pione 0.5.0.alpha.2 → 0.5.0

data/example/SingleParticlesWithRef/SingleParticlesWithRef.pione

@@ -1,103 +1,22 @@
-#
-# Eos for 3D reconstrucion from 2D rois using 3D initail reference
-#
-
-#
-# Variables
-#
-
-# Target structure name
-$TARGET := "all"
-
-#
-# Search Area for 3D
-#
-
-# Rot1
-$ROT1MIN := 0
-$ROT1MAX := 359
-$ROT1D   := 30
-$nRot1   := 12
-
-# Rot2
-$ROT2MIN := 0
-$ROT2MAX := 359
-$ROT2D   := 30
-$nRot2   := 12
-
-# Rot3
-$ROT3MIN := 0
-$ROT3MAX := 0
-$ROT3D   := 30
-$nRot3   := 1
-
-# For 2D
-$STEP   := 12
-$ROTMIN := 0
-$ROTMAX := 359
-$nROT   := 360 / $STEP
-
-# Pad size for 2D
-$PAD_W := 64
-$PAD_H := 64
-
-#
-# Rules
-#
-
-Rule Main
-  input '*.roi'.all
-  input '{$TARGET}.ref3d'
+Rule SingleParticlesWithRef
   input '{$TARGET}.ref2d'
+  input '*.roi'.all
   output '{$TARGET}.3d'
 Flow
-  rule Create3dinfo
+  rule __SingleParticlesWithRef_Create3dinfo_0__
   rule Create3dlst
   rule Create3d
 End
 
-Rule Create3dinfo
-  input '*.roi'
+Rule __SingleParticlesWithRef_Create3dinfo_0__
   input '{$TARGET}.ref2d'
-  output '{$*}.corinfo'
-  output '{$*}.fit'
-  output '{$*}.3dinfo'
-Flow
-  rule ConvertRoiToPad
-  rule ConvertPadToCorinfo
-  rule ConvertCorinfoTo3dinfo
-End
-
-# .roi.pad
-Rule ConvertRoiToPad
   input '*.roi'
-  output '{$*}.pad'
-Action
-  mrcImageWindowing -i {$*}.roi -o {$*}.mask -W 0.1 0.0 0.05 0.0 -m 18
-  mrcImagePad -i {$*}.mask -o {$*}.padtmp -W {$PAD_W} -H {$PAD_H} -m 3
-  mrcImageWindowing -i {$*}.padtmp -o {$*}.pad -W 0.1 0.0 0.1 0.0 -m 2
-End
-
-# .pad.corinfo
-Rule ConvertPadToCorinfo
-  input '*.pad'
-  input '{$TARGET}.ref2d'
-  output '{$*}.corinfo'
-  output '{$*}.fit'
-Action
-  mrcImageAutoRotationCorrelation -i {$*}.pad -r {$TARGET}.ref2d -O {$*}.corinfo -fit {$*}.fit -cor {$*}.cormap -n {$nROT} -m 18 -range {$ROTMIN} {$ROTMAX} -Iter 2 -nRot2 {$nRot2} -nRot1 {$nRot1} -nRot3 {$nRot3} 2> /dev/null
-End
-
-# .corinfo.3dinfo
-Rule ConvertCorinfoTo3dinfo
-  input '*.corinfo'
   output '{$*}.3dinfo'
-Action
-  awk '/Cor/ { print $7,$16,$2,$3,$4,$5,$9,$11,$12}' {$*}.corinfo | sort -r | sed -e s/.pad/.fit/ > {$*}.3dinfolst
-  head -n 1 {$*}.3dinfolst | awk '{print $2,$3,$4,$5,$6,$1}' > {$*}.3dinfo
+  output '{$*}.fit'
+Flow
+  rule Create3dinfo
 End
 
-# .3dinfo.3dlst
 Rule Create3dlst
   input '*.3dinfo'.all
   output '{$TARGET}.3dlst'
@@ -105,12 +24,10 @@ Action
   cat {$I[1].as_string.join(" ")} | sort > {$TARGET}.3dlst
 End
 
