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Commit d63c4e24 authored by Masneri Stefano's avatar Masneri Stefano
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Completed reading metadata of LSMReader

parent cf794928
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+imageIO/@BioReader/BioReader.m
+ 2
− 2
View file @ d63c4e24
......@@ -111,12 +111,12 @@ classdef BioReader < imageIO.ImageIO
rowDiffs = diff(obj.rowTilePos);
rowDiffs(rowDiffs <= 0) = Inf;
adjacentDiff = min(rowDiffs);
obj.tileOverlap = 1 - adjacentDiff / (obj.pixPerTileRow * obj.pixelSizeY);
obj.tileOverlap = 1 - adjacentDiff / (obj.pixPerTileRow * obj.scaleSize(2));
elseif obj.numTilesCol > 1
colDiffs = diff(obj.colTilePos);
colDiffs(colDiffs == 0) = Inf;
adjacentDiff = min(colDiffs);
obj.tileOverlap = 1 - adjacentDiff / (obj.pixPerTileCol * obj.pixelSizeX);
obj.tileOverlap = 1 - adjacentDiff / (obj.pixPerTileCol * obj.scaleSize(1));
else
obj.tileOverlap = 0;
end
......
+imageIO/@LSMReader/LSMReader.m
+ 7
− 10
View file @ d63c4e24
......@@ -16,16 +16,6 @@ classdef LSMReader < imageIO.ImageIO
properties
lsmPtr = 0; % pointer to the lsm file
offsets = []; % offset to each image directory
channelColors; % ChannelColors object
timeStamps; % TimeStamps object
scanInfo; % ScanInfo object
end
properties (Hidden = true)
offsetChannelColors;
offsetTimestamps;
offsetScanInfo;
end
properties (Constant = true)
......@@ -65,6 +55,13 @@ classdef LSMReader < imageIO.ImageIO
ifd = ifdread(obj); % Implemented in separate file
obj = readMetadata(obj); % Implemented in separate file
function obj = setChannelInfo(obj, chanInfo)
for k = 1:obj.channels
chanData = struct('name', chanInfo.names{k}, 'color', chanInfo.colors{k});
obj.channelInfo = [obj.channelInfo, ChannelInfo(chanData, 'LSM')];
end
end
end
end
......
+imageIO/@LSMReader/readMetadata.m
+ 26
− 1
View file @ d63c4e24
......@@ -55,7 +55,7 @@ for i = 1:length(codes.LSMINF)
end
% Read additional small database ChannelColors
obj.originalMetadata.channelColors = LSMChannelColors(obj.lsmPtr, obj.originalMetadata.OFFSET_CHANNELCOLORS);
obj.originalMetadata.channelColors = LSMChannelColors(obj.lsmPtr, obj.originalMetadata.OFFSET_CHANNELSCOLORS);
% Read additional small database TimeStamps
obj.originalMetadata.timeStamps = LSMTimeStamps(obj.lsmPtr, obj.originalMetadata.OFFSET_TIMESTAMPS);
......@@ -63,5 +63,30 @@ obj.originalMetadata.timeStamps = LSMTimeStamps(obj.lsmPtr, obj.originalMetadata
% Read ScanInfo directory
obj.originalMetadata.scanInfo = LSMScanInfo(obj.lsmPtr, obj.originalMetadata.OFFSET_SCANINFO);
% Set the metadata just read into the appropriate properties
obj.height = obj.originalMetadata.DimensionX;
obj.width = obj.originalMetadata.DimensionY;
obj.channels = obj.originalMetadata.DimensionChannels;
obj.stacks = obj.originalMetadata.DimensionZ;
obj.time = obj.originalMetadata.DimensionTime;
obj = obj.setChannelInfo(obj.originalMetadata.channelColors);
obj.scaleSize = obj.originalMetadata.VOXELSIZES;
% Finally, use the BioFormat reader to get info about overlap and number of
% tiles.
