Merge branch 'dev' of ssh://gitlab.openmole.org:10000/openmole/openmole into dev

openmole/bin/org.openmole.modules/src/main/scala/org/openmole/modules/Module.scala

@@ -18,6 +18,7 @@
 package org.openmole.modules
 
 import org.openmole.core.module._
+import org.openmole.plugin.task.spatial.SpatialSampling
 import org.openmole.tool.file._
 import org.openmole.tool.hash._
 
@@ -52,7 +53,7 @@ object module {
       ModuleEntry("CSVSampling", "Generate sampling using CSV files", components(org.openmole.plugin.sampling.csv.CSVSampling), sampling),
       ModuleEntry("LHS", "Generate Latin Hypercube Sampling", components(org.openmole.plugin.sampling.lhs.LHS), sampling),
       ModuleEntry("QuasiRandom", "Generate sampling using low-discrepency sequences", components(org.openmole.plugin.sampling.quasirandom.SobolSampling), sampling),
-      ModuleEntry("QuasiRandom", "Generate spatial samplings", components(org.openmole.plugin.sampling.spatial.SpatialSampling), sampling),
+      ModuleEntry("QuasiRandom", "Generate spatial samplings", components(SpatialSampling), sampling),
       ModuleEntry("Evolution", "Explore/calibrate models using evolutionary algorithms", components(org.openmole.plugin.method.evolution.NSGA2), method),
       ModuleEntry("ABC", "Calibrate models using bayesian algorithms", components(org.openmole.plugin.method.abc.ABC), method),
       ModuleEntry("Sensitivity", "Statistical sensitivity analisys", components(org.openmole.plugin.method.sensitivity.SensitivityMorris), method)

openmole/bin/org.openmole.site/jvm/src/main/scala/org/openmole/site/Pages.scala

@@ -177,15 +177,7 @@ object DocumentationPages {
 
   def allPages = docPages.flatMap { _.sons } ++ tutoPages.sons ++ communityPages.sons ++ downloadPages.sons ++ headPages
 
-  def headPages: Seq[PageTree] = docPages ++ Seq(plugPages, explorePages, scalePages, languagePages, developersPages, tutoPages, communityPages, downloadPages)
-
-  val mainDocPages = plugPages.sons.map {
-    _.page
-  } ++ explorePages.sons.map {
-    _.page
-  } ++ scalePages.sons.map {
-    _.page
-  } ++ Seq(scale, explore, plug)
+  def headPages: Seq[PageTree] = docPages ++ Seq(plugPages, explorePages, scalePages, utilityTaskPages, languagePages, developersPages, tutoPages, communityPages, downloadPages)
 
   // Documentation
   lazy val documentation = DocumentationPage.fromScalatex(name = "Documentation", content = scalatex.documentation.Documentation)
@@ -195,6 +187,7 @@ object DocumentationPages {
     explorePages,
     samplingPages,
     scalePages,
+    utilityTaskPages,
     languagePages,
     advancedConceptsPages,
     developersPages,
@@ -208,7 +201,7 @@ object DocumentationPages {
   val faq = DocumentationPage.fromScalatex(name = "FAQ", content = scalatex.FAQ, title = Some("Frequently Asked Questions"))
 
   // Plug
-  def plugPages = pageNode(plug, Vector(scala, java, container, python, r, netLogo, gama, scilab, tool))
+  def plugPages = pageNode(plug, Vector(scala, java, container, python, r, netLogo, gama, scilab))
 
   lazy val plug = DocumentationPage.fromScalatex(name = "Plug", content = scalatex.documentation.plug.Plug, title = Some("Plug Your Model"))
   lazy val scala = DocumentationPage.fromScalatex(name = "Scala", content = scalatex.documentation.plug.Scala)
@@ -219,14 +212,13 @@ object DocumentationPages {
   lazy val scilab = DocumentationPage.fromScalatex(name = "Scilab", content = scalatex.documentation.plug.Scilab)
   lazy val gama = DocumentationPage.fromScalatex(name = "GAMA", content = scalatex.documentation.plug.GAMA)
   lazy val container = DocumentationPage.fromScalatex(name = "Executable", content = scalatex.documentation.plug.Container)
-  lazy val tool = DocumentationPage.fromScalatex(name = "Tool", content = scalatex.documentation.plug.Tool)
 
