tests for linux and windows10 passed

src/f_CloneClassifier.m

@@ -5,7 +5,6 @@ function [Objects, Preview] = f_CloneClassifier(row, col, ch1Green, ch2Red, ch3B
     %% Image analysis
 
     % Red pos
-    %RedLP = imfilter(ch1Green, fspecial('gaussian', 60, 20), 'symmetric');
     RedLP = imfilter(ch2Red, fspecial('gaussian', 21, 7), 'symmetric');
     %it(ch2Red)
     %it(RedLP)
@@ -13,10 +12,8 @@ function [Objects, Preview] = f_CloneClassifier(row, col, ch1Green, ch2Red, ch3B
     %it(RedPosMask)
 
     % Green Pos
-    %GreenLP = imfilter(ch2Red, fspecial('gaussian', 21, 7), 'symmetric');
     GreenLP = imfilter(ch1Green, fspecial('gaussian', 60, 20), 'symmetric');
     %it(GreenLP)
-    %GreenPosMask = GreenLP > 150;
     GreenPosMask = GreenLP > 200;
     %it(GreenPosMask)
 
@@ -43,15 +40,7 @@ function [Objects, Preview] = f_CloneClassifier(row, col, ch1Green, ch2Red, ch3B
     Objects.ROW = row;
     Objects.COL = col;
 
-%     if (Objects.AreaRedPos / Objects.Area > 0.5) & ~(Objects.AreaGreenPos / Objects.Area > 0.5) & (Objects.Area >= 1e5)
-%         Class = 'Red';
-%     elseif ~(Objects.AreaRedPos / Objects.Area > 0.5) & (Objects.AreaGreenPos / Objects.Area > 0.5) & (Objects.Area >= 1e5)
-%         Class = 'Green';
-%     elseif (Objects.AreaRedPos / Objects.Area > 0.5) & (Objects.AreaGreenPos / Objects.Area > 0.5) & (Objects.Area >= 1e5)
-%         Class = 'RedGreen';
-%     else
-%         Class = 'Neg';
-%     end
+
     if Objects.AreaBluePos / Objects.Area > 0.5
         Class = 'Blue';
     else
@@ -69,11 +58,9 @@ function [Objects, Preview] = f_CloneClassifier(row, col, ch1Green, ch2Red, ch3B
     Objects.Class = {Class};
 
     %% Previews
-
-    %RGB = cat(3, imadjust(ch2Red, [0 0.01], [0 1]), imadjust(ch1Green, [0 0.01], [0 1]), zeros(size(ch1Green), 'uint16'));
     RGB = cat(3, imadjust(ch2Red, [0 0.01], [0 1]), imadjust(ch1Green, [0 0.01], [0 1]),  imadjust(ch3Blue, [0 0.02], [0 1]));
     % imtool(RGB)
-    Preview = imoverlay2(RGB, imdilate(bwperim(SamplingZone), strel('disk', 10)), [1 1 1]);
+    Preview = imoverlay(RGB, imdilate(bwperim(SamplingZone), strel('disk', 10)), [1 1 1]);
     Preview = insertText(Preview, [1 1], Class, 'FontSize', 200, 'BoxColor', 'black', 'TextColor', 'white');
     Preview = imresize(Preview, 1/ShrinkFactor);
     % imtool(Preview)

src/f_Local_Read_Files_Timeseries_Mosaic_BT2.m

@@ -13,9 +13,7 @@ TimepointsTableFilter = cellfun(@(x) ~isempty(x), TimepointsTableClean.Fun_name,
 TimepointsTableFilter = cell2mat(TimepointsTableFilter);
 TimepointsTableClean2 = TimepointsTable(TimepointsTableFilter, TimepointsTable.Properties.VariableNames);
 TimepointFolders = TimepointsTableClean2.name;
-%files = dirrec([hcsDrive, ':\OperaArchiveCol\OB 20141022_MDPD1_3Stains_2Controls', '\', TimepointFolders{timepoint}], '.flex');
 files = dirrec([hcsPath, filesep, barcode, filesep, TimepointFolders{timepoint}], '.flex');
-%[info, areaNames, plateLayout, areaMap] = flexinfo(files);
 [info, areaNames, plateLayout, areaMap] = flexinfoMosaic(files);
 
 end

src/f_LogDependencies.m

@@ -13,7 +13,11 @@ function [FileList] = f_LogDependencies(Name, SavePath)
     FileCount = size(FileList,1);
 
     for i = 1:FileCount
-        FileThis = regexp(FileList{i}, '\\.*\\(.*)', 'tokens'); FileThis = FileThis{:}{:};
+        try % Windows
+            FileThis = regexp(FileList{i}, '\\.*\\(.*)', 'tokens'); FileThis = FileThis{:}{:};
+        catch % Mac
+            FileThis = regexp(FileList{i}, '/.*/(.*)', 'tokens'); FileThis = FileThis{:}{:};
+        end
         SavePathThisFile = [SavePath, filesep, FileThis];
         copyfile(FileList{i}, SavePathThisFile);
     end

