Thumbnail figure

[will-moore]

Adding support for "Thumbnail Figure" in web.

Script dialog has same functionality as Insight, but shows a preview of the Figure while updating parameters, in particular, sorting images by Tag.
The tag sorting strategy has changed a little in the script and UI: If an image is tagged by more than one of the chosen tags, it is shown "nested" in a hierarchy defined by the order the tags were chosen.

To test, need to have a couple of datasets with images tagged with various tags:

• Choose a number of images OR one or more datasets
• Launch Publication Options > Thumbnail Figure (toolbar top of right panel)
• Adjust "Images per row", choose Tags with/without "Include all thumbnails".
• Add and remove Tags and see if the thumbnails layout "makes sense". The thumbnails are grouped first by the first tag(s) chosen, and then grouped by subsequent tags IF they are tagged by more than 1 Tag.
• Compare the figure "Preview" in web UI and the figure generated by the script - should be equivalent, except that the script doesn't yet support "hierarchical" nesting of multiply tagged images (simply listed in order). See Group thumbs by tag (only show each thumb once) omero-scripts#27 for corresponding Script PR.

NB: This layout is a New feature, so it might need some usability feedback.

[ximenesuk]

On the whole this looks good and does what I expect. The final bullet point on comparing the preview raises a couple of issues. It isn't possible to change the preview by altering the images per row (see figure 1) but only by adding removing tags (see figure 2). But doing this by adding and then removing a tag leaves the preview labelled with "NOT TAGGED" (see figure 3) which, if there is no other sorting by tags, shouldn't be there. The label is not there in the generated figure.

So, either the preview should change as the number of images per row is changed or there should be a preview button. And, "NOT TAGGED" shouldn't appear if there are no tags used for sorting the images.

[ximenesuk]

All the changes above are excellent. Tested in Chrome and safari with no problems.

This time I have looked at sorting with multiple tags a little more. I have picked an extreme case where 6 images are tagged progressively with 6 tags, one image has 1 tag, a second has 2, etc. (user-1 andor dataset). If I sort by all the tags in order I get the first figure below, which is fine. If I use a different order I get the second, again fine in terms of the thumbnails. What it odd though is the second level labelling. The top thumbnail is tagged with 'TN-4 TN-6 TN-5' The second is tagged with 'TN-4 TN-6 TN-5' and 'TN-3' but the label above it is 'TN-6 TN-5 TN-3' Should it not be simply labelled 'TN-3', ie the only different tag from the whole set? Similar the ones below. Or, should the label on the left be just 'TN-4' with the top thumbnail being 'TN-6 TN-5'. The this image gives a more extreme example of the labelling where the major label on the left is all of the tags.

More generally, what is the sorting or bucketing strategy? I assume you are looking at the tags from left to right and picking out all the ones with the first tag for a major label on the left? So the order of the tags changes the bucketing?

On a usability point I worked out that the minor labels were above each thumbnail but this isn't obvious from the layout. Is there any way this could be improved to make it absolutely clear? Also, since the order of the tags determines the grouping would it be possible to be able to drag the tags into a new order? If I want to add a new tag at the start of the list I have to remove al the tags and start again.

[will-moore]

Hi Colin, thanks for that.
The tag grouping certainly does depend on the order you put the tags in. Imagine you had tags "A", "B", "C" and images with all combinations of tags, then you chose to group by A, B, C in that order, you'd get

• A
• AB
• ABC
• B
• BC
• C
  This would then be grouped under A, B, and C.
  If you chose to group by B, C, A in that order, you'd get
  • B
  • BC
  • BCA
  • C
  • CA
  • A

You're right that the sub-label 'TN-6 TN-5 TN-3' should be 'TN-3' according to my current strategy.
It's hard to know how to layout the subsets. Maybe I should simply display all the tags above each subset, then it would be clearer that the labels are "above", since the first subset in each bigger group would have a label.

But I think it works OK if you've not got such complexity (see my example in the PR description above)?

Dragging and dropping to order the tags would be nice, but I think it might be a bit too tricky for me just now!

