[ome-users] ImageProcessorReader.getSeriesMetadata() for extracting DICOM tags
Mohammad Samarah
isamarah at mac.com
Wed Apr 16 18:07:13 BST 2014
Dear Dr. Flynn,
Many thanks for your response. We have uploaded three sample images to
qa.openmicroscopy.org.uk. Please let me know if I can provide additional
details.
Best wishes,
M. Samarah
--
Mohammad Samarah, PhD
Email: msamarah at alumni.fit.edu
Time zone: EST/EDT, UTC/GMT -5 hours, UTC/GMT -4 hours
From: Helen Flynn <h.flynn at dundee.ac.uk>
Date: Wed, 16 Apr 2014 08:38:24 +0000
To: "msamarah at alumni.fit.edu" <msamarah at alumni.fit.edu>
Cc: "<melissa at glencoesoftware.com>" <melissa at glencoesoftware.com>,
"ome-users at lists.openmicroscopy.org.uk"
<ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] ImageProcessorReader.getSeriesMetadata() for
extracting DICOM tags
Dear Mohammad,
Sorry to hear this still isn't working for you. Could you submit the image
file via http://qa.openmicroscopy.org.uk so we can do further testing
please?
Regards,
Helen
Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee
http://openmicroscopy.org
On 11 Apr 2014, at 16:25, Mohammad Samarah <isamarah at mac.com> wrote:
> 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));
>>> }
>>> }
>>>
>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
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