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 #!/usr/bin/env python3
 
 import os
 import argparse
 import time
 from datetime import datetime
 
 from orion.client import build_experiment
 from orion.storage.base import get_storage
 
 import acts
 from acts import (
     SurfaceMaterialMapper,
     VolumeMaterialMapper,
     Navigator,
     Propagator,
     StraightLineStepper,
 )
 
 from acts.json import MaterialMapJsonConverter
 
 from acts.examples import (
     Sequencer,
     WhiteBoard,
     AlgorithmContext,
     ProcessCode,
     MaterialMapping,
 )
 
 from acts.examples.root import (
     RootMaterialTrackReader,
     RootMaterialTrackWriter,
 )
 
 from acts.examples.json import (
     JsonMaterialWriter,
     JsonFormat,
 )
 
 from acts.examples.odd import getOpenDataDetector
 
 
 def runMaterialMappingNoTrack(
     trackingGeometry,
     decorators,
     outputDir,
     inputDir,
     mapName="material-map",
     mapSurface=True,
     mapVolume=True,
     format=JsonFormat.Json,
     readCachedSurfaceInformation=False,
     s=None,
 ):
     """
     Implementation of the material mapping that doesn't write the material tracks.
     Used to create the material map that will then be used to compute the material variance.
 
     trackingGeometry : The tracking geometry
     decorators : The decorators for the tracking geometry
     outputDir : Output directory for the material map
     inputDir : Input directory containing the Material track
     mapName : Name of the material map
     mapSurface : Is material being mapped onto surfaces ?
     mapVolume : Is material being mapped onto volumes ?
     format : Json format used to write the material map (json, cbor, ...)
     readCachedSurfaceInformation : If set to true it will be assumed that the surface has already been associated with each material interaction in the input file.
     """
 
     s = s or Sequencer(numThreads=1)
     for decorator in decorators:
         s.addContextDecorator(decorator)
     wb = WhiteBoard(acts.logging.INFO)
     context = AlgorithmContext(0, 0, wb)
     for decorator in decorators:
         assert decorator.decorate(context) == ProcessCode.SUCCESS
 
     # Read material step information from a ROOT TTRee
     s.addReader(
         RootMaterialTrackReader(
             level=acts.logging.INFO,
             outputMaterialTracks="material-tracks",
             fileList=[
                 os.path.join(
                     inputDir,
                     (
                         "optimised-material-map_tracks.root"
                         if readCachedSurfaceInformation
                         else "geant4_material_tracks.root"
                     ),
                 )
             ],
             readCachedSurfaceInformation=readCachedSurfaceInformation,
         )
     )
 
     stepper = StraightLineStepper()
     mmAlgCfg = MaterialMapping.Config(context.geoContext, context.magFieldContext)
     mmAlgCfg.trackingGeometry = trackingGeometry
     mmAlgCfg.inputMaterialTracks = "material-tracks"
 
     if mapSurface:
         navigator = Navigator(
             trackingGeometry=trackingGeometry,
             resolveSensitive=True,
             resolveMaterial=True,
             resolvePassive=True,
         )
         propagator = Propagator(stepper, navigator)
         mapper = SurfaceMaterialMapper(level=acts.logging.INFO, propagator=propagator)
         mmAlgCfg.materialSurfaceMapper = mapper
 
     if mapVolume:
         navigator = Navigator(
             trackingGeometry=trackingGeometry,
         )
         propagator = Propagator(stepper, navigator)
         mapper = VolumeMaterialMapper(
             level=acts.logging.INFO, propagator=propagator, mappingStep=999
         )
         mmAlgCfg.materialVolumeMapper = mapper
 
     jmConverterCfg = MaterialMapJsonConverter.Config(
         processSensitives=True,
         processApproaches=True,
         processRepresenting=True,
         processBoundaries=True,
         processVolumes=True,
         context=context.geoContext,
     )
 
     jmw = JsonMaterialWriter(
         level=acts.logging.VERBOSE,
         converterCfg=jmConverterCfg,
         fileName=os.path.join(outputDir, mapName),
         writeFormat=format,
     )
 