   // Explore
   def explorePages = pageNode(explore, Vector(samplings, calibration, sensitivity, profile, pse, ose, abc))
 
   lazy val explore = DocumentationPage.fromScalatex(name = "Explore", content = scalatex.documentation.explore.Explore, title = Some("Explore Your Model"))
 
-  def samplingPages = pageNode(samplings, Vector(elementarySamplings, highDimensionSamplings, uniformSampling, fileSampling, spatialSampling, customSampling, advancedSampling, aggregationSampling))
+  def samplingPages = pageNode(samplings, Vector(elementarySamplings, highDimensionSamplings, uniformSampling, fileSampling, customSampling, advancedSampling, aggregationSampling))
 
   lazy val samplings = DocumentationPage.fromScalatex(name = "Samplings", content = scalatex.documentation.explore.sampling.Samplings)
   lazy val elementarySamplings = DocumentationPage.fromScalatex(name = "Elementary Samplings", content = scalatex.documentation.explore.sampling.ElementarySamplings)
@@ -238,7 +230,6 @@ object DocumentationPages {
   //  lazy val sobolSampling = DocumentationPage.fromScalatex(name = "Sobol Sampling", content = scalatex.documentation.explore.sampling.SobolSampling)
   lazy val customSampling = DocumentationPage.fromScalatex(name = "Custom Sampling", content = scalatex.documentation.explore.sampling.CustomSampling)
   lazy val fileSampling = DocumentationPage.fromScalatex(name = "Sampling Over Files", content = scalatex.documentation.explore.sampling.FileSampling)
-  lazy val spatialSampling = DocumentationPage.fromScalatex(name = "Spatial Sampling", content = scalatex.documentation.explore.sampling.SpatialSampling)
   lazy val advancedSampling = DocumentationPage.fromScalatex(name = "Operations on Samplings", content = scalatex.documentation.explore.sampling.AdvancedSampling, title = Some("Advanced Operations on Samplings"))
   lazy val aggregationSampling = DocumentationPage.fromScalatex(name = "Aggregate Sampling Results", content = scalatex.documentation.explore.sampling.Aggregation)
 
@@ -260,7 +251,7 @@ object DocumentationPages {
   lazy val dispatch = DocumentationPage.fromScalatex(name = "Dispatch", content = scalatex.documentation.scale.Dispatch, title = Some("Dispatch Jobs on Multiple Environments"))
 
   // Language
-  def languagePages = pageNode(language, Vector(fileManagement, scalaFunction, hook, transition, source, capsule, moleTask))
+  def languagePages = pageNode(language, Vector(fileManagement, scalaFunction, hook, transition, source, capsule))
 
   lazy val language = DocumentationPage.fromScalatex(name = "Language", content = scalatex.documentation.language.Language, title = Some("The OpenMOLE Language"))
   lazy val fileManagement = DocumentationPage.fromScalatex(name = "File Management", content = scalatex.documentation.language.FileManagement)
@@ -270,7 +261,13 @@ object DocumentationPages {
   lazy val transition = DocumentationPage.fromScalatex(name = "Transitions", content = scalatex.documentation.language.advanced.Transition)
   lazy val source = DocumentationPage.fromScalatex(name = "Source", content = scalatex.documentation.language.advanced.Source)
   lazy val capsule = DocumentationPage.fromScalatex(name = "Capsule", content = scalatex.documentation.language.advanced.Capsule)
-  lazy val moleTask = DocumentationPage.fromScalatex(name = "Mole Task", content = scalatex.documentation.language.advanced.MoleTask)
+
+  def utilityTaskPages = pageNode(utilityTask, Vector(templateTask, moleTask, spatialTask))
+
+  lazy val utilityTask = DocumentationPage.fromScalatex(name = "Utility Tasks", content = scalatex.documentation.utilityTask.Task)
+  lazy val templateTask = DocumentationPage.fromScalatex(name = "Template Task", content = scalatex.documentation.utilityTask.TemplateTask)
+  lazy val moleTask = DocumentationPage.fromScalatex(name = "Mole Task", content = scalatex.documentation.utilityTask.MoleTask)
+  lazy val spatialTask = DocumentationPage.fromScalatex(name = "Spatial Task", content = scalatex.documentation.utilityTask.SpatialTask)
 
