various updates and bug fixes

NamelistTemplates/EMEBSD.template

@@ -20,6 +20,10 @@
  energymax = 20.0,
 ! include a realistic intensity background or not ... 
  includebackground = 'y',
+! prefix of filename for individual pattern output (relative to EMdatapathname)
+! this assumes that bitdepth below is set to 8bit; otherwise no images will be written.
+! [Warning: operating systems typically don't like folders with 100,000 files or more...]
+ tiff_prefix = 'undefined',
 ! name of angle file (euler angles or quaternions); path relative to EMdatapathname
  anglefile = 'testeuler.txt',
 ! does this file have only orientations ('orientations') or does it also have pattern center and deformation tensor ('orpcdef')

Source/EMOpenCLLib/Indexingmod.f90

@@ -315,12 +315,22 @@ END SUBROUTINE ProgCallBackTypeErrorDIdriver
 
 ! intercept the case where the exptnumsx/y parameters are set to zero, but 
 ! numsx/y are not...
-if (dinl%exptnumsx.eq.0) dinl%exptnumsx = dinl%numsx
-if (dinl%exptnumsy.eq.0) dinl%exptnumsy = dinl%numsy
-
+!
+! this if statement is a consequence of an error discovered on 08/13/24 that only 
+! affects the Binary inputtype ... 
+if (trim(dinl%inputtype).eq.'Binary') then 
+  if (dinl%exptnumsx.eq.0) dinl%exptnumsx = dinl%numsx/dinl%binning
+  if (dinl%exptnumsy.eq.0) dinl%exptnumsy = dinl%numsy/dinl%binning
 ! binned pattern array size for experimental patterns
-binx = dinl%exptnumsx/dinl%binning
-biny = dinl%exptnumsy/dinl%binning
+  binx = dinl%exptnumsx
+  biny = dinl%exptnumsy
+else
+  if (dinl%exptnumsx.eq.0) dinl%exptnumsx = dinl%numsx
+  if (dinl%exptnumsy.eq.0) dinl%exptnumsy = dinl%numsy
+! binned pattern array size for experimental patterns
+  binx = dinl%exptnumsx/dinl%binning
+  biny = dinl%exptnumsy/dinl%binning
+end if 
 bindx = 1.0/float(dinl%binning)**2
 ! we also force the dictionary patterns to have this size 
 dinl%numsx = binx
@@ -347,9 +357,9 @@ END SUBROUTINE ProgCallBackTypeErrorDIdriver
     ! and then generate the detector arrays
     enl%numsx = dinl%numsx
     enl%numsy = dinl%numsy
-    enl%xpc = dinl%xpc
-    enl%ypc = dinl%ypc
-    enl%delta = dinl%delta
+    enl%xpc = dinl%xpc/dinl%binning
+    enl%ypc = dinl%ypc/dinl%binning
+    enl%delta = dinl%delta*dinl%binning
     enl%thetac = dinl%thetac
     enl%L = dinl%L
     enl%energymin = dinl%energymin

Source/EMsoftHDFLib/NameListHDFwriters.f90

@@ -2911,6 +2911,11 @@ recursive subroutine HDFwriteEBSDNameList(HDF_head, enl)
 hdferr = HDF_writeDatasetStringArray(dataset, line2, 1, HDF_head)
 if (hdferr.ne.0) call HDF_handleError(hdferr,'HDFwriteEBSDNameList: unable to create masterfile dataset',.TRUE.)
 
+dataset = trim(enl%tiff_prefix)
+line2(1) = trim(enl%tiff_prefix)
+hdferr = HDF_writeDatasetStringArray(dataset, line2, 1, HDF_head)
+if (hdferr.ne.0) call HDF_handleError(hdferr,'HDFwriteEBSDNameList: unable to create tiff_prefix dataset',.TRUE.)
+
 dataset = SC_anglefile
 line2(1) = trim(enl%anglefile)
 hdferr = HDF_writeDatasetStringArray(dataset, line2, 1, HDF_head)

Source/EMsoftHDFLib/patternmod.f90

@@ -323,6 +323,8 @@ recursive function openExpPatternFile(filename, npat, L, inputtype, recsize, fun
         end if
         ! get the first byte to check if this file is version 1-3 or 4
         ! version 4 has an extra byte in the header...
+        ! version 5 does as well, offsets the pattern offsets by an additional 25 bytes,
+        ! and increases the pattern headder from 16 to 42 bytes 
         read(unit=funit, pos=1, iostat=ios) header
         ebspversion = 256-iachar(header)
         io_int(1) = ebspversion
@@ -626,11 +628,12 @@ recursive subroutine getExpPatternRow(iii, wd, patsz, L, dims3, offset3, funit,
     case(5)  ! "OxfordBinary"
 
