Example of TableWrapper with ROI

[lldelisle]

Hi,
Sorry, I already have a question.
I would like to create a Table in omero with a column with ROIs.
I have a ResultTable (obtained with Analyze particle) and the corresponding ImageJ ROIs (in the overlay).
I tried to use setProperty on the ImageJ ROIs then add a column in my ResultTable.
But in omero there is no link between my table entries and my ROIs.
I am quite sure something is missing but I don't know what.
Would you mind to give an example?
Thank you.
My attempt was:

// I built previously a Map<String, Roi> map_rois with the rois corresponding to the table where the key is "Slice" in the rt
// Building a list of ROIs to put in omero
List<Roi> rois =  new ArrayList<>(0)
for ( int row = 0;row<rt.size();row++) {
        int t = rt.getValue("Slice", row) as int
        // Get the corresponding ROI
        Roi temp_roi = map_rois.get(t)
        // Set name and property
        temp_roi.setName("Gastruloid_t" + t)
        temp_roi.setProperty("ROI", "Gastruloid_t" + t)
        rois.add(temp_roi)
        // Add a column with the same info
        rt.setValue("ROI", row, "Gastruloid_t" + t)
}
// Save ROIs to omero
image_wpr.saveROIs(user_client, ROIWrapper.fromImageJ(rois as List))	

// Create an omero table:
TableWrapper table_wpr = new TableWrapper(user_client, rt, image_wpr.getId(), rois as List, "ROI")

// upload the table on OMERO
table_wpr.setName(table_name)
image_wpr.addTable(user_client, table_wpr)

[ppouchin]

The ROIs need a "ROI_ID" property set with their ID on OMERO (which is done automatically when retrieving ROIs).
I think you need to add something like this after saving the ROIs:

updatedRois = ROIWrapper.toImageJ(image_wpr.getROIs(user_client), "ROI")
TableWrapper table_wpr = new TableWrapper(user_client, rt, image_wpr.getId(), updatedRois, "ROI")

However, you'll retrieve all the ROIs, so if you have more than what you want, you may have to filter them. Or use Folders.

[ppouchin]

I'll try to improve the documentation...

[lldelisle]

Hi,
Thank you so much for your answer. It worked.
If I understand well this block:

simple-omero-client/src/main/java/fr/igred/omero/annotations/TableWrapper.java

Lines 408 to 435 in 9442f4a

	if (results.columnExists(roiIdProperty)) {
	Variable[] roiCol = results.getColumnAsVariables(roiIdProperty);
	roiColumn = idColumnToROIColumn(roiCol, id2roi);
	colToDelete = roiIdProperty;
	}
	if (roiColumn.length == 0 && results.columnExists(roiProperty)) {
	Variable[] roiCol = results.getColumnAsVariables(roiProperty);
	roiColumn = propertyColumnToROIColumn(roiCol, id2roi, label2roi, name2roi, shape2roi);
	colToDelete = roiProperty;
	}
	if (roiColumn.length != 0 && !colToDelete.isEmpty()) results.deleteColumn(colToDelete);
	String[] headings = results.getHeadings();
	if (roiColumn.length == 0 && Arrays.asList(headings).contains(LABEL)) {
	Variable[] roiCol = results.getColumnAsVariables(LABEL);
	roiColumn = labelColumnToROIColumn(roiCol, shape2roi, (m, s) -> m.keySet()
	.stream()
	.filter(s::contains)
	.findFirst()
	.orElse(null));
	if (roiColumn.length == 0) {
	roiColumn = labelColumnToROIColumn(roiCol, name2roi, (m, s) -> m.keySet()
	.stream()
	.filter(s::contains)
	.findFirst()
	.orElse(null));
	}
	}

Only one of those 2 is sufficient:

• add the same label as in the result table as name: temp_roi.setName("Gastruloid_t" + t)
• add the same label as in the result table as property: temp_roi.setProperty("ROI", "Gastruloid_t" + t)

[ppouchin]

Well, it's also about what you want do display on OMERO:

• setProperty("ROI", index) is used to group 2D shapes into one 3D/4D ROI on OMERO. The value is never stored, and when you retrieve it from OMERO, the default values are integers.
• setName(name) is used to name the 2D shapes on OMERO (and in ImageJ).
• You can also use setProperty("ROI_NAME", name) to give a 3D/4D ROI a name on OMERO.

I try to match against any of those properties when ROIs are passed to a TableWrapper (but you can't mix them though).

[lldelisle]

Thanks for the answer, I am not familiar with 3D/4D ROI on OMERO.
Just for info, when I tried to use setProperty with index of int type I got an error, it seems that it only accepts String...

[ppouchin]

Oh, yes. setProperty only accepts String. I meant that by default, I return integers as strings.

Any string can be used to group 2D shapes, but, by default, I just return a local index (the string has to be parsed).
It seems redundant with "ROI_ID", the property that contains the OMERO ID, but the latter is a Long, which can be troublesome to handle.
The idea is that if you need to retrieve ROIs from OMERO and want to create a label image, you just have to use the "ROI" property, while the "ROI_ID" property would need 32-bit images and would not start at 1, which would be a bit weird.
When creating ROIs though, you can use whatever String you want, but as it is not stored, it does not have to be complex.

At one point, I also merged "ROI" and "ROI_NAME" too, but there was actually no guarantee that ROI names should be unique.