiment,\n",
+    "    sample_model=sample_model,\n",
+    "    instrument_model=instrument_model,\n",
+    "    Q_index=5,\n",
+    ")\n",
+    "\n",
+    "fit_result = my_analysis.fit()\n",
+    "my_analysis.plot_data_and_model()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c055bd93",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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
+}