   // Advanced Concepts
   def advancedConceptsPages = pageNode(advancedConcepts, Vector(geneticAlgorithm, island, stochasticityManagement))

openmole/bin/org.openmole.site/jvm/src/main/scalatex/openmole/documentation/Documentation.scalatex

@@ -20,9 +20,14 @@
       @sitemap.siteMapSection(explorePages.diff(Seq(samplings)))
   @li
     @h3
-        @a(scale.title, href := scale.file)
+      @a(scale.title, href := scale.file)
     @ol
       @sitemap.siteMapSection(scalePages)
+  @li
+    @h3
+      @a(utilityTask.title, href := utilityTask.file)
+    @ol
+      @sitemap.siteMapSection(utilityTaskPages)
   @li
     @h3
         @a(language.title, href := language.file)

openmole/bin/org.openmole.site/jvm/src/main/scalatex/openmole/documentation/explore/sampling/SpatialSampling.scalatex → openmole/bin/org.openmole.site/jvm/src/main/scalatex/openmole/documentation/utilityTask/SpatialTask.scalatex

@@ -15,9 +15,9 @@ More generally, the @aa("spatial data library", href:= "https://github.com/openm
 
 @br
 
-Some of the corresponding spatial generators are included in OpenMOLE as @i{Spatial Samplings}.
+Some of the corresponding spatial generators are included in OpenMOLE as @i{Task}.
 In the current development version, only some grid generators are included, for a reason of types for output prototypes (synthetic networks are difficult to represent as simple types and to feed as inputs to models).
-All generators output the generated grids in a provided prototype, along with the generation parameters for the generators taking factors as arguments.
+All generators output the generated grids in a provided @code{Val[Array[Array[Double]}, along with the generation parameters for the generators taken as arguments.
 
 
 
@@ -25,19 +25,24 @@ All generators output the generated grids in a provided prototype, along with th
 
 A raster with random values:
 
-@br@br
-
 @hl.openmole("""val myGrid = Val[Array[Array[Double]]]
 val myDensity = Val[Double]
 
+val myGenerator =
+  RandomSpatialSamplingTask(
+    grid = myGrid,
+    gridSize = 10,
+    density = myDensity
+  )
+
 val myModel =
   ScalaTask("println(myGrid.size)") set (
     (inputs, outputs) += myGrid
   )
 
 DirectSampling(
-  sampling = (myDensity in (0.0 to 1.0 by 0.1)) x (myGrid is RandomSpatialSampling(gridSize = 10, density = myDensity)),
-  evaluation = myModel
+  sampling = myDensity in (0.0 to 1.0 by 0.1),
+  evaluation = myGenerator -- myModel
 )""", name= "random grid sampling")
 
 @br
@@ -52,14 +57,22 @@ where
 
 A binary grid with random blocks (random size and position). With the same arguments as before, except the factors for the generator parameters: @code{blocksNumber} is the number of blocks positioned, @code{blocksMinSize}/@code{blocksMaxSize} minimal/maximal (exchanged if needed) width/height of blocks, each being uniformly drawn for each block.
 
-@br@br
-
 @hl.openmole("""
 val myGrid = Val[Array[Array[Double]]]
 val myBlocksNumber = Val[Int]
 val myBlocksMinSize = Val[Int]
 val myBlocksMaxSize = Val[Int]
 
+val myGenerator =
+  RandomSpatialSamplingTask(
+    grid = myGrid,
+    gridSize = 10,
+    number = myBlocksNumber,
+    minSize = myBlocksMinSize,
+    maxSize = myBlocksMaxSize
+  )
+
+
 val myModel =
   ScalaTask("println(myGrid.size)") set (
     (inputs, outputs) += myGrid
@@ -69,17 +82,14 @@ DirectSampling(
   sampling =
     (myBlocksNumber in (10 to 15)) x
       (myBlocksMinSize in (1 to 3)) x
-      (myBlocksMaxSize in RangeDomain[Int]("myBlocksMinSize + 3", "myBlocksMinSize + 5")) x
-      (myGrid is BlocksGridSpatialSampling(gridSize = 10, number = myBlocksNumber, minSize = myBlocksMinSize, maxSize = myBlocksMaxSize)),
-  evaluation = myModel
+      (myBlocksMaxSize in RangeDomain[Int]("myBlocksMinSize + 3", "myBlocksMinSize + 5")),
+  evaluation = myGenerator -- myModel
 )""", name="block grid sampling")
 
-
 @h2{Thresholded exponential mixture sampling}
 
 A binary grid created with an exponential mixture, with kernels of the form @code{exp(-r/r0)}. A threshold parameter is applied to produce the binary grid.
 
