pione 0.4.2 → 0.5.0.alpha.1

data/example/CTFCorrection/Package.pione

@@ -0,0 +1 @@
+.@ PackageName :: "CTFCorrection"

data/example/CTFCorrection/Params.pione

@@ -0,0 +1,21 @@
+Basic Param
+  $RESOLUTION := 3.80 # tiff2mrc -r
+  $CTF_DETERMINE_Cc := 0.7 # ctfDetermine -Cc
+  $CTF_DETERMINE_Cs := 2.1 # ctfDetermine -Cs
+End
+
+Advanced Param
+  $TIFF2MRC_m := 0
+  $TIFF2MRC_Offset := 0.0
+  $MRC_IMAGE_CENTER_Nx := 1000 # FIXME
+  $MRC_IMAGE_CENTER_Ny := 1000 # FIXME
+  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_MAX := 65535
+  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_u_HALF := 16384
+  $MRC_IMAGE_ABNORMAL_VALUE_REMOVE_m := 1
+  $MRC_DETERMINE_D := 50000
+  $MRC_DETERMINE_m := 128
+  $MRC_DETERMINE_CutLow := 0.025
+  $MRC_DETERMINE_CutHigh := 0.15
+  $MRC_DETERMINE_d := 3
+  $MRC_IMAGE_CTF_COMPENSATION_m := 1
+End

data/example/CTFCorrection/pione-package.json

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

data/example/ChildPackage/ChildPackage.pione

@@ -0,0 +1,8 @@
+.@ PackageName :: "ChildPackage"
+.@ Parent :: &ParentPackage
+
+Rule DoAction
+  output 'result.txt'.stdout
+Action
+  echo "This is a child's action."
+End

data/example/ChildPackage/pione-package.json

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

data/example/CountChar/CountChar.pione

@@ -0,0 +1,31 @@
+Rule CountChar
+  input '*.txt'
+  output '{$*}.count'
+Flow
+  rule CountUTF8Char
+  rule ConvertToUTF8
+End
+
+Rule CountUTF8Char
+  input '*.utf8'
+  output '{$*}.count'.stdout
+Action
+  #!/usr/bin/env ruby
+  # coding: utf-8
+  
+  table = {}
+  text = File.open("{$I[1]}").read
+  text.split("").each do |c|
+    table[c] =  table.has_key?(c) ? table[c].succ : 1
+  end
+  table.keys.sort {|a,b| table[b] <=> table[a] }.each do |key|
+    puts "#{key.inspect[1..-2]}:#{table[key]}"
+  end
+End
+
+Rule ConvertToUTF8
+  input '*.txt'
+  output '{$*}.utf8'
+Action
+  iconv -c -f Shift_JIS -t UTF-8 {$I[1]} > {$O[1]}
+End

data/example/CountChar/CountChar.pnml

@@ -0,0 +1,239 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--PLEASE DO NOT EDIT THIS FILE
+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">
+      <name>
+        <text>'*.utf8'</text>
+        <graphics>
+          <offset x="400" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="400" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p5">
+      <name>
+        <text>'{$*}.count'.stdout</text>
+        <graphics>
+          <offset x="540" y="140"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="560" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p3">
+      <name>
+        <text>>'{$*}.count'</text>
+        <graphics>
+          <offset x="740" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="740" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p2">
+      <name>
+        <text>'{$*}.utf8'</text>
+        <graphics>
+          <offset x="240" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="240" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <place id="p1">
+      <name>
+        <text>&lt;'*.txt'</text>
+        <graphics>
+          <offset x="70" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="70" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+    </place>
+    <transition id="t3">
+      <name>
+        <text>CountUTF8Char</text>
+        <graphics>
+          <offset x="480" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="480" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t2">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="660" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="660" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t1">
+      <name>
+        <text>ConvertToUTF8</text>
+        <graphics>
+          <offset x="150" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="150" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <transition id="t6">
+      <name>
+        <text/>
+        <graphics>
+          <offset x="320" y="210"/>
+        </graphics>
+      </name>
+      <graphics>
+        <position x="320" y="170"/>
+        <dimension x="40" y="40"/>
+      </graphics>
+      <toolspecific tool="WoPeD" version="1.0">
+        <time>0</time>
+        <timeUnit>1</timeUnit>
+        <orientation>1</orientation>
+      </toolspecific>
+    </transition>
+    <arc id="a11" source="p7" target="t3">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a1" source="p1" target="t1">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a2" source="t1" target="p2">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a3" source="p5" target="t2">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a4" source="t2" target="p3">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a5" source="p2" target="t6">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a6" source="t6" target="p7">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <arc id="a7" source="t3" target="p5">
+      <inscription>
+        <text>1</text>
+      </inscription>
+      <graphics/>
+      <toolspecific tool="WoPeD" version="1.0">
+        <probability>1.0</probability>
+        <displayProbabilityOn>false</displayProbabilityOn>
+        <displayProbabilityPosition x="500.0" y="0.0"/>
+      </toolspecific>
+    </arc>
+    <toolspecific tool="WoPeD" version="1.0">
+      <bounds>
+        <position x="2" y="25"/>
+        <dimension x="1425" y="596"/>
+      </bounds>
+      <scale>100</scale>
+      <treeWidthRight>1129</treeWidthRight>
+      <overviewPanelVisible>true</overviewPanelVisible>
+      <treeHeightOverview>100</treeHeightOverview>
+      <treePanelVisible>true</treePanelVisible>
+      <verticalLayout>false</verticalLayout>
+      <resources/>
+      <simulations/>
+      <partnerLinks/>
+      <variables/>
+    </toolspecific>
+  </net>
+</pnml>

