我们需要在 DigitalMicrograph 中处理来自 FEI 和 Zeiss 工具的 SEM 图像。它们存储为 tif。DigitalMicrograph 可以读取 2D tif，但图像在 X、Y 方向上显示未校准。是否有任何导入插件可以传输校准信息？或者，我可以想象校准可以直接从流中变为红色。有没有人清楚地知道这些数字存储在 tif 流中的偏移量？我对 tif 的组织不是很熟悉，我知道存在一些变化。特别是，FEI 和蔡司 tifs 的组织方式似乎不同。
问问题
752 次
3 回答
2
FEI 和 ZEISS 似乎都将校准信息存储在自己的自定义 ASCII 文本标签中。遵循TIFF 格式规范 (PDF)，可以轻松编写一个脚本，从 TIFF 中提取所有 ASCII 字段。从那里开始，必须执行文本操作才能进行校准并将它们设置为图像。
下面的脚本使用以下信息对 FEI 和 ZEISS 图像执行此操作：
菲
尺寸信息在Form中的文本中：
[Scan]
PixelWidth=8.26823e-010
PixelHeight=8.26823e-010
这指定了[米]中的像素尺寸蔡司
尺寸信息在 Form 中的文本中：
AP_HEIGHT
Height = 343.0 nm
AP_WIDTH
Width = 457.3 nm
这指定了 FOV 尺寸。
PasteBin上的脚本。
// Auxilliary method for stream-reading of values
number ReadValueOfType(object fStream, string type, number byteOrder)
{
number val = 0
TagGroup tg = NewTagGroup()
if ( type == "bool" )
{
tg.TagGroupSetTagAsBoolean( type, 0 )
tg.TagGroupReadTagDataFromStream( type, fstream, byteOrder )
tg.TagGroupGetTagAsBoolean( type, val )
}
else if ( type == "uint16" )
{
tg.TagGroupSetTagAsUInt16( type, 0 )
tg.TagGroupReadTagDataFromStream( type, fstream, byteOrder )
tg.TagGroupGetTagAsUInt16( type, val )
}
else if ( type == "uint32" )
{
tg.TagGroupSetTagAsUInt32( type, 0 )
tg.TagGroupReadTagDataFromStream( type, fstream, byteOrder )
tg.TagGroupGetTagAsUInt32( type, val )
}
else Throw("Invalid read-type:"+type)
return val
}
string ExtractTextFromTiff( string path )
{
string txt
if ( !DoesFileExist(path) ) Throw("File not found.\n"+path)
// Open Stream
number fileID = OpenFileForReading( path )
object fStream = NewStreamFromFileReference(fileID,1)
// Read data byte order. (1 = big Endian, 2= little Endian for Gatan)
number val
number byteOrder = 0
val = fStream.ReadValueOfType( "uint16", byteOrder )
byteOrder = ( 0x4949 == val ) ? 2 : ( 0x4D4D == val ? 1 : 0 )
//Result("\n TIFF endian:"+byteOrder)
// Verify TIFF image
val = fStream.ReadValueOfType( "uint16", byteOrder )
if ( val != 42 ) Throw( "Not a valid TIFF image" )
// Browse all directories
number offset = fStream.ReadValueOfType( "uint32", byteOrder )
while( 0 != offset )
{
fStream.StreamSetPos( 0, offset ) // Start of IFD
number nEntries = fStream.ReadValueOfType( "uint16", byteOrder )
for ( number e=0;e<nEntries;e++)
{
number tag = fStream.ReadValueOfType( "uint16", byteOrder )
number typ = fStream.ReadValueOfType( "uint16", byteOrder )
number count = fStream.ReadValueOfType( "uint32", byteOrder )
number dataOffset = fStream.ReadValueOfType( "uint32", byteOrder )
//Result("\n entry # "+e+": ID["+tag+"]\ttyp="+typ+"\tcount="+count+"\t offset @ "+dataOffset)
if ( 2 == typ ) // ASCII
{
number currentPos = fStream.StreamGetPos()
fStream.StreamSetPos( 0, dataOffset )
string textField = fStream.StreamReadAsText( 0, count )
txt+=textField
fStream.StreamSetPos( 0, currentPos )
}
}
offset = fStream.ReadValueOfType( "uint32", byteOrder ) // this is 0000 for the last directory according to spec
}
return txt
}
String TruncWhiteSpaceBeforeAndAfter( string input )
{
string work = input
if ( len(work) == 0 ) return ""
while ( " " == left(work,1) )
{
work = right( work, len(work) - 1 )
if ( len(work) == 0 ) return ""
}
while ( " " == right(work,1) )
{
work = left( work, len(work) - 1 )
if ( len(work) == 0 ) return ""
}
return work
}
// INPUT: String with line-wise information
// OUTPUT: TagGroup
// Assumptions:
// - Groups are specified in a line in the format: [GroupName]
// - The string contains information line-wise in the format: KeyName=Vale
TagGroup CreateTagsFromString( string input )
{
TagGroup tg = NewTagGroup()
string work = input
string eoL = "\n"
string GroupLeadIn = "["
string GroupLeadOut = "]"
string keyToValueSep= "="
string groupName = ""
number pos = find(work,eoL )
while( -1 != pos )
{
string line = left(work,pos)
work = right(work,len(work)-pos-len(eoL))
number leadIn = find(line,GroupLeadIn)
number leadOut = find(line,GroupLeadOut)
number sep = find(line,keyToValueSep)
if ( ( -1 < leadIn ) && ( -1 < leadOut ) && ( leadIn < leadOut ) ) // Is it a new group? "[GROUPNAME]"
{
groupName = mid(line,leadIn+len(GroupLeadIn),leadOut-leadIn-len(GroupLeadOut))
groupName = TruncWhiteSpaceBeforeAndAfter(groupName)
}
else if( -1 < sep ) // Is it a value? "KEY=VALUE" ?
