Got four basic examples working in Scala.

src/scala/build.sbt

@@ -31,6 +31,8 @@ lazy val root: Project = (project in file(".")).
   dependsOn(minimal % "test->compile")
 
 // To build and run examples
+// run with sbt 'examples/runMain org.openworm.trackercommons.examples.ExampleName'
+// where `ExampleName` is one of the example files, e.g. `CountAnimals`
 lazy val examples: Project = (project in file("src/examples")).
   settings(commonSettings: _*).
   dependsOn(root)

src/scala/src/examples/CircleTravel.scala

@@ -0,0 +1,31 @@
+package org.openworm.trackercommons.examples
+
+import org.openworm.trackercommons._
+
+object CircleTravel extends ExampleTemplate[String] {
+  val defaultLocation = ""
+
+  def run(args: Array[String]): Either[String, String] = {
+    val circle = Create.wcon.
+      setMeta(
+        Create.meta("circle example").addSoftware( Create.software.name("CircleTravel.scala") )
+      ).
+      addData({
+        val w = Create.worm("1").add(0.0, Array(1.0), Array(0.0))
+        for (i <- 1 until 12)
+          w.add(i.toDouble, Array(math.cos(i*math.Pi/6)), Array(math.sin(i*math.Pi/6)))
+        w
+      }).
+      setUnits().
+      result
+    val output = defaultOutput
+    ReadWrite.write(circle, output) match {
+      case Left(err) => Left(err)
+      case _         => Right(output.getPath)
+    }
+  }
+
+  def succeed(s: String) {
+    println(f"Wrote a circularly traveling point animal to $s")
+  }
+}

src/scala/src/examples/CountAnimals.scala

@@ -1,11 +1,17 @@
 package org.openworm.trackercommons.examples
 
+import org.openworm.trackercommons._
+
 object CountAnimals extends ExampleTemplate[Int] {
-  val defaultPath = "../../tests/count_animals.wcon"
+  val defaultLocation = "../../tests/examples/count_animals.wcon"
 
   def run(args: Array[String]): Either[String, Int] = existingFile(args) match {
     case Left(msg) => Left(msg)
-    case Right(file) => Right(-1)
+    case Right(file) =>
+      ReadWrite.readOne(file) match {
+        case Left(err) => Left(err.toString)
+        case Right(ds) => Right(ds.data.map(_.id).toSet.size)
+      }
   }
 
   def succeed(n: Int) {

src/scala/src/examples/ExampleTemplate.scala

@@ -1,12 +1,17 @@
 package org.openworm.trackercommons.examples
 
+
+case class Selected(count: Int, where: String) {}
+
 trait ExampleTemplate[A] {
   def run(args: Array[String]): Either[String, A]
   def succeed(a: A): Unit
-  def defaultPath: String
+  def defaultLocation: String
+  def defaultOutput: java.io.File = (new java.io.File("result.wcon")).getCanonicalFile
 
+  // Expect `run` to call this to get a single file
   def existingFile(args: Array[String]): Either[String, java.io.File] = {
-    val theFileName = args.headOption.getOrElse(defaultPath)
+    val theFileName = args.headOption.getOrElse(defaultLocation)
     val theFile = new java.io.File(theFileName)
     if (!theFile.exists) {
       Left(Seq(
@@ -20,7 +25,7 @@ trait ExampleTemplate[A] {
   def main(args: Array[String]) {
     run(args) match {
       case Left(msg) => println(msg); sys.exit(1)
-      case Right(n)  => 
+      case Right(a)  => succeed(a)
     }
   }
 }