 ! read position of patterns in file for a single row from the header
-    if (ebspversion.eq.4) then
+    if (ebspversion.gt.3) then
         read(unit=funit, pos=(liii-1)*lwd*8+10, iostat=ios) patoffsets
     else
         read(unit=funit, pos=(liii-1)*lwd*8+9, iostat=ios) patoffsets
     end if
+    if (ebspversion.eq.5) patoffsets = patoffsets + 25_8
 
 ! generate a buffer to load individual patterns into
       buffersize = lL
@@ -642,7 +645,11 @@ recursive subroutine getExpPatternRow(iii, wd, patsz, L, dims3, offset3, funit,
 
       do ii=1,lwd
 ! read each pattern into buffer with the 16 bytes of metadata skipped
-        read(unit=funit, pos=patoffsets(ii)+17_8, iostat=ios) buffer
+        if (ebspversion.eq.5) then 
+            read(unit=funit, pos=patoffsets(ii)+43_8, iostat=ios) buffer
+        else
+            read(unit=funit, pos=patoffsets(ii)+17_8, iostat=ios) buffer
+        end if
 
 ! loop over pixels and convert the byte values into single byte integers
         do jj=1_ill,lL
@@ -956,13 +963,18 @@ recursive subroutine getSingleExpPattern(iii, wd, patsz, L, dims3, offset3, funi
       else
           read(unit=funit, pos=(liii-1)*lwd*8+9, iostat=ios) patoffsets
       end if
+      if (ebspversion.eq.5) patoffsets = patoffsets + 25_8
 
 ! generate buffers to load individual pattern into
       buffersize = lL
       allocate(buffer(buffersize), pairs(buffersize))
 
 ! read single pattern into buffer with the 16 bytes of metadata skipped
-      read(unit=funit, pos=patoffsets(l1)+17_8, iostat=ios) buffer
+      if (ebspversion.eq.5) then 
+          read(unit=funit, pos=patoffsets(l1)+43_8, iostat=ios) buffer
+      else
+          read(unit=funit, pos=patoffsets(l1)+17_8, iostat=ios) buffer
+      end if
 
 ! convert the byte values into single byte integers
       pairs = ichar(buffer) 
@@ -2622,7 +2634,7 @@ end subroutine PreProcessPatterns
 !
 !> @date 11/30/18 MDG 1.0 original, based on EBSD routine
 !--------------------------------------------------------------------------
-recursive subroutine PreProcessTKDPatterns(nthreads, inRAM, tkdnl, binx, biny, masklin, correctsize, totnumexpt, &
+recursive subroutine PreProcessTKDPatterns(nthreads, inRAM, tkdnl, binx, biny, mask, correctsize, totnumexpt, &
                                         epatterns, exptIQ)
 !DEC$ ATTRIBUTES DLLEXPORT :: PreProcessTKDPatterns
 
@@ -2645,7 +2657,7 @@ recursive subroutine PreProcessTKDPatterns(nthreads, inRAM, tkdnl, binx, biny, m
 type(TKDIndexingNameListType),INTENT(IN)    :: tkdnl
 integer(kind=irg),INTENT(IN)                :: binx
 integer(kind=irg),INTENT(IN)                :: biny
-real(kind=sgl),INTENT(IN)                   :: masklin(binx*biny)
+real(kind=sgl),INTENT(IN)                   :: mask(binx, biny)
 integer(kind=irg),INTENT(IN)                :: correctsize
 integer(kind=irg),INTENT(IN)                :: totnumexpt
 real(kind=sgl),INTENT(INOUT),OPTIONAL       :: epatterns(correctsize, totnumexpt)
@@ -2834,6 +2846,9 @@ recursive subroutine PreProcessTKDPatterns(nthreads, inRAM, tkdnl, binx, biny, m
           TKDPat(1:binx,kk) = exppatarray((jj-1)*patsz+(kk-1)*binx+1:(jj-1)*patsz+kk*binx)
         end do
 
