How can we read Biopax file in matlab, biopax is special type of xml file. How we can retrieve information from it using matlab.
There is a BioConductor package for reading and manipulating BioPAX files in R (http://bioconductor.org/packages/release/bioc/html/paxtoolsr.html).
Check out the related tutorial on getting set up in R:
https://www.youtube.com/channel/UCWSbcyynroIp-f6O3sfz7jg
AND using PaxtoolsR:
http://bioconductor.org/packages/release/bioc/vignettes/paxtoolsr/inst/doc/using_paxtoolsr.html
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Is there a place to find sample CFD data in this format please?
I am trying to create scripts for Paraview to automate files opening and want to use the track function.
Data from this article can be used to test out the file format:
I am using the program dicomrt2matlab. I was able to convert the dicom RT structure into matlab and I got the .mat file as well. How do I load the .mat file into matlab next? How can I see the RT information in my applied to my dicom files ?
Link - https://github.com/ulrikls/dicomrt2matlab
if you do data=load('myfilename.mat'); data will contain everything on it.
It shoudl have (I think) the following 3 data on it: 'contours', 'rtssheader', 'imageheaders'
you can access it as data.imageheaders
I am trying to convert MathType's equation which is stored as OLE binary file to MathML using MathType's SDK.
The input file for my program is a DocX which would contain embdedd MathType equations. I am looking for a solution thats independent of using MS Word. DocX is a zip file, and once it is extracted we can find the a binary file for each OLE object in the folder "word/embeddings/". Typically the file name would be oleObject1.bin, oleObject2.bin etc.
When I checked with MathType SDK it has a class "ConvertEquation" which has following method:
virtual public bool Convert(EquationInput ei, EquationOutput eo)
EquationInput is an abstract class for which following concrete classes are made available:
EquationInputFileText
EquationInputFileWMF2
EquationInputFileWMF
EquationInputFileGIF
EquationInputFileEPS
In the above listed classes none of them seems to support OLE binary.
According to MathType's SDK doc, MTEF data is saved as the native data format of the object. Whenever an equation object is to be written to an OLE "stream", a 28- byte header is written, followed by the MTEF data. I guess this is exactly what is present in this binary file. But just that there seems to be no way by which this format can be made to be used by SDK to convert it into MathML. Any thoughts?
Thanks
you can convert mathtype wmf file to mathml as follow:
ConvertEquation conv = new ConvertEquation();
var input = EquationInputFileWMF("mathTYpe.wmf");
var output = EquationOutputFileText("MathMLName.txt", "MathML2 (m namespace).tdl"));
conv.Convert(input , input);
the "MathML2 (m namespace).tdl" string stand for "tdl" file which contains in "MathType\Translators" path, if you open the Translators path ,you can find many of type.
You may try MathMagic equation editor (Windows version).
MathMagic can extract all Word embeded equations out of the document(s) (.doc or .docx), and can save/covert them to other format (such as JPG, PNG, BMP, PDF, TeX, LaTeX, MathML, ...) as a batch conversion job.
Unfortunately, their trial version does not support this batch conversion. A valid license (even 1-month or 2-month license) is required to enable the Conversion feature.
how can I create file (PDF file for example) from binary stream I have stored in global? I have stream stored in caché global and I need to create and save the file created by the stream using ObjectScript.
Thanks :)
It is not so easy. There is only one official way to create pdf in Cache, and it is ZEN reports. With ZEN reports you could create not only pdf, also possible to make html, xlsx. ZEN Reports used Apache FOP for generating it, any other ways also possible, but you should do it only by yourself.
Or maybe I misunderstood you, and you mean that your binary stream already contains PDF, and you just want to save it to some file. If so, you just have to copy your globalstream to filestream, with code like this:
set fs=##class(%Stream.FileBinary).%New()
set fs.Filename="c:\temp.pdf"
set tSC=fs.CopyFrom(yourStream)
set tSC=fs.%Save()
I have a text file called "test.txt" which contains data in libsvm format.
Data in this file is represented as follows:
165475 0:246870 1124384:2 342593:7 1141651:1 297582:1 1186846:1 17725:1 656602:1
463304:1 766612:1 573309:1 290046:1 748198:1 216665:1 950594:2 909004:1 29008:1
105623:1 5018:5 806027:1 1125729:1 757846:1 1023921:2 612980:1 120767:1 51340:1
108172:5 674420:2
where 1st term represents the label and remaining represents the feature and its weight(separated by : ).This is a very huge file(with every label having lots of features and weights).
I am using scikit with ipython notebook and want to load this data in notebook to start processing it.
Can someone tell how to do that.Thanks in advance.
Use load_svmlight_file from sklearn.datasets.