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

Posted by Patrick Pirrotte on Apr 15, 2008; 8:08am
URL: http://imagej.273.s1.nabble.com/a-tutorial-on-a-custom-image-format-file-reader-writer-tp3696492p3696502.html

Hi,

I have almost finished updating the LSM_Toolbox to 4.0c, which will accept
CSV files as a list of lsm files to batch process.

The whole batch process will run in the same thread and will not be subject
to race conditions as is the case with the actual verison of the
toolbox/reader.

Furthermore, reading of compressed images has been improved. While 8 bit
compressed images are read correctly since LSM_Toolbox 4.0a, 12 bit
compressed images will work with LSM_Toolbox 4.0c and ImageJ >=v1.40e.

Best regards,

Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Wayne
Rasband
Sent: 14 April 2008 22:34
To: [hidden email]
Subject: Re: a tutorial on a custom image format file reader / writer

You are probably seeing this problem because you are using the LSM_Toobox,
which opens files in a separate thread. Instead, use the LSM_Reader plugin,
which does not return until it has finished reading the file. You will need
to remove LSM_Toolbox.jar from the plugins folder since the
Handle_Extra_File_Types plugin uses it if it is present. Or upgrade to the
latest version of Handle_Extra_File_Types at
<http://rsb.info.nih.gov/ij/plugins/file-handler.html>, which uses the
LSM_Reader if it is present.

-wayne


On Apr 14, 2008, at 1:52 PM, Francis Burton wrote:

> 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]
> West Medical Building,        |
> University of Glasgow,        |  Tel [phone]
> Glasgow, G12 8QQ, Scotland.   |  Fax [phone]
>