-@br@br
 
 @hl.openmole("""
 val myGrid = Val[Array[Array[Double]]]
@@ -87,6 +97,15 @@ val myCenter = Val[Int]
 val myRadius = Val[Double]
 val myThreshold = Val[Double]
 
+val myGenerator =
+  ExpMixtureThresholdSpatialSamplingTask(
+    grid = myGrid,
+    gridSize = 10,
+    center = myCenter,
+    radius = myRadius,
+    threshold = myThreshold
+  )
+
 val myModel =
   ScalaTask("println(myGrid.size)") set (
     (inputs, outputs) += myGrid
@@ -96,9 +115,8 @@ DirectSampling(
   sampling =
     (myCenter in (1 to 20)) x
       (myRadius in (1.0 to 20.0)) x
-      (myThreshold in (2.0 to 30.0)) x
-      (myGrid is ExpMixtureThresholdSpatialSampling(gridSize = 10, center = myCenter, radius = myRadius, threshold = myThreshold)),
-  evaluation = myModel
+      (myThreshold in (2.0 to 30.0)),
+  evaluation = myGenerator -- myModel
 )""", name="block grid sampling")
 
 @br
@@ -120,14 +138,20 @@ A binary grid resembling a labyrinthine building organisation, obtained by perco
 It percolates a grid network until a fixed number of points on the boundaries of the world are linked through the giant cluster.
 The resulting network is transposed to a building configuration by assimilating each link to a street with a given width as a parameter.
 
-@br@br
-
 @hl.openmole("""
 val myGrid = Val[Array[Array[Double]]]
 val myPercolation = Val[Double]
 val myBordPoint = Val[Int]
 val myLinkWidth = Val[Double]
 
+val myGenerator =
+  PercolationGridSpatialSamplingTask(
+    grid = myGrid,
+    gridSize = 10,
+    percolation = myPercolation,
+    bordPoint = myBordPoint,
+    linkWidth = myLinkWidth)
+
 val myModel =
   ScalaTask("println(myGrid.size)") set (
     (inputs, outputs) += myGrid
@@ -137,9 +161,8 @@ DirectSampling(
   sampling =
     (myPercolation in (0.1 to 1.0 by 0.1)) x
       (myBordPoint in (1 to 30)) x
-      (myLinkWidth in (1.0 to 5.0)) x
-      (myGrid is PercolationGridSpatialSampling(gridSize = 10, percolation = myPercolation, bordPoint = myBordPoint, linkWidth = myLinkWidth)),
-  evaluation = myModel
+      (myLinkWidth in (1.0 to 5.0)),
+  evaluation = myGenerator -- myModel
 )""", name="percolation grid sampling")
 
 @br
@@ -159,12 +182,20 @@ Urban morphogenesis model for population density introduced by @aa("(Raimbault,
 
 @b{USE WITH CAUTION - SOME PARAMETER VALUES YIELD VERY LONG GENERATION RUNTIME}
 
-@br@br
-
 @hl.openmole("""
 val myGrid = Val[Array[Array[Double]]]
 val myGrowthRate = Val[Double]
 
+val myGenerator =
+  ReactionDiffusionSpatialTask(
+    grid = myGrid,
+    gridSize = 10,
+    alpha = 10.0,
+    beta = 10.0,
+    nBeta = 10,
+    growthRate = myGrowthRate,
+    totalPopulation = 10)
+
 val myModel =
   ScalaTask("println(myGrid.size)") set (
     (inputs, outputs) += myGrid
@@ -172,9 +203,8 @@ val myModel =
 
 DirectSampling(
   sampling =
-    (myGrowthRate in (1.0 to 10.0)) x
-      (myGrid is ReactionDiffusionSpatialSampling(gridSize = 10, alpha = 10.0, beta = 10.0, nBeta = 10, growthRate = myGrowthRate, totalPopulation = 10)),
-  evaluation = myModel
+    (myGrowthRate in (1.0 to 10.0)),
+  evaluation = myGenerator -- myModel
 )""", name="reaction diffusion grid sampling")
 
