for function¶
cli¶
main.py¶
- auto_sub()
- load_config(filename, is_no_config, dryrun)
- pygate(config, no_config, dryrun)
analysis.py¶
- analysis_kernel(source, target, analysis_type, dryrun)
- predefined(name, source, output)
- script(target, source, output):
clean.py¶
- clean_kernel(is_subdirectories, subdirectory_patterns: Iterable[str],
- root_file_patterns: Iterable[str], is_slurm_outputs, dryrun: bool)
- clean(subdirectories, root_files, slurm_outputs)
initialize.py¶
- init
- generate
- mac_template(filename)
- shell_task_list(tasks)
- shell_run(filename,tasks,gate_version,shell,partition)
- shell_post_run(filename,tasks,gate_version,shell,partition)
- shell_post_run(filename,tasks,gate_version,shell,partition)
- shell()
- cfg(target,format)
- subdir(nb_split,sub_format)
- broadcast_kernel(files,subdirectory_patterns,dryrun)
- bcast(target, no_ext)
- external_to_copy()
- ext()
- auto()
mac_generate.py¶
- mac()
- script()
- predefined()
merge.py¶
- Tasks
- __init__(self,filename,method)
- merge_kernel(tasks:Iterable[Taks], subdir_pattern: Tterable[str],dryrun)
- merge(target, method)
submit.py¶
- Task
- __init__(self, broadcast=None,single=None)
- submit_kernel(taks:Iterable[Task],subdir_patterns:Iterable[str],duyrun)
- submit(broadcast,single)
analysis¶
__init__.py¶
predifined.py¶
- gamma_energy_deposite_distribution(csv_filename, h5_filename)
results.py¶
- ParticleID(Enum)
- ColumnNames
- ResultBase
- __init__(self,data=None)
- d(self)
- Results(Resultbase)
- __init__(self,data:Tuple[ResultBase])
- map(self,func) -> ‘Results’
- fileter(self,func) -> ‘Results’
- call(self, fuc_name) -> ‘Results’
- zip(self, r: ‘Results’)
- first(self) -> ResultBase
- flatten(self) -> ‘Results’
- merge(self) ->ResultBase
- to_list(self)
- ResultsDask(ResultBase)
- ResulltsNamedTuple(ResultBase)
- ResultsWithKeys(Results)
- __init__(self,data: Tuple[Tuple[str,ResultBase]]
- drop_keys(self) -> Results
- to_dict(self)
- select(self,key)
- ResultsWithUnknownKeys(ResultsDask)
- select(self,key)
- drop_keys(self) -> ResultsDask
- Series(ResultBase)
- __init__(self,series: pd.Series)
- columns(self, *cols)
- position(self) -> ‘Vec3’
- source_position(self) ->’Vec3’
- energy_deposit(self) -> float
- DaraFrame(ResultBase)
- __init__(self, dataframe: pd.DataFrame)
- first(self, *columns) -> Series
- split_row(self) -> Results
- merge(self, r) -> ‘DataFrame’
- to_event(self) -> ‘Event’
- Vec3(ResultBase)
- __init__(self, x, y=Mone, z=None)
- x(self) -> float
- y(self) -> float
- z(self) -> float
- to_list(self)
- EnergyDeposit(ResultBase)
- def __init__(self, position,energy)
- position(self)
- energy(self)
- Event(DataFrame)
- __init__(self,dataframe: pd.DataFrame)
- source_position(self) -> Vec3
- first_position(self) -> Vec3
- incident_direction(self) -> Vec3
- energy_deposit_list(self) -> Results
- CSVFile(ResultBase)
- __init__(self,filename:str)
- load(self) -> DataFrame
api¶
archive¶
components¶
geometry¶
geometry.py¶
- GeometryPreInitialise(ObjectWithTemplate)
- __init__(self, world:Volume)
- GeometryPostInitialise(ObjectWitheTempate)
- __init__(self, surfaces)
- Gemetry
- __init__(self, world:Volume)
- render_pre(self)
- render_post(self)
phantom.py¶
- Phantom(ObjectWithTemplate)
- __init__(self, sensitive_detectors: Tuple[Volume]=())
surface.py¶
- Surface(ObjectWithTemplate)
