#pragma rtGlobals=1		// Use modern global access method.

// adding Stitch Panel to Macros Menu
Menu "Macros"
	"Do Stitch", DoStitch()
end

Proc DoStitch()
//creating all variables & strings 
String/G list_edf,list_txt,listHi_edf,listLo_edf,listHi_txt,listLo_txt,BaseName
Variable/G SampleLoI1,SampleHiI1 
Variable/G gapin=1
Variable/G DetShift=30
Variable/G Gap=17
Variable/G ModuleSize=195
//creating Panel
NewPanel /K=1 /W=(3,20,400,200) as "Stitch"
	Button SelectDataPath, pos={11,6}, size={350,31}, fSize=16, fstyle=1, fColor=(0,0,52224), title="Select Data Path", proc=SelectDataPath
	SetVariable gapin,pos={11,81}, size={340,18}, title="gap increase in pixels (± n pixels above and below each gap)",noedit=0,value=gapin 
	SetVariable DetShift, pos={11,101}, size={230,18}, title="shift distance in pixels of the images", noedit=0, value=DetShift 
	Button SelectOutputPath, pos={11,41}, size={350,31}, fSize=16, fstyle=1, fColor=(0,0,52224), title="Select Output Path", proc=SelectOutputPath
	Button Stitch, pos={11,131}, size={350,31}, fSize=16, fstyle=1, fColor=(0,0,52224), title="Stitch", proc=Stitch
end

Function SelectDataPath(ba) : ButtonControl 
	STRUCT WMButtonAction &ba
	SVAR list_edf,list_txt,listHi_edf,listLo_edf,listHi_txt,listLo_txt,BaseName, InputPath
	list_edf = ""
	list_txt = ""
	Variable index=0
	Make/T/O BaseNameWave
	switch( ba.eventCode )
		case 2: 
		NewPath/O/M="Select data folder where files are contained" folder
		if (V_Flag!=0)
			abort
		endif
	do
	String file_edf, file_txt	
		file_edf=indexedfile(folder,index,".edf")  // generating a list of .txt files and a list of .edf files in the folder (this I can discard if I use the open operation instead of new path)
			if (strlen (file_edf) == 0)
				break
			endif
		file_txt=indexedfile(folder,index,".txt")
			if (strlen (file_txt) == 0)
				break
			endif
		list_edf+=file_edf+";" //  add ";" to separate every file name 
		list_txt+=file_txt+";"
		index+=1
	while(1)
	//separating list by appended Hi_(.file extension) and Lo_(.file extension) for both .edf and .txt files
	listHi_edf=ListMatch(list_edf,"*hi_1m.edf") 
	listLo_edf=ListMatch(list_edf,"*lo_1m.edf")
	listHi_txt=ListMatch(list_txt,"*hi_1m.txt")
	listLo_txt=ListMatch(list_txt,"*lo_1m.txt")
	BaseName=replacestring("_hi_1m.edf",listHi_edf,"") //list of basename of the files; here I use the list of files with "hi" appended to obtain the base name of the file
	redimension/N=(ItemsInList(BaseName, ";")) BaseNameWave   // convert basename string into a txtwave
	BaseNameWave = StringFromList(p, BaseName, ";")
	
		break
	endswitch
return 0
End

Function SelectOutputPath(ba) : ButtonControl 
	STRUCT WMButtonAction &ba
	SVAR OutputPath
	switch( ba.eventCode )
		case 2: 
		NewPath/O/M="Select data folder to save output files" output  	
		if (V_Flag!=0)
			abort
		endif
		break
	endswitch
return 0
End


Function Stitch(ba) : ButtonControl 
	STRUCT WMButtonAction &ba
	NVAR Gap, gapin, Detshift, ModuleSize,SampleLoI1,SampleHiI1 
	SVAR list_edf,list_txt,listHi_edf,listLo_edf,listHi_txt,listLo_txt,BaseName, InputPath, OutputPath
	Wave/T BaseNameWave
	redimension/N=(ItemsInList(BaseName, ";")) BaseNameWave
	switch( ba.eventCode )
		case 2: 
		Variable GapSize= Gap-1+2*gapin
		String FileHi_edf,FileLo_edf,FileHi_txt,FileLo_txt
		Variable i,NOF
		
		NOF=numpnts(BaseNameWave)
		For (i=0; i <NOF; i+=1)
			if (stringmatch(listHi_edf,"*"+BaseNameWave[i]+"_hi_1m.edf"+"*") && stringmatch(listLo_edf,"*"+BaseNameWave[i]+"_lo_1m.edf"+"*") && stringmatch(listHi_txt,"*"+BaseNameWave[i]+"_hi_1m.txt"+"*") && stringmatch(listLo_txt,"*"+BaseNameWave[i]+"_lo_1m.txt"+"*"))
			//if the "if" statement is true for basename[i] (basename[i] can be found in all the lists, it proceeds with the following steps:
			
			print "----------------------------------------------------------------------------------"
			
				FileHi_edf=Listmatch(listHi_edf,BaseNameWave[i]+"_hi_1m.edf"+"*"); FileHi_edf=replacestring(";",FileHi_edf,"") // the first command looks for the basename of the file in a particular list. The second command just removes the ";"
				FileLo_edf=Listmatch(listLo_edf,BaseNameWave[i]+"_lo_1m.edf"+"*"); FileLo_edf=replacestring(";",FileLo_edf,"")
				FileHi_txt=Listmatch(listHi_txt,BaseNameWave[i]+"_hi_1m.txt"+"*"); FileHi_txt=replacestring(";",FileHi_txt,"")
				FileLo_txt=Listmatch(listLo_txt,BaseNameWave[i]+"_lo_1m.txt"+"*"); FileLo_txt=replacestring(";",FileLo_txt,"")
						
