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Commit 16fa4386 authored by Eric Wait's avatar Eric Wait
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KLB format now will split files by channel, time, or both. Reader deals.

parent 14e31fe4
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src/MATLAB/+MicroscopeData/Reader.m
+ 2
− 2
View file @ 16fa4386
......@@ -43,8 +43,8 @@ function [im, imD] = Reader(varargin)
end
imPath = imD.imageDir;
klbFile = fullfile(imPath,[imD.DatasetName '.klb']);
if ( exist(klbFile,'file'))
klbFiles = dir(fullfile(imPath,[imD.DatasetName '*.klb']));
if ( ~isempty(klbFiles))
[im,imD] = MicroscopeData.ReaderKLB('imageData',imD, 'chanList',args.chanList, 'timeRange',args.timeRange, 'roi_xyz',args.roi_xyz, 'getMIP',args.getMIP,...
'outType',args.outType, 'normalize',args.normalize, 'imVersion',args.imVersion, 'verbose',args.verbose, 'prompt',false);
else
......
src/MATLAB/+MicroscopeData/ReaderKLB.m
+ 62
− 35
View file @ 16fa4386
......@@ -62,13 +62,14 @@ function [im, imD] = ReaderKLB(varargin)
args.roi_xyz(2,:) = min(args.roi_xyz(2,:),imD.Dimensions);
end
if (~exist(fullfile(imPath,[imD.DatasetName '.klb']),'file'))
klbList = dir(fullfile(imPath,[imD.DatasetName '*.klb']));
if (isempty(klbList))
warning('No image to read!');
return
end
try
inType = class(MicroscopeData.KLB.readKLBroi(fullfile(imPath,[imD.DatasetName '.klb']),ones(2,5)));
inType = class(MicroscopeData.KLB.readKLBroi(fullfile(imPath,klbList(1).name),ones(2,5)));
catch
warning('No images with at this data field!');
return
......@@ -111,6 +112,8 @@ function [im, imD] = ReaderKLB(varargin)
imSize(3) = 1;
end
prgs = Utils.CmdlnProgress(length(args.chanList)*length(args.timeRange(1):args.timeRange(2)),true);
if ( args.verbose )
orgSize = [imD.Dimensions(1),imD.Dimensions(2),imD.Dimensions(3),imD.NumberOfChannels,imD.NumberOfFrames];
fprintf('Reading %s (%d,%d,%d,%d,%d) %s %5.2fMB --> Into (%d,%d,%d,%d,%d) %s %5.2fMB,',...
......@@ -120,43 +123,21 @@ function [im, imD] = ReaderKLB(varargin)
imSize(1),imSize(2),imSize(3),imSize(4),imSize(5),args.outType,...
(prod(imSize)*outBytes)/(1024*1024));
prgs = Utils.CmdlnProgress(length(args.chanList),true);
drawnow
end
if (~strcmpi(args.outType,'logical'))
im = zeros(imSize, args.outType);
else
im = false(imSize);
end
tic
if (~convert && length(args.chanList)==imD.NumberOfChannels && length(args.timeRange(1):args.timeRange(2))==imD.NumberOfFrames)
im = MicroscopeData.KLB.readKLBstack(fullfile(imPath,[imD.DatasetName '.klb']));
else
for c=1:length(args.chanList)
for t=1:imSize(5)
tempIm = MicroscopeData.KLB.readKLBroi(fullfile(imPath,[imD.DatasetName '.klb']),...
[[Utils.SwapXY_RC(args.roi_xyz(1,:)), args.chanList(c), t+args.timeRange(1)-1];...
[Utils.SwapXY_RC(args.roi_xyz(1,:))+imSize(1:3)-1, args.chanList(c), t+args.timeRange(1)-1]]);
if (convert)
tempIm = ImUtils.ConvertType(tempIm,args.outType,args.normalize);
end
if (args.getMIP)
im(:,:,:,c,t) = max(tempIm,[],3);
else
im(:,:,:,c,t) = tempIm;
end
end
filePerC = ~isempty(regexp(klbList(1).name,'_c\d'));
filePerT = ~isempty(regexp(klbList(1).name,'_t\d+'));
prgsIn = [];
if (args.verbose)
prgs.PrintProgress(c);
end
end
prgsIn = prgs;
end
roi_xyz = args.roi_xyz;
roi_xyz(:,4) = [args.chanList(1);args.chanList(2)];
roi_xyz(:,5) = args.timeRange';
im = readKLBChunk(imD,args.outType,roi_xyz,filePerC,filePerT,prgsIn);
if (args.verbose)
prgs.ClearProgress(true);
end
......@@ -188,3 +169,49 @@ function [im, imD] = ReaderKLB(varargin)
imD.ChannelColors = [];
end
end
function im = readKLBChunk(imD,outType,roi_xyz,filePerC,filePerT,prgs)
im = zeros(Utils.SwapXY_RC(roi_xyz(2,:)-roi_xyz(1,:))+1,outType);
