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#------------------------------------------------------------------------------
# File: ZISRAW.pm
#
# Description: Read ZISRAW (CZI) meta information
#
# Revisions: 2020-08-07 - P. Harvey Created
#
# References: 1) https://www.zeiss.com/microscopy/us/products/microscope-software/zen/czi.html
#------------------------------------------------------------------------------
package Image::ExifTool::ZISRAW;
use strict;
use vars qw($VERSION);
use Image::ExifTool qw(:DataAccess :Utils);
$VERSION = '1.01';
%Image::ExifTool::ZISRAW::Main = (
PROCESS_PROC => \&Image::ExifTool::ProcessBinaryData,
GROUPS => { 0 => 'File', 1 => 'File', 2 => 'Image' },
NOTES => q{
As well as the header information listed below, ExifTool also extracts the
top-level XML-based metadata from Zeiss Integrated Software RAW (ZISRAW) CZI
files.
},
0x20 => {
Name => 'ZISRAWVersion',
Format => 'int32u[2]',
PrintConv => '$val =~ tr/ /./; $val',
},
0x30 => {
Name => 'PrimaryFileGUID',
Format => 'undef[16]',
ValueConv => 'unpack("H*",$val)',
},
0x40 => {
Name => 'FileGUID',
Format => 'undef[16]',
ValueConv => 'unpack("H*",$val)',
},
);
#------------------------------------------------------------------------------
# Shorten obscenely long CZI tag names
# Inputs: Tag name
# Returns: Shortened tag name
sub ShortenTagNames($)
{
local $_;
$_ = shift;
s/^HardwareSetting//;
s/^DevicesDevice/Device/;
s/LightPathNode//g;
s/Successors//g;
s/ExperimentExperiment/Experiment/g;
s/ObjectivesObjective/Objective/;
s/ChannelsChannel/Channel/;
s/TubeLensesTubeLens/TubeLens/;
s/^ExperimentHardwareSettingsPoolHardwareSetting/HardwareSetting/;
s/SharpnessMeasureSetSharpnessMeasure/Sharpness/;
s/FocusSetupAutofocusSetup/Autofocus/;
s/TracksTrack/Track/;
s/ChannelRefsChannelRef/ChannelRef/;
s/ChangerChanger/Changer/;
s/ElementsChangerElement/Changer/;
s/ChangerElements/Changer/;
s/ContrastChangerContrast/Contrast/;
s/KeyFunctionsKeyFunction/KeyFunction/;
s/ManagerContrastManager(Contrast)?/ManagerContrast/;
s/ObjectiveChangerObjective/ObjectiveChanger/;
s/ManagerLightManager/ManagerLight/;
s/WavelengthAreasWavelengthArea/WavelengthArea/;
s/ReflectorChangerReflector/ReflectorChanger/;
s/^StageStageAxesStageAxis/StageAxis/;
s/ShutterChangerShutter/ShutterChanger/;
s/OnOffChangerOnOff/OnOffChanger/;
s/UnsharpMaskStateUnsharpMask/UnsharpMask/;
s/Acquisition/Acq/;
s/Continuous/Cont/;
s/Resolution/Res/;
s/Experiment/Expt/g;
s/Threshold/Thresh/;
s/Reference/Ref/;
s/Magnification/Mag/;
s/Original/Orig/;
s/FocusSetupFocusStrategySetup/Focus/;
s/ParametersParameter/Parameter/;
s/IntervalInfo/Interval/;
s/ExptBlocksAcqBlock/AcqBlock/;
s/MicroscopesMicroscope/Microscope/;
s/TimeSeriesInterval/TimeSeries/;
s/Interval(.*Interval)/$1/;
s/SingleTileRegionsSingleTileRegion/SingleTileRegion/;
s/AcquisitionMode//;
s/DetectorsDetector/Detector/;
s/Setup//;
s/Setting//;
s/TrackTrack/Track/;
s/AnalogOutMaximumsAnalogOutMaximum/AnalogOutMaximum/;
s/AnalogOutMinimumsAnalogOutMinimum/AnalogOutMinimum/;
s/DigitalOutLabelsDigitalOutLabelLabel/DigitalOutLabelLabel/;
s/(VivaTomeOpticalSectionInformation)+VivaTomeOpticalSectionInformation/VivaTomeOpticalSectionInformation/;
s/FocusDefiniteFocus/FocusDefinite/;
s/ChangerChanger/Changer/;
s/Calibration/Cal/;
s/LightSwitchChangerRLTLSwitch/LightSwitchChangerRLTL/;
s/Parameters//;
s/Fluorescence/Fluor/;
s/CameraGeometryCameraGeometry/CameraGeometry/;
s/CameraCamera/Camera/;
s/DetectorsCamera/Camera/;
s/FilterChangerLeftChangerEmissionFilter/LeftChangerEmissionFilter/;
s/SwitchingStatesSwitchingState/SwitchingState/;
s/Information/Info/;
s/SubDimensions?//g;
s/Setups?//;
s/Parameters?//;
s/Calculate/Calc/;