+! apply the mask
+        TKDpat = TKDpat * mask 
+
         if (present(exptIQ)) then
 ! compute the pattern Image Quality 
           exptIQ((iii-iiistart)*jjend + jj) = sngl(computeEBSDIQ(binx, biny, TKDPat, ksqarray, Jres, planf))
@@ -2849,15 +2864,15 @@ recursive subroutine PreProcessTKDPatterns(nthreads, inRAM, tkdnl, binx, biny, m
         mi = minval(TKDPat)
 
         TKDpint = nint(((TKDPat - mi) / (ma-mi))*255.0)
-        TKDPat = float(adhisteq(tkdnl%nregions,binx,biny,TKDpint))
+        TKDPat = float(adhisteq(tkdnl%nregions,binx,biny,TKDpint)) * mask
 
 ! convert back to 1D vector
         do kk=1,biny
           exppatarray((jj-1)*patsz+(kk-1)*binx+1:(jj-1)*patsz+kk*binx) = TKDPat(1:binx,kk)
         end do
 
 ! apply circular mask and normalize for the dot product computation
-        exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L) = exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L) * masklin(1:L)
+        exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L) = exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L) ! * masklin(1:L)
         vlen = vecnorm(exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L))
         if (vlen.ne.0.0) then
           exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L) = exppatarray((jj-1)*patsz+1:(jj-1)*patsz+L)/vlen

Source/EMsoftLib/NameListHandlers.f90

@@ -4039,13 +4039,14 @@ recursive subroutine GetEBSDNameList(nmlfile, enl, initonly)
 character(fnlen)        :: masterfile
 character(fnlen)        :: energyfile  ! removed from template file 05/16/19 [MDG]
 character(fnlen)        :: datafile
+character(fnlen)        :: tiff_prefix
 
 ! define the IO namelist to facilitate passing variables to the program.
 namelist  / EBSDdata / stdout, L, thetac, delta, numsx, numsy, xpc, ypc, anglefile, eulerconvention, masterfile, bitdepth, &
                         energyfile, datafile, beamcurrent, dwelltime, energymin, energymax, binning, gammavalue, alphaBD, &
                         scalingmode, axisangle, nthreads, outputformat, maskpattern, energyaverage, spatialaverage, &
                         applyDeformation, Ftensor, includebackground, anglefiletype, makedictionary, hipassw, nregions, &
-                        maskradius, poisson, Fframe
+                        maskradius, poisson, Fframe, tiff_prefix
 
 ! set the input parameters to default values (except for xtalname, which must be present)
 stdout          = 6
@@ -4088,6 +4089,7 @@ recursive subroutine GetEBSDNameList(nmlfile, enl, initonly)
 masterfile      = 'undefined'   ! filename
 energyfile      = 'undefined'   ! name of file that contains energy histograms for all scintillator pixels (output from MC program)
 datafile        = 'undefined'   ! output file name
+tiff_prefix     = 'undefined'   ! used to output individual tiff files for patterns
 spatialaverage  = 'n'
 
 if (present(initonly)) then
@@ -4169,6 +4171,7 @@ recursive subroutine GetEBSDNameList(nmlfile, enl, initonly)
 ! user definition, if any, in the namelist file is overwritten here...
 enl%energyfile = enl%masterfile       ! changed on 05/16/19 [MDG]
 enl%datafile = datafile
+enl%tiff_prefix = tiff_prefix
 enl%spatialaverage = spatialaverage
 end subroutine GetEBSDNameList
 

Source/EMsoftLib/NameListTypedefs.f90

@@ -630,6 +630,7 @@ module NameListTypedefs
         character(fnlen)        :: targetfile
         character(fnlen)        :: energyfile
         character(fnlen)        :: datafile
+        character(fnlen)        :: tiff_prefix
 end type EBSDNameListType
 
 ! namelist for the EMEBSDBatch program

Source/SEM/EMEBSD.f90

@@ -309,6 +309,8 @@ subroutine ComputeEBSDPatterns(enl, mcnl, mpnl, numangles, angles, EBSDMCdata, E
 use timing
 use stringconstants
 use math
+use image
+use, intrinsic :: iso_fortran_env
 
