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ingiehongingiehong
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Added double output to FocusStack. fsStack.AlignedStackDouble(:, :, :, :) now returns aligned stack with NaNs where pixel value is not available.
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4 files changed

+172
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‎@FocusStack/ExtractAlignedFramesDouble.m‎

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function [tfData] = ExtractAlignedFramesDouble(oStack, sSubs)
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% ExtractAlignedFrames - METHOD Extract and align frames from the stack
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% - Convert cell references to a subsref structure
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if (iscell(sSubs))
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subs = sSubs;
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clear sSubs;
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sSubs.subs = subs;
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sSubs.type = '()';
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end
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% -- Check whether the reference is even possible
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if (numel(sSubs) > 1)
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error('FocusStack:ImproperReference', '*** FocusStack/ExtractFrames: Only one referencing level is possible.');
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end
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if (~isequal(sSubs.type, '()'))
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error('FocusStack:ImproperReference', '*** FocusStack/ExtractFrames: Only ''()'' referencing is supported.');
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end
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% -- Check if alignment data exists
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if (isempty(oStack.mfFrameShifts))
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% - No, so just return un-aligned data
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warning('FocusStack:UnalignedStack', '--- FocusStack/ExtractAlignedFrames: Warning: The stack has not yet been aligned. Returning un-aligned stack images.');
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tfData = ExtractFrames(oStack, sSubs);
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return;
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end
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% -- Create aligned frames cache, if it doesn't exist
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vnStackSize = size(oStack);
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if (isempty(oStack.vbCachedAlignedFrames) || isempty(oStack.oAlignedFrameCache))
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% - Allocate a cache
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oStack.vbCachedAlignedFrames = false(vnStackSize(3:4));
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oStack.oAlignedFrameCache = MappedTensor(vnStackSize, 'Class', oStack.strDataClass);
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end
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% -- Align each frame and extract desired pixels
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[nul, cvnRefs, vnDataSize] = GetFullFileRefs(oStack, sSubs.subs);
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vnFrames = cvnRefs{1};
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% - Record data manipulation state
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bSubtractBlack = oStack.bSubtractBlack;
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bSubtractBlank = oStack.bSubtractBlank;
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bConvertToDFF = oStack.bConvertToDFF;
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% Always return double (to allow NaN elements for unavailable pixels)
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strOutputDataClass = 'double';
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% if (bSubtractBlack || bConvertToDFF)
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% strOutputDataClass = 'double';
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% else
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% strOutputDataClass = oStack.strDataClass;
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% end
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% - Determine desired frame size
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if (numel(vnDataSize) == 3)
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tfData = zeros(vnDataSize, strOutputDataClass);
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vnFrameSize = vnDataSize(1);
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elseif (numel(vnDataSize) == 4)
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tfData = zeros([prod(vnDataSize(1:2)) vnDataSize(3:4)], strOutputDataClass);
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vnFrameSize = vnDataSize(1:2);
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else
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% - Shouldn't ever happen
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error('FocusStack:UnexpectedError', '*** FocusStack/ExtractAlignedFrames: Unexpected error in data sizing.');
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end
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% - Turn off data manipulation
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oStack.bSubtractBlack = false;
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oStack.bConvertToDFF = false;
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oStack.bSubtractBlank = false;
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oStack.bDoubleOutput=true;
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try
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for (nFrameIndex = 1:numel(vnFrames))
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% -- Check the aligned frame cache
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if (false) % all(oStack.vbCachedAlignedFrames(vnFrames(nFrameIndex), cvnRefs{2})))
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% - Extract the aligned frames from the cache
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tfAlignedFrame = oStack.oAlignedFrameCache(:, :, vnFrames(nFrameIndex), cvnRefs{2});
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else
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% -- Extract a full frame from the stack
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% - Permute to get channels in the third dimension
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tfThisFrame = permute(oStack.ExtractFrames({':', ':', vnFrames(nFrameIndex), cvnRefs{2}}), [1 2 4 3]);
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% - Compute a translation matrix
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vfThisShift = oStack.mfFrameShifts(vnFrames(nFrameIndex), :);
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if (any(vfThisShift ~= 0))
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mfTranslation = eye(3);
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mfTranslation(3, 1:2) = vfThisShift;
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oTForm = maketform('projective', mfTranslation);
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% - Align the frame according to the pre-calculated shift data
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tfAlignedFrame = imtransform(tfThisFrame, oTForm, 'XData', [1 vnStackSize(1)], 'YData', [1 vnStackSize(2)], 'FillValues', nan);
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else
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tfAlignedFrame = tfThisFrame;
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end
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% - Insert aligned frame into stack
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oStack.oAlignedFrameCache(:, :, vnFrames(nFrameIndex), cvnRefs{2}) = tfAlignedFrame;
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oStack.vbCachedAlignedFrames(vnFrames(nFrameIndex), cvnRefs{2}) = true;
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end
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% - Return only the requested pixels
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tfAlignedFrame = reshape(tfAlignedFrame, [], 1, numel(cvnRefs{2}));
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% - Should we subtract the black?
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if (bSubtractBlack)
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% - Subtract the black trace for this frame
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tfAlignedFrame = double(tfAlignedFrame) - oStack.vfBlackTrace(vnFrames(nFrameIndex));
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end
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% - Reshape data and return
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tfData(:, nFrameIndex, :) = reshape(ipermute(tfAlignedFrame(cvnRefs{3}, :, :), [1 2 4 3]), [prod(vnFrameSize) 1 numel(cvnRefs{2})]);
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end
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% - Should we convert to DFF?
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if (bConvertToDFF)
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% - Extract the blank frame for these frames and divide
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tfBlanks = ExtractBlankFrames(oStack, {cvnRefs{3} cvnRefs{1}});
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tfData = double(tfData) ./ tfBlanks - 1;
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end
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% - Should we subtract the blank?
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if (bSubtractBlank)
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% - Extract the blank frame for these frames and subtract
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tfBlanks = ExtractBlankFrames(oStack, {cvnRefs{3} cvnRefs{1}});
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tfData = double(tfData) - tfBlanks;
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end
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catch err
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% - Restore data manipulation state
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oStack.bSubtractBlack = bSubtractBlack;
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oStack.bConvertToDFF = bConvertToDFF;
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oStack.bSubtractBlank = bSubtractBlank;
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rethrow(err);
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end
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% - Restore data manipulation state
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oStack.bSubtractBlack = bSubtractBlack;
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oStack.bSubtractBlank = bSubtractBlank;
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oStack.bConvertToDFF = bConvertToDFF;
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oStack.bDoubleOutput=false;
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% - Return pixels to correct size
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tfData = reshape(tfData, vnDataSize);
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% --- END ExtractAlignedFrames METHOD ---

