From 3c170054f782fb9ac230c740c32dceac9e50c618 Mon Sep 17 00:00:00 2001
From: Tom-TBT <tom.boissonnet@hhu.de>
Date: Fri, 11 Oct 2024 11:38:48 +0200
Subject: [PATCH 1/2] wider timestamp query when C or Z dim not filled

---
 omero_figure/omeroutils.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/omero_figure/omeroutils.py b/omero_figure/omeroutils.py
index 279d08882..aeed7f0d7 100644
--- a/omero_figure/omeroutils.py
+++ b/omero_figure/omeroutils.py
@@ -29,6 +29,24 @@ def get_timestamps(conn, image):
         " Info.theZ=0 and Info.theC=0 and pixels.id=:pid"
     info_list = conn.getQueryService().findAllByQuery(
         query, params, conn.SERVICE_OPTS)
+
+    if len(info_list) < image.getSizeT():
+        # C & Z dimensions are not always filled
+        # Remove restriction on c0 z0 to catch all timestamps
+        params = ParametersI()
+        params.addLong('pid', image.getPixelsId())
+        query = """
+            from PlaneInfo Info where Info.pixels.id=:pid
+            and Info.id in (
+                select min(subInfo.id)
+                from PlaneInfo subInfo
+                where subInfo.pixels.id=:pid
+                group by subInfo.theT
+            )
+        """
+        info_list = conn.getQueryService().findAllByQuery(
+            query, params, conn.SERVICE_OPTS)
+
     timemap = {}
     # check if any PlaneInfo was found
     if len(info_list) > 0:
@@ -40,6 +58,7 @@ def get_timestamps(conn, image):
                 plane_info = PlaneInfoWrapper(conn, info)
                 delta_t = plane_info.getDeltaT('SECOND')
                 timemap[t_index] = delta_t.getValue()
+
     # double check to see if timemap actually got populated
     if len(info_list) == 0 or len(timemap) == 0:
         # get time info from the timeIncrement of the Pixels
@@ -58,8 +77,14 @@ def get_timestamps(conn, image):
         if converted_value != 0:
             for i in range(image.getSizeT()):
                 timemap[i] = i*converted_value
+
     time_list = []
     for t in range(image.getSizeT()):
         if t in timemap:
             time_list.append(timemap[t])
+        else:
+            # Hopefully never gets here, but
+            # time_list length MUST match image.sizeT
+            time_list.append(0)
+
     return time_list

From 69b42637f74e4caf1feab8af6faae3757be92525 Mon Sep 17 00:00:00 2001
From: Tom Boissonnet <tom.boissonnet@hhu.de>
Date: Tue, 19 Nov 2024 15:10:09 +0100
Subject: [PATCH 2/2] simplified timestamp query

---
 omero_figure/omeroutils.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/omero_figure/omeroutils.py b/omero_figure/omeroutils.py
index aeed7f0d7..a37041d2e 100644
--- a/omero_figure/omeroutils.py
+++ b/omero_figure/omeroutils.py
@@ -36,8 +36,7 @@ def get_timestamps(conn, image):
         params = ParametersI()
         params.addLong('pid', image.getPixelsId())
         query = """
-            from PlaneInfo Info where Info.pixels.id=:pid
-            and Info.id in (
+            from PlaneInfo Info where Info.id in (
                 select min(subInfo.id)
                 from PlaneInfo subInfo
                 where subInfo.pixels.id=:pid