Modern import (from BDV) plugin

[xulman]

Hi,

I wanted to extract "raw"/orig data from XML/HDF5 BDV dataset and I found File->Import->BigDataViewer... plugin/menu item that can do it. This one, however, was doing GUI dialog by its own, and I couldn't use it in --headless mode.

So, I rewrote it into IJ2 environment. This changed the GUI-pieces of the code completely but otherwise (figuring out how many timepoints, setups, mipmaps as well as creating ImagePlus as a result) I haven't changed the functionality.

I also gave it a bit of love to the way GUI dialog behaves now.

As a side effect, the new plugin can run --headless:
~/Apps/Fiji.app/Contents/MacOS/ImageJ-macosx --headless --run "BigDataViewer..." 'xmlFile="/path_to/dataset.xml",timepointVal=15,setupVal=0,mipmapVal=0,openAsVirtualStack=false'
and/or one can batch/headless extract a sequence of timepoints...
(because it is not attempting to build a GUI dialog and img.show() as it was in the original code).

The GUI:

Vlado

[tpietzsch]

@xulman sorry for taking so long to look at it.

What happened if you tried to run the old plugin in headless mode. In principle the GenericDialogPlus should be able to handle that? Maybe all that is required it to add headless=true to the @Plugin annotation.

What you did is still quite nice. It would be cool to have the plugin IJ2-style (regardless of headless issue).
A few things I still don't like:

• When the plugin opens, the xml filename is populated with previous value, but the bounds are not.
  
• When I then click into the filename field and press ENTER, I would expect that the filename is updated and the bounds are set. Instead, this basically clicks OK.
• (a bug) The maxes are off by one. Instead of timepointMax = seq.getTimePoints().size() should be size()-1.
• To get back something like the sliders in the current dialog, I tried to use style = NumberWidget.SLIDER_STYLE. But that does not work properly, because the slider max is not updated when a new max is set. Would be interesting to know how to do that (and whether it's possible).
• The new code is quite a bit longer than the old one which is a bit ironic because everything should be easier with @Parameter. Maybe some of it could be simplified with the standard way of setting min/max ranges in existing dialog. But I don't know how to do that / whether it is possible. Maybe @imagejan @ctrueden could comment?

[ctrueden]

setting min/max ranges in existing dialog. But I don't know how to do that / whether it is possible

Not currently possible, sorry.

There is no issue precisely about that, but here are the closest ones:

• Allow plugin parameters to be hidden
• Differentiate between dynamic and quasi-dynamic modules
• Differentiate between initially dynamic and iteratively dynamic modules

Perhaps could be tackled as part of the SJC3 dialog generator redesign. I am working on some necessary underpinnings for that over the next couple of months, but I don't know how far along the dialog stuff specifically will get in that time-frame.