s/Visibility/Vis/;
s/Orientation/Orient/;
s/ListItems/Items/;
s/Increment/Incr/;
s/Parameter/Param/;
s/(ParfocalParcentralValues)+ParfocalParcentralValue/Parcentral/;
s/ParcentralParcentral/Parcentral/;
s/CorrFocusCorrection/FocusCorr/;
s/(ApoTomeDepthInfo)+Element/ApoTomeDepth/;
s/(ApoTomeClickStopInfo)+Element/ApoTomeClickStop/;
s/DepthDepth/Depth/;
s/(Devices?)+Device/Device/;
s/(BeamPathNode)+/BeamPathNode/;
s/BeamPathsBeamPath/BeamPath/g;
s/BeamPathBeamPath/BeamPath/g;
s/Configuration/Config/;
s/StageAxesStageAxis/StageAxis/;
s/RangesRange/Range/;
s/DataGridDatasGridData(Grid)?/DataGrid/;
s/DataMicroscopeDatasMicroscopeData(Microscope)?/DataMicroscope/;
s/DataWegaDatasWegaData/DataWega/;
s/ClickStopPositionsClickStopPosition/ClickStopPosition/;
s/LightSourcess?LightSource(Settings)?(LightSource)?/LightSource/;
s/FilterSetsFilterSet/FilterSet/;
s/EmissionFiltersEmissionFilter/EmissionFilter/;
s/ExcitationFiltersExcitationFilter/ExcitationFilter/;
s/FiltersFilter/Filter/;
s/DichroicsDichroic/Dichronic/;
s/WavelengthsWavelength/Wavelength/;
s/MultiTrackSetup/MultiTrack/;
s/TrackTrack/Track/;
s/DataGrabberSetup/DataGrabber/;
s/CameraFrameSetup/CameraFrame/;
s/TimeSeries(TimeSeries|Setups)/TimeSeries/;
s/FocusFocus/Focus/;
s/FocusAutofocus/Autofocus/;
s/Focus(Hardware|Software)(Autofocus)+/Autofocus$1/;
s/AutofocusAutofocus/Autofocus/;
return $_;
}
#------------------------------------------------------------------------------
# Extract metadata from a ZISRAW (CZI) image
# Inputs: 0) ExifTool object reference, 1) dirInfo reference
# Returns: 1 on success, 0 if this wasn't a valid CZI file
sub ProcessCZI($$)
{
my ($et, $dirInfo) = @_;
my $raf = $$dirInfo{RAF};
my ($buff, $tagTablePtr);
# verify this is a valid CZI file
return 0 unless $raf->Read($buff, 100) == 100;
return 0 unless $buff =~ /^ZISRAWFILE\0{6}/;
$et->SetFileType();
SetByteOrder('II');
my %dirInfo = (
DataPt => \$buff,
DirStart => 0,
DirLen => length($buff),
);
$tagTablePtr = GetTagTable('Image::ExifTool::ZISRAW::Main');
$et->ProcessDirectory(\%dirInfo, $tagTablePtr);
# read the metadata section
my $pos = Get64u(\$buff, 92) or return 1;
$raf->Seek($pos, 0) or $et->Warn('Error seeking to metadata'), return 0;
$raf->Read($buff, 288) == 288 or $et->Warn('Error reading metadata header'), return 0;
$buff =~ /^ZISRAWMETADATA\0\0/ or $et->Warn('Invalid metadata header'), return 0;
my $len = Get32u(\$buff, 32);
$len < 200000000 or $et->Warn('Metadata section too large. Ignoring'), return 0;
$raf->Read($buff, $len) or $et->Warn('Error reading XML metadata'), return 0;
$et->FoundTag('XML', $buff); # extract as a block
$tagTablePtr = GetTagTable('Image::ExifTool::XMP::XML');
$dirInfo{DirLen} = length $buff;
# shorten tag names somewhat by removing 'ImageDocumentMetadata' prefix from all
$$et{XmpIgnoreProps} = [ 'ImageDocument', 'Metadata', 'Information' ];
$$et{ShortenXmpTags} = \&ShortenTagNames;
$et->ProcessDirectory(\%dirInfo, $tagTablePtr);
return 1;
}
1; # end
__END__
=head1 NAME
Image::ExifTool::ZISRAW - Read ZISRAW (CZI) meta information
=head1 SYNOPSIS
This module is used by Image::ExifTool
=head1 DESCRIPTION
This module contains definitions required by Image::ExifTool to read
metadata from Zeiss Integrated Software RAW (ZISRAW) CZI files.
=head1 AUTHOR
Copyright 2003-2023, Phil Harvey (philharvey66 at gmail.com)
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
=head1 REFERENCES
=over 4
=item L<https://www.zeiss.com/microscopy/us/products/microscope-software/zen/czi.html>
=back
=head1 SEE ALSO
L<Image::ExifTool::TagNames/ZISRAW Tags>,
L<Image::ExifTool(3pm)|Image::ExifTool>
=cut
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