TimeBlock types

cpp/petsird_analysis.cpp

@@ -18,6 +18,7 @@ using petsird::binary::PETSIRDReader;
 #include <xtensor/xview.hpp>
 #include <xtensor/xio.hpp>
 #include <iostream>
+#include <variant>
 
 int
 main(int argc, char* argv[])
@@ -64,13 +65,17 @@ main(int argc, char* argv[])
   float last_time = 0.F;
   while (reader.ReadTimeBlocks(time_block))
     {
-      last_time = time_block.id * header.scanner.listmode_time_block_duration;
-      num_prompts += time_block.prompt_events.size();
-
-      for (auto& event : time_block.prompt_events)
+      if (std::holds_alternative<petsird::EventTimeBlock>(time_block))
         {
-          energy_1 += energy_mid_points[event.energy_indices[0]];
-          energy_2 += energy_mid_points[event.energy_indices[1]];
+          auto& event_time_block = std::get<petsird::EventTimeBlock>(time_block);
+          last_time = event_time_block.start;
+          num_prompts += event_time_block.prompt_events.size();
+
+          for (auto& event : event_time_block.prompt_events)
+            {
+              energy_1 += energy_mid_points[event.energy_indices[0]];
+              energy_2 += energy_mid_points[event.energy_indices[1]];
+            }
         }
     }
 

cpp/petsird_generator.cpp

@@ -129,8 +129,8 @@ get_scanner_info()
     scanner_info.tof_bin_edges = tof_bin_edges;
     scanner_info.tof_resolution = 9.4F; // in mm
     scanner_info.energy_bin_edges = energy_bin_edges;
-    scanner_info.energy_resolution_at_511 = .11F;    // as fraction of 511
-    scanner_info.listmode_time_block_duration = 1.F; // ms
+    scanner_info.energy_resolution_at_511 = .11F; // as fraction of 511
+    scanner_info.event_time_block_duration = 1.F; // ms
   }
 
   return scanner_info;
@@ -217,8 +217,8 @@ main(int argc, char* argv[])
       std::poisson_distribution<> poisson(COUNT_RATE);
       const auto num_prompts_this_block = poisson(gen);
       const auto prompts_this_block = get_events(header, num_prompts_this_block);
-      petsird::TimeBlock time_block;
-      time_block.id = t;
+      petsird::EventTimeBlock time_block;
+      time_block.start = t * header.scanner.event_time_block_duration;
       time_block.prompt_events = prompts_this_block;
       writer.WriteTimeBlocks(time_block);
     }

model/Protocol.yml

@@ -3,21 +3,68 @@ PETSIRD: !protocol
   sequence:
     header: Header
     timeBlocks: !stream
+      # block with information (e.g. events, signals, etc.) occurring at a certain time or in a time interval
+      # Note: multiple time blocks can occur at the same start time
       items: TimeBlock
 
 Header: !record
   fields:
     scanner: ScannerInformation
     exam: ExamInformation?
 
-TimeBlock: !record
+# types of timeBlocks
+# TODO more types could be needed
+TimeBlock: [EventTimeBlock, ExternalSignalTimeBlock, BedMovementTimeBlock, GantryMovementTimeBlock]
+
+EventTimeBlock: !record
   fields:
-   # number of the block. Multiply with listmodeTimeBlockDuration to get time since startOfAcquisition
-   id: uint
+   # start time since ExamInformation.startOfAcquisition in ms
+   # Note: duration is given by ScannerInformation.eventTimeBlockDuration
+   start: uint
+   # TODO encode end time?
    # list of prompts in this time block
    # TODO might be better to use !array
    promptEvents: CoincidenceEvent*
    # optional list of delayed coincidences in this time block
    delayedEvents: CoincidenceEvent*?
    # optional list of triple coincidences in this time block
    tripleEvents: TripleEvent*?
+
+ExternalSignalTypeEnum: !enum
+  values:
+    - ecgTrace
+    - ecgTrigger
+    - respTrace
+    - respTrigger
+    - otherMotionSignal
+    - otherMotionTrigger
+    - externalSync
+    # other options, to be listed in the future
+    - other
+
+ExternalSignalType: !record
+  fields:
+    type: ExternalSignalTypeEnum
+    description: string
+    id: uint
+
+ExternalSignalTimeBlock: !record
+  fields:
+   # start time since ExamInformation.startOfAcquisition in ms
+   start: uint
+   # refer to ExternalSignalType.id
+   signalID: uint
+   # Note for triggers, this field is to be ignored
+   signalValues: float*
+
+BedMovementTimeBlock: !record
+  fields:
+    # start time since ExamInformation.startOfAcquisition in ms
+    start: uint
+    transform: RigidTransformation
+
+GantryMovementTimeBlock: !record
+  fields:
+    # start time since ExamInformation.startOfAcquisition in ms
+    start: uint
+    transform: RigidTransformation

model/ScannerInformation.yml

@@ -52,8 +52,8 @@ ScannerInformation: !record
     # FWHM of photopeak for incoming gamma of 511 keV, expressed as a ratio w.r.t. 511
     energyResolutionAt511: float
 
-    # duration of each time block in ms
-    listmodeTimeBlockDuration: uint
+    # duration of each event time block in ms
+    eventTimeBlockDuration: uint
 
     # Encode how the scanner handles multiple coincidences
     coincidencePolicy: CoincidencePolicy

python/petsird_analysis.py

@@ -37,11 +37,12 @@
         num_prompts = 0
         last_time = 0
         for time_block in reader.read_time_blocks():
-            last_time = time_block.id * header.scanner.listmode_time_block_duration
-            num_prompts += len(time_block.prompt_events)
-            for event in time_block.prompt_events:
-                energy_1 += energy_mid_points[event.energy_indices[0]]
-                energy_2 += energy_mid_points[event.energy_indices[1]]
+            if isinstance(time_block, petsird.TimeBlock.EventTimeBlock):
+                last_time = time_block.value.start  # all TimeBlock types have this field
+                num_prompts += len(time_block.value.prompt_events)
+                for event in time_block.value.prompt_events:
+                    energy_1 += energy_mid_points[event.energy_indices[0]]
+                    energy_2 += energy_mid_points[event.energy_indices[1]]
 
         print(f"Last time block at {last_time} ms")
         print(f"Number of prompt events: {num_prompts}")

python/petsird_generator.py

@@ -119,7 +119,7 @@ def get_scanner_info() -> petsird.ScannerInformation:
         tof_resolution=9.4,  # in mm
         energy_bin_edges=energyBinEdges,
         energy_resolution_at_511=0.11,  # as fraction of 511
-        listmode_time_block_duration=1,  # ms
+        event_time_block_duration=1,  # ms
     )
 
 
@@ -162,9 +162,16 @@ def get_events(
         header = get_header()
         writer.write_header(header)
         for t in range(NUMBER_OF_TIME_BLOCKS):
+            start = t * header.scanner.event_time_block_duration
             num_prompts_this_block = rng.poisson(COUNT_RATE)
             prompts_this_block = list(get_events(header, num_prompts_this_block))
             # Normally we'd write multiple blocks, but here we have just one, so let's write a tuple with just one element
             writer.write_time_blocks(
-                (petsird.TimeBlock(id=t, prompt_events=prompts_this_block),)
+                (
+                    petsird.TimeBlock.EventTimeBlock(
+                        petsird.EventTimeBlock(
+                            start=start, prompt_events=prompts_this_block
+                        )
+                    ),
+                )
             )