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ImageIO/utils/lsmClasses/@LSMScanInformation/LSMScanInformation.m

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classdef LSMScanInformation
%LSMSCANINFORMATION Class representation of ScanInformation in LSM files
% The field u32OffsetScanInformation of the "CZ-Private tag" contains the
% file offset to the start of a block with information of the device settings
% used during acquisition. Note that the image size, channel number and pixel
% distance of the image stored in the file can be different form the settings
% used during acquisition because the image could have been modified by offline
% operations. Information about the image size, channel number and pixel distance
% of the image contents stored in the file can be found in the fields of the "CZ-Private tag"
%
% AUTHOR: Stefano Masneri
% Date: 14.3.2017
properties
entries; % Cell containing all the properties read from the ScanInformation
propertyList; % Cell array matching hex codes to metadata, based on LSM
% file format specifications
end
properties (Hidden = true)
idx = 1;
end
methods
function obj = LSMScanInformation(lsmPtr, byteOrder)
%LSMOVERLAY Constructor
% Assumes the file pointer in the correct position already
obj = obj.createPropertyList();
obj.entries = cell(207, 2);
% The algorithm for reading the scaninfo database depends on keeping track of a
% "level" hierarchy. As the database is read, some entries are level
% instructions, navigating up or down the hierarchy. The database is done when
% the hierarchy steps back to level 0
level = 0;
while (1)
taghex = dec2hex(fread(lsmPtr, 1, 'uint32', byteOrder));
typecode = fread(lsmPtr, 1, 'uint32', byteOrder);
size = fread(lsmPtr, 1, 'uint32', byteOrder);
tag = obj.getTag(['h' taghex]);
switch typecode
case 0 % Special case: this is a level instruction entry
if (hex2dec(taghex) == hex2dec('FFFFFFFF'))
level = level - 1;
else
level = level + 1;
end
case 2 % string
count = size;
value = char(fread(lsmPtr, count, 'uchar', byteOrder)');
value = value(1:end-1);
case 4 % int32
count = size / 4;
value = fread(lsmPtr, count, 'uint32', byteOrder);
case 5 % float64
count = size / 8;
value = fread(lsmPtr, count, 'float64', byteOrder);
otherwise
error('LSMScanInformation: error parsing LSM file')
end
% If this was just a level instruction entry ignore it, otherwise try to
% record entry.
if typecode > 0
if isempty(tag)
propName = [ 'h' taghex ];
else
propName = tag;
end
obj = obj.addEntry(propName, value);
end
if 0 == level
break;
end
end
end
function [keys, values] = getAllEntries(obj)