- __init__(self, base: Volume, insert:Volume)
- SurfaceOerfectAPD(Surface)
- SurfaceRoughTeflonWrapped(Surface)
volume.py¶
- Repeater(ObjectWithTemplate)
- RepeaterRing(Repeater)
- __init__(self, number)
- RepeaterLinear(Repeater)
- __init__(self, number, repeat_vector)
- RepeaterCubic(Repeater)
- __init__(self, scale: Vec3, repeat_vector: Vec3)
- Volume(ObjectWithTemplate)
- __init__(self, name, ,aterial=None, mother=None, position=None, unit=None, repeaters: Repeater=None)
- add_child(self, child)
- Box(Volume)
- __init__(self, name, size, material=None, ,other=None, position=None,unit=None,repeaters: Repeater=None)
- Cylinder(Volume)
- __init__(self, name, rmax, rmin=None, height=None,phi_start=None,delta_phi=NOne,material=None,mother=None,position=None,unit=None,repeaters: Repeater=None)
- Sphere(Volume)
- __init__(self, name, rmax, rmin=None, phi_start=None,delta_phi=None,theta_start=None,delta_theta=None,material=None,mother=None,position=None,unit=None,repeaters:Repeater=None)
- ImageRegularParamerisedVolume(Volume)
- __init__(self, name, image_file, range_file, material=None,mother=None,position=None, init=None,repeaters: Repeater=None)
- Patch(Volume)
- __init__(self, name, patch_file, material=None,mmother=None,position=None, unit=None, repeater:Repeater=None)
camera¶
__init__.py¶
camera.py¶
- Camera(ObjectWithTemplate)
- __init__(self, system:System, sensitive_detectors:Tuple[Volume]=())
system.py¶
- System
- __init__(self)
- PETscanner(System)
- __init__(self,level1, level2, level3, level4, level5, sensitive_detectors=None)
- Ecat(System)
- __init__(self, block=None, crystal=None)
- CylindricalPET(System)
- __init__(self, rsector=None, module=None,submodule=None,crystal=None,layer0=None,layer1=None,layer2=None,layer3=NOne)
- MultiPatchPET(System)
- __init__(self, container, patch_list)
- SPECThead(System)
- __init__(self,crystal,pixel=None)
- OpticalSystem(System)
- __init__(self, crystal,pixel = None)
template¶
digitizer¶
- singles
- blurring.j2
- buffer.j2
- dead_time.j2
- holder.j2
- readout.j2
- singles.j2
- co_incidence_chain.j2
- co_incidence_sorter.j2
- insertable.j2
geometry¶
- volume
- repeater
- cubic.j2
- linear.j2
- repeater.j2
- ring.j2
- box.j2
- cylinder.j2
- image_sphere.j2
- sphere.j2
- volume.j2
- camera.j2
- geometry_post_init.j2
- geometry_pre_init.j2
- phantom.j2
- surface.j2
- system.j2
misc¶
- database.j2
- verbose.j2
- visualisation.j2
parameter¶
- aquisition
- aquisition.j2
- period.j2
- primaries.j2
- output
- output.j2
- root.j2
- sinogram.j2
- random_engine
- random_engine.j2
- parameter.j2
physics¶
- cuts.j2
- list.j2
- model.j2
- physics.j2
- procrss.j2
source¶
- angular
- angular.j2
- iso.j2
- particle
- gamma.j2
- particle
- position.j2
- shape
- annulus.j2
- circle.j2
- cylinder.j2
- ellipse.j2
- ellipsoid.j2
- rectangle.j2
- shape.j2
- sphere.j2
- voxelized.j2
- source_list.j2
- source.j2
simulation.j2¶
test.j2¶
utils.j2¶
vec3.j2¶
__init__.py¶
base.py¶
- ObjectWithTemplate(ObjectWithTemplateBase)
- Renderable
- render(self) -> str
digitizer.py¶
- Insetable(ObjectWithTemplate)
- __init__(self, name=None, is_define_name=False, is_explicit_insert=True)
- Singles(Insertable)
- __init__(self, plugins=None, name=’Singles’, is_define_name=False,is_explicit_insert=False)
- AdderCompton(Insetable)
