I am basically trying to read out all or most attribute values from a DICOM file, using the gdcm C++ library. I am having hard time to get out any non-string values. The gdcm examples generally assume I know the group/element numbers beforehand so I can use the Attribute template classes, but I have no need or interest in them, I just have to report all attribute names and values. Actually the values should go into an XML so I need a string representation. What I currently have is something like:
for (gdcm::DataSet::ConstIterator it = ds.Begin(); it!=ds.End(); ++it) {
const gdcm::DataElement& elem = *it;
if (elem.GetVR() != gdcm::VR::SQ) {
const gdcm::Tag& tag = elem.GetTag();
std::cout << dict.GetDictEntry(tag).GetKeyword() << ": ";
std::cout << elem.GetValue() << "\n";
}
}
It seems for numeric values like UL the output is something like "Loaded:4", presumably meaning that the library has loaded 4 bytes of data (an unsigned long). This is not helpful at all, how to get the actual value? I must be certainly overlooking something obvious.
From the examples it seems there is a gdcm::StringFilter class which is able to do that, but it seems it wants to search each element by itself in the DICOM file, which would make the algorithm complexity quadratic, this is certainly something I would like to avoid.
TIA
Paavo
Have you looked at gdcmdump? You can use it to output the DICOM file as text or XML. You can also look at the source to see how it does this.
I ended up with extracting parts of gdcm::StringFilter::ToStringPair() into a separate function. Seems to work well for simpler DCM files at least...
You could also start by reading the FAQ, in particular How do I convert an attribute value to a string ?
As explained there, you simply need to use gdcm::StringFilter:
sf = gdcm.StringFilter()
sf.SetFile(r.GetFile())
print sf.ToStringPair(gdcm.Tag(0x0028,0x0010))
Try something like this:
gdcm::Reader reader;
reader.SetFileName( absSlicePath.c_str() );
if( !_reader.Read() )
{
return;
}
gdcm::File file = reader.GetFile();
gdcm::DataSet ds = file.GetDataSet();
std::stringstream strm;
strm << ds;
you get a stringstream containing all the DICOM tags-values.
Actually, most of the DICOM classes (DataElement, DataSet, etc) have the std::ostream & operator<< (std::ostream &_os, const *Some_Class* &_val) overloaded. So you can just expand the for loop and use operator<< to put the values into the stringstream, and then into the string.
For example, if you are using QT :
ui->pTagsTxt->append(QString(strm.str().c_str()));
Related
I have a requirement to convert the output of cypher into JSON.
Here is my code snippet.
RestCypherQueryEngine rcqer=new RestCypherQueryEngine(restapi);
String nodeN = "MATCH n=(Company) WITH COLLECT(n) AS paths RETURN EXTRACT(k IN paths | LAST(nodes(k))) as lastNode";
final QueryResult<Map<String,Object>> queryResult = rcqer.query(searchQuery);
for(Map<String,Object> row:queryResult)
{
System.out.println((ArrayList)row.get("lastNode"));
}
Output:
[http://XXX.YY6.192.103:7474/db/data/node/445, http://XXX.YY6.192.103:7474/db/data/node/446, http://XXX.YY6.192.103:7474/db/data/node/447, http://XXX.YY6.192.103:7474/db/data/node/448, http://XXX.YY6.192.103:7474/db/data/node/449, http://XXX.YY6.192.103:7474/db/data/node/450, http://XXX.YY6.192.103:7474/db/data/node/451, http://XXX.YY6.192.103:7474/db/data/node/452, http://XXX.YY6.192.103:7474/db/data/node/453]
I am not able to see the actual data (I am getting URL's). I am pretty sure I am missing something here.
I would also like to convert the output to JSON.
The cypher works in my browser interface.
I looked at various articles around this:
Java neo4j, REST and memory
Neo4j Cypher: How to iterate over ExecutionResult result
Converting ExecutionResult object to json
The last 2 make use of EmbeddedDatabase which may not be possible in my scenario (as the Neo is hosted in another cloud, hence the usage of REST).
Thanks.
Try to understand what you're doing? Your query does not make sense at all.
Perhaps you should re-visit the online course for Cypher: http://neo4j.com/online-course
MATCH n=(Company) WITH COLLECT(n) AS paths RETURN EXTRACT(k IN paths | LAST(nodes(k))) as lastNode
you can just do:
MATCH (c:Company) RETURN c
RestCypherQueryEngine rcqer=new RestCypherQueryEngine(restapi);
final QueryResult<Map<String,Object>> queryResult = rcqer.query(query);
for(Node node : queryResult.to(Node.class))
{
for (String prop : node.getPropertyKeys()) {
System.out.println(prop+" "+node.getProperty(prop));
}
}
I think it's better to use the JDBC driver for what you try to do, and also actually return the properties you're trying to convert to JSON.
