updates to EM4DEBSD program; see wiki for usage instructions

application of reduced ROI still needs to be tested

NamelistTemplates/EM4DEBSD.template

@@ -19,7 +19,7 @@
 !=====================================
 ! if doconvolution = .TRUE., then perform a full data set convolution and store the 
 ! results in the HDF5 file convolvedpatternfile [relative to EMdatapathname]
-! else we do one mask at a time 
+! else we interrogate the convolvedpatternfile
 !=====================================
  doconvolution = .FALSE.,
  convolvedpatternfile = 'undefined', 
@@ -44,7 +44,7 @@
 ! square virtual detector size (should be odd numbers of the form 2*n+1 !)
  VDsize = 5,
 ! Gaussian virtual detector standard deviation
- VDSD = 0.5,
+ VDSD = 2.5,
 ! Hann window alpha parameter
  VDHannAlpha = 0.5, 
 ! stepsize in pixels for VDtype='Array' mode

Source/EMsoftOOLib/mod_filters.f90

@@ -1311,6 +1311,38 @@ recursive subroutine HannWindow(roi_size, window, alpha)
 
 end subroutine HannWindow
 
+!--------------------------------------------------------------------------
+recursive subroutine GaussianWindow(roi_size, window, SD)
+!DEC$ ATTRIBUTES DLLEXPORT :: GaussianWindow
+!
+!> @brief Gaussian windowing function for pattern region of interest
+!
+!> @date 04/21/24 MDG 1.0 original
+!--------------------------------------------------------------------------
+
+IMPLICIT NONE
+
+integer(kind=irg),INTENT(IN)           :: roi_size
+real(kind=dbl),INTENT(INOUT)           :: window(roi_size, roi_size)
+real(kind=dbl),INTENT(IN)              :: SD
+
+integer(kind=irg)                      :: i, j, r
+real(kind=dbl)                         :: h, k, x, y
+
+r = (roi_size-1)/2
+window = 0.D0
+h = 1.D0/(2.D0*cPi*SD)
+k = 1.D0/(2.D0*SD)
+do i=-r,r
+  x = dble(i)**2
+  do j=-r,r
+    y = dble(j)**2
+    window(i+r+1,j+r+1) = h * exp( -k*(x+y))
+  end do
+end do
+
+end subroutine GaussianWindow
+
 !--------------------------------------------------------------------------
 recursive subroutine init_BandPassFilter(dims, high_pass, low_pass, hpmask_shifted, &
                                          lpmask_shifted, inp, outp, planf, planb) 

Source/EMsoftOOLib/program_mods/mod_4DEBSD.f90

@@ -344,11 +344,10 @@ subroutine readNameList_(self, nmlfile, initonly)
    end if
  end if
 
- if (trim(VDtype).eq.'Array') then 
-   if (trim(convolvedpatternfile).eq.'undefined') then 
-    call Message%printError('readNameList:',' convolvedpatternfile file name is undefined in '//nmlfile)
-   end if 
+ if (trim(convolvedpatternfile).eq.'undefined') then 
+   call Message%printError('readNameList:',' convolvedpatternfile file name is undefined in '//nmlfile)
  end if 
+
 end if
 
 self%nml%ipf_ht = ipf_ht
@@ -1460,7 +1459,7 @@ subroutine drawMPpositions_(self, n, ctmp, sz, MP)
 integer(int8)                     :: i8 (3,4)
 integer(int8), allocatable        :: TIFF_image(:,:)
 
-TIFF_filename = 'Debug_MPpositions.tiff'
+TIFF_filename = 'MPpositions.tiff'
 allocate(TIFF_image(sz(1),sz(2)))
 npx = (sz(1)-1)/2 
 w = 2
@@ -1532,7 +1531,7 @@ subroutine drawEBSPpositions_(self, sz, pat)
 integer(int8)                     :: i8 (3,4)
 integer(int8), allocatable        :: TIFF_image(:,:)
 
-TIFF_filename = 'Debug_EBSPpositions.tiff'
+TIFF_filename = 'EBSPpositions.tiff'
 allocate(TIFF_image(sz(1),sz(2)))
 
 ! and generate the tiff output file 
@@ -1807,11 +1806,15 @@ subroutine EBSD4D_(self, EMsoft, progname, HDFnames)
 select case(nml%VDtype)
   case('Flat')
     VDmask = 1.0
+  case('Gaus')
+    call GaussianWindow(nml%VDsize, VDmaskd, dble(nml%VDSD))
+    VDmask = sngl(VDmaskd)
+    call mem%dealloc(VDmaskd, 'VDmaskd')
   case('Hann')
     call HannWindow(nml%VDsize, VDmaskd, dble(nml%VDHannAlpha))
     VDmask = sngl(VDmaskd)
     call mem%dealloc(VDmaskd, 'VDmaskd')
-  case('Array')
+  case('Array') ! we don't need this option, but it should be here so we don't default out
     VDmask = 1.0
 
   case default 
@@ -1861,7 +1864,7 @@ subroutine EBSD4D_(self, EMsoft, progname, HDFnames)
   c = LL * ca
   d = LL*LL
   mv_plane = plane(a,b,c,d)
-  call mv_plane%log(' Detector plane ')
+  call mv_plane%log(' Detector plane multivector ')
   dl = DIFT%nml%delta
 ! for each sampling point, transform all numhatn vectors to the sample frame using the 
 ! corresponding orientation quaternion from the qAR list; then determine where those 
@@ -1932,6 +1935,7 @@ subroutine EBSD4D_(self, EMsoft, progname, HDFnames)
     quat = conjg(quat)
     newctmp = quat%quat_Lp_vecarray(numhatn, transpose(ctmp))
     ! do kk=1,numhatn
+! we will take the same symmetrically equivalent representative as selected above
       mv_line = line(newctmp(1,VDkk),newctmp(2,VDkk),newctmp(3,VDkk))
       mv_line = mv_line%normalized()
       mv = meet(mv_plane, mv_line)