[ome-users] ImageProcessorReader.getSeriesMetadata() for extracting DICOM tags

[Mohammad Samarah]

Hi Melissa,

We tried both options. We are unable to retrieve the nested DICOM tags. Here
is the code fragment in question.

Thanks for your help,
M. Samarah


ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
IMetadata meta = service.createOMEXMLMetadata();

log_message("INFO: Examining file " + imagePath);
r.setMetadataStore(meta);
r.setGroupFiles(false);
r.setId(imagePath);

CoreMetadata data[] = r.getCoreMetadata();
metadata = data[r.getCoreIndex()].seriesMetadata;
Set<String> keys = metadata.keySet();

for(String key: keys)
{
    System.out.println("Value of "+key+" is: "+metadata.get(key));
}

Object obj = r.getSeriesMetadataValue("0008,2228 Primary Anatomic Structure
Sequence");

if (obj instance of List)
{
    System.out.println("obj is a list");
    // order they were found
    //  List values = (List) obj;
    // Object firstCodeMeaning = values.get(0);
}
else {
    // single value
    System.out.println("obj is a single value");
}

> From: Melissa Linkert <melissa at glencoesoftware.com>
> Reply-To: <melissa at glencoesoftware.com>
> Date: Mon, 07 Apr 2014 18:59:58 -0500
> To: "msamarah at alumni.fit.edu" <msamarah at alumni.fit.edu>
> Cc: "ome-users at lists.openmicroscopy.org.uk"
> <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] ImageProcessorReader.getSeriesMetadata() for
> extracting DICOM tags
> 
> Hi Mohammad,
> 
>> We are using ImageProcessorReader to extract DICOM tags from an RVG image.
>> All seems to be well, however it does not seem to return repeating tags
>> particularly tag id 0008,0104.  Are there specific options needed to extract
>> repeated tags? And are there known limitations with the Imetadata class? I
>> have attached the DICOM tags table and Java code in question below.
> 
> Typically if there would be multiple entries in the metadata hashtable
> that have the same key, then a suffix is appended to the relevant keys.
> I would expect something like this to work:
> 
>      metadata = r.getSeriesMetadata();
>      Object firstCodeMeaning = metadata.get("Code Meaning #0");
>      Object secondCodeMeaning = metadata.get("Code Meaning #1");
>      Object thirdCodeMeaning = metadata.get("Code Meaning #2");
> 
> Alternately, you can do this to preserve the original key and access the
> values as a List:
> 
>     metadata = r.getCoreMetadataList().get(r.getCoreIndex()).seriesMetadata;
>     Object value = metadata.get("Code Meaning");
>     if (value instanceof List) {
>       // multiple values for the same key; values are stored in the
>       // order they were found
>       List values = (List) value;
>       Object firstCodeMeaning = values.get(0);
>     }
>     else {
>       // single value
>     }
> 
> If neither of those options work, please let us know.
> 
> Regards,
> -Melissa
> 
> On Fri, Apr 04, 2014 at 01:48:30AM -0400, Mohammad Samarah wrote:
>> We are using ImageProcessorReader to extract DICOM tags from an RVG image.
>> All seems to be well, however it does not seem to return repeating tags
>> particularly tag id 0008,0104.  Are there specific options needed to extract
>> repeated tags? And are there known limitations with the Imetadata class? I
>> have attached the DICOM tags table and Java code in question below.
>> 
>> Thanks for your help,
>> M. Samarah
>> msamarah at alumni.fit.edu
>> 
>> 
>> Tag ID                          VR    VM   Len    Description       Value
>> (0008,2228)                SQ    0      0       Primary Anatomic Structure
>> Sequence
>>    (FFFE,E000)
>>       (0008,0100)
>>       (0008,0102)
>>       (0008,0104)          LO  1        34      Code Meaning    Maxillary
>> right third molar tooth
>>    (FFFE,E000)
>>       (0008,0100)
>>       (0008,0102)
>>       (0008,0104)          LO  1        34      Code Meaning    Maxillary
>> right second molar tooth
>>    (FFFE,E000)
>>       (0008,0100)
>>       (0008,0102)
>>       (0008,0104)       LO  1           34      Code Meaning    Maxillary
>> right first molar tooth
>>    
>> 
>> ImageProcessorReader r = new ImageProcessorReader(new
>> ChannelSeparator(LociPrefs.makeImageReader()));
>> try
>> {
>>     ServiceFactory factory = new ServiceFactory();
>>     OMEXMLService service = factory.getInstance(OMEXMLService.class);
>>     IMetadata meta = service.createOMEXMLMetadata();
>>     log_message("INFO: Examining file " + imagePath);
>>     r.setMetadataStore(meta);
>>     r.setGroupFiles(false);
>>     r.setId(imagePath);
>>   
>>     metadata = r.getSeriesMetadata();
>>     Set<String> keys = metadata.keySet();
>>     for(String key: keys)
>>     {
>>         System.out.println("Value of "+key+" is: "+metadata.get(key));
>>     }
>> }
>> 
> 
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