Open Microscopy Environment

Dear All,

I would like to extract the OME XML metadata for my images using python. I know the image contains the information I am after since when I export it as OME TIFF it contains the following metadata:

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<Plane DeltaT="0.0" ExposureTime="5.000000237487257E-4" PositionX="-40.36" PositionY="63.14" PositionZ="-2.195" TheC="0" TheT="0" TheZ="0"/>


The item that I am interested in is the ExposureTime attribute. I can obtain this through the gateway if I extract the annotations. One of them is 'original_metadata.txt' and will contain a set of key-values pairs for attributes including:

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Image 1. Exposure time=0.500 secs


I can also extract the original log file for the DeltaVision image file and get the exposure time from that.

I would prefer to use the 'original_metadata.txt' as it is easier to parse. However there appears to be a bug in the ImageWrapper.loadOriginalMetadata() function within the API since I do not get any values returned for my image. Reading the source code for this function it loops over the annotations list and for each one checks that it is a file annotation and isOriginalMetadata() is true. However for my image this is not the case. Below I show some python code using the gateway to get the data:

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>>> img = conn.getObject('Image', 2228)
>>> meta = img.loadOriginalMetadata()
>>> print meta
None
>>> for a in img.listAnnotations():
...     print "%s (%s) = %s" % (a.getFileName(), a._obj.ns.val, a.isOriginalMetadata())
...
original_metadata.txt (openmicroscopy.org/omero/import/companionFile) = False
E05_111220_EH3_p184_55_R3D.dv.log (openmicroscopy.org/omero/import/companionFile) = False


I am not sure why the wrapper for original_metadata.txt is not being picked up as the metadata. Is this a genuine bug or am I missing something when creating my wrapper objects (e.g. loading states)?

Within FileAnnotationWrapper.isOriginalMetadata(self) should the following code be changed:

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if self._obj.ns is not None and \
        self._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and \
        self._obj.file.name.val.startswith("original_metadata"):
    return True


to

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if self._obj.ns is not None and \
        self._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and \
        self.getFileName().startswith("original_metadata"):
    return True


At the moment it looks like I will have to manually loop over the annotations myself and identify the metadata file using the name.

Thanking you in advance.

Alex

Update:

I have changed the code in omero_dist/lib/python/omero/gateway/__init__.py as suggested in my previous post to:

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    def isOriginalMetadata(self):
        """
        Checks if this file annotation is an 'original_metadata' file
       
        @return:    True if namespace and file name follow metadata convention
        @rtype:     Boolean
        """
       
        try:
            #if self._obj.ns is not None and self._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and self._obj.file.name.val.startswith("original_metadata"):
            if self._obj.ns is not None and self._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and self.getFileName().startswith("original_metadata"):
                return True
        except:
            logger.info(traceback.format_exc())
        return False


The call to ImageWrapper.loadOriginalMetadata() now returns the metadata.

Regards,

Alex

Thanks Alex,

This bug has been noted and fixed in the development version of OMERO.

Mentioned in these forums (with workarounds):
http://www.openmicroscopy.org/community ... 3333#p3333
http://www.openmicroscopy.org/community ... f=16&t=920

Apologies for the hassle.

Will.

Hi Will,

Thanks for the info.

I started this thread because the forum search returned no results. Instead it produced this message:

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The following words in your search query were ignored because they are too common words: metadata

I get this for most of my searches using the forum search engine. Is there a problem with the forum search? Next time I'll use Google instead. That would have saved me some effort.

Regards,

Alex

Thanks for that Alex. We've fixed some of the search parameters so things should be working a bit better now.

Cheers, Will.