keep functionality separated
This commit is contained in:
Martin Diehl
parent
6d50066a04
commit
1cae6c4533
|
|
@ -0,0 +1,350 @@
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @author Martin Diehl, KU Leuven
|
||||||
|
!> @brief Read file data from the Visualization toolkit
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
module VTK
|
||||||
|
use prec
|
||||||
|
use zlib
|
||||||
|
use base64
|
||||||
|
use IO
|
||||||
|
|
||||||
|
implicit none
|
||||||
|
private
|
||||||
|
|
||||||
|
public :: VTK_readVTI
|
||||||
|
|
||||||
|
contains
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Parse vtk image data (.vti)
|
||||||
|
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
subroutine VTK_readVTI(cells,geomSize,origin,material, &
|
||||||
|
fileContent)
|
||||||
|
|
||||||
|
integer, dimension(3), intent(out) :: &
|
||||||
|
cells ! # of cells (across all processes!)
|
||||||
|
real(pReal), dimension(3), intent(out) :: &
|
||||||
|
geomSize, & ! physical size (across all processes!)
|
||||||
|
origin ! origin (across all processes!)
|
||||||
|
integer, dimension(:), intent(out), allocatable :: &
|
||||||
|
material
|
||||||
|
character(len=*), intent(in) :: &
|
||||||
|
fileContent
|
||||||
|
|
||||||
|
character(len=:), allocatable :: dataType, headerType
|
||||||
|
logical :: inFile,inImage,gotCellData,compressed
|
||||||
|
integer(pI64) :: &
|
||||||
|
startPos, endPos, &
|
||||||
|
s
|
||||||
|
|
||||||
|
|
||||||
|
cells = -1
|
||||||
|
geomSize = -1.0_pReal
|
||||||
|
|
||||||
|
inFile = .false.
|
||||||
|
inImage = .false.
|
||||||
|
gotCelldata = .false.
|
||||||
|
|
||||||
|
!--------------------------------------------------------------------------------------------------
|
||||||
|
! parse XML file
|
||||||
|
startPos = 1_pI64
|
||||||
|
do while (startPos < len(fileContent,kind=pI64))
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
|
||||||
|
|
||||||
|
if (.not. inFile) then
|
||||||
|
if (index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
|
||||||
|
inFile = .true.
|
||||||
|
if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
|
||||||
|
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
|
||||||
|
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
|
||||||
|
end if
|
||||||
|
else
|
||||||
|
if (.not. inImage) then
|
||||||
|
if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
|
||||||
|
inImage = .true.
|
||||||
|
call cellsSizeOrigin(cells,geomSize,origin,fileContent(startPos:endPos))
|
||||||
|
end if
|
||||||
|
else
|
||||||
|
if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
|
||||||
|
gotCellData = .true.
|
||||||
|
do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
|
||||||
|
if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
|
||||||
|
getXMLValue(fileContent(startPos:endPos),'Name') == 'material' ) then
|
||||||
|
|
||||||
|
if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
|
||||||
|
call IO_error(error_ID = 844, ext_msg='format (material)')
|
||||||
|
dataType = getXMLValue(fileContent(startPos:endPos),'type')
|
||||||
|
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
|
||||||
|
material = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
|
||||||
|
exit
|
||||||
|
end if
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
||||||
|
end do
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
|
||||||
|
if (gotCellData) exit
|
||||||
|
startPos = endPos + 2_pI64
|
||||||
|
|
||||||
|
end do
|
||||||
|
|
||||||
|
if (.not. allocated(material)) call IO_error(error_ID = 844, ext_msg='material data not found')
|
||||||
|
if (size(material) /= product(cells)) call IO_error(error_ID = 844, ext_msg='size(material)')
|
||||||
|
if (any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
|
||||||
|
if (any(cells<1)) call IO_error(error_ID = 844, ext_msg='cells')
|
||||||
|
material = material + 1
|
||||||
|
if (any(material<1)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
|
||||||
|
|
||||||
|
contains
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief determine size and origin from coordinates
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
subroutine cellsSizeOrigin(c,s,o,header)
|
||||||
|
|
||||||
|
integer, dimension(3), intent(out) :: c
|
||||||
|
real(pReal), dimension(3), intent(out) :: s,o
|
||||||
|
