Merge branch 'leverjs' of git-bioimage.coe.drexel.edu:bioimage/hydra-image-processor into leverjs

.gitattributes

-*.mexw64 filter=lfs diff=lfs merge=lfs -text
 *.mat filter=lfs diff=lfs merge=lfs -text
 *.ai filter=lfs diff=lfs merge=lfs -text
 *.png filter=lfs diff=lfs merge=lfs -text
+*.mexw64 filter=lfs diff=lfs merge=lfs -text
+*.mexa64 filter=lfs diff=lfs merge=lfs -text
+*.pyd filter=lfs diff=lfs merge=lfs -text
+*.so filter=lfs diff=lfs merge=lfs -text

src/MATLAB/+ImarisProc/CC_BatchSkeleton.m

-%Skeleton for Imaris batch in Matlab
-
-%ImarisLib.jar needs to be in the same folder.
-%Imaris needs to be running when executing the following code 
-
-%CC 2018-01-03 tested with Imaris 9.1.0 
-
-%Get the image folder. Only read *.ims images.
-infolder = uigetdir;
-files = [infolder '/*.ims'];
-listing = dir(files);
-nfiles = size(listing,1);
-
-%open files in Imaris sequentially
-for i = 1:nfiles
-    
-    filename = [infolder '/' listing(i).name];
-    filename = sprintf(filename);
-    vImarisApplication = StartImaris;
-    vImarisApplication.FileOpen(filename,'');
-    
-    %get dataset in Matlab
-    vDataSet = vImarisApplication.GetDataSet;
-    
-    %apply median filter to dataset
-    vImarisApplication.GetImageProcessing.MedianFilterChannel(vDataSet,0,[5 5 5]);
-    
-    %create Surfaces
-    ip = vImarisApplication.GetImageProcessing;
-    vNewSurfaces = ip.DetectSurfaces(vDataSet, [], 0, 1, 0, true, 0, '');
-    vNewSurfaces.SetName(sprintf('New Surface'));
-    vImarisApplication.GetSurpassScene.AddChild(vNewSurfaces,-1);
-    
-    %get Surface stats 
-    vSurpassComponent = vImarisApplication.GetSurpassSelection;
-    vImarisObject = vImarisApplication.GetFactory.ToSurfaces(vSurpassComponent);
-    vAllStatistics = vImarisObject.GetStatistics;
-    vNames = cell(vAllStatistics.mNames);
-    vValues = vAllStatistics.mValues;
-    disp(unique(vNames))
-    
-    %save ims file
-    newFilename = strcat(filename(1:end-4),'new.ims');
-    vImarisApplication.FileSave(newFilename,'');
-    
-    pause(5);
-    
-    %Clear java handles to clear up memory and prevent future errors
-    clear 'Imaris/IApplicationPrxHelper';
-    clear 'Imaris/IDataSetPrxHelper';
-    clear 'Imaris/IDataContainerPrxHelper';
-    clear 'Imaris/IDataItemPrxHelper';
-    clear 'Imaris/cStatisticValues';
-    clear 'ImarisLib';
-    clear 'vSurpassScene';
-    clear 'vDataSet';
-    clear 'vAllStatistics';
-    clear 'err';
-end
-
-%Quit Imaris Application after all is done
-vImarisApplication.SetVisible(~vImarisApplication.GetVisible);
-vImarisApplication.Quit;
-
-function aImarisApplication = StartImaris
-    javaaddpath ImarisLib.jar;
-    vImarisLib = ImarisLib;
-    server = vImarisLib.GetServer();
-    id = server.GetObjectID(0);
-    aImarisApplication = vImarisLib.GetApplication(id);
-    disp(id)
-end
\ No newline at end of file

src/MATLAB/+ImarisProc/ContrastEnhancement.m

-function ContrastEnhancement(imarisAppID)
-    imarisHandle = ImarisHelper.GetAppHandle(imarisAppID);
-    if (isempty(imarisHandle))
-        error('Imaris is not open or the wrong app id!');
-    end
-    
-    imarisDataset = imarisHandle.GetDataSet();
-    physicalSize = ImarisHelper.GetPhysicalSize(imarisDataset);
-    normSize = physicalSize./max(physicalSize);
-    defaultSigs = 35.*normSize;
-    defaultSigsStr = sprintf('[%.2f,%.2f,%.2f]',defaultSigs(1),defaultSigs(2),defaultSigs(3));
-    
-    prompts = {'Enter Channel:','Enter Gaussian Sigmas:','Enter Median Neighborhood:','Inplace:(false=0,true=1)'};
-    dlgTitle = 'Contrast Enhancement';
-    numLines = 1;
-    defaultAns = {'1',defaultSigsStr,'[3,3,3]','0'};
-    answer = inputdlg(prompts,dlgTitle,numLines,defaultAns);
-    
-    if (isempty(answer))
-        return
-    end
-    
-    chan = str2double(answer{1});
-    sigsStr = regexp(answer{2},'\[(.*),(.*),(.*)\]','tokens');
-    sigs = abs(cellfun(@(x)(str2double(x)),sigsStr{1}));
-    medStr = regexp(answer{3},'\[(.*),(.*),(.*)\]','tokens');
-    medNeighborhood = cellfun(@(x)(str2double(x)),medStr{1});
-    medNeighborhood = abs(round(medNeighborhood));
-    
-    inplace = str2double(answer{4})>0;
-    outChannel = ImarisHelper.GetNumChannels(imarisDataset) +1;
-    if (inplace)
-        outChannel = chan;
-    end
-
-    imarisHandle.DataSetPushUndo('Contrast Enhancement');
-    
-    % TODO see if there is enough memory to just capture the entire series
-    % to process faster
-    
-    numFrames = ImarisHelper.GetNumFrames(imarisDataset);
-    im = ImarisHelper.GetImageData(imarisDataset,chan,1:numFrames);
-    prgs = Utils.CmdlnProgress(numFrames,true,'smooth');
-    for t=1:numFrames
-        im(:,:,:,1,t) = ImProc.ContrastEnhancement(im(:,:,:,1,t),sigs,medNeighborhood);
-        prgs.PrintProgress(t);
-    end
-    prgs.ClearProgress(true);
-    imarisDataset = ImarisHelper.SetImage(imarisHandle,imarisDataset,im,outChannel,1:t);
-end

