Binary Stream into Matlab

Good evening,

So far the community has been fantastic in aiding me to learn Matlab so thank you. However a new problem has presented itself, in another program I have saved data to a file using a byte[] array (C#), the file is 100MB large.

The data contained within that file is a depth sensor pixel data stored in a byte[] array and saved to file. I am able to read the file and import the data into a single column and that is as far as I am able to get.

I am looking for assistance in how to visualise the data into possible a imshow()/drawnow method.

Thanks again,

Dan

Answer 1

[Image Analyst]

Why are you reading it into a column when you want a 2D array? You can read directly into a 2D array. Here's a snippet from an m-file of mine:

oneSlice = fread(fileHandle, [x_size y_size], '*uint8');

Ok, then you have a 2D array. Not sure what your difficulty with imshow() is. You can simply do

imshow(oneSlice); % or whatever your matrix is called.

[Dan]

Thanks for the reply, greatly appreciated. The image is captured by use of a depth sensor and saved to a binary file, The aim is to take the binary file and reply the depth image in Matlab is this possible?

[Image Analyst]

Not sure what you mean by "reply the depth image" but yes, you can read in a binary image, display it, and do math on it.

[Dan]

Thanks for the very quick reply, let me try and be a bit clearer. I am using a depth sensor to record a depth image over a 10 second period (640*480) to a binary file. I would now like to "reply", ie show the depth image in Matlab for visual analysis. I think my problem may more be related to understanding how much information is saved per frame to allow me to generate the playback I would need, something for me to explore.

[Image Analyst]

I do have code to read raw binary files into 8 bit and 16 bit volumes and 2D slices if you're interested, but the heart of it is the fread line I already gave you.

[Dan]

It would be a great help, if at all possible.

[Image Analyst]

Here is a function that reads a raw binary image with a 3D image in it. User specifies which slice they want and it retrieves that as a 2D image. Instructions for calling it are in the comments at the beginning.

%  Read_RAW_Slice
%  Reads one slice from a RAW file from disk.
%
%  [oneSlice, stHeader] = Read_RAW_Slice(fullFileName, sliceNumber) 
%  or, alternate usage:
%  [oneSlice, stHeader] = Read_RAW_Slice(fullFileName, stInputParameters) 
%  reads the specified slice from data in 'fullFileName' and 
%  returns the slice data as a 2D array, and the header as a structure stHeader.
%  This method of calling allows for cropping and subsampling.
%
%======== EXAMPLE USAGES =====================================
%  Example #1 usage: Simply read a slice.  No cropping or subsampling.
%  Note that you can pass in just a single number for the second argument and it
%  will be the slice number.  The Subsampling would then be 1.  For example:
%  fullFileName = 'SimulatedData_Distance8Bit.RAW';
%  [oneSlice, stHeader] = Read_RAW_Slice(fullFileName, 10);
%  imshow(oneSlice, []);
%
%  Example #2 usage: Read a slice with subsampling in the x, y, and z directions.
%  Create a MATLAB structure dynamically to hold the input parameters.
%  Use ZStart for the slice number.  You don't need to define any other structure members.
%  stInputParameters.ZStart = 60;
%  stInputParameters.Subsample = 4;  % Same for all 3 directions.
%  fullFileName = 'SimulatedData_Distance8Bit.RAW';
%  [oneSlice, stHeader] = Read_RAW_Slice(fullFileName, stInputParameters);
%  imshow(oneSlice, []);
%
%  Example #3 usage: Read a slice and crop and subsample it in the x, y, and z directions.
%  Create a MATLAB structure dynamically to hold the input parameters.
%  stInputParameters.XStart = 200;
%  stInputParameters.YStart = 1200;
%  stInputParameters.XEnd = 400;
%  stInputParameters.YEnd = 1600;
%  Use ZStart for the slice number.  You don't need to define any other structure members.
%  stInputParameters.ZStart = 70;
%  stInputParameters.Subsample = 4;  % Same for all 3 directions.
%  fullFileName = 'SimulatedData_Distance8Bit.RAW';
%  [oneSlice, stHeader] = Read_RAW_Slice(fullFileName, stInputParameters);
%  imshow(oneSlice, []);
%=============================================================
%
%  Image Analyst, 7/30/2007.
%--------------------------------------------------------------------------------------------

function [oneSlice, stHeader] = Read_RAW_Slice(fullFileName, stInputParameters)

