Is there a way to retrieve OME-XML directly from OMERO?

[Kouichi_C_Nakamura]

From webclient, using General > Download > Export as OME-TIFF, one can generate a OME-TIFF file on the server and then download it. Using command line tools etc, one can then extract the embedded OME-XML metadata.

I wonder if there is a way to directly extract OME-XML from an image in OMERO using Java API. But I could not find relevant Java class in API. Is there any way to achieve this by programming?

[jburel]

Hi Kouichi

You are correct, neither insight nor web expose the option to export the Image as OME-XML.
You can do it using the Exporter service
Follow some pseudo-code using the Java Gateway

Code: Select all

final int INC = 262144 //Maximum size of pixels read at once
SecurityContext ctx;
File f;
ExporterPrx store = gateway.getExporterService(ctx)
long size = store.generateXml();
FileOutputStream stream = new FileOutputStream(f);
for (offset = 0; (offset+INC) < size;) {
    stream.write(store.read(offset, INC));
    offset += INC;
}
stream.write(store.read(offset, (int) (size-offset)));
stream.close();


I hope it is helpful

Cheers

Jmarie

[Kouichi_C_Nakamura]

Thank you for the code snippet.

I've translated it into MATLAB code without understanding what's happening.

Code: Select all

userName = '********';

password = input('password:','s');

host = 'demo.openmicroscopy.org';

INC = 262144; % //Maximum size of pixels read at once



[gateway,user,cred] = loadOmeroGateway(userName, password, host);

ctx = omero.gateway.SecurityContext(user.getGroupId()); % 'omero.gateway.SecurityContext'
store = gateway.getExporterService(ctx); % 'omero.api.ExporterPrxHelper'

SIZE = store.generateXml(); %102

f = java.io.File('out.xml');

stream = java.io.FileOutputStream(f);

offset = 0;
while offset+INC < SIZE
    stream.write(store.read(offset, INC));
    offset = offset + INC;
end

stream.write(store.read(offset, int32(SIZE-offset)));
stream.close();

using loadOmeroGateway.m of mine:
https://gist.github.com/kouichi-c-nakam ... ogateway-m

This resulted in

Code: Select all

<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"/>

I need to specify an image before retrieving XML. How could I do that?

[jburel]

Hi Kouichi

Sorry I forgot a line
You need to add the following after creating the Exporter Service

Code: Select all

store.addImage(imageID);


[Kouichi_C_Nakamura]

WORKED LIKE A MAGIC! Thank you so much, Jmarie.

Best,
Kouichi

Code: Select all

imageID = 56134;

[gateway,user,cred] = loadOmeroGateway(userName, password, host);

ctx = omero.gateway.SecurityContext(user.getGroupId()); % 'omero.gateway.SecurityContext'
store = gateway.getExporterService(ctx); % 'omero.api.ExporterPrxHelper'

store.addImage(imageID);

SIZE = store.generateXml(); %102

f = java.io.File('out.xml');

stream = java.io.FileOutputStream(f);

offset = 0;
while offset+INC < SIZE
    stream.write(store.read(offset, INC));
    offset = offset + INC;
end

stream.write(store.read(offset, int32(SIZE-offset)));
stream.close();

gateway.close();

bfTiffComment('out.xml','Indent','on','outxmlfile','auto')


bfTiffComment.m is here:
https://gist.github.com/kouichi-c-nakam ... fcomment-m

[jburel]

Hi Kouichi

Great that it works
Thanks for letting us know
We will add an example to our documentation.

Cheers

Jmarie