RnkPic21() 
! Measures correlation   Pearson, Rank & Manders, Hcoef
! doicq=1    do the ICQ
! domand=1   do the MOC
! zpp=1     delete images at end of prog   dF1Pic, Mf1pic,  c1his, F1mappic also those from F2Pic
! correct Hcoef - for when ROI is not the whole image


! includes ranking method
! 8 bit data
! Returns   : Rank-fast (rs) (1-6...), Rank-Pearson-calc (rp), Pearson (r), Manders (Mnd), Li (icq)
!      Rank-fast bypassed
Mnd=99 rp=98 r=97 icq=96
! NO Print Option   - turned off

!  PICS
! need 3 input pics,    F1Pic       F2Pic        MPic; !   2 intensities & analysis Mask
! C1His - histogram
! F1MapPic- mapping table for ranking 
! Mf1Pic - mapped pic
! same for F2 image set
!         Variables
! Npixels - number used in analysis
! NNpixels- number of pixels not used in anal
! zppics - keep all images etc if zppics=0
!      need to add in mask to calculations

if set(doMand)=0 doMand=0; ! bypass Manders
if set(doICQ)=0 doICQ=0; ! bypass ICQ (Li)

local Npi,NNp,mea,nx,ny, max,min
! local xod,  yod,  rod,  r2o
! local xevn, yevn, revn, r2evn 

if set(zppics)=0 zppics=1; ! zap pics
bse=22; ! base for lib nextfree

! find data siz from Mask picture
  ver=0;pic MPic siz; sur MPic full; ver=1
   Npixels=mea*nx*ny;; ! number of pixels to be analysed
   NNpixels=nx*ny-Npixels; ! number of pixels outside mask - not used
   ! typ Npixels,NNpixels
! dis F1Pic to dis:2
ver=0;sur F2Pic; ver=1
if max >min dis  F2Pic to dis:3
! min=0 max=1 dis   MPic to dis:4 pre
   ! uns for; ! wait
! Mask Pics
cal :F1Pic*:MPic
  tit F1Pic text ' F1Pic  Masked'
cal :F2Pic*:MPic
  tit F1Pic text ' F2Pic  Masked'
! dis F1Pic to dis:2
ver=0;sur F2Pic; ver=1
! if max>min dis F2Pic to dis:3
   !uns for;! wait

! RANK data, by intensity, mapping table 
!   - highest rank most intense, equal given average rank
! F1Pic
ver=0
lib nextfree; C1His=nxt; min=0 max=255 his F1Pic to C1His pre
  p 0=p(0)-NNpixels;! dis C1His to dis:2
lib nextfree; F1mapPic=nxt; 
 cre F1mapPic siz 256,1 val 0 fp; ori left; tit tex 'C1 map pic'
ndone=0; ! dis C1His
 for n=255,0,-1
    sel C1His; vn=p(n); ! number intensity n   
    if vn=0 next n 
    sel F1mapPic
       Avrank=(Npixels*2-ndone*2-vn)/2+.5; !  average rank
       p n=Avrank; ! insert average rank
       ! typ n,'  ',Avrank,'    ',vn
       ndone=ndone+vn
 loop
! dis F1mapPic to dis:3
lib nextfree; Mf1Pic=nxt
    map from F1Pic  to Mf1Pic  fp with F1mapPic range 0,255; tit Mf1Pic add tex ' Ranked X '
    ! dis Mf1Pic to dis:2