     mmAlgCfg.materialWriters = [jmw]
 
     s.addAlgorithm(MaterialMapping(level=acts.logging.INFO, config=mmAlgCfg))
 
     return s
 
 
 def runMaterialMappingVariance(
     binMap,
     events,
     job,
     inputPath,
     pathExp,
     pipeResult,
     readCachedSurfaceInformation=False,
 ):
     """
     Run the material mapping and compute the variance for each bin of each surface
     Return a dict with the GeometryId value of the surface as a key that stores
     a list of pairs corresponding to the variance and number of tracks associated with each bin of the surface
 
     binMap : Map containing the binning for each surface
     events : Number of event to use in the mapping
     job : ID of the job
     inputPath : Directory containing the input geantino track and the json geometry
     pathExp : Material mapping optimisation path
     pipeResult : Pipe to send back the score to the main python instance
     readCachedSurfaceInformation : Are surface information stored in the material track. Switch to true if the mapping was already performed to improve the speed.
     """
     print(
         datetime.now().strftime("%H:%M:%S") + "    Start mapping for job " + str(job),
         flush=True,
     )
     mapName = "material-map-" + str(job)
     mapSurface = True
     mapVolume = False
 
     # Create a MappingMaterialDecorator based on the tracking geometry
     matDeco = acts.IMaterialDecorator.fromFile(
         str(os.path.join(inputPath, "geometry-map.json"))
     )
     detectorTemp = getOpenDataDetector(matDeco)
     trackingGeometryTemp = detectorTemp.trackingGeometry()
     matMapDeco = acts.examples.MappingMaterialDecorator(
         tGeometry=trackingGeometryTemp, level=acts.logging.ERROR
     )
     # Update the binning using the bin map corresponding to this trial
     matMapDeco.setBinningMap(binMap)
 
     # Decorate the detector with the MappingMaterialDecorator
     detector = getOpenDataDetector(matMapDeco)
     trackingGeometry = detector.trackingGeometry()
     decorators = detector.contextDecorators()
 
     # Sequence for the mapping, only use one thread when mapping material
     sMap = acts.examples.Sequencer(
         events=events, numThreads=1, logLevel=acts.logging.INFO
     )
 
     # Run the material mapping without writing the material track (as they take too much space)
     runMaterialMappingNoTrack(
         trackingGeometry,
         decorators,
         outputDir=pathExp,
         inputDir=inputPath,
         mapName=mapName,
         format=JsonFormat.Cbor,
         mapVolume=mapVolume,
         readCachedSurfaceInformation=readCachedSurfaceInformation,
         s=sMap,
     )
     sMap.run()
 
     # Compute the variance by rerunning the mapping
     print(
         datetime.now().strftime("%H:%M:%S")
         + "    Job "
         + str(job)
         + ": second pass to compute the variance",
         flush=True,
     )
     # Use the material map from the previous mapping as an input
     cborMap = os.path.join(pathExp, (mapName + ".cbor"))
     matDecoVar = acts.IMaterialDecorator.fromFile(cborMap)
     detectorVar = getOpenDataDetector(matDecoVar)
     trackingGeometryVar = detectorVar.trackingGeometry()
     decoratorsVar = detectorVar.contextDecorators()
     s = acts.examples.Sequencer(events=events, numThreads=1, logLevel=acts.logging.INFO)
     for decorator in decoratorsVar:
         s.addContextDecorator(decorator)
     wb = WhiteBoard(acts.logging.ERROR)
     context = AlgorithmContext(0, 0, wb)
     for decorator in decoratorsVar:
         assert decorator.decorate(context) == ProcessCode.SUCCESS
 