 @br

openmole/bin/org.openmole.site/jvm/src/main/scalatex/openmole/documentation/utilityTask/Task.scalatex

+
+
+
+@import org.openmole.site._
+@import org.openmole.site.tools._
+@import DocumentationPages._
+
+
+This part exposes utility task, that might be useful as pre or post processing task when you design your experiments.
+

openmole/build.sbt

@@ -490,7 +490,7 @@ lazy val sensitivity = OsgiProject(pluginDir, "org.openmole.plugin.method.sensit
 
 /* Sampling */
 
-def allSampling = Seq(combineSampling, csvSampling, oneFactorSampling, lhsSampling, quasirandomSampling, spatialSampling)
+def allSampling = Seq(combineSampling, csvSampling, oneFactorSampling, lhsSampling, quasirandomSampling)
 
 lazy val combineSampling = OsgiProject(pluginDir, "org.openmole.plugin.sampling.combine", imports = Seq("*")) dependsOn(exception, modifierDomain, collectionDomain, workflow) settings (pluginSettings: _*)
 
@@ -507,11 +507,6 @@ lazy val quasirandomSampling = OsgiProject(pluginDir, "org.openmole.plugin.sampl
   ) settings (pluginSettings: _*)
 
 
-lazy val spatialSampling = OsgiProject(pluginDir, "org.openmole.plugin.sampling.spatial", imports = Seq("*")) dependsOn(exception, workflow, workspace) settings(
-  libraryDependencies += Libraries.math,
-  libraryDependencies += Libraries.spatialsampling
-  ) settings (pluginSettings: _*)
-
 /* Source */
 
 def allSource = Seq(fileSource)
@@ -521,7 +516,7 @@ lazy val fileSource = OsgiProject(pluginDir, "org.openmole.plugin.source.file",
 
 /* Task */
 
-def allTask = Seq(toolsTask, external, netLogo, netLogo5, netLogo6, jvm, scala, template, systemexec, container, r, scilab, python, gama, cormas, timing)
+def allTask = Seq(toolsTask, external, netLogo, netLogo5, netLogo6, jvm, scala, template, systemexec, container, r, scilab, python, gama, cormas, spatial, timing)
 
 lazy val toolsTask = OsgiProject(pluginDir, "org.openmole.plugin.task.tools", imports = Seq("*")) dependsOn (openmoleDSL) settings (pluginSettings: _*)
 
@@ -559,6 +554,10 @@ lazy val cormas = OsgiProject(pluginDir, "org.openmole.plugin.task.cormas", impo
 
 lazy val timing = OsgiProject(pluginDir, "org.openmole.plugin.task.timing", imports = Seq("*")) dependsOn (openmoleDSL) settings (pluginSettings: _*)
 
+lazy val spatial = OsgiProject(pluginDir, "org.openmole.plugin.task.spatial", imports = Seq("*")) dependsOn(openmoleDSL) settings(
+  libraryDependencies += Libraries.math,
+  libraryDependencies += Libraries.spatialsampling
+) settings (pluginSettings: _*)
 
 /* ---------------- REST ------------------- */
 

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/hook/Hook.scala

@@ -24,6 +24,7 @@ import org.openmole.core.preference.Preference
 import org.openmole.core.serializer.SerializerService
 import org.openmole.core.threadprovider.ThreadProvider
 import org.openmole.core.workflow.builder.{ InfoConfig, InputOutputConfig }
+import org.openmole.core.workflow.mole.Ticket
 import org.openmole.core.workflow.tools._
 import org.openmole.core.workspace.{ TmpDirectory, Workspace }
 import org.openmole.tool.cache.KeyValueCache
@@ -33,6 +34,7 @@ import org.openmole.tool.random.RandomProvider
 
 case class HookExecutionContext(
   cache:                          KeyValueCache,
+  ticket:                         Ticket,
   implicit val preference:        Preference,
   implicit val threadProvider:    ThreadProvider,
   implicit val fileService:       FileService,

