tiffcomment: fix -version, -no-upgrade, -debug, -trace

[melissalinkert]

tiffcomment previously did not allow -version, -debug or -trace, and would incorrectly indicate that -no-upgrade was an unsupported option.

All 4 options should now behave as they do in showinf and bfconvert. In particular, tiffcomment -debug ... should indicate the upgrade check status and tiffcomment -debug -no-upgrade ... should indicate that the upgrade check is skipped.

I have not attempted to modernize option parsing here, as that's a bigger project, and likely something we'd want to do across all of the tools at once. This PR should hopefully help in the near term though.

[sbesson]

With Bio-Formats 8.0.1

sbesson@Sebastiens-MacBook-Pro-3 Downloads % ./bftools/tiffcomment -version
Warning: unknown flag: -version
sbesson@Sebastiens-MacBook-Pro-3 Downloads % ./bftools/tiffcomment -no-upgrade 4D-series.ome.btf 
Warning: unknown flag: -no-upgrade
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.btf"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData></Pixels></Image></OME>
sbesson@Sebastiens-MacBook-Pro-3 Downloads % ./bftools/tiffcomment -debug 4D-series.ome.btf 
Warning: unknown flag: -debug
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.btf"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData></Pixels></Image></OME>

Using a local build from the HEAD of this branch

sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment -version
Version: 8.1.0-SNAPSHOT
Build date: 12 December 2024
VCS revision: f33369f89747ed27d2f7e95de6b533fd39c63302
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment -no-upgrade -debug ~/Downloads/4D-series.ome.btf 
Skipping upgrade check
Using mapped byte buffer? false
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.btf"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData></Pixels></Image></OME>
sbesson@Sebastiens-MacBook-Pro-3 bioformats %  ./tools/tiffcomment -no-upgrade ~/Downloads/4D-series.ome.btf 
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.btf"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.btf">urn:uuid:80e2fbd6-4fc1-42ea-9e7d-048406953227</UUID></TiffData></Pixels></Image></OME>

The changes look good. Can the usage output be updated with the new supported options?

[sbesson]

Thanks @melissalinkert, one nitpicky question about the expected behavior for the -version command. Otherwise, this should be ready to merge once it the latest commits have been validated by a nightly CI build.

[chris-allan]

I'm getting weird behaviour with a local build with the logging (specifically DEBUG logging showing up without -debug). Is this just to do with how the Maven JARs are built?

$ BF_DEVEL=1 CLASSPATH=./components/bundles/bioformats_package/target/bioformats_package-8.1.0-SNAPSHOT.jar tools/tiffcomment ../sticher/emulated.ome.tif -version
Version: 8.1.0-SNAPSHOT
Build date: 12 December 2024
VCS revision: b8d3ae1835477f63fb42ed7ef23318afaf5fcafb

$ BF_DEVEL=1 CLASSPATH=./components/bundles/bioformats_package/target/bioformats_package-8.1.0-SNAPSHOT.jar tools/tiffcomment path/to/blarg.ome.tif
23:10:50.120 [main] DEBUG loci.formats.UpgradeChecker -- No update needed
23:10:50.131 [main] DEBUG loci.common.NIOByteBufferProvider -- Using mapped byte buffer? false
<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
...

[melissalinkert]

Running with BF_DEVEL=1 and without including tools/logback.xml on the CLASSPATH means you get the default "unconfigured" logging. I expect that adding tools/logback.xml to the CLASSPATH should be enough to get normal logging.

[sbesson]

The updated behavior and usage look good

sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment 
Usage:
tiffcomment [-version] [-debug] [-trace] [-no-upgrade] [-set comment] [-edit] file1 [file2 ...]

This tool requires an ImageDescription tag to be present in the TIFF file. 