     # Read material step information from a ROOT TTRee
     reader = RootMaterialTrackReader(
         level=acts.logging.ERROR,
         outputMaterialTracks="material-tracks",
         fileList=[
             os.path.join(
                 inputPath,
                 (
                     "optimised-material-map_tracks.root"
                     if readCachedSurfaceInformation
                     else "geant4_material_tracks.root"
                 ),
             )
         ],
         readCachedSurfaceInformation=readCachedSurfaceInformation,
     )
     s.addReader(reader)
     stepper = StraightLineStepper()
     mmAlgCfg = MaterialMapping.Config(context.geoContext, context.magFieldContext)
     mmAlgCfg.trackingGeometry = trackingGeometryVar
     mmAlgCfg.inputMaterialTracks = "material-tracks"
 
     if mapSurface:
         navigator = Navigator(
             trackingGeometry=trackingGeometryVar,
             resolveSensitive=True,
             resolveMaterial=True,
             resolvePassive=True,
         )
         propagator = Propagator(stepper, navigator)
         surfaceCfg = SurfaceMaterialMapper.Config(
             computeVariance=True
         )  # Don't forget to turn the `computeVariance` to true
         mapper = SurfaceMaterialMapper(
             config=surfaceCfg, level=acts.logging.ERROR, propagator=propagator
         )
         mmAlgCfg.materialSurfaceMapper = mapper
 
     if mapVolume:
         navigator = Navigator(
             trackingGeometry=trackingGeometryVar,
         )
         propagator = Propagator(stepper, navigator)
         mapper = VolumeMaterialMapper(
             level=acts.logging.ERROR, propagator=propagator, mappingStep=999
         )
         mmAlgCfg.materialVolumeMapper = mapper
 
     mapping = MaterialMapping(level=acts.logging.ERROR, config=mmAlgCfg)
     s.addAlgorithm(mapping)
     s.run()
 
     # Compute the scoring parameters
     score = dict()
     for key in binMap:
         objective = 0
         nonZero = 0
         binParameters = mapping.scoringParameters(key)
         # Objective : Sum of variance in all bin divided by the number of bin
         # The variance is scaled by (1.0 + 1.0/(number of hits in the bin)) to encourage larger bin at equal score
         for parameters in binParameters:
             if parameters[1] != 0:
                 objective += parameters[0] * (1.0 + 1.0 / parameters[1])
                 nonZero += 1
         if nonZero != 0:
             objective = objective / nonZero
         score[key] = [dict(name="surface_score", type="objective", value=objective)]
     print(
         datetime.now().strftime("%H:%M:%S")
         + "    Mapping over for job "
         + str(job)
         + " : now sending score",
         flush=True,
     )
     pipeResult.send(score)
 
     os.remove(cborMap)
 
 
 def surfaceExperiment(key, nbJobs, pathDB, pathResult, pipeBin, pipeResult, doPloting):
     """
     This function create an experiment for a given single surface
     Due to how Orion is implemented only one DB can exist per job, this thus need to be call using pythons multiprocessing to circumvent the issue.
 
     key : Id of the surface corresponding to this experiment
     nbJobs : Total number of jobs to be executed simultaneously
     pathDB : Path to the databases
     pathResult : Path to write the result of the optimisation
     pipeBin : Pipe use to send the experiment binning to the main python instance
     pipeResult : Pipe to receive the result of the optimisation
     doPloting : true if we want to plot the result of the optimisation and obtain the optimal material map
     """
     # Create the database
     storage = {
         "database": {
             "name": "database_" + str(key),
             "type": "pickleddb",
             "host": os.path.join(pathDB, "database_" + str(key) + ".pkl"),
             "timeout": 43200,
         },
     }
     # Create the search space, the range of the binning can be chosen here
     # x represent X or phi depending on the type of surface
     # y represent Y, R or Z depending on the type of surface
     space = {
         "x": "uniform(1, 240, discrete=True)",
         "y": "uniform(1, 240, discrete=True)",
     }
     # Build the experiment
     experiments = build_experiment(
         "s_" + str(key),
         version="1",
         space=space,
         algorithms="random",
         storage=storage,
         max_idle_time=43200,
     )
     # Clean trial that haven't been completed
     store = get_storage()
     store.delete_trials(uid=experiments.id, where={"status": {"$ne": "completed"}})
     store.release_algorithm_lock(uid=experiments.id)
 
