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