Merge pull request #20 from KrisThielemans/Triples

add Triple events, multiples strategy and changed CoincidenceEvent

cpp/prd_analysis.cpp

@@ -54,8 +54,8 @@ main(int argc, char* argv[])
 
       for (auto& event : time_block.prompt_events)
         {
-          energy_1 += energy_mid_points[event.energy_1_idx];
-          energy_2 += energy_mid_points[event.energy_2_idx];
+          energy_1 += energy_mid_points[event.energy_indices[0]];
+          energy_2 += energy_mid_points[event.energy_indices[1]];
         }
     }
 

cpp/prd_generator.cpp

@@ -107,10 +107,10 @@ get_events(const prd::Header& header, std::size_t num_events)
     {
       const auto detectors = get_random_pair(header.scanner.NumberOfDetectors());
       prd::CoincidenceEvent e;
-      e.detector_1_id = detectors.first;
-      e.detector_2_id = detectors.second;
-      e.energy_1_idx = get_random_energy_value();
-      e.energy_2_idx = get_random_energy_value();
+      e.detector_ids[0] = detectors.first;
+      e.detector_ids[1] = detectors.second;
+      e.energy_indices[0] = get_random_energy_value();
+      e.energy_indices[1] = get_random_energy_value();
       e.tof_idx = get_random_tof_value();
       events.push_back(e);
     }

model/CoincidenceEvent.yml

@@ -1,9 +1,10 @@
-# All information about a coincidence event specified as identifiers or indices (i.e. discretized).
+# All information about a coincidence event specified as identifiers or indices (i.e. discretized). Indices start from 0.
 # TODO: this might take up too much space, so some/all of these could be combined in a single index if necessary.
 CoincidenceEvent: !record
   fields:
-    detector1Id: uint
-    detector2Id: uint
+    # the pair of detector elements
+    detectorIds: uint*2
+    # an index into the tofBinEdges field in the ScannerInformation
     tofIdx: uint
-    energy1Idx: uint
-    energy2Idx: uint
+    # a pair of indices into the energyBinEdges field in the ScannerInformation
+    energyIndices: uint*2

model/Protocol.yml

@@ -18,6 +18,7 @@ TimeBlock: !record
    # list of prompts in this time block
    # TODO might be better to use !array
    promptEvents: CoincidenceEvent*
-   # list of delayed coincidences in this time block
+   # optional list of delayed coincidences in this time block
    delayedEvents: CoincidenceEvent*?
-
+   # optional list of triple coincidences in this time block
+   tripleEvents: TripleEvent*?

model/ScannerInformation.yml

@@ -9,12 +9,34 @@ Detector: !record
     y: float
     z: float
 
+# Type definition for how to encode how the scanner handles multiple coincidences when recording the prompts.
+# Due to various effects (such as high count rate, prompt gammas), it is possible that multiple single
+# events are detected within the coincidence window. This type encodes some different ways
+# that this multiple events are handled, and recorded in the coincidence stream.
+CoincidencePolicy: !enum
+  values:
+    # multiples will be rejected
+    - rejectMultiples
+
+    # multiples will be stored as a sequence of pairs, e.g. a triple leads to 3 pairs
+    - storeMultiplesAsPairs
+
+    # other options, to be listed in the future
+    - other
+
+
 ScannerInformation: !record
   fields:
     modelName: string?
+
+    # list of geometric information for all detector elements
+    # TODO will be adjusted when properly encoding geometry
     detectors: Detector*
 
     # edge information for TOF bins in mm (given as from first to last edge, so there is one more edge than the number of bins)
+    # 0 corresponds to the same arrival time. Negative numbers indicate that the first detector detected first.
+    # For instance, a coincidence event is stored as 2 detectorIds, denoting the arrival time at the first
+    # detector t1 and the arrival time at the second detector t2, we store (t1-t2)*c/2.
     # TODO: this currently assumes equal size for each TOF bin, but some scanners "stretch" TOF bins depending on length of LOR
     tofBinEdges: !array
       items: float
@@ -32,6 +54,9 @@ ScannerInformation: !record
     # duration of each time block in ms
     listmodeTimeBlockDuration: uint
 
+    # encode how the scanner handles multiple coincidences
+    coincidencePolicy: CoincidencePolicy
+
   computedFields:
     numberOfDetectors: size(detectors)
     numberOfTOFBins: size(tofBinEdges)-1

model/TripleEvent.yml

@@ -0,0 +1,11 @@
+# All information about a triple event specified as identifiers or indices (i.e. discretized).
+TripleEvent: !record
+  fields:
+    detectorIds: uint*3
+    # timing differences (converted to mm) w.r.t. first event, stored as
+    # indices into the tofBinEdges field in the ScannerInformation
+    # Note: only 2, corresponding to the arrival time differences of the second and third detectorId
+    # listed w.r.t. the first detectorId
+    tofIndices: uint*2
+    # indices for each single event into the energyBinEdges field in the ScannerInformation
+    energyIndices: uint*3

python/prd_analysis.py

@@ -23,8 +23,8 @@
             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_1_idx]
-                energy_2 += energy_mid_points[event.energy_2_idx]
+                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/prd_generator.py

@@ -57,10 +57,10 @@ def get_events(header: prd.Header, num_events: int) -> Iterator[prd.CoincidenceE
     detector_count = header.scanner.number_of_detectors()
     for _ in range(num_events):
         yield prd.CoincidenceEvent(
-            detector_1_id=random.randrange(0, detector_count),
-            detector_2_id=random.randrange(0, detector_count),
-            energy_1_idx=random.randrange(0, NUMBER_OF_ENERGY_BINS),
-            energy_2_idx=random.randrange(0, NUMBER_OF_ENERGY_BINS),
+            detector_ids = [random.randrange(0, detector_count),
+                           random.randrange(0, detector_count)],
+            energy_indices = [random.randrange(0, NUMBER_OF_ENERGY_BINS),
+                          random.randrange(0, NUMBER_OF_ENERGY_BINS)],
             tof_idx=random.randrange(0, NUMBER_OF_TOF_BINS),
         )