{
string key = left(line,sep)
string value= right(line,len(line)-sep-len(keyToValueSep))
key = TruncWhiteSpaceBeforeAndAfter(key)
value = TruncWhiteSpaceBeforeAndAfter(value)
string tagPath = groupName + ( "" == groupName ? "" : ":" ) + key
tg.TagGroupSetTagAsString( tagPath, value )
}
pos = find(work,eoL)
}
return tg
}
void ImportTIFFWithTags()
{
string path = GetApplicationDirectory("open_save",0)
if (!OpenDialog(NULL,"Select TIFF file",path, path)) exit(0)
string extractedText = ExtractTextFromTiff(path)
/*
if ( TwoButtonDialog("Show extracted text?","Yes","No") )
result(extractedtext)
*/
tagGroup infoAsTags = CreateTagsFromString(extractedText )
/*
if ( TwoButtonDialog("Output tagstructure?","Yes","No") )
infoAsTags.TagGroupOpenBrowserWindow(path,0)
*/
// Import data and add info-tags
image imported := OpenImage(path)
imported.ImageGetTagGroup().TagGroupSetTagAsTagGroup("TIFF Tags",infoAsTags)
imported.ShowImage()
// Calibrate image, if info is found
// It seems FEI stores this value as [m] in the tags PixelHeight and PixelWidth
// while ZEISS images contain the size of the FOV in the tags "Height" and "Width" as string including unit
number scaleX = 0
number scaleY = 0
string unitX
string UnitY
string hStr
string wStr
if ( imported.GetNumberNote( "TIFF Tags:Scan:PixelWidth", scaleX ) )
{
unitX = "nm"
scaleX *= 1e9
}
if ( imported.GetNumberNote( "TIFF Tags:Scan:PixelHeight", scaleY ) )
{
unitY = "nm"
scaleY *= 1e9
}
if ( imported.GetStringNote( "TIFF Tags:Width", wStr ) )
{
number pos = find( wStr, " " )
if ( -1 < pos )
{
scaleX = val( left(wStr,pos) )
scaleX /= imported.ImageGetDimensionSize(0)
unitX = right( wStr, len(wStr)-pos-1 )
}
}
if ( imported.GetStringNote( "TIFF Tags:Height", hStr ) )
{
number pos = find( hStr, " " )
if ( -1 < pos )
{
scaleY = val( left(hStr,pos) )
scaleY /= imported.ImageGetDimensionSize(1)
unitY = right( hStr, len(hStr)-pos-1 )
}
}
if ( 0 < scaleX )
{
imported.ImageSetDimensionScale(0,scaleX)
imported.ImageSetDimensionUnitString(0,unitX)
}
if ( 0 < scaleY )
{
imported.ImageSetDimensionScale(1,scaleY)
imported.ImageSetDimensionUnitString(1,unitY)
}
}
ImportTIFFWithTags()
编辑 2021：我还为完整的 TIFF 导入编写了一个相关脚本，作为对单独问题的回答发布。
于 2016-03-10T14:07:20.833 回答
2
FEI 对每个工具集使用不同的 TIF 格式（SEM 与 TEM，两者都取决于版本）。TIA 的情况也是如此，新版本打破了广泛使用的 SerReader 脚本。如果需要，我可以发布一个简单的修复。
FEI TIFF for TEM 将所有元数据存储在一个 XML 格式的标签中。比例尺也有单独的标签，但它也被格式化为 XML。我对上面的 BmyGuest 代码做了一个小调整来读取比例。必须解析其他元数据。
// Auxilliary method for stream-reading of values
// BmyGuest's March 10, 2016 code modified to read FEI TEM TIF
number ReadValueOfType(object fStream, string type, number byteOrder)
{
number val = 0
TagGroup tg = NewTagGroup()
if ( type == "bool" )
{
tg.TagGroupSetTagAsBoolean( type, 0 )
tg.TagGroupReadTagDataFromStream( type, fstream, byteOrder )
tg.TagGroupGetTagAsBoolean( type, val )
}
else if ( type == "uint16" )
{
tg.TagGroupSetTagAsUInt16( type, 0 )
tg.TagGroupReadTagDataFromStream( type, fstream, byteOrder )
tg.TagGroupGetTagAsUInt16( type, val )
}
else if ( type == "uint32" )
{
