use mat lab's Tiff class

flatironinstitute · May 8, 2018 · 11c91cf · 11c91cf
1 parent cfbcd44
commit 11c91cf
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Showing 2 changed files with 25 additions and 11 deletions.
diff --git a/apply_shifts.m b/apply_shifts.m
@@ -19,7 +19,7 @@
 if isa(Y,'char')
     [~,~,ext] = fileparts(Y);
     ext = ext(2:end);
-    if strcmpi(ext,'tif') || strcmpi(ext,'tiff');
+    if strcmpi(ext,'tif') || strcmpi(ext,'tiff')
         tiffInfo = imfinfo(Y);
         sizY = [tiffInfo(1).Height,tiffInfo(1).Width,length(tiffInfo)];
         filetype = 'tif';
@@ -30,7 +30,7 @@
         sizY = size(Y,'Y');
         details = whos(Y,'Y');
         data_type = details.class;
-    elseif strcmpi(ext,'hdf5') || strcmpi(ext,'h5');
+    elseif strcmpi(ext,'hdf5') || strcmpi(ext,'h5')
         filetype = 'hdf5';
         fileinfo = hdf5info(Y);
         data_name = fileinfo.GroupHierarchy.Datasets.Name;
@@ -87,7 +87,7 @@
 d1 = sizY(1); d2 = sizY(2);
 if nd == 2; d3 = 1; else d3 = sizY(3); end
 
-if strcmpi(options.shifts_method,'fft');
+if strcmpi(options.shifts_method,'fft')
     % precompute some quantities that are used repetitively for template matching and applying shifts
 
     [xx_s,xx_f,yy_s,yy_f,zz_s,zz_f,xx_us,xx_uf,yy_us,yy_uf,zz_us,zz_uf] = construct_grid(options.grid_size,options.mot_uf,options.d1,options.d2,options.d3,options.min_patch_size);
@@ -186,10 +186,11 @@
 for t = 1:bin_width:T
     switch filetype
         case 'tif'
-            Ytm = zeros(sizY(1),sizY(2),min(t+bin_width-1,T)-t+1,'single');
-            for tt = 1:min(t+bin_width-1,T)-t+1
-                Ytm(:,:,tt) = single(imread(Y,'Index',t+tt-1,'Info',tiffInfo));
-            end
+            Ytm = single(read_file(Y, t, min(t+bin_width-1,T)-t+1, [], tiffInfo));
+%             Ytm = zeros(sizY(1),sizY(2),min(t+bin_width-1,T)-t+1,'single');
+%             for tt = 1:min(t+bin_width-1,T)-t+1
+%                 Ytm(:,:,tt) = single(imread(Y,'Index',t+tt-1,'Info',tiffInfo));
+%             end
         case 'hdf5'
             Ytm = single(h5read(Y,data_name,[ones(1,length(sizY)-1),t],[sizY(1:end-1),min(t+bin_width-1,T)-t+1]));
         case 'mem'

diff --git a/read_file.m b/read_file.m
@@ -1,4 +1,4 @@
-function imData=read_file(path_to_file,sframe,num2read,options)
+function imData=read_file(path_to_file,sframe,num2read,options,im_info)
 
 % Reads uncompressed multipage .tiff, .hdf5, .avi or .raw files 
 % Usage:  my_data=read_file('path_to_data_file, start frame, num to read);
@@ -8,6 +8,8 @@
 % sframe:           first frame to read (optional, default: 1)
 % num2read:         number of frames to read (optional, default: read the whole file)
 % options:          options for reading .raw or .bin files
+% im_info:          information about the file (if already present)
+
 
 % OUTPUT:
 % imData:           data in array format 
@@ -19,9 +21,20 @@
 
 [~,~,ext] = fileparts(path_to_file);
 
-if strcmpi(ext,'.tiff') || strcmpi(ext,'.tif') || strcmpi(ext,'.btf');    
-    imData = loadtiff(path_to_file,sframe,num2read);    
-elseif strcmpi(ext,'.hdf5') || strcmpi(ext,'.h5');
+if strcmpi(ext,'.tiff') || strcmpi(ext,'.tif') || strcmpi(ext,'.btf')  
+    if ~exist('im_info','var')
+        im_info = imfinfo(path_to_file);
+    end
+    TifLink = Tiff(path_to_file, 'r');
+    num2read = min(num2read,length(im_info)-sframe+1);
+    imData = zeros(im_info(1).Height,im_info(1).Width,num2read,'like',TifLink.read());
+    for i=1:num2read
+       TifLink.setDirectory(i+sframe-1);
+       imData(:,:,i)=TifLink.read();
+    end
+    TifLink.close()
+    %imData = loadtiff(path_to_file,sframe,num2read);    
+elseif strcmpi(ext,'.hdf5') || strcmpi(ext,'.h5')
 %     info = hdf5info(path_to_file);
 %     dims = info.GroupHierarchy.Datasets.Dims;
 %     name = info.GroupHierarchy.Datasets.Name;