[ome-users] ZVI time information

[Melissa Linkert]

Hi James,
It looks like you are doing everything correctly - there is probably still a
bug in Bio-Formats.

If you could send one or more ZVI files that exhibit this problem, that
would be extremely helpful in debugging.  Files smaller than 15 MB can be
sent as an email attachment; otherwise, you can send them by FTP (I will
provide server details off-list).

Regards,
-Melissa

On Tue, May 27, 2008 at 11:51 AM, James Chen <james.chenn at gmail.com> wrote:

> 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
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>
>
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