ome.xml indentation

[wmoore]

Discussing with Josh and Andrew today, we should aim to standardise all indentation in XML to 4 spaces.

Generating ome.xml like this:

$ java -Xmx512m loci.formats.tools.ImageInfo -nopix -omexml-only /Path/to/file

produces xml with 3 spaces.

I can subsequently format using

$ export XMLLINT_INDENT="    "    # 4 spaces
$ xmllint --format path/to/file.xml > formatted_file.xml

but this is not ideal!

[mlinkert]

This commit adds an option to specify the number of spaces:

​https://github.com/melissalinkert/bioformats/commit/3e2634e6766837de5202b5b11952b76b7860ac0f

So just add '-xmlspaces 4'. I decided not to make 4 spaces the default, as I didn't want to risk hurting anyone who was relying upon the fact that 3 spaces were being used (e.g. anyone doing a plain diff of the output). If you want, I can wrap all of these new options ('-omexml-only -no-sas -xmlspaces 4') into a single option ('-generate-configuration'?) so that it's easier to work with.

In any case, passing back for validation that this works as desired.

[wmoore]

This is working great.
E.g. I am now doing this:

$ java -Xmx512m loci.formats.tools.ImageInfo -nopix -omexml-only -no-sas -xmlspaces 4 /Users/will/Documents/biology-data/Test-Import-Images/Martin/Leica-SP2/samples-SP2/samples-SP2.lei

<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2011-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2011-06 http://www.openmicroscopy.org/Schemas/OME/2011-06/ome.xsd">
    <Instrument ID="Instrument:0">
        <Detector ID="Detector:0:0" Type="PMT"/>
        <Detector ID="Detector:0:1" Offset="-34.599999999999994" Type="PMT" Voltage="742.0867526377491"/>
...