I hold a volume image in a vtkImageData and need to convert it to DcmDataset (DCMTK). I know that I need to set general DICOM tags like patient data to the data set. That's not the problem.
Especially I'm interested in putting the pixel data to DcmDataset. Does anybody know an example or can explain how to do that?
Thanks in advance
Quoting from the DCMTK FAQ:
Is there a tool that converts common graphic formats like PGM/PPM,
PNG, TIFF, JPEG or BMP to DICOM?
No, unfortunately, there is no such tool in DCMTK. Currently, you have to write your own little program for that purpose.
The following code snippet from the toolkit's documentation could be a starting point:
char uid[100];
DcmFileFormat fileformat;
DcmDataset *dataset = fileformat.getDataset();
dataset->putAndInsertString(DCM_SOPClassUID, UID_SecondaryCaptureImageStorage);
dataset->putAndInsertString(DCM_SOPInstanceUID, dcmGenerateUniqueIdentifier(uid, SITE_INSTANCE_UID_ROOT));
dataset->putAndInsertString(DCM_PatientsName, "Doe^John");
/* ... */
dataset->putAndInsertUint8Array(DCM_PixelData, pixelData, pixelLength);
OFCondition status = fileformat.saveFile("test.dcm", EXS_LittleEndianExplicit);
if (status.bad())
cerr << "Error: cannot write DICOM file (" << status.text() << ")" << endl;
The current snapshot of the DCMTK (> version 3.5.4) contains a new
command line tool "img2dcm" that allows for converting JPEG images to
certain DICOM image SOP classes.
I would perhaps look first at the source code for img2dcm (documented here) to see the general process and then post back with any specific questions. IMHO, DCMTK is very powerful but extremely difficult to understand.
Related
To begin with: I am working on Image Processing using OpenCV C++. After loading a Mat image in a C++ program, I plotted a graph of the image using GNUPLOT.
Now, The Requirement is to log the graphical data of the Mat image.
To do this, I created a BOOST C++ Logger by including all BOOST Libraries. BOOST is an excellent library for Testing and logging data as well but, the problem with the it's Log is that it could log only text messages. Correct me if I'm wrong.
Below is my CODE for plotting graph using GNUPlot in OpenCV:
try
{
Gnuplot g1("lines");
std::vector<double> rowVector;
std::vector<double> rowVectorExp;
for (int i = 0; i < 50; i++)
{
rowVector.push_back((double)i);
rowVectorExp.push_back((double)exp((float)i/10.0));
}
cout << "*** user-defined lists of doubles" << endl;
g1 << "set term png";
g1 << "set output \"test.png\"";
//type of plot pattern
g1.set_grid().set_style("lines");
g1.plot_xy(rowVector, rowVectorExp, "user-defined points 2d");
waitKey(0);
}
catch (GnuplotException ge)
{
cout << ge.what() << endl;
}
cout << endl << "*** end of gnuplot example" << endl;
Here is my BOOST Log CODE:
namespace logging = boost::log;
void PlainGetEdgeVector::init()
{
logging::add_file_log("sample%3N.log");
}
BOOST_LOG_TRIVIAL(info) << "This is my first Log line";
The good news is, my BOOST Logger successfully logs the text message. It would be great if it could log my graphical data as well.
Any suggestions? If anyone knows how to implement the same using BOOST, I would be very grateful or if there are any alternatives, good to know that as well.
The solution to your problem greatly depends on the nature of the data how do you want to use the logged data.
1. Re-consider converting binary data to text
For debugging purposes it is often more convenient to convert your binary data to text. Even with large amounts of data this approach can be useful because there are generally many more tools for text processing than for working with arbitrary binary data. For instance, you could compare two logs from different runs of your application with conventional merge/compare tools to see the difference. Text logs are also easier to filter with tools like grep or awk, which are readily available, as opposed to binary data for which you will likely have to write a parser.
There are many ways to convert binary data to text. The most direct approach is to use the dump manipulator, which will efficiently produce textual view of a raw binary data. It suits graphical data as well because it tends to be relatively large in amounts and it is often easy enough to compare in text representation (e.g. when a color sample fits a byte).
std::vector< std::uint8_t > image;
// Outputs hex dump of the image
BOOST_LOG_TRIVIAL(info) << logging::dump(image.data(), image.size());
A more structured way to output binary data is to use other libraries, such as iterator_range from Boost.Range. This can be useful if your graphical data is composed of something more complex than raw bytes.
std::vector< double > image;
// Outputs all elements of the image vector
BOOST_LOG_TRIVIAL(info) << boost::make_iterator_range(image);
You can also write your own manipulator that will format the data the way you want, e.g. split the output by rows.