if (filePerC)
if (filePerT)
% individual image per c and t
i = 0;
for t=roi_xyz(1,5):roi_xyz(2,5)
for c=roi_xyz(1,4):roi_xyz(2,4)
fileName = sprintf('%s_c%d_t%04d.klb',imD.DatasetName,c,t);
im(:,:,:,c,t) = MicroscopeData.KLB.readKLBroi(fullfile(imD.imageDir,fileName), Utils.SwapXY_RC([[roi_xyz(1,1:3),1,1]; [roi_xyz(2,1:3),1,1]]));
i = i +1;
if (~isempty(prgs))
prgs.PrintProgress(i);
end
end
end
else
% only split by c
i=0;
for c=roi_xyz(1,4):roi_xyz(2,4)
fileName = sprintf('%s_c%d.klb',imD.DatasetName,c);
im(:,:,:,c,:) = MicroscopeData.KLB.readKLBroi(fullfile(imD.imageDir,fileName), Utils.SwapXY_RC([[roi_xyz(1,1:3),1,roi_xyz(1,5)]; [roi_xyz(2,1:3),1,roi_xyz(2,5)]]));
i = i +1;
if (~isempty(prgs))
prgs.PrintProgress(i*imD.NumberOfFrames);
end
end
end
elseif (filePerT)
% only split by t
i = 0;
for t=roi_xyz(1,5):roi_xyz(2,5)
fileName = sprintf('%s_t%04d.klb',imD.DatasetName,t);
im(:,:,:,:,t) = MicroscopeData.KLB.readKLBroi(fullfile(imD.imageDir,fileName), Utils.SwapXY_RC([[roi_xyz(1,1:4),1]; [roi_xyz(2,1:4),1]]));
i = i +1;
if (~isempty(prgs))
prgs.PrintProgress(i*imD.NumberOfChannels);
end
end
else
% only one file
im = MicroscopeData.KLB.readKLBroi(fullfile(imD.imageDir,[imD.DatasetName '.klb']),Utils.SwapXY_RC(roi_xyz));
end
end
src/MATLAB/+MicroscopeData/WriterKLB.m
+ 34
− 7
View file @ 16fa4386
......@@ -36,6 +36,8 @@ function WriterKLB(im, varargin)
addParameter(p,'chanList',[],@isvector);
addParameter(p,'timeRange',[],@(x)(numel(x)==2));
addParameter(p,'multiFile',false,@islogical);
addParameter(p,'filePerT',false,@islogical);
addParameter(p,'filePerC',false,@islogical);
addParameter(p,'verbose',false,@islogical);
......@@ -127,15 +129,40 @@ function WriterKLB(im, varargin)
im = ImUtils.ConvertType(im,outType,false);
end
fileName = fullfile(outDir,[args.imageData.DatasetName '.klb']);
tic
MicroscopeData.KLB.writeKLBstack(im, fileName, -1, [args.imageData.PixelPhysicalSize,1,1]);
fileName = fullfile(outDir,args.imageData.DatasetName);
prgs = Utils.CmdlnProgress(args.imageData.NumberOfChannels*args.imageData.NumberOfFrames,true);
if (args.filePerT)
if (args.filePerC)
for t=1:args.imageData.NumberOfFrames
for c=1:args.imageData.NumberOfChannels
fileNameCT = sprintf('%s_c%d_t%04d',fileName,c,t);
MicroscopeData.KLB.writeKLBstack(im(:,:,:,c,t), [fileNameCT,'.klb'], -1, [args.imageData.PixelPhysicalSize,1,1]);
prgs.PrintProgress(c+(t-1)*args.imageData.NumberOfChannels);
end
end
else
for t=1:args.imageData.NumberOfFrames
fileNameT = sprintf('%s_t%04d',fileName,t);
MicroscopeData.KLB.writeKLBstack(im(:,:,:,:,t), [fileNameT,'.klb'], -1, [args.imageData.PixelPhysicalSize,1,1]);
prgs.PrintProgress(t*args.imageData.NumberOfChannels);
end
end
elseif (args.filePerC)
for c=1:args.imageData.NumberOfChannels
fileNameC = sprintf('%s_c%d',fileName,c);
MicroscopeData.KLB.writeKLBstack(squeeze(im(:,:,:,c,:)), [fileNameC,'.klb'], -1, [args.imageData.PixelPhysicalSize,1,1]);
prgs.PrintProgress(c*args.imageData.NumberOfFrames);
end
else
MicroscopeData.KLB.writeKLBstack(im, [fileNameC,'.klb'], -1, [args.imageData.PixelPhysicalSize,1,1]);
end
if (args.verbose)
f = dir(fileName);
fprintf('Wrote %s %.0fMB-->%.0fMB in %s\n',...
prgs.ClearProgress(true);
f = dir([fileName,'*.klb']);
fBytes = sum([f.bytes]);
fprintf('Wrote %s %.0fMB-->%.0fMB\n',...
args.imageData.DatasetName,...
(bytes*prod(args.imageData.Dimensions)*args.imageData.NumberOfChannels*args.imageData.NumberOfFrames)/(1024*1024),...
f.bytes/(1024*1024),Utils.PrintTime(toc));
(bytes*prod(args.imageData.Dimensions)*args.imageData.NumberOfChannels*args.imageData.NumberOfFrames)/(1024*1024),fBytes/1024/1024);
end
end
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