src/scala/src/examples/MovementSelect.scala

@@ -0,0 +1,70 @@
+package org.openworm.trackercommons.examples
+
+import org.openworm.trackercommons._
+
+object MovementSelect extends ExampleTemplate[Selected] {
+  val defaultLocation = "../../tests/examples/all_movements.wcon"
+
+  def sq(x: Double) = x*x
+
+  def movesFar(d: Data): Boolean = {
+    if (d.ts.length < 2) return false
+
+    val cx, cy, l = new Array[Double](d.ts.length)
+    for (i <- l.indices) {
+      val ni = d.spineN(i)
+      if (ni < 1) {
+        cx(i) = Double.NaN
+        cy(i) = Double.NaN
+        l(i) = 0
+      }
+      else {
+        cx(i) = if (d.cxs.length == 0) (d.x(i, 0) + d.x(i, ni-1))/2 else d.cxs(i)
+        cy(i) = if (d.cys.length == 0) (d.y(i, 0) + d.y(i, ni-1))/2 else d.cys(i)
+        l(i) = math.sqrt(sq(d.x(i, 0) - d.x(i, ni-1)) + sq(d.y(i, 0) - d.y(i, ni-1)))
+      }
+    }
+
+    val longest = l.max
+    if (longest == 0) return false     // Reject worms without a size
+
+    var i0 = 0
+    while (i0 < cx.length && (cx(i0).isNaN || cy(i0).isNaN)) i0 += 1  // i0 is at first valid position
+    var i1 = cx.length -1
+    while (i1 > i0 && (cx(i1).isNaN || cy(i1).isNaN)) i1 -= 1  // i1 at last valid position
+    if (i1 <= i0) return false   // Didn't go anywhere valid
+
+    var distmax = 0.0
+    var i = i0 + 1
+    while (i <= i1) {
+      while (cx(i).isNaN || cy(i).isNaN) i += 1
+      val dist = sq(cx(i) - cx(i0)) + sq(cy(i) - cy(i0))
+      if (dist > distmax) distmax = dist
+      i += 1
+    }
+    distmax = math.sqrt(distmax)
+
+    distmax > longest  // We have to have traveled at least one nose-to-tail distance
+  }
+
+  def run(args: Array[String]): Either[String, Selected] = existingFile(args) match {
+    case Left(msg) => Left(msg)
+    case Right(file) =>
+      ReadWrite.readOne(file) match {
+        case Left(err) => Left(err.toString)
+        case Right(ds) =>
+          val selected = ds.groupByIDs().flatMap(d => if (movesFar(d)) Some(d) else None)
+          val output = defaultOutput
+          ReadWrite.write(selected, output) match {
+            case Left(err) => Left(err)
+            case _         => Right(
+              Selected(selected.data.length, output.getPath)
+            )
+          }
+      }
+  }
+
+  def succeed(s: Selected) {
+    println(f"Found ${s.count} records; wrote to ${s.where}")
+  }
+}

src/scala/src/main/scala/Create.scala

@@ -123,6 +123,9 @@ object Create {
       for (d <- more) w = w.addData(d)
       w
     }
+    def addData(builder: DataBuilder[YesData]): MakeWcon[U, YesData, F] = addData(builder.result)
+    def addData(builder1: DataBuilder[YesData], builder2: DataBuilder[YesData], more: DataBuilder[YesData]*): MakeWcon[U, YesData, F] =
+      addData(builder1.result, builder2.result, more.map(_.result): _*)
     def dropData: MakeWcon[U, NoData, F] = { stale = false; new MakeWcon[U, NoData, F](building.copy(data = Array.empty), 0) }
 
     def putCustom(key: String, value: Json) = {
@@ -221,7 +224,8 @@ object Create {
     def result(implicit ev: I =:= YesID) = underlying
   }
 