     # Suggest one binning per job and then send them via the pipe
     trials = dict()
     binMap = dict()
     for job in range(nbJobs):
         trials[job] = experiments.suggest()
         binMap[job] = (trials[job].params["x"], trials[job].params["y"])
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Binning for job "
             + str(job)
             + " and surface "
             + str(key)
             + " has been selected",
             flush=True,
         )
         pipeBin.send(binMap[job])
     print(
         datetime.now().strftime("%H:%M:%S")
         + "    All binning for surface "
         + str(key)
         + " has been sent",
         flush=True,
     )
     # Store the score resulting for the jobs in the database
     for job in range(nbJobs):
         score = pipeResult.recv()
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Received score for job "
             + str(job)
             + " and surface "
             + str(key),
             flush=True,
         )
         experiments.observe(trials[job], score)
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Score for job "
             + str(job)
             + " and surface "
             + str(key)
             + " has been written",
             flush=True,
         )
 
     # Create some performances plots for each surface
     if doPloting:
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    All the jobs are over. Now creating the optimisation plots",
             flush=True,
         )
 
         pathExpSurface = os.path.join(pathResult, "b_" + str(key))
         if not os.path.isdir(pathExpSurface):
             os.makedirs(pathExpSurface)
 
         regret = experiments.plot.regret()
         regret.write_html(pathExpSurface + "/regret.html")
 
         parallel_coordinates = experiments.plot.parallel_coordinates()
         parallel_coordinates.write_html(pathExpSurface + "/parallel_coordinates.html")
 
         lpi = experiments.plot.lpi()
         lpi.write_html(pathExpSurface + "/lpi.html")
 
         partial_dependencies = experiments.plot.partial_dependencies()
         partial_dependencies.write_html(pathExpSurface + "/partial_dependencies.html")
 
         # Select the optimal binning and send it via the pipe
         df = experiments.to_pandas()
         best = df.iloc[df.objective.idxmin()]
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Best score for surface "
             + str(key)
             + " : "
             + str(best),
             flush=True,
         )
         resultBinMap = (best.x, best.y)
         pipeBin.send(resultBinMap)
 
 
 if "__main__" == __name__:
     print(datetime.now().strftime("%H:%M:%S") + "    Starting")
     # Optimiser arguments
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "--numberOfJobs", nargs="?", default=2, type=int
     )  # number of parallele jobs
     parser.add_argument(
         "--topNumberOfEvents", nargs="?", default=100, type=int
     )  # number of events per trials
     parser.add_argument(
         "--inputPath", nargs="?", default=os.getcwd(), type=str
     )  # path to the input
     parser.add_argument(
         "--outputPath", nargs="?", default="", type=str
     )  # path to the output
     parser.add_argument(
         "--doPloting", action="store_true"
     )  # Return the optimisation plot and create the optimal material map
     parser.add_argument(
         "--readCachedSurfaceInformation", action="store_true"
     )  # Use surface information from the material track
     parser.set_defaults(doPloting=False)
     parser.set_defaults(readCachedSurfaceInformation=False)
     args = parser.parse_args()
 
     # Define the useful path and create them if they do not exist
     pathExp = os.path.join(args.outputPath, "Mapping")
     pathDB = os.path.join(pathExp, "Database")
     pathResult = os.path.join(pathExp, "Result")
     if not os.path.isdir(pathExp):
         os.makedirs(pathExp)
     if not os.path.isdir(pathDB):
         os.makedirs(pathDB)
     if not os.path.isdir(pathResult):
         os.makedirs(pathResult)
 
     # Create the tracking geometry, uses the json file to configure the proto-surfaces
     matDeco = acts.IMaterialDecorator.fromFile(
         str(os.path.join(args.inputPath, "geometry-map.json"))
     )
     detector = getOpenDataDetector(matDeco)
     trackingGeometry = detector.trackingGeometry()
     decorators = detector.contextDecorators()
 
