Re: a tutorial on a custom image format file reader / writer

Posted by Francis Burton on Apr 14, 2008; 5:52pm
URL: http://imagej.273.s1.nabble.com/a-tutorial-on-a-custom-image-format-file-reader-writer-tp3696492p3696493.html

At 12:16 14/04/08 -0500, "Curtis Rueden" <[hidden email]> wrote:
>Thanks for this guide. I think it is very useful currently, but hopefully in
>the future we can improve the ImageJ I/O plugin architecture to reduce the
>need for many of these steps. I have some ideas on how to do so, but have
>not yet had time to work on them.

Recently I have been playing around with getting ImageJ to do conversions
between file formats via command line invocation and macros. (Many thanks
to Patrick Pirrotte for all his help with reading LSM linescan images with
his useful LSMReader/LSMToolbox.)

One outstanding problem concerns the threaded nature of file reading. In
Patrick's own words:

"The problem is that somehow in macro headless mode (no gui) opening and
saving occur in other threads. This means that the LSM_Reader is not
finished opening the image that the macro already tries to save the files.
The results are sometimes weird."

This has necessitated adding a delay instruction in the macro, to allow
reading to finish before any attempt to write the converted data file.

Obviously this is less than ideal because this delay will vary depending
on the speed of the computer and other running processes. It makes it
impossible to write a portable solution unless one incorporates a long
enough delay to cover all existing computers (in practice that is quite
a few seconds' delay!).

Would the solution be to add another command to ImageJ similar to wait(...)
that waits for all i/o to complete before continuing execution (of the
macro)?

I am not in a position to judge if this is a sensible proposition, but if
it is I would be very pleased if this was incorporated into the program.

Cheers,
Francis

--
Dr Francis L Burton,          |  [hidden email]
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