Merge branch 'develop' into Release5.0

NamelistTemplates/EMEBSDDI.template

@@ -91,7 +91,7 @@
 !
 ! name of datafile where the patterns are stored; path relative to EMdatapathname
  exptfile = 'undefined',
-! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF
+! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF, NORDIF
  inputtype = 'Binary',
 ! here we enter the HDF group names and data set names as individual strings (up to 10)
 ! enter the full path of a data set in individual strings for each group, in the correct order,

NamelistTemplates/EMEBSDDIpreview.template

@@ -24,7 +24,7 @@
  numav = 0,
 ! name of datafile where the patterns are stored; path relative to EMdatapathname
  exptfile = 'undefined',
-! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF
+! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF, NORDIF
  inputtype = 'Binary',
 ! here we enter the HDF group names and data set names as individual strings (up to 10)
 ! enter the full path of a data set in individual strings for each group, in the correct order,
@@ -34,4 +34,4 @@
 ! pattern coordinates to be used for the preview
  patx = 1,
  paty = 1,
-/
+/

NamelistTemplates/EMIntegrateSTEM.template

@@ -0,0 +1,31 @@
+ &IntegrateSTEMNamelist
+! DO NOT CHANGE THIS LINE
+!------------------------
+! IO Filenames
+!------------------------
+! Name of the file containing diffraction data
+ inputfilename = 'undefined',
+!------------------------
+! Detector Parameters
+!------------------------
+! Size of detector pixels in nm
+ pixsize = 9000,
+! Inner diameter of the annular detector, if used [mm]
+ id = 4,
+! Outer diamater of the annular detector, if used [mm]
+ od = 10,
+! Camera length [cm]
+ camlen = 3,
+!------------------------
+! Operating Parameters
+!------------------------
+! Operating mode
+! 1 = single reflection, 2 = annular detector
+! default is annular detector 
+ mode = 2,
+! If using a single reflection integration, specify the reflection here
+! Default is the through-beam 0,0,0
+ ref = 0,0,0,
+! Generate a CBED pattern, only works if mode = 2
+ CBED = .False.,
+/ 

NamelistTemplates/EMSphInx.template

@@ -58,7 +58,7 @@
  masterfile = 'undefined',
 ! experimental patter file name [relative to EMdatapathname]
  patfile = 'undefined',
-! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF
+! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF, NORDIF
  inputtype = 'Binary',
 ! here we enter the HDF group names and data set names as individual strings (up to 10)
 ! enter the full path of a data set in individual strings for each group, in the correct order,

NamelistTemplates/EMgetADP.template

@@ -31,7 +31,7 @@
 !
 ! name of datafile where the patterns are stored; path relative to EMdatapathname
  exptfile = 'undefined',
-! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF
+! input file type parameter: Binary, EMEBSD, TSLHDF, TSLup2, OxfordHDF, OxfordBinary, BrukerHDF, NORDIF
  inputtype = 'Binary',
 ! here we enter the HDF group names and data set names as individual strings (up to 10)
 ! enter the full path of a data set in individual strings for each group, in the correct order,