character(len=*), intent(in) :: header
|
||||||
|
|
||||||
|
character(len=:), allocatable :: temp
|
||||||
|
real(pReal), dimension(3) :: delta
|
||||||
|
integer :: i
|
||||||
|
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'Direction')
|
||||||
|
if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') & ! https://discourse.vtk.org/t/vti-specification/6526
|
||||||
|
call IO_error(error_ID = 844, ext_msg = 'coordinate order')
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'WholeExtent')
|
||||||
|
if (any([(IO_intValue(temp,IO_stringPos(temp),i),i=1,5,2)] /= 0)) &
|
||||||
|
call IO_error(error_ID = 844, ext_msg = 'coordinate start')
|
||||||
|
c = [(IO_intValue(temp,IO_stringPos(temp),i),i=2,6,2)]
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'Spacing')
|
||||||
|
delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
||||||
|
s = delta * real(c,pReal)
|
||||||
|
|
||||||
|
temp = getXMLValue(header,'Origin')
|
||||||
|
o = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
||||||
|
|
||||||
|
end subroutine
|
||||||
|
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret Base64 string in vtk XML file as integer of default kind
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
function as_Int(base64_str,headerType,compressed,dataType)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType, & ! header type (UInt32 or Uint64)
|
||||||
|
dataType ! data type (Int32, Int64, Float32, Float64)
|
||||||
|
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
||||||
|
|
||||||
|
integer, dimension(:), allocatable :: as_Int
|
||||||
|
|
||||||
|
select case(dataType)
|
||||||
|
case('Int32')
|
||||||
|
as_Int = int(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)))
|
||||||
|
case('Int64')
|
||||||
|
as_Int = int(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)))
|
||||||
|
case('Float32')
|
||||||
|
as_Int = int(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)))
|
||||||
|
case('Float64')
|
||||||
|
as_Int = int(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)))
|
||||||
|
case default
|
||||||
|
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
||||||
|
end select
|
||||||
|
|
||||||
|
end function as_Int
|
||||||
|
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret Base64 string in vtk XML file as integer of pReal kind
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
function as_pReal(base64_str,headerType,compressed,dataType)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType, & ! header type (UInt32 or Uint64)
|
||||||
|
dataType ! data type (Int32, Int64, Float32, Float64)
|
||||||
|
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
||||||
|
|
||||||
|
real(pReal), dimension(:), allocatable :: as_pReal
|
||||||
|
|
||||||
|
select case(dataType)
|
||||||
|
case('Int32')
|
||||||
|
as_pReal = real(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case('Int64')
|
||||||
|
as_pReal = real(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case('Float32')
|
||||||
|
as_pReal = real(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case('Float64')
|
||||||
|
as_pReal = real(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
|
||||||
|
case default
|
||||||
|
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
||||||
|
end select
|
||||||
|
|
||||||
|
end function as_pReal
|
||||||
|
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret Base64 string in vtk XML file as bytes
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
function asBytes(base64_str,headerType,compressed) result(bytes)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType ! header type (UInt32 or Uint64)
|
||||||
|
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
||||||
|
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
||||||
|
|
||||||
|
if (compressed) then
|
||||||
|
bytes = asBytes_compressed(base64_str,headerType)
|
||||||
|
else
|
||||||
|
bytes = asBytes_uncompressed(base64_str,headerType)
|
||||||
|
end if
|
||||||
|
|
||||||
|
end function asBytes
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interpret compressed Base64 string in vtk XML file as bytes
|
||||||
|
!> @details A compressed Base64 string consists of a header block and a data block
|
||||||
|
! [#blocks/#u-size/#p-size/#c-size-1/#c-size-2/.../#c-size-#blocks][DATA-1/DATA-2...]