- __init__(self, name=’adderCompton’, is_define_name=False)
- Readout(Insertable)
- __init__(self,policy=None,depth=1,name=’readout’,is_define_name=False)
- Blurring(Insertable)
- __init__(self, law=None, resolution=0.15,eor=511, slope=None, name=’blurring’, is_define_name=False)
- Holder(Insetable)
- __init__(self,value,name=None, is_define_name=False)
- ThresHolder(Holder)
- __init__(self, value, name=’thresHolder’)
- UpHolder(Holder)
- __init__(self, value, name=’upholder’)
- TimeResolution(Insetable)
- __init__(self, resolution, name=None, is_define_name=False)
- WithBuffer(Insertable)
- __init__(self, size=NOne, mode=NOne, name=NOne, is_define_name=False)
- MemoryBuffer(WithBuffer)
- __init__(self, read_freq=NOne,size=None,mode=None,name=None,is_define_name=False)
- DeadTimeMulti(WithBuffer)
- __init__(self, volume ,t , mode=None, buffer_size=None, buffer_mode=None, name=’deadtime’, is_define_name=False)
- SingleChain(Singles)
- __init__(self, name, is_define_name=True)
- CoincidenceSorter(Insertable)
- __init__(self, input_=None,window=NOne,offset=None,name=’Coincidences’,is_define_name=False, is_explicit_insert=False)
- CoincidencesChanin(Insertable)
- __ini__(self,input1,input2,name,plugins=None,use_priority=None,conseve_all_event=None, is_define_name=True)
misc.py¶
- Verbose(ObjectWithTemplate)
- __init__(self, physics=0,cuts=0,sd=0,action2=0,actor=0,step=0,error=0,warning=0,output=0,beam=0,volume=0,image=0,geometry=0,core=0,run=0,event=0,tracking=0)
- MateriaDatabase(ObjectWithTemplate)
- __init__(self, path: str=None)
- MaterialDatabaseLocal(MaterialDatabase)
- __init__(self)
- Visualisation(ObjectWithTemplate)
- __init__(self, is_disable=True)
parameter.py¶
- Acquisition(ObjectWithTemplate)
- AcquisitionPrimaries(Acquisition)
- __init__(self,number=10000)
- AcquisitionPeriod(Acquisition)
- __init__(self, start=0.0,end=1.0,step=1.0)
- Output(ObjectWithTemplate)
- __init__(self,file_name)
- Ascii(Output)
- __init__(self, file_name, hit=0, singles=0, coincidences=0)
- Binary(Output)
- __init__(self,file_name,hit=0,singles=0, coincidence=0)
- Root(Output)
- __init__(self,file_name，hit=None,singles=None,coincidences=None,optical=None,delay=NOne)
- Sinogram(Output)
- __init__(self,file_name,input_,radial_bin=None,is_true_only=None,is_raw_output=NOne,tang_blurring=NOne,is_store,delay=None,si_store,scatter=None)
- RandomEngine(ObjectWithTemplate)
- __init__(self,seed=’default’)
- RandomEngineRanlux64(RandomEngine)
- RandomEnginJamesRandom(RandomEngine)
- RandomEngineMersenneTwister(RandomEngine)
- Parameter(ObjectWithTemplate)
- __init__(self,random_engine,outputs: List[output],acquisition)
physics.py¶
- Model(ObjectWithTemplate)
- __init__(self,particle=None)
- PenelopeModel(Model)
- StandarModel(Model)
- LivermoreModer(Model)
- LivermorePolarizeModel(Model)
- PhysicsProcess(ObjectWithTemplate)
- __init__(self, models=NOne)
- content_in_adding(self)
- PhotoElectric(PhysicsProcess)
- Compton(PhysicProcess)
- GammaConversion(PhysicsProcess)
- RayleighScattering(PhysicsProcess)
- __init__(self, models=(PenelopeModel(),))
- ElectronIonisation(PhysicsProcess)
- __init__(self, models=(StandardModel(‘e-‘),StandardModel(‘e+’)))
- Bremsstrahlung(PhysicsProcess)
- __init__(self,models=(StandardModel(‘e-‘),StandardModel(‘e+’)))
- PhysicsProcessWithoutModels(PhysicsProcess)
