Read .seq file in MATLAB

Hi, I have a 20 minute video recording of an insect and i need to process it. Since it is the raw data,its file format is .seq.

Can anyone help me in reading the seq file in matlab?

Thanks

[Walter Roberson]

Was your .seq file created by Cyberpaint or by NorPix ?

[kittu]

Hi, Thanks for the reply.I am not sure about it,as I have not collected the data personally.But i think that it was created by NorPix.

Answer 1

[Walter Roberson]

http://www.norpix.com/support/faq.php#matlab

[kittu]

Hi, Thanks for the quick link and answer. I am trying to replicate the same code on my machine. But i am getting this error message:

    ??? Maximum variable size allowed by the program is exceeded.

I am trying to create a zero matrix for preallocation and for that I need to create a zero matrix.However the size of matrix is about:

    404166936*522198298*9765

Here 404166936 is Image width and 522198298 is Image height while 9765 is the number of Allocated frames. I know it is a huge matrix, but some how the people in MATLAB has written the code and i am only replicating it for my use.

Any suggestions?Is there a way to increase the variable size? I am trying to read the .seq file which is about 50MB big. If the program fails in 50MB file, then how will i process even bigger files which are close to 3GB!

Thanks

[Walter Roberson]

There is no hope of reading in 404166936*522198298*9765: it would require 2E12 gigabytes!

Please recheck the sizes. 400 million pixels wide seems quite unlikely. Even a single frame would be 2E8 gigabytes.

[kittu]

Thanks for replying.Ya, i know..But some how when i am reading the header information then it is showing me these figures. I have this following code for header information:

clc
clear
fid = fopen('1.seq','r','b')
endianType = 'ieee-le';
%Reading Header Version
OFB = {28,1,'long'};
fseek(fid,OFB{1}, 'bof')
headerInfo.Version = fread(fid, OFB{2}, OFB{3}, endianType) %headerInfo is a structure
%Reading Header size
OFB = {32,1,'long'};
fseek(fid,OFB{1}, 'bof');
headerInfo.HeaderSize = fread(fid,OFB{2},OFB{3}, endianType)
%Reading Description Format
OFB = {592,1,'long'};
fseek(fid,OFB{1}, 'bof');
DescriptionFormat = fread(fid,OFB{2},OFB{3}, endianType)'
%Reading Byte Description
OFB = {36,512,'ushort'};
fseek(fid,OFB{1}, 'bof');
headerInfo.Description = fread(fid,OFB{2},OFB{3}, endianType)'
%Reading Image Information
OFB = {548,24,'uint32'};
fseek(fid,OFB{1}, 'bof');
tmp = fread(fid,OFB{2},OFB{3}, 0, endianType)
headerInfo.ImageWidth = tmp(1);
headerInfo.ImageHeight = tmp(2);
headerInfo.ImageBitDepth = tmp(3);
headerInfo.ImageBitDepthReal = tmp(4);
headerInfo.ImageSizeBytes = tmp(5);
vals = [0,100,101,200:100:900];
fmts = {'Unknown','Monochrome','Raw Bayer','BGR','Planar','RGB',...
  'BGRx', 'YUV422', 'UVY422', 'UVY411', 'UVY444'};
headerInfo.ImageFormat =[fmts{vals == tmp(6)}];
%Reading information about number of allocated frames
OFB = {572,1,'ushort'};
fseek(fid,OFB{1}, 'bof');
headerInfo.AllocatedFrames = fread(fid,OFB{2},OFB{3}, endianType);
%Reading information about origin
OFB = {576,1,'ushort'};
fseek(fid,OFB{1}, 'bof');
headerInfo.Origin = fread(fid,OFB{2},OFB{3}, endianType);
%Reading information about true image size i.e number of bytes between the
%first pixel of each successive images.
OFB = {580,1,'ushort'};
fseek(fid,OFB{1}, 'bof');
headerInfo.Origin = fread(fid,OFB{2},OFB{3}, endianType);
%Reading True Image Size
OFB = {580,1,'ulong'};
fseek(fid,OFB{1}, 'bof');
headerInfo.TrueImageSize = fread(fid,OFB{2},OFB{3}, endianType);
%Reading information about fps
OFB = {584,8,'double'};
fseek(fid,OFB{1}, 'bof');
headerInfo.FrameRate = fread(fid,OFB{2},OFB{3}, endianType)

When i run this, i get the following header information: headerInfo =

              Version: 0
           HeaderSize: 36629
          Description: [1x512 double]
           ImageWidth: 404166936
          ImageHeight: 522198298
        ImageBitDepth: 572531232
    ImageBitDepthReal: 639771172
       ImageSizeBytes: 606348324
          ImageFormat: []
      AllocatedFrames: 9765
               Origin: 10280
        TrueImageSize: 673654824
            FrameRate: [8x1 double]

Any suggestions?

[Walter Roberson]

There must be a problem in reading the header. The ImageWidth shown there happens to correspond to hex 0x18171918 which is entirely too regular to be an accident.

[Walter Roberson]

See also https://www.mathworks.com/matlabcentral/fileexchange/68341-readcompressedjpegseq

Answer 2

[Davide Ferraro]

On page: http://people.cs.uchicago.edu/~dinoj/matlab/

There are some routines for working with .seq files in MATLAB. I've not been able to test them.

[kittu]

Hi, Thanks for reply.Unfortunately none of those codes are working. I guess those codes are meant for reading the sequential files which are often generated during the sequence analysis of DNA/RNA etc which are text files. But in my case, these .seq files are raw video files.

I am unable to read this file in MATLAB using any of the reader. Please provide some solution. Thanks

[Julian Marstaller]

hey kittu,

i have the same issue currently. did you solve your problem already?

Thanks!

Here is our file output:

                 width: 1920
                height: 1080
         imageBitDepth: 12
     imageBitDepthReal: 12
        imageSizeBytes: 3110400
           imageFormat: 630
             numFrames: 239
         trueImageSize: 3112960
                   fps: 25.1130
            seqVersion: 5
                 codec: 'imageFormat630'
                 descr: 'StreamPix 6.5.0.0 (x64) Ę䀀  䀀   乐䀴   ㋈䀴     　g   䀴 ⊸3…'
    nHiddenFinalFrames: 0

Answer 3

[Vijay Yadav]

Hey,

Can anyone please share matlab script for reading .seq file

[Walter Roberson]

Vijay Yadav:

We have identified at least 3 different kinds of .seq files. We would need to know what software wrote your files to try to figure out what your file is.

[Vijay Yadav]

Hi Walter,

Thnxs for ur reply.

My .seq raw videos files are from StreamPix.

[Walter Roberson]

Try Paul's utility at https://www.mathworks.com/matlabcentral/fileexchange/68341-readcompressedjpegseq

[Paul Siefert]

You can now read compressed and uncompresed sequences completly, or within a reading window with the above script.