How can one find where are lines located in a document with iText?
Suppose say I have a table in a PDF document, and want to read its contents; I would like to find where exactly the cells are located. In order to do that I thought I might find the intersections of lines.
I think your only option using iText will be to parse the PDF tokens manually. Before doing that I would have a copy of the PDF spec handy.
(I'm a .Net guy so I use iTextSharp but other than some capitalization differences and property declarations they're almost 100% the same.)
You can get the individual tokens using the PRTokeniser object which you feed bytes into from calling getPageContent(pageNum) on your PdfReader.
//Get bytes for page 1
byte[] pageBytes = reader.getPageContent(1);
//Get the tokens for page 1
PRTokeniser tokeniser = new PRTokeniser(pageBytes);
Then just loop through the PRTokeniser:
PRTokeniser.TokType tokenType;
string tokenValue;
while (tokeniser.nextToken()) {
tokenType = tokeniser.tokenType;
tokenValue = tokeniser.stringValue;
//...check tokenValue, do something with it
}
As far a tokenValue, you'd want to probably look for re and l values for rectangle and line. If you see an re then you want to look at the previous 4 values and if you see an l then previous 2 values. This also means that you need to store each tokenValue in an array so you can look back later.
Depending on what you used to create the PDF with you might get some interesting results. For instance, I created a 4 cell table with Microsoft Word and saved as a PDF. For some reason there are two sets of 10 rectangles with many duplicates, but the general idea still works.
Below is C# code targeting iTextSharp 5.1.1.0. You should be able to convert it to Java and iText very easily, I noted the one line that has .Net-specific code that needs to be adjusted from a Generic List (List<string>) to a Java equivalent, probably an ArrayList. You'll also need to adjust some casing, .Net uses Object.Method() whereas Java uses Object.method(). Lastly, .Net accesses properties without gets and sets, so Object.Property is both the getter and setter compared to Java's Object.getProperty and Object.setProperty.
Hopefully this gets you started at least!
//Source file to read from
string sourceFile = "c:\\Hello.pdf";
//Bind a reader to our PDF
PdfReader reader = new PdfReader(sourceFile);
//Create our buffer for previous token values. For Java users, List<string> is a generic list, probably most similar to an ArrayList
List<string> buf = new List<string>();
//Get the raw bytes for the page
byte[] pageBytes = reader.GetPageContent(1);
//Get the raw tokens from the bytes
PRTokeniser tokeniser = new PRTokeniser(pageBytes);
//Create some variables to set later
PRTokeniser.TokType tokenType;
string tokenValue;
//Loop through each token
while (tokeniser.NextToken()) {
//Get the types and value
tokenType = tokeniser.TokenType;
tokenValue = tokeniser.StringValue;
//If the type is a numeric type
if (tokenType == PRTokeniser.TokType.NUMBER) {
//Store it in our buffer for later user
buf.Add(tokenValue);
//Otherwise we only care about raw commands which are categorized as "OTHER"
} else if (tokenType == PRTokeniser.TokType.OTHER) {
//Look for a rectangle token
if (tokenValue == "re") {
//Sanity check, make sure we have enough items in the buffer
if (buf.Count < 4) throw new Exception("Not enough elements in buffer for a rectangle");
//Read and convert the values
float x = float.Parse(buf[buf.Count - 4]);
float y = float.Parse(buf[buf.Count - 3]);
float w = float.Parse(buf[buf.Count - 2]);
float h = float.Parse(buf[buf.Count - 1]);
//..do something with them here
}
}
}
From what I understood here, "V8 has a generational garbage collector. Moves objects aound randomly. Node can’t get a pointer to raw string data to write to socket." so I shouldn't store data that comes from a TCP stream in a string, specially if that string becomes bigger than Math.pow(2,16) bytes. (hope I'm right till now..)
What is then the best way to handle all the data that's comming from a TCP socket ? So far I've been trying to use _:_:_ as a delimiter because I think it's somehow unique and won't mess around other things.
A sample of the data that would come would be something_:_:_maybe a large text_:_:_ maybe tons of lines_:_:_more and more data
This is what I tried to do:
net = require('net');
var server = net.createServer(function (socket) {
socket.on('connect',function() {
console.log('someone connected');
buf = new Buffer(Math.pow(2,16)); //new buffer with size 2^16
socket.on('data',function(data) {
if (data.toString().search('_:_:_') === -1) { // If there's no separator in the data that just arrived...
buf.write(data.toString()); // ... write it on the buffer. it's part of another message that will come.