|
||||||
|
! #blocks = Number of blocks
|
||||||
|
! #u-size = Block size before compression
|
||||||
|
! #p-size = Size of last partial block (zero if it not needed)
|
||||||
|
! #c-size-i = Size in bytes of block i after compression
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
function asBytes_compressed(base64_str,headerType) result(bytes)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType ! header type (UInt32 or Uint64)
|
||||||
|
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated
|
||||||
|
|
||||||
|
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
|
||||||
|
integer(pI64) :: headerLen, nBlock, b,s,e
|
||||||
|
|
||||||
|
|
||||||
|
if (headerType == 'UInt32') then
|
||||||
|
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
|
||||||
|
nBlock = int(temp(1),pI64)
|
||||||
|
headerLen = 4_pI64 * (3_pI64 + nBlock)
|
||||||
|
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
||||||
|
else if (headerType == 'UInt64') then
|
||||||
|
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
|
||||||
|
nBlock = int(temp(1),pI64)
|
||||||
|
headerLen = 8_pI64 * (3_pI64 + nBlock)
|
||||||
|
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
||||||
|
end if
|
||||||
|
|
||||||
|
allocate(size_inflated(nBlock),source=temp(2))
|
||||||
|
size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
|
||||||
|
size_deflated = temp(4:)
|
||||||
|
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
|
||||||
|
|
||||||
|
allocate(bytes(sum(size_inflated)))
|
||||||
|
e = 0_pI64
|
||||||
|
do b = 1, nBlock
|
||||||
|
s = e + 1_pI64
|
||||||
|
e = s + size_deflated(b) - 1_pI64
|
||||||
|
bytes(sum(size_inflated(:b-1))+1_pI64:sum(size_inflated(:b))) = zlib_inflate(bytes_inflated(s:e),size_inflated(b))
|
||||||
|
end do
|
||||||
|
|
||||||
|
end function asBytes_compressed
|
||||||
|
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes
|
||||||
|
!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
|
||||||
|
![#bytes-1/DATA-1][#bytes-2/DATA-2]...
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
function asBytes_uncompressed(base64_str,headerType) result(bytes)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
||||||
|
headerType ! header type (UInt32 or Uint64)
|
||||||
|
|
||||||
|
integer(pI64) :: s
|
||||||
|
integer(pI64), dimension(1) :: nByte
|
||||||
|
|
||||||
|
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
||||||
|
allocate(bytes(0))
|
||||||
|
|
||||||
|
s=0_pI64
|
||||||
|
if (headerType == 'UInt32') then
|
||||||
|
do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64)))
|
||||||
|
nByte = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
|
||||||
|
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+nByte(1))),5_pI64)]
|
||||||
|
s = s + base64_nChar(4_pI64+nByte(1))
|
||||||
|
end do
|
||||||
|
else if (headerType == 'UInt64') then
|
||||||
|
do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64)))
|
||||||
|
nByte = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
|
||||||
|
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+nByte(1))),9_pI64)]
|
||||||
|
s = s + base64_nChar(8_pI64+nByte(1))
|
||||||
|
end do
|
||||||
|
end if
|
||||||
|
|
||||||
|
end function asBytes_uncompressed
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief Get XML string value for given key
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
pure function getXMLValue(line,key)
|
||||||
|
|
||||||
|
character(len=*), intent(in) :: line, key
|
||||||
|
|
||||||
|
character(len=:), allocatable :: getXMLValue
|
||||||
|
|
||||||
|
integer :: s,e
|
||||||
|
#ifdef __INTEL_COMPILER
|
||||||
|
character :: q
|
||||||
|
#endif
|
||||||
|
|
||||||
|
s = index(line," "//key,back=.true.)