! F2Pic
lib nextfree; C2His=nxt; min=0 max=255 his F2Pic to C2His pre
  p 0=p(0)-NNpixels; ! dis C2His to dis:2
lib nextfree; F2mapPic=nxt; 
 cre F2mapPic siz 256,1 val 0 fp; ori left; tit tex 'C2 map pic'
ndone=0; ! dis C2His
 for n=255,0,-1
    sel C2His; vn=p(n); ! number intensity n   
    if vn=0 next n 
    sel F2mapPic
       Avrank=(Npixels*2-ndone*2-vn)/2+.5; !  average rank
       p n=Avrank; ! insert average rank
       ! typ n,'  ',Avrank,'    ',vn
       ndone=ndone+vn
 loop
! dis F2mapPic to dis:3
lib nextfree; Mf2Pic=nxt
   map from F2Pic  to Mf2Pic  fp with F2mapPic range 0,255; tit Mf2Pic add tex ' Ranked X '
  ! dis Mf2Pic to dis:2

jump nquick
! Cal  Spearman Rank- quick method
! typ 'Rank-simple'
!    sum the squarred differences in rank
!    mark on display
lib nextfree; RPic=nxt
cal :Mf1Pic-:Mf2Pic to RPic fp; ! dis RPic to dis:2
cal :RPic^2; ! dis RPic to dis:3
sur RPic full; pic RPic siz
  D=mea*nx*ny;! typ D
rs=1-6*D/(Npixels^3-Npixels)
 !typ '    Spearman Fast rs ',rs; ! typ
nquick:

! Rank Correlation Coef Pic method 2 -Pearson
! typ 'Pearson-Rank'
! dis Mf1pic;  ! dis Mf2pic
pic Mf2Pic siz
ver=0
! find mean - can derive from npi for ranked data
! sur Mf1Pic full
  ! m1=mea*nx*ny/Npixels
  m1=(npi+1)/2
! sur Mf2Pic full
  ! m2=mea*nx*ny/Npixels
  m2=m1
  ! typ 'mean 2 ',m2,(npi+1)/2
! top of equation
  cal (:Mf1Pic-m1) to 999 fp;! 999 to dis:1
  cal (:Mf2Pic-m2) to 998 fp;! 998 to dis:2
      cal :999*:998 to 997;cal :997*:MPic
     sur 997 full;ver=1; Em=mea*nx*ny; ! typ Em
  if zpp=1 del 997,999
 ! underside of eq
pic F1Pic siz
      cal (:Mf1Pic-m1)^2 to 996 fp
          cal :996*:MPic
          ver=0;sur 996 full; E1=root(mea*nx*ny); ! typ 'E1 ',E1
      cal (:Mf2Pic-m2)^2  to 995 fp
          cal :995*:MPic
          ver=0; sur 995 full; E2=root(mea*nx*ny); ! typ 'E2 ',E2
if E1=0 | E2=0 end
rp= em/(E1*E2)
if zpp=1 del 995,996

! Pearson Correlation Coef Pic - unranked data
! typ 'Pearson from pics'
! calculated from images
! Requires that F1Pic and F2Pic are already masked
! Npixels  - number of pixels to be analysed - from MPic
   pic MPic siz; sur MPic full
   Npixels=mea*nx*ny
! dis F1Pic; ! dis F2Pic
pic F2Pic siz
ver=0
sur F1Pic full; m1=mea*nx*ny/Npixels; ! typ 'mean 1 ',m1
sur F2Pic full; m2=mea*nx*ny/Npixels; ! typ 'mean 2 ',m2
! top of equation
  cal (:F1Pic-m1) to 999 fp;! 999 to dis:1
  cal (:F2Pic-m2) to 998 fp; ! 998 to dis:2
      cal :999*:998 to 997;cal :997*:MPic
     sur 997 full;ver=1; Em=mea*nx*ny; ! typ Em
 ! underside of eq
pic F1Pic siz
      cal (:F1Pic-m1)^2 to 996 fp
          cal :996*:MPic
          ver=0;sur 996 full; E1=root(mea*nx*ny); ! typ 'E1 ',E1
      cal (:F2Pic-m2)^2  to 995 fp
          cal :995*:MPic
          ver=0; sur 995 full; E2=root(mea*nx*ny); ! typ 'E2 ',E2
if E1=0 | E2=0 end
r= em/(E1*E2)
if zpp=1 del 995,996