     # Use the MappingMaterialDecorator to create a binning map that can be optimised
     matMapDeco = acts.examples.MappingMaterialDecorator(
         tGeometry=trackingGeometry, level=acts.logging.WARNING
     )
     binDict = matMapDeco.binningMap()
 
     # Create the pipes that will be used to transfer data to/from the jobs
     from multiprocessing import Process, Pipe
 
     binPipes_child = dict()
     resultPipes_child = dict()
     scorePipes_child = dict()
 
     binPipes_parent = dict()
     resultPipes_parent = dict()
     scorePipes_parent = dict()
 
     expJob = dict()
     OptiJob = dict()
 
     # Build one experiment per surface
     # The binning of the surfaces are independent so we split
     # an optimisation problem with a large number of variable into a lot of optimisation with 2
     for key in binDict:
         binPipes_parent[key], binPipes_child[key] = Pipe()
         scorePipes_parent[key], scorePipes_child[key] = Pipe()
         expJob[key] = Process(
             target=surfaceExperiment,
             args=(
                 key,
                 args.numberOfJobs,
                 pathDB,
                 pathResult,
                 binPipes_child[key],
                 scorePipes_child[key],
                 args.doPloting,
             ),
         )
         expJob[key].start()
 
     # Prepare `args.numberOfJobs` material mapping jobs
     for job in range(args.numberOfJobs):
         resultPipes_parent[job], resultPipes_child[job] = Pipe()
         binMap = dict()
         # Collect the binning for all the surfaces and create a bin map
         for key in binDict:
             binMap[key] = binPipes_parent[key].recv()
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Binning for job "
             + str(job)
             + " have been selected, now running the mapping",
             flush=True,
         )
         # Launch the material mapping with the bin map
         OptiJob[job] = Process(
             target=runMaterialMappingVariance,
             args=(
                 binMap,
                 args.topNumberOfEvents,
                 job,
                 args.inputPath,
                 pathExp,
                 resultPipes_child[job],
                 args.readCachedSurfaceInformation,
             ),
         )
         OptiJob[job].start()
 
     # Collect the score from the material mapping, this pauses the script until all the jobs have been completed
     for job in range(args.numberOfJobs):
         scores = resultPipes_parent[job].recv()
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Retried score for job "
             + str(job),
             flush=True,
         )
         for key in binDict:
             score = scores[key]
             scorePipes_parent[key].send(score)
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Job number "
             + str(job)
             + " is over",
             flush=True,
         )
 
     if args.doPloting:
         # The optimal binning has been found.
         # Run the material mapping one last to obtain a usable material map
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Running the material mapping to obtain the optimised material map",
             flush=True,
         )
         resultBinMap = dict()
         for key in binDict:
             resultBinMap[key] = binPipes_parent[key].recv()
         matMapDeco.setBinningMap(resultBinMap)
 
         # Decorate the detector with the MappingMaterialDecorator
         resultDetector, resultTrackingGeometry, resultDecorators = getOpenDataDetector(
             matMapDeco
         )
 
         # Sequence for the mapping, only use one thread when mapping material
         rMap = acts.examples.Sequencer(
             events=args.topNumberOfEvents, numThreads=1, logLevel=acts.logging.INFO
         )
 
         # Run the material mapping
         from material_mapping import runMaterialMapping
 
         runMaterialMapping(
             resultTrackingGeometry,
             resultDecorators,
             outputDir=args.outputPath,
             inputDir=args.inputPath,
             mapName="optimised-material-map",
             format=JsonFormat.Json,
             mapVolume=False,
             s=rMap,
         )
         rMap.run()
     print(
         datetime.now().strftime("%H:%M:%S")
         + "    Waiting for all the score to have been stored",
         flush=True,
     )
 
     # Create a timer that will be used to terminate the Process
     deadline = time.time() + 600
 
     for key in binDict:
         timeout = max(deadline - time.time(), 0)
         expJob[key].join(timeout=timeout)
         expJob[key].terminate()
         print(
             datetime.now().strftime("%H:%M:%S")
             + "    Experiment for surface "
             + str(key)
             + " is over",
             flush=True,
         )

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