tg.TagGroupSetTagAsUInt32( type, 0 )
tg.TagGroupReadTagDataFromStream( type, fstream, byteOrder )
tg.TagGroupGetTagAsUInt32( type, val )
}
else Throw("Invalid read-type:"+type)
return val
}
string ExtractTextFromTiff( string path )
{
string txt
if ( !DoesFileExist(path) ) Throw("File not found.\n"+path)
// Open Stream
number fileID = OpenFileForReading( path )
object fStream = NewStreamFromFileReference(fileID,1)
// Read data byte order. (1 = big Endian, 2= little Endian for Gatan)
number val
number byteOrder = 0
val = fStream.ReadValueOfType( "uint16", byteOrder )
byteOrder = ( 0x4949 == val ) ? 2 : ( 0x4D4D == val ? 1 : 0 )
//Result("\n TIFF endian:"+byteOrder)
// Verify TIFF image
val = fStream.ReadValueOfType( "uint16", byteOrder )
if ( val != 42 ) Throw( "Not a valid TIFF image" )
// Browse all directories
number offset = fStream.ReadValueOfType( "uint32", byteOrder )
while( 0 != offset )
{
fStream.StreamSetPos( 0, offset ) // Start of IFD
number nEntries = fStream.ReadValueOfType( "uint16", byteOrder )
for ( number e=0;e<nEntries;e++)
{
number tag = fStream.ReadValueOfType( "uint16", byteOrder )
number typ = fStream.ReadValueOfType( "uint16", byteOrder )
number count = fStream.ReadValueOfType( "uint32", byteOrder )
number dataOffset = fStream.ReadValueOfType( "uint32", byteOrder )
//Result("\n entry # "+e+": ID["+tag+"]\ttyp="+typ+"\tcount="+count+"\t offset @ "+dataOffset)
if ( 2 == typ ) // ASCII
{
number currentPos = fStream.StreamGetPos()
fStream.StreamSetPos( 0, dataOffset )
string textField = fStream.StreamReadAsText( 0, count )
txt+=textField
fStream.StreamSetPos( 0, currentPos )
}
}
offset = fStream.ReadValueOfType( "uint32", byteOrder ) // this is 0000 for the last directory according to spec
}
return txt
}
String TruncWhiteSpaceBeforeAndAfter( string input )
{
string work = input
if ( len(work) == 0 ) return ""
while ( " " == left(work,1) )
{
work = right( work, len(work) - 1 )
if ( len(work) == 0 ) return ""
}
while ( " " == right(work,1) )
{
work = left( work, len(work) - 1 )
if ( len(work) == 0 ) return ""
}
return work
}
// INPUT: String with line-wise information
// OUTPUT: TagGroup
// Assumptions:
// - Groups are specified in a line in the format: [GroupName]
// - The string contains information line-wise in the format: KeyName=Vale
TagGroup CreateTagsFromString( string input )
{
TagGroup tg = NewTagGroup()
string work = input
string eoL = "\n"
string GroupLeadIn = "["
string GroupLeadOut = "]"
string keyToValueSep= "="
string groupName = ""
number pos = find(work,eoL )
while( -1 != pos )
{
string line = left(work,pos)
work = right(work,len(work)-pos-len(eoL))
number leadIn = find(line,GroupLeadIn)
number leadOut = find(line,GroupLeadOut)
number sep = find(line,keyToValueSep)
if ( ( -1 < leadIn ) && ( -1 < leadOut ) && ( leadIn < leadOut ) ) // Is it a new group? "[GROUPNAME]"
{
groupName = mid(line,leadIn+len(GroupLeadIn),leadOut-leadIn-len(GroupLeadOut))
groupName = TruncWhiteSpaceBeforeAndAfter(groupName)
}
else if( -1 < sep ) // Is it a value? "KEY=VALUE" ?
