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RPread.m
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% loads the ultrasound RF data saved from the Sonix software
%%
%% Inputs:
%% filename - The path of the data to open
%%
%% Return:
%% Im - The image data returned into a 3D array (h, w, numframes)
%% header - The file header information
%%
%% Corina Leung, [email protected]
%% Modified by Ali Baghani, Nov 2012 to support recent changes to the user
%% interface [email protected]
%% Ultrasonix Medical Corporation Nov 2007
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [Im,header] = RPread(varargin)
% to determine whether a later version of Sonix is being used
if nargin > 1
filename = varargin{1};
version = varargin{2}; % Valid versions are: 5 for Sonix versions prior to 6.0
% 6 for newer Sonix versions 6.0.2, 6.0.3, 6.0.4, 6.0.6, etc
else
filename = varargin{1};
version = '6.0.3';
end
fid= fopen(filename, 'r');
fileExt = filename(end-3:end);
if( fid == -1)
error('Cannot open file');
end
% read the header info
hinfo = fread(fid, 19, 'int32');
% load the header information into a structure and save under a separate file
header = struct('filetype', 0, 'nframes', 0, 'w', 0, 'h', 0, 'ss', 0, 'ul', [0,0], 'ur', [0,0], 'br', [0,0], 'bl', [0,0], 'probe',0, 'txf', 0, 'sf', 0, 'dr', 0, 'ld', 0, 'extra', 0);
header.filetype = hinfo(1);
header.nframes = hinfo(2);
header.w = hinfo(3);
header.h = hinfo(4);
header.ss = hinfo(5);
header.ul = [hinfo(6), hinfo(7)];
header.ur = [hinfo(8), hinfo(9)];
header.br = [hinfo(10), hinfo(11)];
header.bl = [hinfo(12), hinfo(13)];
header.probe = hinfo(14);
header.txf = hinfo(15);
header.sf = hinfo(16);
header.dr = hinfo(17);
header.ld = hinfo(18);
header.extra = hinfo(19);
% -------------- memory initialization for speeding up -------------------
switch header.filetype
case {2, 4, 8, 16, 64, 256, 1024, 4096, 8192, 16384, 32768}
Im = zeros(header.h, header.w, header.nframes);
case {32}
Im = zeros(header.h, header.nframes);
case {128}
Im = zeros(header.h, 1, header.nframes);
case {512}
Im = zeros(header.h, header.w * header.extra, header.nframes);
case {2048}
Im = zeros(header.h, header.w * 2, header.nframes);
case {524288}
Im = zeros(header.w, header.nframes);
otherwise
Im = [];
end
h = waitbar(0, 'Generando las lineas RF');
% load the data and save into individual .mat files
for frame_count = 1:header.nframes
if(header.filetype == 2) %.bpr
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end % Each frame has 4 byte header for frame number in older versions
[v,count] = fread(fid,header.w*header.h,'uchar=>uchar');
Im(:,:,frame_count) = reshape(v,header.h,header.w);
elseif(header.filetype == 4) %postscan B .b8
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.w*header.h,'uint8');
temp = int16(reshape(v,header.w,header.h));
Im(:,:,frame_count) = imrotate(temp, -90);
elseif(header.filetype == 8) %postscan B .b32
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.w*header.h,'uint32');
temp = reshape(v,header.w,header.h);
Im(:,:,frame_count) = imrotate(temp, -90);
elseif(header.filetype == 16) %rf
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.w*header.h,'int16');
Im(:,:,frame_count) = int16(reshape(v,header.h,header.w));
elseif(header.filetype == 32) %.mpr
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.h,'int16');
Im(:,frame_count) = v;
elseif(header.filetype == 64) %.m
[v,count] = fread(fid,'uint8');
temp = reshape(v,header.w,header.h);
Im(:,:,frame_count) = imrotate(temp,-90);
elseif(header.filetype == 128) %.drf
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.h,'int16');
Im(:,:,frame_count) = int16(reshape(v,header.h,1));
elseif(header.filetype == 512) %crf
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.extra*header.w*header.h,'int16');
Im(:,:,frame_count) = reshape(v,header.h,header.w*header.extra);
% to obtain data per packet size use:
% Im(:,:,:,frame_count) = reshape(v,header.h,header.w,header.extra);
elseif(header.filetype == 256) %.pw
[v,count] = fread(fid,'uint8');
temp = reshape(v,header.w,header.h);
Im(:,:,frame_count) = imrotate(temp,-90);
