implemented get_timestamps() from timeIncrement attribute

[JensWendt]

Changed get_timestamps() to revert back to the timeIncrement attribute of Pixels of an Image, if no PlaneInfo is found for it, or if the PlaneInfo did not contain DeltaT information. If no timeIncrement attribute is found, it will just return 0 for all timepoints. This does not account for any time offset that might have occured, i.e. the first image always is at 0s.

[will-moore]

Thanks @JensWendt. If there's no timeIncrement, can we just keep the existing behaviour of returning an empty list? Then we know that an empty list means "No timestamps", rather than a list where all the values are 0.

[JensWendt]

Done! now it checks if time_increment != 0 and leaves the dict empty if not, which in turn leaves the list empty again, as it was before.

[JensWendt]

Hold! no merging yet, please. I found a bug.

EDIT: Fixed. we can go ahead.

[JensWendt]

-.- now the timeIncrements are converted to SECOND BUT I cannot open images, where I manually set the timeIncrement with an OMERO.web script, anymore in Figure --> Error Image not found on the server, or you don't have permission to access it at /figure/imgData/584306/ It is my image, nobody else touched it. I could open it just fine before the latest "fix" why is converting the time somehow preventing me from opening the image?

[will-moore]

@JensWendt Are you sure you're still logged in as the same user (your connection hasn't timed out and you're now logged-in as e.g. public user)? Can you still access your other images?

[JensWendt]

nevermind, I simply did not add the new imports in the live omeroutils.py file on our server, only updated the function. I assume somehow this broke the import of the image as soon as TimeI got called, because I could still open Images that were going the route of PlaneInfo. For me everything works now, it should be ready.

[will-moore]

Hi @JensWendt I set timeIncrement based on your code at https://forum.image.sc/t/how-to-correctly-set-a-timeincrement-for-omero-pixels/101600

But the conversion of the time into seconds in this PR wasn't working for me. (are you sure it's working for you?) This is the change I needed to get this working...

--- a/omero_figure/omeroutils.py
+++ b/omero_figure/omeroutils.py
@@ -48,9 +48,9 @@ def get_timestamps(conn, image):
         try:
             pixels = image.getPrimaryPixels()._obj
             time_increment = pixels.getTimeIncrement()
-            time_increment_unit = time_increment.getUnit()
-            converted_value = TimeI.CONVERSIONS[time_increment_unit][
-                UnitsTime.SECOND](time_increment._value)
+            secs_unit = getattr(UnitsTime, "SECOND")
+            seconds = TimeI(time_increment, secs_unit)
+            converted_value = seconds.getValue()

         except Exception as error:

[JensWendt]

Hi,

I just double checked, and yes, it does work on my machine :)

But your solutions seems a lot nicer and more intuitive, if I would have known it works like this I would have done it that way. I think I missed that Constructor because I looked at Time instead of TimeI -.- Once again I am lost in the jungle of OMERO documentation

[will-moore]

Ah, OK I realise what's going on. You can't convert from a 'SECOND' to a 'SECOND'! So if your timeIncrement is already in SECONDS then it fails.

This works OK...

>>> TimeI.CONVERSIONS[UnitsTime.SECOND][UnitsTime.MILLISECOND]
<omero.conversions.Mul object at 0x11007fd30>

Bun this fails (which is the error I was seeing).

>>> TimeI.CONVERSIONS[UnitsTime.SECOND][UnitsTime.SECOND]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
KeyError: SECOND

So I guess your timeIncrement was not in SECONDS?

I agree that this is confusing and docs are lacking, so I think you actually did pretty well! I just happened to remember relevant code at https://github.com/ome/omero-py/blob/4fd72efaa8cdbec9da98e1d28678af16878a86ba/src/omero/gateway/__init__.py#L292 and adapted that.

[JensWendt]

Yes, I tried with minutes and hours, because that was what initially didnt work after my first iteration.

[JensWendt]

did a commit with your solution. Tested it with millisecond, second, minute and it works now as expected/intended

[will-moore]

This is working fine for me now - tested on merge-ci server. Merging...