|
||||||
|
if (s==0) then
|
||||||
|
getXMLValue = ''
|
||||||
|
else
|
||||||
|
e = s + 1 + scan(line(s+1:),"'"//'"')
|
||||||
|
if (scan(line(s:e-2),'=') == 0) then
|
||||||
|
getXMLValue = ''
|
||||||
|
else
|
||||||
|
s = e
|
||||||
|
! https://community.intel.com/t5/Intel-Fortran-Compiler/ICE-for-merge-with-strings/m-p/1207204#M151657
|
||||||
|
#ifdef __INTEL_COMPILER
|
||||||
|
q = line(s-1:s-1)
|
||||||
|
e = s + index(line(s:),q) - 1
|
||||||
|
#else
|
||||||
|
e = s + index(line(s:),merge("'",'"',line(s-1:s-1)=="'")) - 1
|
||||||
|
#endif
|
||||||
|
getXMLValue = line(s:e-1)
|
||||||
|
end if
|
||||||
|
end if
|
||||||
|
|
||||||
|
end function
|
||||||
|
|
||||||
|
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
!> @brief check for supported file format
|
||||||
|
!------------------------------------------------------------------------------------------------
|
||||||
|
pure function fileFormatOk(line)
|
||||||
|
|
||||||
|
character(len=*),intent(in) :: line
|
||||||
|
logical :: fileFormatOk
|
||||||
|
|
||||||
|
fileFormatOk = getXMLValue(line,'type') == 'ImageData' .and. &
|
||||||
|
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
|
||||||
|
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
|
||||||
|
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
|
||||||
|
|
||||||
|
end function fileFormatOk
|
||||||
|
|
||||||
|
end subroutine VTK_readVTI
|
||||||
|
|
||||||
|
end module VTK
|
||||||
|
|
@ -14,8 +14,7 @@ module discretization_grid
|
||||||
use prec
|
use prec
|
||||||
use parallelization
|
use parallelization
|
||||||
use system_routines
|
use system_routines
|
||||||
use base64
|
use VTK
|
||||||
use zlib
|
|
||||||
use DAMASK_interface
|
use DAMASK_interface
|
||||||
use IO
|
use IO
|
||||||
use config
|
use config
|
||||||
|
|
@ -77,7 +76,7 @@ subroutine discretization_grid_init(restart)
|
||||||
|
|
||||||
if (worldrank == 0) then
|
if (worldrank == 0) then
|
||||||
fileContent = IO_read(interface_geomFile)
|
fileContent = IO_read(interface_geomFile)
|
||||||
call readVTI(cells,geomSize,origin,materialAt_global,fileContent)
|
call VTK_readVTI(cells,geomSize,origin,materialAt_global,fileContent)
|
||||||
fname = interface_geomFile
|
fname = interface_geomFile
|
||||||
if (scan(fname,'/') /= 0) fname = fname(scan(fname,'/',.true.)+1:)
|
if (scan(fname,'/') /= 0) fname = fname(scan(fname,'/',.true.)+1:)
|
||||||
call results_openJobFile(parallel=.false.)
|
call results_openJobFile(parallel=.false.)
|
||||||
|
|
@ -166,339 +165,6 @@ subroutine discretization_grid_init(restart)
|
||||||
end subroutine discretization_grid_init
|
end subroutine discretization_grid_init
|
||||||
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Parse vtk image data (.vti)
|
|
||||||
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
subroutine readVTI(cells,geomSize,origin,material, &
|
|
||||||
fileContent)
|
|
||||||
|
|
||||||
integer, dimension(3), intent(out) :: &
|
|
||||||
cells ! cells (across all processes!)
|
|
||||||
real(pReal), dimension(3), intent(out) :: &
|
|
||||||
geomSize, & ! size (across all processes!)
|
|
||||||
origin ! origin (across all processes!)
|
|
||||||
integer, dimension(:), intent(out), allocatable :: &
|
|
||||||
material
|
|
||||||
character(len=*), intent(in) :: &
|
|
||||||
fileContent
|
|
||||||
|
|
||||||
character(len=:), allocatable :: dataType, headerType
|
|
||||||
logical :: inFile,inImage,gotCellData,compressed
|
|
||||||
integer(pI64) :: &
|
|
||||||
startPos, endPos, &
|
|
||||||
s
|
|
||||||
|
|
||||||
|
|
||||||
cells = -1
|
|
||||||
geomSize = -1.0_pReal
|
|
||||||
|
|
||||||
inFile = .false.
|
|
||||||
inImage = .false.
|
|
||||||
gotCelldata = .false.
|
|
||||||
|
|
||||||
!--------------------------------------------------------------------------------------------------
|
|
||||||
! parse XML file
|
|
||||||
startPos = 1_pI64
|
|
||||||
do while (startPos < len(fileContent,kind=pI64))
|
|
||||||
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
|
||||||
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
|
|
||||||
|
|
||||||
if (.not. inFile) then
|
|
||||||
if (index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
|
|
||||||
inFile = .true.
|
|
||||||
if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
|
|
||||||
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
|
|
||||||
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
|
|
||||||
end if
|
|
||||||
else
|
|
||||||
if (.not. inImage) then
|
|
||||||
if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
|
|
||||||
inImage = .true.
|
|
||||||
call cellsSizeOrigin(cells,geomSize,origin,fileContent(startPos:endPos))
|
|
||||||
end if
|
|
||||||
else
|
|
||||||
if (index(fileContent(startPos:endPos),'<CellData',kind=pI64) /= 0_pI64) then
|
|
||||||
gotCellData = .true.
