Commit d4ba0a6e161ab56c7ce1412a5c8d389ecc3bdfc5
Merge branch 'spe' into 'master'
added support for Wei's SPE files See merge request !7
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| 1 | +% Read images of TIFF, SPE2.2(WinSpec) and SPE3.0(Lightfield) | ||
| 2 | +% Version: JTL Jun-9-2016 | ||
| 3 | +% ----------------- READ THIS FIRST !!!!! -------------------------------- | ||
| 4 | +% Change the file name to "readspe" before use | ||
| 5 | +% Example: | ||
| 6 | +% Z = readspe(filename) | ||
| 7 | +% Z = readspe(filename,'info') | ||
| 8 | +% Z = readspe(filename,frame_index) | ||
| 9 | +% Z = readspe(filename,frame_index,'info') | ||
| 10 | +% Input: | ||
| 11 | +% filename - filename string, e.g. 'image.spe' | ||
| 12 | +% frame_index - frame index, start from 1 | ||
| 13 | +% If you have multiple frames, use a "for" loop | ||
| 14 | +% 'info' - flag to show file info, i.e. dimension, number of frames, version | ||
| 15 | +% Output: | ||
| 16 | +% Z - UINT16 image (convert to double if you need) | ||
| 17 | +% ------------------------------------------------------------------------ | ||
| 18 | +% Z = readspe (filename,frame_index,'info') | ||
| 19 | +function Z = readspe (filename,varargin) | ||
| 20 | + | ||
| 21 | +if exist(filename) == 2 | ||
| 22 | + | ||
| 23 | + Nfr = 1; % default read first frame | ||
| 24 | + if nargin >1 | ||
| 25 | + if isa(varargin{1},'numeric') | ||
| 26 | + Nfr = varargin{1}; | ||
| 27 | + end | ||
| 28 | + end | ||
| 29 | + | ||
| 30 | + [~,name,ext] = fileparts(filename); | ||
| 31 | + switch upper(ext) | ||
| 32 | + case '.TIFF' | ||
| 33 | + file_ver = 'TIFF'; | ||
| 34 | + Z = imread(filename); | ||
| 35 | + [Y,X] = size(Z); | ||
| 36 | + % datatype = class(Z) | ||
| 37 | + | ||
| 38 | + case '.SPE' | ||
| 39 | + fid = fopen(filename); | ||
| 40 | + I = fread(fid,Inf,'uint8'); | ||
| 41 | + X = double(typecast(uint8(I(43:44)),'uint16')); | ||
| 42 | + Y = double(typecast(uint8(I(657:658)),'uint16')); | ||
| 43 | + fr = typecast(uint8(I(1447:1450)),'int32'); | ||
| 44 | + spe_ver = typecast(uint8(I(1993:1996)),'single'); | ||
| 45 | + file_ver = ['SPE ' num2str(spe_ver)]; | ||
| 46 | + datatypeN = typecast(uint8(I(109:110)),'int16'); | ||
| 47 | + switch datatypeN | ||
| 48 | + case 0 % 32-bit float | ||
| 49 | + datatype = 'single'; datalength = 4; | ||
| 50 | + case 1 % 32-bit signed integer | ||
| 51 | + datatype = 'int32'; datalength = 4; | ||
| 52 | + case 2 % 16-bit signed integer | ||
| 53 | + datatype = 'int16'; datalength = 2; | ||
| 54 | + case 3 % 16-bit unsigned integer | ||
| 55 | + datatype = 'uint16'; datalength = 2; | ||
| 56 | + case 8 % 32-bit unsigned integer | ||
| 57 | + datatype = 'uint32'; datalength = 4; | ||
| 58 | + end | ||
| 59 | + % A = I(4101:4100+X*Y*2); % Default read first frame | ||
| 60 | + A = I(4101+X*Y*datalength*(Nfr-1):4100+X*Y*datalength*Nfr); | ||
| 61 | + B = typecast(uint8(A),datatype); % important | ||
| 62 | + Z = reshape(B,X,Y); | ||
| 63 | + Z = Z'; | ||
| 64 | + fclose(fid); | ||
| 65 | + end | ||
| 66 | + | ||
| 67 | + if nargin >1 | ||
| 68 | + if varargin{end} == 'info' | ||
| 69 | + display(['X = ' num2str(X)]); | ||
| 70 | + display(['Y = ' num2str(Y)]); | ||
| 71 | + if(exist('fr','var'));display(['Number of Frames: ' num2str(fr)]);end; | ||
| 72 | + display(['File version: ' file_ver]); | ||
| 73 | + end | ||
| 74 | + end | ||
| 75 | + | ||
| 76 | +elseif exist(filename) == 0 | ||
| 77 | + display('File does not exist!'); | ||
| 78 | +end | ||
| 0 | \ No newline at end of file | 79 | \ No newline at end of file |
| 1 | +function spe2envi(filemask, outfile) | ||
| 2 | + | ||
| 3 | + filelist = dir(filemask); | ||
| 4 | + | ||
| 5 | + %get a list of date numbers | ||
| 6 | + datenums = cell2mat({filelist.datenum}); | ||
| 7 | + | ||
| 8 | + %sort the file order based on acquisition time | ||
| 9 | + [~, id] = sort(datenums); | ||
| 10 | + | ||
| 11 | + %get the number of files | ||
| 12 | + Y = length(id); %size of the image along Y | ||
| 13 | + | ||
| 14 | + %load the first file to determine the spectral and X-axis size | ||
| 15 | + temp = readspe(filelist(1).name); | ||
| 16 | + X = size(temp, 1); %size of the image along X | ||
| 17 | + B = size(temp, 2); %number of bands in the image | ||
| 18 | + | ||
| 19 | + %create the cube | ||
| 20 | + I = zeros(X, Y, B); | ||
| 21 | + | ||
| 22 | + %for each line | ||
| 23 | + for y = 1:Y | ||
| 24 | + | ||
| 25 | + %read a SPE file | ||
| 26 | + img = readspe(filelist(id(y)).name); | ||
| 27 | + | ||
| 28 | + I(:, y, :) = permute(img, [1 3 2]); | ||
| 29 | + end | ||
| 30 | + | ||
| 31 | + enviSaveRaw(single(I), outfile, [outfile '.hdr']); | ||
| 32 | + | ||
| 33 | + | ||
| 34 | + |