Re: metadata and time depiction

Posted by Rasband, Wayne (NIH/NIMH) [E] on
URL: http://imagej.273.s1.nabble.com/metadata-and-time-depiction-tp3687079p3687086.html

On Aug 30, 2010, at 5:06 AM, fabrice senger wrote:

> In addition to this mail : when I try to acces creation date a message
> appears in the IJ bar :
>
> "unknown creation date format : 20100722 14:53:38.88"
>
> and when I import my image with metadata in a result window, save that table
> and then reopen it using import results, the table wich opens is still not a
> Results table...and I can not access it (?!)

You can get all the metadata, as a string, of images imported with the Bio-Formats plugin using the getMetadata("info") macro function. In the ImageJ 1.44g daily build, you can retrieve specified metadata values using the getInfo() macro function. For example:

   order = getInfo("DimensionOrder");
   type = getInfo("PixelType");
   sizeC = getInfo("SizeC");

The getInfo() function can also retrieve the value of DICOM tags

   modality = getInfo("0008,0060");
   sliceThickness = getInfo("0018,0050");
   position = getInfo("0020,0032");

and Java properties

   version = getInfo("java.version");
   os = getInfo("os.name");
   home = getInfo("user.home");

-wayne

>> Hi there,
>>
>> I hope it's not to boring, I'm still working on file metadata (stk and nd
>> folders as ganerated by Metamorph).
>> This time i open my files with the LOCI plugin and ask for the metadata
>> depicted in the result table...In my case I would have been happy to get the
>> Results table and not the "Original Metada - filename"...with the Results
>> table I would have been able to extract whatever info to a custom table.
>>
>> So i tried to rename the Original-Metadta- table to Results, but this
>> doesn't work in my hands...
>>
>> Any clue ?
>>
>> Thank you very much,
>>
>> Fabrice.
>>
>>
>> 2010/8/27 Vinay Singh <[hidden email]>
>>
>> Hi all,
>>> I use Metamorph too and have data sets up to 20gb and find it
>>> Difficult to find time stamps specially after making a maximum projection
>>> of the z stacks. Would love to know how you are using loci plugin to get the
>>> time stamp! I am not familiar with programing but I do have the loci plugin
>>> installed would love a fix I could apply without having to write codes
>>> Thanks
>>> Vinay
>>>
>>> Vinay Singh
>>> 4315 FFSC, Duke university
>>> Durham NC 27708
>>> 919-6134456
>>>
>>> On Aug 27, 2010, at 3:05 AM, fabrice senger <[hidden email]>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> I had such a piece of discussion off-list with Dan White.
>>>> As I work with stk files, i have access to the image creation time (this
>>> is
>>>> accurate even you pause the acquisition), I have access to this info
>>> with
>>>> the LOCI plugin and some code Melissa kindly sent me.
>>>>
>>>> What would be of interest is a tool like a time slider as you can get it
>>> in
>>>> Metamorph or in Imaris...or then : "
>>>>
>>>>> Are you suggesting that you would like to see the timestamp in seconds
>>>>> displayed as part of the label at the top of the image window?"
>>>>>
>>>>
>>>>
>>>>
>>>> This is probably a particular situation when you have to pause
>>> acquisition
>>>> for one or two acquisitions but in this case dynamic measurements would
>>> not
>>>> be accurate if based on time intervals (?!)
>>>>
>>>> Thank you for your reply,
>>>>
>>>> Best,
>>>>
>>>> Fabrice.
>>>>
>>>> 2010/8/26 Curtis Rueden <[hidden email]>
>>>>
>>>>> Hi Fabrice,
>>>>>
>>>>> as follow up to a previous mail, i just wonder why the time dimension
>>> is
>>>>>> always depicted as t (time frame) and not in real units as sec.
>>>>>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>>>>>> almost every format.
>>>>>>
>>>>>
>>>>> The Bio-Formats Importer does populate the frame interval in the image
>>>>> properties when that information is available. In the case of variable
>>> time
>>>>> between frames, we average the times and populate the frame interval
>>> with
>>>>> the mean (though the eventual goal is for ImageJ to support variable
>>> time
>>>>> frames directly). And I believe that in general, ImageJ uses the frame
>>>>> interval value for the frames per second when animating—adjustable by
>>> right
>>>>> clicking the Play button next to the time slider.
>>>>>
>>>>> Thus it would be interesting to have direct acces to those parameters.
>>>>>>
>>>>>
>>>>> Are you suggesting that you would like to see the timestamp in seconds
>>>>> displayed as part of the label at the top of the image window?
>>>>>
>>>>
>>>> Yes this is what I think about!
>>>>
>>>>>
>>>>> As example, if you do time-lapse and have to pause your acquisition for
>>> one
>>>>>> or two acquisition, you could not use the time interval, but the
>>> metadata
>>>>>> acqusitionTime is still relevant.
>>>>>>
>>>>>
>>>>> Whether such a pause is properly recorded in the metadata depends on
>>> the
>>>>> file format. As I said above, Bio-Formats averages the timestamps, so
>>> you
>>>>> should still get a reasonable frame interval in the properties, as long
>>> as
>>>>> the correct values are really present in metadata.
>>>>>
>>>>> -Curtis
>>>>>
>>>>> On Thu, Aug 26, 2010 at 5:48 AM, fabrice senger <
>>> [hidden email]
>>>>>> wrote:
>>>>>
>>>>>> as follow up to a previous mail, i just wonder why the time dimension
>>> is
>>>>>> always depicted as t (time frame) and not in real units as sec.
>>>>>> Indeed, using the LOCI plugin it is possible to retrieve metadata from
>>>>>> almost every format.
>>>>>>
>>>>>> Thus it would be interesting to have direct acces to those parameters.
>>>>>>
>>>>>> As example, if you do time-lapse and have to pause your acquisition
>>> for
>>>>> one
>>>>>> or two acquisition, you could not use the time interval, but the
>>> metadata
>>>>>> acqusitionTime is still relevant.
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Fabrice.
>>>>>>
>>>>>
>>>
>>
>>