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

Posted by Francis Burton on Apr 16, 2008; 4:52pm
URL: http://imagej.273.s1.nabble.com/a-tutorial-on-a-custom-image-format-file-reader-writer-tp3696492p3696506.html

Hi Curtis,

Thanks for the suggestion. I'm willing to try anything that will get me
more quickly to my destination - which is to read two images, representing
simultaneous linescan recordings at two different wavelengths, from Zeiss
LSM files into a Delphi program I wrote to space- and time-average bands
in a very interactive way. At the moment, my colleagues are still using the
free Zeiss image browsing software manually to open the LSM file and write
out two uncompressed TIFF files which my program can then read. I haven't yet
reinvented the wheel and written my own LSM importing routine, because I
don't particularly want to have to grapple with the business of reading &
interpreting TIFF header fields and doing LZW decompression if someone else
has solved those problems already!

So I tried some of the Bio-Format tools. First, I tried "showinf", and that
displayed sensible-looking info, showing that I had put the files in the
right place at least:

C:\bftools>showinf 07.lsm
Checking file format [Zeiss Laser-Scanning Microscopy]
Initializing reader
        Reading IFDs
        Populating metadata
        Removing thumbnails
Initialization took 1.344s

Reading core metadata
Filename = 07.lsm
Series count = 1
Series #0:
        Image count = 20000
        RGB = true (2)
        Interleaved = false
        Indexed = false
        Width = 512
        Height = 1
        SizeZ = 1
        SizeT = 20000
        SizeC = 2 (effectively 1)
        Thumbnail size = 3 x 128
        Endianness = intel (little)
        Dimension order = XYZCT (certain)
        Pixel type = uint16
        Metadata complete = true
        -----
        Plane #0 <=> Z 0, C 0, T 0
        Plane #9998 <=> Z 0, C 0, T 9998
        Plane #9999 <=> Z 0, C 0, T 9999
        Plane #10000 <=> Z 0, C 0, T 10000
        Plane #10001 <=> Z 0, C 0, T 10001
        Plane #10002 <=> Z 0, C 0, T 10002
        Plane #19999 <=> Z 0, C 0, T 19999

Reading pixel data (0-19999) ..Terminate batch job (Y/N)? y

Then I tried to "bfconvert" and received the following errors:

C:\bftools>bfconvert -debug 07.lsm 07.tiff
Debugging at level 1
07.lsm java.lang.UnsatisfiedLinkError: no LegacyND2Reader in java.library.path
        at java.lang.ClassLoader.loadLibrary(Unknown Source)
        at java.lang.Runtime.loadLibrary0(Unknown Source)
        at java.lang.System.loadLibrary(Unknown Source)
        at loci.formats.in.LegacyND2Reader.<clinit>(LegacyND2Reader.java:59)
        at java.lang.Class.forName0(Native Method)
        at java.lang.Class.forName(Unknown Source)
        at loci.formats.ClassList.<init>(ClassList.java:90)
        at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:56)

        at loci.formats.ImageReader.<init>(ImageReader.java:90)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:91)

        at loci.formats.tools.ImageConverter.main(ImageConverter.java:146)

1208362874734: ZeissLSMReader: ZeissLSMReader.initFile(07.lsm)
1208362874734: ZeissLSMReader: BaseTiffReader.initFile(07.lsm)
java.lang.ArithmeticException: / by zero
        at loci.formats.in.ZeissLSMReader.parseOverlays(ZeissLSMReader.java:825)

        at loci.formats.in.ZeissLSMReader.initMetadata(ZeissLSMReader.java:400)
        at loci.formats.in.ZeissLSMReader.initFile(ZeissLSMReader.java:757)
        at loci.formats.FormatReader.setId(FormatReader.java:573)
        at loci.formats.FormatHandler.setId(FormatHandler.java:146)
        at loci.formats.ImageReader.setId(ImageReader.java:565)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:103
)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:146)

Terminate batch job (Y/N)? y

Finally, I tried "bfview" and after a few seconds it put up a window with some
sliders labelled N, Z, T & C, and a Progress bar window which is still sitting
at 0% some 20 minutes after I started the batch file. :-/

Any ideas what might be going on (or not going on)?

Cheers!

Francis

At 13:08 15/04/08 -0500, Curtis Rueden <[hidden email]> wrote:

>Hi Francis,
>
>If you want to convert files on the command line, Bio-Formats has a
>"bfconvert" tool that allows this. As you would expect, it can read from any
>supported input format, and write to any supported output format -- see the
>formats table on the web site at <http://www.loci.wisc.edu/ome/formats.html>
>for details; blue striped rows are supported output formats (as of this
>writing: AVI, EPS, JPEG, OME-TIFF, PNG, MOV and TIFF).
>
>The command has a number of optional parameters to control its behavior; if
>what you need isn't there, let me know and perhaps it could be added.
>
>-Curtis
>
>On Mon, Apr 14, 2008 at 12:52 PM, Francis Burton <[hidden email]>
>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]
>>
>
>