} else { // if there is a separator in the data that arrived
parts = data.toString().split('_:_:_'); // the first part is the end of a previous message, the last part is the start of a message to be completed in the future. Parts between separators are independent messages
if (parts.length == 2) {
msg = buf.toString('utf-8',0,4) + parts[0];
console.log('MSG: '+ msg);
buf = (new Buffer(Math.pow(2,16))).write(parts[1]);
} else {
msg = buf.toString() + parts[0];
for (var i = 1; i <= parts.length -1; i++) {
if (i !== parts.length-1) {
msg = parts[i];
console.log('MSG: '+msg);
} else {
buf.write(parts[i]);
}
}
}
}
});
});
});
server.listen(9999);
Whenever I try to console.log('MSG' + msg), it will print out the whole buffer, so it's useless to see if something worked.
How can I handle this data the proper way ? Would the lazy module work, even if this data is not line oriented ? Is there some other module to handle streams that are not line oriented ?
It has indeed been said that there's extra work going on because Node has to take that buffer and then push it into v8/cast it to a string. However, doing a toString() on the buffer isn't any better. There's no good solution to this right now, as far as I know, especially if your end goal is to get a string and fool around with it. Its one of the things Ryan mentioned # nodeconf as an area where work needs to be done.
As for delimiter, you can choose whatever you want. A lot of binary protocols choose to include a fixed header, such that you can put things in a normal structure, which a lot of times includes a length. In this way, you slice apart a known header and get information about the rest of the data without having to iterate over the entire buffer. With a scheme like that, one can use a tool like:
node-buffer - https://github.com/substack/node-binary
node-ctype - https://github.com/rmustacc/node-ctype
As an aside, buffers can be accessed via array syntax, and they can also be sliced apart with .slice().
Lastly, check here: https://github.com/joyent/node/wiki/modules -- find a module that parses a simple tcp protocol and seems to do it well, and read some code.
You should use the new stream2 api. http://nodejs.org/api/stream.html
Here are some very useful examples: https://github.com/substack/stream-handbook
https://github.com/lvgithub/stick
I've been reading through the adobe pdf spec, along with apple's quartz 2d documentation for pdf rendering and parsing. I've also downloaded Voyeur and inspected a local pdf with it to see it's internal data. At this point I'm able to get the document catalog, and then fetch the outlines dictionary from there. I can see that nested within the outlines dictionary dictionaries that there are named "/Dest" nodes with values such as:
G1.1025588
etc
I'm wondering if there is a way for me to use these values to get a reference to page to render using some methods I've seen github projects such as Reader, along with apple documented examples.
PDF processing is definitely a challenge, so any help would be appreciated.
The /Dest entry in an outline item dictionary can either be a name, a string, or an array.
The simplest case is if it's an array; then the first item is the page object the outline entry points to (a dictionary). To get the page number, you have to iterate over all pages in the document and see which one is equal (==) to the dictionary you have (CGPDFPageRefs are actually CGPDFDictionaryRefs). You could also traverse the page tree, which is a bit harder, but may be faster (not as much as you might expect, I wouldn't optimize prematurely here). The other items in the array are position on the page etc., search for "Explicit Destinations" in the PDF spec to learn more.
If the entry is a name or string, it is a named destination. You have to map the name to a destination from the document catalog's /Dests entry which is a dictionary that contains a name tree. A name tree is essentially a tree map that allows fast access to named values without requiring to read all the data at once (as with a plain dictionary). Unfortunately, there's no direct support for name trees in Quartz, so you'll have to do a little more work to parse this structure recursively (see "Name Trees" in the PDF spec).
Note that an outline item doesn't necessarily have a /Dest entry, it can also specify its destination via an /A (action) entry, which is a little bit more complex. In most cases, however, the action will be a "GoTo" action that is essentially a wrapper for a destination.
The mapping of names to destinations can also be stored as a plain dictionary. In that case, it's in the /Dests entry of the /Names dictionary in the document's catalog. I've rarely seen this though and it was deprecated after PDF 1.2 (current is 1.7).
You will definitely need the PDF spec for this: http://www.adobe.com/content/dam/Adobe/en/devnet/pdf/pdfs/PDF32000_2008.pdf
Thanks to Omz, here is a piece of code to retreive a page number for an outline destination in a PDF file :
// Get Page Number from an array
- (int) getPageNumberFromArray:(CGPDFArrayRef)array ofPdfDoc:(CGPDFDocumentRef)pdfDoc withNumberOfPages:(int)numberOfPages
{
int pageNumber = -1;
// Page number reference is the first element of array (el 0)
CGPDFDictionaryRef pageDic;
CGPDFArrayGetDictionary(array, 0, &pageDic);
// page searching
for (int p=1; p<=numberOfPages; p++)
{
CGPDFPageRef page = CGPDFDocumentGetPage(pdfDoc, p);
if (CGPDFPageGetDictionary(page) == pageDic)
{
pageNumber = p;
break;
}
}
return pageNumber;
}
// Get page number from an outline. Only support "Dest" and "A" entries
- (int) getPageNumber:(CGPDFDictionaryRef)node ofPdfDoc:(CGPDFDocumentRef)pdfDoc withNumberOfPages:(int)numberOfPages
{
int pageNumber = -1;
CGPDFArrayRef destArray;
CGPDFDictionaryRef dicoActions;
if(CGPDFDictionaryGetArray(node, "Dest", &destArray))
{
pageNumber = [self getPageNumberFromArray:destArray ofPdfDoc:pdfDoc withNumberOfPages:numberOfPages];
}
else if(CGPDFDictionaryGetDictionary(node, "A", &dicoActions))
{
const char * typeOfActionConstChar;
CGPDFDictionaryGetName(dicoActions, "S", &typeOfActionConstChar);
NSString * typeOfAction = [NSString stringWithUTF8String:typeOfActionConstChar];
if([typeOfAction isEqualToString:#"GoTo"]) // only support "GoTo" entry. See PDF spec p653
{
CGPDFArrayRef dArray;
if(CGPDFDictionaryGetArray(dicoActions, "D", &dArray))
{
pageNumber = [self getPageNumberFromArray:dArray ofPdfDoc:pdfDoc withNumberOfPages:numberOfPages];
}
}
}
return pageNumber;
}
I have several characters that aren't recognized properly.
Characters like:
º
á
ó
(etc..)
This means that the characters encoding is not utf-8 right?
So, can you tell me what character encoding could it be please.
We don't have nearly enough information to really answer this, but the gist of it is: you shouldn't just guess. You need to work out where the data is coming from, and find out what the encoding is. You haven't told us anything about the data source, so we're completely in the dark. You might want to try Encoding.Default if these are files saved with something like Notepad.
If you know what the characters are meant to be and how they're represented in binary, that should suggest an encoding... but again, we'd need to know more information.
read this first http://www.joelonsoftware.com/articles/Unicode.html
There are two encodings: the one that was used to encode string and one that is used to decode string. They must be the same to get expected result. If they are different then some characters will be displayed incorrectly. we can try to guess if you post actual and expected results.
I wrote a couple of methods to narrow down the possibilities a while back for situations just like this.
static void Main(string[] args)
{
Encoding[] matches = FindEncodingTable('Ÿ');
Encoding[] enc2 = FindEncodingTable(159, 'Ÿ');
}
// Locates all Encodings with the specified Character and position
// "CharacterPosition": Decimal position of the character on the unknown encoding table. E.G. 159 on the extended ASCII table
//"character": The character to locate in the encoding table. E.G. 'Ÿ' on the extended ASCII table
static Encoding[] FindEncodingTable(int CharacterPosition, char character)
{
List matches = new List();
byte myByte = (byte)CharacterPosition;
byte[] bytes = { myByte };
foreach (EncodingInfo encInfo in Encoding.GetEncodings())
{
Encoding thisEnc = Encoding.GetEncoding(encInfo.CodePage);
char[] chars = thisEnc.GetChars(bytes);
if (chars[0] == character)
{
matches.Add(thisEnc);
break;
}
}
return matches.ToArray();
}
// Locates all Encodings that contain the specified character
static Encoding[] FindEncodingTable(char character)
{
List matches = new List();
foreach (EncodingInfo encInfo in Encoding.GetEncodings())
{
Encoding thisEnc = Encoding.GetEncoding(encInfo.CodePage);
char[] chars = { character };
byte[] temp = thisEnc.GetBytes(chars);
if (temp != null)
matches.Add(thisEnc);
}
return matches.ToArray();
}
Encoding is the form of modifying some existing content; thus allowing it to be parsed by the required destination protocols.
An example of encoding can be seen when browsing the internet:
The URL you visit: www.example.com, may have the search facility to run custom searches via the URL address:
www.example.com?search=...
The following variables on the URL require URL encoding. If you was to write:
www.example.com?search=cat food cheap
The browser wouldn't understand your request as you have used an invalid character of ' ' (a white space)
To correct this encoding error you should exchange the ' ' with '%20' to form this URL:
www.example.com?search=cat%20food%20cheap
Different systems use different forms of encoding, in this example I have used standard Hex encoding for a URL. In other applications and instances you may find the need to use other types of encoding.
Good Luck!