Open Microscopy Environment

Hi,

If the user, at import time, chooses the "Archive the original imported files(s) to the server" option, is there a way through the API to get those files either as bytes or perhaps the file path(s) that the client app can then access through the file system?

Thanks
John

Hi John
If the user selects the archived option, to retrieve the files you can do:
Use the Query service to retrieve the original files linked to a given pixels set.
You will get the pixels ID from the image itself.

Code: Select all

IQueryPrx service;
ParametersI param = new ParametersI();
param.map.put("id", omero.rtypes.rlong(pixelsID));
List files = service.findAllByQuery(
               "select ofile from OriginalFile as ofile left join " +
               "ofile.pixelsFileMaps as pfm left join pfm.child as " +
               "child where child.id = :id", param);


The call will return a collection of Original files.

Then you can read the data using the RawFileStore
Follow some pseudo-code

Code: Select all

int INC = 262144;
RawFileStorePrx store;
File f;// The file on client's machine
OriginalFile of; //object from the list returned in previous call.
store.setFileId(of.getId().getValue());
stream = new FileOutputStream(f);
size = of.getSize().getValue();
try {
   for (offset = 0; (offset+INC) < size;) {
       stream.write(store.read(offset, INC)); //read the data
      offset += INC;
    }               
} finally {
stream.write(store.read(offset, (int) (size-offset)));
stream.close();
}            


I will probably need to make the method available through one of the services, so it is easier to use.

Thanks
jmarie

Thank you JMarie that worked nicely!