- __init__(self)
- PositronAnnihilation(PhysicsProcessWithoutModels)
- RadioactiveDecay(PhysicsProcessWithoutModels)
- OpticalAbsorption(PhysicsProcessWithoutModels)
- OpticalRayleigh(PhysicsProcessWithoutModels)
- OpticalBoundary(PhysicsProcessWithoutModels)
- OpticalMie(PhysicsProcessWithoutModels)
- OpticalWLS(PhysicsProcessWithoutModels)
- Scintillation(PhysicsProcessWithoutModels)
- MultipleScattering(PhysicsProcessWithoutModels)
- __init__(self, particle)
- content_in_adding(self)
- EMultipleScattering(PhysicsProcessWithoutModels)
- __init__(self,particle)
- content_in_adding(self)
- PhysicsList(ObjectWithTemplate)
- __init__(self,physics_processes:List[PhysicsProcess])
- Cuts(ObjectWithTemplate)
- __init__(self,volume:Volume,cuts:TV(‘CutT’,float,Dict[Volume,float]),max_step: float=None)
- Physics(ObjectWithTemplate)
- __init__(self, physics_list,cut_list)
simulation.py¶
- Simulation(ObjectWithTemplate)
- __init__(self,geometry,physics,digitizers,source,paramerter,material_database=None,visualisation=None)
source.py¶
- Source(ObjectWithTemplate)
- __init__(self,name,particle=None,activity=NOne,angle=None,shape=NOne,position:Vec3=None)
- unified_activity(self, activity)
- bind(self, obj)
- is_voxelized(self)
- Particle(ObjectWithTemplate)
- bind_source(self, source)
- __init__(self, unstable=None, halflife=None)
- ParticlePositron(Particle)
- __init__(self, unstalble=True,halfife=6586)
- ParticleGamma(Particle)
- __init__(self, unstable=True,halflife=6586.2,monoenergy=511,back2back=True)
- Angular(ObjectWithTemplate)
- Shape(ObjectWithTemplate)
- __init__(self,dimension)
- ShapePlane(Shape)
- __init__(self)
- ShapeSurfaceOrVolume(Shape)
- __init__(self,dimension)
- Voxelized(Shape)
- __init__(self,read_table,read_file,reader=’interfile’,translator=’range’,positon=None)
- Cylinder(ShapeSurfaceOrVolume)
- __init__(self,radius,halfz,dimension)
- Sphere(Shape)
- __init__(self,radius,dimension)
- Ellipsoid(Shape)
- __init__(self,half_sie:Vec3,dimension)
- Circle(ShapePlane)
- __init__(slef,radius)
- Annulus(ShapePlane)
- __init__(self,radius0,radius)
- Ellipse(ShapePlane)
- __init__(self,half_size)
- Rectangle(ShapePlane)
- __init__(self,half_size)
- SourceList(ObjectWithTemplate)
- __init__(self,sources:List[Source])
utils.py¶
- Vec3(ObjectWiTemplate)
- __init__(self,x,y,z,unit=None)
predefined¶
- cylindricalPET(world: Volume, cylinder=None,rrh=None,head=None,rcb=None,block=None,rcc=None,crystal=None,lso=None,bgo=None)
- ecat(world: Volume, cylinder=None,rlb=None,rrb=None,block=None,rcc=None,crystal=None)
- opticalsystem(world: Volume,box=None,crystal=NOne,rcp=None,pixel=None)
- optical_gamma(world:Volume,crystal:VolumeLike)
- multipatchPET(world: Volume)
- optocal_surfaces(cam:Camera)
- voxelized_gamma(position,src_name=’voxelized_gamma’,read_table=’act_range.data’,read_file=’act.h33’)
- voxelized_F18(position,src_name=’voxelized_F18’,read_table=’act_range.dat,read_file=’act.h33’)
- cylinder_source(position=Vec3(0,0,0),src_name=’cylinder_source’,cylinder=None,activity=NOne,particle=None,angle=None)
- plane_source(psotion=Vec3(0,0,0),src_name=’plane_source’,rectangle=None,activity=None,particle=None,angle=None)
- sphere_source(position=Vec3(0,0,0),src_name=’sphere_source’,sphere=None,activity=None,particle=None,angle=None)
