I'm in the process of writing an application which converts from a proprietary dataformat to OME-TIFF using the C++ libraries (ome-files-cpp 0.2.2, ome-common 5.3.2, bioformats 5.2.3).
I want to write multiple 2D images/datasets as series into one OME TIFF file.
This works, but I'm struggling to add specific metadata for each series
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for(auto dsn : matches)
{
// read each image dimensions from the dataset
ReadImageDimensions(dsn, dims);
// create meta data as we now know the image size
shared_ptr<ome::files::CoreMetadata> meta = CreateMetaDataForImage(dims[0], dims[1]);
meta->seriesMetadata.set("HDF5 Source Dataset", "some string");
metadataStore->setImageID(ome::files::createID("Image", idx), idx);
fillPixels(*metadataStore, *meta, idx);
ome::xml::meta::OMEXMLMetadata& omexml(dynamic_cast<ome::xml::meta::OMEXMLMetadata&>(*metadataStore));
ome::files::addMetadataOnly(omexml, idx);
idx++;
}
I've now looked at the generated TIFF file using
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ome-files info --omexml
Image: file_with_one_raw_image_raw_img.ome.tiff
Using reader: OME-TIFF (Open Microscopy Environment TIFF)
Reader setup took 00:00:00.083000
Filename = "/.../file_with_one_raw_image_raw_img.ome.tiff"
Used files = ["/.../file_with_one_raw_image_raw_img.ome.tiff"]
Reading core metadata
Series count = 1
Series #0:
Image count = 1
RGB = [false] ([1])
Interleaved = false
Indexed = false
Width = 3000
Height = 2000
SizeZ = 1 (effectively 1)
SizeT = 1 (effectively 1)
SizeC = 1 (effectively 1)
Thumbnail size = 128 × 85
Endianness = little
DimensionOrder = XYZTC (certain)
PixelType = uint16
Bits per Pixel = 16
MetadataComplete = true
ThumbnailSeries = false
Global metadata:
HDF5 File Version: 0.1
HDF5 Source File: /.../file_with_one_raw_image.h5
HDF5 Storage Server compilation timestamp: Jan 29 2016 17:50:06
UserComment: someComment
OME-XML metadata:
<?xml version="1.0" encoding="UTF-8" standalone="no" ?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" UUID="urn:uuid:2cb9eadf-7f62-42f6-a81d-cd9095590a7a" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/O ... 06/ome.xsd"><!-- Warning: this comment is within an OME-XML metadata block, which contains crucial dimensional parameters and other important metadata. Please edit cautiously (if at all), and back up the original data before doing so. For more information, see the OME-TIFF web site: http://www.openmicroscopy.org/site/supp ... /ome-tiff/ --><Image ID="Image:0"><Pixels BigEndian="false" DimensionOrder="XYZTC" ID="Pixels:0" Interleaved="false" SignificantBits="16" SizeC="1" SizeT="1" SizeX="3000" SizeY="2000" SizeZ="1" Type="uint16"><Channel Color="-1" ID="Channel:0:0" SamplesPerPixel="1"/><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="file_with_one_raw_image_raw_img.ome.tiff">urn:uuid:2cb9eadf-7f62-42f6-a81d-cd9095590a7a</UUID></TiffData><Plane TheC="0" TheT="0" TheZ="0"/></Pixels></Image><StructuredAnnotations><XMLAnnotation ID="Annotation:0"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 File Version</Key><Value xmlns="">0.1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:1"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Source File</Key><Value xmlns="">/.../file_with_one_raw_image.h5</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:2"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Storage Server compilation timestamp</Key><Value xmlns="">Jan 29 2016 17:50:06</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:3"><Value><OriginalMetadata xmlns=""><Key xmlns="">UserComment</Key><Value xmlns="">someComment</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:4"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 File Version</Key><Value xmlns="">0.1</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:5"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Source File</Key><Value xmlns="">/.../file_with_one_raw_image.h5</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:6"><Value><OriginalMetadata xmlns=""><Key xmlns="">HDF5 Storage Server compilation timestamp</Key><Value xmlns="">Jan 29 2016 17:50:06</Value></OriginalMetadata></Value></XMLAnnotation><XMLAnnotation ID="Annotation:7"><Value><OriginalMetadata xmlns=""><Key xmlns="">UserComment</Key><Value xmlns="">someComment</Value></OriginalMetadata></Value></XMLAnnotation></StructuredAnnotations></OME>
OME-XML validation successful
but my metadata series entry seems to be not there.
Any hints what I'm doing wrong?