‎@FocusStack/ExtractFrames.m‎

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@@ -30,7 +30,7 @@
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% -- Read from each file in turn
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if (oStack.bSubtractBlack || oStack.bConvertToDFF || oStack.bSubtractBlank)
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if (oStack.bSubtractBlack || oStack.bConvertToDFF || oStack.bSubtractBlank || oStack.bDoubleOutput)
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strOutputDataClass = 'double';
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else
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strOutputDataClass = oStack.strDataClass;

‎@FocusStack/FocusStack.m‎

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% fsStack.AlignedStack(:, :, :, :)
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% fsStack.RawStack(:, :, :, :);
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%
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% To extract aligned frames in double format (including NaN for unavailable pixels:
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% fsStack.AlignedStackDouble(:, :, :, :)
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%
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% To accumulate over the stack:
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% fsStack.SummedFrames(:, :, :, :);
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% fsStack.SummedAlignedFrames(:, :, :, :);
@@ -35,6 +38,7 @@
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cstrFilenames = {};
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bConvertToDFF = false;
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bSubtractBlank = false;
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bDoubleOutput = false;
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end
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properties (SetAccess = private, GetAccess = private)

‎@FocusStack/subsref.m‎

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@@ -37,6 +37,15 @@
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varargout{1} = ExtractAlignedFrames(oStack, sSubs(2));
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case {'AlignedStackDouble'}
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if (numel(sSubs) == 1)
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sSubs(2).type = '()';
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sSubs(2).subs = {':', ':', ':', ':'};
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end
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varargout{1} = ExtractAlignedFramesDouble(oStack, sSubs(2));
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case {'SummedFrames'}
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if (numel(sSubs) == 1)
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sSubs(2).type = '()';

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