-  def meta() = new MakeMeta[NoID](Metadata.empty)
+  def meta(): MakeMeta[NoID] = new MakeMeta[NoID](Metadata.empty)
+  def meta(id: String): MakeMeta[YesID] = meta().setID(id)
 
   final class MakeLab private[trackercommons] (val result: Laboratory) {
     def isEmpty = result.isEmpty

src/scala/src/main/scala/Data.scala

@@ -279,8 +279,9 @@ extends AsJson with Customizable[Data] {
   }
 
   def reshaped(reshaper: Reshape, magic: Magic = Magic.expand, unshaped: Option[Unshaped] = None): Option[Data] = {
-    if (reshaper.length != 1) return None
+    if (reshaper.sizes.length != 1) return None
     val nts = reshaper(Array(ts))
+    if (nts.length == 0) return None
     val nxd = reshaper(Array(xDatas))
     val nyd = reshaper(Array(yDatas))
     val nrx = reshaper(Array(rxs))
@@ -476,9 +477,9 @@ object Data extends FromJson[Data] {
 
   private def BAD(msg: String): Either[JastError, Nothing] = Left(JastError("Invalid data entries: " + msg))
   private def IBAD(id: String, msg: String): Either[JastError, Nothing] =
-    BAD("Data points for " + id + " have " + msg)
+    BAD("Data points for " + id + " are wrong because " + msg)
   private def MYBAD(id: String, t: Double, msg: String): Either[JastError, Nothing] =
-    BAD("Data point for " + id + " at time " + t + " has " + msg)
+    BAD("Data point for " + id + " at time " + t + " is wrong because " + msg)
 
   private[trackercommons] val emptyD = new Array[Double](0)
   private[trackercommons] val zeroD = Array(0.0)
@@ -783,7 +784,7 @@ object Data extends FromJson[Data] {
         case Some(us) =>
           val u = new Unshaped
           val ans = concat(ds, magic, Some(u))
-          us += u
+          if (u.mistakes.nonEmpty) us += u
           id -> ans
         case _ =>
           id -> concat(ds, magic)

src/scala/src/main/scala/DataSet.scala

@@ -9,6 +9,26 @@ extends AsJson with Customizable[DataSet] {
   def map(f: Data => Data) = new DataSet(meta, unitmap, data.map(f), files, custom)
   def flatMap(f: Data => Option[Data]) = new DataSet(meta, unitmap, data.flatMap(x => f(x)), files, custom)
 
+  def groupByIDs(unshaped: Option[collection.mutable.ArrayBuffer[Custom.Unshaped]] = None): DataSet = {
+    val groups = data.zipWithIndex.groupBy(_._1.id).toMap
+    if (groups.size == data.length) this
+    else {
+      val groupedData = groups.map{ case (_, vs) => 
+        val ix = vs.map(_._2).min
+        val ds = vs.map(_._1)
+        val re = Reshape.sortSet(ds.map(_.ts), deduplicate = true)
+        if (unshaped.nonEmpty) {
+          val u = new Custom.Unshaped
+          val join = Data.join(re, ds, unshaped = Some(u))
+          if (u.mistakes.nonEmpty) unshaped.get += u
+          ix -> join
+        }
+        else ix -> Data.join(re, ds)
+      }.toArray.sortBy(_._1).flatMap(_._2)
+      this.copy(data = groupedData)
+    }
+  }
+
   def customFn(f: Json.Obj => Json.Obj) = copy(custom = f(custom))
 
   def json = unitmap.unfix(

src/scala/src/main/scala/Reshape.scala

@@ -71,9 +71,9 @@ object Reshape {
       n
     }
     val elements = {
-      var a = new Array[Int](count)
+      var a = new Array[Int](2*count)
       var i, j = 0
-      while (i < indicator.length) { if (indicator(i)) { a(j) = i; j += 1 }; i +=1 }
+      while (i < indicator.length) { if (indicator(i)) { a(j) = 0; j += 1; a(j) = i; j += 1 }; i += 1 }
       a
     }
     new Reshape(elements, Array(indicator.length))

