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Author: tes24

Useful Functions/readTIFstack.m

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+function oimg = readTIFstack(path)
+
+% Copyright (c) 2012, YoonOh Tak
+% All rights reserved.
+
+% Redistribution and use in source and binary forms, with or without 
+% modification, are permitted provided that the following conditions are 
+% met:
+% 
+%     * Redistributions of source code must retain the above copyright 
+%       notice, this list of conditions and the following disclaimer.
+%     * Redistributions in binary form must reproduce the above copyright 
+%       notice, this list of conditions and the following disclaimer in 
+%       the documentation and/or other materials provided with the distribution
+%     * Neither the name of the Gwangju Institute of Science and Technology (GIST), Republic of Korea nor the names 
+%       of its contributors may be used to endorse or promote products derived 
+%       from this software without specific prior written permission.
+%       
+% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
+% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+% POSSIBILITY OF SUCH DAMAGE.
+
+s = warning('off', 'all'); % To ignore unknown TIFF tag.
+
+% Frame number
+tiff = Tiff(path, 'r');
+frame = 0;
+while true
+    frame = frame + 1;
+    if tiff.lastDirectory()
+        break;
+    end;
+    tiff.nextDirectory();
+end;
+
+k_struct = 0;
+tiff.setDirectory(1);
+for kf = 1:frame
+    if kf == 1
+        n1 = tiff.getTag('ImageWidth');
+        m1 = tiff.getTag('ImageLength');
+        spp1 = tiff.getTag('SamplesPerPixel');
+        sf1 = tiff.getTag('SampleFormat');
+        bpp1 = tiff.getTag('BitsPerSample');
+        if kf ~= frame
+            tiff.nextDirectory();
+        end;
+        continue;
+    end;
+    
+    n2 = tiff.getTag('ImageWidth');
+    m2 = tiff.getTag('ImageLength');
+    spp2 = tiff.getTag('SamplesPerPixel');
+    sf2 = tiff.getTag('SampleFormat');
+    bpp2 = tiff.getTag('BitsPerSample');
+    
+    if n1 ~= n2 || m1 ~= m2 || spp1 ~= spp2 || sf1 ~= sf2 || bpp1 ~= bpp2
+        k_struct = k_struct + 1;
+        tifstruct(k_struct).m = m1;
+        tifstruct(k_struct).n = n1;
+        tifstruct(k_struct).spp = spp1;
+        tifstruct(k_struct).frame = kf-1;
+        tifstruct(k_struct).data_type = DataType(sf1, bpp1);
+    end;
+   
+    if kf ~= frame
+        tiff.nextDirectory();
+    else
+        if k_struct > 0
+            k_struct = k_struct + 1;
+            tifstruct(k_struct).m = m2;
+            tifstruct(k_struct).n = n2;
+            tifstruct(k_struct).spp = spp2;
+            tifstruct(k_struct).frame = kf;
+            tifstruct(k_struct).data_type = DataType(sf2, bpp2);
+        end;
+    end;
+    n1 = n2; m1 = m2; spp1 = spp2; sf1 = sf2; bpp1 = bpp2;
+end;
+
+if k_struct == 0
+    if spp1 == 1
+        oimg = zeros(m1, n1, frame, DataType(sf1, bpp1)); % grayscle
+        for kf = 1:frame
+            tiff.setDirectory(kf);
+            oimg(:, :, kf) = tiff.read();
+        end;
+    else
+        oimg = zeros(m1, n1, spp1, frame, DataType(sf1, bpp1)); % color
+        for kf = 1:frame
+            tiff.setDirectory(kf);
+            oimg(:, :, :, kf) = tiff.read();
+        end;
+    end;
+else
+    k_cell = 1;
+    kf_start = 1;
+    for kc=1:k_struct
+        if tifstruct(kc).spp == 1
+            temp = zeros(tifstruct(kc).m, tifstruct(kc).n, tifstruct(kc).frame-kf_start+1, tifstruct(kc).data_type);
+            for kf=1:tifstruct(kc).frame-kf_start+1
+                tiff.setDirectory(kf+kf_start-1);
+                temp(:, :, kf) = tiff.read();
+            end;
+            oimg{k_cell} = temp; k_cell = k_cell+1;
+        else
+            temp = zeros(tifstruct(kc).m, tifstruct(kc).n, 3, tifstruct(kc).frame-kf_start+1, tifstruct(kc).data_type);
+            for kf=1:tifstruct(kc).frame-kf_start+1
+                tiff.setDirectory(kf+kf_start-1);
+                temp(:, :, :, kf) = tiff.read();
+            end;
+            oimg{k_cell} = temp; k_cell = k_cell+1;
+        end;
+        kf_start = tifstruct(kc).frame + 1;
+    end;
+end;
+
+tiff.close();
+
+warning(s);
+
+end
+
+function out = DataType(sf, bpp)
+switch sf
+    case 1
+        switch bpp
+            case 8
+                out = 'uint8';
+            case 16
+                out = 'uint16';
+            case 32
+                out = 'uint32';
+        end;
+    case 2
+        switch bpp
+            case 8
+                out = 'int8';
+            case 16
+                out = 'int16';
+            case 32
+                out = 'int32';
+        end;
+    case 3
+        switch bpp
+            case 32
+                out = 'single';
+            case 64
+                out = 'double';
+        end;
+end;
+
+end