- make_default_source(simu_name)
- sphere(radius,position:Vec3=Vec3(0.0,0.0,0.0,’mm’),angle:Anular=None,activity:int=1000,particle=None,name=’sphere_source’) -> SourceList
- ecat_digitizer(dtvolume, rdr=None.blur=None,thres=None,uph=None,ddt=None,coin=None,coin_delay=None,coin_chain=None)
- cylindricalPET_digitizer(rdr=None,blur=NOne,thres=None,uph=None,coin=NOne,coin_delay=None)
- optical_digitizer(rdr=None)
- spect_digitizer(blur=None,spblur=None,thres=None,uph=None)
- pet_parameters(acqu=AcquisitionPeriod(),outpits=None,rand=RandomEngine(seed=’auto’))
- optical_parameters(acqu=AcquisitionPrimaries(number=10000),outputs=None,rand=RandomEngineMersenneTwister(seed=’auto’))
- optical_gamma(nb_primaries)
- voxelized_phantom(world,image_file=’phan.h33’,range_file=’mat_range,dat’,position=None)
- pet_physics(cut_pair_list)
- optical_physics(cut_pari_list)
- gamma_physics(cut_pair_list)
- spect_physics(cut_pair_list)
- PredefinedSimulations(Enum)
- make_default_camera(simu_name,world: Volume)
- make_default_surfaces(simu_name,cam: Camera)
- make_default_physics(simu_name,cam:Camera,phan:Phantom,cut_pair_list=None)
- make_default_digitizer(simu_name, cam: Camera)
- make_default_parameter(simu_name)
- make_simulation(simu_name,geo=None,phy=None,digi=None,src=None,para=None)
- simulation(simulation_name:PredefinedSimulations,geometry=None,physics=None,digitizer=None,source=None,parameter=None)
- optical_gamma(source=None,world_size:Vec3=Vec3(400.0,400.0,400.0,’cm’),crystal_size:Vec3=Vec3(30.0,30.0,30.0,’mm’),crystal_position:Vec3=Vec3(0.0,0.0,0.0,’mm’),crystal_material:str=’LYSO’,nb_prmaries=10000)
routine¶
- KEYS
- AnalysisType(Enum)
- OperationAnalysis(OperationOnfile)
- __init(self, source_csv_filename, target_h5_filename, analysis_type:AnalysisType=None)
- source(self,r:RoutineOnDirectory)
- dryrun(self,r:RoutineOnDirectory)
- Operation
- apply(self,routine)
- dryrun(self,routine)
- Routine
- __init__(self,operation:Tterable[Operation]=(),dryrun=False,verbose=0)
- last_result(self)
- work(self)
- echo(self)
- RoutineOnDirectory(Routine)
- OperationOnFile(Operation)
- __init__(self,filename:str)
- target(self,r:RoutineOnDirectory) -> File
- dryrun(self,r:RountineOnDirectory)->Dict[str,Any]
- apply(self,r: RoutineOnDerectory) ->Dict[str,Any]
- OpeartionOnSubdirectories(Operation)
- __init__(self,patterns:Iterable[str])
- subdirectories(self, r: RoutineOnDirectory)
- OpeartionWithShellCall(Operation)
- call_args(self,r:Routine)
- stdout(self, r:Routine)
- run_child_program(self, r:Routine)
- apply(self,r:Routine)
- dryrun(self, r:Routine)->Dict[str, Iterable[str]]
- KEYS
- OpCleanSubdirectories(OperationOnSubdirectories)
- apply(self, r: RoutineOnDirectory)
- dryrun(self, r:RoutineOnDirectiory)
- OpCleanSource(Operation)
- __init__(self,file_patterns:Iterable[str])
- files(self, r: RoutineOnDirectory)
- apply(self, r: RoutineInDirectory)
- dryrun(self,r: RoutineOnDirectory)
- OpCleanFilesInAllDirectories(OperationOnSubdirectories)
- __init__(self,file_patterns:Iterable[str],subdirectory_patterns:Iterable[str])
- files_on_directory(self,d:Directory)
need to be corrected(directroy->directory) - to_remove(self,r:RoutineOnDirectory)
- apply(self,r:RoutineOnDirectory)
- dryrun(self,r:RoutineOnDirectory)
- routine_clean(source_patterns:Iterable[str]=(),is_subdir:bool=False,dryrun:bool=False)