 IMPLICIT NONE
 
@@ -381,8 +383,8 @@ subroutine ComputeEBSDPatterns(enl, mcnl, mpnl, numangles, angles, EBSDMCdata, E
 character(15)                           :: tstrb
 character(15)                           :: tstre
 character(10)                           :: char10
-character(fnlen)                        :: datafile
-logical                                 :: overwrite = .TRUE., insert = .TRUE., singlebatch
+character(fnlen)                        :: datafile, TIFF_filename
+logical                                 :: overwrite = .TRUE., insert = .TRUE., singlebatch, tiff_output=.FALSE.
 character(5)                            :: bitmode
 integer(kind=irg)                       :: numbits
 real(kind=sgl)                          :: bitrange
@@ -392,6 +394,15 @@ subroutine ComputeEBSDPatterns(enl, mcnl, mpnl, numangles, angles, EBSDMCdata, E
                                            Gmatrix(3,3), gs2c(3,3)
 logical                                 :: includeFmatrix=.FALSE., noise
 
+! declare variables for use in object oriented image module
+integer                                 :: iostat
+character(len=128)                      :: iomsg
+logical                                 :: isInteger
+type(image_t)                           :: im
+character(6)                            :: TIFF_number
+integer(int8)                           :: i8 (3,4)
+integer(int8), allocatable              :: TIFF_image(:,:)
+
 !====================================
 ! max number of OpenMP threads on this platform
 maxthreads = omp_get_max_threads()
@@ -412,6 +423,8 @@ subroutine ComputeEBSDPatterns(enl, mcnl, mpnl, numangles, angles, EBSDMCdata, E
   call Message('Program will work in dictionary generation mode')
 end if
 
+if (trim(enl%tiff_prefix).ne.'undefined') tiff_output = .TRUE. 
+
 ! define some energy-related parameters derived from MC input parameters
 !====================================
 noise = .FALSE.
@@ -1133,6 +1146,32 @@ subroutine ComputeEBSDPatterns(enl, mcnl, mpnl, numangles, angles, EBSDMCdata, E
        if (hdferr.ne.0) call HDF_handleError(hdferr,'HDF_writeHyperslabFloatArray3D EBSDpatterns')
      end if
    end if
+
+! ! should we write out individual patterns ? (tiff_output=.TRUE.)
+!    if ((trim(bitmode).eq.'char').and.(tiff_output.eqv..TRUE.)) then 
+!     allocate(TIFF_image(binx,biny))
+! ! Create a tiff file name 
+!     do i=1,dim2
+!       TIFF_filename = trim(EMsoft_getEMdatapathname())//trim(enl%tiff_prefix)
+!       write (TIFF_number,"(I6.6)") iang-1
+!       TIFF_filename = trim(TIFF_filename)//TIFF_number//'.tiff'
+!       TIFF_filename = EMsoft_toNativePath(TIFF_filename)
+!       ma = maxval(ECPpattern)
+!       mi = minval(ECPpattern)
+!       ECPpatternintd = ((ECPpattern - mi)/ (ma-mi))
+!       if (enl%maskpattern.eq.'y')  ECPpatternintd = ECPpatternintd * mask 
+!       TIFF_image = nint(255.0*ECPpatternintd)
+! ! set up the image_t structure
+!       im = image_t(TIFF_image)
+!       if(im%empty()) call Message("EMECP","failed to convert array to image")
+
+! ! create the file
+!       call im%write(trim(TIFF_filename), iostat, iomsg) ! format automatically detected from extension
+!       if(0.ne.iostat) then
+!         call Message("failed to write image to file : "//iomsg)
+!       end if 
+!     end do
+!    end if 
  !end if
 ! =====================================================
 ! end of HDF_FileVersion = 4.0 write statements

Source/SEM/EMEBSDmaster.f90

@@ -780,12 +780,12 @@ subroutine ComputeMasterPattern(emnl, progname, nmldeffile)
   karray(1:3,1) = sngl(ktmp%k(1:3))
   karray(4,1) = sngl(ktmp%kn)
   kij(1:3,1) = (/ ktmp%i, ktmp%j, ktmp%hs /)
-   do ik=2,numk
-     ktmp => ktmp%next
-     karray(1:3,ik) = sngl(ktmp%k(1:3))
-     karray(4,ik) = sngl(ktmp%kn)
-     kij(1:3,ik) = (/ ktmp%i, ktmp%j, ktmp%hs /)
-   end do
+  do ik=2,numk
+    ktmp => ktmp%next
+    karray(1:3,ik) = sngl(ktmp%k(1:3))
+    karray(4,ik) = sngl(ktmp%kn)
+    kij(1:3,ik) = (/ ktmp%i, ktmp%j, ktmp%hs /)
+  end do
 ! and remove the linked list
   call Delete_kvectorlist(khead)