ShockFinder 7.4.2

ShockFinder is an interactive scientic simulation data analysis software based on python and supports multi-process, multi-mode, I/O access and drawing.

ShockFinder

ShockFinder is an interactive scientic simulation data analysis software based on python and supports multi-process, multi-mode, I/O access and drawing.

Author: Junxiang H. & C. B. Singh
If you have any questions and suggestions
Please contact: [e-mail]

You can access Outdate version (i.e., < V7.0) here.

Latest Version: 7.4.0, date: 2024-03-02

Update: The Analyze module now reads saved configuration files and supports secondary modifications.

Install

Please follow one of the ways to install ShockFinder

pip3 install ShockFinder

If you want to use multi-processes during analysis and reading, it is recommended to use the XME interface of the WACMK-Xenon software set, which can be installed through the following command:

pip3 install XME

If you have better multiprocessing engine, you can definde it by using ShockFinder inline command -n=MultiprocessEngine@configname.

At the same time, we are very encourage that you use our GUI engine XenonUI to assist your analysis work. You can install it by following command:

pip3 install XenonUI

Notice: XenonUI supports UNIX and windows systems, but the tkinter libraries have to be installed! More detail see https://www.github.com/wacmkxiaoyi/Xenon-UI.

Useage

Enter the following code and save it into a file (like shockfind.py, version >=7.1)

try:
	import XME
except:
	print("Warning: The default Multiprocess Engine XME is not installed, Multiprocess mode might not be used!")
	print("Please type: pip3 install XME to install")
	print("More infomation see: https://github.com/wacmkxiaoyi/Xenon-Multiprocessing-Engine")
	print("\n")
try:
	import XenonUI
except:
	print("Warning: The default GUI Engine XUI (XenonUI) is not installed, GUI mode might not be used!")
	print("Please type: pip3 install XenonUI to install")
	print("More infomation see: https://github.com/wacmkxiaoyi/Xenon-UI")
	print("\n")

import sys,os
import ShockFinder
from ShockFinder.Config import ShockFinderDir
from ShockFinder.Update import Update_all

def drop_bk(strc):
	if strc!="" and (strc[0]=="'" and strc[-1]=="'" or strc[0]=='"' and strc[-1]=='"'):
		strc=strc[1:-1]
	return strc
if __name__=="__main__":#windows support
	gui=True
	for i in sys.argv[1:]:
		if i.split("=")[0] in ("f","-f","file"):
			ShockFinder.ShockFinder(drop_bk(i.split("=")[1]))
			gui=False
		elif i.split("=")[0] in ("u","-u","update"):
			Update_all()
			gui=False
		elif i.split("=")[0] in ("n","-n","new"):#new=module@filename
			LoaderDir=os.path.join(ShockFinderDir,"Addon","Loader")
			AnalysisToolDir=os.path.join(ShockFinderDir,"Addon","AnalysisTool")
			PainterDir=os.path.join(ShockFinderDir,"Addon","Painter")
			IODir=os.path.join(ShockFinderDir,"Addon","IO")
			MultiprocessEngineDir=os.path.join(ShockFinderDir,"Addon","MultiprocessEngine")
			GUIDir=os.path.join(ShockFinderDir,"Addon","GUI")
			modu=i.split("=")[1].split("@")[0]
			mfname=i.split("=")[1].split("@")[1]
			if modu in ("Loader","AnalysisTool","Painter","IO","MultiprocessEngine","GUI"):
				import shutil
				if modu=="Loader":
					shutil.copy(mfname,LoaderDir)
				elif modu=="AnalysisTool":
					shutil.copy(mfname,AnalysisToolDir)
				elif modu=="Painter":
					shutil.copy(mfname,PainterDir)
				elif modu=="IO":
					shutil.copy(mfname,IODir)
				elif modu=="MultiprocessEngine":
					shutil.copy(mfname,MultiprocessEngineDir)
				elif modu=="GUI":
					shutil.copy(mfname,GUIDir)
			Update_all()
			gui=False
	if gui:
		ShockFinder.ShockFinder()

GUI MODE

GUI mode is used to generate analysis configuration files and visualize analysis results!

Enter GUI mode:

python shockfind.py

The GUI engine for the ShockFinder is XUI (see https://github.com/wacmkxiaoyi/Xenon-UI).