2. For binary data use attributes and a custom sink backend
If you intend to process the logged data by a more specialized piece of software, like an image viewer or editor, you might want to save the data in binary form. This can be done with Boost.Log, but it will require more effort because the sinks provided by the library are text-oriented and you cannot save a binary data into a text file as is. You will have to write a sink backend that will write binary data in the format you want (e.g. if you plan to use an image editor you might want to write files in the format supported by that editor). There is a tutorial here, which shows the interface you have to implement and a sample implementation. The important bit is the consume function of the backend, which will receive a log record view with your data.
typedef boost::iterator_range< const double* > image_data;
BOOST_LOG_ATTRIBUTE_KEYWORD(a_image, "Image", image_data)
class image_writer_backend :
public sinks::basic_sink_backend< sinks::synchronized_feeding >
{
public:
void consume(logging::record_view const& rec)
{
// Extract the image data from the log record
if (auto image = rec[a_image])
{
image_data const& im = image.get();
// Write the image data to a file
}
}
};
In order to pass your image binary data to your sink you will need to attach it to the log record as an attribute. There are multiple ways to do that, but assuming you don't intend to filter log records based on the image, the easiest way to do this is to use the add_value manipulator.
std::vector< double > image;
BOOST_LOG_TRIVIAL(info) << logging::add_value(a_image, image) << "Catch my image";
Caveat: In order to avoid copying the potentially large image data, we're passing a lightweight iterator_range as the attribute value. This will only work with synchronous logging because the image vector needs to stay alive while the log record is being processed. For async logging you will have to pass the image by value or use reference counting.
If you do want to apply filters to the image data then you can use scoped attributes or add the attribute to a logger.
Note that by adding your new sink for writing binary data you do not preclude also writing textual logs with other sinks, so that "Catch my image" message can be processed by a text sink. By using other attributes, like log record counters you can associate log records in different files produced by different sinks.
I am using Tesseract OCR c++ library in QT to get a text from a png image
using this code
const char* lang = "eng";
QString filename = "D:/image.png";
tesseract::TessBaseAPI tess;
tess.Init(NULL, lang, tesseract::OEM_DEFAULT);
tess.SetPageSegMode(tesseract::PSM_AUTO);
FILE* fin = fopen(filename.toStdString().c_str(), "rb");
if (fin == NULL)
{
std::cout << "Cannot open " << filename.toStdString().c_str() << std::endl;
return;
}
fclose(fin);
STRING text;
if (tess.ProcessPages(filename.toStdString().c_str(), NULL, 0, &text))
{
ui->plainTextEdit->setPlainText(QString::fromUtf8(text.string()));
//show result in plainttext qt gui
}
put the data not accurate enough for the data in the table and it gives me strange characters and when I use an online OCR website to convert my image to text (the same image) it does it with 100% accurate so what makes it gives me this wrong text is this a problem with the library? or my code? or if there is a better free library I can use to be more accurate?
I got the image from pdf I use ghost script to get the image with a good quality so the OCR library should get me the correct data
link to download the image
website I use to get the accurate ocr
I am not experienced with cpp, but I think your problem relates to the below line with a great probability:
tess.Init(NULL, lang, tesseract::OEM_DEFAULT);
It must show the tessdata folder. instead of NULL you may write the folder name, for example "C:/tessdata/". Again, I am not experienced with cpp, that's why you may decide slash "/" or backslash "\". This folder should contain the language file(s).
As Eddge mentioned in his comment you should apply some image preprocessing stuff there are bunch of scripts for imagemagick.
Ans of course OpenCV will vastly help in this stuff as well.
The next point could be PSM mode which by default should satisfy your needs to extract whole page information.
Also the result of the online OCR is not 100% as you mentioned.
There is "1 S Days" instead of "15 Days"
There is "Mail: finance(a)" instead of "E Mail: finance#"
There is "TiA THE GREEN HOL1 5" instead of "T/A THE GREEN HOU 5"
etc.
Which Tesseract version are you using? I highly recommend to use 3.05. (4.0 shows much better results but it is not officially released yet).