bfPtr = bfGetReader(obj.fileFullPath);
ome = bfPtr.getMetadataStore();
obj.datatype = char(ome.getPixelsType(0));
try
obj.tile = ome.getImageCount();
catch
obj.tile = 1;
end
obj = obj.setTileProperties(ome);
if obj.tile ~= 1
obj.height = round(obj.pixPerTileRow * (1 + (obj.numTilesRow - 1) * (1 - obj.tileOverlap)));
obj.width = round(obj.pixPerTileCol * (1 + (obj.numTilesCol - 1) * (1 - obj.tileOverlap)));
end
end
+imageIO/@LSMReader/setTileProperties.m 0 → 100644
+ 58
− 0
View file @ d63c4e24
function [ obj ] = setTileProperties( obj, ome )
%SETTILEPROPERTIES Summary of this function goes here
if 1 == obj.tile
obj.rowTilePos = 1;
obj.colTilePos = 1;
obj.numTilesRow = 1;
obj.numTilesCol = 1;
obj.tileOverlap = 0;
obj.pixPerTileRow = ome.getPixelsSizeY(0).getValue();
obj.pixPerTileCol = ome.getPixelsSizeX(0).getValue();
else
obj.rowTilePos = nan(1, obj.tile);
obj.colTilePos = nan(1, obj.tile);
try
for k = 1:obj.tile
obj.rowTilePos(k) = double(ome.getPlanePositionY(k-1,0).value());
obj.colTilePos(k) = double(ome.getPlanePositionX(k-1,0).value());
end
obj.numTilesRow = length(unique(obj.rowTilePos));
obj.numTilesCol = length(unique(obj.colTilePos));
catch
obj.rowTilePos = nan(1, obj.tile);
obj.colTilePos = nan(1, obj.tile);
obj.numTilesRow = nan;
obj.numTilesCol = nan;
end
try
obj.pixPerTileRow = double(ome.getPixelsSizeY(0).getValue());
obj.pixPerTileCol = double(ome.getPixelsSizeX(0).getValue());
catch
obj.pixPerTileRow = NaN;
obj.pixPerTileCol = NaN;
end
try
if obj.numTilesRow > 1
%get the minimum value above zero
rowDiffs = diff(obj.rowTilePos);
rowDiffs(rowDiffs <= 0) = Inf;
adjacentDiff = min(rowDiffs);
obj.tileOverlap = 1 - adjacentDiff / (obj.pixPerTileRow * ...
double(ome.getPixelsPhysicalSizeY(0).value()));
elseif obj.numTilesCol > 1
colDiffs = diff(obj.colTilePos);
colDiffs(colDiffs == 0) = Inf;
adjacentDiff = min(colDiffs);
obj.tileOverlap = 1 - adjacentDiff / (obj.pixPerTileCol * ...
double(ome.getPixelsPhysicalSizeX(0).value()));
else
obj.tileOverlap = 0;
end
catch
obj.tileOverlap = 0;
end
end
end
utils/@ChannelInfo/ChannelInfo.m
+ 8
− 0
View file @ d63c4e24
......@@ -44,6 +44,14 @@ classdef ChannelInfo
catch
obj.color = [255 255 255 255]; % white, arbitrary
end
elseif strcmpi('LSM', whereFrom)
obj.color = data.color;
try
obj.dyeName = data.name;
catch
obj.dyeName = '';
end
obj.gamma = 1;
else
warning('ChannelInfo.ChannelInfo: Unsupported input filetype')
end
......