NamelistTemplates/EMmdSTEM.template

@@ -1,37 +1,52 @@
-&MDSTEMlist 
-! do not change the first line in this file !
-!
-! Note: All parameter values are default values for the program
-!
-!--------------
-! the name of the crystal input file MUST be specified (full pathname)
- xtalname = 'xtalfile',
-! DDD or MD input file MUST be specified
- inputfilename = 'input'
-! output will be stored here (full pathname)
- datafile = 'output.h5',
-! scale factor for DDD data - this MUST be specified based on scaling of your displacement grid (sx,sy,sz,dx,dy,dz)
- scalefactor = sx,sy,sz,dx,dy,dz,
-! size of the CBED disk in pixels
- discsize = 10,
-! orientation of crystal; euler angle representation in degrees
- eu = 0.0,0.0,0.0,
- ! orientation of crystal; euler angle representation in degrees
- eulerconvention = 'bsd',
-! ph1,ph2,phi3
- phi1 = 0.0,
- phi2 = 0.0,
- phi3 = 0.0,
-! minimum d-spacing to be taken into account [nm]
- dmin = 0.06, 
-! microscope accelerating voltage [kV]
+ &MDSTEMlist
+! DO NOT CHANGE THIS LINE
+!------------------------
+! IO Filenames
+!------------------------
+! Name of the crystal structure file
+ xtalname = 'undefined',
+! Name of the file containing displace vectors
+ inputfilename = 'undefined',
+! Output file containing diffracted intensities
+ datafile = 'undefined',
+!------------------------
+! Diffraction Parameters
+!------------------------
+! Accelerating Voltage, in kV
  voltage = 200.0,
-! beam convergence angle
- convergence = 4.0,
-! platform id for opencl
+! Smallest d-spacing to take into account [nm]
+ dmin = 0.08,
+! Convergence angle of the beam cone, in mRad
+ convergence = 3.0,
+! Number of rings in the beam cone discretization
+ discsize = 81,
+!------------------------
+! Crystal Parameters
+!------------------------
+! Crystal orientation Euler angles
+ eu = 0.0, 0.0, 0.0,
+! Nearest zone axis in this orientation
+ ZAindex = 0,0,1,
+! Laue shift values in the basis vectors of the CBED pattern
+ lauec = 0,0,
+! Distance between points in the Z direction in the displacement field, in nm
+ thk = 4.0,
+! Number of subslices to use for each displacement point. E
+subslice = 20,
+!------------------------
+! OpenCL Parameters
+!------------------------
+! Device ID for GPU
  devid = 1,
-! device id for opencl
- platid = 1
-! this last line must be present!
-/
-
+! Platform ID for GPU
+ platid = 1,
+!------------------------
+! Parameters for DDD simulations
+!------------------------
+! Is the data presorted into a 4D array in an h5 file?
+ presorted = .True.,
+! Scaling factor for input data that is not presorted, (x,y,z,dx,dy,dz)
+! If you used a python script similar to the one in the ***** folder, to
+! format your data as an h5 file, this is not used
+ scalefactor = 1,1,1,1,1,1,
+/ 

Source/EMsoftHDFLib/patternmod.f90

@@ -215,6 +215,7 @@ end subroutine invert_ordering_arrays
 !> @date 05/10/18 MDG 1.5 changed .up2 access mode to STREAM to facilitate record positioning
 !> @date 06/21/18 SS  1.6 changed recorsize to L*4 instead of recsize (correctsize*4); recsize has padded 0's
 !> @date 05/01/19 MA  1.7 add support for Oxford Instruments binary pattern files
+!> @date 10/09/19 HWÅ 1.8 support for NORDIF binary pattern files
 !--------------------------------------------------------------------------
 recursive function openExpPatternFile(filename, npat, L, inputtype, recsize, funit, HDFstrings) result(istat)
 !DEC$ ATTRIBUTES DLLEXPORT :: openExpPatternFile
@@ -357,8 +358,13 @@ recursive function openExpPatternFile(filename, npat, L, inputtype, recsize, fun
         ! we can do this because the pmHDF_head pointer is private and has SAVE status for this entire module
 
     case(9)  !  "NORDIF"
-        ! to be written
-        call FatalError("openExpPatternFile","NORDIF input format not yet implemented")
+        open(unit=funit, file=trim(ename), status='old', access='stream', &
+            iostat=ios)
+        if (ios.ne.0) then
+            io_int(1) = ios
+            call WriteValue("File open error; error type ", io_int, 1)
+            call FatalError("openExpPatternFile", "Cannot continue program")
+        end if
 
     case default 
         istat = -1
@@ -395,6 +401,7 @@ end function openExpPatternFile
 !> @date 03/21/19 MDG 1.4 fixed off-by-one error in column labels for up1 and up2 file formats
 !> @date 05/01/19 MA  1.5 add support for Oxford Instruments binary pattern files
 !> @date 09/26/19 MDG 1.6 add option for vertical flip of patterns
+!> @date 10/09/19 HWÅ 1.7 support for NORDIF binary pattern files
 !--------------------------------------------------------------------------
 recursive subroutine getExpPatternRow(iii, wd, patsz, L, dims3, offset3, funit, inputtype, HDFstrings, &
                                       exppatarray, ROI, flipy) 
@@ -622,11 +629,45 @@ recursive subroutine getExpPatternRow(iii, wd, patsz, L, dims3, offset3, funit,
         end do 
 
     case(9)  !  "NORDIF"
-        ! to be written
-        call FatalError("getExpPatternRow","NORDIF input format not yet implemented")
+        ! Buffer for single patterns
+        buffersize = lL
+        allocate(buffer(buffersize))
 
