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docs: update usage notebooks new sympy design
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‎.gitignore

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*.json
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*.npy
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*.pdf
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*.pickle
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*.png
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*.svg
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*.v2

‎cspell.json

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"itertools",
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"jsonschema",
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"jupyter",
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"lineshape",
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"mathbb",
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"matplotlib",
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"mkdir",

‎docs/usage.md

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usage/1_create_model
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usage/2_generate_data
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usage/3_perform_fit
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usage/sympy
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usage/backends
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```

‎docs/usage/1_create_model.ipynb

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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Next we convert the {attr}`~expertsystem.reaction.Result.transitions` into an {class}`~expertsystem.amplitude.model.AmplitudeModel`. This can be done with the {func}`~expertsystem.generate_amplitudes` method."
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"Next we convert the {attr}`~expertsystem.reaction.Result.transitions` into an {class}`~expertsystem.amplitude.helicity.HelicityModel`. This can be done with the {func}`~expertsystem.generate_amplitudes` method."
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{
@@ -92,7 +92,11 @@
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Note that we have to specify the dynamics for the resonances. We choose to use {class}`~expertsystem.amplitude.model.RelativisticBreitWigner` for all resonances:"
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"The heart of the model is a sympy expression that contains the full description of the intensity model. Note two things:\n",
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"1. The coefficients for the different amplitudes are **complex** valued.\n",
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"2. By default there is no dynamics in the model and it still has to be specified.\n",
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"\n",
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"We choose to use {func}`~expertsystem.amplitude.dynamics.lineshape.relativistic_breit_wigner_with_ff` for all resonances. In the HelicityModel `~expertsystem.amplitude.dynamics.set_resonance_dynamics` is an convenience interface for replacing the dynamics for intermediate states."
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"from expertsystem.amplitude.dynamics import set_resonance_dynamics\n",
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"from expertsystem.amplitude.dynamics.builder import (\n",
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" create_relativistic_breit_wigner_with_ff,\n",
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")\n",
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"\n",
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"for name in result.get_intermediate_particles().names:\n",
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" model.dynamics.set_breit_wigner(name)\n",
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"{name: type(dyn) for name, dyn in model.dynamics.items()}"
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" set_resonance_dynamics(\n",
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" model, name, create_relativistic_breit_wigner_with_ff\n",
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" )"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Now let's take another look at the parameters of the model"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"list(model.parameters)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Finally, we can write the [AmplitudeModel](expertsystem.amplitude.model.AmplitudeModel), using the [io.write](expertsystem.io.write) function:"
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"Finally, we can write the [HelicityModel](expertsystem.amplitude.helicity.HelicityModel) via `pickle` to file:"
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]
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"es.io.write(model, \"amplitude_model_helicity.yml\")"
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"import pickle\n",
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"\n",
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"with open(\"helicity_model.pickle\", \"wb\") as model_file:\n",
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" pickle.dump(model, model_file)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Cool, that's it! We now have a recipe for an amplitude model with which to [generate data](./2_generate_data) and [perform a fit](./3_perform_fit)! In the [next steps](./2_generate_data), we will use use this [AmplitudeModel](expertsystem.amplitude.model.AmplitudeModel) as a fit model template for [tensorwaves](tensorwaves)."
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"Cool, that's it! We now have a recipe for an amplitude model with which to [generate data](./2_generate_data) and [perform a fit](./3_perform_fit)! In the [next steps](./2_generate_data), we will use use this {class}`~expertsystem.amplitude.helicity.HelicityModel` as a fit model template for {mod}`tensorwaves`."
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]
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}
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],

