Add progress bar for CZIReader

+imageIO/@BioReader/getDataNoTiles.m

@@ -63,7 +63,7 @@ for s = stacks
     idxT = 1;
     for t = timeseries
       % update progress bar
-      currNum = t + (idxCh-1)*nT + (idxS-1)*nCh*nT;
+      currNum = idxT + (idxCh-1)*nT + (idxS-1)*nCh*nT;
       progBar.update(currNum/maxNum * 100);
       
       %set index

+imageIO/@BioReader/getTiledData.m

@@ -87,7 +87,7 @@ for s = stacks
       for row = tileRow
         for col = tileCol
           % update progress bar
-          currNum = t + (idxCh-1)*nT + (idxS-1)*nCh*nT + ...
+          currNum = idxT + (idxCh-1)*nT + (idxS-1)*nCh*nT + ...
               (col-1)*nS*nCh*nT + (row-1)*nC*nS*nCh*nT;
           progBar.update(currNum/maxNum * 100);
           %set series

+imageIO/@CZIReader/getAllData.m

@@ -5,6 +5,9 @@ function [ data ] = getAllData( obj )
 % AUTHOR: Stefano Masneri
 % Date: 13.10.2016
 
+progBar = TextProgressBar('BioReader --> Extracting data: ', 30);
+numDirEntries = length(obj.directoryEntries);
+
 if obj.wrongMetadata
   %initialize data
   data = zeros(obj.height, obj.width, obj.channels, obj.stacks, obj.time, ...
@@ -12,7 +15,9 @@ if obj.wrongMetadata
  
   %now browse through directory entries again, and extract the subblocks
   % Now go through all the directory entries
-  for k = 1:length(obj.directoryEntries)
+  for k = 1:numDirEntries
+    progBar.update(k/numDirEntries * 100);
+    
     dirEntry = obj.directoryEntries(k);
     % Get image
     tmpImg = obj.readRawSubblockSegm('dirEntry', dirEntry);
@@ -36,7 +41,9 @@ else
     obj.series, obj.datatype);
 
   % Now go through all the directory entries
-  for k = 1:length(obj.directoryEntries)
+  for k = 1:numDirEntries
+    progBar.update(k/numDirEntries * 100);
+    
     dirEntry = obj.directoryEntries(k);
     % Get image
     tmpImg = obj.readRawSubblockSegm('dirEntry', dirEntry);

+imageIO/@CZIReader/getDataNoTiles.m

@@ -47,6 +47,15 @@ series = p.Results.S;
 data = zeros(length(rows), length(cols), length(channels), length(stacks), ...
   length(timeseries), length(series), obj.datatype);
 
+% get numelements in each dimension
+nS = numel(stacks);
+nCh = numel(channels);
+nT = numel(timeseries);
+maxNum = nS * nCh * nT;
+
+% define progress bar
+progBar = TextProgressBar('BioReader --> Extracting data: ', 30);
+
 idxZ = 1;
 for z = stacks
   idxCh = 1;
@@ -55,6 +64,10 @@ for z = stacks
     for t = timeseries
       idxS = 1;
       for s = series
+        % update progress bar
+        currNum = idxS + (idxT-1)*nS + (idxCh-1)*nT*nS;
+        progBar.update(currNum/maxNum * 100);
+        
         %get directory entry
         dirEntry = obj.directoryEntries(obj.dirEntryIndices{ch, z, t, s});
         tmpImg = obj.readRawSubblockSegm('dirEntry', dirEntry);

+imageIO/@CZIReader/getTiledData.m

@@ -68,6 +68,16 @@ sizeCols = round(length(cols) * (1 + (length(tileCols) - 1) * (1 - obj.tileOverl
 data = zeros(sizeRows, sizeCols, length(channels), length(stacks), ...
   length(timeseries), length(series), obj.datatype);
 
+% get numelements in each dimension
+nZ = numel(stacks);
+nC = numel(channels);
+nT = numel(timeseries);
+nS = numel(series);
+maxNum = nZ * nC * nT * nS;
+
+% define progress bar
+progBar = TextProgressBar('BioReader --> Extracting data: ', 30);
+
 %get index of start of each new tile
 pixelStartTileRow = 1 + round((0:length(tileRows)-1) * (1 - obj.tileOverlap) * length(rows));
 pixelStartTileCol = 1 + round((0:length(tileCols)-1) * (1 - obj.tileOverlap) * length(cols));
@@ -82,6 +92,11 @@ for z = stacks
     for t = timeseries
       idxS = 1;
       for s = series
+        % update progress bar
+        currNum = idxS + (idxT-1)*nS + (idxCh-1)*nS*nT + ...
+          (idxZ-1)*nS*nC*nT;
+        progBar.update(currNum/maxNum * 100);
+        
         %get directory entry
         dirEntries = obj.directoryEntries(obj.dirEntryIndices{ch, z, t, s});
         for k = 1:length(dirEntries)