unify different file types

NoRMCorreSetParms.m

@@ -46,6 +46,8 @@
     'use_windowing      ' % flag for windowing data before fft (default: false)
     'window_length      ' % length of window on each side of the signal as a fraction of signal length
                            %    total length = length(signal)(1 + 2*window_length). (default: 0.5)
+    % bitsize for reading .raw files
+    'bitsize            ' % (default: 2 (uint16). other choices 1 (uint8), 4 (single), 8 (double))
    ]; 
 
 [m,n] = size(Names);
@@ -164,6 +166,8 @@
     % use_windowing
     {false}
     {0.5}
+    % bitsize for reading .raw files
+    {2}
     ];
 
 for j = 1:m

apply_shifts.m

@@ -35,8 +35,8 @@
     elseif strcmpi(ext,'raw')
         filetype = 'raw';
         fid = fopen(Y);
-        FOV = [512,512];
-        bitsize = 2;
+        FOV = [options.d1,options.d2];
+        bitsize = options.bitsize;
         imsize = FOV(1)*FOV(2)*bitsize;                                                   % Bit size of single frame
         current_seek = ftell(fid);
         fseek(fid, 0, 1);

demo.m

@@ -12,7 +12,7 @@
     fprintf('done.');
 end
 
-tic; Y = loadtiff(name); toc; % read the file (optional, you can also pass the path in the function instead of Y)
+tic; Y = read_file(name); toc; % read the file (optional, you can also pass the path in the function instead of Y)
 Y = double(Y);      % convert to double precision 
 T = size(Y,ndims(Y));
 %Y = Y - min(Y(:));

normcorre_batch.m

@@ -36,6 +36,19 @@
         data_name = fileinfo.GroupHierarchy.Datasets.Name;
         sizY = fileinfo.GroupHierarchy.Datasets.Dims;
         T = sizY(end);
+    elseif strcmpi(ext,'raw')
+        filetype = 'raw';
+        fid = fopen(Y);
+        FOV = [options.d1,options.d2];
+        bitsize = options.bitsize;
+        imsize = FOV(1)*FOV(2)*bitsize;                                                   % Bit size of single frame
+        current_seek = ftell(fid);
+        fseek(fid, 0, 1);
+        file_length = ftell(fid);
+        fseek(fid, current_seek, -1);
+        T = file_length/imsize;
+        sizY = [FOV,T];
+        fclose(fid);        
     end    
 elseif isobject(Y);
     filetype = 'mem';
@@ -234,6 +247,8 @@
             case 'mat'
                 if nd == 2; Ytm = single(Y(:,:,t:min(t+bin_width-1,T))); end
                 if nd == 3; Ytm = single(Y(:,:,:,t:min(t+bin_width-1,T))); end
+            case 'raw'
+                Ytm = single(read_raw_file(Y,t,min(t+bin_width-1,T)-t+1,FOV,bitsize));                
         end
 
         if nd == 2; Ytc = mat2cell(Ytm,d1,d2,ones(1,size(Ytm,ndims(Ytm)))); end
@@ -412,4 +427,4 @@
     M_final.template = template;
 end
 maxNumCompThreads('automatic');
-end
+end

read_file.m

@@ -1,24 +1,26 @@
-function imData=read_file(path_to_file,sframe,num2read)
+function imData=read_file(path_to_file,sframe,num2read,options)
 
-% Reads uncompressed multipage .tiff, .hdf5, or .avi files 
+% Reads uncompressed multipage .tiff, .hdf5, .avi or .raw files 
 % Usage:  my_data=read_file('path_to_data_file, start frame, num to read);
 
 % INPUTS:
 % path_to_file:     location of file to be read
 % 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
 
 % OUTPUT:
 % imData:           data in array format 
 
 % Written by Eftychios A. Pnevmatikakis, Simons Foundation
 
 if nargin<2 || isempty(sframe); sframe = 1; end
+if nargin<3 || isempty(num2read); num2read = Inf; end
 
 [~,~,ext] = fileparts(path_to_file);
 
 if strcmpi(ext,'.tiff') || strcmpi(ext,'.tif');    
-    imData = loadtiff(path_to_file);    
+    imData = loadtiff(path_to_file,sframe,num2read);    
 elseif strcmpi(ext,'.hdf5') || strcmpi(ext,'.h5');
 %     info = hdf5info(path_to_file);
 %     dims = info.GroupHierarchy.Datasets.Dims;
@@ -50,6 +52,17 @@
             break;
         end
     end
+elseif strcmpi(ext,'.raw')
+    if nargin < 4 || ~isfield(options,'d1') || isempty(options.d1);
+        options.d1 = input('What is the total number of rows? \n');
+    end
+    if nargin < 4 || ~isfield(options,'d2') || isempty(options.d2);
+        options.d2 = input('What is the total number of columns? \n');
+    end
+    if nargin < 4 || ~isfield(options,'bitsize') || isempty(options.bitsize);
+        options.bitsize = 2;
+    end   
+    imData = read_raw_file(path_to_file,sframe,num2read,[options.d1,options.d2],options.bitsize);
 else
     error('Unknown file extension. Only .tiff, .avi and .hdf5 files are currently supported');
 end

read_raw_file.m

@@ -1,6 +1,6 @@
 function A = read_raw_file(filename,framenum,window,FOV,bitsize)
 
-%% Starting from frame number: 'framenum', read 'window' number of frames and get their average 
+%% Starting from frame number: 'framenum', read 'window'
 fid = fopen(filename);
 imsize = FOV(1)*FOV(2)*bitsize;                                                   % Bit size of single frame