src/imoverlay2.m

-function out = imoverlay2(in, mask, color)
-%IMOVERLAY Create a mask-based image overlay.
-%   OUT = IMOVERLAY(IN, MASK, COLOR) takes an input image, IN, and a binary
-%   image, MASK, and produces an output image whose pixels in the MASK
-%   locations have the specified COLOR.
-%
-%   IN should be a grayscale or an RGB image of class uint8, uint16, int16,
-%   logical, double, or single.  If IN is double or single, it should be in
-%   the range [0, 1].  If it is not in that range, you might want to use
-%   mat2gray to scale it into that range.
-%
-%   MASK should be a two-dimensional logical matrix.
-%
-%   COLOR should be a 1-by-3 vector of values in the range [0, 1].  [0 0 0]
-%   is black, and [1 1 1] is white.
-%
-%   OUT is a uint8 RGB image.
-%
-%   Examples
-%   --------
-%   Overlay edge detection result in green over the original image.
-%       
-%       I = imread('cameraman.tif');
-%       bw = edge(I, 'canny');
-%       rgb = imoverlay(I, bw, [0 1 0]);
-%       imshow(rgb)
-%
-%   Treating the output of peaks as an image, overlay the values greater than
-%   7 in red.  The output of peaks is not in the usual grayscale image range
-%   of [0, 1], so use mat2gray to scale it.
-%
-%       I = peaks;
-%       mask = I > 7;
-%       rgb = imoverlay(mat2gray(I), mask, [1 0 0]);
-%       imshow(rgb, 'InitialMagnification', 'fit')
-
-%   Steven L. Eddins
-%   Copyright 2006-2012 The MathWorks, Inc.
-
-% If the user doesn't specify the color, use white.
-DEFAULT_COLOR = [1 1 1];
-if nargin < 3
-    color = DEFAULT_COLOR;
-end
-
-% Force the 2nd input to be logical.
-mask = (mask ~= 0);
-
-% Make the uint8 the working data class.  The output is also uint8.
-in_uint8 = im2uint8(in);
-color_uint8 = im2uint8(color);
-
-% Initialize the red, green, and blue output channels.
-if ndims(in_uint8) == 2
-    % Input is grayscale.  Initialize all output channels the same.
-    out_red   = in_uint8;
-    out_green = in_uint8;
-    out_blue  = in_uint8;
-else
-    % Input is RGB truecolor.
-    out_red   = in_uint8(:,:,1);
-    out_green = in_uint8(:,:,2);
-    out_blue  = in_uint8(:,:,3);
-end
-
-% Replace output channel values in the mask locations with the appropriate
-% color value.
-out_red(mask)   = color_uint8(1);
-out_green(mask) = color_uint8(2);
-out_blue(mask)  = color_uint8(3);
-
-% Form an RGB truecolor image by concatenating the channel matrices along
-% the third dimension.
-out = cat(3, out_red, out_green, out_blue);

src/main.m

@@ -7,7 +7,7 @@ clc
 
 InPath = ['..', filesep, 'dataIn'];
 SavePath = ['..', filesep, 'dataOut'];
-Barcode = {'HO_20180320_Subcloning_snca4correction_1'};
+Barcode = {'HO_20170921_Subcloning_YEL1'};
 DisplayChannel = 1;
 
 %% Initialize variables and prepare Java environment
@@ -28,7 +28,7 @@ for n = 1:size(Barcode, 2)
 
     SavePathThisBarcode = [SavePath, filesep, Barcode];
     AnalysisTimeStamp = datestr(now, 'yyyymmdd_HHMMSS');
-    SavePath = [SavePathThisBarcode, '\Analysis_', AnalysisTimeStamp];
+    SavePath = [SavePathThisBarcode, filesep, 'Analysis_', AnalysisTimeStamp];
     mkdir(SavePathThisBarcode)
     FileNameShort = mfilename;
     newbackup = sprintf('%s_log.m',[SavePathThisBarcode, filesep, FileNameShort]);
@@ -41,7 +41,7 @@ for n = 1:size(Barcode, 2)
     f_LogDependencies(mfilename, SavePathThisBarcode)
 
     %% Load data
-    [files, info, areaNames, plateLayout, areaMap] = f_Local_Read_Files_Timeseries_Mosaic_BT2('S:\OperaQEHS\OperaArchiveCol', Barcode, 1);
+    [files, info, areaNames, plateLayout, areaMap] = f_Local_Read_Files_Timeseries_Mosaic_BT2(InPath, Barcode, 1);
 
     %% Organize images
     % find images for a given mosaic

src/readflexcube.m

@@ -48,10 +48,6 @@ end
 
 cube = zeros([sizeY(), sizeX(), sizeZ, sizeC], 'uint16');
 
-% getZCTCoords = @(i) [mod(i, sizeZ), ...
-%                      mod(floor(i / sizeZ), sizeC), ...
-%                      floor(floor(i / sizeZ) / sizeC)];
-
 getCZTCoords = @(i) [mod(floor(i / sizeC), sizeZ), ...
                      mod(i, sizeC), ...
                      floor(floor(i / sizeC) / sizeZ)];