Merge pull request #589 from JensWendt/timestamp_fix

implemented get_timestamps() from timeIncrement attribute

omero_figure/omeroutils.py

@@ -17,6 +17,8 @@
 
 from omero.sys import ParametersI
 from omero.gateway import PlaneInfoWrapper
+from omero.model.enums import UnitsTime
+from omero.model import TimeI
 
 
 def get_timestamps(conn, image):
@@ -28,13 +30,34 @@ def get_timestamps(conn, image):
  info_list = conn.getQueryService().findAllByQuery(
  query, params, conn.SERVICE_OPTS)
  timemap = {}
- for info in info_list:
- t_index = info.theT.getValue()
- if info.deltaT is not None:
- # Use wrapper to help unit conversion
- plane_info = PlaneInfoWrapper(conn, info)
- delta_t = plane_info.getDeltaT('SECOND')
- timemap[t_index] = delta_t.getValue()
+ # check if any PlaneInfo was found
+ if len(info_list) > 0:
+ # get time info from the PlaneInfo
+ for info in info_list:
+ t_index = info.theT.getValue()
+ if info.deltaT is not None:
+ # Use wrapper to help unit conversion
+ 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
+ time_increment = 0
+ converted_value = 0
+ try:
+ pixels = image.getPrimaryPixels()._obj
+ time_increment = pixels.getTimeIncrement()
+ secs_unit = getattr(UnitsTime, "SECOND")
+ seconds = TimeI(time_increment, secs_unit)
+ converted_value = seconds.getValue()
+
+ except Exception as error:
+ print(f"An exception occured: {error}\n"
+ "maybe the image has no 'timeIncrement' set")
+ 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: