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Hi Mario,
<div class=""> </div>
<div class="">as always thanks for the email and the link to your sample file.</div>
<div class="">Which version of Bio-Formats are you using? With the version 5.1.4 of</div>
<div class="">Bio-Formats, the separator you are mentioning is indeed converted to</div>
<div class="">“ #13 #10” and should be properly handled in the parseXML step [1] [2].</div>
<div class=""><br class="">
</div>
<div class="">So the list of values stored in the first Description property is correctly</div>
<div class="">parsed into metadata key/value pairs when calling showing on your</div>
<div class="">sample file:</div>
<div class=""><br class="">
</div>
<div class=""> $ showinf -nopix bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif <br class="">
Checking file format [Metamorph TIFF]<br class="">
Initializing reader<br class="">
MetamorphTiffReader initializing bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif</div>
<div class="">...<br class="">
Reading global metadata<br class="">
ApplicationName: MetaMorph<br class="">
ApplicationVersion: 5.1.0.46<br class="">
Binning: 1 x 1<br class="">
BitsPerSample: 16<br class="">
Camera Bit Depth: 14<br class="">
Camera Shutter: Always Open<br class="">
Clear Count: 2<br class="">
Clear Mode: CLEAR PRE SEQUENCE<br class="">
Compression: Uncompressed<br class="">
DateTime: 20150828 10:17:04.11<br class="">
Digitizer: 10 MHz<br class="">
Exposure: 10 ms<br class="">
Frames to Average: 1<br class="">
Gain: Gain 1 (0.5x)<br class="">
ImageLength: 1040<br class="">
ImageWidth: 1392<br class="">
ImageXpress Micro Filter Cube: DAPI<br class="">
ImageXpress Micro Objective: 10x Plan Fluor<br class="">
ImageXpress Micro Shutter: Open<br class="">
Lumencor Blue Intensity: 255<br class="">
Lumencor Blue Shutter: Closed<br class="">
Lumencor Cyan Intensity: 255<br class="">
Lumencor Cyan Shutter: Closed<br class="">
Lumencor Green Intensity: 255<br class="">
Lumencor Green Shutter: Closed<br class="">
Lumencor Red Intensity: 255<br class="">
Lumencor Red Shutter: Closed<br class="">
Lumencor Teal Intensity: 255<br class="">
Lumencor Teal Shutter: Closed<br class="">
Lumencor UV Intensity: 255<br class="">
Lumencor UV Shutter: Closed<br class="">
MetaDataPhotometricInterpretation: Monochrome<br class="">
MetaDataVersion: 1<br class="">
NewSubfileType: 2<br class="">
NumberOfChannels: 1<br class="">
Orientation: 1st row - top; 1st column - left<br class="">
PhotometricInterpretation: BlackIsZero<br class="">
Region: 1392 x 1040, offset at (0, 0)<br class="">
SamplesPerPixel: 1<br class="">
Shading: Off<br class="">
Software: MetaSeries<br class="">
Subtract: Off<br class="">
Temperature: -29.75<br class="">
Trigger Mode: Normal (TIMED)</div>
<div class="">…</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">[1] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/src/loci/formats/in/MetamorphTiffReader.java#L244" class="">https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/src/loci/formats/in/MetamorphTiffReader.java#L244</a></div>
<div class="">[2] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java#L128" class="">https://github.com/openmicroscopy/bioformats/blob/v5.1.4/components/formats-gpl/src/loci/formats/in/MetamorphHandler.java#L128</a></div>
<div class=""><br class="">
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<blockquote type="cite" class="">
<div class="">On 4 Sep 2015, at 12:52, Mario Emmenlauer <<a href="mailto:mario@emmenlauer.de" class="">mario@emmenlauer.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><br class="">
Dear Bio-Formats developers,<br class="">
<br class="">
I have a small issue with MetaXpress meta data. I could already track<br class="">
down a bit of detail: The MetaXpress meta data can contain an XML<br class="">
string, that will be read in loci/formats/in/MetamorphTiffReader.java.<br class="">
The XML can contain a value="..." that is itself a list again, which<br class="">
in earlier versions of MetaXpress was separated by "&#13;&#10;"<br class="">
In newer versions of MetaXpress there seems to be a change, that the<br class="">
list is instead separated by " " (note the different ampersand).<br class="">
<br class="">
Now the problem comes around line 244 of MetamorphTiffReader.java, where<br class="">
there is a call to XMLTools.sanitizeXML(ifd.getComment()); After the<br class="">
sanitizing, the ampersand is gone, leaving " #13; #10;" behind, which<br class="">
is a problem for my subsequent parsers. Would it be possible to change<br class="">
the behavior of sanitizeXML() to leave intact the list separator? Or<br class="">
maybe you have another better solution...<br class="">
<br class="">
The image I used is here:<br class="">
<a href="http://data.marssoft.de/bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif" class="">http://data.marssoft.de/bxyz-505_wA03_s1_z1_t1_cDAPI_u1.tif</a><br class="">
<br class="">
All the best, and thanks for your great work,<br class="">
<br class="">
Mario Emmenlauer<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
-- <br class="">
Mario Emmenlauer BioDataAnalysis Mobil: +49-(0)151-68108489<br class="">
Balanstrasse 43 mailto: mario.emmenlauer * <a href="http://unibas.ch" class="">
unibas.ch</a><br class="">
D-81669 München <a href="http://www.marioemmenlauer.de/" class="">http://www.marioemmenlauer.de/</a><br class="">
<br class="">
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</blockquote>
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