setting names/values for Z, C, T

[yuriy_alexandrov]

looking back at Andy's explanations and by opening Will's example data, I believe I've got the picture.

I found this Matlab example useful:
https://github.com/mporter-gre/ImageAnalysis/blob/master/createNewImageFromOldPixels.m

try to summarize:

1) "Pixels" are used to get ZCT "physical sizes"

Code: Select all

    physSizeX = oldPixels.getPhysicalSizeX.getValue; % alive!
    physSizeY = oldPixels.getPhysicalSizeY.getValue; % alive!
    physSizeZ = oldPixels.getPhysicalSizeZ.getValue; % alive!

2) "Pixels" are also used to get wavelength info, albeit not directly but via "Channles":

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pixelsService = factory.getPixelsService();
pixelsDesc = pixelsService.retrievePixDescription(pixels.getId().getValue());
channels = pixelsDesc.copyChannels();
%
for c = 1:sizeC
    ch = channels.get(c-1);
    ch.getLogicalChannel.getName.getValue % alive!
    % ....
end

3) "planeInfo" structure is used to get exposure times and macro times (delays from the beginning of experiment)

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planeInfo00T = getPlaneInfo(factory, getImages(factory, uint64(image.getId().getValue())), 0, 0, []);
%
for k = 1 : planeInfo00T.size()
     z = planeInfo00T(k).getTheZ.getValue;   
     c = planeInfo00T(k).getTheC.getValue;   
     t = planeInfo00T(k).getTheT.getValue;
     exposuretime = planeInfo00T(k).getExposureTime.getValue; % alive!
     deltaT  = planeInfo00T(k).getDeltaT.getValue; % alive!
     % ...
end


settings should work correspondingly.
I hope I interpreted getDeltaT correctly, as returning macro-time.

Many thanks Andy and Will.
...

[sbesson]

Hi Yuriy,

the code snippets you posted above all look sensible and should get you the information you are looking for. One small comment:

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    ch.getLogicalChannel.getName.getValue


will return a java.lang.String object. Thus you may want to convert it before manipulating it:

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    char(ch.getLogicalChannel.getName.getValue)


Best,
Sebastien

[yuriy_alexandrov]

Yes certainly, the type conversions aren't automatic yet, like breathing.

Thanks for the getPlaneInfo function!

Best,
Y.

[yuriy_alexandrov]

....
When importing to Omero the data acquired by multiple cameras with many attributes etc., - it is reasonable to annotate the XY-plane (camera output) with some string - typically the XY-plane Filename.

The "Set***Description" look suitable method and "Plane" is proper place - however there is no setPlaneDescription function so I compiled an example using "setPlaneHashSHA1" instead, that has proper interface

Code: Select all

for ii = 1:num_files
z = 1;
c = 1;
t = 1;
  switch modulo
     case 'ModuloAlongC'
       c = ii;
     case 'ModuloAlongZ'
       z = ii;
     case 'ModuloAlongT'
       t = ii;
     end
     metadata.setPlaneTheC(toInt(c),0,ii-1);
     metadata.setPlaneTheT(toInt(t),0,ii-1);
     metadata.setPlaneTheZ(toInt(z),0,ii-1);                       
     metadata.setPlaneHashSHA1(sprintf(char(file_names{ii})),0,ii-1)                         
end                                                                                     
%
img_description = char(loci.formats.MetadataTools.getOMEXML(metadata));                                                       
% ......
iId = pixelsService.createImage(SizeX, SizeY, SizeZ, SizeT, toJavaList([uint32(0:(SizeC - 1))]), pixelsType, imageName, img_description);


that solves the problem - I realize it is wrong usage of SHA1 field.

Also, strangely, I found that "setImageDescription" method doesn't change Description field, it is only set up properly on image creation by "createImage".

The "bfsave" in Bioformats Matlab, - very instructive, thanks.

Best,
Y.

[wmoore]

One option might be to annotate the PlaneInfo in the same way as a Project, Dataset, Image etc. (there is a PlaneInfoAnnotationLink http://ci.openmicroscopy.org/job/OMERO- ... nLink.html) although this might be a bit of an overkill?

[yuriy_alexandrov]

...
thanks Will - yes, "overkill" is exactly a word that I was thinking when the same idea crossed my mind...
also, the number of planes in some cases can go in thousands.

if Plane's Description field is left private in the structure, one probably can think about accessing it.

Best,
Y.