Unify file handling for CZI and LIF

[stelfrich]

@mutterer Is there a specific reason why the file handling logic differs for CZI and LIF, see FigureJ_Tool#L1401-L1422?

With this implementation, user-defined default values for Bio-Formats are overwritten by our ImporterOptions. I don't see why this is desirable..

[mutterer]

Hi @stelfrich,
options.setFirstTime(false);
options.setUpgradeCheck(false);
->prevents the burden of extra dialogs.

options.setStackFormat(ImporterOptions.VIEW_HYPERSTACK);
->this guarantees that a single window is opened with all channels.

These two points should be set as well for CZI, I agree.

The main concern was with the lif files. They almost always consist of several series and users have to go through the series selection dialog where they can select multiple series. But in our case only one serie should be selected, hence the loop finding the selected serie with the highest index. I think multiseries is also possible with czi, but I have not seen example files for that case.

To avoid and overwrite user defined options in other contexts, maybe a backup of current options could be taken and restored after the panel is filled.

[stelfrich]

These two points should be set as well for CZI, I agree.

That's what I thought.

To avoid and overwrite user defined options in other contexts, maybe a backup of current options could be taken and restored after the panel is filled.

"Overwriting" is ambiguous in this context. The options that are set in the ImporterOptions are not stored or taken as the new default values. I just don't know how the values that are not explicitly set are determined (if there are Bio-Formats defaults or if the user defaults are used). I will look into this.

The main concern was with the lif files. They almost always consist of several series and users have to go through the series selection dialog where they can select multiple series. But in our case only one serie should be selected, hence the loop finding the selected serie with the highest index. I think multiseries is also possible with czi, but I have not seen example files for that case.

Multiseries images in CZI files are most definitely possible and are for us here the default case 😃 which is why I am asking. If I have understood you correctly, the current implementation restricts me to load the series with the highest index from a LIF file (by doing so automatically)? Is that desirable, @mutterer?

[mutterer]

"Overwriting"

If the ImporterOptions are not taken as new values, I should have used: "overriding" instead. I found no way of skipping the main "Bioformats Import Options" while being able to still have the series options dialog, that's why I need to override any unsuitable user choice in the first dialog.

Multiseries images in CZI ... are the defult case

So I agree the logic should be the same as for lif files.

the current implementation restricts me to load the series with the highest index from a LIF

The highest selected index series. The motivation for this is that the raw data for a given figure panel can originate from only one series. The first series is selected by default in the series options dialog, and a user might forget the unselect it, when selecting the desired series.