src/MATLAB/sandbox.m

-im = tiffReader('DAPI Olig2-514 GFAP-488 Dcx-647 Laminin-Cy3 Bcatenin-568 20x1 TopLeft');
\ No newline at end of file

src/MATLAB/showIm.m

-%% print out image
-function showIm(image,label)
-figure
-imagesc(max(image,[],3))
-
-% set(gcf,'Units','normalized');
-% set(gcf,'Position',[0 0 1 1]);
-
-colormap gray
-
-title(label)
-axis image
-end

src/MATLAB/template.m

-function [cTime,mTime,kernelName] = (im,)
-    kernelName = '';
-    cT = tic;
-    imC = HIP.(im,);
-    cTime = toc(cT);
-
-    mT = tic;
-    imM = HIP.(im,,true);
-    mTime = toc(mT);
-end

src/MATLAB/testChunking.m

-figure
-
-plot(0,0,'.w');
-ax = gca;
-hold on
-
-for i=1:length(imChunks)
-    curChunk = imChunks(i);
-    
-    Utils.PlotBox(ax,Utils.SwapXY_RC(curChunk.ImageStart_rc),Utils.SwapXY_RC(curChunk.ImageEnd_rc),'-b',num2str(i));
-    Utils.PlotBox(ax,Utils.SwapXY_RC(curChunk.ImageROIstart_rc),Utils.SwapXY_RC(curChunk.ImageROIend_rc),'--r');
-    Utils.PlotBox(ax,...
-        Utils.SwapXY_RC(curChunk.ImageStart_rc) + Utils.SwapXY_RC(curChunk.ChunkROIstart_rc) - 1,...
-        Utils.SwapXY_RC(curChunk.ImageStart_rc) + Utils.SwapXY_RC(curChunk.ChunkROIstart_rc) -1 + (Utils.SwapXY_RC(curChunk.ChunkROIend_rc)-Utils.SwapXY_RC(curChunk.ChunkROIstart_rc)-1),...
-        ':g');
-end
-axis ij
-axis equal

src/c/Cuda/CudaLoG.cuh

@@ -70,6 +70,7 @@ void cLoG(ImageView<PixelTypeIn> imageIn, ImageView<float> imageOut, Vec<double>
 			{
 				if (!chunks[i].sendROI(imageIn, deviceImages.getCurBuffer()))
 					std::runtime_error("Error sending ROI to device!");
+
 				cudaMultiplySumBias<<<chunks[i].blocks, chunks[i].threads >> > (*(deviceImages.getCurBuffer()), *(deviceImages.getNextBuffer()), constLoGKernelMem_x, MIN_VAL, MAX_VAL, constGausKernelMem_x, true);
 				deviceImages.incrementBuffer();
 				if (sigmas.y!=0)
@@ -91,6 +92,7 @@ void cLoG(ImageView<PixelTypeIn> imageIn, ImageView<float> imageOut, Vec<double>
 			{
 				if (!chunks[i].sendROI(imageIn, deviceImages.getCurBuffer()))
 					std::runtime_error("Error sending ROI to device!");
+
 				if (sigmas.x!=0)
 				{
 					cudaMultiplySum << <chunks[i].blocks, chunks[i].threads >> > (*(deviceImages.getCurBuffer()), *(deviceImages.getNextBuffer()), constGausKernelMem_x, MIN_VAL, MAX_VAL);
@@ -112,6 +114,7 @@ void cLoG(ImageView<PixelTypeIn> imageIn, ImageView<float> imageOut, Vec<double>
 			{
 				if (!chunks[i].sendROI(imageIn, deviceImages.getCurBuffer()))
 					std::runtime_error("Error sending ROI to device!");
+
 				if (sigmas.x!=0)
 				{
 					cudaMultiplySum << <chunks[i].blocks, chunks[i].threads >> > (*(deviceImages.getCurBuffer()), *(deviceImages.getNextBuffer()), constGausKernelMem_x, MIN_VAL, MAX_VAL);