- KEYS
- TargetFileWithContent
- __init__(self,target: TypeVar(‘FileLike’,File,str).is_to_broadcast:bool=True,content:str=None)
- to_dict(self)
- save(self)
- OpAddToBroadcastFile(OperationOnFile)
- __init__(self,filename)
- apply(self,r: RoutineOnDirectory)
- dryrun(self,r: RoutineOnDirectory)
- OpGenerateFile(OperationOnFile)
- __init__(self,filename:str,is_to_broadcast=True)
- content(self,r:RoutineOnDirectory) ->str
- target_file_with_content(self,r:RoutineOnDirectory)
- apply(self,r: RoutineOnDirectory)
- dryrun(self,r:RoutineOnDirectory)
- OpGeneratorMac(OpGenerateFile,OpeartionWithShellCall)
- __init__(self,script_filename:str,mac_config:str=None,mac_filename: str=None)
- call_args(self,r: RoutineOnDirectory)
- OpgenerateMacTemplate(OpGerateFile)
- __init__(self,filename:str,script:Script)
- content(self,r: RoutineOnDirectory)->str
- OpGeneratorShell(OperationOnFile)
- __init__(self,filename:str,script:Script)
- content(self, r:RoutineOnDirectory) ->
- OpGeneratorPhantom(OperationOnFile)
- __init__(self,filename:str)
- OpSubdirectoriesMake(Operation)
- __init__(self,nb_split:int,subdirectory_format:str=”sub.{}”)
- apply(self, r: RoutineOnDirectory)
- dryrun(self, r: RoutineOnDirectory)
- OpBroadcastFile(OperationONsubdirectories)
- files_to_broadcast(self,r: RoutineOnDirectory)
- dryrun(self,r:RoutineOnDirectory)
- apply(self,r: RoutineOndirectory)
- OpMerge(OperationOnFile,OperationOnSubdirectories)
- __init__(self,filename:str,patterns:Iterable[str])
- sources(self, r:RoutineOnDirectory)
- dryrun(self,r: RoutineOnDirectory) -> JSONStr
- OpMergeWithShellCall(OpMerge,OpeartionWithShellCall)
- __init__(self,filename:str,patterns:Iterable[str])
- apply(self,r:RoutineOnDirectory)
- dryrun(self,r:RoutineOnDirectory)
- OpMergeHADD(OpMergeWithShellCall)
- call_args(self,r: RoutinOnDirectory)
- OpMergeCat(OpMergeWithShellCall)
- call_args(self,r:RoutineOnDirectory)
- OpMergePandasConcatenate(OpMerge)
- apply(self,r:RoutineOnDirectory)
- OpMErgeSumBinary(OpMerge)
- hadd(work_derectory:Directory,subdirectory_patterns:Iterable[str],source_filenames:Iterable[str],dryrun=False)
- KEYS
- depens_from_result_dict(r: Dict[str,Any])->Iterable[int]
- append_depens_to_dict(to_submit:Dict[str,Any],previous_result: Dict[str,Any])
- parse_paths_from_dict(r: Doct[str,Any]) -> Doct[str,Any]
- submit_from_dict(r: Dct[str,Any]) -> Dict[str,Any]
- OpSubmitBroadcast(OperationOnSubdirectories,OperationOnFile)
- __init__(self,filename,subdirectory_patterns:Iterable[str])
- to_submit(self, r: RoutineOnDirectory) -> ‘Observable[Dict[str,Any]]’
- apply(self,r:RoutinOnDirectory) -> Dict[str,Iterable[Dict[str,str]]]
- dryrun(self,r :RoutineOnDirectory) -> Dict[str,Iterable[Dict[str,str]]]
- OpSubmitSingleFile(OperationOnFile)
- __init__(self,filename:str)
- to_submit(self, r:RoutineOnDirectory)
- apply(self,r:RoutineOnDirectory) ->Doct[str,Any]
- dryrunn(self,r:RoutineOnDirectory) -> Dict[str,Any]
scripts¶
templates¶
- make_mac.j2
- post_run.j2
- run_loacal.j2
- run.j2
- sbatch.j2
- shell.j2
__init__.py¶
base.py¶
- ObjectWithTemplate(ObjectWithTemplateBase)
helper.py¶
- gate_simulation(mac_filename)
- gate_simulation_with_root_analysis(mac_filename,root_filename,analysis_c_filename)
need to be corrected (gete->gate)
shell.py¶
- Script(ObjectWithTemplate)