|
|
||||||
do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
|
|
||||||
if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
|
|
||||||
getXMLValue(fileContent(startPos:endPos),'Name') == 'material' ) then
|
|
||||||
|
|
||||||
if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
|
|
||||||
call IO_error(error_ID = 844, ext_msg='format (material)')
|
|
||||||
dataType = getXMLValue(fileContent(startPos:endPos),'type')
|
|
||||||
|
|
||||||
startPos = endPos + 2_pI64
|
|
||||||
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
|
||||||
s = startPos + verify(fileContent(startPos:endPos),IO_WHITESPACE,kind=pI64) -1_pI64 ! start (no leading whitespace)
|
|
||||||
material = as_Int(fileContent(s:endPos),headerType,compressed,dataType)
|
|
||||||
exit
|
|
||||||
end if
|
|
||||||
startPos = endPos + 2_pI64
|
|
||||||
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
|
|
||||||
end do
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
|
|
||||||
if (gotCellData) exit
|
|
||||||
startPos = endPos + 2_pI64
|
|
||||||
|
|
||||||
end do
|
|
||||||
|
|
||||||
if (.not. allocated(material)) call IO_error(error_ID = 844, ext_msg='material data not found')
|
|
||||||
if (size(material) /= product(cells)) call IO_error(error_ID = 844, ext_msg='size(material)')
|
|
||||||
if (any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
|
|
||||||
if (any(cells<1)) call IO_error(error_ID = 844, ext_msg='cells')
|
|
||||||
material = material + 1
|
|
||||||
if (any(material<1)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
|
|
||||||
|
|
||||||
contains
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief determine size and origin from coordinates
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
subroutine cellsSizeOrigin(c,s,o,header)
|
|
||||||
|
|
||||||
integer, dimension(3), intent(out) :: c
|
|
||||||
real(pReal), dimension(3), intent(out) :: s,o
|
|
||||||
character(len=*), intent(in) :: header
|
|
||||||
|
|
||||||
character(len=:), allocatable :: temp
|
|
||||||
real(pReal), dimension(:), allocatable :: delta
|
|
||||||
integer :: i
|
|
||||||
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'Direction')
|
|
||||||
if (temp /= '1 0 0 0 1 0 0 0 1' .and. temp /= '') & ! https://discourse.vtk.org/t/vti-specification/6526
|
|
||||||
call IO_error(error_ID = 844, ext_msg = 'coordinate order')
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'WholeExtent')
|
|
||||||
if (any([(IO_intValue(temp,IO_stringPos(temp),i),i=1,5,2)] /= 0)) &
|
|
||||||
call IO_error(error_ID = 844, ext_msg = 'coordinate start')
|
|
||||||
c = [(IO_intValue(temp,IO_stringPos(temp),i),i=2,6,2)]
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'Spacing')
|
|
||||||
delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
|
||||||
s = delta * real(c,pReal)
|
|
||||||
|
|
||||||
temp = getXMLValue(header,'Origin')
|
|
||||||
o = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
|
|
||||||
|
|
||||||
end subroutine
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret Base64 string in vtk XML file as integer of default kind
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function as_Int(base64_str,headerType,compressed,dataType)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType, & ! header type (UInt32 or Uint64)
|
|
||||||
dataType ! data type (Int32, Int64, Float32, Float64)
|
|
||||||
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
|
||||||
|
|
||||||
integer, dimension(:), allocatable :: as_Int
|
|
||||||
|
|
||||||
select case(dataType)
|
|
||||||
case('Int32')
|
|
||||||
as_Int = int(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)))
|
|
||||||
case('Int64')
|
|
||||||
as_Int = int(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)))
|
|
||||||
case('Float32')
|
|
||||||
as_Int = int(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)))
|
|
||||||
case('Float64')
|
|
||||||
as_Int = int(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)))
|
|
||||||
case default
|
|
||||||
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
|
||||||
end select
|
|
||||||
|
|
||||||
end function as_Int
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret Base64 string in vtk XML file as integer of pReal kind