keys = obj.entries.keys();
values = obj.entries.values();
end
end
methods (Access = private)
function tag = getTag(obj, tagHex)
tag = [];
for k = 1:length(obj.propertyList)
if strcmp(tagHex, obj.propertyList{k}{1})
tag = obj.propertyList{k}{2};
break;
end
end
end
function obj = addEntry(obj, propName, value)
try
obj.entries{obj.idx, 1} = propName;
obj.entries{obj.idx, 2} = value;
obj.idx = obj.idx + 1;
catch
error('LSMScanInformation: error adding field to entries')
end
end
function obj = createPropertyList(obj)
cnt = 1;
scan{cnt} = {'h10000000', 'RECORDINGS' }; cnt = cnt+1;
scan{cnt} = {'h10000001', 'ENTRY_NAME' }; cnt = cnt+1;
scan{cnt} = {'h10000002', 'ENTRY_DESCRIPTION' }; cnt = cnt+1;
scan{cnt} = {'h10000003', 'ENTRY_NOTES' }; cnt = cnt+1;
scan{cnt} = {'h10000004', 'ENTRY_OBJECTIVE' }; cnt = cnt+1;
scan{cnt} = {'h10000005', 'PROCESSING_SUMMARY' }; cnt = cnt+1;
scan{cnt} = {'h10000006', 'SPECIAL_SCAN' }; cnt = cnt+1;
scan{cnt} = {'h10000007', 'SCAN_TYPE' }; cnt = cnt+1;
scan{cnt} = {'h10000008', 'SCAN_MODE' }; cnt = cnt+1;
scan{cnt} = {'h10000009', 'STACKS_COUNT' }; cnt = cnt+1;
scan{cnt} = {'h1000000A', 'LINES_PER_PLANE' }; cnt = cnt+1;
scan{cnt} = {'h1000000B', 'SAMPLES_PER_LINE' }; cnt = cnt+1;
scan{cnt} = {'h1000000C', 'PLANES_PER_VOLUME' }; cnt = cnt+1;
scan{cnt} = {'h1000000D', 'IMAGES_WIDTH' }; cnt = cnt+1;
scan{cnt} = {'h1000000E', 'IMAGES_HEIGHT' }; cnt = cnt+1;
scan{cnt} = {'h1000000F', 'NUMBER_OF_PLANES' }; cnt = cnt+1;
scan{cnt} = {'h10000010', 'IMAGES_NUMBER_STACKS' }; cnt = cnt+1;
scan{cnt} = {'h10000011', 'IMAGES_NUMBER_CHANNELS' }; cnt = cnt+1;
scan{cnt} = {'h10000012', 'LINESCAN_X_Y' }; cnt = cnt+1;
scan{cnt} = {'h10000013', 'SCAN_DIRECTION' }; cnt = cnt+1;
scan{cnt} = {'h10000014', 'TIME_SERIES' }; cnt = cnt+1;
scan{cnt} = {'h10000015', 'ORIGINAL_SCAN_DATA' }; cnt = cnt+1;
scan{cnt} = {'h10000016', 'ZOOM_X' }; cnt = cnt+1;
scan{cnt} = {'h10000017', 'ZOOM_Y' }; cnt = cnt+1;
scan{cnt} = {'h10000018', 'ZOOM_Z' }; cnt = cnt+1;
scan{cnt} = {'h10000019', 'SAMPLE_0_X' }; cnt = cnt+1;
scan{cnt} = {'h1000001A', 'SAMPLE_0_Y' }; cnt = cnt+1;
scan{cnt} = {'h1000001B', 'SAMPLE_0_Z' }; cnt = cnt+1;
scan{cnt} = {'h1000001C', 'SAMPLE_SPACING' }; cnt = cnt+1;
scan{cnt} = {'h1000001D', 'LINE_SPACING' }; cnt = cnt+1;
scan{cnt} = {'h1000001E', 'PLANE_SPACING' }; cnt = cnt+1;
scan{cnt} = {'h1000001F', 'PLANE_WIDTH' }; cnt = cnt+1;
scan{cnt} = {'h10000020', 'PLANE_HEIGHT' }; cnt = cnt+1;
scan{cnt} = {'h10000021', 'VOLUME_DEPTH' }; cnt = cnt+1;
scan{cnt} = {'h10000034', 'ROTATION' }; cnt = cnt+1;
scan{cnt} = {'h10000035', 'PRECESSION' }; cnt = cnt+1;