tests/examples/all_movements.wcon

@@ -0,0 +1,29 @@
+{
+  "metadata": {
+    "protocol": "Six animals that travel different distances."
+  },
+  "units": { "t":"s", "x":"mm", "y":"mm" },
+  "data": [
+    { "id":"1", "t":[0, 1, 2, 3],
+      "x":[[1,2], [3,4], [5,6], [7,8]],
+      "y":[[3,4], [4,3], [3,2], [2,3]],
+      "comment":"Length = sqrt(2), travels more than 6 (include)"
+    },
+    { "id":"2", "t":[0, 1, 2, 3],
+      "x":[[0,5], [1,6], [0,5], [-1,4]],
+      "y":[[-3,3], [-3,2], [-3,2], [-2,3]],
+      "comment":"Length over 6, travels less than 3 (reject)"
+    },
+    { "id":"3", "t":[0], "x":[[1,3]], "y":[[3,5]] },
+    { "id":"3", "t":[1], "x":[[2,4]], "y":[[3,5]] },
+    { "id":"3", "t":[2], "x":[[3,5]], "y":[[3,5]] },
+    { "id":"3", "t":[3], "x":[[4,6]], "y":[[3,5]] },
+    { "id":"4", "t":[2], "x":[[-5,-5]], "y":[[3,4]] },
+    { "id":"5", "t":[0, 1, 2, 3],
+      "x":[[2,2,2], [2,2,2], [2,2,2], [2,2,2]],
+      "y":[[4,4,4], [4,4,4], [4,4,4], [4,4,4]] },
+    { "id":"6", "t":[0, 1, 2, 3],
+      "x":[[4], [4], [4], [4]],
+      "y":[[2], [2], [2], [2]] }
+  ]
+}

tests/examples/all_times.wcon

@@ -0,0 +1,27 @@
+{
+  "metadata": {
+    "protocol": "Six animals present for different lengths of time."
+  },
+  "units": { "t":"s", "x":"mm", "y":"mm" },
+  "data": [
+    { "id":"1", "t":[0, 8, 16, 24, 32, 40],
+      "x":[[1,2], [3,4], [5,6], [7,8], [9,8], [7,6]],
+      "y":[[3,4], [4,3], [3,2], [2,3], [1,2], [2,1]]
+    },
+    { "id":"2", "t":[0, 3, 6, 9, 12, 15],
+      "x":[[8,9], [7,9], [6,9], [6,8], [6,7], [6,6]],
+      "y":[[7,6], [6,5], [5,4], [4,3], [3,2], [2,1]]
+    },
+    { "id":"3", "t":[0, 1], "x":[[1,3],[2,3]], "y":[[3,5],[4,5]] },
+    { "id":"3", "t":[5, 11], "x":[[1,3],[2,3]], "y":[[3,5],[4,5]] },
+    { "id":"3", "t":[15, 16], "x":[[1,3],[2,3]], "y":[[3,5],[4,5]] },
+    { "id":"3", "t":[19, 26], "x":[[1,3],[2,3]], "y":[[3,5],[4,5]] },
+    { "id":"3", "t":[33, 34], "x":[[1,3],[2,3]], "y":[[3,5],[4,5]] },
+    { "id":"4", "t":[2], "x":[[-5,-5]], "y":[[3,4]] },
+    { "id":"5", "t":[22], "x":[[-5,-5]], "y":[[3,4]] },
+    { "id":"6", "t":[14, 18, 22, 26],
+      "x":[[-1,-2], [-3,-4], [-5,-6], [-7,-8]],
+      "y":[[-3,-4], [-4,-3], [-3,-2], [-2,-3]]
+    }
+  ]
+}

tests/examples/count_animals.wcon

@@ -0,0 +1,12 @@
+{
+  "metadata": {
+    "protocol": "Three animals created by hand in four data points."
+  },
+  "units": { "t":"s", "x":"mm", "y":"mm" },
+  "data": [
+    {"id":"1", "t":[0], "x":[[1,2]], "y":[[3,4]] },
+    {"id":"2", "t":[0], "x":[[8,9]], "y":[[7,6]] },
+    {"id":"1", "t":[1, 2], "x":[[1,3],[2,3]], "y":[[3,5],[4,5]] },
+    {"id":"3", "t":[2], "x":[[-5,-5]], "y":[[3,4]] }
+  ]
+}