Four pages are available: Analysis, Graph, Help and Exit

The Exit page is used to interrupt multi-thread monitoring and exit Shockfinder. Help displays some basic information about ShockFinder (such as version, author)

Page analysis

The Analysis page has three menus, Save Configuration, Global Settings and Analysis

Global Settings

The menu Global Settings has three submenus:

1. Multiprocess: Regarding the configuration of multi-process analysis, the default multi-process engine is XME (see https://github.com/wacmkxiaoyi/Xenon-Multiprocessing-Engine, some advanced options can be clicked here Link).

2. Database Storage: Configuration used to store analysis data. The default engine is HDF5, the default project name (save target file name) is current timestamp, and Drop Buffer is the buffer analysis process. Medium transparency (default and recommended True)

3. Simulation Data Loader: In this submenu you must define the type of simulation data used.

Analysis

Menu Analysis has two sub-menus:

1. Parameters: in here you can define the global variable during the analyzing

2. Quantities: in here you can define which analysis approch will be used during the analyzing

Save Configurations:

1. Button Test: to test cn the analysis process proceed normally

2. Button Save: save the analysis configuration file

Page Figure

Page Figure has Two Menus, Database, and Figure

Database

Menu Database has two sub-menus:

1. Load: before you figure the picture you like, you should load the after-analyzing data firstly. In this menu, data reading, browsing, and other functions can be performed

2. Global Settings: the configuration of loader of after-analyzing data

Figure

Menu Figure has three sub-menus: Set unit, 2d and 3d (easy to understand without additional explanation)

Parallel analysis mode (PAM)

After producing the analysis configration file (e.g., config1.ini, config2.ini), you can start to analyze:

python shockfinder.py -f=config1.ini -f=config2.ini ...

How to add a new type of simulation or analysis method:

ShockFinder recommends two module models:

1. LoaderModel.py:

#This is a model file for the Loader Addon
#It will be created when creating a new Loader
#Note!!!!: places which marke "<>" have to be updated, and delete "<>".

#File type: <Function> return <Object: Data>
#By Junxiang H., 2023/06/30
#wacmk.com/cn Tech. Supp.

#var filename includes the file_dir

#if you would like to import some packages,
#during the data loading.
#Please put that packages into this folder and using:

'''
try:
	import ShockFinder.Addon.Loader.<package1name> as <package1name>
	import ShockFinder.Addon.Loader.<package2name> as <package2name>
	#...
except:
	import <package1name> #debug
	import <package2name> #debug
	#...
'''


#A default Loader Addon can preprocess the filename,
#into to a formation with (time_index, file_dir, file_type)
#You can denote the below sentence to use it.

'''
try:
	import ShockFinder.Addon.Loader.FileNamePreProcess.FileNamePreProcess as FNPP
except:
	import FileNamePreProcess.FileNamePreProcess #debug
'''

try:
	import ShockFinder.Data
except:
	pass
def load(filename): #updated here
	#Loading Process
	read=<reader Process>(filename) #updated here
	#grid definded
	grid={}
	#GEOMETRY:	SPHERICAL	CYLINDRICAL		POLAR		CARTESIAN
	#			x1-x2-x3	x1-x2			x1-x2-x3	x1-x2-x3
	#			r-theta-phi r-z				r-phi-z		x-y-z
	grid["x1"]=read.<x1> #updated here
	grid["x2"]=read.<x2> #updated here
	grid["x3"]=read.<x3> #updated here 
	#basic quantities
	quantities={}
	quantities["vx1"]=read.<vx1> #updated here
	quantities["vx2"]=read.<vx2> #updated here
	quantities["vx3"]=read.<vx3> #updated here
	quantities["rho"]=read.<rho> #updated here
	quantities["prs"]=read.<prs> #updated here
	quantities["geometry"]=read.<geometry>
	#user definded...
	try:
		return Data.Data(grid,quantities)
	except:
		return (grid,quantities)

2. AnalysisToolModel.py:

#This is a model file for the Loader Addon
#It will be created when creating a new Loader
#Note!!!!: places which marke "<>" have to be updated, and delete "<>".

#File type: <Function> return a new <Object: Data>
#By Junxiang H., 2023/07/01
#wacmk.com/cn Tech. Supp.