‎docs/usage/2_generate_data.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"jupyter": {
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"source_hidden": true
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},
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"tags": [
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"remove-cell"
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]
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},
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"outputs": [],
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"source": [
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"%config Completer.use_jedi = False"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"cell_type": "markdown",
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"source": [
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"In this section, we will use the [AmplitudeModel](expertsystem.amplitude.model.AmplitudeModel) that we created with the expert system in [the previous step](./1_create_model) to generate a data sample via hit & miss Monte Carlo. We do this with the [tensorwaves.data.generate](tensorwaves.data.generate) module.\n",
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"In this section, we will use the {class}`~expertsystem.amplitude.helicity.HelicityModel` that we created with the expert system in [the previous step](./1_create_model) to generate a data sample via hit & miss Monte Carlo. We do this with the {mod}`tensorwaves.data.generate` module.\n",
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"\n",
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"First, we {func}`~.expertsystem.io.load` an {class}`~expertsystem.amplitude.model.AmplitudeModel` that was created in the previous step:"
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"First, we {func}`~.expertsystem.io.load` an {class}`~expertsystem.amplitude.helicity.HelicityModel` that was created in the previous step:"
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"from expertsystem import io\n",
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"# TODO: pickling of the HelicityModel does not work, so we have to currently redo all steps from before...\n",
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"import expertsystem as es\n",
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"\n",
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"model = io.load(\"amplitude_model_helicity.yml\")"
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"result = es.generate_transitions(\n",
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" initial_state=(\"J/psi(1S)\", [-1, +1]),\n",
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" final_state=[\"gamma\", \"pi0\", \"pi0\"],\n",
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" allowed_intermediate_particles=[\"f(0)\"],\n",
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" allowed_interaction_types=\"strong and EM\",\n",
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")\n",
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"model = es.generate_amplitudes(result)\n",
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"from expertsystem.amplitude.dynamics import set_resonance_dynamics\n",
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"from expertsystem.amplitude.dynamics.builder import (\n",
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" create_relativistic_breit_wigner_with_ff,\n",
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")\n",
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"\n",
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"for name in result.get_intermediate_particles().names:\n",
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" set_resonance_dynamics(\n",
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" model, name, create_relativistic_breit_wigner_with_ff\n",
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" )"
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{
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"cell_type": "markdown",
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"source": [
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"An [AmplitudeModel](expertsystem.amplitude.model.AmplitudeModel) defines the kinematics, the particles involved in the reaction, the dynamics used for the model on which to perform the eventual optimization, etc."
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"A {class}`~expertsystem.amplitude.helicity.HelicityModel` defines the kinematics, the particles involved in the reaction, the dynamics used for the model on which to perform the eventual optimization, etc."
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"# TODO: this part will be changed once the kinematics is ported to the expertsystem!\n",
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"from tensorwaves.physics.helicity_formalism.kinematics import (\n",
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" HelicityKinematics,\n",
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" ParticleReactionKinematicsInfo,\n",
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" SubSystem,\n",
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")\n",
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"\n",
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"kin = HelicityKinematics(\n",
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" ParticleReactionKinematicsInfo(\n",
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" initial_state_names=[\n",
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" x.name for x in model.kinematics.initial_state.values()\n",
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" ],\n",
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" final_state_names=[\n",
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" x.name for x in model.kinematics.final_state.values()\n",
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" ],\n",
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" particles=model.particles,\n",
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" fs_id_event_pos_mapping=dict(\n",
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" {k: i for i, k in enumerate(model.kinematics.final_state.keys())}\n",
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" ),\n",
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" )\n",
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")\n",
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"kin.register_subsystem(SubSystem([[3, 4], [2]], [], []))\n",
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"kin.register_subsystem(SubSystem([[3], [4]], [2], []))\n",
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"kin.register_invariant_mass([2, 4])\n",
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"\n",
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"import pickle\n",
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"\n",
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"with open(\"kinematics.pickle\", \"wb\") as kin_file:\n",
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" pickle.dump(kin, kin_file)\n",
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"\n",
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"kin = HelicityKinematics.from_model(model)\n",
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"print(\"Initial state mass:\", kin.reaction_kinematics_info.initial_state_masses)\n",
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"print(\"Final state masses:\", kin.reaction_kinematics_info.final_state_masses)\n",
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"print(\"Involved particles:\", model.particles.names)"
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"'Data samples' are more complicated than phase space samples in that they represent the intensity profile resulting from a reaction. You therefore need an [IntensityTF](tensorwaves.physics.helicity_formalism.amplitude.IntensityTF) object (or, more generally, a [Function](tensorwaves.interfaces.Function) instance) and a phase space over which to generate that intensity distribution. We call such a data sample an **intensity-based sample**.\n",
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"'Data samples' are more complicated than phase space samples in that they represent the intensity profile resulting from a reaction. You therefore need an {class}`~tensorwaves.physics.amplitude.Intensity` object (or, more generally, a [Function](tensorwaves.interfaces.Function) instance) and a phase space over which to generate that intensity distribution. We call such a data sample an **intensity-based sample**.\n",
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"\n",
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"An intensity-based sample is generated with the function [generate_data](tensorwaves.data.generate.generate_data). Its usage is similar to [generate_phsp](tensorwaves.data.generate.generate_phsp), but now you have to give an [Intensity](tensorwaves.physics.amplitude.Intensity) in addition to the [Kinematics](tensorwaves.interfaces.Kinematics) object. An [Intensity](tensorwaves.physics.amplitude.Intensity) object can be created with the [SympyModel](tensorwaves.physics.amplitude.SympyModel) class:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from tensorwaves.physics.amplitude import Intensity, SympyModel\n",
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"\n",
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"sympy_model = SympyModel(\n",
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" expression=model.expression.full_expression,\n",
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" parameters={k: v.value for k, v in model.parameters.items()},\n",
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" variables={},\n",
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")\n",
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"\n",
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"An intensity-based sample is generated with the function [generate_data](tensorwaves.data.generate.generate_data). Its usage is similar to [generate_phsp](tensorwaves.data.generate.generate_phsp), but now you have to give an [IntensityTF](tensorwaves.physics.helicity_formalism.amplitude.IntensityTF) in addition to the [Kinematics](tensorwaves.interfaces.Kinematics) object. An [IntensityTF](tensorwaves.physics.helicity_formalism.amplitude.IntensityTF) object can be created with the [IntensityBuilder](tensorwaves.physics.helicity_formalism.amplitude.IntensityBuilder) class:"
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"intensity = Intensity(sympy_model)"
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"from tensorwaves.physics.helicity_formalism.amplitude import IntensityBuilder\n",
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"import pickle\n",
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"\n",
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"builder = IntensityBuilder(model.particles, kin)\n",
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"intensity = builder.create_intensity(model)"
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"with open(\"sympy_model.pickle\", \"wb\") as model_file:\n",
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" pickle.dump(sympy_model, model_file)"
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"The data set is just a [dict](dict) of kinematic variables (keys are the names, values is a list of computed values for each event). The numbers you see here are final state IDs as defined in the [AmplitudeModel](expertsystem.amplitude.model.AmplitudeModel) member of the [AmplitudeModel](expertsystem.amplitude.model.AmplitudeModel):"
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"The data set is just a [dict](dict) of kinematic variables (keys are the names, values is a list of computed values for each event). The numbers you see here are final state IDs as defined in the {class}`~expertsystem.amplitude.helicity.HelicityModel` member of the {class}`~expertsystem.amplitude.helicity.HelicityModel`:"
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{
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"cell_type": "markdown",
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"In the [next step](./3_perform_fit), we will illustrate how to 'perform a fit' with [tensorwaves](tensorwaves) by optimizing the intensity model to these data samples."
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"In the [next step](./3_perform_fit), we will illustrate how to 'perform a fit' with {mod}`tensorwaves` by optimizing the intensity model to these data samples."
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