  % Check syntax.  Must have two arguments.
  if (nargin ~= 2)
    error('Usage: [image2D, stHeader] = Read_RAW_Slice(fullFileName, stInputParameters)');
  end 
  if (ischar(fullFileName) ~= 1)
    error('Requires a string filename as an argument.');
  end 
  if ~exist(fullFileName, 'file')
    error('Error: file passed in to Read_RAW_Slice\n%s\ndoes not exist.', fullFileName);
  end

  % Read in header and get 3D image array dimensions.
  stHeader = Read_RAW_Header(fullFileName);
  % Note: fread() requires that x_size and y_size be doubles.
  x_size = double(stHeader.x_size);
  y_size = double(stHeader.y_size);
  z_size = double(stHeader.z_size);

  % Determine the parameters that they passed in.
  if isa(stInputParameters, 'double') || isa(stInputParameters, 'integer')
    % They didn't pass in a structure - they just passed in a single number (scalar).
    % Interpret this number as the slice number.
    sliceNumber = int32(stInputParameters);
    % For the rest, just take the entire slice.
    xStart = int32(1);
    yStart = int32(1);
    xEnd = int32(x_size);
    yEnd = int32(y_size);
    Subsampling = int32(1);
  else
    % They passed in a structure.  Make sure they passed in valid numbers.
    % Assign defaults to any fields in stInputParameters that they didn't set.
    stValidParameters = ValidateInputParameters(stInputParameters, x_size, y_size, z_size);
    sliceNumber = int32(stValidParameters.ZStart);
    xStart = int32(stValidParameters.XStart);
    yStart = int32(stValidParameters.YStart);
    xEnd = int32(stValidParameters.XEnd);
    yEnd = int32(stValidParameters.YEnd);
    Subsampling = int32(stValidParameters.Subsample);
  end

  % Make sure they asked for a slice that is within range.
  if (sliceNumber > z_size)
    % Error and exit if they didn't.
    error('Slice number must be within the range 1 to %d.\nYou asked for slice %d.', z_size, sliceNumber);
  end

  % Open file for reading.
  fileHandle = fopen(fullFileName, 'rb', stHeader.EndianArg);
  if (fileHandle == -1)
    error(['Error opening ', fullFileName, ' for input.']);
  end

  % Skip past header of stHeader.HeaderSize bytes.
  bytesToSkip = int32(stHeader.HeaderSize);
  fseek(fileHandle, bytesToSkip, 'bof');

  % Now, additionally, skip past (sliceNumber - 1) slices
  % so that we end up at the beginning byte of the slice that we want.
  bytesToSkip = bytesToSkip + int32(x_size * y_size * stHeader.BytesPerVoxel * (sliceNumber - 1));
  fseek(fileHandle, bytesToSkip, 'bof');

  % Read in image2D image data
  % Get original, full-sized 2-D slice.
  % Note: fread() requires that x_size and y_size be doubles.
  % Note: fread() will return a 2D array if you pass in a 2D array for the number of bytes, as in [x_size y_size].
  if stHeader.BytesPerVoxel == 1
    oneSlice = fread(fileHandle, [x_size y_size], '*uint8');
  elseif stHeader.BytesPerVoxel == 2
    oneSlice = fread(fileHandle, [x_size y_size], '*int16'); % It will be a 2D array after this.
  else
    error('Unsupported BytesPerVoxel %d', stHeader.BytesPerVoxel);
  end

  % Close the file.
  fclose(fileHandle);

  % Subsample and/or crop it, if requested.
  if Subsampling ~= 1 || xStart ~= 1 || yStart ~= 1 || xEnd ~= x_size || yEnd ~= y_size
    oneSlice = oneSlice(xStart:Subsampling:xEnd, yStart:Subsampling:yEnd);
  end

  return;  % from Read_RAW_Slice()

Answer 2

[Walter Roberson]

reshape() to a 2D array, and imshow(TheArray)