multi-file open incorrectly logged

[Elaine Meng]

If I use menu: File... Open and use click + Shift-click to choose multiple files for opening (e.g. DICOM image stack is a series of files), the logged "open" command just names the first file. Thus,
later if you try to reopen the data from File History/Rapid Access, it just opens a single plane.

Assign/prioritize as appropriate...

[pett]

Can you point me towards an example DICOM image stack? I've changed the code to put all the file names into the 'open' command, but for PDB files at least it creates one file-history entry for each file, and I'm worried that it will create a zillion entries for a DICOM stack, so I want something to test with.

[Elaine Meng]

try this tiff stack (10 files in zipped folder)

[pett]

I can make File→Open issue the multi-file 'open' command, but in that case the command uses each file's full path; it doesn't compress them using any type of globbing of course. But the open command will only interpret multiple files as a volume or volume series if the name has wildcard/glob characters in it(!), even if you explicitly say 'vseries true'. So with your data, a long 'open' command gets issued, but you get one volume viewer per file and one file-history entry per file. Not optimal.

There doesn't seem to be any equivalent in the open command to what File→Open has been doing with multiple files, which is to call session.models.open(paths) directly, which creates a single volume out of the files. In order to fix this we need some way to make the 'open' command work then same way when given multiple files.

I am re-assigning this ticket to T.G. and opening a separate ticket for '"open browse" file browser does not allow multi-file selection and opening.'

--Eric

[Elaine Meng]

Could something have changed after my report yesterday? I could have sworn both yesterday and today I was using
UCSF ChimeraX version: 0.9 (2018-12-22)
which I take to mean that nothing has changed since 12/22.  However, in the daily build I just downloaded, I don’t see any command logged when I open an image stack using File… Open and click/Shift-click.  Not with the TIFF stack I attached to the report, nor the same DICOM stack I was looking at yesterday when I made the report, nor another DICOM stack of mouse brain I just downloaded from a public archive.  I also cannot find any entry for the dataset in the File History interface.

So it’s a mystery to me, but today I don’t see any “wrong” thing in the History/Log from opening the stack… instead the action is not logged at all.  However, it would be really nice if it were in the history, so I didn’t have to go into 4 layers of folders each time I want to open a given stack.

[pett]

Seems that when I said "I am reassigning this ticket to T.G.", I didn't actually reassign it!

[Tom Goddard]

Fixed.

I made the open command open all specified paths in one Python call so stacks of 2d images (DICOM, TIFF) and volume series can be specified using multiple paths in the open command. The open file browser makes such commands when a multi-select is used to open several files at once.

The file history mechanism still does not make an entry for open commands that include more than one path or one database id.