#if you would like to import some packages,
#during the data loading.
#Please put that packages into this folder and using:

try:
	from ShockFinder.Addon.AnalysisTool.Basic import *
	#if AvgTh_CAL is True
	#import ShockFinder.Addon.AnalysisTool.Mean as Mean
	#import ShockFinder.Addon.AnalysisTool.<packages name> as <packages name>
except:
	from Basic import *
	#import Mean #debug
	#import <packages name>

need=[]
#args will be inserted into Data Object
#vargs will not be inserted into Data Object
import numpy as np
def get(Dataobj,args={},vargs={}):
	Dataobj.quantities.update(args)
	for i in need:
		if i not in Dataobj.quantities.keys() and i not in vargs.keys():
			print("Warning: args:",i,"is needed without definding")
			return Dataobj
	quantities={
		#operation with dict args
		#...
		<quantity name>:... #update here
	}
	Dataobj.quantities.update(quantities)
	return Dataobj
def result(quantity_name=None,anafname=None):
	return () #this function will return result types shown in GUI
#if AvgTh mode is needed, please set AvgTh_cal=True
#The below code can be ignored, if set to False
AvgTh_cal=False
def get_AvgTh(Dataobj,args={},vargs={"Mean_axis":(1,)}):
	try:
		if AvgTh_cal:
			import copy
			newneed=copy.copy(need)
			if "Mean_axis" not in newneed:
				newneed.append("Mean_axis")
			Dataobj.quantities.update(args)
			for i in newneed:
				if i not in Dataobj.quantities.keys() and i not in vargs.keys():
					print("Warning: args:",i,"is needed without definding")
					return Dataobj
			meanstr=""
			try:
				meanaxis=vargs["Mean_axis"]
			except:
				meanaxis=Dataobj.quantities["Mean_axis"]
			for i in meanaxis:
				meanstr+=str(i)+"@"+str((round(vargs["Mean_axis"+str(i)][0],2),round(vargs["Mean_axis"+str(i)][1],2)))+"_" if "Mean_axis"+str(i) in vargs.keys() else meanstr+=str(i)+"@"+str((round(Dataobj.quantities["Mean_axis"+str(i)][0],2),round(Dataobj.quantities["Mean_axis"+str(i)][1],2)))+"_" if "Mean_axis"+str(i) in Dataobj.quantities.keys() else ""
			quantities={"AvgTh_"+meanstr+"<quantity name>":...} #update here
			Dataobj.quantities.update(quantities)
		else:
			print("Warning: AvgTh mode is not opened: <quantity name>") #update here
	except:
		print("Warning: AvgTh mode is not definded:", __file__) #update here
	return Dataobj

if __name__=="__main__":
	print("Testing Model:",__file__)
	from TestData import TestData
	TestData=get(TestData)
	print("Testing Result:", TestData.quantities[<quantity name>]) #update here!
	if AvgTh_cal:
		TestData=get_AvgTh(TestData)
		print("Testing Result:", TestData.quantities["AvgTh_<quantity name>"]) #update here!

Once done, you must place it into the ShockFinder directory by using

python shockfinder.py -n={module@filename/path}

in the DOC window. The new simulated data type or analysis method will then be displayed in GUI mode.

Example:

We will present here an analytical method suitable for our current working model for calculating mass fluxes (i.e. accretion rates, etc.)

#File BlackHoleMassFlux.py
#WACMK Tech
#Only for 2D data, support SPHERICAL, POLAR, XOY
#	edge: fall into black hole, match accretion rate.
# 		plus : escape from black hole, minor: fall into black hole
#	inj: injet flow
#		plus : accreted into system, minor: escape from system
#	wind: wind
#		plus: back to system, minor: escape from system
#	outflow:
#		plus: back to system, minor: escape from system	
#   jet:
#		plus: escape from bh,....
#in each case, positive flux means material go to accretion region
#ac_begin and ac_end are size of accretion region (Escapt Polar coordinate)

try:
	from ShockFinder.Addon.AnalysisTool.Basic import *
	from ShockFinder.Addon.AnalysisTool.Differential import integrate_sph_sur,integrate_pol_sur,integrate_surface,get_closest_index
	#if AvgTh_CAL is True
	#import ShockFinder.Addon.AnalysisTool.Mean as Mean
	#import ShockFinder.Addon.AnalysisTool.<packages name> as <packages name>
except Exception as err:
	print(err)
	from Basic import *
	#import Mean #debug
	#import <packages name>

need=["MassFlux_x1","MassFlux_x2"]
#args will be inserted into Data Object
#vargs will not be inserted into Data Object
import numpy as np
def get(Dataobj,args={},vargs={}):
	Dataobj.quantities.update(args)
	for i in need:
		if i not in Dataobj.quantities.keys() and i not in vargs.keys():
			print("Warning: args:",i,"is needed")
			return Dataobj

