Merge branch 'master' of https://gitlab.mpcdf.mpg.de/mpibr/scic/ImageIO

+imageIO/@LIFReader/LIFReader.m

@@ -23,6 +23,7 @@ classdef LIFReader < imageIO.ImageIO
       obj = obj@imageIO.ImageIO(filename);
       
       obj.bfPtr = bfGetReader(obj.fileFullPath);
+      obj = obj.readRawMetadata();
       obj = obj.readMetadata();
     end
     
@@ -69,7 +70,8 @@ classdef LIFReader < imageIO.ImageIO
   
   methods (Access = protected)
     
-    obj = readMetadata(obj);        % IMPLEMENTED IN SEPARATE FILE
+    obj = readRawMetadata(obj);     % implemented in separate file
+    obj = readMetadata(obj);        % implemented in separate file
     
     function obj = setTileProperties(obj, ome)
     %SETTILEPROPERTIES Set all properties related to tiles

+imageIO/@LIFReader/readMetadata.m

@@ -213,4 +213,25 @@ else
     end
 end
 
+
+%% read laser settings from raw metadata
+laserLineSettings = regexp(obj.originalMetadata, '<LaserLineSetting ([^/^>]+)/>', 'match');
+if (~isempty(laserLineSettings))
+    laserLineValues = zeros(length(laserLineSettings), 4);
+    for i = 1 : length(laserLineSettings)
+        tag = xml2struct(laserLineSettings{i});
+        laserLine = str2double(tag.LaserLineSetting.Attributes.LaserLine);
+        intensityDev = str2double(tag.LaserLineSetting.Attributes.IntensityDev);
+        isVisible = str2double(tag.LaserLineSetting.Attributes.IsVisible);
+        aobsIntensityLowDev = str2double(tag.LaserLineSetting.Attributes.AOBSIntensityLowDev);
+        laserLineValues(i, :) = [laserLine, intensityDev, isVisible, aobsIntensityLowDev];
+    end
+    idxFilter = (laserLineValues(:,3) == 0) | (laserLineValues(:,4) == -1);
+    laserLineValues(idxFilter,:) = [];
+    obj.wavelengthExc = laserLineValues(:, 1);
+    obj.laserPower = laserLineValues(: ,2);
+end
+
 end
+
+

+imageIO/@LIFReader/readRawMetadata.m

+function obj = readRawMetadata(obj)
+% READRAWMETADATA Access the raw metadata and sets the object properties
+% The function accesses the binary metadata. The method takes as input the
+% object filename and opens the file for binary read
+% https://de.mathworks.com/matlabcentral/fileexchange/78089-rawlifreader
+% https://github.com/bastibe/MatlabXML
+
+    % open file for raw binary read
+    fid = fopen(obj.fileFullPath, 'r', 'l');
+    
+    % read common block header
+    CBHi = 0x70;  % common Block Header identifier (112)
+    ID = fread(fid, 1, '*uint32');
+    assert(ID == CBHi, 'Found %x instead of %x in first metadata block. Not a valid block.', ID, CBHi);
+    CBHsize = fread(fid, 1, '*uint32');
+    
+    % read metadata block header
+    MBHi = 0x2A;  % metadata Block Header identifier (42)
+    ID = fread(fid, 1, '*uint8');
+    assert(ID == MBHi, 'Found %x instead of %x in in first metadata block. Not a valid block.', ID, MBHi);
+    MBHsize = fread(fid, 1, '*uint32');
+    
+    % read raw metadata block
+    mdb = fread(fid, MBHsize, '*uint16');
+    obj.originalMetadata = sprintf('%s', char(mdb));
+    fclose(fid);
+end
\ No newline at end of file

