///\file "parameterisations/Par03/.README.txt"
///\brief Example Par04 README page

/*! \page ExamplePar04 Example Par04

 This example demonstrates how to use the Machine Learning (ML) inference
 to create energy deposits as a fast simulation model using
<a href="https://github.com/microsoft/onnxruntime">ONNX runtime</a>,
 <a href="https://github.com/lwtnn/lwtnn">LWTNN</a>, and
 <a href="https://pytorch.org/cppdocs/frontend.html">LibTorch</a> libraries.

 The model used in this example was trained externally (in Python) on data
 from this examples' full simulation and can be applied to perform fast simulation.
 The python scripts are available in the training folder.

 The geometry used in the example is a cylindrical setup of layers: tungsten
 absorber and silicon as the active material. 3D readout geometry (cylindrical)
 is defined dynamically,  based on the particle direction at the entrance to the
 calorimeter. This is set using a fast simulation model that is triggered at
 detector entrance. Analysis of energy deposits is done in the event action,
 ntuple with hits is stored.

 ## 1. Detector description

 The detector consists of cylindrical layers of passive and active material,
 tungsten and silicon, respectively.

 Fast simulation is attached to the region of the detector.

 Input macro can specify which layer is considered an active layer (sensitive
 detector is attached to it). For fast simulation both layers should be marked
 as sensitive. It is connected to the way the deposits are created: position is
 centre of the layer, which may often fall within the absorber (which is thicker
 than the active material). In a realistic detector setup, the positions used in
 fast simulation would be calculated properly, to deposit energy within the active
 material.

 ## 2. Sensitive detector

### 2.1. Par04SensitiveDetector

This SD scores energy originating from showers, in a cylinder around the particle 
direction and position in the calorimeter.
 Sensitive detector inherits from both base classes:
 - G4VSensitiveDetector: for processing of detailed/non-fast simulation hits
 - G4VFastSimSensitiveDetector: for processing of fast sim (G4FastSim) hits.
 Hits are placed in the same hit collection, with a different flag to distinguish
 between those originated in the full simulation, and those from the fast
 simulation.
 During visualisation, hits are represented as volumes of different colour:
 green for full simulation and red for fast simulation.

### 2.2. Par04ParallelFullSensitiveDetector

This SD represents a physical readout structure to the detector (a regular grid).
UI settings are available to set number of slices (azimuthal segmentation) and number
of rows (segmentation along beam axis). Number of layers cannot be changed as it
corresponds to the number of layers placed at the detector construction time. Only
deposits in the active (sensitive) layers are scored in this SD.

### 2.2. Par04ParallelFastSensitiveDetector

This SD represents a physical readout that takes into account deposits originating
from fast simulation, so cells span over active and passive layers. This allows to
account all energy from the parameterisation.

 ## 3. Primary generation

 Particle gun is used as a primary generator. 10 GeV electron is used by default.
 By default particles are generated along y axis. Those values
 can be changed using /gun/ UI commands.

 ## 4. Physics List

 FTFP_BERT modular physics list is used. On top of it, fast simulation physics
 is registered for selected particles (electrons, positrons).


 ## 5. User actions

 - Par04RunAction : run action used for initialization and termination
                    of the run. Histograms for analysis of shower development
                    in the detector are created.

 - Par04EventAction : event action used for initialization and termination
                      of the event. Analysis of shower development is performed
                      on event-by-event basis.

 ## 6. ML Inference

 - Par04MLFastSimModel : model used for parametrisation of electrons, positrons,
      and gammas. Energy is deposited and
      distributed according to inferred values from the ML model.
      This class triggers the inference setup, asks for values,
      and deposits energies at given positions.

 - Par04InferenceSetup : this class is used to initialize the inference parameters
       (user application specific) such as the inference library,
      the path and name of the inference model and the size of
      the input inference vector(latent dimension and and condition size).
      This class constructs this vector and triggers the interface
      corresponding to the specified input inference library.
      After the inference, the post processing step consists of
      scaling back inferred values to the original range.

 - Par04InferenceInterface : is a base class that allows to read in the ML model, configure
       and execute inference.

 - Par04OnnxInference and Par04LWTNNInference and Par04TorchInference : inference library specific
      classes that inherit from the base class Par04InferenceInterface.


 ## 7. Output

 The execution of the program (examplePar04) produces an output with histograms.
 Ntuples are also stored. They are not merged if the application is run on multiple threads.

 The macro file examplePar04.mac is used to run full simulation. It will simulate 100
 events, for single 10 GeV electron beams.
 If CMake is able to find inference libraries (LWTNN and/or ONNX Runtime and/or LibTorch), a configuration
 macro will be available for that library (examplePar04_lwtnn.mac and/or examplePar04_onnx.mac
 and/or examplePar04_torch.mac). It will use a trained model to run inference and create showers
 in the detector by directly depositing energy.

 ## 8. How to build and run the example

- LWTNN, ONNX Runtime, and LibTorch are available on LCG. In order to use them, you can set a `CMAKE_PREFIX_PATH`:
\verbatim
  % source /cvmfs/sft.cern.ch/lcg/contrib/gcc/11.3.0/x86_64-centos7/setup.sh
  % cmake -DCMAKE_PREFIX_PATH="/cvmfs/sft.cern.ch/lcg/releases/LCG_102b/lwtnn/2.11.1/x86_64-centos7-gcc11-opt/;/cvmfs/sft.cern.ch/lcg/releases/LCG_102b/onnxruntime/1.11.1/x86_64-centos7-gcc11-opt/;/cvmfs/sft.cern.ch/lcg/releases/LCG_102b/torch/1.11.0/x86_64-centos7-gcc11-opt/lib/python3.9/site-packages/torch/" <Par04_SOURCE>
\endverbatim

- Compile and link to generate the executable (in your CMake build directory):
\verbatim
% cmake <Par04_SOURCE>
% make
\endverbatim

- Execute the application (in batch mode):
\verbatim
% ./examplePar04 -m examplePar04.mac
\endverbatim
  which produces two root file for full simulation.