scan{cnt} = {'h10000036', 'SAMPLE_0_TIME' }; cnt = cnt+1;
scan{cnt} = {'h10000037', 'START_SCAN_TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h10000038', 'START_SCAN_TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'h10000039', 'START_SCAN_EVENT' }; cnt = cnt+1;
scan{cnt} = {'h10000040', 'START_SCAN_TIME' }; cnt = cnt+1;
scan{cnt} = {'h10000041', 'STOP_SCAN_TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h10000042', 'STOP_SCAN_TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'h10000043', 'STOP_SCAN_EVENT' }; cnt = cnt+1;
scan{cnt} = {'h10000044', 'START_SCAN_TIME2' }; cnt = cnt+1;
scan{cnt} = {'h10000045', 'USE_ROIS' }; cnt = cnt+1;
scan{cnt} = {'h10000046', 'USE_REDUCED_MEMORY_ROIS' }; cnt = cnt+1;
scan{cnt} = {'h10000047', 'USER' }; cnt = cnt+1;
scan{cnt} = {'h10000048', 'USE_BCCORECCTION' }; cnt = cnt+1;
scan{cnt} = {'h10000049', 'POSITION_BCCORRECTION1' }; cnt = cnt+1;
scan{cnt} = {'h10000050', 'POSITION_BCCORRECTION2' }; cnt = cnt+1;
scan{cnt} = {'h10000051', 'INTERPOLATIONY' }; cnt = cnt+1;
scan{cnt} = {'h10000052', 'CAMERA_BINNING' }; cnt = cnt+1;
scan{cnt} = {'h10000053', 'CAMERA_SUPERSAMPLING' }; cnt = cnt+1;
scan{cnt} = {'h10000054', 'CAMERA_FRAME_WIDTH' }; cnt = cnt+1;
scan{cnt} = {'h10000055', 'CAMERA_FRAME_HEIGHT' }; cnt = cnt+1;
scan{cnt} = {'h10000056', 'CAMERA_OFFSETX' }; cnt = cnt+1;
scan{cnt} = {'h10000057', 'CAMERA_OFFSETY' }; cnt = cnt+1;
scan{cnt} = {'h10000059', 'RT_BINNNING' }; cnt = cnt+1;
scan{cnt} = {'h1000005a', 'RT_FRAME_WIDTH' }; cnt = cnt+1;
scan{cnt} = {'h1000005b', 'RT_FRAME_HEIGHT' }; cnt = cnt+1;
scan{cnt} = {'h1000005c', 'RT_REGION_WIDTH' }; cnt = cnt+1;
scan{cnt} = {'h1000005d', 'RT_REGION_HEIGHT' }; cnt = cnt+1;
scan{cnt} = {'h1000005e', 'RT_OFFSETX' }; cnt = cnt+1;
scan{cnt} = {'h1000005f', 'RT_OFFSETY' }; cnt = cnt+1;
scan{cnt} = {'h10000060', 'RT_ZOOM' }; cnt = cnt+1;
scan{cnt} = {'h10000061', 'RT_LINEPERIOD' }; cnt = cnt+1;
scan{cnt} = {'h10000062', 'PRESCAN' }; cnt = cnt+1;
scan{cnt} = {'h10000063', 'SCAN_DIRECTIONZ' }; cnt = cnt+1;
scan{cnt} = {'h11000000', 'TIMERS' }; cnt = cnt+1;
scan{cnt} = {'h12000000', 'TIMER' }; cnt = cnt+1;
scan{cnt} = {'h12000001', 'TIMER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h12000003', 'INTERVAL' }; cnt = cnt+1;
scan{cnt} = {'h12000004', 'TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h12000005', 'TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'h13000000', 'MARKERS' }; cnt = cnt+1;
scan{cnt} = {'h14000000', 'MARKER' }; cnt = cnt+1;
scan{cnt} = {'h14000001', 'MARKER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h14000002', 'DESCRIPTION' }; cnt = cnt+1;
