Merge pull request #30 from MATLAB-Community-Toolboxes-at-INCF/integrate-custom-datastore

Integrate custom datastore

Author: stevevanhooser

.gitattributes

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+*.fig binary
+*.mat binary
+*.mdl binary diff merge=mlAutoMerge
+*.mdlp binary
+*.mexa64 binary
+*.mexw64 binary
+*.mexmaci64 binary
+*.mlapp binary
+*.mldatx binary
+*.mlproj binary
+*.mlx binary
+*.p binary
+*.sfx binary
+*.sldd binary
+*.slreqx binary merge=mlAutoMerge
+*.slmx binary merge=mlAutoMerge
+*.sltx binary
+*.slxc binary
+*.slx binary merge=mlAutoMerge
+*.slxp binary
+
+## Other common binary file types
+*.docx binary
+*.exe binary
+*.jpg binary
+*.pdf binary
+*.png binary
+*.xlsx binary

.gitignore

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+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+# Compiled MEX binaries (all platforms)
+*.mex*
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace

datastore/DeepInterpolationDataStore.m

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+classdef DeepInterpolationDataStore < matlab.io.Datastore & ...
+                                      matlab.io.datastore.Subsettable & ...
+                                      matlab.io.datastore.Shuffleable
+    %DEEPINTERPOLATIONDATASTORE - custom datastore for DeepInterpolation-MATLAB
+    %
+    % This custom datastore provides flanking frames and the center frame 
+    % upon one read.
+    %
+    % dids = DeepInterpolationDataStore(pathToTiffFile, options);
+    %
+    % Input must be full path to a grayscale, single channel tiff stack of 
+    % >'flankingFrames + 2' frames in order to work (this is according to
+    % the function of the DeepInterpolation network).
+    %
+    % If the image frame dimensions differ from the network input size
+    % the doAutoResize option controls whether the frames will be
+    % automatically resized to outputFrameSize before they are returned.
+    %
+    % Dr. Thomas Künzel, The MathWorks, 2023
+    % [email protected]
+
+    properties
+        fileName string
+        doAutoResize logical
+        numberOfFlankingFrames int32
+        outputFrameSize int32
+        frameCount double
+        dsSetCount double
+        setsAvailable double
+        currentSet double
+        setFramesStartIndex double
+        currentFrameIndex double
+        allSetFrameStartIndices double
+    end
+
+    methods % begin methods section
+        function myds = DeepInterpolationDataStore(filePath, options)
+            arguments
+                filePath
+                options = struct();
+            end
+            if isfield(options, 'doAutoResize')
+                myds.doAutoResize = logical(options.doAutoResize);
+            else % default
+                myds.doAutoResize = false;
+            end
+            if isfield(options, 'numberOfFlankingFrames')
+                assert(options.numberOfFlankingFrames > 0)
+                assert(rem(options.numberOfFlankingFrames, 2) == 0, "Number of flanking frames should be even.")
+                myds.numberOfFlankingFrames = options.numberOfFlankingFrames;
+            else % default
+                myds.numberOfFlankingFrames = 60;
+            end
+            if isfield(options, 'outputFrameSize')
+                if not (myds.doAutoResize)
+                    warning('Specified an output frame size, but auto-resize is turned off.')
+                end
+                outputFrameSize = options.outputFrameSize;
+                if not (isnumeric(outputFrameSize) && isequal(size(outputFrameSize), [1, 2]) && all(outputFrameSize >= 0))
+                    error('outputFrameSize should be an array with dimension 1x2 and non-negative values.');
+                end
+                myds.outputFrameSize = outputFrameSize;
+            else % default
+                myds.outputFrameSize = [512, 512];
+            end
+            assert(isfile(filePath));
+            myds.fileName = filePath;
+            fileInfo = imfinfo(myds.fileName);
+            assert(strcmp(fileInfo(1).Format,'tif'), "Must be tiff format");
+            if ~myds.doAutoResize
+                assert((fileInfo(1).Width == myds.outputFrameSize(1)) ...
+                    && (fileInfo(1).Height == myds.outputFrameSize(2)),...
+                    "Actual frame size is not equal to specified outputFrameSize");
+            end
+            framePerSetCount = myds.numberOfFlankingFrames + 3;