utils/@LSMFileInfo/LSMFileInfo.m deleted 100644 → 0
+ 0
− 265
View file @ cf794928
classdef LSMFileInfo
% LSMFileInfo LSM file metadata information
% This class stores all the metadata related to LSM files created using
% ZEISS confocal microscopes. This class is heavily based on the LSM file
% toolbox developed by Peter Li (available on the Matlab file exchange:
% http://www.mathworks.com/matlabcentral/fileexchange/8412-lsm-file-toolbox)
% The name of the class is based on the Java implementation in the Fiji
% plugin LSM_Reader and has been chosen for consistency
properties
unknown = {}; %ensemble of fields whose meaning is unknown
datatype = {};
dimensions = 0;
timestacksize = 0;
voxelsizes = 0;
scantype = 0;
spectralscan = 0;
magicNumber = 0;
structureSize = 0;
dimensionX = 0;
dimensionY = 0;
dimensionZ = 0;
dimensionChannels = 0;
dimensionTime = 0;
intensityDataType = 0;
thumbnailX = 0;
thumbnailY = 0;
voxelSizeX = 0;
voxelSizeY = 0;
voxelSizeZ = 0;
originX = 0;
originY = 0;
originZ = 0;
scanType = 0;
spectralScan = 0;
dataType = 0;
timeInterval = 0;
displayAspectX = 0;
displayAspectY = 0;
displayAspectZ = 0;
displayAspectTime = 0;
toolbarFlags = 0;
objectiveSphereCorrection = 0;
bitsPerSample = 0;
scanInfo; % instance of ScanInfo class
channelColors; % instance of ChannelColors class
timeStamps; % instance of TimeStamps class
end
methods
function obj = LSMFileInfo(filename) %main function for parameters setting
% if it's a directory, return. Will get the info in some other way
if isdir(filename) || isempty(filename)
return
end
if ~exist(filename, 'file')
error(['Could not find file: ' filename]);
end
%get file ID for each file already opened (used to check whether we
%should close filename or not)
openFilesFIDs = fopen('all');
fid = fopen(filename);
if -1 == fid
error(['Could not open file ', filename]);
end
% Read special LSM IFD
ifd = obj.ifdread();
lsmifd = ifd([ifd.tagcode] == 34412);
if isempty(lsmifd)
error('Could not find LSMINFO IFD entry');
end
%Read LSMINFO Header
codes = LSMSpecs.getInstance();
if fseek(fid, lsmifd.offset, 'bof')
error(['Received error on file seek to LSMInfoOffset(' lsmifd.offset '): ' ferror(fid)]);
end
for i = 1:length(codes.LSMINF)
%ugly hack to allow compatibility with lsminfo (which also uses a
%hack for backward compatibility... ugly)
if 23 == i
fseek(fid, lsmifd.offset, 'bof');
end
mapKey = codes.LSMINF{i}{1};
num = codes.LSMINF{i}{2};
type = codes.LSMINF{i}{3};
[value, readnum] = fread(fid, num, type);
if readnum ~= num
error(['Failed to read more than ' num2str(readnum) ' values for ' field '(' num2str(num) ')']);
end
% If value is character string, convert to char.
if strfind(type, 'char')
value = char(value);
end
if strfind(mapKey, '_')
propName = util.fromUpperToCamelCase(mapKey);
elseif sum(isstrprop(mapKey, 'upper')) == length(mapKey)
propName = lower(mapKey);
else
propName = mapKey;
end
% for "unknown" and "datatype" put all the values together in a
% cell array (consistent with script from Peter Li)
if isstrprop(mapKey(end), 'digit')
propName = propName(1:end-1);
obj.(propName) = [ obj.(propName) value ];
else %otherwise just set property
propName = [ lower(propName(1)) propName(2:end) ];
try
obj.(propName) = value;
catch
disp(['Property ' propName ' does not exist, skipping.'])
end
end
end
%Read additional small database ChannelColors
chanCol = LSMChannelColors(fid, obj.offsetChannelColors);
obj.channelColors = chanCol;
%Read additional small database TimeStamps
timSta = LSMTimeStamps(fid, obj.offsetTimestamps);
obj.timeStamps = timSta;
% Read ScanInfo directory
scanInf = LSMScanInfo(fid, obj.offsetScaninfo);
obj.scanInfo = scanInf;
%if fid was already opened before, then we should leave it open.
if isempty(openFilesFIDs == fid)
fclose(fid);
end
end
end
methods (Access = private)
function [ifd, offset] = ifdread(obj)
% IFDREAD read IFD entries from TIFF file according to TIFF standard
% [IFD,OFFSET] = IFDREAD(FID)
%
% The idf database is read into struct IFD. The OFFSET to the beginning of
% image data is the last piece of information in the database.
%
% Extensively based on the work by Peter Li 30-Aug-05
% Some rights reserved. Licensed under Creative Commons:
% http://creativecommons.org/licenses/by-nc-sa/3.0/
fid = obj.lsmPtr;
ENTRY_LENGTH = 12;
IFD_TAGMAP = struct( ...
'x254' , 'NewSubFileType' ,...
'x256' , 'ImageWidth' ,...
'x257' , 'ImageLength' ,...
'x258' , 'BitsPerSample' ,...
'x259' , 'Compression' ,...
