Accessing Multiple Images (aka Series) programmatically

[waxenegger]

Do note that the terminology here is slightly tricky. OMEXMLReader refers to reading data from an OME-XML file; OMEXMLService/OMEXMLMetadata refers to using objects from the ome.xml.model package (http://downloads.openmicroscopy.org/bio ... mmary.html) to store metadata in a format-independent manner, for querying or when exporting a file to a different format.

well, that clears up a misconception.

in the end, I think, I'm going to deal with my problem in a similar fashion this reader deals with it:
https://github.com/openmicroscopy/bioformats/blob/v5.1.2/components/formats-gpl/src/loci/formats/in/OperettaReader.java by subclassing from FormatReader and overrriding the relevant sections.

I'm going to extract the individual file location from the meta-data (XML) and read the tiff data via the tiff reader. That way I get my desired group behavior and one file extraction logic over the indices (dimensions).

There is only one piece of advice that would be useful: Aiming at accessing OME XML for the purpose of meta-info extraction I struggle to get through the encapsulation used:

Code: Select all

OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) reader.getMetadataStoreRoot();

so working with the OMEXMLMetadataRoot my way from the root upwards to then iterate over some elements (TiffData e.g.) is not exactly elegant (using array out of bounds to know the end) since I could not find convenient getters to do so (and array length). Did I miss a method to get to the elements by name?

I suppose, alternatively, I could abandon the idea in favor of a more custom solution (since I plan to extend from FormatReader) to do it in a fashion the above mentioned reader does (and writing my own handler for the xml):

Code: Select all

  String xmlData = DataTools.readFile(id);
    OperettaHandler handler = new OperettaHandler();
    XMLTools.parseXML(xmlData, handler);


    ArrayList<Plane> planeList = handler.getPlanes();
    ....


[rleigh]

In terms of the metadata encapsulation:

OMEXMLMetadataStore implements both the MetadataStore and MetadataRetrieve methods.
It is a wrapper providing access to a tree of OME-XML model objects (ome.xml.model.*). The root of this model object tree is ome.xml.model.OME, corresponding to the OME root element in the OME-XML ome.xsd schema. The getMetadataStoreRoot() method returns an abstract interface corresponding to whatever provides the concept of "root" metadata object in any concrete implementation of the metadata interfaces. In the case of OMEXMLMetadataStore, that is the OME root element.

For the most part, every method in the MetadataStore and Retrieve interfaces uses indexes into the various lists contained in the tree of OME-XML model objects, with corresponding Count() methods. For example:

Code: Select all

   NonNegativeInteger getTiffDataIFD(int imageIndex, int tiffDataIndex);


To know the valid index values, you would use:

Code: Select all

int getImageCount();
int getTiffDataCount(int imageIndex);


If you were using the OME-XML model objects directly, you could use in ome.xml.model.OME:

Code: Select all

public int sizeOfImageList()
public Image getImage(int index)

This would get you the ome.xml.model.Image object for the image of interest. You would then call on that image:

Code: Select all

public Pixels getPixels()


to get the pixel data for the image, and then on the ome.xml.model.Pixels:

Code: Select all

public int sizeOfTiffDataList()
public TiffData getTiffData(int index)

Finally, with the TiffData object, we can call

Code: Select all

public NonNegativeInteger getIFD()

Using the model objects directly is certainly possible, as you can see. And if you look at the OMEXMLMetadataStoreImpl implementation, you will see that it does the steps outlined above for you, and the same applies to all of its methods, which navigate the object tree appropriately. Essentially, the MetadataStore/Retrive APIs are a convenience to make it easier to manipulate the tree, or at least reduce the amount of effort you need to expend and amount of code you need to write.

I hope this answers your question. If it doesn't please let me know.

[waxenegger]

Thank you very much. I will have another look at the interfaces. Hmm, looking at the java doc online I see the size... getters. Wonder what hierarchies I jumped in eclipse in my frenzy to not see that the first time...