adds individual pattern tiff output to EMECP program

NamelistTemplates/EMECP.template

@@ -25,6 +25,9 @@
  outputformat = 'gui',
 ! output file ; path relative to EMdatapathname
  datafile = 'undefined',
+! file prefix to save individual patterns as tiff files (relative to EMdatapathname)
+! [probably best to save them in a separate folder, so they can be loaded as an image stack in Fiji]
+ tiff_prefix = 'undefined',
 ! number of threads for parallel execution
  nthreads = 1,
 ! tilt of the sample; only one angle incorporated for now

Source/EMsoftHDFLib/NameListHDFwriters.f90

@@ -3388,6 +3388,11 @@ recursive subroutine HDFwriteECPNameList(HDF_head, ecpnl, twolayerflag)
 hdferr = HDF_writeDatasetStringArray(dataset, line2, 1, HDF_head)
 if (hdferr.ne.0) call HDF_handleError(hdferr,'HDFwriteECPNameList: unable to create datafile dataset',.TRUE.)
 
+dataset = 'tiff_prefix'
+line2(1) = ecpnl%tiff_prefix
+hdferr = HDF_writeDatasetStringArray(dataset, line2, 1, HDF_head)
+if (hdferr.ne.0) call HDF_handleError(hdferr,'HDFwriteECPNameList: unable to create tiff_prefix dataset',.TRUE.)
+
 dataset = SC_xtalname
 line2(1) = ecpnl%xtalname
 hdferr = HDF_writeDatasetStringArray(dataset, line2, 1, HDF_head)

Source/EMsoftLib/NameListHandlers.f90

@@ -5797,6 +5797,7 @@ recursive subroutine GetECPNameList(nmlfile, ecpnl, initonly)
 character(fnlen)        :: datafile
 character(1)            :: maskpattern
 character(fnlen)        :: anglefile
+character(fnlen)        :: tiff_prefix
 character(3)            :: eulerconvention
 integer(kind=irg)       :: numangle_anglefile
 real(kind=sgl)          :: gammavalue
@@ -5808,7 +5809,7 @@ recursive subroutine GetECPNameList(nmlfile, ecpnl, initonly)
 
 ! namelist /ECPlist/ stdout, xtalname, voltage, k, fn, dmin, distort, abcdist, albegadist, ktmax, &
 namelist /ECPlist/ stdout, xtalname, xtalname2, fn_f, fn_s, dmin, filmthickness, anglefile, &
-                   nthreads, thetac, npix, maskpattern, eulerconvention, Rin, Rout, &
+                   nthreads, thetac, npix, maskpattern, eulerconvention, Rin, Rout, tiff_prefix, &
                    gF, gS, tF, tS, energyfile, filmfile, subsfile, masterfile, datafile, &
                    numangle_anglefile, gammavalue, outputformat, sampletilt, workingdistance
 
@@ -5832,6 +5833,7 @@ recursive subroutine GetECPNameList(nmlfile, ecpnl, initonly)
 subsfile = 'undefined'
 masterfile = 'undefined'
 datafile = 'undefined'
+tiff_prefix = 'undefined'
 maskpattern = 'y'
 anglefile = 'undefined'
 eulerconvention = 'hkl'
@@ -5880,6 +5882,7 @@ recursive subroutine GetECPNameList(nmlfile, ecpnl, initonly)
 ecpnl%masterfile = masterfile
 ecpnl%maskpattern = maskpattern
 ecpnl%anglefile = anglefile
+ecpnl%tiff_prefix = tiff_prefix
 ecpnl%numangle_anglefile = numangle_anglefile
 ecpnl%eulerconvention = eulerconvention
 ecpnl%gammavalue = gammavalue

Source/EMsoftLib/NameListTypedefs.f90

@@ -1061,6 +1061,7 @@ module NameListTypedefs
         character(fnlen)        :: masterfile
         character(fnlen)        :: datafile
         character(fnlen)        :: anglefile
+        character(fnlen)        :: tiff_prefix
         character(3)            :: eulerconvention
         real(kind=sgl)          :: gammavalue
         character(3)            :: outputformat

Source/SEM/EMECP.f90

@@ -113,6 +113,8 @@ subroutine ECpattern(ecpnl, progname, nmldeffile)
 use distortion
 use filters 
 use stringconstants
+use image
+use, intrinsic :: iso_fortran_env
 