- add_task(self,task)
- Task
- render()
- TaskWithFileArg(Task)
- GateSimulation(TaskWithFileArg)
- RootAnalysis(TaskWithFileArg)
- __init__(self, root_filename, c_file_name)
- render(self)
- PygateAnalysis(TaskWithFileArg)
- __init__(self, source=NOne,target=None,output=None, name=None,analysis_type=None)
- render(self)
- Clean(Task)
- render(self)
- Merge(TaskWithFileArg)
- ScriptRun(Script)
- __init__(self,work_derectory,tasks: Tuple[Task]=(),geant4_version=‘8.0’,shell=’bash’,is_need_source_env=False,partition=’cpu’)
- add_task(self,task)
- ScriptRunLocal(ScriptRun)
- __init__(self,work_directory,tasks:Tuple[Task],geant4_version,shell=’bash’,is_nedd_source_env=False,local_work_directory=None,partition=’cpu’)
- add_task(self,task)
- ScriptPostRun(Script)
- __init__(self,tasks:Tuple[Task]=(),geant4_version=‘8.0’,shell=’bash’,is_need_source_env=False,partition=’cpu’)
- add_task(self,task)
- ScriptMacTemplate(ObjectWithTemplate)
test¶
test
utils¶
__init__.py¶
object_with_template.py¶
- EnvironmentOfPackage
- __init__(self,pkg_name)
- get_or_create_env(self)
- default_suffix(s: str, suffix: str, is_auto_add_point_prefix=True)
- ObjectWithTemplateBase
- template_name(self)
- render(self)
strs.py¶
syscall.py¶
- shell_call(commands: Iterable[str] or str, is_echo=True)
typing.py¶
- JSONStr(str)
__init__.py¶
cleaner.py¶
- Cleaner
- __init__(self,fs,config)
- clean(self)
- msg(self,path)
- _clean_subs(self)
- _clean_sources(self)
conf.py¶
- KEYS
- SUBMIT_KEYS
- CLEAN_KEYS
- ANALYSIS_KEYS
- INIT_KEYS
- BROADCAST_KEYS
- EXTERNAL_KEYS
- MAC_KEYS
- SHELL_KEYS
- PHANTOM_KEYS
config_maker.py¶
- ConfigMaker
- _make_pygate_config(cls,fs,target,congfig_filename=None)
- _make_mac_config(cls,fs,target,config=None,mac_config=None)
- make(cls, fs,target,pygate_config=None,mac_config=None)
config.py¶
configs.py¶
initializer.py¶
- Initializer
- __init__(self,fs,config)
- _copy_sources_from_template(self)
- _make_mac(self)
- _make_phantom(self)
- _sub_dir_name(self,i)
- _nb_sub_dirs(self)
- _make_subdirs(self)
- _make_map_shell_scripts(self)
- _copy_sources_to_subdirs(self)
- pre_sub(self)
- make_sub(self)
merger.py¶
- Merger
- __init__(self,fs,config)
- _path_of_file_in_sub_dirs(self,base_filename)
- msg(self,method,target,sources)
- _hadd(self,task)
- _cat(self,task)
- _sum(self,task)
- _copy(self,task)
- merge(self)
phantom.py¶
- PhantomBinFileMaker:
- __init__(self,fs,phantom_files)
- _load_data(self,source)
- _make_bin(self,target,data)
- make(self)
renderable.py¶
- Renderable
- render(self) ->str
service.py¶
- make_config(target=’.’)
- init(config,method)
- submit(config)
- merge(config)
- clean(config)
shell.py¶
- ShellScriptBase
- __init__(self,fs,workdir:str, output:str,tasks:list,shell=’zsh’,version=‘7.2’)
- _add_if_gate(self,task)
- _add_if_root(self,task)
- _get_workdir_on_local_and_server(self)
- _make(self)
- ShellScriptMerge(ShellScriptBase)
- __init__(self,fs,workdir:str,output:str,tasks:list,shell=’zsh’)
- _make(self)
- ShellScriptMaker
- __init__(self,fs,config)
- make(self)
submitter.py¶
- Submitter
- __init__(self,fs,config)
- _get_map_info(self)
- _get_merge_info(self)
- submit(self)
- _echo(self,info,fout)
- _slurm(self, run_infos,post_infos)
- _hqlf(self,run_infos,post_infos)
utils.py¶
- get_scripts_path
- load_script(name)
- sub_dir_filters(config)