[ome-users] ZVI time information

[Melissa Linkert]

Hi James,
The ZVI timestamp bug should be fixed in the latest trunk build of
Bio-Formats.  Also, please note that there is a typo in the code snippet
that I originally sent you - getPlaneTimingDeltaT returns the number of
seconds since acquisition began, not the number of milliseconds.

Please let us know if you continue to experience problems with OME software.

Regards,
-Melissa

On Tue, May 27, 2008 at 12:10 PM, Melissa Linkert <linkert at wisc.edu> wrote:

> 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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