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Query timestamps from all planes when C or Z dimensions are not filled #598

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merged 2 commits into from
Nov 27, 2024
Merged

Query timestamps from all planes when C or Z dimensions are not filled #598

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3c17005
wider timestamp query when C or Z dim not filled
Tom-TBT Oct 11, 2024
69b4263
simplified timestamp query
Tom-TBT Nov 19, 2024
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24 changes: 24 additions & 0 deletions omero_figure/omeroutils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,23 @@ 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.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:
Expand All @@ -40,6 +57,7 @@ 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
Expand All @@ -58,8 +76,14 @@ 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