-# .3dlst.3d
 Rule Create3d
-  input '{$TARGET}.3dlst'
   input '*.fit'.all
+  input '{$TARGET}.3dlst'
   output '{$TARGET}.3d'
 Action
   mrc2Dto3D -I {$TARGET}.3dlst -o {$TARGET}.3d -InterpolationMode 2 -Double -DoubleCounter {$TARGET}.3dcounter -CounterThreshold 0.5 -m 1 -WeightMode 2
 End
-

data/example/SingleParticlesWithRef/SingleParticlesWithRef.pnml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--PLEASE DO NOT EDIT THIS FILE
-Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
+Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
 <pnml>
   <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID">
     <place id="p7">
@@ -29,7 +29,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </place>
     <place id="p4">
       <name>
-        <text>'*.roi'</text>
+        <text>'*.roi' #1</text>
         <graphics>
           <offset x="390" y="220"/>
         </graphics>
@@ -41,7 +41,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </place>
     <place id="p3">
       <name>
-        <text>&lt;'{$TARGET}.ref2d'</text>
+        <text>&lt;'{$TARGET}.ref2d' #2</text>
         <graphics>
           <offset x="390" y="300"/>
         </graphics>
@@ -362,7 +362,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a19" source="t6" target="p11">
+    <arc id="a8" source="t1" target="p6">
       <inscription>
         <text>1</text>
       </inscription>
@@ -373,7 +373,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a8" source="t1" target="p6">
+    <arc id="a19" source="t6" target="p11">
       <inscription>
         <text>1</text>
       </inscription>
@@ -386,7 +386,7 @@ Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
     </arc>
     <toolspecific tool="WoPeD" version="1.0">
       <bounds>
-        <position x="2" y="22"/>
+        <position x="2" y="25"/>
         <dimension x="1905" y="784"/>
       </bounds>
       <scale>100</scale>

data/example/SingleParticlesWithRef/pione-package.json

@@ -0,0 +1,20 @@
+{
+  "PackageName": "SingleParticlesWithRef",
+  "Parents": [
+
+  ],
+  "Documents": [
+    "Create3dinfo.pione",
+    "Package.pione",
+    "SingleParticlesWithRef.pione"
+  ],
+  "Scenarios": [
+
+  ],
+  "Bins": [
+
+  ],
+  "Etcs": [
+
+  ]
+}

data/example/WorkflowPatterns/07_StructuredSynchronizingMerge/StructuredSynchronizingMerge.pione

@@ -1,71 +1,45 @@
-param $COND1 := true
-$COND2 := not :: $COND1
-
-Rule Main
+Rule StructuredSynchronizingMerge
   output 'o1'
 Flow
-  rule Init
   rule A
+  rule Init
+  rule E
+  rule D
+    if $COND1
   rule B
+  end
+
+    if $COND2
   rule C
-  rule D
-  rule E
-End
+  end
 
-Rule Init
-  output 'i1'.touch
 End
 
 Rule A
   input 'i1'
-  output 'p1' or null
-  output 'p2' or null
-  output 'p4' or null
-  output 'p5' or null
-Flow
-  rule A1
-  rule A2
-  rule A3
-  rule A4
 End
 
-Rule A1
-  output 'p1'.touch
-  constraint $COND1
-End
-
-Rule A2
-  output 'p4'.touch
-  constraint not :: $COND1
+Rule Init
+  output 'i1'
 End
 
-Rule A3
-  output 'p2'.touch
-  constraint $COND2
+Rule C
+  input 'p2'
+  output 'p5'
 End
 
-Rule A4
-  output 'p5'.touch
-  constraint not :: $COND2
+Rule E
+  input 'p5'
+  input 'p4'
+  output 'o1'
 End
 
 Rule B
   input 'p1'
-  output 'p3'.touch
-End
-
-Rule C
-  input 'p2'
-  output 'p5'.touch
+  output 'p3'
 End
 
