ZVI ROI fixes (develop)

[ghost]

As for dev_4_4 (#471)

[ghost]

--test zeiss-zvi

[pwalczysko]

@rleigh-dundee It would be good to have a link to the dev_4_4 PR in here. It is #471.

[pwalczysko]

Imported test_images_roi/zvi folder to gretzky (user-4, group read-write-1, Project test ROI Petr).
Opened first 3 images - no ROIs there (but this might be expected, possibly).
Opened image nr. 4 - no ROIs there (certainly should be something there ?) - see screenshot below.

[ghost]

I don't think that there's a problem here. For the file in question, I've run

% CLASSPATH=artifacts/loci_tools.jar SCIFIO_DEVEL=1 ./tools/showinf -nopix -omexml -novalid /ome/data_repo/test_images_roi/zvi/roi-line.zvi

and in the resulting OME-XML, we get:

   <ROI xmlns="http://www.openmicroscopy.org/Schemas/ROI/2012-06" ID="ROI:0" Name="Text">
      <Union>
         <Shape ID="Shape:0:0" Text="Line (straight)">
            <Label X="2.0" Y="120.0"/>
         </Shape>
         <Shape ID="Shape:0:1" Text="Line (straight)">
            <Rectangle Height="104.0" Width="289.0" X="2.0" Y="120.0"/>
         </Shape>
      </Union>
   </ROI>
   <ROI xmlns="http://www.openmicroscopy.org/Schemas/ROI/2012-06" ID="ROI:1" Name="Line">
      <Union>
         <Shape ID="Shape:1:0">
            <Line X1="49.0" X2="250.00000000000006" Y1="290.0" Y2="341.0"/>
         </Shape>
      </Union>
   </ROI>
   <ROI xmlns="http://www.openmicroscopy.org/Schemas/ROI/2012-06" ID="ROI:2" Name="Line">
      <Union>
         <Shape ID="Shape:2:0">
            <Line X1="66.0" X2="152.0" Y1="395.0" Y2="368.0"/>
         </Shape>
      </Union>
   </ROI>
   <ROI xmlns="http://www.openmicroscopy.org/Schemas/ROI/2012-06" ID="ROI:3" Name="Line">
      <Union>
         <Shape ID="Shape:3:0">
            <Line X1="312.0" X2="296.0" Y1="269.0" Y2="421.0"/>
         </Shape>
      </Union>
   </ROI>
   <ROI xmlns="http://www.openmicroscopy.org/Schemas/ROI/2012-06" ID="ROI:4" Name="Line">
      <Union>
         <Shape ID="Shape:4:0">
            <Line X1="175.0" X2="367.0" Y1="445.0" Y2="451.0"/>
         </Shape>
      </Union>
   </ROI>

[pwalczysko]

Agreed that the ROIs are there - they can be seen using both ImageJ and Fiji. When taking the images from test_images_roi/zvi/ folder one by one in the order of appearance, we have:

1. 18 ROIs
2. 6 ROIs
3. 1 ROI
4. 5 ROIs (=roi-line.zvi)
5. 1 ROI
6. 1 ROI
7. 1 ROI
8. 6 ROIs
9. NO ROI (...scalebar.zvi)

If this is how it should be, than the PR is probably ok.

[ghost]

Hmm, some of those aren't quite right. Some of the more esoteric types (scale bar, angle, length measurement) are being picked up as a single rectangle which is not right. Something is definitely being mis-parsed there.

I'll take a look at exactly what's going on for those types. This also affects 4.4.7/dev_4_4 I'm afraid. I can either open a separate ticket and/or PR for that or fix it for this PR and backport the extra bits to 4.4 after.

[ghost]

Argh, it's definitely this PR that introduces that was well. It's relating to b3a902d where it's parsing the ROI name as the font name, so it's getting confused when it comes to reading the points.

[ghost]

The issues noted with respect to some ROIs not being parsed is now fixed.

[joshmoore]

@rleigh-dundee: will any of the commits need to be re-rebased?

[joshmoore]

Note: see gh-486 for the backporting of these last fixes.

[ghost]

Yes, that's the rebased patches, and everything else in this PR was already merged into dev_4_4/

[melissalinkert]

--test zeiss-zvi

Happy to merge if overnight builds are green.