{
string key = left(line,sep)
string value= right(line,len(line)-sep-len(keyToValueSep))
key = TruncWhiteSpaceBeforeAndAfter(key)
value = TruncWhiteSpaceBeforeAndAfter(value)
string tagPath = groupName + ( "" == groupName ? "" : ":" ) + key
tg.TagGroupSetTagAsString( tagPath, value )
}
pos = find(work,eoL)
}
return tg
}
void ImportTIFFWithTags()
{
string path = GetApplicationDirectory("open_save",0)
if (!OpenDialog(NULL,"Select TIFF file",path, path)) exit(0)
string extractedText = ExtractTextFromTiff(path)
/*
if ( TwoButtonDialog("Show extracted text?","Yes","No") )
result(extractedtext)
*/
tagGroup infoAsTags = CreateTagsFromString(extractedText )
/*
if ( TwoButtonDialog("Output tagstructure?","Yes","No") )
infoAsTags.TagGroupOpenBrowserWindow(path,0)
*/
// Import data and add info-tags
image imported := OpenImage(path)
imported.ImageGetTagGroup().TagGroupSetTagAsTagGroup("TIFF Tags",infoAsTags)
imported.ShowImage()
// Calibrate image, if info is found
// It seems FEI stores this value as [m] in the tags PixelHeight and PixelWidth
// while ZEISS images contain the size of the FOV in the tags "Height" and "Width" as string including unit
number scaleX = 0
number scaleY = 0
string unitX
string UnitY
string scaletemp
number scalestart, scaleend
string hStr
string wStr
if ( imported.GetNumberNote( "TIFF Tags:Scan:PixelWidth", scaleX ) )
{
unitX = "nm"
scaleX *= 1e9
}
if ( imported.GetNumberNote( "TIFF Tags:Scan:PixelHeight", scaleY ) )
{
unitY = "nm"
scaleY *= 1e9
}
if (imported.GetStringNote( "TIFF Tags:<X unit", scaletemp ) )
{
unitX = "nm"
scalestart = scaletemp.find("\">") + 2
scaleend = scaletemp.find("</X>")
scaleX = val(scaletemp.mid(scalestart,scaleend-scalestart))*1e9
}
if ( imported.GetStringNote( "TIFF Tags:<Y unit", scaletemp ) )
{
unitY = "nm"
scalestart = scaletemp.find("\">") + 2
scaleend =scaletemp.find("</Y>")
scaleY = val(scaletemp.mid(scalestart,scaleend-scalestart))*1e9
}
if ( imported.GetStringNote( "TIFF Tags:Width", wStr ) )
{
number pos = find( wStr, " " )
if ( -1 < pos )
{
scaleX = val( left(wStr,pos) )
scaleX /= imported.ImageGetDimensionSize(0)
unitX = right( wStr, len(wStr)-pos-1 )
}
}
if ( imported.GetStringNote( "TIFF Tags:Height", hStr ) )
{
number pos = find( hStr, " " )
if ( -1 < pos )
{
scaleY = val( left(hStr,pos) )
scaleY /= imported.ImageGetDimensionSize(1)
unitY = right( hStr, len(hStr)-pos-1 )
}
}
if ( 0 < scaleX )
{
imported.ImageSetDimensionScale(0,scaleX)
imported.ImageSetDimensionUnitString(0,unitX)
}
if ( 0 < scaleY )
{
imported.ImageSetDimensionScale(1,scaleY)
imported.ImageSetDimensionUnitString(1,unitY)
}
}
ImportTIFFWithTags()
于 2016-04-24T21:45:47.713 回答
1
TIF 或 TIFF（标记图像文件格式）是一种相当通用的格式，其中任何附加信息都可以作为“标记”存储在文件中。（尽管这与 DM 中的标签不同。）标签中写入的具体内容（以及写入位置）取决于写入文件的软件，即本例中的 FEI。我假设物理校准已写入这些标签，但我没有要测试的文件。（您可以上传一个到您的问题？）
我确实相信，但尚未检查，DM 在 TIFF 导入时将所有或部分标签写入其自己的 TagGroup 结构。你检查过了吗？（即，如果您通过 DM 从 FEI 导入一个 TIFF 文件并转到“图像显示 -> 标签”，您会看到什么？可能是校准所需的信息在那里，您可以编写一个简单的脚本来使用这用于校准。
或者，通常可以在文本编辑器中打开 TIFF 文件以查看（除了图像的大量二进制文件）ASCII 文本中的标签。这将使您了解事物存储在此特定 TIFF 文件中的位置。
具备这些知识后，您可以使用 RAW 流式传输命令来查找相应的信息，并编写一个导入脚本来复制校准。
于 2016-03-05T09:39:55.163 回答