'x262' , 'PhotometricInterpretation' ,...
'x273' , 'StripOffsets' ,...
'x277' , 'SamplesPerPixel' ,...
'x279' , 'StripByteCounts' ,...
'x284' , 'PlanarConfiguration' ,...
'x34412' , 'LSMInfoOffset' ...
);
if fseek(fid, 8, 'bof')
error(['Received error on file seek to offset 8: ' ferror(fid)]);
end
numEntries = fread(fid, 1, 'uint16');
entriesStartPos = ftell(fid);
%preallocate ifd
ifd.tagcode = uint16(0);
ifd.typecode = uint16(0);
ifd.count = uint32(0);
ifd.tag='';
ifd.bytes = 0;
ifd.value = 0;
for i = 1:numEntries
% Go to ifd entry i
if fseek(fid, entriesStartPos + ((i - 1) * ENTRY_LENGTH), 'bof')
error(['Received error on file seek to position for entry ' num2str(i) ': ' ferror(fid)]);
end
ifd(i).tagcode = fread(fid, 1, 'uint16');
ifd(i).typecode = fread(fid, 1, 'uint16');
ifd(i).count = fread(fid, 1, 'uint32');
ifd(i).tag = structmap(ifd(i).tagcode, IFD_TAGMAP);
switch ifd(i).typecode
case {1, 2, 6, 7} % uint8, uchar, int8, undef8
ifd(i).bytes = 1;
case {3, 8} % uint16, int16
ifd(i).bytes = 2;
case {4, 9, 11} % uint32, int32, float32
ifd(i).bytes = 4;
case {5, 10, 12} % uint32 / uint32, int32 / int32, float64
ifd(i).bytes = 8;
otherwise
error(['Illegal typecode: ' num2str(ifd(i).typecode) '. Misformed IFD']);
end
% If the data take up more than 4 bytes, then the value is a
% pointer to the data. Otherwise the value is the data.
if ((ifd(i).bytes * ifd(i).count) > 4)
ifd(i).offset = fread(fid, 1, 'uint32');
if fseek(fid, ifd(i).offset, 'bof')
error(['Received error on file seek to data for entry ' num2str(i) '(' num2str(ifd(i).offset) '): ' ferror(fid)]);
end
end
switch ifd(i).typecode
case 1 % uint8
ifd(i).value = fread(fid, ifd(i).count, 'uint8');
case 2 % uchar
ifd(i).value = fread(fid, ifd(i).count, 'uchar');
char(ifd(i).value);
case 3 % uint16
ifd(i).value = fread(fid, ifd(i).count, 'uint16');
case 4 % uint32
ifd(i).value = fread(fid, ifd(i).count, 'uint32');
case 5 % Two uint32, first a numerator, then a denominator, representing a fraction
ifd(i).value = fread(fid, 2 * ifd(i).count, 'uint32');
numerators = fid(i).value(1:2:end);
denominators = fid(i).value(2:2:end);
ifd(i).value = double(numerators) ./ double(denominators);
case 6 % int8
ifd(i).value = fread(fid, ifd(i).count, 'int8');
case 7 % undef8
ifd(i).value = fread(fid, ifd(i).count, 'uint8');
case 8 % int16
ifd(i).value = fread(fid, ifd(i).count, 'int16');
case 9 % int32
ifd(i).value = fread(fid, ifd(i).count, 'int32');
case 10 % Two int32, first a numerator, then a denominator, representing a fraction
ifd(i).value = fread(fid, 2 * ifd(i).count, 'int32');
numerators = fid(i).value(1:2:end);
denominators = fid(i).value(2:2:end);
ifd(i).value = double(numerators) ./ double(denominators);
case 11 % float32
ifd(i).value = fread(fid, ifd(i).count, 'float32');
case 12 % float64
ifd(i).value = fread(fid, ifd(i).count, 'float64');
otherwise
error(['Illegal typecode: ' num2str(ifd(i).typecode) '. Misformed IFD']);
end
end
fseek(fid, entriesStartPos + (numEntries * ENTRY_LENGTH), -1);
offset = fread(fid, 1, 'uint32');
end
end
end
utils/license.txt → utils/license_GetFullPath.txt
+ 0
− 0
View file @ d63c4e24
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