Imagej prep

[jburel]

In this PR,

• Refactor import code to handle imagePlus object.
• Add 2 entries to the OMERO plugin menu.

To Test:

• make sure you can still import images using the standard build.

ImageJ Test

• Add the omero_imageJ to the plugin.
• Add the BF-tools jar. If you have it installed, you will need to update it.

test 1:

• Open an image in ImageJ
• Under the plugin menu. Select OMERO>Upload and Save To OMERO.
• The data manager and the importer dialog should pop up.
• Add the file to the queue and import

test 2:

• Open an image in ImageJ. Crop it for example
• Under the plugin menu. Select OMERO>Upload and Save To OMERO.
• The data manager and the importer dialog should pop up.
• Add the file to the queue and import. An ome-tiff will be generated and imported.

ROIs are not yet supported for test 1

[jburel]

This is still work in progress. It will allow @pwalczysko @gusferguson @bramalingam to check status.

[pwalczysko]

test 1:

• the data manager and importer should pop up -> only the importer popped up, there was a short blink just like if something "wanted" to pop up prior to this, but it did not...

[pwalczysko]

Ah, the data manager did pop up, after a long time (in the meantime, I already used the importer and clicked Add to the queue button (which worked fine)

[pwalczysko]

I can add the image to the queue many times over. The importer will import all of them, but will report the import of only one (the new "import1" tab will have just one item in the list). When checking in the Data Manager, all the images in queue were imported though.

[jburel]

@pwalczysko: last commit should fix the MIF import issue

[pwalczysko]

• open Beta catenin
• select the Series004 and make a crop
• do not close anything
• create an ROI on the cropped Series004 (note that ImageJ changed the name to BetaCatenin.liff - Series004)
• Save it as Overlay
• Still in IJ, select image003 and draw a region, save as overlay
• import to OMERO, selecting "Add from all image windows"
• full Beta catenin MIF imports 1x (expected) & image003 imports as well separately (not expected)
• the image003 has the region I have drawn onto the Series004 originally (not expected)

[pwalczysko]

Additional info to #3329 (comment) - no need to draw any ROIs to reproduce the import problem of the crop. Need just to

• crop the Series004 (this is the stack)
• get the Image003 to focus in IJ
• start the import selecting Add from all image windows -> the *.ome.tiff will not be cropped, and will be matching the Image003 -> not expected

[pwalczysko]

Additional info to #3329 (comment) - the change of focus in the last step is necessary and sufficient condition to reproduce the problem. The image uploaded as .ome-tiff is the one which was last in focus. It is also necessary to make the crop from the multi-z stack (Series004), if crop is made from the single plane images (Image00x), all works fine.

[pwalczysko]

Unfortunately, I am able to reproduce the problem also with free edge.liff from the same folder.
Again,

• select the last image which pops up in the IJ after opening the MIF,
• crop it,
• get focus into the one-but last (not cropped) image
• import to omero
• the .ome-tiff is identical with the one-but last image in the series (= the one which was the last time in focus)

[pwalczysko]

Additional info: the problem #3329 (comment) has nothing to do with MIFs, it just came out because we had enough windows open. You can repeat it with a single file/image dv, by creating the crop and reopening the original dv file again (not closing the crop) and then getting the non-cropeed file into focus -> the same problem happens, the .ome.tiff will not be the cropped image, but the original one (= the one which was in focus).

[jburel]

@pwalczysko: ok I understood the issue. BF plugin only takes into account the current image Plus.
So I need to modify the BF plugin.

[jburel]

Required ome/bioformats#1539

[jburel]

@pwalczysko: to test the last commit
Click "Quit" before logging in. Then go back to the plugin >OMERO menu. Select one of the entries. The login screen should pop up again (it was not before)

[pwalczysko]

The problem with the window selection #3329 (comment) is sorted.
The only follow-up here is the region work on MIFs - unfortunately there is another problem here. The images itself and the crop are all fine (also in the MIF case), but if I have an ROI on the crop and another ROI on the uncropped original MIF, the ROI on the crop will appear fine in OMERO, the ROI on the MIF will not appear at all (Beta catenin.liff).
I think this is a case for another PR, the complex cases like this with MIFs and different regions on different images imported at once can be sorted out later (a simple case of one crop and one non-MIF image, both with different regions, works fine actually, on .dv file).

[pwalczysko]

The Quit problem #3329 (comment).
This does not work. Although there is a second-time splashscreen showing okay, and no crash, there is no action after I login and connect to server.

Workflow:

• import Beta catenin.liff using Bio-formats importer (all 5 images)
• go Plugins > OMERO > Upload and Save to OMERO -> splashscreen appears as expected
• click Quit
• go again Plugins > OMERO > Upload and Save to OMERO -> splashscreen appears as expected
• login and connect to server -> nothing happens, neither Data Manager nor importer appear -> not expected

[jburel]

@pwalczysko:

• Fix the issue when pressing "Quit".
• I have prepared all the code to support overlay on individual MIF. Still need to retrieve the "series" from the OMERO image. Option discussed today with @joshmoore to add a new column "series". So for now the feature will not work.

[pwalczysko]

The "Quit" problem works as expected.

[jburel]

@pwalczysko: all the features are now working. The work to handle the crazy MIF scenario is in place, but I will be fully turned on after DB change.
We should merge this PR so we can move forward with the rest and few PRs are conflicting.
Any objections?

[sbesson]

Got a written agreement from @pwalczysko. Merging

[jburel]

--no-rebase