@science-corporation/synapse 1.1.0 → 2.0.0

package/src/api/proto.json

@@ -150,37 +150,52 @@
             }
           }
         },
-        "SpikeDetectConfig": {
+        "SpikeBinnerConfig": {
           "fields": {
-            "mode": {
-              "type": "SpikeDetectMode",
-              "id": 1
-            },
-            "thresholdUV": {
+            "binSizeMs": {
               "type": "uint32",
-              "id": 2
-            },
+              "id": 1
+            }
+          }
+        },
+        "TemplateMatcher": {
+          "fields": {
             "templateUV": {
               "rule": "repeated",
               "type": "uint32",
-              "id": 3
-            },
-            "sort": {
-              "type": "bool",
-              "id": 4
-            },
-            "binSizeMs": {
+              "id": 1
+            }
+          }
+        },
+        "Thresholder": {
+          "fields": {
+            "thresholdUV": {
               "type": "uint32",
-              "id": 5
+              "id": 1
+            }
+          }
+        },
+        "SpikeDetectorConfig": {
+          "oneofs": {
+            "config": {
+              "oneof": [
+                "thresholder",
+                "templateMatcher"
+              ]
             }
           },
-          "nested": {
-            "SpikeDetectMode": {
-              "values": {
-                "kThreshold": 0,
-                "kTemplate": 1,
-                "kWavelet": 2
-              }
+          "fields": {
+            "thresholder": {
+              "type": "Thresholder",
+              "id": 1
+            },
+            "templateMatcher": {
+              "type": "TemplateMatcher",
+              "id": 2
+            },
+            "samplesPerSpike": {
+              "type": "uint32",
+              "id": 3
             }
           }
         },
@@ -212,7 +227,8 @@
             "kBroadband": 2,
             "kSpiketrain": 3,
             "kTimestamps": 4,
-            "kImage": 5
+            "kImage": 5,
+            "kWaveforms": 6
           }
         },
         "DiskWriterConfig": {
@@ -458,6 +474,11 @@
               "requestType": "QueryRequest",
               "responseType": "QueryResponse"
             },
+            "StreamQuery": {
+              "requestType": "StreamQueryRequest",
+              "responseType": "StreamQueryResponse",
+              "responseStream": true
+            },
             "ListFiles": {
               "requestType": "google.protobuf.Empty",
               "responseType": "ListFilesResponse"
@@ -494,10 +515,11 @@
             "kBroadbandSource": 3,
             "kElectricalStimulation": 4,
             "kOpticalStimulation": 5,
-            "kSpikeDetect": 6,
+            "kSpikeDetector": 6,
             "kSpikeSource": 7,
             "kSpectralFilter": 8,
-            "kDiskWriter": 9
+            "kDiskWriter": 9,
+            "kSpikeBinner": 10
           }
         },
         "NodeConfig": {
@@ -509,10 +531,11 @@
                 "broadbandSource",
                 "electricalStimulation",
                 "opticalStimulation",
-                "spikeDetect",
+                "spikeDetector",
                 "spectralFilter",
                 "diskWriter",
-                "spikeSource"
+                "spikeSource",
+                "spikeBinner"
               ]
             }
           },
@@ -545,8 +568,8 @@
               "type": "OpticalStimulationConfig",
               "id": 8
             },
-            "spikeDetect": {
-              "type": "SpikeDetectConfig",
+            "spikeDetector": {
+              "type": "SpikeDetectorConfig",
               "id": 9
             },
             "spectralFilter": {
@@ -560,6 +583,10 @@
             "spikeSource": {
               "type": "SpikeSourceConfig",
               "id": 12
+            },
+            "spikeBinner": {
+              "type": "SpikeBinnerConfig",
+              "id": 13
             }
           }
         },
@@ -770,6 +797,14 @@
             }
           }
         },
+        "StreamQueryRequest": {
+          "fields": {
+            "request": {
+              "type": "QueryRequest",
+              "id": 1
+            }
+          }
+        },
         "QueryResponse": {
           "oneofs": {
             "response": {
@@ -799,6 +834,38 @@
             }
           }
         },
+        "StreamQueryResponse": {
+          "oneofs": {
+            "response": {
+              "oneof": [
+                "impedance",
+                "selfTest"
+              ]
+            }
+          },
+          "fields": {
+            "code": {
+              "type": "StatusCode",
+              "id": 1
+            },
+            "message": {
+              "type": "string",
+              "id": 2
+            },
+            "timestampNs": {
+              "type": "uint64",
+              "id": 3
+            },
+            "impedance": {
+              "type": "ImpedanceResponse",
+              "id": 4
+            },
+            "selfTest": {
+              "type": "SelfTestResponse",
+              "id": 5
+            }
+          }
+        },
         "StatusCode": {
           "values": {
             "kOk": 0,