tests/LIFfile.m

+classdef LIFfile
+    % Abbriviations
+    % - Leica Image File (lif) <-- what we read here
+    % - Extended Leica File (xlef)
+    % - Extended Leica Image Files (xlif)
+    % - Leica Object File (lof)
+    % - Common Block Header (CBH)
+    % - Metadata Block Header (MBH)
+    % - Binary Block Header (BBH)
+    
+    properties
+        binaryBlockHeaders
+        xmlRaw
+        xmlData
+    end
+    properties (Hidden)
+        fid
+        closed
+        filesize
+        
+    end
+    properties (Constant, Hidden)
+        CBHi = 0x70;  %Common Block Header identifier (112)
+        MBHi = 0x2A;  %Metadata Block Header identifier (42)
+        LBBHi = 0x2A; %LIF Binary Block Header identifier (42)
+        extension = '.lif'
+    end
+    
+    methods
+        function obj = LIFfile(filename)            
+            % LIF file contains a Metadata Block followed by LIF Binary Blocks.
+            if isstruct(filename) %file as structure
+                filename = fullfile(filename.folder,filename.name);
+            end
+            if ~strcmp(filename(end-3:end),obj.extension),filename=[filename,obj.extension];end
+            if ~exist(filename,'file')
+                error('cannot find file')
+            else
+                obj.fid = fopen(filename,'r','l');
+            end
+            d = dir(filename);
+            obj.filesize = d.bytes;
+            
+            % Read the MetadataBlock data
+            obj.xmlRaw = obj.readMetadataBlock('First Metadata Block');
+            xmlStream = java.io.ByteArrayInputStream(uint8(obj.xmlRaw));
+            xmlSource = org.xml.sax.InputSource(xmlStream);
+            xmlData = obj.parseLIFXML(xmlread(xmlSource));
+            
+            % Get information about the binary blocks
+            blockCounter=1;
+            while ftell(obj.fid)<obj.filesize
+                header = getLIFBinaryBlockHeader(obj,sprintf('Binary Block %.0f', blockCounter));
+                binaryBlockHeaders(blockCounter) = header;
+                blockCounter=blockCounter+1;
+            end
+            
+            %couple binaryBlockHeaders to XML blocks
+            for ct = 1:length(binaryBlockHeaders)
+                element = xmlData(ismember(xmlData(:,2),binaryBlockHeaders(ct).identifier),1);
+                binaryBlockHeaders(ct).metadata = element{1};
+                %extract the name of the element
+                theAttributes = binaryBlockHeaders(ct).metadata.getAttributes;
+                numAttributes = theAttributes.getLength;
+                for count = 1:numAttributes
+                    attrib = theAttributes.item(count-1);
+                    if strcmp(char(attrib.getName),'Name')
+                        binaryBlockHeaders(ct).Name=char(attrib.getValue);
+                    end
+                end  
+            end
+            obj.binaryBlockHeaders=binaryBlockHeaders;
+        end
+        function data = getLIFBinaryBlockData(obj,BBid) %get the raw data from a lif file
+            if ischar(BBid) %find the name in the description
+                BBidName = BBid;
+                BBid = find(ismember({obj.binaryBlockHeaders.identifier},BBidName));
+                assert(~isempty(BBid),'Did not find binary block with the name %s',BBidName);
+            end
+            assert(BBid<=length(obj.binaryBlockHeaders),'Could not find binary block %.0f, only %.0f present',BBid,length(obj.binaryBlockHeaders))
+            header = obj.binaryBlockHeaders(BBid);
+            fseek(obj.fid,header.offset,'bof');
+            data = fread(obj.fid,header.datasize,'*uint8');
+        end
+        function header = getLIFBinaryBlockHeader(obj,name)
+            % consists of CBH LifBBH and binary data
+            CBHsize = readCommonBlockHeader(obj,name);
+            ID = fread(obj.fid,1,'*uint8');
+            assert(ID==obj.LBBHi,'Found %x instead of %x in %s. Not a valid block.',ID, obj.LBBHi,name)
+            BDsize = fread(obj.fid,1,'*uint64'); %binary data size
+            ID = fread(obj.fid,1,'*uint8');
+            assert(ID==obj.LBBHi,'Found %x instead of %x in %s. Not a valid block.',ID, obj.LBBHi,name)
+            BDIsize = fread(obj.fid,1,'*uint32'); %binary data identifier size
+            BDI = char(fread(obj.fid,BDIsize,'*uint16')); %binary data indentifier
+            offset = ftell(obj.fid);
+            fseek(obj.fid,BDsize,'cof'); %forward over BDsize
+            header.datasize = BDsize;
+            header.offset = offset;
+            header.identifier = BDI';
+        end
+        function mdb = readMetadataBlock(obj,name)
+            %consist of CBH MDB and metadata
+            CBHsize = obj.readCommonBlockHeader(name);
+            MBHsize = obj.readMetadataBlockHeader(name);
+            mdb = char(fread(obj.fid,MBHsize,'*uint16'));
+        end
+        function CBHsize = readCommonBlockHeader(obj,name)
+            ID = fread(obj.fid,1,'*uint32');
+            assert(ID==obj.CBHi,'Found %x instead of %x in %s. Not a valid block.',ID, obj.CBHi,name)
+            CBHsize = fread(obj.fid,1,'*uint32');
+        end
+        function MBHsize = readMetadataBlockHeader(obj,name)
+            ID = fread(obj.fid,1,'*uint8');
+            assert(ID==obj.MBHi,'Found %x instead of %x in %s. Not a valid block.',ID, obj.MBHi,name)
+            MBHsize = fread(obj.fid,1,'*uint32');
+        end
+        function close(obj)
+            fclose(obj.fid);
+        end
+    end
+    
+    methods(Static) %taken from Matlab https://nl.mathworks.com/help/matlab/ref/xmlread.html
+        function elements = parseLIFXML(theNode)
+            elements = findElements(theNode,{});
+            function elements = findElements(theNode,elements)
+                % Adapted from the ParseXML function
+                if strcmp(char(theNode.getNodeName),'Element')
+                    temp = theNode.cloneNode(true);
+                    %remove the child-node called Children
+                    childNodes = temp.getChildNodes;
+                    numChildNodes = childNodes.getLength;
+                    for count = 1:numChildNodes
+                        theChild = childNodes.item(count-1);
+                        if strcmp(char(theChild.getNodeName),'Children')
+                            elements = findElements(theChild,elements); %Search the Children
+                            temp.removeChild(theChild);
+                        end
+                        if strcmp(char(theChild.getNodeName),'Memory')
+                            theAttributes = theChild.getAttributes;
+                            numAttributes = theAttributes.getLength;
+                            for count = 1:numAttributes
+                                attrib = theAttributes.item(count-1);
+                                if strcmp(char(attrib.getName),'MemoryBlockID')
+                                    MemoryBlockID=char(attrib.getValue);
+                                end
+                            end
+                        end
+                    end
+                    elements{end+1,1}=temp;
+                    elements{end,2}=MemoryBlockID;
+                elseif theNode.hasChildNodes %Look at the children
+                    childNodes = theNode.getChildNodes;
+                    numChildNodes = childNodes.getLength;
+                    for count = 1:numChildNodes
+                        theChild = childNodes.item(count-1);
+                        elements = findElements(theChild,elements);
+                    end
+                end
+            end
+        end
+    end
+end
\ No newline at end of file

tests/testLIF.m

+% TEST LIF FILES
+clc
+clear variables
+close all
+
+%% add path
+path_project = './';
+addpath(genpath(path_project));
+
+%% create pointer
+file_lif = '../../230329.lif';
+
+addpath(genpath('../'));
+obj = imageIOPtr(file_lif);
+disp([obj.wavelengthExc, obj.laserPower]);
+