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function as_pReal(base64_str,headerType,compressed,dataType)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType, & ! header type (UInt32 or Uint64)
|
|
||||||
dataType ! data type (Int32, Int64, Float32, Float64)
|
|
||||||
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
|
||||||
|
|
||||||
real(pReal), dimension(:), allocatable :: as_pReal
|
|
||||||
|
|
||||||
select case(dataType)
|
|
||||||
case('Int32')
|
|
||||||
as_pReal = real(prec_bytesToC_INT32_T(asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case('Int64')
|
|
||||||
as_pReal = real(prec_bytesToC_INT64_T(asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case('Float32')
|
|
||||||
as_pReal = real(prec_bytesToC_FLOAT (asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case('Float64')
|
|
||||||
as_pReal = real(prec_bytesToC_DOUBLE (asBytes(base64_str,headerType,compressed)),pReal)
|
|
||||||
case default
|
|
||||||
call IO_error(844,ext_msg='unknown data type: '//trim(dataType))
|
|
||||||
end select
|
|
||||||
|
|
||||||
end function as_pReal
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret Base64 string in vtk XML file as bytes
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function asBytes(base64_str,headerType,compressed) result(bytes)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType ! header type (UInt32 or Uint64)
|
|
||||||
logical, intent(in) :: compressed ! indicate whether data is zlib compressed
|
|
||||||
|
|
||||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
|
||||||
|
|
||||||
if (compressed) then
|
|
||||||
bytes = asBytes_compressed(base64_str,headerType)
|
|
||||||
else
|
|
||||||
bytes = asBytes_uncompressed(base64_str,headerType)
|
|
||||||
end if
|
|
||||||
|
|
||||||
end function asBytes
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interpret compressed Base64 string in vtk XML file as bytes
|
|
||||||
!> @details A compressed Base64 string consists of a header block and a data block
|
|
||||||
! [#blocks/#u-size/#p-size/#c-size-1/#c-size-2/.../#c-size-#blocks][DATA-1/DATA-2...]
|
|
||||||
! #blocks = Number of blocks
|
|
||||||
! #u-size = Block size before compression
|
|
||||||
! #p-size = Size of last partial block (zero if it not needed)
|
|
||||||
! #c-size-i = Size in bytes of block i after compression
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function asBytes_compressed(base64_str,headerType) result(bytes)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType ! header type (UInt32 or Uint64)
|
|
||||||
|
|
||||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes, bytes_inflated
|
|
||||||
|
|
||||||
integer(pI64), dimension(:), allocatable :: temp, size_inflated, size_deflated
|
|
||||||
integer(pI64) :: headerLen, nBlock, b,s,e
|
|
||||||
|
|
||||||
|
|
||||||
if (headerType == 'UInt32') then
|
|
||||||
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(4_pI64)))),pI64)
|
|
||||||
nBlock = int(temp(1),pI64)
|
|
||||||
headerLen = 4_pI64 * (3_pI64 + nBlock)
|
|
||||||
temp = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
|
||||||
else if (headerType == 'UInt64') then
|
|
||||||
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(8_pI64)))),pI64)
|
|
||||||
nBlock = int(temp(1),pI64)
|
|
||||||
headerLen = 8_pI64 * (3_pI64 + nBlock)
|
|
||||||
temp = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(:base64_nChar(headerLen)))),pI64)
|
|
||||||
end if
|
|
||||||
|
|
||||||
allocate(size_inflated(nBlock),source=temp(2))
|
|
||||||
size_inflated(nBlock) = merge(temp(3),temp(2),temp(3)/=0_pI64)
|
|
||||||
size_deflated = temp(4:)
|
|
||||||
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
|
|
||||||
|
|
||||||
allocate(bytes(sum(size_inflated)))
|
|
||||||
e = 0_pI64
|
|
||||||
do b = 1, nBlock
|
|
||||||
s = e + 1_pI64
|
|
||||||
e = s + size_deflated(b) - 1_pI64
|
|
||||||
bytes(sum(size_inflated(:b-1))+1_pI64:sum(size_inflated(:b))) = zlib_inflate(bytes_inflated(s:e),size_inflated(b))
|
|
||||||
end do
|
|
||||||
|
|
||||||
end function asBytes_compressed
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Interprete uncompressed Base64 string in vtk XML file as bytes
|
|
||||||
!> @details An uncompressed Base64 string consists of N headers blocks and a N data blocks
|
|
||||||
![#bytes-1/DATA-1][#bytes-2/DATA-2]...