package/src/config.ts

@@ -5,7 +5,8 @@ import DiskWriter from "./nodes/disk_writer";
 import ElectricalStimulation from "./nodes/electrical_stimulation";
 import OpticalStimulation from "./nodes/optical_stimulation";
 import SpectralFilter from "./nodes/spectral_filter";
-import SpikeDetect from "./nodes/spike_detect";
+import SpikeBinner from "./nodes/spike_binner";
+import SpikeDetector from "./nodes/spike_detector";
 import SpikeSource from "./nodes/spike_source";
 import StreamIn from "./nodes/stream_in";
 import StreamOut from "./nodes/stream_out";
@@ -19,7 +20,8 @@ const kNodeTypeObjectMap = {
   [synapse.NodeType.kSpikeSource]: SpikeSource,
   [synapse.NodeType.kOpticalStimulation]: OpticalStimulation,
   [synapse.NodeType.kSpectralFilter]: SpectralFilter,
-  [synapse.NodeType.kSpikeDetect]: SpikeDetect,
+  [synapse.NodeType.kSpikeBinner]: SpikeBinner,
+  [synapse.NodeType.kSpikeDetector]: SpikeDetector,
   [synapse.NodeType.kStreamIn]: StreamIn,
   [synapse.NodeType.kStreamOut]: StreamOut,
 };

package/src/device.ts

@@ -18,7 +18,7 @@ class Device {
     if (!status.ok() || !client) {
       throw new Error(`Failed to create client for ${uri}: ${status.message}`);
     }
-    this.rpc = client;
+    this.rpc = client as synapse.SynapseDevice;
   }
 
   async configure(config: Config, options: CallOptions = {}): Promise<Status> {
@@ -90,6 +90,39 @@ class Device {
     });
   }
 
+  async streamQuery(
+    query: synapse.IStreamQueryRequest,
+    options: CallOptions = {},
+    callbacks: {
+      onData: (data: synapse.StreamQueryResponse) => void;
+      onEnd?: () => void;
+      onError?: (err: Error) => void;
+      onStatus?: (status: Status) => void;
+    }
+  ) {
+    const { onData, onEnd, onError, onStatus } = callbacks;
+    const call = this.rpc.streamQuery(query, options);
+    call.on("data", (data: synapse.StreamQueryResponse) => {
+      onData(data);
+    });
+    if (onEnd) {
+      call.on("end", () => {
+        onEnd();
+      });
+    }
+    if (onError) {
+      call.on("error", (err: ServiceError) => {
+        onError(err);
+      });
+    }
+    if (onStatus) {
+      call.on("status", (grpcStatus) => {
+        onStatus?.(new Status(grpcStatus.code, grpcStatus.details));
+      });
+    }
+    return call;
+  }
+
   // Logs
 
   async getLogs(

package/src/nodes/index.ts

@@ -3,7 +3,8 @@ export { default as DiskWriter } from "./disk_writer";
 export { default as ElectricalStimulation } from "./electrical_stimulation";
 export { default as OpticalStimulation } from "./optical_stimulation";
 export { default as SpectralFilter } from "./spectral_filter";
-export { default as SpikeDetect } from "./spike_detect";
+export { default as SpikeBinner } from "./spike_binner";
+export { default as SpikeDetector } from "./spike_detector";
 export { default as SpikeSource } from "./spike_source";
 export { default as StreamIn } from "./stream_in";
 export { default as StreamOut } from "./stream_out";

