[ome-users] ZVI time information

[James Chen]

Hi Melissa,
Thanks for your input. I'm using the matlab version of bio-formats and I
tried running a matlab version of the code you posted below. However, the
results are still the same: the retrieve structure basically has no data in
it. Here is what I ran:

javaaddpath('loci_tools.jar');
store = loci.formats.MetadataTools.createOMEXMLMetadata();
reader = loci.formats.ImageReader();
reader.setMetadataStore(store);

reader.setId(zvi_file);

retrieve = reader.getMetadataStore();

creationDate = retrieve.getImageCreationDate(0);

for plane = 0:reader.getImageCount()
    timestamp = retrieve.getPlaneTimingDeltaT(0,0,plane)
end

When I run a get(retrieve), all the fields in the structure are either 0 or
empty. I made sure I was running the latest daily build of bio-formats and I
double checked to make sure the zvi file had time stamps, but I am still
getting nothing. Am I doing something wrong?

Thanks,
-James


On Mon, May 26, 2008 at 12:33 PM, Melissa Linkert <linkert at wisc.edu> wrote:

> Hi James,
> The latest daily build of Bio-Formats (available at
> http://loci.wisc.edu/ome/formats.html) should fix this problem.  If
> timestamps are present in the file, they will be in the hashtable under the
> key "Timestamp <n>", where <n> is the timepoint number indexed from 0.  Note
> that this will only work for ZVI files - other formats store their
> timestamps using different keys.
>
> I don't how you are using Bio-Formats; if you are using it as a library
> within your own application, then you should consider using the
> MetadataStore API to retrieve timestamps.  Following is some example code:
>
> MetadataStore store = MetadataTools.createOMEXMLMetadata();
> ImageReader reader = new ImageReader();
> reader.setMetadataStore(store);
>
> reader.setId("/path/to/file");
> MetadataRetrieve retrieve = (MetadataRetrieve) reader.getMetadataStore();
>
>  // get the time when acquisition began, in "yyyy-MM-dd'T'HH:mm:ss" format
> String creationDate = retrieve.getImageCreationDate(0);
>
> for (int plane=0; plane<reader.getImageCount(); plane++) {
>   // get the timestamp for this plane
>   // this is the time in milliseconds since acquisition began
>   Float timestamp = retrieve.getPlaneTimingDeltaT(0, 0, plane);
> }
>
> Please let us know if you have any other questions, or if the latest daily
> build does not work for you.
>
> Regards,
> -Melissa
>
> On Thu, May 22, 2008 at 12:22 PM, James Chen <james.chenn at gmail.com>
> wrote:
>
>> Hello everyone,
>> I'm having trouble pulling out time stamp information from a time lapsed
>> series in the ZVI file from bio-formats. I've gone over the entire metadata
>> hashtable but can't seem to find any link to it. Does anyone have any
>> suggestions?
>>
>> Thanks,
>> -James
>>
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>>
>>
>
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