scan{cnt} = {'h14000003', 'TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h14000004', 'TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'h20000000', 'TRACKS' }; cnt = cnt+1;
scan{cnt} = {'h30000000', 'LASERS' }; cnt = cnt+1;
scan{cnt} = {'h40000000', 'TRACK' }; cnt = cnt+1;
scan{cnt} = {'h40000001', 'MULTIPLEX_TYPE' }; cnt = cnt+1;
scan{cnt} = {'h40000002', 'MULTIPLEX_ORDER' }; cnt = cnt+1;
scan{cnt} = {'h40000003', 'SAMPLING_MODE' }; cnt = cnt+1;
scan{cnt} = {'h40000004', 'SAMPLING_METHOD' }; cnt = cnt+1;
scan{cnt} = {'h40000005', 'SAMPLING_NUMBER' }; cnt = cnt+1;
scan{cnt} = {'h40000006', 'ENTRY_ACQUIRE' }; cnt = cnt+1;
scan{cnt} = {'h40000007', 'OBSERVATION_TIME' }; cnt = cnt+1;
scan{cnt} = {'h4000000B', 'TIME_BETWEEN_STACKS' }; cnt = cnt+1;
scan{cnt} = {'h4000000C', 'TRACK_NAME' }; cnt = cnt+1;
scan{cnt} = {'h4000000D', 'COLLIMATOR1_NAME' }; cnt = cnt+1;
scan{cnt} = {'h4000000E', 'COLLIMATOR1_POSITION' }; cnt = cnt+1;
scan{cnt} = {'h4000000F', 'COLLIMATOR2_NAME' }; cnt = cnt+1;
scan{cnt} = {'h40000010', 'COLLIMATOR2_POSITION' }; cnt = cnt+1;
scan{cnt} = {'h40000011', 'BLEACH_TRACK' }; cnt = cnt+1;
scan{cnt} = {'h40000012', 'BLEACH_AFTER_SCAN_NUMBER' }; cnt = cnt+1;
scan{cnt} = {'h40000013', 'BLEACH_SCAN_NUMBER' }; cnt = cnt+1;
scan{cnt} = {'h40000014', 'TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h40000015', 'TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'h40000016', 'IS_RATIO_TRACK' }; cnt = cnt+1;
scan{cnt} = {'h40000017', 'BLEACH_COUNT' }; cnt = cnt+1;
scan{cnt} = {'h40000018', 'SPI_CENTER_WAVELENGTH' }; cnt = cnt+1;
scan{cnt} = {'h40000019', 'PIXEL_TIME' }; cnt = cnt+1;
scan{cnt} = {'h40000020', 'ID_CONDENSOR_FRONTLENS' }; cnt = cnt+1;
scan{cnt} = {'h40000021', 'CONDENSOR_FRONTLENS' }; cnt = cnt+1;
scan{cnt} = {'h40000022', 'ID_FIELD_STOP' }; cnt = cnt+1;
scan{cnt} = {'h40000023', 'FIELD_STOP_VALUE' }; cnt = cnt+1;
scan{cnt} = {'h40000024', 'ID_CONDENSOR_APERTURE' }; cnt = cnt+1;
scan{cnt} = {'h40000025', 'CONDENSOR_APERTURE' }; cnt = cnt+1;
scan{cnt} = {'h40000026', 'ID_CONDENSOR_REVOLVER' }; cnt = cnt+1;
scan{cnt} = {'h40000027', 'CONDENSOR_FILTER' }; cnt = cnt+1;
scan{cnt} = {'h40000028', 'ID_TRANSMISSION_FILTER1' }; cnt = cnt+1;
scan{cnt} = {'h40000029', 'ID_TRANSMISSION1' }; cnt = cnt+1;
scan{cnt} = {'h40000030', 'ID_TRANSMISSION_FILTER2' }; cnt = cnt+1;
scan{cnt} = {'h40000031', 'ID_TRANSMISSION2' }; cnt = cnt+1;
scan{cnt} = {'h40000032', 'REPEAT_BLEACH' }; cnt = cnt+1;
scan{cnt} = {'h40000033', 'ENABLE_SPOT_BLEACH_POS' }; cnt = cnt+1;
scan{cnt} = {'h40000034', 'SPOT_BLEACH_POSX' }; cnt = cnt+1;