If using the '-set' option, the new TIFF comment must be specified and may take any of the following forms:

  * the text of the comment, e.g. 'new comment!'
  * the name of the file containing the text of the comment, e.g. 'file.xml'
  * '-', to enter the comment using stdin.  Entering a blank line will
    terminate reading from stdin.

Additional options:
    -version: print the library version and exit
 -no-upgrade: do not perform the upgrade check
      -debug: enable DEBUG-level logging
      -trace: enable TRACE-level logging
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment -version
Version: 8.1.0-SNAPSHOT
Build date: 13 December 2024
VCS revision: b8d3ae1835477f63fb42ed7ef23318afaf5fcafb
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment -version ~/Downloads/4D-series.ome.tif 
Version: 8.1.0-SNAPSHOT
Build date: 13 December 2024
VCS revision: b8d3ae1835477f63fb42ed7ef23318afaf5fcafb
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment ~/Downloads/4D-series.ome.tif       
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData></Pixels></Image></OME>
sbesson@Sebastiens-MacBook-Pro-3 bioformats % ./tools/tiffcomment ~/Downloads/4D-series.ome.tif -debug
No update needed
Using mapped byte buffer? false
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData></Pixels></Image></OME>

Trying to reproduce @chris-allan scenario using BF_DEVEL, adding the directory containing logback.xml i.e. ./tools to the CLASSPATH allows to pick up the appropriate logging configuration

sbesson@Sebastiens-MacBook-Pro-3 bioformats % BF_DEVEL=1 CLASSPATH=./artifacts/bioformats_package.jar:./tools/logback.xml ./tools/tiffcomment ~/Downloads/4D-series.ome.tif 
10:08:19.865 [main] DEBUG loci.formats.UpgradeChecker -- No update needed
10:08:19.885 [main] DEBUG loci.common.NIOByteBufferProvider -- Using mapped byte buffer? false
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData></Pixels></Image></OME>
sbesson@Sebastiens-MacBook-Pro-3 bioformats % BF_DEVEL=1 CLASSPATH=./artifacts/bioformats_package.jar:./tools/ ./tools/tiffcomment ~/Downloads/4D-series.ome.tif 
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="3" IFD="8" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="4" IFD="9" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="0" IFD="10" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="1" IFD="11" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="2" IFD="12" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="3" IFD="13" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="2" FirstZ="4" IFD="14" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="0" IFD="15" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="1" IFD="16" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="2" IFD="17" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="3" IFD="18" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="3" FirstZ="4" IFD="19" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="0" IFD="20" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="1" IFD="21" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="2" IFD="22" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="3" IFD="23" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="4" FirstZ="4" IFD="24" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="0" IFD="25" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="1" IFD="26" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="2" IFD="27" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="3" IFD="28" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="5" FirstZ="4" IFD="29" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="0" IFD="30" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="1" IFD="31" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="2" IFD="32" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="3" IFD="33" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="6" FirstZ="4" IFD="34" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData></Pixels></Image></OME>
sbesson@Sebastiens-MacBook-Pro-3 bioformats % BF_DEVEL=1 CLASSPATH=./artifacts/bioformats_package.jar:./tools/ ./tools/tiffcomment ~/Downloads/4D-series.ome.tif -debug
No update needed
Using mapped byte buffer? false
<?xml version="1.0" encoding="UTF-8"?><!-- Warning: this comment is an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/. --><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="4D-series.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" SizeC="1" SizeT="7" SizeX="439" SizeY="167" SizeZ="5" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="1" IFD="1" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="2" IFD="2" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="3" IFD="3" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="0" FirstZ="4" IFD="4" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="0" IFD="5" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="6" PlaneCount="1"><UUID FileName="4D-series.ome.tif">urn:uuid:a5ae8c1b-ac04-4544-97c1-bbdd0bdf8629</UUID></TiffData><TiffData FirstC="0" FirstT="1" FirstZ="2" IFD="7" PlaneCount="1"><UUID 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[chris-allan]

👍

All good with adding tools to the CLASSPATH.