	if Dataobj.quantities["geometry"] == "SPHERICAL": #2d spherical
		if "ac_begin" not in vargs.keys() or "ac_end" not in vargs.keys():
			print("Warning: args: ac_begin and ac_end are needed")
			return Dataobj
		edge=integrate_sph_sur(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],rr=("min",),tr=(((vargs["ac_begin"],vargs["ac_end"]),),),surface=("r",))[0]
		jet=integrate_sph_sur(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],rr=("min",),tr=(((Dataobj.grid["x2"][0],vargs["ac_begin"]),(vargs["ac_end"],Dataobj.grid["x2"][-1])),),surface=("r",))[0]
		inj=integrate_sph_sur(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],rr=("max",),tr=(((vargs["ac_begin"],vargs["ac_end"]),),),surface=("-r",))[0]
		outflow=integrate_sph_sur(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],rr=("max",),tr=(((Dataobj.grid["x2"][0],vargs["ac_begin"]),(vargs["ac_end"],Dataobj.grid["x2"][-1])),),surface=("-r",))[0]
		thid1=get_closest_index(vargs["ac_begin"],Dataobj.grid["x2"])
		thid2=get_closest_index(vargs["ac_end"],Dataobj.grid["x2"])
		wind=sum(integrate_sph_sur(Dataobj.quantities["MassFlux_x2"][:,thid1:thid2],Dataobj.grid["x1"],Dataobj.grid["x2"][thid1:thid2],tr=("min","max"),surface=("th","-th")))
	elif Dataobj.quantities["geometry"] == "POLAR": #2d polar
		edge=integrate_pol_sur(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],rr=("min",),surface=("r",))[0]
		jet=0 # no jet in 2D polar
		inj=integrate_pol_sur(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],rr=("max",),surface=("-r",))[0]
		outflow=0#no out flow
		wind=0 #no wind
	else:
		if "ac_begin" not in vargs.keys() or "ac_end" not in vargs.keys():
			print("Warning: args: ac_begin and ac_end are needed")
			return Dataobj
		inner=Dataobj.grid["x1"][0]
		edge=integrate_surface(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],xr=("min",),yr=(((-inner,inner),),),surface=("x"))[0]
		j1index=get_closest_index(-inner,Dataobj.grid["x2"])
		j2index=get_closest_index(inner,Dataobj.grid["x2"])
		jet=integrate_surface(Dataobj.quantities["MassFlux_x2"][:,:j1index],Dataobj.grid["x1"],Dataobj.grid["x2"][:j1index],yr=("max",),xr=(((0,inner),),),surface=("-y"))[0]+integrate_surface(Dataobj.quantities["MassFlux_x2"][:,j2index:],Dataobj.grid["x1"],Dataobj.grid["x2"][j2index:],yr=("min",),xr=(((0,inner),),),surface=("y"))[0]
		wind=sum(integrate_surface(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"][:j1index],xr=("min",),yr=(((Dataobj.grid["x2"][0],-inner),(inner,Dataobj.grid["x2"][-1])),),surface=("x",)))+sum(integrate_surface(Dataobj.quantities["MassFlux_x2"],Dataobj.grid["x1"],Dataobj.grid["x2"],yr=("min","max"),surface=("y","-y")))
		inj=integrate_surface(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],xr=("max",),yr=(((vargs["ac_begin"],vargs["ac_end"]),),),surface=("-x"))[0]
		outflow=integrate_surface(Dataobj.quantities["MassFlux_x1"],Dataobj.grid["x1"],Dataobj.grid["x2"],xr=("max",),yr=(((Dataobj.grid["x2"][0],vargs["ac_begin"]),(vargs["ac_end"],Dataobj.grid["x2"][-1])),),surface=("-x",))[0]
	quantities={
		"MassFlux_edge":edge,
		"MassFlux_wind":wind,
		"MassFlux_inj":inj,
		"MassFlux_outflow":outflow,
		"MassFlux_jet":jet,
		"MassFlux_Toutflow":-(outflow+wind),
		"MassFlux_Accretion":-(edge+jet)
	}
	Dataobj.quantities.update(quantities)
	return Dataobj
def result(quantity_name=None,anafname=None):
	return ("MassFlux_edge","MassFlux_Toutflow") #this function will return result types shown in GUI

python shockfinder.py -n=[e-mail]