data/example/CountChar/Main.pione

@@ -1,36 +1,16 @@
-.@ PackageName :: "CountChar"
-
 Rule Main
-  input '*.txt'
+  input '*.txt'.all
   output 'summary.out'
 Flow
-  rule CountUTF8Char
-  rule ConvertToUTF8
+  rule __Main_CountChar_0__
   rule Summarize
 End
 
-Rule CountUTF8Char
-  input '*.utf8'
-  output '{$*}.count'.stdout
-Action
-  #!/usr/bin/env ruby
-  # coding: utf-8
-  
-  table = {}
-  text = File.open("{$I[1]}").read
-  text.split("").each do |c|
-    table[c] =  table.has_key?(c) ? table[c].succ : 1
-  end
-  table.keys.sort {|a,b| table[b] <=> table[a] }.each do |key|
-    puts "#{key.inspect[1..-2]}:#{table[key]}"
-  end
-End
-
-Rule ConvertToUTF8
+Rule __Main_CountChar_0__
   input '*.txt'
-  output '{$*}.utf8'
-Action
-  iconv -c -f Shift_JIS -t UTF-8 {$I[1]} > {$O[1]}
+  output '{$*}.count'
+Flow
+  rule CountChar
 End
 
 Rule Summarize

data/example/CountChar/Main.pnml

@@ -1,41 +1,29 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--PLEASE DO NOT EDIT THIS FILE
-Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
+Created with Workflow PetriNet Designer Version 3.2.0 (woped.org)-->
 <pnml>
   <net type="http://www.informatik.hu-berlin.de/top/pntd/ptNetb" id="noID">
-    <place id="p7">
-      <name>
-        <text>'*.utf8'</text>
-        <graphics>
-          <offset x="400" y="210"/>
-        </graphics>
-      </name>
-      <graphics>
-        <position x="400" y="170"/>
-        <dimension x="40" y="40"/>
-      </graphics>
-    </place>
     <place id="p6">
       <name>
         <text>'summary.out'.stdout</text>
         <graphics>
-          <offset x="480" y="340"/>
+          <offset x="660" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="480" y="300"/>
+        <position x="660" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
     </place>
     <place id="p5">
       <name>
-        <text>'{$*}.count'.stdout</text>
+        <text>'*.txt'</text>
         <graphics>
-          <offset x="560" y="150"/>
+          <offset x="220" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="560" y="170"/>
+        <position x="220" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
     </place>
@@ -43,11 +31,11 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
       <name>
         <text>>'summary.out'</text>
         <graphics>
-          <offset x="640" y="340"/>
+          <offset x="800" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="640" y="300"/>
+        <position x="800" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
     </place>
@@ -55,64 +43,47 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
       <name>
         <text>'*.count'.all</text>
         <graphics>
-          <offset x="310" y="340"/>
+          <offset x="500" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="310" y="300"/>
+        <position x="500" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
     </place>
     <place id="p2">
       <name>
-        <text>'{$*}.utf8'</text>
+        <text>'{$*}.count'</text>
         <graphics>
-          <offset x="240" y="210"/>
+          <offset x="350" y="150"/>
         </graphics>
       </name>
       <graphics>
-        <position x="240" y="170"/>
+        <position x="360" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
     </place>
     <place id="p1">
       <name>
-        <text>&lt;'*.txt'</text>
+        <text>&lt;'*.txt'.all</text>
         <graphics>
-          <offset x="70" y="210"/>
+          <offset x="80" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="70" y="170"/>
+        <position x="80" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
     </place>
-    <transition id="t3">
-      <name>
-        <text>CountUTF8Char</text>
-        <graphics>
-          <offset x="480" y="210"/>
-        </graphics>
-      </name>
-      <graphics>
-        <position x="480" y="170"/>
-        <dimension x="40" y="40"/>
-      </graphics>
-      <toolspecific tool="WoPeD" version="1.0">
-        <time>0</time>
-        <timeUnit>1</timeUnit>
-        <orientation>1</orientation>
-      </toolspecific>
-    </transition>
     <transition id="t2">
       <name>
         <text/>
         <graphics>
-          <offset x="650" y="210"/>
+          <offset x="150" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="650" y="170"/>
+        <position x="150" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