 Rule D
   input 'p3'
-  output 'p4'.touch
-End
-
-Rule E
-  input 'p4'
-  input 'p5'
-  output 'o1'.touch
+  output 'p4'
 End

data/example/WorkflowPatterns/07_StructuredSynchronizingMerge/pione-package.json

@@ -0,0 +1,19 @@
+{
+  "PackageName": "WCP07_StructuredSynchronizingMerge",
+  "Parents": [
+
+  ],
+  "Documents": [
+    "Package.pione",
+    "StructuredSynchronizingMerge.pione"
+  ],
+  "Scenarios": [
+
+  ],
+  "Bins": [
+
+  ],
+  "Etcs": [
+
+  ]
+}

data/example/WorkflowPatterns/12_MultipleInstancesWithoutSynchronization/MultipleInstancesWithoutSynchronization.pione

@@ -25,5 +25,4 @@ End
 Rule C
   input 'p1'
   output 'o1-{$N}'
-  param $N := 1.upto($SIZE)
 End

data/example/WorkflowPatterns/13_MultipleInstancesWithDesignTimeKnowledge/MultipleInstancesWithDesignTimeKnowledge.pione

@@ -10,7 +10,6 @@ End
 Rule B
   input 'p1'
   output 'p2-{$N}'
-  param $N := 1.upto(5)
 End
 
 Rule A

data/example/WorkflowPatterns/14_MultipleInstancesWithRunTimeKnowledge/MultipleInstancesWithRunTimeKnowledge.pione

@@ -10,7 +10,6 @@ End
 Rule C
   input 'p1'
   output 'p2-{$N}'
-  param $N := 1.upto($NUM)
 End
 
 Rule A

data/example/WorkflowPatterns/33_GeneralizedANDJoin/GeneralizedANDJoin.pione

@@ -16,5 +16,4 @@ Rule Init
   output '{$N}.i1'
   output '{$N}.i2'
   output '{$N}.i3'
-  param $N := (1 | 2 | 3 | 4 | 5)
 End

data/example/WorkflowPatterns/38_GeneralSynchronizingMerge/GeneralSynchronizingMerge.pione

@@ -1,94 +1,54 @@
-param $COND1 := true
-param $COND2 := not :: $COND1
-param $COND3 := true # processing is endless if $COND3 is true
-
-Rule Main
-  output 'o1'
+Rule GeneralSynchronizingMerge
   output 'o2' or null
+  output 'o1'
 Flow
-  rule Init
   rule A
-  rule B
-  rule C
-  rule D
+  rule Init
   rule E
   rule F
-End
-
-Rule Init
-  output 'i1'.touch
-End
-
-Rule A
-  input 'i1'
-  output 'p1' or 'p2'
-Flow
-  rule A1
-  rule A2
-End
+  rule D
+    if $COND1
+  rule B
+  end
 
-Rule A1
-  output 'p1'.touch
-  constraint $COND1
-End
+    if $COND3
+  
+  end
 
-Rule A2
-  output 'p2'.touch
-  constraint $COND2
-End
+    if $COND2
+  rule C
+  end
 
-Rule B
-  input 'p1'
-  output 'p3'.touch
 End
 
-Rule C
-  input 'p2'
-  output 'p5'.touch
+Rule A
+  input 'i1'
 End
 
-Rule D
-  input 'p3'
-  output 'p4'.touch
+Rule Init
+  output 'i1'
 End
 
 Rule E
-  input 'p4' or 'p5'
-  output 'o1'.touch
+  input 'p4'
+  input 'p5'
+  output 'o1'
 End
 
 Rule F
-  input 'p1'
   input 'p4'
-  output 'p1' or 'o2'
-Flow
-  rule Once
-  rule F1
-  rule F2
-End
-
-Rule Once
-  output 'once'.touch
 End
 
-Rule F1
-  input 'p1'
-  input 'once'
-  output 'p1'
-  constraint $COND3
-Flow
-  rule F1Touch
+Rule B
+  output 'p3'
 End
 
-Rule F1Touch
-  input 'p1'
-  input 'once'
-  output 'p1'.touch
-  output 'once'.remove
+Rule D
+  input 'p3'
+  output 'p4'
 End
 
-Rule F2
-  output 'o2'.touch
-  constraint not :: $COND3
+Rule C
+  input 'p2'
+  output 'p5'
 End
-