% elseif(header.filetype == 1024) %.col %The old file format for SONIX version 3.0X
% [v,count] = fread(fid,header.w*header.h,'int');
% temp = reshape(v,header.w,header.h);
% temp2 = imrotate(temp, -90);
% Im(:,:,frame_count) = mirror(temp2,header.w);
%
% elseif((header.filetype == 2048) & (fileExt == '.sig')) %color .sig %The old file format for SONIX version 3.0X
% %Each frame has 4 byte header for frame number
% tag = fread(fid,1,'int32');
% [v,count] = fread(fid,header.w*header.h,'uchar=>uchar');
% temp = reshape(v,header.w,header.h);
% temp2 = imrotate(temp, -90);
% Im(:,:,frame_count) = mirror(temp2,header.w);
elseif(header.filetype == 1024) %.col
[v,count] = fread(fid,header.w*header.h,'int');
temp = reshape(v,header.w,header.h);
temp2 = imrotate(temp, -90);
Im(:,:,frame_count) = mirror(temp2,header.w);
elseif((header.filetype == 2048)) %color .cvv (the new format as of SONIX version 3.1X)
% velocity data
[v,count] = fread(fid,header.w*header.h,'uint8');
temp = reshape(v,header.w,header.h);
temp2 = imrotate(temp, -90);
tempIm1 = mirror(temp2,header.w);
% sigma
[v,count] =fread(fid, header.w*header.h,'uint8');
temp = reshape(v,header.w, header.h);
temp2 = imrotate(temp, -90);
tempIm2 = mirror(temp2,header.w);
Im(:,:,frame_count) = [tempIm1 tempIm2];
elseif(header.filetype == 4096) %color vel
if (regexp(version, '5.*') == 1) tag = fread(fid,1,'int32'); end
[v,count] = fread(fid,header.w*header.h,'uchar=>uchar');
temp = reshape(v,header.w,header.h);
temp2 = imrotate(temp, -90);
Im(:,:,frame_count) = mirror(temp2,header.w);
elseif(header.filetype == 8192) %.el
[v,count] = fread(fid,header.w*header.h,'int32');
temp = reshape(v,header.w,header.h);
temp2 = imrotate(temp, -90);
Im(:,:,frame_count) = mirror(temp2,header.w);
elseif(header.filetype == 16384) %.elo
[v,count] = fread(fid,header.w*header.h,'uchar=>uchar');
temp = int16(reshape(v,header.w,header.h));
temp2 = imrotate(temp, -90);
Im(:,:,frame_count) = mirror(temp2,header.w);
elseif(header.filetype == 32768) %.epr
[v,count] = fread(fid,header.w*header.h,'uchar=>uchar');
Im(:,:,frame_count) = int16(reshape(v,header.h,header.w));
elseif(header.filetype == 65536) %.ecg
[v,count] = fread(fid,header.w*header.h,'uchar=>uchar');
Im = v;
elseif or(header.filetype == 131072, header.filetype == 262144) %.gps
gps_posx(:, frame_count) = fread(fid, 1, 'double'); %8 bytes for double
gps_posy(:, frame_count) = fread(fid, 1, 'double');
gps_posz(:, frame_count) = fread(fid, 1, 'double');
if strcmp(version, '6.0.3')
gps_a(:, frame_count) = fread(fid, 1, 'double');
gps_e(:, frame_count) = fread(fid, 1, 'double');
gps_r(:, frame_count) = fread(fid, 1, 'double');
end
gps_s(:,:, frame_count) = fread(fid, 9, 'double'); %position matrix
if strcmp(version, '6.0.3')
gps_q(:, frame_count) = fread(fid, 4, 'double');
end
gps_time(:, frame_count) = fread(fid, 1, 'double');
gps_quality(:, frame_count) = fread(fid, 1, 'ushort'); % 2 bytes for unsigned short
Zeros(:, frame_count) = fread(fid, 3, 'uint16'); % 6 bytes of padded zeroes
elseif (header.filetype == 524288) % time stamps
LineStartInClkCycles = fread(fid, header.w, 'uint32');
Im(:, frame_count) = LineStartInClkCycles;
else
disp('Data not supported');
end
if (ishandle(h))
waitbar(frame_count/header.nframes, h);
else
h = waitbar(frame_count/header.nframes, 'Generando las senales RF.');
end
end
% Scaling factor (Optional)
Im = Im*1.5;
if or(header.filetype == 131072, header.filetype == 262144) %.gps
Im.gps_posx = gps_posx;
Im.gps_posy = gps_posy;
Im.gps_posz = gps_posz;
Im.gps_s = gps_s;
Im.gps_time = gps_time;
Im.gps_quality = gps_quality;
Im.gps_Zeros = Zeros;
if strcmp(version, '6.0.3')
Im.gps_a = gps_a;
Im.gps_e = gps_e;
Im.gps_r = gps_r;
Im.gps_q = gps_q;
end
end
pause(0.1);
if (ishandle(h))
delete(h);
end
fclose(fid);
% % for RF data, plot both the RF center line and image
% if(header.filetype == 16 || header.filetype == 512)
% RPviewrf(Im, header, 24);
%
% elseif(header.filetype == 128)
% PDRFLine = Im(:,:,1);
% figure, plot(PDRFLine, 'b');
% title('PW RF');
%
% elseif(header.filetype == 256)
% figure, imagesc(Im(:,:,1));
% colormap(gray);
% title('PW spectrum');
% end