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/mole/MoleExecution.scala

@@ -259,6 +259,7 @@ object MoleExecution extends JavaLogger {
           val services = executionContext.services
           HookExecutionContext(
             cache = cache,
+            ticket = ticket,
             preference = services.preference,
             threadProvider = services.threadProvider,
             fileService = services.fileService,
@@ -681,7 +682,7 @@ class MoleExecution(
   def endTime(implicit s: MoleExecution.SynchronisationContext) = sync(_endTime)
 
   private[mole] var ticketNumber = 1L
-  private[mole] val rootTicket = Ticket(id, 0)
+  private[mole] val rootTicket = Ticket.root(0L)
 
   private[mole] var moleId = 0L
 

openmole/core/org.openmole.core.workflow/src/main/scala/org/openmole/core/workflow/mole/Ticket.scala

@@ -18,19 +18,26 @@
 package org.openmole.core.workflow.mole
 
 object Ticket {
-  def apply(category: String, content: Long) = new Ticket(content, null)
+  def root(content: Long) = new Ticket(content, null)
   def apply(parent: Ticket, content: Long) = new Ticket(content, parent)
 
   implicit def ordering = Ordering.by[Ticket, Long](_.content)
+  def toString(t: Ticket): String = t.content.toString
 }
 
-class Ticket(val content: Long, _parent: Ticket) {
-  def parent = Some(_parent)
+sealed class Ticket(val content: Long, _parent: Ticket) {
+  def parent = Option(_parent)
   def parentOrException = parent.getOrElse(throw new InternalError("This is a root ticket, it has no parent."))
 
   def isRoot: Boolean = _parent == null
 
-  override def equals(obj: Any): Boolean = content == obj
+  override def toString = Ticket.toString(this)
+  override def equals(obj: Any): Boolean = obj match {
+    case t: Ticket ⇒ t.content == content
+    case t: Long   ⇒ t == content
+    case _         ⇒ false
+  }
+
   override def hashCode = content.hashCode
 }
 

openmole/plugins/org.openmole.plugin.sampling.spatial/src/main/scala/org/openmole/plugin/sampling/spatial/package.scala

-package org.openmole.plugin.sampling
-
-import org.openmole.spatialsampling
-
-package object spatial {
-
-  type RasterLayerData[N] = spatialsampling.RasterLayerData[N]
-  type RasterData[N] = spatialsampling.RasterData[N]
-  type RasterDim = spatialsampling.RasterDim
-  type Point = spatialsampling.Point
-
-}

openmole/plugins/org.openmole.plugin.sampling.spatial/src/main/scala/org/openmole/plugin/sampling/spatial/Activator.scala → openmole/plugins/org.openmole.plugin.task.spatial/src/main/scala/org/openmole/plugin/task/spatial/Activator.scala

 
-package org.openmole.plugin.sampling.spatial
+package org.openmole.plugin.task.spatial
 
 import org.openmole.core.pluginregistry.PluginRegistry
 import org.osgi.framework.{ BundleActivator, BundleContext }
@@ -14,12 +14,12 @@ class Activator extends BundleActivator {
 
     val keyWords: Vector[HighLight] =
       Vector(
-        SamplingHighLight(objectName(RandomSpatialSampling)),
+        SamplingHighLight(objectName(RandomSpatialSamplingTask)),
         SamplingHighLight(objectName(ExponentialMixtureSpatialSampling)),
-        SamplingHighLight(objectName(ReactionDiffusionSpatialSampling)),
-        SamplingHighLight(objectName(BlocksGridSpatialSampling)),
-        SamplingHighLight(objectName(PercolationGridSpatialSampling)),
-        SamplingHighLight(objectName(ExpMixtureThresholdSpatialSampling))
+        SamplingHighLight(objectName(ReactionDiffusionSpatialTask)),
+        SamplingHighLight(objectName(BlocksGridSpatialSamplingTask)),
+        SamplingHighLight(objectName(PercolationGridSpatialSamplingTask)),
+        SamplingHighLight(objectName(ExpMixtureThresholdSpatialSamplingTask))
       )
 
     PluginRegistry.register(this, Vector(this.getClass.getPackage), highLight = keyWords)

openmole/plugins/org.openmole.plugin.sampling.spatial/src/main/scala/org/openmole/plugin/sampling/spatial/SpatialSampling.scala → openmole/plugins/org.openmole.plugin.task.spatial/src/main/scala/org/openmole/plugin/task/spatial/SpatialSampling.scala

 
 