		// load txt files
		Make/T/O headertxtLo0,headertxtHi0	
		LoadWave/J/O/P=folder/N=headertxtLo/L={0,0,35,0,0}/B="F=-2;" FileLo_txt
		LoadWave/J/O/P=folder/N=headertxtHi/L={0,0,35,0,0}/B="F=-2;" FileHi_txt
		SampleLoI1 = str2num(headertxtLo0[1])
		SampleHiI1 = str2num(headertxtHi0[1]) // obatin I1 values from the txt files, second value in the wave ...input #1 for second value on the wave

		Gbloadwave/P=folder/B/T={32,32}/S=1024/W=1/N=LoadedwaveLo FileLo_edf
		Gbloadwave/P=folder/B/T={32,32}/S=1024/W=1/N=LoadedwaveHi FileHi_edf
 		Redimension/D/N=(981,1043) LoadedwaveLo0,LoadedwaveHi0 //Pilatus 1M Dimensions
		//Normalization
		WAVE LoadedwaveLo0,LoadedwaveHi0
		LoadedwaveLo0/=SampleLoI1
		LoadedwaveHi0/=SampleHiI1
		// 			NewImage/K=1 loadedwaveLo0_N
		//			ModifyImage LoadedwaveLo0_N ctab= {0,100,Terrain,0}
		//			NewImage/K=1 loadedwaveHi0_N
		//			ModifyImage LoadedwaveHi0_N ctab= {0,100,Terrain,0}
		//			   make/o/n=(981,1073)  loadedwavelo01,loadedwavehi01      BLANK+NOISE TEST
		//			   loadedwavelo01+=gnoise(1)
		//			   loadedwavehi01+=gnoise(1)
		killwaves/z test,gm30,gm00, mask, mask00,mask30                         //t01,t02,t03
		make/O/N=(981,1073) test, gm30, gm00, mask        //t01,t02,t03
		gm00[0,980][DetShift,1042+DetShift]= loadedwaveLo0[p][q-DetShift] 
		gm30[0,980][0,1042]= loadedwaveHi0 [p][q] // used to be 30, instead of detshift
//				Duplicate/O gm00, gm00_log
//			       gm00_log = log(gm00)
//				Duplicate/O gm30, gm30_log
//			       gm30_log = log(gm30)
//			
//			       NewImage/K=1 gm00_log
//				ModifyImage gm00_log ctab={*,2,Rainbow,0}
//				NewImage/K=1 gm30_log
//				ModifyImage gm30_log ctab={*,2,Rainbow,0}
				
		Duplicate/O gm00,mask00,mask00_log
		Duplicate/O gm30,mask30,mask30_log
			
		  //Stitching (first approach)			
				
//				t01= (gm00 == 0)
//				t02= (gm30 == 0)
//				t03= (gm00 !=0 & gm30 != 0)
//				
//				test = t02 == 1 ? gm00[p][q] : test
//				test = t01 == 1 ? gm30[p][q] : test
//				test = t03 !=0  ? (gm00[p][q]+gm00[p][q])/2 : test
//				
		//Stitching (Second approach)
				
		Variable n
				
		For (n=1; n<5; n+=1)
			Variable indA=(n*ModuleSize+(n-1)*gap)-gapin
			Variable indB=indA+gapsize
			mask30[0,980][IndA,IndB]=gm00 [p][q]
			mask00[0,980][indA+DetShift,indB+DetShift]=gm30 [p][q]

		endfor
				
//				mask00_log = log(mask00)
//				mask30_log=log(mask30)
//				NewImage/K=1 mask00_log
//				ModifyImage mask00_log ctab={*,2,Rainbow,0}
//				NewImage/K=1 mask30_log
//				ModifyImage mask30_log ctab={*,2,Rainbow,0}
								
//        			mask=.5*(mask30+mask00)
				Make/O/N=(981,1043) final
				final = mask30[p][q]
				
//				Duplicate/O mask, mask_log
//				mask_log=log(mask)
//				NewImage/K=1 mask_log
//				ModifyImage mask_log ctab={*,2,Rainbow,0}
				
//				Duplicate/O final, final_log
//				final_log = log(final)
//				NewImage/K=1 final_log
//				ModifyImage final_log ctab={*,2,Rainbow,0}
//				Make/O/N=(981,1043) final
//				final = test[p][q+30]
				
				string FinalName=BaseNameWave[i]+"_st_1m.GB"
				variable refnum
				
				Open/P=output refnum as FinalName
				fbinwrite/B=3/F=4/U refnum,final 
				Close refnum
				
		//			ImageSave/P=output/F/T="tiff"/O Final as FinalName
				
		//			Duplicate/O final final_log
		//			final_log = log(final)
		//			
		//			NewImage/K=1 final
		//			ModifyImage final ctab={*,1000,Rainbow,0}
		//			NewImage final_log
		//			ModifyImage final_log ctab={*,10,Rainbow,0}
			endif
		endfor
		break
	endswitch
return 0
End