Also the following link could help you with your results: https://github.com/tesseract-ocr/tesseract/wiki/ImproveQuality
P.S. I hope you are eligible to share publicly such financial documentations;)
I am given image data and color table I am trying to export it as a single frame GIF using giflib. I looked into the API, but can't get it to work. The program crashes even at the first function:
GifFileType image_out;
int errorCode = 0;
char* fileName = "SomeName.gif";
image_out = *EGifOpenFileName(fileName,true, &errorCode);
It is my understanding that I first need to open a file by specifying it's name and then update it with fileHandle. Then Fill in the screen description, the extension block the image data and add the 3B ending to the file. Then use EGifSpew to export the whole gif. The problem is that I can't even use EGifOpenFileName(); The program crashes at that line.
Can someone help me the API of giflib? This problem is getting really frustrating.
Thanks.
EDIT:
For the purposes of simple encoding I do not want to specify a color table and I just want to encode a single frame GIF.
The prototype is:
GifFileType *EGifOpenFileName(char *GifFileName, bool GifTestExistance, int *ErrorCode)
You should write as
GifFileType* image_out = EGifOpenFileName(fileName,true, &errorCode);
Note GifFileType is not POD type so you should NOT copy like that.
I need optimize this code. Currently, this code works. I can extract the datetimeoriginal tag in a file using the extern tool "exiftool". But this is too slow when this process is repeated. is there a way the extract this information in variables directly?
void image::add_info_creation_date(char *name_jpg){
//Execute exiftool in bash
stringstream ss;
ss << "exiftool.exe -datetimeoriginal -timezone images\\" << name_jpg << " >> temporal.txt";
error = system(ss.str().c_str());
if (error != 0){
printf("The value returned was: %d.\n", error);
ss.clear();
exit(1);
}
ss.clear();
...
}
Sorry for my grammar, i am not native english speaker.
is there a way the extract this information in variables directly?
Yes, it is possible.
Your options are to either find and use a library which can read the EXIF information for you, or to read & understand the JPEG & EXIF formats, and read the file yourself.
Since a quick search turns up several libraries that do these things, and since at least some documentation is available for both standards, it doesn't seem too hard.
If you read the file yourself, note that the JPEG file format contains multiple tagged sections, including both the image and its metadata - you just need to walk the sections until you find the EXIF data and then parse that.
Executing ExifTool once for each file can be slow, but there's a way to run it so you can feed it a stream of commands. First, create an argument file and keep it open for output; let's call it args.txt. Then launch
exiftool -stay_open True -# args.txt
For each file, write the arguments, one argument per line, something like this, to args.txt:
-datetimeoriginal
-timezone
{filename}
-execute
When finished, write the following to args.txt:
-stay_open
False
This may get you sufficient performance. Don't close args.txt till you're finished, but it will help if you flush any buffers after each -execute.
I will try to be clear ....
My project idea is as follow :
I took several compression algorithms which I implemented using C++, after that I took a text file and applied to it the compression algorithms which I implemented, then applied several encryption algorithms on the compressed files, now I am left with final step which is converting these encrypted files to any format of image ( am thinking about png since its the clearest one ).
MY QUESTION IS :
How could I transform a binary stream into a png format ?
I know the image will look rubbish.
I want the binary stream to be converted to a an png format so I can view it as an image
I am using C++, hope some one out there can help me
( my previous thread which was closed )
https://stackoverflow.com/questions/5773638/converting-a-text-file-to-any-format-of-images-png-etc-c
thanx in advance
Help19
If you really really must store your data inside a PNG, it's better to use a 3rd party library like OpenCV to do the work for you. OpenCV will let you store your data and save it on the disk as PNG or any other format that it supports.
The code to do this would look something like this:
#include <cv.h>
#include <highgui.h>
IplImage* out_image = cvCreateImage(cvSize(width, height), IPL_DEPTH_8U, bits_pr_pixel);
char* buff = new char[width * height * bpp];
// then copy your data to this buff
out_image->imageData = buff;
if (!cvSaveImage("fake_picture.png", out_image))
{
std::cout << "ERROR: Failed cvSaveImage" << std::endl;
}
cvReleaseImage(&out_image);
The code above it's just to give you an idea on how to do what you need using OpenCV.
I think you're better served with a bi-dimensional bar code instead of converting your blob of data into a png image.
One of the codes that you could use is the QR code.
To do what you have in mind (storing data in an image), you'll need a lossless image format. PNG is a good choice for this. libpng is the official PNG encoding library. It's written in C, so you should be able to easily interface it with your C++ code. The homepage I linked you to contains links to both the source code so you can compile libpng into your project as well as a manual on how to use it. A few quick notes on using libpng:
It uses setjmp and longjmp for error handling. It's a little weird if you haven't worked with C's long jump functionality before, but the manual provides a few good examples.
It uses zlib for compression, so you'll also have to compile that into your project.