package/src/nodes/spike_binner.ts

@@ -0,0 +1,30 @@
+import { synapse } from "../api/api";
+import Node from "../node";
+
+class SpikeBinner extends Node {
+  type = synapse.NodeType.kSpikeBinner;
+  config: synapse.ISpikeBinnerConfig;
+
+  constructor(config: synapse.ISpikeBinnerConfig = {}) {
+    super();
+
+    this.config = config;
+  }
+
+  toProto(): synapse.NodeConfig {
+    return super.toProto({
+      spikeBinner: this.config,
+    });
+  }
+
+  static fromProto(proto: synapse.INodeConfig): SpikeBinner {
+    const { spikeBinner } = proto;
+    if (!spikeBinner) {
+      throw new Error("Invalid config, missing spikeBinner");
+    }
+
+    return new SpikeBinner(proto.spikeBinner);
+  }
+}
+
+export default SpikeBinner;

package/src/nodes/spike_detector.ts

@@ -0,0 +1,30 @@
+import { synapse } from "../api/api";
+import Node from "../node";
+
+class SpikeDetector extends Node {
+  type = synapse.NodeType.kSpikeDetector;
+  config: synapse.ISpikeDetectorConfig;
+
+  constructor(config: synapse.ISpikeDetectorConfig = {}) {
+    super();
+
+    this.config = config;
+  }
+
+  toProto(): synapse.NodeConfig {
+    return super.toProto({
+      spikeDetector: this.config,
+    });
+  }
+
+  static fromProto(proto: synapse.INodeConfig): SpikeDetector {
+    const { spikeDetector } = proto;
+    if (!spikeDetector) {
+      throw new Error("Invalid config, missing spikeDetector");
+    }
+
+    return new SpikeDetector(proto.spikeDetector);
+  }
+}
+
+export default SpikeDetector;

package/synapse-api/.github/pull_request_template.md

@@ -0,0 +1,10 @@
+# Summary
+Brief overview of the changes
+
+# Changes
+* Detailed breakdown of what changed and why. If there are new/changed API concepts, explain how they are meant to be used.
+
+# Testing
+How can this change be tested?
+
+Please provide a link to a reference server and client implementation in synapse-python.

package/synapse-api/api/datatype.proto

@@ -9,4 +9,5 @@ enum DataType {
     kSpiketrain = 3;
     kTimestamps = 4;
     kImage = 5;
+    kWaveforms = 6;
 }

package/synapse-api/api/node.proto

@@ -6,12 +6,13 @@ import "api/datatype.proto";
 import "api/nodes/broadband_source.proto";
 import "api/nodes/electrical_stimulation.proto";
 import "api/nodes/optical_stimulation.proto";
-import "api/nodes/spike_detect.proto";
+import "api/nodes/spike_detector.proto";
 import "api/nodes/spectral_filter.proto";
 import "api/nodes/stream_out.proto";
 import "api/nodes/stream_in.proto";
 import "api/nodes/disk_writer.proto";
 import "api/nodes/spike_source.proto";
+import "api/nodes/spike_binner.proto";
 
 enum NodeType {
   kNodeTypeUnknown = 0;
@@ -20,10 +21,11 @@ enum NodeType {
   kBroadbandSource = 3;
   kElectricalStimulation = 4;
   kOpticalStimulation = 5;
-  kSpikeDetect = 6;
+  kSpikeDetector = 6;
   kSpikeSource = 7;
   kSpectralFilter = 8;
   kDiskWriter = 9;
+  kSpikeBinner = 10;
 }
 
 message NodeConfig {
@@ -35,10 +37,11 @@ message NodeConfig {
     BroadbandSourceConfig broadband_source = 5;
     ElectricalStimulationConfig electrical_stimulation = 6;
     OpticalStimulationConfig optical_stimulation = 8;
-    SpikeDetectConfig spike_detect = 9;
+    SpikeDetectorConfig spike_detector = 9;
     SpectralFilterConfig spectral_filter = 10;
     DiskWriterConfig disk_writer = 11;
     SpikeSourceConfig spike_source = 12;
+    SpikeBinnerConfig spike_binner = 13;
   }
 }
 