scan{cnt} = {'h40000035', 'SPOT_BLEACH_POSY' }; cnt = cnt+1;
scan{cnt} = {'h40000036', 'BLEACH_POSITION_Z' }; cnt = cnt+1;
scan{cnt} = {'h40000037', 'ID_TUBELENS' }; cnt = cnt+1;
scan{cnt} = {'h40000038', 'ID_TUBELENS_POSITION' }; cnt = cnt+1;
scan{cnt} = {'h40000039', 'TRANSMITTED_LIGHT' }; cnt = cnt+1;
scan{cnt} = {'h4000003a', 'REFLECTED_LIGHT' }; cnt = cnt+1;
scan{cnt} = {'h4000003b', 'TRACK_SIMULTAN_GRAB_AND_BLEACH' }; cnt = cnt+1;
scan{cnt} = {'h4000003c', 'BLEACH_PIXEL_TIME' }; cnt = cnt+1;
scan{cnt} = {'h50000000', 'LASER' }; cnt = cnt+1;
scan{cnt} = {'h50000001', 'LASER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h50000002', 'LASER_ACQUIRE' }; cnt = cnt+1;
scan{cnt} = {'h50000003', 'LASER_POWER' }; cnt = cnt+1;
scan{cnt} = {'h60000000', 'DETECTION_CHANNELS' }; cnt = cnt+1;
scan{cnt} = {'h70000000', 'DETECTION_CHANNEL' }; cnt = cnt+1;
scan{cnt} = {'h70000003', 'DETECTOR_GAIN' }; cnt = cnt+1;
scan{cnt} = {'h70000005', 'AMPLIFIER_GAIN' }; cnt = cnt+1;
scan{cnt} = {'h70000007', 'AMPLIFIER_OFFSET' }; cnt = cnt+1;
scan{cnt} = {'h70000009', 'PINHOLE_DIAMETER' }; cnt = cnt+1;
scan{cnt} = {'h7000000B', 'ENTRY_ACQUIRE' }; cnt = cnt+1;
scan{cnt} = {'h7000000C', 'DETECTOR_NAME' }; cnt = cnt+1;
scan{cnt} = {'h7000000D', 'AMPLIFIER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h7000000E', 'PINHOLE_NAME' }; cnt = cnt+1;
scan{cnt} = {'h7000000F', 'FILTER_SET_NAME' }; cnt = cnt+1;
scan{cnt} = {'h70000010', 'FILTER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h70000013', 'INTEGRATOR_NAME' }; cnt = cnt+1;
scan{cnt} = {'h70000014', 'DETECTION_CHANNEL_NAME' }; cnt = cnt+1;
scan{cnt} = {'h70000015', 'DETECTOR_GAIN_BC1' }; cnt = cnt+1;
scan{cnt} = {'h70000016', 'DETECTOR_GAIN_BC2' }; cnt = cnt+1;
scan{cnt} = {'h70000017', 'AMPLIFIER_GAIN_BC1' }; cnt = cnt+1;
scan{cnt} = {'h70000018', 'AMPLIFIER_GAIN_BC2' }; cnt = cnt+1;
scan{cnt} = {'h70000019', 'AMPLIFIER_OFFSET_BC1' }; cnt = cnt+1;
scan{cnt} = {'h70000020', 'AMPLIFIER_OFFSET_BC2' }; cnt = cnt+1;
scan{cnt} = {'h70000021', 'SPECTRAL_SCAN_CHANNELS' }; cnt = cnt+1;
scan{cnt} = {'h70000022', 'SPI_WAVE_LENGTH_START' }; cnt = cnt+1;
scan{cnt} = {'h70000023', 'SPI_WAVELENGTH_END' }; cnt = cnt+1;
scan{cnt} = {'h70000026', 'DYE_NAME' }; cnt = cnt+1;
scan{cnt} = {'h70000027', 'DYE_FOLDER' }; cnt = cnt+1;
scan{cnt} = {'h80000000', 'ILLUMINATION_CHANNELS' }; cnt = cnt+1;
scan{cnt} = {'h90000000', 'ILLUMINATION_CHANNEL' }; cnt = cnt+1;
scan{cnt} = {'h90000001', 'ILL_NAME' }; cnt = cnt+1;
scan{cnt} = {'h90000002', 'POWER' }; cnt = cnt+1;
scan{cnt} = {'h90000003', 'WAVELENGTH' }; cnt = cnt+1;