[ximenesuk]

Will, yes all applicable tags above all subsets would make it clear. My test was a bit artificial, I expect any normal user would have a simpler breakdown. But you still need to know whether the subset labels are above or below. The tooltips are very useful in the dialog by the way, but this information is obviously lost by the time a jpeg is produced.

As for dragging, it would be nice for extreme cases like mine but I expect most users will have one or two tags where it really isn't a problem.

[will-moore]

The commit above means that the main groupings are only labelled with a single tag (E.g. just "TN4" instead of "TN4 TN6 TN2" etc. When the subset labels are shown, they are above every row of thumbs and grouped closer to their own row, but they are only shown if there is more than 1 subset. Example screenshot:

[ximenesuk]

The improved spacing looks good. What about the break in the vertical line, that was useful, has it been lost in the spacing changes?

[ximenesuk]

All fixes are fine but I have a couple more "features" now. The first is trivial but it looks like the "Choose tags" in the entry box of the dialog is being truncated to the length of the longest tag that will appear in the drop-down. In the next picture my longest tag is 'TN-6' (well, they are all four characters). This gives:

and after I add a longer tag:

The second problem is with the results JPG and is more serious. Long tag names (or even lots of short tag names) don't render well in the jpg. Is there any reason that the jpg layout is so different from the preview?

Dialog:

JPG:

[will-moore]

Handling long label names in figure scripts has been a known issue for a long time. Finally got around to creating a ticket: https://trac.openmicroscopy.org.uk/ome/ticket/10686

The jpeg layout has been only slightly adapted in ome/omero-scripts#27 to group the thumbnails in the same way as the web UI, but I haven't coded the same hierarchy there yet, as I wanted to be sure it was right in the web first. All the layout in the script generation is done manually in Python (lots harder than using html) so I didn't want to do it more than once.

I'll look into the "Choose Tags" truncation...

[pwalczysko]

The jpeg layout works fine in both Web and Insight (see below).

The problem with too narrow column for picking the tags ("Choose Tags" truncation) is fixed.
Works fine.

During testing of PR #1054 found an RFE which could be dealt with here.

[gusferguson]

Tested using howe Web client in Mac Safari and OMERO.insight-4.4.6-1117-f42474a-ice33-b221-mac

Points raised in this PR tested:

• "not tagged" appearing and disappearing as expected
• "minor labels" appearing above rows as expected
• truncation of "Choose tags" in dialog box sorted - behaves as expected

Issue with the alignment of the rows in the actual figure when long tag is above shorter tags.

• preview in dialogue is as expected, but in actual figure, rows below a long tag name are shifting left so not aligning properly
• as this is consistent between Web and Insight it must be the way the script is doing it
• happens sequentially as tags get shorter
• see screenshot:

Web-Insight Differences:

• Web - show untagged images selected by default - Insight - unselected by default
• Web uses generic "Thumbnail_Figure" for default figure name - Insight uses dataset name

Usability Issues:

• automatically generated thumbnail figure title is very ugly (2 date-time stamps)
• ideally figure creation dialogue should have editable field to allow user to put in header
• if not able to do this - perhaps it is better left blank.

Note:

• Will are you aware this build version has the gallery view in it as well?
• not sure if you meant it to be in this build.

[gusferguson]

@will-moore

Forgot another Web-Insight difference:

• Web filters tags so only those on selected images are available for sorting - Insight presents all tags on system - can be difficult to find relevant tags.

[will-moore]

@gusferguson I'll have a look at the alignment in the script.
The web-insight differences in show untagged - I guess I'd argue that it's better to show by default, otherwise you wonder where all your thumbs go.
I'll try and align the Figure naming.
I can easily remove the date-time stamps for now.
[webgallery PR remains open - but is not due to be merged. Could close it for now?]
Insight could be improved to only show Tags that are on the images.

[will-moore]

The above commit and 2 commits to ome/omero-scripts#27 should address the Figure Name, Date-time stamp and left alignment.

[mtbc]

@aleksandra-tarkowska -- is this PR good to merge? (Marked "Done" in standup.)

[atarkowska]

I do not see any issues, ready to push