package/synapse-api/api/nodes/spike_binner.proto

@@ -0,0 +1,7 @@
+syntax = "proto3";
+
+package synapse;
+
+message SpikeBinnerConfig {
+  uint32 bin_size_ms = 1;
+}

package/synapse-api/api/nodes/spike_detector.proto

@@ -0,0 +1,19 @@
+syntax = "proto3";
+
+package synapse;
+
+message TemplateMatcher {
+  repeated uint32 template_uV = 1;
+}
+
+message Thresholder {
+  uint32 threshold_uV = 1;
+}
+
+message SpikeDetectorConfig {
+  oneof config {
+    Thresholder thresholder = 1;
+    TemplateMatcher template_matcher = 2;
+  }
+  uint32 samples_per_spike = 3;
+}

package/synapse-api/api/query.proto

@@ -55,6 +55,12 @@ message QueryRequest {
   }
 }
 
+message StreamQueryRequest {
+  QueryRequest request = 1;
+
+  // Other options to fill in specific to a stream
+}
+
 message QueryResponse {
   Status status = 1;
   repeated uint32 data = 2;
@@ -62,4 +68,16 @@ message QueryResponse {
     ImpedanceResponse impedance_response = 3;
     SelfTestResponse self_test_response = 4;
   }
-}
+}
+
+message StreamQueryResponse {
+  StatusCode code = 1;
+  string message = 2;
+  uint64 timestamp_ns = 3;
+  
+  // We need to switch on the test being run
+  oneof response {
+    ImpedanceResponse impedance = 4;
+    SelfTestResponse self_test = 5;
+  }
+}

package/synapse-api/api/synapse.proto

@@ -45,6 +45,7 @@ service SynapseDevice {
   rpc Start(google.protobuf.Empty) returns (Status) {}
   rpc Stop(google.protobuf.Empty) returns (Status) {}
   rpc Query(QueryRequest) returns (QueryResponse) {}
+  rpc StreamQuery(StreamQueryRequest) returns (stream StreamQueryResponse) {}
 
   rpc ListFiles(google.protobuf.Empty) returns (ListFilesResponse) {}
   rpc WriteFile(WriteFileRequest) returns (WriteFileResponse) {}

package/dist/nodes/spike_detect.d.ts

@@ -1,11 +0,0 @@
-import { synapse } from "../api/api";
-import Node from "../node";
-declare class SpikeDetect extends Node {
-    type: synapse.NodeType;
-    config: synapse.ISpikeDetectConfig;
-    constructor(config?: synapse.ISpikeDetectConfig);
-    toProto(): synapse.NodeConfig;
-    static fromProto(proto: synapse.INodeConfig): SpikeDetect;
-}
-export default SpikeDetect;
-//# sourceMappingURL=spike_detect.d.ts.map

package/src/nodes/spike_detect.ts

@@ -1,30 +0,0 @@
-import { synapse } from "../api/api";
-import Node from "../node";
-
-class SpikeDetect extends Node {
-  type = synapse.NodeType.kSpikeDetect;
-  config: synapse.ISpikeDetectConfig;
-
-  constructor(config: synapse.ISpikeDetectConfig = {}) {
-    super();
-
-    this.config = config;
-  }
-
-  toProto(): synapse.NodeConfig {
-    return super.toProto({
-      spikeDetect: this.config,
-    });
-  }
-
-  static fromProto(proto: synapse.INodeConfig): SpikeDetect {
-    const { spikeDetect } = proto;
-    if (!spikeDetect) {
-      throw new Error("Invalid config, missing spikeDetect");
-    }
-
-    return new SpikeDetect(proto.spikeDetect);
-  }
-}
-
-export default SpikeDetect;

package/synapse-api/api/nodes/spike_detect.proto

@@ -1,16 +0,0 @@
-syntax = "proto3";
-
-package synapse;
-
-message SpikeDetectConfig {
-  enum SpikeDetectMode {
-    kThreshold = 0;
-    kTemplate = 1;
-    kWavelet = 2;
-  }
-  SpikeDetectMode mode = 1;
-  uint32 threshold_uV = 2;
-  repeated uint32 template_uV = 3;
-  bool sort = 4;
-  uint32 bin_size_ms = 5;
-}