scan{cnt} = {'h90000004', 'ACQUIRE' }; cnt = cnt+1;
scan{cnt} = {'h90000005', 'DETCHANNEL_NAME' }; cnt = cnt+1;
scan{cnt} = {'h90000006', 'POWER_BC1' }; cnt = cnt+1;
scan{cnt} = {'h90000007', 'POWER_BC2' }; cnt = cnt+1;
scan{cnt} = {'hA0000000', 'BEAM_SPLITTERS' }; cnt = cnt+1;
scan{cnt} = {'hB0000000', 'BEAM_SPLITTER' }; cnt = cnt+1;
scan{cnt} = {'hB0000001', 'FILTER_SET' }; cnt = cnt+1;
scan{cnt} = {'hB0000002', 'FILTER' }; cnt = cnt+1;
scan{cnt} = {'hB0000003', 'BS_NAME' }; cnt = cnt+1;
scan{cnt} = {'hC0000000', 'DATA_CHANNELS' }; cnt = cnt+1;
scan{cnt} = {'hD0000000', 'DATA_CHANNEL' }; cnt = cnt+1;
scan{cnt} = {'hD0000001', 'DATA_NAME' }; cnt = cnt+1;
scan{cnt} = {'hD0000004', 'COLOR' }; cnt = cnt+1;
scan{cnt} = {'hD0000005', 'SAMPLETYPE' }; cnt = cnt+1;
scan{cnt} = {'hD0000006', 'BITS_PER_SAMPLE' }; cnt = cnt+1;
scan{cnt} = {'hD0000007', 'RATIO_TYPE' }; cnt = cnt+1;
scan{cnt} = {'hD0000008', 'RATIO_TRACK1' }; cnt = cnt+1;
scan{cnt} = {'hD0000009', 'RATIO_TRACK2' }; cnt = cnt+1;
scan{cnt} = {'hD000000A', 'RATIO_CHANNEL1' }; cnt = cnt+1;
scan{cnt} = {'hD000000B', 'RATIO_CHANNEL2' }; cnt = cnt+1;
scan{cnt} = {'hD000000C', 'RATIO_CONST1' }; cnt = cnt+1;
scan{cnt} = {'hD000000D', 'RATIO_CONST2' }; cnt = cnt+1;
scan{cnt} = {'hD000000E', 'RATIO_CONST3' }; cnt = cnt+1;
scan{cnt} = {'hD000000F', 'RATIO_CONST4' }; cnt = cnt+1;
scan{cnt} = {'hD0000010', 'RATIO_CONST5' }; cnt = cnt+1;
scan{cnt} = {'hD0000011', 'RATIO_CONST6' }; cnt = cnt+1;
scan{cnt} = {'hD0000012', 'RATIO_FIRST_IMAGES1' }; cnt = cnt+1;
scan{cnt} = {'hD0000013', 'RATIO_FIRST_IMAGES2' }; cnt = cnt+1;
scan{cnt} = {'hD0000014', 'DYE_NAME' }; cnt = cnt+1;
scan{cnt} = {'hD0000015', 'DYE_FOLDER' }; cnt = cnt+1;
scan{cnt} = {'hD0000016', 'SPECTRUM' }; cnt = cnt+1;
scan{cnt} = {'hD0000017', 'ACQUIRE' }; cnt = cnt+1;
scan{cnt} = {'h11000000', 'TIMERS' }; cnt = cnt+1;
scan{cnt} = {'h12000000', 'TIMER' }; cnt = cnt+1;
scan{cnt} = {'h12000001', 'TIMER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h12000003', 'TIMER_INTERVAL' }; cnt = cnt+1;
scan{cnt} = {'h12000004', 'TIMER_TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h12000005', 'TIMER_TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'h13000000', 'MARKERS' }; cnt = cnt+1;
scan{cnt} = {'h14000000', 'MARKER' }; cnt = cnt+1;
scan{cnt} = {'h14000001', 'MARKER_NAME' }; cnt = cnt+1;
scan{cnt} = {'h14000002', 'MARKER_DESCRIPTION' }; cnt = cnt+1;
scan{cnt} = {'h14000003', 'MARKER_TRIGGER_IN' }; cnt = cnt+1;
scan{cnt} = {'h14000004', 'MARKER_TRIGGER_OUT' }; cnt = cnt+1;
scan{cnt} = {'hFFFFFFFF', 'END_SUBBLOCK' };
obj.propertyList = scan;
end
end
end