! Li  - ICQ method    uses data from Pearson
if doicq=0 jump nicq
typ 'ICQ ',m1,m2
cal :F1Pic>m1 to 999 byt
cal :F2Pic>m2 to 998 byt
cal :999=:998 to 997 int
cal :997*:Mpic; ! 997
min=0 max=1 dis 999 to dis:2
min=0 max=1 dis 998 to dis:3
min=0 max=1 dis 997 to dis:4 pre
  uns for; wait
min=-10 max=10 his 997 to 996 pre
min=-10 max=10 dis 996 to dis:2 pre
uns for; wait
!typ ' ICQ histrogram'
!for n=9,12;!v=p(n); !typ n,v;!loo
v1=p(11)
v2=p(10)
typ 'icq   v1 ',v1,'   v2 ',v2,'     Npixels ',npixels
icq=v1/Npixels-0.5
typ 'icq = ',v1/Npixels-0.5,(v1/(v1+v2))-.5
!typ 'n pixels ',npix,v1,v1+v2
sur 997 full
typ 'icq from mea    ',mea-.5
typ
nicq:

! Manders Correlation Coef Pic - unranked data
 if  doMand=0  jump nMnders 
! typ 'Manders correlation from pics'
! calculated from images
! Requires that F1Pic and F2Pic are already masked
! Npixels  - number of pixels to be analysed - from MPic
   pic MPic siz; sur MPic full
   Npixels=mea*nx*ny
! dis F1Pic; ! dis F2Pic
pic F2Pic siz
ver=0
! top of equation
      cal :F1Pic*:F2Pic to 997 fp;cal :997*:MPic
     sur 997 full;ver=1; Em=mea*nx*ny; ! typ Em
 ! underside of eq
pic F1Pic siz
      cal (:F1Pic)^2 to 996 fp
          cal :996*:MPic
          ver=0;sur 996 full; E1=root(mea*nx*ny); ! typ 'E1 ',E1
                                           E11=mea*nx*ny
      cal (:F2Pic)^2  to 995 fp
          cal :995*:MPic
          ver=0; sur 995 full; E2=root(mea*nx*ny); ! typ 'E2 ',E2
                                           E12=mea*nx*ny
if E1=0 | E2=0 end
Mnd= Em/(E1*E2)
Md1=Em/root(E11*E12)
! typ Em,E11,E12,root(E11*E12)
nMnders:

! Hp Coef Pic - unranked data
trap=25  if  doHp=0  jump nHp
if rc=25  jump nHp
! typ 'Manders correlation from pics'
! calculated from images
! Requires that F1Pic and F2Pic are already masked
! Npixels  - number of pixels to be analysed - from MPic
   pic MPic siz; sur MPic full
   Npixels=mea*nx*ny
! dis F1Pic; ! dis F2Pic
pic F2Pic siz
ver=0

! top of equation - same as MOC
      cal :F1Pic*:F2Pic to 997 fp;cal :997*:MPic
     sur 997 full;ver=1; Em=mea*nx*ny; ! typ Em

 ! underside of eq
pic F1Pic siz
          cal :F1Pic*:Mpic to 996
          ver=0;sur 996 full; E1=mea*nx*ny; ! typ 'E1 ',E1

          cal :F2Pic*:MPic to 995
          ver=0; sur 995 full; E2=mea*nx*ny; ! typ 'E2 ',E2
if E1=0 | E2=0 end
Hp=    Em/(E1*E2)
Hcoef=npix*Hp
! typ Em,E11,E12,root(E11*E12)
nHp:




! final output - Pictures
! exa F1Pic
! typ rou(r*1000)/1000,'   ',rou(rs*1000)/1000,'   ',rou(rp*1000)/1000

! Print OFF
!  typ rou(r*1000)/1000,'   ',rou(rp*1000)/1000

! Tidy Up
if zppics=0 jump nozap
del F1Pic; del Mf1pic; del c1his; del F1mappic 
del F2Pic; del Mf2pic; del c2his; del F2mappic
! del RPic
nozap:

end
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