-
-    case default 
+        ! Pairs to store all patterns in a row
+        buffersize = lwd * lL
+        allocate(pairs(buffersize))
+
+        ! Loop over pixels and convert byte values into single byte integers
+        do ii = 1, lwd
+            ! pos = [(row-1)*scan_width + column - 1]*pattern_size + 1
+            read(unit=funit, pos=((liii-1)*lwd + ii - 1)*lL + 1, &
+                iostat=ios) buffer
+            do jj = 1_ill, lL
+                pairs((ii-1)*lL + jj) = ichar(buffer(jj))
+            end do
+        end do
+        deallocate(buffer)
+
+        ! Place patterns in experimental pattern array 
+        exppatarray = 0.0
+        ! Pattern pixels to read (might not be full pattern, depending on ROI)
+        pixcnt = (kkstart-1)*dims3(1)*dims3(2) + 1
+        ! Loop over row (might not be full row, depending on ROI)
+        do kk = kkstart, kkend
+            kspot = (kk-kkstart) * patsz
+            ! Loop over rows of pattern pixels
+            do jj = 1, dims3(2)
+                jspot = (jj-1) * dims3(1)
+                ! Loop over columns of pattern pixels, converting into float32
+                do ii = 1, dims3(1)
+                    exppatarray(kspot + jspot + ii) = float(pairs(pixcnt))
+                    pixcnt = pixcnt + 1
+                end do
+            end do
+        end do
+        deallocate(pairs)
+
+    case default
 end select
 
 end subroutine getExpPatternRow
@@ -652,6 +693,7 @@ end subroutine getExpPatternRow
 !
 !> @date 02/20/18 MDG 1.0 original
 !> @date 07/13/19 MDG 1.1 added option to read single pattern from OxfordBinary file
+!> @date 10/09/19 HWÅ 1.7 support for reading single pattern from NORDIF binary file
 !--------------------------------------------------------------------------
 recursive subroutine getSingleExpPattern(iii, wd, patsz, L, dims3, offset3, funit, inputtype, HDFstrings, exppat) 
 !DEC$ ATTRIBUTES DLLEXPORT :: getSingleExpPattern
@@ -839,10 +881,38 @@ recursive subroutine getSingleExpPattern(iii, wd, patsz, L, dims3, offset3, funi
         end do 
 
     case(9)  !  "NORDIF"
-        ! to be written
-        call FatalError("getSingleExpPattern","NORDIF input format not yet implemented")
-
-    case default 
+        ! Use ill-type integers
+        lL = L
+        lwd = wd
+
+        ! Buffers for single patterns
+        buffersize = lL
+        allocate(buffer(buffersize), pairs(buffersize))
+
+        ! Read single pattern into buffer
+        ! offset3(3) = row * scan width + column
+        offset = offset3(3)*lL + 1
+        read(unit=funit, pos=offset, iostat=ios) buffer
+
+        ! Convert byte values into single byte integers
+        pairs = ichar(buffer)
+        deallocate(buffer)
+
+        ! Place pattern in experimental pattern array
+        exppat = 0.0
+        pixcnt = 1
+        ! Loop over rows of pattern pixels
+        do jj = 1, dims3(2)
+            jspot = (jj-1)*dims3(1)
+            ! Loop over columns of pattern pixels, converting into float32
+            do ii = 1, dims3(1)
+                exppat(jspot + ii) = float(pairs(pixcnt))
+                pixcnt = pixcnt + 1
+            end do
+        end do
+        deallocate(pairs)
+
+    case default
 
 end select
 
@@ -897,8 +967,7 @@ recursive subroutine closeExpPatternFile(inputtype, funit)
         deallocate(semix, semiy)
 
     case(9)  !  "NORDIF"
-        ! to be written
-        call FatalError("closeExpPatternFile","input format not yet implemented")
+        close(unit=funit, status='keep')
 
     case default 
         call FatalError("closeExpPatternFile","unknown input format")