-package org.openmole.plugin.sampling.spatial
-
-import com.google.common.collect.DiscreteDomain
-import org.openmole.core.context.{ Val, Variable }
-import org.openmole.core.expansion._
-import org.openmole.core.workflow.domain.{ DiscreteFromContextDomain }
-import org.openmole.core.workflow.sampling._
-import org.openmole.core.workflow.tools.{ OptionalArgument, ScalarOrSequenceOfDouble }
+package org.openmole.plugin.task.spatial
+
+import org.openmole.core.dsl._
+import org.openmole.core.dsl.extension._
 import org.openmole.spatialsampling._
 
 object SpatialSampling {
@@ -50,7 +46,7 @@ object SpatialSampling {
 
 }
 
-object ExpMixtureThresholdSpatialSampling {
+object ExpMixtureThresholdSpatialSamplingTask {
 
   /**
    * Sampling of binary density grids with a thresholded exponential mixture. Parameters are randomly sampled.
@@ -61,10 +57,11 @@ object ExpMixtureThresholdSpatialSampling {
    * @param threshold threshold for the binary grid (max of kernels is at 1)
    */
   def apply(
+    grid:      Val[Array[Array[Double]]],
     gridSize:  FromContext[Int],
     center:    FromContext[Int],
     radius:    FromContext[Double],
-    threshold: FromContext[Double]) = FromContext { p ⇒
+    threshold: FromContext[Double])(implicit scope: DefinitionScope) = Task("ExpMixtureThresholdSpatialSamplingTask") { p ⇒
     import p._
 
     val size = gridSize.from(context)
@@ -73,12 +70,17 @@ object ExpMixtureThresholdSpatialSampling {
     val r = radius.from(context)
     val t = threshold.from(context)
 
-    Generation.expMixtureGrid(Left(size), nc, 1.0, r)(random()).map { _.map { d ⇒ if (d > t) 1.0 else 0.0 } }
-  }
+    Context(
+      grid -> Generation.expMixtureGrid(Left(size), nc, 1.0, r)(random()).map { _.map { d ⇒ if (d > t) 1.0 else 0.0 } }
+    )
+  } set (
+    inputs ++= gridSize.inputs ++ center.inputs ++ radius.inputs ++ threshold.inputs,
+    outputs += grid
+  ) withValidate (gridSize.validate ++ center.validate ++ radius.validate ++ threshold.validate)
 
 }
 
-object PercolationGridSpatialSampling {
+object PercolationGridSpatialSamplingTask {
 
   /**
    * Binary density grids through network percolation
@@ -89,12 +91,13 @@ object PercolationGridSpatialSampling {
    * @param linkWidth size of links
    */
   def apply(
+    grid:         Val[Array[Array[Double]]],
     gridSize:     FromContext[Int],
     percolation:  FromContext[Double],
     bordPoint:    FromContext[Int],
     linkWidth:    FromContext[Double],
-    maxIteration: Int                 = 10000
-  ) = FromContext { p ⇒
+    maxIteration: Int                       = 10000
+  )(implicit scope: DefinitionScope) = Task("PercolationGridSpatialSamplingTask") { p ⇒
     import p._
 
     val size = gridSize.from(context)
@@ -103,11 +106,16 @@ object PercolationGridSpatialSampling {
     val b = bordPoint.from(context)
     val w = linkWidth.from(context)
 
-    Generation.percolationGrid(size, pp, b, w, maxIteration)(random()).map { _.map { d ⇒ if (d > 0.0) 1.0 else 0.0 } }
-  }
+    Context(
+      grid -> Generation.percolationGrid(size, pp, b, w, maxIteration)(random()).map { _.map { d ⇒ if (d > 0.0) 1.0 else 0.0 } }
+    )
+  } set (
+    inputs ++= gridSize.inputs ++ percolation.inputs ++ bordPoint.inputs ++ linkWidth.inputs,
+    outputs += grid
+  ) withValidate (gridSize.validate ++ percolation.validate ++ bordPoint.validate ++ linkWidth.validate)
 }
 
-object BlocksGridSpatialSampling {
+object BlocksGridSpatialSamplingTask {
 
   /**
    * Binary density grid filled with blocks
@@ -118,11 +126,12 @@ object BlocksGridSpatialSampling {
    * @param gridSize size
    */
   def apply(
+    grid:     Val[Array[Array[Double]]],
     gridSize: FromContext[Int],
     number:   FromContext[Int],
     minSize:  FromContext[Int],