+            assert(numel(fileInfo) >= framePerSetCount, "Not enough frames in stack for DeepInterpolation");
+            myds.frameCount = numel(fileInfo);
+            myds.dsSetCount = myds.frameCount - framePerSetCount + 1;
+            myds.allSetFrameStartIndices = 1:myds.dsSetCount;
+            reset(myds);
+        end
+
+        function tf = hasdata(myds)
+            % Return true if more data is available.
+            tf = myds.setsAvailable > 0;
+        end
+
+        function [data,info] = read(myds)
+            % Read data and information about the extracted data.
+            assert(hasdata(myds), "No more data to read");
+            rawRefFrame = imread(myds.fileName,myds.currentFrameIndex);
+            if myds.doAutoResize
+                rawRefFrame = imresize(rawRefFrame,myds.outputFrameSize);
+            end
+            refFrame = single(rawRefFrame);
+            flankingFrames = single( ...
+                ones(myds.outputFrameSize(1), ...
+                myds.outputFrameSize(2), ...
+                myds.numberOfFlankingFrames) ...
+                );
+            framecount = 1;
+            for leftFrame = 0:(myds.numberOfFlankingFrames/2) - 1
+                rawThisFrame = imread(myds.fileName,myds.setFramesStartIndex+leftFrame);
+                if myds.doAutoResize
+                    rawThisFrame = imresize(rawThisFrame,myds.outputFrameSize);
+                end
+                thisFrame = single(rawThisFrame);
+                flankingFrames(:,:,framecount) = thisFrame;
+                framecount = framecount + 1;
+            end
+            %frame myds.numberOfFlankingFrames + 1 is center frame. One
+            %frame before and one after is left out.
+            startRightFrame = myds.numberOfFlankingFrames/2 + 3;
+            for rightFrame = startRightFrame:startRightFrame + myds.numberOfFlankingFrames/2 - 1
+                rawThisFrame = imread(myds.fileName,myds.setFramesStartIndex+rightFrame);
+                if myds.doAutoResize
+                    rawThisFrame = imresize(rawThisFrame,myds.outputFrameSize);
+                end
+                thisFrame = single(rawThisFrame);
+                flankingFrames(:,:,framecount) = thisFrame;
+                framecount = framecount + 1;
+            end
+            data = {flankingFrames, refFrame};
+            info = "set=" + num2str(myds.currentSet) + "/centerframe=" + num2str(myds.currentFrameIndex);
+            myds.currentSet = myds.currentSet + 1;
+            myds.setsAvailable = myds.setsAvailable - 1;
+            if myds.setsAvailable > 0
+                myds.setFramesStartIndex = myds.allSetFrameStartIndices(myds.currentSet);
+                myds.currentFrameIndex = myds.setFramesStartIndex + myds.numberOfFlankingFrames/2 + 1;
+            else
+                myds.setFramesStartIndex = nan;
+                myds.currentFrameIndex = nan;
+            end
+        end
+
+        function reset(myds)
+            % Reset to the start of the data.
+            myds.setsAvailable = myds.dsSetCount;
+            myds.currentSet = 1;
+            myds.setFramesStartIndex = myds.allSetFrameStartIndices(myds.currentSet);
+            myds.currentFrameIndex = myds.setFramesStartIndex + myds.numberOfFlankingFrames/2 + 1;
+        end%
+
+        function shmyds = shuffle(myds)
+            % shmyds = shuffle(myds) shuffles the sets
+            % Create a copy of datastore
+            shmyds = copy(myds);
+
+            % Shuffle files and corresponding labels
+            numObservations = shmyds.dsSetCount;
+            idx = randperm(numObservations);
+            shmyds.allSetFrameStartIndices = myds.allSetFrameStartIndices(idx);
+            reset(shmyds);
+        end
+    end
+
+    methods (Hidden = true)
+        function frac = progress(myds)
+            % Determine percentage of data read from datastore
+            if hasdata(myds)
+                frac = (myds.currentSet-1) / myds.dsSetCount;
+            else
+                frac = 1;
+            end
+        end
+    end
+
+    methods (Access = protected)
+        function subds = subsetByReadIndices(myds, indices)
+            subds = copy(myds);
+            subds.dsSetCount = numel(indices);
+            subds.allSetFrameStartIndices = myds.allSetFrameStartIndices(indices);
+            reset(subds);
+        end
+
+        function n = maxpartitions(myds)
+            n = myds.dsSetCount;
+        end
+    end
+
+end