- Execute the application (in interactive mode):
\verbatim
% ./examplePar04 -i -m vis.mac
\endverbatim
  which allows to visualize hits (from full simulation).

- If ONNX Runtime is available:
\verbatim
% ./examplePar04 -m examplePar04_onnx.mac
\endverbatim
  For interactive mode with visualization:
\verbatim
% ./examplePar04 -i -m vis_onnx.mac
\endverbatim

- If LWTNN is available:
\verbatim
% ./examplePar04 -m examplePar04_lwtnn.mac
\endverbatim
  For interactive mode with visualization:
\verbatim
% ./examplePar04 -i -m vis_lwtnn.mac
\endverbatim

- If LibTorch is available:
\verbatim
% ./examplePar04 -m examplePar04_torch.mac
\endverbatim
  For interactive mode with visualization:
\verbatim
% ./examplePar04 -i -m vis_torch.mac
\endverbatim

- Additional options available:
\verbatim
% ./examplePar04 -m examplePar04.mac -r 0
\endverbatim
For serial run manager mode
\verbatim
% ./examplePar04 -m examplePar04.mac -r 1 -t 8
\endverbatim
For multi-threaded run manager mode with 8 threads
\verbatim
% ./examplePar04 -m examplePar04.mac -r 2
\endverbatim
For tasking run manager mode with number of tasks that can be change via env variable G4FORCE_EVENTS_PER_TASK

 By default, CMake will attempt to build fast simulation with ONNX Runtime and LWTNN. However, if none
 of those libraries is found, it will proceed with full simulation only. The search can be switched
 off manually switching CMake flag `INFERENCE_LIB` to `OFF` (`-DINFERENCE_LIB=OFF`)

 ## 9. Macros

common_settings.mac - A macro with common settings, executed by all other macros (e.g. detector settings).

 vis.mac - Allows to run visualization. Pass it to the example in interactive mode ("-i" passed to the executable).
           It can be used to visualize full simulation.

 vis_onnx.mac - Allows to run visualization with ONNX Runtime inference. Pass it to the example in interactive mode
              ("-i" passed to the executable). It contains necessary settings of the inference.

 vis_lwtnn.mac - Allows to run visualization with LWTNN inference. Pass it to the example in interactive mode
              ("-i" passed to the executable). It contains necessary settings of the inference.

 vis_torch.mac - Allows to run visualization with LibTorch inference. Pass it to the example in interactive mode
              ("-i" passed to the executable). It contains necessary settings of the inference.

 examplePar04.mac - Runs full simulation. It will run 100 events with single electrons, 10 GeV and
                   along y axis.

 examplePar04_onnx.mac - Available only if ONNX Runtime is found by CMake. Runs fast simulation with
                        a NN stored in onnx file.

 examplePar04_lwtnn.mac - Available only if LWTNN is found by CMake. Runs fast simulation with
                        a NN stored in json file.

 examplePar04_torch.mac - Available only if LibTorch is found by CMake. Runs fast simulation with
                        a NN stored in pt file.

 ## 10. UI commands

 UI commands useful in this example:

- activation/disactivation of the fast simulation model:
\verbatim
/param/ActivateModel inferenceModel
/param/InActivateModel inferenceModel
\endverbatim

- particle gun commands
\verbatim
/gun/particle e-
/gun/energy 10 GeV
/gun/direction 0 1 0
/gun/position 0 0 0
\endverbatim

 UI commands defined in this example:
 - detector settings
\verbatim
/Par04/detector/setDetectorInnerRadius 80 cm
/Par04/detector/setDetectorLength 2 m
/Par04/detector/setNbOfLayers 90
/Par04/detector/setAbsorber 0 G4_W 1.4 mm false
/Par04/detector/setAbsorber 1 G4_Si 0.3 mm true
\endverbatim

 - readout mesh
\verbatim
/Par04/mesh/setSizeOfRhoCells 2.325 mm
/Par04/mesh/setSizeOfZCells 3.4 mm
/Par04/mesh/setNbOfRhoCells 18
/Par04/mesh/setNbOfPhiCells 50
/Par04/mesh/setNbOfZCells 45
\endverbatim

 - inference setup
\verbatim
/Par04/inference/setSizeLatentVector 10
/Par04/inference/setSizeConditionVector 4
/Par04/inference/setModelPathName MLModels/Generator.onnx
/Par04/inference/setProfileFlag 0
/Par04/inference/setOptimizationFlag 0
/Par04/inference/setInferenceLibrary ONNX
/Par04/inference/setSizeOfRhoCells 2.325 mm
/Par04/inference/setSizeOfZCells 3.4 mm
/Par04/inference/setNbOfRhoCells 18
/Par04/inference/setNbOfPhiCells 50
/Par04/inference/setNbOfZCells 45
\endverbatim

 ## 11. Python scripts for training

 The scripts available in the training folder were used to firstly convert
 the ROOT files to the h5 files, preprocess the data and then train
 the VAE model of this example. More details can be found in 
 training/README.


 ## 12. Public data

 Data generated with full simulation with this example has been published on <a href="https://doi.org/10.5281/zenodo.6082201">zenodo</a>.

 */