 IMPLICIT NONE
 
@@ -148,20 +150,29 @@ subroutine ECpattern(ecpnl, progname, nmldeffile)
 real(kind=dbl)                          :: dp, MCangle
 real(kind=dbl),parameter                :: Rtod = 57.2957795131D0
 real(kind=dbl),parameter                :: dtoR = 0.01745329251D0
-logical                                 :: switchwfoff = .FALSE.
+logical                                 :: switchwfoff = .FALSE., tiff_output = .FALSE.
 !complex(kind=dbl)                       :: D
 
 type(HDFobjectStackType)                :: HDF_head
 integer(HSIZE_T), dimension(1:3)        :: hdims, offset 
 integer(HSIZE_T)                        :: dims3(3)
 character(fnlen,kind=c_char)            :: line2(1)
-character(fnlen)                        :: groupname, dataset, attributename, HDF_FileVersion
+character(fnlen)                        :: groupname, dataset, attributename, HDF_FileVersion, TIFF_filename
 character(11)                           :: dstr
 character(15)                           :: tstrb
 character(15)                           :: tstre
 character(fnlen)                        :: datafile
 logical                                 :: overwrite = .TRUE., insert = .TRUE.
 
+! declare variables for use in object oriented image module
+integer                                 :: iostat
+character(len=128)                      :: iomsg
+logical                                 :: isInteger
+type(image_t)                           :: im
+character(5)                            :: TIFF_number
+integer(int8)                           :: i8 (3,4)
+integer(int8), allocatable              :: TIFF_image(:,:)
+
 !=================================================================
 ! read Monte Carlo output file and extract necessary parameters
 ! first, we need to load the data from the output of EMMCOpenCL
@@ -220,11 +231,12 @@ subroutine ECpattern(ecpnl, progname, nmldeffile)
     switchwfoff = .TRUE.
 end if
 
-
 !=================================================================
 ! completed reading the file; generating list of incident vectors
 !=================================================================
 
+if (trim(ecpnl%tiff_prefix).ne.'undefined') tiff_output = .TRUE. 
+
 numk = 0
 call GetVectorsCone(ecpnl, khead, numk)
 allocate(kij(2,numk),klist(3,numk),stat=istat)
@@ -376,12 +388,14 @@ subroutine ECpattern(ecpnl, progname, nmldeffile)
 
 ! use OpenMP to run on multiple cores
 !$OMP PARALLEL DEFAULT(SHARED) &
-!$OMP PRIVATE(TID,nthreads,dc,ixy,istat,nix,niy,nixp,niyp,dx,dy,dxm,dym,MCangle,isig,dp,isigp) &
+!$OMP PRIVATE(TID,nthreads,dc,ixy,istat,nix,niy,nixp,niyp,dx,dy,dxm,dym,MCangle,isig,dp,isigp,TIFF_image) &
 !$OMP& PRIVATE(ipx,ipy,ECPpattern,bpat,ECPpatternintd,ma,mi,offset,hdims,dims3,hdferr,qu,idir,wf)
 
 TID = OMP_GET_THREAD_NUM()
 nthreads = OMP_GET_NUM_THREADS()
 
+if (tiff_output.eqv..TRUE.) allocate(TIFF_image(ecpnl%npix,ecpnl%npix))
+
 !$OMP DO SCHEDULE(DYNAMIC)
 angleloop: do iang = 1,ecpnl%numangle_anglefile
     qu(1:4) = angles%quatang(1:4,iang)
@@ -493,11 +507,30 @@ subroutine ECpattern(ecpnl, progname, nmldeffile)
           hdims = (/ ecpnl%npix, ecpnl%npix, ecpnl%numangle_anglefile /)
           dims3 = (/ ecpnl%npix, ecpnl%npix, 1 /)
           hdferr = HDF_writeHyperslabFloatArray3D(dataset, ECPpattern, hdims, offset, dims3, HDF_head, insert)
-! =====================================================
-! end of HDF_FileVersion = 4.0 write statements
-! =====================================================
+    end if
 
+    if (tiff_output.eqv..TRUE.) then 
+! Create a tiff file name 
+      TIFF_filename = trim(EMsoft_getEMdatapathname())//trim(ecpnl%tiff_prefix)
+      write (tiff_number,"(I5.5)") 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 (ecpnl%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 if
+
 !$OMP END CRITICAL
 
 end do angleloop