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
function asBytes_uncompressed(base64_str,headerType) result(bytes)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: base64_str, & ! base64 encoded string
|
|
||||||
headerType ! header type (UInt32 or Uint64)
|
|
||||||
|
|
||||||
integer(pI64) :: s
|
|
||||||
integer(pI64), dimension(1) :: nByte
|
|
||||||
|
|
||||||
integer(C_SIGNED_CHAR), dimension(:), allocatable :: bytes
|
|
||||||
allocate(bytes(0))
|
|
||||||
|
|
||||||
s=0_pI64
|
|
||||||
if (headerType == 'UInt32') then
|
|
||||||
do while(s+base64_nChar(4_pI64)<(len(base64_str,pI64)))
|
|
||||||
nByte = int(prec_bytesToC_INT32_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64)))),pI64)
|
|
||||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(4_pI64+nByte(1))),5_pI64)]
|
|
||||||
s = s + base64_nChar(4_pI64+nByte(1))
|
|
||||||
end do
|
|
||||||
else if (headerType == 'UInt64') then
|
|
||||||
do while(s+base64_nChar(8_pI64)<(len(base64_str,pI64)))
|
|
||||||
nByte = int(prec_bytesToC_INT64_T(base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64)))),pI64)
|
|
||||||
bytes = [bytes,base64_to_bytes(base64_str(s+1_pI64:s+base64_nChar(8_pI64+nByte(1))),9_pI64)]
|
|
||||||
s = s + base64_nChar(8_pI64+nByte(1))
|
|
||||||
end do
|
|
||||||
end if
|
|
||||||
|
|
||||||
end function asBytes_uncompressed
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief Get XML string value for given key
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
pure function getXMLValue(line,key)
|
|
||||||
|
|
||||||
character(len=*), intent(in) :: line, key
|
|
||||||
|
|
||||||
character(len=:), allocatable :: getXMLValue
|
|
||||||
|
|
||||||
integer :: s,e
|
|
||||||
#ifdef __INTEL_COMPILER
|
|
||||||
character :: q
|
|
||||||
#endif
|
|
||||||
|
|
||||||
s = index(line," "//key,back=.true.)
|
|
||||||
if (s==0) then
|
|
||||||
getXMLValue = ''
|
|
||||||
else
|
|
||||||
e = s + 1 + scan(line(s+1:),"'"//'"')
|
|
||||||
if (scan(line(s:e-2),'=') == 0) then
|
|
||||||
getXMLValue = ''
|
|
||||||
else
|
|
||||||
s = e
|
|
||||||
! https://community.intel.com/t5/Intel-Fortran-Compiler/ICE-for-merge-with-strings/m-p/1207204#M151657
|
|
||||||
#ifdef __INTEL_COMPILER
|
|
||||||
q = line(s-1:s-1)
|
|
||||||
e = s + index(line(s:),q) - 1
|
|
||||||
#else
|
|
||||||
e = s + index(line(s:),merge("'",'"',line(s-1:s-1)=="'")) - 1
|
|
||||||
#endif
|
|
||||||
getXMLValue = line(s:e-1)
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
|
|
||||||
end function
|
|
||||||
|
|
||||||
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
!> @brief check for supported file format
|
|
||||||
!------------------------------------------------------------------------------------------------
|
|
||||||
pure function fileFormatOk(line)
|
|
||||||
|
|
||||||
character(len=*),intent(in) :: line
|
|
||||||
logical :: fileFormatOk
|
|
||||||
|
|
||||||
fileFormatOk = getXMLValue(line,'type') == 'ImageData' .and. &
|
|
||||||
getXMLValue(line,'byte_order') == 'LittleEndian' .and. &
|
|
||||||
getXMLValue(line,'compressor') /= 'vtkLZ4DataCompressor' .and. &
|
|
||||||
getXMLValue(line,'compressor') /= 'vtkLZMADataCompressor'
|
|
||||||
|
|
||||||
end function fileFormatOk
|
|
||||||
|
|
||||||
end subroutine readVTI
|
|
||||||
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
!---------------------------------------------------------------------------------------------------
|
||||||
!> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element)
|
!> @brief Calculate undeformed position of IPs/cell centers (pretend to be an element)
|
||||||
!---------------------------------------------------------------------------------------------------
|
!---------------------------------------------------------------------------------------------------
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue