[ome-devel] OME.tiff with FLIM time gates that are not equally spaced in time

[Munro, Ian]

Thanks for the summary Sebastien.
I’ll try and get a PR together when I can.

Best

Ian




On 31 Jul 2018, at 13:39, Sebastien Besson (Staff) <s.besson at dundee.ac.uk<mailto:s.besson at dundee.ac.uk>> wrote:

Hi Ian and Romain,

having briefly discussed the state of the things internally, here is a summary:

- there is nothing in  FormatWriter that handles file existing i.e. the writer will write to the
  specified output stream
- handling file deletion prior to writing is the responsiblity of the caller of the low-level
  writer API
- the `bfconvert` command-line utility contains some logic to detect the output file
  existence and overwrite it either via an interactive opt-in or via the `-overwrite` option
- the `bfsave.m` MATLAB utility does not contain any such logic at the moment. Until
  Bio-Formats 5.9.0 it is the responsibility of the bfsave caller to handle file existence.

Implementing some overwriting logic at the MATLAB level probably controlled by a
key/value option would probably be a reasonable choice if this helped addressing the
issues you and Romain faced. In this case, feel free to suggest your changes as a
Pull Request against the Bio-Formats source code repository.

Best,
Sebastien
________________________________
From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk<mailto:ome-devel-bounces at lists.openmicroscopy.org.uk>> on behalf of Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>>
Sent: Monday, July 30, 2018 8:48:04 PM
To: OME External Developer List
Subject: Re: [ome-devel] OME.tiff with FLIM time gates that are not equally spaced in time

Hi All

Since sending the mail below Romain has been in touch to say
“ There’s just a small problem is that I think it doesn’t overwrite files properly when there’s already a file with the same name.
I got some weird results doing that so I made sure they’re created each time."

This suggests  that a the problem of overwriting existing files, addressed by the 2nd of the 2 code snippets below, remains an issue.
My feeling is that this should be addressed in either the bio-formats Matlab plugin or at an even lower level?

What does the OME team think?

Best Wishes

Ian





On 17 Jul 2018, at 13:20, Munro, Ian <i.munro at imperial.ac.uk<mailto:i.munro at imperial.ac.uk>> wrote:

Hi Romain

Attached is a little Matlab script to create a FLIM OME-TIFF.
The first section just creates some dummy data.
The second part (after the tic at line 28) uses the bio-formats Matlab plugin to write this to a file.
Note that the variable “delays’ can contain any strings not just the regularly spaced ones used here.

This is quite old code now so maybe someone from the core OME team could have a quick look and see if it’s still ok?
In particular this line:

java.lang.System.setProperty('javax.xml.transform.TransformerFactory','com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl’);

may no longer be required.
Also we used to have problems when overwriting existing files. If this has since been addressed,
then this section:

if exist(outputPath, 'file') == 2
    delete(outputPath);
end

May no longer be required.
Hope that helps.

Best wishes.

Ian




<save_as_OMEtiff_Synthetic_Gated.m>


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