       <toolspecific tool="WoPeD" version="1.0">
@@ -123,13 +94,13 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
     </transition>
     <transition id="t1">
       <name>
-        <text>ConvertToUTF8</text>
+        <text>extern CountChar</text>
         <graphics>
-          <offset x="150" y="210"/>
+          <offset x="290" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="150" y="170"/>
+        <position x="290" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
       <toolspecific tool="WoPeD" version="1.0">
@@ -142,11 +113,11 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
       <name>
         <text>Summarize</text>
         <graphics>
-          <offset x="400" y="340"/>
+          <offset x="580" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="400" y="300"/>
+        <position x="580" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
       <toolspecific tool="WoPeD" version="1.0">
@@ -159,11 +130,11 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
       <name>
         <text/>
         <graphics>
-          <offset x="560" y="340"/>
+          <offset x="730" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="560" y="300"/>
+        <position x="730" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
       <toolspecific tool="WoPeD" version="1.0">
@@ -176,28 +147,11 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
       <name>
         <text/>
         <graphics>
-          <offset x="320" y="210"/>
-        </graphics>
-      </name>
-      <graphics>
-        <position x="320" y="170"/>
-        <dimension x="40" y="40"/>
-      </graphics>
-      <toolspecific tool="WoPeD" version="1.0">
-        <time>0</time>
-        <timeUnit>1</timeUnit>
-        <orientation>1</orientation>
-      </toolspecific>
-    </transition>
-    <transition id="t7">
-      <name>
-        <text>.@ PackageName :: "CountChar"</text>
-        <graphics>
-          <offset x="70" y="120"/>
+          <offset x="430" y="210"/>
         </graphics>
       </name>
       <graphics>
-        <position x="70" y="80"/>
+        <position x="430" y="170"/>
         <dimension x="40" y="40"/>
       </graphics>
       <toolspecific tool="WoPeD" version="1.0">
@@ -217,17 +171,6 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a12" source="t2" target="p3">
-      <inscription>
-        <text>1</text>
-      </inscription>
-      <graphics/>
-      <toolspecific tool="WoPeD" version="1.0">
-        <probability>1.0</probability>
-        <displayProbabilityOn>false</displayProbabilityOn>
-        <displayProbabilityPosition x="500.0" y="0.0"/>
-      </toolspecific>
-    </arc>
     <arc id="a10" source="t4" target="p6">
       <inscription>
         <text>1</text>
@@ -239,18 +182,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a11" source="p7" target="t3">
-      <inscription>
-        <text>1</text>
-      </inscription>
-      <graphics/>
-      <toolspecific tool="WoPeD" version="1.0">
-        <probability>1.0</probability>
-        <displayProbabilityOn>false</displayProbabilityOn>
-        <displayProbabilityPosition x="500.0" y="0.0"/>
-      </toolspecific>
-    </arc>
-    <arc id="a1" source="p1" target="t1">
+    <arc id="a11" source="p5" target="t1">
       <inscription>
         <text>1</text>
       </inscription>
@@ -305,7 +237,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a6" source="t6" target="p7">
+    <arc id="a6" source="t6" target="p3">
       <inscription>
         <text>1</text>
       </inscription>
@@ -316,7 +248,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a7" source="t3" target="p5">
+    <arc id="a7" source="p1" target="t2">
       <inscription>
         <text>1</text>
       </inscription>
@@ -327,7 +259,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
         <displayProbabilityPosition x="500.0" y="0.0"/>
       </toolspecific>
     </arc>
-    <arc id="a8" source="p5" target="t2">
+    <arc id="a8" source="t2" target="p5">
       <inscription>
         <text>1</text>
       </inscription>
@@ -340,7 +272,7 @@ Created with Workflow PetriNet Designer Version 1.0 (woped.org)-->
     </arc>
     <toolspecific tool="WoPeD" version="1.0">
       <bounds>
-        <position x="2" y="25"/>
+        <position x="2" y="22"/>
         <dimension x="1425" y="596"/>
       </bounds>
       <scale>100</scale>